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60c7527cee301ceecbc7ac04 | 10.26434/chemrxiv.13299785.v1 | A Bio-Inspired Lanthanum-Ortho Quinone Catalyst for Aerobic Oxidation of Alcohol | <p>Oxidation
reactions are fundamental transformations in organic synthesis and chemical
industry. With oxygen or air as terminal oxidant, aerobic oxidation catalysis provides
the most sustainable and economic oxidation processes. Most aerobic oxidation
catalysis employs redox metal as its active center. While nature provides
non-redox metal strategy as in pyrroloquinoline quinone (PQQ)-dependent
methanol dehydrogenases (MDH), such an effective chemical version is unknown.
Inspired by the recently discovered rare earth metal-dependent enzyme Ln-MDH,
here we show that an open-shell semi-quinone anionic radical species in
complexing with lanthanum could serve as a very efficient aerobic oxidation
catalyst under ambient conditions. In this catalyst, the lanthanum metal serves
only as a Lewis acid promoter and the redox process occurs exclusively on the
semiquinone ligand. The catalysis is initiated by 1e<sup>-</sup>-reduction of
lanthanum-activated <i>ortho</i>-quinone to
a semiquinone-lanthanum complex La(<b>SQ<sup>-.</sup></b>)<sub>2</sub>,
which undergoes a coupled O-H/C-H dehydrogenation for aerobic oxidation of
alcohols with up to 330 h<sup>-1</sup> TOF. This study suggests a possible functional
mode of semiquinone radicals, widely observed with quinoproteins in Nature. Moreover,
this unique reductive activation strategy as well as the resulted radical anion
as redox ligand creates a new turning point in the development of efficient aerobic
oxidation catalysis.</p> | Ruipu Zhang; Long Zhang; Ming-Tian Zhang; Sanzhong Luo | Organic Synthesis and Reactions; Physical Organic Chemistry; Lanthanides and Actinides; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7527cee301ceecbc7ac04/original/a-bio-inspired-lanthanum-ortho-quinone-catalyst-for-aerobic-oxidation-of-alcohol.pdf |
62da45fb27b1e4961e4722da | 10.26434/chemrxiv-2022-s8m5s | Quantum-based modeling of protein-ligand interaction: The complex of RutA with uracil and molecular oxygen | Modern quantum-based methods are employed to model interaction of the flavin-dependent enzyme RutA with the uracil and oxygen molecules. This complex presents the structure of reactants for the chain of chemical reactions of monooxygenation in the enzyme active site, which is important in drug metabolism. In this case, application of quantum-based approaches is an essential issue, unlike conventional modeling of protein-ligand interaction with force fields using molecular mechanics and classical molecular dynamics methods. We focus on two difficult problems to characterize the structure of reactants in the RutA-FMN-O2-uracil complex, where FMN stands for the flavin mononucleotide species. First, location of a small O2 molecule in the triplet spin state in the protein cavities is required. Second, positions of both ligands, O2 and uracil, must be specified in the active site with a comparable accuracy. We show that the methods of molecular dynamics with the interaction potentials of quantum mechanics/molecular mechanics theory (QM/MM MD) allow us to characterize this complex and, in addition, to surmise possible reaction mechanism of uracil oxygenation by RutA. | Igor Polyakov; Alexander Nemukhin; Tatiana Domratcheva; Anna Kulakova; Bella Grigorenko | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2022-07-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62da45fb27b1e4961e4722da/original/quantum-based-modeling-of-protein-ligand-interaction-the-complex-of-rut-a-with-uracil-and-molecular-oxygen.pdf |
60c742f10f50db1347395e0a | 10.26434/chemrxiv.8859098.v1 | Covalent-Fragment Screening of Brd4 Identifies a Ligandable Site Orthogonal to the Acetyl-Lysine Binding Sites | <p>Brd4, a member of the bromodomain and extraterminal domain (BET) family, has emerged as a promising epigenetic target in cancer and inflammatory disorders. All reported BET family ligands bind within the bromodomain acetyl-lysine binding sites and competitively inhibit BET protein interaction with acetylated chromatin. Alternative chemical probes that act orthogonally to the highly-conserved acetyl-lysine binding sites may exhibit selectivity within the BET family and avoid recently reported toxicity in clinical trials of BET bromodomain inhibitors. Here, we report the first identification of a ligandable site on a bromodomain outside the acetyl-lysine binding site. Inspired by our computational prediction of hotspots adjacent to non-homologous cysteine residues within the <i>C</i>-terminal Brd4 bromodomain (Brd4-BD2), we performed a mid-throughput mass spectrometry screen to identify cysteine-reactive fragments that covalently and selectively modify Brd4. Subsequent mass spectrometry, NMR and computational docking analyses of electrophilic fragment hits revealed a novel ligandable site near Cys356 that is unique to Brd4 among all human bromodomains. This site is orthogonal to the Brd4-BD2 acetyl-lysine binding site as Cys356 modification did not impact binding of the pan-BET bromodomain inhibitor JQ1 in fluorescence polarization assays. Finally, we tethered covalent fragments to JQ1 and performed NanoBRET assays to provide proof of principle that this orthogonal site can be covalently targeted in intact human cells. Overall, we demonstrate the potential of targeting sites orthogonal to bromodomain acetyl-lysine binding sites to develop bivalent and covalent inhibitors that displace Brd4 from chromatin.</p> | Michael Olp; Daniel Sprague; Stefan Kathman; Ziyang Xu; Alexandar Statsyuk; Brian Smith | Biochemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742f10f50db1347395e0a/original/covalent-fragment-screening-of-brd4-identifies-a-ligandable-site-orthogonal-to-the-acetyl-lysine-binding-sites.pdf |
60c73d9d0f50dbd580395522 | 10.26434/chemrxiv.5743170.v2 | Study on the influence on the formation of highly ordered porous anodic aluminia membrane | We have studied porous anodic alumina template through the second anodic oxidation of preparation. Observing the morphology of nanoscale AAO template using scanning electron microscope (SEM), the results indicate that the pores are orderly paralleled arranged with uniform pore diameter, perpendicular to the template surface. A detailed study of the influence of different oxidation conditions, such as different type of electrolyte, concentration, voltage and temperature on the template of alumina and its electrochemical mechanism were performed. By changing the oxidation voltage, electrolyte type, concentration, pore diameter and template thickness can be altered in a wide range such that we can obtain the desired aspect ratio. <br /> | O Pong-Sik; Ryang Se-Hun; Sin Gum-Chol; Hwang Guk-Nam; yongson hong | Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2018-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d9d0f50dbd580395522/original/study-on-the-influence-on-the-formation-of-highly-ordered-porous-anodic-aluminia-membrane.pdf |
60c74d5a0f50db85d9397015 | 10.26434/chemrxiv.12606068.v1 | Fatty Acid Sentinels as Covalently Bound Randomization Standards for Triacylglycerol (TAG) Quantitative Analysis | <div>RATIONALE. Quantitative analysis of triacylglycerols (TAG) is impeded by a lack of standards and the huge number of potential TAG molecular species that may be present due to the combinatorial nature of glycerolipids. Randomization of acyl groups yields TAG mixtures with profiles predictable from fatty acid profiles, however their use as calibration mixtures has been limited. METHODS. We introduce here the principle of fatty acid isotopic sentinels that are quantitatively added prior to randomization to enable verification that randomization is complete, and that can be used as internal standards. A mixture of two or more</div><div>isotopically labeled fatty acid methyl esters (FAME) are prepared in quantitative proportions and randomized covalently into the acyl groups of TAG mixtures.</div><div>RESULTS. Reaction with catalytic amounts of NaOCH3 yields complete randomization, such that the product FAME and TAG have the same fatty acid profile. TAG mixture</div><div>analysis reveals that the isotopic sentinels have been covalently incorporated into TAG molecular species and <1% of the expected proportions thus verifying randomization within experimental error.</div><div>CONCLUSIONS. The sentinel principle demonstrated here as covalently incorporated internal standards verifies that randomization chemistry went to completion. It applies in</div><div>general to use of combinatorial chemistry for quantitative standards.</div> | DongHao Wang; Zhen Wang; Secilia Martinez; Herbert Tobias; Tom Brenna | Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d5a0f50db85d9397015/original/fatty-acid-sentinels-as-covalently-bound-randomization-standards-for-triacylglycerol-tag-quantitative-analysis.pdf |
664388b891aefa6ce1fa01be | 10.26434/chemrxiv-2023-3ftxd-v3 | Quantum dot-based FRET nanosensors for Talin-membrane assembly and mechanosensing | Understanding the mechanisms of assembly and disassembly of macromolecular structures in cells relies on solving biomolecular interactions. However, those interactions often remain unclear because tools to track molecular dynamics are not sufficiently resolved in time or space. In this study, we present a straightforward method for resolving inter- and intra- molecular interactions in cell adhesive machinery, using quantum dot (QD) based Förster resonance energy transfer (FRET) nanosensors. Using mechanosensitive protein Talin, one of the major components of focal adhesions, we are investigating mechanosensing ability of proteins to sense and respond to mechanical stimuli. First, we quantified the distances separating Talin and a giant unilamellar vesicle membrane for three Talin variants. These variants differ in molecular length. Second, we investigated the mechanosensing capabilities of Talin, i.e., its conformation changes due to mechanical stretching initiated by cytoskeleton contraction. Our results suggest that in early focal adhesion, Talin undergoes stretching, corresponding to a decrease in the Talin-membrane distance of 2.5 nm. We demonstrate that QD-FRET nanosensors can be applied for the sensitive quantification of mechanosensing with sub-nanometer accuracy. | Audrey Ntadambanya; Julien Pernier; Violaine David; Kimihiro Susumu; Igor Medintz; Mayeul Collot; Andrey Klymchenko; Niko Hildebrandt; Isabelle Le Potier; Christophe Le Clainche; Marcelina Cardoso Dos Santos | Biological and Medicinal Chemistry; Nanoscience; Nanodevices; Biophysics; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664388b891aefa6ce1fa01be/original/quantum-dot-based-fret-nanosensors-for-talin-membrane-assembly-and-mechanosensing.pdf |
60c7532e469df42e1ff44cec | 10.26434/chemrxiv.13417118.v1 | Deconvolving Native and Intact Protein Mass Spectra with UniDec | Intact protein, top-down, and native mass spectrometry (MS) generally require the deconvolution of electrospray ionization (ESI) mass spectra to assign the mass of components from their charge state distribution. For small, well-resolved proteins, the charge can usually be assigned based on the isotope distribution. However, it can be challenging to determine charge states with larger proteins that lack isotopic resolution, in complex mass spectra with overlapping charge states, and in native spectra that show adduction. To overcome these challenges, UniDec uses Bayesian deconvolution to assign charge states and to create a zero-charge mass distribution. UniDec is fast, user-friendly, and includes a range of advanced tools to assist in intact protein, top-down, and native MS data analysis. This chapter provides a step-by-step protocol, an in-depth explanation of the UniDec algorithm, and highlights the parameters that affect the deconvolution. It also covers advanced data analysis tools, such as macromolecular mass defect analysis and tools for assigning potential PTMs and bound ligands. Overall, the chapter provides users with a deeper understanding of UniDec, which will enhance the quality of deconvolutions and allow for more intricate MS experiments.<br /> | Marius Kostelic; Michael Marty | Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7532e469df42e1ff44cec/original/deconvolving-native-and-intact-protein-mass-spectra-with-uni-dec.pdf |
64ccf07f69bfb8925a59cbeb | 10.26434/chemrxiv-2023-5fr92-v2 | Application of dolomite to forested catchments in Nova Scotia improves water quality - but more is needed to meet water quality targets | Populations of Atlantic salmon (Salmo salar) in Nova Scotia have plummeted in recent decades. One of the major threats for these populations is freshwater acidification, which has caused toxic water conditions including elevated stream water concentrations of toxic cationic aluminum (Ali). The only viable management option to reduce the threats of acidification to Atlantic salmon within the timeline needed to save the remaining populations is the addition of alkaline materials to waters or soils, via “liming.” While studies in Europe, the UK, and the northeastern USA show that stream water Ali concentrations decrease in response to terrestrial liming with positive impacts on fish communities, stream chemistry response to terrestrial liming in Nova Scotia has not yet been examined. Here we examine the response of stream water chemistry to terrestrial liming in two types of experimental treatments in Nova Scotia. Our results show that liming decreased streamwater Ali concentrations and increased dissolved calcium concentrations and pH levels. Untreated sites have water chemistry conditions that are toxic to Atlantic salmon, and although water chemistry was improved at treated sites, some parameters still do not meet thresholds for aquatic health, indicating that higher doses or repeated liming treatments are required. Results suggest that expansion of liming activities with higher liming doses may help avoid loss of the remaining wild salmon populations. | Kristin A. Hart; Edmund A. Halfyard; Shannon M. Sterling | Earth, Space, and Environmental Chemistry; Environmental Science; Hydrology and Water Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ccf07f69bfb8925a59cbeb/original/application-of-dolomite-to-forested-catchments-in-nova-scotia-improves-water-quality-but-more-is-needed-to-meet-water-quality-targets.pdf |
6654eb07418a5379b06d79b3 | 10.26434/chemrxiv-2024-g51kp | Asymmetric Csp3-Csp3 Bond Formation via Ni-Catalyzed Regio- and Enantioselective Hydroalkylation of 1,3-Diene through Carbonyl Umpolung | The asymmetric Csp3-Csp3 bond formation has been a grand pursuit in synthetic chemistry. The regio- and enantionselective hydroalkylation of 1,3-diene has emerged as an appealing approach for constructing chiral allylic Csp3-Csp3 bonds. However, this method is presently confined to the use of stabilized Csp3 nucleophilic substrates. Herein, we present a nickel-catalyzed asymmetric hydroalkylation of 1,3-dienes with simple unstablized alkyl carbanion enabled by hydrazones umpolung under mild reaction conditions. A range of simple alkylated chiral allylic compounds were generated in good to excellent yields, with enantiomeric ratio (er) of up to 2:98 in forming the Csp3-Csp3 bond. The protocol is applicable to heterocycles, polyenes and unsaturated hydrazones, as well as amenable for late-stage functionalizations of various complex pharmaceuticals. Density functional theory calculations elucidate the mechanism and enantioselectivity of the reaction. An enantiocontrol model is also proposed, emphasizing the crucial role of a chiral NHC ligand in facilitating this asymmetric reaction, as revealed by the two-layer two-dimensional (2D) contour maps. | Ruofei Cheng; Kangbao Zhong; Xueqiang Chu; Yu Lan; Chao-jun Li | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Stereochemistry; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6654eb07418a5379b06d79b3/original/asymmetric-csp3-csp3-bond-formation-via-ni-catalyzed-regio-and-enantioselective-hydroalkylation-of-1-3-diene-through-carbonyl-umpolung.pdf |
62c6833d5163113bde145761 | 10.26434/chemrxiv-2022-jvg5j | Development of a Universal NADH Detection Assay for High
Throughput Enzyme Evolution Using Fluorescence Activated
Droplet Sorting | Directed evolution is an enzyme engineering approach based on the generation and screening of large mutagenesis libraries, with a view to discovering enzymes with improved properties such as activity, specificity or stability. Recently, droplet-based microfluidics has emerged as a powerful technology enabling ultra-high throughput screening of enzyme libraries and the effective identification and isolation of novel, improved enzyme variants, outperforming conventional enzyme screening platforms by several orders of magnitude in terms of speed and chemical consumption. When using droplet-based platforms fluorescence remains the predominant choice for detection of enzymatic activity due to its high sensitivity and low limits of detection. However, this approach often requires the use of labeled, non-natural substrates, which are typically not commercially available. In addition, fluorescence detection is only suitable for a few enzyme classes such as hydrolases or oxidases, whose reactions can often lead to a fluorescent signal. Herein, we describe an assay that enables fluorescence detection of enzymatic activity through a reaction cascade for the industrially important enzyme subclass of dehydrogenases. By applying a hydrogen peroxide-forming NADH oxidase coupled with peroxidase-catalyzed fluorescence generation, quantification of NADH and dehydrogenase activity becomes possible. We explored the utility of this assay in the evolution of a low performing alcohol dehydrogenase from Sphingomonas species A1 (SpsADH). A fluorescence-activated droplet sorting (FADS) platform was utilized for the screening of a 50,000 variant SpsADH library towards the non-native substrate L-guluronate, a primary component of macroalgae, with the potential to serve as raw material for the bio-based production of chemicals. Significantly, we found an enzyme variant with a 2.6-fold improvement in catalytic efficiency kcat/Km towards the non-native substrate, with only a single round of mutagenesis. The screening of SpsADH libraries confirms the ability of the developed method to enrich active enzyme variants. | Gerassimos Kolaitis; Ankit Jain; Dennis Romeis; Tomas Buryska; Matthias Steiger; Lena Wuerstl; Manuel Doering; Barbara Beer; Stavros Stavrakis; Andrew deMello; Volker Sieber | Catalysis; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c6833d5163113bde145761/original/development-of-a-universal-nadh-detection-assay-for-high-throughput-enzyme-evolution-using-fluorescence-activated-droplet-sorting.pdf |
60c75986ee301c7accc7b915 | 10.26434/chemrxiv.14707233.v1 | Simplifying and Expanding the Scope of Boron Imidazolate Framework (BIF) Synthesis Using Mechanochemistry | Mechanochemistry enables rapid access to boron imidazolate frameworks (BIFs), including ultralight materials based on Li and Cu(I) nodes, as well as new and previously unexplored systems based on Ag(I) nodes. Compared to solution methods, mechanochemistry is faster, provides materials with improved porosity, and replaces harsh reactants (e.g. n-butyllithium) with simpler and safer oxides, carbonates or hydroxides. Periodic density-functional theory (DFT) calculations on polymorphic pairs of BIFs based on Li<sup>+</sup>, Cu<sup>+</sup>, and Ag<sup>+</sup> nodes reveals that heavy-atom nodes increase the stability of the open SOD-framework relative to the non-porous <i>dia</i>-polymorph.<br /> | Cameron Lennox; Jean-Louis Do; Joshua Crew; Mihails Arhangelskis; Hatem M. Titi; Ashlee J Howarth; Omar
K. Farha; Tomislav Friscic | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75986ee301c7accc7b915/original/simplifying-and-expanding-the-scope-of-boron-imidazolate-framework-bif-synthesis-using-mechanochemistry.pdf |
60f456f9f1a54f53b750baf6 | 10.26434/chemrxiv-2021-b1qph-v2 | Origin of The Failure of Density Functional Theories in Predicting Inverted Singlet-Triplet Gaps | Recent experimental and theoretical studies have shown several new organic molecules that violate Hund’s rule and have the first singlet excited state lower in energy than the first triplet excited state. While many correlated single reference wave function methods have successfully predicted excited state energetics of these low-lying states, conventional linear-response time-dependent density functional theory (LR-TDDFT) fails to predict the correct excited state energy ordering. Herein, we have shown that it is possible to get inverted singlet-triplet gaps within the density functional theory framework by taking into account correlation contributed by double excitations and choosing correct exchange-correctional functional. Going beyond Kohn-Sham density functional theory (KS-DFT), we have demonstrated that a combined wave function and density functional method resulting in multiconfiguration pair-density functional theory (MC-PDFT), in some cases, can predict inverted singlet-triplet gaps. Consequently, we have identified that both the missing doubly excited configurations and the form of the exchange-correlation functionals are the foremost grounds for the failure of the LR-TDDFT method. We have also compared the accuracy of single reference correlated wave function methods for these low-lying singlet and triplet excited states to multireference second-order perturbation theory. | Soumen Ghosh; Kalishankar Bhattacharyya | Theoretical and Computational Chemistry; Energy; Computational Chemistry and Modeling; Theory - Computational; Photovoltaics; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f456f9f1a54f53b750baf6/original/origin-of-the-failure-of-density-functional-theories-in-predicting-inverted-singlet-triplet-gaps.pdf |
6435a036a41dec1a56e3a453 | 10.26434/chemrxiv-2023-8k18l | SPSiPs, A New Class of Biphosphine Ligands Based on SPSiOL with a Large Dihedral Angle | Here, we demonstrate the development and the synthetic applications of a novel class of diphosphine ligands (SPSiP) based on chiral spirosilabiindane diol (SPSiOL). Starting from SPSiOL, the biphosphine ligands could be readily prepared in three steps with high efficiency. This novel class of biphosphine ligands features rigid configuration, a large dihedral angle, a large P–M–P angle, and a long P–P distance, which might possess unique catalytic reactivities. The potentials of SPSiPs in asymmetric catalysis have also been preliminary disclosed by Rh-catalyzed asymmetric hydrogenation, Rh-catalyzed tandem hydrosilylation, and Pd-catalyzed asymmetric allylic alkylation. | Hao Li; Peng-Gang Zhao; Cai-Yun Wang; Ruo-Yu Zhang; Jian-Jun Li; Yichen Wu; Peng Wang | Organic Chemistry; Organometallic Chemistry; Ligand Design | CC BY NC 4.0 | CHEMRXIV | 2023-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6435a036a41dec1a56e3a453/original/sp-si-ps-a-new-class-of-biphosphine-ligands-based-on-sp-si-ol-with-a-large-dihedral-angle.pdf |
6564cde4cf8b3c3cd7409156 | 10.26434/chemrxiv-2023-xzzsq-v2 | Electrocatalytic Ammonia Oxidation with a Tailored
Molecular Catalyst Heterogenized via Surface Host-Guest
Complexation | Macrocyclic host molecules bound to electrode surfaces enable the complexation of catalytically active guests for molecular heterogeneous catalysis. We present a surface-anchored host-guest complex with the ability to electrochemically oxidize ammonia in both organic and aqueous solutions. With an adamantyl mo-tif as the binding group on the backbone of the molecular catalyst [Ru(bpy-NMe2)(tpada)(Cl)](PF6) (1) (where bpy-NMe2 is 4,4’-bis(dimethylamino)-2,2’-bipyridyl, tpada is 4'-(adamantan-1-yl)-2,2':6',2''-terpyridine), high binding constants with β-cyclodextrin were observed in solution (in dmso-d6: D2O (7:3), K11 = 492 ± 21 M-1). The strong binding affinities also transferred to a mesoporous ITO (mITO) surface functionalized with a phosphonated derivative of β-cyclodextrin. The newly designed catalyst (1) was com-pared to the previously reported naphthyl-substituted catalyst [Ru(bpy-NMe2)(tpnp)(Cl)](PF6) (2) (where tpnp is 4'-(naphthalene-2-yl)-2,2':6',2''-terpyridine) for its stability during catalysis. Despite the insulating nature of the adamantyl substituent serving as the binding group, the stronger binding of this unit to the host functionalized electrode and the resulting shorter distance between the catalytic active center and the surface led to better performance and higher stability. Both guests are able to oxidize ammonia in both organic and aqueous solutions and the host-anchored electrode can be refunctionalized multiple times (>3) following loss of the catalytic activity, without a reduction in performance. Guest 1 exhibits significantly higher stability in comparison to guest 2 towards basic conditions, which often constitutes a challenge for anchored molecular systems. Ammonia oxidation in water led to the selective formation of NO3- with faradaic efficiencies of up to 98%. | Helena Roithmeyer; Laurent Sévery; Thomas Moehl; Bernhard Spingler; Olivier Blacque; Thomas Fox; Marcella lannuzzi; David Tilley | Catalysis; Organometallic Chemistry; Electrocatalysis | CC BY 4.0 | CHEMRXIV | 2023-11-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6564cde4cf8b3c3cd7409156/original/electrocatalytic-ammonia-oxidation-with-a-tailored-molecular-catalyst-heterogenized-via-surface-host-guest-complexation.pdf |
6361228f18a8cc620b5a0e58 | 10.26434/chemrxiv-2022-kv9g4-v2 | Microfluidic quantum sensing platform for lab-on-a-chip applications | Lab-on-a-chip (LOC) applications have emerged as invaluable physical and life sciences tools. The advantages stem from advanced system miniaturization, thus, requiring far less sample volume while allowing for complex functionality, increased reproducibility, and high throughput. However, LOC applications necessitate extensive sensor miniaturization to leverage these inherent advantages fully. Atom-sized quantum sensors are highly promising to bridge this gap and have enabled measurements of temperature, electric and magnetic fields on the nano- to microscale. Nevertheless, the technical complexity of both disciplines has so far impeded an uncompromising combination of LOC systems and quantum sensors. Here, we present a fully integrated microfluidic platform for solid-state spin quantum sensors, such as the nitrogen-vacancy (NV) center in diamond. Our platform fulfills all technical requirements, such as fast spin manipulation, enabling full quantum sensing capabilities, biocompatibility, and easy adaptability to arbitrary channel and chip geometries. To illustrate the vast potential of quantum sensors in LOC systems, we demonstrate various NV center-based sensing modalities for chemical analysis in our microfluidic platform, ranging from paramagnetic ion detection to high-resolution microscale NV-NMR. Consequently, our work opens the door for novel chemical analysis capabilities within LOC devices with applications in electrochemistry, high throughput reaction screening, bioanalytics, organ-on-a-chip, or single-cell studies.
