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Publications related to Computational Chemistry (10,000)
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Conference Paper
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Computational chemistry started by using computers to do calculations on molecular mechanics and quantum mechanics methods. In 1968,1969 the golem-1 computer in Israel utilized fortran to run molecular mechanics calculations and during that time period quantum mechanics calculations on computers was first done at MIT. The typically start points in...
Article
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The elucidation of viral-receptor interactions and an understanding of virus-spreading mechanisms are of great importance, particularly in the era of a pandemic. Indeed, advances in computational chemistry, synthetic biology, and protein engineering have allowed precise prediction and characterization of such interactions. Nevertheless, the hazards...
Article
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Theoretical calculations based on the Dirac--Coulomb--Breit relativistic coupled cluster method have been carried out for the electron affinities and ionization potentials of the superheavy element nihonium (Nh) and its lighter homologues In and Tl. The In and Tl calculations are in agreement with measurement within uncertainties. For Nh, where exp...
Article
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The glucagon-like peptide 1 receptor (GLP-1R) is a member of the family (or class) B G-protein-coupled receptor (GPCR). The receptor is a regulator of insulin and a key target in treating Type 2 diabetes mellitus. In this investigation, computational chemistry techniques such as molecular docking were combined with in silico ADME/Tox predictions to...
Article
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Recent findings, in vitro and in silico, are strengthening the idea of a simpler, earlier stage of genetically encoded proteins which used amino acids produced by prebiotic chemistry. These findings motivate a re-examination of prior work which has identified unusual properties of the set of twenty amino acids found within the full genetic code, wh...
Article
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A series of σ2R compounds containing benzimidazolone and diazacycloalkane cores was synthesized and evaluated in radioligand binding assays. Replacing the piperazine moiety in a lead compound with diazaspiroalkanes and the fused octahydropyrrolo[3,4-b] pyrrole ring system resulted in a loss in affinity for the σ2R. On the other hand, the bridged 2,...
Article
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Absract Pseudokinases have received increasing attention over the past decade because of their role in different physiological phenomena. Although pseudokinases lack several active-site residues, thereby hindering their catalytic activity, recent discoveries have shown that these proteins can play a role in intracellular signaling thanks to their n...
Article
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Tumors are still one of the main causes of death; therefore, the search for new therapeutic agents that will enable the implementation of effective treatment is a significant challenge for modern pharmacy. One of the important factors contributing to the development of neoplastic diseases is the overexpression of enzymes responsible for the regulat...
Poster
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Hybrid QM/MM simulations advanced the field of computational chemistry for the investigation of complex molecular systems. However, they are computationally expensive and suffer from artifacts at the interface. We developed BuRNN, an NN/MM approach that overcomes those limitations; the introduced Buffer Region reduces artifacts and Neural Networks...
Preprint
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The discovery of new catalysts is one of the significant topics of computational chemistry as it has the potential to accelerate the adoption of renewable energy sources. Recently developed deep learning approaches such as graph neural networks (GNNs) open new opportunity to significantly extend scope for modelling novel high-performance catalysts....
Preprint
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Quantum computational chemistry (QCC) is the use of quantum computers to solve problems in computational quantum chemistry. We develop a high performance variational quantum eigensolver (VQE) simulator for simulating quantum computational chemistry problems on a new Sunway supercomputer. The major innovations include: (1) a Matrix Product State (MP...
Article
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Pt(L1)2, Pt(L2)2 and Pt(L3)2 type four‐coordinated hypothetical platinum‐II complexes were designed and characterized computationally. Where L1, L2 and L3 are the Schiff base anions as 2‐((ethylamino)methyl)‐6‐methoxyphenolate, 2‐((ethylamino)methyl)‐6‐methylphenolate and 2‐((ethylamino)methyl)‐6‐chlorophenolate, respectively. M062X/LANL2DZ/6‐31G(d...
Article
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Conventional machine-learning (ML) models in computational chemistry learn to directly predict molecular properties using quantum chemistry only for reference data. While these heuristic ML methods show quantum-level accuracy with speeds several orders of magnitude faster than traditional quantum chemistry methods, they suffer from poor extensibili...
