Insights into the electronic structure and mechanism of norcarane hydroxylation by OxoMn(V) porphyrin complexes: A density functional theory study.

abstract：:We introduce a new Python interface for the Cassandra Monte Carlo software, molecular simulation design framework (MoSDeF) Cassandra. MoSDeF Cassandra provides a simplified user interface, offers broader interoperability with other molecular simulation codes, enables the construction of programmatic and reproducible m...

journal_title：Journal of computational chemistry

authors： DeFever RS,Matsumoto RA,Dowling AW,Cummings PT,Maginn EJ

更新日期：2021-04-30 00:00:00

abstract：:We propose an efficient and accurate non-iterative method, dubbed uESE, for calculating solvation free energies. Apart from a COSMO-like electrostatic term, the model takes into account non-electrostatic contributions, which depend on atomic surfaces, induced surface charge densities, and the molecular volume. uESE is...

journal_title：Journal of computational chemistry

authors： Vyboishchikov SF,Voityuk AA

更新日期：2021-04-12 00:00:00

abstract：:The full configuration interaction (FCI) method is only applicable to small molecules with few electrons in moderate size basis sets. One of the main alternatives to obtain approximate FCI energies for bigger molecules and larger basis sets is selected CI. However, due to: (a) the lack of a well-defined structure in a...

journal_title：Journal of computational chemistry

authors： Chilkuri VG,Neese F

更新日期：2021-05-30 00:00:00

abstract：:Efficient design and screening of the novel molecules is a major challenge in drug and material design. This paper focuses on a multi-stage pipeline, in which several deep neural network models are combined to map discrete molecular representations into continuous vector space to later generate from it new molecular s...

journal_title：Journal of computational chemistry

authors： Druchok M,Yarish D,Gurbych O,Maksymenko M

更新日期：2021-04-30 00:00:00

abstract：:We introduce iSPECTRON, a program that parses data from common quantum chemistry software (NWChem, OpenMolcas, Gaussian, Cobramm, etc.), produces the input files for the simulation of linear and nonlinear spectroscopy of molecules with the Spectron code, and analyzes the spectra with a broad range of tools. Vibronic s...

journal_title：Journal of computational chemistry

authors： Segatta F,Nenov A,Nascimento DR,Govind N,Mukamel S,Garavelli M

更新日期：2021-04-05 00:00:00

abstract：:In this article, we investigate the effects of the isoleucine (ILE)N amino acid chain growth, N = 1.0.6, the ILE conformational effect as well as the solvent presence on the electrical and magnetic spectroscopic properties when these compounds are in aqueous solution. Computational molecular dynamics simulations were ...

journal_title：Journal of computational chemistry

authors： Mendanha K,Prado RC,Oliveira LBA,Colherinhas G

更新日期：2021-02-15 00:00:00

abstract：:Molecular dynamics on the complexes of inhibitors with Zn-metalloproteins are a privileged area of applications of polarizable molecular mechanics potentials. With which accuracy could these reproduce the QC intermolecular interaction energies in the two mono-zinc cores and in the dizinc core, toward full-fledged MD s...

journal_title：Journal of computational chemistry

authors： Kwapien K,Gavara L,Docquier JD,Berthomieu D,Hernandez JF,Gresh N

更新日期：2021-01-15 00:00:00

abstract：:Evaluating the availability of molecular oxygen (O2 ) and energy of excited states in the retinal binding site of rhodopsin is a crucial challenging first step to understand photosensitizing reactions in wild-type (WT) and mutant rhodopsins by absorbing visible light. In the present work, energies of the ground and ex...

journal_title：Journal of computational chemistry

authors： Hernández-Rodríguez EW,Escorcia AM,van der Kamp MW,Montero-Alejo AL,Caballero J

更新日期：2020-10-05 00:00:00

abstract：:The impact of solvent flexibility and electron correlation on the simulation results of Cu2+ in liquid ammonia has been investigated via an ab initio quantum mechanical charge field molecular dynamics (QMCF MD) simulation approach. To achieve this, three different simulation systems were considered in this study, name...

journal_title：Journal of computational chemistry

authors： Saputri WD,Pranowo HD,Schuler MJ,Hofer TS

更新日期：2020-09-30 00:00:00

abstract：:In this study, we revisited the Ziff-Gulari-Barshad (ZGB) model in order to study the behavior of its phase diagram when two well-known random networks play the role of the catalytic surfaces: the random geometric graph and the Erdös-Rényi network. The connectivity and, therefore, the average number of neighbors of th...

