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62603a6511b1461e422a00b6 | 10.26434/chemrxiv-2022-cn7qr | Approaches for enhancing the analysis of chemical space for drug discovery | Chemical space is a powerful, general, and practical conceptual framework in drug discovery and other areas in chemistry that addresses the diversity of molecules and it has various applications. Moreover, chemical space is a cornerstone of chemoinformatics as a scientific discipline. In response to the increase in the set of chemical compounds in databases, generators of chemical structures, and tools to calculate molecular descriptors, novel approaches to generate visual representations of chemical space in low dimensions are emerging and evolving. Such approaches include a wide range of commercial and free applications, software, and open-source methods. Herein, the current state of chemical space in drug design and discovery is reviewed. The topics discussed herein include advances for efficient navigation in chemical space, the use of this concept in assessing the diversity of different data sets, exploring structure-property/activity relationships for one or multiple endpoints, and compound library design. Recent advances in methodologies for generating visual representations of chemical space have been highlighted, thereby emphasizing open-source methods. It is concluded that quantitative and qualitative generation and analysis of chemical space require novel approaches for handling the increasing number of molecules and their information available in chemical databases (including emerging ultra-large libraries). In addition, it is of utmost importance to note that chemical space is a conceptual framework that goes beyond visual representation in low dimensions. However, the graphical representation of chemical space has several practical applications in drug discovery and beyond. | Fernanda I. Saldívar-González; José L. Medina-Franco | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2022-04-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62603a6511b1461e422a00b6/original/approaches-for-enhancing-the-analysis-of-chemical-space-for-drug-discovery.pdf |
630a27b6521cb7de54a887fc | 10.26434/chemrxiv-2022-lpvvb | Energy transport in dichromic metallo-organic crystals: selective inclusion of spatially-resolved arrays of donor and acceptor dyes in different nanochannels | In this study, the precise positioning and alignment of arrays of two different guest molecules in a crystalline host matrix has been engineered resulting in new optically-active materials. Sub-nm differences in the diameters of two types of 1D channels is sufficient for size-selective inclusion of dyes. Energy transport occurs between the arrays of different dyes that are included in parallel-positioned nanochannels by fluorescence resonance energy transfer (FRET). Dichromism and diattenuation of individual micro-sized crystals are dependent on their relative position under polarized light. This angular-dependent behavior is a result of the geometrically-constrained orientation of the dyes by the crystallographic packing of the host matrix and is concentration dependent. These functionalized crystals can find applications in optical switches and as bulk materials for light harvesting and up-conversion. | Qiang Wen; Naveen Malik; Yoseph Addadi; Maren Maren Weißenfels; Vivek Singh; Linda J. W. Shimon; Michal Lahav; Milko E. van der Boom | Physical Chemistry; Nanoscience; Photochemistry (Physical Chem.); Self-Assembly; Materials Chemistry; Crystallography | CC BY 4.0 | CHEMRXIV | 2022-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/630a27b6521cb7de54a887fc/original/energy-transport-in-dichromic-metallo-organic-crystals-selective-inclusion-of-spatially-resolved-arrays-of-donor-and-acceptor-dyes-in-different-nanochannels.pdf |
666d85f95101a2ffa8a7add3 | 10.26434/chemrxiv-2024-dt7fg | Excited-state Hund’s Rule Violations in Bridged [10]- and [14]Annulene Perimeters | Molecules with Hund’s rule violations between low-lying singlet and triplet states may enable a new generation of fluorescent emitters. However, only a few classes of molecules are known with this property at the current time. Here, we use a high-throughput screening algorithm of the FORMED database to uncover a class of compounds where the first excited state violates Hund’s rule. We examine this class of bridged [10]- and [14]annulene perimeters with saturated bridges, and relate them to known conjugated polycyclic systems with Hund’s rule violations. Despite the structural similarities with the related class of non-alternant polycyclic hydrocarbons, the mechanism is different in these bridged annulene perimeters. Here, two molecular orbital configurations contribute to each excited state. Consequently, a Hund’s rule violation can only be unambiguously assigned based on the symmetry of the lowest excited singlet and triplet states. With several examples of synthetically realistic molecules, the class of bridged [10]- and [14]annulenes thus provides a structural link between the known non-alternant and alternant (azaphenalene) classes of molecules violating Hund’s rule, and may open avenues for design of molecules with inverted singlet-triplet gaps. | J. Terence Blaskovits; Clemence Corminboeuf; Marc H. Garner | Physical Chemistry; Photochemistry (Physical Chem.); Physical and Chemical Properties; Quantum Mechanics | CC BY 4.0 | CHEMRXIV | 2024-06-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/666d85f95101a2ffa8a7add3/original/excited-state-hund-s-rule-violations-in-bridged-10-and-14-annulene-perimeters.pdf |
61e1a5d46afbef3cfb64777d | 10.26434/chemrxiv-2022-m57j9 | Connecting the Geometric and Electronic Structures of the Nitrogenase Iron–Molybdenum Cofactor through Site-selective Labeling | Understanding the chemical bonding in the catalytic cofactor of the Mo nitrogenase (FeMo-co) is foundational for building a mechanistic picture of biological nitrogen fixation. A persistent obstacle in these efforts has been that the 57Fe-based spectroscopic data—although rich with information—reflects all seven Fe sites, and it has therefore not been possible to map individual spectroscopic responses to specific sites in the 3-D structure. We herein overcome this challenge by incorporating 57Fe into a single site of FeMo-co. Spectroscopic analysis of the reduced and oxidized forms of the resting state provides unprecedented insights into the local electronic structure of the terminal (Fe1) site, including its oxidation state and spin orientation. This leads to the discovery that Fe1 is a site of redox reactivity during oxidation of the resting state, and on this basis, we suggest a possible role for Fe1 as an electron reservoir during N2 reduction catalysis. | Edward Badding; Suppachai Srisantitham; Dmitriy Lukoyanov; Brian Hoffman; Daniel Suess | Inorganic Chemistry; Bioinorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61e1a5d46afbef3cfb64777d/original/connecting-the-geometric-and-electronic-structures-of-the-nitrogenase-iron-molybdenum-cofactor-through-site-selective-labeling.pdf |
65afddd566c138172917b5aa | 10.26434/chemrxiv-2024-q9tc4 | A reagent-driven visual method for analyzing chemical reaction data | The increasing use of machine learning and artificial intelligence in chemical reaction studies demands high-quality reaction data, necessitating specialized tools enabling data understanding and cura- tion. Our work introduces a novel methodology for reaction data exploration centered on reagents — essential molecules in reactions that do not contribute atoms to products. We propose an intu- itive tool for creating interactive reagent space maps using distributed vector representations, akin to word2vec in Natural Language Processing, capturing the statistics of reagent usage within datasets. Our approach enables swift assessment of reaction type distributions, identification of alternative reagents, and detection of errors, which we demonstrate using the USPTO dataset. Our contributions include an open-source web application for visual reagent pattern analysis and a table cataloging around six hundred of the most frequent reagents in USPTO annotated with detailed roles. Accessible via GitHub at https://github.com/Academich/reagent_emb_vis, our method supports organic chemists and cheminformatics experts in navigating extensive reaction datasets efficiently. | Mikhail Andronov; Natalia Andronova; Michael Wand; Jürgen Schmidhuber; Djork-Arné Clevert | Theoretical and Computational Chemistry; Organic Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65afddd566c138172917b5aa/original/a-reagent-driven-visual-method-for-analyzing-chemical-reaction-data.pdf |
67571c7a085116a133dcce4f | 10.26434/chemrxiv-2024-6xlc0 | Influence of the Counterion on the Activation of Nickel(σ-Aryl) Precatalysts | Complexes of the type LnNi(σ-aryl)Cl are known to be competitive precatalysts for various transformations, avoiding the use of expensive and sensitive Ni(0) precursors, such as Ni(cod)2. The in situ activation requires a transmetalation step with a nucleophile, yielding the active Ni(0) catalyst after reductive elimination. Steric hindrance is usually implemented in the σ-aryl group (e.g. o tolyl or 1 naphthyl) to enhance kinetic stability. Simultaneously, this steric hindrance can render the activation process slow, thus increasing the reaction time and possibly reducing the amount of active catalyst. To circumvent this issue, we envisaged substitution of the anionic chloride ligand of the precatalyst with more labile ligands that would facilitate transmetalation. In this work, a series of (Xantphos)Ni(o-tolyl)X complexes was successfully synthesized and the effect of the counterion X on the reaction profile was investigated using C–S cross-coupling as the model reaction. (Xantphos)Ni(o-tolyl)OTf was identified as the most efficient precatalyst, probably due to the weak coordinating ability of the triflate anion that facilitated the activation step. Finally, this concept was also studied in Suzuki-Miyaura coupling and Buchwald-Hartwig amination reactions using (dppf)Ni(o tolyl)X precatalysts. | Ivo Lindenmaier; Anna Harzer; Markus Ströbele; Ivana Fleischer | Organic Chemistry; Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Coordination Chemistry (Organomet.); Ligand Design | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67571c7a085116a133dcce4f/original/influence-of-the-counterion-on-the-activation-of-nickel-aryl-precatalysts.pdf |
60c758b5469df419b5f45712 | 10.26434/chemrxiv.14343137.v2 | Combining Evolutionary Conservation and Quantum Topological Analyses to Determine QM Subsystems for Biomolecular QM/MM Simulations | We present an approach that combines protein sequence/structure evolution and electron localization function (ELF) analyses. The combination of these two analysis allows the determination of whether a residue needs to be included in the QM subsystem, or can be represented by the MM environment. We have applied this approach on two systems previously investigated by QM/MM simulations, 4{oxalocrotonate tautomerase (4OT), and ten-eleven translocation-2 (TET2), that provide examples where fragments may or may not need to be included in the QM subsystem. Subsequently, we present the use of this approach to determine the appropriate QM subsystem to calculate the minimum energy path (MEP) for the reaction catalyzed by human DNA polymerase lambda? with a third cation in the active site. | Mark A. Hix; Emmett M. Leddin; G. Andres Cisneros | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758b5469df419b5f45712/original/combining-evolutionary-conservation-and-quantum-topological-analyses-to-determine-qm-subsystems-for-biomolecular-qm-mm-simulations.pdf |
6334b16a08470044848ce3a0 | 10.26434/chemrxiv-2022-v11gc-v2 | Accurate prediction of vertical ionization
potentials and electron affinities from
spin-component scaled CC2 and ADC(2) models | The CC2 and ADC(2) wave function models and their spin-component scaled modifications are adopted for predicting vertical ionization potentials (VIPs) and electron affinities (VEAs). The ionic solutions are obtained as electronic excitations in the continuum orbital formalism, making possible the use of existing, widespread quantum chemistry codes with minimal modifications, in full consistency with the treatment of charge transfer excitations. The performance of different variants is evaluated via benchmark calculations on various sets from previous works, containing small and medium-sized systems, including the nucleobases. It is shown that with the spin-scaled approximate methods, in particular the scaled opposite-spin variant of the ADC(2) method the accuracy of EOM-CCSD is achievable at a fraction of the computational cost, also outperforming many common electron propagator approaches. | Ahmed Shaalan Alag; Dávid P. Jelenfi; Attila Tajti; Péter G. Szalay | Physical Chemistry; Physical and Chemical Properties; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6334b16a08470044848ce3a0/original/accurate-prediction-of-vertical-ionization-potentials-and-electron-affinities-from-spin-component-scaled-cc2-and-adc-2-models.pdf |
61bd107e203b4027d0915396 | 10.26434/chemrxiv-2021-8cjd5 | Bioderived ether design for low emission and high reactivity transport fuels | Bioderived ethers have recently drawn attention as a response to increasing demands on clean alternative fuels. A theory-experiment combined approach was introduced for the five ether molecules representing linear, branched, and cyclic ethers to derive rational design principles for low-emission and high-reactivity ethers. Flow reactor experiments and quantum-mechanical calculations were performed at high (750–1100K) and low temperature (400–700K) regimes to investigate the structural effects on their sooting tendency and reactivity, respectively. At a high-temperature regime, ethers’ high sooting tendency is related to increased C3 and C4 hydrocarbon formation compared to C1 and C2 products from oxidation reactions. On the other hand, the reactivity at the low-temperature regime is determined by the activation energies of reaction steps until ketohydroperoxide formation. These studies found that ethers’ sooting tendency and reactivity are relevant to two structural factors: the carbon type (primary to quaternary) and the relative position of ether oxygen atoms to carbon atoms. These factors were utilized to build a multivariate model to predict the cetane number (CN) and yield sooting index (YSI) of 50 different ethers. The model suggests building blocks with specific carbon types that maximize CN and minimize YSI, leading to the design principles of ethers toward low emissions and high reactivity fuels for transport applications. Ethers with a high CN and low YSI were then proposed using the developed model, and through experimental measurements, it was proved that they are promising biodiesel candidates. | Jaeyoung Cho; Yeonjoon Kim; Brian Etz; Gina Fioroni; Nimal Naser; Junqing Zhu; Zhanhong Xiang; Cameron Hays; Juan Alegre-Requena; Peter St John; Bradley Zigler; Charles McEnally; Lisa Pfefferle; Robert McCormick; Seonah Kim | Theoretical and Computational Chemistry; Chemical Engineering and Industrial Chemistry; Theory - Computational; Machine Learning; Reaction Engineering | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61bd107e203b4027d0915396/original/bioderived-ether-design-for-low-emission-and-high-reactivity-transport-fuels.pdf |
62174d3657a9d2257f682559 | 10.26434/chemrxiv-2022-dpcbt | Optimising the β-lactam Parameters Using the Force
Field Toolkit | In this work we performed force field parameter optimisation for various β-lactams using the Force Field Toolkit (FFTK) and Gaussian calculations. Two problems that users are likely to encounter when optimising other drug molecules are identified. First, inappropriate CGenFF parameters without penalty prediction could cause a difficulty in optimisation. Second, multiple dihedral parameter sets may produce the same molecular mechanics (MM) potentials of similar quality, raising the question on how to choose the right parameter set as the best solution. A systematic protocol incorporating molecular dynamics simulations and a principle for
selecting the dihedral phase shifts are introduced. Using the protocol, we then successfully optimised both neutral and anionic forms of penam and of cephem. Our results highlight the importance of selecting proper phase shifts during the dihedral optimisation, and the protocol proposed in this work is beneficial to other users. | Qiyang Wu; Songyan Xia; Frank Otto; Tzong-Yi Lee; Hsien-Da Huang; Ying-Chih Chiang | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62174d3657a9d2257f682559/original/optimising-the-lactam-parameters-using-the-force-field-toolkit.pdf |
6407673e0e6a36fabae5319c | 10.26434/chemrxiv-2023-4wmgw | A Late-Stage Approach towards Higher Pillar[4]arenes from a Structurally Well-Defined Biomass-Derived Macrocyclic Template. | A late-stage macrocycle-to-macrocycle-to-macrocycle strategy to form a wide range of 9,10-disubstituted- pillar[4]naphthalenes from a common calix[4]furan building block, via pillar[4](1,4-epoxynapthalene) intermediates, is developed. Since post-transformation begins with a structurally well-defined macrocycle template, conventional issues in macrocyclization, such as unwanted polymerization, and non-selective macrocycle formation, are thus avoided. Albeit low conversion, this method even leads to the formation of pillar[4]anthracene, which is confirmed by HR-MALDI spectroscopy. Moreover, pillar[4]naphthalene is shown to be highly selective for NH4+ over other alkali metals in gas phase. Theoretical studies revealed that the selective complexation between pillar[4]naphthalene and NH4+ guest is directed solely by favorable multiple N-H interactions. Collectively, since calix[4]furan template is constructed from bio-renewable resources, our work is expected to inspire future efforts to employ biomass waste-derived building blocks to construct unique petroleum-based functional materials inaccessible by conventional methods. | Zhaoyang Chu; Fang-Zi Liu; Zhiyuan He; KaKing Yan | Organic Chemistry; Supramolecular Chemistry (Org.) | CC BY 4.0 | CHEMRXIV | 2023-03-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6407673e0e6a36fabae5319c/original/a-late-stage-approach-towards-higher-pillar-4-arenes-from-a-structurally-well-defined-biomass-derived-macrocyclic-template.pdf |
62ec300115fdaedeb8227c23 | 10.26434/chemrxiv-2022-kmmkv | Enabling Wide-Gamut Human-Centric Display Lighting
| Monitors, televisions, and smartphones have been revolutionized by the invention of InGaN-based LED backlighting. Yet, regular exposure to the bright blue light emitted by these screens can lead to mood disorders and insomnia. Switching to a "human-centric" display that uses a violet-emitting LED chip and a trichromatic phosphor blend is one materials chemistry solution for this problem. The challenge is finding a blue-emitting phosphor with a sufficiently small Stokes’ shift to down-convert the violet LED light. This study reports a new oxynitride phosphor that meets this need. K3AlP3O9N:Eu2+ exhibits a narrow (45 nm, 2206 cm-1), thermally robust, and efficient blue photoluminescence upon violet excitation. Computational modeling and photoluminescence spectroscopy revealed that a rare combination of preferential excitation and site-selective quenching produce the desired optical properties. Combining K3AlP3O9N:Eu2+ with red- and green-emitting phosphors and a violet LED covers 10% more of the color gamut than a commercial tablet while simultaneously mitigating blue light exposure en route to next-generation, human-centric displays. | Shruti Hariyani; Xinxin Xing; Mahdi Amachraa; Jiming Bao; Shyue Ping Ong; Jakoah Brgoch | Inorganic Chemistry; Solid State Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ec300115fdaedeb8227c23/original/enabling-wide-gamut-human-centric-display-lighting.pdf |
60c74aba842e65651edb2fcd | 10.26434/chemrxiv.12246020.v1 | AP-Net: An Atomic-Pairwise Neural Network for Smooth and Transferable Interaction Potentials | <div>
<div>
<div>
<p>Intermolecular interactions are critical to many chemical phenomena, but their accurate computation using
<i>ab initio</i> methods is often limited by computational cost. The recent emergence of machine learning (ML)
potentials may be a promising alternative. Useful ML models should not only estimate accurate interaction
energies, but also predict smooth and asymptotically correct potential energy surfaces. However, existing
ML models are not guaranteed to obey these constraints. Indeed, systemic deficiencies are apparent in the
predictions of our previous hydrogen-bond model as well as the popular ANI-1X model, which we attribute
to the use of an atomic energy partition. As a solution, we propose an alternative atomic-pairwise framework
specifically for intermolecular ML potentials, and we introduce AP-Net—a neural network model for interaction energies. The AP-Net model is developed using this physically motivated atomic-pairwise paradigm and
also exploits the interpretability of symmetry adapted perturbation theory (SAPT). We show that in contrast to other models, AP-Net produces smooth, physically meaningful intermolecular potentials exhibiting
correct asymptotic behavior. Initially trained on only a limited number of mostly hydrogen-bonded dimers,
AP-Net makes accurate predictions across the chemically diverse S66x8 dataset, demonstrating significant
transferability. On a test set including experimental hydrogen-bonded dimers, AP-Net predicts total interaction energies with a mean absolute error of 0.37 kcal mol−1, reducing errors by a factor of 2-5 across
SAPT components from previous neural network potentials. The pairwise interaction energies of the model
are physically interpretable, and an investigation of predicted electrostatic energies suggests that the model
‘learns’ the physics of hydrogen-bonded interactions.
