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65fac0ed66c1381729628a47 | 10.26434/chemrxiv-2024-sh4gw | Visible Light Induced Organophotoredox Catalyzed β-Hydroxytrifluoromethylation of Unactivated Alkenes | Herein, we report a mild transition metal-free organophotoredox catalyzed approach for β-hydroxytrifluoromethylation of unactivated alkenes using CF3SO2Na and acridinium salt. The protocol is compatible with various mono, di- and tri-substituted aliphatic unactivated alkenes containing numerous functional groups and natural product derivatives. Further, the post-synthetic modifications of synthesized trifluoromethylated products have been demonstrated through cross-coupling and functional group interconversion reactions. The method proved to be scalable and also it works smoothly un-der direct exposure of sunlight. A plausible mechanism has been proposed based on fluorescence quenching experiment and cyclic voltammetry analysis. | Mousumi Behera; Pankaj D. Dharpure; Ajit Kumar Sahu; Dr. Ramakrishna G. Bhat | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Photocatalysis; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65fac0ed66c1381729628a47/original/visible-light-induced-organophotoredox-catalyzed-hydroxytrifluoromethylation-of-unactivated-alkenes.pdf |
60c74514ee301cb184c7922f | 10.26434/chemrxiv.9961718.v1 | The Sensitivity of Cu for Electrochemical Carbon Dioxide Reduction to Hydrocarbons as Revealed by High Throughput Experiments | Electrochemical CO2 reduction to valuable products is a centerpiece of future energy technologies that relies on identificaiton of new catalysts. We present accelerated screening of Cu bimetallic alloys, revealing remarkable sensitivity to alloy concentration that indicates the segregation of alloying elements to critical sites for hydrocarbon formation. | Yunchieh Lai; Ryan J. R. Jones; Yu Wang; Lan Zhou; Matthias Richter; John Gregoire | Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74514ee301cb184c7922f/original/the-sensitivity-of-cu-for-electrochemical-carbon-dioxide-reduction-to-hydrocarbons-as-revealed-by-high-throughput-experiments.pdf |
662faf7d91aefa6ce1be0da6 | 10.26434/chemrxiv-2024-zmmdp | Enantioconvergent carbenoid insertion into carbon−boron bonds | Boron-mediated homologation can potentially access almost any kind of chiral centers
from readily available boronates via asymmetric carbenoid insertion, followed by
versatile transformations of the carbon−boron bonds. However, the current asymmetric
boron homologation strategies exhibit limitations, and enantioselective insertion of
diversely substituted carbenoids remains challenging. Here we report an
enantioconvergent approach for direct insertion of carbon-, oxygen-, nitrogen-, sulfur-,
and silicon-substituted carbenoids into carbon−boron bonds. The excellent
enantioselectivity is enabled by a new class of chiral oxazaborolidines derived from
inexpensive α-amino esters. Computational studies revealed that the non-C2-symmetric
oxazaborolidine features a puckered geometry and the cooperative effects of multiple
substituents create an asymmetric environment for effective enantioinduction. This
method is scalable, and each chiral center can be independently controlled by the chiral
oxazaborolidine without being influenced by nearby stereocenters. Besides forming
singular chiral centers, iterative operations of this asymmetric homologation simplify
synthesis of complex molecules with multiple stereocenters. | Qiqiang Xie; Thomas Tugwell; Jiahao Li; Peng Liu; Guangbin Dong | Organic Chemistry; Organic Synthesis and Reactions; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662faf7d91aefa6ce1be0da6/original/enantioconvergent-carbenoid-insertion-into-carbon-boron-bonds.pdf |
60c74afe469df4395ef43e46 | 10.26434/chemrxiv.12278780.v1 | A Hydrogen Bond Between Linear Tetrapyrrole and Conserved Aspartate Causes the Far-Red Shifted Absorption of Phytochrome Photoreceptors | Photoswitching
of phytochrome photoreceptors between red-absorbing (Pr) and far-red absorbing
(Pfr) states triggers light adaptation of plants, bacteria and other organisms.
Using quantum chemistry, we elucidate the color-tuning mechanism of
phytochromes and identify the origin of the Pfr-state red-shifted spectrum.
Spectral variations are explained by resonance interactions of the protonated
linear tetrapyrrole chromophore. In particular, hydrogen bonding of pyrrole
ring D with the strictly conserved aspartate shifts the positive charge towards
ring D thereby inducing the red spectral shift. Our MD simulations demonstrate
that formation of the ring D–aspartate hydrogen bond depends on interactions
between the chromophore binding domain (CBD) and phytochrome specific domain
(PHY). Our study guides rational engineering of fluorescent phytochromes with a
far-red shifted spectrum. | Egle Maximowitsch; Tatiana Domratcheva | Computational Chemistry and Modeling; Theory - Computational; Chemoinformatics - Computational Chemistry; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74afe469df4395ef43e46/original/a-hydrogen-bond-between-linear-tetrapyrrole-and-conserved-aspartate-causes-the-far-red-shifted-absorption-of-phytochrome-photoreceptors.pdf |
60c755b19abda2146bf8e413 | 10.26434/chemrxiv.14150174.v1 | Nickel-Catalyzed 1,2-Diarylation of Alkenyl Ketones: A Comparative Study of Carbonyl-Directed Reaction Systems | <div><p>A conjunctive cross-coupling reaction of alkenyl ketones, aryl iodides, and arylboronic esters under nickel catalysis is reported. The reaction delivers the desired 1,2-diarylated products with moderate to excellent regiocontrol using a diverse array of ketone starting materials, as illustrated across over 40 examples. To showcase the versatility of this method, a representative product is diversified into a wide range of synthetically useful building blocks, that are not readily accessible via existing 1,2-diarylation reactions. Preliminary mechanistic studies shed light on the binding mode of the substrate, and Hammett analysis shows the effect of electronic factors on initial rates. To our knowledge, this method represents the first example of catalytic 1,2-diarylation of an alkene, directed by a native ketone functional group.</p></div> | Roman Kleinmans; Omar Apolinar; Joseph Derosa; Malkanthi Karunananda; Zi-Qi Li; Van Tran; Steven Wisniewski; Keary Engle | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Homogeneous Catalysis; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755b19abda2146bf8e413/original/nickel-catalyzed-1-2-diarylation-of-alkenyl-ketones-a-comparative-study-of-carbonyl-directed-reaction-systems.pdf |
60c759c6bb8c1a28733dccae | 10.26434/chemrxiv.14724357.v1 | Palladium-Catalyzed Decarbonylative Catellani Reaction | <p><b>The transition
metal-catalyzed Catellani reaction of aryl halides has drawn significant
attentions as an efficient and practical tool for the synthesis of substituted
arenes. We describe herein the palladium-catalyzed, norbornene (NBE)-mediated synthesis
of polysubstituted arenes from aromatic acids via decarbonylative Catellani reaction.
A variety of alkenyl, alkyl, aryl and sulfur moieties could be conveniently introduced
into the<i> ipso</i>-positions of aromatic thioesters. By merging carboxyl-directed
C−H functionalization and the classical Catellani reactions, our protocol
allowed the construction of 1,2,3-trisubstituted and 1,2,3,4-tetrasubstituted arenes
from simple aromatic acids. Furthermore, the late-stage functionalization of a
series of drug molecules highlights the potential utility of the reaction.</b></p> | Huixiong Dai; Ming-Liang Han; Jun-Jie Chen; Hui Xu; Wei Huang; Yue-Wen Liu; Xing Wang; Min Liu; Zi-Qiong Guo; Zhi-Cong Huang | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c759c6bb8c1a28733dccae/original/palladium-catalyzed-decarbonylative-catellani-reaction.pdf |
60c74479bdbb8903aea38801 | 10.26434/chemrxiv.9829442.v1 | Time-dependent Photodynamic Therapy for Multiple Targets: A Highly Efficient AIE-active Photosensitizer for Selective Bacterial Elimination and Cancer Cell Ablation | Pathogen infection and
cancer are the two major human health problems. In this work, we achieved an
organic salt photosensitizer (PS), called 4TPA-BQ with aggregation-induced
emission feature <i>via</i> one-step
reaction. Owing to the aggregation-induced reactive oxygen species generation
effect and sufficient small ΔE<sub>ST</sub>,
4TPA-BQ shows a satisfactorily high <sup>1</sup>O<sub>2</sub> generation
efficiency of 97.8%. <i>In vitro</i> and <i>in vivo</i>
experiments confirmed that 4TPA-BQ exhibited potent photodynamic antibacterial
performance against ampicillin-resistant <i>Escherichia
coli</i> with good biocompatibility in a short time (15 min). When the
incubation time persisted long enough (12 h), cancer cells were ablated
efficiently, leaving normal cells essentially unaffected. This is the first reported
time-dependent fluorescence-guided photodynamic therapy in one individual PS
for ordered and multiple targeting by varying the external conditions. This can
update the design principle of efficient PSs in potential clinical applications. | Qiyao Li; Ying Li; Tianliang Min; Junyi Gong; Lili Du; Kai LI; David Lee Phillips; Junkai Liu; Jacky W. Y. Lam; Herman H.-Y. Sung; Chun Loong Ho; Ian Duncan Williams; Ryan Tsz Kin Kwok; Jianguo Wang; Ben Zhong Tang | Biological Materials | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74479bdbb8903aea38801/original/time-dependent-photodynamic-therapy-for-multiple-targets-a-highly-efficient-aie-active-photosensitizer-for-selective-bacterial-elimination-and-cancer-cell-ablation.pdf |
63a60113a2da4b37500e957b | 10.26434/chemrxiv-2022-68n6h-v2 | Enhancing Semiempirical Quantum Mechanical Scoring with Machine Learning: a new scoring function that accounts for both the enthalpic and entropic contributions to the ligand binding free energy | Identifying hit compounds is a principal step in early-stage drug discovery. While many machine learning (ML) approaches have been proposed, in the absence of binding data, molecular docking is the most widely used option to predict binding modes and score hundreds of thousands of compounds for binding affinity to the target protein. Docking's effectiveness is critically dependent on the protein-ligand (P-L) scoring function (SF), thus re-scoring with more rigorous SFs is a common practice. In this pilot study, we scrutinize the PM6-D3H4X/COSMO semi-empirical quantum mechanical (SQM) method as a docking pose re-scoring tool on 17 diverse receptors and ligand decoy sets, totaling 1.5 million P-L complexes. We investigate the effect of explicitly computed ligand conformational entropy and ligand deformation energy on SQM P-L scoring in a virtual screening (VS) setting, as well as molecular mechanics (MM) versus hybrid SQM/MM structure optimization prior to re-scoring. Our results proclaim that there is no obvious benefit from computing ligand conformational entropies or deformation energies and that optimizing only the ligand's geometry on the SQM level is sufficient to achieve the best possible scores. Instead, we leverage machine learning (ML) to include implicitly the missing entropy terms to the SQM score using ligand topology, physicochemical, and P-L interaction descriptors. Our new hybrid scoring function, named SQM-ML, is transparent and explainable, and achieves in average 9% higher AUC-ROC than PM6-D3H4X/COSMO and 3% higher than Glide SP, but with consistent and predictable performance across all test sets, unlike the former two SFs, whose performance is considerably target-dependent and sometimes resembles that of a random classifier. The code to prepare and train SQM-ML models is available at https://github.com/tevang/sqm-ml.git and we believe that will pave the way for a new generation of hybrid SQM/ML protein-ligand scoring functions. | Thomas Evangelidis; Ilektra-Chara Giassa,; Mario Lovrić | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Machine Learning; Chemoinformatics - Computational Chemistry; Quantum Mechanics | CC BY 4.0 | CHEMRXIV | 2022-12-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63a60113a2da4b37500e957b/original/enhancing-semiempirical-quantum-mechanical-scoring-with-machine-learning-a-new-scoring-function-that-accounts-for-both-the-enthalpic-and-entropic-contributions-to-the-ligand-binding-free-energy.pdf |
624421205ab8df752385b9ea | 10.26434/chemrxiv-2022-54jpx | Study on the tolerance of low-temperature CO methanation with single pulse experiments | In this contribution, single pulse reaction experiments are discussed in the context of dynamic reactor operation and used to determine the tolerance of reactors arising from sorption effects at the catalyst surface. A defined amount of CO is dosed together with an internal standard (He) in a constant H2 stream, and the pulse response is observed with reference to the internal standard, which is representing the fluid dynamics of the injected pulse. Different responses are obtained depending on the catalyst mass (Ni/Al2O3) and the operation temperature (170°C-300°C). The tolerance of the reactor can be deduced from the experimental findings. On the one hand, the catalyst adsorption capacity determines the ability to buffer fluctuations at low reaction temperatures (𝑇<220 °𝐶), which are beneficial for full-conversion, overcoming thermodynamic restrictions. On the other hand, temperature determines the transient response of the system and is independent of the catalyst mass. From these findings the study reveals that reactors represent important buffer systems during load changes in dynamic operation modes and provide an intrinsic tolerance originating from sorption processes at the catalyst surface. | Jens Friedland; Thomas Turek; Robert Güttel | Catalysis; Chemical Engineering and Industrial Chemistry; Reaction Engineering; Heterogeneous Catalysis | CC BY NC 4.0 | CHEMRXIV | 2022-03-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/624421205ab8df752385b9ea/original/study-on-the-tolerance-of-low-temperature-co-methanation-with-single-pulse-experiments.pdf |
65b5c6f366c13817296acb44 | 10.26434/chemrxiv-2024-fkcf8 | Generation of Protocells by Spontaneous Reaction of Cysteine with Short Chain Thioesters | It is unknown how the earliest forms of life were compartmentalized. Several models have suggested a role for single-chain lipids such as fatty acids, but the membranes formed are often unstable, particularly when made from shorter alkyl chains (≤C8) that were likely more prevalent on the prebiotic Earth. We show that the amino acid cysteine can spontaneously react with two short-chain (C8) thioesters to form diacyl lipids, generating protocell-like membrane vesicles. The three-component reaction takes place rapidly in water using low concentrations of reactants. Silica can catalyze the formation of protocells through a simple electrostatic mechanism. Several simple aminothiols react to form diacyl lipids, including short peptides. The protocells formed are compatible with functional ribozymes, suggesting that coupling of multiple short-chain precursors may have provided membrane building blocks during the early evolution of cells. | Christy J. Cho; Taeyang An; Yei-Chen Lai; Alberto Vázquez-Salazar; Alessandro Fracassi; Irene A. Chen; Neal K. Devaraj | Biological and Medicinal Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b5c6f366c13817296acb44/original/generation-of-protocells-by-spontaneous-reaction-of-cysteine-with-short-chain-thioesters.pdf |
645c06c6f2112b41e956d61a | 10.26434/chemrxiv-2023-qv5bh | Catalytic σ-Bond Annulation with Ambiphilic Organohalides Enabled by β-X Elimination | We describe a catalytic cascade sequence involving directed C(sp3)–H activation followed by β-heteroatom elimination to generate a PdII(π-alkene) intermediate that then undergoes redox-neutral annulation with an ambiphilic aryl halide to access 5- and 6-membered (hetero)cycles. Various alkyl C(sp3)–oxygen, nitrogen, and sulfur bonds can be selectively activated, and the annulation proceeds with high diastereoselectivity. The method enables modification of amino acids with good retention of enantiomeric excess, as well as σ-bond ring-opening/ring-closing transfiguration with low-strain heterocycles. Despite its mechanistic complexity, the method employs simple conditions and is operationally straightforward to perform. | Hui-Qi Ni; Jing-Cheng Dai; Shouliang Yang; Richard Loach; Matthew Chuba; Indrawan McAlpine; Keary Engle | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/645c06c6f2112b41e956d61a/original/catalytic-bond-annulation-with-ambiphilic-organohalides-enabled-by-x-elimination.pdf |
6654da5921291e5d1d6a5b07 | 10.26434/chemrxiv-2024-d6qkv | Aromatic Ring-Opening Metathesis | Aromatic compounds have found paramount utility on account of their stability, characteristic interactions, defined molecular shape and the numerous synthetic approaches for their synthesis, which include a diversity of cyclization reactions. In contrast, the cleavage of the inert aromatic carbon-carbon bonds remained largely unfeasible due to the unfavourable energetics of disrupting aromaticity in the formation of ring-opened products. For non- aromatic structures, alkene metathesis catalysed by transition metal alkylidenes is established as one of the most versatile carbon-carbon bond-forming and breaking reactions. However, despite remarkable advancements, strategies to open aromatic compounds by metathesis remained elusive. Herein we disclose the feasibility of aromatic ring-opening metathesis (ArROM) to cleave a diversity of aromatic rings, including tetraphene, naphthalene, indole, benzofuran and phenanthrenes by employing Schrock- Hoveyda molybdenum alkylidene catalysts. The reactions for each of the ring systems thereby proceed through unique alkylidene intermediates. We further show the possibility for stereoselective aromatic ring-opening metathesis with exquisite catalyst control over the configuration of atropisomers. Aromatic ring-opening metathesis is therefore a viable and efficient approach to catalytically transform and interconvert various aromatics without the requirement for any reagents or photoexcitation. | Valeriia Hutskalova; Christof Sparr | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Stereochemistry; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6654da5921291e5d1d6a5b07/original/aromatic-ring-opening-metathesis.pdf |
60c758ec469df43dc3f45779 | 10.26434/chemrxiv.14614152.v1 | Cluster Models of FeMoco with Sulfide and Carbyne Ligands: Effect of Interstitial Atom in Nitrogenase Active Site | <p>Nitrogen-fixing
organisms perform dinitrogen reduction to ammonia at an iron-M (M = Mo, Fe, or
V) cofactor (FeMco) of nitrogenase. FeMoco displays eight metal centers bridged
by sulfides and a carbide having the MoFe<sub>7</sub>S<sub>8</sub>C cluster
composition. The role of the carbide ligand, a unique motif in protein active
sites, remains poorly understood. Toward addressing its function, we isolated
synthetic models of subsite MFe<sub>3</sub>S<sub>3</sub>C displaying sulfides
and a carbyne ligand. We developed synthetic protocols for structurally related
clusters, [Tp*MFe<sub>3</sub>S<sub>3</sub>X]<sup>n-</sup>, where M = Mo or W,
the bridging ligand X = CR, N, NR, S, and Tp* =
tris(3,5-dimethyl-1-pyrazolyl)hydroborate, to study the effects of the identity
of the heterometal and the bridging X group on structure and electrochemistry.
