Synthesis, identification, density functional and Hirshfeld surface studies of 2,2'-disulfanediylbis(tetrahydro-4H-cyclopenta[d][1,3,2]dioxaphosphole-2-sulfide).

abstract：:The prediction of 13 C chemical shifts can be challenging with density functional theory (DFT). In this study 39 different functionals and three different basis sets were tested on three neutral alkylpyrroles and their corresponding protonated species. The calculated shielding constants were compared to experimental d...

journal_title：Journal of computational chemistry

authors： Zahn SLV,Hammerich O,Hansen PE,Sauer SPA

更新日期：2021-04-30 00:00:00

abstract：:There have been significant advances in the biological use of hypervalent selenium and tellurium compounds as cysteine protease inhibitors. However, the full understanding of their reaction mechanisms for and cysteine proteases inhibition is still elusive. Kinetic studies suggest an irreversible inhibition mechanism, ...

journal_title：Journal of computational chemistry

authors： Dias-da-Silva G,L O R Cunha R,D Coutinho-Neto M

更新日期：2021-04-19 00:00:00

abstract：:The stability and bonding of a series of hetero-diatomic molecules with general formula (cAAC)EM(CO)n , where cAAC = cyclic alkyl(amino) carbene; E = group 14 elements (C, Si, and Ge); M = transition metal (Ni, Fe, and Cr) have been studied by quantum chemical calculations using density functional theory (DFT) and en...

journal_title：Journal of computational chemistry

authors： Gorantla SMNVT,Parameswaran P,Mondal KC

更新日期：2021-04-15 00:00:00

abstract：:The Poisson-Boltzmann equation is a widely used model to study electrostatics in molecular solvation. Its numerical solution using a boundary integral formulation requires a mesh on the molecular surface only, yielding accurate representations of the solute, which is usually a complicated geometry. Here, we utilize ad...

journal_title：Journal of computational chemistry

authors： Ramm V,Chaudhry JH,Cooper CD

更新日期：2021-03-09 00:00:00

abstract：:We investigate the performance of a set of recently introduced range-separated double-hybrid functionals, namely ωB2-PLYP, ωB2GP-PLYP, RSX-0DH, and RSX-QIDH models for hard-to-calculate excitation energies. We compare with the parent (B2-PLYP, B2GP-PLYP, PBE0-DH, and PBE-QIDH) and other (DSD-PBEP86) double-hybrid mode...

journal_title：Journal of computational chemistry

authors： Brémond É,Ottochian A,Pérez-Jiménez ÁJ,Ciofini I,Scalmani G,Frisch MJ,Sancho-García JC,Adamo C

更新日期：2021-05-30 00:00:00

abstract：:Cellular membranes are composed of a wide diversity of lipid species in varying proportions and these compositions are representative of the organism, cellular type and organelle to which they belong. Because models of these molecular systems simulated by MD steadily gain in size and complexity, they are increasingly ...

journal_title：Journal of computational chemistry

authors： Crowet JM,Buchoux S,Belloy N,Sarazin C,Lins L,Dauchez M

更新日期：2021-05-30 00:00:00

abstract：:This study aims to apply artificial neural networks for the prediction of the lattice parameters of materials with stannite- and kesterite-type structure, and to compare the results of predictions with that obtained in the calculations exploiting the density functional theory. Crystallographic data for 49 compounds wi...

journal_title：Journal of computational chemistry

authors： Matyszczak G,Zberecki K

更新日期：2021-04-30 00:00:00

abstract：:Two proteins within the β-grasp superfamily, the B1-domain of protein G and the small archaeal modifier protein 1, were investigated to elucidate the key determinants of structural stability at the level of individual interactions. These symmetrical proteins both contain two β-hairpins which form a sheet flanked by a ...

journal_title：Journal of computational chemistry

authors： Bedford JT,Poutsma J,Diawara N,Greene LH

更新日期：2021-04-05 00:00:00

abstract：:A detailed computational exploration of the most relevant steps of iodido Pt(IV) complexes reduction and Pt(II) drugs mechanism of action and eventual deactivation is presented here inspired by the recent findings on iodido Pt(II) complexes and surprising re-evaluation of their cytotoxic activity. Pt(II) and Pt(IV) mo...

journal_title：Journal of computational chemistry

authors： Scoditti S,Vigna V,Dabbish E,Sicilia E

更新日期：2021-04-05 00:00:00

abstract：:In this work the possibility of using the IR intensity of the stretching vibration νs of proton donor group for estimation of hydrogen bond strength was investigated. For a set of complexes with FH···X (X = F, N, O) hydrogen bonds in the wide range of energies (0.1-49.2 kcal/mol) vibrational frequencies νs and their i...

