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671c9c181fb27ce124a411a8 | 10.26434/chemrxiv-2024-54m5x-v2 | Endless Data for Drug Discovery Pipeline Validation for Free – Computational Chemistry’s Gift | Modern virtual high-throughput screening (vHTS) pipelines tend to be overmarketed and undervalidated, with no rigorous studies conclusively demonstrating that every one of their steps reliably adds increasing enrichment atop the baseline random hit rate. Moreover, what little benchmarking studies are available primarily focus on the docking aspect of the pipelines, which is usually only the beginning or near the beginning, and even there, authors tend to use flawed data sets that artificially inflate performance metrics. Herein, we present an alternative method to pipeline validation and data set generation that requires no additional experimental work and expenditure, yet offers negative data that is vastly superior both in terms of quality and quantity to any data set used in vHTS pipeline validation up to now. By randomizing ligands across published experimental structures and generating structural isomers of known binders, practically unlimited amounts of negative data can be generated. Such sets of positive and negative data points match closely in molecular properties and are much more suitable for pipeline validation and have far greater evidentiary value than any of the current sets. Once such sets are generated, they are to be run through any proposed pipeline, assessing performance at every step. We stress the importance of using negative data of adequate quality and quantity in validation studies to definitively and verifiably demonstrate the utility of a given tool or workflow. Our goal is to help distinguish tools and pipelines that truly accelerate hit discovery and lead optimization from ones that promise to do so but actually do not, whereupon academia and industry can begin to tackle the many unaddressed medical needs of the 21st century. | Stefan Ivanov | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-10-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671c9c181fb27ce124a411a8/original/endless-data-for-drug-discovery-pipeline-validation-for-free-computational-chemistry-s-gift.pdf |
61b75e4f689c870f3be280d5 | 10.26434/chemrxiv-2021-l3hzf | Communication and Cross-Regulation Between Multiple Concatenated Enzymatic Reaction Networks | Nature connects multiple fuel-driven chemical/enzymatic reaction networks (CRNs/ERNs) via cross-regulation to hierarchically control biofunctions for a tailored adaption in complex sensory landscapes. In contrast, emerging artificial fuel-driven systems most-ly focus on a single CRN and their implementation to direct self-assembly or material responses. In this work, we introduce a facile example of communication and cross-regulation among multiple DNA-based ERNs regulated by a concatenated RNA transcription regulator. For this purpose, we run two fuel-driven DNA-based ERNs by concurrent NAD+-fueled ligation and restriction via endo-nucleases (REases) in parallel. ERN one allows for the dynamic steady-state formation of the promoter sequence for T7 RNA poly-merase, which activates RNA transcription. The produced RNA regulator can repress or promote the second ERN via RNA-mediated strand displacement. Furthermore, adding RNase H to degrade the produced RNA can restart the reaction or tune the lag time of two ERNs, giving rise to a repression-recovery and promotion-stop processes. We believe that concatenation of multiple CRNs provides a basis for the design of more elaborate autonomous regulatory mechanisms in systems chemistry and synthetic biology. | Mo Sun; Jie Deng; Andreas Walther | Polymer Science; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b75e4f689c870f3be280d5/original/communication-and-cross-regulation-between-multiple-concatenated-enzymatic-reaction-networks.pdf |
623036203599de40e500436e | 10.26434/chemrxiv-2022-h590n | Coordination/Metal–Organic Cages Inside Out | Cage-like molecules, assembled by the coordination of multiple metal ions and organic links, are pushing new frontiers in science due to their design flexibility and the resulting diverse and unique chemical properties. This field has been advanced by two close but distinct chemistry communities. Consequently, the family of molecules referred to as coordination cages (CCs) constituted of metal-pyridine coordination bonds or metal–organic cages (MOCs) based on dinuclear tetracarboxylates paddlewheel complexes in each community had not been reviewed cross-sectionally, even though they are conceptually similar. This review article extracted and compared experimental information on a total of 197 CCs and 78 MOCs from 182 reports to identify their synthetic and structural signatures. We did not merely enumerate the reports we collected; we meta-analyzed the data extracted from the reports and highlighted both the similarities and dissimilarities between CCs and MOCs. As a result, we clarified the key parameters governing the synthetic conditions. Furthermore, we identified a new research direction by visualizing unexplored features and properties of CCs and MOCs. This review article provides a good tutorial both for researchers attempting to cross the boundary between CCs and MOCs and those who are new to the field. | Tomoki Tateishi; Masahiko Yoshimura; Shun Tokuda; Fuyuki Matsuda; Daishi Fujita; Shuhei Furukawa | Inorganic Chemistry; Nanoscience; Coordination Chemistry (Inorg.); Supramolecular Chemistry (Inorg.); Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-03-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/623036203599de40e500436e/original/coordination-metal-organic-cages-inside-out.pdf |
6440d43e83fa35f8f6f0bddd | 10.26434/chemrxiv-2023-tbmtf | PBCNet：Computing Relative Binding Affinity of Ligands to a Receptor Based on a Pairwise Binding Comparison Network for Lead Optimization | Structure-based lead optimization is an open challenge in drug discovery, which is still largely driven by hypotheses and depends on the experience of medicinal chemists. We here propose a pairwise binding comparison network (PBCNet) based on physics-informed graph attention mechanism, specifically tailored for ranking relative binding affinity among congeneric ligands. Benchmarking on two held-out sets (provided by Schrödinger, Inc. and Merck KGaA) containing over 460 ligands and 16 targets, PBCNet demonstrated significant advantages in terms of both prediction accuracy and computational efficiency. Equipped with a fine-tuning operation, the performance of PBCNet reaches that of Schrödinger's FEP+, which is much more computationally intensive and requires significant expert intervention. A further simulation-based experiment showed that active learning-optimized PBCNet may accelerate lead optimization campaigns by 30%. Finally, for the convenience of users, a web service (https://pbcnet.alphama.com.cn/index) for PBCNet is established to facilitate complex relative binding affinity prediction through an easy-to-operate graphical interface. | Jie Yu; Zhaojun Li; Geng Chen; Xiangtai Kong; Jie Hu; Dingyan Wang; Duanhua Cao; Yanbei Li; Xiaohong Liu; Gang Wang; Hualiang Jiang; Xutong Li; Xiaomin Luo; Mingyue Zheng | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-04-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6440d43e83fa35f8f6f0bddd/original/pbc-net-computing-relative-binding-affinity-of-ligands-to-a-receptor-based-on-a-pairwise-binding-comparison-network-for-lead-optimization.pdf |
66e066facec5d6c142aff017 | 10.26434/chemrxiv-2024-zgg6v | Intercalation Phenomena in Two-Dimensional Hybrid Perovskites Featuring Discrete Free Volume Elements | Here, we show using density functional theory that 2D hybrid perovskites assembled with mixtures of organics ligands to create free volume elements within the gallery space render the hybrids amenable to intercalation by organic small molecules. Though these intercalants produce relatively small changes in the materials architecture, their presence has a pronounced effect on the optoelectronic properties of two-dimensional L2PbI4 perovskites | Kevin Whitham; Jisook Hong; Liang Tan; Brett Helms | Theoretical and Computational Chemistry; Theory - Computational; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e066facec5d6c142aff017/original/intercalation-phenomena-in-two-dimensional-hybrid-perovskites-featuring-discrete-free-volume-elements.pdf |
60c747be4c8919bd30ad2d8f | 10.26434/chemrxiv.11733393.v1 | Evaluation of Grey Wolf Optimization Algorithm on Rigid and Flexible Receptor Docking | Protein-ligand docking programs are
indispensable tools for predicting the binding pose of a ligand to the receptor
protein in current structure-based drug design. In this paper, we evaluate the
performance of grey wolf optimization (GWO) in protein-ligand docking. Two
versions of the GWO docking program – the original GWO and the modified one
with random walk – were implemented based on AutoDock Vina. Our rigid docking experiments
show that the GWO programs have enhanced exploration capability leading to
significant speedup in the search while maintaining comparable binding pose
prediction accuracy to AutoDock Vina. For flexible receptor docking, the GWO
methods are competitive in pose ranking but lower in success rates than
AutoDockFR. Successful redocking of all the flexible cases to their holo
structures reveals that inaccurate scoring function and lack of proper
treatment of backbone are the major causes of docking failures. | Kin Meng Wong; Shirley Siu | Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747be4c8919bd30ad2d8f/original/evaluation-of-grey-wolf-optimization-algorithm-on-rigid-and-flexible-receptor-docking.pdf |
650c4f95ed7d0eccc3f62bcc | 10.26434/chemrxiv-2023-pxq1b | Optical and scintillation properties of hybrid manganese(II) halides with formamidinium and acetamidinium cations | In recent years, hybrid manganese(II) halides (HMHs) have attracted wide attention due to their impressive optical properties, low toxicity, and facile synthetic processibility. Being effective reab-sorption-free phosphors, these compounds demonstrate the potential to be used as low-cost solu-tion-processable scintillators. However, most of the HMHs studied to date contain bulk organic cations and, as a result, are characterized by low density and low X-ray stopping power. For this reason, we studied manganese(II) halides with compact organic cations such as formamidinium (FA+) and acetamidinium (Ac+). In particular, we synthesized four new phases, two of which are characterized by octahedral coordination of manganese ions (FAMnBr3, AcMnBr3) and red emis-sion, whereas the other two have tetrahedrally coordinated Mn2+ ions (FA3MnBr5, Ac2MnBr4) and green emission. Photoluminescence (PL) and radioluminescence measurements demonstrated high PL quantum yields and reasonable scintillation light yields of acetamidinium-based compounds. In addition, unlike most known HMH-based scintillators, the discovered materials have a relatively high density, due to the small fraction of the volume occupied by organic cations, so their X-ray attenuation coefficients are comparable to the well-known oxide scintillators. | Sergey Fateev; Vladislava Kozhevnikova; Kirill Kuznetsov; Daria Belikova; Victor Khrustalev; Eugene Goodilin; Alexey Tarasov | Physical Chemistry; Spectroscopy (Physical Chem.); Materials Chemistry; Crystallography | CC BY NC 4.0 | CHEMRXIV | 2023-09-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650c4f95ed7d0eccc3f62bcc/original/optical-and-scintillation-properties-of-hybrid-manganese-ii-halides-with-formamidinium-and-acetamidinium-cations.pdf |
675231985a82cea2fa1f9dcf | 10.26434/chemrxiv-2024-s75wv-v2 | Nanoscale Materials in Biomedical Applications of Sensors: Insights from a Comprehensive Landscape Analysis | Since their inception in the early 1960s, the use of nanoscale materials has progressed in leaps and bounds, and their role in diverse fields ranging from human health to energy is undeniable. Nanosensors are devices having a nanoscale dimension designed to detect, record, and transmit signals to provide valuable data and information. In this report, we utilize the CAS Content Collection, a vast repository of scientific information extracted from journal and patent publications, to identify emerging materials and applications in this field. This involves understanding trends, such as the growth of certain topics over time, as well as establishing relationships between emerging topics.
Our analysis indicates that among the various nanomorphologies explored in nanosensors, nanoparticles, nanotubes and quantum dots tend to lead. In terms of the types of nanosensors, chemical and biological sensors account for nearly 80% of publications. In combination with bibliographic data, we utilized our access to the CAS REGISTRY and identified a host of emerging materials across various substance classes (polymers, small molecules, elements) associated with nanosensor publications. Finally, our analysis indicates that a major application of nanosensors appears to be biomedical in nature (cancer diagnosis and testing and drug discovery etc.). Our findings are highlighted in a CAS TrendScape map that provides an overview of research interest in various concepts in the field. We also provide a snapshot of commercial interest in the development of nanosensors as well as briefly discuss nanosensors currently under development. It is our hope that this report provides a comprehensive overview of the field and serves as a valuable guide to researchers/scientists.
| Kavita A. Iyer; Rumiana Tenchov; Krittika Ralhan; Robert E. Bird; Leilani Lotti Diaz; kevin J. Hughes; Magesh Ganesan; Julian Ivanov; Qiongqiong Zhou | Materials Science; Nanoscience | CC BY 4.0 | CHEMRXIV | 2024-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675231985a82cea2fa1f9dcf/original/nanoscale-materials-in-biomedical-applications-of-sensors-insights-from-a-comprehensive-landscape-analysis.pdf |
67671fd86dde43c908ec6761 | 10.26434/chemrxiv-2024-nsj0f | Automated Multireference Vertical Excitations for Transition Metal Compounds | Excited states of transition metal complexes are generally strongly correlated due to the near-degeneracy of the metal d orbitals. Consequently, electronic structure calculations of such species often necessitate multireference approaches. However, widespread use of multireference methods is hindered due to the active space selection problem, which has historically required system-specific chemical knowledge and a trial-and-error approach. Here, we address this issue with an automated method combining the approximate pair coefficient (APC) scheme for estimating orbital entropies with the discrete variational selection (DVS) approach for evaluating active space quality. We apply DVS-APC to the calculation of 67 vertical excitations in transition metal diatomics as well as to two larger complexes. We show DVS-APC generated active spaces yield NEVPT2 mean absolute errors of 0.18 eV, in line with previous accuracies obtained for organic systems, but larger than errors achieved with hand-selected active spaces (0.14 eV). If instead of using DVS we identify the best results from our trial wave functions, we find improved performance (mean absolute error of 0.1 eV) over the manually selected results. We highlight this deviation between DVS and hand selected active spaces as a possible measure of bias introduced when hand selecting active spaces. However, we find that multiconfiguration pair-density functional theory (MC-PDFT) using the tPBE and tPBE0 functionals is roughly 0.15 eV less accurate than NEVPT2 across this class of diatomic systems, potentially accounting for the decreased performance of DVS-APC, which uses MC-PDFT energies to select between active spaces. We also showcase an ability to ``down-sample'' the DVS-APC wave functions using natural orbital occupancies to achieve smaller minimal active spaces which retain the accuracy of the larger starting active spaces. Finally, DVS-APC and tPBE0 are proven to be effective when applied to modeling excited states in two larger transition metal complexes, suggesting that the transition metal diatomics may be a particular outstanding challenge for DVS-APC and MC-PDFT approaches. | Jacob Wardzala; Daniel King; Laura Gagliardi | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-12-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67671fd86dde43c908ec6761/original/automated-multireference-vertical-excitations-for-transition-metal-compounds.pdf |
65730a805bc9fcb5c95bf294 | 10.26434/chemrxiv-2023-xc820 | Dynamic and solid-state behaviour of bromoisotrianglimine | Solid-state materials formed from discrete imine macrocycles have potential in industrial separations, but dynamic behaviour during both synthesis and crystallisation makes them challenging to exploit. Here, we explore opportunities for structural control by investigating the dynamic nature of a C-5 brominated isotrianglimine in solution and under crystallisation conditions. In solution, the equilibrium between the [3+3] and the less reported [2+2] macrocycle was investigated, and both macrocycles were fully characterised. Solvent templating during crystallisation was used to form new packing motifs for the [3+3] macrocycle and an unreported [4+4] macrocycle. Finally, chiral self-sorting was used to demonstrate how crystallisation conditions can not only influence packing arrangements but also shift the macrocycle equilibrium to yield new structures. This work thus exemplifies three strategies for exploiting dynamic behaviour to form isotrianglimine materials, and highlights the importance of understanding the dynamic behaviour of a system when designing and crystallising functional materials formed using dynamic covalent chemistry. | Abbie Scholes; Laurence Kershaw-Cook; Filip Szczypiński; Benjamin Egleston; Rebecca Greenaway; Anna Slater | Organic Chemistry; Supramolecular Chemistry (Org.); Materials Chemistry; Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65730a805bc9fcb5c95bf294/original/dynamic-and-solid-state-behaviour-of-bromoisotrianglimine.pdf |
6576e2ff7acf130c32f910ac | 10.26434/chemrxiv-2023-9c6fz | Boundary lubrication performance of polyelectrolyte-surfactant complexes on biomimetic surfaces | Aqueous mixtures of oppositely charged polyelectrolytes and surfactants are useful in many industrial applications, including shampoos and hair conditioners. In this work, we investigate the friction between biomimetic hair surfaces in the presence of adsorbed complexes formed from cationic polyelectrolytes and anionic surfactants in aqueous solution. For this purpose, we apply non-equilibrium molecular dynamics (NEMD) simulations using the coarse-grained MARTINI model. We develop new MARTINI parameters for cationic guar gum (CGG), a functionalized, plant-derived polysaccharide. The surface complexation of CGG and the anionic surfactant sodium dodecyl sulfate (SDS) on virgin and bleached hair is studied using a sequential adsorption approach, whereby CGG is deposited first, followed by SDS. The stability of the adsorbed complexes with respect to compression were then tested using squeeze-out simulations, where some of the water and SDS molecules are removed from the contact. Finally, we carry out sliding NEMD simulations to assess the boundary lubrication performance of the polyelectrolyte-surfactant complex compressed between virgin and chemically damaged biomimetic hair surfaces. We observe synergistic friction behaviour for the CGG-SDS complex, which gives lower shear stress than either pure CGG or SDS. We observe large reductions in the shear stress by the CGG-SDS complex at relatively low normal stress (≤ 20 MPa) compared to water. At higher normal stresses, which are probably beyond those usually experienced during hair manipulation, SDS and water are squeezed out and the shear stress with the complex increases to levels higher than those observed for pure water due to increased interdigitation. Thus, the CGG-SDS complex generally increases the friction coefficient, but decreases the adhesive Derjaguin offset compared to pure water. The outcomes of this work are expected to be beneficial to fine-tune and screen sustainable hair care formulations to provide low friction and therefore a smooth feel and superior entanglement behaviour. | Erik Weiand; Peter H. Koenig; Francisco Rodriguez-Ropero; Yuri Roiter; Stefano Angioletti-Uberti; Daniele Dini; James P. Ewen | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Polyelectrolytes - Materials; Computational Chemistry and Modeling; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6576e2ff7acf130c32f910ac/original/boundary-lubrication-performance-of-polyelectrolyte-surfactant-complexes-on-biomimetic-surfaces.pdf |
65a677ad9138d231610ac911 | 10.26434/chemrxiv-2024-b32m2 | A Simple Regeneration Process Using a CO2-switchable Solvent for Cellulose Hydrogels | Cellulose is one of the main components of plant cell walls, abundant on earth, and is a non-edible material that can be acquired at a low cost. Furthermore, there has been increasing interest in its use in environmentally friendly, carbon-neutral, sustainable materials. It is expected that the applications of cellulose will expand with the development of a simple processing method. Previously, it was demonstrated that cellulose can be dissolved in a non-heated, short-duration process using an aqueous pyrrolidinium hydroxide solution. In this study, we dissolved cellulose in aqueous N-butyl-N-methylpyrrolidinium hydroxide solution ([C4mpyr][OH]/H2O) and investigated the cellulose regeneration process based on changes in solubility upon application of CO2 gas. We investigated the effect of transformation of the anion chemical structure on cellulose solubility by flowing CO2 gas into [C4mpyr][OH]/H2O and conducted pH, FT-IR, and 13C NMR measurements. We observed that the changes in anion structure allowed for the modulation of cellulose solubility in [C4mpyr][OH]/H2O, thus establishing a simple and safe cellulose regeneration process. This regeneration process was also applied to enable the production of cellulose hydrogels. The hydrogel formed using this approach was revealed to be of a higher mechanical strength than that of an analogous hydrogel produced using the same dissolution solvent with addition of a cross-linker. The ability to produce cellulose-based hydrogels of different mechanical properties is expected to expand the possible applications. | Arata Matsui; Deandra Ayu Putri; Morgan L. Thomas; Yuko Takeoka; Masahiro Rikukawa; Masahiro Yoshizawa-Fujita | Polymer Science; Chemical Engineering and Industrial Chemistry; Cellulosic materials; Hydrogels; Process Control; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a677ad9138d231610ac911/original/a-simple-regeneration-process-using-a-co2-switchable-solvent-for-cellulose-hydrogels.pdf |
64d0f72e69bfb8925a85ee3b | 10.26434/chemrxiv-2023-k92gw | Improved Quantification of Carbonyl Sub-metabolome by Liquid Chromatography Mass Spectrometry using a Fragment Controlled Multiplexed Isotopic Tag | Background: Carbonyl-containing metabolites are a class of key intermediate in metabolism, which has potentials to be biomarkers. Since their poor ionization, derivatization reagents, such as dansylhydrazine, are usually used to improve the sensitivity and/or to facilitate quantification. However, most current carbonyl derivatization reagents only have two channels, one is isotopically labeled and the other one is non-labeled. To quantify more samples in a run and using data-independent acquisition (DIA) mode to get comprehensive and unbiased mass fragmentation, we proposed a fragment-controlled isotopic tag, called DiMe-FP-NHNH2 (FP) which has five channels: Δ0, Δ3, Δ6, Δ9, and Δ12, thus up to 5 samples can be analyzed in a run. Results:. The most important improvement is that the FP tag can produce multiple characteristic signals in tandem mass, diagnostic ions and neutral losses, which helps to selectively detect aldehydes/ketones for targeted and untargeted analysis. To exhibit all capabilities of the FP tag, we mimicked an untargeted metabolomics experiment, which comprises two steps. First, discovery step, using Data-Independent Analysis (SWATH-MS) and the labeling of two channels (Δ0 and Δ3), we picked out aldehyde/ketone from the pooled urine samples based on three characteristic signals, including isotope patterns, diagnostic ions, and neutral losses. Second, five-plex quantification, relative and absolute quantification were achieved in a single LC-MS analysis. Notably, because of different nominal masses, the FP tag can be used on any low or high resolution mass spectrometers Significance: The benefits and performance of the FP tag are demonstrated by the analysis of urine samples collected from patients from a prostate cancer study, in which more than a thousand features were found based on MS1 fingerprint, but only around 120 aldehyde/ketone candidates were confirmed with characteristic signals and nine of which were quantified showing significant differences from healthy and reference urine samples. | Xiaobo Tian; Gérard Hopfgartner | Analytical Chemistry; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d0f72e69bfb8925a85ee3b/original/improved-quantification-of-carbonyl-sub-metabolome-by-liquid-chromatography-mass-spectrometry-using-a-fragment-controlled-multiplexed-isotopic-tag.pdf |