| Robin Derek Allert; Fleming Bruckmaier; Nick Ruben Neuling; Fabian Alexander Freire-Moschovitis; Kristina Song Liu; Claudia Schrepel; Philip Schätzle; Peter Knittel; Martin Hermans; Dominik Benjamin Bucher | Physical Chemistry; Biological and Medicinal Chemistry; Analytical Chemistry; Analytical Apparatus; High-throughput Screening; Biophysics | CC BY NC 4.0 | CHEMRXIV | 2022-11-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6361228f18a8cc620b5a0e58/original/microfluidic-quantum-sensing-platform-for-lab-on-a-chip-applications.pdf |
661f521691aefa6ce1b86807 | 10.26434/chemrxiv-2022-1vr86-v2 | Environmental metabolomics characterization of modern stromatolites and annotation of ibhayipeptolides | Lithified layers of complex microbial mats known as microbialites are ubiquitous in the fossil record, and modern forms are increasingly identified globally. A key challenge to developing an understanding of microbialite formation and environmental role is how to investigate complex and diverse communities in situ. We selected living, layered microbialites (stromatolites) in a peritidal environment near Schoenmakerskop, Eastern Cape, South Africa to conduct a spatial survey mapping the composition and small molecule production of the microbial communities from environmental samples. Substrate core samples were collected from nine sampling stations ranging from the upper point of the freshwater inflow to the lower marine interface where tidal overtopping takes place. Substrate cores provided material for parallel analyses of microbial community diversity by 16S rRNA gene amplicon sequencing and metabolomics using LC–MS2. Species and metabolite diversities were correlated, and prominent specialized metabolites were targeted for preliminary characterization. A new series of cyclic hexadepsipeptides, named ibhayipeptolides, was most abundant in substrate cores of submerged microbialites. These results demonstrate the detection and identification of metabolites from mass-limited environmental samples and contribute knowledge about microbialite chemistry and biology, which facilitates future targeted studies of specialized metabolite function and biosynthesis. | George Neuhaus; Allegra Aron; Eric Isemonger; Daniel Petras; Samantha Waterworth; Luthando Madonsela; Emily Gentry; Xavier Siwe Noundou; Jarmo-Charles Kalinski; Alexandros Polyzois; Julius Habiyaremye; Margaret Redick; Jason Kwan; Rosemary Dorrington; Pieter Dorrestein; Kerry McPhail | Organic Chemistry; Analytical Chemistry; Earth, Space, and Environmental Chemistry; Bioorganic Chemistry; Natural Products; Chemoinformatics | CC BY NC 4.0 | CHEMRXIV | 2024-04-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661f521691aefa6ce1b86807/original/environmental-metabolomics-characterization-of-modern-stromatolites-and-annotation-of-ibhayipeptolides.pdf |
63405710fee74e417259f9e1 | 10.26434/chemrxiv-2021-lq308-v2 | Quantification of gas-accessible microporosity in metal-organic framework glasses | Metal-organic framework (MOF) glasses are a new class of microporous glass materials with immense potential for applications ranging from gas separation to optics and solid electrolytes. Due to the inherent difficulty to determine the atomistic structure of amorphous glasses, the intrinsic structural porosity of MOF glasses is only poorly understood. In this work, the porosity features of a series of prototypical MOF glass formers from the family of zeolitic imidazolate frameworks (ZIFs) and their corresponding glasses is investigated comprehensively. CO2 gas sorption at 195 K allows to follow the evolution of microporosity when transforming from the crystalline to the glassy state of these materials. Based on these data, the pore volume and the apparent density of the ZIF glasses (i.e. the density including the intrinsic microporosity of the glasses) are quantified for the first time. Additional hydrocarbon sorption data (n-butane, propane and propylene) at variable temperatures together with X-ray total scattering experiments prove that the porosity features (in particular the pore size and the pore limiting diameter) of the ZIF glasses depend on the types of organic linkers present in the glass network. This allows formulating first design principles for a targeted tuning of the intrinsic microporosity of MOF glasses. Importantly, these principles are counterintuitive and contrary to established porosity design concepts for crystalline MOFs but show similarities to strategies previously developed for porous polymers. | Louis Frentzel-Beyme; Pascal Kolodzeiski; Jan-Benedikt Weiß; Andreas Schneemann; Sebastian Henke | Materials Science; Inorganic Chemistry; Hybrid Organic-Inorganic Materials; Coordination Chemistry (Inorg.); Solid State Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63405710fee74e417259f9e1/original/quantification-of-gas-accessible-microporosity-in-metal-organic-framework-glasses.pdf |
65eedffe9138d2316133b1d3 | 10.26434/chemrxiv-2024-f0d4h | 4D printed nanoengineered super bioactive hydrogel scaffold with programmable deformation for potential bifurcated vascular channel construction | Four-dimensional (4D) printing of hydrogel enabled the fabrication of complex scaffold geometries out of static parts. Although current 4D fabrication strategies are promising for creating vascular parts such as tubes, developing branched networks or tubular junctions is still challenging. Here, for the first time, a 4D printing approach is employed to fabricate T-shaped perfusable bifurcation using an extrusion-based multi-material 3D printing process. An alginate/methylcellulose-based dual-component hydrogel system (with defined swelling behavior) is nanoengineered with carbonized alginate (~100 nm) to introduce anti-oxidative, anti-inflammatory, and anti-thrombotic properties and shape-shifting properties. A computational model to predict shape deformations in the printed hydrogels with defined infill angles was designed and further validated experimentally. Shape deformations of the 3D-printed flat sheets were achieved by ionic cross-linking. An undisrupted perfusion of a dye solution through a T-junction with minimal leakage mimicking blood flow through vessels is also demonstrated. Moreover, human umbilical vein endothelial and fibroblast cells seeded with printed constructs show intact morphology and excellent cell viability. Overall, developed strategy paves the way for manufacturing self-actuated vascular bifurcations with remarkable anti-thrombotic properties to potentially treat coronary artery diseases. | Amit Nain; Akshat Joshi; Souvik Debnath; Saswat Choudhury; Jobin Thomas; Jitendra Satija; Chih-Ching Huang; Kaushik Chatterjee | Materials Science; Polymer Science; Nanoscience; Nanostructured Materials - Materials; Biopolymers; Hydrogels | CC BY NC 4.0 | CHEMRXIV | 2024-03-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65eedffe9138d2316133b1d3/original/4d-printed-nanoengineered-super-bioactive-hydrogel-scaffold-with-programmable-deformation-for-potential-bifurcated-vascular-channel-construction.pdf |
65ee3b3a9138d231612af790 | 10.26434/chemrxiv-2024-7v2mk-v2 | Synthesis of N–H Aziridines from Unactivated Olefins Using Hydroxylamine-O-Sulfonic Acids as Aminating Agent | Herein, we presented a practical methodology for the intermolecular aziridination of alkenes, using HOSA as the aminating agent, alongside pyridine or piperidine as the base, within HFIP solvent system. Notably, this approach showcases excellent reactivity, especially with non-activated alkenes, and facilitates the transformation of various alkenes substrates, including mono-, di-, tri, and tetra-substituted alkenes, into aziridines with moderate to excellent yield. This method presents a promising avenue for synthesizing aziridines from a wide range of alkenes, featuring the benefits of straightforward operation, mild reaction conditions, extensive substrate compatibility, and scalability. | Yi Huang; Shiyang Zhu; Gang He; Gong Chen; Hao Wang | Organic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2024-03-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ee3b3a9138d231612af790/original/synthesis-of-n-h-aziridines-from-unactivated-olefins-using-hydroxylamine-o-sulfonic-acids-as-aminating-agent.pdf |
672bb761f9980725cf565e99 | 10.26434/chemrxiv-2024-16402 | Designing Molecular and Two Dimensional Metalloporphyrin Catalysts for the Electrochemical CO2 Reduction Reaction | A computational investigation of the electrocatalytic CO2 reduction (CO2R) on metalloporphyrin (M-POR) catalysts, featuring varying metal centres (Ni, Fe, Cu, and Co), oxidation states, and anchoring ligands, was conducted using density functional theory calculations. The evaluation of the thermodynamic and electrochemical stability of the M-POR systems concluded that neutral systems are more stable than charged systems, with the doubly reduced systems being the most unstable. The reaction free energy profiles for CO2R to the C1 products CO and HCOOH were computed according to two possible mechanisms: coupled proton-coupled electron transfer (PCET) and proton transfer – electron transfer (PT-ET). The PCET pathways was found to be by far the most favourable, leading to the preferential formation of HCOOH over CO. Among the catalysts, Fe-POR exhibited the best catalytic performance for CO/HCOOH formation. To evaluate competition with the competitive hydrogen evolution reaction (HER), overpotentials of the CO2R and HER were compared for all systems. This comparison, along with the PCET analysis, revealed that most systems favour HCOOH production. The most promising M-PORs were then to generate models of two-dimensional (2D) carbonaceous frameworks, exploring their potential for CO2R, with 2D Fe-PORs being active towards C1 formation. | Amira Uddin; Rachel Crespo-Otero; Devis Di Tommaso | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Electrocatalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672bb761f9980725cf565e99/original/designing-molecular-and-two-dimensional-metalloporphyrin-catalysts-for-the-electrochemical-co2-reduction-reaction.pdf |
62f9f03f1ea5f6cd0d74959f | 10.26434/chemrxiv-2022-mkc4d | Investigation and Characterization of Flexible Polyurethane Foams from the use of Chicken Eggshells as Fillers. | Chicken egg shells (ES) with 5%wt, 10%wt and 15%wt were incorporated and characterized as fillers in the production of flexible polyurethane foams. The results obtained were compared with conventional application of calcium carbonate (CaCO3). Physico-mechanical properties of the foam without fillers (unfilled), gave density of 20.87 kg/m3, compression set at room temperature (2.880C) and at higher temperature (70) had 3.960C, elongation at break (651.60%), tensile strength (112.10 KPa) and Indentation Force Deflection (hardness at 400C) was 187.20N. Subsequently, foams with 5% ES and 5% CaCO3 fillers depicted densities (21.72 and 21.50 kg/m3), compression set at room temperatures (3.66 and 3.450C), temperature at 700C (4.33 and 5.460C), elongation at break (312.70 and 328.50%), tensile strength (78.40 and 81.40 KPa) and Indentation Forces Deflections (Hardness at 400C) were 241.80 and 198N respectively. Foams with 10% CaCO3 and 10% ES also revealed densities of 21.68 and 21.80 kg/m3 respectively, Compression set at room temperature (6.96 and 4.120C), temperature at 700C (5.79 and 6.160C), elongation at break (359.50 and 362.40%), tensile strength (85.00 and 94.00 KPa) and Indentation Forces Deflections (Hardness at 400C) were 203.00 and 186.40N respectively. Consequently, 15% CaCO3 and 15% ES fillers depicted densities (22.14 and 22.39 kg/m3), compression set at room temperatures (5.24 and 3.030C), temperature at 700C (5.50 and 6.250C), elongation at break (383.10 and 397.50%), tensile strength (90.40 and 97.60 KPa) and Indentation Forces Deflections (Hardness at 400C) were 197.00 and 169.90N respectively. In all cases, the physcio-mechanical properties increased with increase in fillers weights. However, Eggshell-filled foams showed better quality in terms of density, compression set at room temperature, elongation at break and tensile strength than CaCO3-filled foams. Unfilled foams (foam without fillers) had the best compression set both at room temperature and intermediate temperature. All foam samples produced fell within the ASTM D-3574 set standard range of 1-10% for compression tests of polyurethane foams. | Precious Ebereonwu ; Dayil Dashak; Chris Ogah | Polymer Science | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f9f03f1ea5f6cd0d74959f/original/investigation-and-characterization-of-flexible-polyurethane-foams-from-the-use-of-chicken-eggshells-as-fillers.pdf |
651eda9945aaa5fdbb5b9274 | 10.26434/chemrxiv-2023-l6jjd-v3 | Machine Learning Nucleation Collective Variables with Graph Neural Networks | The efficient calculation of nucleation collective variables (CVs) is one of the main limitations to the application of enhanced sampling methods to the investigation of nucleation processes in realistic environments. Here we discuss the development of a graph-based model for the approximation of nucleation CVs, which enables orders-of-magnitude gains in computational efficiency in the on-the-fly evaluation of nucleation CVs. By performing simulations on a nucleating colloidal system mimicking a multistep nucleation process from solution, we assess the model's efficiency in both postprocessing and on-the-fly biasing of nucleation trajectories with pulling, umbrella sampling and metadynamics simulations. Moreover, we probe and discuss the transferability of graph-based models of nucleation CVs across systems by using the model of a CV based on sixth-order Steinhardt parameters trained on a colloidal system to drive the nucleation of crystalline copper from its melt. Our approach is general and potentially transferable to more complex systems as well as to different CVs. | Florian Dietrich; Xavier Rosas Advincula; Gianpaolo Gobbo; Michael Bellucci; Matteo Salvalaglio | Theoretical and Computational Chemistry; Physical Chemistry; Machine Learning; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-10-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651eda9945aaa5fdbb5b9274/original/machine-learning-nucleation-collective-variables-with-graph-neural-networks.pdf |
65f7e074e9ebbb4db9ec7d6d | 10.26434/chemrxiv-2024-95mdm | Efficient Generation of Torsional Energy Profiles by Multifidelity Gaussian Processes for Hindered-Rotor Corrections | Accurate thermochemistry computations often require a proper treatment of torsional modes. The one-dimensional hindered rotor model has proven to be a computationally efficient solution, given a sufficiently accurate potential energy surface. Methods that provide potential energies at various compromises of uncertainty and computational time demand can be optimally combined within a multifidelity treatment. In this study, we demonstrate how multifidelity modeling leads to: 1. smooth interpolation along low-fidelity scan points with uncertainty estimates, 2. inclusion of high-fidelity data that change the energetic order of conformations, and 3. predict best next-point calculations to extend an initial coarse grid. Our diverse application set comprises molecules, clusters, and transition states of alcohols, ethers, and rings. We discuss limitations for cases where the low-fidelity computation is highly unreliable. Different features of the potential energy curve affect different quantities. To obtain “optimal” fits, we therefore apply strategies ranging from simple minimization of deviations to developing an acquisition function tailored for statistical thermodynamics. Bayesian prediction of best next calculations can save a substantial amount of computation time for one- and multi-dimensional hindered rotors. | Maximilian Fleck; Wassja A. Kopp; Narasimhan Viswanathan; Niels Hansen; Joachim Gross; Kai Leonhard | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Machine Learning; Statistical Mechanics | CC BY 4.0 | CHEMRXIV | 2024-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f7e074e9ebbb4db9ec7d6d/original/efficient-generation-of-torsional-energy-profiles-by-multifidelity-gaussian-processes-for-hindered-rotor-corrections.pdf |
60c747cb337d6c8d0fe27401 | 10.26434/chemrxiv.11796702.v1 | Enantioselective Hydroamination of Alkenes with Sulfonamides Enabled by Proton-Coupled Electron Transfer | <div><p>An enantioselective, radical-based method for the intramolecular hydroamination of alkenes with sulfonamides is reported. These reactions are proposed to proceed <i>via</i> <i>N</i>-centered radicals formed by proton-coupled electron transfer (PCET) activation of sulfonamide N–H bonds. Non-covalent interactions between the neutral sulfonamidyl radical and a chiral phosphoric acid generated in the PCET event are hypothesized to serve as the basis for asymmetric induction in a subsequent C–N bond forming step, achieving selectivities of up to 98:2 er. These results offer further support for the ability of non-covalent interactions to enforce stereoselectivity in reactions of transient and highly reactive open-shell intermediates.</p></div> | Casey B. Roos; Joachim Demaerel; David E. Graff; Robert Knowles | Organic Synthesis and Reactions; Photochemistry (Org.); Stereochemistry; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747cb337d6c8d0fe27401/original/enantioselective-hydroamination-of-alkenes-with-sulfonamides-enabled-by-proton-coupled-electron-transfer.pdf |
6604af7c9138d231617aff11 | 10.26434/chemrxiv-2023-ggd1w-v3 | Comprehensive Encoding of Conformational and Compositional Protein Structural Ensembles through mmCIF Data Structure | In their folded state, biomolecules exchange between multiple conformational states, crucial for their function. However, most structural models derived from experiments and computational predictions only encode a single state. To represent biomolecules more accurately, we must move towards modeling and predicting structural ensembles. Information about structural ensembles exists within experimental data from X-ray crystallography and cryo electron microscopy (cryoEM). While new tools are available to detect conformational and compositional heterogeneity that exist within these ensembles, the legacy PDB data structure does not robustly encapsulate this complexity. We propose modifications to the Macromolecular Crystallographic Information File (mmCIF) to improve the representation and interrelation of conformational and compositional heterogeneity. These modifications will enable improved tools to capture macromolecular ensembles in a way that is human and machine interpretable, potentially catalyzing breakthroughs for ensemble-function predictions, analogous to AlphaFold's achievements with single structure prediction. | Stephanie Wankowicz; James Fraser | Biological and Medicinal Chemistry; Biochemistry; Bioinformatics and Computational Biology; Biophysics | CC BY 4.0 | CHEMRXIV | 2024-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6604af7c9138d231617aff11/original/comprehensive-encoding-of-conformational-and-compositional-protein-structural-ensembles-through-mm-cif-data-structure.pdf |
61efe72663acbad8ce198a9f | 10.26434/chemrxiv-2022-b7s0p | The Dynamic Covalent Chemistry of Amidoboronates: Tuning the rac5/rac6 Ratio via the B-N and B-O Dynamic Covalent Bonds | Amidoboronates were prepared as a mixture of up to three isomers (rac5, meso5 and rac6) from the reductive coupling of N-aryl iminoboronates with either cobaltocene or decamethylcobaltocene in acetonitrile. The interconversion of rac5 and rac6 isomers via rearrangement of their dynamic covalent B N bonds was investigated in solution by redissolving isolated crystals. The aniline para substituent and catechol within the amidoboronates tuned the distribution between the rac5 and rac6 isomers; the rac6 isomer predominated for amidoboronates based on pyrocatechol with electron-withdrawing substituents and no interconversion was observed for the rac5 isomers of amidoboronates based on tetrachlorocatechol. Furthermore, the rac5/rac6 distribution was altered by catechol exchange of pyrocatechol for tetrachlorocatechol exploiting the dynamic covalent B O bonds. | Patrick Harders; Thomas Griebenow; Artjom Businski; Anton Kaus; Lorenz Pietsch; Christian Näther; Anna McConnell | Organic Chemistry; Inorganic Chemistry; Organic Synthesis and Reactions; Main Group Chemistry (Inorg.); Supramolecular Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61efe72663acbad8ce198a9f/original/the-dynamic-covalent-chemistry-of-amidoboronates-tuning-the-rac5-rac6-ratio-via-the-b-n-and-b-o-dynamic-covalent-bonds.pdf |
60c7534d702a9b203518c336 | 10.26434/chemrxiv.13473561.v1 | Electrically-Induced Mixed Valence Causes Resistive Switching in Copper Helical Metallopolymers | <div>Controlling the flow of electrical current at the nanoscale typically requires complex top-down approaches. Here we use a bottom-up approach to demonstrate resistive</div><div>switching within molecular wires that consist of double-helical metallopolymers and are constructed by self-assembly. When we expose the material to an electric field, we determine that approximately 25% of the copper atoms oxidise from Cu(I) to Cu(II) without rupture of the polymer chain. The ability to sustain such high level of oxidation is unprecedented in a copper-based molecule: it is made possible here by the double helix compressing in order to satisfy the new coordination geometry required by Cu(II).</div><div>This mixed-valence structure exhibits a 10<sup>4</sup>-fold increase in</div><div>conductivity, which is projected to last over 10 years. We explain the increase in conductivity as being promoted by the creation, upon oxidation, of partly filled d<sub>z</sub><sup>2</sup></div><div>orbitals aligned along the mixed-valence copper array; the long-lasting nature of the change in conductivity is due to the structural rearrangement of the double-helix, which poses an energetic barrier to re-reduction. This work establishes helical metallopolymers as a new platform for controlling currents at the nanoscale.</div> | Jake L. Greenfield; Daniele Di Nuzzo; Emrys Evans; Satyaprasad P. Senanayak; Sam Schott; Jason T. Deacon; Adele Peugeot; William K. Myers; Henning Sirringhaus; Richard Friend; Jonathan Nitschke | Hybrid Organic-Inorganic Materials; Nanostructured Materials - Materials; Thin Films; Polymer chains; Nanostructured Materials - Nanoscience; Physical and Chemical Properties; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7534d702a9b203518c336/original/electrically-induced-mixed-valence-causes-resistive-switching-in-copper-helical-metallopolymers.pdf |
