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60c74e834c89195071ad3a4d | 10.26434/chemrxiv.12768317.v1 | Tuning Rh(II)-Catalyzed Cyclopropanation with Tethered Thioether Ligands | Dirhodium(II) paddlewheel complexes have high utility in diazo-mediated cyclopropanation reactions and ethyl diazoacetate is one of the most commonly used diazo compounds in this reaction. In this study, we report our efforts to use tethered thioether ligands to tune the reactivity of Rh-carbene mediated cyclopropanation of olefins with ethyl diazoacetate. Microwave methods enabled the synthesis of a family of Rh-complexes in which tethered thioether moieties were coordinated to axial sites of the complex. Different tether lengths and thioether substituents were screened to optimize cyclopropane yeilds and minimize side product formation. Furthermore, good yields were obtained when equimolar diazo and olefin were used. Structural and spectroscopic investigation revealed that tethered thioethers changed the electronic structure of the rhodium core, which was instrumental in the performance of the catalysts. Computational modeling of the catalysts provided further support that the tethered thioethers were responsible for increased yields. | Derek Cressy; Cristian Zavala; Anthony Abshire; William Sheffield; Ampofo Darko | Organic Synthesis and Reactions; Transition Metal Complexes (Inorg.); Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e834c89195071ad3a4d/original/tuning-rh-ii-catalyzed-cyclopropanation-with-tethered-thioether-ligands.pdf |
640dbf27b5d5dbe9e82496d2 | 10.26434/chemrxiv-2023-3k422-v4 | q-Gaussians and the shapes of Raman spectral lines | q-Gaussians are probability distributions having their origin in the framework of Tsallis statistics. A continuous real parameter q is characterizing them so that, in the range 1 < q < 3, the q-functions pass from the usual Gaussian form, for q close to 1, to that of a heavy tailed distribution, at q close to 3. The value q=2 corresponds to the Cauchy-Lorentzian distribution. This behavior of q-Gaussian functions could be interesting for a specific application, that regarding the analysis of Raman spectra, where Lorentzian and Gaussian profiles are the most commonly used line shapes to fit the spectral bands. Therefore, we will discuss q-Gaussians with the aim of comparing the resulting fit analysis with data available in literature. As it will be clear from the discussion, in particular referring to (Meier, 2005), this is a very sensitive issue. Then, we will consider results given in a recently proposed analysis of carbon-based materials, obtained by means of mixed Gaussian and Lorentzian line shapes, defined as GauLors (Tagliaferro et al., 2020). In this paper, we will also provide a detailed discussion about pseudo-Voigt functions. We will show a successfully comparison of q-Gaussians with pseudo-Voigt functions. It is also considered the role of q-Gaussians in EPR spectroscopy (Howarth et al., 2003), where the q-Gaussian is given as the "Tsallis lineshape function". | Amelia Carolina Sparavigna | Materials Science; Carbon-based Materials | CC BY NC 4.0 | CHEMRXIV | 2023-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/640dbf27b5d5dbe9e82496d2/original/q-gaussians-and-the-shapes-of-raman-spectral-lines.pdf |
60c74b76469df4f0baf43f19 | 10.26434/chemrxiv.12339614.v1 | Bis-cyclooctatetraenyl Thulium(II): Highly Reducing Lanthanide Sandwich Single Molecule Magnets | Divalent lanthanide organometallics are well known highly reducing compounds usually used for single electron transfer reactivity and small molecule activation. Thus, their very reactive nature prevented for many years the study of their physical properties, such as magnetic studies on a reliable basis. In this article, the access to rare organometallic sandwich compounds of Tm<sup>II</sup> with the cyclooctatetraenyl (Cot) ligand impacts on the use of divalent organolanthanide compounds as an additional strategy for the design of performing Single Molecule Magnets (SMM). Herein, the first divalent thulium sandwich complex with f<sup>13</sup> configuration behaving as a Single Molecule Magnet in absence of DC field is highlighted. | Jules Moutet; jules Schleinitz; Leo La Droitte; Maxime Tricoire; Frédéric Gendron; Thomas Simler; Carine Clavaguéra; Boris Le Guennic; Olivier Cador; Gregory Nocton | Coordination Chemistry (Organomet.); Spectroscopy (Organomet.); Theory - Organometallic | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b76469df4f0baf43f19/original/bis-cyclooctatetraenyl-thulium-ii-highly-reducing-lanthanide-sandwich-single-molecule-magnets.pdf |
6797a63efa469535b90d5591 | 10.26434/chemrxiv-2025-z7zjr | Exploring the Chemical Design Space of Metal-Organic Frameworks for Photocatalysis | In this work, we introduce a combined DFT and machine learning approach to obtain insights into the chemical design of metal-organic framework (MOF) photocatalysts for hydrogen (HER) and oxygen (OER) evolution reactions. To train our machine learning models, we evaluated a dataset of 314 MOFs using a dedicated DFT workflow that computes a set of five descriptors for both closed and open shell MOFs. Our dataset is composed of a diverse selection of the QMOF database and experimentally reported MOF photocatalysts. In addition, to ensure a balanced dataset, we designed a set of MOFs (CDP–MOF) inspired by insights obtained regarding different types of photocatalytic materials. Our machine-learning approach allowed us to screen the entire QMOF and CDP–MOF databases for promising candidates. Our analysis of the chemical design space shows that we have many materials with a suitable spatial overlap of electron and hole, band gap, band-edge alignment to HER, and charge-carrier effective masses. However, we have identified in the QMOF database only a very small percentage of materials that also have the right band edge alignment to OER. With the CDP–MOF database, we successfully targeted building blocks that potentially have the correct OER band alignment, and indeed obtained a larger percentage of materials that obey this criteria. Among those, a few motifs stood out, such as Au-pyrazolate, Ti clusters and rod-shaped metal nodes, and a particular MOF designed with the Mn4Ca cluster, which mimics the OER center in the photosystem II of photosynthesis. | Beatriz Mouriño; Sauradeep Majumdar; Xin Jin; Fergus McIlwaine; Joren van Herck; Andres Ortega-Guerrero; Susana Garcia; Berend Smit | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational; Machine Learning | CC BY 4.0 | CHEMRXIV | 2025-01-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6797a63efa469535b90d5591/original/exploring-the-chemical-design-space-of-metal-organic-frameworks-for-photocatalysis.pdf |
60c73f85ee301c7b01c78902 | 10.26434/chemrxiv.6230627.v3 | Toward Learned Chemical Perception of Force Field Typing Rules | <div>Molecular mechanics force fields define how the energy and forces of a molecular system are computed from its atomic positions, and enable the study of such systems through computational methods like molecular dynamics and Monte Carlo simulations. Despite progress toward automated force field parameterization, considerable human expertise is required to develop or extend force fields. </div><div>In particular, human input has long been required to define <i>atom types</i>, which encode chemically unique environments that determine which parameters must be assigned. However, relying on humans to establish atom types is suboptimal: the resulting atom types are often unjustified from a statistical perspective, leading to over- or under-fitting; they are difficult to extend in a systematic and consistent manner when new chemistries must be modeled or new data becomes available; and human effort is not scalable when force fields must be generated for new (bio)polymers or materials. We aim to replace human specification of atom types with an automated approach, based on solid statistics and driven by experimental and/or quantum chemical reference data. Here, we describe a novel technology for this purpose, termed <i>SMARTY</i>, which generalizes atom typing by using direct chemical perception with SMARTS strings, and adopting a hierarchical approach to type assignment. The SMARTY technology enables creation of a move set in atom-typing space that can be used in a Monte Carlo optimization approach to atom typing. We demonstrate the power of this approach with a fully automated procedure that is able to re-discover human-defined atom types in the traditional small molecule force field parm99/parm@Frosst. Furthermore, we show how an extension of this approach that makes use of SMIRKS strings to match multiple atoms, which we term <i>SMIRKY</i>, allows us to take full advantage of the advances in direct chemical perception for valence types (bonds, angles, and torsions) afforded by the recently-proposed SMIRNOFF direct chemical perception force field typing language. We assess these approaches using several molecular datasets, including one which covers a diverse molecular subset from DrugBank. </div> | Camila Zanette; Caitlin C. Bannan; Christopher I. Bayly; Josh Fass; Michael Gilson; Michael R. Shirts; John Chodera; David Mobley | Computational Chemistry and Modeling; Theory - Computational; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2018-10-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f85ee301c7b01c78902/original/toward-learned-chemical-perception-of-force-field-typing-rules.pdf |
61a8c8f9772cb2de2c4d7516 | 10.26434/chemrxiv-2021-zmv6h | Size dependent inhibition of sperm motility by
copper particles as a path towards reversible
male contraception | Effective inhibition of sperm motility using a spermicide can be a promising approach in developing non-invasive male contraceptive agents. Copper is known to have
contraceptive properties and has been used clinically for decades as intrauterine contraceptive devices (IUDs) for contraception in females. Beyond that, the spermicidal use
of copper has not been explored much further, even though its use could also subdue
the harmful effects caused by the hormonal contraceptive agents on the environment.
Herein, we study the size, concentration and time dependent in vitro inhibition of
bovine spermatozoa by copper microparticles. The effectivity in inhibiting the sperm motility is correlated to the amount of Cu2+ ions released by the particles during incubation. The copper particles cause direct suppression of sperm cell motility upon
incubation and thereby show potential as sperm inhibiting, hormone free candidate for
male contraception beyond condoms. | Purnesh Chattopadhyay; Veronika Magdanz; Konstantin Borchert; Dana Schwarz; Juliane Simmchen | Biological and Medicinal Chemistry; Biophysics | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61a8c8f9772cb2de2c4d7516/original/size-dependent-inhibition-of-sperm-motility-by-copper-particles-as-a-path-towards-reversible-male-contraception.pdf |
60c753f1bb8c1a0c793dc14e | 10.26434/chemrxiv.13584995.v1 | Ultra-Bright Fluorescent Organic Nanoparticles Based on Small-Molecule Ionic Isolation Lattices | Ultra-bright fluorescent
nanoparticles hold great promise for demanding bioimaging applications.
Recently, extremely bright molecular crystals of cationic fluorophores were
obtained by hierarchical co-assembly with cyanostar anion-receptor complexes of
associated counterions. These small-molecule ionic isolation lattices (SMILES)
ensure spatial and electronic isolation to prohibit dye aggregation quenching.
We report a simple, one-step supramolecular approach to formulate SMILES
materials into nanoparticles. Rhodamine-based SMILES nanoparticles stabilized
by glycol amphiphiles show high fluorescence quantum yield (30%) and brightness
per volume (5000 M<sup>–1</sup> cm<sup>–1</sup> / nm<sup>3</sup>)
with 400 dyes packed into 16-nm particles, corresponding to an absorption
coefficient of 4 × 10<sup>7</sup> M<sup>–1 </sup>cm<sup>–1</sup>. UV
excitation of the cyanostar component leads to highest brightness (>6000 M<sup>–1</sup> cm<sup>–1</sup> /
nm<sup>3</sup>) by energy transfer to rhodamine emitters. Coated nanoparticles
stain cells and are thus promising for bioimaging. | Junsheng Chen; S. M. Ali Fateminia; Laura Kacenauskaite; Nicolai Bærentsen; Stine Grønfeldt Stenspil; Jona Bredehoeft; Karen L. Martinez; Amar Flood; Bo W. Laursen | Dyes and Chromophores | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753f1bb8c1a0c793dc14e/original/ultra-bright-fluorescent-organic-nanoparticles-based-on-small-molecule-ionic-isolation-lattices.pdf |
651cdc37bda59ceb9ad48ab0 | 10.26434/chemrxiv-2023-3k07n | Supramolecular Construction of a Highly Elongated π-Conjugated Structure in the Solid State: Metal-Free Click Reaction Guided by C-H Hydrogen Bonding | A planned topochemical azide-alkyne cycloaddition is developed in the organic solid state to generate a highly elongated π-conjugated 1,2,3-triazole by a metal-free click reaction. The triazole is generated using a binary cocrystal composed of stilbenes that are covalently adjoined in a single-crystal-to-single-crystal transformation. The click reaction is accompanied by a large-scale structural reorganization involving procession-like movements of 1D stacked columns into a 2D layered structure. The formation of the layered structure is guided by newly formed triazoles self-assembling via C-H···N hydrogen bonding. | Shweta Yelgaonkar; Changan Li; Amy Charles; Leonard MacGillivray | Organic Chemistry; Organic Synthesis and Reactions; Supramolecular Chemistry (Org.); Materials Chemistry; Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651cdc37bda59ceb9ad48ab0/original/supramolecular-construction-of-a-highly-elongated-conjugated-structure-in-the-solid-state-metal-free-click-reaction-guided-by-c-h-hydrogen-bonding.pdf |
66deb2e951558a15ef7e3a2d | 10.26434/chemrxiv-2024-0h32j | viAFM - a Python toolset for virtual Atomic Force Microscopy | Atomic Force Microscopy (AFM) is a powerful but demanding imaging technique used also to study the interaction strength of single biomolecules by force spectroscopy. Here we provide a viAFM program designed to facilitate multi- directional steered molecular dynamics simulations and analysis of forces required to disrupt protein complexes thus mimicking AFM force spectroscopy experiments. Our viAFM tool allows for rapid assessment of protein-protein interaction strength, anisotropy, and the impact of ligands or mutations on complex stability, enabling efficient testing of drug candidates. | Katarzyna Walczewska-Szewc; Beata Niklas; Wieslaw Nowak | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Bioinformatics and Computational Biology | CC BY NC 4.0 | CHEMRXIV | 2024-09-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66deb2e951558a15ef7e3a2d/original/vi-afm-a-python-toolset-for-virtual-atomic-force-microscopy.pdf |
646aa633f2112b41e9ed5f1d | 10.26434/chemrxiv-2023-dpm20 | Asymmetric Organocatalyzed Phospha-Michael Addition to Iminochromenes | The potential of phosphites as nucleophiles for the synthesis of chiral chromene derivatives has been overlooked in the literature. Herein, we report a highly promising approach via asymmetric organocatalyzed phospha-Michael addition to iminochromenes, using a bifunctional squaramide. Our optimized protocol provides very good reactivity, affording yields of up to 95% and excellent enantioselectivity, with chiral products exhibiting an outstanding enantiomeric excess of up to 98%. | Eugenia Marqués-López; Isaac G. Sonsona; Miryam Garcés-Marín; M. Concepción Gimeno; Raquel P. Herrera | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Stereochemistry; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646aa633f2112b41e9ed5f1d/original/asymmetric-organocatalyzed-phospha-michael-addition-to-iminochromenes.pdf |
63b3f8bc963bf311a5af0c01 | 10.26434/chemrxiv-2023-qq7ph | MULTI-SEASON MOBILE MONITORING CAMPAIGN OF ON-ROAD AIR POLLUTION IN BENGALURU, INDIA: HIGH-RESOLUTION MAPPING AND ESTIMATION OF QUASI-EMISSION FACTORS | Mobile monitoring can supplement regulatory measurements, particularly in low-income countries where stationary monitors’ density is low. Here, we report results from a ~year-long mobile monitoring campaign of on-road black carbon (BC) mass concentration, ultrafine particle (UFP) number concentration, and carbon dioxide (CO2) in Bengaluru, India. The study route included ~150 unique kms covering urban and peri-urban residential neighborhoods and the central business district (CBD); ~22 repeat measurements were made per monitored road-segment, covering most seasons. After cleaning the data for known instrument artifacts and sensitivities, we generated 30 m high-resolution stable ‘data only’ spatial maps of BC, UFP, and CO2 for the study route. For the urban residential areas, the mean BC levels for residential roads, arterials, and highways were ~10, 22, and 56 µgm-³, respectively. A similar pattern (highways being characterized by highest pollution levels) was also observed for the UFP and CO2. Using the data from repeat measurements, we carried out a Monte Carlo subsampling analysis to understand the minimum number of repeat measures to generate stable maps of pollution in the city. Leveraging the simultaneous nature of the measurements, we also mapped the quasi-emission factors (QEF) of the pollutants under investigation. Finally, the results are discussed in the context of technical aspects of the campaign, limitations, and their policy relevance. | Adithi Upadhya; Meenakshi Kushwaha; Pratyush Agrawal; Jonathan Gingrich; Jai Asundi; Sreekanth V; Julian Marshall; Joshua Apte | Earth, Space, and Environmental Chemistry; Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63b3f8bc963bf311a5af0c01/original/multi-season-mobile-monitoring-campaign-of-on-road-air-pollution-in-bengaluru-india-high-resolution-mapping-and-estimation-of-quasi-emission-factors.pdf |
60c74c58ee301ce15ec7a051 | 10.26434/chemrxiv.12465236.v1 | A Boron-Oxygen Transborylation Strategy for the Asymmetric Reduction of Ketones | The asymmetric reduction of ketones with pinacolborane (HBpin) has been catalysed by an enantioenriched borane catalyst, formed <i>in situ</i> from 9-borabicyclo[3.3.1]nonane (H-<i>B</i>-9-BBN) and β-pinene. While previously only used stoichiometrically, this borane has now been rendered catalytic using a new turnover mechanism, B-O transborylation. Thermodynamic and kinetic parameters of the key B-O/B-H transborylation showed this is a sub-class of σ-bond metathesis. | Kieran Nicholson; Joanne Dunne; Peter DaBell; Alexander Beaton Garcia; Andrew D. Bage; Jamie
H. Docherty; Thomas A. Hunt; Thomas Langer; Stephen P. Thomas | Organic Synthesis and Reactions; Stereochemistry; Main Group Chemistry (Inorg.); Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c58ee301ce15ec7a051/original/a-boron-oxygen-transborylation-strategy-for-the-asymmetric-reduction-of-ketones.pdf |
60c9e3b1551c4fcb2ec4c30c | 10.26434/chemrxiv.14778393.v1 | Mixing and Flow-Induced Silk Fibroin Self-Assembly in Microfluidic and Semi-Batch Nanoprecipitation | <div><div><div><p>Here, we report the modulation of silk fibroin self-assembly by varying factors which control shear and mixing during nanoprecipitation in semi-batch and micro-mixers. For feeds processed at low shear in a semi-batch format, the properties of secondary assemblies (nanoparticles) were scalable by reducing the mixing time by stirring (0 < 400 rpm). For low mixing times, moving from low to high shear processing increased the extent of self-assembly (0.017 < 16.96 mL min-1) for 0.5, 2 and 3% w/v silk. In high shear regimes, the size and polydispersity index of assemblies decreased with mixing time, as stirring rate (800, 400 < 0 rpm) and feed addition height (3.5 < 0 cm) increased. Finally, in conditions of high shear and low mixing time, the feed concentration controlled the assembly shape, size, and polydispersity index in microfluidic (0.5, 3.0 < 2% w/v) and semi-batch format (3.0 < 0.5% w/v). This work provides new insight into the manufacture of low polydispersity, spherical and worm-like silk nanoparticles.</p></div></div></div> | Saphia A. L. Matthew; Refaya Rezwan; Yvonne Perrie; F. Philipp Seib | Biodegradable Materials; Biopolymers | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c9e3b1551c4fcb2ec4c30c/original/mixing-and-flow-induced-silk-fibroin-self-assembly-in-microfluidic-and-semi-batch-nanoprecipitation.pdf |