journal_title：Journal of computational chemistry

authors： Tupikina EY,M Tolstoy P,A Titova A,A Kostin M,S Denisov G

更新日期：2021-03-30 00:00:00

abstract：:We are introducing Pep McConst-a software that employs a Monte-Carlo algorithm to construct 3D structures of polypeptide chains which could subsequently be studied as stand-alone macromolecules or complement the structure of known proteins. Using an approach to avoid steric clashes, Pep McConst allows to create multip...

journal_title：Journal of computational chemistry

authors： Schuhmann F,Korol V,Solov'yov IA

更新日期：2021-03-30 00:00:00

abstract：:A local optimization algorithm for solving the Kohn-Sham equations is presented. It is based on a direct minimization of the energy functional under the equality constraints representing the Grassmann Manifold. The algorithm does not require an eigendecomposition, which may be advantageous in large-scale computations....

journal_title：Journal of computational chemistry

authors： Mrovec M,Berger JA

更新日期：2021-03-15 00:00:00

abstract：:We explore the possible route to approximate natural orbital occupation numbers-based diagnostic of differential multireference character of noncovalent energy differences by techniques based on many-body expansion. It turns out that two-body fragmentation of monomers may lead to a reasonable approximation of such a d...

journal_title：Journal of computational chemistry

authors： Šulka M,Dubecký M

更新日期：2021-03-15 00:00:00

abstract：:The semiempirical INDO/S Hamiltonian is incorporated into a new release of MOPAC2016. The MOPAC2016 software package has long been at the forefront of semiempirical quantum chemical methods (SEQMs) for small molecules, proteins, and solids and until this release has included only NDDO-type SEQMs. The new code enables ...

journal_title：Journal of computational chemistry

authors： Gieseking RLM

更新日期：2021-02-15 00:00:00

abstract：:A simple practical method to compute both d-d and metal-to-ligand charge-transfer (MLCT) excited states of iron(II) polypyridyl complexes is proposed for use in simulation studies. Specifically, a model electronic Hamiltonian developed previously for d-d excited states of [Fe(bpy)3 ]2+ is extended to deal with low-lyi...

journal_title：Journal of computational chemistry

authors： Iuchi S,Koga N

更新日期：2021-01-30 00:00:00

abstract：:FFLUX is a biomolecular force field under construction, based on Quantum Chemical Topology (QCT) and machine learning (kriging), with a minimalistic and physically motivated design. A detailed analysis of the forces within the kriging models as treated in FFLUX is presented, taking as a test example a liquid water mod...

journal_title：Journal of computational chemistry

authors： Konovalov A,Symons BCB,Popelier PLA

更新日期：2021-01-15 00:00:00

abstract：:Antipsychotics represent an effective therapy for schizophrenia (a chronic mental disorder). Their benefits are related to the interaction of the drugs with dopamine D2 receptor (D2R). Antipsychotics are classified as agonists or antagonists. One of the working hypotheses is that there is a charge transfer process bet...

journal_title：Journal of computational chemistry

authors： Del Castillo RM,Ramos E,Martínez A

更新日期：2021-01-05 00:00:00

abstract：:The construction of configuration-interaction (CI) expansions from a matrix product state (MPS) involves numerous matrix operations and the skillful sampling of important configurations in a large Hilbert space. In this work, we present an efficient procedure for constructing CI expansions from MPS employing the paral...

journal_title：Journal of computational chemistry

authors： Wang T,Ma Y,Zhao L,Jiang J

更新日期：2020-12-15 00:00:00

abstract：:Partial atomic charges are important force field parameters. They are usually computed by applying quantum-chemical calculations and the assumed population scheme. In this study polarization consistent scheme of deriving a charge distribution inside solute molecule is proposed. The environment effect is explicitly tak...

journal_title：Journal of computational chemistry

authors： Stachowicz-Kuśnierz A,Korchowiec B,Korchowiec J

更新日期：2020-11-15 00:00:00

abstract：:The quantum theory of atoms in molecules (QTAIM) provides a theoretical foundation to determine the properties of functional groups through additive atomic contributions. Many studies have used QTAIM in their analyses with a variety of electronic structure methods, but it is unknown if the properties measured using on...