60f05fd7446ac34cd59086c0 | 10.26434/chemrxiv-2021-754q4 | Decoupling bulk and interfacial contributions to performance in localized high concentration electrolytes for Li metal batteries | Localized high concentration electrolytes (LHCEs) are a promising class of electrolytes to enable stable cycling of the lithium metal anode. Here, we report the use of operando nuclear magnetic resonance (NMR) spectroscopy to observe electrolyte decomposition during Li stripping/plating and identify the influence of individual components in LHCEs on Li metal battery performance. Data from operando 19F solution NMR indicates that both bis(fluorosulfonyl)imide (FSI–) salt and bis(2,2,2-trifluoroethyl)ether (BTFE) diluent molecules play a key role in solid electrolyte interphase (SEI) formation, in contrast to prior reports that suggest diluents are inert. Using a combination of solution 17O NMR and cyclic voltammetry (CV), we assess differences in solvation and electrochemical reduction in LHCEs and compare to low concentration electrolytes (LCEs). We find that BTFE diluents are chemically (rather than electrochemically) reduced during Li metal battery operation, which can be detected with operando NMR, but not conventional electrochemical methods. Solid-state NMR (SSNMR) and X-ray photoelectron spectroscopy (XPS) measurements confirm that LHCEs decompose to form a SEI on Li metal that contains organic BTFE reduction products as well as high quantities of lithium fluoride from both BTFE and FSI– reduction. Insight into the (electro)chemical reduction mechanisms underpinning SEI formation in LHCEs suggests that fluorinated ethers exhibit tunable reactivity that can be leveraged to control Li deposition behavior. | Richard May; Julia Hestenes; Lauren Marbella | Materials Science; Energy; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f05fd7446ac34cd59086c0/original/decoupling-bulk-and-interfacial-contributions-to-performance-in-localized-high-concentration-electrolytes-for-li-metal-batteries.pdf |
60c73cbf842e655cc8db167a | 10.26434/chemrxiv.14745282.v1 | A Computational Protocol Combining DFT and Cheminformatics for Prediction of pH-Dependent Redox Potentials | <p>We present and validate a robust procedure to calculate the redox potentials of organic molecules at any pH value, using widely available quantum chemistry and cheminformatics methods. Using a consistent experimental data set for validation, we explore and compare a few different methods for calculating reaction free energies, the treatment of solvation, and the effect of pH on redox potentials. We find that the B3LYP hybrid functional with COSMO solvation method, in conjunction with thermal contributions evaluated from BLYP gas-phase harmonic frequencies, yields a good prediction of pH=0 redox potentials at a moderate computational cost. To predict how the potentials are affected by pH, we propose an improved version of the Alberty-Legendre transform that allows the construction of a more realistic Pourbaix diagram by taking into account how the protonation state changes with pH.</p> | Rocco Peter Fornari; Piotr de Silva | Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73cbf842e655cc8db167a/original/a-computational-protocol-combining-dft-and-cheminformatics-for-prediction-of-p-h-dependent-redox-potentials.pdf |
64f9559cdd1a73847f59d172 | 10.26434/chemrxiv-2023-0h4zp | Three-Dimensional Covalent Organic Frameworks Constructed from Irregular Polyhedral Building Blocks | Developing three-dimensional (3D) covalent organic frameworks (COFs) has paramount significance across numerous applications. However, the conventional design approach that relies on regular building blocks significantly restricts the structural diversity of COFs. In this study, we successfully designed and synthesized two 3D COFs, named JUC-643 and JUC-644, employing a novel strategy based on irregular 8-connected (8-c) building blocks. By using a continuous rotation electron diffraction technique combined with powder X-ray diffraction patterns, their structures were solved and revealed a unique linkage with double helical structure, a phenomenon previously unreported in COFs. In order to precisely describe the topology, these structures should be deconstructed into the unprecedented [4+3(+2)]-c nets instead of the traditional [8(+2)]-c or [6(+2)]-c net. Furthermore, one of the materials (JUC-644) has demonstrated exceptional adsorption capability towards C3H8 and n-C4H10 (11.28 and 10.45 mmol g-1 at 298 K and 1 bar respectively), surpassing the adsorption performance of all known porous materials, and breakthrough experiments have also highlighted the remarkable C3H8/C2H6 and n-C4H10/C2H6 selectivity. This pioneering concept of incorporating irregular building blocks in 3D COFs introduces a promising avenue for designing intricate architectures while enhancing their potential application in the recovery of C2H6 from natural gas liquids. | Qianrong Fang; Jianhong Chang; Zeyue Zhang; Haorui Zheng; Hui Li; Jinquan Suo; Chunqing Ji; Fenqian Chen; Valentin Valtchev; Shilun Qiu; Junliang Sun | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f9559cdd1a73847f59d172/original/three-dimensional-covalent-organic-frameworks-constructed-from-irregular-polyhedral-building-blocks.pdf |
60c746fdf96a00a93f286e40 | 10.26434/chemrxiv.11466972.v1 | Catalytic Sulfone Upgrading Reaction with Alcohols via Ru(II) | <a>Sulfones and sulfonamides with an α-CH bond can be easily alkylated by aliphatic alcohols to add the carbon skeleton of the alcohol via a one-step, Ru(II) catalyzed redox neutral reaction. The reaction requires a sub-stoichiometric amount of base and produces only water as a byproduct. A number of pharmaceutically relevant functional groups such as piperidine, morpholine, etc. are well tolerated under the reaction conditions to give higher value-added products in one step from widely available substrates. The reaction proceeds through a sulfone carbanion addition to an in-situ generated aldehyde formed via catalytic dehydrogenation and subsequent catalyst mediated replacement of the secondary alcohol by hydrogen.</a> | Tomas Vojkovsky; Shubham Deolka; Saiyyna P. Stepanova; Michael C. Roy; Eugene Khaskin | Homogeneous Catalysis; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746fdf96a00a93f286e40/original/catalytic-sulfone-upgrading-reaction-with-alcohols-via-ru-ii.pdf |
62ff981d11986c8ae83e4534 | 10.26434/chemrxiv-2022-fvcnb | Linker-templated structure tuning of optical response in plasmonic nanoparticle gels | Gel assemblies of functional nanoparticles, reversibly associated into percolating networks using bifunctional linking molecules, offer promise as versatile materials platforms. Molecular linkers can be customized to template interparticle spacing and modify colloidal network attributes, enabling design for structure-dependent properties. Mechanical properties of gels are commonly studied by molecular simulation, but simulating the optical response of large-scale, disordered assemblies has been computationally intractable, limiting our understanding of light-matter interactions in structurally complex plasmonic networks. Here, we use a recently developed mutual polarization method, capable of predicting optical properties for large disordered configurations of spherical particles, together with an experimentally-informed coarse-grained model to study the behavior of plasmonic linker gels. The simulation results demonstrate how blends of short and long linkers with the same average molecular weight can be chosen to deliberately modulate structure-dependent near- and far-field spectral features of the colloidal gel, while preserving gel mechanical properties. Linker selection can also be used to prepare gel networks with qualitatively different mechano-optical responses. The structural changes occurring under strain shed light on possible origins of experimentally observed red- and blue-shifting of optical extinction of plasmonic nanocomposites under uniaxial extension. | Murari Singh; Zachary M. Sherman; Delia J. Milliron; Thomas M. Truskett | Materials Science; Optical Materials | CC BY 4.0 | CHEMRXIV | 2022-08-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ff981d11986c8ae83e4534/original/linker-templated-structure-tuning-of-optical-response-in-plasmonic-nanoparticle-gels.pdf |
634135e50847002d0599c484 | 10.26434/chemrxiv-2022-qcg0x | Plant Terpenoid Permeability through Biological Membranes Explored via Molecular Simulations | Plants synthesize small molecule diterpenes comprised of twenty carbon from precursors isopentenyl diphosphate and dimethylallyl disphosphate, manufacturing diverse compounds used for defense, signaling, and other functions. Industrially, diterpenes are used as natural aromas and flavoring, as pharmaceuticals, and as natural insecticides or repellents. Despite diterpene ubiquity in plant systems, it remains unknown how plants control diterpene localization and transport. For many other small molecules, plant cells maintain transport proteins that control compound compartmentalization. However, for most diterpene compounds, specific transport proteins have not been identified, and so it has been hypothesized that diterpene may cross biological membranes passively. Through molecular simulation, we study membrane transport for three complex diterpenes from among the many made by members of the Lamiaceae family to determine their permeability coefficient across plasma membrane models. To facilitate accurate simulation, the intermolecular interactions for leubethanol, abietic acid, and sclareol were parameterized through the standard CHARMM methodology for incorporation into molecular simulations. To evaluate the effect of membrane composition on permeability, we simulate the three diterpenes in two membrane models derived from sorghum and yeast lipidomics data. We track permeation events within our unbiased simulations, and compare implied permeation coefficients with those calculated from Replica Exchange Umbrella Sampling calculations using the inhomogeneous solubility diffusion model. The diterpenes are observed to permeate freely through these membranes, indicating that a transport protein may not be needed to export these small molecules from plant cells. Moreover, the permeability is observed to be greater for plant-like membrane compositions when compared against animal-like membrane models. Increased permeability for diterpene molecules in plant membranes suggest that plants have tailored their membranes to facilitate low-energy transport processes for signaling molecules. | Saad Raza; Mykayla Miller; Björn Hamberger; Josh Vermaas | Theoretical and Computational Chemistry; Physical Chemistry; Agriculture and Food Chemistry; Computational Chemistry and Modeling; Biophysical Chemistry; Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634135e50847002d0599c484/original/plant-terpenoid-permeability-through-biological-membranes-explored-via-molecular-simulations.pdf |
60c74978567dfeeb0eec4c05 | 10.26434/chemrxiv.12057900.v1 | NMR-TS: De Novo Molecule Identification from NMR Spectra | <div>NMR spectroscopy is an effective tool for identifying molecules in a sample. Although many previously observed NMR spectra are accumulated in public databases, they cover only a tiny fraction of the chemical space, and molecule identification is typically accomplished manually based on expert knowledge. Herein, we propose NMR-TS, a machine-learning-based python library, to automatically identify any molecule from its NMR spectrum. NMR-TS discovers candidate molecules whose NMR spectra match the target spectrum by using deep learning and density functional theory (DFT)-computed spectra. As a proof-of-concept, we identify prototypical metabolites from their computed spectra. After an average 5451 DFT runs for each spectrum, six of the nine molecules are identified correctly, and proximal molecules are obtained in the other cases. This encouraging result implies that de novo molecule generation can contribute to the fully automated identification of chemical structures. NMR-TS is available at https://github.com/tsudalab/NMR-TS. <br /></div> | Jinzhe Zhang; Kei Terayama; Masato Sumita; Kazuki Yoshizoe; Kengo Ito; Jun Kikuchi; Koji Tsuda | Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74978567dfeeb0eec4c05/original/nmr-ts-de-novo-molecule-identification-from-nmr-spectra.pdf |
60c750ff4c891928edad3e79 | 10.26434/chemrxiv.13107548.v1 | Topological Excitation of Singly Hydrated Hydroxide Complex in Confined Sub-Nanospace for Bright Color Emission and Heterogeneous Catalysis | <p>This
excellent story answered two unresolved questions in the past one century and
two centuries. The first one is that water is colored or noncolored (<b><i>Water
as an Activator of Luminescence. Nature 1930, 125, 706-707</i></b>)? If it is colorful,
why and how does it emit the bright colors? The second question is on the
physical origin of catalysis or catalyst, i.e., the mysterious internal force
of catalysis is what, and how this powerful force determines the chemical
reactivity, including activity, selectivity and life times (or stability of
catalyst)? (<b><i>A Brief History of Catalysis. CATTECH 2003, 7 (4), 130-138.</i></b>)</p>
After reading this
interesting story, both seemingly non-related two questions could be perfectly
answered by topological excitation of singly hydrated hydroxide complex in
confined sub-nanospace. | Xiao-Dan Hu; Taiqun Yang; Bingqian Shan; Bo Peng; Kun Zhang | Heterogeneous Catalysis; Chemical Kinetics; Interfaces; Photochemistry (Physical Chem.); Quantum Mechanics; Quasiparticles and Excitations; Spectroscopy (Physical Chem.); Surface | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750ff4c891928edad3e79/original/topological-excitation-of-singly-hydrated-hydroxide-complex-in-confined-sub-nanospace-for-bright-color-emission-and-heterogeneous-catalysis.pdf |
60c75741567dfed2b6ec665c | 10.26434/chemrxiv.14156816.v1 | Thermotropic Icy Road Sign with Light Scattering and Fluorescence Response | <div>
<div>
<div>
<p>Prototypes of flexible, electricity-free, ice warning signs for roads and pavements have been developed. A thermotropic
response in the form of an upper critical solution (UCST) type phase separation targeted near the freezing point of water
manifests itself through light scattering as a clear-to-opaque transition. It is simultaneously amplified by an enhanced
photoluminescence effect. The conceptual road sign application is a multi-lamellar flexible strip with an active layer of a
polystyrene-based solution. The solvent is a plasticizer, here either dioctylphthalate (DOP) or its alternative 1,2-cyclohexane
dicarboxylic acid diisononyl ester (DINCH). A collection of styrene-based macromolecules were made by free radical
(co)polymerization, varying molecular weight and monomer feed composition. UCST type phase diagrams for the polymer
solutions were constructed from cloud point data measured by a bespoke photographic set-up, in which up to 30 samples
were measured simultaneously using both light scattering, that is opacity, and fluorescence. For the latter, the concept of
restricted motion enhanced photoluminescence, often referred to as aggregation-induced emission (AIE), was used.
Polystyrene labelled with tetraphenylethylene (TPE) was used for this. The contrast between ‘ON’ and ‘OFF’ states in the
prototype ice warning signs was optimized by tuning the polymer concentration and the active layer thickness. Our prototype
signs show full reversibility over many temperature cycles. We believe the concept can be of wider use in electricity-free
signs and labels.
</p>
</div>
</div>
</div> | Joshua Booth; Robert Young; Andrés Richards Gonzales; zachary meakin; Corinna Preuss-Weber; Ross Jaggers; Stefan Bon | Aggregates and Assemblies; Materials Processing; Multilayers; Optical Materials; Organic Polymers; Polymer chains; Industrial Manufacturing; Optics; Physical and Chemical Properties; Self-Assembly; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75741567dfed2b6ec665c/original/thermotropic-icy-road-sign-with-light-scattering-and-fluorescence-response.pdf |
60c751570f50db2cea397772 | 10.26434/chemrxiv.13154261.v1 | The Chirality of Yariv Reagent Aggregates Correlates with AGP–binding Ability | Yariv reagents are glycosylated triphenylazo dyes, some of which bind to the polysaccharide component of arabinogalactan proteins (AGPs), proteoglycans found in plant cell walls. However, the exact reason for the selectivity in the presence/absence of AGP binding ability among Yarivs remains unknown. The Yariv reagents are known to form supramolecular aggregates in solution. We use circular dichroism to show that the Yariv reagent aggregates possess helical chirality, and the AGP binding ability of the Yariv reagents is correlated to its helical chirality. | Raghuraj Hoshing; Blaise W Leeber III; Helene Kuhn; David Caianiello; Brandon Dale; Michael Saladino; Robert Lusi; Natalie Palaychuk; Sarah Weingarten; Amit Basu | Biophysics; Plant Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751570f50db2cea397772/original/the-chirality-of-yariv-reagent-aggregates-correlates-with-agp-binding-ability.pdf |
63a4ce51e8047a098cf27a03 | 10.26434/chemrxiv-2022-sgh97 | Wastewater-based epidemiology for comprehensive community health diagnostics in a national surveillance study: mining biochemical markers in wastewater | This manuscript showcases results from a large scale and comprehensive wastewater-based epidemiology (WBE) study focussed on multi-biomarker suite analysis of both chemical and biological determinants in 10 cities and towns across England equating to a population of ~7 million people. Multi-biomarker suite analysis, describing city metabolism, can provide a holistic understanding to encompass all of human, and human-derived, activities of a city in a single model: from lifestyle choices (e.g. caffeine intake, nicotine) through to health status (e.g. prevalence of pathogenic organisms, usage of pharmaceuticals as proxy for non-communicable disease, NCD, conditions or infectious disease status), and exposure to harmful chemicals due to environmental and industrial sources (e.g. pesticide intake via contaminated food and industrial exposure). Population normalised daily loads (PNDLs) of many chemical markers were found, to a large extent, driven by the size of population contributing to wastewater (especially NCDs). However, there are several exceptions providing insights into chemical intake that can inform either disease status in various communities or unintentional exposure to hazardous chemicals: e.g. very high PNDLs of ibuprofen in Hull resulting from its direct disposal (confirmed by ibuprofen/2-hydroxyibuprofen ratios) and bisphenol A (BPA) in Hull, Lancaster and Portsmouth likely related to industrial discharge. An importance for tracking endogenous health markers such as 4-hydroxy-2-nonenal-mercapturic acid (HNE-MA, an oxidative stress marker) as a generic marker of health status in communities was observed due to increased levels of HNE-MA seen at Barnoldswick wastewater treatment plant that coincided with higher-than-average paracetamol usage and SARS-CoV-2 prevalence in this community. PNDLs of virus markers were found to be highly variable. Being very prevalent in communities nationwide during sampling, SARS-CoV-2 presence in wastewater was to large extent community driven. The same applies to the fecal marker virus, crAssphage, which is very prevalent in urban communities. In contrast, norovirus and enterovirus showed much higher variability in prevalence across all sites investigated, with clear cases of localised outbreaks in some cities while maintaining low prevalence in other locations. In conclusion, this study clearly demonstrates the potential for WBE to provide an integrated assessment of community health which can help target and validate policy interventions aimed at improving public health and well-being. | Barbara Kasprzyk-Hordern; Natalie Sims; Kata Farkas; Kishore Jagadeesan; Kathryn Proctor; Matthew J. Wade; Davey Jones | Biological and Medicinal Chemistry; Analytical Chemistry; Earth, Space, and Environmental Chemistry; Biochemical Analysis; Mass Spectrometry; Microbiology | CC BY NC 4.0 | CHEMRXIV | 2022-12-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63a4ce51e8047a098cf27a03/original/wastewater-based-epidemiology-for-comprehensive-community-health-diagnostics-in-a-national-surveillance-study-mining-biochemical-markers-in-wastewater.pdf |
6162f48b2aca53d3be5ef67b | 10.26434/chemrxiv-2021-bfr9f | Forecasting Nonadiabatic Dynamics using Hybrid Convolutional Neural Network/Long Short-Term Memory Network | Modeling nonadiabatic dynamics in complex molecular or condensed-phase systems has been challenging especially for the long-time dynamics. In this work, we propose a time series machine learning scheme based on the hybrid convolutional neural network/long short-term memory (CNN-LSTM) framework for predicting the long-time quantum behavior given only the short-time dynamics. This scheme takes advantage of both the powerful local feature extraction ability of CNN and the long-term global sequential pattern recognition ability of LSTM. With feature fusion of individually trained CNN-LSTM models for the quantum population and coherence dynamics, the proposed scheme is shown to have high accuracy and robustness in predicting the linearized semiclassical and symmetrical quasiclassical mapping dynamics of various spin-boson models with learning time up to 0.3 ps. Furthermore, if the hybrid network has learned the dynamics of a system, this knowledge is transferable that could significantly enhance the accuracy in predicting the dynamics of a similar system. The hybrid CNN-LSTM network is thus believed to have high predictive power in forecasting the nonadiabatic dynamics in realistic charge and energy transfer processes in photoinduced energy conversion. | Daxin Wu; Zhubin Hu; Jiebo Li; Xiang Sun | Theoretical and Computational Chemistry; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6162f48b2aca53d3be5ef67b/original/forecasting-nonadiabatic-dynamics-using-hybrid-convolutional-neural-network-long-short-term-memory-network.pdf |
617c0b0492abe098e32d6463 | 10.26434/chemrxiv-2021-38dt8 | Selective solvent conditions influence sequence development and supramolecular assembly in step-growth copolymerization | Sequence control in synthetic copolymers remains a tantalizing objective in polymer science due to the influence of sequence on material properties and self-organization. A greater understanding of sequence development throughout the polymerization process will aid the design of simple, generalizable methods to control sequence and tune supramolecular assembly. In previous simulations of solution-based step-growth copolymerizations, we have shown that weak, non-bonding attractions between monomers of the same type can produce a microphase separation among the lengthening nascent oligomers and thereby alter sequence. This work explores the phenomenon further, examining how effective attractive interactions, mediated by a solvent selective for one of the reacting species, impact the development of sequence and the supramolecular assembly in a simple A-B copolymerization. We find that as the effective attractions between monomers increase, an emergent self-organization of the reactants causes a shift in reaction kinetics and sequence development. When the solvent-mediated interactions are selective enough, the simple mixture of A and B monomers oligomerize and self-assemble into structures characteristic of amphiphilic copolymers. The composition and morphology of these structures and the sequences of their chains are sensitive to the relative balance of affinities between the comonomer species. Our results demonstrate the impact of differing A-B monomer-solvent affinities on sequence development in solution-based copolymerizations and are of consequence to the informed design of synthetic methods for sequence controlled amphiphilic copolymers and their aggregates. | Ryan Hamblin; Nhu Nguyen; Kateri DuBay | Theoretical and Computational Chemistry; Polymer Science; Polymerization (Polymers); Polymer morphology; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/617c0b0492abe098e32d6463/original/selective-solvent-conditions-influence-sequence-development-and-supramolecular-assembly-in-step-growth-copolymerization.pdf |
63830e174b1a5fda988ed67a | 10.26434/chemrxiv-2022-zr0vz | Molecular Mechanism of Spectral Tuning by Chloride Binding in Monkey Green Sensitive Visual Pigment | The visual pigments of the cones perceive red, green, and blue colors. The monkey green (MG) pigment possesses a unique Cl− binding site; however, its relationship to the spectral tuning in green pigments remains elusive. Recently, FTIR spectroscopy revealed the characteristic structural modifications of the retinal binding site by Cl− binding. Herein, we report the computational structural modeling of MG pigments and quantum-chemical simulation to investigate its spectral redshift and physicochemical relevance when Cl− is present. Our protein structures reflect the previously suggested structural changes. AlphaFold2 failed to predict these structural changes. Excited-state calculations successfully reproduced the experimental red-shifted absorption energies, corroborating our protein structures. Electrostatic energy decomposition revealed that the redshift results from the His197 protonation state and conformations of Glu129, Ser202, and Ala308; however, Cl− itself contributes to the blueshift. Site-directed mutagenesis supported our analysis. These modeled structures may provide a valuable foundation for studying cone pigments.
