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61d71b6ba16050129f963539 | 10.26434/chemrxiv-2022-249z5 | Biocompatibility and Physiological Thiolytic Degradability of Radically-made Thioester-functional Copolymers | Being non-degradable, vinyl polymers have limited biomedical applicability. Unfortunately, backbone esters incorporated through conventional radical ring-opening methods do not undergo appreciable abiotic hydrolysis under physiologically relevant conditions. Here, PEG acrylate and di(ethylene glycol) acrylamide-based copolymers containing backbone thioesters were prepared through the radical ring-opening copolymerization of the thionolactone dibenzo[c,e]oxepin-5(7H)-thione. The thioesters degraded fully in the presence of 10 mM cysteine at pH 7.4, with the mechanism presumed to involve an irreversible S–N switch. Degradations with N-acetylcysteine and glutathione were reversible through the thiol–thioester exchange polycondensation of R–SC(=O)–polymer–SH fragments with full degradation relying on an increased thiolate:thioester ratio. Treatment with 10 mM glutathione at pH 7.2 (mimicking intracellular conditions) triggered an insoluble–soluble switch of a temperature-responsive copolymer at 37 °C and the release of encapsulated Nile Red (as a drug model) from core-degradable diblock copolymer micelles. Copolymers and their cysteinolytic degradation products were found to be non-cytotoxic, making thioester backbone-functional polymers promising for drug delivery applications. | Nathaniel Bingham; Qamar Nisa; Priyanka Gupta; Neil Young; Eirini Velliou; Peter Roth | Polymer Science; Biopolymers; Drug delivery systems; Organic Polymers | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61d71b6ba16050129f963539/original/biocompatibility-and-physiological-thiolytic-degradability-of-radically-made-thioester-functional-copolymers.pdf |
64907699853d501c0023e040 | 10.26434/chemrxiv-2023-985h7 | High-throughput solubility determination for data-driven materials design and discovery in redox flow battery research | Solubility is crucial for redox flow batteries as it affects their energy density. A data-driven approach based on AI/ML models can speed up the development of highly soluble redox active materials, but accurate solubility prediction remains elusive because of the lack of relevant databases. To overcome this deficiency, we developed a high-throughput experimentation process that combines a robotically controlled platform with high-throughput methodology to collect large-scale and high-quality solubility data. We demonstrate the potential utility and applicability of this high-throughput process by measuring the aqueous and non-aqueous solubilities of redox active materials and studying the effect of additives on their solubilities for both aqueous and non-aqueous redox flow battery applications. A redox flow battery based on our optimized negative electrolyte formulation and ferrocyanide positive electrolyte offers highly stable performance over 18 days (>100 cycles) with consistent capacity and a 24% boost in energy density. | Yangang Liang; Heather Job; Ruozhu Feng; Fred Parks; Xin Zhang; Aaron Hollas; Mark Bowden; Vijayakumar Murugesan; Wei Wang | Materials Science; Energy; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64907699853d501c0023e040/original/high-throughput-solubility-determination-for-data-driven-materials-design-and-discovery-in-redox-flow-battery-research.pdf |
65ecd15a66c1381729a481e2 | 10.26434/chemrxiv-2024-n12vr | Addressing Reproducibility Challenges in High-Throughput Photochemistry | Light-mediated reactions have emerged as an indispensable tool in organic synthesis and drug discovery, enabling novel transformations and providing access to previously unexplored chemical space. Despite their widespread application in both academic and industrial research, the utilization of light as an energy source still encounters challenges regarding reproducibility and data robustness. Herein we present a comprehensive head-to-head comparison of commercially available batch photoreactors, alongside the introduction of the use of batch and flow photoreactors in parallel synthesis. Hence, we aim to establish a reliable and consistent platform for light-mediated reactions in high-throughput mode. Herein, we showcase the identification of several platforms aligning with the rigorous demands for efficient and robust high-throughput experimentation screenings and library synthesis. | Brenda Pijper; Lucía M. Saavedra; Matteo Lanzi; Maialen Alonso; Alberto Fontana; Marta Serrano; José Enrique Gómez; Arjan W. Kleij; Jesús Alcázar; Santiago Cañellas | Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Photochemistry (Org.); Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ecd15a66c1381729a481e2/original/addressing-reproducibility-challenges-in-high-throughput-photochemistry.pdf |
616d2f798b620d6f50535d6b | 10.26434/chemrxiv-2021-bsx14 | Colloidal SERS sensors for inflammatory biomarker detection in urine for patient risk stratification | Consistently raised levels of inflammatory marker - Neopterin, in urine is linked to increased risk of progression of age-related disease and poorer prognosis. We have developed colloidal SERS sensors and demonstrate their ability, and ease of use, for quantification of neopterin in human urine samples. Results with the sensors are comparable and in agreement with those obtained by HPLC and allow individuals to be stratified into ‘risk’ categories based on their results. With an average 17.85% difference in results between the two analytical approaches, SERS with colloidal sensors, demonstrates an alternative method that is rapid, inexpensive, requires minimal sample treatment, can be performed on a portable instrument with little need for complex data analysis, whilst having the analytical strength to reliably demonstrate an individual’s risk category based on inflammatory load. | Rachel Kidd; William Anderson; Josh Prince; Akosua Agyemang-Prempeh; Peter Roach; Tracey Newman; Sumeet Mahajan | Biological and Medicinal Chemistry; Analytical Chemistry; Nanoscience; Biochemical Analysis; Spectroscopy (Anal. Chem.); Plasmonic and Photonic Structures and Devices | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/616d2f798b620d6f50535d6b/original/colloidal-sers-sensors-for-inflammatory-biomarker-detection-in-urine-for-patient-risk-stratification.pdf |
60c746aaee301c4d00c79571 | 10.26434/chemrxiv.11336525.v1 | Enantioselective Michael Addition: An Experimental Introduction to Asymmetric Synthesis | <p>
We
adapted a classical asymmetric Michael addition for a 1-day
experimental session (6-8 hrs) for third or fourth-year undergraduate
students. The experiment follows up three steps : synthesis of a
chiral Lewis Acid, LiAl(BINOL)<sub>2</sub>, then its use as a
catalyst in the Michael addition of diethyl malonate on
cyclopentenone, followed by purification through column
chromatography on silica gel. The desired product can be fully
characterized by 1D and 2D NMR experiments and IR spectroscopy. The
enantiomeric excess can be determined by polarimetry and <sup>1</sup>H
NMR using chiral lanthanide shift reagent Eu(hfc)<sub>3</sub>.</p> | Martin Tiano | Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746aaee301c4d00c79571/original/enantioselective-michael-addition-an-experimental-introduction-to-asymmetric-synthesis.pdf |
6621a4db418a5379b024045c | 10.26434/chemrxiv-2024-6mnwj | Nonergodic complex medium dynamics affecting protein electron transfer | The standard description of long-range protein electron transfer anticipates an exponential decay of the reaction rate with the donor-acceptor distance due to decaying tunneling probability. In contrast, dynamical models of electron transfer predict a rate turnover to a plateau specified by the protein-water dynamics at shorter distances. The turnover distance is affected by the medium dynamics which is often complex, involving a number of relaxation times. The reaction time also specifies the time scale on which the medium dynamics can affect the reaction dynamics, thus imposing a nonergodic cutoff of the medium relaxation spectrum. The model presented here considers the effects of both the complex medium dynamics and the nonergodic dynamical constraints on the distance dependence of the reaction rate. Considering specific parameters of electron transfer in azurin, it shows that that the dynamical turnover disappears for fast reactions in the picosecond time domain due to nonergodic restrictions on the medium relaxation spectrum. | Dmitry Matyushov | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC 4.0 | CHEMRXIV | 2024-04-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6621a4db418a5379b024045c/original/nonergodic-complex-medium-dynamics-affecting-protein-electron-transfer.pdf |
6149299187a02de46f4294ec | 10.26434/chemrxiv-2021-mb1f5 | Explore protein conformational space with variational autoencoder | Molecular dynamic (MD) simulations have been actively used in the study of protein structure and function. However, extensive sampling in the protein conformational space requires large computational resources and takes a prohibitive amount of time. In this study, we demonstrated that variational autoencoders (VAEs), a type of deep learning model, can be employed to explore the conformational space of a protein through MD simulations. VAEs are shown to be superior to autoencoders (AEs) through a benchmark study, with low deviation between the training and decoded conformations. Moreover, we show that the learned latent space in the VAE can be used to generate unsampled protein conformations. Additional simulations starting from these generated conformations accelerated the sampling process and explored hidden spaces in the conformational landscape. | Hao Tian; Xi Jiang; Francesco Trozzi; Sian Xiao; Eric Larson; Peng Tao | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6149299187a02de46f4294ec/original/explore-protein-conformational-space-with-variational-autoencoder.pdf |
612e7555fc08e3cb7b8753ec | 10.26434/chemrxiv-2021-l969j | C2 product formation in the CO2 electroreduction on boron-doped graphene anchored copper clusters | A possible remedy for the increasing CO2 concentration in the atmosphere is capturing, and reducing it into valuable chemicals like methane, methanol, ethylene, ethanol, etc. However, the suitable catalyst for this process is still under extensive research. Small sized copper clusters have gained attention in the recent years due to their catalytic activity in CO2 reduction reaction. Although C2+ products higher economic value, only the formation of C1 products was investigated thoroughly. For the electrochemical reduction of CO2, a supporting material is needed for small copper clusters. Graphene is a promising candidate, as is exhibits good mechanical and electrical properties however, the weak interaction of copper and graphene needs to be addressed. Our DFT computations also revealed, that small Cu clusters on boron-doped graphene support are promising catalysts for the electrochemical reduction of CO2 towards both C1 and C2 products. We demonstrate the most promising reaction pathways towards various C1 products, and ethanol or ethylene as C2 products on both Cu4 and Cu7 clusters on a boron-doped graphene (BDG) support. We also demonstrate the size-tuneable reactivity of these materials: Cu4 is considered a more reactive agent in general, but Cu7 shows a higher selectivity towards C2 products | Tibor Höltzl; Ewald Janssens; Balázs Barhács | Catalysis; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/612e7555fc08e3cb7b8753ec/original/c2-product-formation-in-the-co2-electroreduction-on-boron-doped-graphene-anchored-copper-clusters.pdf |
611ca58ef5c7c30af8dd0ad9 | 10.26434/chemrxiv-2021-h2110 | Nonlinear Correlation between Reduced Mass and Computed Activation Energy | Correlation between activation energies of the aldol and ene reactions and the reduced masses of the raw materials was revealed by semi-empirical molecular orbital calculations. It was found that there is a singular point where the activation energy changes from decreasing to increasing or to nearly unchanging as the reduced mass increases, and the nonlinear change can be approximated by a quadratic curve. When the coefficient of determination of the correlation was greater than 0.8, the the reduced mass at the singular point was 40-120. | Masatoshi Kawashima | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/611ca58ef5c7c30af8dd0ad9/original/nonlinear-correlation-between-reduced-mass-and-computed-activation-energy.pdf |
6366eaa5aa278451595bac2c | 10.26434/chemrxiv-2022-21mb0 | Asymmetric Potential Barrier Lowering Promotes Photocatalytic Nonoxidative Dehydrogenation of Anhydrous Methanol | Photocatalytic nonoxidative dehydrogenation of anhydrous methanol can be a promising approach to producing formaldehyde and hydrogen as it can avoid catalyst degradation occurred at high temperature in conventional catalysis. To facilitate the rate-determining step, we propose to lower the barrier height for semiconductor-cocatalyst interfacial electron transfer by solution acidity modulating, which shifts electroreduction potential and inherently lowers the interface conduction band position. Since this measure does not change the surface conduction band position, the increase in protons does not aggravate leakage of electron from semiconductor. The resulted asymmetric potential barrier lowering endows photocatalyst with larger driving force for enhancing utilization of photogenerated charge carriers. In our demonstrated reaction, a quantum yield of 89.9 % with formaldehyde selectivity of 95.5 % can be realized. | Kun Jia; Xuhui Wei; Yang Xu; Zhijian Wang; Jiazang Chen | Physical Chemistry; Catalysis; Photocatalysis | CC BY NC 4.0 | CHEMRXIV | 2022-11-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6366eaa5aa278451595bac2c/original/asymmetric-potential-barrier-lowering-promotes-photocatalytic-nonoxidative-dehydrogenation-of-anhydrous-methanol.pdf |
621f3d09c45c0b3e5f2246f8 | 10.26434/chemrxiv-2022-wp6l3 | X-band Parallel-Mode and Multifrequency Electron Paramagnetic Resonance Spectroscopy of S = 1/2 Bismuth Centers | The recent successes in the isolation and characterization of several bismuth radicals inspire the development of new spectroscopic approaches for the in-depth analysis of their electronic structure. Electron paramagnetic resonance (EPR) spectroscopy is a powerful tool for the characterization of main group radicals. However, the large electron-nuclear hyperfine interactions of Bi (209Bi, I = 9/2) have presented difficult challenges to fully interpret the spectral properties for some of these radicals. Parallel-mode EPR (B1 || B0) is almost exclusively employed for the study of S > 1/2 systems but becomes feasible for S = 1/2 systems with large hyperfine couplings, offering a distinct EPR spectroscopic method. Herein, we demonstrate the application of conventional X-band parallel-mode EPR for S = 1/2, I = 9/2 spin systems: Bi doped crystalline silicon (Bi:Si) and the molecular Bi radicals: [L(X)Ga]2Bi• (X = Cl, I) and [L(Cl)GaBi(MecAAC)]• (L = HC[MeCN(2,6-iPr2C6H3)]2). In combination with multifrequency perpendicular-mode EPR (X-, Q-, and W-band frequency), we were able to fully refine both of the anisotropic g- and A-tensors of these molecular radicals. The parallel-mode EPR experiments demonstrated and discussed here have the potential to enable the characterization of other S = 1/2 systems with large hyperfine couplings, which is often challenging by conventional perpendicular-mode EPR techniques. Considerations pertaining to the choice of microwave frequency are discussed for relevant spin-systems. | Julia Haak; Julia Krüger; Nikolay Abrosimov; Christoph Helling; Stephan Schulz; George Cutsail III | Physical Chemistry; Inorganic Chemistry; Main Group Chemistry (Inorg.); Spectroscopy (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/621f3d09c45c0b3e5f2246f8/original/x-band-parallel-mode-and-multifrequency-electron-paramagnetic-resonance-spectroscopy-of-s-1-2-bismuth-centers.pdf |
62fb2f136e379698ef7d3217 | 10.26434/chemrxiv-2022-hk6p7 | Revisiting phase transformation mechanisms in LiNi0.5Mn1.5O4 high voltage cathodes with operando microdiffraction | Understanding the phase transition mechanisms of active materials inside Li-ion batteries is critical for rechargability and optimizing the power/energy density of devices. In this work, high-energy microfocused X-ray diffraction is used to measure in operando the state-of-charge heterogeneities inside a high-voltage spinel (LiMn1.5Ni0.5O4, LMNO) cathode. The structure of active material which resists complete delithiation is studied, towards unlocking the full storage capacity of ion-conductive spinels. High-precision diffraction also reveals nonlinear coupling between strain and lithiation state inside the cathode at high voltages, which suggests the phase diagram of this material is more complex than previously assumed. X-ray diffraction depth-profiling shows that large lithiation heterogeneities through the cross-section of the electrode are formed even at low currents, and that decoupling these gradients are necessary to study the phase transitions in detail. | Isaac Martens; Nikita Vostrov; Marta Mirolo; Mattia Colalongo; Peter Kus; Marie-Ingrid Richard; Lianzhou Wang; Xiaobo Zhu; Tobias U. Schulli; Jakub Drnec | Physical Chemistry; Materials Science; Energy; Electrochemistry - Mechanisms, Theory & Study; Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62fb2f136e379698ef7d3217/original/revisiting-phase-transformation-mechanisms-in-li-ni0-5mn1-5o4-high-voltage-cathodes-with-operando-microdiffraction.pdf |
6516ea03ade1178b245bd883 | 10.26434/chemrxiv-2023-d5mn9 | Electronic Relaxation Mechanism of 9-Methyl-2,6-Diaminopurine and 2,6-Diaminopurine-2’-Deoxyribose in Solution | Prolonged ultraviolet exposure results in the formation of adducts such as the cyclobutene pyrimidine dimers (CPDs) in RNA despite the established photostability of the nucleic acids. Therefore, prebiotic photolesion repair mechanisms should have played an important role in the maintenance of the structural integrity of primitive nucleic acids. 2,6-Diaminopurine (2,6DAP) is a prebiotic nucleobase that has been demonstrated to repair CPDs with high efficiency when incorporated into nucleic acid polymers. We investigate the electronic deactivation pathways of 2,6-diaminopurine-2’-deoxyriside (2,6DAP-d) and 9-methyl-2,6-diaminopurine (9Me2,6DAP) in acetonitrile and aqueous solution to shed light on the photophysical and excited state properties of the 2,6DAP chromophore. Spectroscopic measurements, enhanced with electronic-structure calculations, evidence that both are photostable prebiotic compounds that exhibit nearly identical deactivation mechanisms upon population of the S1(ππ* La) state at 290 nm. The electronic relaxation mechanism involves deactivation through two reaction coordinates (C2- and C6-coordinates) and >99% of the excited state population decays through non-radiative pathways involving two conical intersections with the ground state. The results support the idea that 2,6DAP should have accumulated in significant quantities during prebiotic times to participate in the formation of non-canonical RNA oligonucleotides and play a significant role in the protection of the prebiotic genetic code. | Luis A. Ortiz-Rodríguez; Naishka E. Caldero-Rodríguez; Sourav K. Seth; Karitza Díaz-González; Carlos Crespo-Hernández | Theoretical and Computational Chemistry; Physical Chemistry; Biophysical Chemistry; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2023-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6516ea03ade1178b245bd883/original/electronic-relaxation-mechanism-of-9-methyl-2-6-diaminopurine-and-2-6-diaminopurine-2-deoxyribose-in-solution.pdf |
60c7599f702a9b348f18cf03 | 10.26434/chemrxiv.14672094.v2 | C-5 Aryl Substituted Azaspirooxindolinones Derivatives: Synthesis and Biological Evaluation as Potential Inhibitors of Tec Family Kinases | <p>The interleukin-2-inducible kinase (ITK) and Bruton tyrosine kinase (BTK) are two crucial
Tec family kinase members with important roles in the development of hematopoietic
malignancies, autoimmune disorders and
other diseases in human. Thus, ITK and BTK are key targets for drug
development. Spirooxindoles are important scaffolds for the
synthesis of small molecules with broad and potent biological activities. In
this study, we performed a structure-activity relationship study of a new
series of 5'-(benzo[d][1,3]dioxol-5-yl)spiro[piperidine-4,3'-pyrrolo[2,3-b]pyridin]-2'(1'H)-one
linked with N-acyl and C-5 aryl-substituted scaffolds in a panel of ITK and BTK cancer cell lines. Four compounds <b>11</b>, <b>12</b>, <b>14</b> and <b>15</b> showed high antiproliferative activity against ITK and BTK cell
lines. Compounds <b>11</b> and <b>12</b> with a C-5 benzodioxole group and
gem-dialkyl group attached to carbonyl on piperidine were highly effective in
ITK-high Jurkat and CEM cell lines, and compound <b>14, </b>a<strong> </strong>biotin analogue, was identified as a good inhibitor
of BTK-high RAMOS cells. Compound <b>15 </b>with
cyclopropyl group attached to carbonyl on piperidine also showed good activity
in ITK and BTK cell lines.<b> </b></p> | Gopal Mudasani; Kalyani Paidikondala; Soňa Gurská; Shambabu Joseph Maddirala; Petr Džubák; Viswanath Das; Rambabu Gundla | Bioinorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7599f702a9b348f18cf03/original/c-5-aryl-substituted-azaspirooxindolinones-derivatives-synthesis-and-biological-evaluation-as-potential-inhibitors-of-tec-family-kinases.pdf |