journal_title：Journal of computational chemistry

authors： Vilela EB,Fernandes HA,Paranhos Costa FL,Gomes PF

更新日期：2020-08-15 00:00:00

abstract：:A classical 6-12 Lennard-Jones (LJ) equation has been widely used to model materials and is the potential of choice in studies when the focus is on fundamental issues. Here we report a systematic study comparing the pair interaction potentials within solid-state materials (i.e., [Co6 Se8 (PEt3 )6 ][C60 ]2 , [Cr6 Te8 (...

journal_title：Journal of computational chemistry

authors： Sikorska C,Gaston N

更新日期：2020-08-15 00:00:00

abstract：:Nitrate ( NO 3 - ) and nitrite ( NO 2 - ...

journal_title：Journal of computational chemistry

authors： Yadav S,Chandra A

更新日期：2020-07-30 00:00:00

abstract：:Density functional theory methods were employed to clarify the adsorption/desorption behaviors of the thione-containing mercaptopurine and thioguanine drugs on the gold surface using both small Au6 and Au8 clusters as model reactants. Structural features, thermodynamic parameters, bonding characteristics, and electron...

journal_title：Journal of computational chemistry

authors： Nhat PV,Si NT,Tram NTT,Duong LV,Nguyen MT

更新日期：2020-07-15 00:00:00

abstract：:Multicanonical molecular dynamics based dynamic docking was used to exhaustively search the configurational space of an inhibitor binding to the N-terminal domain of heat-shock protein 90 (Hsp90). The obtained structures at 300 K cover a wide structural ensemble, with the top two clusters ranked by their free energy c...

journal_title：Journal of computational chemistry

authors： Bekker GJ,Araki M,Oshima K,Okuno Y,Kamiya N

更新日期：2020-06-30 00:00:00

abstract：:The semiclassical tunneling method is applied to evaluate the tunneling splitting of tropolone due to the intramolecular proton transfer in the electronic excited state, first time, in a framework of the trajectory on-the-fly molecular dynamics (TOF-MD) approach. To prevent unphysical zero-point vibrational energy tra...

journal_title：Journal of computational chemistry

authors： Ootani Y,Satoh A,Harabuchi Y,Taketsugu T

更新日期：2020-06-15 00:00:00

abstract：:Positron binding energies (PBEs) of 41 polyatomic molecules were calculated using the positron-electron correlation-polarization potential (CPP) approach and compared with experimentally measured values. In this approach, the short-range positron-electron potential is modeled using the density-functional expression, w...

journal_title：Journal of computational chemistry

authors： Sugiura Y,Suzuki H,Otomo T,Miyazaki T,Takayanagi T,Tachikawa M

更新日期：2020-06-30 00:00:00

abstract：:Anionic species of aspartic acid, Asp- , having a zwitterionic backbone and a deprotonated side chain, appears to be a good example for analyzing dipole-ion and ion pair interactions. Density functional theory calculations were herein performed to investigate the low energy conformers of Asp- embedded in a dielectric ...

journal_title：Journal of computational chemistry

authors： Hernández B,Pflüger F,Ghomi M

更新日期：2020-05-30 00:00:00

abstract：:A new simple and conceptual theoretical scheme is proposed for estimating one-electron excitation energies using Kohn-Sham (KS) solutions. One-electron transitions that are dominated by the promotion from one initially occupied orbital to one unoccupied orbital of a molecular system can be expressed in a two-step proc...

journal_title：Journal of computational chemistry

authors： Hirao K,Chan B,Song JW,Bhattarai K,Tewary S

更新日期：2020-05-30 00:00:00

abstract：:The search for new dyes to be used as photosensitizers in photodynamic therapy (PDT) is a field of great interest from both experimental and theoretical viewpoints. In this study, the main photophysical properties (excitation energies, singlet-triplet energy gap, and spin orbit coupling matrix elements) of some unsubs...

journal_title：Journal of computational chemistry

authors： Alberto ME,De Simone BC,Liuzzi S,Marino T,Russo N,Toscano M

更新日期：2020-05-30 00:00:00

abstract：:Pressure-induced insulator-to-metal transition (IMT) has been studied in the van der Waals compound iron thiophosphate (FePS3 ) using first-principles calculations within the periodic linear combination of atomic orbitals method with hybrid Hartree-Fock-DFT B3LYP functional. Our calculations reproduce correctly the IM...

journal_title：Journal of computational chemistry

authors： Evarestov RA,Kuzmin A

更新日期：2020-05-30 00:00:00

abstract：:In this paper we present the implementation and benchmarking of a Time Dependent Density Functional Theory approach in conjunction with Double Hybrid (DH) functionals. We focused on the analysis of their performance for through space charge-transfer (CT) excitations which are well known to be very problematic for comm...