Article
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The ideas of quantum simulation and advances in quantum algorithms to solve quantum chemistry problems have been discussed. Theoretical proposals and experimental investigations both have been studied to gauge the extent to which quantum computation has been applied to solve quantum chemical problems till date. The distinctive features and limitati...
Article
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Phosphinylidenes are an important class of organophosphorus compounds that can exhibit tautomerization between tricoordinated P(III) hydroxide (R 1 R 2 POH) and a pentacoordinated P(V) oxide (R 1 R 2 P(O)H) form. Herein we show, using the canonical variational transition state theory combined with multidimensional small‐curvature tunneling approxim...
Article
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Machine learning and other artificial intelligence methods are gaining increasing prominence in chemistry and materials sciences, especially for materials design and discovery, and in data analysis of results generated by sensors and biosensors. In this paper, we present a perspective on this current use of machine learning, and discuss the prospec...
Preprint
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Nowadays, many chemical investigations are supported by routine calculations of molecular structures, reaction energies, barrier heights, and spectroscopic properties. The lion's share of these quantum-chemical calculations applies density functional theory (DFT) evaluated in atomic-orbital basis sets. This work provides best-practice guidance on t...
Article
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Ethnopharmacology, through the description of the beneficial effects of plants, has provided an early framework for the therapeutic use of natural compounds. Natural products, either in their native form or after crude extraction of their active ingredients, have long been used by different populations and explored as invaluable sources for drug de...
Article
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Lithium‐ion batteries (LIBs) are vital energy‐storage devices in modern society. However, the performance and cost are still not satisfactory in terms of energy density, power density, cycle life, safety, etc. To further improve the performance of batteries, traditional “trial‐and‐error” processes require a vast number of tedious experiments. Compu...
Article
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Antibiotics constitute one of the emerging categories of persistent organic pollutants, characterised by their expansion of resistant pathogens. Antibiotic pollutants create a major public health challenge, with already identifiable detrimental effects on human and animal health. A fundamental aspect of controlling and preventing the spread of poll...
Article
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In this study, FDA-approved HCV antiviral drugs and their structural analogues—several of them in clinical trials—were tested for their inhibitory properties toward the SARS-CoV-2 spike protein bound to angiotensin-converting enzyme 2 (6M0J) using a virtual screening approach and computational chemistry methods. The most stable structures and the c...
Article
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We present a data set from a first-principles study of amino-methylated and acetylated (capped) dipeptides of the 20 proteinogenic amino acids – including alternative possible side chain protonation states and their interactions with selected divalent cations (Ca2+, Mg2+ and Ba2+). The data covers 21,909 stationary points on the respective potentia...
Article
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Predicting transition state geometries is one of the most challenging tasks in computational chemistry, which often requires expert-based knowledge and permanent human intervention. This short communication reports technical details and preliminary results of a python-based tool (AMADAR) designed to generate any Diels–Alder (DA) transition state ge...
Article
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Identification of molecular structural features is a central part of computational chemistry. It would be beneficial if pattern recognition techniques could be incorporated to facilitate the identification. Currently, the quantification of the structural dissimilarity is mainly carried out by root-mean-square-deviation (RMSD) calculations such as i...
Cover Page
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Computational chemistry allows for in-depth examination of molecules. Antioxidants have recently piqued the interest of researchers due to their ability to scavenge free radicals, whose elevated levels cause serious damage to organic and inorganic matter. This review assembles methods that are currently in use in the studies on them.
Article
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Transition metal macrocyclic complexes are appealing catalysts for electrochemical oxygen reduction reaction (ORR). Here, we perform first-principles calculations to gain a comprehensive understanding on the structure-property relationship of the metal macrocyclic complex systems. Various modifications of the complexes are considered, including cen...
Preprint
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High-dimensional Partial Differential Equations (PDEs) are a popular mathematical modelling tool, with applications ranging from finance to computational chemistry. However, standard numerical techniques for solving these PDEs are typically affected by the curse of dimensionality. In this work, we tackle this challenge while focusing on stationary...
