On the intrinsic reactivity index for electrophilicity/nucleophilicity responses.

abstract：:Hyaluronan lyase from Streptococcus pneumoniae can degrade hyaluronic acid, which is one of the major components in the extracellular matrix. Hyaluronan can regulate water balance, osmotic pressure, and act as an ion exchange resin. Followed by our recent work on the catalytic reaction mechanism and substrate binding ...

journal_title：Journal of molecular modeling

authors： Li F,Xu D

更新日期：2015-08-01 00:00:00

abstract：:Despite encouraging progress over the past decade, malaria caused by the Plasmodium parasite continues to pose an enormous disease burden and is one of the major global health problems. The extreme challenge in malaria management is the resistance of parasites to traditional monochemotherapies like chloroquine and sul...

journal_title：Journal of molecular modeling

authors： Sharma D,Soni R,Patel S,Joshi D,Bhatt TK

更新日期：2016-09-01 00:00:00

abstract：:Molecular modeling and docking studies along with three-dimensional quantitative structure relationships (3D-QSAR) studies have been used to determine the correct binding mode of glycogen synthase kinase 3beta (GSK-3beta) inhibitors. The approaches of comparative molecular field analysis (CoMFA) and comparative molecu...

journal_title：Journal of molecular modeling

authors： Kim KH,Gaisina I,Gallier F,Holzle D,Blond SY,Mesecar A,Kozikowski AP

更新日期：2009-12-01 00:00:00

abstract：:In this work, the effect of the external electric field (EF) on the drug delivery performance of peptide-based metal-organic framework (MPF) for 6-mercaptopurine (6-MP) drug is investigated by means of the molecular dynamics (MD) simulations. It is found that the strength interaction of drug molecule with MPF is decre...

journal_title：Journal of molecular modeling

authors： Shahabi M,Raissi H

更新日期：2019-09-06 00:00:00

abstract：:In this work, the low-lying states of several isomers of ScSi n-/0 (n = 4-6) were investigated with the B3LYP functional and CASPT2 method. The ground states of the anionic clusters were predicted to be the singlet states of the trigonal bipyramid ScSi4- (A-ScSi4-), the face-capped trigonal bipyramid ScSi5- (A-ScSi5-)...

journal_title：Journal of molecular modeling

authors： Nguyen MT,Tran QT,Tran VT

更新日期：2017-09-20 00:00:00

abstract：:Through the B3LYP/6-311++G(d,p) calculations, theoretical studies of structural parameters, electronic properties, infrared vibration modes, and charge density topologies on the C2H4O∙∙∙HX and C2H5N∙∙∙HX (X = F or O-F) heterocylic hydrogen complexes are presented. The H-bond distances and high energies point out stron...

journal_title：Journal of molecular modeling

authors： Oliveira BG

更新日期：2015-11-01 00:00:00

abstract：:The chain tacticity of a polymer is a key influence on its structure and dynamics, which ultimately determine its properties. While they have great potential to elucidate the influence of chain tacticity, all-atom molecular simulations are often restricted to short chains and small systems. In this work, two typical s...

journal_title：Journal of molecular modeling

authors： Wu C

更新日期：2014-08-01 00:00:00

abstract：:A series of no-chlorine and oxygen-rich hydrazine derivatives (hydrazine modified with -NO₂ and NO₃(-) groups) was designed and optimized to obtain molecular geometries and electronic structures at density functional theory-B3PW91/6-311++G(3df,3pd) level. Some important properties such as bond dissociation enthalpy, d...

journal_title：Journal of molecular modeling

authors： Wang PC,Zhu ZS,Xu J,Zhao XJ,Lu M

更新日期：2013-06-01 00:00:00

abstract：:A theoretical investigation is completed on the mechanism of electrical breakdown strength increment of polyethylene. It is shown that it is one of the most important factors for increasing electrical breakdown strength of polyethylene through keto-enol isomerization of acetophenone and its analogues at the ground sta...

journal_title：Journal of molecular modeling

authors： Zhang H,Shang Y,Zhao H,Han B,Li Z

更新日期：2013-10-01 00:00:00

abstract：:Cation-π interactions are known to be one of the strongest noncovalent forces in the gas phase, but they rarely occur in a fully solvated environment. The present work used two different ab initio molecular dynamics-based approaches to describe the correlation between the strength of the cation-π interactions and the ...

journal_title：Journal of molecular modeling

authors： Larrucea J

更新日期：2012-09-01 00:00:00

abstract：:A coarse-grained Brownian dynamics model was used to simulate two proteins of similar sizes inside model membrane pores of varying size and hydrophobicity. The two proteins, which have radii of gyration of approximately 9.5 Å in their native states, are a 36-residue hydrophilic villin head piece (HP-36) and a 40-resid...