| Kazuhiro J. Fujimoto; Fumika Minowa; Michiya Nishina; Shunta Nakamura; Sayaka Ohashi; Kota Katayama; Hideki Kandori; Takeshi Yanai | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Biophysics; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63830e174b1a5fda988ed67a/original/molecular-mechanism-of-spectral-tuning-by-chloride-binding-in-monkey-green-sensitive-visual-pigment.pdf |
6586ed2e66c1381729e11a6d | 10.26434/chemrxiv-2023-gxht4 | Elucidating the Role of O2 Uncoupling for the Adaptation of Bacterial Biodegradation Reactions Catalyzed by Rieske Oxygenases | Oxygenation of aromatic and aliphatic hydrocarbons by Rieske oxygenases is the initial step of various biodegradation pathways for environmental organic contaminants. Microorganisms carrying Rieske oxygenases are able to quickly adapt their substrate spectrum to alternative carbon and energy sources that are structurally related to the original target substrate, yet the molecular events responsible for this rapid adaptation are not well understood. Here, we evaluated the hypothesis that reactive oxygen species (ROS) generated by unproductive activation of O2, the so-called O2 uncoupling, in the presence of the alternative substrate exert a selective pressure for increasing the oxygenation efficiency of Rieske oxygenases. To that end, we studied wild-type 2-nitrotoluene dioxygenase (2NTDO) from Acidovorax sp. strain JS42 and five enzymes variants that have evolved from laboratory evolution experiments with 3- and 4-nitrotoluene as alternative growth substrates. The enzyme variants showed a substantially increased oxygenation efficiency towards the new target substrates concomitant with a reduction of ROS production, while mechanisms and kinetics of enzymatic O2 activation remained unchanged. Structural analyses and docking studies suggest that point mutations in enzyme variants occurred at residues lining both substrate and O2 transport tunnels enabling tighter binding of the target substrates in the active site. Increased oxygenation efficiencies measured in vitro for the various enzyme (variant)-substrate combinations correlated linearly with in vivo changes in growth rates for evolved Acidovorax strains expressing the variants. Our data suggest that the selective pressure from oxidative stress towards more efficient oxygenation by Rieske oxygenases was most notable when O2 uncoupling exceeded 60%. | Charlotte E. Bopp; Nora M. Bernet; Fabian Meyer; Riyaz Khan; Serina L. Robinson; Hans-Peter E. Kohler; Rebecca Buller; Thomas Hofstetter | Earth, Space, and Environmental Chemistry | CC BY 4.0 | CHEMRXIV | 2023-12-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6586ed2e66c1381729e11a6d/original/elucidating-the-role-of-o2-uncoupling-for-the-adaptation-of-bacterial-biodegradation-reactions-catalyzed-by-rieske-oxygenases.pdf |
66ab9127c9c6a5c07ab4c832 | 10.26434/chemrxiv-2024-k27ps-v2 | Spatially resolved uncertainties for machine learning potentials | Machine learning potentials have become an essential tool for atomistic simulations, yielding results close to ab-initio simulations at a fraction of computational cost. With recent improvements on the achievable accuracies, the focus has now shifted on the dataset composition itself. The reliable identification of erroneously predicted configurations to extend a given dataset is therefore of high priority. Yet, uncertainty estimation techniques have achieved mixed results for machine learning potentials. Consequently, a general and versatile method to correlate energy or atomic force uncertainties with the model error has remained elusive to date. In the current work, we show that epistemic uncertainty cannot correlate with model error by definition, but can be aggregated over groups of atoms to yield a strong correlation. We demonstrate that our method correctly estimates prediction errors both globally per structure, and locally resolved per atom. The direct correlation of local uncertainty and local error is used to design an active learning framework based on identifying local sub-regions of a large simulation cell, and performing ab-initio calculations only for the sub-region subsequently. We successfully utilize this method to perform active learning in the low-data regime for liquid water. | Esther Heid; Johannes Schörghuber; Ralf Wanzenböck; Georg. K. H. Madsen | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning | CC BY 4.0 | CHEMRXIV | 2024-08-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ab9127c9c6a5c07ab4c832/original/spatially-resolved-uncertainties-for-machine-learning-potentials.pdf |
661dd99b418a5379b0ee73fc | 10.26434/chemrxiv-2024-fqll9 | Diversity-driven, efficient exploration of a MOF design space to optimize MOF properties: application to NH3 adsorption | Metal-organic frameworks (MOFs) promise to engender technology-enabling properties for numerous applications. However, one significant challenge in MOF development is their overwhelmingly large design space, which is intractable to fully explore even computationally. To find diverse optimal MOF designs without exploring the full design space, we develop Vendi Bayesian optimization (VBO), a new algorithm that combines traditional Bayesian optimization with the Vendi Score, a recently introduced interpretable diversity measure. Both Bayesian optimization and the Vendi Score require a kernel similarity function, we therefore also introduce a novel similarity function in the space of MOFs that accounts for both chemical and structural features. This new similarity metric enables VBO to find optimal MOFs with properties that may depend on both chemistry and structure. We statistically assessed VBO by its ability to optimize three NH3-adsorption dependent performance metrics that depend, to different degrees, on MOF chemistry and structure. With ten simulated campaigns done for each metric, VBO consistently outperformed random search to find high-performing designs within a 1,000-MOF subset for i) NH3 storage, ii) NH3 removal from membrane plasma reactors, and iii) NH3 capture from air. Then, with one campaign dedicated to finding optimal MOFs for NH3 storage in a “hybrid” ~10,000-MOF database, we identify twelve extant and eight hypothesized MOF designs with potentially record-breaking working capacity ∆NNH3 between 300 K and 400 K at 1 bar. Specifically, the best MOF designs are predicted to i) achieve ∆NNH3 values between 23.6 and 29.3 mmol/gm, potentially surpassing those that MOFs previously experimentally tested for NH3 adsorption would have at the proposed operation conditions, ii) be thermally stable at the operation conditions and iii) require only ca. 10% of the energy content in NH3 to release the stored molecule from the MOF. Finally, the analysis of the generated simulation data during the search indicates that a pore size of around 10 Å, a heat of adsorption around 33 kJ/mol, and the presence of Ca could be part of MOF design rules that could help optimize NH3 working capacity at the proposed operation conditions | Tsung-Wei Liu; Quan Nguyen; Adji Bousso Dieng; Diego Gomez-Gualdron | Theoretical and Computational Chemistry; Materials Science; Chemical Engineering and Industrial Chemistry; Hybrid Organic-Inorganic Materials; Computational Chemistry and Modeling; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661dd99b418a5379b0ee73fc/original/diversity-driven-efficient-exploration-of-a-mof-design-space-to-optimize-mof-properties-application-to-nh3-adsorption.pdf |
60c751cc0f50db39b139783e | 10.26434/chemrxiv.13211012.v1 | Supramolecular Recognition in Crystalline Nanocavities Through Monte Carlo and Voronoi Network Algorithms | Computational screening of templating molecules enables the discovery of new synthesis routes for zeolites. Despite decades of work in molecular modeling of organic structure-directing agents (OSDAs), the development and benchmarking of algorithms for docking molecules in nanoporous materials has received scarce attention. Here, we introduce Voronoi Organic-Inorganic Docker (VOID) a method based on Voronoi diagrams to dock molecules in crystalline materials, and release it as a Python package. Benchmarks of the implementation show it generates docked poses up to 95 times faster than the traditional Monte Carlo docking scheme. We then evaluate the algorithm by obtaining binding energies for about 120 zeolite-OSDA pairs of industrial relevance. The computed host-guest interactions explain experimental outcomes for traditional synthesis routes from the literature. The results further suggest new OSDAs to synthesize known zeolites. Finally, we exemplify the generality of VOID by docking molecules inside a metal-organic framework and on a metal surface. The proposed method and software provide a low-cost computational approach for generating molecule-material interfaces. | Daniel Schwalbe-Koda; Rafael Gomez-Bombarelli | Hybrid Organic-Inorganic Materials; Supramolecular Chemistry (Inorg.); Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751cc0f50db39b139783e/original/supramolecular-recognition-in-crystalline-nanocavities-through-monte-carlo-and-voronoi-network-algorithms.pdf |
6415ba072bfb3dc251f90166 | 10.26434/chemrxiv-2023-gxkj5 | Copper(II) and copper(I) complexes with a bidentate hydrazinic dithiocarbazate: synthesis and crystal structures | In this work, we explored the ability of N-methyl-S-methyl dithiocarbazate ([H2N-N(CH3)C(=S)SCH3]; DTCZ) to form coordination complexes with copper starting from different copper (II, I) sources. Data proved that the type of used salt affects the stoichiometry and structure of the obtained coordination complexes. Copper complexes of general empirical formula [Cu(DTCZ)Cl2] (1), [Cu(DTCZ)2NO3]NO3 (2), [Cu(DTCZ)2(OH2)]SO4 (3), [Cu(DTCZ)2]PF6 (4), [Cu(DTCZ)(PPh3)2]NO3 (5) and [Cu(DTCZ)2]Br (6) were synthesized in high yield and characterized by elemental analysis, UV-Vis and IR spectroscopy. Molecular structures of 1-6 and also of side- products [Cu(DTCZ)2SO4] (3a), [Cu(DTCZ)2](PF6)(OH) (4b) and [CuBr(C3H7NS2)]n (6a) were determined by single crystal X-ray diffraction (XRD). In all cases, DTCZ binds the metal in the neutral form through the hydrazine nitrogen (NH2) and thione sulphur (S) atom set, forming monosubstituted and disubstituted complexes having tetrahedral, square planar, or square pyramidal geometries, depending on the copper source. In addition, two one-dimensional (1D) coordination polymers and water channels have been observed in the crystal states. | Michele Di Palma; Nicola Salvarese; Carolina Gobbi; Alessandro Dolmella; Cristina Bolzati | Inorganic Chemistry; Coordination Chemistry (Inorg.); Transition Metal Complexes (Inorg.); Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6415ba072bfb3dc251f90166/original/copper-ii-and-copper-i-complexes-with-a-bidentate-hydrazinic-dithiocarbazate-synthesis-and-crystal-structures.pdf |
60c7449aee301c7a53c79199 | 10.26434/chemrxiv.9860891.v1 | Solvent-Free Powder Synthesis and MOF-CVD Thin Films of the Mesoporous Metal-Organic Framework MAF-6 | A simple solvent- and catalyst-free method is presented for the synthesis of the mesoporous metal-organic framework (MOF) MAF-6 (RHO-Zn(eIm)2) based on the reaction of ZnO with 2-ethylimidazole vapor at temperatures ≤ 100 °C. By translating this method to a chemical vapor deposition (CVD) protocol, mesoporous crystalline films could be deposited for the first time entirely from the vapor phase. A combination of PALS and Kr physisorption measurements confirmed the porosity of these MOF-CVD films and the size of the MAF-6 supercages (diam. ~2 nm), in close agreement with powder data and calculations. MAF-6 powders and films were further characterized by XRD, TGA, SEM, FTIR, PDF and EXAFS. The exceptional uptake capacity of the mesoporous MAF-6 in comparison to the microporous ZIF-8 is demonstrated by vapor-phase loading of a molecule larger than the ZIF-8 windows. | Timothée Stassin; Ivo Stassen; Joao Marreiros; Alexander John Cruz; Rhea Verbeke; Min Tu; Helge Reinsch; Marcel Dickmann; Werner Egger; Ivo Vankelecom; Dirk De Vos; Rob Ameloot | Hybrid Organic-Inorganic Materials | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7449aee301c7a53c79199/original/solvent-free-powder-synthesis-and-mof-cvd-thin-films-of-the-mesoporous-metal-organic-framework-maf-6.pdf |
64f0589679853bbd78c8306c | 10.26434/chemrxiv-2023-mfltj | Unlocking the Reactivity of Diazo Compounds on Red Light with the Use of Photochemical Tools | Photoinduced bioorthogonal reactions constitute a valuable class of chemical transformations that enable spatiotemporal con-trol of biomacromolecules. Among them, those involving carbenes proved effective in various bioapplications, but they require ultraviolet or blue-light irradiation. Using lower energetic radiation, however, offers deeper penetration and diminishes photo-damages. Thus, herein, we describe the photochemistry of structurally diversified diazo reagents under red light irradiation. Reactive intermediates can be generated via direct photolysis or taking advantage of porphyrin chemistry via photosensitisa-tion and photoredox catalysis. | Dorota Gryko; Orłowska Katarzyna; Klaudia Łuczak; Piotr Krajewski; Joao V. Santiago; Katarzyna Rybicka-Jasińska | Organic Chemistry; Catalysis | CC BY NC 4.0 | CHEMRXIV | 2023-08-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f0589679853bbd78c8306c/original/unlocking-the-reactivity-of-diazo-compounds-on-red-light-with-the-use-of-photochemical-tools.pdf |
60c741679abda20199f8be78 | 10.26434/chemrxiv.8040380.v1 | Revealing the reactivity of the Iridium trioxide intermediate for the oxygen evolution reaction in acidic media | We report a strategy to isolate IrO<sub>3</sub> as an intermediate for the oxygen evolution reaction (OER). Its reactivity is studied using X-ray absorption spectroscopy, X-ray and neutron diffraction and X-ray photoelectron spectroscopy. Its stability is assessed by using on-line mass spectroscopy and inductively coupled plasma optical emission spectroscopy and presented herein. Upon reaction with water in acidic conditions, we could observe the formation of a new protonated iridate phase of composition H<sub>2</sub>IrO<sub>3</sub>. Coupling OER measurements and dissolution rate determination, we could show that its activity and stability are governed by a yet ill-described charge compensation mechanism enlisting reversible bulk proton insertion inside the catalyst structure. This singular property enables an enhanced activity and stability towards dissolution compared to the stellar IrO<sub>x</sub>/SrIrO<sub>3</sub> catalyst. Such a finding opens the route towards the design of new OER catalysts enlisting proton insertion that could be competitive for water splitting in acidic media.<br /> | Paul Pearce; Chunzhen Yang; Antonella Iadecola; Juan Rodriguez-Carvajal; Gwenaëlle Rousse; Rémi Dedryvère; Artem M. Abakumov; Domitille Giaume; Michael Deschamps; Jean-Marie Tarascon; Alexis Grimaud | Acid Catalysis; Electrocatalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741679abda20199f8be78/original/revealing-the-reactivity-of-the-iridium-trioxide-intermediate-for-the-oxygen-evolution-reaction-in-acidic-media.pdf |
60c75163337d6c77d0e28508 | 10.26434/chemrxiv.13087319.v1 | Organic Molecules with Inverted Gaps between First Excited Singlet and Triplet States and Appreciable Fluorescence Rates | One of the recent proposals for the design of state-of-the-art emissive materials for organic light emitting diodes (OLEDs) is the principle of thermally activated delayed fluorescence (TADF). The underlying idea is to enable facile thermal upconversion of excited state triplets, which are generated upon electron-hole recombination, to excited state singlets by minimizing the corresponding energy difference resulting in devices with up to 100% internal quantum efficiencies (IQEs). Ideal emissive materials potentially surpassing TADF emitters should have both negative singlet-triplet gaps and appreciable fluorescence rates to maximize reverse intersystem crossing (rISC) rates from excited triplets to singlets while minimizing ISC rates and triplet state occupation leading to long-term operational stability. However, molecules with negative singlet-triplet gaps are extremely rare and, to the best of our knowledge, not emissive. In this work, based on computational studies, we describe the first molecules with negative singlet-triplet gaps and considerable fluorescence rates and show that they are more common than hypothesized previously. | Robert Pollice; Pascal Friederich; Cyrille Lavigne; Gabriel dos Passos Gomes; Alan Aspuru-Guzik | Physical Organic Chemistry; Carbon-based Materials; Optical Materials; Computational Chemistry and Modeling; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75163337d6c77d0e28508/original/organic-molecules-with-inverted-gaps-between-first-excited-singlet-and-triplet-states-and-appreciable-fluorescence-rates.pdf |
674fc43f7be152b1d0dc3c8c | 10.26434/chemrxiv-2024-cbwhd | Crystallization of Small Molecules in Lyotropic Liquid Crystals | Single-crystal X-ray diffraction analysis emerges as the most dependable method for structural determination. It serves as the definitive method, particularly in challenging cases where other approaches fail to yield precise results. However, the generation of high-quality single crystals remains a frequently encountered obstacle. Here, we present a strategy employing an alignment medium to enhance the growth of single crystals for small organic compounds. Furthermore, a mathematical crystallization model based on the classical nucleation theory was conducted specifically designed for alignment media. The hypothesis suggests that alignment media effectively reduce solution entropy, thereby lowering the free energy barrier associated with crystal nucleus formation and facilitating the crystallization process. Employing an alignment medium derived from self-assembled oligopeptide nanotubes (AAKLVFF), we successfully cultivated single crystals of diverse organic compounds. Our discovery unveils an innovative strategy and an accessible approach for acquiring single crystals. | Xinxiang Lei; Wen-Xuan Wang; Li-Wen Bai; Yong-Liang Shao; Xiao-Yang Han; Jun He; Jing Li | Analytical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674fc43f7be152b1d0dc3c8c/original/crystallization-of-small-molecules-in-lyotropic-liquid-crystals.pdf |
6391d7567b7c917683e86b83 | 10.26434/chemrxiv-2022-nmg78 | Unexpected quasi-axial conformer in thermally activated delayed fluorescence DMAC-TRZ. Demonstrating how to turn green OLEDs into blue. | Although there have been several studies on the mechanism of thermally activated delayed fluorescence (TADF), providing useful models to understand the behaviour of TADF molecules, some photophysical features cannot be explained. Here, we investigate the hidden phenomena taking place in the very well-known TADF emitter, DMAC-TRZ. A molecule that, based on its structure, was considered not to fulfil the required criteria to have more than one ground and excited state conformation. However, based on experimental and computational studies, we have found two conformers, a quasi-axial (QA) and a quasi-equatorial (QE), and explored the effect of their co-existence on both optical and electrical excitation. Although the relative population of the QA conformer appears to be small, its effect is disproportionate because it has high local excited state character. The energy transfer efficiency from the QA to the QE conformer is shown to be high, even at low concentrations, and changes depending on the hosting environment. The currently known triplet energy of DMAC-TRZ quoted from experiment is shown to originate from the QA conformer, completely changing the understanding we have so far for this donor-acceptor molecule. The contribution of the QA conformer in devices has been explored and its presence explains the good performance of the material in neat emissive layer devices. Moreover, hyperfluorescnece (HF) devices, using v-DABNA as the terminal emitter show direct energy transfer from the QA conformer to v-DABNA, explaining the relative improved Förster resonance energy transfer (FRET) efficiency compared to similar HF systems. Using this approach, we demonstrate highly efficient organic light emitting diodes (OLEDs) were green light (TADF only devices) is converted to blue light (HF devices) with the maximum external quantum efficiency remaining high and close to 30%. | Kleitos Stavrou; Larissa Gomes Franca; Tobias Böhmer; Luka Duben; Christel Marian; Andrew Monkman | Materials Science | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6391d7567b7c917683e86b83/original/unexpected-quasi-axial-conformer-in-thermally-activated-delayed-fluorescence-dmac-trz-demonstrating-how-to-turn-green-ole-ds-into-blue.pdf |
6349c4dc1df68876f9909906 | 10.26434/chemrxiv-2022-tzmt9 | Introducing state-of-the-art forensics into instrumental analysis laboratory: detection of document forgery with laser desorption/ionization mass spectrometry
| Forensics has long been viewed by chemical educators as a field with great potential as far as providing inspiration for modifying chemistry laboratory curriculum and enhancing students’ learning experience at different levels. While most experiments are based on adaptation of laboratory procedures routinely used in criminalistics, very exciting (but frequently overlooked) opportunities are presented by state-of-the-art analytical technologies that are available on university and college campuses, but have not yet become commonly accepted tools in the armamentarium of forensic analysis. We illustrate this using as an example laser desorption/ionization mass spectrometry (LDI MS), a technique which has been actively evaluated in recent years in forensic community as a tool to detect forgery in various printed and hand-written documents. Two possible uses of this technique in the undergraduate laboratory are described, one focusing on fraudulent alteration of a personal check, and another focusing on detecting forgery in a printed document. Both experiments are open-ended, in that the initial findings invite additional questions and encourage further work. As such, these themes can be used not only as modules in analytical or instrumental laboratory, but also as templates for more in-depth work, such as independent study by chemistry majors and advanced high school students. | Igor Kaltashov; Kenyon Kowalski; Ryan Sullivan; Alyssa Marsico; Nicholas DeGraan-Weber | Analytical Chemistry; Chemical Education; Imaging; Mass Spectrometry | CC BY 4.0 | CHEMRXIV | 2022-10-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6349c4dc1df68876f9909906/original/introducing-state-of-the-art-forensics-into-instrumental-analysis-laboratory-detection-of-document-forgery-with-laser-desorption-ionization-mass-spectrometry.pdf |
652bbd12bda59ceb9aa08ff2 | 10.26434/chemrxiv-2023-tflfq | Crown Ether Active Template Synthesis of Rotaxanes | Abstract Rotaxanes are interlocked molecules that consist of a macrocycle encircling a stoppered thread. The ability to control relative component positions makes rotaxanes ideal building blocks for constructing functional and responsive molecular machines. Despite the potential of rotaxanes, their challenging synthesis limits their application. One approach to construct rotaxanes is to use an active template synthesis, where a reaction that forms the thread is accelerated in the cavity of a macrocycle. An emerging method of active template synthesis that exploits the ability of crown ether macrocycles to accelerate simple organic reactions is discussed herein. Crown ether active template synthesis (CEATS) permits the rapid and simple synthesis of rotaxanes containing a wide range of functionality. Integrating rotaxane formation with chemical reaction networks has permitted the construction of molecular machines. The simplification of rotaxane synthesis will facilitate their widespread study and application. | Stephen Fielden | Organic Chemistry; Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652bbd12bda59ceb9aa08ff2/original/crown-ether-active-template-synthesis-of-rotaxanes.pdf |