674a3adaf9980725cf83b8e5 | 10.26434/chemrxiv-2024-pg3f1 | Synthesis and characterization of rare and highly hydrolysis-resistant boronium (+3) cations | Boronium (+3) cations, L4B3+, are rare and scarcely studied. But, thanks to their rigid tetrahedral shape and high cationic charge they may be promising tectons for creating hybrid organic-inorganic solids, especially since a single cation can serve as a nucleating center around which three anions can be assembled. However, the few boronium (+3) cations which have been reported are generally water-sensitive, a factor which is a potential impediment to the former endeavor (as is the case with many perovskite photovoltaics). Herein we report the synthesis and characterization (X-ray, NMR, DSC, TGA, CV) of multiple boronium (+3) salts, all of which are highly water stable across the 1-14 pH range. And, as a preliminary investigation of the template-tecton hypothesis, the BETI- [bis(pentafluoroethanesulfonyl)imide] salt of a representative cation was prepared. Significantly, the crystals of the latter were determined by X-ray crystallography to feature continuous, fluorine-rich veins. | Margaret Crowley; Christopher Stachurski; James Davis; Andrzej Wierzbicki; E. Alan Salter; Richard O'Brien; Gabriel Merchant; Paul Trulove; David Durkin; Matthias Zeller | Inorganic Chemistry; Coordination Chemistry (Inorg.); Main Group Chemistry (Inorg.); Materials Chemistry; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674a3adaf9980725cf83b8e5/original/synthesis-and-characterization-of-rare-and-highly-hydrolysis-resistant-boronium-3-cations.pdf |
60c758e09abda28071f8e9ae | 10.26434/chemrxiv.14604720.v1 | Proteochemometric Models Using Multiple Sequence Alignments and a Subword Segmented Masked Language Model | <div>Proteochemometric (PCM) models of protein-ligand activity combine information from both the ligands and the proteins to which they bind. Several methods inspired by the field of natural language processing (NLP) have been proposed to represent protein sequences. </div><div>Here, we present PCM benchmark results on three multi-protein datasets: protein kinases, rhodopsin-like GPCRs (ChEMBL binding and functional assays), and cytochrome P450 enzymes. Keeping ligand descriptors fixed, we evaluate our own protein embeddings based on subword-segmented language models trained on mammalian sequences against pre-existing NLP-based descriptors, protein-protein similarity matrices derived from multiple sequence alignments (MSA), dummy protein one-hot encodings, and a combination of NLP-based and MSA-based descriptors. Our results show that performance gains over one-hot encodings are small and combining NLP-based and MSA-based descriptors increases predictive performance consistently across different splitting strategies. This work has been presented at the 3rd RSC-BMCS / RSC-CICAG Artificial Intelligence in Chemistry in September 2020.</div> | Héléna Alexandra Gaspar; Mohamed Ahmed; Thomas Edlich; Benedek Fabian; Zsolt Varszegi; Marwin Segler; Joshua Meyers; Marco Fiscato | Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758e09abda28071f8e9ae/original/proteochemometric-models-using-multiple-sequence-alignments-and-a-subword-segmented-masked-language-model.pdf |
60c74cb8337d6ce704e27cbd | 10.26434/chemrxiv.12523136.v1 | Discovery of Fungal Metabolites Bergenin, Quercitrin and Dihydroartemisinin as Potential Inhibitors Against Main Protease of SARS-CoV-2 | Emergence
of severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) infection has
given rise to COVID-19 pandemic, that is wreaking havoc worldwide. Therefore,
there is an urgent need to find out novel drugs to combat SARS-CoV-2 infection.
In this backdrop, the present study was aimed to assess potent bioactive
compounds from different fungi as
potential inhibitors of SARS-CoV-2 main protease (M<sup>pro</sup>) using an <i>in-silico</i>
analysis. Nearly 118 bioactive compounds were extracted from <i>Dictyophora
indusiata</i>, <i>Geassstrum triplex</i> and <i>Cyathus stercoreus </i>and
identified using HR LC/MS analysis. Of which, only bergenin (<i>D. indusiata</i>), quercitrin (<i>G. triplex</i>) and
dihydroartemisinin (<i>C. stercoreus</i>) were selected based on their
medicinal uses, binding score and active site covered. The 6LU7, a protein crystallographic structure of SARS-CoV-2 M<sup>pro</sup>,
was docked with bergenin, quercitrin and dihydroartemisinin using Autodock 4.2
and the binding energies obtained were -7.86, -10.29 and -7.20 kcal/mol,
respectively. Bergenin, quercitrin and dihydroartemisinin formed hydrogen bond,
electrostatic interactions and hydrophobic interactions with foremost active
site amino acids THR190, GLU166, GLN189, GLY143, HIS163, HIS164, CYS145 and
PHE140. Present investigation suggests that these three drugs may be used as
alternative inhibitors against SARS-CoV-2 M<sup>pro</sup>. However, further research is necessary to
assess <i>in vitro</i> potential of these drugs. To the
best of our knowledge, present investigation reported these three bioactive
compounds of fungal origin for the first time. | Ravi Patel; Akash Vanzara; Nimisha Patel; Ajit Vasava; Sachin Patil; Kishore Rajput | Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74cb8337d6ce704e27cbd/original/discovery-of-fungal-metabolites-bergenin-quercitrin-and-dihydroartemisinin-as-potential-inhibitors-against-main-protease-of-sars-co-v-2.pdf |
63e2b56e3067856f18b6d90a | 10.26434/chemrxiv-2023-4mlfq | Understanding the Fate of the Banert Cascade of Propargylic Azides. Sigmatropic versus Prototropic Pathway | The Banert cascade is an efficient synthetic strategy for obtaining 4,5-disubstituted 1,2,3-triazoles. The reaction can proceed via a sigmatropic or prototropic mechanism depending on the substrate and the conditions. In this work, the mechanism of both pathways from propargylic azides with different electronic features were investigated using DFT, QTAIM and NBO approaches. The calculated energies barriers were consistent with the experimental data. Three patterns of electron density distribution on the transition structures were observed, which reflected the behaviours of the reactants in the Banert cascade. The stronger conjugative effects were associated with lower/higher free activation energies of sigmatropic/prototropic reactions, respectively. A clear relationship between the accumulation of the charge at the C3 atom of propargylic azides with the energy barriers for prototropic reactions was found. Thus, the obtained results would allow the prediction of the reactions course evaluating reactants. | Miguel Villareal-Parra; Gabriel E. Di Gresia; Guillermo R. Labadie; Margarita M. VALLEJOS | Organic Chemistry; Physical Organic Chemistry; Process Chemistry | CC BY 4.0 | CHEMRXIV | 2023-02-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63e2b56e3067856f18b6d90a/original/understanding-the-fate-of-the-banert-cascade-of-propargylic-azides-sigmatropic-versus-prototropic-pathway.pdf |
60c740e1842e655b59db1d76 | 10.26434/chemrxiv.7851503.v1 | Perturbation of Hydrogen Bonding Networks over Supported Lipid Bilayers by Poly (Allylamine Hydrochloride) | <div><div><div><p>Water is vital to many biochemical processes and is necessary for driving many fundamental interactions of cell membranes with their external environments, yet it is difficult to probe the membrane/water interface directly and without the use of external labels. Here, we employ vibrational sum frequency generation (SFG) spectroscopy to understand the role of interfacial water molecules above bilayers formed from zwitterionic (phosphatidylcholine, PC) and anionic (phosphatidylglycerol, PG, and phosphatidylserine, PS) lipids as they are exposed to the common polycation poly (allylamine hydrochloride) (PAH) in 100 mM NaCl. We show that as the concentration of PAH is increased, the interfacial water molecules are irreversibly displaced and find that it requires 10 times more PAH to displace interfacial water molecules from membranes formed from purely zwitterionic lipids when compared to membranes that contain the anionic PG and PS lipids. This outcome is likely due to difference in (1) the energy with which water molecules are bound to the lipid headgroups, (2) the number of water molecules bound to the headgroups, which is related to the headgroup area, and (3) the electrostatic interactions between the PAH molecules and the negatively charged lipids that are favored when compared to the zwitterionic lipid headgroups. The findings presented here contribute to establishing causal relationships in nanotoxicology and to understanding, controlling, and predicting the initial steps that lead to the lysis of cells exposed to membrane disrupting polycations, or to transfection.</p></div></div></div> | Naomi Dalchand; Merve Dogangun; Paul E. Ohno; Emily Ma; Alex Martinson; Franz Geiger | Cell and Molecular Biology; Biophysical Chemistry; Interfaces; Optics; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740e1842e655b59db1d76/original/perturbation-of-hydrogen-bonding-networks-over-supported-lipid-bilayers-by-poly-allylamine-hydrochloride.pdf |
6405ed25cc600523a3be7837 | 10.26434/chemrxiv-2023-91b0s | Why does the UL49.5 of herpes simplex 1 virus fail to inhibit the TAP-dependent antigen presentation? | Herpes simplex virus type 1 (HSV-1) is a well-studied herpesvirus that causes a number of human diseases. The HSV-1, like other herpesviruses, produces transmembrane glycoprotein N (gN / UL49.5 protein). Although this protein is conserved throughout the herpesvirus family, little is known about its function in HSV-1. The amino-acid sequence and length of UL49.5 proteins differ between herpesvirus species. It is, therefore, crucial to determine whether and to what extent the spatial structure of UL49.5 orthologs that are TAP inhibitors (i.e., of BoHV-1 virus) differs from that of non-TAP inhibitors (i.e., of HSV-1 virus). As a result, the primary goal of our study was to examine the 3D structure of HSV-1-encoded UL49.5 protein in an advanced model of the endoplasmic reticulum (ER) membrane. Circular dichroism (CD), 2D nuclear magnetic resonance (NMR), and multiple-microsecond all-atom molecular dynamics (MD) simulations in the ER membrane mimetic environment were used to determine the final structure of the HSV-1 UL49.5 protein. According to our findings, the N-terminus of HSV-1 UL49.5 adopts a highly flexible, unordered structure in the extracellular part due to the presence of a large number of Pro and Gly residues. In contrast to the UL49.5 protein from BoHV-1, the transmembrane region of HSV-1-encoded UL49.5 is formed by a single long transmembrane -helix, rather than two helices oriented perpendicularly, while the cytoplasmic part of the protein (C-terminus) has a short unordered structure. Our findings provide experimental structural information on HSV-1-encoded UL49.5 protein and structure-based insight into its lack of biological activity in inhibiting the TAP-independent antigen presentation pathway. | Sylwia Rodziewicz-Motowidło; Paweł Krupa; Natalia Karska; Igor Zhukov; Andrea Lipińska | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Biophysics; Chemical Biology; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2023-03-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6405ed25cc600523a3be7837/original/why-does-the-ul49-5-of-herpes-simplex-1-virus-fail-to-inhibit-the-tap-dependent-antigen-presentation.pdf |
638da22b44ccbcfdc40e9b97 | 10.26434/chemrxiv-2022-kjq9z | Fluorescence Lifetime Control of NV Centers in Nanodiamonds for Long-Term Information Storage | Today’s huge amount of data generation and transfer induced an urgent requirement for long-term data storage. Here, we demonstrate and discuss a novel concept for long-term storage using NV centers inside nanodiamonds. The approach is based upon the radiation-induced generation of additional vacancies (so-called GR1 states), which quench the initial NV centers, resulting in a reduced overall fluorescence lifetime of the NV center. Using the tailored fluorescence lifetime of the NV center to code the information we demonstrate a “beyond binary” data storage density per bit. We also demonstrate that this process is reversible by heating the sample or the spot of information. This proof of principle shows that our technique may be a promising alternative data storage technology, especially in terms of long-term storage due to the high stability of the involved color centers. In addition to the proof of principle demonstration using macroscopic samples, we suggest and discuss the usage of focused electron beams to write information in nanodiamond materials, to read it out with focused low-intensity light, and to erase it on a macro, micro, or nanoscale. | Christian Laube; Robert Temme; Andrea Prager; Jan Griebel; Wolfgang Knolle; Bernd Abel | Materials Science; Nanoscience; Carbon-based Materials; Optical Materials; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/638da22b44ccbcfdc40e9b97/original/fluorescence-lifetime-control-of-nv-centers-in-nanodiamonds-for-long-term-information-storage.pdf |
60c753b2702a9b775718c3d7 | 10.26434/chemrxiv.13536005.v1 | The Ranked-Orbital Approach to Selecting Active Spaces | The past decade has seen a great increase in the application of high-throughput
computation to a variety of important problems in chemistry. However, one area which
has been resistant to the high-throughput approach is multireference wave function
methods, in large part due to the technicalities of setting up these calculations and
in particular the not always intuitive challenge of active space selection. As we look
towards a future of applying high-throughput computation to all areas of chemistry,
it is important to prepare these methods for large-scale automation. Here, we propose a ranked-orbital approach to selecting active spaces with the goal of standardizing
multireference methods for high-throughput computation. This method allows for the
meaningful comparison of different active space selection schemes and orbital localizations, and we demonstrate the utility of this approach across 1120 multireference
calculations for the excitation energies of small molecules. Additionally, we propose
our own active space selection scheme that estimates the importance of an orbital for
the active space through a pair-interaction framework from orbital energies and features
of the Hartree-Fock exchange matrix. We call this new scheme the "Approximate Pair
Coefficient" (APC) method and it performs quite well for the test systems presented | Daniel King; Laura Gagliardi | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753b2702a9b775718c3d7/original/the-ranked-orbital-approach-to-selecting-active-spaces.pdf |
64cacd8269bfb8925a413153 | 10.26434/chemrxiv-2023-gkfl8 | A Paradigm Shift in Catalysis: Electro- and Photomediated Nickel-Catalyzed Cross-Coupling Reactions | Transition-metal cata-lyzed cross-coupling reactions are fundamental reactions in organic chemistry, facilitating strategic bond formations for accessing natural products, organic mate-rials, agrochemicals, and pharmaceuticals. Redox chemistry enables access to elusive cross-coupling mechanisms through single-electron processes as an alternative to classical two-electron strategies, which are predominated by palladium catalysis. The hallmark of this redox platform is the systematic modulation of transition-metal oxidation states by a photoredox catalyst or at a heterogeneous electrode sur-face. Electrocatalysis and photocatalysis enhance transition metal catalysis’ capacity for bond formation through electron- or energy-transfer processes. Cross-coupling conditions promoted by electrocatalysis and photocatalysis are mild and bond formation proceeds with exceptionally high chemoselectivity and wide functional group tolerance. The interfacing of abundant first-row transition-metal catalysis with electrocatalysis and photocatalysis has brought about a paradigm shift in cross-coupling technology. In particular, the merger of Ni catalysis with electro- and photochemistry ushered in a new era for carbon-carbon and carbon-heteroatom cross-couplings. We have developed enabling photo- and electrochemical methods throughout our research experience in industry (BMS, AstraZeneca), academia (Professor Baran, Scripps Research), and cross-disciplinary collaborative environments. In this Account, we will outline recent progress from our past and present labs in photo- and electrochemically mediated Ni-catalyzed cross-couplings. By highlighting these cross-coupling methodologies, we will also compare mechanistic features of both electro– and photochemical strategies for forging C(sp2)–C(sp3), C(sp3)–C(sp3), C–O, C–N, and C–S bonds. In each case study where we did not specifically develop both approaches, we will highlight related work from others for education. Through these side-by-side comparisons, we hope to demystify the subtle differences between the two complementary tools to enact redox control over transition metal catalysis. Finally, building off the collective experience of ourselves and the rest of the community, we propose a user guide to photo- and electrochemically-driven cross-coupling reactions to aid the practitioner in rapidly applying such tools in their synthetic designs. | Maximilian Palkowitz; Megan Emmanuel; Martins Oderinde | Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY 4.0 | CHEMRXIV | 2023-08-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64cacd8269bfb8925a413153/original/a-paradigm-shift-in-catalysis-electro-and-photomediated-nickel-catalyzed-cross-coupling-reactions.pdf |
67d401a581d2151a0258e83d | 10.26434/chemrxiv-2025-0tl66 | Self-organization of gold nanoparticles capped with liquid crystalline azobenzene ligands: the effect of terminal groups on particle arrangements | The ligands immobilized on the surface of gold nanoparticles (AuNPs) can be classified into two main types: end-on and side-on ligands. In order to investigate the effect of the terminal group of the end-on ligand on the nanoparticle arrangement, three types of AuNPs were employed by using azobenzene ligands with three different terminal groups (ethyl, acetyl, and nitrile). The obtained AuNPs with ethyl group (Au-L1e/d) are in a weakly ordered state, those with acetyl group (Au-L2e) show a hexagonal columnar liquid crystalline phase upon heating, and those with nitrile groups (Au-L3e) are highly aggregated and do not melt even when heated up to 220°C. According to DFT calculations, the dipole moments of each ligand are in the order of ethyl < acetyl < nitrile. There is a trade-off between the magnitude of the dipole moment and the aggregation/assembly behavior of the AuNPs. Au-L1e/d and Au-L2e exhibit trans-cis isomerization of the azobenzene ligands upon photoirradiation both in dispersed solution and in the film state. Furthermore, they also exhibit a gradual color change from orange to purple in solution, when the solutions are allowed to stand at rt for 24 h after photoirradiation. By means of tunneling electron microscopy (TEM), it is found that the nanoparticles irreversibly coalesce into a non-uniform morphology after being left to stand for 24 h. Prior to photoirradiation, the ligands are found to be densely packed on the gold surface; this dense packing may be responsible for the desorption after the isomerization to cis forms and the particle growth. | Jun Yoshida; Nobuyuki Hara; Ran Kato | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d401a581d2151a0258e83d/original/self-organization-of-gold-nanoparticles-capped-with-liquid-crystalline-azobenzene-ligands-the-effect-of-terminal-groups-on-particle-arrangements.pdf |
61c0480c02c21442332bd57e | 10.26434/chemrxiv-2021-t7mfj | A ruthenium-based catalyst on carbon electrodes for electrochemical water splitting | Electrochemical water splitting constitutes one of the most promising strategies for converting water into hydrogen-based fuels, and this technology is predicted to play a key role in our transition towards a carbon-neutral energy economy. To enable the design of cost-effective electrolysis cells based on this technology, new and more efficient anodes with augmented water splitting activity and stability will be required. Herein, we report an active molecular Ru-based catalyst for electrochemically-driven water oxidation and two simple methods for preparing anodes by attaching this catalyst onto multi-walled carbon nanotubes. The anodes modified with the molecular catalyst were characterized by a broad toolbox of microscopy and spectroscope techniques, and interestingly no RuO2 formation was detected during electrocatalysis over 4 h. These results demonstrate that the herein presented strategy can be used to prepare anodes that rival the performance of state-of-the-art metal oxide anodes. | Lin Li; Biswanath Das; Ahibur Rahaman; Andrey Shatskiy; Fei Ye; Peihong Cheng; Chunze Yuan; Zhiqi Yang; Oscar Verho; Markus Kärkäs; Joydeep Dutta; Tsu-Chien Weng; Björn Åkermark | Organic Chemistry; Catalysis; Electrocatalysis; Heterogeneous Catalysis; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2021-12-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61c0480c02c21442332bd57e/original/a-ruthenium-based-catalyst-on-carbon-electrodes-for-electrochemical-water-splitting.pdf |