journal_title：Journal of computational chemistry

authors： Ottochian A,Morgillo C,Ciofini I,Frisch MJ,Scalmani G,Adamo C

更新日期：2020-05-15 00:00:00

abstract：:Advances to the distributed, multi-core and fully cross-platform QuBiLS-MIDAS software v2.0 (http://tomocomd.com/qubils-midas) are reported in this article since the v1.0 release. The QuBiLS-MIDAS software is the only one that computes atom-pair and alignment-free geometrical MDs (3D-MDs) from several distance metrics...

journal_title：Journal of computational chemistry

authors： García-Jacas CR,Marrero-Ponce Y,Vivas-Reyes R,Suárez-Lezcano J,Martinez-Rios F,Terán JE,Aguilera-Mendoza L

更新日期：2020-05-05 00:00:00

abstract：:The virtual-reality framework AVATAR (Advanced Virtual Approach to Topological Analysis of Reactivity) for the immersive exploration of potential-energy landscapes is presented. AVATAR is based on modern consumer-grade virtual-reality technology and builds on two key concepts: (a) the reduction of the dimensionality o...

journal_title：Journal of computational chemistry

authors： Martino M,Salvadori A,Lazzari F,Paoloni L,Nandi S,Mancini G,Barone V,Rampino S

更新日期：2020-05-15 00:00:00

abstract：:Determination of the ligand-binding affinity is an extremely interesting problem. Normally, the free energy perturbation (FEP) method provides an appropriate result. However, it is of great interest to improve the accuracy and precision of this method. In this context, temperature replica exchange molecular dynamics i...

journal_title：Journal of computational chemistry

authors： Ngo ST,Nguyen TH,Tung NT,Nam PC,Vu KB,Vu VV

更新日期：2020-03-15 00:00:00

abstract：:Based on the molecular dynamics software package CovalentMD 2.0, the fastest molecular dynamics simulation for covalent crystalline silicon with bond-order potentials has been implemented on the third highest performance supercomputer "Sunway TaihuLight" in the world (before June 2019), and already obtained 16.0 Pflop...

journal_title：Journal of computational chemistry

authors： Hou C,Zhang C,Ge W,Wang L,Han L,Pang J

更新日期：2020-03-15 00:00:00

abstract：:Density functional theory has been used to study the biologically important coenzyme NADPH and its oxidized form NADP+ . It was found that free NADPH prefers a compact structure in gas phase and exists in more extended geometries in aqueous solution. Ultraviolet-visible absorption spectra in aqueous solution were calc...

journal_title：Journal of computational chemistry

authors： Cao X,Wu L,Zhang J,Dolg M

更新日期：2020-02-05 00:00:00

abstract：:Accurate identification of ligand-binding sites and discovering the protein-ligand interaction mechanism are important for understanding proteins' functions and designing new drugs. Meanwhile, accurate computational prediction and mechanism research are two grand challenges in proteomics. In this article, ligand-bindi...

journal_title：Journal of computational chemistry

authors： Hu X,Ge R,Feng Z

更新日期：2020-01-15 00:00:00

abstract：:ClC-ec1 is a Cl- /H+ antiporter that exchanges Cl- and H+ ions across the membrane. Experiments have demonstrated that several mutations, including I109F, decrease the Cl- and H+ transport rates by an order of magnitude. Using reactive molecular dynamics simulations of explicit proton transport across the central regi...

journal_title：Journal of computational chemistry

authors： Wang Z,Swanson JMJ,Voth GA

更新日期：2020-03-05 00:00:00

abstract：:G-protein-coupled receptors (GPCRs) are the largest family of human membrane proteins and serve as primary targets of approximately one-third of currently marketed drugs. In particular, adenosine A1 receptor (A1 AR) is an important therapeutic target for treating cardiac ischemia-reperfusion injuries, neuropathic pain...

journal_title：Journal of computational chemistry

authors： Bhattarai A,Wang J,Miao Y

更新日期：2020-02-15 00:00:00

abstract：:The absolute solvation energies (free energies and enthalpies) of the proton in ammonia are used to compute the pKa of species embedded in ammonia. They are also used to compute the solvation energies of other ions in ammonia. Despite their importance, it is not possible to determine experimentally the solvation energ...

journal_title：Journal of computational chemistry

authors： Malloum A,Fifen JJ,Conradie J

更新日期：2020-01-05 00:00:00