677d9fe081d2151a023ebad7 | 10.26434/chemrxiv-2025-htb6x | Catalytic allylation of native hexoses and pentoses in water with indium | Carbohydrates are an abundant, inexpensive, and renewable biomass feedstock that could be a cornerstone for sustainable chemical manufacturing, but scalable and environmentally friendly methods that leverage these feedstocks are lacking. For example, 1-allyl sorbitol is the foundational building block for the polypropylene (PP) clarifying agent Millad® NX® 8000 which is produced on multi-ton scale annually, but the current manufacturing process requires superstoichiometric amounts of tin. , The NX 8000 additives dominate about 80% of the global clarified PP market, used in concentrations of 0.01% to 1% during PP production to improve its transparency and resistance to high temperatures, which translates to 300-30,000 tons annually. The market volume of PP in 2022 was approximately 79.01 million metric tons (MMT), with demand expected to rise by nearly 33% to 105 MMT by 2030. The cost and sustainability benefits of clarified PP are driving this demand, necessitating more clarifying agents. Herein, we report a high-yielding allylation of unprotected carbohydrates in water using a catalytic amount of indium metal and either allylboronic acid or the pinacol ester (allylBpin) as donors. Aldohexoses, aminohexoses, ketohexoses, and aldopentoses are all allylated in high yield under mild conditions, and the indium metal is recoverable and reusable with no loss of catalytic activity. Leveraging these features, this process was translated to a scalable continuous synthesis of 1-allyl sorbitol in flow with high yield and productivity through Bayesian optimization of reaction parameters. | Tapas Adak; Travis Menard; Matthew Albritton; Federico Florit; Martin Burke; Klavs Jensen; Scott Denmark | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677d9fe081d2151a023ebad7/original/catalytic-allylation-of-native-hexoses-and-pentoses-in-water-with-indium.pdf |
63db025401ecc690f91d5b68 | 10.26434/chemrxiv-2023-qwhz1 | Deconstructing Allostery: Computational Assessment of the Binding Determinants of Allosteric PTP1B Modulators | It is currently challenging to predict whether fragment hits that do not bind to an orthosteric site could be elaborated into allosteric modulators, as in these cases binding does not necessarily translate into a functional effect. We propose a workflow using Markov State Models (MSMs) with steered molecular dynamics (sMD) to assess the allosteric potential of known binders. sMD simulations are employed to sample protein conformational space inaccessible to routine equilibrium MD timescales. Protein conformations sampled by sMD provide starting points for seeded MD simulations, which are combined into MSMs. The methodology is demonstrated on a dataset of protein tyrosine phosphatase 1B ligands. Experimentally confirmed allosteric inhibitors are correctly classified as inhibitors, whereas the deconstructed analogues show reduced inhibitory activity. Analysis of the MSMs provide insights into preferred protein-ligand arrangements that correlate with functional outcomes. The present methodology may find applications for progressing fragments towards lead molecules in FBDD campaigns. | Adele Hardie; Benjamin P Cossins; Silvia Lovera; Julien Michel | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2023-02-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63db025401ecc690f91d5b68/original/deconstructing-allostery-computational-assessment-of-the-binding-determinants-of-allosteric-ptp1b-modulators.pdf |
60c73cc09abda232a0f8b5d7 | 10.26434/chemrxiv.14740425.v1 | Complexions at the Electrolyte/Electrode Interface in Solid Oxide Cells | Rapid deactivation presently limits a wide spread use of high-temperature solid oxide cells (SOCs) as otherwise highly efficient chemical energy converters. With deactivation triggered by the ongoing conversion reactions, an atomic-scale understanding of the active triple-phase boundary (TPB) between electrolyte, electrode and gas phase is essential to increase cell performance. Here we use a multi-method approach comprising transmission electron microscopy and first-principles calculations and molecular simulations to untangle the atomic arrangement of the prototypical SOC interface between a lanthanum strontium manganite (LSM) anode and an yttria-stabilized zirconia (YSZ) electrolyte. We identify an interlayer of self-limited width with partial amorphization and strong compositional gradient, thus exhibiting the characteristics of a complexion that is stabilized by the confinement between two bulk phases. This offers a new perspective to understand the function of SOCs at the atomic scale. Moreover, it opens up a hitherto unrealized design space to tune the conversion efficiency. | Hanna Türk; Franz-Philipp Schmidt; Thomas Götsch; Frank Girgsdies; Adnan Hammud; Danail Ivanov; Izaak C. Vinke; L.G.J. (Bert) de Haart; Rüdiger-A. Eichel; Karsten Reuter; Robert Schlögl; Axel Knop-Gericke; Christoph Scheurer; Thomas Lunkenbein | Computational Chemistry and Modeling; Fuel Cells; Interfaces; Structure | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73cc09abda232a0f8b5d7/original/complexions-at-the-electrolyte-electrode-interface-in-solid-oxide-cells.pdf |
63179473bada381737bb75b6 | 10.26434/chemrxiv-2022-nnbhf | Conformal CVD of boron-rich BxC thin films from triethylboron | We report conformal chemical vapor deposition (CVD) of boron carbide thin films on silicon substrates with 8:1 aspect-ratio morphologies, using triethylboron (TEB, B(C2H5)3) as single source CVD precursor. Step coverage (SC) calculated from the cross-sectional scanning electron microscopy measurements shows that films deposited at ≤450 °C were perfectly conformal (SC = 1). We attribute this to the low reaction probability at low substrate temperatures enabling more gas phase diffusion into the features. The chemical state of the material, determined by X-ray photoelectron spectroscopy, shows as carbide with B-B, B-C, C-B and C-C chemical bonds. Quantitative analysis by time-of-flight elastic recoil detection analysis reveals that films deposited at 450 °C are boron-rich with around 82.5 at.% B, 15.6 at.% C, 1.3 at.% O and 0.6 at.% H, i.e., about B5C. The film density as measured by X-ray reflectometry, varies from 1.9 to 2.28 g/cm3 depending on deposition temperature. | Arun Choolakkal; Hans Högberg; Jens Birch; Henrik Pedersen | Physical Chemistry; Materials Science; Nanoscience; Coating Materials; Thin Films; Surface | CC BY 4.0 | CHEMRXIV | 2022-09-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63179473bada381737bb75b6/original/conformal-cvd-of-boron-rich-bx-c-thin-films-from-triethylboron.pdf |
67d3787581d2151a024cb4e3 | 10.26434/chemrxiv-2025-fr2wj | Mini review | This mini review explores the development and performance of bacteria-based self-healing concrete and mortar, emphasizing the role of microorganisms such as Bacillus sphaericus and Bacillus subtilis in enhancing mechanical properties and promoting autonomous crack repair. The study examines the effects of bacterial concentration, curing conditions, and the incorporation of steel fibers and polyvinyl alcohol (PVA) fibers on the compressive, tensile, and flexural strengths of concrete. The primary self-healing mechanism is identified as microbially induced calcite precipitation (MICP), where bacterial activity facilitates calcium carbonate (CaCO₃) deposition to seal cracks. Advanced characterization techniques such as Scanning Electron Microscopy (SEM), Energy-Dispersive X-ray Spectroscopy (EDS), Fourier-transform infrared spectroscopy (FTIR), and X-ray diffraction (XRD) confirm the formation of CaCO₃ and its impact on the material’s microstructure. The review highlights significant long-term strength improvements due to bacterial incorporation and presents bio-concrete as an eco-friendly alternative to conventional cement, contributing to sustainability by reducing the carbon footprint of construction materials. While the research demonstrates promising advancements, further studies are required to assess the long-term durability of microbial-treated materials under diverse environmental conditions and to evaluate the economic feasibility of large-scale implementation. This review underscores the potential of microbial intervention in advancing durable, self-healing, and sustainable concrete technologies. | ASHRAF ABBAS; Osama A I Ali | Materials Science | CC BY 4.0 | CHEMRXIV | 2025-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d3787581d2151a024cb4e3/original/mini-review.pdf |
62d17c664689331b3659e834 | 10.26434/chemrxiv-2022-z1d96 | Temperature-Controlled Mechanochemistry for the Nickel-Catalyzed Suzuki-Miyaura-Type Coupling of Aryl Sulfamates via Ball Milling and Twin-Screw Extrusion | The use of temperature-controlled mechanochemistry to enable the mechanochemical nickel-catalyzed Suzuki-Miyaura coupling is herein described. Transitioning from a capricious room-temperature protocol, through to a heated, PID-controlled programmable jar heater manifold was required to deliver an efficient method for the coupling of aryl sulfamates (derived from ubiquitous phenols) and aryl boronic acid species. Furthermore, this process is conducted using a base-metal nickel catalyst, in the absence of bulk solvent, and in the absence of air/moisture sensitive reaction set-ups. This methodology is showcased through translation to large-scale twin-screw extrusion methodology enabling 200-fold scale increase, producing decagram quantities of C-C coupled material. | Robert Bolt; Sarah Raby-Buck; Katharine Ingram; Jamie Leitch; Duncan Browne | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Process Chemistry; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62d17c664689331b3659e834/original/temperature-controlled-mechanochemistry-for-the-nickel-catalyzed-suzuki-miyaura-type-coupling-of-aryl-sulfamates-via-ball-milling-and-twin-screw-extrusion.pdf |
64e87020dd1a73847f7a7f74 | 10.26434/chemrxiv-2023-q9fd7 | Highly defective ultra-small M(IV)-MOF nanocrystals | A precise and concomitant control of both the size and defects in inorganic materials is of importance in many applications, particularly catalysis, as it often results in enhanced properties or emerging new features. So far, applying the strategy of modulation chemistry has been unable to afford high-quality functional Metal-Organic Frameworks (MOFs) nanocrystals with minimized size while exhibiting maximized defects. We report here a general sustainable strategy for the design of highly defective and ultra-small M(IV)-MOFs crystals (ca. 35% missing linker, 4-6 nm). Advanced characterizations have been performed to shed light on the main factors governing the crystallization mechanism and to identify the nature of the defects. The ultra-small Zr-MOFs showed excellent performance in peptide hydrolysis reaction, including high reactivity, selectivity, diffusion, stability, and show emerging tailorable reactivity and selectivity towards peptide bond formation simply by changing the reaction solvent. Therefore, these highly defective ultra-small tetravalent MOFs particles open new perspectives for the development of heterogeneous MOF catalysts with dual functions. | Shan Dai; Charlotte Simms; Gilles Patriarche; Marco Daturi; Antoine Tissot; Tatjana Parac-Vogt; Christian Serre | Catalysis; Nanoscience; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-08-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e87020dd1a73847f7a7f74/original/highly-defective-ultra-small-m-iv-mof-nanocrystals.pdf |
653b7e0648dad23120791450 | 10.26434/chemrxiv-2023-chd0q-v3 | Proposal of a new empirical model with flow velocity to improve time-weighted average concentration estimates from the Polar Organic Chemical Integrative Samplers | It is now widely recognized that the sampling rate of Polar Organic Chemical Integrative Samplers (POCIS) is significantly affected by flow velocity, which can cause a consequent bias when determining time-weighted average concentrations (TWAC). In previous works, we observed the desorption of a compound such as deisopropylatrazine (DIA) over time when added to the receiving phase of a POCIS. In particular, it was found in situ that its desorption rate was also influenced by flow velocity, in an agitated water environment. In the method presented here, we calibrated 30 pesticides under controlled laboratory conditions, varying the flow velocity over four levels. At the same time, we studied the desorption rate of DIA-d5 (a deuterated form of DIA) over time. An empirical model based on a power law involving flow velocity was used to process the information provided by the accumulation kinetics of the compounds of interest and the elimination of DIA-d5. With this type of model, it was possible to take into account the effect of this crucial factor on exchange kinetics, and then to obtain more accurate TWACs, with reduced bias and more acceptable dispersion of the results. | Nicolas Mazzella; Marion Bernard ; Robin Guibal; Sebastien Boutry; Sophie Lissalde; Gilles Guibaud | Analytical Chemistry; Earth, Space, and Environmental Chemistry; Environmental Science; Analytical Chemistry - General; Environmental Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653b7e0648dad23120791450/original/proposal-of-a-new-empirical-model-with-flow-velocity-to-improve-time-weighted-average-concentration-estimates-from-the-polar-organic-chemical-integrative-samplers.pdf |
63490bf94a18762edbe33f62 | 10.26434/chemrxiv-2022-pmstk | Transition of Self-assembled Structures in Poly(N- octadecyl acrylamide-co-hydroxylethyl acrylamide) Random Copolymer Films | This paper shows that a simple random copolymer can form self-assembled lamellae, the structure of which depends upon the comonomer composition and annealing temperature. A random copolymer of octadecyl acrylamide and hydroxyethyl acrylamide [p(ODA/HEAm)] was prepared via free racial copolymerization. Thin films of p(ODA/HEAm) were prepared via a spin-coating method and their structures were studied using X-ray diffraction. It was found that copolymers with a HEAm content between 28% and 50% formed self-assembled lamellae upon annealing at 10 ˚C above the glass-transition temperature. The self-assembled form has a “side-chain-mixed” lamellar structure in which the ODA and HEAm side chains are oriented perpendicularly to the lamellar plane composed of the polymer main chain. Interestingly, a copolymer with HEAm content between 36% and 50% transforms from the side-chain-mixed lamellar structure to form a “side-chain-segregated” lamellar structure upon annealing at a much higher temperature (160 ˚C). In this structure, the ODA and HEAm side chains are oriented perpendicularly to the lamellar plane and in opposite directions to each other. We concluded that the lamellar structure that is formed is determined by the strain force generated during self-assembly and by the segregation force between the comonomers. | Mao Kikuchi; Nozomi Saito; Mizuki Ohke; Shotaro Nishitsuji; Shusaku Nagano; Jun Matsui | Polymer Science; Polymer morphology | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63490bf94a18762edbe33f62/original/transition-of-self-assembled-structures-in-poly-n-octadecyl-acrylamide-co-hydroxylethyl-acrylamide-random-copolymer-films.pdf |
60e15a73f7373f690d44e32a | 10.26434/chemrxiv-2021-hwh2d-v2 | Uncertainty Quantification of Reactivity Scales | According to Mayr, polar organic synthesis can be rationalized by a simple empirical relationship linking bimolecular rate constants to as few as three reactivity parameters. Here, we propose an extension to Mayr’s reactivity method that is rooted in uncertainty quantification and transforms the reactivity parameters into probability distributions. Through uncertainty propagation, these distributions can be transformed into uncertainty estimates for bimolecular rate constants. Chemists can exploit these virtual error bars to enhance synthesis planning and to decrease the ambiguity of conclusions drawn from experimental data. We demonstrate the above at the example of the reference data set released by Mayr and co-workers [J. Am. Chem. Soc. 2001, 123, 9500; J. Am. Chem. Soc. 2012, 134, 13902]. As by-product of the new approach, we obtain revised reactivity parameters for 36 π-nucleophiles and 32 benzhydrylium ions. | Jonny Proppe; Johannes Kircher | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Physical Organic Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60e15a73f7373f690d44e32a/original/uncertainty-quantification-of-reactivity-scales.pdf |
60e35b7df7373f9ea3455b89 | 10.26434/chemrxiv-2021-6n36h-v2 | Determining the Ethanol Concentrations in Ethyl Alcohol-Based Hand Sanitizers with Different Expiration Dates Using Fourier-Transform Infrared Spectroscopy (FT-IR) | Hand sanitizer has proved to be an essential public health tool in slowing the spread of the coronavirus (COVID-19). However, amid the COVID-19 pandemic, the availability of recently manufactured hand sanitizer can be limited. The product expiration date set by manufacturers is also minimally regulated. The efficacy of hand sanitizer is entirely determined by its most volatile ingredient, alcohol, which must remain at a concentration greater than 60% (v/v) to kill bacterial and viral pathogens. In our undergraduate Chem 2123W course (Introductory Quantitative Analysis Laboratory) in spring 2021, we designed and conducted an experiment to investigate the alcohol concentration of ethyl alcohol-based commercial hand sanitizers with varying expiration dates. The presence of a primary alcohol functional group in ethyl alcohol can be observed by Fourier-transform infrared spectroscopy (FT- IR). Through a series of standard additions of ethyl alcohol to the diluted hand sanitizer sample, we measured the changes in the integration of the FT-IR primary alcohol C-O stretch. The signal changes in integration were used to generate a standard addition curve using ethanol concentration and calculate the initial ethanol concentration of each sample. Our approach accounts for this matrix effect and does not rely on a compositional approximation. All the samples studied were found to exceed the minimum concentration required to effectively exhibit antimicrobial properties despite three of the four samples being expired. However, the expired samples remained close to the 60% threshold and with consideration of error analysis, the effectiveness of these hand sanitizers remains uncertain. The samples analyzed in this study varied in reported initial ethyl alcohol concentration, manufacturer, color, perfume, and other ingredients. The heterogeneity of our samples coupled with our consistent results provided insight into consumer use of expired ethyl alcohol-based hand sanitizers. | Max Shlafstein; Emily Hannah; Ling Hao | Analytical Chemistry; Chemical Education; Chemical Education - General; Analytical Chemistry - General; Spectroscopy (Anal. Chem.) | CC BY NC 4.0 | CHEMRXIV | 2021-07-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60e35b7df7373f9ea3455b89/original/determining-the-ethanol-concentrations-in-ethyl-alcohol-based-hand-sanitizers-with-different-expiration-dates-using-fourier-transform-infrared-spectroscopy-ft-ir.pdf |
662cf99421291e5d1ddd2779 | 10.26434/chemrxiv-2024-ztpdg | Disulfide-based poly-pseudorotaxanes with locked and on demand unlocked degradability | Materials containing labile linkages are in great demand due to their inherent degradability and recyclability. However, this generally comes at the cost of their stability during a use phase and synthesis. Here we present a concept of supramolecular polymers with locked and on demand unlocked labile linkages, rendering the materials robust yet degradable. We designed disulfides with polymerizable handles forming inclusion complexes (pseudorotaxanes) with cucurbit[6]uril (CB6) macrocycle positioned specifically around the disulfide bond. CB6 endowed the disulfide group with significantly improved photo-, thermo- and chemical stability. The polymerization of these monomers delivered poly-pseudorotaxanes with locked disulfide bonds. pH-triggered removal of the ionic host-guest interactions allowed for the dissociation of the poly-pseudorotaxane into the unlocked polydisulfide, amenable for further degradation, and CB6 in its free form. The former was subsequently depolymerized into dithiols under mild reduction of disulfide bonds. | Elena Subbotina; Paul Anastas | Polymer Science; Organic Polymers; Polymer scaffolds; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662cf99421291e5d1ddd2779/original/disulfide-based-poly-pseudorotaxanes-with-locked-and-on-demand-unlocked-degradability.pdf |
66602583418a5379b02056e9 | 10.26434/chemrxiv-2024-hmc97 | Control of crystallization pathways in the BiFeO3 - Bi2Fe4O9 system | Bismuth ferrates, specifically perovskite-type BiFeO₃ and mullite-type Bi₂Fe₄O₉, hold significant technological promise as catalysts, photovoltaics, and room-temperature multiferroics. However, challenges arise due to their frequent co-crystallization, particularly in the nano-regime, hindering the production of phase pure materials. This study unveils a controlled sol-gel crystallization approach, elucidating the phase formation complexities in the bismuth ferrate oxide system by coupling thermochemical analysis and total scattering with pair distribution function analysis. We tune the crystallization pathways by adjusting the metal to complexing agent ratio and pH during precursor preparation resulting in preferential crystallization of either BiFeO3 or Bi2Fe4O9. Although all precursors undergo an amorphization process during heating, our results demonstrate a consistent correlation between the crystallization pathway and the initial structural entities formed during gel formation. Pair distribution function analysis reveals structural differences in the intermediate amorphous structures, which preferentially crystallize into either BiFeO3 or Bi2Fe4O9. This study offers mechanistic insights into the formation process and synthetic guidance for controlled synthesis of BiFeO₃ and Bi₂Fe₄O₉ nanomaterials. Additionally, it elucidates the unusual growth behavior and structural size-dependence of Bi₂Fe₄O₉, particularly highlighting significant distortions in the local structure likely induced by the proximity of Bi's stereoactive lone electron pairs at small sizes. | Andrea Kirsch; Guilherme B. Strapasson; Niels Lefeld; Mathias Gogolin; Mark C. Videbæk; Soham Banerjee; Heloisa N. Bordallo; Kirsten M. Ø. Jensen | Inorganic Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Kinetics and Mechanism - Inorganic Reactions; Materials Chemistry; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66602583418a5379b02056e9/original/control-of-crystallization-pathways-in-the-bi-fe-o3-bi2fe4o9-system.pdf |
62be57a7e60d98a34cf3bae4 | 10.26434/chemrxiv-2022-gf5dz | Metabolomics of Non-Saccharomyces Yeasts in Fermented Beverages | Fermented beverages have been consumed for millennia and today support a global industry producing
diverse products. Saccharomyces yeasts currently dominate the fermented beverage industry, but
consumer demands for alternative products with a variety of sensory profiles and actual or perceived
health benefits are driving the diversification and use of non-Saccharomyces yeasts. The diversity of
flavours, aromas, and other sensory characteristics that can be obtained by using non-Saccharomyces
yeasts in fermentation is, in large parts, due to the diverse secondary metabolites they produce compared
to conventional Saccharomyces yeast. Here, we review the use of metabolomic analyses of non-
Saccharomyces yeasts to explore their impact on the sensory characteristics of fermented beverages.