journal_title：Journal of molecular modeling

authors： Zhang Y,Zhang Y,McCready MJ,Maginn EJ

更新日期：2019-04-25 00:00:00

abstract：:Conjugate peak refinement (CPR) is a powerful and robust method to search transition states on a molecular potential energy surface. Nevertheless, the method was to the best of our knowledge so far only implemented in CHARMM. In this paper, we present PyCPR, a new Python-based implementation of the CPR algorithm withi...

journal_title：Journal of molecular modeling

authors： Gisdon FJ,Culka M,Ullmann GM

更新日期：2016-10-01 00:00:00

abstract：:The Fbw7-Skp1 complex is an essential component in the formation and development of the mammalian cardiovascular system; the complex interaction is mediated through binding of Skp1 C-terminal peptide (qGlu-peptide) to the F-box domain of Fbw7. By visually examining the crystal structure, we identified a typical cation...

journal_title：Journal of molecular modeling

authors： Zhou J,Wang YS

更新日期：2017-09-26 00:00:00

abstract：:Understanding the interaction between graphene and polymers is of essential interest when designing novel nanocomposites with reinforced mechanical and electrical properties. In this computational study, the interaction of pristine graphene (PG) and graphene oxide (GO) with a series of functional groups, representativ...

journal_title：Journal of molecular modeling

authors： Güryel S,Alonso M,Hajgató B,Dauphin Y,Van Lier G,Geerlings P,De Proft F

更新日期：2017-02-01 00:00:00

abstract：:The formation of silaspiropentane from addition of singlet silacyclopropylidene 1 and silacyclopropylidenoid 8 to ethylene has been investigated separately at the B3LYP, X3LYP, WB97XD, and M05-2X theories using the 6-31+G(d,p) basis set. The silacycloproylidenoid addition follows a stepwise route. In contrast, a conce...

journal_title：Journal of molecular modeling

authors： Yildiz CB,Azizoglu A

更新日期：2016-07-01 00:00:00

abstract：:To determine the kinase inhibitory potential of natural products that could be utilized in lung cancer therapy in the near future, a pharmacophore-based activity profiling protocol using parallel pharmacophore-based virtual screening of ZINC-a natural product database-was employed. The work presented here is based on ...

journal_title：Journal of molecular modeling

authors： Singh PK,Silakari O

更新日期：2018-10-20 00:00:00

abstract：:The structural features, spectroscopic properties, and interaction energies of the linear proton-bound complexes of OCH(+) and its sulfur analog SCH(+) with N2 were investigated using the high-level ab initio methods MP2 and CCSD(T) as well as density functional theory with the aug-cc-pVXZ (X = D, T) basis sets. The r...

journal_title：Journal of molecular modeling

authors： Begum S,Subramanian R

更新日期：2016-01-01 00:00:00

abstract：:Density functional theory (DFT) was used to study the stereochemistry, thermodynamic stability, and spectra of recently synthesized bis-Betti base derivatives of 2,3-dihydroxynaphthalene obtained through multicomponent reactions of 2,3-dihydroxynaphthalene with aminoisoxazole and benzaldehyde derivatives. The stereoch...

journal_title：Journal of molecular modeling

authors： Zamani M,Shafiee M,Keshavarz MH

更新日期：2016-04-01 00:00:00

abstract：:Molecular dynamics simulations are conducted to investigate the buckling characteristics of functionalized carbon nanotubes (f-CNTs) under axial compression at various temperatures. The influences of functionalization, content of functional groups, chirality and diameter, as well as temperature on buckling response of...

journal_title：Journal of molecular modeling

authors： Mehralian F,Tadi Beni Y

更新日期：2017-11-04 00:00:00

abstract：:The UV absorption spectra of ten N,N'-bisarylmalonamides have been recorded in the range 200-400 nm in a set of selected solvents. The solute-solvent interactions have been analyzed on the basis of the linear solvation energy relationship (LSER) concept proposed by Kamlet and Taft. The effects of substituents on the a...

journal_title：Journal of molecular modeling

authors： Arsovski VM,Božić BĐ,Mirković JM,Vitnik VD,Vitnik ZJ,Fabian WM,Petrović SD,Mijin DZ

更新日期：2014-08-01 00:00:00

abstract：:The complementarity plot (CP) is an established validation tool for protein structures, applicable to both globular proteins (folding) as well as protein-protein complexes (binding). It computes the shape and electrostatic complementarities (Sm, Em) for amino acid side-chains buried within the protein interior or inte...