Article
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The synthesis, structure, and spectroscopic characterization of a pincer-type compound; N,N′-di(pyridine-4-yl)-pyridine-3,5-dicarboxamide is described. The tricationic pro-ligand (C20H22N5O2)³⁺ bearing two pendant alkylated 4-pyridyl arms at the 3,5-positions of the central pyridyl group features three triflate anions (CF3SO3⁻) in the asymmetric un...
Article
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Scientists’ ability to detect drug-related metabolites at trace concentrations has improved over recent decades. High-resolution instruments enable collection of large amounts of raw experimental data. In fact, the quantity of data produced has become a challenge due to effort required to convert raw data into useful insights. Various cheminformati...
Article
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Sustainable practices in chemical sciences can be better realized by adopting interdisciplinary approaches that combine the advantages of machine learning (ML) on the initially acquired small data in reaction discovery. Developing new reactions generally remains heuristic and even time and resource intensive. For instance, synthesis of fluorine-con...
Article
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Corrosion has caused serious damage to our society, lives and environments. Although the corrosion of metals and their alloys was inevitable, it was controllable using the certain protection method. Using corrosion inhibitors was a feasible strategy to protect metals and alloys from corrosion. Traditional inorganic and organic inhibitors were toxic...
Article
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Breast cancer (BC) is the most frequently diagnosed cancer and is the second-most common cause of death in women worldwide. Because of this, the search for new drugs and targeted therapy to treat BC is an urgent and global need. Histone deacetylase 6 (HDAC6) is a promising anti-BC drug target associated with its development and progression. In the...
Article
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The organization and management of large amounts of data has become a major point in almost all areas of human knowledge. In this context, semantic approaches propose a structure for the target data, defining ontologies that state the types of entities on a certain field and how these entities are interrelated. In this work, we introduce OntoRXN, a...
Article
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Abraham’s measure of the solute hydrogen bond basicity, β2H\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\beta_{2}^{{\text{H}}}$$\end{document}, is analyzed in terms...
Article
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The use of machine learning techniques in computational chemistry has gained significant momentum since large molecular databases are now readily available. Predictions of molecular properties using machine learning have advantages over the traditional quantum mechanics calculations because they can be cheaper computationally without losing the acc...
Article
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Traditionally, chemistry has been developed to obtain thermodynamically stable and isolable compounds such as molecules and solids by chemical reactions. However, recent developments in computational chemistry have placed increased importance on studying the dynamic assembly and disassembly of atoms and molecules formed in situ. This study directly...
Article
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Finding accurate solutions to the Schrödinger equation is the key unsolved challenge of computational chemistry. Given its importance for the development of new chemical compounds, decades of research have been dedicated to this problem, but due to the large dimensionality even the best available methods do not yet reach the desired accuracy. Recen...
Article
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The sampling problem is one of the most widely studied topics in computational chemistry. While various methods exist for sampling along a set of reaction coordinates, many require system-dependent hyperparameters to achieve maximum efficiency. In this work, we present an alchemical variation of adaptive sequential Monte Carlo (SMC), an irreversibl...
Book
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Obesity is not a lifestyle choice; it is a disease with multiple causes. It is a risk factor for chronic pathologies (diabetes, cardiovascular and respiratory diseases, etc.) and also has major psychological and social consequences. It can be prevented, especially in its severe forms. Recourse to surgery is appropriate only in very specific cases....
Article
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Nonadiabatic dynamics simulations in the long timescale (much longer than 10 ps) are the next challenge in computational photochemistry. This paper delimits the scope of what we expect from methods to run such simulations: they should work in full nuclear dimensionality, be general enough to tackle any type of molecule and not require unrealistic c...
Article
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New hydrazone derivate, (1Z,2E)-2-(2-(1-(1,3-dimethyl-2,4,6-trioxotetrahydropyrimidin-5(2H)-ylidene)ethyl)hydrazineylidene)-2-(p-tolyl)acetaldehyde oxime (H2L) was synthesized by 5-acetyl-1,3-dimethyl-barbituric acid and p-methyl isonitrosophenylhydrazine. Its molecular and crystal structures were determined by single crystal X-ray analysis. It bel...
Article
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A green and effective approach for the synthesis of structurally diversed α-hydroxyphosphonates via hydrophosphonylation of aldehydes under solventless conditions and promoted by biosourced catalysts, called ecocatalysts “Eco-MgZnOx” is presented. Ecocatalysts were prepared from Zn-hyperaccumulating plant species Arabidopsis halleri, with simple an...