We highlight several key species currently used in the industry, including Brettanomyces, Torulaspora,
Lachancea, and Saccharomycodes, and emphasize the future potential for the use of non-
Saccharomyces yeasts in the production of diverse fermented beverages. | Daniel Ellis; Edward Kerr; Gerhard Schenk; Benjamin Schulz | Organic Chemistry; Analytical Chemistry; Agriculture and Food Chemistry; Biochemical Analysis; Mass Spectrometry | CC BY 4.0 | CHEMRXIV | 2022-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62be57a7e60d98a34cf3bae4/original/metabolomics-of-non-saccharomyces-yeasts-in-fermented-beverages.pdf |
60c7541b0f50db3cc8397ca3 | 10.26434/chemrxiv.13614176.v1 | Multiple C–H Activation Enabled Modular Construction of Densely Functionalized Sulfur-Contained Arenes | <div>
<p>Modular construction of multiple
functionalized arenes from abundant feedstocks, stands as an unremitting pursue
goal in synthetic chemistry, which would accelerate the discovery of new drugs
an advanced materials. Herein, by using multiple C-H activation strategy,
through judicious choice of versatile imidate ester as the key directing group,
expedi-ent delivery of molecular libraries of densely functionalized
sulfur-contained arenes. Further synthetic application was demonstrated by
multiple C-H modification of fused arenes and pharmaceuticals such as
Ibuprofen, and concise con-struction of biologically active molecules, Madam
dihydrochloride and Bipenamol, was also achieved.</p>
</div>
<br /> | Wensen Ouyang; Jianhang Rao; Jie Wang; Yang Gao; Yanping Huo; Qian Chen; Xianwei Li | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7541b0f50db3cc8397ca3/original/multiple-c-h-activation-enabled-modular-construction-of-densely-functionalized-sulfur-contained-arenes.pdf |
64882fd84f8b1884b739e886 | 10.26434/chemrxiv-2023-z4cwr | Multiscale reactive model for 1,3,5-triamino-2,4,6-trinitrobenzene inferred by reactive MD simulations and unsupervised learning | When high-energy-density materials are subjected to thermal or mechanical insults at extreme conditions (shock loading), a coupled response between the thermo-mechanical and chemical behavior is systematically induced. We develop a reaction model for the fast chemistry of 1,3,5-triamino-2,4,6- trinitrobenzene (TATB) at the mesoscopic scale where the chemical behavior is determined by underly- ing microscopic reactive simulations. The slow carbon clusters formation is not discussed in the present work. All-atom reactive MD simulations are performed with the ReaxFF potential and a reduced-order chemical kinetics model for TATB is fitted on isothermal and adiabatic simulations of single crystal chemical decomposition. Unsupervised machine learning techniques based on the non-negative matrix factorization are applied to MD trajectories to model the decomposition kinetics of TATB in terms of a four components model. The associated heats of reaction are fit to the temperature evolution from adiabatic decomposition trajectories. Using a chemical species analysis, we show that NMF captures the main chemical decomposition steps of TATB, and provides an accurate estimation of their evolution with temperature. The final analytical formulation, coupled to a diffusion term, is incorporated into a continuum formalism and simulation results are compared one-to-one against MD simulations of a 1D reaction propagation along different crystallographic directions and with different initial temperatures. A good agreement is found for both temporal and spatial evolution of the temperature field. | Paul Lafourcade; Jean-Bernard Maillet; Jérôme Roche; Michael Sakano; Brenden Hamilton; Alejandro Strachan | Physical Chemistry; Materials Science; Chemical Kinetics; Physical and Chemical Processes; Physical and Chemical Properties; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64882fd84f8b1884b739e886/original/multiscale-reactive-model-for-1-3-5-triamino-2-4-6-trinitrobenzene-inferred-by-reactive-md-simulations-and-unsupervised-learning.pdf |
66cc1af4a4e53c4876a51c36 | 10.26434/chemrxiv-2024-1dr51 | From chemical fingerprints to environmental footprints: Advancing feed production through near-infrared spectroscopy | Animal feed production involves balancing nutritional quality, profitability and environmental sustainability. Although near-infrared spectroscopy (NIRS) is currently used for real-time quality control of feed ingredients, we demonstrate that NIRS can also predict their environmental sustainability in a resource-efficient way. We use NIRS to determine ingredient origins and combine these with global spatially-explicit life cycle assessment (LCA) to estimate environmental footprints. By incorporating ingredient prices and transport, we then optimize feeds towards the triple goals of quality, profitability and sustainability. We show 3.3-39% reductions in climate change and land stress impacts on biodiversity while reducing profitability by only 0.82-2.4% over current production and ensuring quality. Our approach provides a suite of optimal feed ratios and identifies footprint-profitability trade-offs, aiding decision-makers in moving towards more environmentally sustainable feed. We conclude that NIRS-LCA is a powerful combination for enhancing sustainability that can be extended beyond feed to food, fiber and other biobased commodities. | Maria Cairoli; Anne Ottenbros; Sin Yong Teng; Steef Hanssen; Mark Schoot; Christiaan Kapper; Rosalie van Zelm; Lutgarde Buydens; Mark Huijbregts; Jeroen Jansen | Theoretical and Computational Chemistry; Analytical Chemistry; Agriculture and Food Chemistry; Environmental Analysis; Spectroscopy (Anal. Chem.); Machine Learning | CC BY 4.0 | CHEMRXIV | 2024-08-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66cc1af4a4e53c4876a51c36/original/from-chemical-fingerprints-to-environmental-footprints-advancing-feed-production-through-near-infrared-spectroscopy.pdf |
60c75423ee301c3bd0c7af00 | 10.26434/chemrxiv.13615853.v1 | Local Electric Fields as a Natural Switch of Heme-Iron Protein Reactivity | Heme-iron oxidoreductases operating through the
high-valent Fe<sup>IV</sup>O intermediates perform crucial and complicated
transformations, such as oxidations of unreactive saturated hydrocarbons. These
enzymes share the same Fe coordination, only differing by the axial ligation,
e.g., Cys in P450 oxygenases, Tyr in catalases, and His in peroxidases. By
examining ~200 heme-iron proteins, we show that the protein hosts exert
highly specific intramolecular electric fields on the active sites, and there
is a strong correlation between the direction and magnitude of this field and
the protein function. In all heme proteins, the field is preferentially aligned
with the Fe‒O bond (<b><i>F<sub>z</sub></i></b>). The Cys-ligated P450
oxygenases have the highest average <b><i>F<sub>z</sub></i></b> of
28.5 MV cm<sup>-1</sup>, i.e., most enhancing the oxyl-radical character of the
oxo group, and consistent with the ability of these proteins to activate strong
C‒H bonds. In contrast, in Tyr-ligated proteins, the average <b><i>F<sub>z</sub></i></b> is
only 3.0 MV cm<sup>-1</sup>, apparently suppressing single-electron
off-pathway oxidations, and in His-ligated proteins, <b><i>F<sub>z</sub></i></b> is
–8.7 MV cm<sup>-1</sup>. The operational field range is given by the trade-off
between the low reactivity of the Fe<sup>IV</sup>O Compound I at the more
negative <b><i>F<sub>z</sub></i></b>, and the low selectivity at the more
positive <b><i>F<sub>z</sub></i></b>. Consequently, a heme-iron site
placed in the field characteristic of another heme-iron protein class loses its
canonical function, and gains an adverse one. Thus, electric fields
produced by the protein scaffolds, together with the nature of the axial
ligand, control all heme-iron chemistry. | Daniel Bím; Anastassia N. Alexandrova | Bioinorganic Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75423ee301c3bd0c7af00/original/local-electric-fields-as-a-natural-switch-of-heme-iron-protein-reactivity.pdf |
61f59b2e71868d4570c304ca | 10.26434/chemrxiv-2022-ppjpd | ¹H and ¹³C NMR Assignment of Sunitinib Malate in Aqueous Media | Despite expanding therapeutic application of sunitinib and advances in its formulation, pharmacochemical and spectroscopical study on its aqueous solution is rather insufficient due to poor solubility of its base or salt form. In this report, ¹H (900 MHz) and ¹³C (225 MHz) NMR spectra of sunitinib malate in H₂O/D₂O=9/1 have been analyzed, whose spectral peaks have been assigned to each hydrogen and carbon atom, assisted by a combination of two-dimensional homo- and heteronuclear NMR: COSY, HSQC-DEPT, and HMBC. The assignment of labile H-N hydrogens in ¹H NMR spectrum is of particular interest in aqueous media, where such labile hydrogens could be potentially affected by intermolecular interactions (e.g., hydrogen bonding) with co-solvated constituents. Peak splitting patterns and corresponding ⁿJ(H-H), ⁿJ(H-F), and ⁿJ(C-F) coupling constants observed in each assigned spectrum have been jointly discussed, and ⁿJ(C-F) coupling constants were compared to those taken in DMSO-d6. | Myungjo J. Kim; Jong Hoa Ok; Chul Hwan Kim; Joo Young Oh | Biological and Medicinal Chemistry | CC BY 4.0 | CHEMRXIV | 2022-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61f59b2e71868d4570c304ca/original/1h-and-13c-nmr-assignment-of-sunitinib-malate-in-aqueous-media.pdf |
66708d83c9c6a5c07aadf4fe | 10.26434/chemrxiv-2024-lc3kf | Geometric Tuning of Coordinatively Unsaturated Copper(I) Sites in Metal–Organic Frameworks for Ambient-Temperature Hydrogen Storage | Porous solids can accommodate and release molecular hydrogen readily, making them attractive for minimizing the energy requirements for hydrogen storage relative to physical storage systems. However, H2 adsorption enthalpies in such materials are generally weak (−3 to −7 kJ/mol), leading to low capacities at ambient temperature. Metal–organic frameworks with well-defined structures and synthetic modularity could allow for tuning adsorbent–H2 interactions for ambient-temperature storage. Recently, Cu2.2Zn2.8Cl1.8(btdd)3 (H2btdd = bis(1H-1,2,3-triazolo-[4,5-b],[4′,5′-i])dibenzo[1,4]dioxin; CuI-MFU-4l) was reported to show a large H2 adsorption enthalpy of −32 kJ/mol owing to π-backbonding from CuI to H2, exceeding the optimal binding strength for ambient-temperature hydrogen storage (−15 to −25 kJ/mol). Toward realizing optimal H2 binding, we sought to modulate the π-backbonding interactions by tuning the pyramidal geometry of the trigonal CuI sites. A series of isostructural frameworks, Cu2.7M2.3X1.3(btdd)3 (M = Mn, Cd; X = Cl, I; CuIM-MFU-4l), was synthesized through post-synthetic modification of the corresponding materials M5X4(btdd)3 (M = Mn, Cd; X = CH3CO2, I; MX-MFU-4l). This strategy adjusts the H2 adsorption enthalpy at the trigonal pyramidal CuI sites as a function of the ionic radius of the central metal ion of the pentanuclear cluster node, leading to −33 kJ/mol for M = ZnII (0.74 Å), −27 kJ/mol for M = MnII (0.83 Å), and −23 kJ/mol for M = CdII (0.95 Å). Thus, CuICd-MFU-4l provides a second, more stable example of optimal H2 binding energy for ambient-temperature storage among reported metal–organic frameworks. Structural, computational, and spectroscopic studies indicate that a larger central metal planarizes trigonal CuI sites, weakening the π-backbonding to H2. | Yuto Yabuuchi; Hiroyasu Furukawa; Kurtis M. Carsch; Ryan A. Klein; Nikolay V. Tkachenko; Adrian J. Huang; Yongqiang Cheng; Keith M. Taddei; Eric Novak; Craig M. Brown; Martin Head-Gordon; Jeffrey R. Long | Inorganic Chemistry; Coordination Chemistry (Inorg.); Solid State Chemistry; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-06-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66708d83c9c6a5c07aadf4fe/original/geometric-tuning-of-coordinatively-unsaturated-copper-i-sites-in-metal-organic-frameworks-for-ambient-temperature-hydrogen-storage.pdf |
60c749539abda23aaff8cbd3 | 10.26434/chemrxiv.12017796.v2 | Total Synthesis of the Antitumor Depsipeptide FE399 and its S-Benzyl Derivative: A Macrolactamization Approach | <div>An efficient and practical method for the synthesis of (9R,14R,17R)-FE399, a novel antitumor bicyclic depsipeptide, was developed. A 2-methyl-6-nitrobenzoic anhydride (MNBA)-mediated dehydration condensation reaction was effectively employed for the formation of the 16-membered macrocyclic depsipeptide moiety of FE399. FE399 was found to exist as an inseparable equilibrium mixture of conformational isomers; the mixture was quantitatively transformed into the corresponding S-benzyl product and isolated as a single isomer. Thus, we could confirm that the molecular structure of FE399 obtained by this method is identical to that of the natural product.</div> | Takayuki Tonoi; Miyuki Ikeda; Teruyuki Sato; Takehiko Inohana; Ryo Kawahara; Takatsugu Murata; Isamu Shiina | Natural Products | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749539abda23aaff8cbd3/original/total-synthesis-of-the-antitumor-depsipeptide-fe399-and-its-s-benzyl-derivative-a-macrolactamization-approach.pdf |
60cbcb1d461f5627524764ab | 10.26434/chemrxiv-2021-v9rzc | E2EDNA: Simulation Protocol for DNA Aptamers with Ligands | We present E2EDNA, a simulation protocol and accompanying code for the molecular
biophysics and materials science communities. This protocol is both easy to use and sufficiently
efficient to simulate single-stranded (ss)DNA and small analyte systems that are central to
cellular processes and nanotechnologies such as DNA aptamer-based sensors. Practical aptamer optimization often requires higher accuracy
predictions for only a small subset of sequences suggested e.g., by SELEX experiments, but in
the absence of a streamlined procedure this task is extremely time and expertise intensive. We
address this gap by introducing E2EDNA, a computational framework that accepts a DNA
sequence in the FASTA format and the structures of the desired ligands, and performs
approximate folding followed by a refining step, analyte complexation, and molecular dynamics
sampling at the desired level of accuracy. As a case study we simulate a DNA-UTP (uridine triphosphate) complex in water using AMOEBA force field. https://github.com/InfluenceFunctional/E2EDNA. | Michael Kilgour; Tao Liu; Brandon Walker; Pengyu Ren; Lena Simine | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Biophysics; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2021-06-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60cbcb1d461f5627524764ab/original/e2edna-simulation-protocol-for-dna-aptamers-with-ligands.pdf |
64e89c58dd1a73847f7ef9f9 | 10.26434/chemrxiv-2023-jb7xw | Yield-stress shear thinning and shear thickening fluid flows in deformable channels | Yield stress shear thinning/thickening fluids flow through flexible channels, tubes are widespread in the natural world with many technological applications [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11]. In this paper, we have derived analytical formulae for the velocity profiles and flow rate using the Herschel-Bulkley rheological model in the rigid and deformable shallow channels under lubrication approximation. To represent deformable walls, we have utilized small displacement structural mechanics and perturbation theory presented by Gervais et al. [12] and Christov et al. [13], respectively. The newly derived formulae also facilitate the flow dynamics of Newtonian fluids, power-law fluids, and Bingham fluids as its limiting cases, which have been previously derived in the literature [12, 13, 14, 15]. We find that the deformability increases the effective channel height and the flow rate in the channel. We find many scalings for the flow rate under different regimes of applied pressure and the deformability parameter. We also find that increasing the yield stress leads to a decrease in the velocity in the plug flow as well as in the non-plug flow regions. Increasing yield stress also leads to increasing the yield surface height and the solid plug in the central region due to which decreasing in the flow rate. We also find that the shear thinning/thickening index does not affect the plug height, although as the index increases, the flow rate starts to decrease due to the corresponding increase in shear thickening of the material. | Ashish Garg; Pranjal Prasad | Polymer Science; Chemical Engineering and Industrial Chemistry; Fluid Mechanics; Process Control; Transport Phenomena (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e89c58dd1a73847f7ef9f9/original/yield-stress-shear-thinning-and-shear-thickening-fluid-flows-in-deformable-channels.pdf |
67d38d8481d2151a024e6c19 | 10.26434/chemrxiv-2025-1tlh1 | Microenvironments Explain the Mismatch between Photochemical Absorptivity and Reactivity | Photochemistry is at the forefront of many modern technologies, from additive manufacturing to phototherapeutics, to sun protection and organic synthesis. For centuries, it was believed that an absorbance spectrum – showing the likelihood of a photon to be absorbed by a chromophore at a given wavelength – is an accurate predictor of how well a photochemical process will proceed when irradiated with different colours of light. Over the last decade this paradigm has been repeatedly challenged for many photochemical systems, as a distinct mismatch between the absorption spectrum and the wavelength resolved photochemical reactivity has been observed. Herein, we unravel the underlying mechanisms behind the mismatched reactivity and absorbance. Initially, we probe the impact that an equilibrium established between reversible photochemical processes has on the mismatch. Subsequently, we establish a critical link between photophysics and photochemistry with a theory based on the selective excitation of specific microenvironments leading to molecular transitions that allow for favourable wavelength-dependent reactivity. Time-resolved and steady-state fluorescence spectroscopy measurements confirm the presence of this selectivity, with both displaying significant red-edge effects that are observed in fluorescence spectroscopy literature, further supporting our theory. By synthetically tethering chromophores together, we further evidence the importance of microenvironments and their wavelength-dependent excited-state lifetimes, presenting the missing link that explains the mismatch for many photochemical systems. The implications of the theory presented herein stretch from additive manufacturing to photodynamic therapy and beyond, meaning that researchers can leverage photochemical mismatches of their design by simply changing the properties of the environment surrounding the chromophore. | Joshua A. Carroll; Fred Pashley-Johnson; Maciej Klein; Theresa Stephan; Ajay K. Pandey; Michael Walter; Andreas-Neil Unterreiner; Christopher Barner-Kowollik | Physical Chemistry; Photochemistry (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2025-03-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d38d8481d2151a024e6c19/original/microenvironments-explain-the-mismatch-between-photochemical-absorptivity-and-reactivity.pdf |
666325fbe7ccf7753a3a337c | 10.26434/chemrxiv-2024-mhv7n | An atomic radii set and Generalized Born implicit solvation model trained using explicit water solvation free energy data | Compared with the other common implicit and explicit water models, Generalized Born (GB) models can provide a fast approximation of solvation free energy that is reasonably accurate but fast enough to use in molecular dynamics (MD) simulations. This enhances conformational sampling of the solute molecules, and also can be a valuable component of multi-scale simulations. We previously developed the GB-Neck2 model, which exhibited improved secondary structure balance and was used to successfully fold a series of small proteins. More recent simulations using GB-Neck2 with updated protein models suggest that α-helices remain somewhat over-stabilized. Here, we develop a more self-consistent model, retraining both the intrinsic solvation radii as well as the GB model parameters, using the solvation free energies of an explicit water model as training references. The new radii set, named MIRO, when used with the GBNSR6 implicit solvent model leads to improved reproduction of solvation free energies calculated in explicit water. The new GB-Neck3 model shows a good balance of secondary structures: the stability of β-sheets is improved, while the previously over-stabilized α-helices became less favorable, as expected. GB-Neck3 and MIRO radii should extend the range of problems accessible to biomolecular simulation. | Yuzhang Wang; Chuan Tian; Jorge Pincay; Carlos Simmerling | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/666325fbe7ccf7753a3a337c/original/an-atomic-radii-set-and-generalized-born-implicit-solvation-model-trained-using-explicit-water-solvation-free-energy-data.pdf |
60c73dd5842e6580b4db183b | 10.26434/chemrxiv.6187253.v1 | Tuning the Electrochemical Potential of Perfunctionalized Dodecaborate Clusters Through Vertex Differentiation | We report a new class of redox-‐active vertex-‐differentiated dodecaborate clusters featuring pentafluoroaryl groups. These [B12(OR)11NO2] clusters share several unique photophysical properties with their [B12(OR)12] analogues, while exhibiting significantly higher (+0.5 V) redox potentials. This work describes the synthesis, characterization, and isolation of [B12(O-‐CH2C6F5)11NO2] clusters in all 3 oxidation states (dianion, radical, and neutral). Reactivity to post-‐functionalization with thiol species via SNAr on the pentafluoroaryl groups is also demonstated. | Alex I. Wixtrom; Zeeshan Parvez; Miles A. Savage; Elaine A. Qian; Dahee Jung; Saeed I. Khan; Arnold L. Rheingold; Alexander Spokoyny | Bonding; Electrochemistry; Main Group Chemistry (Inorg.); Clusters | CC BY NC ND 4.0 | CHEMRXIV | 2018-04-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dd5842e6580b4db183b/original/tuning-the-electrochemical-potential-of-perfunctionalized-dodecaborate-clusters-through-vertex-differentiation.pdf |