journal_title：Journal of computational chemistry

authors： Lefrancois-Gagnon KM,Mawhinney RC

更新日期：2020-11-01 00:00:00

abstract：:Pd-PEPPSI type complexes are widely used as precatalyst in a variety of organic reactions, including the Negishi, Kumada and Suzuki-Miyaura cross-coupling reactions. The aim of this research is to determine potential proposed reaction pathways 1, 2, or 2' (See Schemes 1 and S1-S4) for Pd-PEPPSI precatalyst activation ...

journal_title：Journal of computational chemistry

authors： Ahmadvand Z,Bayat M,Zolfigol MA

更新日期：2020-10-05 00:00:00

abstract：:Photo-switchable lipids are synthetic lipid molecules used in photo-pharmacology to alter membrane lateral pressure and thus control opening and closing of mechanosensitive ion channels. The molecular picture of how photo-switchable lipids interact with membranes or ion channels is poorly understood. To facilitate all...

journal_title：Journal of computational chemistry

authors： Klaja O,Frank JA,Trauner D,Bondar AN

更新日期：2020-10-15 00:00:00

abstract：:We present an update on recently developed methodology and functionality in the computer program Local Orbital Basis Suite Toward Electronic-Structure Reconstruction (LOBSTER) for chemical-bonding analysis in periodic systems. LOBSTER is based on an analytic projection from projector-augmented wave (PAW) density-funct...

journal_title：Journal of computational chemistry

authors： Nelson R,Ertural C,George J,Deringer VL,Hautier G,Dronskowski R

更新日期：2020-08-05 00:00:00

abstract：:A major challenge in computer-aided drug design is the accurate estimation of ligand binding affinity. Here, a new approach that combines the adaptive steered molecular dynamics (ASMD) and partial atomic charges calculated by semi-empirical quantum mechanics (SQMPC), namely ASMD-SQMPC, is suggested to predict the liga...

journal_title：Journal of computational chemistry

authors： Peng C,Wang J,Xu Z,Cai T,Zhu W

更新日期：2020-07-15 00:00:00

abstract：:Correction of calculation errors in the original article led to the change of bead type for the unprotonated beads in the coarse-grained polyethylenimine model. The original model was still of good quality while the updated model showed better performance in describing the interaction between polyethylenimine and DNA....

journal_title：Journal of computational chemistry

authors： Mahajan S,Tang T

更新日期：2020-07-05 00:00:00

abstract：:While the natural transition orbital (NTO) method has allowed electronic excitations from time-dependent Hartree-Fock and density functional theory to be viewed in a traditional orbital picture, the extension to multicomponent molecular orbitals such as those used in relativistic two-component methods or generalized H...

journal_title：Journal of computational chemistry

authors： Kasper JM,Li X

更新日期：2020-06-15 00:00:00

abstract：:The realization that noncoding RNA is implicated in numerous cellular processes, makes it imperative to understand and predict RNA-folding. RNA secondary structure prediction is more tractable than tertiary structure or protein structure. Yet insights into RNA structure-function relationships are complicated by coupli...

journal_title：Journal of computational chemistry

authors： Alaidi O,Aboul-Ela F

更新日期：2020-06-15 00:00:00

abstract：:We have evaluated the performance of various density functionals, covering generalized gradient approximation (GGA), global hybrid (GH) and range-separated hybrid (RSH), using time dependent density functional theory (TDDFT) for computing vertical excitation energies against experimental absorption maximum (λmax ) for...

journal_title：Journal of computational chemistry

authors： Narsaria AK,Ruijter JD,Hamlin TA,Ehlers AW,Guerra CF,Lammertsma K,Bickelhaupt FM

更新日期：2020-06-05 00:00:00

abstract：:A relativistic density functional theory (DFT) study is reported which aims to understand the complexation chemistry of An4+ ions (An = Th, U, Np, and Pu) with a potential decorporation agent, 5-LIO(Me-3,2-HOPO). The calculations show that the periodic change of the metal binding free energy has an excellent correlati...

journal_title：Journal of computational chemistry

authors： Sadhu B,Dolg M,Kulkarni MS

更新日期：2020-06-05 00:00:00

abstract：:This work demonstrates the potential of machine learning (ML) method to predict catalytic activity of transition metal complex precatalyst toward ethylene polymerization. For this purpose, 294 complexes and 15 molecular descriptors were selected to build the artificial neural network (ANN) model. The catalytic activit...

journal_title：Journal of computational chemistry

authors： Yang W,Fidelis TT,Sun WH

更新日期：2020-04-30 00:00:00