64b30426b053dad33a4ff7be | 10.26434/chemrxiv-2023-vlb3f | Multi-stage heterogeneous bubble nucleation under negative pressures | In this paper, we investigate homogeneous and heterogeneous bubble nucleation processes in systems under tension using molecular dynamics simulations. The maximum pressure (nucleation pressure, $\sigma_{min}$) sustained by the system is used a as measure of the system's propensity to nucleate a vapor bubble. In the presence of a planar gold substrate, nucleation pressure is essentially the same as homogeneous values when strong interaction exists between the gold atoms and water molecules; at weaker interactions, a significant lowering of nucleation pressure is observed, signifying that nucleation from such surfaces is easier. Reduction in nucleation pressure with decreasing gold-water surface interaction strength obtained from our simulations shows a good qualitative agreement with classical heterogeneous nucleation theory. As compared to planar surfaces, surfaces with grooves show a further reduction in nucleation barrier only for weak interfacial interactions. Furthermore, the groove dimensions also influence $\sigma_{min}$ -- an optimal groove geometry exists for which $\sigma_{min}$ is minimized; our results indicate that this occurs when the length scale of the defect is comparable to that of the critical (homogeneous) bubble nucleation radius. Moreover, in the presence of defects, multiple barriers to nucleation exist. Our findings provide design guidelines for surface grooves for controllable generation of vapor bubbles; such hydrophobic grooves should be avoided for maximizing overheat or can be used for spatially controlled boiling. | Anirban Chandra; Harrison Lee; Shekhar Garde; Pawel Keblinski | Theoretical and Computational Chemistry; Materials Science; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2023-07-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b30426b053dad33a4ff7be/original/multi-stage-heterogeneous-bubble-nucleation-under-negative-pressures.pdf |
60c9e3b1059ce2022676bb47 | 10.26434/chemrxiv.14744202.v1 | The Effect of the Mixture Composition of BmimBF4-Acetonitrile on the Excited State Relaxation Dynamics of a Solar Cell Dye D149: An Ultrafast Transient Absorption Study | It has been recognized that the understanding of the photo physic of the dyes used in solar cells in an important step in improving their efficiency. Certainly using ionic liquid as an electrolyte is a good solution as it stabilizes the excited state of the dye, however, because of the high viscosity, the diffusion of the components of the solar cell (dye, electrolyte, the chosen redox couple) is very low and has consequences on the other processes (Forward and backward processes). One of the ideas, is to modulate the viscosity of the ionic liquid by mixing the ionic liquid with a solvent. The goal then of this work is to quantify the mixture composition dependence of the excited state relaxation times. Other studies should be carried out to quantify the mixture dependence on the time characteristics of other processes (charge injection, collection etc.) to optimize the working optimal conditions of the solar cell. Following this goal, the present study is devoted to characterize the relaxation time of in the whole mixture composition of BmimBF4 and acetonitrile and in the neat components. For the first time, the decay relaxation times of the first excited electronic state of D149 dye, as obtained by transient absorption spectroscopy (TAS). These relaxation times are monitored by a gradual change of the local structure around a dye, from the one dominated by the interionic interactions, high viscosity and low polarity (as quantified by the static dielectric constant) in BmimBF4 to the one that is dominated by dipole-dipole interactions, low viscosity and high polarity in acetonitrile.<br /> | Nishith Maity; Piotr Piatkowski; Kamil Polok; Francois-Alexandre Miannay; Abdenacer Idrissi | Optics; Photochemistry (Physical Chem.); Physical and Chemical Processes; Physical and Chemical Properties; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c9e3b1059ce2022676bb47/original/the-effect-of-the-mixture-composition-of-bmim-bf4-acetonitrile-on-the-excited-state-relaxation-dynamics-of-a-solar-cell-dye-d149-an-ultrafast-transient-absorption-study.pdf |
67d02bff81d2151a02fdd892 | 10.26434/chemrxiv-2025-klwrw | Enhancing Thermal Conductivity and Flame Resistance of Carbon Fiber Composites using CNT-infused Multiphase Graphene Resins | Carbon fiber composites (CFC) are distinguished by their remarkable strength-to-weight ratio, rendering them exceptionally suitable for various applications. This study explores replacing the conventional polymer epoxy matrix in CFCs with macropore-infused graphene nanocomposite emulsion thermosets (MINETs). The explored MINETs are formed utilizing epoxy resin, graphene particles, and different oils as working fluids. This approach allows CFCs to exhibit multifunctional properties, including enhanced thermal conductivity and flame resistance, making them ideal for fire-proof drone enclosures, electronic casings, and thermal-energy-storage equipment applications. The thermal conductivity was further increased by adding carbon nanotubes (CNT) to the MINET matrix. The rheological properties of MINET allowed for CNT loading concurrently alongside graphene, without preventing processing. Rheological evaluations and Vickers hardness assessments were conducted to optimize the maximum CNT loading for efficient molding and robust mechanical properties. Thermal conductivity analysis demonstrated that CNT-reinforced MINET composites have a higher thermal conductivity when compared to standard graphene-MINET formulations. Infrared thermal imaging confirmed that CFC MINET composites have better dynamic heat transfer properties than CFC epoxy samples. Flammability tests indicated an improved flame resistance, particularly for silicone oil CFC MINET CNT formulations. The results indicate that CNT-infused CFC MINET exhibits exceptional thermal management and enhanced fire resistance co-optimized with mechanical properties, thus rendering it ideal for high heat dissipation, thermal stability, and flame retardancy. | Yogin Patel; Pei Huan Sun; Bryan Llumiquinga; Nandi Bao; Adrien Duran; Charm Nicholas; Rituparna Mohanty; Nare Cho; Stephen Tse; Jonathan Singer | Materials Science; Carbon-based Materials; Composites; Nanostructured Materials - Materials | CC BY NC 4.0 | CHEMRXIV | 2025-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d02bff81d2151a02fdd892/original/enhancing-thermal-conductivity-and-flame-resistance-of-carbon-fiber-composites-using-cnt-infused-multiphase-graphene-resins.pdf |
6684f842c9c6a5c07a246005 | 10.26434/chemrxiv-2024-zfj3p-v2 | A Short Overview of Benzalkonium Chloride in Pharmaceutical Sector: Safety, Environmental Impact and Alternatives | This paper provides an overview of the environmental and safety concerns associated with benzalkonium chloride (BAC), a chemical widely used in pharmaceuticals. The review covers BAC’s various applications, toxicity, and environmental considerations. It explores the industrial processing of BAC, its role as a preservative in drug formulations, and the negative consequences linked to its usage. Furthermore, the review highlights the potential allergic reactions following the initial application of BAC. The study also refers to the various concentrations of BAC employed in different formulations and their administration for safety purposes. Additionally, initiatives to use alternatives to BAC in order to mitigate the potential side effects are explored. | Batool Wali; Niga Othman; Sara Rashid; Sima Hamid; Hayder Issa | Biological and Medicinal Chemistry; Earth, Space, and Environmental Chemistry; Environmental Science; Wastes; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2024-07-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6684f842c9c6a5c07a246005/original/a-short-overview-of-benzalkonium-chloride-in-pharmaceutical-sector-safety-environmental-impact-and-alternatives.pdf |
677bf347fa469535b9f77105 | 10.26434/chemrxiv-2025-0txsj | Degradable Water-Soluble Polymer Prodrugs for Subcutaneous Delivery of Irritant Anticancer Drugs | Chemotherapy is primarily administered intravenously (IV), but this route poses significant challenges (e.g., high costs, patient discomfort, logistical difficulties, side effects such as infections from catheter use). Although oral and subcutaneous (SC) routes are preferred for their convenience and have the potential for better patient comfort and cost reduction, oral chemotherapy faces issues like poor bioavailability and adherence, while SC delivery is unsuitable for irritant or vesicant drugs due to local toxicity. To overcome these limitations, the polymer prodrug strategy has been explored, where drugs are linked to a polymer, reducing toxicity and enhancing drug delivery. Recent work has focused on creating water-soluble polymer prodrugs for SC delivery of paclitaxel (Ptx), a hydrophobic and vesicant drug, which was successfully conjugated to polyacrylamide (PAAm), a very hydrophilic biocompatible polymer, resulting in safer SC injection and enhanced therapeutic efficacy in tumor-bearing mice. However, this strategy's potential depends on adapting it to other vesicant anticancer drugs. Making the polymer degradable for facilitated excretion would also be a key improvement. In this work, this approach has been successfully extended to gemcitabine (Gem), a widely used but irritant anticancer drug, and to a degradable PAAm-based promoiety, having cleavable ester groups in the main chain. The resulting Gem-based prodrugs featured upper critical solution temperature to ensure complete solubility at the temperature of the SC tissue, sustained Gem release, significant degradation under physiological conditions, improved systemic toxicity and absence of local toxicity compared to free Gem. Remarkably, Gem-PAAm polymer prodrugs exhibited significant anticancer efficacy in mice bearing Mia Pa-Ca 2 tumors, outperforming Gemzar®, the commercial formulation of Gem. These advances suggest the potential of these hydrophilic polymer prodrugs to transform SC chemotherapy, enabling the use of a broader range of anticancer drugs while reducing side effects and improving patient outcomes. | Léa Guerassimoff; Jingming Cao; Michaelle Auguste; Amaury Bossion; Chen Zhu; Dao Le; Catherine Cailleau; Safa Mohamed Ismail; Françoise Mercer-Nomé; Julien Nicolas | Polymer Science; Drug delivery systems | CC BY NC 4.0 | CHEMRXIV | 2025-01-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677bf347fa469535b9f77105/original/degradable-water-soluble-polymer-prodrugs-for-subcutaneous-delivery-of-irritant-anticancer-drugs.pdf |
6720640e83f22e42147f7c5a | 10.26434/chemrxiv-2024-0dxz6 | Harnessing the power of microfluidics in sustainable sonochemistry: case study of ultra-fast removal of methyl orange from wastewater. | The oxidation of renewable resources is a promising process that has great potential in addressing the climate change and building the circular economic, sustainable society and green chemical supply chain. This study explores the application of ultrasound in oxidation processes using the wastewater treatment as a case study. Advanced oxidation processes (AOPs) are highly effective for degrading the pollutants in wastewater through the generation of oxidative radicals, with ultrasound emerging as a promising AOP method due to its mild conditions and synergistic potential with other methods. However, ultrasound alone faces challenges in efficiently degrading complex compounds like azo dyes, partly due to issues with cavitation bubble stability and non-uniform ultrasonic fields. Microfluidic reactor combined with microbubble technology offers a solution to enhance ultrasound efficiency by improving bubble stability and energy distribution. In this study, we investigate microbubble formation in a microfluidic reactor with T-junction and flow-focusing inlets, aiming to enhance ultrasound-driven AOPs. The flow-focusing design successfully generates relatively small and monodisperse bubbles allowing for effective ultrasound application at 108.5 kHz using a piezoelectric transducer. Our results demonstrate a relatively high H2O2 generation rate of 0.54 μM/s, among the highest reported in the literature, and a methyl orange (MO) degradation efficiency of 35% in just 2.9 seconds - significantly surpassing conventional systems and prior microfluidic studies. This work demonstrates the novelty of integrating microbubble technology with microfluidic reactors to enhance the energy efficiency of ultrasound - assisted oxidation processes, providing an efficient approach to the chemo-selective conversion of renewable resources to high-value specialty chemicals that are inaccessible via conventional routes. | Quang Thang Trinh; Yuran Cheng; Haotian Cha; Kin Un Tai; Lingxi Ouyang; Prince Nana Amaniampong; Jun Zhang; Hongjie An; Zuojun Wei; Nam-Trung Nguyen | Physical Chemistry; Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry; Environmental Science; Fluid Mechanics; Reaction Engineering | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6720640e83f22e42147f7c5a/original/harnessing-the-power-of-microfluidics-in-sustainable-sonochemistry-case-study-of-ultra-fast-removal-of-methyl-orange-from-wastewater.pdf |
661dc770418a5379b0eda2f9 | 10.26434/chemrxiv-2024-smqf9 | Bonding-Directed Crystallization of Ultra-Long One-Dimensional NbS3 van der Waals Nanowires | The rediscovery of one-dimensional (1D) and quasi-1D (q-1D) van der Waals (vdW) crystals ushered the realization of nascent physical properties in 1D that are suitable for applications including photonics, electronics, and sensing. However, despite renewed interest in the creation and understanding of the physical properties of 1D and q-1D vdW crystals, the lack of accessible synthetic pathways for growing well-defined nanostructures that extend across several length scales remains. Using the highly anisotropic 1D vdW NbS3-I crystal as a model phase, we present a catalyst-free and bottom-up synthetic approach to access ultra-long nanowires, with lengths reaching up to 7.9 mm and with uniform thicknesses ranging from 13 to 190 nm between individual nanowires. Control over the synthetic parameters enabled the modulation of intra- and inter-chain growth modalities to selectively yield 1D nanowires or quasi-2D nanoribbons. Comparative synthetic and density functional theory (DFT) studies with a closely related non-dimerized phase, ZrS3, show that the unusual preferential growth along 1D can be correlated to the strongly anisotropic bonding and dimeric nature of NbS3 Type-I. These results, owing to the ubiquity of dimerization in Peierls-distorted 1D crystals, will open opportunities to grow ultra-long nanowires for high-fidelity optical and electronic devices approaching the sub-nanoscale regime. | Diana Lopez; Yinong Zhou; Dmitri Cordova; Griffin Milligan; Kaleolani Ogura; Ruqian Wu; Maxx Arguilla | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661dc770418a5379b0eda2f9/original/bonding-directed-crystallization-of-ultra-long-one-dimensional-nb-s3-van-der-waals-nanowires.pdf |
6788154ffa469535b92f6230 | 10.26434/chemrxiv-2025-6xg5d | Empowering scientists: delivering AI tools through an ELN framework at the enterprise level | Artificial intelligence (AI) holds immense potential to revolutionize drug discovery, yet its widespread adoption within scientific enterprises faces significant hurdles. Key challenges include ensuring user-friendliness, managing complex workflows, and integrating diverse datasets. To address these issues, we propose a novel framework that leverages the familiar Electronic Lab Notebook (ELN) paradigm. By seamlessly integrating AI workflows as ELN protocols and AI job runs as ELN experiments, our approach provides a user-centric and scalable solution that aligns with established scientific practices. This ELN-based framework, implemented at Sygnature Discovery, adheres to FAIR principles, enhancing data findability, accessibility, interoperability, and reusability. By mirroring the intuitive ELN interface, our solution empowers bench scientists to easily access and utilize cutting-edge AI tools, accelerating drug discovery efforts and maximizing the return on AI investments. | Ting Qin; Aparna Chandrasekaran; Oran Maguire; Jack Hoffman; Jason Shiers; Tarun Jain; Colin Sambrook Smith | Theoretical and Computational Chemistry; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6788154ffa469535b92f6230/original/empowering-scientists-delivering-ai-tools-through-an-eln-framework-at-the-enterprise-level.pdf |
65ae65a49138d231617b6ecf | 10.26434/chemrxiv-2024-lctpz | Pharmaceutical Digital Design: From Chemical Structure through Crystal Polymorph to Conceptual Crystallization Process | A workflow for the digital design of crystallization processes starting from the chemical structure of the active pharmaceutical ingredient (API) is a multi-step, multi-disciplinary process. A simple version would be to first predict the API crystal structure and from it the corresponding properties of solubility, morphology, and growth rates, assume that the nucleation would be controlled by seeding, and then use these parameters to design the crystallization process. This is usually an over-simplification as most APIs are polymorphic, and the most stable crystal of the API alone may not have the required properties for development into a drug product. This perspective, from the experience of a Lilly Digital Design project, considers the fundamental theoretical basis of crystal structure prediction (CSP), free energy, solubility, morphology and growth rate prediction, and the current state of nucleation simulation. This is illustrated by applying the modeling techniques to real examples, olanzapine and succinic acid. We demonstrate the promise of using ab initio computer modeling for solid form selection and process design in pharmaceutical development. We also identify open problems in the application of current computational modeling and achieving the accuracy required for immediate implementation that are currently limiting the applicability of the approach. | Christopher L. Burcham; Michael F. Doherty; Baron G. Peters; Sarah L. Price; Matteo Salvalaglio; Susan M. Reutzel-Edens; Louise S. Price; Ravi Kumar Reddy Addula; Nicholas Francia; Vikram Khanna | Theoretical and Computational Chemistry; Chemical Engineering and Industrial Chemistry; Pharmaceutical Industry | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ae65a49138d231617b6ecf/original/pharmaceutical-digital-design-from-chemical-structure-through-crystal-polymorph-to-conceptual-crystallization-process.pdf |
60c73f7cbb8c1a53f03d9b7f | 10.26434/chemrxiv.7387103.v1 | Li-ion Conductive Li3PO4-Li3BO3-Li2SO4 Mixture: Prevision through Density Functional Molecular Dynamics and Machine Learning | The development of high Li-ion conductive solid electrolytes is crucial for the practical use of all solid-state Li-ion batteries. The mixing of hetero Li-ion conductive substances is a known method for enhancing the Li-ion conductivity more than in the original substances. In this study, using computer simulations, we proved that a ternary Li<sub>3</sub>PO<sub>4</sub>-Li<sub>3</sub>BO<sub>3</sub>-Li<sub>2</sub>SO<sub>4</sub>system has the potential to demonstrate improved Li-ion conductivity based on the introduction of a quasi-Li/oxygen vacancy. The Li-ion conductivities of this ternary system were calculated using several model systems based on the density functional molecular dynamics under an isothermal-isobaric ensemble. However, an exploration using the density functional molecular dynamics cannot cover the entire combinatorial space owing to a lack of computational capability. To search through a vast combinatorial space, we conducted analyses using a machine learning technique. The analysis results clarify the relationship between Li-ion conductivity and phonon free energy, and allow the optimum composition ratio with the highest Li-ion conductivity to be predicted. | Masato Sumita; Ryo Tamura; Kenji Homma; Chioko Kaneta; Koji Tsuda | Computational Chemistry and Modeling; Machine Learning; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2018-11-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f7cbb8c1a53f03d9b7f/original/li-ion-conductive-li3po4-li3bo3-li2so4-mixture-prevision-through-density-functional-molecular-dynamics-and-machine-learning.pdf |
659bf0c29138d231617324ed | 10.26434/chemrxiv-2024-lbdl5 | Predicting Two-Dimensional Semiconductors Using Conductivity Effective Mass | In this paper we investigate the relationship between the conductivity effective mass and exfoliation energy of materials to assess whether automatic sampling of the electron band structure can predict the presence of and ease of separating chemically bonded layers. We assess 22,976 materials from the Materials Project database, screen for only those that are thermodynamically stable and identify the 1,000 materials with the highest standard deviation for p-type and the 1,000 materials with the highest standard deviation for n-type internal conductivity effective mass tensors. We calculate the exfoliation energy of these 2,000 materials and report on the correlation between effective mass and exfoliation energy. A relationship is found which is used to identify a previously unconsidered two-dimensional material and could streamline the modelling of other two-dimensional materials in the future. | Wenjun Zhang; Zhikun Yao; Lee Burton | Materials Science; Inorganic Chemistry; Multilayers; Solid State Chemistry; Theory - Inorganic | CC BY 4.0 | CHEMRXIV | 2024-01-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/659bf0c29138d231617324ed/original/predicting-two-dimensional-semiconductors-using-conductivity-effective-mass.pdf |
60c74b9d702a9b96d218b49c | 10.26434/chemrxiv.12362996.v1 | Myricetin Preferentially Binds to Interfacial Regions in Domains 1 – 3 to Inhibit Cholesterol-Dependent Cytolysins: A Molecular Docking Study | <p>Cholesterol-dependent cytolysins (CDCs)
are proteinaceous toxins secreted as monomers by some Gram-positive and