While the nature of M results in minor changes, the μ<sub>3</sub>-bridging
ligand X has a large impact on reduction potentials, with differences higher
than 1 V, even for the same formal charge, the most reducing clusters being
supported by the carbyne ligand. </p> | Linh Le; Gwendolyn Bailey; Anna Scott; Theodor Agapie | Bioinorganic Chemistry; Coordination Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758ec469df43dc3f45779/original/cluster-models-of-fe-moco-with-sulfide-and-carbyne-ligands-effect-of-interstitial-atom-in-nitrogenase-active-site.pdf |
6169a534fb8619755bf95ac8 | 10.26434/chemrxiv-2021-1wh3l-v3 | Activating [FeFe] hydrogenase mimic for hydrogen evolution under visible light | Inspired by the active center of the natural [FeFe] hydrogenases, we designed a compact and precious metal-free photosensitizer-catalyst dyad (PS-CAT) for photocatalytic hydrogen evolution under visible light irradiation. PS-CAT represents a prototype dyad comprising pi-conjugated oligothiophenes as light absorbers. PS-CAT and its interaction with the sacrificial donor 1,3-dimethyl-2-phenylbenzimidazoline were studied by steady-state and time-resolved spectroscopy coupled with electrochemical techniques and visible light-driven photocatalytic investigations. Operando EPR spectroscopy revealed the formation of an active [Fe(I)Fe(0)] species – in accordance with theoretical calculations – presumably driving photocatalysis effectively (TON ≈ 210). | Philipp Buday; Chizuru Kasahara; Elisabeth Hofmeister; Daniel Kowalczyk; Michael K. Farh; Saskia Riediger; Martin Schulz; Maria Wächtler; Shunsuke Furukawa; Masaichi Saito; Dirk Ziegenbalg; Stefanie Gräfe; Peter Bäuerle; Stephan Kupfer; Benjamin Dietzek-Ivanšić; Wolfgang Weigand | Catalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6169a534fb8619755bf95ac8/original/activating-fe-fe-hydrogenase-mimic-for-hydrogen-evolution-under-visible-light.pdf |
67999b606dde43c908c86c50 | 10.26434/chemrxiv-2025-652kn | Differentiation Between Bulk and Interfacial Properties: Analysis of Time-Dependent Carrier Injection in Perovskite Solar Cells | Perovskite solar cells (PSCs) have developed rapidly in the last decade, primarily because of improvements in their photovoltaic (PV) performance. However, methods of characterization and analyses for PSCs remain immature, mostly because of the complex multilayered PSC structure. The sandwiched structure of i-type perovskite photoabsorbers having both p-type hole transport materials (HTMs) and n-type electron transport materials (ETMs) facilitates charge separation in the perovskite photoabsorber and thus plays a crucial role in developing efficient PSCs. However, this structure forms multiple heterointerfaces, which more easily undergo structural changes than the bulk and are difficult to characterize independently. Herein, we propose a method for differentiating the bulk and heterointerface properties in PSCs in terms of their carrier dynamics by using excitation power dependence on photoluminescence lifetime (EPD-PLL) measurements. This method exploits the intrinsically different carrier mobility behavior of the PSC components; specifically, the carrier mobilities within perovskite photoabsorbers are significantly higher (by over three orders of magnitude) than those in carrier-transport materials (CTMs). Strong excitation causes carrier accumulation in the CTM bulk, resulting in time-dependent carrier injection, which could be indicative of the bulk CTM properties. In contrast, weak excitation leads to time-independent carrier injection from the perovskite to CTMs, correlating with heterointerface properties. Hence, EPD-PLL measurements differentiate carrier dynamics between the CTM bulk and heterointerfaces. The method was tested by investigating the thermal degradation mechanism of typical Spiro-OMeTAD-based PSCs, revealing that the contribution of heterointerface deterioration by thermal stress can be neglected. The degraded PSCs had unusual PV properties, unlike those of fresh PSCs, and the EPD-PLL results confirmed these unusual properties, facilitating effective PSC characterization. The proposed method can be applied to the characterization of other PSCs, contributing to the further development of PSCs by addressing a missing point: the characterization and analysis of PSCs. | Naoyuki Nishimura; Ranjan Kumar Behera; Daisuke Kubota; Hiroyuki Kanda; Kohei Yamamoto; Hiroyuki Yaguchi; Takurou N. Murakami; Hiroyuki Matsuzaki | Materials Science | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67999b606dde43c908c86c50/original/differentiation-between-bulk-and-interfacial-properties-analysis-of-time-dependent-carrier-injection-in-perovskite-solar-cells.pdf |
642d6b29736114c963f50391 | 10.26434/chemrxiv-2023-08z77 | A simple, sustainable route to flexible microporous carbon cloth for energy storage applications | Activated carbon cloth (ACC) has the potential to be extremely useful in gas capture and storage applications as it combines high porosity, robustness, and flexibility with ease of handling. While it has been produced by a few researchers, the synthesis methods used to date either do not yield a product with high porosity, or if appropriate textural properties are achieved the synthesis is com- plex and arduous. Following a systematic study, we show that an almost exclusively microporous flexible ACC can be achieved with surface area >1900 m2 g−1 via stabilisation with NH4Cl only, followed by activation with benign activating agent potassium oxalate (PO). After extensive opti- misation and simplification of the process, it was found that the stabilisation step can be omitted in a synthesis route requiring only a simple carbonisation step to produce a flexible microporous carbon with surface area >2200 m2 g−1, thus further reducing the need for additional solvents and reagents. The CO2 and CH4 uptake of the ACCs developed in this work is comparable to that previously reported for flexible porous carbons prepared via more complicated routes and the porosity of the ACCs can be tuned to specific gas uptake applications according to the synthesis conditions. | Thria Alkhaldi; L. Scott Blankenship; Robert Mokaya | Physical Chemistry; Energy; Energy Storage; Physical and Chemical Properties; Surface; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-04-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/642d6b29736114c963f50391/original/a-simple-sustainable-route-to-flexible-microporous-carbon-cloth-for-energy-storage-applications.pdf |
60c751bcbb8c1a25f83dbd4b | 10.26434/chemrxiv.13017149.v2 | Efficient Polymer-Mediated Delivery of Ribonucleoprotein Payloads Through Combinatorial Design & Parallelized Experimentation | Genome editing is almost completely reliant on viral delivery to achieve therapeutic goals, hindering widespread clinical adoption. Chemically defined delivery vehicles such as cationic polymers are versatile alternatives to engineered viruses, but their clinical translation hinges on rapidly exploring vast chemical design spaces and deriving structure-function relationships governing delivery performance. Here, we discovered a polymer for efficient ribonucleoprotein (RNP) delivery through combinatorial polymer design and parallelized experimental workflows. A chemically diverse library of 43 statistical copolymers was synthesized via combinatorial RAFT polymerization, realizing systematic variations in physicochemical properties. We selected cationic monomers that varied in their pK<sub>a</sub> values (8.1 to 9.2) as well as in the steric bulk and lipophilicity of their alkyl substituents. We also incorporated co-monomers of varying hydrophilicity and elucidated the roles of protonation equilibria and hydrophobic-hydrophilic balance. We screened our multiparametric vector library through image cytometry and rapidly uncovered a hit polymer (P38), which outperforms state-of-the-art commercial transfection reagents, achieving nearly 60\% editing efficiency via non-homologous end-joining. Structure-function correlations underlying editing efficiency, cellular toxicity, and RNP uptake were probed through unbiased statistical learning approaches to uncover the physicochemical basis of P38's performance. Although cellular toxicity and RNP uptake were solely determined by polyplex size distribution and protonation degree respectively, these two polyplex design parameters were found to be inconsequential during RNP delivery. Instead, polymer hydrophobicity and the Hill coefficient, a parameter describing cooperativity-enhanced polymer deprotonation, were identified as the critical determinants of RNP delivery. Our unconventional approach not only discovered a novel polymeric vehicle that may have remained inaccessible to chemical intuition, but also yielded statistically derived design rules to guide the synthesis of future polymer libraries. | Ramya Kumar; Ngoc Le; Zhe Tan; Mary E. Brown; Shan Jiang; Theresa M. Reineke | Biocompatible Materials; Polyelectrolytes - Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751bcbb8c1a25f83dbd4b/original/efficient-polymer-mediated-delivery-of-ribonucleoprotein-payloads-through-combinatorial-design-parallelized-experimentation.pdf |
66b50d425101a2ffa899ddf1 | 10.26434/chemrxiv-2024-bzt5g | Understanding ligand exchange and surface passivation in CdS quantum dots from first principles | The capping ligands on quantum dots (QDs) play a critical role in determining their stability and properties, making the ligand exchange process pivotal. However, rational design rules for selecting ligands to effectively passivate QD surfaces are lacking. In this study, we employ first-principles density functional theory and many-body perturbation theory to systematically examine how various ligands affect surface passivation and modulate the electronic and optical properties of QDs. We focus on the (111) and (100) facets of zinc blende CdS QDs and survey several common ligands: chlorine (-Cl), amine (-NH2), oleic acid [CH3(CH2)7CH=CH(CH2)7COOH], stearic acid [CH3(CH2)16COOH], and thioglycolic acid (HS-CH2-COOH). We elucidate the trends in surface passivation based on an electron counting argument. We discuss different effects associated with the ligand exchange, including the interface dipole, ligand binding mode, and many-body interaction. Our work provides structure-property relationships to pave the way for the rational design of effective QD ligands. | Joseph Frimpong; Sandip Aryal; Tejas Karun; Zhen-Fei Liu | Theoretical and Computational Chemistry; Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b50d425101a2ffa899ddf1/original/understanding-ligand-exchange-and-surface-passivation-in-cd-s-quantum-dots-from-first-principles.pdf |
60c74c01842e6578f4db323f | 10.26434/chemrxiv.12410597.v1 | Quantitative Analysis of Ethyl Carbamate in Distillers Grains Co-products and Bovine Plasma by GC-MS | <p><b>ABSTRACT
: </b>Ethyl
carbamate (EC) is a fermentation byproduct in foods and beverages and
classified as a Group 2A probable human carcinogen. Each year greater than 40
million metric tons of fermentation co-products from the U.S. ethanol industry
are fed to food animals. A GC-MS assay was developed to analyze EC extracted
from various distillers grains co-products with a limit of detection at 0.7
ng/g. EC was detected in all the distillers grains co-products surveyed in this
study. Corn condensed distillers solubles contained the highest level of EC
ranging from 1618 to 2956 ng/g. The levels of EC in the semi-solid co-products
varied from 17 to 917 ng/g. Cattle fed on these fermentation co-products were
found to contain 2-3 ng/mL of EC in blood plasma. No EC was detected in control
animal blood plasma. The presence of EC in animal feeds and subsequently in
animals may pose an animal health risk.</p><br /> | Linxing Yao; Kaitlyn Maloley; Corey D. Broeckling; Steve Ensley; Scott Crain; Robert Coffey | Feed; Food | CC BY 4.0 | CHEMRXIV | 2020-06-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c01842e6578f4db323f/original/quantitative-analysis-of-ethyl-carbamate-in-distillers-grains-co-products-and-bovine-plasma-by-gc-ms.pdf |
65a904b39138d23161345c1e | 10.26434/chemrxiv-2024-lzs12 | A Dinuclear Ru(II) Schiff-Base Complex Catalyzed One-pot Synthesis of Quinolines through Acceptorless Dehydrogenative Coupling of Secondary Alcohols with 2-Nitrobenzyl Alcohol | Dinuclear Ru(II) complexes [(p-cymene)2(RuCl)2L1]2X (X = BF4 (Ru1); X = PF6 (Ru2)) and mononuclear [(p-cymene)(RuCl)L2]BF4 (Ru3) (where L1 = N,N'-(3,3',5,5'-tetraisopropyl-[1,1'-biphenyl]-4,4'-diyl)bis(1-(pyridin-2-yl)methanimine); L2 = N-(2,6-diisopropyl-phenyl)-1-(pyridin-2-yl)-methanimine) have been synthesized and characterized by spectroscopic and analytical techniques. Dinuclear Ru1 and Ru2 orchestrate direct transformation 2-nitrobenzyl alcohols to quinolines under mild conditions with significant efficiency even when employed at a minimal catalyst loading of 0.1 mol%. Proportional experiments carried out with the corresponding mononuclear complex Ru3 by keeping the Ru content same (0.2 mol% of Ru3) reveal superior activity by the bimetallic system Ru1 for the one-pot quinoline synthesis. Late-stage functionalization of bioactive steroids and scale-up synthesis, demonstrate the practical applicability of the present catalyst system. A probable mechanism of this conversion is proposed based on trapping of many of the intermediates by ESI-mass spectroscopy. These mechanistic studies have further been substantiated by React-IR studies by monitoring the progress of the reaction in real-time. | Gopal Deshmukh; Santosh J. Gharpure; Ramaswamy Murugavel | Organic Chemistry; Inorganic Chemistry; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a904b39138d23161345c1e/original/a-dinuclear-ru-ii-schiff-base-complex-catalyzed-one-pot-synthesis-of-quinolines-through-acceptorless-dehydrogenative-coupling-of-secondary-alcohols-with-2-nitrobenzyl-alcohol.pdf |
636d495b924538918587fd39 | 10.26434/chemrxiv-2022-vg4jr | Toward liquid cell quantum sensing: Ytterbium complexes with ultra-narrow absorption | In quantum technology (such as atomic vapor cells used in precision magnetometry), the energetic disorder induced by a fluctuating liquid environment acts in direct opposition to the precise control required for coherence-based sensing. Overcoming fluctuations requires a protected quantum subspace that only weakly interacts with the local environment. Herein, we report a ferrocene-supported ytterbium complex ((thiolfan)YbCl(THF), thiolfan = 1,1′-bis(2,4-di-tert-butyl-6-thiomethylenephenoxy)ferrocene) that exhibits an extraordinarily narrow absorption linewidth in solution at room temperature with a full-width at half-maximum of 0.625 ± 0.006 meV. A detailed spectroscopic analysis allows us to assign all near infrared (NIR) transitions to atom-centered f-f transitions, protected from the solvent environment. A combination of density functional theory and multireference methods match experimental transition energies and oscillator strengths, illustrating the role of spin-orbit coupling and asymmetric ligand field in enhancing absorption and pointing toward molecular design principles that create well-protected yet observable electronic transitions in lanthanide complexes. Narrow linewidths allow for a demonstration of extremely low-field magnetic circular dichroism at room temperature, employed to sense and image magnetic fields, down to Earth scale. We term this system an ‘atom-like molecular sensor’ (ALMS), and propose approaches to improve its performance. | Ashley J. Shin; Changling Zhao; Yi Shen; Claire E. Dickerson; Barry Y. Li; Daniel Bím; Timothy L. Atallah; Paul H. Oyala; Lianne K. Alson; Anastassia N. Alexandrova; Paula L. Diaconescu; Wesley C. Campbell; Justin R. Caram | Theoretical and Computational Chemistry; Physical Chemistry; Inorganic Chemistry; Lanthanides and Actinides; Sensors; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636d495b924538918587fd39/original/toward-liquid-cell-quantum-sensing-ytterbium-complexes-with-ultra-narrow-absorption.pdf |
661f7dbd21291e5d1d026b84 | 10.26434/chemrxiv-2024-vnh4k | Reparameterization of GFN1-xTB for Atmospheric Molecular Clusters: Applications to Multi-Acid–Multi-Base Systems | Atmospheric molecular clusters, the onset of secondary aerosol formation, are a ma- jor part of the current uncertainty in modern climate models. Quantum chemical (QC) methods are usually employed in a funneling approach to identify the lowest free energy cluster structures. However, the funneling approach highly depends on the accuracy of low-cost methods to ensure that important low-lying minima are not missed. Here we present a reparameterized GFN1-xTB model based on the Clusteromics I–V datasets for studying atmospheric molecular (AMC) clusters, denoted AMC-xTB. The AMC- xTB model reduces the mean of electronic binding energy errors from 7–11.8 kcal/mol to roughly 0 kcal/mol and the root mean square deviation from 7.6–12.3 kcal/mol to 0.81–1.45 kcal/mol. In addition, the minimum structures obtained with AMC-xTB are closer to the ωB97X-D/6-31++G(d,p) level of theory compared to GFN1-xTB. We employ the new parameterization in two new configurational sampling workflows that include an additional meta-dynamics sampling step using CREST with the AMC-xTB model. The first workflow, denoted the “independent workflow”, is a commonly used funneling approach with an additional CREST step, and the second, the “improvement workflow”, where the best configuration currently known in the literature is improved with a CREST+AMC-xTB step. Testing the new workflow we find configurations lower in free energy for all the literature clusters with the largest improvement being up to 21 kcal/mol. Lastly, employing the improvement workflow we massively screened 288 multi-acid– multi-base clusters containing up to 8 different species. For these new multi-acid–multi- cluster systems we observe that the improvement workflow finds configurations lower in free energy for 245 out of 288 (85.1%) cluster structures. Most of the improvements are within 2 kcal/mol, but we see improvements up to 8.3 kcal/mol. Hence, we can recommend this new workflow based on the AMC-xTB model for future studies on atmospheric molecular clusters. | Yosef Knattrup; Jakub Kubečka; Haide Wu; Frank Jensen; Jonas Elm | Theoretical and Computational Chemistry; Physical Chemistry; Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Theory - Computational; Thermodynamics (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2024-04-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661f7dbd21291e5d1d026b84/original/reparameterization-of-gfn1-x-tb-for-atmospheric-molecular-clusters-applications-to-multi-acid-multi-base-systems.pdf |