6670249601103d79c5654c6a | 10.26434/chemrxiv-2023-b4btj-v2 | Unhindered Biplane-Shaped N-Heterocyclic Carbenes as Powerful Ligands in Challenging Ru-Catalysed Olefin Metathesis of Sterically-Crowded Substrates | Despite notable progress, olefin metathesis methods for preparing sterically crowded C-C double bonds remain scarce. They are commonly based on specialised ruthenium catalysts with sterically reduced N-heterocyclic carbene (NHC) ligands, able to accommodate more crowded olefinic substrates during the catalytic steps. Yet, although being highly active, these complexes are rather unstable. In the case of Ru complexes containing NHC ligands with N-aryl groups, the catalyst deactivation is mainly due to intramolecular C-H activation at the ortho position of the N-aryl group of the NHC ligand. Considering that the deleterious C-H activation process requires the rotation of the N-aryl arm of the NHC ligand, we introduced a second decker of aromatic groups in benzimidazolylidene-based N-phenyl NHC ligands, which led to robust and highly efficient ruthenium metathesis catalysts in challenging metathesis reactions of tri-and tetra-substituted olefins. The beneficial effect of these upper aromatic “wings” on the stability and activity of the Ru-complexes is rationalised through the experimental determination of the stereoelectronic properties of the NHC ligands, complemented by DFT calculations on the nature of the through-space interactions between the aromatics and on the decomposition pathway of these second-generation Hoveyda precursors. | Paweł Krzesiński; Chiara Dinoi ; Iker Del Rosal; Laure Vendier; Pavel Kumandin; Stéphanie Bastin; Vincent César; Anna Kajetanowicz; Karol Grela | Catalysis | CC BY 4.0 | CHEMRXIV | 2024-06-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6670249601103d79c5654c6a/original/unhindered-biplane-shaped-n-heterocyclic-carbenes-as-powerful-ligands-in-challenging-ru-catalysed-olefin-metathesis-of-sterically-crowded-substrates.pdf |
65957d349138d231611ad8f7 | 10.26434/chemrxiv-2024-5p9j4 | Challenges in high-throughput inorganic material prediction and autonomous synthesis | Materials discovery lays the foundation for many technological advancements. Predicting and discovering new materials are not simple tasks. We here outline some basic principles of solid-state chemistry, which might help to advance both, and discuss pitfalls and challenges in materials discovery. Using the recent work of Szymanski et al., which reported the autonomous discovery of 43 novel materials, as an example, we discuss problems that can arise in unsupervised materials discovery, and hope that by addressing these, autonomous materials discovery can be brought closer to reality. We discuss all 43 synthetic products and point out four common shortfalls in the analysis. These errors unfortunately lead to the conclusion that no new materials have been discovered in that work. We conclude that there are two important points of improvement that require future work from the community: (i) automated Rietveld analysis of powder x-ray diffraction data is not yet reliable. Future improvement of such, and the development of a reliable artificial intelligence-based tool for Rietveld fitting, would be very helpful, not only to autonomous materials discovery, but also the community in general. (ii) We find that disorder in materials is often neglected in predictions. The predicted compounds investigated herein have all their elemental components located on distinct crystallographic positions, but in reality, elements can share crystallographic sites, resulting in higher symmetry space groups and - very often - known alloys or solid solutions. This error might be related to the difficulty of modeling disorder in a computationally economical way, and needs to be addressed both by computational and experimental material scientists. We find that two-thirds of the claimed successful materials in Szymanski et al are likely to be known, compositionally disordered versions of the predicted, ordered compounds. We highlight important issues in materials discovery, computational chemistry, and autonomous interpretation of x-ray diffraction. We discuss concepts of materials discovery from an experimentalist point of view, which we hope will be helpful for the community to further advance this important new aspect of our field. | Josh Leeman; Yuhan Liu; Joseph Stiles; Scott Lee; Prajna Bhatt; Leslie Schoop; Robert Palgrave | Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-01-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65957d349138d231611ad8f7/original/challenges-in-high-throughput-inorganic-material-prediction-and-autonomous-synthesis.pdf |
67d794cf6dde43c9080f7772 | 10.26434/chemrxiv-2025-t70d5 | Exploring foundational machine learned potentials for treating the high temperature dynamics of metal-organic frameworks | Metal-organic framework (MOF) derived materials, formed through high temperature processes, show great potential as catalysts. However, knowledge of the structure-property relationships between the initial MOF and final MOF-derived catalyst is limited, as their amorphous nature challenges standard structural characterization methods. Additionally, current molecular simulation methods, such as ab initio molecular dynamics, are computationally demanding and unable to follow pyrolysis over large temporal and spatial scales. One solution is the use of neural network approaches for learning interatomic potentials from density functional theory (DFT). Here we explored the pyrolysis of CALF-20 and ZIF-8 using machine learned potentials and established potentials that can simulate high temperature decomposition at near DFT accuracy. Standard random sampling and two biased sampling techniques were tested in an effort to sample the phase space of average zinc coordination number and bond length. These biased sampling methods showed significant improvement over random sampling; the resulting models were able to successfully recreate the environments seen in a DFT simulation. Using this model, we then simulated a one nanosecond quench of CALF-20 and ZIF-8 at 1500 K and 1750 K, respectively. This gave atomistic details of how the MOF behaved at high temperatures including gas formation, changes in zinc coordination environment and decomposition of linkers. This demonstrates the potential of using MLPs to simulate complex, high temperature processes in MOFs to gain a better understanding of reactivity and predict the features needed for new catalytic materials. | Connor W. Edwards; Jack D. Evans | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2025-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d794cf6dde43c9080f7772/original/exploring-foundational-machine-learned-potentials-for-treating-the-high-temperature-dynamics-of-metal-organic-frameworks.pdf |
64be66c1ae3d1a7b0d406da6 | 10.26434/chemrxiv-2023-0gjch | Ligand-Induced Symmetry Breaking as Origin of Multiexponential Photoluminescence Decay in CdSe Quantum Dots | The bright photoluminescence (PL) of colloidal CdSe quantum dots (QDs) makes them interesting for optical applications. For most of them well-defined PL properties, dominated by a single excitonic state, are required. However, in many PL experiments on QD ensembles multiexponential decay was observed. Based on spin-orbit density functional theory and screened configuration interaction calculations, we show that highly symmetric and defect-free CdSe QDs with diameters of 1.7 nm and 2.0 nm possess a multiexponential PL at the single-dot level. This is a consequence of a ligand-induced symmetry breaking with a subsequent rearrangement of the lowest eight excitonic states in two sets of four singly degenerate excitonic states. For each set, the lowest state is dark and the other three bright. We find that the splitting between the sets can be modified by the ligand coverage and the ligand choice, which facilitates engineering the PL properties of CdSe QDs. | Torben Steenbock; Tobias Dittmann; Surender Kumar; Gabriel Bester | Theoretical and Computational Chemistry; Physical Chemistry; Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64be66c1ae3d1a7b0d406da6/original/ligand-induced-symmetry-breaking-as-origin-of-multiexponential-photoluminescence-decay-in-cd-se-quantum-dots.pdf |
60c75203702a9b818318c04c | 10.26434/chemrxiv.13095551.v2 | Widely Used Catalysts in Biodiesel Production: A Review | <p>An ever-increasing energy demand and
environmental problems associated with exhaustible fossil fuels have led to the
search for an alternative renewable source of energy. In this context, biodiesel
has attracted attention worldwide as an alternative to fossil fuel for being
renewable, non-toxic, biodegradable, carbon-neutral; hence eco-friendly. Despite
homogeneous catalyst has its own merits, currently, much attention has been paid
to chemically synthesize heterogeneous catalysts for biodiesel production as it
can be tuned as per specific requirement, easily recovered, thus enhance
reusability. Recently, biomass-derived heterogeneous catalysts have risen to
the forefront of biodiesel productions because of their sustainable, economical
and eco-friendly nature. Further, nano and bifunctional catalysts have emerged
as a powerful catalyst largely due to their high surface area and potential to
convert free fatty acids and triglycerides to biodiesel, respectively. This
review highlighted the latest synthesis routes of various types of catalysts
including acidic, basic, bifunctional and nanocatalysts derived from different chemicals
as well as biomass. In addition, the impacts of different methods of
preparation of catalysts on the yield of biodiesel are also discussed in
details.</p> | Bishwajit Changmai; Vanlalveni Chhangte; Rahul Bhagat; Avinash P. Ingle; Samuel Lalthazuala Rokhum | Fuels - Energy Science | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75203702a9b818318c04c/original/widely-used-catalysts-in-biodiesel-production-a-review.pdf |
64fc2abbb6ab98a41c1fede7 | 10.26434/chemrxiv-2023-lx165 | Copper-Mediated Hydrogen Atom Transfer Enabling General Catalytic Hydrofunctionalization of Olefins | The renaissance of catalytic hydrogen atom transfer from a metal hydride (MHAT) offers advanced tools for practicing sophisticated radical chemistry on simple olefins. While 3d transition metals like cobalt, iron, and manganese have been extensively studied in catalytic MHAT, the potential of copper remains unexplored. This is due to the polar reactivity exhibited by classical nucleophilic Cu(I) hydrides. Here we report the first examples of catalytic hydrofunctionalization reactions enabled by copper-mediated MHAT. The Cu-MHAT process produces alkyl radicals in high chemo- and regioselectivity, which are subsequently captured by Cu(II) species to undergo coupling reactions with an exceptionally broad scope of oxygen-, nitrogen-, halogen-, and carbon-based nucleophiles. The distinct reactivity and selectivity observed in Cu-MHAT system is attributed to the involvement of Cu(II)–H species, a hydrogen atom donor that possesses substantially altered charge distribution and weakened bonding in contrast to conventional Cu(I) hydrides. Preliminary results suggest potential extension to asymmetric catalysis and radical polymerization are viable. This work opens up new opportunities for MHAT chemistry by going beyond the common oxidation states. | Jun-Jie Wang; He Huang; Han-Li Sun; Fan Yang; Rong Zhu | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64fc2abbb6ab98a41c1fede7/original/copper-mediated-hydrogen-atom-transfer-enabling-general-catalytic-hydrofunctionalization-of-olefins.pdf |
60c7532d337d6c19cce2880e | 10.26434/chemrxiv.13416272.v1 | An uncomplicated electrochemical sensor combining a perfluorocarbon SAM and ACE2 as the bio-recognition element to sensitively and specifically detect SARS-CoV-2 in complex samples. | Emerging in late 2019, the SARS-CoV-2 virus has had a devastating health and economic effects around the world forcing governments to enact restrictions on day to day life, resulting in severe economic and social disruption. The virus has stimulated new research in the fields of drug development, vaccinology and diagnostic testing. Here we present the basis for a simple, mass manufacturable saliva based electrochemical assay for the SARS-CoV-2 virus acheived through adsorption of the Angiotsnsin Converting Enzyme 2 (ACE2) into thiolated amphiphobic prefluoro monolayer assemled on a gold sensor surface. Following sensor preparation, it is possible to measure specific binding of recombinant spike protein and discriminate positive and negative samples of inactivated SARS-CoV-2 following 30 minutes incubation under ambient conditions. Representative calculations of limits of detection are made for recombinant spike protein (1.68 ng/ml) and inactivated virus (37.8 dC/mL). The assay as presented ultimately shows discrimination between positive and negative inactivated SARS-CoV-2 samples originating from clinical molecular standards kit intended for clinical and biomedical assay validation, and which is designed to mimic clinical samples through presence of cells and proteins in the sample medium. The simple design of the label free measurement and the selection of reagents involved means the assay has clear potential for transfer onto mass producible units such as screen-printed electrodes similar to glucose-format test strips, to enable widespread, low cost and rapid testing for SARS-CoV-2 in the general population | Vincent Vezza; Adrian Butterworth; Perrine Lasserre; Ewen O Blair; Alexander MacDonald; Stuart Hannah; Christopher Rinaldi; Paul A Hoskisson; Andrew C Ward; Alistair Longmuir; Steven Setford; Michael E Murphy; Damion Corrigan | Analytical Chemistry - General; Electrochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7532d337d6c19cce2880e/original/an-uncomplicated-electrochemical-sensor-combining-a-perfluorocarbon-sam-and-ace2-as-the-bio-recognition-element-to-sensitively-and-specifically-detect-sars-co-v-2-in-complex-samples.pdf |
650ce869b927619fe796902f | 10.26434/chemrxiv-2023-wdj45 | Tunable magnetic order in Fe-Mg co-doped montmoril- lonite nano-clay interfaced with amino acids. | The present study investigates the tunable magnetic order as well as the electrostatic and magnetic interactions due to the adsorption of the amino acids (AA) on the insulating montmorillonite (MMT) nano-clay in vacuum and in aqueous medium using the first principle density functional theory (DFT). A single layer MMT clay of thickness 0.68 nm has been co- doped with impurity atoms, Fe(II) and Mg(II), each of concentration 12.5 %. Our calculated values of interaction energies suggest that the water molecules enhances the binding affinity of AA molecules due to the formation of a strong hydrogen bonding with substantial charge transfer between AA molecules (charge donor) and nano-clay (charge acceptor). We also predicted the possible transition in magnetic orders (ferromagnetism, antiferromagnetism, and ferrimagnetism) due to adsorption of AA molecules while going from vacuum to aqueous medium which has not been reported yet. Such kind of study possess potential applications in tissue engineering, pharmacology, magnetic resonance imaging, and chemical engineering. | Dinesh Thapa; Steven Westra; Dmitri Kilin; Svetlana Kilina | Organometallic Chemistry; Chemical Engineering and Industrial Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650ce869b927619fe796902f/original/tunable-magnetic-order-in-fe-mg-co-doped-montmoril-lonite-nano-clay-interfaced-with-amino-acids.pdf |
67583209085116a133ef166b | 10.26434/chemrxiv-2024-mlcss-v2 | Synthetic Strategy for mRNA Encapsulation and Gene Delivery with Metal-Organic Frameworks | In the past two decades, metal-organic frameworks (MOFs) have evolved from uses in catalysis and gas storage to exciting applications in biomedicine, particularly in drug delivery. Initially, MOFs were primarily used to deliver small molecules, but recent innovations have shifted focus toward more complex nucleic acids like DNA, short guide RNA (sgRNA), and short interfering RNA (siRNA). Remarkably, no studies to date have demonstrated the successful encapsulation and delivery of fragile messenger RNA (mRNA) via MOFs in vitro and in vivo. This study tackles that gap by identifying optimal synthetic conditions to encapsulate and deliver mRNA using nanoscale zeolitic imidazole framework-8 (ZIF-8). Early attempts showed mRNA loading in ZIF-8 but failed to retain mRNA in biological media. To overcome this challenge, we incorporated polyethyleneimine (PEI) into the framework, forming a robust polymer complex core-MOF shell particle. This system not only stabilized mRNA complexes but delayed their release, resulting in effective protein expression in multiple cell lines and mice, performing on par with commercial lipid-based transfection reagents and surpassing PEI alone. Moreover, we present the first investigation into thermally stable mRNA storage using ZIF-8, demonstrating successful protein expression after three months of room-temperature storage in vitro and one month in vivo. Our findings broaden the scope of MOF-based therapeutic delivery and open new avenues for long-term mRNA storage and transport. | Harrison Lawson; Huy Nguyen; Keng Lee; Nattarat Wongsuwan; Ayesha Tupe ; Mariah Arral; Anne Behre; Mengrou Lu; Adam Feinberg; Kathryn Whitehead; Si-Yang Zheng | Biological and Medicinal Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Bioengineering and Biotechnology; Drug Discovery and Drug Delivery Systems; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67583209085116a133ef166b/original/synthetic-strategy-for-m-rna-encapsulation-and-gene-delivery-with-metal-organic-frameworks.pdf |
65d9f441e9ebbb4db9223dcf | 10.26434/chemrxiv-2024-s1fzw | Single-benzene-based clickable fluorophores for in vitro and in vivo bioimaging | A series of clickable single-benzene-based fluorophores derived from tetrafluoroterephthalonitrile (4F-2CN) is reported. Fluorophores based on a tetrahydroquinoxaline skeleton (2F-2CN-(β-NH2Ala)) exhibited improved photophysical properties owing to better planarity and conjugation over those with dihydro[1,4]thiazine skeleton (2F-2CN-Cys). These easily produced clickable fluorophores were successfully applied in in vitro and in vivo bioimaging after protein conjugation. | Raja Mohanrao; Clyde S. Pinto; Andrejus Suchenko; Guy J. Clarkson; Martin Wills; Stefan Roesner; Michael Shipman; Mohan K. Balasubramanian | Biological and Medicinal Chemistry; Organic Chemistry; Analytical Chemistry; Organic Compounds and Functional Groups; Imaging; Biochemistry | CC BY 4.0 | CHEMRXIV | 2024-02-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d9f441e9ebbb4db9223dcf/original/single-benzene-based-clickable-fluorophores-for-in-vitro-and-in-vivo-bioimaging.pdf |
642d530c736114c963f3f382 | 10.26434/chemrxiv-2023-5f00r-v3 | A Roadmap for Achieving Scalable, Safe, and Low-cost Direct Air Carbon Capture and Storage | Direct air carbon capture and storage (DACCS) involves a set of approaches for capturing CO2 directly from the air and its subsequent long-term storage. DACCS is at an early stage of technical development and currently faces a variety of challenges, including high cost and energy requirements. Building on publicly available data, this paper provides: (i) an overview and classification of DACCS systems, (ii) a harmonization of technical and economic performance of direct air capture technologies, (iii) a comprehensive list of technical- and infrastructure-based obstacles to scaling DACCS systems, and (iv) a roadmap and list of priority initiatives for research, development, demonstration, and deployment of DACCS. Our intent is to drive progress against high-impact priority actions, with a focus on accelerating research, development, and deployment of safe, scalable, and low cost DACCS as a component of the broader carbon dioxide removal portfolio. | Lukas Küng; Silvan Aeschlimann; Charithea Charalambous; Fergus McIlwaine; John Young; Noah Shannon; Karen Strassel; Cara Maesano; Rudy Kahsar; Daniel Pike; Mijndert van der Spek; Susana Garcia | Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry | CC BY 4.0 | CHEMRXIV | 2023-04-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/642d530c736114c963f3f382/original/a-roadmap-for-achieving-scalable-safe-and-low-cost-direct-air-carbon-capture-and-storage.pdf |
62cee93f7aab585379bbe40b | 10.26434/chemrxiv-2022-4fj0r | The Rise and Fall of Hydroxychloroquine (HCQ) in COVID Era: A Therapeutic Journey and Synthetic Progress
| With no proven therapy against COVID-19, the repurposing of existing drugs is an ongoing exercise. In this context, an antimalarial drug, hydroxychloroquine (HCQ) received immediate stardom when the US-FDA issued an Emergency Use Authorization (EUA) for HCQ against COVID-19 based on the limited clinical study. However, on 17 June 2020, WHO announced the stoppage of the HCQ trial for COVID-19 treatment based on data received from the Solidarity trial and UK's Recovery trials indicating HCQ does not result in the reduction of mortality of hospitalized COVID-19 patients when compared with standard of care. In this context, the present review aims to provide a developmental journey of HCQ including medicinal chemistry highlighting the essential pharmacology and the current studies exploring its effectiveness against COVID-19, and its synthetic advancement.