Gram-negative bacteria that contribute to their pathogenicity. These toxins
bind to either cholesterol or human CD59, leading to massive structural changes,
toxin oligomerization, formation of very large pores, and ultimately cell death,
making these proteins promising targets for inhibition. Myricetin, and its
related flavonoids, have been previously identified as a candidate small
molecule inhibitor of specific CDCs such as listeriolysin O (LLO) and suilysin
(SLY), interfering with their oligomerization. In this work, molecular docking
was performed to assess the interaction of myricetin with other CDCs whose
crystal structures are already known. Results indicated that although myricetin
bound to the hitherto identified cavity in domain 4 (D4), much more efficient
and stable binding was obtained in sites along the interfacial regions of
domains 1 – 3 (D1 – D3). This was common among the tested CDCs, which was primarily
due to much more extensive stabilizing intermolecular interactions, as
indicated by post-docking analysis. Specifically, myricetin bound to (1) the
interface of the three domains in anthrolysin O (ALO), perfringolysin O (PFO),
pneumolysin (PLY), SLY, and vaginolysin (VLY), (2) at/near the D1/D3 interface
in LLO and streptolysin O (SLO), and (3) along the D2/D3 interface in
intermedilysin (ILY). These findings provide theoretical basis on the
possibility of using myricetin and its related compounds as a broad-spectrum
inhibitor of CDCs to potentially address the diseases associated with these pathogens.</p> | Rafael Espiritu | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b9d702a9b96d218b49c/original/myricetin-preferentially-binds-to-interfacial-regions-in-domains-1-3-to-inhibit-cholesterol-dependent-cytolysins-a-molecular-docking-study.pdf |
60c741aaf96a00667e2864af | 10.26434/chemrxiv.8108735.v1 | Observation of Hyperpositive Non-Linear Effects in Asymmetric Catalysis | Asymmetric amplification is a phenomenon that plays a key role in the emergence of homochirality in life. In asymmetric catalysis, theoretical and experimental models have been investigated for understanding how chiral amplification is possible, in particular through non-linear effect. In the most remarkable cases, the degree of enantio-induction from a non-enantiopure catalyst can be as high as with an enantiopure reference system. Interestingly, it has been proposed a quarter century ago that chiral catalysts, when not enantiopure may be more enantioselective than their enantiopure counterparts, though such a case has never been observed to date. We show here than such hyperpositive non-linear effect in asymmetric catalysis is absolutely possible. A depth study into the underlying mechanism was carried out and our conclusion differs from the proposed models.<br /> | Yannick Geiger; thierry achard; aline maisse-françois; Stephane Bellemin-Laponnaz | Stereochemistry; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741aaf96a00667e2864af/original/observation-of-hyperpositive-non-linear-effects-in-asymmetric-catalysis.pdf |
67a87f146dde43c9082a374d | 10.26434/chemrxiv-2025-bzv25 | Dynamics and Resilience for Design of Sustainable Processes, Industrial Networks and Supply Chains: Review and Perspective | Engineers are increasingly faced with the question of sustainable design of processes, industrial networks and supply chains. Conventional steady-state methodologies prevalent for sustainability assessment are inadequate to address the dynamic complexities of multiscale systems with which this community deals. This review systematically examines the evolution of sustainability assessment frameworks, highlighting the limitations of static approaches in capturing the nonlinearity, feed- back loops, and temporal variability inherent across the multiple scales. We explore the transition to dynamic, data-driven methodologies, emphasizing the integration of hybrid mechanistic-machine learning models that bridge first-principles knowledge with data. Further, we highlight the importance of transdisciplinary concepts from ecological sciences such as non-linear dynamics and resilience to the design of industrial networks and supply chains. The perspective uncovers how these dynamic phenomena influence system stability, adaptability, and long-term sustainability by incorporating concepts such as time delays, hysteresis, and time-variant characteristics. We further examine stability landscapes and adaptive cycles to demonstrate how resilience thinking redefines process design and control strategies in the face of global uncertainties. The emergence of advanced computational tools, such as spatial-temporal deep learning architectures and adaptive process control strategies, is reshaping the sustainability of manufacturing supply chains. These innovations enable robust performance under dynamic conditions while aligning with circular economy objectives. By synthesizing resilience principles with dynamic sustainability assessments, this review establishes a transformative paradigm for chemical process network design, offering both theoretical insights and practical strategies to advance sustainability in chemical engineering practice and the future trajectory of research. | Abhimanyu Shekhar; William Farlessyost; Shweta Singh | Chemical Engineering and Industrial Chemistry; Industrial Manufacturing | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a87f146dde43c9082a374d/original/dynamics-and-resilience-for-design-of-sustainable-processes-industrial-networks-and-supply-chains-review-and-perspective.pdf |
67885fef81d2151a0255216c | 10.26434/chemrxiv-2025-rnbdx | Ultrastrong Coupling by Assembling Plasmonic Metal Oxide Nanocrystals in Open Cavities | Plasmon polaritons created by coupling optical cavity modes with plasmonic resonances offer widely tunable frequencies and strong light-matter interaction. While metallic nanocrystals (NCs) are compelling building blocks, existing approaches for their photonic integration are not scalable, limiting systematic study and potential applications. Here, we assemble colloidal tin-doped indium oxide NCs in a straightforward Salisbury screen configuration to realize an 'open' cavity structure, where the infrared resonance frequencies of the NC assembly and the photonic mode are independently controlled and strongly coupled. By modeling each NC layer as an effective medium, we designed cavities with plasmon-polariton spectra tuned to target frequencies, for example approximating the two atmospheric transparency windows. NCs with varying ligands and doping concentrations can be stacked in the assemblies to customize the spectral lineshape and control the spatial distribution of the electric near-field within the assembly. We anticipate applications in chemosensing and photonic technologies. | Woo Je Chang; Benjamin Roman; Tanay Paul; Zarko Sakotic; Priyansh Vora; Kihoon Kim; Daniel Wasserman; Thomas Truskett; Delia Milliron | Physical Chemistry; Materials Science; Nanoscience; Optical Materials; Nanostructured Materials - Nanoscience; Plasmonic and Photonic Structures and Devices | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67885fef81d2151a0255216c/original/ultrastrong-coupling-by-assembling-plasmonic-metal-oxide-nanocrystals-in-open-cavities.pdf |
60c73ed7702a9b8fdf189e31 | 10.26434/chemrxiv.7108706.v1 | Influence of Metal Substitution on the Pressure-Induced Phase Change in Flexible Zeolitic Imidazolate Frameworks | <p>Metal–organic frameworks that display step-shaped adsorption profiles arising from discrete pressure-induced phase changes are promising materials for applications in both high-capacity gas storage and energy-efficient gas separations. The thorough investigation of such materials through chemical diversification, gas adsorption measurements, and <i>in situ </i>structural characterization is therefore crucial for broadening their utility. We examine a series of isoreticular, flexible zeolitic imidazolate frameworks (ZIFs) of the type M(bim)<sub>2</sub> (SOD; M = Zn<sup> </sup>(ZIF-7), Co (ZIF-9), Cd (CdIF-13); bim<sup>–</sup> = benzimidazolate), and elucidate the effects of metal substitution on the pressure-responsive phase changes and the resulting CO<sub>2</sub> and CH<sub>4</sub> step positions, pre-step uptakes, and step capacities. Using ZIF-7 as a benchmark, we reexamine the poorly understood structural transition responsible for its adsorption steps and, through high-pressure adsorption measurements, verify that it displays a step in its CH<sub>4 </sub>adsorption isotherms. The ZIF-9 material is shown to undergo an analogous phase change, yielding adsorption steps for CO<sub>2</sub> and CH<sub>4</sub> with similar profiles and capacities to ZIF-7, but with shifted threshold pressures. Further, the Cd<sup>2+</sup> analogue CdIF-13 is reported here for the first time, and shown to display adsorption behavior distinct from both ZIF-7 and ZIF-9, with negligible pre-step adsorption, a ~50% increase in CO<sub>2</sub> and CH<sub>4</sub> capacity, and dramatically higher threshold adsorption pressures. Remarkably, a single-crystal-to-single-crystal phase change to a pore-gated phase is also achieved with CdIF-13, providing insight into the phase change that yields step-shaped adsorption in these flexible ZIFs. Finally, we show that the endothermic phase change of these frameworks provides intrinsic heat management during gas adsorption. </p> | C. Michael McGuirk; Tomče Runčevski; Julia Oktawiec; Ari Turkiewicz; mercedes K. taylor; Jeffrey R. Long | Coordination Chemistry (Inorg.); Inorganic Acid/Base Chemistry; Main Group Chemistry (Inorg.); Supramolecular Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2018-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73ed7702a9b8fdf189e31/original/influence-of-metal-substitution-on-the-pressure-induced-phase-change-in-flexible-zeolitic-imidazolate-frameworks.pdf |
65cbc352e9ebbb4db94a358b | 10.26434/chemrxiv-2024-274k4 | Theoretical and experimental insights into the spatial distribution of functional groups in multivariate flexible metal-organic framework JUK-8(Br)(NO2) | Dynamic multicomponent metal-organic frameworks, comprising numerous functional groups attached to a flexible backbone, expedite the complexity of coordination chemistry. Both factors, stimuli-responsiveness, and non-homogeneous environ-ments, are pivotal for creating complex systems that bring scientists closer to understanding biological structures, nevertheless, com-prehension of such systems remains largely unexplored. Inspired by this concept, we prepared a series of flexible multivariate JUK-8(NO2)x(Br)1-x (0 < x < 1) compounds (MTV-MOFs) and introduced experimental and theoretical methodologies for their investiga-tion. 1H-NMR was employed to determine the molar fraction of the linker in the bulk sample, whereas single crystal X-ray diffraction verified this value for single crystals. CO2 adsorption studies at 195 K revealed that the monosubstituted JUK-8(NO2) transitioned from a less porous to a porous phase at p/p0 ~ 0.20, while for JUK-8(Br), this process occurred at p/p0 ~ 0.58. For the MTV-MOFs, in contrast to the anticipated steady increase in transformation pressure with the molar fraction of Br-pip, xBr, we observed a constant gate opening pressure, p/p0 ~ 0.33, across a broad range of xBr,
0.27-0.63, and then its gradual increase up to p/p0 ~ 0.48 for xBr up to 0.96. Resolving the crystal structure of the closed phases of JUK-8(Br) and JUK-8(NO2) allowed us to identify the crucial interactions governing this phenomenon. Finally, by constructing theo-retical models of a multivariate structure and employing solid-state NMR crystallography supported by DFT simulation, we shed light on the possible spatial arrangement of functional groups in JUK-8(NO2)0.50(Br)0.50. Overall, our report introduces a methodology that could potentially be utilized for investigating multicomponent flexible MOFs. | Kornel Roztocki; Monika Szufla; Filip Formalik; Volodymyr Bon; Anna Krawczuk; Piotr Paluch; Marta K. Dudek; Stefan Kaskel; Dariusz Matoga | Materials Science; Inorganic Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65cbc352e9ebbb4db94a358b/original/theoretical-and-experimental-insights-into-the-spatial-distribution-of-functional-groups-in-multivariate-flexible-metal-organic-framework-juk-8-br-no2.pdf |
6616685991aefa6ce13fa40e | 10.26434/chemrxiv-2024-87mtm | Synthesis, characterization and stability of phosphonium phenolate zwitterions derived from a (diphenylphosphino)phenol derivative and oxiranes | Phosphonium phenolate zwitterions have been synthesized from 2,4-di-tert-butyl-6-(diphenylphosphino)phenol and five different oxirane derivatives. The reaction does not proceed at a detectable rate when the two reactants are combined in dichloromethane at room temperature. Despite the substantial ring strain, the reaction proceeds only with the addition of methanol, which acts as a hydrogen transfer shuttle, allowing a slow conversion to the desired zwitterions. The compounds have been fully characterized and single crystal X-ray crystallography has been performed on the methyloxirane and the phenyl glycidyl ether-derived zwitterion. The phosphonium phenolate units exhibit an ylidic bonding situation as evidenced by spectroscopic and crystallographic analysis. Glycidyl ethers were found to react faster than alkyl and aryloxiranes. Decomposition studies of the zwitterions showed high thermal stability in solution under ambient conditions. Under forced conditions (150 °C, 6 h), decomposition to the corresponding phosphine oxide and secondary aliphatic alcohols, the formally hydrogenated oxirane derivative, was observed. | Matthias Steiner; Christoph Marschner; Judith Baumgartner; Johann Hlina; Christian Slugovc | Organic Chemistry; Polymer Science; Organic Synthesis and Reactions | CC BY NC 4.0 | CHEMRXIV | 2024-04-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6616685991aefa6ce13fa40e/original/synthesis-characterization-and-stability-of-phosphonium-phenolate-zwitterions-derived-from-a-diphenylphosphino-phenol-derivative-and-oxiranes.pdf |
60c74998337d6c6a56e2773e | 10.26434/chemrxiv.12084672.v1 | Stereoselective Synthesis of Unnatural α-Amino Acids through Photoredox Catalysis | A protocol for stereoselective C-radical addition to a chiral glyoxylate-derived sulfinyl imine was developed through visible light-promoted photoredox catalysis, providing a convenient method for the synthesis of unnatural α-amino acids. The developed protocol allows the use of ubiquitous carboxylic acids as radical precursors without prior derivatization. The protocol utilizes near-stoichiometric amounts of the imine and the acid radical precursor in combination with a catalytic amount of an organic acridinium-based photocatalyst. The mechanism for the developed transformation is discussed and the stereodetermining radical addition step was studied by the DFT calculations. | Andrey Shatskiy; Anton Axelsson; Björn Blomkvist; Jian-Quan Liu; Peter Dinér; Markus Kärkäs | Photocatalysis; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74998337d6c6a56e2773e/original/stereoselective-synthesis-of-unnatural-amino-acids-through-photoredox-catalysis.pdf |
64675f5afb40f6b3eed5ab49 | 10.26434/chemrxiv-2023-rk0k1 | A New Low-Barrier Hydrogen Bond System: Free-Base Corrole Anion
| Free-base corroles have long been known to be acidic, readily undergoing deprotonation by mild bases and in polar solvents. The conjugate base, however, has not been structurally characterized until now. Presented here is a first crystal structure of a free-base corrole anion, derived from tris(p-cyanophenyl)corrole, as the tetrabuylammonium salt. The low-temperature (100 K) structure reveals localized hydrogens on a pair of opposite pyrrole nitrogens. DFT calculations identify such a structure as the global minimum but also point to two cis tautomers only 4-7 kcal/mol above the ground state. In terms of free energy, however, the cis tautomers are above or essentially flush with the trans-to-cis barrier so the cis tautomers are unlikely to exist or be observed as true intermediates. Thus, the hydrogen bond within each dipyrrin unit on either side of the molecular pseudo-C2 axis through C10 (i.e., between pyrrole rings A and B, or between C and D) qualifies as or very closely approaches a low-barrier hydrogen bond. Proton migration across the pseudo-C2 axis entails much higher activation energies > 20 kcal/mol, reflecting the relative rigidity of the molecule along the C1-C19 pyrrole-pyrrole linkage. | Arup Tarai; Jyoti Prakash Mallick; Pranjali Singh; Jeanet Conradie; Sanjib Kar; Abhik Ghosh | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Physical Organic Chemistry; Computational Chemistry and Modeling; Crystallography – Organic | CC BY 4.0 | CHEMRXIV | 2023-05-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64675f5afb40f6b3eed5ab49/original/a-new-low-barrier-hydrogen-bond-system-free-base-corrole-anion.pdf |
60c74149842e65255bdb1e55 | 10.26434/chemrxiv.8003717.v1 | A New Phase of the Na+ Ion Conductor Na3PS4 | <div>
<p>Solid electrolytes are crucial for next‑generation
solid‑state batteries and Na<sub>3</sub>PS<sub>4</sub> is one of the most
promising Na<sup>+</sup> conductors for such applications. At present, two
phases of Na<sub>3</sub>PS<sub>4</sub> have been identified and it had been
thought to melt above 500 °C. In contrast, we show that it remains solid above this temperature
and transforms into a third polymorph, γ, exhibiting superionic behavior. We
propose an orthorhombic crystal structure for γ‑Na<sub>3</sub>PS<sub>4</sub>
based on scattering density analysis of diffraction data and density functional
theory calculations. We show that the Na<sup>+</sup> superionic behavior is associated
with rotational motion of the thiophosphate polyanions pointing to a rotor
phase, based on <i>ab initio</i> molecular
dynamics simulations and supported by high‑temperature synchrotron and neutron
diffraction, thermal analysis and impedance spectroscopy. These findings are of
importance for the development of new polyanion‑based solid electrolytes.</p>
</div> | Theodosios Famprikis; James Dawson; François Fauth; Emmanuelle Suard; Benoit Fleutot; Matthieu Courty; Jean-Nöel Chotard; Saiful Islam; Christian Masquelier | Solid State Chemistry; Computational Chemistry and Modeling; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74149842e65255bdb1e55/original/a-new-phase-of-the-na-ion-conductor-na3ps4.pdf |
60c753560f50db1afc397b53 | 10.26434/chemrxiv.13477275.v1 | Surface-Induced Dissociation of Protein Complexes Selected by Trapped Ion Mobility Spectrometry | <p><a>Native
mass spectrometry, particularly in conjunction with gas-phase ion mobility
spectrometry measurements, has proven useful as a structural biology tool for
evaluating the stoichiometry, conformation, and topology of protein complexes. Here,
we demonstrate the combination of trapped ion mobility spectrometry (TIMS) and
surface-induced dissociation (SID) on a Bruker SolariX XR 15 T FT-ICR mass spectrometer
for structural analysis of protein complexes. We successfully performed SID on
mobility-selected protein complexes, including streptavidin tetramer and cholera
toxin B with bound ligand. Additionally, TIMS-SID was employed on a mixture of
peptides bradykinin desR1 and desR9 to mobility separate and identify the
individual peptides. Importantly, results show that native-like conformations
can be maintained throughout the TIMS analysis. The TIMS-SID spectra are
analogous to SID spectra acquired using quadrupole mass selection, indicating
little measurable, if any, structural rearrangement during mobility selection.
Mobility parking was used on the ion or mobility of interest and 50 to 200 SID
mass spectra were averaged. High quality TIMS-SID spectra were acquired over a
period of 2-10 minutes, comparable to or slightly longer than SID coupled with
ion mobility on various instrument platforms in our laboratory. The ultrahigh
resolving power of the 15 T FT-ICR allowed for the identification and relative
quantification of overlapping SID fragments with the same nominal <i>m/z</i>
based on isotope patterns and shows promise as a platform to probe small mass
differences, such as protein-ligand binding or post-translational modifications.
These results represent the potential of TIMS-SID-MS for the analysis of both
protein complexes and peptides.</a></p> | Erin Panczyk; Dalton Snyder; Mark. E. Ridgeway; Arpad Somogyi; Melvin A. Park; Vicki Wysocki | Analytical Apparatus; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753560f50db1afc397b53/original/surface-induced-dissociation-of-protein-complexes-selected-by-trapped-ion-mobility-spectrometry.pdf |
60c74db8469df42e84f4433f | 10.26434/chemrxiv.12654602.v1 | Fc-Binding Antibody-Recruiting Molecules Targeting Prostate-Specific Membrane Antigen: Defucosylation of Antibody for Efficacy Improvement | <div>
<div>
<div>
<p>Synthetic small molecules that redirect endogenous antibodies to target cells are promising
drug candidates because they overcome the potential shortcomings of therapeutic antibodies,
such as immunogenicity. Previously, we reported a novel class of bispecific molecules
targeting the antibody Fc region and folate receptor, named Fc-binding antibody-recruiting
molecules (Fc-ARMs). Fc-ARMs can theoretically recruit most endogenous antibodies,
inducing cancer cell elimination via antibody-dependent cell-mediated cytotoxicity (ADCC).
Here, we describe new Fc-ARMs that target prostate cancer (Fc-ARM-Ps). Fc-ARM-Ps
recruited antibodies to cancer cells expressing prostate membrane-specific antigen but did so
with lower efficiency compared with Fc-ARMs targeting folate receptor. Upon recruitment by
Fc-ARM-P, defucosylated antibodies efficiently activated natural killer cells and induced
ADCC, whereas antibodies with intact N-glycans did not. The results suggest that the affinity
between recruited antibodies and CD16a, a type of Fc receptor expressed on immune cells,
could be a key factor controlling immune activation in the Fc-ARM strategy.