64df9c3200bbebf0e66790e8 | 10.26434/chemrxiv-2023-mmxqx | Quantification of Residual Water in Pharmaceutical Frozen Solutions via 1H Solid-state NMR | Freezing is essential for the stability of biological drug substances and products, particularly in frozen solution formulations and during the primary drying of lyophilized preparations. However, the unfrozen segment within the frozen matrix can alter solute concentration, ionic strength, and stabilizer crystallization, posing risks of increased biophysical instability and faster chemical degradation. While quantifying the unfrozen water content is crucial for designing stable biopharmaceuticals, there is a lack of analytical techniques for in situ quantitative measurements. In this study, we introduce a 1H magic angle spinning NMR technique to identify the freezing point (T_ice) and quantify mobile water content in frozen biologics. Our quantitative results demonstrate that water freezing is influenced by buffer salt properties and formulation composition, including the presence of sugar cryoprotectants and protein concentration. Additionally, the 1H chemical shift can probe pH in the unfrozen phase, potentially predicting the microenvironmental acidity in the frozen state. Our proposed methodology provides fresh insights into the analysis of freeze-concentrated solutions, enhancing our understanding of the stability of frozen and lyophilized biopharmaceuticals. | Yong Du; Yongchao Su | Analytical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64df9c3200bbebf0e66790e8/original/quantification-of-residual-water-in-pharmaceutical-frozen-solutions-via-1h-solid-state-nmr.pdf |
62d18c6cfe12e3c5a1a3cd01 | 10.26434/chemrxiv-2022-d5smv-v2 | Effect of Calcium on the Atomic and Electronic Structures of CdSe QDs Embedded Soda-Lime-Silica Glasses | In this work, we have investigated effects of calcium on the atomic and electronic structures of CdSe QDs by ab initio molecular dynamics. The increase of CaO content in glass is found to break the linkage between Na and O atoms, while interactions between Cd atoms and non-bridging oxygens are not disrupted. The presence of the CdSe QD promotes the migration of Na atoms from the glass matrix to the interface, and even the interior of CdSe QD, while Ca atoms are only found to be present at the QD/glass interface and in glass matrices far from QD. However, on the basis of radial concentration distribution, the CdSe QD only impacts the structure of glass at short-range near the interface. The increase in CaO content is also shown to increase the HOMO-LUMO gap of CdSe QDs embedded glasses. Our findings can extend understanding of the effect of calcium on the structural and luminescence properties of CdSe QDs embedded glasses. | Wenke Li; Xiujian Zhao; François-Xavier Coudert; Chao Liu | Materials Science | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62d18c6cfe12e3c5a1a3cd01/original/effect-of-calcium-on-the-atomic-and-electronic-structures-of-cd-se-q-ds-embedded-soda-lime-silica-glasses.pdf |
6102c081537d10350580560a | 10.26434/chemrxiv-2021-3z7sj-v2 | Operando Studies of Iodine Species in an Advanced Oxidative Water Treatment Reactor | We present an electrochemical advanced oxidation process (eAOP) reactor employing expanded graphite, potassium iodide (KI), and electrical current, which demonstrates an exceptionally high rate of inactivation of E. coli (6log reduction in viable cells) at low current density 0.12 mA/cm^2), with low contact time (5 minutes) and low concentration of KI (10 ppm). Operando X-ray fluorescence mapping is used to show the distribution of iodine species in the reactor, and operando X-ray absorption spectroscopy in the anodic chamber reveals iodine species with higher effective oxidation state than periodate. Operando electrochemical measurements confirm the conditions in the anodic chambers are favourable for the creation of highly oxidized iodine products. The killing efficiency of this new eAOP reactor far exceeds that expected from either traditional iodine-based electrochemical water treatment or advanced oxidation systems alone, a phenomenon that may be associated with the production of highly oxidized iodine species reported here. | Ahmed Moustafa; Alex Evans; Simmon Hofstetter; Jenny Boutros; Parastoo Pourrezaei; Cheng Zhang; Laura Patterson-Fortin; Charles Laing; Carter Goertzen; Richard Smith; Kenneth R Code; Ning Cheng; Peter E R Blanchard; Nathan Bettman; Raquibul Alam; Kerry McPhedran; Zohreh Fallah; Edward P L Roberts; Michael Gaultois | Physical Chemistry; Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry; Wastes; Electrochemistry - Mechanisms, Theory & Study; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6102c081537d10350580560a/original/operando-studies-of-iodine-species-in-an-advanced-oxidative-water-treatment-reactor.pdf |
60c74c60bdbb891499a39777 | 10.26434/chemrxiv.12465371.v1 | AiZynthFinder: A Fast Robust and Flexible Open-Source Software for Retrosynthetic Planning | We present the
open-source AiZynthFinder software that can be readily used in retrosynthetic
planning. The algorithm is based on a Monte Carlo tree search that recursively
breaks down a molecule to purchasable precursors. The tree search is guided by
an artificial neural network policy that suggests possible precursors by
utilizing a library of known reaction templates. The software is fast and can typically find a
solution in less than 10 seconds and perform a complete search in less than 1
minute. Moreover, the writing of the code was guided by a range of software
engineering principles such as automatic testing, system design and continuous
integration leading to robust software. The object-oriented design makes the
software very flexible and can straightforwardly be extended to support a range
of new features. Finally, the software is clearly documented and should be easy
to get started with. The software is available at http://www.github.com/MolecularAI/aizynthfinder. | Samuel Genheden; Amol Thakkar; Veronika Chadimova; Jean-Louis Reymond; Ola Engkvist; Esben Jannik Bjerrum | Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c60bdbb891499a39777/original/ai-zynth-finder-a-fast-robust-and-flexible-open-source-software-for-retrosynthetic-planning.pdf |
60c73e9b4c89191935ad1e26 | 10.26434/chemrxiv.7069658.v1 | Ligand-Accelerated Non-Directed C–H Cyanation of Arenes | <p>We herein report the first example of a 2-pyridone
accelerated non-directed C−H cyanation
with an arene as the limiting reagent. This protocol is compatible with a broad
scope of arenes, including advanced intermediates, drug molecules, and natural
products. A kinetic isotope experiment (k<sub>H</sub>/k<sub>D</sub> = 4.40)
indicates that the C–H bond cleavage is the
rate-limiting step. Also, the
reaction is readily scalable, further showcasing the synthetic utility of this
method.<i></i></p> | Luoyan Liu; Kap-Sun Yeung; jin-quan yu | Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2018-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e9b4c89191935ad1e26/original/ligand-accelerated-non-directed-c-h-cyanation-of-arenes.pdf |
623ad7452c5010b0fb855490 | 10.26434/chemrxiv-2022-mw5gb | Impact of Tether Length and Flexibility on the Efficiency of Analyte Capture by Tethered Receptors | Structure and functionality of molecular layers play a crucial role in determining the outcome of analyte-receptor interactions on affinity biosensors. The control over the structure of these molecular layers gives an independent means to enhance the sensor performance. Here we study the impact of the length and flexibility of molecular tethers on analyte capture by tethered receptors on quartz crystal microbalance and surface plasmon resonance sensors. Our results show clear enhancement of analyte-receptor interactions when receptors are bound to the sensor via flexible, and longer tethers. The findings further reveal a qualitative similarity of the impact of tether length on widely different type of binding interactions, viz. gold nanoparticle binding to tethered amine layers, and neutravidin binding to tethered biotin layers. By independent determination of tether densities, our investigations decouple the impact of receptor densities, and the tether conformations, and confirm the role of tether length on adsorption densities and kinetics. The results agree with theoretical reports in literature that predict enhanced analyte capture by receptors anchored to surface via long, flexible tethers, owing to enhanced freedom of movement and thereby its ability to “seek” the analyte in solution. These findings highlight the significance of factoring in the structure of the molecular tether to enhance analyte capture by tethered receptors, and thereby the performance of affinity biosensors. | Matteo Beggiato; Christine Dupont-Gillain; Sivashankar Krishnamoorthy | Physical Chemistry; Analytical Chemistry; Nanoscience; Biochemical Analysis; Interfaces; Transport phenomena (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2022-03-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/623ad7452c5010b0fb855490/original/impact-of-tether-length-and-flexibility-on-the-efficiency-of-analyte-capture-by-tethered-receptors.pdf |
665f21c821291e5d1d0dd4ae | 10.26434/chemrxiv-2024-tbjtw | Catalytic Hydrogenation of Alkylphenols for Renewable Caprolactone | Selective hydrogenation of lignin-derived alkyl-phenol to alkyl-cyclohexanone is a key step in the synthesis of renewable caprolactone from lignin-derived monomers. Selective hydrogenation of p-cresol, a model compound for lignin-derived monomers, to 4-methyl-cyclohexanone was conducted using Pd/γ-Al2O3 in a continuous three-phase flow reactor, with side products of 4-methyl cyclohexanol. High conversion (85%) and selectivity (>93%) was demonstrated at ambient reaction pressure. Evaluation of the hydrogenation at different reaction parameters showed that the reaction selectivity was determined by the surface coverage of p-cresol and 4-methyl cyclohexanone. High selectivity to 4-methyl cyclohexanone was also attributed to the lower apparent activation barrier of p-cresol hydrogenation (67 ± 2 kJ/mol) compared to hydrogenation 4-methyl cyclohexanone (92 ± 11 kJ/mol), with a faster rate of initial hydrogenation of p-cresol relative to carbonyl hydrogenation of 4-methyl-cyclohexanone. | Jimmy Soeherman; Jaeheon Kim; Tzia Ming Onn; Theresa Reineke; Paul Dauenhauer | Catalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/665f21c821291e5d1d0dd4ae/original/catalytic-hydrogenation-of-alkylphenols-for-renewable-caprolactone.pdf |
6224a84a50b6218d51eb5543 | 10.26434/chemrxiv-2022-zwssl | Hollow Microneedle Array Fabrication with Rational Design to Prevent Skin Clogging in Transdermal Drug Delivery | Microneedle (MN) technology is a promising candidate to replace hypodermic needles for practical use and painless drug delivery. However, the complex top-down fabrication process of functional MN arrays is a bottleneck that hinders their widespread use. Here, we fabricate the tapered hollow MN array with a unique bi-level-tip by combining strain-engineering and capillary self-assembly of carbon nanotube (CNT) microstructures. Strain-engineering facilitated by the offset pattern of the catalyst enables the growth of bent, bi-level CNT microstructures while capillary self-assembly helps constituting the tapered geometry of MNs. The bottom-up fabrication that consists of only two standard photolithography steps and CNT growth to form the scaffold of MNs followed by a polymer (polyimide) reinforcement step to impart mechanical stiffness to MNs provides scalable and less processing steps. The tapered shape of the MN allows 8 times less force to pierce and penetrate the skin compared to the straight MN. The liquid delivery rate of the bi-level-tip MN is measured to be 26% better than the flat tip MN of the same lumen size as its geometry reduces skin clogging effect at the needle tip. In addition, cytotoxicity tests verify that the polyimide reinforced CNT-MNs are biocompatible for future in-vivo applications. | Nur Unver; Gokcen Birlik Demirel; Sedat Odabas; Osman Tolga Gul | Materials Science; Carbon-based Materials; Controlled-Release Systems; Nanostructured Materials - Materials | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6224a84a50b6218d51eb5543/original/hollow-microneedle-array-fabrication-with-rational-design-to-prevent-skin-clogging-in-transdermal-drug-delivery.pdf |
60c7459fbb8c1a56dc3da701 | 10.26434/chemrxiv.10072973.v1 | Iodane-Guided C-H Cleavage to Synthesize Densely Functionalized Arenes | We describe a strategy for the iodane-guided functionalization of sterically congested C-H bonds, which is distinct from electronic, steric or proximity guided C-H functionalization methods. Readily accessible aryl(Mes)iodonium salts serve as the starting materials in these reactions and produce complex 1,2,3,4-substituted arenes via aryne intermediates. This approach is especially powerful when coupled with the innate C-H functionalization reactivity of simple arenes, to replace two C-H bonds with two C-C or C-heteroatom bonds while over-riding steric effects that typically inhibit such reactions. DFT stud-ies reveal a contribution of inductive, resonance, and steric effects on the regioselectivity of C-H cleavage and aryne generatation. | Aleksandra Nilova; Paul A. Sibbald; Edward. J. Valente; Gisela Gonzalez-Monteil; H. Camille Richardson; Kevin S. Brown; Paul Cheong; David Stuart | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7459fbb8c1a56dc3da701/original/iodane-guided-c-h-cleavage-to-synthesize-densely-functionalized-arenes.pdf |
60c73e9ebb8c1a083b3d9966 | 10.26434/chemrxiv.7075127.v1 | Fabrication of Highly Ordered Sn Nanowires in Anodic Aluminum Oxide Templates by Using AC Electrochemical Method | <div>Sn and its nanostructures are one of the promising candidates to replace graphite in the anode of Lithium-ion batteries due to their higher capacity.</div><div>One of the challenges, which limited the usage of Sn anodes for the Lithium-ion batteries, is Tin's high volumetric strain and its low cyclability.</div><div>On the other hand, nanostructures show lower volume change during charge/discharge and as a result could address the cyclability issues.</div><div>In this research, an alternating current (AC) electrochemical method is developed in order to facilitate the industrial scale production of Sn nanowires. The developed electrodeposition technique shows reliable controllability over chemical composition and crystalline structure of Sn nanowires. Also, the order structure of nanowires could be adjusted more accurately in comparison to conventional fabrication techniques.</div><div>As a result, the Sn nanowires as well as Aluminum Oxide templates synthesized by using the developed electrochemical method are examined due to their morphology, chemical composition, and their crystalline structure in order to develop a practical relation between electrochemical composition of the solution and materials properties of Sn nanowires.</div><div>The results show that the proposed electrodeposition method maintains a highly-ordered morphology as well as industrially acceptable controllability over crystalline structure of nanowires, which could be used to optimize the procedure for industrial applications due to low cost and simple experimental setup.</div> | Mastooreh Seyedi; Mozhdeh Saba | Electrochemical Analysis; Nanostructured Materials - Nanoscience; Electrochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2018-09-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e9ebb8c1a083b3d9966/original/fabrication-of-highly-ordered-sn-nanowires-in-anodic-aluminum-oxide-templates-by-using-ac-electrochemical-method.pdf |
644227bde4bbbe4bbfff123d | 10.26434/chemrxiv-2023-md4ww | Inkjet Printed CNT-Antibody Bioink for Detecting HBV Surface Antigen | A new bioink consisted of single-walled carbon nanotubes (SWCNTs) conjugated with anti-HBsAg antibodies (SWCNT-Ab) was applied for the detection of HBsAg. The electrical conductivity of the printed film was optimized by printing multiple layers of the SWCNT-Ab bioink. The biosensors showed a linear response range from 1-10 mM HBsAg, and the response began to plateau after 10 mM, with a detection limit of 0.5 mM. The inkjet printed biosensors showed stable resistance and a linear response to increasing concentrations of HBsAg. The study suggests that this method has the potential for producing low-cost and sensitive biosensors for the early detection and accurate diagnosis of HBV in resource-limited settings. | Feng Yuan; Wei Wong | Analytical Chemistry; Analytical Chemistry - General; Analytical Apparatus | CC BY 4.0 | CHEMRXIV | 2023-04-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644227bde4bbbe4bbfff123d/original/inkjet-printed-cnt-antibody-bioink-for-detecting-hbv-surface-antigen.pdf |
66b2a097c9c6a5c07a362ff1 | 10.26434/chemrxiv-2024-tmtsd-v2 | The spatial distribution of lipophilic cations in gradient copolymers regulates pDNA binding interactions, polyplex aggregation, and transgene expression | Synthetic polymers—chemically versatile and affordable materials—are promising nanocarriers for the intracellular delivery of nucleic acids. Copolymers comprising of lipophilic cations and neutral hydrophilic co-monomers effectively complex and deliver bulky nucleic acid payloads such as plasmids (pDNA). In this work, we demonstrate that the spatial distribution of lipophilic cations governs the complexation pathways, serum stability, and biological performance of polymer–pDNA complexes (polyplexes). Hitherto, investigators focused predominantly on block and statistical copolymers while largely ignoring gradient copolymers, where the density of lipophilic cations diminishes (gradually or steeply) along polymer backbones. Our goal is to engineer gradient copolymers that combine the colloidal stability of polyplexes formed from block copolymers with the high transfection efficacy of statistical copolymers. We synthesized length- and compositionally-equivalent gradient copolymers (G1–G3) via reversible addition fragmentation chain transfer polymerization in addition to equivalent statistical (S) and block (B) copolymers. We mapped microstructure-dependent differences in pDNA loading per polyplex, pDNA conformational changes, and polymer–pDNA binding thermodynamics via static light scattering, circular dichroism spectroscopy, and isothermal titration calorimetry, respectively. B exhibited vastly different pDNA complexation profiles from the other four copolymers while loading the most pDNA per polyplex. Further, we discovered that subtle modulation of gradient steepness effectively negotiates trade-offs among pDNA delivery efficiency, cytotoxicity, and colloidal stability in serum. For instance, G1 overcame the colloidal instability of S polyplexes in serum, while maintaining comparable transfection efficiency and cell viability. Microstructural contrasts did not elicit differences in complement activation but governed polycation-triggered hemolysis. Our work demonstrates that the spatial distribution of lipophilic cations is an effective, albeit underutilized, design handle to improve polyplex physical properties and pDNA delivery capacity. | Jessica L. Lawson; Ram Prasad Sekar; Aryelle R. E Wright; Grant Wheeler; Jillian Yanes; Jordan Estridge; Chelsea Johansen; Nikki Farnsworth; Praveen Kumar; Jian Wei Tay; Ramya Kumar | Materials Science; Polymer Science; Nanoscience; Biological Materials; Polyelectrolytes - Polymers; Polymerization (Polymers) | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b2a097c9c6a5c07a362ff1/original/the-spatial-distribution-of-lipophilic-cations-in-gradient-copolymers-regulates-p-dna-binding-interactions-polyplex-aggregation-and-transgene-expression.pdf |
676074dcfa469535b9d64973 | 10.26434/chemrxiv-2024-8svsk | Blueprints for the Geometric Control of NHC-CDI Isomers | Rational control of the 3-dimensional presentation of atoms—stereochemistry—lies at the heart of syn-thetic organic and materials chemistries. Here, we report detailed computational studies on conforma-tional isomerism in N-heterocyclic carbene–carbodiimide (NHC–CDI) zwitterionic adducts. By varying the steric and electronic parameters of the NHC and CDI components, criteria for controlling isomerization (thermo)dynamics and predicting energetically favorable conformations were identi-fied. These criteria were validated experimentally using a novel synthetic approach to NHC-CDIs, which exploits the thermodynamic equilibrium be-tween sterically unencumbered NHC dimers to ac-cess NHC-CDI adducts with low barriers to confor-mational isomerization, including the first example of an (E/E)-NHC-CDI. | Craig Day; Niklas Grabicki; Daniel Chu; Allison Keys; Avni Singhal; Vyshnavi Vennelakanti; Ilia Kevlishvili; Rafael Gómez-Bombarelli; Heather Kulik; Jeremiah Johnson | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Physical and Chemical Properties; Structure | CC BY 4.0 | CHEMRXIV | 2024-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676074dcfa469535b9d64973/original/blueprints-for-the-geometric-control-of-nhc-cdi-isomers.pdf |
60c758c4842e65a928db48be | 10.26434/chemrxiv.14571546.v1 | Z-Matrix template-based substitution approach for enumeration of 3D molecular structures | <p>The exhaustive enumeration of 3D chemical
structures based on Z-matrix templates has recently been used in the quantum
chemical investigation of constitutional isomers, diastereomers and rotamers.
