jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Giang N. Tran | Bailey S. Bouley | Liviu M. Mirica
Source: ChemRxiv (preprint, 2022-08-21)
Field: Chemistry — Organic Chemistry

Isolation and Catalytic Reactivity of Mononuclear Palladium(I) Complexes Palladium complexes are among the most commonly used transition metal catalysts for different organic transformations with wide applications in the chemical synthesis. Currently, catalytic transformations involving Pd(0)/Pd(II) catalytic cycles are very well-known, and processes involving Pd(II)/Pd(III)/Pd(IV) intermediates are also gaining interest in recent years due to the increasing relevance of high-valent Pd species. By contrast, isolated low-valent Pd(I) complexes, especially mononuclear Pd(I) species, are very rare. Herein, we report the isolation of two heteroleptic Pd(I) complexes stabilized by dithiapyridinophane ligands that were fully characterized by single-crystal X-ray diffraction, EPR, IR, and UV-Vis spectroscopies, and computational studies. Excitingly, these Pd(I) complexes are shown to be superior catalysts for the C<i>sp<sup>2</sup></i>-C<i>sp<sup>3</sup> </i>Kumada cross-coupling reaction vs. their Pd(0) or Pd(II) analogs. Palladium ; Catalysis ; Chemistry ; Reactivity (psychology) ; Transition metal ; Single crystal ; Metal ; Coupling reaction ; Combinatorial chemistry ; Crystallography ; Organic chemistry Catalytic Cross-Coupling Reactions ; Organometallic Complex Synthesis and Catalysis ; Asymmetric Hydrogenation and Catalysis
Authors: Claudio Cazorla
Source: arXiv (Cornell University) (preprint, 2022-08-10)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Atomistic simulation of barocaloric effects Due to critical environmental issues there is a pressing need to switch from current refrigeration methods based on compression of greenhouse gases to novel solid-state cooling technologies. Solid-state cooling capitalizes on the thermal response of materials to external fields named "caloric effect". The barocaloric (BC) effect driven by hydrostatic pressure is particularly promising from a technological point of view since typically presents larger cooling potential than other caloric variants (e.g., magnetocaloric and electrocaloric effects driven by magnetic and electric fields, respectively). Atomistic simulation of BC effects represents an efficient and physically insightful strategy for advancing solid-state cooling by complementing, and in some cases even guiding, experiments. Atomistic simulation of BC effects involves approaches ranging from computationally inexpensive force fields to computationally very demanding, but quantitatively accurate, first-principles methods. Here, we survey several methods and strategies involved in atomistic simulation of BC effects like the quasi-harmonic approximation and direct/quasi-direct estimation approaches. The Review finalizes with a collection of case studies in which some of these methods were employed to simulate and predict original BC effects. Magnetic refrigeration ; Refrigeration ; Hydrostatic pressure ; Hydrostatic equilibrium ; Solid-state ; Statistical physics ; Computer science ; Materials science ; Mechanical engineering ; Mechanics ; Magnetic field ; Engineering physics ; Physics ; Engineering ; Magnetization Magnetic and transport properties of perovskites and related materials ; Ferroelectric and Piezoelectric Materials ; Electronic and Structural Properties of Oxides
Authors: Daniele Ongari | Leopold Talirz | Kevin Maik Jablonka | Daniel W. Siderius | Berend Smit
Source: ChemRxiv (preprint, 2022-02-01)
Field: Chemistry — Inorganic Chemistry

Data-driven matching of experimental crystal structures and gas adsorption isotherms of metal-organic frameworks Porous metal-organic frameworks are a class of materials with great promise in gas separation and gas storage applications. Due to the large material space, computational screening techniques have long been an important part of the scientific toolbox. However, a broad validation of molecular simulations in these materials is hampered by the lack of a connection between databases of gas adsorption experiments and databases of the atomic crystal structure of corresponding materials. This work aims to connect the gas adsorption isotherms of metal-organic frameworks collected in the NIST/ARPA-E Database of Novel and Emerging Adsorbent Materials to a corresponding crystal structure in the Cambridge Structural Database. With tens of thousands of isotherms and crystal structures reported to date, an automatic approach is needed to establish this link, which we describe in this paper. As a first application and consistency check, we compare the pore volume deduced from low-temperature argon or nitrogen isotherms to the geometrical pore volume computed from the crystal structure. Overall, 545 argon or nitrogen isotherms could be matched to a corresponding crystal structure. We find that the pore volume computed via the two complementary methods shows acceptable agreement only in about 35% of these cases. We provide the subset of isotherms measured on these materials as a seed for a future, more complete reference data set for computational studies. Adsorption ; Argon ; Metal-organic framework ; Volume (thermodynamics) ; Crystal (programming language) ; NIST ; Toolbox ; Materials science ; Sorption ; Crystal structure ; Chemistry ; Computer science ; Thermodynamics ; Physical chemistry ; Physics ; Organic chemistry Metal-Organic Frameworks: Synthesis and Applications ; Carbon dioxide utilization in catalysis ; Catalytic Processes in Materials Science
Authors: Roelant Hilgers | Sin Yong Teng | Anamarija Briš | Aleksandr Y. Pereverzev | Paul B. White | Jeroen Jansen | Jana Roithová
Source: ChemRxiv (preprint, 2022-04-12)
Field: Chemistry — Spectroscopy