66cdda9d20ac769e5f02f47b | 10.26434/chemrxiv-2024-pzclt-v2 | Reactivity of Pseudozyma antarctica lipase B towards the Synthesis of End-capped Polycaprolactone for Drug Delivery | State-of-the-art delivery systems currently rely on chemical synthesis routes for drug encapsulation. However, these methods have inherent drawbacks concerning toxicity, selectivity, and the potential for burst release. To overcome these limitations, the enzymatic synthesis of polymer-drug conjugates emerges as a promising alternative to promote ecofriendliness and safety in production and grants precise control over the resulting structures. In this study, we delved into the reactivity of Pseudozyma (Candida) antarctica lipase B for polyesters’ capping with small molecules. For that purpose, Quantum Mechanics/Molecular Mechanics simulations were used to predict the conjugation reactions. These predictions were translated to the laboratory, where the enzymatic reactions were replicated, subsequently benchmarking them against metal-catalysed reactions. The outcome of our experiments was the successful generation of end-capped oligo/polycaprolactone, with their molecular weights spanning from 540 to 2600 g/mol with an enzymatic approach, and slightly higher when applying conventional catalysis, and with isolation yields up to 68.4%. This work underscores the potential of enzyme-driven strategies in fabricating precisely engineered drug delivery | Pedro R. Figueiredo; Armando J.D. Silvestre; Andreia F. Sousa; Alexandra T.P. Carvalho | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Biocatalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66cdda9d20ac769e5f02f47b/original/reactivity-of-pseudozyma-antarctica-lipase-b-towards-the-synthesis-of-end-capped-polycaprolactone-for-drug-delivery.pdf |
60c74357842e653b52db2253 | 10.26434/chemrxiv.9114413.v1 | Highly Porous Hybrid Metallosilicate Materials Prepared by Non-Hydrolytic Sol-Gel: Hydrothermal Stability and Catalytic Properties in Ethanol Dehydration | <div>
<p>Herein, we
present novel phenylene- and xylylene-bridged silica and metallosilicate materials
prepared by non-hydrolytic sol-gel. The hybrid silica are highly porous, chemically
similar to periodic mesoporous organosilica (PMO), but amorphous. Analogous
hybrid metallosilicates are obtained by directly incorporating Al, Nb, or Sn in
the hybrid silica framework. Exhibiting open texture, surface acidity and
tunable hydrophobicity, these materials are excellent candidates for catalytic
alcohol dehydration reactions. The gas-phase hydrothermal and thermal stability
of these materials is examined. While the hybrid silica is expectedly stable, a
stark decrease in stability is observed for phenylene bridged silsesquioxanes upon
metal introduction. The extent of the hydrolytic Si−C(sp<sup>2</sup>) bond
cleavage is quantitatively followed by <sup>29</sup>Si MAS NMR, TG analysis,
and GC-FID analysis of effluent coming from samples exposed to water vapor. Two
important features affecting the hydrothermal and thermal stability are
identified: (i) the homogeneity of metal dispersion within the silica matrix,
and (ii) the electronegativity of the incorporated metal. The stability of
hybrid metallosilicates is significantly improved by replacing the phenylene
bridges with xylylene bridges, due to the presence of more stable Si−C(sp<sup>3</sup>)
bonds. Interestingly, the latter hybrid metallosilicate proves to be an active catalyst
for the dehydration of ethanol to ethylene. Unlike the other hybrid materials
presented here, it reaches high ethylene yields without undergoing degradation
and deactivation.</p>
</div> | Ales Styskalik; Imene Kordoghli; Claude Poleunis; Arnaud Delcorte; Carmela Aprile; Luca Fusaro; Damien Debecker | Catalysts; Acid Catalysis; Heterogeneous Catalysis; Interfaces; Physical and Chemical Properties | CC BY NC 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74357842e653b52db2253/original/highly-porous-hybrid-metallosilicate-materials-prepared-by-non-hydrolytic-sol-gel-hydrothermal-stability-and-catalytic-properties-in-ethanol-dehydration.pdf |
656c3d8a29a13c4d478c53df | 10.26434/chemrxiv-2023-8v6dr-v2 | Highly modified cephalotane-type diterpenoids from Cephalotaxus fortunei var. alpina and C. sinensis | Six undescribed cephalotane-type diterpenoids and/or norditerpenoids, ceforloids A–F (1–6), were isolated from Cephalotaxus fortunei var. alpina and C. sinensis. Their structures were elucidated by comprehensive analysis of spectroscopic data. Compound 1 possesses an unprecedented norditerpenoid skeleton featuring an unusual acetophenone moiety, and originated putatively from a disparate biogenetic pathway. Compounds 4 and 5 incorporate a unique 12,13-p-hydroxybenzylidene acetal motif. Compound 6 is a rare cephalotane-type diterpenoid glycoside. Immunosuppressive assays showed that compounds 2 and 6 exhibited mild suppressive activity against the activated T and B lymphocytes proliferation. | Zhan-Peng Ge; Jin-Biao Xu; Peng Zhao; Mai Xiang; Yu Zhou; Ze-Min Lin; Jian-Ping Zuo; Jin-Xin Zhao; Jian-Min Yue | Biological and Medicinal Chemistry; Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656c3d8a29a13c4d478c53df/original/highly-modified-cephalotane-type-diterpenoids-from-cephalotaxus-fortunei-var-alpina-and-c-sinensis.pdf |
60c74580842e657127db263e | 10.26434/chemrxiv.10046525.v1 | Iridium-Catalyzed Silylation of Five-Membered Heteroarenes: High Sterically Derived Selectivity from a Pyridyl-Imidazoline Ligand | <div>We report that the silylation of five-membered ring heteroarenes occurs with high sterically derived regioselectivity when catalyzed by the combination of</div><div>[Ir(cod)(OMe)]2 and a phenanthroline ligand or a new pyridylimidazoline ligand that further increases the regioselectivity. The silylation reactions with these catalysts produce high yields of heteroarylsilanes from functionalization at the most sterically accessible C–H bonds of these rings under conditions that the borylation of C–H bonds with previously reported catalysts formed mixtures of products or products that are unstable.</div> | Caleb Karmel; Camille Rubel; Elena Kharitonova; John Hartwig | Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74580842e657127db263e/original/iridium-catalyzed-silylation-of-five-membered-heteroarenes-high-sterically-derived-selectivity-from-a-pyridyl-imidazoline-ligand.pdf |
60dacfa02962502258e5916f | 10.26434/chemrxiv-2021-mxk4c | Synthesis and Exploitation of the Biological Profile of Novel Guanidino Xylofuranose Derivatives | The synthesis of novel guanidino sugars as potential mimetics of nucleosides and their biological evaluation is described. 5-Guanidino xylofuranoses containing different O-substituents at C-3, including saturated/unsaturated hydrocarbon chains and aromatic-containing moieties, were accessed from 5-azido xylofuranose precursors through reduction followed by guanidinylation of the obtained amines with N,N′-bis(tert-butoxycarbonyl)-N′′-triflylguanidine. A 5-azido 3-O-methyl-branched N-benzyltriazole isonucleoside was converted into the corresponding 5-guanidino-containing isonucleoside, whose structure includes both the guanidine and triazole moieties as nucleobase-like motifs connected to the xylofuranose template. In alternative, this structurally new type of compound was synthesized via cycloaddition between a 5-guanidino-3-O-propargyl xylofuranose derivative and benzyl azide in the presence of a CuI/Amberlyst A-21 catalytic system, along with the 5-iodotriazole derivative as a secondary product, which, in turn was the sole product when using equimolar CuI and a catalytic amount of 4-dimethylaminopyridine. A guanidinomethyltriazole 3′-O-dodecyl xylofuranos-5′-yl isonucleoside, which comprise a novel isonucleosidic framework having a guanidine system appended on the sugar-linked triazole motif, was obtained from the related aminomethyltriazole 5’-isonucleoside via guanidinylation. Bioactivity screening revealed 2 compounds as selective inhibitors of acetylcholinesterase (AChE), namely the guanidinomethyltriazole derivative, with moderate inhibition (Ki = 22.87 µM) and the 3-O-dodecyl (N-Boc)guanidino xylofuranose, which was the most active compound (Ki = 7.49 µM) acting as a non-competitive inhibitor. The latter also displayed moderate antiproliferative effects in chronic myeloid leukemia (K562, GI50 =31.02 μM) and in breast cancer (MCF-7, GI50 = 26.89 μM) cells. The aminomethyltriazole 5’-isonucleoside was the most potent molecule with single-digit micromolar GI50 values against both cells (GI50 = 6.33 μM and 8.45 μM), similar to that of the standard drug 5-fluorouracil against MCF-7 cells. | Nuno Manuel Xavier; Andreia Fortuna; Rita Gonçalves-Pereira; Paulo J. Costa; Radek Jorda; Veronika Vojáčková; Niels V. Heise; René Csuk; M. Conceição Oliveira | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Organic Synthesis and Reactions; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60dacfa02962502258e5916f/original/synthesis-and-exploitation-of-the-biological-profile-of-novel-guanidino-xylofuranose-derivatives.pdf |
627b68e2809e323af88bc3b7 | 10.26434/chemrxiv-2022-d0f7d | Influence of structural dynamics on cell uptake investigated with single-chain polymeric nanoparticles | Most nanoparticles’ parameters affect their interactions with cells. To date, all the parameters studied are basically static (e.g., size, shape, ligands, charge). This is unfortunate, as proteins have structural dynamics that most nanoparticles do not possess. Here we study single-chain polymeric nanoparticles (SCPNs), whose structure undergoes dynamic changes. We produced multiple sets of particles from identical polymer chains via a supramolecular reshuffling approach that allowed iterative reshuffling between a compact/static and a sparse/dynamic form. These particles are topological isomers as they have identical molecular formulas differing in connectivity, and thus structural dynamics. We show that cell uptake discriminates these SCPN topological isomers. Through different endocytic pathways, the sparse/dynamic isomers are uptaken more, but the compact/static isomers access the cytosol more efficiently as evidenced by a glucocorticoid translocation assay. These results highlight the importance of structural dynamics’ role in cellular interactions. | Suiyang Liao; Lixia Wei; Arthur Boucheza; Francesco Stellacci | Materials Science; Polymer Science; Nanoscience; Drug delivery systems; Polymer chains; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/627b68e2809e323af88bc3b7/original/influence-of-structural-dynamics-on-cell-uptake-investigated-with-single-chain-polymeric-nanoparticles.pdf |
668da25cc9c6a5c07acb32dc | 10.26434/chemrxiv-2024-tr710-v3 | Rapid, Accurate, Ranking of Protein-Ligand Binding Affinities with VM2, the 2nd –Generation Mining Minima Method | The structure-based technologies most widely used to rank the affinities of candidate small molecule drugs for proteins range from faster but less reliable docking methods to slower but more accurate explicit solvent free energy methods. In recent years, we have advanced another technology, which is called mining minima because it “mines” out the main contributions to the chemical potentials of the free and bound molecular species by identifying and characterizing their main local energy minima. The present study provides systematic benchmarks of the accuracy and computational speed of mining minima, as implemented in the VeraChem Mining Minima Generation 2 (VM2) code, across two well-regarded protein-ligand benchmark datasets for which there are already benchmark data for docking, free energy, and other computational methods. A core result is that VM2’s accuracy approaches that of explicit solvent free energy methods at far lower computational cost. In finer grained analyses, we also examine the influence of various run settings, such as the treatment of crystallographic water molecules, on accuracy, and define the costs in time and dollars of representative runs on Amazon Web Services (AWS) compute instances with various CPU and GPU combinations. We also use the benchmark data to determine the importance of VM2’s correction from generalized Born to finite-difference Poisson-Boltzmann results for each energy well and find that this correction affords a remarkably consistent improvement in accuracy at modest computational cost. The present results establish VM2 as a distinctive technology for early-stage drug discovery, which provides a strong combination of efficiency and predictivity. | Michael K. Gilson; Lawrence E. Stewart; Michael J. Potter; Simon P. Webb | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668da25cc9c6a5c07acb32dc/original/rapid-accurate-ranking-of-protein-ligand-binding-affinities-with-vm2-the-2nd-generation-mining-minima-method.pdf |
632035a0185684558413ff22 | 10.26434/chemrxiv-2022-24mtj | Techno-economic feasibility of a sunflower husk fast pyrolysis value chain for the production of advanced biofuels | Biofuels are required to reach the target set out by the European Commission’s Transport mandate in the RED II (Renewable Energy Directive) for 2020 – 2030. To avoid indirect land use change, waste biomass resources such as sunflower husks can be used for advanced biofuel production. A process simulation and technoeconomic assessment of three fast pyrolysis plant scenarios were conducted. The nature of the waste feedstock has an effect on the value chain configuration, fast pyrolysis, and upgrading process design. Considering the difficulties with the transport and storage of biogenic waste due to low bulk density or hazardous and pathogenic content in case of transporting untreated sunflower husks, it is recommended to use a hub-and-spoke type of decentralized value chain configuration. The fast pyrolysis plants are located close to the feedstock, and the fast pyrolysis bio-oil (FPBO) is transported to a single upgrading facility, colocated at an existing refinery. The upgraded FPBO is then cofed into an FCC (fluidized catalyst cracker), where partially green biofuels such as gasoline and diesel are produced. For the fast pyrolysis process design, Scenario 2, treating 10 t/h of dry biomass with electricity and steam as coproducts, has the most favorable economic results with a total capital investment (TCI) of 78 million Euro and operating expenses (OPEX) of 6 million Euro. | Mieke Nieder-Heitmann; Sadaf S. Savadkouhi; Robbie Venderbosch; Evert Leijenhorst; Evert van der Pol; Hank Vleeming | Energy; Fuels - Energy Science | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/632035a0185684558413ff22/original/techno-economic-feasibility-of-a-sunflower-husk-fast-pyrolysis-value-chain-for-the-production-of-advanced-biofuels.pdf |
63ea269efcfb27a31fb63896 | 10.26434/chemrxiv-2023-6sf4l | Overcoming a Solid Solution System on Chiral Resolution: Combining Thermodynamics of Crystallization and Kinetics of Enantioselective Dissolution | We have successfully performed chiral resolution of a key synthetic intermediate of ozanimod, rac-4-cyano-1-aminoindane, by combining crystallization and enantioselective dissolution. 4-Cyano-1-aminoindane forms a diastereomeric salt with di-p-toluoyl-L-tartaric acid, however the single crystallization gave moderate enantiomeric excess, which indicated the formation of solid solution. The formation of solid solution is typical trouble in chiral resolution, and the limitation of enrichment by the crystallization was indicated by the construction of binary and ternary phase diagrams. Thorough phase diagram study revealed the solid-state landscape of the diastereomeric salt and determined the condition for chiral resolution. Additionally, further enrichment was achieved by following enantioselective dissolution using the difference in dissolution rates of the diastereomeric pairs. This combination of crystallization and dissolution demonstrated chiral resolution of 4-cyano-1-aminoindane up to 96%, and proposed a new solution to the solid solution formation which is typical trouble of chiral resolution for the first time. | Ryusei Oketani; Koki Shiohara; Ichiro Hisaki | Physical Chemistry; Organic Chemistry; Chemical Engineering and Industrial Chemistry; Process Chemistry; Thermodynamics (Physical Chem.); Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63ea269efcfb27a31fb63896/original/overcoming-a-solid-solution-system-on-chiral-resolution-combining-thermodynamics-of-crystallization-and-kinetics-of-enantioselective-dissolution.pdf |
61a9cd2363557c81ab95115e | 10.26434/chemrxiv-2021-cpq5j-v2 | Clustering and Halogen Effects Enabled Red/Near-Infrared Room Temperature Phosphorescence from Aliphatic Cyclic Imides | <a>Pure organics with room temperature
phosphorescence (RTP) are urgently demanded in advanced optoelectronic and
bioelectronic applications. However, currently reported phosphors are mostly
aromatics and restricted to blue to orange colors. It remains an enormous
challenge to achieve red and near-infrared (NIR) RTP, particularly for those
from nonaromatics. Here we demonstrate a series of cyclic imides derived from
succinimide, which can emit red (665, 690 nm) and even NIR (745 nm) RTP with
outstanding efficiencies of up to 9.2%, despite their rather limited molecular
conjugations. Such unique emission should be ascribed to the presence of the
imide unit and heavy atoms, effective molecular clustering, and the electron
delocalization of halogens, which not only greatly facilitate intersystem
crossing, but also afford significantly extended through-space conjugation and
rigidified conformations.</a> These results pave the way to the rational
construction of red and NIR nonconventional luminophores through synergistic
clustering and halogen effects. | Tianwen Zhu; Tianjia Yang; Qiang Zhang; Wang Zhang Yuan | Physical Chemistry; Clusters; Optics; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61a9cd2363557c81ab95115e/original/clustering-and-halogen-effects-enabled-red-near-infrared-room-temperature-phosphorescence-from-aliphatic-cyclic-imides.pdf |
60c740de337d6c06e5e26792 | 10.26434/chemrxiv.7848446.v1 | Hydroalkylation of Olefins to form Quaternary Carbons | Metal-hydride hydrogen atom transfer (MHAT) functionalizes unbiased alkenes with predictable branched (Markovnikov) selectivity. The breadth of these transformations has been confined to π-radical traps; no sp<sup>3 </sup>electrophiles have been reported. Here we describe a Mn/Ni dual catalytic system that allows for the hydroalkylation of unactivated olefins by unactivated alkyl halides, yielding aliphatic quaternary carbons. | Samantha Green; Tucker R. Huffman; Ruairí McCourt; Vincent van der Puyl; Ryan Shenvi | Redox Catalysis; Reaction (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-03-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740de337d6c06e5e26792/original/hydroalkylation-of-olefins-to-form-quaternary-carbons.pdf |
6540fffd48dad23120c63ae0 | 10.26434/chemrxiv-2023-qbmm5 | A dual photobase system for directing the pathway of pH-sensitive chemical reactions with light | Light-gated chemical reactions allow spatial and temporal control of chemical processes. Here, we suggest a new system for controlling pH-sensitive processes with light using two photobases of Arrhenius and Brønsted types. Only after light excitation do Arrhenius photobases undergo hydroxide ion dissociation, while Brønsted photobases capture a proton. However, none can be used alone to reversibly control pH due to the limitations arising from excessively fast or overly slow photoreaction timescales. We show here that combining the two types of photobases allows light-triggered and reversible pH control. We show an application of this method in directing the pH-dependent reaction pathways of the organic dye Alizarin Red S simply by switching between different wavelengths of light, i.e., irradiating each photobase separately. The concept of a light-controlled system shown here of a sophisticated interplay between two photobases can be integrated into various smart functional and dynamic systems. | Anna Yucknovsky; Nadav Amdursky | Physical Chemistry; Chemical Kinetics; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2023-11-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6540fffd48dad23120c63ae0/original/a-dual-photobase-system-for-directing-the-pathway-of-p-h-sensitive-chemical-reactions-with-light.pdf |