612741fab817b45a000afef6 | 10.26434/chemrxiv-2021-k5n6s-v2 | Contact Map Fingerprints of Protein-Ligand Unbinding Trajectories Reveal Mechanisms Determining Residence Times Computed from Scaled Molecular Dynamics | <div>The binding kinetic properties of potential drugs may significantly influence their subsequent clinical efficacy. Predictions of these properties based on computer simulations provide a useful alternative to their expensive and time-demanding experimental counterparts, even at an early drug discovery stage.</div><div>Herein, we perform Scaled Molecular Dynamics (ScaledMD) simulations on a set of 27 ligands of HSP90 belonging to more than 7 chemical series in order to estimate their relative residence time. We introduce two new techniques for the analysis and the classification of the simulated unbinding trajectories. The first technique, which helps in estimating the limits of the free energy well around the bound state and the second one, based on a new contact map fingerprint, allows the description and the comparison of the paths that lead to unbinding.</div><div>Using these analyses, we find that ScaledMD’s relative residence time generally enables the identification of the slowest unbinders. We propose an explanation for the underestimation of the residence times of a subset of compounds and we investigate how the biasing in ScaledMD can affect the mechanistic insights that can be gained from the simulations.</div> | Marc Bianciotto; Paraskevi Gkeka; Daria B. Kokh; Rebecca Wade; Minoux Hervé | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/612741fab817b45a000afef6/original/contact-map-fingerprints-of-protein-ligand-unbinding-trajectories-reveal-mechanisms-determining-residence-times-computed-from-scaled-molecular-dynamics.pdf |
67b71eeafa469535b92584fb | 10.26434/chemrxiv-2025-2r8s1 | Unraveling the Effects of Pore Size and Diamine Functionalization on CO2 Diffusion in Metal-Organic Frameworks using Machine-Learning Interatomic Potentials
| M2(dobdc) (dobdc4- = 2,5-dioxido-1,4-benzenedicarboxylate; M = Mg, Mn, Fe, Co, Ni, Cu, Zn), commonly referred to as M-MOF-74, and its variants have been extensively studied for their outstanding CO2 capture performance. In particular, diamine-functionalized M2(dobpdc) (dobpdc4- = 4,4’-dioxidobiphenyl-3,3’-dicarboxylate), an extended analogue of M2(dobdc), has demonstrated exceptional CO2 selectivity under humid conditions owing to its unique cooperative CO2 capture mechanism. Despite these advantages, its CO2 diffusion behavior—a critical parameter for practical applications—remains poorly understood. Here, we systematically investigate the effects of pore size and diamine functionalization on CO2 diffusion in Mg2(dobpdc). By employing machine-learning interatomic potentials (MLPs), we achieve quantum-level accuracy within classical molecular dynamics (MD) simulations, enabling the examination of large-scale systems comprising over 4,000 atoms on nanosecond timescales. To elucidate the CO2 diffusion behavior, we compare Mg2(dobpdc) with its smaller-pore counterpart Mg2(dobdc) and larger-pore analogue Mg2(dotpdc) (2,5-dioxido-1,4-terephthalate). Four distinct diamines–m-2 (N-N'-methylethylenediamine), m-2-m (N,N’-dimethylethylenediamine), e-2 (N-ehylethylenediamine), and e-2-e (N,N’-diethylethylenediamine)–are appended to Mg2(dobpdc) and Mg2(dotpdc) to evaluate their influence on CO2 diffusion. The developed MLPs exhibit root mean square errors (RMSEs) of less than 5 meV/atom for energies and 0.3 eV/Å for forces, compared to density functional theory (DFT) calculations, with MLP-optimized lattice parameters deviating from DFT values by no more than ±2%. For bare MOFs, our MLPs accurately predict CO2 binding enthalpies and the localized CO2 feature near open Mg sites, consistent with experimental observations. This results in low diffusion coefficients (2.0 x 10-11 m2/s – 3.1 x 10-10 m2/s) at low CO2 uptake. For Mg2(dobpdc) and Mg2(dotpdc), which possess larger pore sizes than Mg2(dobdc), the diffusion coefficients increase with increasing CO2 uptake. This trend is attributed to the saturation of Mg sites, which reduces interactions between free CO2 molecules and Mg ions. At one CO2 per Mg, the diffusion coefficients are calculated as 2.1 x 10-9 m2/s and 3.7 x 10-9 m2/s for Mg2(dobpdc) and Mg2(dotpdc), respectively. Diamine functionalization further enhances CO2 diffusion (0.8 x 10-9 m2/s ~ 13.2 x 10-9 m2/s) by reducing access to open Mg sites and introducing complex interactions between diamine units and CO2 and between ammonium carbamate units and CO2. However, at high CO2 loadings, steric hindrance caused by functionalized diamines decreases the diffusion coefficients (1.6 x 10-9 m2/s ~ 6.1 x 10-9 m2/s), particularly in Mg2(dobpdc) due to its smaller pore size relative to Mg2(dotpdc). These findings provide valuable insights into the interplay between pore architecture, functionalization, and CO2 diffusion in bare and diamine-functionalized MOFs. Our results not only deepen the understanding of CO2 capture mechanisms but also provide a framework for designing next-generation materials optimized for carbon capture applications. | Joharimanitra Randrianandraina; Chang Seop Hong; Jung-Hoon Lee | Theoretical and Computational Chemistry; Materials Science | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b71eeafa469535b92584fb/original/unraveling-the-effects-of-pore-size-and-diamine-functionalization-on-co2-diffusion-in-metal-organic-frameworks-using-machine-learning-interatomic-potentials.pdf |
66d754d712ff75c3a14abf53 | 10.26434/chemrxiv-2024-wbj8k-v2 | Revealing the Role of Redox Reaction Selectivity and Mass Transfer in Current–Voltage Predictions for Ensembles of Photocatalysts | Photocatalysts are conceptually simple reaction units where nanoscale semiconductors integrated with catalysts drive a pair of redox reactions on illumination. However, the proximity of reaction sites performing cathodic and anodic reactions poses dire challenges to realize large light-to-fuel conversion efficiencies. In this study, a powerful, yet straightforward, equivalent-circuit detail-balance modeling framework is developed and applied to evaluate the performance of photocatalytic systems featuring multiple light absorbers. Specifically, low bandgap iridium-doped strontium titanate is modeled a Z-scheme photocatalyst to effect desired hydrogen evolution and iron-based redox shuttle oxidation reactions. Our model has unique capabilities to simulate competing redox reactions and address mass-transfer limitations. In a significant departure from state-of-the-art circuit models, our study develops tools to perform load-line analyses by incorporating a net electrochemical load curve that includes both desired and competing redox reactions. Consequently, reaction selectivity is predicted from equivalent circuit models for photocatalytic and photoelectrochemical systems. Our investigation into ensembles comprised of multiple, semi-transparent light absorbers reveals their potential to outperform a single, optically thick light absorber, particularly when operated under mass-transfer-limited conditions. However, this outcome hinges on minimizing mass-transfer rates of select redox species to prevent undesired reactions of hydrogen oxidation and/or redox shuttle reduction. Our findings demonstrate that reaction selectivity can be achieved by tuning asymmetry in redox species mass-transfer even with perfectly symmetric electrocatalytic charge-transfer coefficients. The influences of various kinetic, mass-transfer, and thermodynamic parameters are explored to offer crucial insights to inform the next-generation of photocatalysts, selective coatings, and reactor designs. | Luisa Barrera; Bradley Layne; Zejie Chen; Kenta Watanabe; Akihiko Kudo; Daniel Esposito; Shane Ardo; Rohini Bala Chandran | Energy; Chemical Engineering and Industrial Chemistry; Transport Phenomena (Chem. Eng.); Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d754d712ff75c3a14abf53/original/revealing-the-role-of-redox-reaction-selectivity-and-mass-transfer-in-current-voltage-predictions-for-ensembles-of-photocatalysts.pdf |
657ba3ac66c1381729340d4f | 10.26434/chemrxiv-2023-2kl8s | Sensitive thermochromic behavior of InSeI, a highly anisotropic and tubular 1D van der Waals Crystal | Thermochromism, the change in color of a material with temperature, is the fundamental basis of optical thermometry. A longstanding challenge in realizing sensitive optical thermometers for widespread use is identifying materials with pronounced thermometric optical performance in the visible range. To this end, we demonstrate that single crystals of indium selenium iodide (InSeI), a 1D van der Waals (vdW) solid consisting of weakly-bound helical chains, exhibit considerable visible range thermochromism. We show a strong temperature-dependent optical band edge absorption ranging from 450 to 530 nm (2.8 to 2.3 eV) over a 380 K temperature range with an experimental (dEg/dT)max value extracted to be 1.26 × 10-3 eV K-1. This value appreciably lies above most dense conventional semiconductors in the visible range and is comparable to soft lattice solids. We further sought to understand the origin of this unusually sensitive thermochromic behavior and found that it arises from strong electron-phonon interactions and anharmonic phonons that significantly broaden band edges and lower the Eg with increasing temperature. Our identification of structural signatures resulting to sensitive thermochromism in exfoliable 1D vdW crystals opens avenues in discovering low-dimensional solids with strong temperature-dependent optical response across broad spectral windows, dimensionalities, and nanoscale size regimes. | Dmitri Leo Cordova; Yinong Zhou; Griffin Milligan; Leo Cheng; Tyler Kerr; Joseph Ziller; Ruqian Wu; Maxx Arguilla | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657ba3ac66c1381729340d4f/original/sensitive-thermochromic-behavior-of-in-se-i-a-highly-anisotropic-and-tubular-1d-van-der-waals-crystal.pdf |
66df48ae12ff75c3a1e25e46 | 10.26434/chemrxiv-2024-ngfvp | Residue interactions guide translational diffusion of proteins | Diffusion at the molecular level involves random collisions between particles, the structure of local microscopic environments, and interactions between the molecules involved. Sampling all these aspects, along with correcting for finite-size effects, can make calculation of infinitely dilute diffusion coefficients computationally difficult. We present a new approach for estimating the translational diffusion coefficient of biomolecular structures by encapsulating these driving forces of diffusion through piece-wise assembly of the component residues of protein structure. By linking the local chemistry of a solvent-exposed patch of a molecule to its contribution to the overall hydrodynamic radius, an accurate prediction of the computationally and experimentally comparable diffusion coefficients can be constructed following a solvent-excluded surface area calculation. We demonstrate that the resulting predictions for diffusion coefficients from peptides through to protein structures are comparable to explicit molecular simulations and improve on statistical mass-based predictions, which tend to rely on limited training data. As this approach uses the chemical identity of molecular structures, we find that it is able to predict and identify differences in diffusivity for structures that would be indistinguishable by mass information alone. | Elham Fazelpour; Jennifer Haseleu; Christopher Fennell | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Biophysics; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66df48ae12ff75c3a1e25e46/original/residue-interactions-guide-translational-diffusion-of-proteins.pdf |
60c73f5bbb8c1a3ce13d9aaf | 10.26434/chemrxiv.7323989.v1 | N-Heterocyclic carbene-functionalized magic number gold nanoclusters | Magic number metal nanoclusters are atomically precise nanomaterials that have enabled unprecedented insight into structure-property relationships in nanoscience. Thiolates are the most common ligand, binding to the cluster via a staple motif in which only central gold atoms are in the metallic state. The lack of other strongly-bound ligands for nanoclusters with different bonding modes has been a significant limitation in the field. Herein, we report a previously unknown ligand for gold (0) nanoclusters: N-heterocyclic carbenes (NHCs), which feature a robust metal-carbon single bond, and impart high stability to the corresponding gold cluster. The addition of a single NHC to gold nanoclusters results in significantly improved stability and catalytic properties in the electrocatalytic reduction of CO<sub>2</sub>. By varying the conditions, nature and number of equivalents of the NHC, predominantly or exclusively monosubstituted NHC-functionalized clusters result. Clusters can also be obtained with up to five NHCs, as a mixture of species. | Mina R. Narouz; Kimberly
M. Osten; Phillip J. Unsworth; Renee
W. Y. Man; Kirsi Salorinne; Shinjiro Takano; Ryohei Tomihara; Sami Kaappa; Sami Malola; Cao Thang Dinh; J. Daniel Padmos; Kennedy Ayoo; Garrett
J. Patrick; Masakazu Nambo; J. Hugh Horton; Edward H. Sargent; Hannu Häkkinen; Tatsuya Tsukuda; Cathleen Crudden | Nanocatalysis - Catalysts & Materials; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2018-11-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f5bbb8c1a3ce13d9aaf/original/n-heterocyclic-carbene-functionalized-magic-number-gold-nanoclusters.pdf |
65643eeccf8b3c3cd73715b4 | 10.26434/chemrxiv-2023-0wrwb | Host-Guest UiO-66 Based Supra-MOF Assembly for Custom Designed Opto-Electronic Device | Supramolecular chemistry adopted by the hybrid systems of metal ions and organic linkers of metal-organic frameworks (MOFs) offers not only the molecular level porous architecture but also an approach for assembly-within-assembly: Supra-MOF, for creating simpler yet multifunctional host-guest based smart material couples. In this work, Supra-MOF approach is smoothly translated to a well-known UiO-66 MOF compound to form luminescent CQDUiO-66 (CQD: carbon quantum dots) and used as a main probe in custom-designed 3D printed opto-electronic device. The device mainly explored on the basis of quenching of fluorescence ability of Iodine for the purpose of identifying the quality of edible oil samples from different commercially available brands. The photodiode based signal output from the device was used to identify the changes in the incident fluorescent light of aqueous dispersion of CQDUiO-66 affected by the rejected iodine from the oil portion. The application of MOF based compound in a proof-of-concept opto-electronic device sheds light on the impact of temperature (heating) with the time on edible oil saturation/unsaturation levels using a quick and newly developed method of determining iodine value (Iv) of oil samples. | Abhijeet Chaudhari; Umesh Chandrashekar | Inorganic Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Coordination Chemistry (Inorg.); Sensors; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65643eeccf8b3c3cd73715b4/original/host-guest-ui-o-66-based-supra-mof-assembly-for-custom-designed-opto-electronic-device.pdf |
64c24b15ce23211b20a321ff | 10.26434/chemrxiv-2023-6vvnn | Scaling-up electroorganic synthesis using a spinning electrode electrochemical reactor in batch and flow mode | Technology for the rapid scale-up of synthetic organic electrochemistry from milligrams to multi-grams or multi-100 gram quantities is highly desirable. Traditional parallel plate flow electrolysis cells can produce large quantities of material, but transfer from batch to this flow technology requires re-optimization of the reaction conditions and fully homogeneous reaction mixtures. Moreover, single-pass processing is often difficult to accomplish due to gas generation and the low flow rates typically used in continuous mode. Herein we present a novel reactor design, based on a rotating cylinder electrode concept, that enables seamless scale up from small scale batch experimentation to gram and even multi-kilogram per day quantities. The device can operate in batch and flow mode and it is able to easily process slurries without clogging of the system or fouling of the electrodes. Continuous operation is also demonstrated using three reactors in series that act as a continuous stirred electrochemical reactor cascade, providing kilogram per day productivities in a single pass. | Nikola Petrović; Bhanwar K. Malviya; C. Oliver Kappe; David Cantillo | Organic Chemistry; Organic Synthesis and Reactions; Process Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c24b15ce23211b20a321ff/original/scaling-up-electroorganic-synthesis-using-a-spinning-electrode-electrochemical-reactor-in-batch-and-flow-mode.pdf |
654e4a79dbd7c8b54b048a2c | 10.26434/chemrxiv-2022-3qc9t-v3 | BigBind: Learning from Nonstructural Data for Structure-Based Virtual Screening | Deep learning methods that predict protein-ligand binding have recently been used for structure-based virtual screening. Many such models have been trained using protein-ligand complexes with known crystal structures and activities from the PDBBind dataset. However, because PDBbind only includes 20K complexes, models typically fail to generalize to new targets, and model performance is on par with models trained with only ligand information. Conversely, the ChEMBL database contains a wealth of chemical activity information but includes no information about binding poses. We introduce BigBind, a dataset that maps ChEMBL activity data to proteins from the CrossDocked dataset. BigBind comprises 583K ligand activities and includes 3D structures of the protein binding pockets. Additionally, we augmented the data by adding an equal number of putative inactives for each target. Using this data, we developed BANANA (BAsic NeurAl Network for binding Affinity), a neural network-based model to classify active from inactive compounds, defined by a 10 μM cutoff. Our model achieved an AUC of 0.72 on BigBind’s test set, while a ligand-only model achieved an AUC of 0.59. Furthermore, BANANA achieved competitive performance on the LIT-PCBA benchmark (median EF1\% 1.81) while running 16,000 times faster than molecular docking with GNINA. We suggest that BANANA, as well as other models trained on this dataset, will significantly improve the outcomes of prospective virtual screening tasks. | Michael Brocidiacono; Paul Francoeur; Rishal Aggarwal; Konstantin Popov; David Koes; Alexander Tropsha | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry | CC BY 4.0 | CHEMRXIV | 2023-11-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/654e4a79dbd7c8b54b048a2c/original/big-bind-learning-from-nonstructural-data-for-structure-based-virtual-screening.pdf |
636cf1d59245387888879d8d | 10.26434/chemrxiv-2022-pp66f | Optode-based chemical imaging of laboratory burned soil reveals millimeter-scale heterogeneous biogeochemical responses | Soil spatial responses to fire are unclear. Using optical chemical sensing with planar ‘optodes’, pH and dissolved O2 concentration were tracked spatially with a resolution of 360 µm per pixel for 72 hours after burning soil in the laboratory with a butane torch (~ 1300 °C) and then sprinkling water to simulate a postfire moisture event. Imaging data from planar optodes correlated with microbial activity (quantified via RNA transcripts). Post-fire and post-wetting, soil pH increased throughout the entire ~ 13 cm × 17 cm × 20 cm rectangular cuboid of sandy loam soil. Dissolved O2 concentrations were not impacted until the application of water postfire. pH and dissolved O2 both negatively correlated (p < 0.05) with relative transcript expression for galactose metabolism, the degradation of aromatic compounds, sulfur metabolism, and narH. Additionally, dissolved O2 negatively correlated (p < 0.05) with carbon fixation pathways in Bacteria and Archaea, amoA/amoB, narG, nirK, and nosZ. nifH was not detected in any samples. Only amoB and amoC correlated with depth in soil (p < 0.05). Results demonstrate that postfire soils are spatially complex on a mm scale and that using optode-based chemical imaging as a chemical navigator for RNA transcript sampling is effective. | Alexander S. Honeyman; Theresa Merl; John R. Spear; Klaus Koren | Analytical Chemistry; Earth, Space, and Environmental Chemistry; Soil Science; Biochemical Analysis; Imaging | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636cf1d59245387888879d8d/original/optode-based-chemical-imaging-of-laboratory-burned-soil-reveals-millimeter-scale-heterogeneous-biogeochemical-responses.pdf |
60c73ed9bb8c1a5d833d99bb | 10.26434/chemrxiv.6940796.v2 | DNA Detection Using Programmed Bilayer Nanopores | <p>Pore-functionalization
has been explored by several groups as a strategy to control DNA translocation
through solid-state nanopores. Here we present a hybrid nanopore system
consisting of single-layer graphene and a DNA origami layer to achieve
base-selective control of DNA translocation rate through aligned nanopores of
the two layers. This is achieved by incorporating unpaired dangling bases
called overhangs to the origami near the pore region. Molecular dynamics
simulations were used to optimize the design of the origami nanopore and the
overhangs. Specifically, we considered the influence of the number and spatial
distribution of overhangs on translocation times. The simulations revealed that
specific interactions between the overhangs and the translocating single
stranded DNA resulted in base-specific residence times. <b></b></p> | Ramkumar Balasubramanian; Sohini Pal; Himanshu Joshi; Banani Chakraborty; Akshay Naik; Manoj Varma; Prabal