This simple yet powerful initial structure generation approach can apply beyond
the investigation of compounds of identical formula by quantum chemical
methods. This paper aims to provide a short description of the overall concept
followed by a practical tutorial to the approach. </p>
<p>· - The four
steps required for Z-matrix template-based substitution are template
construction, generation of tuples for substitution sites, removal of duplicate
tuples and substitution on the template. </p>
<p>· -The
generated tuples can be used to create chemical identifiers to query compound
properties from chemical databases. </p>
<p>· - All of
these steps are demonstrated in this paper by common model compounds and are
very straightforward for an undergraduate audience to reproduce. A comparison
of the approach in this tutorial and other options is also discussed.<b></b></p><br /> | Wanutcha Lorpaiboon; Taweetham Limpanuparb | Bioinformatics and Computational Biology; Computational Chemistry and Modeling; Theory - Computational; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2021-05-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758c4842e65a928db48be/original/z-matrix-template-based-substitution-approach-for-enumeration-of-3d-molecular-structures.pdf |
67579833085116a133e39d86 | 10.26434/chemrxiv-2024-spw5s | Evaluating the functional importance of conformer-dependent atomic partial charge assignment | Physics-based methods such as protein-ligand binding free energy calculations have been increasingly adopted in early-stage drug discovery to prioritize promising compounds for synthesis. However, the accuracy of these methods is highly dependent on details of the calculation and choices made while preparing the ligands and protein ahead of running calculations. During ligand preparation, researchers typically assign partial atomic charges to each ligand atom using a specific ligand conformation for charge assignment, often the input conformer. While it is a well known problem that partial charge assignment is dependent on conformation, little investigation has explored the downstream effects of varied partial charge assignment on free energy estimates. Preliminary benchmarks from Open Free Energy Project show that generating partial charges from different input conformers leads to variation of up to ±5.3 kcal/mol in calculated relative binding free energies due to variation in partial charges alone. In this study, we more systematically explore this issue, investigating systems where differences in partial charge generation (such as those caused by input conformer choice, partial charge engine, and hardware) may lead to differences in calculated absolute hydration free energy (AHFE) values. We demonstrate that supplying different input conformers to a partial charge engine can result in atomic partial charge discrepancies of up to 0.681 e, resulting in differences in calculated AHFE of 6.9 ± 0.1 kcal/mol. We find that even relatively small variations in partial charge assignment can result in notable differences in calculated AHFE, and thus care should be taken when assigning partial charges to ensure reproducibility and accuracy of any resulting free energy calculations. | Meghan Osato; Hannah Baumann; Jennifer Huang; Irfan Alibay; David Mobley | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2024-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67579833085116a133e39d86/original/evaluating-the-functional-importance-of-conformer-dependent-atomic-partial-charge-assignment.pdf |
625875115b9009a36d0e6949 | 10.26434/chemrxiv-2022-zsk04 | Identification of potential anti-COVID-19 drug leads from Medicinal Plants through Virtual High-Throughput Screening | Natural compounds are widely used as attractive and valuable starting points for drug lead discovery. The present study aims to identify phytochemical compounds found in medicinal plants as potential COVID-19 inhibitors, using ensemble docking simulations. To this end, a phytochemical library from the PHCD database – a database of natural chemical compositions of Persian medicinal herbs (https://persianherb.com) – have been virtually screened against four key protein targets in the SARS-CoV-2 life cycle – the Mpro and PLpro proteases and the Spike and human ACE2 proteins. Several potential antiviral lead candidates have been identified based on the “Computational Multitarget Screening” approach, in which favourite candidates interact simultaneously with all four targets. Four of the bioactive phytochemicals identified – Chelidimerine, Gallagyldilacton, Hinokiflavone, and Physalin Z – show the highest binding affinities to all the targets and are suggested to be the best choices for drug design research. Also, several important medicinal plants, including Chelidonium majus L., Punica granatum, Rhus coriaria, Capparis spinose, Cichorium intybus, and Cynara scolymus, with the most phytochemicals interacting with all the host and viral proteins, have been identified that can be considered as the most important herbal resources for drug development with the medicinal plant formulations against COVID-19. | Rohoullah Firouzi; Mitra Ashouri | Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/625875115b9009a36d0e6949/original/identification-of-potential-anti-covid-19-drug-leads-from-medicinal-plants-through-virtual-high-throughput-screening.pdf |
669a8fbcc9c6a5c07add5300 | 10.26434/chemrxiv-2024-6c9kc | Synthesis of 3,3-Disubstituted Thietane Dioxides | 4-Membered heterocycles have been increasingly exploited in medicinal chemistry and as small polar motifs often show important influence on activity and physicochemical properties. Thietane dioxides similarly offer potential in both agricultural and pharmaceutical applications but are notably understudied. Here we report a divergent approach to 3,3-disubstituted thietane dioxide derivatives by forming carbocations on the 4-membered ring with catalytic Lewis or Brønsted acids. Benzylic tertiary alcohols of the thietane dioxides are coupled directly with arenes, thiols and alcohols. | Peerawat Saejong; Jianing Zhong; Juan J. Rojas; Andrew J. P. White; Chulho Choi; James A Bull | Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Acid Catalysis | CC BY 4.0 | CHEMRXIV | 2024-07-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669a8fbcc9c6a5c07add5300/original/synthesis-of-3-3-disubstituted-thietane-dioxides.pdf |
6626cbd991aefa6ce11fc9a8 | 10.26434/chemrxiv-2024-990q0 | A Universal Framework for Fast, Flexible and Fun(ctional) Autonomous Laboratories | The construction of autonomous chemical laboratories is complex, laborious, and expensive. It is imperative to develop highly usable, flexible, and powerful development framework to unify efforts. Current platforms have high adoption barriers, whether through their high price of adoption, high complexity to implement, or limited implementation on diverse hardware and software systems. Furthermore, there are no studies to date which examine the practical usability of current platforms with state-of-the-art scientific studies. In this work we engineer a new, flexible laboratory automation platform (FLAB) to resolve these issues. With a unique, user-centric and agile approach, we develop this platform through eight different experimental studies, which represent the broad spectrum of activities in the integration of chemical laboratories and artificial intelligence. By beginning with a generalized, modular architecture in Python, each study created a generalized feature that evolved the platform’s utility and ease of use. Such features include advanced methods for synchronous processing, data manipulation and a user-interface for rapid prototyping. Ultimately, this study yields a simpler, more accessible and powerful toolset for the creation of autonomous chemical laboratories. | Nicholas A. Jose; Peace Adesina; Kevin Ballu; Aniket Chitre; Dogancan Karan; Anna Katsarou; Alexander Pomberger; Song Zhai; Alexei Lapkin | Materials Science; Chemical Engineering and Industrial Chemistry; Chemical Education; Chemical Education - General; Reaction Engineering | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6626cbd991aefa6ce11fc9a8/original/a-universal-framework-for-fast-flexible-and-fun-ctional-autonomous-laboratories.pdf |
67a4be6c81d2151a02605f53 | 10.26434/chemrxiv-2025-cqhf1 | Chemical functionalization of a unique 2D material – Computational prediction for cyclooctyne on the biphenylene network | The chemical functionalization of the biphenylene network with the organic adsorbate cyclooctyne is predicted using density functional theory. As a novel 2D material, the biphenylene network has attracted a lot of attention in the material science community due to possible applications in superconductivity, photocatalysis, or hydrogen storage. First studies show the decoration of the biphenylene network using metal atoms, hydrogenation, or the adsorption of simple molecules like CO2. However, covalent functionalization of the material is an unsolved challenge, which could allow tailoring of the material's properties owing to the variability of organic adsorbates. We show that the biphenylene network can be functionalized with cyclooctyne by exploiting its strained triple bond. The reaction mechanism proceeds via the asynchronous [2+2] cycloaddition found for cyclooctyne adsorption before using the energy decomposition analysis for extended systems (pEDA). Chemical functionalization leads to a coverage-dependent change in the effective band structure with the disappearance of the type II Dirac cone known for pristine biphenylene for higher coverages. A brief comparison with other 2D carbon materials shows the high reactivity of the biphenylene network, making it a promising first study for exploring new avenues for the creation of novel functional materials and interfaces and the chemical tuning of their electronic structure. | Hendrik Weiske; Ralf Tonner-Zech | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2025-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a4be6c81d2151a02605f53/original/chemical-functionalization-of-a-unique-2d-material-computational-prediction-for-cyclooctyne-on-the-biphenylene-network.pdf |
672da3795a82cea2fa782330 | 10.26434/chemrxiv-2024-7f2l6-v2 | Carbon footprint comparison of liquid organic hydrogen carriers cycled thermochemically and electrochemically | Hydrogen (H2) has been proposed as a way to store energy for long durations with minimal carbon footprint. The challenges of using H2 to store energy are that it has very low volumetric density and diffuses rapidly through container walls. Liquid organic hydrogen carriers (LOHCs) have been proposed as a method of storing hydrogen in the molecular backbone of stable organic chemicals, addressing many of the concerns of molecular hydrogen. The majority of LOHC systems proposed have utilized thermochemical cycling for the hydrogenation (to store hydrogen) and dehydrogenation (to release hydrogen). Thermochemical cycling requires heating of the reactors, which results in an increased carbon footprint, and is not easily amenable to dynamic operating with the variable renewable electricity grid. Electrochemical LOHC cycling has been proposed as an alternative to thermochemical cycling because it can pair directly with the variable renewable grid and operate more dynamically. To understand the viability of the thermochemical and electrochemical processes, a comparative carbon footprint analysis is necessary. The analysis showed that the electrochemical LOHC cycling process achieves the lowest carbon footprint when using highly concentrated LOHCs as the feed or when a downstream separation process was not needed. The carbon footprint in electrochemical cycling of diluted LOHC was primarily contributed to by the LOHC distillation separation process. A sensitivity analysis showed the carbon footprint LOHC concentration dependence during the electrochemical cycling process. Moreover, the electrolyte composition significantly affects the carbon footprint during electrochemical LOHC cycling. Decisions regarding use of thermochemical versus electrochemical cycling need to include separation system boundaries, not just the reactors themselves. | Moses D. Chilunda; Sarvarjon A. Talipov; Elizabeth J. Biddinger | Catalysis; Energy; Chemical Engineering and Industrial Chemistry; Reaction Engineering; Electrocatalysis; Energy Storage | CC BY 4.0 | CHEMRXIV | 2024-11-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672da3795a82cea2fa782330/original/carbon-footprint-comparison-of-liquid-organic-hydrogen-carriers-cycled-thermochemically-and-electrochemically.pdf |
649d59e89ea64cc1672abe4b | 10.26434/chemrxiv-2023-jgl5l | Metal-organic framework based nanomaterials: An advanced review of their synthesis and energy storage applications | Metal-organic frameworks (MOFs) have emerged as a versatile class of porous materials with enormous potential for various applications, including energy storage devices. In this review, we present a comprehensive analysis of the recent advancements and applications of MOFs in the field of energy storage. We begin by providing a brief overview of the fundamental aspects of MOFs, including their synthesis, structural diversity, and tuneable properties. We then focus on the utilisation of MOFs in advanced energy storage systems with a particular focus on supercapacitors. MOFs can be employed as electrode materials, separators, and catalysts, offering enhanced electrochemical performance, improved charge/discharge rates, and prolonged cycling stability. The unique tunability of MOFs allows for the rational design of tailored materials with desired properties, such as high specific capacity, excellent conductivity, and superior cycling stability. We will further discuss in detail the recent developments in MOF-based electrochemical capacitors, highlighting the significant progress made in achieving high energy and power densities. The exceptional charge storage capacity of MOFs combined with their facile synthesis and scalability make them promising candidates for next-generation energy storage technologies. The review further sheds light on the challenges and opportunities in the practical implementation of MOFs in energy storage devices with an eye on future research and development in the MOFs for energy applications. The manuscript discusses perspectives and future directions and, we believe, the insights presented are timely and will be of particular help to young and early-stage researchers. | Mudasir Ahmad Yatoo; Jhalak Gupta; Faiza Habib; Akram Alfantazi; Zahid Ansari; Zubair Ahmad | Energy; Energy Storage | CC BY 4.0 | CHEMRXIV | 2023-06-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649d59e89ea64cc1672abe4b/original/metal-organic-framework-based-nanomaterials-an-advanced-review-of-their-synthesis-and-energy-storage-applications.pdf |
6332ebfde665bd7cbb146491 | 10.26434/chemrxiv-2022-dcbd8 | Concise synthesis of (–)-cotylenol, a 14-3-3 PPI molecular glue | Small molecules that modulate the 14-3-3 protein-protein interaction (PPI) network represent valuable therapeutics and tool com-pounds. However, access has been lost to 14-3-3 PPI molecular glues of the cotylenin class, leading to investigations into practi-cal chemical syntheses. Here we report a concise synthesis of (–)-cotylenol via a 10-step entry into the 5-8-5 cotylenin binding region using a convergent fragment coupling and Claisen-ene cascade. | Tucker Huffman; Akihiro Kuroo; Ryota Sato; Ryan Shenvi | Organic Chemistry; Natural Products; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6332ebfde665bd7cbb146491/original/concise-synthesis-of-cotylenol-a-14-3-3-ppi-molecular-glue.pdf |
60c745aeee301c4480c7937c | 10.26434/chemrxiv.10059935.v1 | Phase Dependent Encapsulation and Release Profile of ZIF-Based Biocomposites | Here we systematically varied the composition of the relative amounts of ligand (2-methylimidazole), metal precursor (Zn(OAc)2∙2H2O, and protein to prepare a series of protein@ZIF biocomposites. The effect of post synthetic treatments (i.e. washes with water or water/ethanol) was investigated. The XRD data of the examined samples were used to construct ternary diagrams. Five different phases were identified. The encapsulation efficiency (of bovine serum albumin and insulin) were phase dependent. | Francesco Carraro; Miriam Velasquez; Efwita Astria; Weibin Liang; liam Twight; chiara parise; meng ge; Zhehao Huang; Raffaele Ricco; Xiaodong Zou; laura villanova; C. Oliver Kappe; Christian Doonan; paolo falcaro | Nanostructured Materials - Materials | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745aeee301c4480c7937c/original/phase-dependent-encapsulation-and-release-profile-of-zif-based-biocomposites.pdf |
61de7dd26be42018d32bac8d | 10.26434/chemrxiv-2022-w0hg4 | Fullerene-Tetrabenzofluorene (C60-TBF) in Multivalent Photosensitisation for Enhanced ZnO-based Photo-catalysts: Mono vs. Hexakis Adduct | Photo-catalysts offer a simple catalytic method with widespread applications like degradation of polluting dyes, hydrogen generation from water, etc., in the presence of a photon source like sunlight. The development of a second-generation photo-catalyst in the form of a nanocomposite is an integral part of research to improve the practical usefulness and efficiency of the process. A systematic study using the active material with controlled functional groups is required to understand the process in detail as well as to develop efficient photocatalytic systems. In this paper, we report the design, synthesis, detailed physicochemical studies, and self-assembly of interesting materials where fullerenes have been functionalized with polycyclic, aromatic, conjugated, butterfly-shaped molecules like Tetrabenzofluorene (TBF) using a well-known click chemistry approach. Detailed analyses using spectroscopic, electrochemical, and microscopic or X-ray diffraction (single crystal) techniques were undertaken for a clear understanding of their photophysical or self-assembly behavior. The functionalized fullerene material was mainly used so that comparative results could be presented where two units (mono adduct) or twelve units (hexakis adduct) of TBF molecules were attached separately. These comparative studies were beneficial for unambiguous interpretation of results and drawing definitive conclusions regarding the energy transfer with cascade-type systems. Finally, those results were useful for the logical understanding of photo-catalytic experiments using those designer fullerene materials. | Munusamy Krishnamurthy; Philip Hope; P Ramar; A. A. Boopathi; Srinivasan Sampath; Marc K. Etherington; Alyssa-Jennifer Avestro; debasis samanta | Materials Science; Catalysis; Carbon-based Materials; Catalysts; Photocatalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61de7dd26be42018d32bac8d/original/fullerene-tetrabenzofluorene-c60-tbf-in-multivalent-photosensitisation-for-enhanced-zn-o-based-photo-catalysts-mono-vs-hexakis-adduct.pdf |
61659aecbe10744e149a5ba2 | 10.26434/chemrxiv-2021-tn0x7 | Microbial fuel cell power overshoot studied with microfluidics: from quantification to elimination | Power overshoot can hinder determination of maximum power densities in microbial fuel cells (MFCs). In this work, a microfluidic approach was used to study overshoot in an MFC containing a pure culture of electroactive biofilms (EAB) containing Geobacter sulfurreducens. After 1-month operation under constant flow of an ideal nutrient medium, the MFC health began to degrade, marked by voltage loss and the appearance of anomalies in the power density curves. One such anomaly was a chronic power overshoot, accompanying a loss of both measured power and current density on the high-current side of the power density curve. The degree of power overshoot was quantified while certain flow-based interventions were applied, notably the shear
erosion of the EAB outer layer. Next, two approaches to acclimation were demonstrated to treat the remaining overshoot. The standard approach, which acclimates the MFC to high currents before a standard polarization test, eliminated the remaining overshoot and returned maximum
power densities to initial levels, but maximum current density remained lower than the initial level. A microfluidic-assisted “long-hold polarization test” enabled efficient in situ acclimation of each external resistor during the measurement. Despite the health-compromised MFC, this
method provided long-term stability during the polarization test, resulting in power and current density measurements that exceeded those made on the healthy MFC using the standard polarization test. We conclude that slower electron transfer kinetics in unhealthy MFCs can provoke overshoot by prolonging the time to reach steady state during the polarization test, but a properly designed measurement overcomes this problem. | Mehran Abbaszadeh Amirdehi; Lingling Gong; Nastaran Khodaparastasgarabad; Bruce E. Logan; Jesse Greener | Catalysis; Analytical Chemistry; Energy; Electrochemical Analysis; Electrocatalysis; Fuel Cells | CC BY 4.0 | CHEMRXIV | 2021-10-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61659aecbe10744e149a5ba2/original/microbial-fuel-cell-power-overshoot-studied-with-microfluidics-from-quantification-to-elimination.pdf |
60c744beee301c9ccec791ce | 10.26434/chemrxiv.9911627.v1 | Single Particle Inductively Coupled Plasma Mass Spectrometry: Investigating Nonlinear Response Observed in Pulse Counting Mode and Extending the Linear Dynamic Range by Compensating for Dead Time Related Count Losses on a Microsecond Timescale | <p>The article demonstrates the importance of using
a suitable approach to compensate for dead time relate count losses (a certain
measurement artefact) whenever short, but potentially strong transient signals are
to be analysed using inductively coupled plasma mass spectrometry (ICP-MS).