67324ad57be152b1d0c35fcc | 10.26434/chemrxiv-2024-37bpl | Active Learning High Coverage Sets of Complementary Reaction Conditions | Chemical reaction conditions capable of producing high yields over diverse reactants will be a key component of future self driving labs. While much work has been done to discover general reaction conditions, any single conditions are necessarily limited over increasingly diverse chemical spaces. A potential solution to this problem is to identify small sets of complementary reaction conditions that, when combined, cover a much larger chemical space than any one general reaction condition. In this work, we analyze experimentally derived datasets to assess the relative performance of individual general reaction conditions vs sets of complementary reaction conditions. We then propose and benchmark active learning methods to efficiently discover these complimentary sets of conditions. The results show the value of active learning in exploring sets of reaction conditions and provide an avenue for improving synthetic hit rates in high-throughput synthesis campaigns. | Sofia Sivilotti; David Friday; Nicholas Jackson | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Combinatorial Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67324ad57be152b1d0c35fcc/original/active-learning-high-coverage-sets-of-complementary-reaction-conditions.pdf |
6556dbc32c3c11ed718e7a20 | 10.26434/chemrxiv-2023-5vpzk-v2 | Dual Ratiometric Fluorescence Monitoring of Mechanical Polymer Chain Stretching and Subsequent Strain-Induced Crystallization | Tracking the behavior of mechanochromic molecules provides valuable insights into force transmission and associated microstructural changes in soft materials under load. Herein, we report a dual ratiometric fluorescence (FL) analysis for monitoring both mechanical polymer chain stretching and strain-induced crystallization (SIC) of polymers. SIC has recently attracted renewed attention as an effective mechanism for improving the mechanical properties of polymers. A polyurethane (PU) film incorporating a trace of a dual-emissive flapping force probe (N-FLAP, 0.008 wt%) exhibited a blue-to-green FL spectral change in a low stress region (< 20 MPa), resulting from conformational planarization of the probe in mechanically stretched polymer chains. Only at higher probe concentrations (~0.65 wt%), the PU film showed a second spectral change from green to yellow during the SIC growth (20–65 MPa) due to self-absorption of scattered FL in a short wavelength region. The reversibility of these spectral changes was demonstrated by load-unload cycles. With these results in hand, the degrees of the polymer chain stretching and SIC were quantitatively mapped and monitored by dual ratiometric imaging based on different FL ratios (I525/I470 and I525/I600). Simultaneous analysis of these two mappings revealed a spatio-temporal gap in the distribution of the polymer chain stretching and the SIC. The combinational use of the dual-emissive force probe and the ratiometric FL imaging is a universal approach for the development of soft matter physics. | Kensuke Suga; Takuya Yamakado; Shohei Saito | Physical Chemistry; Materials Science; Polymer Science; Organic Polymers; Polymer chains; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6556dbc32c3c11ed718e7a20/original/dual-ratiometric-fluorescence-monitoring-of-mechanical-polymer-chain-stretching-and-subsequent-strain-induced-crystallization.pdf |
60c7543f337d6c2a97e289f3 | 10.26434/chemrxiv.13634885.v1 | Novel copper(I) complex of 2,5-Bis(2-pyridyl)phosphole: Synthesis, Characterization, Catalytic Activity and DFT Calculations | <p>A
copper(I) complex [CuCl{<i>k</i><sup>1</sup>(P)-<b>1a</b>}{k<sup>2</sup>(P,N)-<b>1a</b>}]
(<b>1a</b> = 2,5-bis(2-pyridyl)-1-phenylphosphole) with pseudo tetrahedral
geometry was synthesized. In solution, <b>1a</b> displays a hemilabile
behaviour leading to a dynamic equilibrium between four and three-coordinate
specie. Its catalytic potential was tested in synthesis of propargylamines and
1,2,3-triazoles via three-component reactions. <a>Experimental
results discussed on base to DFT calculations. </a></p> | Jeremy Guaramato; Franmerly Fuentes; Rocío Rivera-Campos; Deivi Oliveros; José R. Mora; Andreas Reiber; Edward Ávila; Yomaira Otero; Juan Manuel Garcia Garfido | Coordination Chemistry (Inorg.); Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7543f337d6c2a97e289f3/original/novel-copper-i-complex-of-2-5-bis-2-pyridyl-phosphole-synthesis-characterization-catalytic-activity-and-dft-calculations.pdf |
60c74df6702a9b665a18b952 | 10.26434/chemrxiv.12678290.v1 | Site-Specific and Trigger-Activated Modification of Proteins by Means of Catalytic Hemin/G-quadruplex (hGQ) DNAzyme Nanostructures | <div>Synthetic DNA that forms various G-quadruplex nanostructures, in combination with hemin, <i>N</i>-methyl luminol derivatives, and H2O2 can site-specifically modify proteins (i.e. evidence is provided for lysozyme and human alpha-thrombin). The catalytic modification is completed in 15-30 mins, and the site-specificity is influenced by the G-quadruplex topology (a total of 22 G-quadruplex forming sequences was tested). We also show that the heavy chain of the therapeutic antibody trastuzumab is modified, which facilitates the preparation of antibody-drug conjugates. Furthermore, a trigger can be programmed into this synthetic DNA so that the protein modification chemistry is made dependent on an external trigger.</div><div><br /></div>Techniques used: HPLC, SDS-PAGE, LC-MS/MS, NMR. | Jordi Keijzer; Bauke Albada | Bioorganic Chemistry; Organic Synthesis and Reactions; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74df6702a9b665a18b952/original/site-specific-and-trigger-activated-modification-of-proteins-by-means-of-catalytic-hemin-g-quadruplex-h-gq-dn-azyme-nanostructures.pdf |
60c740220f50db437f3958f9 | 10.26434/chemrxiv.7640414.v1 | A Portable 3D-Printed Platform for Point-of-Care Diagnosis of Clostridium Difficile Infection and Malaria | Here,
we integrate 3D-printing technology with low-cost open source electronics to
develop a portable diagnostic platform suitable for a wide variety of
diagnostic and sensing assays. We demonstrate two different clinical
applications in the diagnosis of <i>Clostridium
difficile</i> infection and malaria. | Soichiro Tsuda; Lewis A. Fraser; Salah Sharabi; Mohammed Hezwani; Andrew Kinghorn; Shaolin Liang; Gillian Douce; Julian Tanner; Leroy Cronin | Analytical Apparatus; Biochemical Analysis; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2019-01-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740220f50db437f3958f9/original/a-portable-3d-printed-platform-for-point-of-care-diagnosis-of-clostridium-difficile-infection-and-malaria.pdf |
628d1d58a42e9cef904c5d1e | 10.26434/chemrxiv-2022-flcwb | Transition State Spectroscopy of the F + NH3 Reaction | Transition state spectroscopy experiments based on negative ion photodetachment directly probe the vibrational structure and metastable resonances that are characteristic of the neutral reactive potential energy surface (PES). Here, we study the five-atom reaction F + NH3 → HF + NH2 using slow photoelectron velocity-map imaging spectroscopy of cryogenically cooled FNH3¯ anions. Reduced-dimensional quantum dynamical simulations performed on a global potential energy surface show excellent agreement with the experimental results, allowing for the assignment of spectral structure and demonstrating that key dynamics of this bimolecular reaction are well described by this theoretical framework. Our combined experimental-theoretical study reveals features associated with a manifold of vibrational Feshbach resonances in the product well of the F + NH3 PES. At higher energies, the spectra reveal structure attributed to resonances localized across the transition state and into the reactant complex well, which may impact the bimolecular reaction dynamics. | Mark Babin; Martin DeWitt; Jascha Lau; Marissa Weichman; Jongjin Kim; Hongwei Song; Hua Guo; Daniel Neumark | Physical Chemistry | CC BY 4.0 | CHEMRXIV | 2022-05-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628d1d58a42e9cef904c5d1e/original/transition-state-spectroscopy-of-the-f-nh3-reaction.pdf |
64559ff627fccdb3ea8f54d7 | 10.26434/chemrxiv-2023-2dfrv-v2 | Ligand Accelerated Hydrogen Isotope Exchange: Switching C-H Activation from Functionalization Towards C-D Bond Formation | Hydrogen isotope exchange (HIE) has emerged as a unique strategy for labelling, affording plenty of deuterated chemicals with varieties in patterns. Although the HIE based on electrophilic C-H activation could utilize the economic heavy water as deuterium source, the poor kinetic feature, as well as the side reactions still hampered its further application. In this work, an acceleration strategy for HIE development had been proposed based on ligand-modified C-H activation intermediate. According to the strategy, high efficiency HIE condition could be stemmed from the moderate-potency conditions in the corresponding functionalizations, which may fail in balancing the C-H activation and the subsequent coupling. Thus, as a proof of concept, experimental evidence was provided by different ligand preferences of HIE and functionalizations based on a non-directed Pd-catalyzed dual-ligand system. The competing experiment suggested the functionalization could be partially suppressed by using steric MPAA ligands, which facilitated the progression of C-D bond formation. | Zhi-Jiang Jiang; Dawei Xu; Jiakai Lu; Jianfei Bai; Bencan Tang; Jia Chen; Zhanghua Gao | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC 4.0 | CHEMRXIV | 2023-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64559ff627fccdb3ea8f54d7/original/ligand-accelerated-hydrogen-isotope-exchange-switching-c-h-activation-from-functionalization-towards-c-d-bond-formation.pdf |
6455042c07c3f0293740f17a | 10.26434/chemrxiv-2023-pqtpd | Reliable Gas Phase Reaction Rates at Affordable Cost by Means of the Parameter-Free junChS-F12 Model Chemistry | A recently developed strategy for the computation at affordable cost of reliable barrier heights ruling reactions in the gas-phase (junChS, [Barone et al. J. Chem. Theory Comput. 2021, 17, 4913-4928]) has been extended to the employment of explicitly-correlated (F12) methods. A thorough benchmark based on a wide range of prototypical reactions shows that the new model (referred to as junChS-F12), which employs cost-effective revDSD-PBEP86-D3(BJ) reference geometries, has an improved performance with respect to its conventional counterpart and outperforms the most well-known model chemistries without the need of any empirical parameter and at an affordable computational cost. Several benchmarks show that revDSD-PBEP86- D3(BJ) structures and force fields provide zero point energies and thermal contributions, which can be confidently used, together with junChS-F12 electronic energies, for obtaining accurate reaction rates in the framework of the master equation approach based on the ab initio transition-state theory. | Vincenzo Barone; Jacopo Lupi; Zoi Salta; Nicola Tasinato | Theoretical and Computational Chemistry; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2023-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6455042c07c3f0293740f17a/original/reliable-gas-phase-reaction-rates-at-affordable-cost-by-means-of-the-parameter-free-jun-ch-s-f12-model-chemistry.pdf |
62923fd0d3c73a9eedd36847 | 10.26434/chemrxiv-2022-vldj6 | Aqueous mid-infrared electrically switchable opaque building envelopes for all-season radiative thermoregulation | Radiative thermoregulation has been considered a promising approach for reducing the heating, ventilation, and air-conditioning (HVAC) energy consumption of buildings and solving the global climate change issues. Electrochromism is a powerful way to dynamically control the heat balance of buildings in response to fluctuating weather conditions, but it has been largely limited to visible and near-infrared wavelength regimes. Here, we develop an aqueous flexible electrochromic system based on graphene ultra-wideband transparent conductive electrode and reversible electrodeposition, which can non-volatilely tune the thermal emissivity between 0.07 (heating) and 0.92 (cooling) with substantial long-term stability and durability. Building energy simulation demonstrates that applying our electrochromic device to building envelopes can save the year-round operational HVAC energy consumption across the U.S., especially in cold climate zone (up to 43.1 MBtu on average among climate zones 5-8). Furthermore, such a dynamic building envelope shows more profound benefits on less insulated buildings, with up to 19.44% of the year-round operational HVAC energy saving for building with only 25% insulation layer, which can serve as a technological solution to retrofit historical buildings or to complement newly constructed buildings with less insulation for lower embodied carbon. | Chenxi Sui; Jiankun Pu; Ting-Hsuan Chen; Yi-Ting Lai; Yunfei Rao; Xiuqiang Li; Jiawei Liang; Venkatasubramanian Viswanathan; Po-Chun Hsu | Physical Chemistry; Materials Science; Energy; Metamaterials; Radiation | CC BY 4.0 | CHEMRXIV | 2022-05-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62923fd0d3c73a9eedd36847/original/aqueous-mid-infrared-electrically-switchable-opaque-building-envelopes-for-all-season-radiative-thermoregulation.pdf |
65398e36a8b423585a368281 | 10.26434/chemrxiv-2021-spcd9-v3 | Transforming CeO2 nanoparticles into ultra small ceria clusters on alumina enhances catalytic activity | Ceria nanoparticles supported on alumina have found wide applications for various catalytic reactions, especially in contact with precious metals. We discovered that treatment of these catalysts at temperatures between 750 and ~1,000 ºC under the flow of CO and NO in the presence of steam (reactive aging in reducing atmosphere) leads to dispersion of ceria nanoparticles and creates a novel catalytic architecture with high density (up to 10 wt%) of atomically dispersed, ultra small CexOy clusters densely covering alumina, as confirmed by XPS, FTIR and AC-STEM characterization. These clusters possess markedly higher oxygen mobility (and therefore oxygen storage capacity), leading to easier extraction of oxygen with the formation of abundant Ce+3 sites and oxygen vacancies. Because of this, these catalysts (in the absence or presence noble metals, such as Rh and Pt) possess much improved activity for multiple industrially important catalytic reactions such as NO and N2O reduction, as well as CO and NO oxidation even after exposure to harsh aging conditions, with activity superior to fresh catalyst even for aged samples, providing a general pathway to creating more efficient PGM/ceria catalysts. Our study therefore reveals novel catalyst architecture with atomically dispersed ceria clusters with superior redox properties under conditions where typical catalyst sintering is generally assumed to occur and allows to utilize these materials as supports for more effective general catalysis. | Konstantin Khivantsev; Hien Pham; Mark Engelhard; Hristiyan Aleksandrov; Libor Kovarik; Xiaohong Li; Jinshu Tian; Iskra Koleva; Inhak Song; Wenda Hu; Xinyi Wei; Yipeng Sun; Pascaline Tran; Trent Graham; Dong Jiang; David P. Dean; Christian J. Breckner; Jeffrey T. Miller; Georgi Vayssilov; Janos Szanyi; Abhaya Datye; Yong Wang | Catalysis; Heterogeneous Catalysis; Redox Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65398e36a8b423585a368281/original/transforming-ce-o2-nanoparticles-into-ultra-small-ceria-clusters-on-alumina-enhances-catalytic-activity.pdf |
643467ce736114c963477b64 | 10.26434/chemrxiv-2023-g9sm2-v2 | Growth and Passivation of Individual Carbon Nanoparticles by C2H2 addition at High Temperatures: Dependence of Growth Rate and Evolution on Material and Size | Absolute kinetics for reactions of C2H2 with a series of ~60 individual carbon nanoparticles (NPs) from graphite, graphene, graphene oxide, carbon black, diamond, and nano-onion feedstocks were measured for temperatures (TNP) ranging from 1200 to 1700 K. All the NPs were observed to gain mass by carbon addition under conditions that varied with feedstock, but with large variations in initial growth rate. Long reaction periods were studied to allow the evolution of the growth rates over time to be observed. Diamond NPs were found to passivate against C2H2 addition if heated above ~1400 K, and the highly variable initial reactivity for carbon nano-onions was found to depend on the presence of non-onion-structure surface carbon. For graphitic and carbon black NPs, three distinct growth modes were observed, correlated with the initial NP mass (M¬initial). Smallest graphitic and carbon black NPs, with masses < ~25 MDa, initially grew rapidly but also passivated quickly after adding < 4% of Minitial. NPs in the 20 to 50 MDa range also passivated, but only after multiple waves of fast growth separated by periods of low reactivity, with up to ~11% total mass gain before passivation. The largest carbon black and graphitic NPs, with Minitial > 50 MDa, grew rapidly and continuously, adding up to ~300% of Minitial with no sign of rate slowing as long as C2H2 was present. The efficiencies for C2H2 addition and etching by O2 are strongly correlated, but the correlation changes as the NPs passivate. Growth and passivation mechanisms are discussed. | Chris Lau; Daniel Rodriguez; Abigail Friese; Scott Anderson | Physical Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Chemical Kinetics; Physical and Chemical Processes; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-04-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643467ce736114c963477b64/original/growth-and-passivation-of-individual-carbon-nanoparticles-by-c2h2-addition-at-high-temperatures-dependence-of-growth-rate-and-evolution-on-material-and-size.pdf |
61cb922502c214cc3a3572c2 | 10.26434/chemrxiv-2021-z4w2d | Aza-Yang Cyclization—Buchner Aromatic Ring Expansion: Collective Synthesis of Cycloheptatriene-containing Azetidine Lactones | We prepared a collection of complex cycloheptatriene-containing azetidine lactones by ap- plying two key photochemical reactions: “aza-Yang” cyclization and Buchner carbene insertion into aromatic rings. While photolysis of phenacyl amines leads to a rapid charge transfer and elimination, we found that a simple protonation of the amine enables the formation of azetidinols as single diastereomers. We provide evidence, through ultrafast spectroscopy, for the electron transfer from free amines in the excited state. Further, we characterize aza-Yang re- action by establishing the dependence of initial reaction rates on rates of photon absorption. Unanticipated change in reactivity in morpholine analogs is explained through interactions with the tosylate anion. Buchner reaction proceeds with slight preference for one diastereomer over the other, and successful reaction requires electron-donating carbene-stabilizing substituents. Overall, sixteen compounds were prepared over seven steps. Guided by an increase in structural complexity, efforts such as this one extend reach of chemists into unexplored chemical space and provide useful quantities of new compounds for studies focused on their properties. | Manvendra Singh; Bryce Gaskins; Daniel Johnson; Christopher Elles; Zarko Boskovic | Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.); Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61cb922502c214cc3a3572c2/original/aza-yang-cyclization-buchner-aromatic-ring-expansion-collective-synthesis-of-cycloheptatriene-containing-azetidine-lactones.pdf |