K. Maiti | Bioengineering and Biotechnology; Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2018-09-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73ed9bb8c1a5d833d99bb/original/dna-detection-using-programmed-bilayer-nanopores.pdf |
632df608e615025e06240a16 | 10.26434/chemrxiv-2022-9zh2v-v2 | Multi-scale Methane Measurements at Oil and Gas Facilities Reveal Necessary Framework for Improved Emissions Accounting | Methane mitigation from the oil and gas (O&G) sector represents a key near-term global climate action opportunity. Recent legislation in the United States requires updating of current methane reporting programs for oil and gas facilities with empirical data. While technological advances had led to improvements in methane emissions measurements and monitoring, the overall effectiveness of mitigation strategies rests on quantifying spatially and temporally varying methane emissions more accurately than current approaches. In this work, we demonstrate a quantification, monitoring, reporting, and verification framework that pairs snapshot measurements with continuous emissions monitoring systems (CEMS) to reconcile measurements with inventory estimates and account for intermittent emissions events. We find site-level emissions exhibit significant intra-day and daily emissions variation. Snapshot measurements of methane can span over three orders of magnitude and may have limited application in developing annualized inventory estimates at site-level. Consequently, while official inventories underestimate methane emissions on average, emissions at individual facilities can be higher or lower than inventory estimates. Using CEMS, we characterize distributions of frequency and duration of intermittent emission events. Technologies that allow high sampling frequency such as CEMS, paired with a mechanistic understanding of facility-level events, are key to accurate accounting of short-duration, episodic, and high-volume events that are often missed in snapshot surveys, and to scale snapshot measurements to annualized emissions estimates. | Jiayang (Lyra) Wang; William Daniels; Dorit Hammerling; Matthew Harrison; Kaylyn Burmaster; Fiji George; Arvind Ravikumar | Energy; Earth, Space, and Environmental Chemistry; Environmental Science; Fuels - Energy Science | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/632df608e615025e06240a16/original/multi-scale-methane-measurements-at-oil-and-gas-facilities-reveal-necessary-framework-for-improved-emissions-accounting.pdf |
673b43b67be152b1d07c8021 | 10.26434/chemrxiv-2024-prw8k | Affordable robotic arm system for benchtop hyperpolarization-enhanced NMR experiments | Optimization of nuclear spin hyperpolarization experiments often require varying one system parameter at a time (or several parameters in a nontrivial manner) as well as multiple repetitions of signal measurements. Use of automated robotic systems can significantly streamline this optimization process, accelerating data acquisition and improving reproducibility in the long term. In this work we show an exemplary system built on open-source components and demonstrate several benchtop experiments employing photo-CIDNP and SABRE-derived hyperpolarization. This work illustrates that open-source platforms employing benchtop NMR and robotic systems built in a modular manner with remote operation allow the implementation of various (including unconventional) experiments in a reproducible manner. | Kirill Sheberstov; Erik Van Dyke; Jingyan Xu; Raphael Kircher; Liubov Chuchkova; Yinan Hu; Sulaiman Alvi; Dmitry Budker; Danila Barskiy | Physical Chemistry; Analytical Chemistry; Chemical Education; Analytical Apparatus; Spectroscopy (Physical Chem.); Robotics | CC BY NC 4.0 | CHEMRXIV | 2024-11-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673b43b67be152b1d07c8021/original/affordable-robotic-arm-system-for-benchtop-hyperpolarization-enhanced-nmr-experiments.pdf |
60c74f85702a9bdb1e18bbbd | 10.26434/chemrxiv.12906227.v1 | Graphitic Nitrogen in Carbon Catalysts Important for the Reduction of Nitrite Revealed by 15N NMR Spectroscopy at Natural Abundance | Metal-free nitrogen-doped carbon is considered as a green functional material, but the structural determination of the atomic positions of nitrogen remains challenging. We recently demonstrated that directly-excited solid state <sup>15</sup>N NMR (ssNMR) spectroscopy is a powerful tool for the determination of such positions in an N-doped carbon at natural <sup>15</sup>N isotope abundance. Here we present a green chemistry approach to the synthesis of N-doped carbon using cellulose as precursor, and a study of the catalytic properties and atomic structures of the related catalyst. The N-doped carbon (NH<sub>3</sub>) was obtained by oxidation of cellulose with HNO<sub>3</sub> followed by ammonolysis at 800°C. It had a N content of 6.5 wt.% and a surface area of 557 m<sup>2 </sup>g<sup>–1</sup>, and <sup>15</sup>N ssNMR spectroscopy provided evidence for graphitic nitrogen besides of regular pyrrolic and pyridinic nitrogen. This structure determination enabled probing the role of graphitic nitrogen for electrocatalytic reactions, such as the hydrogen evolution reaction (HER), oxygen evolution reaction (OER), and nitrite reduction reaction. The N-doped carbon catalyst (NH<sub>3</sub>) had higher electrocatalytic activities in OER and HER under alkaline conditions and a higher activity for nitrite reduction, as compared with a catalyst prepared by carbonization of the HNO<sub>3</sub>-treated cellulose in N<sub>2</sub>. The electrocatalytic selectivity for nitrite reduction of the N-doped carbon catalyst (NH<sub>3</sub>) was directly related to the graphitic nitrogen functions. Complementary structural analysis by means of <sup>13</sup>C and <sup>1</sup>H ssNMR, scanning electron microscopy (SEM), transmission electron microscopy (TEM), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), Raman spectroscopy, and low-temperature N<sub>2 </sub>adsorption were preformed and provided support to the findings. The results show that directly-excited <sup>15</sup>N ssNMR at natural <sup>15</sup>N abundance is generally capable to provide information on N-doped carbon materials, and it is expected that the approach can be applied to a wide range of solids with an intermediate amount of N atoms. | Zheng Chen; Aleksander Jaworski; Jianhong Chen; Tetyana Budnyak; Ireneusz Szewczyk; Anna Rokicińska; Richard Dronskowski; Niklas Hedin; Piotr Kustrowski; Adam Slabon | Nanocatalysis - Catalysts & Materials; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f85702a9bdb1e18bbbd/original/graphitic-nitrogen-in-carbon-catalysts-important-for-the-reduction-of-nitrite-revealed-by-15n-nmr-spectroscopy-at-natural-abundance.pdf |
6441ed8fe4bbbe4bbffc4bb0 | 10.26434/chemrxiv-2023-zztqm | Preparation of Resilient Organic Electrochemical Transistors Based on Blend Films with Flexible Crosslinkers | Organic electrochemical transistors (OECTs) exhibit high biocompatibility and are expected to be applied in biological sensors. This study focused on crosslinking agents in blend films of a mixed conducting polymer, poly(3,4-ethylenedioxythiophene)-poly(styrenesulfonate) (PEDOT:PSS), and a thermoresponsive polymer, poly(N-isopropylacrylamide) (PNIPAM), as channel layers to realize reversible temperature response. In addition to the conventional (3-glycidyloxypropyl) trimethoxysilane (GOPS) crosslinker, a poly(ethylene glycol) diglycidyl ether (PEGDE) flexible crosslinker was used to overcome the volume expansion caused by the temperature change. Structural analysis revealed that PNIPAM was segregated on the surface and that the PEGDE crosslinker increased the crystallinity of PEDOT. Blend films with binary crosslinkers (PEGDE and GOPS) exhibited reversible response to temperature cycling. Therefore, the use of a flexible crosslinker in functional blend films can facilitate the fabrication of biosensing OECT devices with higher resilience to the fluctuation of surrounding conditions. | Shuhei Kindaichi; Ryosuke Matsubara; Atsushi Kubono; Shunsuke Yamamoto; Masaya Mitsuishi | Physical Chemistry; Polymer Science; Conducting polymers; Polymer morphology; Electrochemistry - Mechanisms, Theory & Study; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6441ed8fe4bbbe4bbffc4bb0/original/preparation-of-resilient-organic-electrochemical-transistors-based-on-blend-films-with-flexible-crosslinkers.pdf |
60c744f9469df47af6f43419 | 10.26434/chemrxiv.9936473.v1 | Importance of Model Size in Quantum Mechanical Studies of DNA Intercalation | There is currently a dearth of effective computational tools to design nucleobase-targeting small molecules and molecular mechanics force-fields for nucleobases lag behind their protein-focused counterparts. While quantum chemical methods can provide reliable interaction energies for small molecule-nucleobase interactions, these come at a steep computational cost. As a first step toward refining available tools for predicting small molecule-nucleobase interactions, we assessed the convergence of DFT-computed interaction energies with increasing binding site model size. We find that while accurate intercalator interaction energies can be derived from binding site models featuring only the flanking nucleotides for uncharged intercalators that bind parallel to the DNA base pairs, errors remain significant even when including distant nucleotides for intercalators that are charged, exhibit groove-binding tails that engage in non-covalent interactions with distant nucleotides, or that bind perpendicular to the DNA base pairs. Consequently, binding site models that include at least three adjacent nucleotides are required to consistently predict converged binding energies. The computationally inexpensive HF-3c method is shown to provide reliable interaction energies and can be routinely applied to such large models.<br /> | Drew P. Harding; Laura J. Kingsley; Glen Spraggon; Steven Wheeler | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744f9469df47af6f43419/original/importance-of-model-size-in-quantum-mechanical-studies-of-dna-intercalation.pdf |
60c73dd5ee301c042dc7864c | 10.26434/chemrxiv.6199340.v1 | The Hydration Structure of Methylthiolate from QM/MM Molecular Dynamics | Thiols are widely present in biological systems, most notably as the side chain of cysteine amino acids in proteins. Thiols can be deprotonated to form a thiolate, which affords a diverse range of enzymatic activity and modes for chemical modification of proteins. Parameters for modeling thiolates using molecular mechanical force fields have not yet been validated, in part due to the lack of structural data on thiolate solvation. Here, the CHARMM36 and Amber models for thiolates in aqueous solutions are assessed using free energy perturbation and QM/MM MD simulations. The hydration structure of methylthiolate was calculated from 1 ns of QM/MM MD (PBE0/def2-TZVP//TIP3P), which show that the water–S- distances are approximately 2 Å. The CHARMM thiolate parameters predict a thiolate S radius close to the QM/MM value and predict a hydration Gibbs energy of -331 kJ/mol, close to the experimental value of -318 kJ/mol. The cysteine thiolate model in the Amber force field underestimates the thiolate radius by 0.2 Å and overestimates the thiolate hydration energy by 119 kJ/mol because it uses the same Lennard-Jones parameters for thiolates as for thiols. A recent Drude polarizable model for methylthiolate with optimized thiolate parameters also performs well. SAPT2+ analysis indicates exchange repulsion is larger for the methylthiolate, consistent with it having a more diffuse electron density distribution in comparison to the parent thiol. These data demonstrate that it is important to define distinct non-bonded parameters for the protonated/deprotonated states of amino acid side chains in molecular mechanical force fields. | Ernest Awoonor-Williams; Christopher Rowley | Physical Organic Chemistry; Computational Chemistry and Modeling; Biophysical Chemistry; Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2018-04-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dd5ee301c042dc7864c/original/the-hydration-structure-of-methylthiolate-from-qm-mm-molecular-dynamics.pdf |
67af5b0381d2151a026d8f25 | 10.26434/chemrxiv-2025-g6kg4 | A near-infrared-II molecular probe for early diagnosis of acute kidney injury induced by diverse etiologies | Acute kidney injury (AKI) is a clinical syndrome characterized by complex etiologies and usually lacks obvious clinical manifestations at the early stage. Compared with traditional imaging methods, optical imaging is broadly considered to be a promising technique for diagnosis of kidney dysfunction own to the merits of noninvasiveness, high sensitivity and fast feedback speed. Herein, we report a water-soluble fluorophore, PEG-TBSe, for in vivo imaging across diverse AKI models in the second near-infrared (NIR-II, 1000–1700 nm) window. Notably, PEG-TBSe possesses an ultrasmall size (~5.5 nm) that is suitable for renal clearance, allowing for comprehensive assessment of AKI severity in pre-renal, renal and post-renal models. In addition, the real-time imaging capacities of PEG-TBSe are sensitive to early changes in AKI, enabling the noninvasive identification of renal lesions earlier than common clinical assays. Overall, this study demonstrates the first NIR-II small molecular probe for the early diagnosis and evaluation of the severity of kidney dysfunction in different AKI models. | Yiqi Zhu; Dingyuan Yan; Jun Zhu; Hongbo Xu; Weijie Zhang; Jianquan Hou; Dong Wang; Ben Zhong Tang | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67af5b0381d2151a026d8f25/original/a-near-infrared-ii-molecular-probe-for-early-diagnosis-of-acute-kidney-injury-induced-by-diverse-etiologies.pdf |
60c74b859abda2c531f8d077 | 10.26434/chemrxiv.12344459.v1 | Classification of Platinum Nanoparticle Catalysts using Machine Learning | Computer simulations and machine learning provide complementary ways of identifying structure/property relationships that are typically targeting toward predicting the ideal singular structure to maximise the performance on a given application. This can be inconsistent with experimental observations that measure the collective properties of entire samples of structures that contain distributions or mixture of structures, even when synthesized and processed with care. Metallic nanoparticle catalysts are an important example. In this study we have used a multi-stage machine learning workflow to identify the correct structure/property relationships of Pt nanoparticles relevant to oxygen reduction (ORR), hydrogen oxidation (HOR) and hydrogen evolution (HER) reactions. By including classification prior to regression we identified two distinct classes of nanoparticles, and subsequently generate the class-specific models based on experimentally relevant criteria that are consistent with observations. These multi-structure/multi-property relationships, predicting properties averaged over a large sample of structures, provide a more accessible way to transfer data-driven predictions into the lab. | Amanda J. Parker; George Opletal; Amanda Barnard | Nanocatalysis - Catalysts & Materials; Nanostructured Materials - Nanoscience; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence; Electrocatalysis; Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b859abda2c531f8d077/original/classification-of-platinum-nanoparticle-catalysts-using-machine-learning.pdf |
623235d8a4ed95400222c8cd | 10.26434/chemrxiv-2022-jvh37 | Synthesis and styrene copolymerization of novel ring-substituted isobutyl phenylcyanoacrylates | Novel ring-substituted isobutyl phenylcyanoacrylates, RPhCH=C(CN)CO2CH2CH(CH3)2, where R is 2-fluoro-5-iodo, 2-fluoro-6-iodo, 2-trifluoromethyl, 3-trifluoromethyl, 4-trifluoromethyl, 2-trifluoromethoxy, 3-trifluoromethoxy, 4-trifluoromethoxy, 2,4,5-trimethyl, 2,4,6-trimethyl, 2,3,5,6-tetramethyl, pentamethyl, 2,3-dimethyl-4-methoxy, 2,5-dimethyl-4-methoxy, 2,4-dimethoxy-3-methyl, 2,4-dimethoxy-6-methyl were synthesized by the piperidine catalyzed Knoevenagel condensation of ring-substituted benzaldehydes and isobutyl cyanoacetate and characterized by CHN analysis, IR, 1H and 13C NMR. The acrylates were copolymerized with styrene in solution with radical initiation (ABCN) at 70C. The compositions of the copolymers were calculated from nitrogen analysis. | Alessandra Cimino; Amaan M. Azeemullah; Danielle E. Comp; Sydney C. Hunt; Madison M. Janakis; Sonia S. Khan; Patryk Labedz; Christopher Lee; Monique L.P. Lotto; Yasmeen Lowe; Raza Malik; Raisa A. Munshi; Udita Persaud; Saikrupa Rajaramsiva; Maximillian A. Ramirez; Claire P. Rossi; Sara M. Rocus; William Schjerven; Gregory Kharas | Organic Chemistry; Polymer Science; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Organic Polymers | CC BY 4.0 | CHEMRXIV | 2022-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/623235d8a4ed95400222c8cd/original/synthesis-and-styrene-copolymerization-of-novel-ring-substituted-isobutyl-phenylcyanoacrylates.pdf |
60c748bf0f50db34073967db | 10.26434/chemrxiv.11911077.v2 | The Pyruvate Aldol Condensation Product: A Metabolite that Escaped Synthetic Preparation for Over a Century | <p>The homo-aldol condensation
product of pyruvate, <a>2-methyl-4-oxopent-2-enedioic acid (OMPD)
</a>has been recently implicated as a catabolic intermediate in the bacterial
degradation of lignin and previously identified from other biological sources
in reports ranging over sixty years. Yet, while a preparation of the pyruvate aldol-product
precursor, 4-hydroxy-4-methyl-2-oxoglutaric acid (HMOG) was first reported in
1901, there has not been a complete published synthesis of OMPD. Analysis of reaction mixtures have helped
identify that it is zymonic acid, the lactone of HMOG, that is the direct
precursor to OMPD. The reaction appears to proceed through an acid or base
mediated ring opening that does not involve formal lactone hydrolysis. In addition to a preparative protocol we
provide a proposed mechanism for the formation of methylsuccinic acid that
arises from the non-oxidative decarboxylation of OMPD. Lastly, we report on the relative stability
of the possible isomers of the condensation product and find that at all pH
values, Z-OMPD is the most abundant.</p> | Andro Rios; Partha Bera; Jennifer Moreno; George Cooper | Bioorganic Chemistry; Organic Synthesis and Reactions; Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748bf0f50db34073967db/original/the-pyruvate-aldol-condensation-product-a-metabolite-that-escaped-synthetic-preparation-for-over-a-century.pdf |
652eafa745aaa5fdbb3429dc | 10.26434/chemrxiv-2023-96z34 | Constant-pH Simulations with the Polarizable Atomic Multipole AMOEBA Force Field | Classical mechanical simulation of molecular models at constant pH is an advanced technique for studying conformational dynamics in the presence of proton titration which is critical to pharmaceutical design. The algorithms presented previously have been limited to fixed charge force fields. This work introduces the first constant pH molecular dynamics (CpHMD) algorithm compatible with multipolar electrostatics and polarizability. Additionally, our implementation in the open-source Force Field X software has the unique ability to handle titration state changes in crystalline systems, including flexible support for all 230 space groups. Evaluation of the constant pH AMOEBA model was performed on 11 crystal peptide systems that span the titrating amino acids Asp, Glu, His, Lys, and Cys. Accurate titration state predictions for these crystals, including for the coordination of Zn+2 by cysteines, demonstrates the promise of the method for constant pH
molecular dynamics simulations of proteins in the context of pKa predictions, assessment of protein conformational ensembles, and for the calculation of protein-ligand binding affinity. | Andrew Thiel; Matthew Speranza; Sanika Jadhav; Lewis Stevens; Daniel Unruh; Pengyu Ren; Jay Ponder; Jana Shen; Michael Schnieders | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Biochemistry; Biophysics; Computational Chemistry and Modeling; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652eafa745aaa5fdbb3429dc/original/constant-p-h-simulations-with-the-polarizable-atomic-multipole-amoeba-force-field.pdf |
60fd7834d03b3d13a602dbfc | 10.26434/chemrxiv-2021-cg9p8 | MoleGuLAR: Molecule Generation using Reinforcement Learning with Alternating Rewards | Design of new inhibitors for novel targets is a very important problem especially in the current scenario with the world being plagued by COVID-19. Conventional approaches undertaken to this end, like, high-throughput virtual screening require extensive combing through existing datasets in the hope of finding possible matches. In this study we propose a computational strategy for de novo generation of molecules with high binding affinities to the specified target. A deep generative model is built using a stack augmented recurrent neural network for initially generating drug like molecules and then it is optimized using reinforcement learning to start generating molecules with desirable properties--primarily the binding affinity. The reinforcement learning section of the pipeline is further extended to multi-objective optimization showcasing the model's ability to generate molecules with a wide variety of properties desirable for drug like molecules, like, LogP, Quantitative Estimate of Drug Likeliness etc.. For multi-objective optimization, we have devised a novel strategy in which the property being used to calculate the reward is changed periodically. In comparison to the conventional approach of taking a weighted sum of all rewards, this strategy shows enhanced ability to generate a significantly higher number of molecules with desirable properties.