Prediction of enantioselectivity by monitoring reaction intermediates Enantioselective reactions are at the core of chemical synthesis. Their development mostly relies on prior knowledge, laborious product analysis and post-rationalization by theoretical methods. Here, we introduce a simple and fast method to determine enantioselectivities based on mass spectrometry. The method is based on ion mobility separation of diastereomeric intermediates, formed from a chiral catalyst and prochiral reactants, and delayed reactant labeling experiments to link the mass spectra with the reaction kinetics in solution. The data provide rate constants along the reaction paths of the individual diastereomeric intermediates, revealing the origins of enantioselectivity. Using the derived kinetics, the enantioselectivity of the overall reaction can be predicted. Hence, this method can offer a rapid discovery and optimization of enantioselective reactions in the future. We illustrate the method for the addition of cyclopentadiene (CP) to an α,β-unsaturated aldehyde catalyzed by a diarylprolinol silyl ether. Enantioselective synthesis ; Chemistry ; Diastereomer ; Catalysis ; Silyl ether ; Mass spectrometry ; Aldehyde ; Chemical kinetics ; Computational chemistry ; Silylation ; Organic chemistry ; Kinetics ; Combinatorial chemistry ; Chromatography Mass Spectrometry Techniques and Applications ; Analytical Chemistry and Chromatography ; Molecular spectroscopy and chirality
Authors: Mengxian Yu | Yajuan Shi | Qingzhu Jia | Qiang Wang | Zheng‐Hong Luo | Fangyou Yan | Yin‐Ning Zhou
Source: Research Square (preprint, 2022-11-08)
Field: Materials Science — Polymers and Plastics

Ring Repeating Unit: A Deterministic Structure Representation of Polymers for Property Predictions Abstract Deterministic structure representation of polymers plays a crucial role in developing models for polymer property prediction and polymer design by data-centric approaches. Currently, unique structure representations of polymers, especially the polymers with heteroatomic backbones, are unavailable. In this contribution, we propose a so-called ring repeating unit (RRU) method that can uniquely represent polymers with a broad range of structure diversity. To prove the rationality of RRU-based structure representation for generating feature descriptors, a quantitative structure property relationship (QSPR) model for glass transition temperature ( T g ) was established for 1321 polyimides with good accuracy ( R 2 = 0.8793). Comprehensive model validations including external, internal, and Y -random validations were performed, providing T g prediction result with an average absolute error (AAE) of 19.38 ℃. It is believed that the as-developed RRU method allows for dealing with any macromolecular structure and targeted property, enabling for reliable polymer property prediction and high-performance polymer design by data-driven approaches. Property (philosophy) ; Unit (ring theory) ; Representation (politics) ; Ring (chemistry) ; Mathematics ; Computer science ; Chemistry ; Law ; Philosophy ; Epistemology ; Political science ; Organic chemistry Synthesis and properties of polymers ; Epoxy Resin Curing Processes ; Polymer Nanocomposites and Properties
Authors: Marco Gibaldi | Ohmin Kwon | Andrew J. P. White | Jake Burner | Tom K. Woo
Source: ChemRxiv (preprint, 2022-06-22)
Field: Chemistry — Inorganic Chemistry