60c744fdee301c6128c79220 | 10.26434/chemrxiv.9946931.v1 | Interlayer Engineering of Flexible and Large Area Red Organic Light Emitting Diodes Based on a N-Annulated Perylene Diimide Dimer | <p>Flexible red
OLEDs based on a quadruple layer stack in-between electrodes with 160 mm<sup>2</sup>
active area were fabricated in ambient air on PET via slot-die coating. For the
OLED structure PET/ITO/PEDOT:PSS/PVK/PFO:tPDI<sub>2</sub>N-EH/ZnO/Ag the ink
formulations and coating parameters for each layer were systematically
evaluated and optimized. The air-stable red-light emitting material tPDI<sub>2</sub>N-EH
was successfully utilized as blended homogeneous film with PFO for the emitting
layer. The use of an organic hole-transport layer (PVK) and inorganic electron
injection layer (ZnO) significantly improved the brightness of the reference
device from 4 cd/m<sup>2</sup> to 303 cd/m<sup>2</sup>. Surface analysis using AFM
measurements showed that PVK interlayer reduced the surface roughness of the hole
injection layer (PEDT:PSS) from 0.45 nm to 0.17 nm, which improved the ability
to form uniform emitting layers on top. In addition, the ZnO interlayer improved
the average roughness of the device from 1.26 nm to 0.85 nm and reduced the
turn-on voltage of the device from 5.0 V to 2.8 V.</p> | Mohammad Rahmati; Majid Pahlevani; Gregory Welch | Optical Materials | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744fdee301c6128c79220/original/interlayer-engineering-of-flexible-and-large-area-red-organic-light-emitting-diodes-based-on-a-n-annulated-perylene-diimide-dimer.pdf |
66bddb21f3f4b05290f1dc7e | 10.26434/chemrxiv-2024-kbkvg | Thioester-mediated chemoselective aminoacylation of RNA in water. | Selective aminoacylation of RNA in water is a key challenge that must be resolved to elucidate the origin of peptide biosynthesis. To date there are no chemical methods to effectively and selectively aminoacylate RNA-2′,3′-diols, with the breadth of proteinogenic amino acids, in water. Here we demonstrate that prebiotic nitriles, aminoacyl-adenylates and N-carboxyanhydrides all react with thiols (including enzyme-cofactors) to selectively yield aminoacyl-thiols, which in turn aminoacylate RNA in high yield and selectivity for 2',3'-diols. Broad sidechain scope for both thioester synthesis and aminoacylation are demonstrated, including Ala, Asp, Arg, Glu, Gln, Gly, His, Leu, Lys, Phe, Pro, Ser and Val. Asp reacts with high (kinetic) alpha-aminoacylation selectivity, even upon dual activation of alpha- and beta-carboxylates, and Glu gamma-aminoacylation is blocked by pyroglutamate formation. Arg-aminoacylation is catalysed and enhanced by unprecedented sidechain nucleophilic catalysis. Thioester formation suppresses amine coupling and native-duplex is shown to direct chemoselective 2′,3′-aminoacylation of RNA. Our results suggest an important role for thiol cofactors in RNA-aminoacylation prior to the evolution of proteinaceous synthetase enzymes. | Jyoti Singh; Benjamin Thoma; Daniel Whitaker; Yuan Yao; Matthew Powner | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66bddb21f3f4b05290f1dc7e/original/thioester-mediated-chemoselective-aminoacylation-of-rna-in-water.pdf |
64396acc73c6563f14d92042 | 10.26434/chemrxiv-2023-w3fgw | Surfactant Assisted Exfoliation of Near Infrared Fluorescent Silicate Nanosheets | Fluorophores that emit light in the near infrared (NIR) are advantageous in photonics and imaging due to minimal light scattering, absorption, phototoxicity and autofluorescence in this spectral region. The layered silicate Egyptian Blue (CaCuSi4O10) emits as bulk material bright and stable fluorescence in the NIR and is a promising NIR fluorescent material for (bio)photonics. Here, we demonstrate a surfactant-based (mild) exfoliation procedure to produce nanosheets (EB-NS) of high monodispersity, heights down to 1 nm and diameters <20 nm in large quantities. The approach combines planetary ball milling, surfactant assisted bath sonication and centrifugation steps. It avoids the impurities that are typical for the harsh conditions of tip-sonication. Several solvents and surfactants were tested and we find the highest yield for sodium dodecyl benzyl sulfate (SDBS) and water. The NIR fluorescence emission (λem≈930-940 nm) is not affected by this procedure, is extremely stable and is not affected by quenchers. This enables the use of EB-NS for macroscopic patterning/barcoding of materials in the NIR. In summary, we present a simple and mild route to NIR fluorescent nanosheets that promise high potential as NIR fluorophores for optical applications. | Bjoern Hill; Smitha Abraham; Anas Akhtar; Gabriele Selvaggio; Kristina Tschulik ; Sebastian Kruss | Physical Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-04-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64396acc73c6563f14d92042/original/surfactant-assisted-exfoliation-of-near-infrared-fluorescent-silicate-nanosheets.pdf |
623fe1b18ab3732446738f4d | 10.26434/chemrxiv-2022-jgh1c | Mechanochemical Synthesis of Phosphonate-based Proton Conducting Metal Organic Frameworks | The rational design of new type of water stable metal–organic frameworks (MOFs) as promising proton-conductors has attracted great attention owing to their applications in proton-exchange membrane fuel cells (PEMFC). Herein, we report the mechanochemical gram scale synthesis of three new mixed ligand phosphonate-based MOFs, {Co(H2PhDPA)(4,4ʹ-Bipy)(H2O)·2H2O}n (BAM-1), {Fe(H2PhDPA)(4,4ʹ-Bipy)(H2O)·2H2O}n (BAM-2) and {Cu(H2PhDPA)(Dpe)2(H2O)2·2H2O}n (BAM-3) [where H2PhDPA = Phenylenediphosphonate 4,4ʹ-Bipy = 4,4ʹ-Bipyridine, and Dpe = 1,2-Di(4-pyridyl)ethylene]. Single crystal X-ray diffraction measurements revealed that BAM-1 and BAM-2 are isostructural and possess a three-dimensional (3D) network structure comprising1D channels filled with guest water molecules. Whereas BAM-3 displays a one-dimensional (1D) network structure extended to 3D supramolecular structure by hydrogen-bonding bridging and π-π interactions. In all three structures, guest water molecules are interconnected with uncoordinated acidic hydroxylgroups of the phosphonate moieties and coordinated water molecules by means of extended hydrogen-bonding interactions. BAM-1 and BAM-2 showed gradual increase of proton conductivities with increasing temperature and reached to 4.9 × 10–5 and 4.4 × 10–5 S cm–1 at 90 C and 98% RH. In case of BAM-3, the highest proton conductivity recorded was 1.4 × 10–5 S cm–1 at 50 C and 98% RH. Upon further heating, BAM-3 undergoes dehydration followed by phase transition to another crystalline form which largely effects the performance. All compounds exhibited a proton hopping (Grotthuss model) mechanism as suggested by their low activation energy. | Biswajit Bhattacharya; Max Rautenberg; Chayanika Das; Franziska Emmerling | Inorganic Chemistry; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-03-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/623fe1b18ab3732446738f4d/original/mechanochemical-synthesis-of-phosphonate-based-proton-conducting-metal-organic-frameworks.pdf |
6464fa1fa32ceeff2dcce578 | 10.26434/chemrxiv-2023-cd90t | Effect of Solvent on the Interaction of Lignin
with Zeolite Nanosheet in the Condensed | Lignin is the essential building block of lignocellulosic biomass, an excellent renewable source of different aromatic monomers for the polymer and biofuel industry. The depolymerization of lignin into value-added chemicals and fuels through the catalytic process poses a significant challenge due to the complex structure of lignin. Understanding lignin's conformational diversity and dynamics in the liquid phase is crucial for designing an effective depolymerization process. Here, we conducted all-atom molecular dynamics simulations to understand the conformation and dynamics of softwood lignin on the all-silica zeolite nanosheet based on the MFI topology in a binary mixture of water-methanol at three different molar compositions (0%, 50%, 100% methanol). We observed that methanol-surface interaction is stronger than water-surface, and methanol readily diffused into the MFI core. Lignin and surface contact decreases with increasing methanol composition due to higher solubility and dynamics. Lignin dynamics on the surface in neat water is an order of magnitude smaller than methanol. We also found that lignin adopts a slightly extended conformation when it stays on the surface than in the bulk solution phase for the pure water case, whereas for pure methanol and the binary structures are statistically similar. | Md Masrul Huda; Neeraj Rai | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Computational Chemistry and Modeling; Interfaces; Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6464fa1fa32ceeff2dcce578/original/effect-of-solvent-on-the-interaction-of-lignin-with-zeolite-nanosheet-in-the-condensed.pdf |
626f293fd048ed361258f371 | 10.26434/chemrxiv-2022-n6mp5 | Conductive SWCNT/PDMS bottlebrush elastomers for ultrasoft electronics | Understanding biological systems and mimicking their functions require electronic tools that can interact with biological tissues with matched softness. Conductive materials that match the softness of biological tissue are thus highly demanded for the construction of ultrasoft electronics. However, the commonly employed intrinsically stretchable materials usually contain solvents that limit stability for long-term use or possess low electronic conductivity. Additionally, integrating such ultrasoft and conductive materials into electronic devices is poorly explored. This article reports a solvent-free, ultrasoft and conductive PDMS bottlebrush elastomer composite with single-wall carbon nanotubes as conductive fillers. The conductive SWCNT/BBE with a filler concentration of 0.4−0.6 wt % reveals an ultralow Young’s modulus (<11 kPa) and satisfactory conductivity (>2 S/m) as well as strong wet-adhesion property. Furthermore, we fabricate ultrasoft electronics based on laser cutting and 3D printing of conductive and non-conductive BBEs and demonstrate their potential applications in wearable sensing, soft robotics, and electrophysiological recording. | Pengfei Xu; Shaojia Wang; Angela Lin; Hyun-Kee Min; Zhanfeng Zhou; Xi Huang; Helen Tran; Xinyu Liu | Materials Science; Polymer Science; Composites; Elastic Materials; Polymer brushes; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/626f293fd048ed361258f371/original/conductive-swcnt-pdms-bottlebrush-elastomers-for-ultrasoft-electronics.pdf |
60c74451bdbb894200a387c6 | 10.26434/chemrxiv.9777632.v1 | Record High External Quantum Efficiency of 19.2% Achieved in Light-Emitting Diodes of Colloidal Quantum Wells Enabled by Hot-Injection Shell Growth | <p> Colloidal quantum
wells (CQWs) are regarded as a new, highly promising class of
optoelectronic materials thanks to their unique excitonic characteristics of high
extinction coefficient and ultranarrow emission bandwidth. Although the exploration
of CQWs in light-emitting diodes (LEDs) is impressive, the performance of
CQW-LEDs lags far behind compared with other types of LEDs (e.g., organic LEDs,
colloidal quantum-dot LEDs, and perovskite LEDs). Herein, for the first time, the authors show high-efficiency CQW-LEDs reaching
close to the theoretical limit. A key factor for this high performance is the
exploitation of hot-injection shell (HIS) growth of CQWs, which enables a near-unity photoluminescence
quantum
yield (PLQY), reduces nonradiative channels, ensures smooth films and enhances
the stability. Remarkably, the PLQY remains 95% in solution and 87% in film despite
rigorous cleaning. Through
systematically understanding their shape-, composition- and device- engineering, the CQW-LEDs using CdSe/Cd<sub>0.25</sub>Zn<sub>0.75</sub>S
core/HIS CQWs exhibit a maximum external quantum efficiency of 19.2%. Additionally, a high luminance of 23,490 cd m<sup>-2</sup>, extremely saturated red color with the Commission
Internationale de L’Eclairage coordinates of (0.715, 0.283) and stable emission
are obtained. The findings indicate that HIS grown CQWs enable high-performance
solution-processed LEDs, which may pave the path for CQW-based display and
lighting technologies.</p> | Baiquan Liu; Yemliha Altintas; Lin Wang; Sushant Shendre; Manoj Sharma; Handong Sun; Evren Mutlugun; Hilmi Volkan Demir | Nanodevices | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74451bdbb894200a387c6/original/record-high-external-quantum-efficiency-of-19-2-achieved-in-light-emitting-diodes-of-colloidal-quantum-wells-enabled-by-hot-injection-shell-growth.pdf |
66d6c7fc51558a15efe623a2 | 10.26434/chemrxiv-2024-2cp8z | Photocyclization of Fluorinated Acetophenones Unlocks an Efficient Way to Solar Energy Storage | The development of light-driven isomerization offers a promising avenue for energy storage applications. However, a persistent challenge lies in controlling the stability of the photoisomeric state and in catalyzing the thermal reversal effec-tively. In this work, we introduce the molecular pair ortho-methylacetophenone ⇄ benzocyclobutenol as a promising platform for long-term energy storage. To obtain an overall good performance, a trifluoromethyl group is strategically introduced. This group prevents unproductive reaction pathways during the photochemical cyclization (yield >99%), ensures stable photoisomers, and facilitates back-isomerization by critically lowering the pKa of the benzocyclobutenol scaffold. Thus, efficient reversal using simple organic bases is achieved, capitalizing on substantial rate differences for normal vs. anionic electrocyclic ring-openings. Ultimately, this discovery enables controlled heat release under ambient conditions. | Henning Maag; Matthias Schmitz; Alexander Sandvoß; Domenik Mundil; Abhilash Pedada; Felix Glaser; Christoph Kerzig; Johannes Markus Wahl | Organic Chemistry; Catalysis; Energy; Photochemistry (Org.); Physical Organic Chemistry; Energy Storage | CC BY NC 4.0 | CHEMRXIV | 2024-09-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d6c7fc51558a15efe623a2/original/photocyclization-of-fluorinated-acetophenones-unlocks-an-efficient-way-to-solar-energy-storage.pdf |
60e0cf6195d7ff1e24bc7ef8 | 10.26434/chemrxiv-2021-m7dh3 | Revealing Substrate Positioning Dynamics in Non-heme Fe(II)/αKG-dependent Halogenases Through Spectroscopically Guided Simulation | Non-heme iron halogenases, such as SyrB2, WelO5, and BesD, halogenate unactivated carbon atoms of diverse substrates at ambient conditions with exquisite selectivity seldom matched by non-biological catalysts. Although crystallography, spectroscopy, and kinetic measurements provide foundational knowledge of enzyme structure and function, critical gaps remain in our understanding of how the protein environment dynamically reorganizes to a catalytically active state capable of halogenation. Using experimentally-guided molecular dynamics (MD) simulations augmented with multi-scale (i.e., QM/MM) simulations of substrate-bound complexes of BesD and WelO5, we investigate substrate/active-site dynamics that enable selective halogenation. Our simulations reveal that active-site configurational isomerization is necessary in WelO5 to attain substrate/active-site geometry consistent with its observed chemo- and regioselectivity. Conversely, a slight reorientation of the substrate from its crystal-structure position is sufficient to enable regioselective chlorination in BesD without the need to invoke active-site isomerization. We observe how substrate-protein interactions evolve during experimentally-motivated MD of halogenases. We relate the nature of these interactions to the distinct substrates. For BesD, we resolve the uncertainty around the mechanistic relevance of Asn219 based on a prior mutagenesis study. By quantifying the presence of thermodynamically competitive C-H bonds on substrates of SyrB2, BesD, and WelO5, we confirm the need for the protein environment to strategically position the substrate to impart regioselectivity to halogenases. Our simulations reveal that the optimum substrate/active-site geometry also outweighs interactions between active site ligands and the protein environment in facilitating the required chemoselectivity in halogenases. | Rimsha Mehmood; Vyshnavi Vennelakanti; Heather Kulik | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Catalysis; Computational Chemistry and Modeling; Theory - Computational; Biocatalysis | CC BY NC 4.0 | CHEMRXIV | 2021-07-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60e0cf6195d7ff1e24bc7ef8/original/revealing-substrate-positioning-dynamics-in-non-heme-fe-ii-kg-dependent-halogenases-through-spectroscopically-guided-simulation.pdf |
66f3d9dacec5d6c142248e03 | 10.26434/chemrxiv-2024-r3rjr | FMOPhore for hotspot identification and efficient fragment-to-lead growth strategies | Fragment based drug design (FBDD) is like a chess game in that a good or a bad move can dramatically influence the outcome. At the start of the design process, it is important to identify the key binding site residues (hotspots) that can have a substantial impact on ligand efficiency (LE) and binding. Here, we introduce a novel, fully automated algorithm named FMOPhore, which performs Quantum Mechanics Fragment Molecular Orbital (QM-FMO) calculations on 3D-protein-ligand pharmacophore models. This is implemented in a novel scoring function named FP-score to classify binding site residues in two classes: 1) Hotspot residues (further delineated into three categories; Anchor, Transient, and Accessible) and 2) Non-hotspot residues. We apply our algorithm in two different scenarios: holo-complex and apo-structure scenarios, testing its robustness on sixteen different protein targets including the application for fragment growing and target selectivity. We demonstrate that handling protein binding site flexibility using Dy-FMOPhore improves hotspots detection. The FMOPhore algorithm can be a powerful tool in identifying and quantifying binding site hotspots to enable an efficient design strategy for fragment-to-lead optimization. | Peter E.G.F. Ibrahim; Ulrich Zachariae; Ian Gilbert; Mike Bodkin | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-10-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f3d9dacec5d6c142248e03/original/fmo-phore-for-hotspot-identification-and-efficient-fragment-to-lead-growth-strategies.pdf |
631b8b1d173b5d98f9f78997 | 10.26434/chemrxiv-2022-qj2fg-v2 | Synthesis and styrene copolymerization of novel bromo, chloro, and fluoro ring-disubstituted tert-butyl phenylcyanoacrylates | Novel ring-disubstituted tert-butyl phenylcyanoacrylates, RPhCH=C(CN)CO2C(CH3)3, where R is 3,5-dibromo, 2,4-dichloro, 2,6-dichloro, 3,4-dichloro, 2,4-difluoro, 2,5-difluoro,
2,6-difluoro, 3,4-difluoro, 3,5-difluoro, were prepared and copolymerized with styrene. The acrylates were synthesized by the piperidine catalyzed Knoevenagel condensation of ring-disubstituted benzaldehydes and tret-butyl cyanoacetate, and characterized by CHN analysis, IR, 1H and 13C NMR. All the acrylates were copolymerized with styrene in solution with radical initiation at 70C. The compositions of the copolymers were calculated from nitrogen analysis.