</p>
</div>
</div>
</div> | Koichi Sasaki; Minori Harada; Takuma Yoshikawa; Hiroshi Tagawa; Yui Harada; Yoshikazu Yonemitsu; Taka-aki Ryujin; Akihiro Kishimura; Takeshi Mori; Yoshiki Katayama | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74db8469df42e84f4433f/original/fc-binding-antibody-recruiting-molecules-targeting-prostate-specific-membrane-antigen-defucosylation-of-antibody-for-efficacy-improvement.pdf |
610a5f1e18911d80b6d9b3d0 | 10.26434/chemrxiv-2021-hkth2-v2 | The Phospha-Bora-Wittig Reaction | We report the phospha-bora-Wittig reaction for the direct preparation of phosphaalkenes from aldehydes, ketones, esters, or amides. The transient phosphaborene Mes*P=B-NR2 reacts with carbonyl compounds to form 1,2,3-phosphaboraoxetanes, analogues of oxaphosphetane intermediates in the classical Wittig reaction. 1,2,3-phosphaboraoxetanes undergo thermal or Lewis acid-promoted cycloreversion, yielding phosphaalkenes. Experimental and density functional theory studies reveal far-reaching similarities between classical and phospha-bora-Wittig reactions. | Andryj Borys; Ella Rice; Gary Nichol; Michael Cowley | Inorganic Chemistry; Organometallic Chemistry; Frustrated Lewis Pairs; Kinetics and Mechanism - Inorganic Reactions; Main Group Chemistry (Inorg.) | CC BY NC 4.0 | CHEMRXIV | 2021-08-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/610a5f1e18911d80b6d9b3d0/original/the-phospha-bora-wittig-reaction.pdf |
633c7396975e94051f93bda3 | 10.26434/chemrxiv-2022-43vvb | Synthesis of pyrrothiamine, a novel thiamine analogue, and evaluation of derivatives as potent and selective inhibitors of pyruvate dehydrogenase | Inhibition of thiamine pyrophosphate (TPP)-dependent enzymes with thiamine/TPP analogues that have the central thiazolium ring replaced with other rings is well established, but a limited number of central rings have been reported. We report a novel analogue, pyrrothiamine, with a central pyrrole ring. We further develop pyrrothiamine derivatives as potent and selective inhibitors of pyruvate dehydrogenase, which might have anti-cancer potential. | Alex H. Y. Chan; Terence C. S. Ho; Kwasi Agyei-Owusu; Finian James Leeper | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC 4.0 | CHEMRXIV | 2022-10-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/633c7396975e94051f93bda3/original/synthesis-of-pyrrothiamine-a-novel-thiamine-analogue-and-evaluation-of-derivatives-as-potent-and-selective-inhibitors-of-pyruvate-dehydrogenase.pdf |
63ed6cb0fcfb27a31fdbb159 | 10.26434/chemrxiv-2023-8tm82 | Probing the Mechanism of Hydrolytic Degradation of Nerve Agent Simulant with Zirconium-based Metal-Organic Frameworks | Metal-organic frameworks (MOFs) have been reported to effectively detoxify chemical warfare agents (CWAs) and their simulants. Early studies of Zr-MOF-catalyzed hydrolytic degradation of an organophospho-ester type CWA, Sarin, and its simulant, dimethyl-4-nitrophenylphosphate (DMNP), suggested that the activity originates from ZrIV-OH-ZrIV moieties that resemble the structure of the active-site phosphotriesterase enzyme. Measurements of pKa values for hexa-zirconium-node-sited bridging hydroxo, terminal hydroxo, and aqua ligands reveal essentially complete conversion of mu-hydroxo ligands to substitution-inert mu-oxo ligands at alkaline pHs, ruling out a primary role for ZrIV-OH-ZrIV moieties, despite the resemblance to the phosphotriesterase enzyme active-site. The measurements also rule out a secondary role as a hydrogen bond donor/stabilizer of bound DMNP. Additionally, the measurements show that reactant-displaceable node-aqua ligands become increasingly scarce in increasingly alkaline environments. Here, rates of catalyzed hydrolysis reaction were examined experimentally to ascertain reaction orders and, in turn, interrogate the mechanism. In striking contrast to the ubiquitous Zr-MOF, UiO-66, for which simulant displacement of water as a node ligand is rate-determining, and the rate of catalysis (in alkaline environments) increases with decreasing pH, catalysis by NU-1000 is rate-limited by solution hydroxide attack of the nitrophenoxide-phosphorous bond of the MOF-activated simulant, with the overall hy-drolysis rate being remarkably insensitive to pH (or pOH). Underlying the unusually weak sensitivity of rates of hydroly-sis to pH is almost exact counter-balancing of the prevalence of catalyst active-sites (Zr-OH2 sites) with activity of the re-action nucleophile, free hydroxide ion, as a function of pH. We ascribe the residual pH dependence of the overall rate to a charge-based modulation of the equilibrium constant for simulant binding to the node. In contrast to overall hydrolysis rates, the catalyst turnover frequencies per Zr-OH2 active-site are strongly pH dependent, exceeding 30,000 s-1 at pH 10.5. | Yijun Liao; Thomas Sheridan; Jian Liu; Zhiyong Lu; KaiKai Ma; Omar Farha; Joseph Hupp | Inorganic Chemistry; Catalysis; Heterogeneous Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63ed6cb0fcfb27a31fdbb159/original/probing-the-mechanism-of-hydrolytic-degradation-of-nerve-agent-simulant-with-zirconium-based-metal-organic-frameworks.pdf |
64efa6b7dd1a73847fd871f5 | 10.26434/chemrxiv-2023-w3mmv | Alternative synthetic routes for the encapsulation of proteins: overcoming the elusive mineralization of HKUST-1 in water | Alternative synthetic procedures to obtain protein@HKUST-1 composites from protein@Cu-BTC dense composites are reported. pH dependent dense phase precursors are first obtained and their biocompatible transformations into HKUST-1 are characterized. Encapsulation efficiency is affected by the nature of the protein, and can be modulated by the sequential or simultaneous addition of the MOF precursors. | Jesús Cases Díaz; Mónica Giménez-Marqués | Inorganic Chemistry; Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64efa6b7dd1a73847fd871f5/original/alternative-synthetic-routes-for-the-encapsulation-of-proteins-overcoming-the-elusive-mineralization-of-hkust-1-in-water.pdf |
661d7d3891aefa6ce19ff124 | 10.26434/chemrxiv-2023-0t2w2-v2 | Dynamic partitioning of surfactants into non-equilibrium emulsion droplets | Characterizing the propensity of molecules to distribute between fluid phases is key to describing chemical concentrations in heterogenous mixtures and the corresponding physiochemical properties of a system. Usually, partitioning is studied under equilibrium multiphase conditions. However, there are situations where a mixture may form only a single phase at equilibrium but can exist in multiple phases when out-of-equilibrium. Emulsion droplets, such as oil-in-water droplets stabilized by surfactant, are one such example. Droplets are often thermodynamically unstable and persist under non-equilibrium conditions for some time while disappearing by dissolution or solubilization over longer timescales. Consequently, equilibrium properties like partition coefficients or interfacial tensions may not necessarily describe the properties of an out-of-equilibrium droplet. Here, the partitioning of nonionic surfactants between microscale oil droplets and water is investigated under non-equilibrium conditions wherein the droplets shrink in volume over time via solubilization and only a single phase exists at equilibrium. Quantitative mass spectrometry is used to analyze the composition of individual micro-droplets as a function of time under conditions of varying surfactant composition, concentration, and oil molecular structure. Common nonionic surfactants partition into oil micro-droplets within minutes and reach a non-equilibrium steady state concentration that can be orders of magnitude higher than the aqueous phase. Over timescales of hours, the droplet solubilizes and sheds accumulated surfactant back into the water. Transiently high concentrations of oil and surfactant accumulate near the oil droplet - water interface over time, which leads to the localized evolution of a microemulsion phase and unexpectedly low interfacial tension. The introduction of an ionic surfactant that forms mixed micelles with the nonionic surfactant reduces the nonionic surfactant transfer into oil. Based on this observation, we use stimuli-responsive ionic surfactants to trigger phase separation and mixing inside binary oil droplets via modulation of the nonionic surfactant partitioning. This study thus reveals generalizable non-equilibrium states and conditions experienced by solubilizing droplets that govern emulsion properties. | Rebecca Balaj; Wangyang Xue; Parvin Bayati; Stewart Mallory; Lauren Zarzar | Physical Chemistry; Interfaces; Solution Chemistry; Transport phenomena (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661d7d3891aefa6ce19ff124/original/dynamic-partitioning-of-surfactants-into-non-equilibrium-emulsion-droplets.pdf |
62dfac10dc4c7868da3fe8a7 | 10.26434/chemrxiv-2022-f0mfq | [4]Triangulenes with Three Oxygen-Boron-Oxygen (OBO) Units and Anti-Kasha Emissions | Triangulenes have attracted enormous interest due to the intriguing properties. However, the limited synthetic approach and intrinsic instability make the investigation of their properties inaccessible. The synthesis of heteroatom-doped triangulenes becomes an alternative strategy of studying triangulenes. Herein, we report the synthesis of three [4]triangulenes, which are edge-modified by three oxygen-boron-oxygen (OBO) units. The structure of OBO-doped [4]triangulene is confirmed by the single-crystal X-ray diffraction analysis, revealing an off-plane core with three edge-modified OBO units. These OBO-doped [4]triangulenes exhibit high stability towards air and moisture. Both theoretical calculations and photophysical investigation of OBO-doped [4]triangulenes indicate that this kind of molecules display anti-Kasha fluorescence and phosphorescence emissions. The binding behaviors of (OBO)3-[4]triangulenes toward pyridine were also studied. | Xiaobin Chen; Dehui Tan; Jiaqi Dong; Tinghao Ma; Deng-Tao Yang | Organic Chemistry; Organic Compounds and Functional Groups; Photochemistry (Org.); Materials Chemistry; Crystallography – Organic | CC BY NC 4.0 | CHEMRXIV | 2022-07-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62dfac10dc4c7868da3fe8a7/original/4-triangulenes-with-three-oxygen-boron-oxygen-obo-units-and-anti-kasha-emissions.pdf |
67a1e93281d2151a022179a8 | 10.26434/chemrxiv-2025-tq3bh | The Quasi-bound State as a Predictor of Relative Binding Free Energy | Relative binding free energy (ΔΔGbind) predictions have become the main approach to evaluate the potency of a congeneric series of compounds. They are enabled by alchemical transformations coupled to free energy methods, tools that have become essential in drug design. Yet, they are computationally expensive and are limited to small and relatively simple transformations. The ever-increasing size of virtual screening databases demands faster methods to assess virtual hits. Here, we show that the structural robustness of protein-ligand complexes, measured as the quasi-bound free energy (ΔGQB) by Dynamic Undocking (DUck), is well suited to detect outliers in the structure-activity continuum (i.e., activity cliffs), which are particularly challenging for knowledge-based approaches. On congeneric series of HSP90α, CDK2 and BACE-1 inhibitors, we demonstrate that ΔGQB can deliver excellent predictions, despite the local nature of the measurement, in some cases, comparable to the much more computationally demanding alchemical transformation methods. We find that for systems following a one-step dissociation model, ΔGQB actually informs about the free energy of the transition state, which allows us to predict relative binding kinetics and, when the series present relatively constant on-rates, also ΔΔGbind.This work has important implicatinos for drug discovery, as it shows that within a well-defined applicability domain, high-throughput computational dissociation studies can deliver ΔΔGbind predictions that compare well with rigorous alchemical transformation methods. | Álvaro Serrano-Morrás; Yvonne Westermaier; Maciej Majewski; Xavier Barril | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2025-02-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a1e93281d2151a022179a8/original/the-quasi-bound-state-as-a-predictor-of-relative-binding-free-energy.pdf |
66e3a03bcec5d6c142e9f3f6 | 10.26434/chemrxiv-2024-ld2k6 | Physics-Guided Neural Networks for Transferable Prediction of Polymer Properties | The architectural, compositional, and chemical complexities of polymers are fundamentally important to their properties; however, these same factors obfuscate effective predictions. Machine learning offers a promising approach for predicting polymer properties, but model transferability remains a major challenge, particularly when data is insufficient due to high acquisition costs and practical limitations. We explore the integration of polymer physics theory with machine learning architectures to enhance the predictive capabilities of polymer properties. Using a dataset of 18,450 polymers with diverse architectures, molecular weights, compositions, and chemical patterns, we focus on transferability tasks for predicting moments of the distribution of squared radius of gyration. Our tandem model, GC-GNN, which combines a graph neural network with a fittable model based on ideal Gaussian chain theory, surpasses both standalone polymer-physics and graph neural network models in predictive accuracy and transferability. We also demonstrate that predictive transferability varies with polymer architecture due to deviations from the ideal Gaussian chain assumption. This study highlights the potential of combining polymer physics with data-driven models to improve predictive transferability across diverse conditions and also pathways for improvement. | Shengli Jiang; Michael Webb | Theoretical and Computational Chemistry; Materials Science; Polymer Science; Polymer chains; Polymer morphology; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e3a03bcec5d6c142e9f3f6/original/physics-guided-neural-networks-for-transferable-prediction-of-polymer-properties.pdf |
67637673fa469535b9093148 | 10.26434/chemrxiv-2024-bm3b9 | SeroWare: An Open-Source Software Suite for
Voltammetry Data Acquisition and Analysis | Voltammetry is widely used for fast, data-dense measurements of redox-active analytes in versatile environments, including the brain. Voltammetry requires minimal hardware beyond a potentiostat, a front-end amplifier, and a computer. Nonetheless, researchers must often develop or modify software packages for application-specific uses. Of the voltammetry software available, significant issues exist with source code inaccessible for updating or customization, non-configurable data processing procedures, and hardware incompatibilities. These limitations, coupled with the recent proliferation of waveform types and increased demands for high bandwidth data acquisition and efficient data processing, create the need for sophisticated, powerful, and flexible voltammetry software. We report developing ‘SeroWare’, an open-source, end-to-end voltammetry acquisition and analysis software designed to handle a wide variety of use cases encountered by voltammetry users. Although inspired by neurochemical analyses, this software is flexible, customizable, and compatible with open-source toolkits. The modular software architecture enables users to generate, acquire, and analyze voltammetry data of different types, ranging from pulse and sweep waveforms to fast and slow scans via easily accessible and exportable file formats. Template code is provided for communicating with a variety of standard external devices. We report several novel features for waveform applications and data flow. In-depth documentation in a User Guide and video tutorials are provided to enable new research directions, particularly regarding shareability and lowering the barriers to entry for new investigators. | Cameron Movassaghi; Rahul Iyer; Maya Curry; Mila Wesely ; Miguel Alcañiz ; Anne Andrews | Analytical Chemistry; Electrochemical Analysis | CC BY NC 4.0 | CHEMRXIV | 2024-12-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67637673fa469535b9093148/original/sero-ware-an-open-source-software-suite-for-voltammetry-data-acquisition-and-analysis.pdf |
60c755e6702a9b7b7f18c7db | 10.26434/chemrxiv.13547774.v2 | Organic Functionalization at the Si(001) Dimer Vacancy Defect – Structure, Bonding and Reactivity | In this density functional theory study, the influence of the dimer vacancy on the reactivity of the Si(001) surface is investigated. To this end, electronic and structural properties of the defect are analyzed. Band structure calculations reveal a higher-lying valence band which would suggest increased reactivity. However, the opposite is found when organic molecules for interface formation (acetylene, ethylene and cyclooctyne) are adsorbed at the defect. Significant reaction barriers have to be overcome in order to form bonds with defect atoms, while adsorption on the pristine surface is mostly direct. This suggests the presence of a, rather weak, Si-Si bond across the defect which must be dissociated before organic adsorbates can react. A rich adsorption and reaction network is found in addition to the structures known from the pristine surface. All three investigated adsorbates show different bonding characteristics. For acetylene and ethylene, the preferred thermodynamic sink is the insertion into the defect, with the latter molecule even dissociating. Bulky cyclooctyne on the other hand avoids reaction with the defect due to steric demands imposed by the small defect cavity. The DV has no effect on reactivity of neighboring dimers. A combination of defect creation and hydrogen-precoverage could be a promising approach for selective surface functionalization. We thus show the influence of a non-ideal surface on organic functionalization and interface build-up reactions for a prototypical interface. <br /> | Jan-Niclas Luy; Ralf Tonner | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755e6702a9b7b7f18c7db/original/organic-functionalization-at-the-si-001-dimer-vacancy-defect-structure-bonding-and-reactivity.pdf |
63d36d8b1125967e607c0549 | 10.26434/chemrxiv-2023-hjtr2 | Pentaenolate Activation in the Organocatalytic Allylic Alkylation of Indene-2-carbaldehydes | In the manuscript, the application of pentaenolate chemistry for the allylic alkylation of indene-2-carbaldehydes with Morita-Baylis-Hillman (MBH) carbonates is described. The reaction has been realized in a highly enantio- and diastereoselective manner owing to the use of chiral tertiary amine acting as nucleophilic catalyst. Developed reactivity constitutes the first application of organocatalytic pentaenolate activation in asymmetric synthesis expanding the arsenal of catalytic methods. It leads to the formation of synthetically useful building blocks for target oriented synthesis as confirmed in selected transformations of the products. | Adam Cieśliński; Sebastian Frankowski; Łukasz Albrecht | Organic Chemistry; Catalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d36d8b1125967e607c0549/original/pentaenolate-activation-in-the-organocatalytic-allylic-alkylation-of-indene-2-carbaldehydes.pdf |
66f28447cec5d6c1420a66e3 | 10.26434/chemrxiv-2024-6fcxp | Transient Kinetic Investigation of Chain Growth during CO Hydrogenation on Co/TiO2 under Fischer-Tropsch Conditions: Elemental Balance of Species Adsorbed at the Catalyst Surface | CO hydrogenation is a promising approach for the storage of renewable energy in the form of hydrocarbons via the Fischer-Tropsch synthesis (FTS). Since transient operation of FTS reactors might be necessary and even be beneficial, transient kinetics for a rational catalyst and reactor design are essential. In order to advance the development of such transient kinetics, the periodic transient kinetics (PTK) method was applied to the CO hydrogenation on a Co/TiO2 catalyst under FT-like conditions. It was revealed that there are two carbon species of different reactivity, Cα and Cβ, present on the catalyst surface during the reaction. Cα forms fast within a few seconds and is highly reactive, while Cβ forms slowly, is accumulating on the surface over a longer time and imposes an inhibiting effect. However, a contribution of Cβ to the chain growth reaction was shown. Finally, the transient experimental results are evaluated based on a material balance and the amounts of Cα and Cβ present on the catalyst surface during the reaction were determined. | Max Gäßler; Simon Hermann; Jens Friedland; Jakob Stahl; Lutz Mädler; Robert Güttel | Catalysis; Chemical Engineering and Industrial Chemistry; Reaction Engineering; Heterogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2024-09-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f28447cec5d6c1420a66e3/original/transient-kinetic-investigation-of-chain-growth-during-co-hydrogenation-on-co-ti-o2-under-fischer-tropsch-conditions-elemental-balance-of-species-adsorbed-at-the-catalyst-surface.pdf |
67bc2f93fa469535b9ae2304 | 10.26434/chemrxiv-2025-nt0jx | QC-Augmented GNNs for Few-Shot Prediction of Amorphous Polymer Properties via Multi-Scale Microstructures | Accurate prediction of polymer properties is essential for material design. However, traditional methods often struggle with efficiency due to the limited availability of experimental data and insufficient understanding of polymer microstructures, particularly in the case of small datasets for amorphous polymers. To address this hallenge, we introduce a novel paradigm based on "local clusters", structural motifs whose properties are efficiently computed using quantum chemistry (QC) methods. These clusters, simulated across multiple scales, serve as key descriptors that encapsulate essential microstructural features of polymers. By integrating these QC-derived descriptors with graph convolutional networks (GNNs) or neural networks (NNs), we have developed Locluster, a multiscale, microstructure-driven predictive model tailored for data-scarce environments in amorphous polymer research. Notably, Locluster requires only 2–5 descriptors and as few as two dozen training samples to accurately predict critical polymer properties, including density, refractive index, dielectric constant, and glass transition temperature. The model achieves predictive performance comparable to approaches trained on large datasets, thereby effectively mitigating the data scarcity challenge in polymer informatics. This work provides an effective option for the rational design and accelerated discovery of novel polymeric materials. | Yiwen Zhang; Zihao YE; Dejun HU; Shutao QI; Zuobang SUN; Junfeng YANG; Yan MA; Yi ZHANG; Junliang ZHANG; Zhiming LI | Theoretical and Computational Chemistry; Polymer Science | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67bc2f93fa469535b9ae2304/original/qc-augmented-gn-ns-for-few-shot-prediction-of-amorphous-polymer-properties-via-multi-scale-microstructures.pdf |
60c7587f567dfeb2bdec6882 | 10.26434/chemrxiv.14556072.v1 | Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations | <p>The control of the crystal form is a central issue in the pharmaceutical industry. The identification of putative polymorphs through Crystal Structure Prediction (CSP) methods is based on lattice energy calculations, which are known to significantly over-predict the number of plausible crystal structures. A valuable tool to reduce overprediction is to employ physics-based, dynamic simulations to coalesce lattice energy minima separated by small barriers into a smaller number of more stable geometries once thermal effects are introduced. Molecular dynamics simulations and enhanced sampling methods can be employed in this context to simulate crystal structures at finite temperature and pressure. </p><p>Here we demonstrate the applicability of approaches based on molecular dynamics to systematically process realistic CSP datasets containing several hundreds of crystal structures. The system investigated is ibuprofen, a conformationally flexible active pharmaceutical ingredient that crystallises both in enantiopure forms and as a racemic mixture. By introducing a hierarchical approach in the analysis of finite-temperature supercell configurations, we can post-process a dataset of 555 crystal structures, identifying 65% of the initial structures as labile, while maintaining all the experimentally known crystal structures in the final, reduced set. Moreover, the extensive nature of the initial dataset allows one to gain quantitative insight into the persistence and the propensity to transform of crystal structures containing common hydrogen-bonded intermolecular interaction motifs.</p> | Nicholas Francia; Louise Price; Matteo Salvalaglio | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7587f567dfeb2bdec6882/original/reducing-crystal-structure-overprediction-of-ibuprofen-with-large-scale-molecular-dynamics-simulations.pdf |