</p>
</div>
</div>
</div> | Zachary Glick; Derek Metcalf; Alexios Koutsoukas; Steven Spronk; Daniel Cheney; David Sherrill | Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence; Clusters | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74aba842e65651edb2fcd/original/ap-net-an-atomic-pairwise-neural-network-for-smooth-and-transferable-interaction-potentials.pdf |
67db185281d2151a0209b35f | 10.26434/chemrxiv-2024-mf7f8-v2 | The Role of Counterion Size in Defining Star-Shaped Polyelectrolytes Thermodynamics, Conformations, and Ion Dynamics | In this work, we systematically investigate the impact of counterion size on the behavior of star-shaped strong polyelectrolytes in dilute aqueous solutions using Langevin simulations and a primitive model of electrolytes. Varying both the counterion diameter and the number of arms of the polyelectrolyte, we demonstrated that both characteristics significantly impact polyelectrolyte conformations and counterions absorption. Counterions dynamics is also affected, the most interesting aspect being the presence of a fraction of mobile ions slowly diffusing, compared to the average behavior, which increases with polyelectrolyte branching and their size. Informed by the results on systems with single-size counterions, we also investigate possible changes in behavior of these polyelectrolytes when neutralized by a binary mixture of bulky and small counterions at different relative concentration. Our results show that small counterions demonstrate a greater tendency for remaining located within the inner regions of the polyelectrolyte, particularly when their molar fraction is low and the polyelectrolyte is highly branched. This results in the spatial separation of the two species into core-shell-like structures, which dramatically decreases the diffusivity of the smaller counterions. By investigating the partitioning of counterions between the solution and the regions internal to the polyelectrolytes, it is shown that the selectivity toward the smaller species can be significantly enhanced by increasing the number of arms and operating under conditions of counterion scarcity. | Andrea Tagliabue; Massimo Mella | Theoretical and Computational Chemistry; Physical Chemistry; Polymer Science; Polyelectrolytes - Polymers; Computational Chemistry and Modeling; Theory - Computational | CC BY NC 4.0 | CHEMRXIV | 2025-03-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67db185281d2151a0209b35f/original/the-role-of-counterion-size-in-defining-star-shaped-polyelectrolytes-thermodynamics-conformations-and-ion-dynamics.pdf |
63f05e90fcfb27a31ff9c5de | 10.26434/chemrxiv-2023-0dddr | Electrochemical Hydrogen Isotope Exchange of Amines Controlled by Alternating Current Frequency | Here, we report an electrochemical protocol for hydrogen isotope exchange (HIE) at -C(sp3)-H amine sites. Tetrahydroisoquinoline and pyrrolidine are selected as two model substrates because of their different proton transfer (PT) and hydrogen atom transfer (HAT) kinetics at the -C(sp3)-H amine sites, which are utilized to control the HIE reaction outcome at different applied alternating current (AC) frequencies. We found the highest deuterium incorporation for tetrahydroisoquinolines at 0 Hz (i.e., direct current (DC) electrolysis condition) and pyrrolidines at 0.5 Hz. Analysis of the product distribution and D incorporation at different frequencies reveals that HIE of tetrahydroisoquinolines is limited by its slow HAT, whereas HIE of pyrrolidines is limited by the overoxidation of its -amino radical intermediates. The AC-frequency-dependent HIE of amines can be potentially used to achieve elective labeling of -amine sites in one drug molecule, which will significantly impact the pharmaceutical industry. | Nibedita Behera; Disni Gunasekera; Jyoti Mahajan; Joseph Frimpong; Zhenfei Liu; Long Luo | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63f05e90fcfb27a31ff9c5de/original/electrochemical-hydrogen-isotope-exchange-of-amines-controlled-by-alternating-current-frequency.pdf |
6292e70b24011edf7a0e5da8 | 10.26434/chemrxiv-2022-cq479 | A theoretical study of the structure and binding energies of dimers of Zn(II)-Porphyrin derivatives | Zinc complexed porphyrin and chlorophyll derivatives form functional aggregates with remarkable photophysical and optoelectronic properties. Understanding the type and strength of intermolecular interactions between these molecules is essential for designing new materials with desired morphology and functionality. The dimer interactions of a molecular set comprised of porphyrin derivatives obtained by substitutional changes starting from free-base porphyrin is studied. It is found that B97M-rV/def2-TZVP level of theory provides a good compromise between the accuracy and cost to get the dimer geometries and interaction energies. The neglect of the relaxation energy due to the change in the monomer configurations upon complex formation, causes a more significant error than the basis set superposition error. The metal complexation increases the binding energy by about -6 to -8 kcal/mol, and the introduction of keto and hydroxy groups further stabilizes the dimers by -10 to -15 kcal/mol. Although the saturation of one of the pyrrol double bonds does not change the interaction energy, the addition of R groups increases it.
| Sule Atahan-Evrenk | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6292e70b24011edf7a0e5da8/original/a-theoretical-study-of-the-structure-and-binding-energies-of-dimers-of-zn-ii-porphyrin-derivatives.pdf |
6111680f18911d335cdd2353 | 10.26434/chemrxiv-2021-wpjjk | Investigating the Impact of Solid-Electrolyte Interface on Dendrite Formation: A Case Study Based on Zinc Metal Electrodes | The formation of dendrites is the bottleneck to harvest the high theoretical capacities of metal anodes such as Li, Na, Mg, and Zn batteries. The critical current density, interfacial instabilities, and the characteristic of the solid-electrolyte interface (SEI) layer play a major role in the formation mechanisms of dendrites. In this study, we investigated the impact of the SEI layer on the electroplating of zinc metals in organic and aqueous electrolytes by using electrochemical techniques coupled with electron microscopy and X-ray photoelectron spectroscopy. First, the electrochemical response of Zn plating in organic or aqueous electrolytes was compared with the ones for Li and Na metal plating by using analogous perchlorate salt dissolved in the same organic solvent. Under similar charge conditions, the cycle life of the metal electrodes was longer in the order of Zn (aqueous) > Li > Zn (organic) > Na. The impact of the SEI layer is then investigated by electroplating Zn in aqueous for 20 cycles, and then switching it to organic electrolytes and vice versa. In organic electrolytes, the cycle life of the PAO-Zinc is almost three-fold longer than the as-received zinc electrodes. PAO stands for pre-cycled in aqueous electrolyte for twenty times. Overall, our study demonstrated the impact of surface chemistry and morphology on the formation of Zn dendrites. The methodology established here can be used to study the impact of electrolyte salt and additives on the formation of dendrites on metal electrodes. | Darrell Gregory; Collin Britten; Keisha Walters; Ömer Özgür Çapraz | Materials Science; Energy; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6111680f18911d335cdd2353/original/investigating-the-impact-of-solid-electrolyte-interface-on-dendrite-formation-a-case-study-based-on-zinc-metal-electrodes.pdf |
6756de5a7be152b1d0690d80 | 10.26434/chemrxiv-2024-8hxsh | Design of D-π-A type cyclo[18]carbon derivatives with excellent optical nonlinearity: A theoretical perspective | The geometric and electronic structures, photophysical property, and optical nonlinearity of four cyclo[18]carbon (C18) derivatives containing hydrogen (-H), amino (-NH2) and/or nitro (-NO2) groups were theoretically explored. The carbon-atom skeleton of molecules with different functional groups do not differ obviously, but their electronic properties are noticeably different. Electronic excitation analysis shows that with the introduction of -NH2 and/or -NO2 groups, the maximum wavelength absorption of derivatives red-shifts slightly and the absorption intensity decreases gradually, and the four molecules all have an excellent infrared (IR) transparency in the wavelength range of 800 to 4000 nm. The essence of electronic transition in derivatives was illustrated through charge-transfer spectrum (CTS) analysis and hole-electron analysis. Derivative molecules with different combinations of functional groups exhibit markedly different response properties, and the first hyperpolarizability reaches the maximum when -NH2 and -NO2 are introduced simultaneously to form NH2-C18-NO2. The differences in first hyperpolarizability between four C18 derivatives are revealed by analyzing hyperpolarizability tensor, hyperpolarizability density, and hyperpolarizability decomposition. The comprehensive analysis indicated that donor-π-bridge-acceptor (D-π-A) type NH2-C18-NO2 can be considered as potential candidates for novel IR nonlinear optical (NLO) materials. | Jingbo Xu; Jiaojiao Wang; Xiaohui Chen; Wenwen Zhao; Xiufen Yan; Zeyu Liu; Tian Lu; Aihua Yuan | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2024-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6756de5a7be152b1d0690d80/original/design-of-d-a-type-cyclo-18-carbon-derivatives-with-excellent-optical-nonlinearity-a-theoretical-perspective.pdf |
65e8d20466c13817296247d8 | 10.26434/chemrxiv-2024-cmwjx | Adaptive and Space-Filling Peptide Self-Assembly Upon Drying | Peptides have tremendous potential as building blocks of designer materials with wide-ranging applications. These materials are stabilized by strongly directional hydrogen bonding patterns giving rise to one-, or two-dimensional assembly. It remains a challenge to mimic biology’s context-adaptive and flexible structures. Here, we introduce minimalistic tripeptide sequences that form dynamic ensembles through incorporation of multivalent sidechain interactions that collectively self-optimize depending on their context. Notably, we observed that these dispersions undergo drying-induced liquid to solid phase separation involving interface stabilization and expansion, resulting in formation of films of stiff, and densely packed, porous peptide microparticles that can be instantaneously redispersed upon re-introduction of water. Air-drying of aqueous peptide dispersions in the presence of proteins or small molecule payloads results in spontaneous and efficient encapsulation, and retention of protein stability after redispersion. These supramolecular tripeptide dispersions show promise for emulsification, encapsulation, and storage of biomacromolecules. | Dhwanit R. Dave; Salma Kassem; Mona Tayarani-Najjaran; Maeva Coste; Lele Xu; Sheng Zhang; Darjan Podbevsek; Luis Ortuno Macias; Deborah Sementa; Muniyat A. Choudhury; Kelly Veerasammy; Selma Doganata; Cory Weng; Jorge Morales; Tong Wang; Mateusz Marianski; Tai-De Li; Xi Chen; Raymond Tu; Ye He; Rein Ulijn | Biological and Medicinal Chemistry; Nanoscience; Bioengineering and Biotechnology; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e8d20466c13817296247d8/original/adaptive-and-space-filling-peptide-self-assembly-upon-drying.pdf |
60c7488b842e655e72db2bf1 | 10.26434/chemrxiv.11919948.v1 | Membrane Trafficking Inspired Hydrolysis of Non-Activated Esters at Physiological pH | Natural enzymes establish the proximity of the substrates to perform challenging reactions in aqueous medium, whereas most chemical catalysts typically follow stochastic way and are less efficient. Inspired by the membrane trafficking, a core biological process, herein we report that positively charged micro heterogeneous vehicles loaded with substrate could be trafficked suitably at the site of the reaction to promote the localization and proximity of the reactants. The guided vehicular delivery coupled with electrolysis overcomes the entropic barrier related to the proximity of the reactants and allows the hydrolysis of non-activated esters at physiological pH. Mechanistic investigations suggest that the reaction utilizes the electrochemical energy to generate hydroxide ion at the cathode and the positively charged micellar vehicles (loaded with substrates) trafficked selectively near cathode to promote the hydrolysis. The in situ modulation of surface charge was exploited to accelerate or inhibit the hydrolysis in a controlled manner akin to cofactors or zymogens of natural enzymes. We believe this elegant membrane trafficking inspired approach paves the way for the further applications of proximity controlled selective transformations in organic synthesis using green aqueous medium.<br /> | Pradip Kumar Tarafdar; Suman De Sarkar; Raki Mandal; Kingshuk Mahanty; Subhendu Mandal | Bioorganic Chemistry; Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7488b842e655e72db2bf1/original/membrane-trafficking-inspired-hydrolysis-of-non-activated-esters-at-physiological-p-h.pdf |
61b6356002d90d6fe15fdabd | 10.26434/chemrxiv-2021-8x13n | TeachOpenCADD 2021: Open Source and FAIR Python Pipelines to Assist in Structural Bioinformatics and Cheminformatics Research | Computational pipelines have become a crucial part of modern drug discovery campaigns. Setting up and maintaining such pipelines, however, can be challenging and time-consuming --- especially for novice scientists in this domain.
TeachOpenCADD is a platform that aims to teach domain-specific skills and to provide pipeline templates as starting points for research projects. We offer Python-based solutions for common tasks in cheminformatics and structural bioinformatics in the form of Jupyter notebooks and based on open source resources only. Including the 12 newly released additions, TeachOpenCADD now contains 22 notebooks that each cover both theoretical background as well as hands-on programming.
To promote reproducible and reusable research, we apply software best practices to our notebooks such as testing with an automated continuous integration and adhering to a more idiomatic Python style. The new TeachOpenCADD website is available at https://projects.volkamerlab.org/teachopencadd and all code is deposited on GitHub. | Dominique Sydow; Jaime Rodríguez-Guerra; Talia B. Kimber; David Schaller; Corey J. Taylor; Yonghui Chen; Mareike Leja; Sakshi Misra; Michele Wichmann; Armin Ariamajd; Andrea Volkamer | Theoretical and Computational Chemistry; Chemical Education; Chemical Education - General; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2021-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b6356002d90d6fe15fdabd/original/teach-open-cadd-2021-open-source-and-fair-python-pipelines-to-assist-in-structural-bioinformatics-and-cheminformatics-research.pdf |
60c75194567dfe8c1cec5ab2 | 10.26434/chemrxiv.13177364.v1 | Guest Size Limitation in Metal-Organic Framework Crystal-Glass Composites | <p></p><p>Metal-organic framework
crystal-glass composites (MOF CGCs) have previously been formed by embedding
crystalline MIL-53(Al) within a ZIF-62 glass (<i>a</i><sub>g</sub>ZIF-62)
matrix. Here we highlight thermal stability considerations in the formation of
MOF CGCs, and subsequently report the synthesis of two novel MOF CGCs, by
incorporating MIL-118, and UL-MOF-1 within <i>a</i><sub>g</sub>ZIF-62. These
new materials, alongside the prototypical MOF CGC formed using MIL-53(Al), were
studied using scanning electron microscopy, powder X-ray diffraction, and gas
sorption techniques. The gas uptake in composites formed from MIL-118C and
UL-MOF-1 is largely dominated by the <i>a</i><sub>g</sub>ZIF-62 matrix,
suggesting that to improve the porosity of the MOF CGC, the matrix porosity
must be improved, or a percolation threshold must be overcome.</p><br /><p></p> | Christopher Ashling; Lauren K. Macreadie; Thomas J. F. Southern; Yiming Zhang; Lauren N. McHugh; Rachel Evans; Stefan Kaskel; Shane G. Telfer; Thomas Bennett | Hybrid Organic-Inorganic Materials; Coordination Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75194567dfe8c1cec5ab2/original/guest-size-limitation-in-metal-organic-framework-crystal-glass-composites.pdf |
646e58974f8b1884b737a7eb | 10.26434/chemrxiv-2023-l3sgl | An alternative to R^2 to characterize the quality of fit for linear least squares using offsets of variable orientation related to uncertainties in the data. | It is not appropriate to use the determination coefficient, R^2, to characterize the quality of fit for a least squares fitted line. In this paper, the maximum of R^2 is found as a function of the rotation angle of the data and gives the quality of fit for the line found by linear least squares with perpendicular offsets. The same rotation method is used to derive the perpendicular offset fit to the data, which yields two possible solutions where the correct root can be identified by a simple discriminant. These results are then generalized for any arbitrarily oriented offset, bringing about a new measure for the quality fit of a line, Q^2. Unlike the determination coefficient, R^2, this quality of fit measure is invariant to rotational transformations of the data and is specific to the offset’s orientation, which is directly related to the uncertainties in x- or y-data. Finally, this paper provides a method to determine the slope and intercept of a fitted line, as well as its quality of fit, given any estimate of the uncertainty ratio. | Lewis Wedgewood; Cody Mischel | Chemical Engineering and Industrial Chemistry; Chemical Education; Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646e58974f8b1884b737a7eb/original/an-alternative-to-r-2-to-characterize-the-quality-of-fit-for-linear-least-squares-using-offsets-of-variable-orientation-related-to-uncertainties-in-the-data.pdf |
60c745e5702a9b6e5a18aac3 | 10.26434/chemrxiv.10284104.v1 | Dearomative Photocatalytic Construction of Bridged 1,3-Diazepanes | The construction of diverse sp3-rich skeletal ring systems is of importance to drug discovery programmes and natural product synthesis. Herein, we report the photocatalytic construction of 2,7-diazabicyclo[3.2.1]octanes (bridged 1,3-diazepanes) via a reductive diversion of the Minisci reaction. The fused tricyclic product is proposed to form via radical addition to the C4 position of 4-substituted quinoline substrates, with subsequent Hantzsch ester-promoted reduction to a dihydropyridine intermediate which undergoes in situ two-electron ring closure to form the bridged diazepane architecture. A wide scope of N-arylimine and quinoline derivatives was demonstrated and good efficiency was observed in the construction of sterically congested all-carbon quaternary centers. Computational and experimental mechanistic studies provide insights into the reaction mechanism and observed regioselectivity/diastereoselectivity.<br /> | Jamie Leitch; Tatiana Rogova; Fernanda Duarte; Darren J. Dixon | Photochemistry (Org.); Photocatalysis; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745e5702a9b6e5a18aac3/original/dearomative-photocatalytic-construction-of-bridged-1-3-diazepanes.pdf |
61543464d1fc3358a7f8223c | 10.26434/chemrxiv-2021-5wn7m | Poly(thioether phenyl acrylate) Based Micelles Show Exclusively ROS-triggered Breakdown
| In certain tumor and diseased tissues, reactive oxygen species (ROS), such as H2O2, are produced in higher concentrations than in healthy cells. To date, only few examples of drug delivery and release systems responds selectively to these small but significantly elevated ROS concentrations. In addition, assuring the stability of the polymer-based carrier in “healthy” biological conditions is still a challenge in the field of oxidation-sensitive materials.
Here, we present ROS-responsive block copolymer micelles capable of achieving micellar disruption over days in the presence of 2 mM H2O2 and within hours under higher concentrations of H2O2 (60 – 600 mM). At the same time, these micelles are stable for over two weeks in oxidant-free physiological (pH = 7.4, 37°C) and for at least six days in mildly acidic (pH = 5.0 and pH = 6.0, 37°C) conditions. The observed selectivity is programmed into the material using a 4-(methylthio)phenyl ester based logic gate. Here, oxidation of the thioether moiety results in a large increase in ester hydrolytic lability, effectively switching the ester hydrolysis from off to on. The concept represents a step forward to realize signal responsive drug delivery materials capable of selective action in biological environments.
| Irene Piergentili; Pepijn R. Bouwmans; Luuk Reinalda; Reece W. Lewis; Benjamin Klemm; Huanhuan Liu; Robin M. de Kruijff; Antonia G. Denkova; Rienk Eelkema | Biological and Medicinal Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Supramolecular Chemistry (Org.); Drug Discovery and Drug Delivery Systems; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2021-09-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61543464d1fc3358a7f8223c/original/poly-thioether-phenyl-acrylate-based-micelles-show-exclusively-ros-triggered-breakdown.pdf |
60c74924bb8c1a5c6d3dadca | 10.26434/chemrxiv.12033774.v1 | Molecular Docking study of Receptor Binding Domain of SARS-CoV-2 Spike Glycoprotein with Saikosaponin, a Triterpenoid Natural Product | The appearance of SARS-CoV-2 has resulted ~19000
deaths and ~423000 infections worldwide as of March 24, 2020. Coronavirus spike
(S) glycoproteins hooks on target cells and binds to the angiotensin-converting
enzyme 2 (ACE2) receptor. Recent researches speculated that residues 331 to 524
of the S glycoprotein of the receptor binding domain (RDB) of the spike is the
most crucial target and this side was very important for computational docking.