| Huzefa Chaudhary; Paulina Dobryk; Klodiana Duraku; Kylie T. Gaeta; Talia S. Gierut; Nora D. Henley; Erhunmwunsee Igbinovia; Sebastian Krzywinski; Leonie L.N. Mbouguen; Sara M. Schjerven; Nicholas M. Tassone; Gregory B. Kharas | Organic Chemistry; Polymer Science; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Organic Polymers | CC BY 4.0 | CHEMRXIV | 2022-09-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/631b8b1d173b5d98f9f78997/original/synthesis-and-styrene-copolymerization-of-novel-bromo-chloro-and-fluoro-ring-disubstituted-tert-butyl-phenylcyanoacrylates.pdf |
6412b80daad2a62ca1d6b0f3 | 10.26434/chemrxiv-2023-8jwmj | Group 10 Metal Allyl Amidinates: A Family of Readily Accessible and Stable Molecular Precursors to Generate Supported Nanoparticles | The synthesis of well-defined materials as model systems for catalysis and related fields is an important pillar in the understanding of catalytic processes at a molecular level. Various approaches employing organometallic precursors have been developed and established to make monodispersed supported nanoparticles, nanocrystals, and films. Using rational design principles, a new family of precursors based on group 10 metals suitable for the generation of small and monodispersed nanoparticles on metal oxides has been developed. Particle formation on SiO2 and Al2O3 supports is demonstrated, as well as the potential in the synthesis of bimetallic catalyst materials exemplified with a PdGa/SiO2 system capable in the hydrogenation of CO2 to methanol. In addition to surface organometallic chemistry (SOMC), it is envisioned that these precursors could also be employed in related applications such as atomic layer deposition, due to their inherent volatility and relative thermal stability. | Christian Ehinger; Xiaoyu Zhou; Max Candrian; Scott R. Docherty; Stephan Pollitt; Christophe Copéret | Inorganic Chemistry; Catalysis; Organometallic Chemistry | CC BY 4.0 | CHEMRXIV | 2023-03-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6412b80daad2a62ca1d6b0f3/original/group-10-metal-allyl-amidinates-a-family-of-readily-accessible-and-stable-molecular-precursors-to-generate-supported-nanoparticles.pdf |
6584941f9138d2316136191d | 10.26434/chemrxiv-2023-4bmwq | Spaces of mathematical chemistry | In an effort to expand the domain of mathematical chemistry and inspire research beyond the realms of graph theory and quantum chemistry, I explore five mathematical chemistry spaces and their interconnectedness through mappings. These spaces are characterised by their elements and the concept of proximity that binds these elements within the space. These spaces comprise the chemical space, which encompasses substances and reactions; the space of reaction conditions, spanning the physical and chemical aspects involved in chemical reactions; the space of reaction grammars, which encapsulates the rules for creating and breaking chemical bonds; the space of substance properties, covering all documented measurements regarding substances; and the space of substance representations, composed of the various ontologies for characterising substances. | Guillermo Restrepo | Theoretical and Computational Chemistry; Theory - Computational; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-12-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6584941f9138d2316136191d/original/spaces-of-mathematical-chemistry.pdf |
67573ed9085116a133debe0c | 10.26434/chemrxiv-2024-xh6t3-v2 | Vulcanization accelerators and silica coupling agents in polyisoprene melts | The achievement of sufficient dispersion of vulcanization accelerators is critical to tailoring superior cross-linked elastomers. Modern recipes rely on multicomponent formulations with silica particles covered by coupling agents. We study the molecular properties of select accelerators in polyisoprene melts and their affinity for functionalized surfaces via extensive all-atom molecular dynamics simulations. We focus on the common (N-cyclohexyl)-2-benzothiazole sulfenamide (CBS), 1,6-Bis((dibenzylthiocarbamoyl)disulfanyl) hexane (DBTH) and diphenyl guanidine (DPG) molecules and their mixing characteristics at curing temperatures. Our results support a low association affinity for CBS and DBTH with polyisoprene, whereas DPG forms small hydrogen-bonded aggregates. Subsequently, we examine systems in contact with silica interfaces, bare or grafted with (3-Mercaptopropyl) triethoxysilane (MPTES), (3- Octanoylthio) 1-propyl-triethoxysilane (NXT), and bis (triethoxypropyl) disulfide (TESPD). Accelerator-substrate affinity is first assessed at infinite dilution using free energy calculations and subsequently at finite concentrations. Accelerators exhibit high substrate affinity (DPG >CBS >DBTH) irrespective of functionalization. However, coupling agents are able to displace from the surface a significant amount that increases with the grafting density and the size of the coupling agent. Finally, we investigate the behavior of DPG in binary DPG-CBS formulations, where the former can act as a covering agent that solubilizes CBS into the bulk polymer | Nikolaos Patsalidis; George Papakonstantopoulos; Jan Domurath; Patrycja Polinska; Craig Burkhart; Vagelis Harmandaris; Manolis Doxastakis | Theoretical and Computational Chemistry; Polymer Science; Chemical Engineering and Industrial Chemistry; Computational Chemistry and Modeling; Thermodynamics (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67573ed9085116a133debe0c/original/vulcanization-accelerators-and-silica-coupling-agents-in-polyisoprene-melts.pdf |
65a4df12e9ebbb4db93090bd | 10.26434/chemrxiv-2023-cljlr-v2 | Comparative Structure Based Virtual Screening Utilizing Optimized AlphaFold Model Identifies Selective HDAC11 Inhibitor | HDAC11 is a class IV histone deacylase with no crystal structure reported so far. The catalytic domain of HDAC11 shares low sequence identity with other HDAC isoforms which makes the conventional homology modeling less reliable. AlphaFold is a neural network machine learning approach that can predict the 3D structure of proteins with high accuracy even in absence of similar structures. However the fact that AlphaFold models are predicted in absence of small molecules and ions/cofactors complicate their utilization for drug design. Previously we optimized an HDAC11 AlphaFold model by adding the catalytic zinc ion and minimization in the presence of reported HDAC11 inhibitors. In the current study we implement a comparative structure-based virtual screening approach utilizing the previously optimized HDAC11 AlphaFold model to identify novel and selective HDAC11 inhibitors. The stepwise virtual screening approach was successful in identifying a hit that was subsequently tested using an in vitro enzymatic assay. The hit compound showed an IC50 value of 3.5 µM for HDAC11 and could selectively inhibit HDAC11 over other HDAC subtypes at 10 µM concentration. In addition we carried out molecular dynamics simulations to further confirm the binding hypothesis obtained by the docking study. These results reinforce the previously presented AlphaFold optimization approach and confirm the applicability of AlphaFold models in the search for novel inhibitors for drug discovery. | Fady Baselious; Sebastian Hilscher; Dina Robaa; Cyril Barinka; Mike Schutkowski; Wolfgang Sippl | Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a4df12e9ebbb4db93090bd/original/comparative-structure-based-virtual-screening-utilizing-optimized-alpha-fold-model-identifies-selective-hdac11-inhibitor.pdf |
60c741e7842e65424edb1f96 | 10.26434/chemrxiv.8150666.v1 | Convolutional Neural Network of Atomic Surface Structures to Predict Binding Energies for High-Throughput Screening of Catalysts | We present an application of deep-learning convolutional neural network of atomic surface structures using atomic and Voronoi polyhedra-based neighbor information to predict adsorbate binding energies for the application in catalysis. | Seoin Back; Junwoong Yoon; Nianhan Tian; Wen Zhong; Kevin Tran; Zachary Ulissi | Theory - Computational; Machine Learning; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741e7842e65424edb1f96/original/convolutional-neural-network-of-atomic-surface-structures-to-predict-binding-energies-for-high-throughput-screening-of-catalysts.pdf |
60c73dd1bdbb89b26ba37cd9 | 10.26434/chemrxiv.6104054.v1 | Palladium and platinum 2,4-cis-amino azetidine and related complexes | Crystal structures and structural interpretation of complexes of azetidine (and related) ligands coordinated to palladium(II) and platinum(II). | Akina Yoshizawa; Antonio Feula; Andrew G. Leach; Louise Male; John Fossey | Coordination Chemistry (Inorg.); Ligands (Inorg.); Transition Metal Complexes (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2018-04-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dd1bdbb89b26ba37cd9/original/palladium-and-platinum-2-4-cis-amino-azetidine-and-related-complexes.pdf |
60c740ec9abda2f30ff8bdb0 | 10.26434/chemrxiv.7880996.v1 | How Chemistry Computes: Language Recognition by Non-Biochemical Chemical Automata | This manuscript contains the experimental realization of one instance of each automata in the theory of computation using chemistry and not using biochemistry. All automata are implemented in a 1-pot reactor. The Finite Automaton (FA) is represented by a precipitation reaction, the 1-stack Push Down Automaton (PDA) by a pH reaction network and the Turing machine (TM) by the Belousov-Zhabotinsky chemical reaction. The computation (consisting on recognizing if chemically transcribed abstract sequences belong to appropriate languages in the Chomsky hierarchy) is carried out by a chemical reaction recognizing the molecules and their order. Once the sequence is introduced in the reactor (very much as mRNA is introduced in the ribosome) the reaction does all the recognition without any need for external not strictly chemical help from reaction/diffusion set-ups or chemical gates. The result of the computation has a straightforward thermodynamic/information theory interpretation. These results are of interest for soft-robotics, chemically self-assembled systems, chemical neural networks, artificial intelligence and of course chemical computing (i. e., computing done by chemistry at molecular scales which translates to larger scales by the power of Avogadro's number) as well as natural computing and analog/digital computing. | Marta Dueñas-Diez; Juan Perez-Mercader | Theory - Computational; Artificial Intelligence; Redox Catalysis; Thermodynamics (Physical Chem.); Robotics | CC BY NC ND 4.0 | CHEMRXIV | 2019-03-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740ec9abda2f30ff8bdb0/original/how-chemistry-computes-language-recognition-by-non-biochemical-chemical-automata.pdf |
60c7569f337d6c6290e28e5f | 10.26434/chemrxiv.14273651.v1 | Probing Interfacial Effects on Ionization Energies: The Surprising Banality of Anion-Water Hydrogen Bonding at the Air/Water Interface | Liquid microjet photoelectron spectroscopy is an increasingly common technique to measure vertical ionization energies (VIEs) of aqueous solutes, although the interpretation of these experiments is subject to questions regarding sensitivity to bulk versus interfacial solvation environments. Here, we compute aqueous-phase VIEs for a set of inorganic anions, some of which partition preferentially at the air/water interface, using a combination of molecular dynamics simulations and electronic structure calculations. The results are in excellent agreement with experiment, regardless of whether the simulation data are restricted to ions at the air/water interface or to those in bulk liquid water. Although the computed VIEs are sensitive to ion-water hydrogen bonding, we find that the short-range solvation structure is sufficiently similar in the bulk and interfacial environments that it proves impossible to discriminate between the two on the basis of the VIE, a conclusion that has important implications for the interpretation of liquid-phase photoelectron spectroscopy. More generally, analysis of the simulation data suggests that partitioning of soft anions at the air/water interface is largely a second (or third) solvation shell effect, arising from disruption of water-water hydrogen bonds and not from significant changes in first-shell anion-water hydrogen bonding. <br /> | Suranjan Paul; John Herbert | Computational Chemistry and Modeling; Theory - Computational; Interfaces; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7569f337d6c6290e28e5f/original/probing-interfacial-effects-on-ionization-energies-the-surprising-banality-of-anion-water-hydrogen-bonding-at-the-air-water-interface.pdf |
6540375c48dad23120bbacfa | 10.26434/chemrxiv-2023-frr55 | Harvesting Water from Air with High-Capacity, Stable Furan-Based Metal–Organic Frameworks | We synthesized two isoreticular furan-based metal–organic frameworks (MOFs), MOF-LA2-1(furan) and MOF-LA2-2(furan) with rod-like secondary building units (SBUs) featuring 1D channels, as sorbents for atmospheric water harvesting (LA = long arm). These aluminum-based MOFs demonstrated a combination of high water uptake and stability, exhibiting working capacities of 0.41 and 0.48 g of water per g of MOF (under isobaric conditions of 1.70 kPa), respectively. Remarkably, both MOFs showed negligible loss in water uptake after 165 adsorption-desorption cycles. These working capacities rival those of MOF-LA2-1(pyrazole), which has a working capacity of 0.55 g of water per g of MOF. The current MOFs stand out for their high water stability as evidenced by 165 cycles of water uptake and release. MOF-LA2-2(furan) is the first aluminum MOF to employ a double 'long arm' extension strategy, confirmed through single-crystal X-ray diffraction (SCXRD). The MOFs were synthesized using a straightforward synthesis route. This study offers valuable insights into designing durable, water-stable MOFs and underscores their potential for efficient water harvesting. | Ali H. Alawadhi; Saumil Chheda; Gautam D. Stroscio; Zichao Rong; Daria Kurandina; Ha L. Nguyen; Nakul Rampal; Zhiling Zheng; Laura Gagliardi; Omar Yaghi | Inorganic Chemistry; Organometallic Chemistry; Coordination Chemistry (Organomet.); Theory - Organometallic; Materials Chemistry; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6540375c48dad23120bbacfa/original/harvesting-water-from-air-with-high-capacity-stable-furan-based-metal-organic-frameworks.pdf |
66a8b07d01103d79c5361170 | 10.26434/chemrxiv-2024-xrx41 | Electroredox N-Heterocyclic Carbene-Catalyzed Enantioselective (3+3) Annulation of Enals with 2-Naphthols | In recent years, asymmetric electrocatalysis has emerged as a powerful and efficient tool for constructing enantioenriched compounds. However, developing asymmetric transformations using N-heterocyclic carbene (NHC)-catalyzed radical reactions is still very desirable and challenging. Herein, we report an iodide-promoted β-carbon activation of enals via electroredox carbene catalysis coupled with a hydrogen evolution reaction (HER). This strategy offers an environmentally friendly and sustainable route for rapidly assembling synthetically useful chiral naphthopyran-3-one in good to excellent yield and enantioselectivity, using traceless electrons as an inexpensive and greener oxidant. The mechanistic studies and cyclic voltammetry suggest that the reaction proceeds via direct single electron oxidation (SET) of the in-situ Breslow intermediate. | Vikas Kale; Sayan Shee; Shiv Dutt; Nidhi Sinha; Akkattu T. Biju; Prabal Banerjee | Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Electrocatalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a8b07d01103d79c5361170/original/electroredox-n-heterocyclic-carbene-catalyzed-enantioselective-3-3-annulation-of-enals-with-2-naphthols.pdf |
60c753d9bb8c1a695c3dc124 | 10.26434/chemrxiv.12776222.v2 | First Principle Investigations of Long-range Magnetic Exchange Interactions via Polyacene Coupler | <div>The electronic and magnetic properties of polyacenes become quite fascinating as the number of linearly conjugated benzene rings increases. Higher-order conjugated polyacenes develop radicaloid characters due to the transition of electronic structures from closed-shell to the open-shell system. Here we have investigated the role of such polyacenes as the magnetic coupler when placed between the two spin-sources based on nitroxy radicals. To do so, the magnetic exchange interactions (<i>2J</i>) are computed employing electronic structure theories, i.e. broken-symmetry (BS) approach within the density functional theory (DFT) as well as symmetry-adopted wave function based multi-configurational methods. In the former approach, various genre of exchange-correlation (XC) functionals such as generalized gradient approximation (GGA), meta-GGA, hybrid functional, constrained spin density (i.e. CDFT) and on-site Coulomb correlation corrected GGA+<i>U</i> functionals are adopted. All DFT based calculations estimate an exponential increase in <i>2J</i> values with the length of the couplers, especially for the higher-order acenes. This is indeed an unexpected observation and also there is no experimental report available in support of the DFT calculations. The complexity in the electronic structure enhances with the increasing number of benzene rings due to an increase in near-degenerate or quasi-degenerate molecular orbitals (MOs) and also the reduction of the energy gap with the low-lying excited states. Consequently, it invokes a severe challenge in the computations of the magnetic exchange interactions in DFT. As an alternative approach, the wave function based multi-reference calculations, e.g. CASSCF/NEVPT2 methods are also adopted. In the later calculations, it has been realized that the π-orbitals of the couplers play a crucial role in the exchange interactions. For larger polyacenes (i.e. hexacene to decacene) such calculations become prohibitively expensive and rigorous as the number of π-orbitals increases, thus expanding the active space enormously. The limited active spaces calculations indicate quite strong ferromagnetic exchange interactions, thus <i>in principle,</i> reinforcing long-range magnetic exchange interactions.</div> | Prabhleen Kaur; Md. Ehesan Ali | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753d9bb8c1a695c3dc124/original/first-principle-investigations-of-long-range-magnetic-exchange-interactions-via-polyacene-coupler.pdf |
60c743af469df4d9d2f4322d | 10.26434/chemrxiv.7218272.v3 | Functionalized Azetidines Via Visible Light-Enabled Aza Paternò-Büchi Reactions | <p>Azetidines are four-membered nitrogen-containing heterocycles that hold great promise in current medicinal chemistry due to their desirable pharmacokinetic effects. However, a lack of efficient synthetic methods to access functionalized azetidines has hampered their incorporation into pharmaceutical lead structures. As [2+2] cycloaddition reaction between imines and alkenes, the aza Paternò-Büchi reaction arguably represents the most direct approach to functionalized azetidines. Currently, competing reaction paths accessible upon photochemical excitation of the substrates greatly restrict the synthetic utility of these transformations. We herein report the development of a visible light-enabled aza Paternò-Büchi reaction that surmounts existing limitations and represents a general solution for the direct formation of functionalized azetidines from imine and alkene containing precursors.<br /></p><br /><p></p> | Marc R. Becker; Alistair D. Richardson; Corinna S. Schindler | Photochemistry (Org.); Photocatalysis; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743af469df4d9d2f4322d/original/functionalized-azetidines-via-visible-light-enabled-aza-paterno-buchi-reactions.pdf |
60c744774c89192cc4ad27e6 | 10.26434/chemrxiv.9808508.v1 | Vibrational Ultra Strong Coupling of Water and Ice | Water is of vital importance for life and human activities on Earth—it exhibits unique properties due to its interlinked and multipoint hydrogen bonding network. Here, we experimentally show that water can undergo vibrational ultra strong coupling (V-USC) in both the liquid and solid forms when the OH stretching mode of water or ice is resonantly coupled with an optical mode of an infrared Fabry−Pérot cavity. The light-coupled H<sub>2</sub>O under V-USC reveals the largest Rabi splitting ever reported, reaching 22% and 26% of the vibrational energy for water and ice, respectively. We confirm that the extraordinarily large Rabi splitting stems from the densely packed minuscule molecular structures, large vibrational energies, and broad and intense absorptions due to intermolecular hydrogen bonding. These new findings offer a brand-new platform in polaritonic chemistry for controlling the properties of water with an ultra strong light-matter interaction. | Hidefumi Hiura; Atef Shalabney; Jino George | Spectroscopy (Anal. Chem.); Physical and Chemical Properties; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744774c89192cc4ad27e6/original/vibrational-ultra-strong-coupling-of-water-and-ice.pdf |
667b1aa75101a2ffa87dfc54 | 10.26434/chemrxiv-2024-0kks1-v2 | Transformative Natural Product-Drug Combinations Pioneering Techniques for Enhanced Efficacy Against Drug-Resistant Pathogens for drug discovery and development. | This study aims to develop, modify, or optimize potent active compounds by utilizing combinatorial synthetic methods involving phytoconstituents from plant extracts to enhance efficacy and reduce resistance potential. We employed ATR-FTIR, GC-MS, and antibacterial results from related literature to validate these strategies. The methodology involved careful harvesting, pre-treatment, and extraction processes to ensure the quality and efficacy of plant extracts. We used various extraction methods and solvents to isolate specific phytoconstituents, followed by further purification using chromatography. The study proposes three strategies: (1) reacting single or multiple plant extracts with reagents like acids or catalysts, (2) combining plant extracts with ineffective drugs to induce structural changes that enhance antibacterial efficacy, and (3) combining plant extracts with drugs not originally intended for the target disease to explore new structural functionalities. Notable results included the synergistic effects observed in combining Psidium guajava and Calotropis procera extracts with antibiotics, significantly increasing zones of inhibition against resistant bacteria. GC-MS analysis identified numerous bioactive compounds, some with known anticancer properties, suggesting potential applications beyond antibacterial effects. Our findings demonstrate that these innovative combinatorial approaches can yield new compounds with enhanced antimicrobial properties, highlighting the potential of plant extracts in drug discovery and development. This study underscores the promise of harnessing natural products to combat multi-drug resistance, paving the way for advanced research and development in pharmaceutical applications. | Mathew Gideon | Biological and Medicinal Chemistry; Analytical Chemistry; Analytical Chemistry - General; Spectroscopy (Anal. Chem.); Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2024-06-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667b1aa75101a2ffa87dfc54/original/transformative-natural-product-drug-combinations-pioneering-techniques-for-enhanced-efficacy-against-drug-resistant-pathogens-for-drug-discovery-and-development.pdf |
60c7575b0f50dbb856398260 | 10.26434/chemrxiv.14397176.v1 | High-performance Photoacoustic Probe for Biopsy-free Assessment of Copper Status in Murine Models of Wilson’s Disease and Liver Metastasis | <p>The
development of high-performance photoacoustic (PA) probes that can monitor
disease biomarkers in deep-tissue has the potential to replace invasive medical
procedures such as a biopsy. However, such probes must be highly optimized for <i>in
vivo</i> performance and exhibit an exceptional safety profile. In this study,
we have developed PACu-1, the first PA probe designed for biopsy-free
assessment (BFA) of hepatic Cu via photoacoustic imaging. PACu-1 features a
Cu(I)-responsive trigger appended to an aza-BODIPY dye platform that has been
optimized for ratiometric sensing. Owing to its excellent performance, we were
able to detect basal levels of Cu in healthy wildtype mice, as well as elevated
Cu in a Wilson’s disease model and in a liver metastasis model. To showcase the
potential impact of PACu-1 for BFA, we conducted a blind study where we were
able to successfully identify a Wilson’s disease animal from a group of healthy
control mice with greater than 99.7% confidence.</p> | Melissa Lucero; Yuqi Tang; Chloe Zhang; ShengZhang Su; Joseph Forzano; Valeria Garcia; Xin Huang; David Moreno; Jefferson Chan | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7575b0f50dbb856398260/original/high-performance-photoacoustic-probe-for-biopsy-free-assessment-of-copper-status-in-murine-models-of-wilson-s-disease-and-liver-metastasis.pdf |
667e9d14c9c6a5c07aac150f | 10.26434/chemrxiv-2024-kbcr5 | Nonconventional Fluorescent Non-Isocyanate Polyurethane Foams for Multipurpose Sensing Applications | Fluorescent foams with interconnected pores are attractive for the detection and quantification of various products. However, many fluorescent probes are suffering from aggregation-caused fluorescence quenching in their solid/aggregated state, are costly, and/or not straightforward to incorporate in foams, limiting their utility for this application. Herein, non-isocyanate polyurethane foams (NIPUF), prepared by the simple water-induced self-blowing process, present a nonconventional fluorescence behaviour, i.e. they are intrinsically fluorescent with a multicolor emission without requiring ex-situ traditional fluorescent probes. These foams demonstrate utility for capturing-sensing gaseous formaldehyde (an emblematic indoor air pollutant), as well as for detecting and quantifying various metal ions (Fe2+, Cu2+, Fe3+, Hg2+). They are also able to selectively sense tetracycline antibiotic in a ratiometric way with a high sensitivity. By exploiting the unique multicolor photoluminescent foam properties, a smartphone-compatible device is used for the facile antibiotic quantification. This nonconventional fluorescence behaviour is discussed experimentally and theoretically, and is mainly based on clusteroluminescence originating from multiple hydrogen bonding and hetero-atomic sub-luminophores, thus from aggregation-induced emission luminogens that are naturally present in the foams. This work illustrates that easily accessible non-conventional fluorescent NIPU foams characterized by a modular emission wavelength have an enormous potential for multiple substrates detection and, in some cases, their quantification. | Manas Mahapatra; Maxime Bourguignon; Bruno Grignard; Marylène Vandevenne; Moreno Galleni; Christophe Detrembleur | Materials Science; Polymer Science; Organic Polymers; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667e9d14c9c6a5c07aac150f/original/nonconventional-fluorescent-non-isocyanate-polyurethane-foams-for-multipurpose-sensing-applications.pdf |
6103fb367bf0c9e2b861d67e | 10.26434/chemrxiv-2021-2wlll | Coupling of photoactive transition metal complexes to a functional polymer matrix | Conductive polymers represent a promising alternative to semiconducting oxide electrodes typically used in dye-sensitized cathodes as they more easily allow a tuning of the physicochemical properties. This can then also be very beneficial for using them in light-driven catalysis. In this computational study, we address the coupling of Ru-based photosensitizers to a polymer matrix by combining two different first-principles electronic structure approaches. We use a periodic density functional theory code to properly account for the delocalized nature of the electronic states in the polymer. These ground state investigations are complemented by time-dependent density functional theory simulations to assess the Franck-Condon photophysics of the present photoactive hybrid material based on a molecular model system. Our results are consistent with recent experimental observations and allow to elucidate the light-driven redox chemical processes -- eventually leading to charge separation -- in the present functional hybrid systems with potential application as photocathode materials. | Miftahussurur Hamidi Putra; Sebastian Seidenath; Stephan Kupfer; Stefanie Gräfe; Axel Gross | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Computational Chemistry and Modeling; Electrocatalysis; Photochemistry (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2021-08-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6103fb367bf0c9e2b861d67e/original/coupling-of-photoactive-transition-metal-complexes-to-a-functional-polymer-matrix.pdf |
60c73fc6bdbb89c8d8a3806a | 10.26434/chemrxiv.7295534.v2 | On the Choice of Coordinates in Anharmonic Theoretical Vibrational Spectroscopy | <div>By a suitable choice of coordinates,the computational effort required for calculations of anharmonic vibrational spectra can be reduced significantly. By using suitable localized-mode coordinates obtained from an orthogonal transformation of the conventionally used normal-mode coordinates, anharmonic couplings between modescan be significantly reduced. However, such a transformation introduces harmonic couplings between the localized modes. To elucidate the role of these harmonic couplings, we consider vibrational self-consistent field (VSCF) / vibrational configuration interaction (VCI) calculations for both few-mode model systems and for ethene as a molecular test case. We show that large harmonic couplings can result in significant errors in localized-mode L-VSCF/L-VCI calculations and study the convergence with respect to the size of the VCI excitation space. To further elucidate the errors introduced by harmonic couplings, we discuss the connection between L-VSCF/L-VCI and vibrational exciton models. With the help of our results, we propose an algorithm for the localization of normal modes in suitable subsets that are chosen to strictly limit the errors introduced by the harmonic couplings while still leading to maximally localized modes.<br /></div> | Paweł T. Panek; Adrian Hoeske; Christoph R. Jacob | Computational Chemistry and Modeling; Theory - Computational; Quantum Mechanics; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2018-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73fc6bdbb89c8d8a3806a/original/on-the-choice-of-coordinates-in-anharmonic-theoretical-vibrational-spectroscopy.pdf |
62721ddad048ed83a45b797c | 10.26434/chemrxiv-2022-kt9v3-v2 | Anomalous viscosity of a racemate: a simple experiment demonstrating chirally induced spin selectivity
| It has been known for over a century that racemic solutions of hydrogen-bonded compounds are less viscous than their component enantiomers, but this fact has so far remained unexplained. Here we confirm it using enantiomers of lactic acid, and compare it to molecular dynamics simulations of lactic acid viscosity. The effect is absent in classical MD. We suggest that the anomalous viscosity of racemates may be due to a recently discovered magnetic intermolecular force due to spin-dependent charge reorganization.
