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67063eaccec5d6c142aae619 | 10.26434/chemrxiv-2024-tpm29-v3 | Thermodynamics of Solids Including Anharmonicity Through Quasiparticle Theory | The quasiharmonic approximation (QHA) in combination with density-functional theory is the main computational method used to calculate thermodynamic properties under arbitrary temperature and pressure conditions. QHA can predict thermodynamic phase diagrams, elastic properties and temperature- and pressure-dependent equilibrium geometries, all of which are important in various fields of knowledge. The main drawbacks of QHA are that it makes spurious predictions for the volume and other properties in the high temperature limit due to its approximate treatment of anharmonicity, and that it is unable to model dynamically stabilized structures. In this work, we propose an extension to QHA that fixes these problems. Our approach is based on four ingredients: i) the calculation of the n-th order force constants using randomly displaced configurations and regularized regression, ii) the calculation of temperature-dependent effective harmonic frequencies omega(V,T) within the self-consistent harmonic approximation (SCHA), iii) Allen's quasiparticle (QP) theory, which allows the calculation of the anharmonic entropy from the effective frequencies, and iv) a simple Debye-like numerical model that enables the calculation of all other thermodynamic properties from the QP entropies. The proposed method is conceptually simple, with a computational complexity similar to QHA but requiring more supercell calculations. It allows incorporating anharmonic effects to any order. The predictions of the new method coincide with QHA in the low-temperature limit and eliminate the QHA blowout at high temperature, recovering the experimentally observed behavior of all thermodynamic properties tested. The performance of the new method is demonstrated by calculating the thermodynamic properties of geologically relevant minerals MgO and CaO. In addition, using cubic SrTiO3 as an example, we show that, unlike QHA, our method can also predict thermodynamic properties of dynamically stabilized phases. We expect this new method to be an important tool in geochemistry and materials discovery. | Ernesto Blancas; Álvaro Lobato; Fernando Izquierdo Ruiz; Antonio M. Márquez; J. Manuel Recio; Pinku Nath; José J. Plata; Alberto Otero de la Roza | Theoretical and Computational Chemistry; Materials Science; Geological Materials; Computational Chemistry and Modeling; Machine Learning; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-10-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67063eaccec5d6c142aae619/original/thermodynamics-of-solids-including-anharmonicity-through-quasiparticle-theory.pdf |
6772bbb881d2151a0263d14d | 10.26434/chemrxiv-2024-wsgjp | Photobiocatalytic Enantioselective C(sp3)–H Acylation Enabled by Thiamine-dependent Enzymes via Intermolecular Hydrogen Atom Transfer | Hydrogen atom transfer (HAT) constitutes a powerful mechanism exploited in biology and chemistry alike to functionalize otherwise inert C(sp3)–H bonds in organic molecules. Despite its synthetic potential, achieving stereocontrol in chemical HAT-mediated C–H functionalization transformations remains challenging. By merging the radical reactivity of thiamine (ThDP)-dependent enzymes with chemical hydrogen atom transfer, we report here a photobiocatalytic strategy for the enantioselective C(sp3)–H acylation of an organic substrate, a transformation not found in nature, nor currently attainable by chemical means. This method enables the direct functionalization of benzylic C(sp3)–H sites in a broad range of substrates to furnish valuable enantioenriched ketone motifs with good to high enantioselectivity (up to 96% e.e.). Mechanistic and reactivity studies support the involvement of radical species derived from the Breslow intermediate and C–H substrate, along with the critical role of the photocatalyst and hydrogen atom abstraction reagent for productive catalysis. This study illustrates the productive integration of ThDP-mediated biocatalysis with chemical HAT, expanding the range of asymmetric C(sp3)–H functionalization transformations accessible through biocatalysis. | Yen-Chu Lu; Ronald Adukure; Satyajit Roy; Derek Chien; Matthew McGill; Karl Scheidt; Rudi Fasan | Organic Chemistry; Catalysis; Biocatalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6772bbb881d2151a0263d14d/original/photobiocatalytic-enantioselective-c-sp3-h-acylation-enabled-by-thiamine-dependent-enzymes-via-intermolecular-hydrogen-atom-transfer.pdf |
669b8f9301103d79c5a8e62e | 10.26434/chemrxiv-2024-7jj5n | On the Origin of Electrocatalytic Selectivity during the Oxygen Reduction Reaction on Au(111) | A puzzling observation during the oxygen reduction reaction (ORR) on weak- binding electrodes such as Au is the preference to form hydrogen peroxide (H2O2), instead of the thermodynamically favored water product. This selectivity cannot be explained on the basis of thermodynamic reaction models that simply assume a series of proton-coupled electron transfers (PCETs). Here, we use ab initio molecular dynamics along with umbrella sampling to obtain free energy profiles for competing key ORR steps on Au(111). Our comparison includes not only PCETs, but also “chemical” reaction steps that do not include an explicit faradaic charge transfer, such as desorption or surface dissociation. This allows to explore favorable reaction paths, while varying the capacitive charging to represent realistic ORR potentials. Our results show that all reaction steps competing with H2O2 formation have sizeable kinetic barriers and are thus prohibited, even though they may be thermodynamically favored. We find that this situation does not change under more reducing conditions and specifically determine the “nobleness” of Au as playing a decisive role in preventing O-O bond scission. It is thus not the applied potential, but the underlying chemistry that drives the ORR selectivity. Our study overall further highlights the kinetic competition between PCET and non-PCET steps that cannot be resolved via simple Brønsted-Evans-Polanyi scaling relations. | Elias Diesen; Alexandra M. Dudzinski; Karsten Reuter; Vanessa Jane Bukas | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Theory - Computational; Electrocatalysis | CC BY 4.0 | CHEMRXIV | 2024-07-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669b8f9301103d79c5a8e62e/original/on-the-origin-of-electrocatalytic-selectivity-during-the-oxygen-reduction-reaction-on-au-111.pdf |
60c73d939abda25cb7f8b72a | 10.26434/chemrxiv.5944228.v1 | Understanding the Capacity Loss in LNMO-LTO Lithium-Ion Cells at Ambient and Elevated Temperatures | The high voltage spinel LiNi<sub>0.5</sub>Mn<sub>1.5</sub>O<sub>4</sub> (LNMO) is an attractive positive electrode due to its operating voltage around 4.7 V (vs Li/Li<sup>+</sup>) and high power capability. However, problems including electrolyte decomposition at high voltage and transition metal dissolution, especially at elevated temperatures, have limited its potential use in practical full cells. In this paper, a fundamental study for LiNi<sub>0.5</sub>Mn<sub>1.5</sub>O<sub>4</sub> || Li<sub>4</sub>Ti<sub>5</sub>O<sub>12</sub> (LTO) full cells has been performed to understand the effect of different capacity fading mechanisms contributing to overall cell failure. Electrochemical characterization of cells in different configurations (regular full cells, back-to-back pseudo-full cells and 3-electrode full cells) combined with an intermittent current interruption technique have been performed. Capacity fade in the full cell configuration was mainly due to progressively limited lithiation of electrodes caused by a more severe degree of parasitic reactions at the LTO electrode, while the contributions from active mass loss from LNMO or increases in internal cell resistance were minor. Comparison of cell formats constructed with and without the possibility of cross-talk indicate that the parasitic reactions on LTO occur because of the transfer of reaction products from the LNMO side. The efficiency of LTO is more sensitive to temperature causing a dramatic increase in the fading rate at 55 °C. These observations show how important the electrode interactions (cross-talk) can be for the overall cell behaviour. Additionally, internal resistance measurements showed that the positive electrode was mainly responsible for the increase of resistance over cycling, especially at 55 °C. Surface characterization showed that LNMO surface layers were relatively thin when compared to the SEI on LTO. The SEI on LTO does not contribute significantly to overall cell resistance even though these films are relatively thick. XANES measurements showed that the Mn and Ni observed on the anode were not in metallic state; the presence of elemental metals in the SEI is therefore not implicated in the observed fading mechanism through a simple reduction process of migrated metal cations.<br /> | Burak Aktekin; Matthew J. Lacey; Tim Nordh; Reza Younesi; Carl Tengstedt; Wolfgang Zipprich; Daniel Brandell; Kristina Edström | Electrochemistry; Solid State Chemistry; Spectroscopy (Inorg.); Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2018-03-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d939abda25cb7f8b72a/original/understanding-the-capacity-loss-in-lnmo-lto-lithium-ion-cells-at-ambient-and-elevated-temperatures.pdf |
67cae93b6dde43c908ea85ff | 10.26434/chemrxiv-2025-5k8qx | Structural transitions at the bilayer graphene–methanol interface from ab initio molecular dynamics | The precise tailoring of the atomic architecture of 2D carbon-based materials, which results in the modulation of their physical properties, promises to open new pathways for the design of technological devices in electronics, spintronics, and energy storage. High-pressure conditions can lead to the synthesis of complex materials starting from multi-layer graphene, often relying on chemical transformations at the interface between carbon and pressure-transmitting media like water or alcohol. Unfortunately, the experimental characterization of molecular-scale mechanisms at interfaces is very challenging. On the other side, the sheer cost of ab initio simulations strongly limited, so far, the computational works in literature to simplified models that, often, do not capture the complexity of the materials and finite-temperature effects. In this work, we provide for the first time an extensive computational study of complex, realistic models of bilayer graphene-methanol interfaces at high pressure and finite temperature. Our simulations allow to gain fundamental insight on several questions raised from previous experimental works about structural, electronic and reactivity properties of this challenging material. The exploitation of state-of-the-art enhanced sampling techniques combined with topological electronic descriptors allowed to characterize barrier activated functionalization processes, unveiling a major catalytic effect of carbon defects and pressure towards sp3 formation. | Flavio Siro Brigiano; Thomas Thevenet; Alexis Markovits; Julia Contreras Garcia; Alfonso San Miguel; Fabio Pietrucci | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2025-03-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67cae93b6dde43c908ea85ff/original/structural-transitions-at-the-bilayer-graphene-methanol-interface-from-ab-initio-molecular-dynamics.pdf |
60c7447e567dfe37feec42cf | 10.26434/chemrxiv.7851461.v4 | Highly proton conductive membranes based on carboxylated cellulose nanofibres and their performance in proton exchange membrane fuel cells | <p>The performance of thin carboxylated cellulose nanofiber-based (CNF) membranes as proton exchange membranes in fuel cells has been measured in-situ as a function of CNF surface charge density (600 and 1550 µmol g<sup>-1</sup>), counterion (H<sup>+</sup>or Na<sup>+</sup>), membrane thickness and fuel cell relative humidity (RH 55 to 95 %). The structural evolution of the membranes as a function of RH, as measured by Small Angle X-ray scattering, shows that water channels are formed only above 75 % RH. The amount of absorbed water was shown to depend on the membrane surface charge and counter ions (Na<sup>+</sup>or H<sup>+</sup>). The high affinity of CNF for water and the high aspect ratio of the nanofibers, together with a well-defined and homogenous membrane structure, ensures a proton conductivity exceeding 1 mS cm<sup>-1</sup>at 30 °C between 65 and 95 % RH. This is two orders of magnitude larger than previously reported values for cellulose materials and only one order of magnitude lower than Nafion 212. Moreover, the CNF membranes are characterized by a lower hydrogen crossover than Nafion, despite being ≈ 30 % thinner. Thanks to their environmental compatibility and promising fuel cell performance the CNF membranes should be considered for new generation proton exchange membrane fuel cells.</p> | Valentina Guccini; Annika Carlson; Shun Yu; Göran Lindbergh; Rakel Wreland Lindström; Germán Salazar-Alvarez | Nanostructured Materials - Materials; Fuel Cells | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7447e567dfe37feec42cf/original/highly-proton-conductive-membranes-based-on-carboxylated-cellulose-nanofibres-and-their-performance-in-proton-exchange-membrane-fuel-cells.pdf |
60c751574c89196232ad3f27 | 10.26434/chemrxiv.13154147.v1 | Saturation Transfer Difference NMR Spectroscopy Using Glycopolymers | <p>We report the use of Saturation Transfer Difference (STD) NMR spectroscopy to observe the interaction of various phenylboronic acids (PBAs) with synthetic glycopolymers presenting galactose and glucose. After optimizing experimental parameters to maximize spin diffusion, the binding of boronic acids to the glycopolymers was examined using STD NMR. Efficient amplification factor build-up curves which were used to generate an epitope map for the boronic acid binding to the glycopolymers. STD-NMR was also used to detect the interaction between indole and a galactosylated glycopolymer, providing an indole-based view of this C-H – π interaction.</p> | janet muzulu; Amit Basu | Organic Polymers | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751574c89196232ad3f27/original/saturation-transfer-difference-nmr-spectroscopy-using-glycopolymers.pdf |
611909b730231a8bfd0ac45e | 10.26434/chemrxiv-2021-hrlf1 | Boosting the Efficiency and Stability of Blue TADF Emitters by Deuteration | Deep-blue organic light-emitting diodes (OLEDs) with both high efficiency and stability remain exclusive in scientific literatures after decades of research. A key reason is the chemical bond dissociation through conical intersections between potential energy surfaces (PESs) of energetically-hot excited states and dissociative states. Here, we report a deuteration strategy to stabilize blue thermally activated delayed fluorescence (TADF) emitters. It is unveiled that deuteration would lower high-frequency vibrations to create shallower PESs in both ground and excited states, energetically retarding the cross of the conical intersection point in dissociative process and alleviate vibrational coupling to eliminate nonradiative decay. With a deuterated blue TADF compound, namely 2,3,4,5,6-pentakis(9H-carbazol-9-yl-d8) benzonitrile, as the sensitizer, a deep-blue OLED simultaneously achieves a peak external quantum efficiency of 30.3%, a Commission Internationale de L’Eclairage coordinate y value (CIEy) of 0.17, and a superb LT80 (time to 80% of initial luminance) of 227 h at 1000 cd/m2. And a blue OLED with a CIEy~0.19 shows an even longer LT80 of 456 h at 1000 cd/m2.
| Tianyu Huang; Dongdong Zhang; Ge Zhan; Qi Wang; Guomeng Li; Xiangchen Hong; Ziyang Liu; Lian Duan | Physical Chemistry; Materials Science; Optical Materials; Photochemistry (Physical Chem.); Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2021-08-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/611909b730231a8bfd0ac45e/original/boosting-the-efficiency-and-stability-of-blue-tadf-emitters-by-deuteration.pdf |
64274e26db1a20696e51ab8d | 10.26434/chemrxiv-2023-0j38z | Towards exploring the activity landscape of peptide datasets using MAP4 fingerprint | Peptides are a re-emerged strategy to fight a plethora of diseases and their utility has been expanded to new areas. Now sequence-based peptide design opens up new possibilities to develop peptidic molecular entities. However, its methodological limitations (e.g., its inefficiency in designing large peptides and that do not allow the analysis of post-traductional modification) limit their applicability domain. In contrast, ligand-based molecular design approaches have demonstrated their extensive applicability domain, although the peptide design-based in this method continues been not exploited. The main limitation has been the complex molecular structure of peptides, which has not been studied using classical fingerprints tuned for small organic compounds. Towards this end, MAP4 is a recently developed universal fingerprint that allows quantifying the sequence/structure diversity of natural products or peptides. As part of the peptide design, there is a current trend to develop predictive models which are founded on the available structure-activity data available. Before developing such models, it is essential to characterize in detail the structure-activity relationship and identify if any activity cliffs: subtle structural modifications that have a large and unexpected effect on the biological activity. In this study, we map the structure-activity landscape of an exemplary dataset with 165 peptides (anti-methicillin-resistant Staphylococcus aureus peptides) using a similarity metric based on MAP4 fingerprint. Specifically, we characterized the activity landscape of this data set, and we identified key amino acids (AAs) and structural motifs that play a key role in the activity of the anti-methicillin-resistant Staphylococcus aureus peptides. To the best of our knowledge, this is the first chemoinformatics approach to systematically explore the activity landscape of peptides emphasizing the quantification of the structural similarity. The approach is general and can be extended to analyze the presence of activity cliffs in any set of peptides. Identifying activity cliffs has practical implications during the development of predictive models. | Edgar López-López; Oscar Robles; Fabien Plisson; José L. Medina-Franco | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-04-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64274e26db1a20696e51ab8d/original/towards-exploring-the-activity-landscape-of-peptide-datasets-using-map4-fingerprint.pdf |
60c749044c891947f7ad2ffd | 10.26434/chemrxiv.12012411.v1 | Ni(I)-Alkyl Complexes Bearing Phenanthroline Ligands: Experimental Evidence for CO2 Insertion at Ni(I) Centers | ABSTRACT: Although the catalytic carboxylation of unactivated alkyl electrophiles has reached remarkable levels of sophistication, the intermediacy of (phenanthroline)Ni(I)-alkyl species – complexes proposed in numerous Ni-catalyzed reductive cross-coupling reactions – has been subject to speculation. Herein, we report the synthesis of such elusive (phenanthroline)Ni(I) species and their reactivity with CO2, allowing us to address a long-standing challenge related to metal-catalyzed carboxylation reactions. <div>
</div> | Rosie Somerville; Carlota Odena; Marc Obst; Nilay Hazari; Kathrin Hopmann; Ruben Martin | Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749044c891947f7ad2ffd/original/ni-i-alkyl-complexes-bearing-phenanthroline-ligands-experimental-evidence-for-co2-insertion-at-ni-i-centers.pdf |
64e6056a79853bbd78421e53 | 10.26434/chemrxiv-2023-hgsql | Navigating the Chemical Space and Chemical Multiverse of a Unified Latin American Natural Product Database: LANaPDB | The number of databases of natural products (NPs) have increased substantially. Latin America is extraordinarily rich in biodiversity enabling the identification of novel NPs, which has encouraged both the development of databases and the implementation of those that are being created or are under development. In a collective effort from several Latin American countries, herein we introduce the first version of Latin American Natural Products Database (LANaPDB), a public compound collection that gathers the chemical information of NPs contained in diverse databases from this geographical region. The current version of LANaPD unifies the information from six countries and contains 12,959 chemical structures. The structural classification showed that the most abundant compounds are the terpenoids 63.2%, phenylpropanoids 18% and the alkaloids 11.8%. From the analysis of the distribution of properties of pharmaceutical interest, it was observed that many LaNaPDB compounds satisfy some drug-like rules of thumb for physicochemical properties. The concept of the chemical multiverse was employed to generate multiple chemical spaces from two different fingerprints and two dimensionality reduction techniques. Comparing LaNaPDB with FDA-approved drugs and the major open-access repository of NPs, COCONUT it was concluded that the chemical space covered by LaNaPDB completely overlaps with COCONUT and in some regions with FDA-approved drugs. LANaPD will be updated adding more compounds from each database plus the addition of databases from other Latin American countries. The database is freely available at https://github.com/alexgoga21/LaNaPDB. | Alejandro Gómez-García; Daniel A. Acuña Jiménez; William J. Zamora; Haruna L. Barazorda-Ccahuana; Miguel Á. Chávez-Fumagalli; Marilia Valli; Adriano D. Andricopulo; Vanderlan da S. Bolzani; Dionisio A. Olmedo; Pablo N. Solís; Marvin J. Núñez; Johny R. Rodríguez Pérez; Hoover A. Valencia Sánchez; Héctor F. Cortés Hernández; José L. Medina-Franco | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Agriculture and Food Chemistry; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-08-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e6056a79853bbd78421e53/original/navigating-the-chemical-space-and-chemical-multiverse-of-a-unified-latin-american-natural-product-database-la-na-pdb.pdf |
60c75944567dfe69ceec69ee | 10.26434/chemrxiv.13502571.v3 | Activation Energy and NBO Interaction Approaches to Torquoselectivity and its Dependence on the Conformational Profile of the Substituent | The torquoselectivity of ring opening of 3-fluoromethylcyclobutenes, 2-fluoromethyl-3-oxetenes
and perfluoro-3-methyl-cyclobutene have been studied at the MP2/cc-pVTZ level
of theory and the results analysed by using the activation energy approach and
also the NBO interactions of the breaking ring bond with the substituent bond.