6520af778bab5d2055cca01e | 10.26434/chemrxiv-2023-b8ggw | Lattice-guided assembly of optoelectronically-active π-conjugated peptides on 1D van der Waals single crystals | The utility of organic functional units for high-performance materials and devices is highly dependent on the formation of ordered domains across extended regimes. As such, the development of synthetic approaches to achieve precisely ordered material building blocks, a process often complicated by the dynamic and sensitive nature of supramolecular interactions in many organic molecules, is critical in realizing efficient functional devices and emergent physical properties. To this end, we leveraged the long-range anisotropic ordering intrinsic to a class of 1D van der Waals (vdW) crystals comprised of sub-nanometer-thick transition metal trichalcogenide (MCh3; M = Ti, Zr, Hf, Nb, Ta; Ch = S, Se) chain subunits to guide the assembly of supramolecular π-conjugated peptide building blocks. Through this synthetic strategy, we realized morphologically well-defined organic-inorganic heterointerfaces that display drastically altered photophysical properties and are capable of photocurrent generation. Owing to the structural correspondence between the π-π interactions of the organic quaterthiophene (4T)-based π-conjugated peptides (DDD-4T) and the periodic sulfur ordering along the (100) planes of inorganic niobium sulfide (NbS3) 1D vdW crystals, we found that organic π-conjugated peptide monomers can readily form 1D supramolecular assemblies on the surface of the underlying inorganic crystal. Optimal assembly conditions allowed for the controlled deposition and growth of the peptide assemblies on the crystal surfaces as validated by a combination of fluorescence microscopy, photoluminescence map-ping, Raman spectroscopy, atomic force microscopy, and computational molecular dynamics simula-tions. The resulting DDD-4T/NbS3 heterointerfaced assemblies exhibit a significantly improved visi-ble-range photocurrent generation compared to the freestanding π-conjugated peptide films assembled from solution. Altogether, our study demonstrates the important role of lattice matching in the for-mation of ordered low-dimensional organic-inorganic heterointerfaces, offering a new approach to-wards directing the assembly of supramolecular organic building blocks endowed with improved opti-cal and optoelectronic properties. | Ze-Fan Yao; Dmitri Leo Cordova; Griffin Milligan; Diana Lopez; Steven Allison; Yuyao Kuang; Herdeline Ardona; Maxx Arguilla | Inorganic Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Solid State Chemistry; Supramolecular Chemistry (Inorg.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6520af778bab5d2055cca01e/original/lattice-guided-assembly-of-optoelectronically-active-conjugated-peptides-on-1d-van-der-waals-single-crystals.pdf |
649a92e79ea64cc1670a2dbf | 10.26434/chemrxiv-2023-17m4w-v2 | Immobilization of biotinylated antibodies through streptavidin binding aptamer | Liquid biopsy approaches are powerful strategies that potentially allow the diagnosis and prognosis of a number of diseases. The field is continuously and rapidly growing, encouraging the discovery of novel predictory biomarkers. Antibodies are usually exploited in sensors to validate biomarker candidates. Unfortunately, the immobilization of antibodies on the surface of sensors represents a challenging task. Immobilization strategies need to be optimized for each antibody, representing a huge obstacle to overcome in the discovery of new biomarkers. Herein we propose a novel strategy for the immobilization of antibodies, based on the use of a streptavidin-binding aptamer. Using this approach it is possible to immobilize antibodies on the surface of sensors with no need for optimization, with the only requirement for antibody to be biotinylated. The proposed strategy potentially paves the way towards a straightforward immobilization of antibodies on biosensors, making their use in biomarker validation more accessible. | Dario Brambilla; Laura Sola; Francesco Damin; Alessandro Mussida; Marcella Chiari | Analytical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649a92e79ea64cc1670a2dbf/original/immobilization-of-biotinylated-antibodies-through-streptavidin-binding-aptamer.pdf |
6461bfd9a32ceeff2dab16ff | 10.26434/chemrxiv-2022-fbggw-v2 | Development of Imidazolium-Based Parameters for AMOEBA–IL | A new approach for the efficient parametrization of the polarizable ionic liquid potential AMOEBA–IL, and its application to develop parameters for imidazoliumbased cations is presented. The new approach relies on the development of parameters for fragments that can be transferred to generate new molecules. The parametrization uses the original AMOEBA–IL parametrization approach, including the use of Gaussian Electrostatic Model Distributed Multipoles (GEM–DM) for the permanent multipoles and approximation of the Van der Waals parameters using quantum mechanics energy decomposition analysis (QM–EDA) data. Based on this, functional groups of the selected initial structures are employed as building blocks to develop parameters for new imidazolium-based cations (symmetric or asymmetric) with longer alkyl chains. The parameters obtained with this proposed method were compared with inter-molecular interactions from QM references via energy decomposition analysis using Symmetry Adapted Perturbation Theory (SAPT) and counterpoise-corrected total inter-molecular interactions. The validation of the new parametrized cations was carried out by running molecular dynamics simulations on a series of imidazolium-based ionic liquids with different anions to compare selected thermodynamic and transport properties, including density ρ, enthalpy of vaporization ΔHvap, radial distribution function g(r), and diffusion coefficients D±, with experimental data. Overall, the calculated gas-phase and bulk properties show good agreement with the reference data. The new procedure provides a straightforward approach to generating the required AMOEBA–IL parameters for any imidazolium-based cation. | JOSE ENRIQUE VAZQUEZ CERVANTES; G. Andres Cisneros | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2023-05-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6461bfd9a32ceeff2dab16ff/original/development-of-imidazolium-based-parameters-for-amoeba-il.pdf |
60c742ec9abda22ad8f8c0ce | 10.26434/chemrxiv.8835728.v1 | Cellulose Separators with Integrated Carbon Nanotube Interlayers for Lithium-Sulfur Batteries: An Investigation into the Complex Interplay Between Cell Components | This work aims to address two major roadblocks in the development of lithium-sulfur (Li-S) batteries: the inefficient deposition of Li on the metallic Li electrode and the parasitic "polysulfide redox shuttle". These roadblocks are here approached, respectively, by the combination of a cellulose separator with a cathode-facing conductive porous carbon interlayer, based on their previously reported individual benefits. The cellulose separator increases cycle life by 33%, and the interlayer by a further 25%, in test cells with positive electrodes with practically relevant specifications and a relatively low electrolyte/sulfur (E/S) ratio. Despite the prolonged cycle life, the combination of the interlayer and cellulose separator increases the polysulfide shuttle current, leading to reduced Coulombic efficiency. Based on XPS analyses, the latter is ascribed to a change in the composition of the solid electrolyte interphase (SEI) on Li. Meanwhile, electrolyte decomposition is found to be slower in cells with cellulose-based separators, which explains their longer cycle life. These counterintuitive observations demonstrate the complicated interactions between the cell components in the Li-S system and how strategies aiming to mitigate one unwanted process may exacerbate another. This study demonstrates the value of a holistic approach to the development of Li-S chemistry.<br /> | Yu-Chuan Chien; Ruijun Pan; Ming-Tao Lee; Leif Nyholm; Daniel Brandell; Matthew Lacey | Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742ec9abda22ad8f8c0ce/original/cellulose-separators-with-integrated-carbon-nanotube-interlayers-for-lithium-sulfur-batteries-an-investigation-into-the-complex-interplay-between-cell-components.pdf |
640b82907290f69f8ec67f95 | 10.26434/chemrxiv-2023-2svfb-v2 | Energy Flows in Static and Programmable Catalysts | Programmable catalysts that change on the time scale of a catalytic cycle provide a new opportunity to control the flow of energy to reactants and products to promote faster and more selective chemistry. While traditional chemical manufacturing processes consume energy to achieve favorable reaction conditions, programmable catalysts aim to dynamically add or remove energy to catalytic cycles through perturbations of the catalytic surface via strain, charge, or light. These surface energy flows are quantified by the changes in adsorbate binding energy with time, and the overall efficiency relating energy inputs to catalytic performance are defined by the characteristics of the undulating catalytic surface. Understanding and quantification of energy flows in programmable catalysts provides baseline definitions and metrics for comparing dynamic conditions and identifying optimal catalytic performance for more efficient chemical manufacturing. | Omar Abdelrahman; Paul Dauenhauer | Catalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/640b82907290f69f8ec67f95/original/energy-flows-in-static-and-programmable-catalysts.pdf |
60c7401e337d6c6e7de26628 | 10.26434/chemrxiv.7599803.v1 | Free Standing Nanoporous Pd Alloys as CO Poisoning Tolerant Electrocatalysts for the Electrochemical Reduction of CO2 to Formate | CO2 electrochemical reduction to formate has emerged as one of the promising routes for CO2 conversion to useful chemicals and renewable energy storage. Palladium has been shown to make formate with a high selectivity at minimal overpotential. However, production of CO as a minor product quickly deactivates the catalyst during extended electrolysis. Here, we present nanoporous Pd alloys (np-PdX) formed by electrochemical dealloying of Pd15X85 alloys (X = Co, Ni, Cu, and Ag) as active free standing electrocatalysts with high formate selectivity and superior CO poisoning tolerance. Rate of deactivation under constant potential electrolysis, due to CO passivation, is strongly correlated to the identity of the transition metal alloying component. We purport that this composition dependent behavior is due to the induced electronic changes in the active Pd surface, affecting both the CO adsorption strength and the near surface hydrogen solubility which can impact the adsorption strength of active/inactive intermediates and reaction selectivity. Free-standing np-PdCo is found to exhibit high areal formate partial current densities, > 40 mA cm-2, with superior CO poisoning tolerance and minimal active area loss at cathodic potentials, demonstrating the utility of these materials for selective and stable CO2 electrolysis | Swarnendu Chatterjee; Charles D. Griego; James Hart; Yawei Li; Mitra Taheri; John Keith; Joshua Snyder | Nanostructured Materials - Materials; Electrochemistry; Electrocatalysis; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2019-01-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7401e337d6c6e7de26628/original/free-standing-nanoporous-pd-alloys-as-co-poisoning-tolerant-electrocatalysts-for-the-electrochemical-reduction-of-co2-to-formate.pdf |
60c750da567dfe1315ec592f | 10.26434/chemrxiv.13084265.v1 | Molecular Dynamics Simulations of Two-Step Process Enable Room-Temperature Synthesis of α-FAPbI3 | It is well established that the lack of understanding the crystallization process in two-step sequential deposition has a direct impact on efficiency, stability and reproducibility of perovskite solar cells. Here, we try to understand the solid-solid phase transition occuring during two-step sequential deposition of methylammonium lead iodide and formamidinium lead iodide. Using metadynamics, X-ray diffraction and Raman spectroscopy, we reveal the microscopic details of this process. We find that the formation of perovskite proceeds through intermediate structures and report polymorphs found for methylammonium lead iodide and formamidinium lead iodide. From simulations, we discover a possible crystallization pathway for the highly efficient metastable α-phase of formamidinium lead iodide. Guided by these simulations, we perform experiments that results in the room temperature crystallization of α-formamidinium lead iodide. | Paramvir Ahlawat; Haizhou Lu; Amita Ummadisingu; Haiyang Niu; Michele Invernizzi; Shaik M. Zakeeruddin; Anders Hagfeldt; Michael Grätzel; Ursula Rothlisberger; Michele Parrinello | Hybrid Organic-Inorganic Materials; Computational Chemistry and Modeling; Theory - Computational; Photovoltaics | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750da567dfe1315ec592f/original/molecular-dynamics-simulations-of-two-step-process-enable-room-temperature-synthesis-of-fa-pb-i3.pdf |
628999d687d01ff873edc7d2 | 10.26434/chemrxiv-2022-q5zgx-v4 | Classifying the toxicity of pesticides to honey bees via support vector machines with random walk graph kernels | Pesticides benefit agriculture by increasing crop yield, quality, and security. However, pesticides may inadvertently harm bees, which are valuable as pollinators. Thus, candidate pesticides in development pipelines must be assessed for toxicity to bees.
Leveraging a data set of 382 molecules with toxicity labels from honey bee exposure experiments, we train a support vector machine (SVM) to predict the toxicity of pesticides to honey bees. We compare two representations of the pesticide molecules: (i) a random walk feature vector listing counts of length-L walks on the molecular graph with each vertex- and edge-label sequence and (ii) the MACCS structural key fingerprint (FP), a bit vector indicating the presence/absence of a list of pre-defined subgraph patterns in the molecular graph. We explicitly construct the MACCS FPs, but rely on the fixed-length-L random walk graph kernel (RWGK) in place of the dot product for the random walk representation. The L-RWGK-SVM achieves an accuracy, precision, recall, and F1 score (mean over 2000 runs) of 0.81, 0.68, 0.71, and 0.69 on the test data set---with L=4 the mode optimal walk length. The MACCS-FP-SVM performs on par/marginally better than the L-RWGK-SVM, lends more interpretability, but varies more in performance. We interpret the MACCS-FP-SVM by illuminating which subgraph patterns in the molecules tend to strongly push them towards the toxic/non-toxic side of the separating hyperplane. | Ping Yang; E. Adrian Henle; Xiaoli Fern; Cory M. Simon | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2022-05-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628999d687d01ff873edc7d2/original/classifying-the-toxicity-of-pesticides-to-honey-bees-via-support-vector-machines-with-random-walk-graph-kernels.pdf |
60c74df20f50db404d39710e | 10.26434/chemrxiv.12678974.v1 | Structural Evolution in Photodeposited Nickel (Oxy)hydroxide Oxygen Evolution Electrocatalysts | <div>Amorphous metal oxides expand the range of material parameters significantly compared to their crystalline counter parts. However, predictions of the exact nature of the amorphous phase and its effect on material properties are still elusive. Thorough structure-property investigations of well-known model systems are thus necessary before predictive control of useful material properties is obtained. In this work, we fabricate a series of photodeposited nickel (oxy)hydroxide (NiO<sub>x</sub>) thin films and anneal them at temperatures up to 1000 <sup>o</sup>C. EXAFS, XRD and XPS are used to determine the local structure, allowing us to correlate it to measured electrochemical properties. We find an amorphous Ni(OH)<sub>2</sub>-like local structure for annealing conducted below 250 <sup>o</sup>C, followed by an amorphous-to-amorphous phase transition to a NiO-like structure by 300 <sup>o</sup>C, thus supplying evidence for different amorphous polymorphs in this Ni-O system. Above 400 <sup>o</sup>C a cubic NiO XRD diffraction pattern is detected. Electrochemically, we find a stepwise increase of the onset overpotential at this transition, indicating a change in potential-determining step and possibly OER reaction mechanism. The Tafel slope decreases linearly with annealing temperature, which we attribute to a decrease in (Ni)OOH reaction intermediary coverage, supported by <i>in-operando</i> UV-Vis electrochromism. Furthermore, we find that the (Ni)OOH coordination is increasingly strained with annealing temperature, which manifests in higher electrochromic coloring rates and lower binding energies. We identify this as the root cause of the lowered intermediary coverage. Thus, nano-crystalline NiO should kinetically be a superior catalyst to amorphous Ni(OH)<sub>2</sub>. However, at our benchmarking value of 10 mA cm<sup>-2</sup> the amorphous material exhibits lower overpotential, due to a combination of lower onset potential, large chemically active surface area and mass transport limitations under our conditions.</div> | Martin Schoen; Nicholas Randell; Oliver Calderon; Santiago Jimenez Villegas; Zachary Thomson; Roman Chernikov; Simon Trudel | Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74df20f50db404d39710e/original/structural-evolution-in-photodeposited-nickel-oxy-hydroxide-oxygen-evolution-electrocatalysts.pdf |
6256dd7e1033884c92eaf563 | 10.26434/chemrxiv-2022-f76tr | Static Quasi-Double Emulsions as Programmable Microcrystallizers for Controllable Polymorphic Crystallization | Controlling crystal polymorphism is critical in many fields such as pharmaceuticals, biomineralization, and catalysis. However, it is challenging for conventional batch crystallization approaches to effectively control the polymorphism of obtained crystals. In this work, we introduce a novel approach for controlling polymorphic crystallization by using quasi-double-emulsions (QDEs) as programmable microcrystallizers. The QDEs utilize a thin oil layer to separate aqueous droplets trapped in a high-density microwell array from the continuous aqueous phase, forming a large number of water-oil-water (W/O/W) structures similar to double emulsions. Benefitting from the semi-permeability of its middle oil film, the QDEs platform can facilely and flexibly vary the supersaturation rate and solvent composition of its inner aqueous phase (IAP) via changing its outer aqueous phase (OAP). Such variations can tune the kinetics of crystallization in the IAP, thus achieving highly controlled polymorphic crystallization and obtaining desired crystal polymorphs. In a proof-of-concept application, we demonstrated the convenience and versatility of the QDE platform by applying it for regulating the polymorph of glycine. Compared to traditional crystallizers, the QDEs platform provides more controllability and flexibility in polymorphic crystallization, being a powerful tool for solid form screening in pharmaceutical, fine chemicals, and food industries. | Yin Wu; Nankun Xiong; Yanwu Liu; Tengbao Xie; Qiang Zhao; Gang Li | Physical Chemistry; Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6256dd7e1033884c92eaf563/original/static-quasi-double-emulsions-as-programmable-microcrystallizers-for-controllable-polymorphic-crystallization.pdf |
67a7dd1d81d2151a02aeee38 | 10.26434/chemrxiv-2024-6bj22-v3 | MBX v1.2: Accelerating Data-Driven Many-Body Molecular Dynamics Simulations | The MBX software provides an advanced platform for molecular dynamics simulations, leveraging state-of-the-art MB-pol and MB-nrg data-driven many-body potential energy functions. Developed over the past decade, these potential energy functions integrate physics-based and machine-learned many-body terms trained on electronic structure data calculated at the ``gold standard'' coupled cluster level of theory. Recent advancements in MBX have focused on optimizing its performance, resulting in the release of MBX v1.2. While the inherently many-body nature of MB-pol and MB-nrg ensures high accuracy, it poses computational challenges. MBX v1.2 addresses these challenges with significant performance improvements, including enhanced parallelism that fully harnesses the power of modern multicore CPUs. These advancements enable simulations on nanosecond timescales for condensed-phase systems, significantly expanding the scope of high-accuracy, predictive simulations of complex molecular systems powered by data-driven many-body potential energy functions. | Shreya Gupta; Ethan F. Bull-Vulpe; Henry Agnew; Shishir Iyer; Xuanyu Zhu; Ruihan Zhou; Christopher Knight; Francesco Paesani | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Physical and Chemical Processes; Physical and Chemical Properties; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a7dd1d81d2151a02aeee38/original/mbx-v1-2-accelerating-data-driven-many-body-molecular-dynamics-simulations.pdf |
672fddb5f9980725cfb059a8 | 10.26434/chemrxiv-2024-s1fs5-v3 | ChIMES Carbon 2.0: A Transferable Machine-Learned Interatomic Model Harnessing Multifidelity Training Data | We present a new parameterization of the ChIMES physics informed machine- learned interatomic model for simulating carbon under conditions ranging from 300 K and 0 GPa to 10,000 K and 100 GPa, along with a new multi-fidelity active learning strategy. The resulting model shows significant improvement in accuracy and temperature/pressure transferability relative to the original ChIMES carbon model developed in 2017, and can serve as a foundation for future transfer-learned ChIMES parameter sets. Model applications to carbon melting point prediction, shockwave-driven con- version of graphite to diamond, and thermal conversion of nanodiamond to graphitic nanoonion are provided. Ultimately, we find our new model to be robust, accurate, and well-suited for modeling evolution in carbon systems under extreme conditions. | Rebecca Lindsey; Sorin Bastea; Sebastien Hamel; Yanjun Lyu; Nir Goldman; Vincenzo Lordi | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Carbon-based Materials; Computational Chemistry and Modeling; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672fddb5f9980725cfb059a8/original/ch-imes-carbon-2-0-a-transferable-machine-learned-interatomic-model-harnessing-multifidelity-training-data.pdf |
6670e2095101a2ffa8cf30c6 | 10.26434/chemrxiv-2024-8kqnq | Mineralogical Analysis of Solid Sample Flame Emission Spectra by Machine Learning | Solid pre-concentrated ore samples used in pyrometallurgical copper smelters are analyzed by flame emission spectroscopy using a specialized flame OES system. Over 8500 complex spectra are categorized using an artificial neural network, ANN, that was optimized to have ten hidden layers with 40 nodes per layer. The ANN was able to quantify the elemental content of all samples to within better than 1.5% w/w, and was able to identify the prevalent minerals to within better than 2.5%w/w. The flame temperature was obtained with an uncertainty of 3 K and the particle sizes to within 2 m. The results are found to be superior to those obtained to a non-linear partial least squares fit model, which is equivalent to an ANN having no hidden layers. | Adam Bernicky; Boyd Davis; Milen Kadiyski; Hans-Peter Loock | Analytical Chemistry; Chemoinformatics; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6670e2095101a2ffa8cf30c6/original/mineralogical-analysis-of-solid-sample-flame-emission-spectra-by-machine-learning.pdf |