| Manan Goel; Shampa Raghunathan; Siddhartha Laghuvarapu; U. Deva Priyakumar | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60fd7834d03b3d13a602dbfc/original/mole-gu-lar-molecule-generation-using-reinforcement-learning-with-alternating-rewards.pdf |
6636548891aefa6ce124f3d1 | 10.26434/chemrxiv-2024-9j85m-v2 | Neural network potentials for exploring condensed phase chemical reactivity | Recent advances in machine learning oer powerful tools for exploring complex reaction mechanisms in condensed phases via reactive simulations. In this tutorial review, we describe the key challenges associated with simulating reactions in condensed phases, we introduce neural network potentials and detail how they can be trained. We emphasize the importance of active learning to construct the training set, and show how these reactive force elds can be integrated with enhanced sampling techniques, including transition path sampling. We illustrate the capabilities of these new methods with a selection of applications to chemical reaction mechanisms in solution and at interfaces. | Axel Gomez; Miguel de la Puente; Rolf David; Damien Laage | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6636548891aefa6ce124f3d1/original/neural-network-potentials-for-exploring-condensed-phase-chemical-reactivity.pdf |
617ba1b38ac7a29a355ff356 | 10.26434/chemrxiv-2021-qvx0l | Resistive Pulse Sensing with Micro-fabricated Nanopores (NP-RPS) for Sub-micron Biomolecule and Bionanoparticle Analysis | Biomolecules and bionanoparticles, such as nucleic acids, proteins, microorganisms and extracellular vesicles (EVs), are recognized as important targets for fundamental research, clinical diagnostic and therapeutic applications. To gain detailed information of those bionanoparticles, we demonstrate an electroosmotic (EO) driven transport behavior in silicon and silicon nitride-based nanopore, towards an accurate measure of concentration and sizing of sub-micro particles for a general biological interest. | Ke LIU | Biological and Medicinal Chemistry; Analytical Chemistry; Nanoscience; Analytical Apparatus; High-throughput Screening; Nanofabrication | CC BY NC 4.0 | CHEMRXIV | 2021-11-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/617ba1b38ac7a29a355ff356/original/resistive-pulse-sensing-with-micro-fabricated-nanopores-np-rps-for-sub-micron-biomolecule-and-bionanoparticle-analysis.pdf |
67471c385a82cea2fa1c5803 | 10.26434/chemrxiv-2024-f123c-v2 | Generative AI-Powered Inverse Design for Tailored
Narrowband Molecular Emitters | In organic displays, developing molecules that produce a broad color gamut with exceptional color purity is of critical importance. AI-assisted molecular screening can expedite the design process of emission molecules. However, the efficiency of current methodologies is constrained by their limited candidate pools and poor hit rates. Here we present MEMOS, a cutting-edge molecular generation framework that, through Markov molecular sampling techniques, facilitates the targeted inverse design of molecules across a nearly boundless chemical space, tailored to emit the narrow spectral bands associated with desired colors. Notably, by employing a self-improving iterative process, MEMOS achieves an impressive hit rate of up to 80%. Our method showcases the pioneering capability to rapidly navigate through millions of molecular possibilities, efficiently pinpointing thousands of high-potential candidates within a 24-hour period. This breakthrough accelerates the design of novel organic luminescent materials, setting the stage for the advancement of the next generation of high-quality organic displays. | Mianzhi Pan; Tianhao Tan; Yawen Ouyang; Qian Jin; Yougang Chu; Wei-Ying Ma; Jianbing Zhang; Lian Duan; Dong Wang; Hao Zhou | Organic Chemistry; Materials Science; Optical Materials; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-11-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67471c385a82cea2fa1c5803/original/generative-ai-powered-inverse-design-for-tailored-narrowband-molecular-emitters.pdf |
60c74e064c891923cbad391b | 10.26434/chemrxiv.12661214.v2 | Natures Therapy for COVID-19: Targeting the Vital Non-Structural Proteins (NSP) from SARS-CoV-2 with Phytochemicals from Indian Medicinal Plants | Containing COVID-19 is still a global challenge. It has affected the "normal" world by<br />targeting its economy and health sector. Research is more focused on finding a cure to this<br />disease and is less concerned about other life threatening diseases like cancer. Thus we need to<br />develop a medical solution at the earliest. In this context the present work aimed to understand<br />the efficacy of 22 rationally screened phytochemicals from Indian medicinal plants obtained<br />from our previous work, following drug-likeness properties, against 6 non-structural-proteins<br />(NSP) from SARS-CoV-2. 100 ns molecular dynamics simulations were performed and<br />relative binding free energies were computed by MM/PBSA. Further, principal component<br />analysis, dynamic cross correlation and hydrogen bond occupancy were analyzed to<br />characterize protein–ligand interactions. Biological pathway enrichment analysis was also<br />carried out to elucidate the therapeutic targets of the phytochemicals in comparison to SARS-<br />CoV-2. The potential binding modes and favourable molecular interaction profile of 9<br />phytochemicals, majorly from Withania sominifera with lowest free binding energies, against<br />the SARS-CoV-2 NSP targets were identified. It was understood that phytochemicals and<br />repurposed drugs with steroidal moieties in their chemical structures formed stable interactions<br />with the NSPs. Additionally, human target pathway analysis for SARS-CoV-2 and<br />phytochemicals showed that cytokine mediated pathway and phosphorylation pathways were<br />with the most significant p-value. To summarize this work, we suggest a global approach of<br />targeting multiple proteins of SARS-CoV-2 with phytochemicals as a natural alternative<br />therapy for COVID-19. We also suggest that these phytochemicals need to be tested<br />experimentally to confirm their efficacy. | Pratap Kumar Parida; Dipak Paul; Debamitra Chakravorty | Bioinformatics and Computational Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e064c891923cbad391b/original/natures-therapy-for-covid-19-targeting-the-vital-non-structural-proteins-nsp-from-sars-co-v-2-with-phytochemicals-from-indian-medicinal-plants.pdf |
61d6391ce7b751fa558eb501 | 10.26434/chemrxiv-2021-7mfxf-v3 | Aluminum Electrodeposition from Chloride-Rich and Chloride-Free Organic Electrolytes | The corrosivity of chloride-based electrolytes is a major shortcoming in the practical realization of rechargeable aluminum batteries. Herein, the effect of Cl- on Al speciation and electrochemistry in tetrahydrofuran was measured by employing theoretical and experimental approaches for three systems: Al(OTF)3/THF, Al(OTF)3 plus LiCl in THF, and AlCl3/THF. The high consistency between measured and computed spectroscopic aspects associated with Al(OTF)3/THF electrolyte provided both a rationale for understanding Al complex-ion formation in a Cl- free environment and an approach for examining the effect of Cl- on Al speciation. Room-temperature Al plating was achieved from dilute solutions ([Al] = 0.1M) at potentials ≥ 0V (vs. Al⁄Al3+). Cl- is found to enable facile Al plating and SEM reveals that Al is electrochemically deposited as nanocrystalline grains. | Zaher Slim; Erik Menke | Physical Chemistry; Energy; Electrochemistry - Mechanisms, Theory & Study; Spectroscopy (Physical Chem.); Surface; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61d6391ce7b751fa558eb501/original/aluminum-electrodeposition-from-chloride-rich-and-chloride-free-organic-electrolytes.pdf |
661d28b7418a5379b0e44459 | 10.26434/chemrxiv-2024-891rw | Pt-Pd Nanoparticles from Green Synthesis Combined with Multi-walled Carbon Nano-tubes as a Modifying Layer on a Glassy Carbon Electrode for the Electrochemical Detection of Pyrene | A glassy carbon electrode was modified with Pt-Pd nanoparticles (NPs) and multi-walled carbon nanotubes (MWCNTs) for electrochemical detection of pyrene, a polycyclic aromatic hydrocarbon suggested by environmental authorities for monitoring. The Pt-Pd NPs were synthesized using metal salt precursors and an aqueous extract of E. grandis leaves. This offered an alternative synthesis route that eliminates use of the conventional hazardous reductive chemicals. The size of the NPs was optimized by varying the proportions of the Pt and Pd ions in the precursor solutions. Square wave voltammetry and cyclic voltammetry were used in the electrochemical analysis of pyrene. The electrode modification resulted in an increase of the peak current for pyrene oxidation by up to 200 %. The electrochemical process was determined to be both adsorption- and diffusion-controlled making it necessary to have a pre-concentration time before analysis. The linear range of analysis for the electrochemical sensor was 66–130 µM with R2 of 0.99516. The lower limit of detection was determined to be 23 µM. Pt-Pd NPs from a green process could be used together with MWCNTs to modify an electrode for relatively sensitive electrochemical detection of pyrene. An increase in the separation between the oxidation peaks of pyrene and anthracene at the modified electrode provides a slight improvement in selectivity. | Fredrick M. Mwazighe; Rudolf Holze | Physical Chemistry; Analytical Chemistry; Electrochemical Analysis; Electrochemistry - Mechanisms, Theory & Study; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-04-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661d28b7418a5379b0e44459/original/pt-pd-nanoparticles-from-green-synthesis-combined-with-multi-walled-carbon-nano-tubes-as-a-modifying-layer-on-a-glassy-carbon-electrode-for-the-electrochemical-detection-of-pyrene.pdf |
60c7575f469df44a40f45465 | 10.26434/chemrxiv.14398067.v1 | RedDB, a Computational Database of Electroactive Molecules for Aqueous Redox Flow Batteries | An increasing number of electroactive compounds have recently been explored for their use in high-performance redox flow batteries for grid-scale energy storage. Given the vast and highly diverse chemical space of the candidate compounds, it is alluring to access their physicochemical properties in a speedy way. High-throughput virtual screening approaches, which use powerful combinatorial techniques for systematic enumerations of large virtual chemical libraries and respective property evaluations, are indispensable tools for an agile exploration of the designated chemical space. Herein, RedDB: a computational database that contains 31,677 molecules from two prominent classes of organic electroactive compounds, quinones and aza-aromatics, has been presented. RedDB incorporates miscellaneous physicochemical property information of the compounds that can potentially be employed as battery performance descriptors. RedDB’s development steps, including: i)chemical library generation, ii) molecular property prediction based on quantum chemical calculations, iii) aqueous solubility prediction using machine learning, and iv) data processing and database creation, have been described. | Elif Sorkun; Qi Zhang; Abhishek Khetan; murat cihan sorkun; Süleyman Er | Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7575f469df44a40f45465/original/red-db-a-computational-database-of-electroactive-molecules-for-aqueous-redox-flow-batteries.pdf |
60c755e0702a9b013f18c7c1 | 10.26434/chemrxiv.14176523.v1 | Influence of a Cu-Zirconia Interface Structure on CO2 Adsorption and Activation | We have screened different Cu-ZrO<sub>2</sub> interface structures and analysed the influence of the interface structure on CO<sub>2</sub> binding strength using density functional theory calculations. Our results demonstrate that a Cu nanorod favours one position on both tetragonal and monoclinic ZrO<sub>2</sub> surfaces, where the bottom Cu atoms are placed close the lattice oxygens. CO<sub>2</sub> prefers a bent bidentate configuration at the interface and the molecule is clearly activated being negatively charged. Altogether, our results highlight that CO<sub>2</sub> adsorption and activation depend sensitively on the chemical composition and atomic structure of the interface used in the calculations. <div><br /></div> | Lars Gell; Aku Lempelto; toni Kiljunen; Karoliina Honkala | Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755e0702a9b013f18c7c1/original/influence-of-a-cu-zirconia-interface-structure-on-co2-adsorption-and-activation.pdf |
60c749520f50db451d3968c8 | 10.26434/chemrxiv.12052677.v1 | Beta-PdBi2 Monolayer: Two-Dimensional Topological Metal with Superior Catalytic Activity for Carbon Dioxide Electroreduction to Formic Acid | The lack of efficient electrocatalysts has been a main obstacle for the large-scale commercialization of CO<sub>2</sub> electroreduction. In this work, we demonstrate that two-dimensional (2D) beta-PdBi<sub>2</sub> mono-layer is a promising solution for this issue. beta-PdBi<sub>2</sub> monolayer is a stable 2D crystal and the three-dimensional (3D) bulk interlayer energy is similar as for other layered materials that can be exfoliated into 2D crystals. Interestingly, beta-PdBi<sub>2</sub> monolayer has rather intri-guing electronic properties: while being metallic, it also has a non-trivial topological point. Remarkably, the extra electronic states at the Fermi level induced by the intrinsic spinorbit coupling (SOC) effect significantly enhance the adsorption of OCHO* intermediate on beta-PdBi<sub>2</sub> monolayer, resulting in a rather small onset potential of -0.26 V vs. RHE for CO<sub>2</sub> electroreduction to HCOOH. These results not only suggest a promising candidate for CO<sub>2</sub> electrolysis but also deepen our understanding of the factors dominating the catalytic activity of 2D materials. <br /> | Xiaorong Zhu; Yu Wang; Yu Jing; Thomas Heine; Yafei Li | Computational Chemistry and Modeling; Electrocatalysis; Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749520f50db451d3968c8/original/beta-pd-bi2-monolayer-two-dimensional-topological-metal-with-superior-catalytic-activity-for-carbon-dioxide-electroreduction-to-formic-acid.pdf |
60c75191bb8c1afedd3dbcfb | 10.26434/chemrxiv.13177367.v1 | Surface Ligand Removal in Atomic Layer Deposition of GaN Using Triethylgallium | Gallium nitride (GaN) is one of the most important semiconductor materials in modern electronics. While GaN films are routinely deposited by chemical vapor deposition at around 1000 °C, low-temperature routes for GaN deposition need to be better understood. Herein, we present an atomic layer deposition (ALD) process for GaN-based on triethyl gallium (TEG) and ammonia plasma and show that the process can be improved by adding a reactive pulse between the TEG and ammonia plasma, making it an ABC-type pulsed process. We show that the material quality of the deposited GaN is not affected by the B-pulse, but that the film growth per ALD cycle increase when a B-pulse is added. We suggest that this can be explained by removal of ethyl ligands from the surface by the B-pulse, enabling a more efficient nitridation by the ammonia plasma. We show that the B-pulsing can be used to enable GaN deposition with a thermal ammonia pulse, albeit of X-ray amorphous films. | Petro Deminskyi; Chih-Wei Hsu; Babak Bakhit; Polla Rouf; Henrik Pedersen | Thin Films; Organometallic Compounds; Ligands (Organomet.); Main Group Chemistry (Organomet.); Interfaces; Physical and Chemical Processes; Surface | CC BY 4.0 | CHEMRXIV | 2020-11-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75191bb8c1afedd3dbcfb/original/surface-ligand-removal-in-atomic-layer-deposition-of-ga-n-using-triethylgallium.pdf |
65f29f789138d231616dede2 | 10.26434/chemrxiv-2024-2tvmv | Computational Investigations of the Detailed Mechanism of Reverse Intersystem Crossing in Inverted Singlet-Triplet Gap Molecules | Inverted singlet-triplet gap (INVEST) materials have promising photophysical properties for optoelectronic applications due to an inversion of their lowest singlet (S1) and triplet (T1) excited states. This results in an exothermic reverse intersystem crossing (rISC) process that potentially enhances triplet harvesting, compared to thermally activated delayed fluorescence (TADF) emitters with endothermic rISCs. However, the processes and phenomena that facilitate conversion between excited states for INVEST materials are underexplored. We investigate the complex potential energy surfaces (PESs) of the excited states of three heavily studied azaphenalene INVEST compounds, namely cyclazine, pentazine and heptazine using two state-of-the-art computational methodologies, namely RMS-CASPT2 and SCS-ADC(2) methods. Our findings suggest that ISC and rISC processes take place directly between the S1 and T1 electronic states in all three compounds through a minimum-energy crossing point (MECP) with an activation energy barrier between 0.11 to 0.58 eV above the S1 state for ISC and between 0.06 to 0.36 eV above the T1 state for rISC. We predict that higher-lying triplet states are not populated, since the crossing point structures to these states are not energetically accessible. Furthermore, the conical intersection (CI) between the ground and S1 states are high in energy for all compounds (between 0.4 to 2.0 eV) which makes nonradiative decay back to the ground state a relatively slow process. We demonstrate that the spin-orbit coupling (SOC) driving the S1-T1 conversion is enhanced by vibronic coupling with higher-lying singlet and triplet states possessing vibrational modes of proper symmetry. We also rationalize that the experimentally-observed anti-Kasha emission of cyclazine is due to the energetically inaccessible CI between the bright S2 and the dark S1 states, hindering internal conversion. Finally, we show that SCS-ADC(2) is able to qualitatively reproduce excited state features, but consistently overpredict relative energies of excited state structural minima compared to RMS-CASPT2. The identification of these excited state features elaborates design rules for new INVEST emitters with improved emission quantum yields. | Danillo Valverde; Cher Tian Ser; Gaetano Ricci; Kjell Jorner; Robert Pollice; Alan Aspuru-Guzik; Yoann Olivier | Theoretical and Computational Chemistry; Materials Science; Dyes and Chromophores; Optical Materials; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f29f789138d231616dede2/original/computational-investigations-of-the-detailed-mechanism-of-reverse-intersystem-crossing-in-inverted-singlet-triplet-gap-molecules.pdf |
6797cc236dde43c9089b2b71 | 10.26434/chemrxiv-2025-r2h91 | Ultrafast Solvent Migration in an Iron Complex Revealed by Nonadiabatic Dynamics Simulations | The response of a solvation shell to molecular solute photoexcitation is an ubiquitous phenomenon of great relevance in chemistry. This response can occur within just few tens of femtoseconds, making it very challenging to resolve experimentally. Thus, elucidating the homogeneity of the response around a solute, the presence of coherent solvent fluctuations, hydrogen bond reorganization mechanisms, and the intricate interplay between electronic, spin, nuclear, and solvent dynamics in detail remains elusive. Here, we report large-scale nonadiabatic molecular dynamics simulations of [Fe(CN)4(bipy)]2− (bipy=2,2’-bipyridine) in water, where the electronic evolution from singlet metal-to-ligand charge transfer (MLCT) states to triplet MLCT and metal-centered (MC) states overlaps temporally with the molecule’s nuclear motion and a strong solvent shell response. We leverage vibronic coupling model potentials combined with electrostatic embedding, within our so-called vibronic coupling/molecular mechanics (VC/MM) method, to be able to compute several thousand nonadiabatic excited-state trajectories, including all relevant singlet and triplet states as well as over 5000 explicit water molecules. This superior statistics affords an unprecedented view on the three-dimensional solvent distribution dynamics at few-fs and sub-Å resolution. The results reveal a direct solvent migration mechanism, where excitation to the MLCT states leads to the breaking of hydrogen bonds to the cyanide ligands within less than 100 fs, followed by the formation of hydrogen bonds with the negatively charged bipyridyl ligand by the same water molecules. Furthermore, the MLCT and MC states show very distinct solvent responses, which are overlapping in time, as governed by the electronic dynamics. | Severin Polonius; Leticia González; Sebastian Mai | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Photochemistry (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2025-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6797cc236dde43c9089b2b71/original/ultrafast-solvent-migration-in-an-iron-complex-revealed-by-nonadiabatic-dynamics-simulations.pdf |
60c73dd0567dfe070eec36c9 | 10.26434/chemrxiv.6097688.v1 | A Photoactivatable α5β1-Specific Integrin Ligand | In order to study how dynamic changes of α5β1 integrin engagement affect cellular behaviour, photoactivatable derivatives of α5β1 specific ligands are presented in this article. The presence of the photoremovable protecting group (PRPG) introduced at a relevant position for integrin recognition, temporally inhibits ligand bioactivity. Light exposure at cell-compatible dose efficiently cleaves the PRPG and restores functionality. Selective cell response (attachment, spreading, migration) to the activated ligand on the surface is achieved upon controlled exposure. Spatial and temporal control of the cellular response is demonstrated, including the possibility to in situ activation. Photoactivatable integrin-selective ligands in model microenvironments will allow the study of cellular behavior in response to changes in the activation of individual integrins as consequence of dynamic variations of matrix composition. | Roshna Vakkeel; Aleeza Farrukh; Aranzazu del Campo | Bioorganic Chemistry; Photochemistry (Org.); Biocompatible Materials; Cell and Molecular Biology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2018-04-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dd0567dfe070eec36c9/original/a-photoactivatable-5-1-specific-integrin-ligand.pdf |