The outward or inward opening that has lower activation energy in the activation
energy approach or larger interaction in the NBO approach constitutes the
preferred mode. The CHF<sub>2</sub> and CH<sub>2</sub>F substituents on
cyclobutene and oxetene can adopt three distinct conformations with respect to
the cleaving ring bond. It has been discovered that each conformer exhibits a distinct
level of torquoselectivity and some higher lying conformer may even significantly
contribute to the overall selectivity. The conformational profile of the
substituent, therefore, is recommended for taking into consideration in any serious
treatment of the subject. The experimental selectivity, if otherwise, is likely
to be a consequence of secondary reactions such as the reaction equilibration,
which honours the relative thermodynamic stabilities of the ring opened
products. | Veejendra Yadav | Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75944567dfe69ceec69ee/original/activation-energy-and-nbo-interaction-approaches-to-torquoselectivity-and-its-dependence-on-the-conformational-profile-of-the-substituent.pdf |
62feb60cf07ee16fd9e8e054 | 10.26434/chemrxiv-2022-7hq66 | Radical-Polar Crossover Catalysis with a d0 Metal Enabled by a Redox-Active Ligand | Radical-polar crossover mechanisms are invoked in numerous late transition metal and photocatalyzed reactions. To the best of our knowledge, reductive radical-polar crossover mechanisms are not invoked for group 3 early transition metals due to their propensity to exist in high oxidation states. Through use of a redox-active (tris)amido ligand we have accessed this mechanism for use with early transition metals. This mechanism is showcased through enabling product formation for a wide variety of elimination products from -halo substituted benzylic bromides. The mechanism of this new type of reactivi-ty with Sc is explored and Hammett analysis reveals an anionic intermediate. The wide functional group tolerance of this reaction is also demonstrated. | Joshua Gavin; Roman Belli; Courtney Roberts | Organometallic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62feb60cf07ee16fd9e8e054/original/radical-polar-crossover-catalysis-with-a-d0-metal-enabled-by-a-redox-active-ligand.pdf |
6134fad4fc08e350a88b374c | 10.26434/chemrxiv-2021-jf8r2-v2 | Overcoming the Challenges towards Selective C(6)-H Alkylation of 2-Pyridone with Maleimide through Mn(I)-Catalyst: Migration of directing group through cleavage of C-N bond for the formation of all-carbon quaternary carbon center | An earth-abundant and inexpensive Mn(I)-catalyzed alkylation of 2-pyridone with maleimide has been reported for the first time, in contrast to previously reported Diels-alder product. The directing group was easily removed after functionalization. Notably, unexpected migration of pyridine ring has been discovered in presence of acetic acid, which also provides unique class of compounds with three different N-heterocycles with an all-carbon quaternary carbon center. Furthermore, single crystal X-ray and HRMS revealed a five-membered manganacycle intermediate. This methodology tolerates a wide variety of functional groups delivering the alkylated products in moderate to excellent yields. | Smruti Ranjan Mohanty; Namrata Prusty; Shyam Kumar Banjare; Tanmayee Nanda; Ponneri C. Ravikumar | Organic Chemistry; Catalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6134fad4fc08e350a88b374c/original/overcoming-the-challenges-towards-selective-c-6-h-alkylation-of-2-pyridone-with-maleimide-through-mn-i-catalyst-migration-of-directing-group-through-cleavage-of-c-n-bond-for-the-formation-of-all-carbon-quaternary-carbon-center.pdf |
65ad3f3f66c1381729f2c2c9 | 10.26434/chemrxiv-2024-twmpk | “Systems thinking encourages a safe space to offer different perspectives and insights”: Student perspectives and experiences with ST activities | Researchers and educators have been exploring systems thinking (ST) in chemistry education to better equip citizens for 21st century challenges; however, little is known about students’ perspectives and experiences. In this study, we investigated students’ perspectives of ST and their experiences with ST activities. We designed and implemented a ST intervention, performed individually and collaboratively, as well as follow up interviews. Twenty-four undergraduate and graduate students participated in this study and reported a variety of experiences and perspectives. For students’ experiences, we found that: (1) while collaborating, participants recognized and appreciated different perspectives, (2) participants included chemistry concepts and connections in their system maps despite having difficulties, (3) system maps emphasized problems/solutions and causes/effects and differed in terms of organization and intended purpose, and (4) limitations to system map construction included time, knowledge, and technology skills. Students also expressed positive perspectives of a ST approach based on their experience engaging with the ST intervention and believed a ST approach (1) is beneficial to learning, (2) captures interest and engagement, (3) allows perspectives to be shared and gained, and (4) provides personal, social, and professional relevance. Based on these findings, we suggest aspects to consider when planning and implementing ST activities and identify future research required to better understand the impacts of ST in chemistry education. | Alisha Renee Szozda; Zahra Lalani; Samira Behroozi; Peter G Mahaffy; Alison B. Flynn | Chemical Education | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ad3f3f66c1381729f2c2c9/original/systems-thinking-encourages-a-safe-space-to-offer-different-perspectives-and-insights-student-perspectives-and-experiences-with-st-activities.pdf |
65f01f6266c1381729d48f5a | 10.26434/chemrxiv-2024-62zmf | Accessing a Diverse Set of Functional Red-Light Photoswitches by Selective Copper-Catalyzed Indigo N-Arylation | The ability to correlate the structure of a molecule to its properties is the key to a rational and accelerated design of new functional compounds and materials. Taking photoswitches as an example, the thermal stability of meta-stable state is a crucial property that dictates their application in molecular systems. Indigos have recently emerged as an attractive motif for designing photoswitchable molecules due to their red-light addressability, which can be advantageous in biomedical and material applications. The absence of comprehensive synthetic techniques and a thorough understanding of the impact of structural factors on the photochemical and thermal properties of this widely available dye hinders its broad application. Herein, we report an efficient copper-catalyzed indigo N-arylation that enables the installation of a wide variety of aryl moieties carrying useful functional groups. The exclusive selectivity for mono-arylation likely originates from a bimetallic cooperative mechanism through a binuclear copper-indigo intermediate. Functional N-aryl-N′-alkylindigos were prepared and shown to photoisomerize efficiently under red light. Moreover, this design allows for the modulation of thermal half-lives through N-aryl substituents, while the N′-alkyl groups enable the independent attach-ment of functional moieties without affecting the photochromic properties. Strong correlation between the structure of N-aryl moiety and the thermal stability of the photogenerated Z-isomers was achieved by multivariate linear regression models obtained through a straightforward data-science workflow. This work thus builds an avenue leading to versatile red-light photoswitches and a general method for structure-property correlation that is expected to be broadly applicable to the design of photoresponsive molecules. | Amit K. Jaiswal; Priya Saha; Julong Jiang; Kimichi Suzuki; Anna Jasny; Bernd M. Schmidt; Satoshi Maeda; Stefan Hecht; Chung-Yang (Dennis) Huang | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f01f6266c1381729d48f5a/original/accessing-a-diverse-set-of-functional-red-light-photoswitches-by-selective-copper-catalyzed-indigo-n-arylation.pdf |
60c752fdbdbb89bc8ea3a3b1 | 10.26434/chemrxiv.13372475.v1 | Clustering of Synthetic Routes Using Tree Edit Distance | <div>We present a novel algorithm to compute the distance between synthesis routes based on a tree edit distance calculation. Such distances can be used to cluster synthesis routes from a retrosynthesis prediction tool. We show that the clustering of routes from a retrosynthesis analysis is performed in less than ten seconds on average, and only constitutes seven percent of the total time (prediction + clustering). Furthermore, we are able to show that representative routes from each cluster can be used to reduce the set of predicted routes. Finally, we show with a number of examples that the algorithm gives intuitive clusters that can be easily rationalized. The algorithm is included in the latest version of the open-source AiZynthFinder software.</div> | Samuel Genheden; Ola Engkvist; Esben Jannik Bjerrum | Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752fdbdbb89bc8ea3a3b1/original/clustering-of-synthetic-routes-using-tree-edit-distance.pdf |
60db7449bcab04720569bcde | 10.26434/chemrxiv-2021-mwk57 | A monoanionic pentadentate ligand platform for scandium-pnictogen multiple bonds | A new monoanionic pentadentate ligand is designed to accommodate Sc=E bonds (E = N, P). The imido complex is stable enough to isolate and characterize, and reacts rapidly with CO2. The phosphinidene, on the other hand, is highly reactive and induces C-C bond cleavage to yield a phosphido-pyridyl complex which also undergoes rapid reacton with CO2. | Evan Patrick; Yan Yang; Warren Piers; Laurent Maron; Benjamin Gelfand | Theoretical and Computational Chemistry; Inorganic Chemistry; Organometallic Chemistry; Bonding; Lanthanides and Actinides; Ligand Design | CC BY NC 4.0 | CHEMRXIV | 2021-06-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60db7449bcab04720569bcde/original/a-monoanionic-pentadentate-ligand-platform-for-scandium-pnictogen-multiple-bonds.pdf |
60c73fa1bb8c1a56a33d9bea | 10.26434/chemrxiv.7461569.v1 | Catalytic Hydrogenation of α,β-Unsaturated Carboxylic Acid Derivatives Using copper(I)/N-Heterocyclic Carbene Complexes | A simple and air-stable copper(I)/N-heterocyclic carbene complex enables the catalytic hydrogenation of hitherto unreactive enoates and enamides employing H2 as terminal reducing agent. This atom economic transformation replaces commonly employed hydrosilanes and can also be carried out in an asymmetric fashion.<br /><br /> | Birte Zimmermann; Johannes F. Teichert | Organic Synthesis and Reactions; Homogeneous Catalysis; Bond Activation; Catalysis; Coordination Chemistry (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2018-12-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73fa1bb8c1a56a33d9bea/original/catalytic-hydrogenation-of-unsaturated-carboxylic-acid-derivatives-using-copper-i-n-heterocyclic-carbene-complexes.pdf |
6604e9da9138d231617e483d | 10.26434/chemrxiv-2024-s9td8 | Molecular Ball Joints: Mechanochemical Perturbation of Bullvalene Hardy-Cope Rearrangements in Polymer Networks | The solution-state fluxional behavior of bullvalene, first investigated over 60 years ago, has fascinated physical organic and supramolecular chemists alike. Little effort, however, has been put into investigating bullvalene applications in the bulk, partially due to difficulties in characterizing such dynamic systems. To address this fundamental knowledge gap, herein we probe whether bullvalene Hardy-Cope rearrangements can be mechanically perturbed in bulk polymer networks. We first demonstrate the impact of bullvalene fluxionality in bulk thermoset elastomers using modulated differential scanning calorimetry; enhanced enthalpic relaxation events are observed in the non-reversing heat flow for bullvalene-containing materials relative to “static” control networks. Then, we use dynamic mechanical analysis to demonstrate that the activation barrier to glass transition is significantly elevated for bullvalene-containing materials (ca. 90 kcal/mol) relative to “static” control networks (ca. 50 kcal/mol). Furthermore, bullvalene rearrangements can be “mechanically activated” at low temperature in the glassy region; such behavior facilitates energy dissipation (at least ca. 3-fold increase in hysteresis energy) and polymer chain alignment to stiffen the material (at least ca. 2-fold increase in Young’s modulus) under load. Collectively, this work showcases bullvalene as a reversible chemical mechanophore in the modulation of viscoelastic behaviors. | Peiguan Sun; Meredith Pomfret; Matthew Elardo; Progyateg Chakma; Sheila Keating; Chuqiao Chen; Yunze Wu; Rowina Bell; Stuart Rowan; Matthew Golder | Organic Chemistry; Polymer Science; Organic Polymers | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6604e9da9138d231617e483d/original/molecular-ball-joints-mechanochemical-perturbation-of-bullvalene-hardy-cope-rearrangements-in-polymer-networks.pdf |
676094756dde43c9085fdf78 | 10.26434/chemrxiv-2024-hbbn1 | Repurposing Lateral Flow Assays as a Versatile and Rapid Characterization Tool for Bioconjugation of Nanoparticles | This study explores the use of lateral flow assays (LFAs), recognized for their simplicity and ease-of-use, as a tool for characterizing nanoparticles functionalized with various biomolecules (e.g., proteins, antibodies and nucleic acids). A half-strip model system was developed using ovalbumin (OVA) conjugated to gold nanoparticles (AuNPs). The characterization results obtained with LFAs were compared to those from traditional methods such as infrared spectroscopy and fluorescence labelling. The advantages of LFAs in characterizing such conjugated nanosystems were clearly demonstrated. The use of half-strip assays could not only confirm the presence of OVA on AuNPs but also enable the quantification of OVA bound per nanoparticle, offering a rapid and quantitative characterization method. Additionally, the assay showcased its versatility, as it was successfully applied to optimize the covalent coupling conditions of OVA on AuNPs, as well as to differentiate between covalently bound and adsorbed proteins. Furthermore, LFAs were employed to detect antibodies on functionalized nanoparticles, optimize their coupling to a newly developed organic coating, and confirm both the grafting of nucleic acids onto the surface and their pairing with complementary strands. These findings underscore the remarkable adaptability of LFAs for characterizing diverse nanoconjugates. Overall, LFAs stand out as a versatile and accessible tool for characterizing complex bioconjugated nanosystems, making them highly suitable for rapid Quality Control (QC) analysis and bioconjugation optimization. | Bryan Gosselin; Raphael Dutour; Ivan Jabin; Gilles Bruylants | Nanoscience; Plasmonic and Photonic Structures and Devices | CC BY NC 4.0 | CHEMRXIV | 2024-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676094756dde43c9085fdf78/original/repurposing-lateral-flow-assays-as-a-versatile-and-rapid-characterization-tool-for-bioconjugation-of-nanoparticles.pdf |
63791b42355119822d394a4e | 10.26434/chemrxiv-2022-fmwrk | Reclaiming Polycarbonate from Compact Discs and its Use in Synthesizing Hollow Micro Spheres by Electrospraying | This paper reports the use of polycarbonate reclaimed from compact disks for synthesis of hollow microspheres by electrospraying from solution. Compact disks are predominantly made up of polycarbonate and it is possible to reclaim the polycarbonate easily by using mechanical methods. The reclaimed polycarbonate has been subjected to GPC analysis and compared to virgin polycarbonate to ensure that no significant change in properties of virgin and reclaimed polycarbonate exist. Microspheres were synthesized by electrospraying the polycarbonate solution of varying concentrations which was then collected on a water bed. Evaporation of the tetrahydrofuran solvent from the polymer solution result in the formation of pores on the surface of the microspheres. Rotational rheometry has been used to study the effect of viscosity of the polycarbonate solution on the electrospraying process. Also, the pendant drop method has been used to analyze the surface tension of the polymer solution, and to correlate it to the effect that surface tension has on the polymer solution. Using this process, microspheres on 10μm diameter with pores of around 1μm have been synthesized. | Manoj Praharaj Bhatnagar | Polymer Science; Nanoscience; Organic Polymers; Nanofabrication | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63791b42355119822d394a4e/original/reclaiming-polycarbonate-from-compact-discs-and-its-use-in-synthesizing-hollow-micro-spheres-by-electrospraying.pdf |
6602e024e9ebbb4db995c81f | 10.26434/chemrxiv-2024-470n4 | Beyond Ridge Regression: Enhancing Distribution of Relaxation Times Deconvolution | The distribution of relaxation times (DRT) has emerged as a promising method for analyzing
electrochemical impedance spectroscopy (EIS) data. The standard approach for reconstructing the DRT
from measured impedances consists of regularized regression, which usually leverages the
Euclidean norm. In this work, we show for the first time that the 1-norm is often more accurate
than ridge regression and the infinity-norm. We also demonstrate that the 1-norm is more robust
against discontinuities in the DRT and outliers in the impedance data. Overall, this work is
expected to enhance regularized regression of non-parametric methods when analyzing EIS
spectra. | Baptiste Py; Francesco Ciucci | Energy; Energy Storage | CC BY 4.0 | CHEMRXIV | 2024-03-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6602e024e9ebbb4db995c81f/original/beyond-ridge-regression-enhancing-distribution-of-relaxation-times-deconvolution.pdf |
67ce1d9b6dde43c90834e2bd | 10.26434/chemrxiv-2025-cxwjt-v2 | Predicting Solubility and Size-Exclusivity Towards the Rational Design of Porous Liquid Solutions | Porous liquids are a sub-class of porous materials that combine permanent porosity, typically associated with solids, with the fluidity and fast mass-transfer capabilities of liquids, making them ideal candidates for gas storage and separation applications. One strategy to form porous liquids is the dissolution of discrete and permanently porous molecular species at relatively high concentrations in cavity-excluded solvents, thus introducing permanent porosity into the liquid in which it is dissolved and ensuring a solution of reasonable porosity is obtained. To access high-performance porous liquids for target applications, the selection of both the porous molecular species and the cavity-excluded solvent is key to ensuring the solvent is permanently excluded and the pore carrier is highly soluble. Finding new solvents that fit both these requirements is challenging, often resulting in a trial-and-error approach. While predictive data-driven models may be attractive, the youth of the porous liquid field currently limits the availability of data necessary to train robust models. Here, we present a computational workflow for the discovery of new porous liquid solutions combining solubility prediction software and a size-exclusivity prediction algorithm that correctly predicts size-exclusivity; this is followed by experimental validation with a representative system. Our workflow yielded size-excluded solvent and soluble porous organic cage pairs, leading to the realisation of a new porous liquid with enhanced methane uptake compared to previous systems discovered in a purely experimental high-throughput brute-force manner, highlighting the advantages of incorporating a computational workflow in the discovery of new porous liquids. | Austin Mroz; Benjamin Egleston; James Sherwood; Ruby Morel; Kim Jelfs; Rebecca Greenaway | Theoretical and Computational Chemistry; Materials Science | CC BY 4.0 | CHEMRXIV | 2025-03-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ce1d9b6dde43c90834e2bd/original/predicting-solubility-and-size-exclusivity-towards-the-rational-design-of-porous-liquid-solutions.pdf |
60c73d0c567dfe6144ec3581 | 10.26434/chemrxiv.5336200.v1 | Facile fabrication of marshmallow-like gels as flexible thermal insulators and liquid nitrogen retention materials: Application to a cryopreserved embryo container | <p>Low bulk density porous monoliths were prepared by
using two types of silicon alkoxide methyltrimethoxysilane (MTMS) and
dimethyldimethoxysilane (DMDMS) as precursors and controlling phase separation
under appropriate conditions. By changing the ratio of the aqueous solution to
the precursors in the starting composition, it was possible to control the
microstructure of the resulting porous monoliths or to prepare microparticles.