| Dinesh Kumar; Gargi Nikhil Vaidya; Ashwini Venkatesh; Deep Rohan Chatterjee; Pooja Rana; Mithilesh Nagpure; Dinesh Parshuram Satpute; Shyam Lokhande; Kiran Kalia | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2022-07-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62cee93f7aab585379bbe40b/original/the-rise-and-fall-of-hydroxychloroquine-hcq-in-covid-era-a-therapeutic-journey-and-synthetic-progress.pdf |
646706cff2112b41e9c9ccc2 | 10.26434/chemrxiv-2023-3295p | From Diaminosilylenes to Silapyramidanes: Making Sense of the Stability of Divalent Silicon Compounds
| Since the discovery of decamethylsilicocene over three decades ago, chemists have successfully isolated a variety of divalent silicon compounds by orchestrating steric and electronic effects to their advantage. Two broad strategies of electronic stabilization appear to have been widely deployed, namely -conjugation as in diaminosilylenes and -complexation as in decamethylsilicocene and silapyramidanes. Herein, we have attempted to identify quantitative metrics for the electronic stabilization of silylenes. Singlet-triplet gaps and electron affinities, both physical observables, appear to be useful in this regard. Thus, the most stable silylenes exhibit unusually high singlet-triplet gaps and very low or negative gas-phase electron affinities. Both metrics signify low electrophilicity, i.e., a low susceptibility to nucleophilic attack. The ionization potential associated with the Si-based lone pair also gives an indication of nucleophilic reactivity. | Kristian Torstensen; Abhik Ghosh | Theoretical and Computational Chemistry; Physical Chemistry; Inorganic Chemistry; Bonding; Main Group Chemistry (Inorg.); Theory - Inorganic | CC BY 4.0 | CHEMRXIV | 2023-05-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646706cff2112b41e9c9ccc2/original/from-diaminosilylenes-to-silapyramidanes-making-sense-of-the-stability-of-divalent-silicon-compounds.pdf |
64701bbbe64f843f41c8a4b8 | 10.26434/chemrxiv-2023-4vdb1 | Fundamental Insight into Humid CO2 Uptake in Direct Air Capture Nanocomposites Using Fluorescence and Portable NMR Relaxometry | Direct air capture (DAC) technology is being explored as a pathway for reducing greenhouse gas emissions through the efficient removal of CO2 from the atmosphere. However, there remains a knowledge gap regarding structure-property-performance factors that impact the behavior of these systems in diverse, real-world environments. In aminopolymer-based DAC systems, gas diffusion is tightly coupled with polymer mobility, which is in turn affected by a large matrix of variables, including interactions with the pore wall of the support, nanoconfinement, the presence of co-adsorbates (moisture), and electrostatic crosslinks that develop as a function of CO2 chemisorption. Higher throughput, benchtop techniques for studying and understanding mobility in these systems would lead to more rapid advances in the field. Here, we demonstrate the value of a fluorescence technique for monitoring polymer mobility within nanocomposite capture materials as a function of CO2 and water adsorption in a series of humidified polyethylenimine-Al2O3 composite materials. The approach allows us to correlate changes in mobility with CO2 adsorption kinetics as a function of relative humidity. We further couple this information with NMR relaxometry data attained using a portable single-sided magnetic resonance device, and we employ diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) to correlate the formation of different relative amounts of carbamates and carbonates with the environmental conditions. These results provide a blueprint for using benchtop techniques to promote fundamental understanding in DAC systems that can in turn enable more efficient operation in real-world conditions. | Glory Russell-Parks; Noemi Leick; Maxwell Marple; Nicholas Strange; Brian Trewyn; Simon Pang; Wade Braunecker | Physical Chemistry; Nanoscience; Physical and Chemical Processes; Spectroscopy (Physical Chem.); Transport phenomena (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64701bbbe64f843f41c8a4b8/original/fundamental-insight-into-humid-co2-uptake-in-direct-air-capture-nanocomposites-using-fluorescence-and-portable-nmr-relaxometry.pdf |
60c7496c702a9bdbed18b136 | 10.26434/chemrxiv.12061152.v1 | Incorporating Functionalized Cellulose to Increase the Toughness of Covalent Adaptable Networks | <p>Covalent adaptable networks (CANs) are cross-linked polymers that have mechanical properties similar to thermosets at operating conditions, yet can be reprocessed by cross-link exchange reactions that are activated by a stimulus. Although CAN exchange dynamics have been studied for many polymer compositions, the tensile properties of these demonstration systems are often inferior compared to commercial thermosets. In this study, we explore toughening CANs capable of forming covalent bonds with a reactive filler to characterize the trade-off between improved toughness and longer reprocessing times. Polycarbonate (PC) and polyurethane (PU) CANs were toughened by incorporating cellulose modified with cyclic carbonate groups as a reactive filler with loadings from 1.3-6.6 wt%. The addition of 6.6 wt% of the cellulose derivative resulted in a 3.2-fold increase in average toughness for the PC CANs, yet only increased the characteristic relaxation time of stress relaxation (*) via disulfide exchange at 180 °C from 63 s to 365 s. The cellulose-containing samples also showed >80% recovery in crosslinking density and mechanical properties after reprocessing. The addition of 3.2 wt% of the functionalized cellulose into a PEG-based PU CAN led to a 2.3-fold increase in toughness, while increasing * at 140 °C from 106 s to 157 s. These findings demonstrate the promise of functionalized cellulose as an inexpensive, renewable, and sustainable filler that toughens CANs containing hydroxyl groups. </p> | Jeremy Swartz; William Dichtel | Cellulosic materials; Organic Polymers; Polymerization (Polymers) | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7496c702a9bdbed18b136/original/incorporating-functionalized-cellulose-to-increase-the-toughness-of-covalent-adaptable-networks.pdf |
61fc587fc86ae289ad158fef | 10.26434/chemrxiv-2021-hr1r0-v3 | Free and Open Source Software for Computational Chemistry Education | Long in the making, computational chemistry for the masses [J. Chem. Educ. 1996, 73, 104] is finally here. Our brief review on free and open source software (FOSS) packages points out the existence of software offering a wide range of functionality, all the way from approximate semiempirical calculations with tight-binding density functional theory to sophisticated ab initio wave function methods such as coupled-cluster theory, covering both molecular and solid-state systems. Combined with the remarkable increase in the computing power of personal devices, which now rivals that of the fastest supercomputers in the world in the 1990s, we demonstrate that a decentralized model for teaching computational chemistry is now possible thanks to FOSS packages, enabling students to perform reasonable modeling on their own computing devices in the bring your own device (BYOD) scheme. FOSS software can be made trivially simple to install and keep up to date, eliminating the need for departmental support, and also enables comprehensive teaching strategies, as various algorithms' actual implementations can be used in teaching. We exemplify what kinds of calculations are feasible with four FOSS electronic structure programs, assuming only extremely modest computational resources, to illustrate how FOSS packages enable decentralized approaches to computational chemistry education within the BYOD scheme. FOSS also has further benefits driving its adoption: the open access to the source code of FOSS packages democratizes the science of computational chemistry, and FOSS packages can be used without limitation also beyond education, in academic and industrial applications, for example. | Susi Lehtola; Antti Karttunen | Theoretical and Computational Chemistry; Chemical Education; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2022-02-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61fc587fc86ae289ad158fef/original/free-and-open-source-software-for-computational-chemistry-education.pdf |
621c4a7bc3e9dac94b7ad6da | 10.26434/chemrxiv-2022-jqbf0 | Mechanically Enhanced Proline Ring-Opening in Proteins | Proteins such as collagen and elastin are subjected to highly repetitive stresses in the cardiovascular system. These proteins can have half-lives of many decades and, therefore, experience many tens or hundreds of millions of stress-strain cycles. Such a large number of cycles, even for a modest level of stress, subjects these molecules bond breaking and fatigue failure. To gain further insight into bond breaking in mechanically stressed proteins, the mechanical strength of bonds in the polypeptide backbone are estimated using bond dissociation energies from model compounds for individual amino acids. This analysis shows that the N-Cα bond in proline has a bond dissociation energy that is ~60 kJ/mol less than the next weakest bond in a polypeptide backbone. Thus, when mechanically stressed, the pyrrolidine ring of proline will open before other backbone bonds break. Such mechanically enhanced proline ring-opening would maintain structural continuity of the peptide backbone while increasing the length of the backbone by ~0.3 nm per ring-opening. The increase in length would redistribute forces to nearby molecules, thus effectively remodeling the mechanical properties of the tissue involved. | Jan Hoh | Physical Chemistry; Biological and Medicinal Chemistry; Polymer Science; Biopolymers; Polymer chains; Biochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/621c4a7bc3e9dac94b7ad6da/original/mechanically-enhanced-proline-ring-opening-in-proteins.pdf |
659daa7ae9ebbb4db9cd192d | 10.26434/chemrxiv-2024-ng6c0 | Modular Synthesis of alpha-Branched Secondary Alkylamines via Visible-light-mediated Carbonyl Alkylative Amination | The development of methods for the assembly of alpha-branched secondary alkylamines remains a central challenge to chemical synthesis because of their critical importance in modulating the physical properties of biologically active molecules. Despite decades of intensive research, chemists still rely on selective N-alkylation and carbonyl reductive amination to make most amine products. Here we report the further evolution of a carbonyl alkylative amination process that, for the first time, brings together primary amines, aldehydes and alkyl iodides in a visible-light-mediated multicomponent coupling reaction for the synthesis of a wide range of -branched secondary alkylamines. In addition to exploring the structural tolerance and limitations in each reaction component, we also report preliminary applications to the telescoped synthesis of -branched N-heterocycles and a primary-selective N-alkylation protocol based on carbonyl alkylative amination. We believe that this method will enable practitioners of synthetic chemistry in academic and industrial settings to approach the synthesis of these important molecules in a manner that is distinct from established approaches. | Matthew Gaunt; Milo Smith; Ryan Kang; Roopender Kumar; Biswarup Roy | Organic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2024-01-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/659daa7ae9ebbb4db9cd192d/original/modular-synthesis-of-alpha-branched-secondary-alkylamines-via-visible-light-mediated-carbonyl-alkylative-amination.pdf |
663dbd5121291e5d1de7f530 | 10.26434/chemrxiv-2024-1pxc6 | Development of QSAR Models on the Fouling-Release Performance of Silicone Oil-modified Siloxane Polyurethane Coatings | Polymer coatings with a fouling release activity is an effective method to prevent marine biological fouling caused by large number of marine organisms (over 4000) and ensure stability and safety of marine facilities. In this study, a novel cheminformatics-based approach was employed to investigate the fouling-release performance of siloxane-PU coating system. The structure-fouling release activity relationship was modeled for a set of 18 siloxane PU coatings by incorporation phenylmethyl silicones oils (PMM-1025, PMM-1043, PMM-5021, PMM-6025, PMM-0021, PMM-0025 of 1, 2 and 5 wt%). A specific structural descriptors encoding approach was applied for these systems, based on a mixture-based encoding, to feed the complex polymeric systems in machine learning algorithms. Several predictive quantitative structure-fouling release relationships models were developed using machine learning techniques, from multiple linear regression to nonlinear random forest methods, followed by scoring them based on high performance accuracy and validation with rigorous internal fit R2 train values between 0.73 to 0.95 and external predictivity R2ext between 0.68 to 0.88. Random Forest method was the best nonlinear one for predicting diatom removal activity. This work indicates that both linear and nonlinear machine learning-based modeling can be beneficial to predict fouling release properties of polymer coatings with an effective fouling release performance. | Achiya Khanam; Gerardo Casanola-Martin; Amirreza Daghighi; Dean Webster; Bakhtiyor Rasulev | Theoretical and Computational Chemistry; Materials Science; Polymer Science; Coating Materials; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/663dbd5121291e5d1de7f530/original/development-of-qsar-models-on-the-fouling-release-performance-of-silicone-oil-modified-siloxane-polyurethane-coatings.pdf |
670ae3e651558a15efe298d0 | 10.26434/chemrxiv-2024-q30x2 | How Do Microbial Metabolites Interact with Their Protein Targets? | The design of drugs and nutraceutics that mimic microbial metabolites is an emerging drug modality in medicinal chemistry that attempts to modulate the myriad of interactions that these molecules establish with host and microbial proteins. Understanding how microbial metabolites interact with their target proteins is key to perform a rational design of metabolite mimetic molecules for therapeutic usage. In the present work we answer that question by analyzing the functional groups of these molecules, and the interactions they display in a set of more than 71 K protein-metabolite interactions from the PDB. Significant differences in the functional group distributions, their chemical features, and their co-occurrences, are observed for distinct subsets of these molecules. The same is true for the distributions of interaction types. By correlating both datasets, we are able to explain the observed interaction patterns in terms of observed functional group patterns. These results will shed light on the rational design of novel metabolite mimetic molecules for therapeutic purposes. | Mario Astigarraga; Andrés Sánchez-Ruiz; Aminata Diop-Aw; Raquel Quintero; Gonzalo Colmenarejo | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670ae3e651558a15efe298d0/original/how-do-microbial-metabolites-interact-with-their-protein-targets.pdf |
6123595bded28a50d9868081 | 10.26434/chemrxiv-2021-pfdcx-v2 | Lifting the discrepancy between experimental results and the theoretical predictions for the catalytic activity of RuO2 (110) towards Oxygen Evolution Reaction | Developing new efficient catalyst materials for the oxygen evolution reaction (OER) is essential for widespread proton exchange membrane water electrolyzer use. Both RuO2(110) and IrO2(110) have been shown to be highly active OER catalysts, however DFT predictions have been unable to explain the high activity of RuO2. We propose that this discrepancy is due to RuO2 utilizing a different reaction pathway, as compared to the conventional IrO2 pathway. This hypothesis is supported by comparisons between experimental data, DFT data and the proposed reaction model. | Spyridon Divanis; Adrian Frandsen; Tugce Kutlusoy; Jan Rossmeisl | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Theory - Computational; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6123595bded28a50d9868081/original/lifting-the-discrepancy-between-experimental-results-and-the-theoretical-predictions-for-the-catalytic-activity-of-ru-o2-110-towards-oxygen-evolution-reaction.pdf |
661a702a91aefa6ce17a9536 | 10.26434/chemrxiv-2024-ts5k7 | Reactivity Manipulation of Ionic Liquid Based on Alkyl Primary Ammonium: Protonation Control Using Pyridine Additive for Effective Spontaneous Passivation of Perovskite via Hole Transport Material Deposition | Alkyl-primary-ammonium-based room-temperature ionic liquids (RTILs) designed to exhibit specific reactivities allowing the functions that cannot be achieved by the current major RTILs (e.g., pyridine-based RTILs) have recently emerged. The archetype of the reactive RTILs is n-octylammonium bis(trifluoromethanesulfonyl)imide (OA-TFSI), which has promising functions as an additive for the hole transport material (HTM) in perovskite solar cells (PCSs); the high reactivity of the OA cations on the perovskite surface allows effective spontaneous perovskite passivation via HTM deposition, significantly improving the PV performance of the PSC. However, although the reactivity manipulation of the reactive RTILs is instrumental for exploiting their potential functions and exploring their application scope, methods for reactivity control have not been developed. In this study, we propose and demonstrate that the co-addition of a pyridine moiety can effectively manipulate the reactivity of OA-TFSI by controlling the protonation between OA and the 2,2',7,7'-tetrakis-(N,N-di-4-methoxyphenylamino)-9,9'-spirobifluorene (Spiro-OMeTAD) HTM. The pyridine prevented OA deprotonation presumably via stabilization of the OA cation, thus retaining its ammonium form, which allowed effective spontaneous perovskite passivation. Although the proton being with OA owing to pyridine addition is disadvantageous for Spiro-OMeTAD radical formation via its protonation, which is crucial when conventional RTILs are used, a supportive function of the spontaneous perovskite passivation (i.e., the absence of cationic species in the HTM core) likely facilitated Spiro-OMeTAD radical formation, mitigating the requirement of Spiro-OMeTAD protonation. Therefore, overall, optimal pyridine addition significantly enhanced the PV performance, revealing the preference of protonation in the OA-TFSI system used in this study, which is opposite to that in conventional RTILs and represents the specificity of the reactive RTILs. This study provides valuable guidance for developing spontaneous perovskite passivation techniques, which can lead to further advancement of PCSs. Furthermore, this first proposal of a means in manipulating reactivity of the reactive RTILs will develop the nascent RTILs and contribute to further development of material science. | Naoyuki Nishimura; Hiroaki Tachibana; Ryuzi Katoh; Hiroyuki Kanda; Takurou N. Murakami | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661a702a91aefa6ce17a9536/original/reactivity-manipulation-of-ionic-liquid-based-on-alkyl-primary-ammonium-protonation-control-using-pyridine-additive-for-effective-spontaneous-passivation-of-perovskite-via-hole-transport-material-deposition.pdf |