659622489138d2316125d14c | 10.26434/chemrxiv-2024-lxk6x | Performance of density functionals for excited-state properties of isolated chromophores and exciplexes: Emission spectra, solvatochromic shifts, and charge-transfer character | This study assesses the performance of various meta-generalized gradient approximation (meta-GGA), global hybrid, and range-separated hybrid (RSH) density functionals in capturing excited-state properties of organic chromophores and their excited-state complexes (exciplexes). Motivated by their uses in solar energy harvesting and photoredox CO2 reduction, we use oligo-(p-phenylenes) and their excited-state complexes with triethylamine as model systems. We focus on the fluorescence properties of these systems, specifically emission energies, solvatochromic shifts, and wavefunction characteristics. The latter is described using reduced quantities such as natural transition orbitals (NTOs) and exciton descriptors. The functionals are benchmarked against the experimental fluorescence spectra and the equation-of-motion coupled-cluster method with single and double excitations (EOM-CCSD). The results show that, both in isolated chromophores and in exciplexes, meta-GGA functionals drastically underestimate the emission energies, and exhibit significant exciton delocalization and anti-correlation between electron and hole pair. The performance of global hybrid functionals depends strongly on the percentage of exact exchange. RSH GGAs are the best-performing functionals identified in our study, with ωPBE demonstrating the best agreement with experimental results. RSH meta-GGAs often overestimate emission energies in exciplexes and yield larger hole NTOs. Their performance can be improved by optimally tuning the range-separation parameter. | Abhilash Patra; George Baffour Pipim; Anna I. Krylov; Shaama Mallikarjun Sharada | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/659622489138d2316125d14c/original/performance-of-density-functionals-for-excited-state-properties-of-isolated-chromophores-and-exciplexes-emission-spectra-solvatochromic-shifts-and-charge-transfer-character.pdf |
60c753fdbb8c1a04683dc153 | 10.26434/chemrxiv.12678404.v2 | Stabilization of Supramolecular Membrane Protein-Lipid Bilayer Assemblies Through Immobilization in a Crystalline Exoskeleton | <div>
<div>
<div><div><div><p>Artificial native-like lipid bilayer systems constructed from phospholipids assembling into unilamellar liposomes allow the reconstitution of detergent-solubilized transmembrane proteins into supramolecular lipid-protein assemblies called proteoliposomes, which mimic cellular membranes. Stabilization of these complexes remains challenging because of their chemical composition, the hydrophobicity and structural instability of membrane proteins, and the lability of interactions between protein, detergent, and lipids within micelles and lipid bilayers. In this work we demonstrate that metastable lipid, protein-detergent, and protein-lipid supramolecular complexes can be successfully generated and immobilized within zeolitic-imidazole framework (ZIF) to enhance their stability against chemical and physical stressors. Upon immobilization in ZIF bio-composites, blank liposomes, and model transmembrane metal transporters in detergent micelles or embedded in proteoliposomes resist elevated temperatures, exposure to chemical denaturants, aging, and mechanical stresses. Extensive morphological and functional charac- terization of the assemblies upon exfoliation reveal that all these complexes encapsulated within the framework maintain their native morphology, structure, and activity, which is otherwise lost rapidly without immobilization.</p></div></div></div>
</div>
</div> | Fabian C. Herbert; Sameera Abeyrathna; Nisansala Abeyrathna; Yalini Wijesundara; Olivia Brohlin; Francesco Carraro; Heinz Amenitsch; paolo falcaro; Michael A. Luzuriaga; Alejandra Durand-Silva; Shashini D. Diwakara; Ronald A. Smaldone; Gabriele Meloni; Jeremiah J. Gassensmith | Nanofabrication; Nanostructured Materials - Nanoscience; Biochemistry; Bioengineering and Biotechnology | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753fdbb8c1a04683dc153/original/stabilization-of-supramolecular-membrane-protein-lipid-bilayer-assemblies-through-immobilization-in-a-crystalline-exoskeleton.pdf |
60c7480cee301cb3f3c797f1 | 10.26434/chemrxiv.11848968.v1 | Reversible Iodine Intercalation into Tungsten Ditelluride | The new compound WTe2I was prepared by a reaction of WTe2 with iodine in a fused silica vessel at temperatures between 40 and 200 °C. Iodine atoms are intercalated into the van der Waals gap between tungsten ditelluride layers. As a result, the WTe2 layer separation and therefore the c-axis length is significantly increased, and the orthorhombic space group is preserved. Iodine atoms form planar layers between each tungsten ditelluride layer. Due to oxidation by iodine the semi-metallic nature of WTe2 is changed, as shown by comparative band structure calculations for WTe2 and WTe2I based on density functional theory. The calculated phonon band structure of WTe2I suggests a charge density wave instability at low temperature.<br /> | Patrick Schmidt; Philipp Schneiderhan; Markus Ströbele; Carl P. Romao; H.-Jürgen Meyer | Reaction (Inorg.); Solid State Chemistry; Theory - Inorganic; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7480cee301cb3f3c797f1/original/reversible-iodine-intercalation-into-tungsten-ditelluride.pdf |
667d75625101a2ffa8a64edf | 10.26434/chemrxiv-2024-198l5 | Ambient Cationic Ring-opening Polymerization of Dibenzo[c,e]oxepine-5(7H)-thione (DOT): Thermal and Nucleophile-initiated Depolymerization | With rising concern over plastic waste accumulation worldwide, the quantitative depolymerization of polymers into small molecule building blocks offers avenues toward a circular polymer economy. But a tuning of the polymer stability versus degradation efficiency remains challenging. Herein, the thionolactone dibenzo[c,e]oxepine-5(7H)-thione (DOT) is shown to undergo cationic ring-opening polymerization (CROP) under ambient conditions without the need for inert atmosphere or dry solvents. Involving S–O isomerization, the polymerization gave polythioesters in near-quantitative conversions with tuneable SEC-measured molar masses from 1.3–50 kg/mol and dispersities between 1.5–2.0. The polythioesters could be degraded with an excess of amine, with substoichiometric amounts of thiolate (which was shown to involve depolymerization from a thiolate ω-end group), or thermally. The latter two conditions produced the thiolactone dibenzo[c,e]thiepine-5(7H)-one (DTO). While anionic ring-opening polymerization (the common route to polythioesters) gives thiol end groups, the CROP presented herein provided end-capped polymers. Interestingly, the choice of initiator (and resulting end cap) was shown to have a drastic influence on the thermal stability. While a boron trifluoride-initiated polymer showed only 6% decomposition when heated to 140 °C without solvent, a comparable methyl triflate-initiated polymer underwent 35% degradation to DTO when heated to the same temperature overnight. | Swarnali Neogi; Qamar un Nisa; Rohani Abu Bakar; Nathaniel Bingham; Peter Roth | Polymer Science; Polymerization (Polymers); Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-06-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667d75625101a2ffa8a64edf/original/ambient-cationic-ring-opening-polymerization-of-dibenzo-c-e-oxepine-5-7h-thione-dot-thermal-and-nucleophile-initiated-depolymerization.pdf |
60c74f2e567dfeeecfec563b | 10.26434/chemrxiv.12847499.v1 | The Virtual Circular Genome Model for Primordial RNA Replication | Our manuscript describes a hypothesis for the replication of primordial RNA genomes by entirely nonenzymatic processes. Our proposal circumvents long standing problems such as the difficulty of copying long templates by nonenzymatic chemistry, the need for defined primers, and the so-called ‘last base addition problem’. Our hypothesis leads to surprising predictions, notably that the replication of an ensemble of oligonucleotides could be mediated by the template-directed extension of all oligos by as little as one nucleotide, on average. We propose experimental tests of our model, and discuss its implications for the origin of life. | Lijun Zhou; Dian Ding; Jack Szostak | Biochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f2e567dfeeecfec563b/original/the-virtual-circular-genome-model-for-primordial-rna-replication.pdf |
62fa6148e1594bfdfdd11f05 | 10.26434/chemrxiv-2022-9f544 | Heteroatom-Doped [4]Triangulene: Facile Synthesis and Two-Dimensional On-Surface Self-Assemblies | Synthesis of nanographenes (NGs) with structural precision has attracted enormous interest in organic chemistry and materials science. However, their ordered two-dimensional (2D) self-assembled structures on surfaces, which are of great importance for the future nanotechnologies, remain challenging. In this work, embedding heteroatoms (oxygen-boron-oxygen) into the zigzag edges of NGs is proven as a useful strategy to afford ordered 2D self-assemblies based upon intermolecular hydrogen bonding. We have thus synthesized OBO-doped [4]triangulenes, whose planar geometry is revealed by single-crystal X-ray diffraction. Their photophysical and electrochemical properties show significant differences from those of pristine [4]triangulene. Self-assembly on metal surfaces is explored by scanning tunneling microscopy (STM) associated with the minimum spanning tree (MST) analysis. Highly ordered 2D superstructures can be demonstrated and the packing modes depend sensitively upon the substrate. | Cheng Chen; Jiayi Lu; Yang Lv; Yuyi Yan; Qiang Sun; Akimitsu Narita; Klaus Müllen; Xiao-Ye Wang | Physical Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Self-Assembly; Surface; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62fa6148e1594bfdfdd11f05/original/heteroatom-doped-4-triangulene-facile-synthesis-and-two-dimensional-on-surface-self-assemblies.pdf |
60c7555dbb8c1a1cb43dc3c5 | 10.26434/chemrxiv.14095639.v1 | Exploration of Steam Explosion Treatment for the Recovery of Phenolic Compounds | <p>Steam explosion (SE) is a versatile tool for the pretreatment of lignocellulosic plant 27 materials and the further separation of their main constitutive components, <i>i.e. </i>cellulose, 28 hemicellulose, lignin, etc. In this study, we propose to evaluate the effects of SE 29 treatment on the recovery of secondary metabolites. As a case study, the well-known 30 grape pomace phenolic compounds were considered. Our results demonstrate that the 31 efficiency of the steam explosion in term of yield (900 mg polyphenols per kg of dry 32 grape pomace) was relatively similar to conventional maceration methods in alcoholic 33 media (800 mg/kg). Advantages of SE compared to maceration were highlighted: the 34 process is organic solvent free, destabilize the biomass structure and release insoluble 35 bound phenolic compounds. In addition, it offers the possibility to modulate distinct 36 polyphenols profiles by modifying the process conditions. </p> | Thomas Berchem; Quentin Schmetz; Thibaut Istasse; Nicolas Jacquet; Eric Haubruge; Aurore Richel | Food | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7555dbb8c1a1cb43dc3c5/original/exploration-of-steam-explosion-treatment-for-the-recovery-of-phenolic-compounds.pdf |
60dd4ef46b8d894a0c6a9a73 | 10.26434/chemrxiv-2021-87m9w | Simultaneous monitoring of monoclonal antibody variants by strong cation-exchange chromatography hyphenated to mass spectrometry to assess biosimilar-ity of rituximab-based biotherapeutics | The increasing importance of biosimilars in the biopharmaceutical market leads to high demands for enhanced protein characterization methods. Different manufacturing processes can lead to a significant variability of biotherapeutics arising from chemical and enzymatic post translational modifications (PTMs), resulting in the co-existence of a plethora of proteoforms with different physicochemical properties. Thus, biosimilarity to the originator product must be proven rigorously. Among these PTMs, N-terminal pyroglutamate formation, C-terminal lysine clipping, glycosylation, glycation, and deamidation lead to differences in the net charge of the protein, resulting in charge variants (CV). To unravel the heterogeneity of these proteoforms, Strong Cat-ion eXchange (SCX) High-Performance Liquid Chromatography (HPLC) is routinely used. However, the use of non-volatile salts makes the technique incompatible for hyphenation to mass spectrometry (MS). Recently, an approach employing volatile salts and a pH gradient was applied for CV analysis, opening the era of SCX-HPLC-MS approaches. Here, we apply an already established SCX-HPLC-MS approach by Füssl et al. to characterize two Rituximab-based biotherapeutics, the originator MabThera® and its Indian copy product Reditux™. The study assessed molecular differences between the two drug products and constitutes the basis for biosimilarity characterization using a fast SCX-HPLC-MS approach. | Fiammetta Di Marco; Thomas Berger; Wolfgang Esser-Skala; Erdmann Rapp; Christof Regl; Christian G. Huber | Analytical Chemistry; Biochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60dd4ef46b8d894a0c6a9a73/original/simultaneous-monitoring-of-monoclonal-antibody-variants-by-strong-cation-exchange-chromatography-hyphenated-to-mass-spectrometry-to-assess-biosimilar-ity-of-rituximab-based-biotherapeutics.pdf |
60c75240337d6c2da4e286cf | 10.26434/chemrxiv.13272980.v1 | The Role of Al3+-Based Aqueous Electrolytes in the Charge Storage Mechanism of MnOx Cathodes | <p>Rechargeable aqueous aluminium batteries
are the subject of growing interest, but the charge storage mechanisms at manganese
oxide-based cathodes remain poorly understood with as many mechanisms as
studies. Here, we use an original <i>in situ</i>
spectroelectrochemical methodology to unambiguously demonstrate that the reversible
proton-coupled MnO<sub>2</sub>-to-Mn<sup>2+</sup> conversion is the main charge
storage mechanism occurring at MnO<sub>2</sub> cathodes over a range of slightly
acidic Al<sup>3+</sup>-based aqueous electrolytes. In Zn/MnO<sub>2</sub> assemblies,
this mechanism is associated with high gravimetric capacity and discharge
potentials, up to 560 mAh·g<sup>-1</sup> and 1.76 V respectively, attractive
efficiencies (<i>CE</i> > 98.5 % and <i>EE</i> > 80%) and excellent cyclability (>
750 cycles at 10 A·g<sup>-1</sup>). Finally, we conducted a critical analysis of the
data previously published on MnO<sub>x</sub> cathodes in Al<sup>3+</sup>-based
aqueous electrolytes to conclude on a universal charge storage mechanism, <i>i.e.</i>, the reversible
electrodissolution/electrodeposition of MnO<sub>2</sub>.<i></i></p> | Véronique Balland; Mickaël Mateos; Kenneth D. Harris; Benoit Limoges | Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75240337d6c2da4e286cf/original/the-role-of-al3-based-aqueous-electrolytes-in-the-charge-storage-mechanism-of-mn-ox-cathodes.pdf |
60c744b1bb8c1a0c7d3da532 | 10.26434/chemrxiv.8850320.v2 | Protein Dynamics from Accurate Low-Field Site-Specific Longitudinal and Transverse Relaxation | <div><div><div><p>Nuclear magnetic relaxation provides invaluable quantitative site-specific information on the dynamics of complex systems. Determining dynamics on nanosecond timescales requires relaxation measurements at low magnetic fields, incompatible with high-resolution NMR. Here, we use a two-field NMR spectrometer to measure carbon-13 transverse and longitudinal relaxation rates at a field as low as 0.33 T (proton Larmor frequency 14 MHz) in specifically labeled sidechains of the protein ubiquitin. The use of radiofrequency pulses enhances the accuracy of measurements as compared to high-resolution relaxometry approaches, where the sample is moved in the stray field of the superconducting magnet. Importantly, we demonstrate that accurate measurements at a single low magnetic field provide enough information to characterize complex motions on low nanosecond timescales, which opens a new window for the determination of site- specific nanosecond motions in complex systems such as proteins.</p></div></div></div> | Pavel Kaderavek; Nicolas Bolik-Coulon; Samuel Cousin; Thorsten Marquardsen; Jean-Max Tyburn; Jean-Nicolas Dumez; Fabien Ferrage | Biophysical Chemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744b1bb8c1a0c7d3da532/original/protein-dynamics-from-accurate-low-field-site-specific-longitudinal-and-transverse-relaxation.pdf |
60c74c894c89195505ad3652 | 10.26434/chemrxiv.12497690.v1 | The Influence of Electronic Structure Modelling and Junction Structure on First-Principles Chiral Induced Spin Selectivity | <br />We have carried out a comprehensive study of the influence of electronic structure modeling and junction structure description on the first-principles calculation of the spin polarization in molecular junctions caused by the chiral induced spin selectivity (CISS) effect. We explore the limits and the sensitivity to modelling decisions of a Landauer / Green’s function / density functional theory approach to CISS. We find that although the CISS effect is entirely attributed in the literature to molecular spin filtering, spin-orbit coupling being partially inherited from the metal electrodes plays an important role in our calculations, even though this effect cannot explain the experi- mental conductance results. Also, an important dependence on the specific description of exchange interaction and spin–orbit coupling is manifest in our approach. This is important because the interplay between exchange effects and spin-orbit coupling may play an important role in the description of the junction magnetic response. Our calculations are relevant for the whole field of spin-polarized electron transport and electron transfer because there is still an open discussion in the literature about the detailed underlying mechanism and the magnitude of relevant physical parameters that need to be included to achieve a consistent description of the CISS effect<br /> | Martin Sebastian Zöllner; Vladimiro Mujica; Carmen Herrmann | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c894c89195505ad3652/original/the-influence-of-electronic-structure-modelling-and-junction-structure-on-first-principles-chiral-induced-spin-selectivity.pdf |
62137a327a054a3c5b151608 | 10.26434/chemrxiv-2022-536jc | Densified HKUST-1 Monoliths as a Route to High Volumetric and Gravimetric Hydrogen Storage Capacity | We are currently witnessing the dawn of the hydrogen (H2) economy, where H2 will become a primary fuel for heating, transportation, and long-distance and long-term energy storage. Among the diverse possibilities, H2 can be stored as a pressurized gas, cryogenic liquid, or solid fuel via adsorption onto porous materials. Metal-organic frameworks (MOFs) have emerged as the adsorbent materials with the theoretical highest H2 storage densities on both a volumetric and gravimetric basis. However, a critical bottleneck for the use of H2 as a transportation fuel has been the lack of densification methods capable of shaping MOFs into practical formulations whilst maintaining their adsorptive performance. Here, we report a high-throughput screening and deep analysis of a database of MOFs to find optimal materials, followed by the synthesis, characterisation, and performance evaluation of an optimal monolithic MOF (monoMOF) for H2 storage. After densification, this monoMOF stores 46 g L-1 H2 at 50 bar, 77 K, and delivers 41 and 42 g L-1 H2 at operating pressures of 25 and 50 bar, respectively, when deployed in a combined temperature–pressure (25-50 bar/77 K → 5 bar/160 K) swing gas delivery system. This performance represents up to an 80% reduction in the operating pressure requirements for delivering H2 gas when compared with benchmark materials, and an 83% reduction compared to compressed H2 gas. Our findings represent a substantial step forward in the application of high-density materials for volumetric H2 storage applications. | David Madden; Daniel O'Nolan; Nakul Rampal; Robin Babu; Ceren Camur; Ali Al Shakhs; Shi-Yuan Zhang; Graham Rance; Javier Perez; Nicola Casati; Carlos Cuadrado-Collados; Denis O'Sullivan; Nicholas Rice; Thomas Gennett; Philip Parilla; Sarah Shulda; Katherine Hurst; Vitalie Stavila; Mark Allendorf; Joaquin Silvestre-Albero; Alexander Forse; Neil Champness; Karena Chapman; David Fairen-Jimenez | Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-02-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62137a327a054a3c5b151608/original/densified-hkust-1-monoliths-as-a-route-to-high-volumetric-and-gravimetric-hydrogen-storage-capacity.pdf |
63f47bd41d2d184063da9344 | 10.26434/chemrxiv-2022-0w70n-v2 | Reflective microscopy for mechanistic insights in corrosion research | Reflective microscopy (RM) is a robust, label free optical imaging technique that allows fast operando measurements of structural changes on metal interfaces at nanoscale in a wide field. Based on the analysis of the reflected light, RM can be simply understood as “video camera” to produce optical photographs of studied interfaces and thus, it has been used for many years as a complementary tool for the visual inspection. However, recent developments in the optical models and refining the experimental design provided means for the quantitative conversion of reflected light intensities into the variations in roughness, thickness of surface films, chemical composition etc., all indispensable for the surface sciences. This review highlights recent advances and contemporary challenges in the methodological developments of RM specifically tailored for the corrosion research. | Viacheslav Shkirskiy; Frédéric Kanoufi | Physical Chemistry; Analytical Chemistry; Nanoscience; Imaging; Electrochemistry - Mechanisms, Theory & Study; Optics | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63f47bd41d2d184063da9344/original/reflective-microscopy-for-mechanistic-insights-in-corrosion-research.pdf |
60c755c50f50dbb68f397f96 | 10.26434/chemrxiv.14160968.v1 | Redox-neutral S-nitrosation Mediated by a Dicopper Center | An unprecedented redox-neutral <i>S</i>-nitrosation of thiol has been achieved at dicopper(I,I)
center. Treatment of dicopper (I,I) complex with excess NO<sup>•</sup> and
thiol generates a dicopper
(I,I) di-<i>S</i>-nitrosothiol complex [Cu<sup>I</sup>Cu<sup>I</sup>(RSNO)<sub>2</sub>]<sup>2+</sup> or
dicopper (I,I) mono-<i>S</i>-nitrosothiol complex [Cu<sup>I</sup>Cu<sup>I</sup>(RSNO)]<sup>2+</sup>, which readily
release RSNO in 88-94% yield. The <i>S</i>-nitrosation reaction proceeds
through a mixed-valence [Cu<sup>II</sup>Cu<sup>III</sup>(<i>m</i>-O)(<i>m</i>-NO)]<sup>2+</sup><i> </i>species, which deprotonates RS-H at the
basic <i>m</i>-O site and
nitrosates the RS<sup>-</sup> at the <i>m</i>-NO site.