The HEALED SBU library of chemically realistic building blocks for construction of hypothetical metal-organic frameworks Advancements in hypothetical metal-organic framework (hMOF) databases and construction tools have resulted in a rapidly expanding chemical design space for nanoporous materials. The bulk of these hypothetical structures are constructed using structural building units (SBUs) derived from experimental MOF structures, often collected from the CoRE-MOF database. Recent investigations into the state of these deposited experimental structures’ chemical accuracy identified an array of common structural errors—including omitted protons, missing counterions, and disordered structures. These structural errors propagate into the SBUs mined from experimental MOFs, culminating in inaccurate hMOF structures possessing net charges or missing atoms which were not accounted for previously. This work demonstrates how manual investigation was applied to diagnose structural errors in SBUs obtained from several popular hMOF construction tools and databases. An analysis of the prevailing errors discovered during the examination process is provided along with representative cases to aid with error detection in future studies involving SBU extraction and hMOF construction. A novel repair protocol was established and employed to generate a library of SBUs that are hand-examined and labeled with enhanced detail (HEALED). This repaired library of SBUs contains 952 inorganic SBUs and 568 organic SBUs ideally suited for the generation of hypothetical frameworks that are chemically accurate and properly charge labelled. Additionally, case studies following the effects of SBU errors on electrostatic potential-fitted charges and GCMC-simulated gas adsorption predictions are presented to highlight the significance of using chemically accurate hMOF structures exclusively in all screening efforts going forward. SBus ; Computer science ; Template ; Process (computing) ; Materials science ; Algorithm ; Nanotechnology ; Adsorption ; Metal-organic framework ; Chemistry ; Physical chemistry Metal-Organic Frameworks: Synthesis and Applications ; X-ray Diffraction in Crystallography ; Machine Learning in Materials Science
Authors: Maria Fischer Susanne | Petra Kaschnitz | Christian Slugovc
Source: ChemRxiv (preprint, 2022-07-19)
Field: Chemistry — Organic Chemistry

Tris(2,4,6-trimethoxyphenyl)phosphine - a Lewis base able to compete with phosphazene bases in catalysing oxa-Michael reactions The performance of the strong Lewis base tris(2,4,6-trimethoxyphenyl)phosphine (TTMPP) in catalysing oxa-Michael reactions is assessed and compared with other electron-rich tertiary arylphosphines and, as the benchmark, with the Brønsted base 1-tert-butyl-2,2,4,4,4-pentakis-(dimethylamino)-2λ5,4λ5-catenadi-(phosphazen) (P2-tBu). A matrix of five varyingly strong Michael acceptors and four varyingly acidic alcohols is used to evaluate the activity of the catalysts. The study attributes TTMPP a significant superiority over other arylphosphine based Lewis bases and a similar activity as P2-tBu under highly concentrated, quasi solvent free conditions. Furthermore, the performance of TTMPP and P2-tBu is compared in the oxa-Michael polymerisation reactions of 2-hydroxyethyl acrylate (HEA) and of 1,4-butanediol diacrylate (BDDA) with diols under solvent free conditions. In the case of HEA TTMPP is to be preferred over P2-tBu because the latter gave a not fully soluble polymeric product. TTMPP is the first Lewis base capable of catalysing the oxa-Michael polymerisation of diacrylates and diols, albeit P2-tBu catalysis results in higher molar masses in this polymerisation reaction. Furthermore, the performance of the catalysts under diluted conditions was assessed and the activity of TTMPP is distinctly more concentration dependent than the activity of P2-tBu. The use of the polar, protic solvent t-butanol mitigates the negative impact of dilution exerted by nonpolar, aprotic and polar, aprotic solvents such as toluene or dimethylformamide. Finally, data attesting TTMPP a limited, but for practical work under air still acceptable, stability to oxygen are disclosed. Chemistry ; Lewis acids and bases ; Michael reaction ; Phosphazene ; Phosphine ; Polymer chemistry ; Catalysis ; Frustrated Lewis pair ; Solvent ; Base (topology) ; Acrylate ; Polymerization ; Organic chemistry ; Medicinal chemistry ; Copolymer ; Polymer Coordination Chemistry and Organometallics ; Synthesis and characterization of novel inorganic/organometallic compounds ; Organophosphorus compounds synthesis
Authors: Prajay Patel | Zheng Feng Lu | Mehrafshan G. Jafari | Cristina Hernandez-Prieto | Pavel Zatsepin | Daniel J. Mindiola | David M. Kaphan | A. Jeremy Kropf | Massimiliano Delferro | Cong Liu
Source: ChemRxiv (preprint, 2022-03-09)
Field: Materials Science — Materials Chemistry