Those marshmallow-like monoliths with a skeleton diameter of a few micrometers
and pore diameter of several tens micrometers has high flexibility against
compression and bending, and shows low thermal conductivity of ~30 mW m<sup>−1</sup>
K<sup>−1</sup> at room temperature. We show that those materials can be used as
a simple cryopreserved embryo container like small dry shippers by packing gels
and adsorbing liquid nitrogen in a vacuum-insulated water bottle.</p> | Gen Hayase; Yasutaka Ohya | Elastic Materials; Hybrid Organic-Inorganic Materials | CC BY NC ND 4.0 | CHEMRXIV | 2017-11-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d0c567dfe6144ec3581/original/facile-fabrication-of-marshmallow-like-gels-as-flexible-thermal-insulators-and-liquid-nitrogen-retention-materials-application-to-a-cryopreserved-embryo-container.pdf |
65058b0eb6ab98a41c8a6f5f | 10.26434/chemrxiv-2023-zdpcs | Design of phenanthroline and diindolocarbazole based emitter for efficient upconversion of triplet excitons by improving rISC | There has been significant advancement in display technology in recent times. However, synthetic efforts toward designing more efficient emitters are still underway. TADF emitters offer the advantage of an all organic based design with IQEmax of 100%. To study the effect of phenanthroline-based moieties, we designed and synthesized two yellow-green thermally activated delayed fluorescent (TADF) emitters, DICz-DBPZ and DICz-DPPN. Due to structural variations associated with steric strain, the two emitters displayed different photophysical and organic light-emitting diode (OLED) performances. For DICz-DPPN, the absorption and emission maxima were recorded at 313-368 nm and 516 nm, respectively, while for DICz-DBPZ, they were observed at 311-393 nm and 559 nm. The DPPN-substituted TADF emitter had an EQE of 5.0% and color coordinates of (0.37, 0.53), whereas the DBPZ-substituted emitter displayed a high EQE of 15% with color coordinates of (0.47, 0.51). Due to the closed structure of DICz-DBPZ, thermal decomposition temperature occurred at 269oC as compared to 213oC for DICz-DPPN, which significantly influenced the difference in EQE between the two emitters. In order to simultaneously obtain high EQE and a long lifetime, this study offers an approach to synthesize yellow TADF emitters by utilizing a combination of diindolocarbazole (DICz) and 1,10-phenanthroline-5,6-diamine as a stable donor-acceptor. | Atul Chaskar; Gokul Ganesan; Farah Ansari; Vipin Kumar; Yi-Ting Chen; Guan-Yu Su; Prabhakar Chetti; Chih-Hao Chan | Organic Chemistry; Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65058b0eb6ab98a41c8a6f5f/original/design-of-phenanthroline-and-diindolocarbazole-based-emitter-for-efficient-upconversion-of-triplet-excitons-by-improving-r-isc.pdf |
62a22291f85b597f99033268 | 10.26434/chemrxiv-2022-gcz36 | Residue-specific high-resolution 17O solid-state NMR of peptides: multidimensional indirect 1H detection and magic-angle spinning | Oxygen is an integral component of proteins and nucleic acids, but remains sparsely studied in such samples because its only NMR active isotope, 17O, is a low sensitivity and resolution species. These properties are a consequence of its low natural abundance (0.039%) and the fact that 17O is a S = 5/2 nuclide with large quadrupolar couplings (6-11 MHz). In this work, we address these issues with efficient isotopic labeling, high magnetic fields, fast magic-angle spinning and indirect 1H detection. This combination of refinements, in conjunction with multidimensional heteronuclear correlation experiments, improves sensitivity and permits observation of oxygen sites specific to each amino acid residue in a model dipeptide sample in a manner consistent with the goal of high resolution. In particular, double-quantum cross-polarization at high sample spinning frequencies is found to provide efficient polarization transfer between 13C and 17O nuclei. Notably, the use of 17O as the initial source of polarization for experiments, as opposed to 1H, is found to be advantageous in terms of sensitivity per unit time due to the short 17O T1 relaxation. Additionally, the second-order quadrupolar broadening in the 17O dimension is averaged by incorporation of a low-power multiple-quantum sequence to yield sharp isotropic peaks. Comparison of isotropic and anisotropic 17O spectra allows extraction of quadrupolar parameters for each oxygen site. Finally, the high 17O resolution obtained is used in 3D experiments in combination with 13C polarization transfers and subsequent 1H detection to demonstrate the potential to determine sequential assignments and long range distance restraints. Collectively, these results suggest that 17O correlation spectroscopy can become an essential tool in the repertoire of techniques for biomolecular structure determination with the backbone 17O that has not yet been fully utilized. | Ivan Hung; Eric G. Keeler; Wenping Mao; Peter L. Gor'kov; Robert G. Griffin; Zhehong Gan | Physical Chemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a22291f85b597f99033268/original/residue-specific-high-resolution-17o-solid-state-nmr-of-peptides-multidimensional-indirect-1h-detection-and-magic-angle-spinning.pdf |
60c75214bdbb890ea4a3a1f0 | 10.26434/chemrxiv.13235348.v1 | 3D Fuzzy Graphene Microelectrode Array for Neurotransmitter Sensing at Sub-cellular Spatial Resolution | <div>Dopamine (DA) is a monoamine neurotransmitter involved in the modulation of various physiological brain functions, including learning, motivation, reward, and motor functions. The development of a high sensitivity real-time sensor for multi-site detection of DA with high spatial resolution has critical implications for both neuroscience and clinical communities to improve understanding and treatments of neurological and neuropsychiatric disorders. Here, we present high-surface area out-of-plane grown three-dimensional (3D) fuzzy graphene (3DFG) microelectrode arrays (MEAs) for highly selective, sensitive, and stable DA electrochemical sensing. 3DFG microelectrodes present a remarkable sensitivity to DA (2.87 ± 0.25 nA/nM, with</div><div>LOD of 990±15 pM), the highest reported for nanocarbon MEAs using Fast Scan Cyclic Voltammetry (FSCV). The high surface area of 3DFG allows for miniaturization of electrode down to 2 x 2 μm^2, without compromising the electrochemical performance. Moreover, 3DFG MEAs are electrochemically stable under 7.2 million scans of continuous FSCV cycling, present exceptional selectivity over the most common interferents in vitro with minimum fouling by electrochemical byproducts, and can discriminate DA and serotonin (5-HT) in response to the injection of their 50:50 mixture. These results highlight the potential of 3DFG MEAs as a promising platform for FSCV based multi-site detection of DA with high sensitivity, selectivity, and spatial resolution.</div> | Elisa Castagnola; Raghav Garg; Sahil Rastogi; Tzahi Cohen-Karni; Xinyan Tracy Cui | Nanostructured Materials - Materials; Electrochemical Analysis; Nanostructured Materials - Nanoscience; Sensors | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75214bdbb890ea4a3a1f0/original/3d-fuzzy-graphene-microelectrode-array-for-neurotransmitter-sensing-at-sub-cellular-spatial-resolution.pdf |
60c7535e469df4cdeff44d52 | 10.26434/chemrxiv.13482681.v1 | Gold-Catalyzed Carboamination of Allenes by Tertiary Amines Proceeding with Benzylic Group Migration | <p>Tertiary
amines bearing a benzyl-type group (CH<sub>2</sub>Ar) undergo Au(I)-catalyzed
intramolecular addition to allenes. A formal 1,3-transfer of the CH<sub>2</sub>Ar
group takes place during the cyclization. As demonstrated by both experimental
and DFT studies, these unprecedented intramolecular carboaminations involve two
consecutive [3,3] rearrangements via a dearomatized intermediate. Because of
the poor stability of the enamine products, protocols were developed to convert
them in situ to more stable polycyclic chiral compounds.</p> | Pierre Milcendeau; Vincent Gandon; Xavier Guinchard | Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7535e469df4cdeff44d52/original/gold-catalyzed-carboamination-of-allenes-by-tertiary-amines-proceeding-with-benzylic-group-migration.pdf |
60c73fc20f50db5eee395811 | 10.26434/chemrxiv.6450380.v2 | Femtosecond Pumping Rate Dependence of Fragmentation Mechanisms in Matrix-Assisted Laser Desorption Ionization | The fragmentation mechanisms of matrix-assisted laser desorption/ionization (MALDI) for femtosecond ultraviolet laser pulses in a transmission geometry are characterized on the basis of the well-known benzyltriphenylphosphonium (BTP) thermometer ion. We demonstrate that the survival yield of BTP approaches unity under these conditions, which suggests that a minimal amount of fragmentation is occurring. It is shown that, while the survival yield of BTP is insensitive to the fluence within the studied fluence range, the magnitude of fragmentation for the matrix increased notably with increasing fluence. While nonlinear absorption and ionization are expected to lead to large matrix fragmentation rates, the high BTP survival yields indicate a reduced amount of energy being transferred from the matrix to these BTP thermometer ions. The femtosecond ablation employed here results in increased heating rates and occurs within the fully stress-confinement regime, which minimizes the matrix-analyte interaction during the ablation event. This interpretation is supported by our finding that angiotensin was the largest biomolecule which could be routinely be measured with femtosecond pulses. The spatio-temporal overlap between a neutral biomolecule and matrix ions resulting from this process is too short to result in sufficient proton exchange for ionization.<br /> | Cornelius Pieterse; Frederik Busse; Friedjof Tellkamp; Wesley D. Robertson; R. J. Dwayne Miller | Imaging; Mass Spectrometry; Biophysical Chemistry; Photochemistry (Physical Chem.); Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2018-11-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73fc20f50db5eee395811/original/femtosecond-pumping-rate-dependence-of-fragmentation-mechanisms-in-matrix-assisted-laser-desorption-ionization.pdf |
62f234568dba6868e81ccadf | 10.26434/chemrxiv-2022-6ccfd-v2 | Tidying up the conformational ensemble of a disordered peptide by computational prediction of spectroscopic fingerprints | The most advanced structure prediction methods are powerless in exploring the conformational ensemble of disordered peptides and proteins and for this reason the "protein folding problem" remains unsolved.
We present a novel methodology that enables the accurate prediction of spectroscopic fingerprints (Circular Dichroism, Infrared, Raman, and Raman Optical Activity), and by this allows for "tidying up" the conformational ensembles of disordered peptides and disordered regions in proteins.
This concept is elaborated for and applied to a dodecapeptide, whose spectroscopic fingerprint is measured and theoretically predicted by means of enhanced-sampling Molecular Dynamics coupled with Quantum Mechanical calculations.
Following this approach, we demonstrate that peptides lacking a clear propensity for ordered secondary-structure motifs are not randomly, but only conditionally disordered.
This means that their conformational landscape, or phase-space, can be well represented by a basis-set of conformers including about 10 to 100 structures.
The implications of this finding have profound consequences both for the interpretation of experimental electronic and vibrational spectral features of peptides in solution and for the theoretical prediction of these features using accurate and computationally expensive techniques.
The here-derived methods and conclusions are expected to fundamentally impact the rationalization of so-far elusive structure-spectra relationships for disordered peptides and proteins, towards improved and versatile structure prediction methods. | Monika Michaelis; Lorenzo Cupellini; Carl Mensch; Carole C. Perry; Massimo Delle Piane; Lucio Colombi Ciacchi | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Physical and Chemical Properties; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2022-08-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f234568dba6868e81ccadf/original/tidying-up-the-conformational-ensemble-of-a-disordered-peptide-by-computational-prediction-of-spectroscopic-fingerprints.pdf |
60c73e16ee301c056bc786a5 | 10.26434/chemrxiv.6462887.v1 | First Principles Insights into Amorphous Mg2Sn Alloy Anode for Mg-ion Batteries | <p>Rechargeable Mg-ion batteries (MIBs) are an advantageous alternative solution to Li-ion batteries in many ways. Mg is safer and abundant in the Earth, and has a high electrochemical capacity owing to its divalent nature. It is yet relatively less studied largely due to primal success of Li-base batteries and challenges associated with the design of MIBs including high performance electrode materials. Herein, using first principles calculation, we study the electrochemical and mechanical properties of the most viable alloy anode Mg<sub>2</sub>Sn with special attention to its amorphous phase—unavoidable phase forming during cyclic Sn magnesiation in MIBs due to volume changes. We create amorphous Mg<sub>2</sub>Sn via simulated annealing technique using <i>ab initio</i> molecular dynamics. We find while Mg<sub>2</sub>Sn undergoes a substantial atomic-level structural changes during the crystal-to-amorphous transformation, its polycrystalline properties degrade slightly and become softer by only 20 % compared to the crystal phase. Moreover, we predict competitive electrochemical properties for the amorphous phase assuming it goes under similar reaction path as the average electronic charge on Mg ions almost remain unaffected. This work thus not only demonstrate that a-Mg<sub>2</sub>Sn phase could be a bypass to combat the challenges associated with the crystal cracking during volume change, but also serves as first step to better understand the widely used Mg<sub>2</sub>Sn alloy anode in MIBs.</p> | Majid Mortazavi; Edmund Soon; Nikhil V. Medhekar | Nanostructured Materials - Materials; Electrochemistry; Theory - Computational; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2018-06-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e16ee301c056bc786a5/original/first-principles-insights-into-amorphous-mg2sn-alloy-anode-for-mg-ion-batteries.pdf |
6757d4eef9980725cf93c698 | 10.26434/chemrxiv-2024-tkjr1 | Stereochemistry-aware string-based molecular generation | This study investigates the impact of incorporating stereochemical information, a crucial aspect of computational drug discovery and materials design, in molecular generative modelling. We present a comprehensive comparison of stereochemistry-aware and conventionally stereochemistry-unaware string-based generative approaches, utilizing both genetic algorithms and reinforcement learning-based techniques. To evaluate these models, we introduce novel benchmarks specifically designed to assess the importance of stereochemistry-aware generative modelling. Our results demonstrate that stereochemistry-aware models generally perform on par with or surpass conventional algorithms across various stereochemistry-sensitive tasks. However, we also observe that in scenarios where stereochemistry plays a less critical role, stereochemistry-aware models may face challenges due to the increased complexity of the chemical space they must navigate. This work provides insights into the trade-offs involved in incorporating stereochemical information in molecular generative models and offers guidance for selecting appropriate approaches based on specific application requirements. | Gary Tom; Edwin Yu; Naruki Yoshikawa; Kjell Jorner; Alán Aspuru-Guzik | Theoretical and Computational Chemistry; Physical Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6757d4eef9980725cf93c698/original/stereochemistry-aware-string-based-molecular-generation.pdf |
651a66070065940912460deb | 10.26434/chemrxiv-2023-txhw5 | TransPTM: a Transformer-Based Model for Non-Histone Acetylation Site Prediction | Protein acetylation is one of the extensively studied post-translational modifications (PTMs) for its sig- nificant roles across a myriad of biological processes. Although many computationl tools for acetylation site identification have been developed, there is a lack of benchmark dataset and bespoke predictors for non-histone acetylation site prediction. To address those problems, we have contributed to both dataset creation and predictor benchmark in this study. Firstly, we construct a non-histone acetylation site bench- mark dataset, namely NHAC, which includes 11 subsets according to the sequence length ranging from 11 to 61 amino acids. There are totally 886 positive samples and 4707 negative samples for each sequence length. Secondly, we propose a transformer-based neural network model, TransPTM, for non-histone acetylation site predication. Our model introduces a pre-trained protein language model ProtT5 to con- struct the site’s feature space. The GNN framewrk consists of three TransformerConv layers for feature extraction and a multilayer perceptron (MLP) module for classification. In experiments, TransPTM has the competitive performance for non-histone acetylation site prediction over 3 SOTA tools. It improves our comprehension on the PTM mechanism and provides a theoretical basis for developing drug targets for diseases. Moreover, the created PTM datasets fills the gap in non-histone acetylation site datasets and is beneficial to the related communities. The source code and data utilized by TransPTM are accessible at https://www.github.com/TransPTM. | Lingkuan Meng; Xingjian Chen; Ke Cheng; Nanjun Chen; Zetian Zheng; Fuzhou Wang; Hongyan Sun; Ka-Chun Wong | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651a66070065940912460deb/original/trans-ptm-a-transformer-based-model-for-non-histone-acetylation-site-prediction.pdf |
60c755434c89196565ad465b | 10.26434/chemrxiv.14060948.v1 | Ab Initio Calculations of Dissociation Energy of Water Molecule on Near-Term Quantum Devices Using the Pennylane Interface to Quantum Hardware | <br /><br />Fault-tolerant quantum computers may be far off, however solving real world quantum chemistry problems on near-term quantum devices is possible through the Pennylane which provides interface to use any of the quantum hardware provided by any of the quantum hardware providers such as IBM, Google or Microsoft. A demonstrated use of Pennylane to solve real world quantum chemical problems on near-term quantum devices is shown. Ab initio quantum chemical calculations of dissociation energy of water molecule on the near-term quantum hardware using the Pennylane interface yielded a dissociation energy comparable to experiment and therefore it is recommended that the quantum chemistry community use near-term quantum devices to leverage quantum computing advantage to solve quantum chemical problems.<br /><br /> | Ben Geoffrey A S | Computational Chemistry and Modeling; Quantum Computing; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755434c89196565ad465b/original/ab-initio-calculations-of-dissociation-energy-of-water-molecule-on-near-term-quantum-devices-using-the-pennylane-interface-to-quantum-hardware.pdf |
64ea83d2dd1a73847f9656fc | 10.26434/chemrxiv-2023-v72j0 | Extraction Yield Prediction for the Large-Scale Recovery of Botanicals | The extraction of compounds from natural sources is essential to organic chemistry, from identifying bioactive molecules for potential therapeutics to obtaining complex, chiral molecule building blocks. Similar to chemical syntheses, anticipating the extraction conditions (flow rate, time, pressure, etc.) that will lead to the highest purity or recovery of a target molecule is difficult. Machine learning algorithms have been demonstrated to streamline reaction optimization processes by constraining the parameter space to be physically tested to predicted regions of high performance; however, it is not altogether clear if these techniques extend to the optimization of extractions where the process conditions are even more expensive to evaluate, limiting the data available for assessment. Combining information from several sources could provide access to the requisite data necessary for implementing a data-driven approach to optimization, but little data has been made publicly available. To address this challenge and to evaluate the capabilities of machine learning for optimizing extraction processes, we built a dataset on the carbon dioxide supercritical fluid extraction (CO2 SFE) of botanicals by harmonizing data from various companies. Using this combinatorial dataset and new techniques for maximizing the information obtained from a single large scale experiment, we built robust machine learning models to accurately predict extraction yields. The resulting machine learning models also allow for the prediction of out-of-sample biomass variations, process conditions, and scales. | Hart Plommer; Isaiah Betinol; Tom Dupree; Markus Roggen; Jolene Reid | Theoretical and Computational Chemistry; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ea83d2dd1a73847f9656fc/original/extraction-yield-prediction-for-the-large-scale-recovery-of-botanicals.pdf |
669602a05101a2ffa8809aa3 | 10.26434/chemrxiv-2024-l6hs1-v2 | Incubation of Amyloidogenic Peptides in Reverse Micelles Allow Active Control of Oligomer Size and Study of Protein–Protein Interactions | Studies of the structure and dynamics of oligomeric aggregates of amyloidogenic peptides pose challenges due to their transient nature. This concept article provides a brief overview of various nucleation mechanisms with reference to the classical nucleation theory and illustrates the advantages of incubating amyloidogenic peptides in reverse micelles (RMs). The use of RMs not only facilitates size regulation of oligomeric aggregates but also provides an avenue to explore protein–protein interactions among the oligomeric aggregates of various amyloidogenic peptides. Additionally, we envision the feasibility of preparing brain tissue-derived oligomeric aggregates using RMs, potentially advancing the development of monoclonal antibodies with enhanced potency against these pathological species in vivo. | Han-Wen Chang; Chien-I Yang; Jerry Chun Chung Chan | Physical Chemistry; Biological and Medicinal Chemistry; Biophysics; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669602a05101a2ffa8809aa3/original/incubation-of-amyloidogenic-peptides-in-reverse-micelles-allow-active-control-of-oligomer-size-and-study-of-protein-protein-interactions.pdf |
60c74aeb337d6c0d87e279bf | 10.26434/chemrxiv.12252965.v1 | Repurposing Therapeutics to Identify Novel Inhibitors Targeting 2'-O-Ribose Methyltransferase Nsp16 of SARS-CoV-2 | <p>Three
coronaviruses (CoVs): severe acute respiratory syndrome coronavirus
(SARS-CoV-1), Middle East respiratory syndrome coronavirus (MERS-CoV), and the
recently identified SARS-CoV-2 in December 2019, have caused deadly pneumonia
in humans since the beginning of the 21st century. The SARS-CoV-2 causes
coronavirus disease-19 (COVID-19) with influenza-like symptoms ranging from
mild discomfort to severe lung injury and multi-organ failure, eventually
leading to death. As of April 30, 2020, more than three million (3,175,207)
COVID-19 cases were reported worldwide, and more than 220,000 (224,172)
patients have died
(https://www.who.int/emergencies/diseases/novel-coronavirus-2019). Effective
treatments and vaccines for SARS-CoV-2 infection do not currently exist. Thus,
it will be of great benefit to identify and repurpose already
well-characterized compounds and approved drugs for use in combating COVID-19.</p>
<p> </p>
<p>CoVs are
positive-sense RNA viruses that replicate in the cytoplasm of infected cells.