In the present study we have considered a series of saikosaponins and molecular
docking was performed. Most of the docked molecules bind favorably to the RDB
region of the spike glycoprotein and among them Saikosaponin B4 is the best
inhibitor. | Tamal Goswami; Bhaskar Bagchi | Drug Discovery and Drug Delivery Systems; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74924bb8c1a5c6d3dadca/original/molecular-docking-study-of-receptor-binding-domain-of-sars-co-v-2-spike-glycoprotein-with-saikosaponin-a-triterpenoid-natural-product.pdf |
66e291fb12ff75c3a11b656c | 10.26434/chemrxiv-2024-rbs2q | Defluorinative C−O Coupling between Trifluoromethylarenes and Alcohols via Copper Photoredox Catalysis | Fluorine-containing compounds have shown unparalleled impacts in the realm of functional molecules, and the ability to prepare novel structures has been crucial in unlocking new properties for pharmaceutical and materials science. Herein, we report a copper-catalyzed, photoinduced defluorinative C‒O coupling between trifluoromethylarenes and alcohols. This method allows for direct access to a wide selection of difluorobenzylether (ArCF2OR) molecules, including a com-pound displaying liquid crystal behavior. Through slight modification of the protocol, we were able to generate ArCF2I products, another class of synthetically useful fluorine-bearing molecules. Comprehensive mechanistic investigations first suggested ArCF2I as a reservoir to steadily supply the key ArCF2• radical species. Furthermore, experimental evi-dence supported a mechanism consisting of two collaborative cycles: C‒F activation operated by a homoleptic Cu(I) co-ordinated by two bisphosphine ligands as the photocatalyst and C‒O coupling promoted by a Cu(I) ligated by a single bisphosphine ligand. The critical roles of the two salt additives, lithium iodide and zinc acetate, in orchestrating the two cycles were also elucidated. This dual-role copper catalyst demonstrates the power of base metal photoredox catalysis in achieving both substrate activation and chemical bond formation via a single catalytic system. | Priya Saha; Mingoo Jin; Dennis Chung-Yang Huang | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e291fb12ff75c3a11b656c/original/defluorinative-c-o-coupling-between-trifluoromethylarenes-and-alcohols-via-copper-photoredox-catalysis.pdf |
63640b0f311072e325fbee90 | 10.26434/chemrxiv-2022-vx8w8 | Simultaneous N-deglycosylation and digestion of complex samples on S-Traps enables efficient glycosite hypothesis generation | N-linked glycosylation is an important post-translational modification that is difficult to identify and quantify in traditional bottom-up proteomics experiments. Enzymatic deglycosylation of proteins by peptide:N-glycosidase F (PNGase F) prior to digestion and subsequent mass spectrometry analysis has been shown to improve coverage of various N-linked glycopeptides, but inclusion of this step may add up to a day to an already lengthy sample preparation process. An efficient way to integrate deglycosylation with bottom-up proteomics would be a valuable contribution to the glycoproteomics field. Here, we demonstrate a proteomics workflow in which deglycosylation and proteolytic digestion of samples occurs simultaneously using suspension trapping (S-Trap). This approach adds no additional time to standard digestion protocols. Applying this sample preparation strategy to a human serum sample, we demonstrate improved identification of potential N-glycosylated peptides in deglycosylated samples compared with non-deglycosylated samples, identifying 156 unique peptides that contain the N-glycosylation motif (Asparagine–X–Serine/Threonine), the deamidation modification characteristic of PNGase F, and an increase in peptide intensity over a control sample. We expect that this rapid sample preparation strategy will assist in the identification and quantification of both known and potential glycoproteins. Data are available via ProteomeXchange with identifier PXD037921. | Christine DeRosa; Simon Weaver; Chien-Wei Wang; Naviya Schuster-Little; Rebecca Whelan | Analytical Chemistry | CC BY 4.0 | CHEMRXIV | 2022-11-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63640b0f311072e325fbee90/original/simultaneous-n-deglycosylation-and-digestion-of-complex-samples-on-s-traps-enables-efficient-glycosite-hypothesis-generation.pdf |
649ea2926e1c4c986b9592a2 | 10.26434/chemrxiv-2022-rcq28-v2 | Crystallographic and geometrical dependence of water oxidation activity in Co-based layered hydroxides | Cobalt-based layered hydroxides (LHs) stand out as one of the best families of electroactive materials for the alkaline oxygen evolution reaction (OER). However, fundamental aspects such as the influence of the crystalline structure and its connection with the geometry of the catalytic sites remain poorly understood. Thus, to address this topic we have conducted a thorough experimental and in silico study on the most important divalent Co-based LHs (i.e.: ɑ-LH, β-LH and LDH) which allows us to understand the role of the layered structure and coordination environment of divalent Co atoms on the OER performance. The ɑ-LH, containing both octahedral and tetrahedral sites, behaves as the best OER catalyst in comparison to the other phases, pointing out the role of the chemical nature of the crystalline structure. Indeed, density functional theory (DFT) calculations confirm the experimental results which can be explained in terms of the more favourable reconstruction into active Co(III)-based oxyhydroxide-like phase (dehydrogenation process) as well as the significantly lower calculated overpotential across the OER mechanism for the ɑ-LH structure (exhibiting lower Egap). Furthermore, ex-situ X-ray diffraction and absorption spectroscopy reveal the permanent transformation of ɑ-LH phase into a highly reactive oxyhydroxide-like stable structure under ambient conditions. Hence, our findings highlight the key role of tetrahedral sites on the electronic properties of the LH structure as well as their inherent reactivity towards OER catalysis, paving the way for the rational design of more efficient and low-maintenance electrocatalysts. | Roger Sanchis-Gual; Diego Hunt; Camilo Jaramillo-Hernandez; Álvaro Seijas-Da Silva; Martín Mizrahi; Carlo Marini; Víctor Oestreicher; Gonzalo Abellán | Inorganic Chemistry; Catalysis; Energy; Electrochemistry; Solid State Chemistry; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649ea2926e1c4c986b9592a2/original/crystallographic-and-geometrical-dependence-of-water-oxidation-activity-in-co-based-layered-hydroxides.pdf |
60c745fcee301c52eac79423 | 10.26434/chemrxiv.10299428.v1 | Extension and Evaluation of the D4 London Dispersion Model for Periodic Systems | <div>London-dispersion effects are of great relevance to many aspects of materials science and for various condensed matter problems. In this work we present an adaptation and implementation of the DFT-D4 model [Caldeweyher et al., J. Chem. Phys., 2019, 150, 154122] for periodic systems. The main new ingredient are better computed reference polarizabilities for high coordination numbers (including alkaline metals, earth alkaline metals, and d-metals of group 3-5), which are consistently derived from periodic electrostatically embedded cluster calculations. Some technical extensions have been added concerning the coordination number, the partial charges, and the dispersion energy expression. To demonstrate the performance of the improved scheme, several test cases are considered, for which we compare D4 results to those of its predecessor D3(BJ) as well as to several other dispersion corrected methods. The largest improvements are observed for solid state polarizabilities of 16 inorganic salts, where the new D4 model achieves an unprecedented accuracy, surpassing its predecessor as well as other, computationally much more demanding approaches. For cell volumes and lattice energies of two sets of chemically diverse molecular crystals, the accuracy gain is less pronounced compared to the already excellently performing D3(BJ) method. For the challenging adsorption energies of small organic molecules on metallic as well as on ionic surfaces, DFT-D4 provides high accuracy similar to MBD/HI or uncorrected DFT/SCAN approaches. These results suggest the standard application of the proposed periodic D4 model as a physically improved yet computationally efficient dispersion correction for standard DFT calculations as well as low-cost approaches like semi-empirical or even force-field models.</div> | Eike Caldeweyher; Jan-Michael Mewes; Sebastian Ehlert; Stefan Grimme | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745fcee301c52eac79423/original/extension-and-evaluation-of-the-d4-london-dispersion-model-for-periodic-systems.pdf |
66310dbf21291e5d1d186bda | 10.26434/chemrxiv-2023-9ggbk-v2 | Influence of Strong pi-Acceptor Ligands on Cr-K-edge X-Ray Absorption Spectral Signatures and Consequences on Interpretation of Surface Sites in the Phillips Catalyst | X-ray absorption spectroscopy (XAS) is one of the most powerful characterization techniques, that has been intensively employed to study the Phillips polymerization catalyst (CrO3/SiO2). While Cr K-edge XAS signatures are used to evaluate the nature of surface (active) sites, they are highly sensitive to oxidation state, geometry and types of ligands, making interpretation challenging. In the specific case of CrO3/SiO2, CO has been particularly used both as a reductant to generate the expected low valent Cr sites and a probe to understand surface Cr sites. Considering the electronic properties of CO, a strong sigma-donor and pi-acceptor ligand, one may wonder the impact of the coordination of CO on Cr on its XAS signature. We herein built a molecular low-valent Cr library bearing isocyanide ligands, which mimic CO as its isoelectronic counterpart, as a model of low-valent Cr sites interacting with pi-acceptor ligand. Cr K-edge XAS augmented with DFT calculations elucidated the profound effect of isocyanide ligand on both XANES and EXAFS regions giving a rise to characteristic features as well as the significant stabilization of low-spin Cr(II/III) species, which potentially alter the ease of interpretation of XAS spectra. Taking the herein demonstrated effect of pi-acceptor ligand into account, experimental Cr K-edge spectra of reduced Phillips catalyst at different temperatures, with/without interaction with CO, were nicely reproduced. | Yuya Kakiuchi; Svetlana Shapovalova; Bogdan Protsenko; Sergey Guda; Olga V. Safonova; Alexander Guda; Christophe Copéret | Inorganic Chemistry; Catalysis; Spectroscopy (Inorg.); Transition Metal Complexes (Inorg.); Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66310dbf21291e5d1d186bda/original/influence-of-strong-pi-acceptor-ligands-on-cr-k-edge-x-ray-absorption-spectral-signatures-and-consequences-on-interpretation-of-surface-sites-in-the-phillips-catalyst.pdf |
65a1ad619138d23161c97bc3 | 10.26434/chemrxiv-2024-rwj5z | A robust “bottom up” proteomics pipeline is integral for assessing protein structure using hydroxyl radical protein footprinting mass spectrometry. | Hydroxyl Radical Protein Footprinting (HRPF) monitors macromolecular structure and dynamics by utilizing hydroxyl radicals to probe the solvent-accessible side chains of proteins. Hydroxyl radicals form irreversible covalent bonds with protein side chains based on their solvent accessibility and intrinsic reactivity. Following labeling, bottom-up proteomics which involves protease digestion and liquid chromatography (LC-MS/MS) coupled with mass spectrometry, is routinely employed to detect and quantify the modified protein side chains. The HRPF technique has been a breakthrough in the field of structural biology, enabling the assessment of structures and interrelationships between proteins, protein-drug complexes or such macromolecular mixtures. It is now being extended to complex applications such as in-cell and in-vivo studies. This perspective focuses on detailing aspects of peptide separations technology in HRPF, with a particular emphasis on chromatography. The discussion further encompasses the HRPF methodology, its current limitations, recent developments, and proposed ideas for future developments for selected research fields. | Rohit Jain; Nayeon Jeon; Janna Kiselar; Mark R. Chance | Analytical Chemistry; Analytical Chemistry - General; Mass Spectrometry; Separation Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a1ad619138d23161c97bc3/original/a-robust-bottom-up-proteomics-pipeline-is-integral-for-assessing-protein-structure-using-hydroxyl-radical-protein-footprinting-mass-spectrometry.pdf |
628f975f9e332683f6fadb2f | 10.26434/chemrxiv-2022-4qxd5-v2 | Non-bonded force field parameters from MBIS partitioning of the molecular electron density improve CB7 host-guest affinity predictions | Binding affinity prediction by means of computer simulation has been increasingly incorporated in drug discovery projects. Its wide application, however, is limited by the prediction accuracy of the free energy calculations. The main error sources are force fields used to describe molecular interactions and incomplete sampling of the configurational space. Organic host-guest systems have been used to address force field quality because they share similar interactions found in ligands and receptors, and their rigidity facilitates configurational sampling. Here, we test the binding free energy prediction accuracy for 14 guests with aromatic or adamantane core and the CB7 host using molecular electron density derived non-bonded force field parameters. We developed a computational workflow written in Python to derive atomic charges and Lennard-Jones parameters with the minimal basis iterative stockholder method using the polarized electron density of several configurations of each guest in the bound and unbound state. The resulting non-bonded force field parameters improve binding affinity prediction, especially for guests with adamantane core in which repulsive exchange and dispersion interactions to the host dominate. | Duvan Gonzalez; Luis Macaya; Carlos Castillo-Orellana; Toon Verstraelen; Stefan Vogt-Geisse; Esteban Vöhringer-Martinez | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Computational Chemistry and Modeling; Theory - Computational; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628f975f9e332683f6fadb2f/original/non-bonded-force-field-parameters-from-mbis-partitioning-of-the-molecular-electron-density-improve-cb7-host-guest-affinity-predictions.pdf |
619ca21158bc4bdfb19f9981 | 10.26434/chemrxiv-2021-gjt11 | Selective extraction of biomolecules using a bidirectional flow filter | We present a microfluidic device for selective separation and extraction of molecules based on their diffusivity. The separation relies on electroosmotically-driven bidirectional flows in which high diffusivity species experience a net-zero velocity, and lower diffusivity species are advected to a collection reservoir. The device can operate continuously and is suitable for processing low sample volumes. Using several model systems, we showed that the extraction efficiency of the system is maintained at more than 90% over tens of minutes, with a purity of more than 99%. We demonstrate the applicability of the device to the extraction of genomic DNA from short DNA fragments. | Vesna Bacheva; Federico Paratore; Maya Dolev; Baruch Rofman; Govind Kaigala; Moran Bercovici | Analytical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/619ca21158bc4bdfb19f9981/original/selective-extraction-of-biomolecules-using-a-bidirectional-flow-filter.pdf |
62b7cd020bba5de62e753c8c | 10.26434/chemrxiv-2022-1vs9p | Techno-economic analysis on recent heterogeneous catalysts for ammonia synthesis | The economic performance of recently developed catalysts for ammonia synthesis, Ru/Ca(NH2)2 and Ru/Pr2O3, are evaluated by process simulation using ASPEN Plus. The results show that catalyst costs are high due to expensive ruthenium; thus, the catalysts' lifetime significantly influences the total cost. Besides, the new catalysts are advantageous when the electricity cost is high and the production scale is small, which are the characteristics of the case in which renewable energy is employed. Finally, the future direction of the catalyst developments is discussed. | Takaya Ogawa; Masaki Yoshida; Keiichi Ishihara N. | Theoretical and Computational Chemistry; Chemical Engineering and Industrial Chemistry; Industrial Manufacturing; Thermodynamics (Chem. Eng.); Transport Phenomena (Chem. Eng.) | CC BY 4.0 | CHEMRXIV | 2022-06-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b7cd020bba5de62e753c8c/original/techno-economic-analysis-on-recent-heterogeneous-catalysts-for-ammonia-synthesis.pdf |
62ec08a03b834e2a53e50c7f | 10.26434/chemrxiv-2022-spw0d-v4 | Absence of Relevant Thermal Conversion of Cannabidiol (CBD) to Tetrahydrocannabinol (THC) in E-Cigarette Vapor and Low-THC Cannabis Smoke | Introduction: Recent research claimed that cannabidiol (CBD) in commercial electronic cigarette (e-cigarette) liquids can be converted into psychotropic amounts of ∆9-tetrahydrocannabinol (THC). This study aims to validate this claim using a realistic e-cigarette setup. Additionally, this study also investigates if such a conversion may occur during smoking of CBD-rich cannabis joints.
Methods: Two different CBD liquids were vaporized using two different e-cigarette models, one of which was operated at extreme energy settings (0.2 Ω and 200 W). The smoke of six CBD joints was collected using a rotary smoking machine according to ISO 4387:2019. Analyses were conducted using nuclear magnetic resonance (NMR) spectrometry as well as liquid chromatography tandem mass spectrometry (LC-MS/MS).
Results: For the condensed e-cigarette liquids, no increase in THC concentration could be observed. For the CBD joints, no THC formation was provable. The recovered THC concentrations were ranging between 1% and 48% (0.034 mg and 0.73 mg) of the THC amount initially contained in the joints before smoking.
Conclusions: Using realistic conditions of consumer exposure, relevant conversion of CBD to THC appears to not be occurring. The health risk of CBD liquids for electronic cigarettes, as well as low-THC cannabis intended for smoking, can be assessed by concentrations in the source material without the need to consider significant changes in psychotropic compounds during use by consumers.