The [Cu<sup>II</sup>Cu<sup>III</sup>(<i>m</i>-O)(<i>m</i>-NO)]<sup>2+</sup>
complex is also competent for <i>O</i>-nitrosation of MeOH, which is isoelectronic
to thiol. In this case, a rare [Cu<sup>II</sup>Cu<sup>II</sup>(<i>m</i>-NO)(OMe)]<sup>2+</sup> intermediate has been
isolated and fully characterized, suggesting the <i>S</i>-nitrosation proceeds
through the intermediary of analogous [Cu<sup>II</sup>Cu<sup>II</sup>(<i>m</i>-NO)(SR)]<sup>2+</sup> species. The redox- and
proton-neutral <i>S-</i>nitrosation process reported here represents the first
functional model of ceruloplasmin in mediating <i>S</i>-nitrosation of external
thiols, adding further implications for biological copper sites in the
interconversion of NO<sup>•</sup>/RSNO. | Wenjie Tao; Curtis Moore; Shiyu Zhang | Bioinorganic Chemistry; Coordination Chemistry (Inorg.); Organometallic Compounds; Small Molecule Activation (Inorg.); Spectroscopy (Inorg.); Transition Metal Complexes (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755c50f50dbb68f397f96/original/redox-neutral-s-nitrosation-mediated-by-a-dicopper-center.pdf |
625d4534742e9fe205623028 | 10.26434/chemrxiv-2022-w89tc | Virtual reality sampled pathways guide free energy calculation of protein-ligand binding | We describe a novel two-step approach for combining cloud-mounted interactive molecular dynamics in virtual reality (iMD-VR) with free energy sampling (FES) approaches to quantitatively explore the dynamics of biological processes at the molecular level. The combined approach we refer to as the iMD-VR-FES protocol. Stage one involves using a state-of-the-art iMD-VR framework to quickly sample a diverse range of protein-ligand unbinding pathways, benefitting from the sophistication of human spatial and chemical intuition. Stage two involves using the iMD-VR-sampled pathways as initial guesses for defining a path-based reaction coordinate from which we can obtain a corresponding free energy profile using FES methods. To investigate the performance of the method, we apply iMR-VR-FES to investigate the unbinding of a benzamidine ligand from a trypsin protein. Unbinding free energies calculated using iMD-VR-FES show good internal consistency, and broadly agree with previous literature values. Moreover, the resulting free energy profiles can distinguish energetic differences corresponding to various protein-ligand conformations (e.g., helping to identifying favorable vs. unfavorable pathways) and also enable identification of metastable states along the unbinding pathways. The two-step iMD-VR-FES approach offers an intuitive way for researchers to test various hypotheses of dynamical and conformational change, in order to quickly obtain both qualitative and quantitative insight. | Helen Deeks; Kirill Zinovjev; Jonathan Barnoud; Adrian Mulholland; Marc van der Kamp; David Glowacki | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Computational Chemistry and Modeling; Theory - Computational | CC BY NC 4.0 | CHEMRXIV | 2022-04-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/625d4534742e9fe205623028/original/virtual-reality-sampled-pathways-guide-free-energy-calculation-of-protein-ligand-binding.pdf |
60c73dd4702a9b9c9b189c4f | 10.26434/chemrxiv.6159335.v1 | Catalytic Asymmetric Synthesis of Geminal-Dicarboxylates | <p>Stereogenic acetals, spiroacetals and ketals are well-studied stereochemical features that bear two heteroatoms at a common carbon atom. These stereocenters are normally found in cyclic structures while linear (or acyclic) analogues bearing two heteroatoms are rare. Chiral geminal-dicarboxylates are illustrative, there is no current way to access this class of compounds while controlling the stereochemistry at the carbon center bound to two oxygen atoms. Here we report a rhodium-catalyzed asymmetric carboxylation of ester-containing allylic bromides to form stereogenic carbon centers bearing two different carboxylates with high yields and enantioselectivities. The products, which are surprisingly stable to a variety of acidic and basic conditions, can be manipulated with no loss of enantiomeric purity as demonstrated be ring closing metathesis reactions to form chiral lactones, which have been extensively used as building blocks in asymmetric synthesis.<br /></p> | Nisha Mistry; Stephen P. Fletcher | Organic Synthesis and Reactions; Acid Catalysis; Base Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2018-04-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dd4702a9b9c9b189c4f/original/catalytic-asymmetric-synthesis-of-geminal-dicarboxylates.pdf |
6541c7cfc573f893f18c703e | 10.26434/chemrxiv-2023-vp6ns-v3 | Consistent Density Functional Theory-Based Description of Ion Hydration Through Density-Corrected Many-Body Representations | Delocalization error constrains the accuracy of density functional theory (DFT) in describing molecular interactions in ion–water systems. Using Na+ and Cl− in water as model systems, we calculate the effects of delocalization error in the SCAN functional for describing ion–water and water–water interactions in hydrated ions, and demonstrate that density-corrected SCAN (DC-SCAN) predicts n-body and interaction energies with an accuracy approaching coupled cluster theory. The performance of DC-SCAN is size-consistent, maintaining an accurate description of molecular in- teractions well beyond the first solvation shell. Molecular dynamics simulations at ambient conditions with MB-SCAN(DC) potentials, derived from the many-body expansion, predict the solvation structure of Na+ and Cl− in quantitative agreement with reference data, while simultaneously reproducing the structure of liquid water. Beyond rationalizing the accuracy of density-corrected models of ion hydration, our findings suggest that our unified density-corrected many-body formalism holds great promise for efficient DFT-based simulations of condensed-phase systems with chemical accuracy. | Etienne Palos; Alessandro Caruso; Francesco Paesani | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Computational Chemistry and Modeling; Theory - Computational; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6541c7cfc573f893f18c703e/original/consistent-density-functional-theory-based-description-of-ion-hydration-through-density-corrected-many-body-representations.pdf |
61510f3ba7b249ff5e3a39f2 | 10.26434/chemrxiv-2021-fgnrk-v2 | Speeding up quantum dissipative dynamics of open systems with kernel methods | The future forecasting ability of machine learning (ML) makes ML a promising tool for predicting long-time quantum dissipative dynamics of open systems. In this Article, we employ nonparametric machine learning algorithm (kernel ridge regression as a representative of the kernel methods) to study the quantum dissipative dynamics of the widely-used spin-boson model. Our ML model takes short-time dynamics as an input and is used for fast propagation of the long-time dynamics, greatly reducing the computational effort in comparison with the traditional approaches. Presented results show that the ML model performs well in both symmetric and asymmetric spin-boson models. Our approach is not limited to spin-boson model and can be extended to complex systems. | Arif Ullah; Pavlo O. Dral | Theoretical and Computational Chemistry; Theory - Computational; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61510f3ba7b249ff5e3a39f2/original/speeding-up-quantum-dissipative-dynamics-of-open-systems-with-kernel-methods.pdf |
65626beb29a13c4d47fc685a | 10.26434/chemrxiv-2023-w1ngh | Molecular Origin of Novichok Nerve Agents | Nerve gasses have a devastating effect on the human body through their inhibition of the acetylcholinesterase enzyme, a crucial part of muscle control. In this review, we focus on the molecular aspects of the infamous Novichok nerve gasses. In addition to briefly outlining their development history, we place a lot of attention for the mode of action of these poisons. Secondary effects, medical treatment and legal aspects are also briefly reviewed. This document stands out from other reviews in this field by placing a focus on the (dynamic) properties of acetylcholinesterase, and by studying novichok as a carrier of a covalent warhead. In addition, by making use of recent crystal structures, the non-covalent binding aspects of novichok are described for the first time. | Jonas Verhellen | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2023-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65626beb29a13c4d47fc685a/original/molecular-origin-of-novichok-nerve-agents.pdf |
60f79168393cc90b294de63e | 10.26434/chemrxiv-2021-8blf6 | Reduction of Sulfur Dioxide to Sulfur Monoxide by Ferrous Porphyrin | Reduction of SO¬2 to fixed forms of sulfur can address the growing concerns regarding its detrimental effect on health and environment as well as enable its valorization into valuable chemicals. While the coordination of SO2 to transition metals are documented, its reduction using molecular catalysts has remained elusive. Alternatively, the naturally occurring heme en-zyme sulfite reductase is known to reduce SO2 to H2S and is an integral part of the global sulfur cycle. However, its action is not yet mimicked in artificial systems outside of the protein matrix even after several decades of its structural elucidation. Here reduction of SO2 by iron (II) porphyrin, a synthetic analogue of heme, is demonstrated. A combination of spectroscop-ic and analytical methods indicates that SO2 is reduced by 2e-/2H+ by FeIITPP to form an intermediate [FeIII-SO]+ species which releases SO. The SO obtained from the chemical reduction of SO2 could be valorized in the form of a Diels-Alder ad-duct of butadiene resulting in an organic sulfoxide. | Aishik Bhattacharya; Arnab Nath; Arnab Ghatak; Abhijit Nayek; Rajat Saha; Somdatta Dey; Abhishek Dey | Inorganic Chemistry; Catalysis; Kinetics and Mechanism - Inorganic Reactions; Reaction (Inorg.); Spectroscopy (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f79168393cc90b294de63e/original/reduction-of-sulfur-dioxide-to-sulfur-monoxide-by-ferrous-porphyrin.pdf |
60c74e8fbb8c1a76ff3db778 | 10.26434/chemrxiv.12771254.v1 | Kekulene: On-Surface Synthesis, Orbital Structure, and Aromatic Stabilization | We revisit the question of kekulene’s aromaticity by focusing on the electronic structure of its frontier orbitals as determined by angle-resolved photoemission spectroscopy. To this end, we have developed a specially designed precursor, 1,4,7(2,7)-triphenanthrenacyclononaphane-2,5,8-triene, which allows us to prepare sufficient quantities of kekulene of high purity directly on a Cu(111) surface, as confirmed by scanning tunneling microscopy. Supported by density functional calculations, we determine the orbital structure of kekulene’s highest occupied molecular orbital by photoelectron tomography. In agreement with a recent aromaticity assessment of kekulene based solely on C–C bond lengths, we conclude that the π-conjugation of kekulene is better described by the Clar model rather than a superaromatic model. Thus, by exploiting the capabilities of photoemission tomography, we shed light on the question which consequences aromaticity holds for the frontier electronic structure of a π-conjugated molecule.<br /> | Anja Haags; Alexander Reichmann; Qitang Fan; Larissa Egger; Hans Kirschner; Tim Naumann; Simon Werner; Tobias Vollgraff; Jörg Sundermeyer; Lukas Eschmann; Xiaosheng Yang; Dominik Brandstetter; François C. Bocquet; Georg Koller; Alexander Gottwald; Mathias Richter; Michael G. Ramsey; Michael Rohlfing; Peter Puschnig; Michael Gottfried; Serguei Soubatch; F. Stefan Tautz | Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e8fbb8c1a76ff3db778/original/kekulene-on-surface-synthesis-orbital-structure-and-aromatic-stabilization.pdf |
60c7436dbdbb894d87a38642 | 10.26434/chemrxiv.9125201.v1 | Sortase-Modified Cholera Toxoids Show Specific Golgi Localization | Cholera toxoid is an established tool for use in cellular tracing in neuroscience and cell biology. We use a sortase-labelling approach to generate site-specifically <i>N</i>-terminally modified variants of both the A2-B<sub>5</sub> heterohexamer and B<sub>5</sub> pentamer forms of the toxoid. Both forms of the toxoid are endocytosed by GM1-positive mammalian cells, and while the heterohexameric toxoid was principally localized in the ER, the B<sub>5</sub> pentamer showed an unexpected localization in the <i>medial/trans</i> Golgi. This study suggests a future role for specifically-labelled cholera toxoids in live-cell imaging beyond their current applications in neuronal tracing and labelling of lipid-rafts in fixed cells. | Darren Machin; Daniel Williamson; Peter Fisher; victoria miller; Gemma Wildsmith; James Ross; Christopher Wasson; Andrew MacDonald; Benjamin I. Andrews; Daniel Ungar; W. Bruce Turnbull; Michael Webb | Cell and Molecular Biology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7436dbdbb894d87a38642/original/sortase-modified-cholera-toxoids-show-specific-golgi-localization.pdf |
60c75388bdbb89541aa3a48b | 10.26434/chemrxiv.13347353.v1 | Augmenting Photosynthesis through Facile AIEgen-Chloroplast Conjugation and Efficient Solar Energy Utilization | <p>Photosynthesis is regarded as the foundation for sustaining planet living, and light-harvesting is the initial step of
photosystems and activates the subsequent photochemical reactions. However, the
incomplete match between the solar radiation spectrum and absorption profile of
chloroplasts limited the full absorption and utilization of sunlight by the
photosynthetic pigments. Here, we designed two new aggregation-induced emission
(AIE)-active molecules with activated alkyl groups (TPE-PPO and TPA-TPO), and
realized the substantial manipulation of live chloroplasts via facile metal-free
“Click” reaction. Owing to the matched photophysical properties, the AIE
luminogens (AIEgens) could harvest harmful ultraviolet radiation (HUVR) and
photosynthetically inefficient radiation (PIR), and further convert them into
photosynthetically active radiation (PAR) for chloroplasts absorption. As a
result, the AIEgen-chloroplasts bioconjugation exhibited better capability of
water splitting and election separation for adenosine triphosphate (ATP)
generation, which are important processes in photosynthesis. This is the first
AIEgen-based conjugation strategy reported for improving solar-energy
utilization and augmenting photosynthetic efficiency.<b></b></p> | Haotian Bai; Haixiang Liu; Xu Chen; Rong Hu; MENG LI; Wei He; jian du; Anjun Qin; Jacky W. Y. Lam; Zhiyang Liu; Ryan Tsz Kin Kwok; Ben Zhong Tang | Biological Materials; Optical Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75388bdbb89541aa3a48b/original/augmenting-photosynthesis-through-facile-ai-egen-chloroplast-conjugation-and-efficient-solar-energy-utilization.pdf |
6404ef6b63e8d44e596c3b8e | 10.26434/chemrxiv-2023-6hsh2 | Structural characterisation of α-synuclein-membrane interactions and the resulting aggregation using small angle scattering | The presence of amyloid fibrils is a hallmark of several neurodegenerative diseases. Some amyloidogenic proteins, such as α-synuclein and amyloid β, can interact with lipids, and this interaction can strongly favor the formation of amyloid fibrils. In particular the primary nucleation step, i.e. the de novo formation of amyloid fibrils, has been shown to be accelerated by lipids. However, the exact mechanism of this acceleration is still mostly unclear. Here we use a range of scattering methods, such as dynamic light scattering (DLS) and small angle X-ray and neutron scattering (SAXS and SANS) to obtain structural information on the binding of α-synuclein to vesicles formed from negatively charged lipids and their co-assembly into amyloid fibrils. We find that the lipid vesicles do not simply act as a surface that catalyses the nucleation reaction, but that lipid molecules take an active role in the reaction. The binding of α-synuclein to the lipid vesicles immediately induces a major structural change in the lipid assembly, which leads to a break-up into small, cylindrical and disc-like lipid-protein
particles. This transition can be largely reversed by temperature changes or proteolytic protein removal. Incubation of these small, cylindrical and disc-like lipid-α-synuclein particles for several hours, however, yields amyloid fibril formation, whereby the lipids are incorporated into the fibrils. | Celine Galvagnion; Abigail Barclay; Katarzyna Makasewicz; Frederik Ravnkilde Marlet; Martine Moulin; Juliette Devos; Sara Linse; Anne Martel; Lionel Porcar; Emma Sparr; Martin Cramer Pedersen; Felix Roosen-Runge; Lise Arleth; Alexander Kai Büll | Physical Chemistry; Biophysical Chemistry; Physical and Chemical Properties; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6404ef6b63e8d44e596c3b8e/original/structural-characterisation-of-synuclein-membrane-interactions-and-the-resulting-aggregation-using-small-angle-scattering.pdf |
60c73dd49abda24819f8b7a8 | 10.26434/chemrxiv.6152435.v1 | Boosting the Performance of Iron-Phthalocyanine as Cathode Electrocatalyst for Alkaline Polymer Fuel Cells Through Edge-Closed Conjugation | One-pot
microwave conjugation results in a polymerized iron-phthalocyanine (pFePc) which
exhibits extremely high ORR performance,, showing
activity much better than that of the FePc monomer and 20 wt % Pt/C, and similar
to that of the 60 wt % Pt/C under the same catalyst loading. Furthermore, we proposed an edge-closing strategy to significantly
enhance the stability of the pFePc
catalyst in alkaline media by eliminating the edge anhydride groups. Using the edge-closed pFePc as cathode catalyst in APFC,
a power density as high as 452 mW∙cm<sup>-2</sup> is achieved, which is among
the best performance of non-noble metal catalyst-based APFCs so far reported. | Heyou Zhang; Shiming Zhang; Ying Wang; Jiaojiao Si; Yingting Chen; Lin Zhuang; Shengli Chen | Fuels - Materials; Theory - Computational; Fuel Cells | CC BY NC ND 4.0 | CHEMRXIV | 2018-04-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dd49abda24819f8b7a8/original/boosting-the-performance-of-iron-phthalocyanine-as-cathode-electrocatalyst-for-alkaline-polymer-fuel-cells-through-edge-closed-conjugation.pdf |