Replication and transcription of the CoV RNA genome are achieved by a complex
RNA replication/transcription machinery, consisting of at least 16 viral
nonstructural proteins (nsp). Previous studies demonstrated that nsp16 proteins
of SARS-CoV-1 and MERS-CoV have methyltransferase (MTase) activities that
catalyze methylation of the first transcribed nucleotide at the ribose 2’-O
position (2’-O-Me). The 2’-O-Me of virus cap RNAs protects itself from
degradation by 5′-3′ exoribonucleases, ensures efficient translation, and helps
to prevent recognition by the host innate immune system. The importance of
nsp16 2'-O-MTase activity for CoV infection and pathogenesis was previously
documented by in vitro and in vivo studies. For SARS-CoV-1, the absence of
nsp16 2′-O-MTase activity results in significant attenuation characterized by
decreased viral replication, reduced weight loss, and limited breathing dysfunction
in mice. In addition, nsp16 down-regulates the activities of innate immune
sensing factors: retinoic acid-inducible gene I (RIG-I) and melanoma
differentiation-associated gene 5 protein (MDA5). Thus, inhibition of nsp16
2’-O-MTase activities should restrain viral replication and enable recognition
by the host innate immune system, making the nsp16-MTase a promising target for
the identification of new anti-SARS-CoV-2 drugs. </p>
<p> </p>
<p>In the
present study, we employed structural analysis, virtual screening, and
systematic drug repurposing approaches to identify “approved” drugs which can
act as promising inhibitors against nsp16 2′-O-MTase of SARS-CoV-2. We first
performed comparative analysis of primary amino acid sequences and crystal
structures of seven human CoVs and defined the key residues for nsp16
2-O’-MTase functions. From the virtual screening against nsp16 2′-O-MTase of
SARS-CoV-2, we provide a ranking of the predicted binding affinities of 1,380
top hit compounds corresponding to 967 “approved” drugs. Furthermore, we have
calculated various structural parameters of our top-ranking drugs. Our studies
provided the foundation to further test and repurpose these candidate drugs
experimentally and clinically for COVID-19 treatment. </p><br /> | Yuanyuan Jiang; Lanxin Liu; Morenci Manning; Madison Bonahoom; Aaron Lotvola; Zeng-Quan Yang | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74aeb337d6c0d87e279bf/original/repurposing-therapeutics-to-identify-novel-inhibitors-targeting-2-o-ribose-methyltransferase-nsp16-of-sars-co-v-2.pdf |
65fcadf366c138172980092b | 10.26434/chemrxiv-2024-wl2lr | Defluorination of Persistent Perfluoroalkyl Substances by Visible Light Under Ambient Conditions | Perfluoroalkyl substances (PFASs) have been extensively utilized in various industries. However, their extremely high stability poses significant challenges, such as environmental persistence and waste treatment. Current PFAS decomposition approaches typically require harsh conditions. Thus, there is a pressing need to develop a new technique capable of decomposing them under mild conditions. Here, we showcase a method wherein perfluorooctanesulfonate, known as a "persistent chemical," and Nafion, a widely utilized sulfonated perfluoropolymer for ion-exchange membranes, undergo efficient decomposition into fluorine ions under ambient conditions via the irradiation of incoherent visible LED light onto semiconductor nanocrystals (NCs). This decomposition reaction is driven by cooperative mechanisms involving light-induced ligand displacements and Auger-induced electron injections via hydrated electrons and higher excited states. Our findings not only demonstrate the feasibility of efficiently breaking down various PFASs under mild conditions but also pave the way for advancing toward a sustainable fluorine-recycling society. | Yuzo Arima; Yoshinori Okayasu; Yuki Nagai; Yoichi Kobayashi | Catalysis; Nanoscience; Nanocatalysis - Catalysts & Materials; Nanocatalysis - Reactions & Mechanisms; Photocatalysis; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-03-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65fcadf366c138172980092b/original/defluorination-of-persistent-perfluoroalkyl-substances-by-visible-light-under-ambient-conditions.pdf |
6628b25891aefa6ce1478cd2 | 10.26434/chemrxiv-2024-mfbd6 | Validation of the identification reliability of known and assumed UDMH transformation products using gas chromatographic retention indices and machine learning | Thirty two commercially available standards were used to determine chromatographic retention indices (RIs) for three different stationary phases. The selected compounds were nitrogen-containing heterocycles and amides, which are unsymmetrical dimethylhydrazine (UDMH) transformation products or its assumed transformation products. UDMH is a highly toxic compound widely used in the space industry, that forms a number of different compounds in the environment. Well-known transformation products may exceed UDMH itself in their toxicity, but most of the products are poorly investigated, while posing a huge environmental threat. Experimental RIs for the stationary phases, RIs from the NIST database, and predicted RIs are presented in this paper. It is shown that there are virtually no RIs for UDMH transformation products in the NIST database. In addition, even among those compounds for which RIs were known, inconsistencies were identified. Adding RIs to the database and eliminating erroneous data would allow for more reliable identification when standards are not available. The discrepancies identified between experimental RI values and predicted values will allow for adjustments to the machine learning models that are used for prediction. Previously proposed compounds as possible transformation products without the use of standards and NMR method were confirmed. | Anastasia Karnaeva; Anastasia Sholokhova | Theoretical and Computational Chemistry; Analytical Chemistry; Earth, Space, and Environmental Chemistry; Environmental Science; Analytical Chemistry - General; Machine Learning | CC BY 4.0 | CHEMRXIV | 2024-04-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6628b25891aefa6ce1478cd2/original/validation-of-the-identification-reliability-of-known-and-assumed-udmh-transformation-products-using-gas-chromatographic-retention-indices-and-machine-learning.pdf |
60c73f204c8919dda2ad1f13 | 10.26434/chemrxiv.7258214.v1 | The Bicyclo[2.2.2]octane Motif: A Class of Saturated Group 14 Quantum Interference Based Single-molecule Insulators | The electronic transmission through σ-conjugated molecules can be fully suppressed by destructive quantum interference, which makes them potential candidates for single-molecule insulators. The first molecule with clear suppression of the single-molecule conductance due to σ-interference was recently found in the form of a functionalized bicyclo[2.2.2]octasilane. Here we continue the search for potential single-molecule insulators based on saturated group 14 molecules. Using a high-throughput screening approach, we assess the electron transport properties of the bicyclo[2.2.2]octane class by systematically varying the constituent atoms between carbon, silicon, and germanium, thus exploring the full chemical space of 771 different molecules. The majority of the molecules in the bicyclo[2.2.2]octane class are found to be highly insulating molecules. Though the all-silicon molecule is a clear-cut case of σ-interference, it is not unique within its class and there are many potential molecules that we predict to be more insulating. The finding of this class of quantum interference based single-molecule insulators indicates that a broad range of highly insulating saturated group 14 molecules are likely to exist | Marc H. Garner; Mads Koerstz; Jan H. Jensen; Gemma C. Solomon | Theory - Computational | CC BY 4.0 | CHEMRXIV | 2018-10-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f204c8919dda2ad1f13/original/the-bicyclo-2-2-2-octane-motif-a-class-of-saturated-group-14-quantum-interference-based-single-molecule-insulators.pdf |
6435059c0784a63aeeeb3039 | 10.26434/chemrxiv-2023-d9d92 | Recent advances in Carbon Nanotube Based Field-Effect Transistor Biosensors for Established Biomarkers for the Diagnosis of Alzheimer's Disease | Alzheimer's disease (AD) is a neurodegenerative disorder that affects millions of people worldwide. Early screening is crucial to prevent potential damages, and researchers are exploring alternative approaches such as multiplexed assays and emerging technologies such as microfluidics, nanotechnology, and biosensors. Current mainstream and conventional tests for AD biomarkers have limitations due to their insufficient sensitivity, which has led to the development of next-generation biosensing techniques that use nanomaterial-based field-effect transistors (FETs) for high-sensitivity and high-integration label-free biosensing. This review provides an overview of AD biomarkers, the working principle of FET biosensors, recent advances in CNT-based FET biosensors for the detection of AD biomarkers, and their potential for clinical diagnosis. FET biosensors have the potential to revolutionize the clinical detection of AD biomarkers, but there are challenges that need to be addressed for their successful translation into practical applications. In this review, we will provide an overview of the current understanding of AD biomarkers, describe the working principle of FET biosensors, and highlight recent advances in the development of CNT-based FET biosensors for the detection of AD biomarkers, with a particular emphasis on Aβ and tau proteins. We will also discuss the potential of these biosensors for clinical diagnosis and the challenges that need to be addressed for their successful translation into practical applications. | Yu Shen | Analytical Chemistry; Analytical Chemistry - General; Analytical Apparatus; Electrochemical Analysis | CC BY 4.0 | CHEMRXIV | 2023-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6435059c0784a63aeeeb3039/original/recent-advances-in-carbon-nanotube-based-field-effect-transistor-biosensors-for-established-biomarkers-for-the-diagnosis-of-alzheimer-s-disease.pdf |
60c745e1bb8c1a6c093da770 | 10.26434/chemrxiv.10279751.v1 | Synthesis and Styrene Copolymerization of Novel Fluoro and Oxy Ring-Disubstituted Isopropyl Phenylcyanoacrylates | <p>Novel
fluoro and oxy ring-disubstituted isopropyl phenylcyanoacrylates, RPhCH=C(CN)CO<sub>2</sub>CH(CH<sub>3</sub>)<sub>2
</sub>(where R is 2-fluoro-3-methoxy, 2-fluoro-4-methoxy, 2-fluoro-5-methoxy, 2-fluoro-6-methoxy,
3-fluoro-4-methoxy, 4-fluoro-3-methoxy, 5-fluoro-2-methoxy, 4-fluoro-3-phenoxy)
were prepared and copolymerized with
styrene. The monomers were synthesized by the piperidine catalyzed Knoevenagel
condensation of ring-substituted benzaldehydes and isopropyl cyanoacetate and
characterized by CHN elemental analysis, IR, <sup>1</sup>H- and <sup>13</sup>C-NMR.
All the ethylenes were copolymerized with styrene in solution with radical
initiation (ABCN) at 70°C. The composition of the copolymers was
calculated from nitrogen analysis, and the structures were analyzed by IR, <sup>1</sup>H
and <sup>13</sup>C-NMR, GPC, DSC, and TGA. </p> | Abby R. Krause; Haley E. Aynessazian; Monica C. Gonzalez; Adnan M. Khan; Lara R. Lieberman; Meghan H. McNicholas; Nina M. Pelsi; Zachary S. Pierard; Sara M. Rocus; William S. Schjerven; Gregory Kharas | Organic Polymers; Polymerization (Polymers) | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745e1bb8c1a6c093da770/original/synthesis-and-styrene-copolymerization-of-novel-fluoro-and-oxy-ring-disubstituted-isopropyl-phenylcyanoacrylates.pdf |
60c74003842e65850adb1bee | 10.26434/chemrxiv.7303988.v2 | Ion Mobility Mass Spectrometry Measures the Conformational Landscape of p27 and Its Domains and How This Is Modulated upon Interaction with Cdk2/cyclin A | Intrinsically disordered proteins have been reported to undergo ‘disorder to order’ transitions upon binding to their partners in the cell. The extent of the ordering on binding and the lack of order prior to binding is difficult to visualize with classical structure determination methods. Binding of p27 to the Cdk2/cyclin A complex is accompanied by partial folding of p27 in the KID domain, with the retention of dynamic behaviour for function, particularly in the C-terminal half of the protein, positioning it as an exemplary system to probe conformational diversity. Here we employ native ion mobility with mass spectrometry (IM-MS) to measure the intrinsic dynamic properties of p27, both in isolation and within the trimeric complex with Cdk2/cyclin A. This stepwise approach reveals the conformational distributions of the constituent proteins and how they are restructured on complex formation; the trimeric Cdk2/cyclin A/p27-KID complex possesses significant structural heterogeneity cf. Cdk2/cyclin A. These findings support the formation of a fuzzy complex in which both the N and C termini of p27 interact with Cdk2/cyclin A in multiple closely associated states. | Rebecca Beveridge; Lukasz Migas; Richard Kriwacki; Perdita E. Barran | Mass Spectrometry; Cell and Molecular Biology; Biophysical Chemistry | CC BY NC 4.0 | CHEMRXIV | 2018-12-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74003842e65850adb1bee/original/ion-mobility-mass-spectrometry-measures-the-conformational-landscape-of-p27-and-its-domains-and-how-this-is-modulated-upon-interaction-with-cdk2-cyclin-a.pdf |
63bee9603af973983464cec4 | 10.26434/chemrxiv-2023-qqmt7 | Catalytic Generation of ortho-Quinone Dimethides via Donor/Donor Rhodium Carbenes | Substrates engineered to undergo a 1,4-C–H insertion to yield benzocyclobutenes resulted in a novel elimination reaction to yield ortho¬-quinone dimethide (o-QDM) products that undergo Diels-Alder or hetero-Diels-Alder cycloadditions. The analogous benzylic acetals or ethers avoid the C–H insertion pathway completely and, after hydride transfer, undergo a de-aromatizing elimination reaction to o-QDM at ambient temperature. The resulting dienes undergo a variety of cycloaddition reactions with high diastereo- and regio-selectivity. This is one of the few examples of catalytic generation of o-QDM without the intermediacy of a benzocyclobutene and represents one of the mildest, ambient temperature processes to access to these useful intermediates. This proposed mechanism is supported by DFT calculations. Moreover, the methodology was applied to the synthesis of (±)-isolariciresinol in 42% overall yield. | Mingchun Gao; Jose Ruiz; Emily Jimenez; Anna Lo; Croix Laconsay; James Fettinger; Dean Tantillo; Jared Shaw | Organic Chemistry; Natural Products; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63bee9603af973983464cec4/original/catalytic-generation-of-ortho-quinone-dimethides-via-donor-donor-rhodium-carbenes.pdf |
60c74f4dee301cd7afc7a6a5 | 10.26434/chemrxiv.12753173.v2 | Discovery of a Two-Dimensional Type I Superionic Conductor | <div>
<div>
<div>
<p>Type I superionic conductors (e.g., AgI, Ag<sub>2</sub>Se, etc.) are defined by an abrupt transition to the superionic state and
have so far been found exclusively in 3D crystal structures. Here, we reveal a new 2D type I superionic conductor, α-KAg<sub>3</sub>Se<sub>2</sub> by
total scattering techniques and complementary simulations. Quasi-elastic neutron scattering (QENS) from the high temperature superionic phase match a simple Fickian diffusion mechanism with a diffusion coefficient of ~10<sup>-5</sup> cm<sup>2</sup> s<sup>-1</sup> between 710 and 740 K. Ab
initio molecular dynamics simulations confirm that the mobile Ag<sup>+</sup> ions are confined to 4 Å thick layers, in addition to reproducing
the experimental diffusion coefficient from QENS and the local structure obtained from X-ray powder pair-distribution-function
analysis. Finally, chemical substitutions suggest that the nature of alkali metal ions comprising the charge-balancing layers can facilitate or inhibit the phase transition temperature.
</p>
</div>
</div>
</div> | Alex Rettie; Jingxuan Ding; Michael Johnson; Christos Malliakas; Naresh Osti; Duck Young Chung; Raymond Osborn; Olivier Delaire; Stephan Rosenkranz; Mercouri Kanatzidis | Ceramics; Solid State Chemistry; Physical and Chemical Properties; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f4dee301cd7afc7a6a5/original/discovery-of-a-two-dimensional-type-i-superionic-conductor.pdf |
60c749089abda2672bf8cb48 | 10.26434/chemrxiv.11955273.v2 | Exploring the Active Compounds of Traditional Mongolian Medicine Agsirga in Intervention of Novel Coronavirus (2019-nCoV) Based on HPLC-Q-Exactive-MS/MS and Molecular Docking Method | <p><a></a><a></a><a></a><a><b>Objective</b></a>:
To screen all compounds of Agsirga based on the HPLC-Q-Exactive high-resolution
mass spectrometry and find potential inhibitors that can respond to 2019-nCoV
from active compounds of Agsirga by molecular docking technology.</p>
<p><b>Methods</b>: HPLC-Q-Exactive high-resolution mass
spectrometry was adopted to identify the complex components of Mongolian
medicine Agsirga, and separated by the high-resolution mass spectrometry
Q-Exactive detector. Then the Orbitrap detector was used in tandem
high-resolution mass spectrometry, and the related molecular and structural
formula were found by using the chemsipider database and related literature,
combined with precise molecular formulas (errors ≤ 5 × 10<sup>−6</sup>) ,
retention time, primary mass spectra, and secondary mass spectra information,
The fragmentation regularities of mass spectra of these compounds were deduced.