| Pascal Hindelang; Andreas Scharinger; Patricia Golombek; Miriam Laible; Sandra Tamosaite; Stephan G. Walch; Dirk W. Lachenmeier | Biological and Medicinal Chemistry; Analytical Chemistry; Agriculture and Food Chemistry; Mass Spectrometry; Spectroscopy (Anal. Chem.); Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2022-08-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ec08a03b834e2a53e50c7f/original/absence-of-relevant-thermal-conversion-of-cannabidiol-cbd-to-tetrahydrocannabinol-thc-in-e-cigarette-vapor-and-low-thc-cannabis-smoke.pdf |
60c748c64c89197b8aad2fa0 | 10.26434/chemrxiv.11967735.v1 | Engineering of Ultrafast High Efficiency Light-Harvesters | Nature provides evidence that there is no fundamental limit for harvesting and funneling nearly all scattered sun-photons onto smaller conversion centers by ultra-fast emergy transfer processes. Recently, a proof-of-principle study showed that this can also be achieved by artificial systems containing light-harvesting pools of randomly oriented molecules that funnel energy to individual, aligned light-redirecting molecules.<br />However, capturing the entire solar spectrum requires engineering of complex multi-element structures considering macroscopic refraction and wave guiding of different spectral ranges of multijunction photovoltaics as well as ultrafast, nanoscopic light-harvesting, energy transfer and funneling, anisotropic absorption and emission and the spectra of a multitude of pigments of different orientations and concentrations. So far, no tool excited that allowed model such structures in one system.<br />Here we present a ray tracing tool allowing to model and analyze such multi-scale structures, including molecular, ultrafast energy transfer and funneling as well as anisotropic absorption and emission as well as micro-and macroscopic waveguiding and raytracing in one tool. We present first results of solar concentrator architectures with the highest theoretical energy conversion efficiency reported so far.<br />A novel tool is provided that allows to construct, model and analyze any desired complex ultrafast light-harvesting/photovoltaic architecture with the highest efficiencies by considering molecular, nanometric energy transfer and funneling as well as microscopic waveguiding and raytracing. | Andreas Albrecht; Julia Nowak; Peter Walla | Photovoltaics | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748c64c89197b8aad2fa0/original/engineering-of-ultrafast-high-efficiency-light-harvesters.pdf |
6789b97d81d2151a02773344 | 10.26434/chemrxiv-2025-r709q | Phase engineering of 1T′-MoS2 via organic enwrapment | Molybdenum disulfide (MoS2) is a layered material known to show various phases. Most studies on it have focused on its semiconductor phase, but it is known to also have a metallic 1T′ phase. This 1T′ phase has also drawn attention as a quantum spin Hall phase, but the 1T′ phase is metastable, and the method of transforming or stabilizing it has not been established. This paper demonstrates a method of effectively transforming the monolayer or the topmost layer of multilayer semiconductor MoS2 (the 1H or 2H phase) into the 1T′ phase via ultraviolet-ozone (UVO) treatment, followed by polymer enwrapment of the MoS2 surface. UVO induces the transformation of the 1H (2H) phase into the 1T′ phase, but the generated phase is unstable. The enwrapment procedure with the polymer poly-L-lysine was found to be effective in transforming the 1H (2H) phase into the 1T′ phase and stabilizing it. Moreover, this procedure transformed only the topmost layer and generated a vertical 1T′/2H heterostructure in multilayer cases. This study shows the high potential of surface organic chemical procedures to control the phases in 2D transition metal dichalcogenides. | Keigo Matsuyama; Limi Chen; Kohei Aso; Kaito Kanahashi; Kosuke Nagashio; Yoshifumi Oshima; Daisuke Kiriya | Materials Science; Hybrid Organic-Inorganic Materials; Nanostructured Materials - Materials; Thin Films | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6789b97d81d2151a02773344/original/phase-engineering-of-1t-mo-s2-via-organic-enwrapment.pdf |
62056dd6cbb4f40603bca0ed | 10.26434/chemrxiv-2022-v8zlp | Fischerazoles A-C, cyanobacterial polychlorinated lipids featuring fatty acyl chain rearrangement | Fatty acyl moieties are a very common feature of cyanobacterial secondary metabolites. Using a recently developed method to discover fatty acyl-containing natural products, we detected and isolated three new lipopeptides – fisch-erazoles A-C (1-3) – from the cyanobacterium Fischerella sp. PCC 9431. These metabolites present extensive halo-genation in their fatty acyl moiety as well as an unusual pendant allyl alcohol. We analyzed the genome sequence of the producing cyanobacterium and identified a putative biosynthetic gene cluster associated with the fischera-zoles, based on bioinformatic analysis. Using stable-isotope precursor feeding experiments, we identified the key substrates for the biosynthesis of 1-3. Surprisingly, we found that hexadecanoic acid was fully incorporated into fischerazoles, despite the fact that these compounds have a linear 15-carbon chain. Additional feeding experiments with stable-isotope labeled fatty acids established a one-carbon contraction of the palmitic acid-derived alkyl chain, and that the remaining carbon branches out as part of the pendant allyl alcohol group. This rearrangement, which leads to the functionalization of a mid-chain aliphatic carbon, might be of interest for biocatalysis. Our findings reinforce the utility of metabolomics-based methods to uncover natural product scaffolds with a high degree of novelty. | Sandra Figueiredo; Kathleen Abt; Teresa Martins; Iñaki Lacomba; Abel Forero; Carlos Jiménez; Jaime Rodríguez; Pedro Leão | Biological and Medicinal Chemistry; Biochemistry; Chemical Biology; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62056dd6cbb4f40603bca0ed/original/fischerazoles-a-c-cyanobacterial-polychlorinated-lipids-featuring-fatty-acyl-chain-rearrangement.pdf |
63c95b6930e3e57fe6962e7b | 10.26434/chemrxiv-2022-285bs-v2 | Anaerobic Hydroxylation of C(sp3)–H Bonds Enabled by the Synergistic Nature of Photoexcited Nitroarenes | A photoexcited nitroarene-mediated, anaerobic C–H hydroxylation of aliphatic systems is reported. The success of this reaction is due to the bifunctional nature of the photoexcited nitroarenes, which serve as the C–H bond activator and the oxygen atom source. Compared to previous methods, this approach is cost and atom economical due to the commercial availability of the nitroarene, the sole mediator of the reaction. Owing to the anaerobic conditions of the transformation, a noteworthy expansion in substrate scope can be obtained compared to prior reports. Mechanistic studies support that the photoexcited nitroarenes engage in successive hydrogen atom transfer and radical recombination events with hydrocarbons, leading to N-arylhydroxylamine ether intermediates. Spontaneous fragmentation of these intermediates leads to the key oxygen atom transfer products. | Joshua Paolillo; Alana Duke; Emma Gogarnoiu; Dan Wise; Marvin Parasram | Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63c95b6930e3e57fe6962e7b/original/anaerobic-hydroxylation-of-c-sp3-h-bonds-enabled-by-the-synergistic-nature-of-photoexcited-nitroarenes.pdf |
622774605f1d9ae793b510c4 | 10.26434/chemrxiv-2022-w2x2w | Hydrogen Bond Redistribution Effects in Mixtures of Protic Ionic Liquids Sharing the Same Cation: Nonideal Mixing
with Large Negative Mixing Enthalpies | We report a joint experimental and theoretical study characterising the hydrogen bond (HB) redistribution in mixtures of two different protic ionic liquids (PILs) sharing the same cation: triethylammonium-methanesulfonate ([TEA][OMs]) and triethylammonium-trifluoromethanesulfonate ([TEA][OTf]). The mixing behaviour deviates strongly from ideality, exhibiting large negative energies of mixing. In the PIL, the [TEA] cation acts as a HB donor, being able to donate a single HB. Both, the [OMs] and the [OTf] anions can act as HB acceptors, which can accept multiple HBs via their respective SO3-groups. We use a combination of molecular dynamics (MD) simulations, calorimetry, and $^1$H-NMR chemical shift measurements to determine the difference in HB strength between the two species to be about 13 kJ/mol, favouring the [TEA]-[OMs] interaction. Based on our MD simulations we are able to formulate a lattice model, discriminating between HB and nonspecific intermolecular interactions. We demonstrate that, due to the ordered structure of the PILs, only the HB interactions contribute to the mixing energy. This allows to us to connect the equilibrium of HBs to each of the two anion species with the mixing energies by a simple relation, which is obeyed by both, MD-simulation as well as experimental calorimetry and 1H-NMR chemical shift data. | Benjamin Golub; Daniel Ondo; Viviane Overbeck; Ralf Ludwig; Dietmar Paschek | Physical Chemistry; Physical and Chemical Properties | CC BY NC 4.0 | CHEMRXIV | 2022-03-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/622774605f1d9ae793b510c4/original/hydrogen-bond-redistribution-effects-in-mixtures-of-protic-ionic-liquids-sharing-the-same-cation-nonideal-mixing-with-large-negative-mixing-enthalpies.pdf |
66c71a9aa4e53c48763b9880 | 10.26434/chemrxiv-2024-7414b | β-Selective 2-Deoxy- and 2,6-Dideoxyglucosylations Catalyzed by Bis-Thioureas | We present methods for β-selective 2-deoxy and 2,6-dideoxyglucosylations of natural products, carbohydrates, and amino acids using bis-thiourea hydrogen-bond-donor catalysts. Disarming ester protecting groups were necessary to counter the high reactivity of 2-deoxyglycosyl electrophiles toward non-stereospecific SN1 pathways. Alcohol and phenol nucleophiles with both base- and acid-sensitive functionalities were compatible with the catalytic protocol, enabling access to a wide array of 2-deoxy-β-O-glucosides. | Peyton D. Beyer; Michael M. Nielsen; Elias N. Picazo; Eric N. Jacobsen | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Stereochemistry; Organocatalysis | CC BY 4.0 | CHEMRXIV | 2024-08-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c71a9aa4e53c48763b9880/original/selective-2-deoxy-and-2-6-dideoxyglucosylations-catalyzed-by-bis-thioureas.pdf |
61c945ba02c214b800336892 | 10.26434/chemrxiv-2021-955q8-v2 | Dynamic Pt-OH-•H2O-Ag Species Mediate Synergetic Electron and Proton Transfer for Catalytic Hydride Reduction of 4-Nitrophenol at Confined Nanoscale Interface | The nature of interfacial state and/or bonding at heterogeneous nanoscale surface of bimetals remains elusive. For very classical probe reaction of catalytic hydride catalytic reduction of –NO2 to NH2 (herein reduction of 4-NP to 4-AP as an example), three abnormal experimental phenomena cannot be elucidated as such: 1) the hydrogen source of final product of 4-AP is originated from water solvent, rather than NaBH4 reducer; 2) reverse electron transfer between bimetals was observed, which is resisted to the normal thermaldynamic law; 3) even in the absence of any metals, for example just using carbon nanodots as supports, the reaction occurs. These observations indicates that the reduction of –NO2 groups did not follow the classical metal-centered electron and hydride transfer mechanism, i.e., Langmuir-Hinshelwood (L-H) mechanism. We herein provide strong evidence that, the catalytic hydride reduction of 4-NP to 4-AP is though a completely new surface hydrous hydroxyl specie mediated concerted electron and proton transfer process, wherein owing to the space overlapping of p orbitals in hydrous hydroxyl intermediate, an ensemble of interface states are dynamically formed, which could be alternative channels for concerted electron and proton transfer. The main role of second metal of Pt is to regulate the density of surface hydrous hydroxyl intermediate and its interactive strength with metals. This new mechanism not only answers all the abnormal experimental observations above mentioned, but also provide some new insights to water and/or hydroxyl group promoted reaction involved the activation of small molecules (CO2, CO, N2, H2O etc.) in areas of electrochemistry, energy storage and metalloenzyme catalysis. | kun zhang; Meng Ding; bingqian shan; bo peng; jiafeng zhou | Physical Chemistry; Catalysis; Homogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61c945ba02c214b800336892/original/dynamic-pt-oh-h2o-ag-species-mediate-synergetic-electron-and-proton-transfer-for-catalytic-hydride-reduction-of-4-nitrophenol-at-confined-nanoscale-interface.pdf |
6673e6d65101a2ffa807ea0a | 10.26434/chemrxiv-2024-29x1w-v3 | Interactional fingerprints offer an accessible, rapid, means to characterise graphene oxide. | Graphene-based materials (GBMs), including graphene oxide and graphene, are atomically thin materials with great promise, but efforts to realise this promise have been hampered by inconsistent material supply and the lack of rapid, accessible, characterisation methods. Here we present a new approach, based on surface interaction with a series of probe molecules, to rapidly provide a qualitative characterisation of graphene oxide materials at low cost, using widely available instruments. We demonstrate that our method can make qualitative comparisons, allowing us to observe if batches of material differ. Furthermore, in some circumstances it can quantify systematic differences, such as surface modification. We propose this approach may prove a valuable quality control method for materials producers and users alike and, since many applications of graphene oxide ¬— and 2D materials in general — depend on surface interactions, and suggest this kind characterisation may be valuable beyond rapid QC, in GBMs and other materials. | B. Ivonne Vergara-Arenas; Esmé Shepherd; Ivan Alfaro; Edward Cross; Huong Le; Andrew Surman | Analytical Chemistry; Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6673e6d65101a2ffa807ea0a/original/interactional-fingerprints-offer-an-accessible-rapid-means-to-characterise-graphene-oxide.pdf |
6572d9215bc9fcb5c959bf5c | 10.26434/chemrxiv-2023-9xcpw-v2 | Subsystem Density-Functional Theory (Update) | The past years since the publication of our review on subsystem density-functional theory (sDFT) [WIREs Comput. Mol. Sci. 2014, 4:325--362] have witnessed a rapid development and diversification of quantum mechanical fragmentation and embedding approaches related to sDFT and frozen-density embedding (FDE). In this follow-up article, we provide an update addressing formal and algorithmic work on FDE/sDFT, novel approximations developed for treating the non-additive kinetic energy in these DFT/DFT hybrid methods, new areas of application and extensions to properties previously not accessible, projection-based techniques as an alternative to solely density-based embedding, progress in wavefunction-in-DFT embedding, new fragmentation strategies in the context of DFT which are technically or conceptually similar to sDFT, and the blurring boundary between advanced DFT/MM and approximate DFT/DFT embedding methods. | Christoph Jacob; Johannes Neugebauer | Theoretical and Computational Chemistry; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2023-12-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6572d9215bc9fcb5c959bf5c/original/subsystem-density-functional-theory-update.pdf |
638589294b1a5f25a090e82e | 10.26434/chemrxiv-2022-wgdf7 | Kylin 1.0: An Ab-Initio Density Matrix Renormalization Group Quantum Chemistry Program | The accurate evaluation of electron correlations is highly necessary for the proper descriptions of the electronic structures in strongly correlated molecules, ranging from bond-dissociating molecules, polyradicals, to large conjugated molecules and transition metal complexes. For this purpose, in this paper, a new ab-initio quantum chemistry program Kylin 1.0 for electron correlation calculations at various quantum many-body levels, including configuration interaction (CI), perturbation theory (PT), and density matrix renormalization group (DMRG), is presented. In addtion, fundamental quantum chemical methods such as Hartree-Fock self-consistent field (HF-SCF) and the complete active space SCF (CASSCF) are aslo implemented. The Kylin 1.0 program possesses these features: (1) efficient DMRG implementation based on the matrix product operator (MPO) formulation for describing static electron correlation within a large active space composed of more than 100 orbitals, supporting both $\rm U(1)_{n} \times U(1)_{S_z}$ and $\rm U(1)_{n} \times SU(2)_{S}$ symmetries; (2) efficient second-order DMRG-self-consistent field (SCF) implementation; (3) externally-contracted multi-reference CI (MRCI) and Epstein-Nesbet PT with DMRG reference wave functions for including the remaining dynamic electron correlation outside the large active spaces. In this paper, we introduce the capabilities and numerical benchmark examples of the Kylin 1.0 program. | Zhaoxuan Xie; Yinxuan Song; Fangwen Peng; Jianhao Li; Yifan Cheng; Lingzhi Zhang; Yingjin Ma; Yingqi Tian; Zhen Luo; Haibo Ma | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/638589294b1a5f25a090e82e/original/kylin-1-0-an-ab-initio-density-matrix-renormalization-group-quantum-chemistry-program.pdf |
63dccd80fcfb27a31f5cc7cf | 10.26434/chemrxiv-2023-jg187 | Self-assembly of insulin-derived chimeric peptides into two-component amyloid fibrils: the role of Coulombic interactions | Canonical amyloid fibrils are composed of covalently identical polypeptide chains. Here, we employ kinetic assays, atomic force microscopy (AFM), infrared spectroscopy, circular dichroism (CD), and molecular dynamics (MD) to study fibrillization patterns of two chimeric peptides, ACC1-13E8 and ACC1-13K8, in which potent amyloidogenic stretch derived from the N-terminal segment of insulin A-chain (ACC1-13) is coupled to octaglutamate or octalysine segments, respectively. While the large electric charges on monomers of either peptide prevent aggregation at neutral pH, stoichiometric mixing of ACC1-13E8 and ACC1-13K8 triggers rapid self-assembly of two-component fibrils driven by favorable Coulombic interactions. The role of low-symmetry non-polar ACC1-13 pilot sequence is crucial in enforcing the amyloidal parallel -sheet motif as self-assembly of free poly-E and poly-K chains under similar conditions results in amorphous antiparallel -sheet conformation. Interestingly, the pathway to highly ordered fibrils is accessible to ACC1-13E8 also when paired with non-polypeptide polycationic amines such as branched poly-ethylenimine, PEI, instead of ACC1-13K8. Remarkably, such synthetic polycations are more effective in triggering fibrillization of ACC1-13E8 than poly-K (or poly-E in the case of ACC1-13K8). High conformational flexibility of these polyamines makes up for the apparent mismatch in periodicity of charged groups. The results are discussed in the context of mechanisms of heterogenous disease-related amyloidogenesis. | Mateusz Fortunka; Robert Dec; Wojciech Puławski; Marcin Guza; Wojciech Dzwolak | Physical Chemistry; Biological and Medicinal Chemistry; Biophysical Chemistry; Self-Assembly; Structure; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63dccd80fcfb27a31f5cc7cf/original/self-assembly-of-insulin-derived-chimeric-peptides-into-two-component-amyloid-fibrils-the-role-of-coulombic-interactions.pdf |
672e14dbf9980725cf908c37 | 10.26434/chemrxiv-2024-g66jr | Synthesis of 2-Aminobenzo[b]thiophenes via an Intramolecular Dehydrogenative C–S Bond Formation Effected by Iodine(III) Reagents | A direct synthesis of medicinal chemistry-relevant 2- aminobenzo[b]thiophenes has been achieved from substituted thioamides of 2-arylacetic acids through a fast intramolecular cross-dehydrogenative cyclization, mediated by hydroxy(tosyloxy)iodobenzene (HTIB, Koser’s reagent). This synthetic approach is operationally simple, uses easily accessible substrates, and tolerates a variety of substituents at different sites, providing an opportunity for diversification. | Dmitry Bugaenko; Alexander Karchava | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672e14dbf9980725cf908c37/original/synthesis-of-2-aminobenzo-b-thiophenes-via-an-intramolecular-dehydrogenative-c-s-bond-formation-effected-by-iodine-iii-reagents.pdf |
60c746fff96a00bf6c286e42 | 10.26434/chemrxiv.11472264.v1 | Ester Dance Reaction on the Aromatic Ring | Aromatic rearrangement reactions are useful tools in the organic chemist’s toolbox when generating uncommon substitution patterns. However, it is difficult to precisely translocate a functional group in (hetero)arene systems, with the exception of halogen atoms in a halogen dance reaction. Herein, we describe an unprecedented “ester dance” reaction: a predictable translocation of an ester group from one carbon atom to another on an aromatic ring. Specifically, a phenyl carboxylate substituent can be shifted from one carbon to an adjacent carbon on a (hetero)aromatic ring under palladium catalysis to often give a thermodynamically favored, regioisomeric product with modest to good conversions. The obtained ester moiety can be further converted to various aromatic derivatives through the use of classic as well as state-of-the-art transformations including an amidation, acylations and decarbonylative couplings. | Kaoru Matsushita; Ryosuke Takise; Kei Muto; Junichiro Yamaguchi | Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746fff96a00bf6c286e42/original/ester-dance-reaction-on-the-aromatic-ring.pdf |
6708a3c051558a15efbfefe5 | 10.26434/chemrxiv-2024-wdkmm | Mechanistic insights into early stages of iron corrosion under electrochemical conditions: A DFT study | Iron corrosion is a persistent issue across a wide range of industries, leading to both economic setbacks and safety concerns. This process is driven by electrochemical reactions that occur when the metal interacts with its surrounding environment. However, the complexity of electrochemical interfaces hinders good understanding for corrosion behaviour at the atomic scale. In this work, we employed grand canonical density functional theory (GC-DFT) along with a hybrid explicit and implicit solvation model to study the interactions between iron surface and its primary corrosive species, water and oxygen. The simulations revealed that the water molecules at the interface adopt specific orientations to achieve the optimal interactions with the surface. The GC-DFT simulations further revealed that the adsorption of water molecules strengthens at positive potentials, whereas atomic oxygen adsorption weakens under the same conditions. Moreover, water dissociation, the key step in iron corrosion, is found to be catalysed by the oxygens adsorbed on the O-bridge sites of the Fe(100) surface. The findings offer valuable insights into the initial stage electrochemical behaviour of water and oxygen on iron surfaces, contributing to a better understanding and prevention of iron corrosion. | Lakshitha Jasin Arachchige; Li Chungqing; Feng Wang | Nanoscience; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-10-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6708a3c051558a15efbfefe5/original/mechanistic-insights-into-early-stages-of-iron-corrosion-under-electrochemical-conditions-a-dft-study.pdf |