60c746fbbdbb89c0e4a38cca | 10.26434/chemrxiv.11446224.v1 | Resolving the Quadruple Bonding Conundrum in C2 Using Insights Derived from Excited State Potential Energy Surfaces: A Molecular Orbital Perspective | The question of quadruple bonding in C<sub>2</sub> has emerged as a hot button issue, with opinions sharply divided between the practitioners of Valence Bond (VB) and Molecular Orbital (MO) theory. Here, we have systematically studied the Potential Energy Curves (PECs) of low lying high spin sigma states of C<sub>2</sub>, N<sub>2</sub> and Be<sub>2</sub> and HC≡CH using several MO based techniques such as CASSCF, RASSCF and MRCI. The analyses of the PECs for the<sup> 2S+1</sup>Σ<sub>g/u</sub> (with 2S+1=1,3,5,7,9) states of C<sub>2</sub> and comparisons with those of relevant dimers and the respective wavefunctions were conducted. We contend that unlike in the case of N<sub>2</sub> and HC≡CH, the presence of a deep minimum in the <sup>7</sup>Σ state of C<sub>2</sub> and CN<sup>+</sup> suggest a latent quadruple bonding nature in these two dimers. Hence, we have struck a reconciliatory note between the MO and VB approaches. The evidence provided by us can be experimentally verified, thus providing the window so that the narrative can move beyond theoretical conjectures. | Ishita Bhattacharjee; Debashree Ghosh; Ankan Paul | Theory - Computational | CC BY NC 4.0 | CHEMRXIV | 2019-12-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746fbbdbb89c0e4a38cca/original/resolving-the-quadruple-bonding-conundrum-in-c2-using-insights-derived-from-excited-state-potential-energy-surfaces-a-molecular-orbital-perspective.pdf |
60c74b84bb8c1a275a3db24a | 10.26434/chemrxiv.12341057.v1 | Scalable Synthesis of Crystalline One-Dimensional Carbon Nanothreads Through Modest-Pressure Polymerization of Furan | <div><div><div><p>Carbon nanothreads, which are unique one-dimensional sp3-rich polymers, combine high tensile strength with flexibility owing to subnanometer widths and diamond-like cores. These extended carbon solids are constructed through pressure-induced polymerization of sp2 molecules such as benzene. Whereas a few examples of carbon nanothreads have been reported, the need for high onset pressures ( ≥ 17 GPa) to synthesize them precludes scalability and limits scope. Herein, we report the scalable synthesis of carbon nanothreads based on molecular furan, which can be achieved through ambient temperature pressure-induced polymerization with an onset reaction pressure of only 10 GPa due to its lessened aromaticity relative to other molecular precursors. When slowly compressed to 15 GPa and gradually decompressed to 1.5 GPa, a sharp six-fold diffraction pattern is observed in situ, indicating a well‐ordered crystalline material formed from liquid furan. Single-crystal X-ray diffraction of the reaction product exhibits three distinct d-spacings from 4.75 to 4.9 Å, whose size, angular spacing, and degree of anisotropy are consistent with our atomistic simulations for crystals of furan nanothreads. Further evidence for polymerization was obtained by powder XRD and Raman/IR spectroscopy. Comparison of the IR spectra with computed vibrational modes provides identification of spectral features characteristic of specific nanothreads, namely syn, anti, and syn/anti configurations. Furan therefore presents a strategic entry toward scalable carbon nanothreads.</p></div></div></div> | Steven Huss; Sikai Wu; Bo Chen; Tao Wang; Margaret Gerthoffer; Roald Hoffmann; Vincent Crespi; John Badding; Elizabeth Elacqua | Organic Polymers; Polymerization (Polymers); Polymer scaffolds | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b84bb8c1a275a3db24a/original/scalable-synthesis-of-crystalline-one-dimensional-carbon-nanothreads-through-modest-pressure-polymerization-of-furan.pdf |
6241a102d6d3ed40f2a24c15 | 10.26434/chemrxiv-2022-cvmqf | Carboxylate catalyzed isomerization of β,γ-unsaturated NAC thioesters | We demonstrate herein the capacity of simple carboxylate salts – tetrametylammo-nium and tetramethylguanidinium pivalate – to act as catalysts in the isomerization of β,γ-unsaturated thioesters to α,β-unsaturated thioesters. The carboxylate catalysts gave reaction rates comparable to those obtained with DBU, but with fewer side reactions. The reaction exhibits a normal secondary kinetic isotope effect (k1H/k1D = 1.065±0.026) with a β,γ-deuterated substrate. Computational analysis of the mechanism provides a similar value (k1H/k1D = 1.05) with a mechanism where -reprotonation of the enolate intermediate is rate determining.We demonstrate herein the capacity of simple carboxylate salts – tetrametylammo-nium and tetramethylguanidinium pivalate – to act as catalysts in the isomerization of β,γ-unsaturated thioesters to α,β-unsaturated thioesters. The carboxylate catalysts gave reaction rates comparable to those obtained with DBU, but with fewer side reactions. The reaction exhibits a normal secondary kinetic isotope effect (k1H/k1D = 1.065±0.026) with a deuterated substrate. Computational analysis of the mechanism provides a similar value (k1H/k1D = 1.05) with a mechanism where γ-reprotonation of the enolate intermediate is rate determining. | Saara Riuttamäki; Gergely Laczko; Adam Madarasz; Tamas Földes; Imre Papai; Anton Bannykh; Petri Pihko | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Physical Organic Chemistry; Theory - Computational; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6241a102d6d3ed40f2a24c15/original/carboxylate-catalyzed-isomerization-of-unsaturated-nac-thioesters.pdf |
65e213db9138d23161709107 | 10.26434/chemrxiv-2024-0bqpc-v2 | Domain Orientation and Molecular Ordering in Thin Films of Small Molecule Donor for Organic Photovoltaics | The relationship between the nanomorphology and the charge transport characteristics in solution-processed organic thin films has been the focus of extensive research, as it is key to the further advancement of organic photovoltaics. Understanding the nanostructured domains and their dependence on the applied thermal annealing conditions is one crucial challenge. Here, the conjugated small-molecule donor p-DTS(FBTTh2)2 is used as a model system to demonstrate how isothermal annealing alone, without addition of any processable additives during solution casting, leads to a high ordering of domain structures. Using scanning transmission X-ray microspectroscopy (STXM), the domain structures are probed at the resonance energy of 284.7 eV corresponding to the C1s to Pi* transition. The STXM data analysis reveals the in-plane orientation of the conjugated backbone comprising the heterocyclic aromatic compounds dithienosilole (DTS), bithiophene (BT), and fluorobenzothiadiazole (FBT). The analysis further exhibits the presence of ordered domains accompanied by the disordered boundaries in thin films where the increase in the domain sizes and the high degree of molecular order (anisotropy) is associated to the relatively slow crystallization dynamics of p-DTS(FBTTh2)2 molecules during isothermal annealing at 90 °C. The analysis of the out-of-plane component of the directed resonance intensity shows deviations in the local out-of-plane tilt angles to the lower values, for the most ordered regions in the thin film, suggesting the more out-of-plane orientation of Pi* resonance. These results manifest a promising role of STXM technique in enhancing the knowledge of domain structures in small molecule organic semiconductors. | Nilesh Patil; Benjamin Watts; Leander Michels; Raf Claessens; David Kleiven; Eirik Torbjørn Bakken Skjønsfjell; Niko Van den Brande; Bruno Van Mele; Dag Werner Breiby | Materials Science; Nanoscience; Energy; Thin Films; Energy Storage; Photovoltaics | CC BY NC 4.0 | CHEMRXIV | 2024-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e213db9138d23161709107/original/domain-orientation-and-molecular-ordering-in-thin-films-of-small-molecule-donor-for-organic-photovoltaics.pdf |
64f1e7a03fdae147fa448937 | 10.26434/chemrxiv-2023-hjsx5 | Iron-Catalyzed Asymmetric Csp3–H/Csp3–H Coupling：Improve the Chirality Induction by Mechanochemical Liquid-Assisted Grinding | The iron-catalyzed asymmetric oxidative coupling is a challenging transformation that is typically restricted to naphthol substrates (Csp2–H) with carefully designed chiral ligands. Herein, we established a mechanochemical protocol for iron-catalyzed asymmetric Csp3–H/ Csp3–H coupling between glycines and β-ketoesters. By using size-tunable liquid additives via non-covalent bond interaction with simply designed chiral salen ligands and substrates under mechanochemical treatment, it is possible to improve the asymmetric induction and offer a variety of structurally diverse α-amino acid derivatives in high enantiopurity. Mechanistic study revealed that the iminium ion derived from acid assisted aerobic oxidation of glycine ester was the key intermediate of the reaction, and the liquid additive t-BuOH act both as a stabilizer for the iminium ion via N–H···O interaction and as an assistant for enantio-control. Moreover, a safer, cleaner, and more energy-conservation route via mechanochemical accelerated aging was first disclosed for this asymmetric Csp3–H/ Csp3–H coupling reaction. | Ping Ying; Tao Ying; Hong Chen; Keyu Xiang; Weike Su; Jingbo Yu | Organic Chemistry; Catalysis; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Stereochemistry | CC BY NC 4.0 | CHEMRXIV | 2023-09-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f1e7a03fdae147fa448937/original/iron-catalyzed-asymmetric-csp3-h-csp3-h-coupling-improve-the-chirality-induction-by-mechanochemical-liquid-assisted-grinding.pdf |
65089d5d99918fe53730c955 | 10.26434/chemrxiv-2023-v3v1x | Electron beam assisted zinc nanocrystal growth from ZnO nanorod | Here, we investigate room temperature in-situ zinc nanocrystal growth from single crystalline [001] ZnO nanorods by high resolution transmission electron microscopy (HRTEM) and put forward a possible mechanism of the nanocrystal formation. A time dependent exposure of ZnO nanorods under electron beam shows formation of crystalline zinc layers and successive deterioration of wurtzite crystallinity in the nanorods. It is interpreted that shrinking size of ZnO reduces zinc and oxygen vacancy formation energy at the ZnO surfaces which may favor Schottky defect generation by simultaneous creation of zinc and oxygen vacancies during electron and ZnO atom interaction. This degrades ZnO nanorod crystallinity followed by zinc nanocrystal formation. | Moumita Ghosh; Michael Seibt | Materials Science; Nanostructured Materials - Materials | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65089d5d99918fe53730c955/original/electron-beam-assisted-zinc-nanocrystal-growth-from-zn-o-nanorod.pdf |
65248efabda59ceb9a345314 | 10.26434/chemrxiv-2023-jhhm2 | Wavelength Tunable Infrared Perfect Absorption in Plasmonic Nanocrystal Monolayers | The ability to efficiently absorb light in ultrathin subwavelength) layers is essential for modern electro-optic devices, including detectors, sensors, and nonlinear modulators. Tailoring these ultrathin films’ spectral, spatial, and polarimetric properties is highly desirable for many, if not all, of the above applications. Doing so, however, often requires costly lithographic techniques or exotic materials, limiting scalability. Here we propose, demonstrate, and analyze a mid-infrared absorber architecture leveraging
monolayer films of nano-plasmonic colloidal tin-doped indium oxide nanocrystals (ITO NCs). We fabricate a series of ITO NC monolayer films using the liquid-air interface method; by synthetically varying the Sn dopant concentration in the NCs, we achieve spectrally selective perfect absorption tunable between wavelengths of two and five micrometers. We achieve monolayer thickness-controlled coupling strength tuning by varying NC size, allowing access to different coupling regimes. Furthermore, we synthesize a bilayer film that enables broadband absorption covering the entire mid-wave IR region (λ = 3−5 μm). With perfect absorption in monolayer films only hundredths of a wavelength in thickness, we demonstrate a scalable platform enabling strong light-matter interaction, with potential applications for molecular detection and ultrafast nonlinear optical applications. | Woo Je Chang; Zarko Sakotic; Alexander Ware; Allison M. Green; Benjamin J. Roman; Kihoon Kim; Thomas M. Truskett; Daniel Wasserman; Delia J. Milliron | Physical Chemistry; Nanoscience; Nanodevices; Optics | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65248efabda59ceb9a345314/original/wavelength-tunable-infrared-perfect-absorption-in-plasmonic-nanocrystal-monolayers.pdf |
63dc191a805bad91da1085fd | 10.26434/chemrxiv-2023-x86xp | Single-Shot Flow Synthesis of D-Proteins for Mirror-Image Phage Display | Mirror-image biological systems have the potential for broad-reaching impact in health and diagnostics, but their study has been greatly limited by the lack of routine access to synthetic D-proteins. We demonstrate that automated fast flow peptide synthesis (AFPS) can reliably produce novel mirror-image protein targets without prior sequence engineering. We synthesized 12 D-proteins, along with their L-counterparts. All 24 synthetic proteins were folded into active structures in vitro, and characterized using biochemical and biophysical techniques. From these chiral protein pairs, we chose MDM2 and CHIP to carry forward into mirror-image phage display screens, and identified macrocyclic D-peptides that bind the recombinant targets. We report 6 mirror-image peptide ligands with unique binding modes: three to MDM2, and three to CHIP, each confirmed with X-ray co-crystal structures. Reliable production of mirror-image proteins with AFPS stands to enable not only the discovery of D-peptide drug leads, but to the study of mirror-image biological systems more broadly. | Alex J. Callahan; Satish Gandhesiri; Tara L. Travaline; Lia Lozano Salazar; Stephanie Hanna; Yen-Chun Lee; Kunhua Li; Olena S. Tokareva; Jean-Marie Swiecicki; Andrei Loas; Gregory L. Verdine; John H. McGee; Bradley L. Pentelute | Biological and Medicinal Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Bioengineering and Biotechnology; Drug Discovery and Drug Delivery Systems; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63dc191a805bad91da1085fd/original/single-shot-flow-synthesis-of-d-proteins-for-mirror-image-phage-display.pdf |
668fff1d5101a2ffa8172aea | 10.26434/chemrxiv-2024-h7173 | Different photo-dissociation mechanisms in Fe(CO)5 and Cr(CO)6 evidenced with femtosecond valence photoelectron spectroscopy and excited-state molecular dynamics simulations | Measured and calculated time-resolved photoelectron spectra and excited-state molecular dynamics simulations of photoexcited gas phase Fe(CO)5 and Cr(CO)6 are presented. Samples were excited with 266 nm pump pulses and probed with 23 eV photons from a femtosecond high- order harmonic generation source. Photoelectron intensities are seen to blue-shift as a function of time from binding energies characteristic of bound electronic excited states via dissociated-state energies towards the energies of the dissociated species for both Fe(CO)5 and Cr(CO)6 but differences are apparent. The excited-state and dissociation dynamics are found to be faster in Cr(CO)6 because repopulation from bound excited to dissociative excited states is faster. This may be due to a stronger coupling between bound and dissociative states in Cr(CO)6, a notion supported by the observation that the manifolds of bound and dissociative states overlap in a narrow energy range in this system. | Henning Schröder; Michael Coates; Raphael Jay; Ambar Banerjee; Nomi Sorgenfrei; Christian Weniger; Rolf Mitzner; Alexander Föhlisch; Michael Odelius; Philippe Wernet | Physical Chemistry; Inorganic Chemistry; Organometallic Chemistry; Spectroscopy (Inorg.); Transition Metal Complexes (Organomet.); Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668fff1d5101a2ffa8172aea/original/different-photo-dissociation-mechanisms-in-fe-co-5-and-cr-co-6-evidenced-with-femtosecond-valence-photoelectron-spectroscopy-and-excited-state-molecular-dynamics-simulations.pdf |
61654532fb86192823f59ac5 | 10.26434/chemrxiv-2021-7qlf5-v4 | Linear Atomic Cluster Expansion Force Fields for
Organic Molecules: beyond RMSE | We demonstrate that fast and accurate linear force fields can be built for molecules using the Atomic Cluster Expansion (ACE) framework. The ACE models parametrize the Potential Energy Surface in terms of body ordered symmetric polynomials making the functional form reminiscent of traditional molecular mechanics force fields. We show that the 4 or 5-body ACE force fields improve on the accuracy of the empirical force fields by up to a factor of 10, reaching the accuracy typical of recently proposed machine learning based approaches.
We not only show state of the art accuracy and speed on the widely used MD17 and ISO17 benchmark datasets, but also go beyond RMSE by comparing a number of ML and empirical force fields to ACE on more important tasks such as normal mode prediction, high temperature molecular dynamics, dihedral torsional profile prediction and even bond breaking.
We also demonstrate the smoothness, transferability and extrapolation capabilities of ACE on a new challenging benchmark dataset comprising a potential energy surface of a flexible drug-like molecule. | David Peter Kovacs; Cas van der Oord; Jiri Kucera; Alice Allen; Daniel Cole; Christoph Ortner; Gabor Csanyi | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61654532fb86192823f59ac5/original/linear-atomic-cluster-expansion-force-fields-for-organic-molecules-beyond-rmse.pdf |
6601746766c1381729c64c01 | 10.26434/chemrxiv-2023-vwwt5-v2 | Template-dependent DNA ligation for the synthesis of modified oligonucleotides | Chemical modification of DNA is a common strategy to improve the properties of oligonucleotides, particularly for therapeutics and nanotechnology. Existing synthetic methods essentially rely on phosphoramidite chemistry or the polymerization of nucleoside triphosphates but are limited in terms of size, scalability, and sustainability. Herein, we report a robust alternative method for the de novo synthesis of modified oligonucleotides using template-dependent DNA ligation of shortmer fragments. Our approach is based on the fast and scaled accessibility of chemically modified shortmer monophosphates as substrates for the T3 DNA ligase. This method has shown high tolerance to chemical modifications, flexibility and overall efficiency, thereby granting access to an ultimately broad range of modified oligonucleotides of different lengths (20 → 120 nucleotides). We have applied this method to the synthesis of clinically relevant antisense drugs and diversely modified ultramers. Furthermore, the designed chemoenzymatic approach has great potential for diverse applications in therapeutics and biotechnology. | Nazarii Sabat; Andreas Stämpfli; Steven Hanlon; Serena Bisagni; Filippo Sladojevich; Kurt Püntener; Marcel Hollenstein | Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Bioorganic Chemistry; Biochemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6601746766c1381729c64c01/original/template-dependent-dna-ligation-for-the-synthesis-of-modified-oligonucleotides.pdf |
60c759844c891996fead4d9f | 10.26434/chemrxiv.14706036.v1 | The Control of pH and Ionic Strength Gradients on the Interaction of Low-Molecular-Weight Organic Acids and Siderophores | <div>A wide range of organic ligands are found in the rhizosphere. Two important groups are low-molecular-weight organic acids (LMWOAs) and siderophores. We know that LMWOAs and siderophores coexist in the rhizosphere and it has been proposed that they interact, but it is not clear what controls this. Such knowledge gaps undermine biofortification efforts. In this study test the hypothesis that pH and ionic strength gradients make it possible for LMWOAs and siderophores to function synergistically during micronutrient cycling in the rhizosphere.</div> | George Northover; Yiru Mao; MD Hanif; Salvador Blasco; Ramon Vilar; Enrique Garcia-España; Dominik Weiss | Environmental Science; Geochemistry; Soil Science; Bioinorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c759844c891996fead4d9f/original/the-control-of-p-h-and-ionic-strength-gradients-on-the-interaction-of-low-molecular-weight-organic-acids-and-siderophores.pdf |
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