K-edge XANES Analysis for Catalytically Relevant Molecular and Supported Vanadium Complexes X-ray Absorption Near-Edge Structure (XANES) spectroscopy is a powerful tool to reveal key structural and electronic features of isolated catalytic sites, yet insights into molecular structure and more detailed orbital analysis through a combination of experimental and computed XANES analysis are necessary for accurate interpretation of the spectra, especially when significant heterogeneity exits among the catalytic sites. Herein, we present an integrated computational and experimental strategy to determine both primary and secondary bonding interactions within the XANES pre-edge region for organovanadium complexes, which was developed using a series of well-defined molecular vanadium complexes and then applied to the characterization of a supported organovanadium olefin hydrogenation catalyst. Time-dependent density functional theory is used to predict the energy of pre-edge XANES features for a series of vanadium complexes with a variety of oxidation states and local coordination environments. A calibration scheme incorporating different density functionals and basis sets is established, resulting in an optimized scheme that accurately predicts pre-edge energies with a mean absolute error of 0.40 eV. Second-shell coordination (e.g., V---V) effects within XANES are identified through the analysis of the computed dominant orbital contributions for multi-vanadium complexes. Orbital analysis also provided confirmation that the vanadium-hydride formation combined with the heterogeneity of the catalytic active species in olefin hydrogenation caused the energy shift and broadening of the pre-edge peak after hydrogen treatment of the silica-supported organovanadium pre-catalyst. This work further elucidates computational XANES simulations and techniques potentially guiding characterization in surface organometallic chemistry. XANES ; Vanadium ; Density functional theory ; Catalysis ; Chemistry ; Characterization (materials science) ; Olefin fiber ; Computational chemistry ; Materials science ; Spectroscopy ; Chemical physics ; Physical chemistry ; Inorganic chemistry ; Nanotechnology ; Organic chemistry ; Physics Catalytic Processes in Materials Science ; Catalysis and Oxidation Reactions ; Electrocatalysts for Energy Conversion
Authors: Gemechis D. Degaga | Amanda Studinger | Loredana Valenzano
Source: ChemRxiv (preprint, 2022-05-17)
Field: Chemistry — Inorganic Chemistry

A Quantum Mechanical Description of the Diffusion Properties of C1-C2 Hydrocarbon Molecules in MOF-74-Mg Among the numerous metal organic framework (MOF) families, of significant importance is the MOF-74-M series (M = metal, -also known as CPO-27-M), characterized by a high density of not fully coordinated open metal site centers; this peculiarity has been demonstrated to translate into a higher hydrocarbons’ separation potential than other known MOFs and zeolites. To provide a more comprehensive description of the behavior of the hydrocarbon molecules within the MOF-74 cavity, diffusion processes and corresponding diffusion barriers of small hydrocarbons in the MOF-74-Mg were modeled. This work provides a description of the molecular transport processes of CH4, C2H2, C2H4 and C2H6 within and along the cavity of MOF-74-Mg; in addition, the influence of pre-adsorbed water molecules is also addressed. Density functional theory (DFT), as implemented within a plane-wave (PW) approach under periodic boundary conditions (PBC), has been used to investigate the diffusion mechanisms using the climbing-image nudge elastic band (CI-NEB) method, coupled with the van der Waals functional (vdW-DF) and ultra-soft pseudopotentials. Two transport mechanisms were identified: M1, referring to the molecular migrations within the MOF cavity; and M2, referring to the molecular migrations along the MOF longitudinal channel. The M1 transport mechanism was further analyzed to address the molecular migration from one metal atom to its adjacent one (M1a), and with respect to the second metal over (M1b). All the transport mechanisms considered show that the diffusion of paraffin molecules in MOF-74-Mg is energetically more favorable than that of olefin molecules. An interesting trend is observed across all the diffusion mechanisms where the stronger the molecule binds to the open metal site, the higher the diffusion barrier it needs to overcome. For all the small hydrocarbons considered in this study, transport mechanism M1a is significantly more energetically favorable than M1b, showing that it is easier for molecules to drift along the longitudinal cavity than to remain trapped cross-sectionally within the cavity itself. This work shows how this computational approach can be successfully applied not only to reveal the molecular transport in other MOF-74 isostructural species, but also in the fundamental understanding of the screening of MOFs and other nano-porous materials for gas separation applications. Metal-organic framework ; Molecule ; Density functional theory ; van der Waals force ; Chemical physics ; Chemistry ; Diffusion ; Hydrocarbon ; Computational chemistry ; Adsorption ; Molecular dynamics ; Physical chemistry ; Thermodynamics ; Physics ; Organic chemistry Metal-Organic Frameworks: Synthesis and Applications ; Magnetism in coordination complexes ; Zeolite Catalysis and Synthesis
Authors: Allison Green | Sanket Kadulkar | Zachary M. Sherman | Thomas M. FitzSimons | Charles K. Ofosu | Jiajun Yan | David Zhao | Ján Ilavský | Adrianne M. Rosales | Brett A. Helms | Venkat Ganesan | Thomas M. Truskett | Delia J. Milliron
Source: ChemRxiv (preprint, 2022-09-05)
Field: Materials Science — Materials Chemistry