Article
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Ab initio molecular dynamics (AIMD) is an established method for revealing the reactive dynamics of complex systems. However, the high computational cost of AIMD restricts the explorable length and time scales. Here, we develop a fundamentally different approach using molecular dynamics simulations powered by a neural network potential to investiga...
Thesis
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Human society has progressed by polluting ecosystems since the early industrial revolution. Thus, large amounts of harmful chemical compounds have been dispersed in soils, seas, groundwaters and wildlife habitats, leading to a persistent toxicological load on the environment. Pollution is a threat to biodiversity, to the health of ecosystems, and t...
Article
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Quantum mechanical calculations are routinely used as a major support in mid-infrared (MIR) and Raman spectroscopy. In contrast, practical limitations for long time formed a barrier to developing a similar synergy between near-infrared (NIR) spectroscopy and computational chemistry. Recent advances in theoretical methods suitable for calculation of...
Article
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The concept of chemical space is a cornerstone in chemoinformatics, and it has broad conceptual and practical applicability in many areas of chemistry, including drug design and discovery. One of the most considerable impacts is in the study of structure–property relationships where the property can be a biological activity or any other characteris...
Article
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A series of triazolium and imidazolium based protic ionic liquids were synthesized using a solvent-free method design to address several limitations encountered with other commonly used methods. Using this method, pure (98-99% m/m) and dry (128-553 ppm of water) protic ionic liquids were synthesized (in a laboratory scale) without the need for puri...
Article
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In this work it is demonstrated that enantiomerically enriched N-alkyl 2-oxazolinylazetidines undergo exclusive α-lithiation, and that the resulting lithiated intermediate is chemically stable but configurationally labile under the given experimental conditions that afford enantioenriched N-alkyl-2,2-disubstituted azetidines. Although this study re...
Article
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Hybrid quantum mechanics/molecular mechanics (QM/MM) simulations have advanced the field of computational chemistry tremendously. However, they require the partitioning of a system into two different regions that are treated at different levels of theory, which can cause artifacts at the interface. Furthermore, they are still limited by high comput...
Preprint
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While in principle exact, Kohn-Sham density functional theory -- the workhorse of computational chemistry -- must rely on approximations for the exchange-correlation functional. Despite staggering successes, present-day approximations still struggle when the effects of electron-electron correlation play a prominent role. The limit in which the elec...
Article
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Electropolymerization has become a convenient method for synthesizing and characterizing complex organic copolymers having intrinsic electronic conductivity, including the donor (D)-acceptor (A) class of electronically conducting polymers (ECPs). This review begins with an introduction to the electrosynthesis of common second-generation ECPs. The i...
Preprint
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Nowadays, many chemical investigations can be supported theoretically by routine molecular structure calculations, conformer ensembles, reaction energies, barrier heights, and predicted spectroscopic properties. Such standard computational chemistry applications are most often conducted with density functional theory (DFT) and atom-centered atomic...
Article
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Complex metal oxides (CMOs) are used broadly in applications including electroreactive forms found in lithium-ion battery technology. Computational chemistry can provide unique information about how the properties of CMO cathode materials change in response to changes in stoichiometry, for example, changes of the lithium (Li) content during the cha...
Preprint
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Considering smooth mappings from input vectors to continuous targets, our goal is to characterise subspaces of the input domain, which are invariant under such mappings. Thus, we want to characterise manifolds implicitly defined by level sets. Specifically, this characterisation should be of a global parametric form, which is especially useful for...
Article
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We present several workflows for protein-ligand docking and free energy calculation for use in the workflow management system Galaxy. The workflows are composed of several widely used open-source tools, including rDock and GROMACS, and can be executed on public infrastructure using either Galaxy’s graphical interface or the command line. We demonst...
Article
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Glycine (Gly), NH2CH2COOH, is the simplest amino acid. Although it has not been directly detected in the interstellar gas-phase medium, it has been identified in comets and meteorites, and its synthesis in these environments has been simulated in terrestrial laboratory experiments. Likewise, condensation of Gly to form peptides in scenarios resembl...