Taking ACE2 as the receptor and deduced compounds as the ligand, all of them
were pretreated by discover studio, autodock and Chem3D. The molecular docking
between the active ingredients and the target protein was studied by using
AutoDock molecular docking software. The interaction between ligand and
receptor is applied to provide a choice for screening anti-2019-nCoV drugs.</p>
<p><b>Result</b>:
Based on the fragmentation patterns of the reference compounds and consulting
literature, a total of 96 major alkaloids and stilbenes were screened and
identified in Agsirga by the HPLC-Q-Exactive-MS/MS method. Combining with
molecular docking, a conclusion was got that there are potential active
substances in Mongolian medicine Agsirga which can block the binding of
ACE2 and 2019-nCoV at the molecular level.</p> | Jie Cheng; Yuchen Tang; Baoquan Bao; Ping Zhang | Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749089abda2672bf8cb48/original/exploring-the-active-compounds-of-traditional-mongolian-medicine-agsirga-in-intervention-of-novel-coronavirus-2019-n-co-v-based-on-hplc-q-exactive-ms-ms-and-molecular-docking-method.pdf |
60c7517c842e6534bedb3bc1 | 10.26434/chemrxiv.13173674.v1 | Transformer: Linking Atom Mapping and Neural Machine Translation | <div><br /></div><div><p> Atom mapping reveals the corresponding relationship between reactant and product atoms in chemical reactions, which is important for drug design, exploration for underlying chemical mechanism, reaction classification and so on. Here, we present a new method that links atom mapping and neural machine translation using the transformer model. In contrast to the previous algorithms, our method runs reaction prediction and captures the information of corresponding atoms in parallel. Meanwhile, we use a set of approximately 360K reactions without atom mapping information for obtaining general chemical knowledge and transfer it to atom mapping task on another dataset which contains 50K atom-mapped reactions. With manual evaluation, the top-1 accuracy of the transformer model in atom mapping reaches 91.4%. we hope our work can provide an important step toward solving the challenge problem of atom mapping in a linguistic perspective.</p></div> | Chengyun Zhang; Ling Wang; Yejian Wu; Yun Zhang; An Su; Hongliang Duan | Organic Synthesis and Reactions; Chemoinformatics; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7517c842e6534bedb3bc1/original/transformer-linking-atom-mapping-and-neural-machine-translation.pdf |
60c73ed3842e650f17db198c | 10.26434/chemrxiv.7001054.v2 | Re-Designing Hazardous Chemicals with Target-Specific Toxicities by Learning from Structure-Based Drug Design | Chemicals are the basis of our society and economy, yet many existing chemicals are known to have unintended adverse effects on human and environmental health. Testing all existing and new chemicals on animals is both economically and ethically unfeasible. In this paper, a new in silico framework is presented that affords redesign of existing hazardous chemicals in commerce based on specific molecular initiating events in their adverse outcomes pathways. Our approach is based on a successful methodology implemented in computational drug discovery, and promises to dramatically lower costs associated with new chemical development by synergistically addressing chemical function and safety at the design stage. <br /> | Traci Clymer; Vanessa Vargas; Eric Corcoran; Robin Kleinberg; Jakub Kostal | Environmental Science; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2018-08-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73ed3842e650f17db198c/original/re-designing-hazardous-chemicals-with-target-specific-toxicities-by-learning-from-structure-based-drug-design.pdf |
6275655244bdd5bec2594b36 | 10.26434/chemrxiv-2022-k6pgj | Ultrafast Laser Pulse Generation by Mode Locking: Matlab-based Demonstrations | Ultrafast laser spectroscopy is a valuable and increasingly accessible technique for studies of rapid chemical reactions. Critical to ultrafast spectroscopy is the concept of mode-locking, a technique that enables a fixed phase relationship between laser modes, resulting in laser pulses with very short duration (in the fs or ps range). Despite an increasing importance of ultrafast lasers in chemistry, the introduction of key concepts behind their operation into the undergraduate and graduate chemistry coursework has been limited. To help the incorporation of these topics into chemistry courses, we report here a hands-on activity that helps students develop an intuitive understanding of the factors that impact electromagnetic wave evolution in optical cavities and the process of mode-locking. We first provide the theoretical background by introducing cavity modes and contrasting them with well-known propagating electromagnetic waves. We then explore what happens when modes are added and how the relative phase between the modes affect their behavior. In the second section of the manuscript, three teaching modules are provided, along with associated Matlab codes and animated images, that can be used in the classroom to introduce concepts of cavity modes and mode-locking. These teaching modules start by contrasting propagating electromagnetic waves with cavity modes, then illustrate what happens when multiple modes are present in the cavity and how the relative phase between the modes affects the overall electromagnetic fields in the cavity. | Alexei Goun; Ksenija Glusac | Chemical Education; Chemical Education - General | CC BY NC 4.0 | CHEMRXIV | 2022-05-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6275655244bdd5bec2594b36/original/ultrafast-laser-pulse-generation-by-mode-locking-matlab-based-demonstrations.pdf |
63d790dc246f166242d1e638 | 10.26434/chemrxiv-2023-n2l6k | The design and synthesis of green emissive iridium(III) complexes guided by calculations of the vibrationally-resolved emission spectra | A key challenge in developing emissive materials for organic light-emitting diodes is to optimize their colour saturation, which means targeting narrowband emitters. In this combined theoretical and experimental study, we investigate the use of heavy atoms in the form of trimethylsilyl groups as a tool to reduce the intensity of the vibrations in the 2-phenylpyridinato ligands of emissive iridium(III) complexes that contribute to the vibrationally coupled modes that broaden the emission profile. An underutilised computational technique, Frank-Condon vibrationally coupled electronic spectral modelling, was used to identify the key vibrational modes that contribute to the broadening of the emission spectra in known benchmark green-emitting iridium(III) complexes. Based on these results, a family of eight new green-emitting iridium complexes containing trimethylsilyl groups substituted at different positions of the cyclometalating ligands has been prepared to explore the impact that these substituents have on reducing the intensity of the vibrations and the resulting reduction in the contribution of vibrationally coupled emission modes to the shape of the emission spectra. We have demonstrated that locating a trimethylsilyl group at the N4 or N5 position of the 2-phenylpyridine ligand damps the vibrational modes of the iridium complex and provides a modest narrowing of the emission spectrum of 8-9 nm (or 350 cm-1). The strong correlation between experimental and calculated emission spectra highlights the utility of this computational method to understand how the vibrational modes contribute to the profile of the emission spectra in phosphorescent iridium(III) emitters. | Campbell Mackenzie; Seung-Yeon Kwak; Sungmin Kim; Eli Zysman-Colman | Inorganic Chemistry; Organometallic Compounds; Spectroscopy (Inorg.) | CC BY 4.0 | CHEMRXIV | 2023-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d790dc246f166242d1e638/original/the-design-and-synthesis-of-green-emissive-iridium-iii-complexes-guided-by-calculations-of-the-vibrationally-resolved-emission-spectra.pdf |
60c73d504c8919b4faad1bbc | 10.26434/chemrxiv.5662201.v1 | Nanowire Transfer Enabled by Incomplete Wetting and Mechanical Tearing for Low-Cost Flexible Bactericidal Surfaces withMulti-Scale Superhydrophobicity | <p>In
this work, we report a large-area fabrication of a flexible superhydrophobic
bactericidal surface decorated with copper hydroxide nanowires. This involves a
simple two-step method which involves growth followed by transfer of the
nanowires onto the polydimethylsiloxane (PDMS) surface by mechanical peeling.
Additional roughness in PDMS is obtained through incomplete wetting of the
nanoscale gaps which leads to multi-scale superhydrophobicity with contact
angle of 169°
and hysteresis of less than 2°.
The simplicity of the process makes it low-cost and easily scalable. The
process allows fabrication of non-planar 3D surfaces. The surface shows blood
repellence and antimicrobial activity against <i>E. coli </i>with<i> </i>more than 5
log reductions in bacterial colony. The surface also shows hemocompatible
behaviour making it suitable for healthcare applications. The fabricated
surface is found to be extremely robust against stretching, twisting, sand
paper abrasion, solid weight impact, and tape peel test. The surface is found
to withstand human weight multiple times without losing its hydrophobicity
making it suitable for several practical scenarios in healthcare and household
applications. </p> | ABINASH TRIPATHY; ARVIND KUMAR; SYAMA SREEDHARAN; GIRISH MURALIDHARAN; AMITAVA PRAMANIK; DIPANKAR NANDI; PROSENJIT SEN | Nanofabrication; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2017-12-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d504c8919b4faad1bbc/original/nanowire-transfer-enabled-by-incomplete-wetting-and-mechanical-tearing-for-low-cost-flexible-bactericidal-surfaces-with-multi-scale-superhydrophobicity.pdf |
660fad8591aefa6ce1d9ab88 | 10.26434/chemrxiv-2024-1t8rk | Recent Developments in Materials and Applications of Triplet Dynamic Nuclear Polarization | Dynamic nuclear polarization (DNP) is a method for achieving high levels of nuclear spin polarization by transferring spin polarization from electrons to nuclei by microwave irradiation, resulting in higher sensitivity in NMR/MRI. In particular, DNP using photoexcited triplet electron spins (triplet-DNP) can provide hyperpolarized nuclear spin state at room temperature and low magnetic field. In this review article, we highlight recent developments in materials and instrumentation for the application of triplet-DNP. First, a brief history and principles of triplet-DNP will be presented. Next, important advances in recent years will be outlined: new materials to hyperpolarize water and biomolecules; high-sensitivity solution NMR by dissolution triplet-DNP; and strategies for further improvement of the polarization. In view of these developments, the future directions for the wider range of application of triplet-DNP will be discussed. | Tomoyuki Hamachi; Nobuhiro Yanai | Physical Chemistry; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660fad8591aefa6ce1d9ab88/original/recent-developments-in-materials-and-applications-of-triplet-dynamic-nuclear-polarization.pdf |
67530c957be152b1d02570bc | 10.26434/chemrxiv-2024-bv03m | NO2 reduction to HONO by small α-hydroxycarbonyls: a laboratory investigation in
relevance to nighttime production of atmospheric HONO | This report presents a study on the reduction of NO2 (nitrogen dioxide) to HONO (nitrous
acid) by two atmospherically significant volatile organic compounds, glycolaldehyde (Gla)
and hydroxyacetone (HAc) in the gas phase under simulated tropospheric condition. The
FTIR spectroscopic probing clearly reveals that HONO is the predominant product of the
reactions. It is demonstrated that the reactions occur in 2:1 stoichiometry with respect to NO2
and Gla/HAc, and from a thermochemical viewpoint, the reactions are energetically
favorable. In each case the overall reaction occurs as a 3rd order process, and the
corresponding rate constants are (1.46±0.04) ×10-34 cm6 molecule-2 s
-1 and (2.06±0.06) ×10-35
cm
6 molecule-2
s
-1 for the reaction of NO2 with Gla and HAc respectively. A brief discussion
is also presented about the atmospheric implications of the findings. | Subhasis Mandal; Rinjini Saha; Tapas Chakraborty | Physical Chemistry; Chemical Kinetics; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67530c957be152b1d02570bc/original/no2-reduction-to-hono-by-small-hydroxycarbonyls-a-laboratory-investigation-in-relevance-to-nighttime-production-of-atmospheric-hono.pdf |
67735c866dde43c908d73fd7 | 10.26434/chemrxiv-2024-6zxh1 | Hydrogen Tunneling and Conformational Motions in Nonadiabatic Proton-Coupled Electron Transfer between Interfacial Tyrosines in Ribonucleotide Reductase | Ribonucleotide reductase is essential for DNA synthesis and repair in all living organisms. The mechanism of E. coli RNR requires long-range radical transport through a proton-coupled electron transfer (PCET) pathway spanning two different protein subunits. Herein, the direct PCET reaction between the interfacial tyrosine residues, Y356 and Y731, is investigated with a vibronically nonadiabatic theory that treats the transferring proton and all electrons quantum mechanically. The input quantities to the PCET rate constant expression are computed with a combination of density functional theory and molecular dynamics simulations. The calculations highlight the importance of hydrogen tunneling in this PCET reaction. Compression of the distance between the proton donor and acceptor oxygen atoms of the interfacial tyrosine residues is essential to facilitate hydrogen tunneling by increasing the overlap between the reactant and product proton vibrational wavefunctions. This compression occurs by thermal conformational fluctuations of these interfacial tyrosine residues. N733 and R411 are identified as key residues that can hydrogen bond to Y731 and Y356, respectively, and thereby compete with the hydrogen-bonding interaction between Y731 and Y356 required for direct PCET. Understanding the roles of hydrogen tunneling and conformational motions in this interfacial PCET reaction, as well as identifying other residues that may impact the kinetics, is important for targeted protein engineering efforts to modulate RNR activity. | Jiayun Zhong; Qiwen Zhu; Alexander Soudackov; Sharon Hammes-Schiffer | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Theory - Computational; Biophysical Chemistry; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67735c866dde43c908d73fd7/original/hydrogen-tunneling-and-conformational-motions-in-nonadiabatic-proton-coupled-electron-transfer-between-interfacial-tyrosines-in-ribonucleotide-reductase.pdf |
60c74481842e65fa89db2485 | 10.26434/chemrxiv.9850301.v1 | Exploring Diamond-Like Lattice Thermal Conductivity Crystals via Feature-Based Transfer Learning | Ultrahigh lattice thermal
conductivity materials hold great importance since they play a critical role in
the thermal management of electronic and optical devices. Models using machine
learning can search for materials with outstanding higher-order properties like
thermal conductivity. However, the lack of sufficient data to train a model is
a serious hurdle. Herein we show that big data can complement small data for
accurate predictions when lower-order feature properties available in big data
are selected properly and applied to transfer learning. The connection between
the crystal information and thermal conductivity is directly built with a
neural network by transferring descriptors acquired through a pre-trained model
for the feature property. Successful transfer learning shows the ability of
extrapolative prediction and reveals descriptors for lattice anharmonicity.
Transfer learning is employed to screen over 60000 compounds to identify novel
crystals that can serve as alternatives to diamond. Even though most materials in the top list are
superhard materials, we reveal that superhard property do not necessarily lead
to high lattice thermal conductivity. Large hardness means high elastic
constants and group velocity of phonons in the linear dispersion regime, but
the lattice thermal conductivity is determined also by other important factor
such as the phonon relaxation time. What’s more, the average or maximum dipole
polarizability and the van der Waals radius are revealed to be the leading
descriptors among those that can also be qualitatively related to
anharmonicity.<br /> | Shenghong Ju; Ryo Yoshida; Chang Liu; Kenta Hongo; Terumasa Tadano; Junichiro Shiomi | Thermal Conductors and Insulators; Machine Learning; Physical and Chemical Properties; Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74481842e65fa89db2485/original/exploring-diamond-like-lattice-thermal-conductivity-crystals-via-feature-based-transfer-learning.pdf |
6433d5030784a63aeee15191 | 10.26434/chemrxiv-2023-c4w8x | MHAT-initiated redox radical cyclization of alkenylsilane enables concise syntheses of (–)-habiterpenol and (+)-2,3-epi-habiterpenol | The concise syntheses of (–)-habiterpenol and (+)-2,3-epi-habiterpenol from (3aR)-(+)-sclareolide and 6-methoxyindanone in 11 and 12 steps, respectively, was enabled by the regioselective addition of the TMS-indenyl anion and facile stereoselective MHAT-initiated redox radical cyclization of alkenylsilane. | Haruki Taguchi; Mayuko Kawaguchi; Tohru Nagamitsu; Masaki Ohtawa | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6433d5030784a63aeee15191/original/mhat-initiated-redox-radical-cyclization-of-alkenylsilane-enables-concise-syntheses-of-habiterpenol-and-2-3-epi-habiterpenol.pdf |
60c753e79abda26359f8e0a0 | 10.26434/chemrxiv.13571075.v1 | Catalyst-Controlled Regiodivergence in Rearrangements of Indole-Based Onium Ylides | We have developed catalyst-controlled regiodivergent rearrangements of onium-ylides derived from indole substrates. Oxonium ylides formed <i>in situ</i> from substituted indoles selectively undergo [2,3]- and [1,2]-rearrangements in the presence of a rhodium and copper catalyst, respectively. The combined experimental and density functional theory (DFT) computational studies indicate divergent mechanistic pathways involving a metal-free ylide in the rhodium catalyzed reaction favoring [2,3]-rearrangement, and a metal-coordinated ion-pair in the copper catalyzed [1,2]-rearrangement that recombines in the solvent-cage. The application<br />of our methodology was demonstrated in the first total synthesis of the indole alkaloid (±)-sorazolon B, which enabled the stereochemical reassignment of the natural product. Further functional group transformations of the rearrangement products to generate valuable synthetic intermediates were also demonstrated. | Vaishnavi Nair; Volga Kojasoy; Croix Laconsay; Dean Tantillo; Uttam Tambar | Natural Products; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Catalysts; Computational Chemistry and Modeling; Theory - Computational; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753e79abda26359f8e0a0/original/catalyst-controlled-regiodivergence-in-rearrangements-of-indole-based-onium-ylides.pdf |
6641eea7418a5379b02375bd | 10.26434/chemrxiv-2024-9xh38-v2 | Beyond Predefined Ligand Libraries: A Genetic Algorithm Approach for De Novo Discovery of Catalysts for the Suzuki Coupling Reactions | This study introduces a novel approach for the unrestricted de novo design of transition metal catalysts, leveraging the power of genetic algorithms (GAs) and density functional theory (DFT) calculations. By focusing on the Suzuki reaction, known for its significance in forming carbon-carbon bonds, we demonstrate the effectiveness of fragment-based and graph-based genetic algorithms in identifying novel ligands for palladium-based catalytic systems. Our research highlights the capability of these algorithms to generate ligands with desired thermodynamic properties, moving beyond the restriction of enumerated chemical libraries. Limitations in the applicability of machine learning models are overcome by calculating thermodynamic properties from first principle. The inclusion of synthetic accessibility scores further refines the search, steering it towards more practically feasible ligands. Through the examination of both palladium and alternative transition metal catalysts like copper and silver, our findings reveal the algorithms' ability to uncover unique catalyst structures within the target energy range, offering insights into the electronic and steric effects necessary for effective catalysis. This work not only proves the potential of genetic algorithms in the cost-effective and scalable discovery of new catalysts but also sets the stage for future exploration beyond predefined chemical spaces, enhancing the toolkit available for catalyst design. | Julius Seumer; Jan H. Jensen | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-05-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6641eea7418a5379b02375bd/original/beyond-predefined-ligand-libraries-a-genetic-algorithm-approach-for-de-novo-discovery-of-catalysts-for-the-suzuki-coupling-reactions.pdf |
60c7453ff96a0079d9286b7b | 10.26434/chemrxiv.9999734.v1 | Extraction on Paper, an Active Learning Technique to Facilitate Student Understanding of Liquid-Liquid Extraction | <p>Undergraduate
students often find it difficult to understand the chemical principles
underlying liquid-liquid extractions. Explanations on how extractions work at
the molecular level in textbook and internet resources are plentiful, but
students still do not seem able to grasp how extractions work before having to
perform the technique in a laboratory course. To address this difficulty in
understanding, we developed an Extraction on Paper Activity. We envision this
activity as a tool to help students understand and apply the chemical
principles underlying liquid-liquid extractions outside of and before entering
into a laboratory setting.</p> | Kate J. McKnelly; William J. Howitz; Simon Lam; Renee Link | Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7453ff96a0079d9286b7b/original/extraction-on-paper-an-active-learning-technique-to-facilitate-student-understanding-of-liquid-liquid-extraction.pdf |
60c74b71bdbb89f84ea395d8 | 10.26434/chemrxiv.12335933.v1 | ACE-2-derived Biomimetic Peptides for the Inhibition of Spike Protein of SARS-CoV-2 | <p>SARS-CoV-2, a novel coronavirus causing overwhelming death and infection worldwide, has emerged as a pandemic. Compared to its predecessor SARS-CoV, SARS-CoV-2 is more infective for being highly contagious and exhibiting tighter binding with host angiotensin-converting enzyme 2 (hACE-2). The entry of the virus into host cells is mediated by the interaction of its spike protein with hACE-2. Thus, a peptide that has a resemblance to hACE-2 but can overpower the spike protein-hACE-2 interaction will be a potential therapeutic to contain this virus. The non-interacting residues in the receptor-binding domain of hACE-2 have been mutated to generate a library of 136 new peptides. Out of this library, docking and virtual screening discover seven peptides that can exert a stronger interaction with the spike protein than hACE-2. A peptide derived from simultaneous mutation of all the non-interacting residues of hACE-2 yields two-fold stronger interaction than hACE-2 and thus turns out here to be the best peptide-inhibitor of the novel coronavirus. The binding of the spike protein and the best peptide-inhibitor with hACE-2 is explored further by molecular dynamics, free energy, and principal component analysis to demonstrate its efficacy. Further, the inhibition assay study with the best peptide inhibitor is in progress. </p> | Saroj Kumar Panda; Parth Sarthi Sen Gupta; Satyaranjan Biswal; Abhik Kumar Ray; Malay Kumar Rana | Bioinformatics and Computational Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b71bdbb89f84ea395d8/original/ace-2-derived-biomimetic-peptides-for-the-inhibition-of-spike-protein-of-sars-co-v-2.pdf |
60c73d51f96a00d3f7285d69 | 10.26434/chemrxiv.5758665.v1 | Azobenzene as a Photoregulator Covalently Attached to RNA: A Quantum Mechanics/Molecular Mechanics-Surface Hopping Dynamics Study | The photoregulation of nucleic acids by azobenzene photoswitches has
recently attracted considerable interest in the context of emerging
biotechnological applications. To understand the mechanism of
photoinduced isomerisation and conformational control in these complex
biological environments, we employ a Quantum Mechanics/Molecular Mechanics (QM/MM) approach in conjunction with nonadiabatic Surface
Hopping (SH) dynamics. Two representative RNA-azobenzene complexes are
investigated, both of which contain the azobenzene chromophore
covalently attached to an RNA double strand via a beta-deoxyribose
linker. Due to the pronounced constraints of the local RNA environment, it is found that trans-to-cis isomerization is slowed down to a time scale of ~15 picoseconds, in contrast to 500 femtoseconds in vacuo, with a quantum yield reduced by a factor of two. By contrast, cis-to-trans isomerization remains in a sub-picosecond regime. A volume-conserving isomerization mechanism is found, similarly to the pedal-like mechanism previously identified for azobenzene in solution phase. Strikingly, the chiral RNA environment induces opposite right-handed and left-handed helicities of the ground-state cis-azobenzene chromophore in the two RNA-azobenzene complexes, along with an almost completely chirality conserving photochemical pathway for these helical enantiomers. | Padmabati Mondal; Giovanni Granucci; Dominique Rastädter; Maurizio Persico; Irene Burghardt | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2018-01-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d51f96a00d3f7285d69/original/azobenzene-as-a-photoregulator-covalently-attached-to-rna-a-quantum-mechanics-molecular-mechanics-surface-hopping-dynamics-study.pdf |
60c755a24c8919caa2ad46f4 | 10.26434/chemrxiv.14138636.v1 | Predicting Single-Substance Phase Diagrams: A Kernel Approach on Graph Representations of Molecules | <p>This work presents a
Gaussian process regression (GPR) model on top of a novel graph representation
of chemical molecules that predicts thermodynamic properties of pure substances
in single, double, and triple phases. A transferable molecular graph
representation is proposed as the input for a marginalized graph kernel, which
is the major component of the covariance function in our GPR models. Radial
basis function kernels of temperature and pressure are also incorporated into
the covariance function when necessary. We predicted three types of
representative properties of pure substances in single, double, and triple phases,
i.e., critical temperature, vapor-liquid equilibrium (VLE) density, and
pressure-temperature density. The data is collected from Knovel
Data Analysis Beta: NIST ThermoDynamics Pure Compounds. The accuracy of the
models is nearly identical to the precision of the experimental measurements.