Depletion-driven assembly of polymer-coated nanocrystals Depletion-driven assembly has been widely studied for micron-sized colloids, but questions remain at the nanoscale where the governing physics are impacted by the stabilizing surface ligands or wrapping polymers, whose length scales are on the same order as those of the colloidal core and the depletant. Here, we probe how wrapping colloidal tin-doped indium oxide nanocrystals with polymers affects their depletion-induced interactions and assembly in solutions of polyethylene glycol. Copolymers of polyacrylic acid grafted with polyethylene oxide provide nanocrystal wrappings with different effective polymer graft densities and molecular weights. (Ultra) small angle X-ray scattering, coarse-grained molecular dynamics simulation, and molecular thermodynamic theory were combined to analyze how depletant size and polymer wrapping characteristics affect depletion interactions, structure, and phase behavior. The results show how depletant molecular weight, as well as surface density and molecular weight of polymer grafts, set thresholds for assembly. These signatures are unique to depletion-driven assembly of nanoscale colloids and mirror phase behaviors of grafted nanoparticle--polymer composites. Optical and rheological responses of depletion-driven assemblies of nanocrystals with different polymer shell architectures were probed to learn how their structural differences impact properties. We discuss how these handles for depletion-driven assembly at the nanoscale may provide fresh opportunities for designing responsive depletion interactions and dynamically reconfigurable materials. Polymer ; Materials science ; Nanocrystal ; Nanoscopic scale ; Nanotechnology ; Dispersity ; Polyacrylic acid ; Polyethylene glycol ; Nanoparticle ; Oxide ; Indium tin oxide ; Nanostructure ; Colloid ; Molecular dynamics ; Chemical engineering ; Chemical physics ; Polymer chemistry ; Thin film ; Chemistry ; Composite material ; Computational chemistry Pickering emulsions and particle stabilization ; Polymer Surface Interaction Studies ; Quantum Dots Synthesis And Properties
Authors: Nicodemo Di Pasquale | Aaron R. Finney | Joshua Elliott | Paola Carbone | Matteo Salvalaglio
Source: arXiv (Cornell University) (preprint, 2022-12-07)
Field: Materials Science — Polymers and Plastics

Constant Chemical Potential-Quantum Mechanical-Molecular Dynamics simulations of the Graphene-electrolyte double layer We present the coupling of two frameworks -- the pseudo-open boundary simulation method known as constant potential Molecular Dynamics simulations (C$μ$MD), combined with QMMD calculations -- to describe the properties of graphene electrodes in contact with electrolytes. The resulting C$μ$QMMD model was then applied to three ionic solutions (LiCl, NaCl and KCl in water) at bulk solution concentrations ranging from 0.5 M up to 6 M in contact with a charged graphene electrode. The new approach we are describing here provides a simulation protocol to control the concentration of the electrolyte solutions while including the effects of a fully polarizable electrode surface. Thanks to this coupling, we are able to accurately model both the electrode and solution side of the double layer and provide a thorough analysis of the properties of electrolytes at charged interfaces, such as the screening ability of the electrolyte and the electrostatic potential profile. We also report the calculation of the integral electrochemical double layer capacitance in the whole range of concentrations analysed for each ionic species, while the QM simulations provide access to the differential and integral quantum capacitance. We highlight how subtle features, such as the adsorption of potassium at the interface or the tendency of the ions to form clusters, emerge from our simulations, contribute to explaining the ability of graphene to store charge and suggest implications for desalination. Graphene ; Molecular dynamics ; Electrolyte ; Chemical physics ; Constant (computer programming) ; Materials science ; Quantum ; Quantum chemical ; Double layer (biology) ; Dynamics (music) ; Layer (electronics) ; Nanotechnology ; Molecule ; Computational chemistry ; Chemistry ; Physics ; Quantum mechanics ; Physical chemistry ; Computer science ; Electrode Conducting polymers and applications ; Molecular Junctions and Nanostructures