60c74fcf4c8919392aad3c85 | 10.26434/chemrxiv.12948587.v1 | Monte-Carlo Method Based QSAR Model to Discover Phytochemical Urease Inhibitors Using SMILES and GRAPH Descriptors | We developed a Monte-Carlo method based<br />QSAR model to predict urease inhibiting potency of molecules using SMILES and GRAPH<br />descriptors on an existing diverse database of urease inhibitors. The QSAR model satisfies all<br />the statistical parameters required for acceptance as a good model. The model is applied to<br />identify urease inhibitors among the wide range of compounds in the phytochemical database,<br />NPACT, as a test case. We combine the ligand-based and structure-based drug discovery<br />methods to improve the accuracy of the prediction. The method predicts pIC50 and estimates<br />docking score of compounds in the database. The method may be applied to any other database<br />or compounds designed in silico to discover novel drugs targeting urease. | Kumar Sambhav Chopdar; Ganesh Chandra Dash; Pranab Kishor Mohapatra; Binata Nayak; Mukesh Kumar Raval | Biochemistry; Bioinformatics and Computational Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74fcf4c8919392aad3c85/original/monte-carlo-method-based-qsar-model-to-discover-phytochemical-urease-inhibitors-using-smiles-and-graph-descriptors.pdf |
65eb2e449138d23161070396 | 10.26434/chemrxiv-2024-0qbj7 | Electron-deficient multicenter bonding in phase change materials: A chance for reconciliation | In the last years, a controversy has been raised regarding the nature of the chemical bond in phase change materials. Two bonding models have claimed to be able to explain their extraordinary properties: the metavalent bonding model and the hypervalent (electron-rich multicenter) bonding model. In this work, we comment that both approaches can be reconciled if we think differently by considering the pros and cons of both models and agree with a third way; i.e. phase change materials are governed by electron-deficient multicenter bonds. | Francisco Javier Manjón Herrera; Hussien Helmy Osman; Matteo Savastano; Ángel Vegas | Physical Chemistry; Inorganic Chemistry; Bonding; Materials Chemistry; Crystallography | CC BY 4.0 | CHEMRXIV | 2024-03-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65eb2e449138d23161070396/original/electron-deficient-multicenter-bonding-in-phase-change-materials-a-chance-for-reconciliation.pdf |
60c750e0567dfe2380ec5931 | 10.26434/chemrxiv.13088882.v1 | Improved Band Gaps and Structural Properties from Wannier-Fermi-Lowdin Self-Interaction Corrections for Periodic Systems | The accurate prediction of band gaps and structural properties in periodic systems continues to be one of the central goals of electronic structure theory. However, band gaps obtained from popular exchange-correlation functionals (such as LDA and PBE) are severely underestimated partly due to the spurious self-interaction error (SIE) inherent to these functionals. In this work, we present a new formulation and implementation of Wannier function-derived Fermi-Lowdin (WFL) orbitals for correcting the SIE in periodic systems. Since our approach utilizes a variational minimization of the self-interaction energy with respect to the Wannier charge centers, it is computationally more efficient than the HSE hybrid functional and other self-interaction corrections that require a large number of transformation matrix elements. Calculations on several (17 in total) prototypical molecular solids, semiconductors, and wide-bandgap materials show that our WFL self-interaction correction approach gives better band gaps and bulk moduli compared to semilocal functionals, largely due to the partial removal of self-interaction errors. | Ravindra Shinde; Sharma Yamijala; Bryan Wong | Optical Materials; Theory - Inorganic; Computational Chemistry and Modeling; Theory - Computational; Physical and Chemical Properties; Quantum Mechanics; Structure; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750e0567dfe2380ec5931/original/improved-band-gaps-and-structural-properties-from-wannier-fermi-lowdin-self-interaction-corrections-for-periodic-systems.pdf |
6637abb191aefa6ce139fc72 | 10.26434/chemrxiv-2024-h523h | Single vs. Blended Electrolyte Additives: Impact of a Sulfur-Based Electrolyte Additive on Electrode Cross-talk and Electrochemical Performance of LiNiO2||Graphite Cells | Lithium nickel oxide (LNO) is an attractive positive electrode active material for lithium ion batteries (LIBs) due to its high reversible specific capacity and absence of cobalt. Nevertheless, it is prone to structural instabilities that lead to rapid capacity fading, safety concerns and shows in average a lower voltage than mixtures with cobalt, limiting its applicability to date. Herein we introduce the sulfur-based electrolyte additive, benzo[d][1,3,2]dioxathiole 2,2-dioxide (DTDPh), to stabilize the LNO electrode and study its effects on interphase compositions by means of complementary electrochemical and spectroscopic techniques. Obtained results demonstrate an improved galvanostatic cycling performance in terms of cycle life and achievable specific discharge capacity that significantly outperform the common film-forming additive vinylene carbonate (VC). The cycle life was increased from 102 to 147 cycles compared to the baseline electrolyte and the accumulated discharge energy until end of life was increased by 45%. This study furthermore provides strong evidence of a significant cross-talk and negative interplay between DTDPh and VC when both are present in the electrolyte formulation. Mechanistic consideration based on density functional theory (DFT) calculations suggest the formation of mobile poly(VC) species, which is supported by the results of post mortem analysis of the resulting interphases. | Christian Wölke; Anass Benayad; Thanh-Loan Lai; Felix Hanke; Giorgio Baraldi; María Echeverría; Ekin Esen; Elixabete Ayerbe; Alex Neale; Jacqui Everitt; Laurence Hardwick; Peng Yan; Marcin Poterała; Władysław Wieczorek; Martin Winter; Isidora Cekic-Laskovic | Energy; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6637abb191aefa6ce139fc72/original/single-vs-blended-electrolyte-additives-impact-of-a-sulfur-based-electrolyte-additive-on-electrode-cross-talk-and-electrochemical-performance-of-li-ni-o2-graphite-cells.pdf |
67c0939881d2151a02528e14 | 10.26434/chemrxiv-2025-m2nqq | ANI-1xBB: an ANI based reactive potential | Reactive potentials serve as essential tools for investigating chemical reactions with moderate computational costs. However, traditional reactive potentials often depend on fixed, semi-empirical parameters, which limits their accuracy and transferability. Overcoming these limitations can significantly expand the applicability of reactive potentials, enabling the simulation of a broader range of reactions under diverse conditions and the prediction of reaction properties, such as barrier heights. This work introduces ANI-1xBB, a novel ANI-based reactive ML potential trained on off-equilibrium molecular conformers generated through an automated bond-breaking workflow. ANI-1xBB significantly enhances the prediction of reaction energetics, barrier heights, and bond dissociation energies, surpassing conventional ANI models. Our results show that ANI-1xBB improves transition state modeling and reaction pathway prediction while generalizing effectively to pericyclic reactions and radical-driven processes. Furthermore, the automated data generation strategy supports the efficient construction of large-scale, high-quality reactive datasets, reducing reliance on expensive QM calculations. This work highlights ANI-1xBB as a practical model for accelerating the development of reactive machine learning potentials, offering new opportunities for modeling reaction phenomena. | Shuhao Zhang; Roman Zubatyuk; Yinuo Yang; Adrian Roitberg; Olexandr Isayev | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c0939881d2151a02528e14/original/ani-1x-bb-an-ani-based-reactive-potential.pdf |
64a2d02f9ea64cc1675f89d7 | 10.26434/chemrxiv-2023-lh8vr-v3 | On the role of charge transfer in many-body non-covalent interactions | Charge transfer is one of the mechanisms involved in non-covalent interactions. In molecular dimers, its contribution to pairwise interaction energies has been studied extensively using a variety of interaction energy decomposition schemes. In polar interactions such as hydrogen bonds, it can contribute ten or several tens of percent of the interaction energy. Less is known about its importance in higher-order interactions in many-body systems, mainly because of the lack of methods applicable to this problem. In this work, we extend our method for the quantification of the charge-transfer energy based on constrained DFT to many-body cases and apply it to model trimers extracted from molecular crystals. Our calculations show that charge transfer can account for a large fraction of the total three-body interaction energy. This also has implications for DFT calculations of many-body interactions in general as it is known that many DFT functionals struggle to describe charge-transfer effects correctly. | Jan Řezáč; Aurélien de la Lande | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a2d02f9ea64cc1675f89d7/original/on-the-role-of-charge-transfer-in-many-body-non-covalent-interactions.pdf |
60c74fb0f96a0051ed287cbe | 10.26434/chemrxiv.12845849.v2 | Expanding the Scope of Palladium-Catalyzed B – N Cross- Coupling Chemistry in Carboranes | <p>Here we show that azide, sulfonamide, cyanate, and phosphoramidate nucleophiles can be straightforwardly cross-coupled onto the B(9) vertices of the o- and m-carborane core from readily accessible precursors without significant deboronation by-products, laying the</p>
<p>groundwork for further study into the utility and properties of these new B-aminated carborane species.</p> | Xin Mu; Rafal Dziedzic; Arnold L. Rheingold; Ellen Sletten; Jonathan Axtell; Alexander Spokoyny; Morgan Hopp | Main Group Chemistry (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74fb0f96a0051ed287cbe/original/expanding-the-scope-of-palladium-catalyzed-b-n-cross-coupling-chemistry-in-carboranes.pdf |
66cf8923a4e53c4876ed16ac | 10.26434/chemrxiv-2024-x7xkz-v2 | Modeling and Comparative Analysis of CO2 Absorption Columns in Electrochemical and Thermochemical Carbon Capture Systems | Deployment of post-combustion carbon dioxide (CO2) capture technologies is needed to reduce emissions from power and industrial sources. Comparisons between existing thermochemical CO2 capture methods and emerging electrochemical concepts can help contextualize the promise of these new approaches. Here, we investigate the required absorber sizes for three capture systems: amine scrubbing using monoethanolamine (MEA), direct electrochemical (redox-active sorbent), and indirect electrochemical (pH-swing). For the electrochemical systems, we study how column size varies as a function of molecular properties and operating conditions, finding that parameters most closely related to CO2 uptake rates (i.e., rate constants and pKa) have the greatest impact. Through a Monte Carlo analysis, we find that the direct process can be designed to have column sizes similar to the thermochemical process, however, the CO2 uptake rate in the indirect process is too slow to enable smaller columns. Broadly, this work connects system input parameters to absorber performance for electrochemical CO2 capture and provides a foundation for technoeconomic and engineering analyses. | Katelyn M. Ripley; Fikile R. Brushett | Chemical Engineering and Industrial Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66cf8923a4e53c4876ed16ac/original/modeling-and-comparative-analysis-of-co2-absorption-columns-in-electrochemical-and-thermochemical-carbon-capture-systems.pdf |
64ea952b3fdae147fae6022b | 10.26434/chemrxiv-2023-r1pps | Structural Characterization and Ligand-Induced Conformational Changes of SenB, a Se-Glycosyltransferase Involved in Selenoneine Biosynthesis | Selenium (Se) is an essential micronutrient that is found naturally in proteins, nucleic acids, and natural products. Unlike selenoproteins and selenonucleic acids, little is known about the structures of the biosynthetic enzymes that incorporate Se into small molecules. Here, we report the X-ray crystal structure of SenB, the first known Se-glycosyltransferase that was recently found to be involved in the biosynthesis of the Se-containing metabolite selenoneine. SenB catalyzes C–Se bond formation using selenophosphate and an activated uridine diphosphate sugar as a Se and glycosyl donor, respectively, making it the first known selenosugar synthase and only one of four bona fide C–Se bond-forming enzymes discovered to date. Our crystal structure, determined to 2.25 Å resolution, reveals that SenB is a type B glycosyltransferase, displaying the prototypical fold with two globular Rossmann-like domains and a catalytic interdomain cleft. By employing complementary structural biology techniques, we find that SenB undergoes both local and global substrate-induced conformational changes, demonstrating a significant increase in α-helicity and a transition to a more compact conformation. Our results provide the first structure of SenB and set the stage for further biochemical characterization in the future. | Kendra Ireland; Chase Kayrouz; Jonathan Huang; Mohammad Seyedsayamdost; Katherine Davis | Biological and Medicinal Chemistry; Biochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ea952b3fdae147fae6022b/original/structural-characterization-and-ligand-induced-conformational-changes-of-sen-b-a-se-glycosyltransferase-involved-in-selenoneine-biosynthesis.pdf |
6448e8dbdf78ec5015694d2b | 10.26434/chemrxiv-2023-rsb4t | Zero- to Low-field Relaxometry of Chemical and Biological Fluids | NMR relaxometry is an analytical method that provides information about the molecular environment, including even NMR “silent” molecules (spin-0), by analyzing the properties of NMR signals versus the magnitude of the longitudinal field. Conventionally, this technique has been performed at fields much higher than Earth’s magnetic field, but in this work, we present NMR relaxometry at zero and ultra-low magnetic fields (ZULFs). Operation under ZULFs allows us to investigate many slow (bio)chemical processes, whose timescale (milliseconds-seconds) coincides with a timescale of spin evolution. ZULFs regime also limits the detrimental role of T2 dephasing, which, in heterogeneous samples, is induced by magnetic susceptibility and often leads to line broadening, hence low-resolution spectra. Finally, in contrast to their high-field NMR, ZULF NMR measurements can be performed with inexpensive, portable/small-size sensors (atomic magnetometers). Here, we use ZULF NMR relaxometry in the analysis of (bio)chemical compounds containing 1H 13C, 1H-15N, and 1H-31P spin pairs. We also detected high-quality ULF NMR spectra of human whole blood at 0.8 μT, despite a shortening of spin relaxation by blood proteomes (e.g., hemoglobin). Information on relaxation times of blood, a potential early biomarker of inflammation, can be obtained in less than a minute and without the need for a sophisticated apparatus. | Seyma Alcicek; Piotr Put; Adam Kubrak; Fatih Celal Alcicek; Danila Barskiy; Stefan Gloeggler; Jakub Dybas; Szymon Pustelny | Physical Chemistry; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2023-04-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6448e8dbdf78ec5015694d2b/original/zero-to-low-field-relaxometry-of-chemical-and-biological-fluids.pdf |
60c750c30f50db1405397608 | 10.26434/chemrxiv.13078913.v1 | An Efficient Discovery of Active, Selective and Stable Catalysts for Electrochemical H2O2 Synthesis Through Active Motif Screening | <div>
<div>
<div>
<p>Electrochemical reduction of O2 provides a clean and decentralized pathway to produce H2O2 compared to the current energy-intensive anthraquinone process. As the
electrochemical reduction of O2 proceeds via either two-electron or four-electron path-
way, it is thus essential to control the selectivity as well as to maximize the catalytic
activity. Siahrostami et al. demonstrated a novel approach to control the reaction
pathway by optimizing an adsorption ensemble to tune adsorption sites of reaction
intermediates, and identified Pt-Hg catalysts from density functional theory (DFT)
calculations and experimentally validated this catalyst (Nat. Mater. 2013, 12, 1137).
Inspired by this concept, in this work, we apply a state-of-the-art high-throughput
screening to develop O2 reduction catalyst for selective H2O2 production. Starting
from Materials Project database, we evaluate activity, selectivity and electrochemical stability. To efficiently perform the screening, we introduce an active motif based
approach which pre-screens unpromising materials and only performs DFT calculations for promising materials, which significantly reduce the number of the required
calculations. We not only provide a list of promising candidates identified by DFT calculations, but also suggest element species to achieve high catalytic activity or H2O2
selectivity for future experimental attempts. Finally, we discuss a strategy for efficient future high-throughput screening using a machine learning pipeline consisting of
a non-linear dimension reduction and a density-based clustering.
</p>
</div>
</div>
</div> | Seoin Back; Jonggeol Na; Zachary Ulissi | High-throughput Screening; Electrocatalysis; Heterogeneous Catalysis; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750c30f50db1405397608/original/an-efficient-discovery-of-active-selective-and-stable-catalysts-for-electrochemical-h2o2-synthesis-through-active-motif-screening.pdf |
60f15de5e0c60f02aae11be3 | 10.26434/chemrxiv-2021-hzbc5 | Functionalization of mono- and bimetallic MIL-100(Al,Fe) MOFs by ethylenediamine: post-functionalization, Brønsted acido-basicity and unique CO2 sorption behaviour | The metal sites of MIL-100(Fe), MIL-100(Fe,Al) and MIL-100(Al) MOFs were decorated with ethylenediamine (EN). Interestingly, the Al-containing MOFs presented hierachized porosity, and their structural integrity was maintained upon functionalization. Solution and solid-state NMR confirmed the grafting efficiency in the case of MIL-100(Al) and the presence of a free amine group. It was shown that MIL-100(Al) can be functionalized by only one EN molecule by trimeric Al3O cluster unit, whereas the two other aluminium sites are occupied by an hydroxyl and a water molecule. The -NH2 sites of the grafted ethylenediamine can be used for further post-functionalization through amine chemistry and is responsible for basicity of the functionalized material. Furthermore, the presence of coordinated water molecules on the Al-MOF is responsible for simultaneous Brønsted acidity and for a unique carbon dioxide sorption mecanism, that distinguishes this material from its iron and chromium counterparts. | Timothy Steenhaut; Luca Fusaro; Koen Robeyns; Séraphin Lacour; Xiao Li; Julien G. Mahy; Véronique Louppe; Nicolas Grégoire; Gabriella Barozzino-Consiglio; Jean-François Statsijns; Carmela Aprile; Yaroslav Filinchuk; Sophie Hermans | Inorganic Chemistry; Coordination Chemistry (Inorg.); Main Group Chemistry (Inorg.); Solid State Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f15de5e0c60f02aae11be3/original/functionalization-of-mono-and-bimetallic-mil-100-al-fe-mo-fs-by-ethylenediamine-post-functionalization-br-nsted-acido-basicity-and-unique-co2-sorption-behaviour.pdf |
647469034f8b1884b775b20f | 10.26434/chemrxiv-2023-g81cw | Beyond Born-Oppenheimer pharmaceutical quantum chemistry of thalidomide analogs and deuterium substituents | Thalidomide and its analogs, designed as sedatives or sleep medications, have been diverted as effective immuno- modulatory imide drugs, although their teratogenicity led by racemization had been a problem. Reducing the racemization initiated by proton dissociation from the chiral center is essential to reduce the side effect. This study applied density functional theory calculations considering nuclear quantum effects to understand the differences in the racemization among them in aqueous conditions. It was clarified that the kinetic isotope effect of Lenalidomide is over three times larger than the others by carbonyl group lack in the phthalimide ring, leading to structural differences upon hydration. This supports previous reports that deuteration of Lenalidomide stabilizes the enantiomers, i.e., significantly reducing racemization. | Kohei Motoki; Hirotoshi Mori | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/647469034f8b1884b775b20f/original/beyond-born-oppenheimer-pharmaceutical-quantum-chemistry-of-thalidomide-analogs-and-deuterium-substituents.pdf |
611fb16651cfecd23196382b | 10.26434/chemrxiv-2021-m8kbg-v4 | Correlating ZnSe Quantum Dot Absorption with Particle Size and Concentration | The focus on heavy metal-free semiconductor nanocrystals has increased interest in ZnSe semiconductor quantum dots (QDs) over the past decade. Reliable and consistent incorporation of ZnSe cores into core/shell heterostructures or devices requires empirical fit equations correlating the lowest energy electron transition (1S peak) to their size and molar extinction coefficients (ε). While these equations are known and heavily used for CdSe, CdTe, CdS, PbS, etc., they are not well established for ZnSe and are non-existent for ZnSe QDs with diameters < 3.5 nm. In this study, a series of ZnSe QDs with diameters ranging from 2 to 6 nm were characterized with small angle X-ray scattering (SAXS), transmission electron microscopy (TEM), UV-Vis spectroscopy, and microwave plasma atomic emission spectroscopy (MP-AES). SAXS-based size analysis enabled practical inclusion of small particles in the evaluation, and elemental analysis with MP-AES elucidates a non-stoichiometric Zn:Se ratio consistent with zinc-terminated spherical ZnSe QDs. Using these combined results, empirical fit equations correlating QD size with its lowest energy electron transition (i.e., 1S peak position), Zn:Se ratio, and molar extinction coefficients for 1S peak, 1S integral, and high energy wavelengths are reported. Finally, the equations are used to track the evolution of a ZnSe core reaction. These results will enable the consistent and reliable use of ZnSe core particles in complex heterostructures and devices. | Reyhaneh Toufanian; Xingjian Zhong; Joshua Kays; Alexander Saeboe; Allison Dennis | Materials Science; Nanoscience; Dyes and Chromophores; Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/611fb16651cfecd23196382b/original/correlating-zn-se-quantum-dot-absorption-with-particle-size-and-concentration.pdf |
633c0ed2114b7e19f827e4c5 | 10.26434/chemrxiv-2022-pr7wg | The effect of pulling and twisting forces on chameleon sequence peptides | Chameleon sequences are amino acid sequences found in several experimental structures in distinct configurations. As such they challenge our understanding of the link between sequence and structure, and provide an interesting target to study the fundamental ideas underlying our understanding of structural competition in proteins. Here, we study the energy landscapes for three such sequences, and interrogate how pulling and twisting forces impact the available structural ensembles.