Findings strongly support the theory that inadequate time resolution, and
therefore insufficient compensation for these count losses, is one of the main
reasons for size underestimation observed when analysing inorganic
nanoparticles using ICP-MS, a topic still controversially discussed.</p> | Ingo Strenge; Carsten Engelhard | Analytical Chemistry - General; Analytical Apparatus; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744beee301c9ccec791ce/original/single-particle-inductively-coupled-plasma-mass-spectrometry-investigating-nonlinear-response-observed-in-pulse-counting-mode-and-extending-the-linear-dynamic-range-by-compensating-for-dead-time-related-count-losses-on-a-microsecond-timescale.pdf |
6714a0cfcec5d6c142ab56e0 | 10.26434/chemrxiv-2024-cd8ht | The path to the triplet state in LOV domains | Upon blue light absorption, LOV domains efficiently undergo intersystem crossing (ISC) to the triplet state. Several factors potentially contribute to this efficiency. One often proposed in the literature is the heavy atom effect from the nearby (and eventually adduct-forming) cysteine. However, some LOV domain derivatives missing the cysteine residue also undergo ISC efficiently. Using hybrid multi-reference quantum mechanical / molecular mechanical (QM/MM) models, we investigate the effect of the protein electrostatic environment in a prototypal LOV domain, AtLOV2, compared to the effect of the dielectric of a solvent. We find that the AtLOV2's electrostatic environment is especially well tuned to stabilize a triplet (nN,π*) state, which we posit is the state involved in the ISC step. Other low-lying triplet states having (π,π*) and (nO,π*) character are ruled out based on energetics and/or their orbital shape. The mechanistic picture that emerges from the calculations is one that involves ISC of photoexcited flavin to a triplet (nN,π*) state followed by rapid internal conversion to a triplet (π,π*) state, which is the state detected spectroscopically. This insight into the ISC mechanism can provide guidelines for tuning flavin's photophysics through mutations that alter the protein electrostatic environment and potentially helps explain why ISC (and subsequent flavin photochemistry) doesn't occur more frequently in many classes of flavin-binding enzymes | Paulami Ghosh; Stephen O. Ajagbe; Samer Gozem | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Theory - Computational; Biophysical Chemistry; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6714a0cfcec5d6c142ab56e0/original/the-path-to-the-triplet-state-in-lov-domains.pdf |
672337757be152b1d08c6368 | 10.26434/chemrxiv-2024-rbdj0 | Light-modulated self-assembly of synthetic nanotubes | Artificial biomolecular polymers with the capacity to respond to stimuli are emerging as a key component to develop living materials and synthetic cells. Here, we demonstrate artificial DNA tubular nanostructures that form in response to light in a dose-dependent manner. These nanotubes assemble from programmable DNA tile motifs that are engineered to include a UV-responsive domain, so that UV irradiation activates nanotube self-assembly. We demonstrate that nanotube formation speed can be tuned by adjusting the UV dose. We then couple light-dependent activation of tiles with RNA transcription, making it possible to control nanotube formation via concurrent physical and biochemical stimuli. Finally, we illustrate how UV activation effectively controls nanotube assembly in confinement, as a rudimentary stimulus-responsive cytoskeletal system that can achieve various conformations in a minimal synthetic cell. This study contributes new tile designs that are immediately useful to build biomolecular scaffolds with controllable dynamics in response to multiple stimuli. | Mahdi Dizani; Siddharth Agarwal; Dino Osmanovic; Elisa Franco | Nanoscience; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672337757be152b1d08c6368/original/light-modulated-self-assembly-of-synthetic-nanotubes.pdf |
66fcefdbcec5d6c142dff018 | 10.26434/chemrxiv-2024-q9hss | A Computational Approach to Modeling Excitation-Energy Transfer and Quenching in Light-Harvesting Complexes | Light-harvesting complexes (LHC) are known to regulate the flux of energy in different light conditions and activate quenching processes to prevent photodamage in case of high light. However, the molecular mechanisms behind these photoprotective processes remain unclear. A widely accepted model suggests an excitation-energy transfer from excited chlorophylls to neighboring carotenoids which finally act as quenchers. Herein, we present a computational protocol to model the energy pathways in the LHC, focusing specifically on the minor CP29 antenna complex of plants. We explore the factors that modulate the switch between light-harvesting and quenched states. The protocol includes modeling the exciton Hamiltonian of the chlorophylls/lutein aggregate, and calculating population dynamics using a kinetic model based on the Redfield-Forster approach. Our analysis reveals a highly tunable excited-state lifetime for the complex, that can switch between quenched and unquenched state depending on the lutein S1 energy, in accordance with recent experiments. Moreover, we observe that the s-trans lutein conformers are more likely to exhibit the characteristics of the quencher. | Chris John; Laura Milena Pedraza González; Elena Betti; Lorenzo Cupellini; Benedetta Mennucci | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational | CC BY NC 4.0 | CHEMRXIV | 2024-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fcefdbcec5d6c142dff018/original/a-computational-approach-to-modeling-excitation-energy-transfer-and-quenching-in-light-harvesting-complexes.pdf |
6773527f6dde43c908d65400 | 10.26434/chemrxiv-2024-5c808-v2 | Machine Learning Approaches for Developing Potential Surfaces: Applications to OH-(H2O)n (n=1-3) Complexes | An approach for obtaining high-level ab initio potential surfaces is described. The approach takes advantage of machine learning strategies in a two-step process. In the first, the molecular-orbital based machine learning (MOB-ML) model uses Gaussian process regression to learn the correlation energy at the CCSD(T) level using the molecular orbitals obtained from Hartree-Fock calculations. In this work, the MOB-ML approach is expanded to use orbitals obtained using a smaller basis set, aug-cc-pVDZ, as features for learning the correlation energies at the complete basis set (CBS) limit. This approach is combined with the development of a neural-network potential, where the sampled geometries and energies that provide the training data for the potential are obtained using a diffusion Monte Carlo (DMC) calculation, which was run using the MOB-ML model. Protocols are developed to make full use of the structures that are obtained from the DMC calculation in the training process. These approaches are used to develop potentials for OH-(H2O) and H3O+(H2O), which are used for subsequent DMC calculations. The results of these calculations are compared to those performed using previously reported potentials. Overall, the results of the two sets of DMC calculations are in good agreement for these very floppy molecules. Potentials are also developed for OH-(H2O)2 and OH-(H2O)3, for which there are not available potential surfaces. The results of DMC calculations for these ions are compared to those for the correspondingOH-(H2O)2 and OH-(H2O)3 ions. It is found that the level of delocalization of the shared proton is similar for a hydroxide or hydronium ion bound to the same number of water molecules. This finding is consistent with the experimental observation that these sets of ions have similar spectra. | Greta Jacobson; Lixue Cheng; Vignesh Bhethanabotla; Jiace Sun; Anne McCoy | Theoretical and Computational Chemistry; Theory - Computational; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6773527f6dde43c908d65400/original/machine-learning-approaches-for-developing-potential-surfaces-applications-to-oh-h2o-n-n-1-3-complexes.pdf |
60c741e8bdbb8979eaa383e0 | 10.26434/chemrxiv.8159642.v1 | Rapid and Accurate Automatic Temperature Calibration of Disposable Screen-printed Heated Gold Electrodes | Joule-heated electrodes have been used to enhance electrochemical analysis. Due to such direct heating, a steep temperature gradient is created near the electrode surface. The heating device that provides the high-frequency AC (50 kHz or more) has to be calibrated, in order to apply the desired temperature during analysis. The applied temperature of the working electrode influences both its electrical resistance and the electrochemical potential of a redox couple. Open circuit potentiometric (OCP) measurements were performed automatically with screen-printed gold loop electrodes (Au-LE), while applying 50 kHz AC heating pulses of increasing intensity provided by a ThermaLab® AC generator. Potentiometric temperature calibrations were performed using 5 mM equimolar ferri/ferrocyanide in 0.1 M of potassium chloride at 20 °C bulk temperature. Potential differences produced during each heat pulse were used to automatically calculate the electrode temperature using the temperature coefficient of this redox couple (-1.6 mV/K). The electrode resistance values at each heating pulse were obtained by measuring the heating voltage and heating current. The automatic temperature calibration experiments with five Au-LEs were shown to be highly reproducible and precise, with an RSD for the temperature of 0.24% and 4% for resistance. The average margin error of OCP temperatures were ±0.66 K at a 95% confidence level. The temperature coefficient (α) of electrical resistivity of the screen-printed gold layers was found to be 0.0025 °C<sup>-1</sup>, which is 27% lower than the theoretical value for gold metal. These findings were confirmed by DC resistance measurements using a potentiostat. Comparing the OCP temperature with the resistivity method, the temperature difference was about 0.94 °C (2.8%). Both methods enable quick, reproducible and accurate temperature calibration for disposable Au-LE, which were also used for trace mercury detection in lake water samples | Sonivette Colón-Rodríguez; Martin Schönhoff; Juhaina Abdulkhalek; Tatiana Quiñones-Ruíz; Stephen W. Bentham; Gourav Bhowmik; Mengbing Huang; Peter Langer; Igor K. Lednev; Gerd-Uwe Flechsig | Electrochemical Analysis; Environmental Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741e8bdbb8979eaa383e0/original/rapid-and-accurate-automatic-temperature-calibration-of-disposable-screen-printed-heated-gold-electrodes.pdf |
639b52a0dadddc02ed8fb00b | 10.26434/chemrxiv-2022-1n56p | Methods for Non-Destructive, High Precision Mass/Charge Determination for Single, Trapped, GigaDalton Nanoparticles | Several methods for non-destructive mass measurements on single, trapped nanoparticles in the megadalton(MDa) to gigadalton (GDa) mass ranges are demonstrated, and the trade-offs between speed, precision, and ease of use are discussed. Charged nanoparticles are introduced into vacuum by electrospray ionization, and trapped in a quadrupole ion (Paul) trap, with detection by light scattering. Four different methods for measuring the mass/charge ratios of trapped particles are discussed, all based on measuring the secular frequency for motion of the particle in the trap, working in either the time or frequency domains. The charge is then measured by driving single electron charge changes using either a discharge or vacuum ultraviolet lamp. Several related topics such as the effects of pressure on secular resonance width and the spectrum of simultaneously trapped particles are also discussed. | David M. Bell; Collin R. Howder; Bryan A. Long; Scott Anderson | Physical Chemistry; Analytical Chemistry; Nanoscience; Mass Spectrometry; Physical and Chemical Processes | CC BY NC 4.0 | CHEMRXIV | 2022-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/639b52a0dadddc02ed8fb00b/original/methods-for-non-destructive-high-precision-mass-charge-determination-for-single-trapped-giga-dalton-nanoparticles.pdf |
60c758f6bdbb893727a3ae6c | 10.26434/chemrxiv.14538576.v2 | Quantum Chemistry for Molecules at Extreme Pressure on Graphical Processing Units: Implementation of Extreme Pressure Polarizable Continuum Model | Pressure plays essential roles in chemistry by altering structures and controlling chemical reactions. The extreme-pressure polarizable continuum model (XP-PCM) is an emerging method with an efficient quantum mechanical description of small and medium-size molecules at high pressure (on the order of GPa). However, its application to large molecular systems was previously hampered by CPU computation bottleneck: the Pauli repulsion potential unique to XP-PCM requires the evaluation of a large number of electric field integrals, resulting in significant computational overhead compared to the gas-phase or standard-pressure polarizable continuum model calculations. Here, we exploit advances in Graphical Processing Units (GPUs) to accelerate the XP-PCM integral evaluations. This enables high-pressure quantum chemistry simulation of proteins that used to be computationally intractable. We benchmarked the performance using 18 small proteins in aqueous solutions. Using a single GPU, our method evaluates the XP-PCM free energy of a protein with over 500 atoms and 4000 basis functions within half an hour. The time taken by the XP-PCM-integral evaluation is typically 1\% of the time taken for a gas-phase density functional theory (DFT) on the same system. The overall XP-PCM calculations require less computational effort than that for their gas-phase counterpart due to the improved convergence of self-consistent field iterations. Therefore, the description of the high-pressure effects with our GPU accelerated XP-PCM is feasible for any molecule tractable for gas-phase DFT calculation. We have also validated the accuracy of our method on small molecules whose properties under high pressure are known from experiments or previous theoretical studies. | Ariel Gale; Eugen Hruska; Fang Liu | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758f6bdbb893727a3ae6c/original/quantum-chemistry-for-molecules-at-extreme-pressure-on-graphical-processing-units-implementation-of-extreme-pressure-polarizable-continuum-model.pdf |
65355d8487198ede0709275c | 10.26434/chemrxiv-2023-tlwq1 | Atomistic Insights into Hydrogen-Bonded Supramolecular Capsule Self-Assembly Dynamics | In this work, we have delved into the intricate assembly dynamics of hydrogen-bonded supramolecular calixarene capsules, particularly focusing on the disparities between resorcinarenes and pyrogallolarenes. Through enhanced sampling simulations, we have mapped out the fundamental thermodynamic, structural, and mechanistic details governing the assembly of these capsules in apolar solvents. Notably, our findings highlight the paramount influence of dimer formations, mediated substantially by inter- and intramolecular hydrogen bonding interactions. Furthermore, we have observed that water plays an instrumental role in the assembly of resorcinarene, though its kinetic contribution is mitigated by its swift diffusion. Solvent encapsulation analysis suggests that pyrogallolarene capsules can accommodate more solvent molecules relative to their resorcinarene counterparts, an attribute most likely resultant from the absence of water in pyrogallolarene structures. These insights not only offer a detailed understanding of the calixarene assembly dynamics but also showcase the potential adaptability of the methodology to other assembly systems, thereby propelling its implications into broader chemical and biological domains. | Riccardo Capelli; GiovanniMaria Piccini | Theoretical and Computational Chemistry; Physical Chemistry; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65355d8487198ede0709275c/original/atomistic-insights-into-hydrogen-bonded-supramolecular-capsule-self-assembly-dynamics.pdf |
676aa5236dde43c9082d2c1d | 10.26434/chemrxiv-2024-rjgwd-v2 | Pore Network Tortuosity Controls Fast-Charging in Supercapacitors | Ionic transport within porous carbon electrodes is crucial for optimizing charge/discharge rates in supercapacitors, yet the material properties governing ion dynamics remain poorly understood. Contrary to the traditional viewpoint, we find that mesoporosity does not necessarily correlate with high supercapacitor rate capability. Instead, we employed pulsed field gradient nuclear magnetic resonance to directly measure anionic effective diffusivities in the carbon pores, offering a probe of ionic transport in supercapacitors. Our findings reveal a significant discrepancy between short-range and long-range diffusivities, which captures the tortuosity of the pore network. Short-range diffusivities lack correlation with supercapacitor rate capability, whereas long-range diffusivities correlate strongly. Ultimately, low-tortuosity nanoporous carbons exhibited superior rate capability, highlighting the importance of well-interconnected pore networks for efficient ion transport. Our study reveals pore network tortuosity as a key factor that governs charging rates in amorphous nanoporous carbons and guides the design of electrodes with optimized transport channels to enhance supercapacitor performance. | Thomas Kress; Xinyu Liu; Alexander Forse | Physical Chemistry | CC BY 4.0 | CHEMRXIV | 2024-12-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676aa5236dde43c9082d2c1d/original/pore-network-tortuosity-controls-fast-charging-in-supercapacitors.pdf |
639766ff14d92db56eac2ad9 | 10.26434/chemrxiv-2022-f6mjt | Deciphering the antioxidative role of p53 against H2O2-induced DNA damage using ion mobility mass spectrometry | The transcription factor p53 is exquisitely sensitive and selective to a broad variety of cellular environments. Several studies have reported that oxidative stress weakens the p53-DNA binding affinity for certain promoters depending on the oxidation mechanism. Despite this body of work, the precise mechanisms by which the physiologically relevant DNA-p53 tetramer complex senses cellular stresses caused by H2O2 are still unknown. Here, we employed native mass spectrometry (MS) and ion mobility (IM)-MS coupled to chemical labelling and chemical oxidation to examine the mechanism of redox regulation of the p53-p21 complex. Our approach has found that two reactive cysteines in p53 protect against H2O2-induced oxidative DNA damage by forming sulfenates. A harsh H2O2 insult that exceeds the antioxidant capability of p53 causes DNA oxidation followed by p53 dissociation. The DNA-free p53 is further oxidized to form disulfides leading to function and structure impairment. | Manuel David Peris-Díaz; Artur Krężel; Perdita Barran | Physical Chemistry; Biological and Medicinal Chemistry; Analytical Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-12-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/639766ff14d92db56eac2ad9/original/deciphering-the-antioxidative-role-of-p53-against-h2o2-induced-dna-damage-using-ion-mobility-mass-spectrometry.pdf |
63f27f82fcfb27a31f11d368 | 10.26434/chemrxiv-2023-6mg3w-v2 | Carboxylate catalysis: a mild catalytic O-silylative aldol reaction of aldehydes and ethyl diazoacetate | A mild catalytic variant of the aldol reaction between ethyl diazoacetate and aldehydes is described using a combination of N,O-bis(trimethylsilyl)acetamide and catalytic tetramethylammonium pivalate as catalyst. The reaction proceeds rapidly at ambient temperature to afford the O-silylated aldol products in good to excellent yield, and the acetamide byproducts can be removed by simple filtration. | Saara Riuttamäki; Anton Bannykh; Anniina Kiesilä; Petri Pihko | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Base Catalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63f27f82fcfb27a31f11d368/original/carboxylate-catalysis-a-mild-catalytic-o-silylative-aldol-reaction-of-aldehydes-and-ethyl-diazoacetate.pdf |
60c73f62bb8c1a0cb23d9b2d | 10.26434/chemrxiv.7373969.v1 | Asymmetric Synthesis of Griffipavixanthone Employing a Chiral Phosphoric Acid-Catalyzed Cycloaddition | Asymmetric synthesis of the biologically active xanthone
dimer griffipavixanthone (GPX) is reported along with its absolute
stereochemistry determination. Synthesis of the natural product is accomplished
<i>via</i> dimerization of a <i>p-</i>quinone methide (<i>p-</i>QM) using a chiral phosphoric acid (CPA) catalyst to afford a
protected precursor in excellent diastereo- and enantioselectivity. Mechanistic
studies, including an unbiased computational investigation of chiral ion-pairs
using parallel tempering (PT), were performed in order to probe the mode of asymmetric
induction | Michael Smith; Kyle Reichl; Randolph Escobar; Thomas Heavey; David Coker; Scott Schaus; John Porco | Natural Products; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2018-11-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f62bb8c1a0cb23d9b2d/original/asymmetric-synthesis-of-griffipavixanthone-employing-a-chiral-phosphoric-acid-catalyzed-cycloaddition.pdf |
66f0101e51558a15efc6e666 | 10.26434/chemrxiv-2024-v691w | On-chip Electrochemical Detection of Dissolved Oxygen: Eliminating the Requirement for Permeable Selective Membrane | Dissolved Oxygen (DO) quantification is an important measure of the overall health of a water system. Fluctuations from normal values can indicate the presence of contaminants, and predict further events, for example, fish deaths resulting from eutrophication. DO can vary due to a variety of environmental factors, including altitude, so regular monitoring is crucial to understanding the baseline water conditions. Electrochemical approaches offer good accuracy and ease of use but are currently limited by their requirement for an oxygen permeable membrane to remove interference. To this end, we propose the use of interdigitated electrode arrays to facilitate the quantification of DO, without the need for a membrane, by measuring the by-product of the oxygen reduction reaction: hydrogen peroxide. In this paper, we show the use of mixed metal electrode arrays to sufficiently produce, and subsequently quantify, hydrogen peroxide as a proxy measure of dissolved oxygen, with a detection limit of 0.36 ppm DO. We further show that this technique is adequate for the detection of DO in tidal river water, and can be reliably used in the presence of chlorine and iron, which have electrochemical activity in the same potential range. | Ian Seymour; Fiona Barry; James F Rohan; Alan O'Riordan | Analytical Chemistry; Electrochemical Analysis | CC BY 4.0 | CHEMRXIV | 2024-09-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f0101e51558a15efc6e666/original/on-chip-electrochemical-detection-of-dissolved-oxygen-eliminating-the-requirement-for-permeable-selective-membrane.pdf |