| Ekin Daplan; Umberto Terranova; Luca Turin | Theoretical and Computational Chemistry; Physical Chemistry; Chemical Education; Computational Chemistry and Modeling; Physical and Chemical Properties; Solution Chemistry | CC BY 4.0 | CHEMRXIV | 2022-05-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62721ddad048ed83a45b797c/original/anomalous-viscosity-of-a-racemate-a-simple-experiment-demonstrating-chirally-induced-spin-selectivity.pdf |
60c73f9d842e650051db1b17 | 10.26434/chemrxiv.7427867.v1 | Ru Passivated and Ru Doped e-TaN surfaces as Combined Barrier and Liner Material for Copper Interconnects: A First Principles Study | <div>As the critical dimensions of transistors continue to be scaled down to facilitate improved performance and device speeds, new ultrathin materials that combine diffusion barrier and seed/liner properties are needed for copper interconnects at these length scales. Ideally, to facilitate coating of high aspect ratio structures, this alternative barrier+liner material should only consist of one or as few layers as possible. We studied TaN, the current industry standard for Cu diffusion barriers, and Ru, which is a</div><div>suitable liner material for Cu electroplating, to explore how combining these two materials in a barrier+liner material influences the adsorption of Cu atoms in the early stage of Cu film growth. To this end, we carried out first-principles simulations of the adsorption and diffusion of Cu adatoms at Ru-passivated and Ru-doped e-TaN(1 1 0) surfaces. For comparison, we also studied the behaviour of Cu and Ru adatoms at the low index surfaces of e-TaN, as well as the interaction of Cu adatoms with the (0 0 1) surface of hexagonal Ru. Our results confirm the barrier and liner properties of TaN and Ru, respectively while also highlighting the weaknesses of both materials. Ru passivated TaN was found to have improved binding with Cu adatoms as compared to the bare TaN and Ru surfaces.</div><div>On the other hand, the energetic barrier for Cu diffusion at Ru passivated TaN surface was lower than at the bare TaN surface which can promote Cu agglomeration. For Ru-doped TaN however, a decrease in Cu binding energy was found in addition to favourable migration of the Cu adatoms toward the doped Ru atom and unfavourable migration away from it or into the bulk. This suggests that Ru doping sites in the TaN surface can act as nucleation points for Cu growth with high migration barrier preventing agglomeration and allow electroplating of Cu. Therefore Ru-doped TaN is proposed as a candidate for a combined barrier+liner material with reduced thickness.</div> | Suresh Natarajan; Cara-Lena Nies; Michael Nolan | Coating Materials; Materials Processing; Multilayers; Thin Films; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2018-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f9d842e650051db1b17/original/ru-passivated-and-ru-doped-e-ta-n-surfaces-as-combined-barrier-and-liner-material-for-copper-interconnects-a-first-principles-study.pdf |
60c744374c89196bbdad2781 | 10.26434/chemrxiv.9759302.v1 | 5-Benzylidene-4-Oxazolidinones are Synergistic with Antibiotics for the Treatment of Staphylococcus Aureus Biofilms | <div>The failure of frontline antibiotics in the clinic is one of the most serious threats to human health and requires a multitude of novel therapeutics and innovative treatment approaches to curtail the growing crisis. In addition to traditional resistance mechanisms resulting in the lack of efficacy of many antibiotics, most chronic and recurring infections are further made tolerant to antibiotic action by the presence of biofilms. Herein, we report an expanded set of 5-benzylidene-4-oxazolidinones that are able to inhibit the formation of Staphylococcus aureus biofilms, disperse preformed biofilms and in combination with common antibiotics are able to significantly reduce the bacterial load in a robust collagen-matrix model of biofilm infection.</div> | Bram Frohock; Jessica M. Gilbertie; Jennifer C. Daiker; Lauren V. Schnabel; Joshua Pierce | Drug Discovery and Drug Delivery Systems; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744374c89196bbdad2781/original/5-benzylidene-4-oxazolidinones-are-synergistic-with-antibiotics-for-the-treatment-of-staphylococcus-aureus-biofilms.pdf |
62d9c9a84e76bf4e049a306c | 10.26434/chemrxiv-2022-k7wdb | Catalyst-Free Transfer Hydrogenation of Activated Alkenes Exploit-ing Isopropanol as the Sole and Traceless Reductant | Both metal-catalyzed and organocatalytic transfer hydrogenation reactions are widely employed for the reduction of C=C, C=O and C=N bonds. Described herein is an unconventional catalyst-free transfer hydrogenation reaction of activated al-kenes using isopropanol as an eco-friendly reductant and solvent. The reaction gives convenient synthetic access to a wide range of substituted malonic acid half oxyesters (SMAHOs) in moderate to good yields. Mechanistic investigations point to-wards an unprecedented hydrogen bond-assisted transfer hydrogenation process. | Tamal Kanti Das; Agustin Rodriguez Trevino; Sanjay Pandiri; Sini Irvankoski; Juha Siitonen; Sara M Rodriguez; Muhammed Yousufuddin; Laszlo Kurti | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62d9c9a84e76bf4e049a306c/original/catalyst-free-transfer-hydrogenation-of-activated-alkenes-exploit-ing-isopropanol-as-the-sole-and-traceless-reductant.pdf |
672c1de17be152b1d0465a35 | 10.26434/chemrxiv-2024-rwlb4 | Quantifying the kinetics factors of the oxidase-like Ce/Fe-bimetallic nanozymes | The kinetics factors of the oxidase-like Ce/Fe-bimetallic nanozymes were quantified. The Michaelis–Menten kinetic model was used for the evaluation of the kinetic of the nanozyme-mediated oxidation of 3,3′,5,5′-tetramethylbenzidine. To provide the quantitative and accurate values of kinetics parameters, Km and Vmax, the linear plot of Lineweaver–Burk was constructed. The results exhibited a Vmax as high as 67.56 nM min-1 for the oxidase-like Ce/Fe-bimetallic nanozymes. Besides, Km was found to be as low as 0.06 mM for the as-prepared nanozymes, revealing the high affinity of the nanozymes toward 3,3′,5,5′-tetramethylbenzidine. | Mohammad Reza Hormozi Jangi | Analytical Chemistry | CC BY 4.0 | CHEMRXIV | 2024-11-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672c1de17be152b1d0465a35/original/quantifying-the-kinetics-factors-of-the-oxidase-like-ce-fe-bimetallic-nanozymes.pdf |
6436587e1d262d40ea4be72c | 10.26434/chemrxiv-2023-psqq6 | Angstrom-scale interface modification extensively tunes thermodynamic ordering of strongly correlated protons in ice | The static and dynamic behaviour of strongly correlated many-body protons in nanoscale hydrogen-bond networks plays crucial roles in a wide range of physicochemical, biological and geological phenomena in nature. However, because of the difficulty of probing and manipulating the proton configuration in nanomaterials, controlling the cooperative behaviour of many-body protons remains challenging. By combining proton-order sensitive nonlinear optical spectroscopy and well-defined interface modification at molecular/atomic scale, we demonstrate the possibility of extensively tuning the emergent physical properties of strongly correlated protons beyond the thermodynamic constraints of bulk hydrogen bonds. Focusing on heteroepitaxially grown crystalline ice films as a model of a strongly correlated and frustrated proton system, we show that the emergence and disappearance of a high-Tc proton order on the nano- to mesoscale can be readily switched by angstrom-scale interface engineering. These results and concept are also applicable to other hydrogen-bonded materials, thus paving the way to the design and control of emergent properties of correlated proton systems. | Norihiro Aiga; Toshiki Sugimoto | Physical Chemistry; Materials Science; Nanoscience; Multilayers; Interfaces; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6436587e1d262d40ea4be72c/original/angstrom-scale-interface-modification-extensively-tunes-thermodynamic-ordering-of-strongly-correlated-protons-in-ice.pdf |
60c74651f96a006f59286d37 | 10.26434/chemrxiv.11302556.v1 | Caryophyllene as a Precursor of Cross-Linked Materials | <p></p><p>This paper aims at the synthesis of a new type of
elastomers from caryophyllene. The adopted strategy was to cross-link the polycaryophyllene,
which was synthesized by ring-opening metathesis polymerization (ROMP). The polycaryophyllene
obtained showed <i>M<sub>n</sub></i> = 2 x
10<sup>4</sup> g.mol<sup>-1</sup> (Đ = 1.5) with a glass transition temperature
(<i>T</i><sub>g</sub>) of -35 °C. On the first
hand, thermal crosslinking was performed in the presence of organic peroxides or
sulfur system. On the second hand, thiol-ene coupling initiated by UV-light at
room temperature was also investigated as an alternative pathway to cross-link
the polycaryophyllene. The materials obtained were analyzed by TGA, DSC, and
DMA. The T<sub>g </sub><sup> </sup>of
cross-linked polycaryophyllene could be easily modulated from<sub> </sub>-35
°C to a range between -25 and 10 °C by changing the type of cross-linking agent.
The curing process led to the improvement of thermal stability ranging from 200
°C to around 340 °C. Finally, the network storage modulus varied from 1 to 100
MPa at room temperature.</p><br /><p></p> | Anderson Medeiros; Cédric Le Coz; Etienne Grau | Polymerization (Polymers) | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74651f96a006f59286d37/original/caryophyllene-as-a-precursor-of-cross-linked-materials.pdf |
66f6e6f712ff75c3a1b17086 | 10.26434/chemrxiv-2024-683hl | Stereoselective Access to Gamma,Gamma-Dihalo-Beta-enols from Alkynes via Photobiocatalysis | Merging different catalytic strategies in one-pot is attracting considerable attention for the straightforward and sustainable synthesis of novel organic compounds. In particular, the exquisite selectivity displayed by enzymes and the possibility to couple biotransformations with metal-, photo and electrocatalytic processes opens new avenues for stereoselective synthesis. Herein, the preparation of chiral (hetero)aryl-3,3-halo-prop-2-en-1-ols has been described for the first time. To achieve this aim, a photochemical and biocatalytic one-pot sequence has been followed employing visible light irradiation and the action of stereoselective alcohol dehydrogenases (ADHs) for the transformation of commercial acetylenes into a series of optically active gamma,gamma-dihalo-beta-enols in aqueous medium. The one-pot two-step sequential approach consisted of the free-photocatalyst reaction between a series of terminal and internal alkynes with polyhalomethanes (CClBr3 or CBr4) leading to gem-dihaloenones, which were subsequently enzymatically reduced with ADHs. After optimisation of individual steps and finding conditions to perform both processes in one-pot, the use of complementary ADHs has allowed the synthesis of a novel family of optically active allylic alcohols with high stereodiscrimination, whose applicability has been demonstrated, for example, towards the synthesis of a chiral propargylic alcohol. | Laura Rodríguez-Fernández; Iván Lavandera; Manuel Plaza ; Vicente Gotor-Fernández | Organic Chemistry; Bioorganic Chemistry; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f6e6f712ff75c3a1b17086/original/stereoselective-access-to-gamma-gamma-dihalo-beta-enols-from-alkynes-via-photobiocatalysis.pdf |
6564ec3e5bc9fcb5c9835f42 | 10.26434/chemrxiv-2023-78l98 | Large-scale Comparison of Fe and Ru Polyolefin C–H Activation Catalysts | We performed a large-scale density functional theory comparison of polyolefin C–H hydroxylation trends across over 200 Fe and Ru catalysts that are identical except for their metal centers for the radical-rebound conversion of propane to propanol. We observed a strong spin-state dependence: higher-spin states had more favorable metal-oxo formation and isopropanol release in Ru catalysts, while hydrogen atom transfer (HAT) was more favorable in Fe catalysts. While the widely studied metal-oxo formation vs. HAT linear free-energy relationship held for Ru, it was more easily disrupted for Fe. Ru catalysts have a spin-forbidden C–H hydroxylation pathway, while Fe catalysts favor a spin-allowed, intermediate spin pathway. Calculation of reaction coordinates on representative catalysts corroborated these spin–reactivity trends and showed comparable energetic spans for Fe and Ru analogues, as well as strong Brønsted–Evans–Polanyi relationships for both the metal-oxo formation and HAT steps, motivating expanded study of Fe catalysts. | Husain Adamji; Ilia Kevlishvili; Aditya Nandy; Yuriy Roman-Leshkov; Heather Kulik | Theoretical and Computational Chemistry; Inorganic Chemistry; Catalysis; Transition Metal Complexes (Inorg.); Theory - Computational | CC BY 4.0 | CHEMRXIV | 2023-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6564ec3e5bc9fcb5c9835f42/original/large-scale-comparison-of-fe-and-ru-polyolefin-c-h-activation-catalysts.pdf |
60c73f63f96a00062e2860d0 | 10.26434/chemrxiv.7376489.v1 | Size-Control by Anion Templating in Mechanochemical Synthesis of Hemicucurbiturils in the Solid State | Self-organization is one of the most intriguing phenomena of chemical matter. While the self-assembly of macrocycles and cages in dilute solution has been extensively studied, it remains poorly understood in solvent-free environments. Here, we provide the first example of using anionic templates to achieve selective assembly of differently sized macrocycles in a solvent-free system. Using the acid-catalyzed synthesis of cyclohexanohemicucurbiturils as a model system, we demonstrate size-controlled quantitative synthesis of 6- or 8-membered macrocycles, taking place through spontaneous anion-directed re-organization of mechanochemically-obtained oligomers in the solid state.<br /> | Sandra Kaabel; Robin Stein; Maria Fomitšenko; Ivar Järving; Tomislav Friscic; Riina Aav | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Physical Organic Chemistry; Supramolecular Chemistry (Org.); Solid State Chemistry; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2018-11-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f63f96a00062e2860d0/original/size-control-by-anion-templating-in-mechanochemical-synthesis-of-hemicucurbiturils-in-the-solid-state.pdf |
63e861db1d2d184063524016 | 10.26434/chemrxiv-2023-fghrc | Selective capture and separation of potent greenhouse gases with gallium- and vanadium-based metal-organic frameworks | Four novel metal-organic frameworks (MOFs) composed of 1,3,6,8-tetrakis(4-carboxyphenyl)pyrene (TBAPy4-) or 1,2,4,5-tetrakis(4-carboxlatephenyl)benzene (TCPB4-) linkers with gallium (Ga) or vanadium (V) were synthesized in this work. 3D electron diffraction patterns combined with high-resolution electron microscopy images were employed to investigate the structure of these MOFs. All four MOFs were highly porous with specific Langmuir surface area ranging from ~900 to over ~1800 m2 g-1. The MOFs also showed high uptake of greenhouse gas and especially selective towards SF6 (110 cm3 cm-3, 293 K 1 bar) and CO2 over N2 (or CH4). Sorption kinetics were investigated in detail and the MOF with the highest gas uptake had pore channels with diameters of approx. 9.1 13.6 and 6.5 13.7 in dimension. These Ga- and V-MOFs are potentially interesting candidate sorbents for greenhouse gas capture and separation applications, especially for the separation of SF6 and CO2 from N2, which are relevant in the electronics and chemical industry, respectively. | Michelle Åhlén; Yi Zhou; Daniel Hedbom; Hae Sung Cho; Maria Strømme; Osamu Terasaki; Ocean Cheung | Materials Science; Inorganic Chemistry; Hybrid Organic-Inorganic Materials; Materials Chemistry; Crystallography – Inorganic | CC BY NC 4.0 | CHEMRXIV | 2023-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63e861db1d2d184063524016/original/selective-capture-and-separation-of-potent-greenhouse-gases-with-gallium-and-vanadium-based-metal-organic-frameworks.pdf |
60c744fe702a9b570318a947 | 10.26434/chemrxiv.9947054.v1 | Probing the Versatility of Shape-Persistent Tetraphenylmethane Dendrimers by Modification of the Skeleton | Tetraphenylmethane has emerged as a recurrent building block for advanced porous materials such as COFs, PAFs and hypercrosslinked polymers. Guided by a similar design principle, we have previously synthesized shape-persistent dendrimers with tetraphenylmethane nodes and ethynylene linkers. Here we report the generality of our approach by describing new dendritic architectures built from tetraphenylmethane. First, we prepared expanded dendrimers where the tetrahedral units are bonded through larger rigid rod spacers. Among the different synthetic strategies tested, the convergent route, with alternating steps of Pd-catalyzed Sonogashira coupling and alkyne activation by removal of TMS masking groups, efficiently afforded the first- and second-generation dendrimers. A second type of compounds having a linear diyne at the core is also described. The dendrimers of generations 1-2 were also synthesized by a convergent approach, with the diyne being assembled in the last step of the synthesis by a Glaser oxidative homocoupling of the corresponding dendrons bearing a terminal alkyne at the focal point. A third-generation dendrimer was also successfully prepared by a double-phase strategy.<br /> | Julio Ignacio Urzúa; Sandra Campana; Massimo Lazzari; Mercedes Torneiro | Organic Polymers | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744fe702a9b570318a947/original/probing-the-versatility-of-shape-persistent-tetraphenylmethane-dendrimers-by-modification-of-the-skeleton.pdf |
61b8ce461e13eb78abf89110 | 10.26434/chemrxiv-2021-vl2vz-v2 | A Complementary Silicon Quantum Dot-Enzyme
Platform for Selective Detection of Nitroaromatics
Compounds | To address the issue of poor selectivity in nanotechnology-driven, portable nitroaromatics sensors, we have coupled a ratiometric photoluminescence sensor based on silicon quantum dots and fluorescent proteins with a colorimetric enzyme-based sensor. Together, the sensors allow differentiation of nitroaromatic compounds – specifically, distinguishing acetylcholinergic nerve agents from the explosive compounds explored herein. The combined system can detect 2,4,6-trinitrotoluene, 2,4-dinitrotoluene and 4-nitrophenol with micromolar detection limits and affords subsequent differentiation from the nitro-containing nerve agent paraoxon. This demonstrates the advantage of merging elements of materials chemistry and biochemistry to devise customized sensors which can accurately identify hazardous chemical species. | Leanne Milburn; Christopher Jay Robidillo; Rochelin Dalangin; Jonathan Veinot | Biological and Medicinal Chemistry; Materials Science; Nanoscience; Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience; Biochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b8ce461e13eb78abf89110/original/a-complementary-silicon-quantum-dot-enzyme-platform-for-selective-detection-of-nitroaromatics-compounds.pdf |