Chameleon sequences do not necessarily exhibit multiple structural ensembles on a multifunnel energy landscape when we consider them in isolation. The application of even small forces leads to drastic changes in the energy landscapes. For pulling forces, we observe sharp transitions from helical to extended structures in a very small span of forces. For twisting forces, the picture is much more complex, and highly dependent on the magnitude and handedness of the applied force as well as the reference angle for the twist. Depending on these parameters, more complex and more simplistic energy landscapes are observed alongside more and less diverse structural ensembles.
The impact of even small forces is significant, confirming their likely role in folding events. In addition, small forces exerted by the remaining scaffold of a protein may be sufficient to lead to the adoption of a specific structural ensemble by a chameleon sequence. | James Meadows; Konstantin Röder | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Physical and Chemical Properties; Structure | CC BY NC 4.0 | CHEMRXIV | 2022-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/633c0ed2114b7e19f827e4c5/original/the-effect-of-pulling-and-twisting-forces-on-chameleon-sequence-peptides.pdf |
656861f529a13c4d475563ee | 10.26434/chemrxiv-2023-698l0-v2 | Cerium Phosphate-Assisted Formation of Nucleosides and Nucleotides from Formamide in a One-Pot (Photo)catalytic Reaction | The abiotic formation of nucleotides from small, simple molecules is of large interest in the context of elucidating the origin of life scenario. In what follows it is shown that nucleosides and nucleotides can be formed from formamide in a one-pot reaction utilizing the mineral cerium phosphate (CePO4) as both a photocatalyst, a catalyst and a reactant that supplies the necessary phosphate groups. While the most abundant RNA / DNA building blocks were thymidine and thymidine monophosphate, considerable yield of other building blocks such as cytidine, cytidine monophosphate and adenosine cyclic monophosphate were found. Comparing the yield of nucleosides and nucleotides under light conditions to that in the dark suggests that in the presence of cerium phosphate, light promotes the formation of nucleobases, whereas the formation of nucleotides from nucleosides take place even in the absence of light. The scenario described herein is considerably simpler than other scenarios involving several steps and several reactants. Therefore, by virtue of the principle of Occam’s razor, should be of large interest for the community. | Shoval Gilboa; Larisa Panz; Nitai Arbell; Yaron Paz | Catalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656861f529a13c4d475563ee/original/cerium-phosphate-assisted-formation-of-nucleosides-and-nucleotides-from-formamide-in-a-one-pot-photo-catalytic-reaction.pdf |
60c73e98567dfe3f78ec3841 | 10.26434/chemrxiv.7038818.v1 | Reaction Networks in Propane Ammoxidation to Acrylonitrile Over Orthorhombic Mo-V-Nb-Te-O Catalyst | We investigated propane ammoxidation to acrylonitrile over hydrothermal Mo-V-Nb-TeO
catalyst containing the dominant M1 phase, recently proposed as active and selective in this
selective ammoxidation reaction. The reaction kinetics was studied in a tubular quartz reactor at
600-700K operated in both differential and integral regimes at 5-60% propane conversion. The
results obtained in this study were examined on the basis of two reaction networks involving
propane transformation via (1) parallel routes to propylene, acrylonitrile and carbon oxides and
(2) propylene as the reaction intermediate for acrylonitrile. The results obtained indicated only a
slight preference for the reaction network involving the propylene intermediate, which may be
explained on the basis of catalytic behavior of the M1 and M2 phases present in the
hydrothermal Mo-V-Nb-Te-O catalyst. The dominant M1 phase was capable of catalyzing all of
the above transformation steps, whereas the M2 impurity phase was only active in propylene
ammoxidation to acrylonitrile. The contribution of the M2 phase to propylene ammoxidation is
expected to be less significant at industrially relevant high propane conversions because of the
improved ability of the M1 phase to covert propylene into acrylonitrile at longer residence times. | Salil Bhatt; Soon-Jai Khang; Vadim Guliants | Heterogeneous Catalysis; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e98567dfe3f78ec3841/original/reaction-networks-in-propane-ammoxidation-to-acrylonitrile-over-orthorhombic-mo-v-nb-te-o-catalyst.pdf |
60c741a99abda23230f8bed5 | 10.26434/chemrxiv.8100203.v1 | SuCOS is Better than RMSD for Evaluating Fragment Elaboration and Docking Poses | One of the fundamental assumptions of fragment-based drug discovery is that the fragment’s binding mode will be conserved upon elaboration into larger compounds. The most common way of quantifying binding mode similarity is Root Mean Square Deviation (RMSD), but Protein Ligand Interaction Fingerprint (PLIF) similarity and shape-based metrics are sometimes used. We introduce SuCOS, an open-source shape and chemical feature overlap metric. We explore the strengths and weaknesses of RMSD, PLIF similarity, and SuCOS on a dataset of X-ray crystal structures of paired elaborated larger and smaller molecules bound to the same protein. Our redocking and cross-docking studies show that SuCOS is superior to RMSD and PLIF similarity. When redocking, SuCOS produces fewer false positives and false negatives than RMSD and PLIF similarity; and in cross-docking, SuCOS is better at differentiating experimentally-observed binding modes of an elaborated molecule given the pose of its non-elaborated counterpart. Finally we show that SuCOS performs better than AutoDock Vina at differentiating actives from decoy ligands using the DUD-E dataset. SuCOS is available at https://github.com/susanhleung/SuCOS . <br /> | Susan Leung; Michael Bodkin; Frank von Delft; Paul Brennan; Garrett Morris | Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741a99abda23230f8bed5/original/su-cos-is-better-than-rmsd-for-evaluating-fragment-elaboration-and-docking-poses.pdf |
60c74a944c8919226aad3277 | 10.26434/chemrxiv.12218276.v1 | General Chemistry Without Orbitals | We illustrate the solutions of Schroedinger's equation for the hydrogen atom in coordinates of all four systems, and differentiate the applicability of orbitals in these four systems. We present reasons that future textbooks of general chemistry should exclude orbitals and discuss the teaching of general chemistry on this basis. The incompatibility of molecular structure and quantum mechanics is discussed before a conclusion that quantum mechanics and its orbital artifacts are irrelevant for general chemistry. | Guy Lamoureux; J. F. Ogilvie | Chemical Education - General; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a944c8919226aad3277/original/general-chemistry-without-orbitals.pdf |
60c73d91337d6cfc6ce2616e | 10.26434/chemrxiv.5883142.v1 | Probing Substrate Diffusion in Interstitial MOF Chemistry with Kinetic Isotope Effects | <p>Metal-organic frameworks (MOFs) have garnered substantial interest as platforms for site-isolated catalysis. Efficient diffusion of small molecule substrates to interstitial lattice-confined catalyst sites is critical to leveraging unique opportunities of these materials as catalysts. Understanding the rate of substrate diffusion in MOFs is challenging and few <i>in situ </i>chemical tools are available to evaluate substrate diffusion during interstitial MOF chemistry. Here, we demonstrate nitrogen-atom transfer (NAT) from a lattice-confined Ru2 nitride to toluene to generate benzylamine. We use a comparison of the <i>intramolecular </i>deuterium kinetic isotope effect (KIE), determined for amination of a partially deuterated substrate, with the <i>intermolecular </i>KIE, determined by competitive amination of a mixture of perdeuterated and undeuterated substrates, to establish the relative rates of substrate diffusion and interstitial chemistry. We anticipate the developed KIE-based experiments will contribute to the development of porous materials for group-transfer catalysis</p> | David Powers; Chen-Hao Wang; Anuvab Das; Wen-Yang Gao | Catalysts; Heterogeneous Catalysis; Kinetics and Mechanism - Organometallic Reactions; Ligands (Organomet.); Chemical Kinetics | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d91337d6cfc6ce2616e/original/probing-substrate-diffusion-in-interstitial-mof-chemistry-with-kinetic-isotope-effects.pdf |
635c0365ee31860cfa7653c9 | 10.26434/chemrxiv-2022-jvdqw | Light-driven reductive cleavage of sulfonamides promoted by thiourea organophotosensitizers | We have developed a practical method to perform the reductive photocleavage of sulfonamides using thioureas as organophotocatalysts. This transformation, which tolerates a variety of substrates, occurs under mild reaction conditions in the presence of tetrabutylammonium borohydride as a reducing agent. Experimental and theoretical mechanistic investigations complete the study, shedding light on the nature of the active species involved in the photocatalytic process. | Jules Brom; Antoine Maruani; Laurent Micouin; Erica Benedetti | Organic Chemistry; Catalysis; Photochemistry (Org.); Organocatalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635c0365ee31860cfa7653c9/original/light-driven-reductive-cleavage-of-sulfonamides-promoted-by-thiourea-organophotosensitizers.pdf |
60c7516c842e654352db3bad | 10.26434/chemrxiv.13166717.v1 | Conducting PEEK Nanocomposites with Electrophoretically Deposited Bioactive Coating for Bone Tissue Regeneration and Multi-Modal Therapeutic Applications | The use of polyetheretherketone (PEEK) has grown exponentially in the biomedical
field in recent decades due to its outstanding biomechanical properties. However, its lack of
bioactivity/osteointegration remains an unresolved issue towards its wide use in orthopedic
applications. In this work, graphene nanosheets have been incorporated into PEEK to obtain
multifunctional nanocomposites. Due to the formation of electrical percolation network and the
π-π* conjugation between graphene and PEEK, the resulting composites have achieved twelve
order of magnitude enhancement in its electrical conductivity, and have enabled electrophoretic
deposition of bioactive/anti-bacterial coating consisting of stearyltrimethylammonium chloride
(STAC) modified hydroxyapatite (HA). The coated composite implant showed significant
boosting of BMSC cell proliferation in vitro. In addition, the strong photothermal conversion
effect of the graphene nanofillers have enabled laser induced heating of our nanocomposite
implants, where the temperature of the implant can reach 45 oC in 150 s. The unique
multi-functionality of our composite implant has also been demonstrated for photothermal
applications such as enhancing bacterial (E. coli and S. aureus) eradication and tumor cell (MG63)
inhibition, as well as bone tissue regeneration in vivo. The results suggest the strong potential of
our multi-functional implant in bone repair applications as well as multi-modal therapy of
challenging bone diseases such as osteosarcoma and osteomyelitis | Miaomiao He; Ce zhu; Huan Xu; dan Sun; Chen Chen; Ganjun Feng; Limin Liu; Li Zhang | Biocompatible Materials | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7516c842e654352db3bad/original/conducting-peek-nanocomposites-with-electrophoretically-deposited-bioactive-coating-for-bone-tissue-regeneration-and-multi-modal-therapeutic-applications.pdf |
675211d9f9980725cf2ea3a0 | 10.26434/chemrxiv-2024-sftwx-v2 | Dinitroacetylene: Can it be Made? | With a predicted record heat formation, energy density, and an outstanding performance as a rocket propellant, dinitroacetylene stretches the imagination for what is possible in terms of organic chemical explosives and monopropellants. In this study, we employ quantum chemical methods to predict its thermodynamic properties, ionization potential, electron affinity, UV/Vis spectra, NMR, and vibrational spectra, and to investigate proposed decomposition mechanisms. While unimolecular decomposition pathways are predicted to have high activation energies, NOx radical species – commonly present in reaction mixtures of energetic materials – are found to significantly catalyze the decomposition of dinitroacetylene. This catalytic effect may explain previous unsuccessful synthesis attempts. A frontier orbital analysis suggests that partial reduction could increase C–N bond order, offering a strategy to stabilize this elusive high-energy-density material. | Lara Harter; Martin Rahm; Guillaume Bélanger-Chabot | Inorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675211d9f9980725cf2ea3a0/original/dinitroacetylene-can-it-be-made.pdf |
60c758f9567dfebc67ec693e | 10.26434/chemrxiv.12806819.v3 | CAVIAR: a method for automatic cavity detection, description and decomposition into subcavities | <p></p><p>The accurate description of protein binding
sites is essential to the determination of similarity and the application of
machine learning methods to relate the binding sites to observed functions.
This work describes CAVIAR, a new open source tool for generating descriptors for
binding sites, using protein structures in PDB and mmCIF format as well as
trajectory frames from molecular dynamics simulations as input. The
applicability of CAVIAR descriptors is showcased by computing machine learning
predictions of binding site ligandability. The method can also automatically
assign subcavities, even in the absence of a bound ligand. The defined
subpockets mimic the empirical definitions used in medicinal chemistry
projects. It is shown that the experimental binding affinity scales relatively
well with the number of subcavities filled by the ligand, with compounds
binding to more than three subcavities having nanomolar or better affinities to
the target. The CAVIAR descriptors and methods can be used in any machine
learning-based investigations of problems involving binding sites, from protein
engineering to hit identification. The full software code is available on
GitHub and a conda package is hosted on Anaconda cloud.</p><p></p> | Jean-Rémy Marchand; Bernard Pirard; Peter Ertl; Finton Sirockin | Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758f9567dfebc67ec693e/original/caviar-a-method-for-automatic-cavity-detection-description-and-decomposition-into-subcavities.pdf |
674682dc7be152b1d0fb49f7 | 10.26434/chemrxiv-2024-826pr | Achieving Single-cell Resolution via Desorption Electrospray Ionization Mass Spectrometry Imaging (DESI-MSI) | Desorption Electrospray Ionization Mass Spectrometry Imaging (DESI-MSI) is a powerful technique for molecular analysis of surfaces; however, its application of single cell studies has not been previously published. In the current work, a commercial DESI setup (DESI XS) coupled to a mass spectrometer was used to analyze cultured mammalian cells attached onto glass coverslips. A series of experiments have been performed to obtain optimized experimental conditions, and MS images of metabolites with the single-cell level resolution were obtained using 10 µm x 10 µm pixel size. This established method can be readily adopted to extend the power of commercial DESI-MSI techniques in metabolomics studies requiring cellular resolution. | Nathan Colwell; Dan Chen; Zhibo Yang | Analytical Chemistry | CC BY 4.0 | CHEMRXIV | 2024-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674682dc7be152b1d0fb49f7/original/achieving-single-cell-resolution-via-desorption-electrospray-ionization-mass-spectrometry-imaging-desi-msi.pdf |
628f1f6f7087675d7b60b233 | 10.26434/chemrxiv-2022-9t6vf-v2 | Molecular Mechanism of Autodissociation in Liquid Water: Density Functional Theory Molecular Dynamics Simulations | Autodissociation in liquid water is one of the most important processes in various topics of physical chemistry, such as acid-base chemistry. Molecular simulations have elucidated most of the molecular mechanisms at the atomic level, yet quantitative analysis to compare with experiments using the potential of mean force (PMF) remains a hurdle, including the definition of reaction coordinates and accuracy of liquid structures by ab initio molecular dynamics (AIMD) simulations with density functional theory (DFT) methods. Here, we perform AIMD simulations with the revPBE-D3 exchange-correlation functional to compute the PMF profiles of autoionization, or proton transfer (PT), in liquid water. For the quantitative analysis with physically meaningful reaction coordinates, we employ a PT coordinate, donor-acceptor (OH--H3O+) distance, and hydrogen (H)-bond number. The one-dimensional (1D) PMF profile along the PT coordinate shows no local minimum in the product state of PT (OH- and H3O+), which is necessary to accurately compute acid dissociation constant (or pKa). On the other hand, the 2D PMF profiles along the PT coordinate and donor-acceptor distance show local minima in the product state and reaction barriers, and the computed pKw is comparable to the experiment. In addition, the 2D PMF profiles along the PT coordinate and the H-bond number reveal the molecular mechanism of the H-bond rearrangement concomitant with PT, in which the H-bond breaking before PT is slightly preferable. These findings indicate that accurate evaluation of pKa by MD simulations requires the donor-acceptor distance in addition to the conventional PT coordinate. | Tatsuya Joutsuka | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Solution Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628f1f6f7087675d7b60b233/original/molecular-mechanism-of-autodissociation-in-liquid-water-density-functional-theory-molecular-dynamics-simulations.pdf |
653fa626c573f893f16fede4 | 10.26434/chemrxiv-2023-zthnc | Discovery of the Polyketide Lagriamide B by Integrated Genome Mining, Isotopic Labeling, and Untargeted Metabolomics | Microorganisms from the order Burkholderiales have been the source of a number of important classes of natural products in recent years. For example, study of the beetle-associated symbiont Burkholderia gladioli led to the discovery of the antifungal polyketide lagriamide; an important molecule from the perspectives of both biotechnology and chemical ecology. As part of a wider project to sequence Burkholderiales genomes from our in-house Burkholderiales library we identified a strain containing a biosynthetic gene cluster (BGC) similar to the original lagriamide BGC. Structure prediction failed to identify any candidate masses for the products of this BGC from untargeted metabolomics mass spectrometry data. However, genome mining from publicly available databases identified fragments of this BGC from a culture collection strain of Paraburkholderia. Whole genome sequencing of this strain revealed the presence of a homologue of this BGC with very high sequence identity. Stable isotope feeding of the two strains in parallel using our newly developed IsoAnalyst platform identified the product of this lagriamide-like BGC directly from the crude fermentation extracts, affording a culturable supply of this important class of antifungal agents. Using a combination of bioinformatic, computational and spectroscopic methods we defined the absolute configurations for all 11 chiral centers in this new metabolite, which we named lagriamide B. Biological testing of lagriamide B against a panel of 21 bacterial and fungal pathogens revealed selective antifungal activity against the opportunistic human pathogen Aspergillus niger. | Claire H. Fergusson; Julia Saulog; Bruno S. Paulo; Darryl M. Wilson; Dennis Y. Liu; Nicholas J. Morehouse; Samantha Waterworth; John Barkei; Christopher A. Gray; Jason C. Kwan; Alessandra S. Eustaquio; Roger Linington | Biological and Medicinal Chemistry; Organic Chemistry; Analytical Chemistry; Natural Products; Chemoinformatics; Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653fa626c573f893f16fede4/original/discovery-of-the-polyketide-lagriamide-b-by-integrated-genome-mining-isotopic-labeling-and-untargeted-metabolomics.pdf |
64657359f2112b41e9b9f6ed | 10.26434/chemrxiv-2023-v0dwk | GraphVAMPnets for Uncovering Slow Collective Variables of Self-Assembly Dynamics | Uncovering slow collective variables (CVs) of self-assembly dynamics is important to elucidate its numerous kinetic assembly pathways and drive the design of novel structures for advanced materials through the bottom-up approach. However, identifying the CVs for self-assembly presents several challenges. First, self-assembly systems often consist of identical monomers and the feature representations should be invariant to permutations and rotational symmetries. Physical coordinates, such as aggregate size, lack the high-resolution detail, while common geometric coordinates like pairwise distances are hindered by the permutation and rotational symmetry challenge. Second, self-assembly is usually a downhill process, and the trajectories often suffer from insufficient sampling of backward transitions that correspond to the dissociation of self-assembled structures. Popular dimensionality reduction methods, like tICA, impose detailed balance constraints, potentially obscuring the true dynamics of self-assembly. In this work, we employ GraphVAMPnets which combines graph neural networks with variational approach for Markovian process (VAMP) theory to identify the slow CVs of the self-assembly processes. First, GraphVAMPnets bears the advantages of graph neural networks, in which the graph embeddings can represent self-assembly structures in a high-resolution while being invariant to permutations and rotational symmetries. Second, it is built upon VAMP theory that studies Markov processes without forcing detailed balance constraint, which addresses the out-of-equilibrium challenge in self-assembly process. We demonstrate GraphVAMPnets for identifying slow CVs of self-assembly kinetics in two systems: aggregation of two hydrophobic molecules and self-assembly of patchy particles. We expect that our GraphVAMPnets can be widely to applied to molecular self-assembly. | Bojun Liu; Mingyi Xue; Yunrui Qiu; Kirill Konovalov; Michael O’Connor; Xuhui Huang | Theoretical and Computational Chemistry; Artificial Intelligence | CC BY NC 4.0 | CHEMRXIV | 2023-05-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64657359f2112b41e9b9f6ed/original/graph-vam-pnets-for-uncovering-slow-collective-variables-of-self-assembly-dynamics.pdf |
61bb5a41a53f1b45949dd96c | 10.26434/chemrxiv-2021-bz14q | Role of conical intersection seam topography in the chemiexcitation of 1,2-dioxetanes | Chemiexcitation, the generation of electronic excited states by a thermal reaction initiated on the ground state, is an essential step in chemiluminescence, and it is mediated by the presence of a conical intersection that allows a nonadiabatic transition from ground state to excited state. Conical intersections classified as sloped favor chemiexcitation over ground state relaxation. The chemiexcitation yield of 1,2-dioxetanes is known to increase upon methylation. In this work we explore to which extent this trend can be attributed to changes in the conical intersection topography or accessibility. Since conical intersections are not isolated points, but continuous seams, we locate regions of the conical intersection seams that are close to the configuration space traversed by the molecules as they react on the ground state. We find that conical intersections are energetically and geometrically accessible from the reaction trajectory, and that topographies favorable to chemiexcitation are found in all three molecules studied. Nevertheless, the results suggest that dynamic effects are more important for explaining the different yields than the static features of the potential energy surfaces.