65e78afae9ebbb4db9fa4a59 | 10.26434/chemrxiv-2024-wg9xj | Charge Delocalization and Global Aromaticity in a Partially Fused 12-Porphyrin Nanoring | Aromatic and antiaromatic ring currents can reveal global electronic delocalization around the circumference of pi-conjugated macrocycles, although these phenomena are poorly understood in large rings. Here we present the template-directed synthesis of a fully pi-conjugated cyclic porphyrin 12-mer consisting of six b,meso,b-edge-fused porphyrin dimers connected by six butadiyne bridges. The lowest energy pi-pi* absorption band of this partially fused nanoring is shifted far into the NIR, confirming the strong pi-conjugation around the circumference of the macrocycle. Investigation of the oxidized and reduced nanoring-template complex by 1H and 19F NMR spectroscopy demonstrates the presence of coherent global (anti)aromatic ring currents, consistent with DFT calculations. The stronger -conjugation enables global charge delocalization even at low levels of oxidation or reduction. These findings open new avenues for the engineering of cyclic molecular wires. | Sebastian Kopp; Henrik Gotfredsen; Janko Hergenhahn; Arnau Rodríguez-Rubio; Jie-Ren Deng; He Zhu; Wojciech Stawski; Harry Anderson | Organic Chemistry; Nanoscience; Organic Synthesis and Reactions; Physical Organic Chemistry; Supramolecular Chemistry (Org.) | CC BY NC 4.0 | CHEMRXIV | 2024-03-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e78afae9ebbb4db9fa4a59/original/charge-delocalization-and-global-aromaticity-in-a-partially-fused-12-porphyrin-nanoring.pdf |
64596c281ca6101a45015aa7 | 10.26434/chemrxiv-2023-lczzd | Drugit: Crowd-sourcing molecular design of non-peptidic VHL binders | Given the role of human intuition in current drug design efforts, crowd-sourced 'citizen scientist' games have the potential to greatly expand the pool of potential drug designers. Here, we introduce ‘Drugit', the small molecule design mode of the online ‘citizen science’ game Foldit. We demonstrate its utility for design with a use case to identify novel binders to the von Hippel Lindau E3 ligase. Several thousand molecule suggestions were obtained from players in a series of 10 puzzle rounds. The proposed molecules were then evaluated by in silico methods and by an expert panel and selected candidates were synthesized and tested. One of these molecules, designed by a player, showed dose-dependent shift perturbations in protein-observed NMR experiments. The co-crystal structure in complex with the E3 ligase revealed that the observed binding mode matched in major parts the player’s original idea. The completion of one full design cycle is a proof of concept for the Drugit approach and highlights the potential of involving citizen scientists in early drug discovery. | Thomas Scott; Christian Alan Paul Smethurst; Yvonne Westermaier; Moriz Mayer; Peter Greb; Roland Kousek; Tobias Biberger; Gerd Bader; Zuzana Jandova; Philipp S. Schmalhorst; Julian E. Fuchs; Aniket Magarkar; Christoph Hoenke; Thomas Gerstberger; Steven A. Combs; Richard Pape; Saksham Phul; Sandeepkumar Kothiwale; Andreas Bergner; Alex G. Waterson; Foldit Players; Harald Weinstabl; Darryl B. McConnell; Jark Böttcher; Jens Meiler; Rocco Moretti | Biological and Medicinal Chemistry; Bioengineering and Biotechnology; Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2023-05-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64596c281ca6101a45015aa7/original/drugit-crowd-sourcing-molecular-design-of-non-peptidic-vhl-binders.pdf |
60c73f190f50db0420395731 | 10.26434/chemrxiv.7217819.v1 | On the Geometrical Representation of Classical Statistical Mechanics | In this work a
geometrical representation of equilibrium and near equilibrium statistical
mechanics is proposed. Using a formalism consistent with the Bra-Ket notation
and the definition of inner product as a Lebasque integral, we describe the
macroscopic equilibrium states in classical statistical mechanics by “properly
transformed probability Euclidian vectors” that point on a manifold of
spherical symmetry. Furthermore, any macroscopic thermodynamic state “close” to
equilibrium is described by a triplet that represent the “infinitesimal volume”
of the points, the Euclidian probability vector at equilibrium that points on a
hypersphere of equilibrium thermodynamic state and a Euclidian vector a vector
on the tangent bundle of the hypersphere. The necessary and sufficient
condition for such representation is expressed as an invertibility condition on
the proposed transformation. Finally, the relation of the proposed geometric
representation, to similar approaches introduced under the context of differential
geometry, information geometry, and finally the Ruppeiner and the Weinhold
geometries, is discussed. It turns out that in the case of thermodynamic
equilibrium, the proposed representation can be considered as a Gauss map of a
parametric representation of statistical mechanics. | Georgios C. Boulougouris | Theory - Computational; Physical and Chemical Processes; Physical and Chemical Properties; Statistical Mechanics; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f190f50db0420395731/original/on-the-geometrical-representation-of-classical-statistical-mechanics.pdf |
660dfd42418a5379b0038d23 | 10.26434/chemrxiv-2024-3chlm | Optimizing the Prediction of Adsorption in Metal-Organic Frameworks Leveraging Q-Learning | The application of machine learning (ML) techniques in materials science has revolutionized the pace and scope of materials research and design. In the case of metal-organic frameworks (MOFs), a promising class of materials due to their tunable properties and versatile applications in gas adsorption and separation, ML has helped survey the vast material space. This study explores the integration of reinforcement learning (RL), specifically Q-learning, with Gaussian processes (GPs) for predictive modeling of adsorption in MOFs. We demonstrate the effectiveness of the RL-driven framework in guiding the selection of training data points and optimizing predictive model performance for methane and carbon dioxide adsorption, using two different reward metrics. Our results highlight the adaptability and versatility of RL in navigating the adsorption predictions in MOFs, with the integration of GPs enhancing the robustness and reliability of predictive modeling. | Etinosa Osaro; Yamil Colón | Materials Science; Chemical Engineering and Industrial Chemistry | CC BY 4.0 | CHEMRXIV | 2024-04-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660dfd42418a5379b0038d23/original/optimizing-the-prediction-of-adsorption-in-metal-organic-frameworks-leveraging-q-learning.pdf |
67b809c5fa469535b93d49dd | 10.26434/chemrxiv-2025-mvj7j | Key Parameters Controlling Energy Performance in Manganese Cathodes | Ideal battery performance can be characterized by high energy density that remains stable over many charge-discharge cycles. While energy degradation is typically unavoidable as batteries age, we observed a unique phenomenon in cells using low-cost, high-manganese (Mn) disordered rocksalt-type cathodes: energy gains, accompanied by voltage stabilization during cycling—an effect linked to phase transformations. To understand and enhance this unconventional performance, we introduce a new methodology that identifies key Mn cathode parameters using newly proposed critical energy metrics, such as maximum energy density, total energy throughput, and energy degradation. Through a range of analytical techniques, we reveal how enhanced kinetics and facilitated phase transformations influence performance. Our analysis investigates cathode active material properties, including conductivity, particle morphology, length-dependent structure, chemical state distributions, and cathode reactivity under varying temperature, current, and voltage window. By mapping the interplay of these factors, our study provides a mechanistic understanding of the newly discovered phenomena that drive maximized energy density, along with strategies for materials engineering and electrochemical protocols to enhance battery efficiency and durability. | Juhyeon Ahn; Matthew J. Crafton; Krishna Prasad Koirala; Tianyu Li; Raphaële J. Clément; Yanbao Fu; Vincent Battaglia; Dennis Nordlund; Chongmin Wang; Bryan D. McCloskey; Stephen J. Harris; Marca M. Doeff; Guoying Chen | Materials Science; Energy; Materials Processing; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b809c5fa469535b93d49dd/original/key-parameters-controlling-energy-performance-in-manganese-cathodes.pdf |
638a3df4b103af9b0f07f63b | 10.26434/chemrxiv-2022-zj8hx | Global potential energy surface and dynamics for the OH + CH3OH reaction | Using as functional form a combination of valence bond and mechanic molecular terms a new full-dimensional potential energy surface was developed for the title reaction, named PES-2022, which was fitted to high-level ab initio calculations at the coupled-cluster singles, doubles and perturbative triples-F12 explicitly correlated level on a representative number of points describing the reactive system. This surface simultaneously describes the two reaction channels, hydrogen abstraction from the methyl group (R1 path) and from the alcohol group (R2 path) of methanol to form water. PES-2022 is a smooth and continuous surface which reasonably describes the topology of this reactive system from reactants to products, including the intermediate complexes present in the system. Based on PES-2022 an exhaustive dynamics study was performed using quasi-classical trajectory calculations under two different initial conditions: at a fixed room temperature, for direct comparison with the experimental evidence and at different collision energies, to analyse possible mechanisms of reaction. In the first case, the available energy was mostly deposited as water vibrational energy, with the vibrational population inverted in the stretching modes and not inverted in the bending modes, reproducing the experimental evidence. In the second case, the analysis of different dynamics magnitudes (excitation functions, product energy partitioning and product scattering distributions), allows us to suggest different mechanisms for both R1 and R2 paths: a direct mechanism for the R2 path versus an indirect one, related with “nearly-trapped” trajectories in the intermediate complexes, for the R1 path. | Joaquin Espinosa-Garcia; Cipriano Rangel | Physical Chemistry; Physical and Chemical Processes | CC BY NC 4.0 | CHEMRXIV | 2022-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/638a3df4b103af9b0f07f63b/original/global-potential-energy-surface-and-dynamics-for-the-oh-ch3oh-reaction.pdf |
64da39124a3f7d0c0d28eb23 | 10.26434/chemrxiv-2023-vdjzr | Green hydrogen production: Process design and capacity expansion integrating economic and operational autonomy objectives | Green hydrogen is an attractive energy vector due to its zero carbon emission in production and use, supporting many industries in their transition to cleaner operations. However, the production of green hydrogen has a fundamental challenge in resilience since it requires renewable energy (RE) systems that are subject to variability. This study develops an optimization-based decision-making framework for the design and capacity expansion of hydrogen production systems at a regional level. A novel resilience objective function that considers external RE-derived fluctuations, as well as internal plant failures, is proposed. An illustrative case study using data from five regions in Chile verifies that consideration of resiliency in the objective function results in a system that is able to overcome the variance without greatly increasing the equilibrium cost for hydrogen. These designs are based on dual storage capacities with different expansion profiles. | Andrés I. Cárdenas; Felipe Díaz-Alvarado; Ana I. Torres | Energy; Chemical Engineering and Industrial Chemistry; Energy Storage; Fuels - Energy Science | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64da39124a3f7d0c0d28eb23/original/green-hydrogen-production-process-design-and-capacity-expansion-integrating-economic-and-operational-autonomy-objectives.pdf |
63d3361a112596c4557be563 | 10.26434/chemrxiv-2023-03j7h | Binuclear Two-Coordinate Coinage Metal Complexes | The model for rational design of carbene metal amide (cMa) complexes with large
oscillator strengths while also decreasing the energy of the singlet and triplet splitting (dEST) is
presented. A series of binuclear cMa complexes bearing Janus carbenes have been synthesized and
studied. The binuclear cMa complexes exhibit short lifetimes (tau = 200-300 ns) with high
photoluminescence efficiencies (PL >95%). The radiative rates of binuclear cMa complexes are
3~4 times faster than that of the corresponding mononuclear cMa complexes. Analysis of
temperature-dependent luminescence data indicates that the fluorescent lifetime for the singlet
state (tS1) of binuclear cMa complexes are near 12 ns with a dEST of 40-50 meV. The presented
compounds provide a general design for cMa complexes to achieve small values for dEST while
retaining high radiative rates. | Jie Ma; Jonas Schaab; Peter Djurovich; Mark Thompson | Organic Chemistry; Inorganic Chemistry; Analytical Chemistry; Spectroscopy (Anal. Chem.); Spectroscopy (Inorg.); Transition Metal Complexes (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d3361a112596c4557be563/original/binuclear-two-coordinate-coinage-metal-complexes.pdf |
61bcdf027284d0312defbbdd | 10.26434/chemrxiv-2021-m6k5f | AutoDesigner, a De Novo Design Algorithm for Rapidly Exploring Large Chemical Space for Lead Optimization: Application to the Design and Synthesis of D-Amino Acid Oxidase Inhibitors | The lead optimization stage of a drug discovery program generally involves the design, synthesis and assaying of hundreds to thousands of compounds. The design phase is usually carried out via traditional medicinal chemistry approaches and/or structure based drug design (SBDD) when suitable structural information is available. Two of the major limitations of this approach are (1) difficulty in rapidly designing potent molecules that adhere to myriad project criteria, or the multiparameter optimization (MPO) problem, and (2) the relatively small number of molecules explored compared to the vast size of chemical space. To address these limitations we have developed AutoDesigner, a de novo design algorithm. AutoDesigner employs a cloud-native, multi-stage search algorithm to carry out successive rounds of chemical space exploration and filtering. Millions to billions of virtual molecules are explored and optimized while adhering to a customizable set of project criteria such as physicochemical properties and potency. Additionally, the algorithm only requires a single ligand with measurable affinity and a putative binding model as a starting point, making it amenable to the early stages of a SBDD project where limited data is available. To assess the effectiveness of AutoDesigner, we applied it to the design of novel inhibitors of D-amino acid oxidase (DAO), a target for the treatment of schizophrenia. AutoDesigner was able to generate and efficiently explore over 1 billion molecules to successfully address a variety of project goals. The compounds generated by AutoDesigner that were synthesized and assayed (1) simultaneously met not only physicochemical criteria, clearance and central nervous system (CNS) penetration (Kp,uu) cutoffs, but also potency thresholds; (2) fully utilize structural data to discover and explore novel interactions and a previously unexplored subpocket in the DAO active site. The reported data demonstrate that AutoDesigner can play a key role in accelerating the discovery of novel, potent chemical matter within the constraints of a given drug discovery lead optimization campaign.
| Pieter H Bos; Evelyne M. Houang; Fabio Ranalli; Abba E. Leffler; Nicholas A. Boyles; Volker A. Eyrich; Yuval Luria; Dana Katz; Haifeng Tang; Robert Abel; Sathesh Bhat | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61bcdf027284d0312defbbdd/original/auto-designer-a-de-novo-design-algorithm-for-rapidly-exploring-large-chemical-space-for-lead-optimization-application-to-the-design-and-synthesis-of-d-amino-acid-oxidase-inhibitors.pdf |
641b04822bfb3dc2512e473f | 10.26434/chemrxiv-2023-r18p7 | Polarizing agents beyond pentacene for efficient triplet dynamic nuclear polarization in glass matrices | Triplet dynamic nuclear polarization (triplet-DNP) is a technique that can obtain high nuclear polarization under moderate conditions. However, in order to obtain practically useful polarization, large single crystals doped with a polarizing agent must be strictly oriented with respect to the magnetic field to sharpen the electron spin resonance (ESR) spectra, which is a fatal problem that prevents its application to truly useful biomolecular targets. Instead of this conventional physical approach of controlling crystal orientation, here, we propose a chemical approach, i.e., molecular design of polarizing agents; pentacene molecules, the most typical triplet-DNP polarizing agent, are modified so as to make the triplet electron distribution wider and more isotropic without loss of the triplet polarization. In fact, the modification of pentacene with thiophene moieties makes the ESR spectrum sharper and stronger than that of pentacene. To elucidate the effect of the substitutions on spin polarization and zero-field splitting parameters, which determine ESR spectrum, state-of-the-art quantum chemical calculations were performed and revealed that the direction of the spin polarization is altered by the modification with thiophene moieties and the size of D and E parameters are reduced from parent pentacene due to the partial delocalization of spin densities on the thiophene moieties. The triplet-DNP with the new polarizing agent successfully exceeds the previous highest 1H polarization of glassy materials by a factor of 5. This demonstrates the feasibility of a polarizing agent that can surpass pentacene, the best polarizing agent for more than 30 years since triplet-DNP was first reported, in the unoriented state. This work provides a pathway toward practically useful high nuclear polarization of various biomolecules by triplet-DNP. | Keita Sakamoto; Tomoyuki Hamachi; Katsuki Miyokawa; Kenichiro Tateishi; Tomohiro Uesaka; Yuki Kurashige; Nobuhiro Yanai | Physical Chemistry; Photochemistry (Physical Chem.); Physical and Chemical Properties; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/641b04822bfb3dc2512e473f/original/polarizing-agents-beyond-pentacene-for-efficient-triplet-dynamic-nuclear-polarization-in-glass-matrices.pdf |
66abc3e3c9c6a5c07abb8b6d | 10.26434/chemrxiv-2024-bmw1n | MatFold: systematic insights into materials discovery models' performance through standardized cross-validation protocols | Machine learning (ML) models in the materials sciences that are validated by overly simplistic cross-validation (CV) protocols can yield biased performance estimates for downstream modeling or materials screening tasks. This can be particularly counterproductive for applications where the time and cost of failed validation efforts (experimental synthesis, characterization, and testing) are consequential. We propose a set of standardized and increasingly difficult splitting protocols for chemically and structurally motivated CV that can be followed to validate any ML model for materials discovery. Among several benefits, this enables systematic insights into model generalizability, improvability, and uncertainty, provides benchmarks for fair comparison between competing models with access to differing quantities of data, and systematically reduces possible data leakage through increasingly strict splitting protocols. A general-purpose, model-agnostic toolkit, MatFold, is provided to automate the construction of these CV splits and encourage further community use. | Matthew Witman; Peter Schindler | Theoretical and Computational Chemistry; Materials Science; Energy; Computational Chemistry and Modeling; Machine Learning | CC BY 4.0 | CHEMRXIV | 2024-08-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66abc3e3c9c6a5c07abb8b6d/original/mat-fold-systematic-insights-into-materials-discovery-models-performance-through-standardized-cross-validation-protocols.pdf |
64664394f2112b41e9c2fba0 | 10.26434/chemrxiv-2023-7wsqv | Step-induced double-row pattern of interfacial water on rutile TiO2(110) at electrochemical conditions | Metal oxides are promising (photo)electrocatalysts for sustainable energy technologies due to their good activity and abundant resources. Their applications such as photocatalytic water splitting predominantly involve aqueous inter- faces at electrochemical conditions, but in situ probing oxide-water interfaces is proven to be extremely challenging. Here, we present an electrochemical scanning tunneling microscopy (EC-STM) study on the rutile TiO2(110)-water interface, and by tuning surface redox chemistry with careful potential control we are able to obtain high quality images of interfacial structures with atomic details. It is interesting to find that the interfacial water exhibits an unexpected double-row pattern that has never been observed. This finding is confirmed by performing a large scale simulation of a stepped interface model enabled by machine learning accelerated molecular dynamics (MLMD) at ab initio accuracy. Furthermore, we show that this pattern is induced by the steps present on the surface, which can propagate across the terraces by interfacial hydrogen bonds. Our work demonstrates that by combining EC-STM and MLMD we can obtain new atomic details of interfacial structures that are valuable to understand the activity of oxides at realistic conditions. | Yan Sun; Cheng-Rong Wu; Feng Wang; Rui-Hao Bi; Yong-Bin Zhuang; Shuai Liu; Ming-Shu Chen; Kelvin H.-L. Zhang; Jia-Wei Yan; Bing-Wei Mao; Zhong-Qun Tian; Jun Cheng | Physical Chemistry; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64664394f2112b41e9c2fba0/original/step-induced-double-row-pattern-of-interfacial-water-on-rutile-ti-o2-110-at-electrochemical-conditions.pdf |