60c74b17337d6c67dae27a12 | 10.26434/chemrxiv.12283967.v1 | Revealing the Molecular Mechanisms of Proteolysis of SARS-CoV-2 Mpro from QM/MM Computational Methods. | SARS-CoV-2 M<sup>pro</sup> is one of the enzymes essential for the replication process of the virus responsible of the COVID-19 pandemic. This work is focused on exploring its proteolysis reaction by means of QM/MM methods. The resulting free energy landscape of the process provides valuable information on the species appearing along the reaction path and suggests that the mechanism of action of this enzyme, taking place in four steps, slightly differs from other cysteine proteases. Our predictions, supported by the agreement with some recently published experimental data, can be used to guide the design of COVID-19 antiviral compounds with clinical potential. | Katarzyna Swiderek; Vicent Moliner | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b17337d6c67dae27a12/original/revealing-the-molecular-mechanisms-of-proteolysis-of-sars-co-v-2-mpro-from-qm-mm-computational-methods.pdf |
637b92493551190cc33b635f | 10.26434/chemrxiv-2022-4kzp1 | Data-driven Reaction Template Fingerprints | Chemical reactions can be classified into distinct categories that encapsulate concepts for how one molecule is transformed into another. One can encode these concepts in rules specifying the set of atoms and bonds that change during a transformation, which is commonly known as a reaction template. While there exist multiple possibilities to represent a chemical reaction in a vector representation, or fingerprint, this is not the case for reaction templates. As a consequence, methods to navigate the space of reaction templates are limited. In this work, we introduce the first reaction template fingerprint. To this end, we follow a data-driven approach relying on a masked language modelling task on SMIRKS strings. We combine unsupervised pre-training with fine-tuning on the classification of templates according to the RXNO ontology, for which we achieve up to 98.4% classification accuracy. We highlight how the learned embeddings can be extracted and used in downstream applications. | Anubhab Chakraborty; Amol Thakkar; Alain C. Vaucher; Teodoro Laino | Theoretical and Computational Chemistry; Organic Chemistry; Materials Science; Organic Synthesis and Reactions; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/637b92493551190cc33b635f/original/data-driven-reaction-template-fingerprints.pdf |
6781597181d2151a029cfe02 | 10.26434/chemrxiv-2025-pvdm9 | Progress in flow-battery shunt current investigations:
a species-resolved foundational approach | Shunt currents are elusive effects occurring in stacks of flow batteries which received partial attention despite being a major cause of internal losses, directly affecting efficiency and operability. Existing studies model them with electric networks of resistors. For the first time, this paper presents a foundational analysis of the charge carriers moving in the fluid electrolytes due to the electric potential differences among homologous electrodes. Taking the vanadium chemistry as a study case, the conductive, diffusive and convective motions of ions V2+, V3+, VO2+, VO2+, H+, HSO4–, SO42– were analyzed with Navier-Stokes, Nernst-Planck and conservation equations. 3D and 2D numerical implementations allowed analyzing both steady state and transient conditions. Shunt current contributions were computed in stacks of different size and under different load, revealing that power losses ranged from 0.17% in a 5-cell stack to 6.9% in a 40-cell stack, being higher at lower load currents. The methodology allows identifies the primary factors affecting shunt currents, such as membrane permeability, electrode porosity, and flow channel design. These results shed light on the strategies to mitigate shunt currents in order to improve efficiency. | Davide Bordignon; Massimo Guarnieri | Theoretical and Computational Chemistry; Energy; Chemical Engineering and Industrial Chemistry; Computational Chemistry and Modeling; Transport Phenomena (Chem. Eng.); Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6781597181d2151a029cfe02/original/progress-in-flow-battery-shunt-current-investigations-a-species-resolved-foundational-approach.pdf |
67d97ed66dde43c90847ed62 | 10.26434/chemrxiv-2025-nk82p | Regulation of Chemical Transformation in Designer Peptide Biomolecular Condensates | Biomolecular condensates, formed through liquid-liquid phase separation (LLPS), serve as dynamic platforms for biochemical regulation. Inspired by these natural systems, we developed designer peptide-based condensates to modulate chemical transformations, focusing on the Cu(I)-catalyzed azide-alkyne cycloaddition click reaction between hydrophobic reactants as a model system. By incorporating varying number of isoleucine residues into peptide sequences, we tuned hydrophobicity of the condensates, influencing reaction rate and conversion. Condensates formed by a peptide with a single isoleucine enhanced reactant recruitment and reaction efficiency, while excessive hydrophobicity resulted in solid-like condensates that impeded catalysis. Notably, we deciphered the factors that affect reactant recruitment, eventually resulting in a complete spatial regulation of product localization inside the condensates. The study highlights the critical balance of hydrophobicity for optimal reaction performance in condensates, demonstrating a new approach to regulate chemical transformations in water-based systems. This work establishes a foundation for engineering biomolecular condensates as green chemistry platforms and reaction vessels for applications in biotechnology and biomedicine. | Shirel Veretnik; Avigail Baruch Leshem; Ayala Lampel | Organic Chemistry; Materials Science; Catalysis; Supramolecular Chemistry (Org.); Aggregates and Assemblies; Biocompatible Materials | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d97ed66dde43c90847ed62/original/regulation-of-chemical-transformation-in-designer-peptide-biomolecular-condensates.pdf |
670819a112ff75c3a1130890 | 10.26434/chemrxiv-2024-2g6px | ESIPT fluorescence turn-on sensors for detection of short chain inorganic polyphosphate in water | We introduce two water-soluble excited state intramolecular proton transfer (ESIPT) based fluorescent turn-on probes responding to inorganic polyphosphates. These ESIPT probes enable specific detection of short-chain inorganic polyphosphates over a range of different other condensed phosphates. The probes are weakly emissive in their off state due to the blocking of ESIPT by Cu2+ coordination. Removal of the copper ion through decomplexation by the analyte accesses the on-state. The probes detect polyphosphates over other biologically occurring phosphates, pyrophosphate, and nucleotides such as ATP, ADP, GTP. An optimal fluorescence response is observed with the short-chain polyphosphate polyP8. Furthermore, the probe shows selectivity towards linear polyphosphates over cyclic metaphosphates. The rapid ‘turn-off―turnon’ fluorescence responses upon consecutive addition of Cu2+ and polyP8 are reversible, further highlighting sensor performance in an aqueous environment. One of the sensors is then applied to monitor polyP digestion by an exopolyphosphatase (PPX). | Subhra Roy; Sandra Moser; Tobias Dürr-Mayer; Rahel Hinkelmann; Henning Jessen | Biological and Medicinal Chemistry; Organic Chemistry; Analytical Chemistry; Bioorganic Chemistry; Biochemical Analysis; Biochemistry | CC BY 4.0 | CHEMRXIV | 2024-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670819a112ff75c3a1130890/original/esipt-fluorescence-turn-on-sensors-for-detection-of-short-chain-inorganic-polyphosphate-in-water.pdf |
66bf3980f3f4b052900e61e4 | 10.26434/chemrxiv-2024-ljkf8-v2 | Computational Design of an Improved Photoswitchable Psychedelic Based on Light Absorption, Membrane Permeation and Protein Binding | Psychedelic compounds can induce rapid-acting and
long-lasting antidepressant benefits. Understanding the
role of their hallucinatory effects is crucial for shaping
the future trajectory of antidepressant drug development.
Photoswitchable compounds targeting the 5-HT2AR offer
precise spatio-temporal control over the activation of
different downstream pathways. In this work, we
computationally discovered PQ-azo-N,N-DMT (34), a
photoswitch with improved features compared to the
previously synthesized azo-N,N-DMT (1). The new
compound shows tight binding to the 5-HT2AR, retaining all
important interactions of lysergic acid diethylamide (LSD),
exhibits positive membrane permeability, and has a strong
red-shifted absorption that would allow photocontrol in the
visible spectrum. | Vito F. Palmisano; Claudio Agnorelli; Shirin Faraji; Juan J. Nogueira | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66bf3980f3f4b052900e61e4/original/computational-design-of-an-improved-photoswitchable-psychedelic-based-on-light-absorption-membrane-permeation-and-protein-binding.pdf |
63d0b355246f165db7cc0249 | 10.26434/chemrxiv-2023-bwsf6 | Molecular insights into the Stereospecificity of Arginine in RNA tetraloop folding | One of the possible hypotheses for the homochirality of amino acids in the context of the origin of life is that only a particular stereoisomer provides preferential stability to RNA folding by acting as a chemical chaperon. This study probes into the molecular understanding of such preferential stability for a small GAAA RNA tetraloop in the presence of chiral arginine amino acids using a combination of umbrella sampling and parallel bias metadynamics involving five collective variables to tackle the multi-dimensional free energy landscape for faster, better, and more efficient estimation with controlled sampling. Our results show that the free energetic stability of RNA differs significantly in the presence of D- and L- arginine, giving rise to different un-folding rates. Interestingly, the folding rates are not altered. We show that the origin of the chirality difference in RNA folding–unfolding dynamics is due to the differences in configurational diversity of RNA by adopting different unnatural conformations accompanied by different binding modes of D-arginine and L-arginine towards the given RNA motif. | Amal Vijay; Arnab Mukherjee | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Biophysical Chemistry; Thermodynamics (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2023-01-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d0b355246f165db7cc0249/original/molecular-insights-into-the-stereospecificity-of-arginine-in-rna-tetraloop-folding.pdf |
60c747c7f96a00d5f9286fad | 10.26434/chemrxiv.11786088.v1 | Autonomous flipping of azobenzene assemblies under light irradiation (II) | <p>To create autonomous microrobots which move in the presence of a
constant energy source, their mechanical motion must have a capacity for
self-control. This is realized when a structural change occurs with conversion
of energy facilitated by cofactors, with a self-regulation component to prevent
reaching a static state. Here, we present a single crystal structure analysis of
azobenene derivatives which reveals a mille-feuille-like layered structure of
sparse and dense layers of six independent azobenzene moieties. In this
anisotropic structure, a specific azobenzene molecule acts as a reaction center
for a light-to-mechanical function process. The other molecules in the crystal act
as modulators. Moreover, depending on the photoisomerisation process
activated by a polarized light source, different cyclic motions are observed. We
clarify the mechanism by which the self-organized mechanical behavior of these azobenzene
molecules is achieved at the molecular level. Thus, the present results
demonstrate that autonomously driven molecular materials can exhibit
information-responsive and self-sustainable motion by incorporating
stimulus-responsive sensors. </p> | Yoshiyuki Kageyama; Tomonori Ikegami; Shinnosuke Satonaga; Kazuma Obara; Hiroyasu Sato; Sadamu Takeda | Nanostructured Materials - Materials | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747c7f96a00d5f9286fad/original/autonomous-flipping-of-azobenzene-assemblies-under-light-irradiation-ii.pdf |
66db0adf12ff75c3a1964fb4 | 10.26434/chemrxiv-2024-s4qxg | Non-van-der-Waals oriented two-dimensional UiO-66 films by rap-id aqueous synthesis at room temperature | The synthesis of MOFs in two-dimensional (2D) film morphology is attractive for several applications including molecular and ionic separation. However, 2D MOFs have only been reported from structures that crystallize in lamellar morphology where layers are held together by van-der-Waals (vdW) interaction. For example, UiO-66, one of the most studied MOFs thanks to its exceptional chemical stability, has only been reported in three-dimensional (3D) morphology. 2D UiO-66 is challenging to obtain given the robust isotropic bonds in its cubic crystal structure. Herein, we report the first synthesis of non-vdW 2D UiO-66-NH2 by developing crystal growth conditions that promote in-plane growth over out-of-plane growth. Continuous, oriented UiO-66-NH2 film with thickness tunable in the range of 0.5 to 2 unit cells could be obtained by sustain-able, scalable chemistry which yielded attractive ion-ion selectivity. The preparation of non-vdW 2D MOF is highly attrac-tive to advance the field of MOF films for diverse applications. | Heng-Yu Chi; Kangning Zhao; Kuang-Jung Hsu; Qi Liu; Shuqing Song; Arthur Allaire; Kumar Varoon Agrawal | Materials Science; Inorganic Chemistry; Chemical Engineering and Industrial Chemistry; Thin Films; Crystallography – Inorganic | CC BY 4.0 | CHEMRXIV | 2024-09-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66db0adf12ff75c3a1964fb4/original/non-van-der-waals-oriented-two-dimensional-ui-o-66-films-by-rap-id-aqueous-synthesis-at-room-temperature.pdf |
60c74ba1842e65ed2ddb31d5 | 10.26434/chemrxiv.12366308.v1 | Nuclear Spin Induced Optical Rotation of Functional Groups in Hydrocarbons | Nuclear spin-induced optical rotation (NSOR) is a nuclear magneto-optic effect manifesting as a change of polarization of light induced by nuclear magnetic moments within a molecule. NSOR probes molecular optical properties through localized nuclear interactions and has a potential to be developed into a new spectroscopic tool. However, so far the connection between the molecular structure and NSOR response has not been systematically investigated. To obtain insight into this relation and to assess its viability as a foundation for a new spectroscopic method, NSOR of a set of hydrocarbon molecules with various structural motifs is theoretically investigated using density functional theory calculations. The results reveal that NSOR intensities are correlated with several structural features of the molecules, such as the position of the nucleus in the carbon chain, isomerism and presence of nearby unsaturated groups. Specific patterns connecting NSOR to the local chemical environment of the nucleus can be observed. It is also shown that this effect can be to a good approximation modelled as a sum of individual contributions from nearby chemical groups, allowing for a rapid estimation of its values. The demonstrated systematic dependence of NSOR signal on the molecular structure is a desirable feature for theoretical and experimental development of new spectroscopic methods based on this phenomenon. | Petr Štěpánek | Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ba1842e65ed2ddb31d5/original/nuclear-spin-induced-optical-rotation-of-functional-groups-in-hydrocarbons.pdf |
60c747040f50db1fd7396526 | 10.26434/chemrxiv.11350079.v2 | A Caged E3 Ligase Ligand for PROTAC-Mediated Protein Degradation with Light | A
caging group has been appended to a widely used Von Hippel Lindau (VHL) E3
ligase ligand for targeted protein degradation with PROTACs. Proteolysis is
triggered only after a short irradiation time allowing spatiotemporal control
of the protein’s fate. | Cyrille Kounde; Maria M. Shchepinova; Edward Tate | Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2019-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747040f50db1fd7396526/original/a-caged-e3-ligase-ligand-for-protac-mediated-protein-degradation-with-light.pdf |
636c7aadb58850f12345fadc | 10.26434/chemrxiv-2022-bpzwt | Understanding Formation and Roles of Ni(II) Aryl Amido and Ni(III) Aryl Amido Intermediates in Ni-Catalyzed Electrochemical Aryl Amination Reactions | Ni-catalyzed electrochemical aryl amination (e-amination) is an attractive, emerging approach to forging C−N bonds as it uses air-stable Ni catalysts and efficiently proceeds at room temperature. However, in-depth mechanistic understandings of this new C−N cross-coupling methodology remain underexplored. Herein, extensive experimental and computational studies were conducted to examine the mechanism of Ni-catalyzed electrochemical aryl amination reactions. The results suggest coordination of an amine to the Ni(II) catalyst occurs before the cathodic reduction and oxidative addition steps. A stable Ni(II) aryl amido intermediate is produced from the cathodic half-reaction, a critical step in controlling the selectivity between cross-coupling and undesired homo-coupling reaction pathways. In addition, redox-active bromide in the supporting electrolyte functions as a redox mediator to promote the oxidation of the stable Ni(II) aryl amido intermediate to a Ni(III) aryl amido intermediate. Subsequently, the Ni(III) aryl amido intermediate undergoes facile reductive elimination to provide a C−N cross-coupling product at room temperature. These mechanistic insights about the Ni-catalyzed aryl e-amination are valuable for understanding and developing new Ni-catalyzed aryl e-amination reactions and also other Ni-catalyzed electrosynthetic reactions such as C−C and C−O cross-couplings. | Jian Luo; Michael Davenport; Chad Callister; Shelley Minteer; Daniel Ess; Tianbiao Liu | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Synthesis and Reactions; Electrocatalysis; Homogeneous Catalysis | CC BY NC 4.0 | CHEMRXIV | 2022-11-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636c7aadb58850f12345fadc/original/understanding-formation-and-roles-of-ni-ii-aryl-amido-and-ni-iii-aryl-amido-intermediates-in-ni-catalyzed-electrochemical-aryl-amination-reactions.pdf |
60c749caf96a005f3c2872f2 | 10.26434/chemrxiv.12103284.v1 | Droplet Shape Control Using Microfluidics and Designer Biosurfactants | <p>Many uses of emulsion droplets require precise control
over droplet size and shape. Here we report a ‘shape-memorable’ micro-droplet
formulation stabilized by a polyethylene glycol (PEG)-modified
protein-surfactant, the droplets are stable against coalescence for months and
can maintain non-spherical shapes for hours, depending on the surface coverage
of PEGylated protein. Monodisperse droplets with aspect ratios ranging from 1.0
to 3.4 were controllably synthesized with a flow-focusing microfluidic device.
Mechanical properties of the interfacial protein network were explored to
elucidate the mechanism behind the droplet shape conservation phenomenon.