| Ignacio Fernández Galván; Anders Brakestad; Morgane Vacher | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61bb5a41a53f1b45949dd96c/original/role-of-conical-intersection-seam-topography-in-the-chemiexcitation-of-1-2-dioxetanes.pdf |
63f51b231d2d184063e2e1f2 | 10.26434/chemrxiv-2022-jpd8f-v2 | Leveraging graphical models to enhance in situ analyte identification via multiple voltammetric techniques | Voltammetry is a powerful analytical technique for evaluating electrochemical reactions and holds particular promise for interrogating electrolyte solutions suitable for energy storage technologies, including examining features such as state-of-charge and state-of-health. However, individual voltammetry techniques are likely to be subcomponents of broader analytical workflows that incorporate complementary methods to diagnose evolving electrolyte solutions of uncertain composition. As such, we demonstrate that jointly evaluating electrolyte solutions with distinct voltammetric modes can enhance the capabilities and sensitivities of characterization protocols. Specifically, by considering both macroelectrode cyclic square wave and microelectrode cyclic voltammograms in sequential ("one after another") and simultaneous ("all at once") manners, the composition of an electrolyte solution may be estimated with greater accuracy, and analytes that exhibit near identical electrode potentials may be more readily differentiated. We additionally explore means of further improving this method, finding that protocol accuracy increases when multiple voltammetry techniques are included in the training dataset. We also observe that the algorithm typically becomes more confident--but not necessarily more accurate--when the number of data points increases. Overall, these studies show that the sequential and simultaneous methods may hold utility when evaluating multiple voltammetry datasets that, in turn, may be leveraged to streamline diagnostic workflows used to examine electrolyte solutions within electrochemical technologies. | Alexis Fenton, Jr.; Fikile Brushett | Energy; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63f51b231d2d184063e2e1f2/original/leveraging-graphical-models-to-enhance-in-situ-analyte-identification-via-multiple-voltammetric-techniques.pdf |
60c75454842e656eb2db411e | 10.26434/chemrxiv.13645622.v1 | Stereoselective Diels-Alder Reactions of gem-Diborylalkenes: Toward the Synthesis of gem-Diboron-Based Polymers via ROMP | Although gem-diborylalkenes are known to be among the most valuable reagents in modern organic synthesis, providing a rapid access to a wide array of transformations, including the construction of C−C and C‐heteroatom bonds, their use as dienophile-reactive groups has been rare. Herein we report the Diels-Alder (DA) reaction of (unsymmetrical) gem-diborylalkenes. These reactions provide a general and efficient method for the stereoselective conversion of gem-diborylalkenes to rapidly access 1,1-bisborylcyclohexenes. Using the same DA reaction manifold with borylated-dienes and gem-diborylalkenes, we also developed a concise, highly regioselective synthesis of 1,1,2-tris- and 1,1,3,4-tetrakis(boronates)cyclohexenes, a family of compounds that currently lack efficient synthetic access. Furthermore, DFT calculations provided insight into the underlying factors that control the chemo-, regio, and stereoselectivity of these DA reactions. This method also provides stereodivergent syntheses of gem-diboryl-norbornenes. The utility of the gem-diboryl-norbornene building blocks was demonstrated by ring-opening metathesis polymerization (ROMP), providing a highly modular approach to the first synthesis of the gem-diboron-based polymers. Given its simplicity and versatility, we believe that this novel DA and ROMP approach holds great promise for organoboron synthesis as well as organoboron-based polymers and that it will result in more novel transformations in both academic and industrial research.<br /> | Nadim Eghbarieh; nicole hanania; Alon Zamir; Molhm Nassir; Tamar Stein; Ahmad Masarwa | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75454842e656eb2db411e/original/stereoselective-diels-alder-reactions-of-gem-diborylalkenes-toward-the-synthesis-of-gem-diboron-based-polymers-via-romp.pdf |
62aa76fdf5524a0693141382 | 10.26434/chemrxiv-2022-6v14d | Discovery of Potent Plasmodium falciparum Protein Kinase 6 (PfPK6) Inhibitors with a Type II Inhibitor Pharmacophore | Malaria is a devastating disease that causes significant global morbidity and mortality. The rise of drug resistance against artemisinin-based combination therapy, the frontline treatment for malaria, demonstrates the necessity to develop alternative antimalarials with novel mechanisms of action. Inhibition of Plasmodium protein kinases presents an underexplored opportunity for drug development. PfPK6 has been identified as an essential kinase for P. falciparum asexual blood stage proliferation, but has not been subjected to medicinal chemistry campaigns for inhibitor development. In this work, we report the discovery of Ki8751 as a PfPK6 inhibitor (IC50 = 14 nM) determined using the KinaseSeeker assay, utilizing split-luciferase three-hybrid technology. A series of 79 1-phenyl-3-(4-(quinolin-4-yloxy)phenyl)urea derivatives of Ki8751 were designed, synthesized and evaluated for PfPK6 inhibition and antiplasmodial activity. Using group efficiency analyses, we established the importance of the key groups on the scaffold for inhibition of PfPK6 consistent with a type II inhibitor pharmacophore. We highlight modifications on the tail group that contribute to antiplasmodial activity. We report the discovery of compound 67, a potent PfPK6 inhibitor (IC50 = 13 nM) active against the P. falciparum blood stage (EC50 = 160 nM), and compound 79, an excellent PfPK6 inhibitor (IC50 < 5 nM) with dual-stage antiplasmodial activity against P. falciparum blood stage (EC50 = 39 nM) and against P. berghei liver stage (EC50 = 220 nM). These results lay the foundation for this chemotype to be further developed into novel antimalarials and into chemical probes targeting PfPK6, enabling further investigation into PfPK6 function. | Han Wee Ong; Anna Truong; Frank Kwarcinski; Chandi de Silva; Krisha Avalani; Tammy Havener; Michael Chirgwin; Kareem Galal; Caleb Willis; Andreas Krämer; Shubin Liu; Stefan Knapp; Emily Derbyshire; Reena Zutshi; David Drewry | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62aa76fdf5524a0693141382/original/discovery-of-potent-plasmodium-falciparum-protein-kinase-6-pf-pk6-inhibitors-with-a-type-ii-inhibitor-pharmacophore.pdf |
662a9ef921291e5d1db6e753 | 10.26434/chemrxiv-2024-tgjlc | LC-HRMS analysis of phospholipids bearing oxylipins | Several oxylipins including hydroxy- and epoxy-polyunsaturated fatty acids (PUFA) act as lipid mediators. In biological samples they dominantly occur esterified in phospholipids (PL). Esterified oxylipins are usually quantified indirectly after alkaline hydrolysis as non-esterified oxylipins. Here, a liquid chromatography high-resolution mass spectrometry (LC-HRMS) method for the direct analysis of oxylipins bound to PL was developed. Optimized reversed phase LC separation enabled the separation of isobaric and isomeric PL from different lipid classes bearing oxylipin positional isomers, by both the polar head groups as well as the fatty acyl chains. Each individual PL bearing oxylipins was tentatively identified based on the combination of retention time, precursor ion and specific product ions. The oxylipin was characterized based on product ions resulting from the characteristic α cleavage occurring at the hydroxy/epoxy group. Phospholipid sn 1/sn 2 isomers were identified based on the neutral loss of the fatty acyl in the sn 2 position as a ketene. A total of 422 individual oxPL species from 7 different lipid classes i.e., PI, PS, PC, PE, PC P, PC O, and PE P, bearing hydroxy- and epoxy-PUFA were detected in human serum and cells. This method was applied to investigate in which PL class supplemented oxylipins are incorporated in HEK293 cells. 153 individual oxPL species were characterized and semi-quantified using one internal standard per lipid class: 20:4;15OH, 20:4;14Ep, and 20:5;14Ep were mostly bound to PI. 20:4;8Ep and 20:5;8Ep were esterified to PC and PE while other hydroxy- and epoxy-PUFA were mainly found in PC. The developed LC-HRMS method enables the direct and comprehensive analysis of PL bearing oxylipins and to investigate their biological role. | Laura Carpanedo; Katharina M. Rund; Luca M. Wende; Nadja Kampschulte; Nils Helge Schebb | Biological and Medicinal Chemistry; Analytical Chemistry; Mass Spectrometry; Biochemistry; Cell and Molecular Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662a9ef921291e5d1db6e753/original/lc-hrms-analysis-of-phospholipids-bearing-oxylipins.pdf |
675db44df9980725cf145092 | 10.26434/chemrxiv-2024-tf510-v3 | Fast and Effective Preparation of Highly Cytotoxic Hybrid Molecules of Schweinfurthin E and OSW-1 | Herein, we present the first synthesis of hybrid molecules combining the pharmacophores of two natural compounds, schweinfurthin E (SW-E) and the glycosidic moiety of OSW-1. These hybrids were designed leveraging the complementary binding of SW-E and OSW-1 to their biological target. The synthetic process highlights, in particular, one-pot functionalization and glycosylation of an L-arabinose unit using a D-xyloside donor and a CuAAC click reaction involving a polyfunctionalized prenylated stilbene derived from SW-E. The cytotoxicity of the four SW-E and OSW-1 hybrids is also reported, two of them being much more cytotoxic than SW-E on a glioblastoma cancer cell line. Finally, a molecular modeling study is conducted to rationalize the biological results obtained. | Baptiste Schelle; Jules Fargier; Clément Grisel; Laurie Askenatzis; Jean-François Gallard; Sandy Desrat; Jérome Bignon; Fanny Roussi; Stephanie Norsikian | Biological and Medicinal Chemistry; Organic Chemistry; Natural Products; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675db44df9980725cf145092/original/fast-and-effective-preparation-of-highly-cytotoxic-hybrid-molecules-of-schweinfurthin-e-and-osw-1.pdf |
60c75272bb8c1a5a063dbea9 | 10.26434/chemrxiv.13296956.v1 | Harnessing Plasma Environments for Ammonia Catalysis: Mechanistic Insights from Experiments and Large-Scale Ab-initio Molecular Dynamics | By
combining experimental measurements with <i>ab initio</i> molecular dynamics
simulations, we provide the first microscopic description of the interaction
between metal surfaces and a low-temperature nitrogen-hydrogen plasma. Our
study focuses on the dissociation of hydrogen and nitrogen as the main
activation route. We find that ammonia forms via an Eley-Rideal mechanism where
atomic nitrogen abstracts hydrogen from the catalyst surface to form ammonia on
an extremely short timescale (a few picoseconds). On copper, ammonia formation
occurs via the interaction between plasma-produced atomic nitrogen and the
H-terminated surface. On platinum, however, we find that surface saturation
with NH groups is necessary for ammonia production to occur. Regardless of the
metal surface, the reaction is limited by the mass transport of atomic
nitrogen, consistent with the weak dependence on catalyst material that we
observe and has been reported by several other groups. This study represents a significant
step towards achieving a mechanistic, microscopic-scale understanding of
catalytic processes activated in low-temperature plasma environments. | Sharma Yamijala; Giorgio Nava; Zulfikhar A. Ali; Davide Beretta; Bryan Wong; Lorenzo Mangolini | Catalysts; Materials Processing; Computational Chemistry and Modeling; Theory - Computational; Reaction Engineering; Base Catalysis; Heterogeneous Catalysis; Homogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms; Chemical Kinetics; Interfaces; Physical and Chemical Processes; Quantum Mechanics; Structure; Surface; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75272bb8c1a5a063dbea9/original/harnessing-plasma-environments-for-ammonia-catalysis-mechanistic-insights-from-experiments-and-large-scale-ab-initio-molecular-dynamics.pdf |
67a7bbeffa469535b98fc1c1 | 10.26434/chemrxiv-2025-qh9rh | Real-time Atomic Oxygen Detection Using Transition Metal Oxide Coated Hydrogen-Terminated Diamond Surface | Atomic oxygen (AO) is a major cause for the deterioration of spacecraft materials, such as polymers, composites and optical coatings, in low Earth orbit (LEO). AO exposure can degrade thermal, mechanical, or optical system performance, potentially leading to premature mission failure. Future missions, especially for remote sensing, are designed for very low Earth orbit (VLEO) where thermospheric density and AO flux variations are more significant than in higher orbits. Therefore, accurate real-time assessment of the AO fluence impinging upon spacecraft surfaces becomes a crucial issue for mission success, as well as for improving current thermospheric density models.
We present a compact, solid-state sensor with high sensitivity and fast response to AO. The sensor is based on two semiconductor components that exhibit unique electrical properties when assembled together: hydrogenated diamond substrate and transition-metal oxide (TMO) coating. The Diamond:H-Transitional Metal Oxide AO sensor (DiMO) was characterized using RF plasma-based and laser detonation AO facilities. Tungsten oxide, WO3, with thickness ranging from 6 nm to 30 nm was used as the TMO coating of choice. The results showed a linear increase in electrical resistance as a function of AO fluence of up to 2×1020 O-atoms∙cm-2, as tested in a laser detonation AO beam facility. The sensitivity of the sensor was found to be tunable, ranging from 10-14 to 10-15 Ω∙O-atoms-1∙cm2, and inversely dependent on the coating thickness. This work demonstrates the potential usage of diamond-based devices for VLEO real-time AO flux monitoring. Furthermore, the compact dimensions and minimal power consumption of the DiMO sensor make it an ideal low-cost solution for the emerging "new-space" era, including nanosatellite applications.