65525b70dbd7c8b54b3110a2 | 10.26434/chemrxiv-2023-zcww7-v2 | Probing Electrochemical Strain Generation in Sodium Chromium Oxide (NaCrO2) Cathode in Na-ion Batteries during Charge/Discharge | Sodium chromium oxide, NaCrO2, exhibits promising features as a cathode electrode in Na-ion batteries, yet it encounters challenges with its capacity fading and poor cycle life. NaCrO2 undergoes multiple phase transitions during Na ion intercalation, eventually leading to chemical instabilities and mechanical deformations. This study aims to investigate the reversible and irreversible mechanical deformations in NaCrO2 using an operando digital image correlation (DIC) coupled with electrochemical techniques. Electrochemical strains were recorded during either cyclic voltammetry or galvanostatic cycling. The electrode undergoes significant irreversible mechanical deformations in the initial cycle, and irreversibility decreases in the subsequent cycles. During desodiation and sodiation, the electrode initially undergoes volume contraction followed by expansion. The strain derivative peaks align well with the peak of the capacitive derivatives, indicating the phase-transition-induced deformations in the electrode. Cumulative irreversible strains demonstrate a linear relationship with the square root of cycling time, indicating irreversibility arising from forming a cathode-electrolyte interphase layer. The outcome of this study provides valuable insights into mechanical deformations in NaCrO2 electrodes during battery cycling and guides the design of mechanically robust cathodes for Na-ion batteries. | Minal Wable; Batuhan Bal; Ömer Özgür Çapraz | Energy; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65525b70dbd7c8b54b3110a2/original/probing-electrochemical-strain-generation-in-sodium-chromium-oxide-na-cr-o2-cathode-in-na-ion-batteries-during-charge-discharge.pdf |
626b20d8ef2ade44934135d5 | 10.26434/chemrxiv-2022-kzvcj-v2 | Free Metallophosphines: Extremely Electron-Rich Phosphorus Superbases that are Electronically and Sterically Tunable | A variety of research fields ranging from catalysis to materials science benefit from readily accessible electron-rich ancillary ligands such as phosphines with diverse stereoelectronic properties. We report herein a facile and highly modular access to an intriguing class of free Au-substituted phosphines (AuPhos), namely (LAu)nPR3-n (L = singlet carbene ligand; R = H, aryl, alkyl, silyl) (n = 1-3). The Tolman electronic parameter (TEP) values coupled with theoretical investigations showcase that Au-substitution can boost the electron-releasing ability of AuPhos, thus leading to an electronically and sterically tunable, extremely electron-rich phosphorus center. The high basicity of AuPhos is attributed to the d-p lone pair π-repulsion arising from interaction between electron-rich d10 Au substituents and the lone pair at P. A series of multi-nuclear transition metal complexes (i.e. Rh, Ir, Pd, Au, W, Mn) ligated by AuPhos are readily prepared via a straightforward process. Preliminary catalytic results reveal the facilitation of Pd-catalyzed C-N coupling reactions and Ir-catalyzed decarbonylation reactions via AuPhos. This work provide insights for future development of electron-rich ligands. | Rui Wei; Shaoying Ju; Liu Leo Liu | Inorganic Chemistry; Main Group Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/626b20d8ef2ade44934135d5/original/free-metallophosphines-extremely-electron-rich-phosphorus-superbases-that-are-electronically-and-sterically-tunable.pdf |
64b6ddbcae3d1a7b0dee9f7f | 10.26434/chemrxiv-2023-ppgxg | Impact of Fluorination Degree of Ether-Based Electrolyte Solvent on Li-metal Battery Performance | Electrolytes using fluorinated solvents have proven effective in improving the cycling life of Li-metal batteries, by forming a robust solid-electrolyte interphase through decomposition of anion and fluorinated solvent molecules. Herein, we modulated the fluorination degree of ether-based electrolyte solvents to investigate their performance in Li-metal batteries. We tuned the fluorination degree by installing a monofluorine substituent on one ethoxy group of 1,2-diethoxyethane (DEE) and varying the fluorination degree on the other one, providing three fluorinated DEE solvent molecules (i.e., F1F0, F1F1 and F1F2) with a relatively low fluorination degree. All the three electrolytes showed improved solvation strength and ionic conductivities compared with previous highly fluorinated DEE elec-trolytes, while retaining good oxidative stability. Full cell test using Li-metal anode and nickel-rich cathode revealed that a higher degree of fluorination is beneficial to the cycling performance, and the cycling stability follows F1F0 < F1F1 < F1F2. Specifically, F1F0 exhibited poor cycling stability due to its instability against both anode and cathode. While F1F1 and F1F2 both showed good stability against Li-metal anode, their relative long-term oxidative stability was responsive for the distinct performance, in which the cycle numbers at 80% capacity retention for F1F1 and F1F2 were ~20 and ~80, respectively. This work shows the importance to modulate the fluorination degree of elec-trolyte solvents, and this approach is suitable for various cathode materials. | Yangju Lin; Zhiao Yu; Weilai Yu; Sheng-Lun Liao; Zhuojun Huang; Yuelang Chen; Elizabeth Zhang; Jian Qin; Yi Cui; Zhenan Bao | Energy; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b6ddbcae3d1a7b0dee9f7f/original/impact-of-fluorination-degree-of-ether-based-electrolyte-solvent-on-li-metal-battery-performance.pdf |
61af898d25f39a393dd040b4 | 10.26434/chemrxiv-2021-gq85t | Glycosylation as a key for enhancing drug recognition into spike glycoprotein of SARS-CoV-2 | The emergence of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and its spread since 2019 represents the major public health problem worldwide nowadays, generating a high number of infections and deaths. That’s why, in addition to vaccination campaigns, the design of a drug to help in the treatment of severe cases of COVID-19 is being investigated. In relation to SARS-CoV-2, one of its most studied proteins is the spike protein (S protein), which mediates host-cell entry and is heavily glycosylated. Regarding the latter, several investigations have been carried out, since it plays an important role in the evasion of the host's immune system and contributes to protein folding and the thermostability of the viral particle. For that reason, our objective was to evaluate the impact of glycosylations on the drug recognition on two domains of the S protein, the receptor-binding domain (RBD) and the N-terminal domain (NTD) through molecular dynamics simulations and computational biophysics analysis. Our results show that glycosylations in the S protein induce structural stability and changes in rigidity/flexibility related to the number of glycosylations in the structure. These structural changes are important for its biological activity as well as the correct interaction of ligands in the RBD and NTD regions. Additionally, we evidenced a roto-translation phenomenon in the interaction of the ligand with RBD in the absence of glycosylation, which disappears due to the influence of glycosylation and the convergence of metastable states in RBM. Similarly, glycosylations in NTD promote an induced-fit phenomenon, which is not observed in the absence of glycosylations; this process is decisive for the activity of the ligand at the cryptic site. Altogether, these results provide an explanation of glycosylation relevance in biophysical properties and drug recognition to S protein of SARS-CoV-2 which must be considered in the rational drug development and virtual screening targeting S protein. | Georcki Ropón-Palacios; Jhon Pérez-Silva; Ricardo Rojas-Humpire; Gustavo E. Olivos-Ramírez; Manuel Chenet-Zuta; Victor Cornejo-Villanueva; Sheyla Carmen-Sifuentes; Kewin Otazu; Yaritza L. Ramirez-Díaz; Ihosvany Camps | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Biochemistry; Bioinformatics and Computational Biology; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61af898d25f39a393dd040b4/original/glycosylation-as-a-key-for-enhancing-drug-recognition-into-spike-glycoprotein-of-sars-co-v-2.pdf |
6770ea186dde43c908ab48f6 | 10.26434/chemrxiv-2024-2ksw1 | Osmium(IV) tetraaryl complexes formed from pre-functionalized ligands | Metal(IV) tetraaryl, M(aryl)4, complexes hold great promise as functional building blocks for complex organometallic materials, yet their widespread utility depends on the development of improved synthetic protocols and a deeper understanding of their chemical structure-property relationship(s). Here we show that Os(aryl)4 complexes with pre-installed functional groups (-F, -Cl, -Br, -I, and -SMe) can be prepared from reactions between (Oct4N)2[OsBr6] and Grignard reagents formed by halogen/magnesium insertion or exchange. This approach provides access to compounds that may otherwise prove challenging to prepare through post-functionalization strategies, such as those comprising halogens in the 2- or 5-positions. Furthermore, we show that these tetrahedral complexes can be stabilized by ortho-chloride substituents, moving beyond the alkyl groups that have previously been exploited for this purpose. We characterize these, as well as previously reported, materials using single-crystal X-ray diffraction, solution voltammetry, and UV-vis spectroscopy. We find these compounds, while typically appearing as black or darkly colored in the solid state, yield differently colored CH2Cl2 solutions due to small changes in the λmax and variations in the relative intensity of their four primary absorbance features. Through a comparison of 13 differently substituted complexes, we identify correlations between their electrochemical and optical gaps, and between the E1/2 of their 0/1+ redox event and an adjusted Hammett parameter that accounts for all aryl ligand substituents. This work provides a foundation for advancing new preparative methods to further derivatize such species, and a robust experimental dataset to help benchmark future experimental and computational compound characterization. | Clarissa Olivar; Joseph Parr; Cynthia Avedian; Thomas Saal; Luana Zagami; Ralf Haiges; Mukund Sharma; Michael Inkpen | Organometallic Chemistry; Electrochemistry - Organometallic; Ligands (Organomet.); Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6770ea186dde43c908ab48f6/original/osmium-iv-tetraaryl-complexes-formed-from-pre-functionalized-ligands.pdf |
60c75747337d6c712ae28ff8 | 10.26434/chemrxiv.14390828.v1 | Additives for Ambient 3D Printing with Visible Light | With 3D printing we desire to be “limited only by
our imagination”, and although remarkable advancements have been made in recent
years the scope of printable materials remains narrow compared to other forms
of manufacturing. Light-driven polymerization methods for 3D printing are
particularly attractive due to unparalleled speed and resolution, yet the
reliance on high energy UV/violet light in contemporary processes limits the
number of compatible materials due to pervasive absorption, scattering, and
degradation at these short wavelengths. Such issues can be addressed with
visible light photopolymerizations. However, these lower-energy methods often
suffer from slow reaction times and sensitivity to oxygen, precluding their
utility in 3D printing processes that require rapid hardening (curing) to maximize
build speed and resolution. Herein, multifunctional thiols are identified as simple
additives to enable rapid high resolution visible light 3D printing under
ambient (atmospheric O<sub>2</sub>) conditions that rival modern UV/violet-based
technology. The present process is universal, providing access to commercially
relevant acrylic resins with a range of disparate mechanical responses from
strong and stiff to soft and extensible. Pushing forward, the insight presented
within this study will inform the development of next generation 3D printing
materials, such as multicomponent hydrogels and composites. | Dowon Ahn; Lynn Stevens; Kevin Zhou; Zachariah Page | Materials Processing; Polymerization (Polymers); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75747337d6c712ae28ff8/original/additives-for-ambient-3d-printing-with-visible-light.pdf |
60c74a4dbdbb89bbffa3934a | 10.26434/chemrxiv.12146106.v1 | cgbind: A Python Module and Web App for Automated Metallocage Construction and Host-Guest Characterization | Metallocages offer a diverse and underexplored region of chemical space to search for novel catalysts and substrate hosts. However, the ability to tailor such structures towards applications in binding and catalysis is a challenging task. Here, we present an open-source computational toolkit, cgbind, that facilitates the characterization and prediction of functional metallocages. It employs known structural scaffolds as starting points, and computationally efficient approaches for the evaluation of geometric and chemical properties. To illustrate the applicability of cgbind, we evaluate the likelihood of 102 substrates to bind within M2L4 and M4L6 cages and achieve accuracy comparable or better than semi-empirical electronic structure methods. The cgbind code presented here is freely available at github.com/duartegroup/cgbind and also via a web-based graphical user interface at cgbind.chem.ox.ac.uk. The protocol described here paves the way for high-throughput virtual screening of potential supramolecular structures, accelerating the search for new hosts and catalysts. | Tom A. Young; Razvan Gheorghe; Fernanda Duarte | Supramolecular Chemistry (Org.); Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a4dbdbb89bbffa3934a/original/cgbind-a-python-module-and-web-app-for-automated-metallocage-construction-and-host-guest-characterization.pdf |
62a9aec74483987a9076b5c9 | 10.26434/chemrxiv-2022-vjcpx | Molecular glues: The adhesive connecting targeted
protein degradation to the clinic | Targeted protein degradation is a rapidly exploding drug discovery strategy which uses small molecules to recruit disease-causing proteins for rapid destruction mainly via the ubiquitin-proteasome pathway. It shows great potential for treating diseases such as cancer, infectious, inflammatory, and neurodegenerative diseases, especially for those with “undruggable” pathogenic protein targets. With the recent rise of the ‘molecular glue’ type of protein degraders, which tighten and simplify the connection of an E3 ligase with a disease-causing protein for ubiquitination and subsequent degradation, new therapies for unmet medical needs are being designed and developed. Here we use data from the CAS Content Collection and the publication landscape of recent research on targeted protein degraders to provide insights into these molecules, with a special focus on molecular glues. We also outline the advantages of the molecular glues and summarize the advances in drug discovery practices for molecular glue degraders. We further provide a thorough review of drug candidates in targeted protein degradation through E3 ligase recruitment. Finally, we highlight the progression of molecular glues in drug discovery pipelines and their targeted diseases. Overall, our paper provides a comprehensive reference to support the future development of molecular glues in medicine. | Janet M. Sasso; Rumiana Tenchov; DaSheng Wang; Linda S. Johnson; Xinmei Wang; Qiongqiong Angela Zhou | Biological and Medicinal Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2022-06-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a9aec74483987a9076b5c9/original/molecular-glues-the-adhesive-connecting-targeted-protein-degradation-to-the-clinic.pdf |
63774e273551196fbc37d002 | 10.26434/chemrxiv-2021-bpg5d-v2 | Material flows and Embodied Energy of Direct Air Capture | Direct air capture (DAC) is an essential nexus of CO2 chemistry and climate mitigation. Life cycle assessment (LCA) is often used to validate the environmental potential of emerging technologies. Consequently, an increased number of ex-ante LCAs is expected in this field. However, a comprehensive description through paramterized modelling of life cycle inventories of distinc technological pathways, which is essential for transparency, has recently been missing from the international literature. To fill this gap, the present study analyzes three selected DAC technologies to create an inventory. Amine-based adsorption and absorption, as well as alkali-based absorption, were modelled.
The energy consumption of the operation, cradle-to-gate embodied energy, and sensitivity analysis based on parameter variations were carried out. The “cradle-to-gate” energy requirement of DAC often lies in the range or above the formation energy of CO2 (8.94 GJ energy can be obtained by formation of 1t CO2 from elementary C and O2). This indicates that theoretically more energy is required for capture, as can be obtained during the formation of CO2. Because energy has continuously growing economic and ecological value, this energy intensity of DAC implies that DAC might have important role in CCU to add directly measurable economic value. The parametrized model includes over 60 parameters, resulting in an array of possible energy and material requirements. The use of this wide range of figures in life cycle assessment sheds light on real opportunities for direct air capture in future product systems. The option of varying parameters enables the tailoring of the calculation to a particular situation or design. In this way, the calculator offers a common base for LCA, fostering an early stage analysis of DAC technologies.
| Bálint Simon | Energy; Chemical Engineering and Industrial Chemistry; Industrial Manufacturing; Natural Resource Recovery; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63774e273551196fbc37d002/original/material-flows-and-embodied-energy-of-direct-air-capture.pdf |
627d33346cae1c222e07be5c | 10.26434/chemrxiv-2022-b4j5n | A Designed Photoenzyme Promotes Enantioselective [2+2]-Cycloadditions via Triplet Energy Transfer | The ability to programme new modes of catalysis into proteins would allow the development of enzyme families with functions beyond those found in nature. To this end, genetic code expansion methodology holds particular promise, as it allows the site-selective introduction of new functional elements into proteins as non-canonical amino acid side chains. Here, we exploit an expanded genetic code to develop a photoenzyme that operates via triplet energy transfer catalysis, a versatile mode of reactivity in organic synthesis that is currently not accessible to biocatalysis. Installation of a genetically encoded photosensitiser into the beta-propeller scaffold of DA_20_00 converts a de novo Diels-Alderase into a photoenzyme for [2+2]-cycloadditions (EnT1.0). Subsequent development and implementation of a platform for photoenzyme evolution afforded an efficient and enantioselective enzyme (EnT1.3, up to 99% e.e.) that can promote selective cycloadditions that have proven challenging to achieve with small molecule catalysts. EnT1.3 performs >300 turnovers and, in contrast to small molecule photocatalysts, can operate effectively under aerobic conditions. A 1.7 Å resolution X-ray crystal structure of an EnT1.3-product complex shows how multiple functional components work in synergy to promote efficient and selective photocatalysis. This study opens the door to a wealth of new excited-state chemistry in protein active sites and establishes the framework for developing a new generation of evolvable photocatalysts with efficiencies and specificities akin to natural enzymes. | Jonathan S. Trimble; Rebecca Crawshaw; Florence J. Hardy; Colin W. Levy; Murray J.B. Brown; Douglas E. Fuerst; Derren Heyes; Richard Obexer; Anthony P. Green | Catalysis; Biocatalysis | CC BY 4.0 | CHEMRXIV | 2022-05-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/627d33346cae1c222e07be5c/original/a-designed-photoenzyme-promotes-enantioselective-2-2-cycloadditions-via-triplet-energy-transfer.pdf |
62f1dd4c69f3a528d2b0d366 | 10.26434/chemrxiv-2022-5mbcp | “Magic Chloro”: Profound Effects of the Chlorine Atom in Drug Discovery | Chlorine is one of the most common atoms present in small-molecule drugs beyond carbon, hydrogen, nitrogen and oxygen. There are currently more than 250 FDA-approved chlorine-containing drugs, yet the beneficial effect of the chloro substituent has not yet been reviewed. The simple substitution of a hydrogen atom (R = H) with a chlorine atom (R = Cl) can result in incredible improvements in potency of up to 100,000-fold, and can lead to profound effects on pharmacokinetic parameters such as clearance, half-life, and drug exposure in vivo. Following the literature terminology of “magic methyl effect” in drugs, the term “magic chloro effect” has been coined herein. Reports of 500-fold or >1000-fold potency improvement are often serendipitous discoveries that can be considered “magic” rather than planned. However, hypotheses made to explain the magic chloro effect can lead to lessons that accelerate the cycle of drug discovery. With this in mind, we believe that medicinal chemists should place chlorine atoms into their lead scaffolds in judicious fashion, and organic chemists should invent more methods to place chlorine atoms selectively onto complex molecules. | Debora Chiodi; Yoshihiro Ishihara | Biological and Medicinal Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f1dd4c69f3a528d2b0d366/original/magic-chloro-profound-effects-of-the-chlorine-atom-in-drug-discovery.pdf |
65e3833de9ebbb4db9c44e76 | 10.26434/chemrxiv-2023-7c4s5-v3 | Intensive Microalgal Cultivation and Tertiary Phosphorus Recovery from Wastewaters via the EcoRecover Process | Mixed community microalgal wastewater treatment technologies have the potential to advance the limit of technology for biological nutrient recovery while producing a renewable carbon feedstock, but a deeper understanding of their performance is required for system optimization and control. In this study, we characterized the performance of a 568 m3·day-1 Clearas EcoRecover system for tertiary phosphorus removal (and recovery as biomass) at an operating water resource recovery facility (WRRF). The process consists of a (dark) mix tank, photobioreactors (PBRs), and a membrane tank with ultrafiltration membranes for the separation of hydraulic and solids residence times. Through continuous on-line monitoring, long-term on-site monitoring, and on-site batch experiments, we demonstrate (i) the importance of carbohydrate storage in PBRs to support phosphorus uptake under dark conditions in the mix tank and (ii) the potential for polyphosphate accumulation in the mixed algal communities. Over a 3 month winter period with limited outside influences (e.g., no major upstream process changes), the effluent total phosphorus (TP) concentration was 0.03 ± 0.03 mg-P·L-1 (0.01 ± 0.02 mg-P·L-1 orthophosphate). Core microbial community taxa included Chlorella spp., Scenedesmus spp., and Monoraphidium spp., and key indicators of stable performance included near-neutral pH, sufficient alkalinity, and a diel rhythm in dissolved oxygen. | Hannah Molitor; Ga-Yeong Kim; Elaine Hartnett; Benjamin Gincley; Md Mahbubul Alam; Jianan Feng; Nickolas Avila; Autumn Fisher; Mahdi Hodaei; Yalin Li; Kevin McGraw; Ro Cusick; Ian Bradley; Ameet Pinto; Jeremy Guest | Chemical Engineering and Industrial Chemistry; Natural Resource Recovery; Water Purification | CC BY 4.0 | CHEMRXIV | 2024-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e3833de9ebbb4db9c44e76/original/intensive-microalgal-cultivation-and-tertiary-phosphorus-recovery-from-wastewaters-via-the-eco-recover-process.pdf |
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