Characterization of the protein film revealed that the presence of a PEG layer
at interfaces alters the mechanical responses of the protein film, resulting in
interfacial networks with improved strength. Taking advantage of the prolonged
stabilization of non-spherical droplets, we demonstrate the possibility of
functionalization of the droplet interface with accessible biotin moieties. The
stabilization of micro-droplet shape with surface-active proteins that also
serve as an anchor for integrating functional moieties, provides a tailorable
interface for diverse applications.</p> | Yuan Gao; Chun-Xia Zhao; Frank Sainsbury | Surfactants; Biopolymers; Physical and Chemical Processes; Self-Assembly; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749caf96a005f3c2872f2/original/droplet-shape-control-using-microfluidics-and-designer-biosurfactants.pdf |
65e1a2a4e9ebbb4db9a43ce4 | 10.26434/chemrxiv-2024-jt5sc | Impact of Wall-Slip on Real Shear Thickening Fluid Flow Behavior in Rectangular Channels: Insights from LBM and Theoretical Modeling | The liquid slip phenomenon are pivotal for understanding fluid behavior at small scales and has been investigated using the lattice Boltzmann method (LBM). Boundary conditions for the lattice Boltzmann liquid flow simulation, however, are much beyond from ideal and how to precisely determine the boundary conditions for liquid flow with slip remains a challenge. In this study, we integrate the slip boundary condition for fluid flow for Newtonian as well as non-Newtonian fluid. Our primary emphasis is to comprehend the influence of slip effects on the flow characteristics of real shear-thickening fluid (STF), encompassing Newtonian, shear-thinning, and shear-thickening behaviors under varying applied stresses or strain rates. In order to achieve this, we have introduced the combination of modified bounce back and specular reflection (MBSR) scheme and half way bounce back and specular reflection (HBSR) scheme. In theory, the interactions between the parameters of the combination and the slip length are explicitly deduced. The specified combination parameter is decided by the slip length given and the relaxation time. These slip boundary conditions are analyzed for their distinct results. Our process has been tested for accuracy and reliability for Newtonian flow as well as non-Newtonian flow and the results are compared with the analytical solution. We also develop a theoretical model to elucidate the flow characteristics of real shear-thickening fluid (STF) in a channel with slip effects. Investigating pressure and channel height variations, we observe nuanced responses. Initially, under increasing pressure, the regime with Newtonian flow rate $Q1$ dominates, reaching a peak. As pressure rises yielding dominance to another regime with shear-thinning flow rate $Q2$, while regime with shear-thickening flow rate $Q3$ remains zero. Further pressure escalation prompts a monotonically increasing trend in $Q3$, achieving dominance. Simultaneously, $Q1$ and $Q2$ approach zero. These trends hold true with and without slip effects, with higher flow rates in the presence of slips for a given pressure drop and viscosity. Additionally, as channel height increases, $Q1$ predominates at lower heights, transitioning to dominance by $Q2$ and then $Q3$ at larger heights. | Garima Vishal; Ashish Garg; Jayati Sarkar; Sudip Kumar Pattanayek | Nanoscience; Chemical Engineering and Industrial Chemistry; Nanostructured Materials - Nanoscience; Fluid Mechanics; Transport Phenomena (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e1a2a4e9ebbb4db9a43ce4/original/impact-of-wall-slip-on-real-shear-thickening-fluid-flow-behavior-in-rectangular-channels-insights-from-lbm-and-theoretical-modeling.pdf |
66982e05c9c6a5c07a8ea853 | 10.26434/chemrxiv-2024-363tw | Exploring the computational aspects of propylene
oligomerization catalysis using Fe2M type
trimetallic MOF nodes | Metal-organic frameworks (MOFs) have emerged as promising materials in the field of catalysis. They offer an optimal ground for screening catalysts and tailoring their catalytic properties. In this work, we investigate the catalytic activity of the propylene oligomerization reaction on the trimetallic MOF nodes, Fe2Ni, by varying the active metal Ni with other 3d-transition metals ranging from Sc to Cu, aiming to grasp the impact of altering the active atoms on the catalyst’s activity. Additionally, we examined how substituting the spectator atom, Fe, in Fe2Ni with other transition metals, i.e., from Sc to Cu, affects these energy barriers. In addition, we found a correlative relationship between spin-density from natural population analysis and energy barriers in the realm of C-C bond formation, whereby an elevation in spin density is found to be inversely proportional to the magnitude of energy barriers. Moreover,
we calculated the energy barriers for C-C coupling and β-hydride elimination using multireference NEVPT2 calculations on top of the CASSCF wavefunction to validate the rate-determining step of the reaction. | Rishu Khurana; Valay Agarawal; Cong Liu | Theoretical and Computational Chemistry; Catalysis; Organometallic Chemistry; Computational Chemistry and Modeling; Heterogeneous Catalysis; Polymerization (Organomet.) | CC BY 4.0 | CHEMRXIV | 2024-07-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66982e05c9c6a5c07a8ea853/original/exploring-the-computational-aspects-of-propylene-oligomerization-catalysis-using-fe2m-type-trimetallic-mof-nodes.pdf |
60c740e4469df42095f42cfb | 10.26434/chemrxiv.7538720.v2 | Computational Insights into the Mechanism of the Selective Catalytic Reduction of NOx: Fe- Versus Cu-Doped Zeolite Catalysts | <div>
<div>
<div>
<p>We computationally investigate the mechanism of the reduction half-cycle of the
selective catalytic reduction (SCR) of nitrogen oxides with ammonia. We compare
both Fe- and Cu-doped zeolite catalysts and aim at exploring all accessible reaction
pathways. From our calculations, a comprehensive picture emerges that unifies sev-
eral previous mechanistic proposals. We find that both for Fe and for Cu catalysts,
different reaction pathways are feasible, but some of the possible reaction pathways
differ in these two cases. Our computational results provide a basis for the inter-
pretation of in situ spectroscopic investigations that can possibly distinguish the
different mechanistic pathways.
</p>
</div>
</div>
</div> | Julian Rudolph; Christoph R. Jacob | Computational Chemistry and Modeling; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740e4469df42095f42cfb/original/computational-insights-into-the-mechanism-of-the-selective-catalytic-reduction-of-n-ox-fe-versus-cu-doped-zeolite-catalysts.pdf |
610835f6171fc70170ba65e8 | 10.26434/chemrxiv-2021-dkkdb | Potassium fluoride and carbonate lead to immediate cell failure in potassium-ion batteries | While Li-ion is the prevailing commercial battery chemistry, development of batteries using earth abundant alkali metals (e.g., Na and K) alleviates reliance on Li with potentially cheaper technologies. While electrolyte engineering has been a major thrust of Li-ion battery (LIB) research, it is unclear if the same electrolyte design principles apply to K-ion batteries (KIBs). Fluoroethylene carbonate (FEC) is a well-known additive used in Li-ion electrolytes, because the products of its sacrificial decomposition aid in forming a stable solid electrolyte interphase (SEI) on the anode surface. Here, we show that FEC addition to KIBs containing hard carbon anodes results in a dramatic decrease in capacity and cell failure in only two cycles, whereas capacity retention remains high (> 90% over 80 cycles at C/10 for both KPF6 and KFSI) for electrolytes that do not contain FEC. Using a combination of 19F solid-state nuclear magnetic resonance (SSNMR) spectroscopy, X-ray photoelectron spectroscopy (XPS), and electrochemical impedance spectroscopy (EIS), we show that FEC decomposes during galvanostatic cycling to form insoluble KF and K2CO3 on the anode surface, which correlate with increased interfacial resistance. Our results strongly suggest KIB performance is sensitive to accumulation of an inorganic SEI, likely due to sluggish K diffusion in these compounds. This mechanism of FEC decomposition was confirmed in two separate electrolyte formulations using KPF6 or KFSI. Interestingly, the salt anions do not decompose themselves, unlike their Li analogues. Insight from these results indicates that electrolyte decomposition pathways and favorable SEI components are significantly different in KIBs and LIBs, suggesting that entirely new approaches to KIB electrolyte engineering are needed. | Lauren Marbella; Andrew Ells; Richard May | Materials Science; Energy; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/610835f6171fc70170ba65e8/original/potassium-fluoride-and-carbonate-lead-to-immediate-cell-failure-in-potassium-ion-batteries.pdf |
66def10612ff75c3a1dcbdc3 | 10.26434/chemrxiv-2024-vpvtp | Self-Brushing Block Copolymers for Defect Self-Healing in
Directed Self-Assembly | We report the use of a block copolymer (BCP) self-brushing mechanism for surface modification of Si substrates to heal defects in patterns generated for directed self-assembly (DSA). Our model system uses a lamellae-forming BCP consisting of a polystyrene block (PS) and a poly(glycidyl methacrylate) block (PG) that is modified via thiol “click” chemistry with nonpolar and polar thiols (BSH and CSH, respectively) to create a random copolymer (PG(B-r-C)). The ratio of B and C is tuned so that the two blocks of the PS-b-PG(B-r-C) BCP have equal surface energy, wherein the repeat units of the PG(B-r-C) block possess hydroxyl moieties that can irreversibly graft to Si substrates. We show on unpatterned substrates that the self-brushing mechanism can occur on pristine Si substrates as well as substrates previously modified with a penetrable polymer brush. On chemically patterned substrates for DSA with 3x density multiplication, we observe self-healing of defects in aligned polymer patterns through sequential rounds of polymer film deposition. Upon annealing, a BCP monolayer grafts to the substrate and retains the phase separation of the original polymer film, generating a 1:1 chemical guiding pattern. The 1:1 chemical guiding pattern enables healing of defects in films as thick as 60 nm or 3 times the pitch of the BCP. Our system for pattern rectification does not rely on additives to the polymer film, such as end-functionalized homopolymers, and therefore can more easily scale down to lithographically relevant sub-10 nm dimensions. | Whitney Loo; Hongbo Feng; Beihang Yu; Scott Dhuey; Ricardo Ruiz; Paul Nealey | Polymer Science; Nanoscience; Polymer brushes; Nanofabrication; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-09-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66def10612ff75c3a1dcbdc3/original/self-brushing-block-copolymers-for-defect-self-healing-in-directed-self-assembly.pdf |
60c74e3df96a002fd1287ab6 | 10.26434/chemrxiv.12728384.v1 | Diboron- and Diaza-Doped Anthracenes and Phenanthrenes: Their Electronic Structures for Being Singlet Fission Chromophores | <p>We used quantum chemistry methods at the levels of mixed-reference spin-flipping time-dependent density functional theory and multireference perturbation theory to study diboron- and diaza-doped anthracenes and phenanthrenes. This class of structures recently surged as potential singlet fission chromophores. We studied electronic structures of their excited states and clarify the reasons why they satisfy or fail to satisfy the energy criteria for singlet fission chromophores. Many studied structures have their S<sub>1</sub> states not dominated by HOMO->LUMO excitation, so that they cannot be described using the conventional two sites model. This is attributed to frontier orbital energy shifts induced by the doping and different charge transfer energies in different one-electron singlet excitations, or in other words different polarizations of hole and/or particle orbitals in their S<sub>1</sub> and T<sub>1</sub> states. There is a mirror relation between the orbital energy shifts induced by diboron- and diaza-dopings, which, together with alternant hydrocarbon pairings of occupied and unoccupied orbitals, leads to more mirror relations between the excited states' electronic structures of the two types of doped structures. </p> | Ekadashi Pradhan; Tao Zeng | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e3df96a002fd1287ab6/original/diboron-and-diaza-doped-anthracenes-and-phenanthrenes-their-electronic-structures-for-being-singlet-fission-chromophores.pdf |
60c75979ee301cc11dc7b8f3 | 10.26434/chemrxiv.14702748.v1 | Improving Cycle Life Through Fast Formation Using a Super-Concentrated Phosphonium Based Ionic Liquid Electrolyte for Anode-Free and Lithium Metal Batteries | <p>ABSTRACT </p><p>Cell formation of lithium-ion cells impacts the evolution of the solid electrolyte interphase (SEI) and the cell cycle stability. Lithium metal anodes are an important step in the development of high energy density batteries owing to the high theoretical specific capacity of lithium metal. However, most lithium metal battery research has used a conventional lithium-ion formation protocol; this is time consuming, costly and does not account for the different properties of the lithium metal electrode. Here, we have used a recently reported promising phosphonium bis(fluorosulfonyl)imide ionic liquid electrolyte coupled with an NMC622 high areal capacity cathode (>3.5 mAh/cm2) to investigate the effect of cell formation rates. A faster formation protocol comprised of a pulsed 1.25C current decreased the formation time by 56 % and gave a 38 % greater capacity retention after 50 cycles when compared to formation at C/20. Electrochemical impedance spectroscopy measurements showed that the fast formation gave rise to a lower-resistance SEI. Column-like lithium deposits with reduced porous lithium domains between the particles were observed using scanning electron microscope imaging. To underline the excellent performance of these high energy-density cells, a 56 % greater stack specific energy was achieved compared to the analogous graphite-based lithium-ion cell chemistries. </p> | Thushan Pathirana; Dmitrii Rakov; Fangfang Chen; Maria Forsyth; Robert Kerr; Patrick
C. Howlett; Dmitrii A. Rakov | Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75979ee301cc11dc7b8f3/original/improving-cycle-life-through-fast-formation-using-a-super-concentrated-phosphonium-based-ionic-liquid-electrolyte-for-anode-free-and-lithium-metal-batteries.pdf |
6176ca0a0f3eebe8396ff51a | 10.26434/chemrxiv-2021-8w57d | Highly efficient water oxidation via a bimolecular reaction mechanism on rutile structured mixed-metal oxyfluorides | Mixed-metal oxides are generally considered to be the highest-performance catalysts for alkaline water oxidation. Despite significant efforts dedicated to understanding and accelerating their efficiency, most works have been limited investigations of Ni, Co, and Fe oxides, thus overlooking beneficial effects of hetero-anion incorporation. To this end, we report on the development of Co0.5Fe0.5O0.5F1.5 oxyfluoride materials featuring a rutile crystal structure and porous morphology via a scalable and green synthetic route. The catalyst surface, enhanced through electron withdrawing effects imparted by the fluoride ions, give rise to highly effective catalytic sites for electrochemical water oxidation. In particular, their performance across metrics of Tafel slope (27 mV/dec), mass activity (846 A/g at 1.53 V vs. RHE), turnover frequency (21/s at 1.53 V vs. RHE), overpotential (220 mV for 10 mA/cm2), and stability (27 days of continuous operation) largely surpasses most known Co-based catalysts. Mechanistic studies suggest that this performance is driven by a bimolecular, oxygen coupling reaction mechanism through proximal active sites on the catalyst surface, thus enabling a new avenue for achieving accelerated oxygenic electrocatalysis. | Zahra Gohari-Bajestani; Xiao Wang; Amandine Guiet; Romain Moury; Jean-Marc Grenèche; Annie Hémon-Ribaud; Yuxuan Zhang; Daniel Chartrand; Vincent Maisonneuve; Ali Seifitokaldani; Nikolay Kornienko; Jérôme Lhoste | Catalysis; Electrocatalysis; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms | CC BY 4.0 | CHEMRXIV | 2021-10-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6176ca0a0f3eebe8396ff51a/original/highly-efficient-water-oxidation-via-a-bimolecular-reaction-mechanism-on-rutile-structured-mixed-metal-oxyfluorides.pdf |
646e5ff94f8b1884b737e698 | 10.26434/chemrxiv-2023-8qnfl | Uncoupling Short-Range Bond Exchange From Long-Range Viscoelastic Flow in Circular Polydiketoenamine Elastomers | Here, we show how to architect dynamic covalent polydiketoenamine (PDK) elastomers prepared from polyetheramine and triketone monomers, not only for energy-efficient circularity, but also outstanding creep resistance at high temperature. By appending polytopic crosslinking functionality at the chain ends of flexible polyetheramines, we reduced creep from >200% to less than 1%, relative to monotopic controls, producing mechanically robust and stable elastomers and carbon-reinforced rubbers that are readily depolymerized to pure monomer in high yield. We also found that the multivalent chain end was essential for ensuring complete PDK deconstruction. | Eric Dailing; Pawan Khanal; Alexander Epstein; Jeremy Demarteau; Kristin Persson; Brett Helms | Theoretical and Computational Chemistry; Polymer Science; Organic Polymers; Theory - Computational; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646e5ff94f8b1884b737e698/original/uncoupling-short-range-bond-exchange-from-long-range-viscoelastic-flow-in-circular-polydiketoenamine-elastomers.pdf |
67878e316dde43c908a7931a | 10.26434/chemrxiv-2025-f6615 | Extending quantum-mechanical benchmark accuracy to biological ligand-pocket interactions | Predicting the binding affinity of ligand molecules to protein pockets is a key step in the drug design pipeline. The flexibility of ligand-pocket motifs arises from a wide range of attractive and repulsive electronic interactions invoked upon binding. Accurately accounting for all these interactions on equal footing requires robust quantum-mechanical (QM) benchmarks, which are scarce for ligand-pocket systems. In addition, the puzzling disagreement between ``gold standard'' Coupled Cluster (CCSD(T)) and Quantum Monte Carlo (QMC) methods [Nat. Commun. 12, 3927 (2021)] casts doubt on many existing benchmarks for larger non-covalent systems. Here, we introduce the ``Quantum Interacting Dimer'' (QUID) benchmark framework containing 170 non-covalent systems spanning equilibrium and non-equilibrium geometries that model chemically and structurally diverse ligand-pocket motifs. Symmetry-adapted perturbation theory shows that QUID broadly covers non-covalent binding motifs and energetic (exchange-repulsion, electrostatic, induction, and dispersion) contributions. Robust and reproducible binding energies are obtained using two complementary QM methods: LNO-CCSD(T) and QMC, achieving mutual agreement of 0.3 kcal/mol. Analysis of this benchmark data reveals that several dispersion-inclusive density functional approximations provide accurate energy predictions, though they exhibit discrepancies in magnitude and orientation of atomic van der Waals forces, which could influence the dynamics of ligands within the pocket. On the contrary, semiempirical methods and widely used empirical force fields require improvements, particularly in capturing non-covalent interactions (NCIs) for out-of-equilibrium geometries. The wide span of molecular dipole moments and polarizabilities in QUID also demonstrates flexibility in designing pocket structures to achieve desired binding properties. Therefore, QUID sets a new ``platinum standard'' for reliable and reproducible QM benchmarks of NCIs in larger systems and enhances our understanding of biomolecular ligand-pocket interactions. | Mirela Puleva; Leonardo Medrano Sandonas; Balázs Lőrincz; Jorge Charry; David M. Rogers; Péter R. Nagy; Alexandre Tkatchenko | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Physical and Chemical Properties | CC BY 4.0 | CHEMRXIV | 2025-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67878e316dde43c908a7931a/original/extending-quantum-mechanical-benchmark-accuracy-to-biological-ligand-pocket-interactions.pdf |
65bd0adb66c1381729d0fd24 | 10.26434/chemrxiv-2023-gk1zv-v2 | Molecular insights into the influence of ions on water structure. I. Alkali metal ions in solution | In this study, we explore the impact of alkali metal ions (Li+, Na+, K+, Rb+, and Cs+) on the hydration structure of water using molecular dynamics simulations carried out with the MB-nrg potential energy functions (PEFs). Our analyses include radial distribution functions, coordination numbers, dipole moments, and infrared spectra of water molecules, calculated as a function of solvation shells. The results collectively indicate a highly local influence of all the alkali metal ions on the hydrogen-bond network established by the surrounding water molecules, with the smallest and most densely charged Li+ ion exerting the most pronounced effect. Remarkably, the MB-nrg PEFs demonstrate excellent agreement with available experimental data for the position and size of the first solvation shells, underscoring their potential as predictive models for realistic simulations of ionic aqueous solutions across various thermodynamic conditions and environments. | Roya Savoj; Henry Agnew; Ruihan Zhou; Francesco Paesani | Theoretical and Computational Chemistry; Physical Chemistry; Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Physical and Chemical Properties; Solution Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65bd0adb66c1381729d0fd24/original/molecular-insights-into-the-influence-of-ions-on-water-structure-i-alkali-metal-ions-in-solution.pdf |
6528486f8bab5d2055398bca | 10.26434/chemrxiv-2021-n0xm9-v3 | Beyond strain release: Delocalization-enabled organic reactivity | The release of strain energy is a fundamental driving force for organic reactions. However, absolute strain energy alone is an insufficient predictor of reactivity, as evidenced by the similar ring strain but disparate reactivity of cyclopropanes and cyclobutanes. In this work, we demonstrate that electronic delocalization is a key factor that operates alongside strain release to boost, or even dominate, reactivity. This delocalization principle extends across a wide range of molecules containing three-membered rings such as epoxides, aziridines and propellanes, and also applies to strain-driven cycloaddition reactions. Our findings lead to a ‘rule of thumb’ for the accurate prediction of activation barriers in such systems, which can be easily applied to reactions involving many of the strained building blocks commonly encountered in organic synthesis, medicinal chemistry, polymer science and bioconjugation. Given the significance of electronic delocalization in organic chemistry, for example in aromatic 𝜋-systems and hyperconjugation, we anticipate that this concept will serve as a versatile tool to understand and predict strain-based organic reactivity. | Alistair Sterling; Russell Smith; Edward Anderson; Fernanda Duarte | Theoretical and Computational Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Physical Organic Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2023-10-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6528486f8bab5d2055398bca/original/beyond-strain-release-delocalization-enabled-organic-reactivity.pdf |
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