61000e5e1f990c17c5a50412 | 10.26434/chemrxiv-2021-r1gxj | Engineered Substrates Reveal Species-Specific Inorganic Cues for Coral Larval Settlement
| The widespread loss of stony reef-building coral populations has been compounded by pervasive recruitment failure, i.e., the low or absent settlement and survival of coral juveniles. To combat global coral reef stressors and rebuild coral communities, restoration practitioners have developed workflows to rear and settle vulnerable coral larvae in the laboratory and subsequently outplant settled juveniles back to natural and artificial reefs. These workflows often make use of the natural biochemical settlement cues present in crustose coralline algae (CCA), which can be presented to swimming larvae as extracts, fragments, or live algal sheets to induce settlement. In this work, we investigated the potential for inorganic chemical cues to complement these known biochemical effects. We designed settlement substrates made from lime mortar (CaCO3) and varied their composition with the use of synthetic and mineral additives, including sands, glasses, and alkaline earth carbonates. In experiments with larvae of two Caribbean coral species, Acropora palmata (elkhorn coral) and Diploria labyrinthiformis (grooved brain coral), we saw additive-specific settlement preferences (>10-fold settlement increase) in the absence of any external biochemical cues. Interestingly, these settlement trends were independent of bulk surface properties such as surface roughness and wettability. Instead, our results suggest that not only can settling coral larvae sense and positively respond to soluble inorganic materials, but that they can also detect localized topographical features more than an order of magnitude smaller than their body width. Our findings open a new area of research in coral reef restoration, in which engineered substrates can be designed with a combination of organic and inorganic additives to increase larval settlement, and perhaps also improve post-settlement growth, mineralization, and defense. | Mark A. Levenstein; Kristen L. Marhaver; Zachary A. Quinlan; Haley M. Tholen; Lucas Tichy; Joaquín Yus; Ian Lightcap; Linda Wegley Kelly; Gabriel Juarez; Mark J. A. Vermeij; Amy J. Wagoner Johnson | Materials Science; Earth, Space, and Environmental Chemistry; Biocompatible Materials; Environmental Science; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2021-08-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61000e5e1f990c17c5a50412/original/engineered-substrates-reveal-species-specific-inorganic-cues-for-coral-larval-settlement.pdf |
6154c53a700ea60776728af5 | 10.26434/chemrxiv-2021-hr5zb | Deep Learning for the Automation of Particle Analysis
in Catalyst Layers for Polymer Electrolyte Fuel Cells | The rapidly growing use of imaging infrastructure in the energy materials domain drives significant data accumulation in terms of their amount and complexity. The applications of routine techniques for image processing in materials research are often \textit{ad hoc}, indiscriminate, and empirical, which renders the crucial task of obtaining reliable metrics for quantifications obscure. Moreover, these techniques are expensive, slow, and often involve several preprocessing steps. This paper presents a novel deep learning-based approach for the high-throughput analysis of the particle size distributions from transmission electron microscopy (TEM) images of carbon-supported catalysts for polymer electrolyte fuel cells. Our approach employs training an instance segmentation model, called StarDist [Schmidt et al. Medical Image Computing and Computer-Assisted Intervention – MICCAI 2018, Lecture Notes in Computer Science, vol 11071. Springer, Cham], which resolves the main challenge in the pixel-wise localization of nanoparticles in TEM images: the overlapping particles. The segmentation maps outperform models reported in the literature, and the results on particle size analyses agree well with manual particle size measurements, albeit at a significantly lower cost. | André Colliard-Granero; Mariah Batool; Jasna Jankovic; Jenia Jitsev; Michael H. Eikerling; Kourosh Malek; Mohammad Javad Eslamibidgoli | Materials Science; Nanoscience; Energy; Nanocatalysis - Catalysts & Materials; Fuel Cells | CC BY NC 4.0 | CHEMRXIV | 2021-09-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6154c53a700ea60776728af5/original/deep-learning-for-the-automation-of-particle-analysis-in-catalyst-layers-for-polymer-electrolyte-fuel-cells.pdf |
62d983c7468933537563e0e1 | 10.26434/chemrxiv-2022-43sd6 | Dipole Effects in the Photoelectron Angular Distributions of the Sulfur Monoxide Anion | Photoelectron angular distributions (PADs) in SO- photodetachment using linearly polarized 355 nm (3.49 eV), 532 nm (2.33 eV), and 611 nm (2.03 eV) light were investigated via photoelectron imaging spectroscopy. The measurements at 532 and 611 nm access the X-^3-Σ^- and a-^1-Delta electronic states of SO, whereas the measurements at 355 nm also access the b-^1Σ^+ state. In aggregate, the photoelectron anisotropy parameter values follow the general trend with respect to electron kinetic energy (eKE) expected for π* orbital photodetachment. The trend is similar to O2-, but the minimum of the SO- curve is shifted to smaller eKE. This shift is attributed mainly to the exit-channel interactions of the departing electron with the dipole moment of the neutral SO core, rather than the differing shapes of the SO- and O2- molecular orbitals. Of the several ab initio models considered, two approaches yield good agreement with the experiment: one representing the departing electron as a superposition of eigenfunctions of a point dipole-field Hamiltonian, and another describing the outgoing electron in terms of Coulomb waves originating from two separated charge centers, with a partial positive charge on the sulfur and an equal negative charge on the oxygen. These fundamentally related approaches support the conclusion that electron-dipole interactions in the exit channel of SO- photodetachment play an important role in shaping the PADs. While a similar conclusion was previously reached for photodetachment from sigma orbitals of CN- (Hart, Lyle, Spellberg, Krylov, Mabbs, J. Phys. Chem. Lett., 2021, 12, 10086-10092), the present work includes the first extension of the dipole-field model to detachment from π* orbitals. | Beverly Ru; C. Annie Hart; Richard Mabbs; Samer Gozem; Anna I. Krylov; Andrei Sanov | Theoretical and Computational Chemistry; Physical Chemistry | CC BY 4.0 | CHEMRXIV | 2022-07-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62d983c7468933537563e0e1/original/dipole-effects-in-the-photoelectron-angular-distributions-of-the-sulfur-monoxide-anion.pdf |
60c757aabdbb894c03a3ac41 | 10.26434/chemrxiv.14445327.v1 | Alkyl vs Aryl Modifications: A Comparative Study on Modular Modifications of Triphenylphosphonium Mitochondrial Vectors | Triphenylphosphonium (TPP+) moieties are commonly conjugated to drug molecules to confer mitochondrial selectivity due to their positive charge and high lipophilicity. Although optimisation of lipophilicity can be achieved by modifying the length of the alkyl linkers between the TPP+ moiety and the drug molecule, it is not always possible. While methylation of the TPP+ moiety is a viable alternative to increase lipophilicity and mitochondrial accumulation, there are no studies comparing these two separate modular approaches. Thus, we have systematically designed, synthesised and tested a range of TPP+ molecules with varying alkyl chain lengths and degree of aryl methylation to compare the two modular methodologies for modulating lipophilicity. The ability of aryl/alkyl modified TPP+ to deliver cargo to the mitochondria was also evaluated by confocal imaging with a TPP+-conjugated fluorescein-based fluorophore. Furthermore, we have employed molecular dynamics simulations to understand the translocation of these molecules through biological membrane model systems. These results provides further insights into the thermodynamics of this process and the effect of alkyl and aryl modular modifications<br /> | How Chee Ong; João T.S. Coimbra; Maria João Ramos; Bengang Xing; Pedro Alexandrino Fernandes; Felipe Garcia | Bioinorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757aabdbb894c03a3ac41/original/alkyl-vs-aryl-modifications-a-comparative-study-on-modular-modifications-of-triphenylphosphonium-mitochondrial-vectors.pdf |
676991d96dde43c9081a6437 | 10.26434/chemrxiv-2024-k3074 | Genetically-targeted photocatalytic organic dyes for spatiotemporally controlled organic synthesis directed by specific living cells | Catalytic reactions of a broad range of abiotic molecules and macromolecules are beyond the native capabilities of mammals. Natural enzymes from prokaryotes or plant-based eukaryotes have limited substrate scopes. Therefore, broadening the range of catalytic bond-forming reactions that function in physiological conditions would enable the syntheses of a vast array of molecules directly within biological systems. This approach may provide an alternative way to modulate cellular behaviors if such molecules can be synthesized with spatiotemporal control on specific cell types in living systems; furthermore, restricting synthesis to well-defined cells or cell-types would enable a potentially transformative approach of treating cells as separable reaction vessels within living organisms. Herein, we use genetic targeting to incorporate an organic photocatalytic dye onto specific cell types to enable in-situ light-controlled and spatially defined chemical synthesis of non-natural molecules. We demonstrate, for the first time, a photo-patterned organic coupling reaction in the extracellular matrix of living cells under dilute, aqueous, aerobic physiological conditions. A 6-fold contrast in reaction yield can be achieved between two adjacent HEK293FT cells with and without light exposure. The above photocatalysis can be initiated using mild confocal laser stimulation as low as 16 μW/mm2 at multiple wavelengths. Furthermore, the cell-type specific photocatalyzed C-H functionalization coupling reactions taking place on cell surfaces are used to demonstrate anabolic construction of non-natural products. The above findings lay an important foundation for developing future abiotic cell-type specific chemical syntheses in living organisms. | Spencer Zhao; Kang Yong Loh; Jonathan Tyson; Chandan Kadur; Carolyn Bertozzi; Karl Deisseroth; Zhenan Bao | Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Chemical Biology; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676991d96dde43c9081a6437/original/genetically-targeted-photocatalytic-organic-dyes-for-spatiotemporally-controlled-organic-synthesis-directed-by-specific-living-cells.pdf |
61931fe458bc4b14f494cf87 | 10.26434/chemrxiv-2021-zjk59 | First-principles surface characterization and water adsorption of Fe3P schreibersite | The meteoritic mineral schreibersite, e.g., Fe3P, is a proposed abiotic source of phosphorus for phosphate ion (PO4-) production, needed for nucleobases, phospholipids, and other life building materials. Schreibersite could have acted as both a source of elemental phosphorus and as a catalyst, and the hostile conditions on early Earth could have accelerated its degradation in different environments. Here, we present results from quantum calculations of bulk schreibersite and of its low Miller index surfaces. We also investigate water surface adsorption and identify possible dissociation pathways on the most stable facet. Our calculations provide useful chemical insights into schreibersite interactions in aqueous environments, paving the way for further detailed investigation on more reactive surfaces. Our results help provide a ``bottom-up'' understanding for phosphorylated organic synthesis on the primitive planet and its role in producing life building molecules. | Riccardo Dettori; Nir Goldman | Theoretical and Computational Chemistry; Materials Science; Earth, Space, and Environmental Chemistry; Geological Materials; Geochemistry; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2021-11-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61931fe458bc4b14f494cf87/original/first-principles-surface-characterization-and-water-adsorption-of-fe3p-schreibersite.pdf |
6781151a81d2151a029650c2 | 10.26434/chemrxiv-2024-jj18c-v2 | Optimal power-law fluid flow in tree-like branching network with self-similar and uniform roughness models | This study presents an analytical model for the flow of a power-law non-Newtonian fluid through a roughened tree-like branching network under volume and surface area constraint. We assume steady-state, axisymmetric, and laminar flow with non-slip boundary conditions along the network walls. We investigate two different roughness models (1) a self-similar roughness length scale aligned with the branching network pattern, and (2) a uniform roughness length scale and compare the results. We find that in case of the self-similar roughness model, the effective conductance remains the same as that of the smooth channels forming the network. However, in case of the uniform roughness model, the effective conductance presents an overall decrease. We argue that the uniform roughness model is a more realistic one. Further, the optimal effective conductance and the critical geometrical scaling parameter, such as diameter ratio, are analyzed as functions of network geometry and fluid rheology with power-law index. Under both volume and surface area constraint, increasing geometrical parameters such as daughter branches and network generations generally reduced optimal effective conductance, especially for shear-thickening fluids, while shear-thinning fluids were less affected. In macroscopic networks where roughness is relatively small, its effect on the optimal effective conductance is negligible; however, in microscopic networks, where roughness approaches the scale of the smallest channels, it leads to pronounced conductance reduction. Further constrained surface area shows significantly lower optimal effective conductance values compared to volume-constrained systems. Furthermore, we find that uniform surface roughness model predicts the scaling laws for optimal flow varying with all geometrical and rheology parameters. Moreover, in the case of self-similar roughness, the scaling laws for optimal flows are the same as those for the smooth network. These are the function of the branch-spitting number N, for volume constraint, and for both N and n, for surface area constraint. For macroscopic networks under the uniform roughness assumption, an approximation for the critical geometrical scaling parameter was derived using linearization with respect to the roughness intensity parameter, and it was found in good agreement with the full model equations. | J. V. Fontana; Ashish Garg | Chemical Engineering and Industrial Chemistry; Fluid Mechanics; Transport Phenomena (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6781151a81d2151a029650c2/original/optimal-power-law-fluid-flow-in-tree-like-branching-network-with-self-similar-and-uniform-roughness-models.pdf |
66e5642012ff75c3a14d0679 | 10.26434/chemrxiv-2024-vqjlz | CMOS and CCD detection in Raman spectroscopy: a comparison using spontaneous and multiplex coherent anti-Stokes Raman scattering (CARS) | Cooled CCD cameras are used widely in spectroscopy, mainly due to their sensitivity and low noise operating under low light conditions, and relatively high image and spectral readout rates. Despite their many advantages, CCD cameras have limitations. Particularly under bright light conditions, such as those encountered with coherent Raman spectroscopies, where the finite readout time of CCD chips is limiting. Furthermore, where weak signals need to be observed close to intense signals, blooming and smearing limit the signal to noise ratios achievable. Scientific complementary mixed oxide (sCMOS) based sensors are relatively new. Although they still show much higher readout noise than cooled CCDs, their application to spectroscopy is certainly of interest given the higher readout rates, and dynamic ranges possible. Here, we evaluate sCMOS sensors for specific spectroscopic applications, including multiplex (50 picosecond) CARS and spontaneous Raman spectroscopy. We compare the performance of a sCMOS based camera to a state-of-the-art (EM)CCD detector for these applications. The EMCCD camera outperforms the sCMOS camera in terms of limits of detection, while the sCMOS camera performs better than the CCD in terms of dynamic range and readout rate. Importantly, sCMOS camera does not suffer from interference due to blooming and smearing seen with CCD cameras, which enables observation of weak bands (e.g., Raman overtones) close to much more intense signals. Here we show that, at moderate readout rates, the relative performances of the two detector types are not substantially different. We anticipate that sCMOS based cameras will find application for bright spectroscopies, such as multiplex CARS, as well as spontaneous Raman spectroscopy, and Raman spectral imaging. | W. J. Niels Klement; Philippe Leproux; Wesley Browne; Hideaki Kano | Physical Chemistry; Analytical Chemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e5642012ff75c3a14d0679/original/cmos-and-ccd-detection-in-raman-spectroscopy-a-comparison-using-spontaneous-and-multiplex-coherent-anti-stokes-raman-scattering-cars.pdf |
631a10083940c20533f81566 | 10.26434/chemrxiv-2022-6h628 | Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization At Scale | The development of accurate transferable force fields is key to realizing the full potential of atomistic modelling in the study of biological processes such as protein--ligand binding for drug discovery. State-of-the-art transferable force fields, such as those produced by the Open Force Field Initiative, use modern software engineering and automation techniques to progressively yield accuracy improvements. However, force field torsion parameters, which must effectively account for many stereoelectronic and steric effects, are generally considered to be less transferable than other force field parameters and are therefore often targets for bespoke parametrization. Here, we present the Open Force Field QCSubmit and BespokeFit software packages that, when combined, facilitate the fitting of torsion parameters to quantum mechanical reference data at scale. We demonstrate the use of QCSubmit for simplifying the process of creating and archiving large numbers of quantum chemical calculations, by generating a dataset of 671 torsion scans for drug-like fragments. We use BespokeFit to derive individual torsion parameters for each of these molecules, thereby reducing the root mean squared error in the potential energy surface from 1.1 kcal/mol, using the original transferable force field, to 0.4 kcal/mol using the bespoke version. Furthermore, we employ the bespoke force fields to compute the relative binding free energies of a congeneric series of inhibitors of the TYK2 protein, and demonstrate further improvements in accuracy, compared to the base force field (MUE reduced from 0.56$^{0.77}_{0.39}$ to 0.42$^{0.59}_{0.28}$ kcal/mol and R$^2$ correlation improved from 0.72$^{0.87}_{0.35}$ to 0.93$^{0.97}_{0.84}$). | Joshua Horton; Simon Boothroyd; Jeffrey Wagner; Joshua Mitchell; Trevor Gokey; David Dotson; Pavan Behara; Venkata Ramaswamy; Mark Mackey; John Chodera; Jamshed Anwar; David Mobley; Daniel Cole | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2022-09-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/631a10083940c20533f81566/original/open-force-field-bespoke-fit-automating-bespoke-torsion-parametrization-at-scale.pdf |
659fffab9138d23161b1e894 | 10.26434/chemrxiv-2023-z3zg0-v2 | Is Mn(I) more promising than Fe(II) – A comparison of Mn vs. Fe complexes for olefin metathesis | Olefin metathesis is one of the most significant transformations in organic chemistry and an excellent example for efficient homogeneous catalysis. Although most currently used catalysts are primarily based on 4d and 5d metals, cycloaddition and cycloreversion reactions can also be attributed to first-row transition metals, such as Fe. Surprisingly, the potential of Mn(I) based catalysts for olefin metathesis has been unexplored, despite its prominence in homogeneous catalysis and its diagonal relationship to Ru(II). In the present study, we have investigated the prospective capabilities of Mn complexes for cycloaddition and reversion reactions, using density functional theory. Therefore, we have initially compared literature known iron model systems and their isoelectronic Mn counterparts regarding reactivity and electronic structure. Next, we constructed potential Mn complexes derived from synthetically accessible species including carbonyl ligands and obeying octahedral geometry. Based on thermodynamic parameters and the calculation of electronic descriptors, we were able to validate the isodiagonal relationship. Our study serves as guidance for the experimental chemist. | Jan Pecak; Radu A. Talmazan; Dennis Svatunek; Karl Kirchner; Maren Podewitz | Theoretical and Computational Chemistry; Catalysis; Organometallic Chemistry | CC BY 4.0 | CHEMRXIV | 2024-01-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/659fffab9138d23161b1e894/original/is-mn-i-more-promising-than-fe-ii-a-comparison-of-mn-vs-fe-complexes-for-olefin-metathesis.pdf |
60c74c12842e65b1dfdb3262 | 10.26434/chemrxiv.12417872.v1 | Enhancing Cycling Stability of Tungsten Oxide Supercapacitor Electrodes via a Boron Cluster-Based Molecular Cross-Linking Approach | <div><div><div><div><p>We report our discovery of utilizing perhydroxylated dodecaborate clusters ([B12(OH)12]2-) as a molecular cross-linker to generate a hybrid tungsten oxide material. We further demonstrate how these robust B12-based clusters in the resulting hybrid tungsten oxide material can effectively preserve the specific capacitance up to 4000 cycles and reduce the charge transfer resistance as well as the response time compared to that of pristine tungsten oxide. </p></div></div></div></div> | Dahee Jung; Mit Muni; Gustavo Marin; Roshini Ramachandran; Maher