63d48559112596efd97d0081 | 10.26434/chemrxiv-2023-2r2gn | Electrified Operando-Freezing of Electrocatalytic CO2 Reduction Cells for Cryogenic Electron Microscopy | The ability to freeze and stabilize reaction intermediates in their metastable states and obtain their structural and chemical information with high spatial resolution would be very powerful to unravel the fundamentals in many important materials technologies such as catalysis and batteries. Here, we develop an electrified operando-freezing methodology for the first time to preserve these metastable states under electrochemical reaction conditions for cryogenic electron microscopy (cryo-EM) imaging and spectroscopy. Using Cu catalysts for CO2 reduction as a model system, we observe restructuring of the Cu catalyst in a CO2 atmosphere while the same catalyst remains intact in an air atmosphere at the nanometer scale. Furthermore, we discover the existence of single valance Cu (1+) state and C-O bonding at the electrified liquid-solid interface of the operando-frozen samples, which are key reaction intermediates that traditional ex situ measurements fail to detect. This work highlights our novel technique to study the local structure and chemistry of electrified liquid-solid interfaces, which has broad impact for many electrochemical reactions. | Yanbin Li; Yunzhi Liu; Zewen Zhang; Weijiang Zhou; Jinwei Xu; Yusheng Ye; Yucan Peng; Xin Xiao; Wah Chiu; Robert Sinclair; Yuzhang Li; Yi Cui | Materials Science; Nanoscience; Energy; Nanocatalysis - Catalysts & Materials; Nanostructured Materials - Nanoscience; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d48559112596efd97d0081/original/electrified-operando-freezing-of-electrocatalytic-co2-reduction-cells-for-cryogenic-electron-microscopy.pdf |
60c73d91ee301c6884c7859a | 10.26434/chemrxiv.5872461.v1 | Site-Selective C-C Modification of Proteins at Neutral pH Using Organocatalyst-Mediated Cross Aldol Ligations | The bioconjugation of proteins with small molecules has proved an invaluable strategy for probing and perturbing dynamic biological mechanisms. The general use of chemical methods for the functionalisation of proteins remains limited however by the frequent requirement for complicated reaction partners to be present in large excess, and harsh reaction conditions which are incompatible with many protein scaffolds. Herein we describe a site-selective organocatalyst-mediated protein aldol ligation (OPAL) that affords stable carbon-carbon linked bioconjugates at neutral pH under biocompatible conditions. OPAL enables rapid chemical modification of proteins within an hour using simple aldehyde probes in minimal excess, and is utilised here in the selective affinity tagging of proteins in cell lysate. Furthermore we demonstrate that the b-hydroxy aldehyde product of the OPAL can be functionalised a second time at neutral pH in a subsequent organocatalyst-mediated oxime ligation. This tandem strategy is showcased in the ‘chemical mimicry’ of a previously inaccessible natural dual post-translationally modified protein integral to the pathogenesis of the neglected tropical disease Leishmaniasis. <br /> | Martin A. Fascione; Richard J. Spears; Robin L. Brabham; Darshita Budhadev; Tessa Keenan; Sophie McKenna; Julia Walton; James. A. Brannigan; A. Marek Brzozowski; Anthony J. Wilkinson; Michael Plevin | Bioorganic Chemistry; Chemical Biology; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2018-02-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d91ee301c6884c7859a/original/site-selective-c-c-modification-of-proteins-at-neutral-p-h-using-organocatalyst-mediated-cross-aldol-ligations.pdf |
60c7494f9abda22429f8cbbe | 10.26434/chemrxiv.12052422.v1 | A Microfluidic Sensing System with a Multichannel Surface Plasmon Resonance Chip: Damage-free Characterization of Cells by Pattern Recognition | <p>The development of a versatile sensing strategy for the damage-free characterization of cultured cells is of great importance for both fundamental biological research and industrial applications. Here, we present a pattern-recognition-based cell-sensing approach using a multichannel surface plasmon resonance (SPR) chip. The chip, in which five cysteine derivatives with different structures are immobilized on Au films, is capable of generating five unique SPR sensorgrams for the cell-secreted molecules that are contained in cell culture media. An automatic statistical program was built to acquire kinetic parameters from the SPR sensorgrams and to select optimal parameters as “pattern information” for subsequent multivariate analysis. Our system rapidly (~ 10 min) provides the complex information by merely depositing a small amount of cell culture media (~ 25 µL) onto the chip, and the amount of information obtained is comparable to that furnished by a combination of conventional laborious biochemical assays. This non-invasive pattern-recognition-based cell-sensing approach could potentially be employed as a versatile tool for characterizing cells. </p> | Hiroka Sugai; Shunsuke Tomita; Sayaka Ishihara; Kyoko Yoshioka; Ryoji Kurita | Analytical Chemistry - General | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7494f9abda22429f8cbbe/original/a-microfluidic-sensing-system-with-a-multichannel-surface-plasmon-resonance-chip-damage-free-characterization-of-cells-by-pattern-recognition.pdf |
658c8f1f9138d23161a3ba15 | 10.26434/chemrxiv-2023-p6zln | Crowd Control of Ions in the Astral Analyzer | Space charge effects are the Achilles’ heel of all high-resolution ion optical devices. In time-of-flight mass analyzers these may manifest as reduction of resolving power, mass measurement shift, peak coalescence and/or transmission losses, whilst highly sensitive modern ion sources and injection devices ensure that such limits are easily exceeded. Space charge effects have been investigated, by experiment and simulation study, for the Astral multi-reflection analyzer, incorporating ion focusing via a pair of converging ion mirrors, and fed by a pulsed extraction ion trap. Major factors were identified as the resonant effect between ~103 ions of similar m/z in-flight, and the expansion of trapped packets of ~104-5 ions prior to extraction. Optimum operation and compensated ion mirror calibration strategies were then generated and described based on these findings. | Hamish Stewart; Dmitry Grinfeld; Johannes Petzoldt; Bernd Hagedorn; Michael Skoblin; Alexander Makarov; Christian Hock | Biological and Medicinal Chemistry; Analytical Chemistry; Analytical Apparatus; Mass Spectrometry | CC BY NC 4.0 | CHEMRXIV | 2023-12-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/658c8f1f9138d23161a3ba15/original/crowd-control-of-ions-in-the-astral-analyzer.pdf |
60c7526cf96a00b7882881ec | 10.26434/chemrxiv.12911939.v2 | Electronic Properties and Photocatalytic Hydrogen Evolution Rates for Alternating Conjugated Copolymers: Predictions and Insights by Data-Driven Models | Alternating conjugated copolymers have been regarded
as promising candidates for photocatalytic hydrogen evolution due to the adjustability
of their molecular structures and electronic properties. In this work, machine
learning (ML) models with molecular fingerprint of segment descriptors (SD)
have been successfully constructed to promote the accurate and universal
prediction of electronic properties such as electron affinity, ionization
potential and optical bandgap. Moreover, without any experimental values, a
high-performance prediction classifier model toward photocatalytic hydrogen
production of alternating copolymers has been developed with high accuracy
(real-test accuracy = 0.91). Consequently, our results demonstrate accurate
regression and classification models to disclose valuable influencing factors
concerning hydrogen evolution rate (HER) of alternating copolymers. | Yuzhi Xu; Cheng-Wei Ju; Bo Li; Qiu-Shi Ma; Lianjie Zhang; Junwu Chen | Conducting polymers | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7526cf96a00b7882881ec/original/electronic-properties-and-photocatalytic-hydrogen-evolution-rates-for-alternating-conjugated-copolymers-predictions-and-insights-by-data-driven-models.pdf |
66fbecc412ff75c3a10c5903 | 10.26434/chemrxiv-2024-65bxp | Electrostatic Embedding Machine Learning for Ground and Excited State Molecular Dynamics of Solvated Molecules | The application of quantum mechanics (QM) / molecular mechanics (MM) models for studying dynamics in complex systems is nowadays well established. However, their significant limitation is the high computational cost, which restricts their use for larger systems and long-timescale processes. We propose a machine-learning (ML) based approach to study the dynamics of solvated molecules on the ground- and excited-state potential energy surfaces. Our ML model is trained on QM/MM calculations and is designed to predict energies and forces within an electrostatic embedding framework. We built a socket-based interface of our machinery with AMBER to run ML/MM molecular dynamics simulations. As an application, we investigated the excited state intramolecular proton transfer of 3-hydroxyflavone in two different solvents: methanol and methylcyclohexane. Our ML/MM simulations accurately distinguished between the two solvents, effectively reproducing the solvent effects on proton transfer dynamics. | Patrizia Mazzeo; Edoardo Cignoni; Amanda Arcidiacono; Lorenzo Cupellini; Benedetta Mennucci | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Machine Learning; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fbecc412ff75c3a10c5903/original/electrostatic-embedding-machine-learning-for-ground-and-excited-state-molecular-dynamics-of-solvated-molecules.pdf |
64e3627300bbebf0e68c9e31 | 10.26434/chemrxiv-2023-mk57s | A new water soluble, highly selective Pyrene-based fluorescent sensor for detection of Fe+3 metal ion | In the context of selective detection of Fe+3, we have shed light on the structure-property relationship and successfully synthesized APTS (sodium 8-aminopyrene-1,3,6-trisulfonate) and APSS (sodium (E)-4-hydroxy-3-((pyren-1-ylimino)methyl)benzenesulfonate) molecules having the sulfonate group in order to increase its applicability in neat aqueous samples. Interestingly these water-soluble fluorescent turn-off sensors exhibited excellent selectivity and sensing properties and were able to detect Fe+3 ion in the nanomolar range showing the limit of detection (LOD) 45.6 nM and 45.9 nM, with the binding stoichiometry of 2:1 and 1:1 for APTS and APSS respectively. Further, the binding mechanism study using Density Functional Theory (DFT) is in progress | Atul Chaskar; Aniket Chaudhari; Omkar Patil; Hardik Janwadkar; Gokul Ganesan; Bhimrao Patil | Organic Chemistry; Organic Compounds and Functional Groups; Physical Organic Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e3627300bbebf0e68c9e31/original/a-new-water-soluble-highly-selective-pyrene-based-fluorescent-sensor-for-detection-of-fe-3-metal-ion.pdf |
60c746ccf96a00402b286e07 | 10.26434/chemrxiv.11301896.v2 | Improving the Stability of Wastewater Derived Microalgae Carbon Materials: Products Characterization, and Kinetic Modelling | <p>Microalgae-derived char contains low stability and
heating values with relatively high nitrogen content than lignocellulosic char.
This study showed that co-pyrolysis helped improve the overall properties of
char than individual pyrolysis of these feedstocks. Two batches of experiments were conducted (a) single step pyrolysis and
(b) two-step pyrolysis in the range of
highest treatment temperature of 400 – 600 °C. Single step pyrolysed char
showed, lower aromaticity, higher yield, ash content and heating values of the
char than two-step pyrolysed char. Similarly, ignition temperature and
activation energy were higher during combustion by single step pyrolysed char
than two-step char. Hence, two-step pyrolysed char is suitable in the
energy applications, and low-temperature
processing (400 – 500 °C) will result in optimum properties in terms of yield and heating values. </p> | Ali Akhtar; Ivo Jiricek; Vladimir Krepl; Abbas Mehrabadi; Tatiana ivanova | Carbon-based Materials; Natural Resource Recovery; Fuels - Energy Science | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746ccf96a00402b286e07/original/improving-the-stability-of-wastewater-derived-microalgae-carbon-materials-products-characterization-and-kinetic-modelling.pdf |
6570da8229a13c4d47cd8558 | 10.26434/chemrxiv-2023-l3lcl | How to build plasmon-driven molecular jackhammers that disassemble cell membranes and cytoskeletons in cancer | Plasmon-driven molecular machines with ultrafast motion at the femtosecond scale are effective for treatment of cancer and other diseases. We recently showed that cyanine dyes act as molecular jackhammers (MJH) through vibronic (vibrational and electronic mode coupling) driven activation that causes the molecule to stretch longitudinally and axially through concerted whole molecule vibrations. However, the theoretical and experimental underpinnings of these plasmon-driven motions in molecules are difficult to assess. Here we describe the use of near-infrared (NIR) light activated plasmons in a broad array of MJH that mechanically disassemble membranes and cytoskeletons in human melanoma A375 cells. The characteristics of plasmon-driven molecular mechanical disassembly of supramolecular biological structures are observed and recorded using real-time fluorescence confocal microscopy. Molecular plasmon resonances in MJH are quantified through a new experimental plasmonicity index method. This is done through the measurement of the UV-vis-NIR spectra in various solvents, and quantification of the optical response as a function of the solvent polarity. Structure-activity relationships were used to optimize the synthesis of plasmon-driven MJH, applying them to eradicate human melanoma A375 cells at low lethal concentrations of 75 nM and 80 mWcm-2 of 730 nm NIR-light for 10 min. | Ciceron Ayala-Orozco; Gang Li; Bowen Li; Vardan Vardanyan; Anatoly Kolomeisky; James Tour | Biological and Medicinal Chemistry; Organic Chemistry; Nanoscience; Photochemistry (Org.); Nanodevices; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6570da8229a13c4d47cd8558/original/how-to-build-plasmon-driven-molecular-jackhammers-that-disassemble-cell-membranes-and-cytoskeletons-in-cancer.pdf |
60c741ca4c89192fc7ad234f | 10.26434/chemrxiv.8113172.v1 | Pitfalls of the Martini Model | <div>
<div>
<div>
<p>The computational and conceptual simplifications realized by coarse-grain (CG)
models make them an ubiquitous tool in the current computational modeling landscape.
Building block based CG models, such as the Martini model, possess the key advantage
of allowing for a broad range of applications without the need to reparametrize the force
field each time. However, there are certain inherent limitations to this approach, which
we investigate in detail in this work. We first study the consequences of the absence of
specific cross Lennard-Jones parameters between different particle sizes. We show that
this lack may lead to artificially high free energy barriers in dimerization profiles. We
then look at the effect of deviating too far from the standard bonded parameters, both
in terms of solute partitioning behavior and solvent properties. Moreover, we show that
too weak bonded force constants entail the risk of artificially inducing clustering, which
has to be taken into account when designing elastic network models for proteins. These results have implications for the current use of the Martini CG model and provide clear
directions for the reparametrization of the Martini model. Moreover, our findings are
generally relevant for the parametrization of any other building block based force field. </p>
</div>
</div>
</div> | Riccardo Alessandri; Paulo C. T. Souza; Sebastian Thallmair; Manuel N. Melo; Alex H. de Vries; Siewert-Jan Marrink | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741ca4c89192fc7ad234f/original/pitfalls-of-the-martini-model.pdf |
60c74667469df40f43f43643 | 10.26434/chemrxiv.11316455.v1 | SilverSil: A New Class of Antibacterial Materials of Broad Scope | Consisting of organically modified silica (ORMOSIL) physically doped with Ag nanoparticles, the SilverSil new class of antibacterial materials of broad scope reported herein shows remarkably high and stable activity against representative Gram-positive and Gram-negative bacteria. The low cost, ease of application and excellent health and environmental profile of SilverSil hybrid glassy coatings open the route to their widespread utilization across domestic, hospital, school, industrial and commercial environments and in consumer products.<br /> | Keren Trabelsi; Rosaria Ciriminna; Yael Albo; Mario Pagliaro | Coating Materials; Hybrid Organic-Inorganic Materials; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74667469df40f43f43643/original/silver-sil-a-new-class-of-antibacterial-materials-of-broad-scope.pdf |
60c7549e842e652f8cdb41ac | 10.26434/chemrxiv.13695994.v1 | Laser-induced, Surface Plasmon-enhanced Two-photon Excitation for Efficient Chemical Functionalization of Nanostructured Gold Surfaces | Functionalized gold nanostructures with efficient, broadband absorption
properties are of interest for a variety of biomedical applications. In
this study, we report a plasmon-enhanced functionalization methodology
that results in selective surface conjugation of a fluorescent probe <em>via</em>
two-photon excitation under visible-wavelength laser irradiation. The
fluorescent probe was designed to incorporate a thiolated
4-piperidinyl-1,8-naphthalimide (SNaph) entity, carrying a photolabile
6-nitroveratryl (NV) protecting group, straightforwardly synthesized in a
few steps in good yield. Efficient plasmon-enhanced photodeprotection
of the NV-group, followed by thiol-gold bond formation on gold
nanoisland substrates was recorded upon exposure to 650 nm laser light,
supported by confocal laser scanning microscopy (CLSM). Photolysis of
the labile NV-group, thereby efficiently exposing the free mercapto
group of the thiolated 1,8-naphthalimide, was recorded upon
UV-irradiation at 350 nm, whereas no cleavage occurred at 650 nm. No
conjugation occurred on featureless, gold-plated flat substrates under
the same conditions. Surface plasmon-enhanced two-photon excitation at
plasmonic hotspots in the absorber layer thus resulted in selective and
efficient conjugation of the fluorescent probe to the structured
surfaces. The resulting laser-assisted approach introduces the advantage
of accomplishing selective molecular functionalization at plasmonic
hotspots, owing to the combined, simultaneous effects of long-wavelength
deprotection and spontaneous conjugation. | Kitjanit Neranon; Mattias Äslund; Max Yan; Hao Xu; Ying Fu; Ingemar Petermann; Per Björk; Olof Ramstrom | Photochemistry (Org.); Plasmonic and Photonic Structures and Devices | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7549e842e652f8cdb41ac/original/laser-induced-surface-plasmon-enhanced-two-photon-excitation-for-efficient-chemical-functionalization-of-nanostructured-gold-surfaces.pdf |
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