| Asaf Bolker; Irina Gouzman; Moshe Tordjman; Nurit Atar; Brian E. Riggs; Yakov Carmiel; Ronen Verker; Eitan Grossman; Rafi Kalish; Timothy K. Minton | Physical Chemistry; Materials Science; Earth, Space, and Environmental Chemistry; Space Chemistry; Physical and Chemical Processes; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a7bbeffa469535b98fc1c1/original/real-time-atomic-oxygen-detection-using-transition-metal-oxide-coated-hydrogen-terminated-diamond-surface.pdf |
628376adf053df4d9c1ec036 | 10.26434/chemrxiv-2022-c4zb6-v2 | Copper-catalysed glutathione oxidation is accelerated by the anticancer thiosemicarbazone Dp44mT and further boosted at lower pH | Glutathione (GSH) is the most abundant thiol in mammalian cells and plays a crucial role in maintaining the redox state of many biomolecules, in detoxification and in antioxidant defence. The thiols of two GSH molecules can be oxidized to the disulphide GSSG. The cytosolic GSH/GSSG ratio is very high (> 100), and its decrease can lead to apoptosis or necrosis, which are of interest in cancer research. CuII ions are very efficient oxidants of thiols, but with an excess of GSH, the formed CuIn(GS)m clusters are only slowly re-oxidized by O2 at pH 7.4, and even more slowly at lower pH. Here, the oxidation of GSH by CuII was investigated in the presence of the anticancer thiosemicarbazone Dp44mT. The results showed that CuII-Dp44mT oxidizes GSH faster than CuII alone at pH 7.4, and hence accelerates the production of the very reactive hydroxyl radicals. Interestingly, the GSH oxidation and hydroxyl radical production by CuII-Dp44mT were accelerated at the acidic pH found in lysosomes, where CuII-Dp44mT was previously shown to accumulate and induce lysosomal membrane permeabilization. To decipher this unusually faster thiol oxidation a lower pH, Density Functional Theory (DFT) calculations and spectroscopic studies were performed. The results suggest that the acceleration is due to the protonation of CuII-Dp44mT on the hydrazinic nitrogen, which favours the rate-limiting reduction step without subsequent dissociation of the CuI-complex. Furthermore, preliminary biological studies in cell culture using the proton pump inhibitor bafilomycin A1 indicated that the lysosomal pH plays a role in the activity of Dp44mT. | Enrico Falcone; Alessandra Ritacca; Sonja Hager; Bertrand Vileno; Youssef El Khoury; Petra Hellwig; Christian R. Kowol; Petra Heffeter; Emilia Sicilia; Peter Faller | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Inorganic Chemistry; Bioinorganic Chemistry; Coordination Chemistry (Inorg.); Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628376adf053df4d9c1ec036/original/copper-catalysed-glutathione-oxidation-is-accelerated-by-the-anticancer-thiosemicarbazone-dp44m-t-and-further-boosted-at-lower-p-h.pdf |
634098c7084700b016990ef2 | 10.26434/chemrxiv-2022-z1bt9 | Quantifying Vertical Resonance Energy in Aromatic Systems with Natural Bond Orbitals | Natural bond orbitals (NBOs) provide the familiar Lewis type (2c-2e-) localized description of a molecule. Interactions between nearly filled (2e-) orbitals and empty (π* or σ*) anti-bonding orbitals represent delocalization in the system and creates a framework to study stereoelectronic interactions. Here we show that deleting the interactions between π and π* orbitals in aromatic systems and acquiring the energy with the NBO program provides a highly intuitive and quantitative picture of π-aromaticity that correlates with the well-established nucleus-independent chemical shift (NICS) method. This natural bond orbital resonance energy (NBO-RE) measures the vertical resonance energy (VRE) of aromatic systems without the use of an external reference structure. The NBO-RE method is applicable to the study of local aromaticity in polycyclic aromatic hydrocarbons (PAHs) and other non-planar systems. | Karnjit Parmar; Michel Gravel | Theoretical and Computational Chemistry; Organic Chemistry; Physical Organic Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634098c7084700b016990ef2/original/quantifying-vertical-resonance-energy-in-aromatic-systems-with-natural-bond-orbitals.pdf |
6561262229a13c4d47eb8c09 | 10.26434/chemrxiv-2023-mhb4c | Machine Learning Prediction of the Experimental Transition Temperature of Fe(II) Spin-Crossover Complexes | Spin crossover (SCO) complexes are materials that exhibit changes in spin state in response to external stimuli with potential applications in molecular electronics. It is challenging to know a priori how to design ligands to achieve the delicate balance of entropic and enthalpic contributions needed to tailor a transition temperature close to room temperature. We leverage the SCO complexes from the previously curated SCO-95 data set [Vennelakanti et al. J. Chem. Phys. 159, 024120 (2023)] to train three ML models for transition temperature (T1/2) prediction, using graph-based revised autocorrelations as features. We perform feature selection using random forest-ranked recursive feature addition (RF-RFA) to identify the features essential to model transferability. Of the ML models considered, the full feature set random forest (RF) and recursive feature addition RF models perform best, achieving moderate correlation to experimental T1/2 values. We then compare ML T1/2 predictions to those from three previously identified best- performing density functional approximations (DFAs) which accurately predict SCO behavior across SCO-95, finding that the ML models predict T1/2 more accurately than the best-performing DFAs. In addition, we study ML model predictions on the set of 18 SCO complexes for which only estimated T1/2 values are available. Upon excluding outliers from this set, the RF-RFA RF model shows strong correlation to estimated T1/2 values with a Pearson’s r of 0.82. In contrast, DFA-predicted T1/2 values have large errors and show no correlation to estimated T1/2 values over the same set of complexes. Overall, our study demonstrates reasonable performance of ML models in comparison to some of the best-performing DFAs, and we expect ML models to improve further as larger data sets of SCO complexes are curated and become available for model training. | Vyshnavi Vennelakanti; Irem Kilic; Gianmarco Terrones; Chenru Duan; Heather Kulik | Theoretical and Computational Chemistry; Inorganic Chemistry; Theory - Inorganic; Transition Metal Complexes (Inorg.); Machine Learning | CC BY 4.0 | CHEMRXIV | 2023-11-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6561262229a13c4d47eb8c09/original/machine-learning-prediction-of-the-experimental-transition-temperature-of-fe-ii-spin-crossover-complexes.pdf |
673249975a82cea2facf8a18 | 10.26434/chemrxiv-2024-04r0l | Access to Arynes from Arenes via Formal Dehydrogenation: Increased Efficiency and Scope, Synthetic Applications and Mechanistic Analysis | Arynes undergo a wide range of diverse chemical transformations making them highly versatile reactive in-termediates for organic synthesis. Access to arynes has long been dominated by pre-functionalized reagents such as the venerable o-trimethylsilylaryl triflate class of substrates. However, a move toward the development of methods to access arynes that are both mild and efficient has prompted research into aryl “onium” aryne precursors. We have leveraged aryl “onium” species as intermediates in an overall net dehydrogenation of simple arenes as an efficient way to generate and trap arynes. Herein, we describe two strategies to achieve mild and efficient access to arynes. 1) The development of a one-pot method that converts simple arenes into aryl thianthrenium salts and uses them in situ to generate arynes; the net transformation of arene to trapped aryne is achieved within two hours. 2) The development of a two-step process to convert arenes into aryl(Mes)iodonium salts and ultimately trapped arynes to expand the scope of arenes compatible; the net transformation is complete within four hours. Mechanistic analysis through competition experiments, deuterium kinetic isotope effects (DKIE) and Density Functional Theory (DFT) provide key insight into the similarity and differences of the two approaches described in this work and yield a user’s guide for selecting the appropriate strategy based on the arene. | Riley Roberts; Bryan Metze; Nicole Javaly; Theresa McCormick; David Stuart | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2024-11-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673249975a82cea2facf8a18/original/access-to-arynes-from-arenes-via-formal-dehydrogenation-increased-efficiency-and-scope-synthetic-applications-and-mechanistic-analysis.pdf |
60c74d1fbdbb89868fa3991f | 10.26434/chemrxiv.12588059.v1 | Enhanced Ion Transport in an Ether Aided Super Concentrated Ionic Liquid Electrolyte for Long-Life Practical Lithium Metal Battery Applications | We explore a novel ether aided superconcentrated
ionic liquid electrolyte; a combination of ionic liquid, <i>N</i>-propyl-<i>N</i>-methylpyrrolidinium
bis(fluorosulfonyl)imide (C<sub>3</sub>mpyrFSI) and ether solvent, <i>1,2</i> dimethoxy ethane (DME) with 3.2
mol/kg LiFSI salt, which offers an alternative ion-transport mechanism and
improves the overall fluidity of the electrolyte. The molecular dynamics (MD)
study reveals that the coordination environment of lithium in the ether aided
ionic liquid system offers a coexistence of both the ether DME and FSI anion
simultaneously and the absence of ‘free’, uncoordinated DME solvent. These
structures lead to very fast kinetics and improved current density for lithium
deposition-dissolution processes. Hence the electrolyte is used in a lithium
metal battery against a high mass loading (~12 mg/cm<sup>2</sup>) LFP cathode
which was cycled at a relatively high current rate of 1mA/cm<sup>2</sup> for
350 cycles without capacity fading and offered an overall coulombic efficiency
of >99.8 %. Additionally, the rate
performance demonstrated that this electrolyte is capable of passing current
density as high as 7mA/cm<sup>2</sup> without any electrolytic decomposition
and offers a superior capacity retention. We have also demonstrated an ‘anode
free’ LFP-Cu cell which was cycled over 50 cycles and achieved an average
coulombic efficiency of 98.74%. The coordination chemistry and
(electro)chemical understanding as well as the excellent cycling stability
collectively leads toward a breakthrough in realizing the practical applicability
of this ether aided ionic liquid electrolytes in lithium metal battery
applications, while delivering high energy density in a prototype cell. | Urbi Pal; Fangfang Chen; Derick Gyabang; Thushan Pathirana; Binayak Roy; Robert Kerr; Douglas Macfarlane; Michel Armand; Patrick
C. Howlett; Maria Forsyth | Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d1fbdbb89868fa3991f/original/enhanced-ion-transport-in-an-ether-aided-super-concentrated-ionic-liquid-electrolyte-for-long-life-practical-lithium-metal-battery-applications.pdf |
6705375112ff75c3a1db56bd | 10.26434/chemrxiv-2024-8kv5g | Hematite Nanoparticle-Modified Carbon Paper as a Promising Electrochemical Sensor for Atropine Detection in Beverages | This study describes the electroanalytical determination of atropine in beverages using a carbon paper (CP) electrode modified with Fe2O3 nanostructures. The incorporation of nanoparticles of a transition metal oxide on CP led to an improvement in the electrochemical response of the electrode using the technique: square wave voltammetry (SWV). Morphological characterization of CPE/Fe2O3 developed by Field Emission Scanning Electron Microscopy (FESEM), shows a relatively uniform distribution of Fe2O3 nanoparticles on the CP surface. The optimization of variables of pH and the amount of modifying agent were relevant to maximize the efficiency of the modified electrode. The evaluation of the pH effect shows that the maximum current response occurs at pH 11.5 in Britton-Robinson buffer, and the optimum amount of Fe2O3 was 1 mg/mL, giving the best response, standing out for an optimum active surface for the detection of atropine. Electrostatic calculations show that at pH 11 the surfaces become negatively charged, having better affinity with protonated atropine, compared the deprotonated state. This pH is beyond atropine pKa, hence, the peak in current at pH 11.5 indicates that the surface induces a shift in pKa, allowing the prevalence of protonated atropine at this high pH. The limit of detection and quantification (LD and LQ) recorded using the CP/Fe2O3 electrode were 0.075 and 0.250 mM, respectively. In the case of real samples, using the standard addition method, the presence of interferents did not significantly affect the detection of atropine, obtaining satisfactory recovery percentages. | Andrea Cabezas; Scarlett Aguilera; Sergio A. Urzúa; Christopher D. Cooper; Cristian Vera; María Aguirre; Paulina Márquez; Jaime Pizarro | Physical Chemistry; Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6705375112ff75c3a1db56bd/original/hematite-nanoparticle-modified-carbon-paper-as-a-promising-electrochemical-sensor-for-atropine-detection-in-beverages.pdf |
60c75338702a9b043a18c309 | 10.26434/chemrxiv.13440179.v1 | Catalytic Mechanism of the Colistin Resistance Protein MCR-1 | <div>
<div>
<div>
<p>The mcr-1 gene encodes a membrane-bound Zn2+-metalloenzyme, MCR-1, which catalyzes phosphoethanolamine transfer onto bacterial lipid A, making
bacteria resistant to colistin, a last-resort antibiotic. Mechanistic understanding of this process remains incomplete. Here, we investigate possible catalytic
pathways using DFT and ab initio calculations on cluster models and identify a complete two-step reaction mechanism. The first step, formation of a covalent
phosphointermediate via trans-fer of phosphoethanolamine from a membrane phospholipid donor to the acceptor Thr285, is rate-limiting and proceeds with
a single Zn2+ ion. The second step, transfer of the phosphoethanolamine group to lipid A, requires an additional Zn2+. The calculations suggest the involment
of the Zn2+ orbitals directly in the reaction is limited, with the second Zn2+ acting to bind incoming lipid A and direct phosphoethanolamine addition. The new
level of mechanistic detail obtained here, which distinguishes these enzymes from other phosphotransferases, will aid in the development of inhibitors specific
to MCR-1 and related bacterial phosphoethanolamine transferases.
</p>
</div>
</div>
</div> | Reynier Suardiaz; Emily Lythell; Philip Hinchliffed; Marc van der Kamp; James Spencer; Natalie Fey; Adrian Mulholland | Biochemistry; Chemical Biology; Computational Chemistry and Modeling; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75338702a9b043a18c309/original/catalytic-mechanism-of-the-colistin-resistance-protein-mcr-1.pdf |
64b5b086b053dad33a6cdcaf | 10.26434/chemrxiv-2023-r728q | The Fallacy of Hyaluronic Acid Binding a Thousand Times Its Weight In Water | This study re-examined experimental reports and past literature of water binding by the humectant hyaluronic acid, in comparison with another common humectant, glycerol, to critically evaluate the common claim that hyaluronic acid binds a thousand times its weight in water, which makes it especially suited to be a cosmetic moisturizer. Thermal gravimetric analysis (TGA) and differential scanning calorimetry (DSC) were used to study aqueous solutions of glycerol and hyaluronic acid. A 0.1 weight % aqueous solution of hyaluronic acid is a clear, flowing liquid, comparable to a 10 weight % aqueous solution of glycerol. The melting point and melting heat of fusion for the hyaluronic acid solution were effectively the same as pure water, while both were reduced for the glycerol solution. There is imperceptible freezing point depression by HA, whereas that by glycerol is as expected. No experimental evidence was found for any special ability of hyaluronic acid to bind water at the claimed level of a thousand times by weight. The origin of the fallacy that it binds water at that level can be traced to older literature that has been misunderstood for the meaning of binding, as compared to other physical properties such as hydrodynamics. | Scott Borchers; Michael Pirrung | Physical Chemistry; Organic Chemistry; Biophysical Chemistry; Physical and Chemical Properties; Thermodynamics (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b5b086b053dad33a6cdcaf/original/the-fallacy-of-hyaluronic-acid-binding-a-thousand-times-its-weight-in-water.pdf |
64f202bbdd1a73847ff70dfa | 10.26434/chemrxiv-2023-hlfmp | Qualitative monitoring of proto-peptide condensation by differential FTIR spectroscopy | Condensation processes such as wet-dry cycling are thought to have played significant roles in the emergence of proto-peptides. Here, we describe a simple and low-cost method, differential Fourier transform infrared (FTIR) spectroscopy, for qualitative analysis of peptide condensation products in model primordial reactions. This method is optimized for depsipeptides and is used to investigate their polymerization in the presence of extraterrestrial dust simulants. | Keon Rezaeerod; Hanna Heinzmann; Alexis Torrence; Jui Patel; Jay Forsythe | Analytical Chemistry; Earth, Space, and Environmental Chemistry; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f202bbdd1a73847ff70dfa/original/qualitative-monitoring-of-proto-peptide-condensation-by-differential-ftir-spectroscopy.pdf |
61f2fc004b9500809d0c59c7 | 10.26434/chemrxiv-2022-nx92n | “Activated Borane” – A Porous Borane Cluster Network | The unprecedented co-thermolysis of nido-decaborane (B10H14) and toluene results in a novel porous material (that we have named “Activated Borane”) containing micropores of 1.0 and 1.5 nm in diameter and a specific surface area of 774 m2 g-1 (Ar, 87 K) that is thermally stable up to 1000 oC. Solid-state 1H, 11B and 13C MAS NMR, UV-vis and IR spectroscopies suggest an amorphous structure of borane clusters interconnected by toluene moieties in a ratio of about three toluene molecules for every borane cluster. In addition, the structure contains Lewis-acidic tri-coordinated boron sites giving it some unique properties. Activated Borane displays high sorption capacity for pollutants such as sulfamethoxazole, tramadol, diclofenac and bisphenol A that exceed the capacity of commercially-available activated carbon. The consistency in properties for each batch made, and the ease of its synthesis, make Activated Borane a promising porous material worthy of broad attention. | Daniel Bůžek; Karel Škoch; Soňa Ondrušová; Matouš Kloda; Dmytro Bavol; Andrii Mahun; Libor Kobera; Kamil Lang; Michael G. S. Londesborough; Jan Demel | Inorganic Chemistry; Polymer Science; Inorganic Polymers; Polymers; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61f2fc004b9500809d0c59c7/original/activated-borane-a-porous-borane-cluster-network.pdf |
60c73e979abda27b22f8b8e6 | 10.26434/chemrxiv.7019579.v1 | A Conserved Asparagine in a Ubiquitin Conjugating Enzyme Positions the Substrate for Nucleophilic Attack | We present classical molecular dynamics (MD), Born-Oppenheimer molecular dynamics (BOMD), and hybrid quantum mechanics/molecular mechanics (QM/MM) data. MD was performed using the GPU accelerated pmemd module of the AMBER14MD package. BOMD was performed using CP2K version 2.6. The reaction rates in BOMD were accelerated using the Metadynamics method. QM/MM was performed using ONIOM in the Gaussian09 suite of programs. Relevant input files for BOMD and QM/MM are available. | Walker M. Jones; Aaron G. Davis; R. Hunter Wilson; Katherine L. Elliott; Isaiah Sumner | Biochemistry; Computational Chemistry and Modeling; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2018-08-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e979abda27b22f8b8e6/original/a-conserved-asparagine-in-a-ubiquitin-conjugating-enzyme-positions-the-substrate-for-nucleophilic-attack.pdf |
67560bbff9980725cf73e349 | 10.26434/chemrxiv-2024-q1w8k | Biological potential of methanol extracts from plants of the genus Spiraea L. growing in Russia | The genus Spiraea is well-represented in the flora of Russian Federation which were only minimally addressed so far in respect of their metabolite profiles and characteristic biological activities. Therefore, phytochemical profiling of the major secondary metabolites in the first year Spiraea shoot extracts, accompanied with comprehensive screening of the activities exerted by these isolates, appears to be a remarkable step forwards. Obviously, this work will deliver new valuable information on the structure-activity relationships (SAR) for the major natural product constituents of these extracts. Indeed, although numerous phytochemical studies with Spiraea plants were reported so far, these works relied on limited numbers of species (or even on individual accessions), while, to the best of our knowledge, no full-scale screening with any logically completed set of Spiraea species was accomplished till now. Because of this, the data on the quantitative profiles of the principal secondary metabolites in the isolates prepared from different Spiraea species are quite fragmentary and require further supplementation and systematization. Therefore, our study aims filling this gap and covers the whole list of the Spiraea species naturally occurring in Russia. Moreover, here we successfully combined a metabolite profiling survey with a comprehensive screening of biological activities of the same extracts to address the Russian spirea species as promising sources of biologically active complexes for use in medical practice. For this, we address the relationships between the relative abundances of individual natural products occurring as their major extract constituents and the biological effects of the corresponding isolates in reliable laboratory models. Specifically, altogether 33 major components representing flavonoids (quercetin and kaempferol derivatives) and hydroxycinnamic acids (caffeic acid, ferulic acid, coumaric acid derivatives) were identified based on chromato-mass spectrometric (LC-MS) analysis. Further, the relative contents of these identified major components in the extracts, obtained from different Spiraea species, were addressed. The analysis of antioxidant potential revealed high activity of all extracts in the models of antiradical activity (DPPH assay), activity against cation radicals (TEAC assay) and superoxide anion radical (NBT assay). The screening of antiviral and antimicrobial activities of the same extracts revealed significant antiviral activity at a concentration of 2 µg/mL, and was assessed high (MIC < 1 mg/mL) or moderate (1 mg/mL ≤ MIC ≤ 4 mg/mL) antibacterial activity against the Gram-positive and Gram-negative bacteria strains. | Anastasia Orlova; Alena Soboleva ; Elena Tsvetkova ; Svetlana Silinskaia ; Yana Esaulkova; Tatiana Veklich ; Vladimir Zarubaev ; Ksenia Fedoseeva ; Ilya Akberdin; Semyon Kolmykov ; Vera Kostikova ; Andrej Frolov | Biological and Medicinal Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67560bbff9980725cf73e349/original/biological-potential-of-methanol-extracts-from-plants-of-the-genus-spiraea-l-growing-in-russia.pdf |
62f24871e78f70c25f351387 | 10.26434/chemrxiv-2022-tt6ww | Transmembrane transport of bicarbonate
by anion receptors | The development of synthetic anion transporters is motivated by their potential application as treatment for diseases that originate from deficient anion transport by natural proteins. Transport of bicarbonate is important for crucial biological functions such as respiration and digestion. Despite this biological relevance, bicarbonate transport has not been as widely studied as chloride transport. Herein we present an overview of the synthetic receptors that have been studied as bicarbonate transporters, together with the different assays used to perform transport studies in large unilamellar vesicles. We highlight the most active transporters and comment on the nature of the functional groups present in active and inactive compounds. We also address recent mechanistic studies that have revealed different processes that can lead to net transport of bicarbonate, as well as studies reported in cells and tissues and comment on the key challenges for the further development of bicarbonate transporters. | Luis Martínez-Crespo; Hennie Valkenier | Biological and Medicinal Chemistry; Organic Chemistry; Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f24871e78f70c25f351387/original/transmembrane-transport-of-bicarbonate-by-anion-receptors.pdf |
645cfaa9f2112b41e963edff | 10.26434/chemrxiv-2023-xq4v4 | AutoDock-SS: AutoDock for Multiconformational Ligand-based Virtual Screening | Ligand-based virtual screening (LBVS) is widely employed in drug discovery to identify potential leads when the crystallographic structure of the target protein remains unknown. In this study, we introduce a novel three-dimensional LBVS workflow incorporating newly designed ligand-based grid maps and AutoDock-GPU, referred to as AutoDock-SS (Similarity Searching).
AutoDock-SS features two modes supporting either single query ligands or multiple pre-aligned ligands as input. The virtual screening performance of AutoDock-SS single-reference mode was evaluated using the standard Directory of Useful Decoys – Enhanced (DUD-E) dataset, with the method outperforming alternative state-of-the-art 3D LBVS methods. The mean area under the receiver operating characteristics curve (AUC) reached 0.775 (exceeding the maximum of 0.755 for alternative methods), and the enrichment factor at one percentage (EF1%) was 25.72.
AutoDock-SS multi-reference mode was assessed on the augmented DUD-E dataset (DUD-E+) using five pre-aligned query ligands, displaying statistically significant superior prediction accuracy (mean AUC of 0.843, p < 10-5) and higher mean EF1% (34.59) compared to the singe-reference mode.
Overall, the findings suggested that AutoDock-SS exhibits enhanced binding conformation prediction when screening the original DUD-E dataset. The proposed method accounts for the shape, pharmacophore, and electrostatic potential of the query ligand(s) to improve prediction accuracy and includes a built-in conformational sampling algorithm that natively considers compounds as naturally conformationally flexible—an aspect not present in existing LBVS methods.
| Boyang Ni; Haoying Wang; Huda Khalaf; Vincent Blay-Roger; Douglas R Houston | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-05-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/645cfaa9f2112b41e963edff/original/auto-dock-ss-auto-dock-for-multiconformational-ligand-based-virtual-screening.pdf |
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