F. El-Kady; Tanya Balandin; Richard B. Kaner; Alexander Spokoyny | Main Group Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c12842e65b1dfdb3262/original/enhancing-cycling-stability-of-tungsten-oxide-supercapacitor-electrodes-via-a-boron-cluster-based-molecular-cross-linking-approach.pdf |
62dad7b581efd048c4b7cae0 | 10.26434/chemrxiv-2022-qvrsd | Asymmetric Polymerization-Induced Crystallization-Driven Self-Assembly of Helical, Rod-Coil Poly(Aryl Isocyanide) Block Copolymers | The helical motif is ubiquitous in naturally occurring chemical systems where it confers numerous useful and distinct material properties. Accordingly, a great many synthetic materials have been produced in efforts to mimic biological systems. As an inherently chiral structural feature, the helix provides a modular platform for the creation of chiral nanomaterials exhibiting a diverse range of capabilities. Nonetheless, the development of rapid, scalable methods for production of chiral nanomaterials presents a formidable challenge. However, recent advances in both amphiphilic block copolymer (BCP) synthesis and self-assembly provide tractable means to do just that. In this work, polymerization induced crystallization-driven self-assembly (PI-CDSA) is combined, for the first time, with helical, rod-coil BCP self-assembly to enable scalable and controllable in situ synthesis of chiral nanostructures with variable shape, size, and dimensionality. Herein, we detail the use of newly developed Asymmetric PI-CDSA methodologies in the synthesis and in situ self-assembly of chiral, rod-coil BCPs comprised of poly(aryl isocyanide) (PAIC) rigid-rod and poly(ethylene glycol) (PEG) random-coil components. Using PEG-based Ni(II) macroinitiators, chiral PAIC-BCP nanostructures are constructed in a controlled, scalable fashion forming variable chiral morphologies including 1D twisted nanofibers, 2D hexagonal nanosheets and 3D twisted spirangles (i.e., spirally arranged hexagonal nanosheet stacks). Using seeded, living asymmetric PI-CDSA, the lengths and heights of 1D nanofiber and 3D spirangle nanostructures, respectively, can be selectively tuned via alterations in unimer-to-seed ratios. The formation of these nanostructures is dictated by the liquid crystalline nature of PAIC blocks and the hierarchical assembly of these BCPs, with chirality translated across length scales and in multiple dimensions (i.e., spirangles), led to large amplifications in chiroptical activity with high Kuhn’s dissymmetry factors reaching 0.029. | Randall Scanga; Ali Shahrokhinia; Jake Borges; Michael Ross; James Reuther | Polymer Science; Nanoscience; Organic Polymers; Polymerization (Polymers); Nanofabrication; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62dad7b581efd048c4b7cae0/original/asymmetric-polymerization-induced-crystallization-driven-self-assembly-of-helical-rod-coil-poly-aryl-isocyanide-block-copolymers.pdf |
66b9cbcec9c6a5c07afc0e35 | 10.26434/chemrxiv-2024-s7vqn | Integrating Compositional and Structural Diversity in Heterometallic Titanium Frameworks by Metal Exchange Methods | The increasing use of Metal-Organic Frameworks (MOFs) in separation, catalysis or storage is linked to the targeted modifi-cation of their composition or porosity metrics. While modification of pore shape and size necessarily implies the assembly of alternative nets, compositional changes often rely on post-synthetic modification adapted to the functionalisation or exchange of the organic linker, or the modification of the inorganic cluster by metal exchange methods. We describe an alternative methodology that enables the integration of both types of modification, structural and compositional, in titanium MOFs by metal exchange reaction of the heterometallic cluster Ti2Ca2. A systematic analysis of this reactivity with MUV-10 is used to understand which experimental variables are crucial to enable replacement of calcium only, or to integrate metal exchange with structural transformation. The isoreticular expanded framework MUV-30, is next used to template the formation of MUV-301, a titanium framework not accessible by direct synthesis that displays the largest mesoporous cages reported to date. Given that the interest of Ti MOFs in photoredox applications often meets the limitations imposed by the challenges of titanium solution chemistry to design concrete candidates, this soft strategy based on pre-assembled frameworks will help integrating specific combinations of metals into highly porous architectures. | Carlos Martí-Gastaldo; Eloy P. Gómez-Oliveira; Javier Castells-Gil; Clara Chinchilla-Garzón; Andrés Uscategui-Linares; Josep Albero; Neyvis Almora-Barrios; Sergio Tatay; Natalia M. Padial | Inorganic Chemistry; Coordination Chemistry (Inorg.); Solid State Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b9cbcec9c6a5c07afc0e35/original/integrating-compositional-and-structural-diversity-in-heterometallic-titanium-frameworks-by-metal-exchange-methods.pdf |
60c742f1567dfe7801ec3feb | 10.26434/chemrxiv.8863517.v1 | Green Light Powered Molecular State Motor Enabling Eight-Shaped Unidirectional Rotation | Molecular motors convert external energy into directional motions at the nanoscale. To date unidirectional circular rotations and linear motions have been realized but more complex directional trajectories remain unexplored on the molecular level. In this work we present a molecular motor powered by green light allowing to produce an eight-shaped geometry change during its unidirectional rotation around the central molecular axis. Motor motion proceeds in four different steps, which alternate between light powered double bond isomerizations and thermal hula-twist isomerizations. The result is a fixed sequence of populating four different isomers in a fully unidirectional trajectory possessing one crossing point. This motor system opens up new avenues for the construction and mechanisms of molecular machines and will therefore not only expand the toolbox of responsive molecular devices but enable unprecedented applications in the field of miniaturized technology in the future.<br /> | Aaron Gerwien; Peter Mayer; Henry Dube | Photochemistry (Org.); Stereochemistry; Nanodevices; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742f1567dfe7801ec3feb/original/green-light-powered-molecular-state-motor-enabling-eight-shaped-unidirectional-rotation.pdf |
653a73eba8b423585a46e894 | 10.26434/chemrxiv-2023-zx04p | Poacic Acid, a Plant-Derived Stilbenoid, Augments Cell-Wall Chitin Production, but Its Antifungal Activity Is Hindered by this Polysaccharide and by Fungal Essential Metals | Climate and environmental changes have modified the habitats of fungal pathogens, inflicting devastating effects on livestock and crop production. Additionally, drug-resistant fungi are increasing worldwide, driving the urgent need to identify new molecular scaffolds for development of antifungal agents for humans, animals, and plants. Poacic acid (PA), a plant-derived stilbenoid, was recently discovered to be a novel molecular scaffold that inhibits the growth of several fungi. Its antifungal activity has been associated with perturbation of the production/assembly of fungal cell wall β-1,3-glucan, but its mode of action is not resolved. In this study, we investigated the antifungal activity of PA and its derivatives on a panel of yeast. PA had a fungistatic effect on S. cerevisiae and a fungicidal effect on plasma membrane-damaged Candida albicans mutants. Live cell fluorescent microscopy experiments revealed that PA increases chitin production and modifies its cell wall distribution. Chitin production and cell growth returned to normal after prolonged incubation. The antifungal activity of PA was reduced in the presence of exogenous chitin, suggesting that potentiation of chitin production is a stress response that helps the yeast cell overcome the effect of this antifungal stilbenoid. Growth inhibition was also reduced by metal ions, indicating that PA affects metal homeostasis. These findings suggest that PA has a complex antifungal mechanism of action that involves perturbation of cell wall β-1,3-glucan production/assembly, chitin production, and metal homeostasis. | Adi Yona; Micha Fridman | Biological and Medicinal Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC 4.0 | CHEMRXIV | 2023-10-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653a73eba8b423585a46e894/original/poacic-acid-a-plant-derived-stilbenoid-augments-cell-wall-chitin-production-but-its-antifungal-activity-is-hindered-by-this-polysaccharide-and-by-fungal-essential-metals.pdf |
646243cafb40f6b3eea29a98 | 10.26434/chemrxiv-2023-c4mw6 | Bottom-up design of peptide nanoshapes in water using oligomers of N-methyl-L/D-alanine | De novo design of peptide nanoshapes is of great interest in biomolecular science since the local peptide nanoshapes formed by a short peptide chain in the proteins are often key to the biological activities. Here, we show that the de novo design of peptide nanoshapes with sub-nanometer conformational control can be realized using peptides consisting of N-methyl-L-alanine and N-methyl-D-alanine residues as studied by NMR, X-ray and XFEL crystallographic and computational analyses as well as by direct imaging of the dynamics of the peptide’s nanoshape using cinematographic electron microscopic technique. The conformation of N-methyl-L/D-alanine residue is largely fixed because of the restricted bond rotation, and hence can serve as a scaffold on which we can build a peptide into a designed nanoshape. The local shape control by per-residue conformational restriction by torsional strains starkly contrasts with the global shape stabilization of proteins based on many remote interactions. The oligomers allow the bottom-up design of diverse peptide nanoshapes with a small number of amino acid residues and would offer unique opportunities to realize the de novo design of biofunctional molecules, such as catalysts and drugs. | Jumpei Morimoto; Yota Shiratori; Marin Yokomine; Takumi Ueda; Takayuki Nakamuro; Kiyofumi Takaba; Saori Maki-Yonekura; Koji Umezawa; Koichiro Miyanishi; Yasuhiro Fukuda; Takumu Watanabe; Wataru Mizukami; Koh Takeuchi; Koji Yonekura; Eiichi Nakamura; Shinsuke Sando | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Combinatorial Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646243cafb40f6b3eea29a98/original/bottom-up-design-of-peptide-nanoshapes-in-water-using-oligomers-of-n-methyl-l-d-alanine.pdf |
66d01546a4e53c4876f8ae8b | 10.26434/chemrxiv-2024-lh925-v2 | Ferroelectric Polarization-Induced Performance Enhancements in BiFeO3-Based Photoanodes for Photoelectrochemical Water Splitting | Photoelectrochemical (PEC) processes will play a crucial role in future clean energy systems, however severe charge recombination and sluggish charge transfer kinetics have hindered their practical adoption. Exploiting ferroelectric polarization-controlled charge dynamics promises an additional lever that can potentially enable the performance limits of traditional static photoelectrodes to be surpassed. Here we report one of the most notable ferroelectric polarization-induced photocurrent enhancements, using a heterostructure of the multiferroic bismuth ferrite (BFO) and the photoactive bismuth vanadate (BVO) in a neutral pH electrolyte. In contrast to previous works, we report enhancements for both poling directions, of 136% for down-poled BFO/BVO and of 70% for the up-poled BFO/BVO, at 1.23 VRHE in comparison to the unpoled, delivering a Faradaic efficiency of more than 95% for prolonged oxygen evolution reaction. Extensive PEC and surface analyses complemented by DFT calculations reveal the improvements are attributed to the modulation of gradients in BFO band energies, changes in band-bending and offsets at the interfaces. Given the scalability of the employed sol-gel synthesis method and the use of environmentally benign materials and PEC conditions, our findings pave the way for multifunctional materials as new-generation agile and dynamic catalyst and photoelectrode systems. | Michael Gunawan; Owen Bowdler ; Shujie Zhou; Xueqing Fang; Qi Zhang; Yasuhiro Sakamoto; Kaiwen Sun; Denny Gunawan; Shery Chang; Rose Amal; Nagarajan Valanoor ; Jason Scott; Judy N. Hart; Cui Ying Toe | Materials Science; Catalysis; Energy; Catalysts; Nanocatalysis - Reactions & Mechanisms; Photocatalysis | CC BY NC 4.0 | CHEMRXIV | 2024-08-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d01546a4e53c4876f8ae8b/original/ferroelectric-polarization-induced-performance-enhancements-in-bi-fe-o3-based-photoanodes-for-photoelectrochemical-water-splitting.pdf |
678ac9bbfa469535b970389c | 10.26434/chemrxiv-2024-27934-v3 | Viscosity and phase state of wildfire smoke particles in the stratosphere from pyrocumulonimbus events: an initial assessment | Understanding the viscosity and phase state of biomass-burning organic aerosol (BBOA) from wildfires and pyrocumulonimbus (pyroCb) events in the stratosphere is critical for predicting their role in stratospheric multiphase chemistry and ozone depletion. However, the viscosity and phase state of BBOA under stratospheric conditions, including interactions with sulfuric acid (H₂SO₄), remain largely unquantified. In this study, we combine laboratory data with a thermodynamic model to predict the viscosity and phase state of BBOA under stratospheric conditions. Our results suggest that BBOA with a H₂SO₄-to-BBOA mass ratio of 0.37—an estimated upper limit for pyroCb smoke in the lower stratosphere after two months of aging— is highly viscous and frequently exists in a glassy state. Even at a higher H₂SO₄-to-BBOA mass ratio of 0.79 – an estimated upper limit after nine months of aging – BBOA can still transition to a glassy state under certain stratospheric conditions. In the glassy state, bulk reactions are suppressed, and multiphase chemistry may be limited to the particle surfaces. We also highlight key areas for future research needed to better constrain the viscosity and phase state of BBOA in the stratosphere and its subsequent impact on ozone. | Mei Fei Zeng; Andreas Zuend; Nealan G. A. Gerrebos; Pengfei Yu; Gregory P. Schill; Daniel M. Murphy; Allan K. Bertram | Earth, Space, and Environmental Chemistry; Atmospheric Chemistry | CC BY 4.0 | CHEMRXIV | 2025-01-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678ac9bbfa469535b970389c/original/viscosity-and-phase-state-of-wildfire-smoke-particles-in-the-stratosphere-from-pyrocumulonimbus-events-an-initial-assessment.pdf |
60c74969ee301c82dcc79a45 | 10.26434/chemrxiv.12057996.v1 | In Silico Analysis of Intermediate Hosts and Susceptible Animals of SARS-CoV-2 | COVID-19, caused by SARS-CoV-2 with major symptom of pneumonia is bringing huge disasters to the people around the world. Recent research indicates that the natural host of SARS-CoV-2 may be bats, but its intermediate host is still unclear. Only by finding natural and intermediate host for SARS-CoV-2 can cut off the source and prevent the virus from being transmitted to humans. In this study, we established a new method for the mining of intermediate host. We selected 82 representative ACE2 sequences from the 1000 sequences with the closest homology to the human ACE2 protein. All these selected ACE2 proteins were modeled by homology modeling. The potential natural and intermediate hosts, as well as susceptible animals of SARS-CoV-2 were analyzed systematically by calculating the binding free energy of ACE2 protein with the RBD of SARS-CoV-2. Based on this study, Rhinolophus sinicus was suggested to be the natural host, and the virus may be transmitted directly from bats to humans. Primates, some wild Felidae, civet, goats, spotted hyenas and golden hamsters may be susceptible to SARS-CoV-2 and could be intermediate hosts, while pangolins are unlikely to be intermediate hosts, and birds and reptiles are not intermediate hosts. Mice, rats and guinea pig are not susceptible to SARS-CoV-2. Considering the possible susceptibility of non-human primates, goats and golden hamsters, they can be used as experimental animals directly for the SARS-CoV-2 infection models without transgenic operation. Herein, the possible candidates of natural and intermediate hosts of SARS-CoV-2 were suggested, which will provide guiding significance for subsequent researches.<br /> | Canrong Wu; Mengzhu Zheng; Yueying Yang; Mingxue Li; Yang Liu; Peng Zhang; Yali Wang; Qiqi Wang; Yang Xu; Lixia Chen; Hua Li | Bioinformatics and Computational Biology; Biophysics; Chemical Biology; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74969ee301c82dcc79a45/original/in-silico-analysis-of-intermediate-hosts-and-susceptible-animals-of-sars-co-v-2.pdf |
61aa39367ce05667438789be | 10.26434/chemrxiv-2021-9s6wz | Upstream rheotaxis of catalytic Janus spheres | Fluid flow is ubiquitous in many environments that form habitats for microorganisms. The tendency of organisms to navigate towards or away from flow is
termed rheotaxis. Therefore, it is not surprising that both biological and artificial microswimmers show responses to flows that are determined by the interplay of chemical and physical factors. In particular, to deepen understanding of how different systems respond to flows, it is crucial to comprehend the influence played by swimming pattern. In recent studies, pusher-type Janus particles exhibited cross-stream migration in externally applied flows. Earlier, theoretical studies predicted a positive rheotactic response for puller-type spherical Janus micromotors. To compare to a different swimmer, we introduce Cu@SiO2 micromotors that swim towards their catalytic cap. Based on
experimental observations, and supported by flow field calculations using a model for self-electrophoresis, we hypothesize that they behave effectively as a puller-type system. We investigate the effect of externally imposed flow on these spherically symmetrical Cu@SiO2 active Janus colloids, and we indeedobserve a steady upstream directional response. Through a simple squirmer
model for a puller, we recover the major experimental observations. Additionally, the model predicts a unique “jumping” behaviour for puller-type micro- motors at high flow speeds. Performing additional experiments at high flow speeds, we capture this phenomenon, in which the particles “roll” with their
swimming axes aligned to the shear plane, in addition to being dragged down- stream by the fluid flow. | Priyanka Sharan; Zuyao Xiao; Viviana Mancuso; William E. Uspal; Juliane Simmchen | Physical Chemistry; Materials Science; Biophysical Chemistry; Transport phenomena (Physical Chem.); Robotics | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61aa39367ce05667438789be/original/upstream-rheotaxis-of-catalytic-janus-spheres.pdf |
669b9f4b01103d79c5a99132 | 10.26434/chemrxiv-2024-cs31x | Using Chemical Substitution to Engineer Photomechanical Cinnamalmalononitrile Crystals | The cinnamalmalononitrile (CM) family of molecules can undergo a [2+2] photodimerization in the solid-state and generate photomechanical response. Derivatives exhibit two different crystal packing motifs: head-to-head (HH) in which the molecules stack with the phenyl rings on the same side of the stack, and head-to-tail (HT) in which the phenyl rings of adjacent molecules are on opposite sides. The [2+2] photodimerization is only observed for HT packing motif. Attempts to identify chemical substitution patterns that favor the reactive HT packing based on simple steric and electrostatic considerations fail to reliably predict crystal packing, and fluorination generated both motifs in more-or-less random fashion. Empirically, substitution at the 3-position favors HT packing while substitution at the 4-position favors HH packing. Computational modeling suggests that the tendency for HH or HT packing arrangements stems from complex many-body interactions with the rest of the lattice. Modeling with periodic density functional theory shows that interactions with the rest of the lattice also explain why the HT motif is photochemically active while the HH motif is inert. Chemical substitution can also affect the photomechanical work output, with a significant variation in work between HT polymorphs composed of different molecules. In order to obtain a reactive HT polymorph, the best strategy appears to entail placing a strong electron-withdrawing group at the 3-position of the phenyl, and we confirm that an HT polymorph of 3-trifluoromethyl-cinnamalmalononitrile is a highly photosalient crystal, with a predicted ideal work density of 40 MJ/m3. | Thomas J. Gately ; Cody J. Perry; Sophie Weiss; Kevin Lam; Imadul Islam; Mohammed N. Almtiri; Veronica Carta; Gregory J. O. Beran; Rabih O. Al-Kaysi; Christopher J. Bardeen | Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.); Materials Chemistry; Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669b9f4b01103d79c5a99132/original/using-chemical-substitution-to-engineer-photomechanical-cinnamalmalononitrile-crystals.pdf |
60c747cb9abda23eb3f8c9a0 | 10.26434/chemrxiv.11796129.v1 | Bis(pentafluorophenyl)phenothiazylborane – A Pseudo Frustrated Radical Pair for the Catalytic Dehydrocoupling of Stannanes | The understanding of the mechanism by which frustrated Lewis pairs activate small molecules has been evolving with the discovery that both heterolytic and homolytic bond activation is possible. Herein we characterized a novel Lewis acidic aminoborane containing a phenothiazyl substituent and demonstrate its potential to catalytically promote the dehydrocoupling of tin hydrides. The reactivity observed implies this species promotes homolytic bond activation, however computational analysis suggests a heterolytic mechanism for this reaction. This result represents the first frustrated Lewis pair system to blur the lines between heterolytic and homolytic reactivity. | Jordan
N. Bentley; Ekadashi Pradhan; Tao Zeng; Christopher B. Caputo | Frustrated Lewis Pairs | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747cb9abda23eb3f8c9a0/original/bis-pentafluorophenyl-phenothiazylborane-a-pseudo-frustrated-radical-pair-for-the-catalytic-dehydrocoupling-of-stannanes.pdf |
60c74789702a9b95a118add9 | 10.26434/chemrxiv.11708496.v1 | C2: More complicated than it sounds | <p>The
present work is another contribution to a better understanding of the chemical
bond in C<sub>2</sub>. A density functional approach is employed, and the
obtained results (bond distance and bond dissociation energy) agrees very well
with the previously [2-4] valence bond results. The obtained results also
points to a bond order of four, reinforcing previously obtained data [3].