journal_title：Journal of molecular modeling

authors： Basu S

更新日期：2017-12-07 00:00:00

abstract：:Given the increasing complexity of simulated molecular systems, and the fact that simulation times have now reached milliseconds to seconds, immense amounts of data (in the gigabyte to terabyte range) are produced in current molecular dynamics simulations. Manual analysis of these data is a very time-consuming task, a...

journal_title：Journal of molecular modeling

authors： Victor Paul Raj FR,Exner TE

更新日期：2014-04-01 00:00:00

abstract：:Prussian Blue is a paradigmatic mixed valence material and a parent compound to a broad family of electronically, optically, and magnetically active materials. Its exact composition varies greatly depending on the preparation route, leading to large variations in its electronic properties. The influence of water molec...

journal_title：Journal of molecular modeling

authors： Wojdeł JC

更新日期：2009-06-01 00:00:00

abstract：:Two important classes of organic molecules, perylene diimide (PDI) and pyrene derivatives have been found to possess relatively excellent photophysical and photochemical properties and especially high two-photon absorption cross sections (δ(T)(max)). Herein, one-photon absorption (OPA) and two-photon absorption (TPA) ...

journal_title：Journal of molecular modeling

authors： Liu XT,Zhao Y,Ren AM,Feng JK

更新日期：2011-06-01 00:00:00

abstract：:Human dihydrofolate reductase-like 1 (DHFRL1) has been identified as a second human dihydrofolate reductase (DHFR) enzyme. Although DHFRL1 have high sequence homology with human DHFR, dihydrofolate (DHF) exhibits a lowered binding affinity to DHFRL1 and the corresponding molecular mechanism is still unknown. To addres...

journal_title：Journal of molecular modeling

authors： Gao J,Cui W,Du Y,Ji M

更新日期：2013-12-01 00:00:00

abstract：:Multilayer-shaped compression and slide models were employed to investigate the complex sensitive mechanisms of cocrystal explosives in response to external mechanical stimuli. Here, density functional theory (DFT) calculations implementing the generalized gradient approximation (GGA) of Perdew-Burke-Ernzerhof (PBE) w...

journal_title：Journal of molecular modeling

authors： Gao HF,Zhang SH,Ren FD,Gou RJ,Han G,Wu JB,Ding X,Zhao WH

更新日期：2016-05-01 00:00:00

abstract：:The pathway and ab initio direct kinetics of the decomposition 5-aminotetrazole (5-ATZ) to HN(3) and NH(2)CN was investigated. Reactant, products and transition state were optimized with MP2 and B3LYP methods using 6-311G** and aug-cc-pVDZ basis sets. The intrinsic reaction coordinate curve of the reaction was calcula...

journal_title：Journal of molecular modeling

authors： Zhang JG,Feng LN,Zhang SW,Zhang TL,Zheng HH

更新日期：2008-05-01 00:00:00

abstract：:CD44 is a cell-surface glycoprotein and receptor for hyaluronan, one of the major components of the tumor extracellular matrix. There is evidence that the interaction between CD44 and hyaluronan promotes breast cancer metastasis. Recently, the molecule F-19848A was shown to inhibit hyaluronan binding to receptor CD44 ...

journal_title：Journal of molecular modeling

authors： Nguyen TT,Tran DP,Pham Dinh Quoc Huy,Hoang Z,Carloni P,Van Pham P,Nguyen C,Li MS

更新日期：2016-07-01 00:00:00

abstract：:The mechanism and regioselectivity of [3+2] cycloaddition (32CA) reactions of benzonitrile oxide with ethyl trans-cinnamate, ethyl crotonate and trans-2-penten-1-ol has been studied in gas phase and in acetonitrile, ethyl acetate and tetrahydrofuran using the B3LYP functional in connection with 6-31G(d) basis set. The...

journal_title：Journal of molecular modeling

authors： Abbiche K,Acharjee N,Salah M,Hilali M,Laknifli A,Komiha N,Marakchi K

更新日期：2020-09-22 00:00:00

abstract：:Amorphous molecular simulation to model the reaction species in the synthesis of chemically inert and energetic 1,1-diamino-2,2-dinitroethene (DADNE) explosive material was performed in this work. Nitromethane was selected as the starting reactant to undergo halogenation, nitration, deprotonation, intermolecular conde...

journal_title：Journal of molecular modeling

authors： Liu MH,Liu CW

更新日期：2017-01-01 00:00:00