Moreover, the reliability of our predictions can be quantified on a per-sample
basis using the posterior uncertainty of the GPR model. We compare our model
against Morgan fingerprints and a graph neural network to further demonstrate
the advantage of the proposed method. The
marginalized graph kernel is computed using GraphDot package at <a href="https://github.com/yhtang/GraphDot">https://github.com/yhtang/GraphDot</a>. All codes used in this work can be found at <a href="https://github.com/Xiangyan93/Chem-Graph-Kernel-Machine">https://github.com/Xiangyan93/Chem-Graph-Kernel-Machine</a>.</p> | Yan Xiang; Yu-Hang Tang; Hongyi Liu; Guang Lin; Huai Sun | Artificial Intelligence; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755a24c8919caa2ad46f4/original/predicting-single-substance-phase-diagrams-a-kernel-approach-on-graph-representations-of-molecules.pdf |
60c747e6702a9b55dd18ae82 | 10.26434/chemrxiv.11815830.v1 | A Boron-Boron Double Transborylation Strategy for the Synthesis of gem-Diborylalkanes | 9-Borabicyclo[3.3.1]nonane
(H-<i>B</i>-9-BBN) has been used as a catalyst
for the sequential double hydroboration of alkynes with pinacolborane (HBpin) to give alkyl gem-di-pinacol boronic esters. This
strategy, which is effective for a wide range of terminal alkynes, is
predicated upon a key C(<i>sp</i><sup>3</sup>)-B
/ B-H transborylation reaction.
Transition-state thermodynamic parameters and 10-boron-isotopic labelling
experiments are indicative of an <i>σ</i>-bond
metathesis exchange pathway. | Jamie Docherty; Kieran Nicholson; Andrew P Dominey; Stephen Thomas | Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747e6702a9b55dd18ae82/original/a-boron-boron-double-transborylation-strategy-for-the-synthesis-of-gem-diborylalkanes.pdf |
66e53e5bcec5d6c142053293 | 10.26434/chemrxiv-2024-2d1m1-v2 | New Frontiers of Triazolate-based MOFs: Amine-Functionalization for Enhanced Diluted CO2 Capture Performance | Capturing CO2 at low concentrations is essential for mitigating indoor air pollution and meeting the increasing demand for effective carbon capture technologies in environments where even trace levels of CO2 can significantly impact human health. This study introduces preparation of novel Zn(II)-based metal-organic framework, NICS-24, featuring diaminotriazole and oxalate linkers which form two types of square-shaped channels. NICS-24 was compared with compositionally related triazolate oxalate (CALF-20) and aminotriazolate oxalate (CALF-15) materials to evaluate the impact of amino functions on CO2 capture capabilities. While CALF-20 showed the highest CO2 uptake at 1 bar, NICS-24 excelled in capturing CO2 at low partial pressures, achieving 1.2 mmol/g at 2 mbar. The presence of amine functions in NICS-24 significantly enhanced CO2 binding and improved selectivity over N2 and O2, driven by narrower pores in comparison to CALF-20. In humid environment, NICS-24 maintained its structural integrity but exhibited reduced CO2 capture performance. In-depth investigation into CO2 adsorption mechanism under humid conditions was conducted, through the aspects of sorption breakthrough experiments, atomistic NMR studies and DFT computational approach. Competitive adsorption mechanism is in favour to water due to the specific framework hydrogen-bonding interactions. Gained understanding of the interaction between CO2 and water within the MOF framework could guide the modification via rational design with improved performance under real-world condition. | Klara Klemenčič; Andraž Krajnc; Andreas Puškarić; Matej Huš; Dana Marinič; Blaž Likozar; Nataša Zabukovec Logar; Matjaž Mazaj | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e53e5bcec5d6c142053293/original/new-frontiers-of-triazolate-based-mo-fs-amine-functionalization-for-enhanced-diluted-co2-capture-performance.pdf |
653d69a948dad231209b07f6 | 10.26434/chemrxiv-2023-kmjst | Unaddressed Uncertainties When Scaling Regional Aircraft Emissions Surveys to Basin Emission Estimates | Wide-area aerial methods provide comprehensive screening of methane emissions from oil and gas (O&G) facilities in production basins. Emissions detections (`plumes') from these studies are also frequently scaled to basin level. However, little information exists to determine if plumes detected fugitive emissions or known, reported, maintenance activities. This study analyzed an aircraft field study in the Denver-Julesberg basin to quantify how often plumes identified maintenance events, using a geospatial inventory of 12,629 O&G facilities with facility outlines. Study partners (7 midstream and production operators) provided timing and location of 5910 maintenance events that occurred in a 6-week period. Results indicated three substantial uncertainties with potential bias unaddressed by current prior studies. First, plumes often detect maintenance events, which short-duration, large, and poorly estimated by aircraft methods: 9.2% to 48% [35% to 62%] of plumes on production were likely due to known maintenance events. Second, data indicated that plumes on midstream facilities were both infrequent and unpredictable, calling into question whether these estimates were representative of midstream emissions. Finally, 4 plumes attributed to O&G, representing 19% of all emissions, were not aligned with any location that would logically create emissions. While it is unclear how frequently this occurs, in this study it had material impact on emissions estimates and was detectable only with complete geospatial information. While aircraft emissions detection remains a powerful tool for identifying methane emissions on oil and gas facilities, this study indicates that additional data inputs, such as detailed GIS data, a more nuanced analysis of emission persistence and frequency, and improved sampling strategies are required to accurately scale plume estimates to basin emissions. | Daniel Zimmerle; Sonu Dileep; Casey Quinn | Energy; Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Environmental Science | CC BY 4.0 | CHEMRXIV | 2023-10-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653d69a948dad231209b07f6/original/unaddressed-uncertainties-when-scaling-regional-aircraft-emissions-surveys-to-basin-emission-estimates.pdf |
65d2fb369138d231616f7bc9 | 10.26434/chemrxiv-2024-sbv85-v2 | Completely Solvent-free Synthesis of Double Heterohelicenes and Their Further Ring Fusion Using Mechanochemical Reaction | In this study, we developed a simple and efficient method for synthesizing double heterohelicenes (DHHs) composed of two heteroacenes bearing an NH group, such as benzo[b]phenoxazine (BPO) and dibenzo[b,i]phenoxazines (DBPO), using mechanochemical oxidative C–N coupling reactions, allowing complete solvent-free synthesis from commercially available compounds. Our new synthetic method afforded more than 1 g of DHH, which has a high dissymmetry factor for circularly polarized luminescence (gCPL) of > 1 × 10−2, in a one-pot mechanochemical reaction using BPO as a reactant. In addition, mechanochemical oxidative coupling also allows for further fusion reactions of DHHs, leading to semi- or fully planarized molecules, which have not been previously achieved through solution-phase reactions. We isolated semi-planarized heterohelicenes 5 and 6 and determined their structures using single-crystal X-ray analysis. Compounds 5 and 6 exhibited enhanced electron donor properties compared to DHHs 3 and 4. The enantiomers of 6 exhibited clear CPL emissions with a |gCPL| value of 2 × 10−3. The magnitudes of the transition magnetic dipole moment (TMDM) of 5 and 6 increased compared to those of 3 and 4. Transition moment density analysis revealed that large TMDM densities appeared on the newly formed C–C bonds, providing a unique molecular design guideline for enhancing the magnitude of the TMDM without expanding the molecular structure. | Honoka Sada; Daisuke Sakamaki; Masayuki Gon; Kazuo Tanaka; Takashi Hirose; Hideki Fujiwara | Physical Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Physical Organic Chemistry; Structure; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d2fb369138d231616f7bc9/original/completely-solvent-free-synthesis-of-double-heterohelicenes-and-their-further-ring-fusion-using-mechanochemical-reaction.pdf |
60c743e4bb8c1ab59d3da3d8 | 10.26434/chemrxiv.9685481.v1 | Molecular Engineering of β-Substituted Oxoporphyrinogens for Hydrogen-Bond Donor Catalysis | <p>A
new class of bifunctional hydrogen-bond donor organocatalyst using
oxoporphyrinogens with increased intramolecular hydrogen-bond donor distances
is reported. Oxoporphyrinogens are highly non-planar rigid macrocycles
containing a multiple hydrogen bond forming binding site. In this work we
report the first example of non-planar OxPs as hydrogen-bond donor catalysts. The
introduction of β-substituents is key to the catalytic activity and the
catalysts are able to catalyze 1,4-conjugate additions and sulfa-Michael
additions, as well as, Henry and aza-Henry reactions at low catalyst loadings
(≤ 1 mol%) under mild conditions. Preliminary mechanistic studies have been
carried out and a possible reaction mechanism has been proposed based on the
bi-functional activation of both substrates through hydrogen-bonding
interactions.</p> | Mandeep K. Chahal; Daniel Payne; Yoshitaka Matsushita; Jan Labuta; Katsuhiko Ariga; Jonathan P. Hill | Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743e4bb8c1ab59d3da3d8/original/molecular-engineering-of-substituted-oxoporphyrinogens-for-hydrogen-bond-donor-catalysis.pdf |
631d528a49042ad4acd30fcc | 10.26434/chemrxiv-2022-mlmf3 | Machine Learning-Enhanced High-Throughput Fabrication and Optimization of Quasi-2D Ruddlesden-Popper Perovskite Solar Cells | Organic-inorganic perovskite solar cells (PSCs) are promising candidates for next-generation, inexpensive solar panels due to their high power conversion efficiency, which is on par with their commercial silicon counterparts. However, PSCs suffer from poor stability. A new subset of PSCs, quasi-two-dimensional Ruddlesden-Popper PSCs (quasi-2D RP PSCs), is known for improved photostability and superior resilience to environmental conditions in comparison with three-dimensional (3D) metal-halide PSCs. To expedite the search of new quasi-2D RP PSCs we report a combinatorial, machine learning (ML) enhanced high-throughput perovskite film fabrication and optimization study. We designed a bespoke experiment strategy and produced perovskite films with a range of different compositions through a fully automated drop-casting process. The performance and characterization data of these solar cells were used to train a ML model that allowed for material parameter optimization and directed the design of improved materials. The ML optimized quasi-2D RP perovskite films yielded solar cells with power conversion efficiencies reaching 16.3%. | Nastaran Meftahi; Maciej Adam Surmiak; Sebastian O. Furer; Kevin James Rietwyk; Jianfeng Lu; Sonia Ruiz Raga; Caria Evans; Monika Michalska; Hao Deng; David P. McMeekin; Tuncay Alan; Dechan Angmo; Doojin Vak; Anthony Chesman; Andrew J. Christofferson; David A. Winkler; Udo Bach; Salvy P. Russo | Theoretical and Computational Chemistry; Materials Science; Energy; Machine Learning; Artificial Intelligence; Photovoltaics | CC BY 4.0 | CHEMRXIV | 2022-09-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/631d528a49042ad4acd30fcc/original/machine-learning-enhanced-high-throughput-fabrication-and-optimization-of-quasi-2d-ruddlesden-popper-perovskite-solar-cells.pdf |
60c759b0337d6cb59be29455 | 10.26434/chemrxiv.14720844.v1 | Data-Driven Prediction of Formation Mechanisms of Lithium Ethylene Monocarbonate with an Automated Reaction Network | <div><div><div><p>Interfacial reactions are notoriously difficult to characterize and robust prediction of the chemical evolution and associated functionality of the resulting surface film is one of the grand challenges of materials chemistry. The solid–electrolyte interphase (SEI), critical to the operation of Li-ion batteries (LIB), exemplifies such a surface film and despite decades of work, considerable controversy remains regarding the major components of the SEI as well as their formation mechanisms. In this work, we present pioneering results of a newly developed data-driven reaction network addressing the recent question whether lithium ethylene monocarbonate (LEMC) or lithium ethylene dicarbonate (LEDC) is the major organic component of the LIB SEI. Our data-driven, automated methodology is based on a systematic generation of relevant species using a general fragmentation/recombination procedure which provides the basis for our vast thermodynamic reaction landscape, calculated with density functional theory (DFT). The graph implementation of the reaction landscape is subsequently explored using shortest pathfinding algorithms, identifying reactions to LEMC from EC, Li+ and H2O under the electron chemical potential of Li metal. Confirming the viability of our approach, the reaction network automatically recovers previously-proposed formation mechanisms of LEMC from EC and LEDC through hydrolysis, among which the direct hydrolysis of EC under basic conditions is found to be the most kinetically favorable. We also identify several other new reaction pathways to LEMC, illustrating the complex and competitive landscape of possible electrochemical electrolyte decomposition reactions. For example, we recover a LEMC formation mechanism that generates lithium hydride as a by-product and a radical mechanism through breaking the (CH2)O–C(–O)OLi bond in LEDC, neither of which has been proposed previously. Most importantly, we find that all identified paths, which are also kinetically favorable under the explored conditions, require water as a reactant. This condition severely limits the amount of LEMC that can form, as compared to LEDC, a conclusion that has direct impact on our understanding of SEI formation in Li-ion energy storage systems. Finally, we emphasize that our framework demonstrates robust, automated, data-driven predictions of novel interfacial reaction mechanisms and this framework is generally applicable to other reactive systems.</p></div></div></div> | Xiaowei Xie; Evan Spotte-Smith; Hetal Patel; Samuel Blau; Kristin Persson | Electrochemistry; Computational Chemistry and Modeling; Electrochemistry - Mechanisms, Theory & Study; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c759b0337d6cb59be29455/original/data-driven-prediction-of-formation-mechanisms-of-lithium-ethylene-monocarbonate-with-an-automated-reaction-network.pdf |
6603e396e9ebbb4db9a9c47a | 10.26434/chemrxiv-2024-2jwqj | Aggregation of N-Heteropolycyclic Aromatic Molecules: The Acridine Dimer and Trimer | Polycyclic aromatic hydrocarbons and their nitrogen-substituted analogues are of great interest for various applications in organic electronics. The performance of such devices is determined not only by the properties of the single molecules, but also by the structure of their aggregates, which often form via self-aggregation. Gaining insight into such aggregation processes is a challenging task, but crucial for a fine-tuning of the materials properties. In this work, an efficient approach for the generation and characterisation of aggregates is described, based on matrix-isolation experiments and quantum-chemical calculations. This approach is exemplified for aggregation of acridine. The acridine dimer and trimer are thoroughly analysed on the basis of matrix-isolation spectroscopy over two spectral ranges and quantum chemical calculations, which agree well with each other. Thereby a novel structure of the acridine dimer is found, which disagrees with a previously reported one. In addition, a structure of the trimer is determined and new insight into the photophysics of small acridine aggregates is gained. Finally, an outlook is given on how even higher aggregates can be made accessible through experiment. | Hans-Jörg Himmel; Stefan Germer; Marco Bauer; Olaf Hübner; Andreas Dreuw | Physical Chemistry; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6603e396e9ebbb4db9a9c47a/original/aggregation-of-n-heteropolycyclic-aromatic-molecules-the-acridine-dimer-and-trimer.pdf |
60c73f5b567dfe506bec39c9 | 10.26434/chemrxiv.7315043.v1 | Proton Conductivity, Stability and Potential for Polymorphism in Metal-Organic Framework Minerals | We demonstrate that rare metal-organic framework (MOF) minerals stepanovite and zhemchuzhnikovite can exhibit properties comparable to known oxalate MOFs, including high proton conductivity at 25 <sup>o</sup>C, and retention of the framework structure upon thermal dehydration. They also have high thermodynamic stability, with a pronounced stabilizing effect of substituting aluminium for iron, illustrating a simple design to access stable, highly proton-conductive MOFs without using complex organic ligands. <br /> | Igor Huskić; Novendra Novendra; Dae-Woo Lim; Filip Topic; Hatem M. Titi; Igor Pekov; Sergey Krivovichev; Alexandra Navrotsky; Hiroshi Kitagawa; Tomislav Friscic | Geochemistry; Organometallic Compounds; Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2018-11-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f5b567dfe506bec39c9/original/proton-conductivity-stability-and-potential-for-polymorphism-in-metal-organic-framework-minerals.pdf |
60c747e0469df41f89f438fc | 10.26434/chemrxiv.9778967.v2 | Spectroscopic investigations under whole cell conditions provide new insight into the metal hydride chemistry of [FeFe]-hydrogenase | Hydrogenases are among the fastest H2 evolving catalysts known to date and have been extensively studied under in vitro conditions. Here, we report the first mechanistic investigation of an [FeFe]-hydrogenase under in vivo conditions. Functional [FeFe]-hydrogenase from the green alga Chlamydomonas reinhardtii is generated in genetically modified Escherichia coli cells, by addition of a synthetic cofactor to the growth medium. The assembly and reactivity of the resulting semi-synthetic enzyme was monitored using whole-cell electron paramagnetic resonance as well as Fourier-transform infrared spectroscopy. Through a combination of gas treatments, pH titrations and isotope editing, we were able to corroborate the physiological relevance of a number of proposed catalytic intermediates, including reactive iron-hydride species. We demonstrate the formation of the so-called hydride state in vivo. Moreover, two previously uncharacterized redox species are reported herein, illustrating the complex metal hydride chemistry of [FeFe]-hydrogenase.<br /> | Lívia S. Mészáros; Pierre Ceccaldi; Marco Lorenzi; Holly J. Redman; Emanuel Pfitzner; Joachim Heberle; Moritz Senger; Sven T. Stripp; Gustav Berggren | Biochemistry; Biophysics; Cell and Molecular Biology; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747e0469df41f89f438fc/original/spectroscopic-investigations-under-whole-cell-conditions-provide-new-insight-into-the-metal-hydride-chemistry-of-fe-fe-hydrogenase.pdf |
65834c6e66c1381729aa3fcb | 10.26434/chemrxiv-2023-zntk5 | Discerning ambiguous internal fragment assignments that are generated in top-down mass spectrometry with cyclic ion-mobility enhances protein sequence information | Top-down mass spectrometry (TD-MS) has become a central technique for the analysis of intact proteins, and internal fragments (fragments containing neither the C- nor N-terminus) have been utilized to enhance the sequence information extracted from such experiments. A key obstacle to including internal fragments in TD-MS workflows stems from potential ambiguities in their assignments, which can severely impact the confidence of assignments and increase false discovery. To utilize internal fragments in TD-MS precisely, it is therefore crucial to discern ambiguous internal fragment assignments. Here, we demonstrate that by including ion mobility, ambiguous internal fragments can be discerned to enable more confident assignments. For example, the β-Casein-derived internal fragments a115¬-x132 and a114¬-x131 were both assigned to 1000.51 m/z; however, ion mobility of this m/z showed two different arrival time distributions: 25.5 ms and 30.0 ms. The different theoretical volumes of a115¬-x132 and a114¬-x131 – 680.6 and 682.3 respectively – enabled their assignments to the respective 25.5 ms and 30.0 ms arrival times. For the test proteins myoglobin, carbonic anhydrase II, β-Casein, and bovine serum albumin, the inclusion of ion mobility discerned internal fragments increased sequence coverage from <55% to >85%, which is near complete sequence coverage for these proteins. By applying this method to a protein complex, trustuzamab, the sequence coverage and sequence information returned for both the heavy and light chains were 85% and 90% respectively. These data demonstrate that the inclusion of ion mobility in TD-MS experiments can enhance the confidence of internal fragment assignments, and significantly extend protein sequence information relative to TD-MS experiments that do not incorporate ion mobility. | Muhammad Zenaidee; Tyren Dodgen; Luke Carroll; Gene Hart-Smith | Analytical Chemistry; Analytical Chemistry - General; Biochemical Analysis; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65834c6e66c1381729aa3fcb/original/discerning-ambiguous-internal-fragment-assignments-that-are-generated-in-top-down-mass-spectrometry-with-cyclic-ion-mobility-enhances-protein-sequence-information.pdf |