Furthermore, based on the calculated IR and Raman spectra, is proposed that C<sub>2</sub>
exhibits, at an electronic level, an asymmetry, and that such molecule has not,
in fact, a centre of inversion. </p> | Robson de Farias | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74789702a9b95a118add9/original/c2-more-complicated-than-it-sounds.pdf |
60c74e65702a9b175618b9d7 | 10.26434/chemrxiv.12746729.v1 | Hybrid Chemo-Biocatalysts Prepared in One Step from Zeolite Nanocrystals and Enzyme-Polyelectrolyte Complexes | The combination of heterogeneous catalysts and enzymes, in so-called hybrid catalysts, is an attractive strategy to effectively run chemoenzymatic reactions. Yet, the preparation of such bifunctional materials remains challenging because both the inorganic and the biological moieties must be integrated in the same solid, while preserving their intrinsic activity. Combining an enzyme and a zeolite, for example, is complicated because the pores of the zeolite are too small to accommodate the enzyme and a covalent anchorage on the surface is often ineffective. Herein, we developed a new pathway to prepare a hybrid catalyst built from glucose oxidase and TS-1 zeolite. Such hybrid material can catalyze the in situ formation of H2O2, which is subsequently used by the zeolite to trigger the epoxidation of allylic alcohol. Starting from an enzymatic solution and a suspension of zeolite nanocrystals, the hybrid catalyst is obtained in one step, using a continuous spray drying method. While enzymes are expectedly unable to resist the conditions used in spray drying (temperature, shear stress, etc.), we leverage on the preparation of “enzyme-polyelectrolyte complexes” (EPCs) to increase the enzyme stability. Importantly, the use of EPCs also appears to prevent enzyme leaching and to stabilize the enzyme against pH changes. We show that the one-pot preparation by spray drying gives access to hybrid catalysts with unprecedented performance in the targeted chemoenzymatic reaction. Interestingly, the hybrid catalyst performs much better than the two catalysts operating as separate entities. We anticipate that this strategy could be used as an adaptable method to prepare other types of multifunctional materials.<br /> | Margot Van der Verren; Valentin Smeets; Aurélien vander Straeten; Christine C. Dupont-Gillain; Damien Debecker | Catalysts; Hybrid Organic-Inorganic Materials; Nanocatalysis - Catalysts & Materials; Biocatalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e65702a9b175618b9d7/original/hybrid-chemo-biocatalysts-prepared-in-one-step-from-zeolite-nanocrystals-and-enzyme-polyelectrolyte-complexes.pdf |
60c74f80567dfe55c7ec56e6 | 10.26434/chemrxiv.12910259.v1 | Operando Tracing and Quantifying Inactive Li in Lithium Metal Battery | we revive the application of operando NMR technique in the study of LMBs. The combination of AFBs and operando NMR completely avoid the interference of lithium metal anode on the analysis of electrochemistry related Li metal, and thus observe the deposition and dissolution processes of lithium metal during cycling in real-time. Combining with the practical battery configuration and the novel data-processing method, we can operando monitor the evolution of capacity loss caused by the dead Li metal and SEI during the whole cycling process | Yuxuan Xiang; Guiming Zhong; Mingming Tao; Ziteng Liang; Guorui Zheng; Xiangsi Liu; Yanting Jin; Michel Armand; Ji-Guang Zhang; Kang Xu; Riqiang Fu; Yong Yang | Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f80567dfe55c7ec56e6/original/operando-tracing-and-quantifying-inactive-li-in-lithium-metal-battery.pdf |
64664bb0f2112b41e9c33a47 | 10.26434/chemrxiv-2023-hlmf6 | Online Buffer Exchange Enables Automated Membrane Protein Analysis by Native Mass Spectrometry | Membrane proteins represent the majority of clinical drug targets and are actively involved in a range of cellular processes. However, the complexity of membrane mimetics for membrane protein solubilization poses challenges for native mass spectrometry (MS) analyses. The most common approach for native MS analyses of membrane proteins remains offline buffer exchange into native MS-compatible buffers prior to manual sample loading into static nano-ESI emitters. This laborious process requires relatively high sample consumption and optimization for individual proteins. Here, we developed online buffer exchange coupled to native mass spectrometry (OBE-nMS) for analyzing membrane proteins in different membrane mimetics, including detergent micelles and nanodiscs. Detergent screening for OBE-nMS reveals mobile phases containing ammonium acetate with lauryl-dimethylamine oxide is most universal for characterizing both bacterial and mammalian membrane proteins in detergent. Membrane proteins in nanodiscs simply require ammonium acetate as the mobile phase. To preserve the intact nanodiscs, a novel switching electrospray approach was used to capture the high-flow separation on column with a low-flow injection to MS. Rapid OBE-nMS completes each membrane protein measurement within minutes and thus enables higher-throughput assessment of membrane protein integrity prior to its structural elucidation. | Weijing Liu; Hiruni Jayasekera; James Sanders; Guozhi Zhang; Rosa Viner; Michael Marty | Biological and Medicinal Chemistry; Analytical Chemistry; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64664bb0f2112b41e9c33a47/original/online-buffer-exchange-enables-automated-membrane-protein-analysis-by-native-mass-spectrometry.pdf |
64b1735ab053dad33a3c2044 | 10.26434/chemrxiv-2023-bb6p4 | Surveying the Conformational Landscape of α-Synuclein Using Native Crosslinking, Ion Mobility-Mass Spectrometry and Ensemble Modeling | Intrinsically disordered proteins (IDPs) contain highly flexible regions and bind to different protein partners to help maintain proper cellular function. Misfolded IDPs form higher order structures and aggregates that are linked to neurodegenerative diseases. In particular, α-Synuclein (αSN) is a major component of Lewy bodies, which are a defining characteristic of Parkinson’s disease. αSN adopts various conformers in solution and learning how the αSN conformational ensemble relates to aggregation is critical in understanding disease progression. Here, native protein crosslinking, ion mobility (IM) separations and tandem mass spectrometry (MS/MS) are combined to identify intramolecular crosslinks from multiple αSN monomer charge states (z = +8, +9, +11 and +13). IM provides overall size measurements of the different conformer subpopulations while crosslinks inform on localized interresidue distance constraints. Together with an initial αSN ensemble generated computationally by IDPConformerGenerator, our approach results in a realistic αSN conformational landscape comparable to a published ensemble obtained using distances derived from spin label nuclear magnetic resonance experiments as restraints in molecular dynamics simulations. The representative structures, resulting from structural clustering of the final αSN ensemble, contain characteristic features previously studied in the context of αSN aggregation. Overall, our findings validate the applicability of our approach in accurately describing the conformationally diverse ensemble of an IDP such as αSN. | Melanie Cheung See Kit; Ian Webb | Physical Chemistry; Biological and Medicinal Chemistry; Analytical Chemistry; Mass Spectrometry; Chemical Biology; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b1735ab053dad33a3c2044/original/surveying-the-conformational-landscape-of-synuclein-using-native-crosslinking-ion-mobility-mass-spectrometry-and-ensemble-modeling.pdf |
6718cf2fd433919392f13f12 | 10.26434/chemrxiv-2024-9cw1g | FULL-DIMENSIONAL POTENTIAL ENERGY SURFACE AND DYNAMICS OF THE OH + CH3SH GAS-PHASE REACTION | In the present work we have developed for the first time an analytical full-dimensional potential energy surface, PES-2024, describing the polyatomic OH + CH3SH gas-phase reaction. This reaction presents some intrinsic difficulties, such as 18 degrees of freedom, two reactive channels and the presence of intermediate complexes in the entrance and exit channels. In the valence bond-molecular mechanics, VB-MM, framework, we have developed this potential based on a reduced number of high-level ab initio calculations, the input data. The new PES has been subjected to a series of stringent tests. PES-2024 simultaneously describes the two reaction paths, hydrogen abstraction from the methyl group (R1 path) and from the thiol group (R2 path) forming the water molecule, and reasonably describing the topology of the reaction: high exothermicities, low barriers and the presence of intermediate complexes. Based on this surface, quasi-classical trajectory calculations (QCT) were performed at room temperature, with special emphasis on the H2O(v1,v2,v3) product stretching and bending vibrational excitations, and the results compared with the experimental evidence. The available energy was mostly deposited as water vibrational energy, 49%, simulating the experimental evidence. Agreement with experiments of these detailed state-to-state results lend confidence to the new surface. | Cipriano Rangel; Joaquin Espinosa-Garcia | Physical Chemistry | CC BY 4.0 | CHEMRXIV | 2024-10-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6718cf2fd433919392f13f12/original/full-dimensional-potential-energy-surface-and-dynamics-of-the-oh-ch3sh-gas-phase-reaction.pdf |
66914b28c9c6a5c07a186df6 | 10.26434/chemrxiv-2024-b32c5 | Photoredox/Pyridine N-oxide Catalyzed Carbohydroxylation and Aminohydroxylation of α-Olefins. | Anti-Markovnikov carbohydroxylation and aminohydroxylation of α-olefins were developed in this research by photore-dox catalyst and pyridine N-oxide. This approach offers the catalytic and direct conversion of unactivated alkenes to a series of primary alcohols including the ones bearing β-quaternary carbon centers and β-amino alcohols. The anti-Markovnikov selective transformation is enabled by the radical addition of α-olefin from pyridine N-oxy radical, which is generated from readily available pyridine N-oxide via photoredox catalyzed single-electron oxidation. Mechanistic stud-ies reveal that the reaction might occur with an N-alkoxypyridinium intermediate and following nucleophilic substitu-tion. The implications of this method for anti-Markovnikov addition of α-olefins were further demonstrated by the exam-ples of carboetherification, carboesterification, and lactone formation. | Cristina Ascenzi Pettenuzzo; Lichuan Liu; Jujhar Singh; Gabe Cuffel; Yongming Deng | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66914b28c9c6a5c07a186df6/original/photoredox-pyridine-n-oxide-catalyzed-carbohydroxylation-and-aminohydroxylation-of-olefins.pdf |
60c744fc337d6c1bf2e26edc | 10.26434/chemrxiv.9943943.v1 | Sensitive Mechanocontrolled Luminescence in Cross-Linked Polymer Films | Direct translation of mechanical force into changes in chemical behavior on a molecular level has important implication not only for the fundamental understanding of mechanochemical processes, but also for the development of new stimuli-responsive materials. In particular, detection of mechanical stress in polymers via non-destructive methods is important in order to prevent material failure and to study the mechanical properties of soft matter. Herein, we report that highly sensitive changes in photoluminescence intensity can be observed in response to the mechanical stretching of cross-linked polymer films when using stable, (pyridinophane)Cu-based dynamic mechanophores. Upon stretching, the luminescence intensity increases in a fast and reversible manner even at small strain (< 50%) and applied stress (< 0.1 MPa) values. Such sensitivity is unprecedented when compared to previously reported systems based on organic mechanophores. The system also allows for the detection of weak mechanical stress by spectroscopic measurements or by direct visual methods.<br /> | Ayumu Karimata; Pradnya Patil; Eugene Khaskin; Sébastien Lapointe; Robert R. Fayzullin; Pavlos Stampoulis; Julia Khusnutdinova | Organic Polymers; Coordination Chemistry (Organomet.); Ligand Design | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744fc337d6c1bf2e26edc/original/sensitive-mechanocontrolled-luminescence-in-cross-linked-polymer-films.pdf |
6108d386393cc912f250b924 | 10.26434/chemrxiv-2021-k7fwf | Molecular Field Analysis Using Computational-Screening Data in Asymmetric N-Heterocyclic Carbene-Copper Catalysis toward Data-driven in silico Catalyst Optimization | A molecular-field-based regression analysis using computational screening data for N-heterocyclic carbene (NHC)-Cu-catalyzed asymmetric carbonyl additions of a silylboronate to aldehydes is reported. A computational screening was performed to collect enantioselectivity data (ΔΔG‡: energy differences between the transitions states leading to each enantiomer) via transition-state (TS) calculations using density functional theory (DFT) methods. A molecular field analysis (MFA) was carried out using the obtained calculated ΔΔG‡ values and TS structures (30 samples in total). Important structural infor-mation for enantioselectivity extracted by the MFA was visualized on the TS structures, which provided insight into an asymmetric induction mechanism. Based on the obtained information, chiral NHC ligands were designed, which showed improved enantioselectivity in these carbonyl additions. | Masakiyo Mukai; Kazunori Nagao; Shigeru Yamaguchi; Hirohisa Ohmiya | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6108d386393cc912f250b924/original/molecular-field-analysis-using-computational-screening-data-in-asymmetric-n-heterocyclic-carbene-copper-catalysis-toward-data-driven-in-silico-catalyst-optimization.pdf |
6296f9d582f956392ccbc592 | 10.26434/chemrxiv-2022-qplkf-v2 | Substituent Effects at the 5,10-Positions of Dianilinotripyrrins on Their Dimerization Dynamics | Control of the association behavior by the molecular design is one of the most essential benefits in artificial supramolecular systems. 1,14-Dianilinotripyrrin has recently emerged as a novel conjugated molecule which forms a double helix in non-polar solvents with the aid of multiple interstrand hydrogen bonding interactions. In this work, we investigated the substituent effects at the 5,10-positions of tripyrrin on their association dynamics. This study illuminated two key findings; 1) electronic tuning by the para-substituents reduce the entropic costs thereby slightly improve the association constants, and 2) ortho-substituents force the tripyrrin core to be relatively planar, which significantly decrease the association constant due to less feasible π-stacking. | Ayane Nishiyama; Kento Ueta; Masataka Umetani; Yuki Akamatsu; Takayuki Tanaka | Organic Chemistry; Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6296f9d582f956392ccbc592/original/substituent-effects-at-the-5-10-positions-of-dianilinotripyrrins-on-their-dimerization-dynamics.pdf |
60c73f1b0f50db3801395736 | 10.26434/chemrxiv.7236029.v1 | Extracting Knowledge from DFT: Experimental Band Gap Predictions Through Ensemble Learning | The field of materials science has seen an explosion in the amount of accessible high quality data. With this sudden surge of data, the application of machine learning (ML) onto materials data has led to great results. Particular success has been found in training models based on chemical formula. Such models have traditionally focused on learning from density functional theory (DFT) or experimental data. Though some researchers have explored the use of DFT calculated properties as features for learning, this has not gained much traction since the machine learning predictions would be limited by the DFT computation time and accuracy. In this work, we explore the use of a stacked ensemble learning system that combines machine learning from DFT calculations to improve learning on experimental data. This is accomplished by handling the DFT and experimental data separately, training distinct models for each. The DFT models are used to generate a "predicted DFT" value for the formulae in the experimental data. A meta-learner-trained using predictions generated by the experimental models combined with predictions from the DFT models-is shown to improve root-mean-squared-error by over 9% in the test data, when compared to a baseline model that only learns from the training data. | Taylor Sparks; Steven Kauwe; Taylor Welker | Theory - Computational; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2018-10-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f1b0f50db3801395736/original/extracting-knowledge-from-dft-experimental-band-gap-predictions-through-ensemble-learning.pdf |
679c0258fa469535b97d03a4 | 10.26434/chemrxiv-2025-mkmn0 | A framework for general-purpose chemical synthesis in the aerosol phase and its automated implementation in an open hardware platform | Aerosols have emerged as a medium promising accelerated reactivity and significantly modified product distribution, yet exploration of these properties have so far only been confined to specific reactions. Wider deployment in chemical synthesis and discovery is impeded by the lack of a general-purpose formalism for conceiving multi-step aerosol syntheses, nor standardized building blocks to enable adaptation of existing synthesis procedures to execution in the aerosol phase. Here we propose a framework based on the timed release of reagents as atomized solutions that provides the minimum necessary building blocks for synthesis in an adaptable aerosol reactor. This framework both connects synthesis in traditional bulk media with aerosols and lays the foundation for massively parallel discovery in aerosols. To validate our proposed formalism with a concrete methodology we demonstrate a prototype hardware platform and examples of automated procedures, with early demonstration of the utility of optical microscopy to interrogate the spatial distribution of droplet compositions. | Jakub Wosik; Chaoyi Zhu; S. Hessam M. Mehr | Physical Chemistry; Organic Chemistry; Analytical Chemistry; Organic Synthesis and Reactions; Imaging; Robotics | CC BY 4.0 | CHEMRXIV | 2025-02-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/679c0258fa469535b97d03a4/original/a-framework-for-general-purpose-chemical-synthesis-in-the-aerosol-phase-and-its-automated-implementation-in-an-open-hardware-platform.pdf |
65c6037a66c1381729474c7e | 10.26434/chemrxiv-2024-37p57 | Conversion of Alkyl Azides to Diazo Compounds and the Azide-Site Selectivity: One-Pot Phosphine-Mediated Transient Protection of Azido Groups and Deprotective Transformation to Diazo Groups | A one-pot conversion of alkyl azides to diazo compounds is outlined. After azido group protection of α-azidocarbonyl compounds, treatment of the resulting phosphazides with silica gel in a wet solvent afforded α-diazo carbonyl products by azide-deprotective conversion. Competitive reactions of α-azido amides with alkyl and aryl azides demonstrate azide-site selectivity. Azide-site selective click functionalization by this one-pot sequence is also demonstrated with diazido compounds. | Hiroki Tanimoto; Ryo Adachi; Kodai Tanisawa; Takenori Tomohiro | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c6037a66c1381729474c7e/original/conversion-of-alkyl-azides-to-diazo-compounds-and-the-azide-site-selectivity-one-pot-phosphine-mediated-transient-protection-of-azido-groups-and-deprotective-transformation-to-diazo-groups.pdf |
60c74ba5702a9bc34d18b4c2 | 10.26434/chemrxiv.12367472.v1 | Trichloro(Dinitrogen)platinate(II) | <p>Zeise’s salt, [PtCl<sub>3</sub>(H<sub>2</sub>C=CH<sub>2</sub>)]<sup>–</sup><sub>,</sub>
is the oldest known organometallic complex, featuring ethylene strongly bound
to a platinum salt. Many derivatives are known, but none involving dinitrogen,
and indeed dinitrogen complexes are unknown for both platinum and palladium.
Electrospray ionization mass spectrometry of K<sub>2</sub>[PtCl<sub>4</sub>]
solutions generate strong ions corresponding to [PtCl<sub>3</sub>(N<sub>2</sub>)]<sup>–</sup>,
whose identity was confirmed through ion mobility spectroscopy and MS/MS
experiments that proved it to be distinct from its isobaric counterparts [PtCl<sub>3</sub>(C<sub>2</sub>H<sub>4</sub>)]<sup>–</sup>
and [PtCl<sub>3</sub>(CO)]<sup>–</sup>. Computational analysis established a
gas-phase platinum-dinitrogen bond strength of 116 kJ mol<sup>-1</sup>,
substantially weaker than the ethylene and carbon monoxide analogues but stronger
than for polar solvents such as water, methanol and dimethylformamide, and
strong enough that the calculated N-N bond length of 1.119 Å represents weakening
to a degree typical of isolated dinitrogen complexes. </p> | Gilian T. Thomas; Sofia Donnecke; Irina Paci; J Scott McIndoe | Bonding; Ligands (Inorg.); Small Molecule Activation (Inorg.); Transition Metal Complexes (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ba5702a9bc34d18b4c2/original/trichloro-dinitrogen-platinate-ii.pdf |
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