60c73d35337d6c19dce260f5 | 10.26434/chemrxiv.5509120.v1 | C-H bond Activation/Arylation over Arene-Ruthenium(II)-picolinate Complexes: Synthesis, Structure and Catalytic Activity | <p>A
series of water soluble arene-ruthenium(II) complexes [(<i>η</i><sup>6</sup>-arene)RuCl(κ<sup>2</sup>-L)]<sup>n+</sup> (n = 0, 1) (<b>[Ru]-1</b> – <b>[Ru]-12</b>) containing pyridine based N,O or N,N ligands (<b>L1-L6</b>) were synthesized and employed
for the catalytic C-H bond activation/ arylation of 2-phenylpyridine with aryl
halides in water. Efficient C-H bond activation/ arylation of a wide range of
substituted 2-phenylpyridines and aryl halides were achieved to afford corresponding
mono and biarylated products. Exploring the reactivity of the synthesized
complexes, our investigation with ruthenium catalysts inferred that pyridine
based N,O donor ligands afforded enhanced catalytic activity compared to those
obtained with the iminopyridine (N,N donor) ligands. Further, mass
spectrometric investigations, during the catalytic and controlled reaction
conditions, evidenced the presence of the crucial cycloruthenated species {(<i>η</i><sup>6</sup>-<i>p</i>-cymene)Ru(<i>κ</i><sup>2</sup>-<i>CN</i>-phenylpyridine)}<sup>+</sup> (m/z [M<sup>+</sup>]
390.0), along with a ligand coordinated species, {(<i>η</i><sup>6</sup>-<i>p</i>-cymene)Ru(<b>L1</b>)(<i>κ</i><sup>2</sup>-<i>CN</i>-phenylpyridine)}<sup>+</sup> (m/z [M<sup>+</sup>]+Na
539.0), suggesting the important role such intermediate species in C-H bond
activation reactions. Moreover, molecular structures for few of the representative
complexes were also authenticated by single crystal X-ray diffraction studies.</p> | Chinky Binnani; Rohit K. Rai; Deepika Tyagi; Shaikh M Mobin; Sanjay Kumar Singh | Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2017-10-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d35337d6c19dce260f5/original/c-h-bond-activation-arylation-over-arene-ruthenium-ii-picolinate-complexes-synthesis-structure-and-catalytic-activity.pdf |
6787d6a7fa469535b925c5fc | 10.26434/chemrxiv-2025-j7f10 | “Writing” Crystal Phases in Amorphous Calcium Carbonate via Bio-Inspired Laser-Induced Patterned Transformations | Biomineralization demonstrates nature's remarkable ability to precisely regulate mineral formation, controlling both polymorph selection and spatial organization. This fascinating level of precision has inspired our investigation into spatially controlled, laser-induced crystallization. To this end, we employed laser-induced patterned crystallization within a Mg-stabilized amorphous calcium carbonate (ACC) matrix, generating four distinct phases: calcite, stable dehydrated ACC, monohydrocalcite, and hydromagnesite. We investigated the parameters affecting phase formation and determined that it is governed by laser power and scanning rate. Our calculations allowed us to determine the temperature generated under these conditions, spanning a range of laser powers and scan rates, leading to the development of a model explaining the formation of each phase. This allowed us to reproducibly "write" crystal phases on the surface in a spatially controlled and rationally designed manner. This research presents a novel approach to laser-induced spatial patterning of multiple crystallographic phases through an amorphous precursor, opening new avenues for bio-inspired studies and offering fresh insights into crystallization mechanisms from amorphous precursors. | Hadar Shaked; Iryna Polishchuk; Niv Ben-Arie; Daniela Dobrynin ; Javier Gainza; Alexander Katsman ; Boaz Pokroy | Materials Science; Inorganic Chemistry; Ceramics; Minerals; Materials Chemistry; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6787d6a7fa469535b925c5fc/original/writing-crystal-phases-in-amorphous-calcium-carbonate-via-bio-inspired-laser-induced-patterned-transformations.pdf |
6682a6c25101a2ffa8024d13 | 10.26434/chemrxiv-2024-7hj35-v2 | Structural Heterogeneity of the Humanised IgGk NIST Monoclonal Antibody Probed by Tandem-Trapped Ion Mobility Spectrometry and Mobility-Resolved Collision-induced Unfolding. | Investigating the structural heterogeneity of monoclonal antibodies is crucial to achieving optimal therapeutic outcomes. We show that tandem-trapped ion mobility spectrometry enables collision-induced unfolding measurements of antibody subpopulations. Our data suggest that such non-ensemble measurements will improve the structural characterisation of complex biotherapeutics such as multivalent antibodies. | Fanny C. Liu; Jusung Lee; Thais Pedrete; Erin M. Panczyk; Stuart Pengelley; Christian Bleiholder | Analytical Chemistry; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6682a6c25101a2ffa8024d13/original/structural-heterogeneity-of-the-humanised-ig-gk-nist-monoclonal-antibody-probed-by-tandem-trapped-ion-mobility-spectrometry-and-mobility-resolved-collision-induced-unfolding.pdf |
60c7436d4c891968f7ad2627 | 10.26434/chemrxiv.9101405.v1 | Mechanistic Insights into Fe Catalyzed α-C-H Oxidations of Tertiary Amines | We report detailed mechanistic investigations of an iron-based catalyst system, which allows the α-C-H oxidation of a wide variety of amines, including acyclic tertiary aliphatic amines, to afford dealkylated or amide products. In contrast to other catalysts that affect α-C-H oxidations of tertiary amines, the system under investigation employs exclusively peroxy esters as oxidants. More common oxidants (e.g. tBuOOH) previously reported to affect amine oxidations via free radical pathways do not provide amine α-C-H oxidation products in combination with the herein described catalyst system. Motivated by this difference in reactivity to more common free radical systems, the investigations described herein employ initial rate kinetics, kinetic profiling, Eyring studies, kinetic isotope effect studies, Hammett studies, ligand coordination studies, and EPR studies to shed light on the Fe catalyst system. The obtained data suggest that the catalytic mechanism proceeds through C-H abstraction at a coordinated substrate molecule. This rate-determining step occurs either at an Fe(IV) oxo pathway or a 2-electron pathway at a Fe(II) intermediate with bound oxidant. We further show via kinetic profiling and EPR studies that catalyst activation follows a radical pathway, which is initiated by hydrolysis of PhCO3 tBu to tBuOOH in the reaction mixture. Overall, the obtained mechanistic data support a non-classical, Fe catalyzed pathway that requires substrate binding, thus inducing selectivity for α-C-H functionalization.<br /> | Christopher J. Legacy; Frederick T. Greenaway; Marion Emmert | Organic Synthesis and Reactions; Physical Organic Chemistry; Coordination Chemistry (Inorg.); Ligands (Inorg.); Reaction (Inorg.); Spectroscopy (Inorg.); Transition Metal Complexes (Inorg.); Homogeneous Catalysis; Redox Catalysis; Bond Activation; Catalysis; Kinetics and Mechanism - Organometallic Reactions; Ligand Design; Ligands (Organomet.); Reaction (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7436d4c891968f7ad2627/original/mechanistic-insights-into-fe-catalyzed-c-h-oxidations-of-tertiary-amines.pdf |
60c74afd842e657a2fdb3048 | 10.26434/chemrxiv.12278588.v1 | Identification of Potential Binders of the SARS-Cov-2 Spike Protein via Molecular Docking, Dynamics Simulation and Binding Free Energy Calculation | <p>The
pandemic outbreak of COVID-19 virus (SARS-CoV-2) has become critical
global health issue. The biophysical and structural evidence shows that SARS-CoV-2
spike protein possesses higher binding affinity towards angiotensin-converting
enzyme 2 (ACE2) and hemagglutinin-acetylesterase (HE) glycoprotein receptor.
Hence, it was selected as a target to generate the potential candidates for the
inhibition of HE glycoprotein. The present study focuses on extensive
computational approaches which contains molecular docking, ADMET prediction
followed by molecular dynamics simulations and free energy calculations.
Furthermore, virtual screening of NPACT compounds identified 3,4,5-Trihydroxy-1,8-bis[(2R,3R)-3,5,7-trihydroxy-3,4-dihydro-2H-chromen-2-yl]benzo[7]annulen-6-one,
Silymarin, Withanolide D, Spirosolane and Oridonin were interact with high
affinity. The ADMET prediction revealed pharmacokinetics and drug-likeness
properties of top-ranked compounds. Molecular dynamics simulations and binding
free energy calculations affirmed that these five NPACT compounds were robust
HE inhibitor.</p> | Dr. Chirag N. Patel; Dr. Prasanth Kumar S.; Dr. Himanshu A. Pandya; Dr. Rakesh M. Rawal | Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74afd842e657a2fdb3048/original/identification-of-potential-binders-of-the-sars-cov-2-spike-protein-via-molecular-docking-dynamics-simulation-and-binding-free-energy-calculation.pdf |
61892793ef38c045946b90b3 | 10.26434/chemrxiv-2021-1c0c4 | Quantifying Fluctuations of Average Environments for Embedding Calculations | In the context of employing embedding methods to study spectroscopic properties, the viability and effectiveness of replacing an ensemble of calculations by a single calculation using an average description of the system of study are evaluated. This work aims to provide a baseline of the expected fluctuations in the average description of the system obtained in the two cases: from calculations of an ensemble of geometries, and from an average environment constructed with the same ensemble. To this end, the classical molecular dynamics simulation of a very simple system was used: a rigid molecule of acetone in a solution of rigid water. We perform a careful numerical analysis of the fluctuations of the electrostatic potential felt by the solute, as well as the fluctuations in the effect on its electronic density, measure through the dipole moment and the atomic charges derived from the corresponding potential. At the same time, we inspect the accuracy of the methods used to construct average environments. Finally, the proposed approach to generate the embedding potential from an average environment density is applied to estimate the solvatochromic shift of the first excitation of acetone. In order to account for quantum-confinement effects that may be important in certain cases, the fluctuations on the shift due to the interaction with the solvent are evaluated using Frozen-Density Embedding Theory. Our results demonstrate that, for normally-behaved environments, the constructed average environment is a reasonably good representation of a discrete solvent environment. | Cristina Gonzalez; Christopher A. Rumble; Daniel Borgis; Tomasz A. Wesolowski | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Spectroscopy (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2021-11-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61892793ef38c045946b90b3/original/quantifying-fluctuations-of-average-environments-for-embedding-calculations.pdf |
60c750c70f50dba327397626 | 10.26434/chemrxiv.13083887.v1 | Polysulfide Anions as Visible Light Photoredox Catalysts for Aryl Cross-Couplings | Herein, we disclose the use of polysulfide anions as visible light photoredox catalysts for aryl cross-coupling reactions. The reaction design enables single-electron-reduction of aryl halides upon photo-excitation of tetrasulfide dianions (S<sub>4</sub><sup>2–</sup>). The resulting aryl radicals are engaged in (hetero)biaryl cross-coupling, borylation, and hydrogenation in a redox catalytic regime involving S<sub>4</sub><sup>•–</sup>/S<sub>4</sub><sup>2–</sup> and S<sub>3</sub><sup>•–</sup>/S<sub>3</sub><sup>2–</sup> redox couples. | Haoyu Li; Xinxin Tang; Jia Hao Pang; Xiangyang Wu; Edwin K. L. Yeow; Jie Wu; Shunsuke Chiba | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750c70f50dba327397626/original/polysulfide-anions-as-visible-light-photoredox-catalysts-for-aryl-cross-couplings.pdf |
649b36d5ba3e99daef228672 | 10.26434/chemrxiv-2023-bt02b | Microstructural model of Indacenodithiophene-co-benzothiadiazole Polymer: π-crossing interactions and their potential impact on charge transport | Morphological and electronic properties of Indacenodithiophene-co-benzothiadiazole (IDTBT) co-polymer with varying molecular weights are calculated through combined molecular dynamics (MD) and quantum chemical (QC) methods. Our study focuses on the polymer chain arrangements, interchain connectivity pathways, and interplay between morphological and electronic structure properties of IDTBT. Our models, which are verified against X-ray scattering measurements, show a considerable number of BT-BT π-π interactions with a (preferential) perpendicular local orientation of polymer chains due to the steric hinderance of bulky sidechains around IDT. The BT-BT (interchain) crossing points show some degree of order in spatial arrangement which most likely result in a mesh-like structure for the polymer and provide efficient pathways for interchain charge transport. | Hesam Makki; Colm Burke; Alessandro Troisi | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2023-06-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649b36d5ba3e99daef228672/original/microstructural-model-of-indacenodithiophene-co-benzothiadiazole-polymer-crossing-interactions-and-their-potential-impact-on-charge-transport.pdf |
6250071985d81407b401b1e1 | 10.26434/chemrxiv-2022-6lvgb | DNA-Origami surface patterning through polymer conjugation | The combination of DNA-origami and synthetic polymers paves the way to a new class of structurally precise biohybrid nanomaterials for diverse applications. Herein, we introduce the grafting to method with high conversions (70-90%) under ambient conditions to generate DNA-polymer conjugates, which can hybridized precisely to DNA-origami architectures. We generated homo and block copolymers from three different polymer families (acrylates, methacrylates and acrylamides), coupled them to single stranded DNA (ssDNA) and pattern different DNA-origami architectures to demonstrate the formation of precise surface nanopatterns.
| Nico Alleva; Pia Winterwerber; Colette J. Whitfield; David Ng; Tanja Weil | Polymer Science; Nanoscience; Biopolymers; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6250071985d81407b401b1e1/original/dna-origami-surface-patterning-through-polymer-conjugation.pdf |
648fc466be16ad5c572269d6 | 10.26434/chemrxiv-2023-6j4nx | Prediction of antibacterial interaction between essential oils via graph embedding approach | Essential oils contain a variety of volatile metabolites, and are expected to be utilized in wide fields such as antimicrobials, insect repellents and herbicides. However, it is difficult to foresee the effect of mixing the oils because hundreds of compounds can be involved in synergistic and antagonistic interactions. For efficient formula optimization, we have developed and evaluated a machine learning method to classify antibacterial interactions between the oils. Cross-validation showed that graph embedding improved areas under the ROC curves for synergistic-versus-rest classification. Furthermore, antibacterial assay against Staphylococcus aureus revealed that oregano–ajowan, lemongrass–hiba, cinnamon–lemongrass and ajowan–ginger combinations exhibited synergistic interaction as predicted. These results indicate that graph embedding approach is useful for predicting synergistic interaction between antibacterial essential oils. | Hiroaki Yabuuchi; Kazuhito Hayashi; Akihiko Shigemoto; Makiko Fujiwara; Yuhei Nomura; Mayumi Nakashima; Takeshi Ogusu; Megumi Mori; Shin-ichi Tokumoto; Kazuyuki Miyai | Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems; Plant Biology | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/648fc466be16ad5c572269d6/original/prediction-of-antibacterial-interaction-between-essential-oils-via-graph-embedding-approach.pdf |
6690cfd401103d79c5c94f88 | 10.26434/chemrxiv-2024-rh4m7 | Anti-Schistosomal Activity and ADMET Properties of 1,2,5-Oxadiazinane-Containing Compound Synthesized by Visible-Light Photoredox Catalysis | The incorporation of saturated nitrogen-containing heterocycle 1,2,5-oxadiazinane into small molecules represents a compelling avenue in drug discovery due to its unexplored behavior within biological systems and incomplete protocols for synthesis. In this study, we present 1,2,5-oxadiazinane, an innovative heterocyclic bioisostere of piperizin-2-one and novel chemotype of the anti-schistosomal drug praziquantel (PZQ), which has been the only clinical drug available for three decades. PZQ is associated with significant drawbacks, including poor solubility, a bitter taste, and low metabolic stability. Therefore, the discovery of a new class of anti-schistosomal agents is imperative. To address this challenge, we introduce a pioneering method for the synthesis of 1,2,5-oxadiazinane derivatives through the cycloaddition of nitrones with N,N,N',N'-tetraalkyldiaminomethane in the presence of an IrIII complex photosensitizer. This transformative reaction offers a streamlined route to various kinds of 1,2,5-oxadiazinanes that is characterized by mild reaction conditions and broad substrate scope. Mechanistic investigations suggest that the photoredox pathway underlies the [3+3] photocycloaddition process. Thus, based on bioisosteric replacement, we identified a remarkable molecule as a new chemotype of a potent anti-schistosomal compound that not only exhibits superior solubility, but also retains the potent biological activity inherent to PZQ. | Kennosuke Itoh; Hiroki Nakahara; Atsushi Takashino; Aya Hara; Akiho Katsuno; Yuriko Abe; Takaaki Mizuguchi; Fumika Karaki; Shigeto Hirayama; Kenichiro Nagai; Reiko Seki; Noriko Sato; Kazuki Okuyama; Masashi Hashimoto; Ken Tokunaga; Hitoshi Ishida; Fusako Mikami; Kofi Dadzie Kwofie; Hayato Kawada; Bangzhong Lin; Kazuto Nunomura; Toshio Kanai; Takeshi Hatta; Naotoshi Tsuji; Junichi Haruta; Hideaki Fujii | Biological and Medicinal Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.); Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6690cfd401103d79c5c94f88/original/anti-schistosomal-activity-and-admet-properties-of-1-2-5-oxadiazinane-containing-compound-synthesized-by-visible-light-photoredox-catalysis.pdf |
60c73df2702a9bd5af189c8f | 10.26434/chemrxiv.6223694.v1 | Isomeric Equilibria, Nuclear Quantum Effects, and Vibrational Spectra of M+(H2O)n=1−3 Clusters, with M = Li, Na, K, Rb, and Cs, Through Many-Body Representations | <div>
<div>
<div>
<p>A quantitative characterization of the molecular mechanisms that regulate ion solvation is key to the microscopic understanding of fundamental processes taking place in
aqueous environments, with major implications for different fields, from atmospheric
chemistry to materials research and biochemistry. This study presents a systematic
analysis of isomeric equilibria for small M<sup>+</sup>(H<sub>2</sub>O)<sub>n</sub> clusters, with M = Li, Na, K, Rb,
and Cs, from 0 K to 200 K. To determine the relative stability of different isomers of each M<sup>+</sup>(H<sub>2</sub>O)<sub>n </sub>cluster as a function of temperature, replica exchange simulations are
carried out at both classical and quantum levels with the recently developed many-body
MB-nrg potential energy functions, which have been shown to exhibit chemical accuracy. Anharmonic vibrational spectra are then calculated within the local monomer
approximation and found to be in agreement with the available experimental data,
providing further support for the accuracy of the MB-nrg potential energy functions.
The present analysis indicates that nuclear quantum effects become increasingly im-
portant for larger M<sup>+</sup>(H<sub>2</sub>O)<sub>n </sub>clusters containing the heavier alkali metal ions, which
is explained in terms of competing ion-water and water-water interactions along with
the interplay between energetic and entropic effects. Directly connecting experimental
measurements with molecular properties calculated at the quantum mechanical level,
this study represents a further step toward the development of a consistent picture of
ion hydration from the gas to the condensed phase. </p>
</div>
</div>
</div> | Marc Riera; Sandra
E. Brown; Paesani Lab | Computational Chemistry and Modeling; Clusters; Physical and Chemical Properties; Quantum Mechanics; Spectroscopy (Physical Chem.); Statistical Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2018-05-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73df2702a9bd5af189c8f/original/isomeric-equilibria-nuclear-quantum-effects-and-vibrational-spectra-of-m-h2o-n-1-3-clusters-with-m-li-na-k-rb-and-cs-through-many-body-representations.pdf |
6501db3eb6ab98a41c61e16a | 10.26434/chemrxiv-2023-vsmbm | Automatic Mechanism Generation Involving Kinetics of Surface Reactions with Bidentate Adsorbates | New features have been added to the open-source Reaction Mechanism Generator (RMG) that enhance its ability to handle multidentate adsorbates. New reaction families and improved thermophysical estimation routines have been added, based upon ab-initio data from 26 reactions involving CxOyHz bidentate adsorbates with two heavy atoms on Pt(111). Non-oxidative dehydrogenation of ethane over Pt(111) is used as a case study to demonstrate the effectiveness of these new features. RMG not only discovered the pathways from prior literature, but it also uncovered new elementary steps involving abstraction reactions. Various mono- and bimetallic catalysts for this process were screened using linear scaling relations within RMG, where a unique mechanism is generated for each catalyst. These results are consistent with prior literature trends, but they add additional insight into the rate determining steps across the periodic table. With these additions, RMG can now explore more intricate reaction mechanisms of heterogeneously catalyzed processes for the conversion of larger molecules, which will be particularly important in fuel synthesis. | Bjarne Kreitz; Katrin Blöndal; Kirk Badger; Richard H. West; C. Franklin Goldsmith | Theoretical and Computational Chemistry; Catalysis; Chemical Engineering and Industrial Chemistry; Computational Chemistry and Modeling; Reaction Engineering | CC BY NC 4.0 | CHEMRXIV | 2023-09-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6501db3eb6ab98a41c61e16a/original/automatic-mechanism-generation-involving-kinetics-of-surface-reactions-with-bidentate-adsorbates.pdf |
620d6a27bd05a05b13099bf5 | 10.26434/chemrxiv-2022-wz83x | Autoinducer-Fluorophore Conjugates Enable FRET in LuxR Proteins in Vitro and in Cells | Cell-to-cell signaling, or quorum sensing (QS), in Gram-negative bacteria is governed by small molecule signals (N-acyl L-homoserine lactones, AHLs) and their cognate intracellular receptors (LuxR-type proteins). The mechanistic underpinnings of QS in these bacteria are severely limited due to the challenges of isolating and manipulating most LuxR-type proteins. Quantitative assays to characterize the direct binding of ligands to these receptors are largely non-existent. We report herein a Förster Resonance Energy Transfer (FRET) assay that leverages (i) conserved endogenous tryptophans located in the LuxR-type protein ligand-binding site and synthetic fluorophore-AHL conjugates, and (ii) isolation/stabilization of the proteins bound to weak agonists. The FRET assay permits straightforward measurement of ligand-binding affinities with receptor—either in vitro or in cells—and was shown to be compatible with six LuxR-type receptors. These methods will advance fundamental investigations of the mechanisms of LuxR-type proteins and the development of small molecule modulators of QS. | Matthew Styles; Michelle Boursier; Margaret McEwan; Emma Santa; Margrith Mattmann; Betty Slinger; Helen Blackwell | Biological and Medicinal Chemistry; Organic Chemistry; Biochemistry; Chemical Biology; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/620d6a27bd05a05b13099bf5/original/autoinducer-fluorophore-conjugates-enable-fret-in-lux-r-proteins-in-vitro-and-in-cells.pdf |
60c7456dee301c0913c792e7 | 10.26434/chemrxiv.9999971.v1 | Synthesis of 1,2-Dihydroisoquinolines by a Modified Pomeranz-Fritsch Cyclization | Isoquinolines and their derivatives are present in many natural products
and biologically active small molecules. Herein, we report a modified
procedure for the Classical Pomeranz-Fritsch protocal, which expands the
scope of 1,2-dihydroisoquinoline products. | Xiang Ji; Zheng Huang; Jean-Philip Lumb | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7456dee301c0913c792e7/original/synthesis-of-1-2-dihydroisoquinolines-by-a-modified-pomeranz-fritsch-cyclization.pdf |
60c741e7702a9b649118a338 | 10.26434/chemrxiv.8153198.v1 | Tuning the Electric Field Response of MOFs by Rotatable Dipolar Linkers | Recently the possibility of using electric fields as a further stimulus to trigger structural changes in metal-organic frameworks (MOFs) has been investigated. In general, rotatable groups or other types of mechanical motion can be driven by electric fields. In this study we demonstrate how the electric response of MOFs can be tuned by adding rotatable dipolar linkers, generating a material that exhibits paralectric behavior in two dimensions and dielectric behavior in one dimension. The suitability of four different methods to compute the relative permittivity κ by means of molecular dynamics simulations was validated. The dependency of the permittivity on temperature T and dipole strength μ was determined. It was found that the herein investigated systems exhibit a high degree of tunability and substantially larger dielectric constants as expected for MOFs in general. The temperature dependency of κ obeys the Curie-Weiss law. In addition, the influence of dipolar linkers on the electric field induced breathing behavior was investigated. With increasing dipole moment, lower field strength are required to trigger the contraction. These investigations set the stage for an application of such systems as dielectric sensors, order-disorder ferroelectrics or any scenario where movable dipolar fragments respond to external electric fields. | Johannes P. Dürholt; Babak Farhadi Jahromi; Rochus Schmid | Hybrid Organic-Inorganic Materials; Computational Chemistry and Modeling; Theory - Computational; Structure | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741e7702a9b649118a338/original/tuning-the-electric-field-response-of-mo-fs-by-rotatable-dipolar-linkers.pdf |
60c74b63f96a0043f72875d3 | 10.26434/chemrxiv.12327569.v1 | Scalable One-Pot - Liquid-Phase Oligonucleotide Synthesis for Model Network Hydrogels | Solid-phase oligonucleotide synthesis (SPOS) based on phosphoramidite chemistry is currently the most widespread technique for DNA and RNA synthesis, but suffers from scalability limitations and high reagent consumption. Liquid-phase oligonucleotide synthesis (LPOS) uses soluble polymer supports and has the potential of being scalable. However, at present, LPOS requires 3 separate reaction steps and 4-5 precipitation steps per nucleotide addition. Moreover, long acid exposure times during the deprotection step degrade sequences with high A-content (adenine) due to depurination and chain cleavage. In this work, we present the first one-pot liquid-phase DNA synthesis technique, which allows the addition of one nucleotide in a one-pot reaction of sequential coupling, oxidation and deprotection, followed by a single precipitation step. Furthermore, we demonstrate how to suppress depurination during the addition of adenine nucleotides. We showcase the potential of this technique to prepare high-purity 4-arm PEG‑T<sub>20</sub> (T = thymine) and 4-arm PEG-A<sub>20</sub>building blocks in multi-gram scale. Such complementary 4-arm PEG-DNA building blocks reversibly self-assemble into supramolecular model network hydrogels, and facilitate the elucidation of bond lifetimes. These model network hydrogels exhibit new levels of mechanical properties, high stability at room temperature (melting at 44 °C), and thus open up pathways to next-generation, scalable DNA-materials programmable through sequence recognition and available for macroscale applications<i>.</i> | Guido Creusen; Cecilia Oluwadunsin Akintayo; Katja Schumann; Andreas Walther | Biopolymers; Hydrogels; Polymerization (Polymers); Polymer morphology | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b63f96a0043f72875d3/original/scalable-one-pot-liquid-phase-oligonucleotide-synthesis-for-model-network-hydrogels.pdf |
61c363d3d6dcc26d454189b7 | 10.26434/chemrxiv-2021-gzlwx-v2 | Total Mercury Concentration of Wild Caught Fish Purchased from Grocery Stores: A Potential Public Health Concern | Methylmercury is a highly toxic organic compound that bioaccumulates and biomagnifies in the human body when absorbed by the gastrointestinal tract after ingestion.1 Thus, monitoring methylmercury levels in fish is crucial for protecting public health and preventing dramatic scenarios such as the Minamata disease crisis in Japan. In this study, three different species of wild caught fish – Sockeye Salmon (Oncorhynchus nerka) from Alaska, USA; tuna imported from Vietnam; and swordfish (Xiphias gladius) imported from Indonesia – were collected from a Harris Teeter grocery store in Washington D.C. Total mercury concentration was measured by ICP-MS and the analyzed samples’ concentrations were 19.8 ± 2.9 ppb, 2.67 ± 0.01 ppm, and 380 ± 9 ppb for Sockeye Salmon, swordfish, and tuna, respectively. | Miguel Aristu; Taylor Pollak | Earth, Space, and Environmental Chemistry; Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61c363d3d6dcc26d454189b7/original/total-mercury-concentration-of-wild-caught-fish-purchased-from-grocery-stores-a-potential-public-health-concern.pdf |
6388c07444ccbc74d909352d | 10.26434/chemrxiv-2022-htgms | Fast, Low cost, and facile phenothiazine radical based photoinduced sensors for rapid detection of chloroform and chlorinated solvents in liquid and gas phases† | Dramatic emission change of PTZ a phenothiazine-based molecule with chloroform and different chlorinated hydrocarbons (CHCs) is providing an effective method for CHCs detection with naked eyes. The visual detection range can reach low concentration as low 30 mM in acetone and water for both volatile chloroform sensing and for liquid. Fabrication of one-time use paper sensors for volatile chloroform and glass-based sensors for liquid chloroform along with using a light source sun or solar box to allow on site detection of chloroform. | MOHAMED MAGDY HASSAN DESOKY | Physical Chemistry; Organic Chemistry; Analytical Chemistry; Photochemistry (Org.); Analytical Chemistry - General; Environmental Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6388c07444ccbc74d909352d/original/fast-low-cost-and-facile-phenothiazine-radical-based-photoinduced-sensors-for-rapid-detection-of-chloroform-and-chlorinated-solvents-in-liquid-and-gas-phases.pdf |
63b8d6c71699ca4cffe637d4 | 10.26434/chemrxiv-2023-b105f | DFT studies on electronic and structure properties of PbSe1-xSx alloys using VCA and EBS | In this study, density functional theory has been used to investigate the structural and electronic properties of lead selenide (PbSe) and lead sulfide (PbS) semiconductors and their alloys PbSe1-xSx using the virtual crystal approximation (VCA) and random structure (RS) generations. The generalized gradient approximation (GGA) has been used to obtain lattice parameters which are compared with theory and experimental results. The generalized gradient approximation (MGGA) of TB09LDA has been used to calculate the electronic bands, for different sulfur compositions (0≤x≤1, ∆x=0.1). It has been observed that the transition from the valence band to the conduction band takes place at the L point, which agrees with previous theoretical investigations. It has been observed that both the bandgap and lattice parameters of the alloys obey Vegard's law. Effective band diagrams obtained from the unfolding of supercell band diagrams, reported for the first time for this system, show that the impacts of alloy disorder are low in the vicinity of the L point, indicating that the alloy composition do not appear to influence the transport phenomena. This work shows the suitability of the VCA approximation and the band unfolding method, to deal and describe the composition-dependent properties of the PbSe1-xSx pseudo binary alloys. | Sergio Montiel-Perales; Cesia Guarneros-Aguilar; Mourad Boujnah; Felipe Caballero-Briones | Theoretical and Computational Chemistry; Materials Science; Alloys; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63b8d6c71699ca4cffe637d4/original/dft-studies-on-electronic-and-structure-properties-of-pb-se1-x-sx-alloys-using-vca-and-ebs.pdf |
60c748cc0f50dbbbde396800 | 10.26434/chemrxiv.11973372.v1 | Fourteen-Membered Macrocyclic Fe Complexes for Oxygen Reduction Catalysis Inspired by FeN4 Centers Hosted by Graphene | For the globalization of polymer
electrolyte fuel cells, the development of non-precious-metal (NPM) catalysts
for oxygen reduction is extremely important. To date, many NPM catalysts have
been synthesized by pyrolyzing Fe-, N-, and C-containing precursors, but they
suffer from the density and uncertain chemical structure of their active sites. This
study reports a 14-membered macrocyclic Fe complex, which was inspired by FeN<sub>4</sub>
centers in the pyrolyzed catalysts, whereas typical macrocyclic MN<sub>4</sub>
complexes have 16-membered rings. This 14-membered macrocycle has strong Fe-N
bonding with an average bond distance of 1.90 Å, which has been evidenced by
single-crystal X-ray diffraction, and is markedly shorter than that in
porphyrin, 2.0 Å. Promising electrocatalytic activities for oxygen reduction
have been demonstrated in both of acidic and basic media. | Makoto Moriya; Ryo Takahama; Kazuki Kamoi; Junya Ohyama; Shin Kawashima; Ryoichi Kojima; Mariko Okada; Teruaki Hayakawa; Yuta Nabae | Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748cc0f50dbbbde396800/original/fourteen-membered-macrocyclic-fe-complexes-for-oxygen-reduction-catalysis-inspired-by-fe-n4-centers-hosted-by-graphene.pdf |
66e4a3a812ff75c3a13f8f27 | 10.26434/chemrxiv-2024-bzg3p | Zero-Point Energies from Bond Orders and Populations Relationships | We report two analytical models for calculating quantum mechanical zero point energies (ZPEs) based on data from just a single-point quantum chemistry energy calculation. Fol- lowing our earlier model that partitioned molecular atomization energies and bond ener- gies using bond orders and orbital population analyses (i.e. the BEBOP method), the ZPE- BOPn methods reported here partition molecular zero-point energies from bond orders and orbital populations. As a starting point, the ZPE-BOP1 model employs a Mulliken orbital populations via a minimal population localization from a B3LYP/6-311+G(3d2f,2df,2p) calculation and leverages an extended Hückel-type vibrational bond energy term with two atom-pairwise parameters that are fit to reproduce scaled ZPEs from B3LYP calculations. For improved accuracy, the ZPE-BOP2 model employs Mulliken orbital populations via a minimal population localization from an ROHF/6-311+G(3d2f,2df,2p) calculation and employs an extended Hückel-type vibrational bond energy term, a short-range anharmonic energy term, and a coupled three-body oscillator energy term with seven atom-pairwise parameters. Both methods efficiently predict ZPEs in molecules without the need for a costly Hessian calculation, but ZPE-BOP2 outperforms ZPE-BOP1 in strained and long- chain molecules and provides reasonable predictions of ZPEs from Hessian calculations using semiempirical quantum chemistry methods (e.g., AM1, PM6, and PM7). This work shows progress toward computational approximations to predict useful chemical physical properties from orbital populations without intensive Hessian calculations. | Barbaro Zulueta; Colin Rude; Jesse Mangiardi; George Petersson; John Keith | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Quantum Mechanics; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e4a3a812ff75c3a13f8f27/original/zero-point-energies-from-bond-orders-and-populations-relationships.pdf |
67af13befa469535b94a2554 | 10.26434/chemrxiv-2025-0bt3h | Highly Efficient Removal of Perfluorooctanoic Acid from Water using Zirconium Terephthalate (UiO-66) Gel | The extensive use and environmental release of perfluoroalkyl substances (PFAS), often referred to as “forever chemicals”, has raised significant health and environmental concerns. Due to their persistence and resistance to natural degradation, PFAS appear in concerningly high concentrations, e.g., in our drinking water. Among these substances, perfluorooctanoic acid (PFOA) is particularly prevalent. This study explores the application of synthesized zirconium terephthalate (UiO-66) metal-organic framework (MOF) gel for highly efficient removal of PFOA from water. The UiO-66 gel not only maintains the structural stability of its powder form but also offers improved ease of handling. Structural characterization by PXRD and TEM analyses revealed the gel's nanocrystalline structure (~20 nm in size), which was further confirmed by electron diffraction. Quantitative NMR spectroscopy demonstrated a PFOA removal efficiency of 96%. The successful absorption of the polyfluoro compound into the UiO-66 gel after filtration was confirmed by the detection of fluoride within the gel structure using STEM-EDS elemental mapping. In addition, to demonstrate the potential of developing membrane platforms as practical and scalable solutions for environmental remediation, the performance of a MOF gel filter was successfully tested. | Giuseppe Di Palma; Pritam Banerjee; Kasper Enemark-Rasmussen; Sara Talebi Deylamani; Joerg R. Jinschek | Organometallic Chemistry; Earth, Space, and Environmental Chemistry; Environmental Science; Coordination Chemistry (Organomet.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67af13befa469535b94a2554/original/highly-efficient-removal-of-perfluorooctanoic-acid-from-water-using-zirconium-terephthalate-ui-o-66-gel.pdf |
65f018a0e9ebbb4db98946fa | 10.26434/chemrxiv-2023-74041-v2 | Can Large Language Models Predict Antimicrobial Peptide Activity and Toxicity? | Antimicrobial peptides (AMPs) are naturally occurring or designed peptides up to a few tens of amino acids which may help address the antimicrobial resistance crisis. However, their clinical development is limited by toxicity to human cells, a parameter which is very difficult to control. Given the similarity between peptide sequences and words, large language models (LLMs) might be able to predict AMP activity and toxicity. To test this hypothesis, we fine-tuned LLMs using data from the Database of Antimicrobial Activity and Structure of Peptides (DBAASP). GPT-3 performed well but not reproducibly for activity prediction and hemolysis, taken as a proxy for toxicity. The later GPT-3.5 performed more poorly and was surpassed by recurrent neural networks (RNN) trained on sequence-activity data or support vector machines (SVM) trained on MAP4C molecular fingerprint-activity data. These simpler models are therefore recommended, although the rapid evolution of LLMs warrants future re-evaluation of their prediction abilities. | Markus Orsi; Jean-Louis Reymond | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-03-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f018a0e9ebbb4db98946fa/original/can-large-language-models-predict-antimicrobial-peptide-activity-and-toxicity.pdf |
61215f8730688d2cee967305 | 10.26434/chemrxiv-2021-729bm | Chemical Interpretation of Charged Point Defects in Semiconductors: A Case Study of Mg2Si | The number of excess charge carriers generated by a point defect, defined by the "charge state" of a defect, is oftentimes an important quantity used to engineer the electronic properties of semiconductors. Here, we develop a molecular orbital theory-based framework for interpreting the charge state(s) of a point defect, which is based on local chemical interactions between the defect and the atoms surrounding the defect site. We demonstrate how the framework can be applied to native defects in Mg2Si, such as interstitials, vacancies, and antisite defects, by utilizing symmetry principles and Density Functional Theory calculations. We anticipate that such an interpretive framework will guide efforts to engineer electronic and optical properties of semiconductors through manipulation of intrinsic and extrinsic defects. | Michael Toriyama; Madison Brod; G Jeffrey Snyder | Materials Science; Inorganic Chemistry; Bonding; Solid State Chemistry; Theory - Inorganic; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2021-08-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61215f8730688d2cee967305/original/chemical-interpretation-of-charged-point-defects-in-semiconductors-a-case-study-of-mg2si.pdf |
60c758e5bb8c1a1f343dcafd | 10.26434/chemrxiv.14610600.v1 | Combined Paper-Based Substrates for Electrochemical Detection of Copper Ions in Serum | <p>The electroanalytical field has exploited great advantages in using paper-based substrates, even if the word “paper” might be general. In fact, the mainly adopted paper-based substrates are often chromatographic and office ones. They are characterized by main features (and drawbacks): chromatographic paper is well-established for storing reagents/treating samples but the sensitivity compared to traditional screen-printed is lower (due to porosity), while office paper represents a sustainable alternative to plastic (with similar sensitivity) but its porosity is not enough to load reagents. To overcome the limitations that might arise due to the adoption of a type of individual paper-based substrate, herein we describe for the first time, the development of a 2D merged paper-based devices for electrochemical copper ions detection in serum. In this work we report a novel configuration to produce an integrated all-in-one electrochemical device, in which no additional working media has to be added by the end user and the sensitivity can be tuned by rapid pre-concentration on porous paper, with the advantage of making the platform adaptable to real matrix scenario. The novel architecture has been obtained by combining office paper to screen-print a sustainable and robust electrochemical strip, the printed electrochemical strips and chromatographic one to 1) store the reagents, 2) collect real sample and 3) pre-concentrate the analyte of interest. The novel sensing platform has allowed to obtain a detection limit for copper ions down to 5 ppb in all the solutions that have been interrogated, namely standard solution and serum, and a repeatability of ca. 10% has been obtained.</p> | Antonella Miglione; Stefano Cinti | Analytical Chemistry - General; Electrochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758e5bb8c1a1f343dcafd/original/combined-paper-based-substrates-for-electrochemical-detection-of-copper-ions-in-serum.pdf |
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