Natural bond orbital/natural J-coupling study of vicinal couplings.

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：:Tuberculosis still remains one of the most deadly infectious diseases. The emergence of drug resistant strains has fuelled the quest for novel drugs and drug targets for its successful treatment. Thymidine monophosphate kinase (TMPK) lies at the point where the salvage and de novo synthetic pathways meet in nucleotide...

journal_title：Journal of molecular modeling

authors： Kumar M,Sharma S,Srinivasan A,Singh TP,Kaur P

更新日期：2011-05-01 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：:Polymer and molecular-based electronic materials incorporating heterocycles like thiophenes and pyrroles are attractive possibilities as substitutes for semimetal materials. Heterocyclic materials are heavily studied in this regard due to the large variations in possible substrates. Herein we evaluated four different ...

journal_title：Journal of molecular modeling

authors： Wild S,Tice N

更新日期：2021-01-31 00:00:00

abstract：:Through comparison with ab initio reference data, we have evaluated the performance of various density functionals for describing pi-pi interactions as a function of the geometry between two stacked benzenes or benzene analogs, between two stacked DNA bases, and between two stacked Watson-Crick pairs. Our main purpose...

journal_title：Journal of molecular modeling

authors： Swart M,van der Wijst T,Fonseca Guerra C,Bickelhaupt FM

更新日期：2007-12-01 00:00:00

abstract：:The unusual π-halogen bond interactions are investigated between (BNN)₃⁺ and X1X2 (X1, X2 = F, Cl, Br) employing MP2 at 6-311 + G(2d) and aug-cc-pVDZ levels according to the "CP (counterpoise) corrected potential energy surface (PES)" method. The order of the π-halogen bond interactions and stabilities of the complexe...

journal_title：Journal of molecular modeling

authors： Qi HT,Ren FD,Zhang JL,Wang JY

更新日期：2011-05-01 00:00:00

abstract：:During thermal transition and variation of pH, structural properties of 35 proteins and their complexes (bound with substrate and co-factor) were analyzed in detail. During pH alteration, these proteins were shown to have substantial differences in conformations. pH conformers were analyzed in detail. Free energy and ...

journal_title：Journal of molecular modeling

authors： Bhattacharya P,Ganeshan T,Nandi S,Srivastava A,Singh P,Rehan M,Rashkush R,Subbarao N,Lynn A

更新日期：2009-09-01 00:00:00

abstract：:B-C binary monolayers and fullerenes (borafullerenes) have received considerable attention in recent years. Inspired by the newly reported B4C3 semiconducting boron carbide monolayer isovalent to graphene (Tian et al., Nanoscale, 2019, 11, 11099), we predict herein at density functional theory level a new class of bor...

journal_title：Journal of molecular modeling

authors： Yan M,Tian XX,Pei L,Ma YY,Zan WY,Mu YW,Li SD

更新日期：2020-07-07 00:00:00

abstract：:Since the human body for many reasons can adapt and become resistant to drugs, it is important to develop and validate computer aided drug design (CADD) methods that could help predict binding affinity changes that can result from these resistant enzymes. The free energy perturbation (FEP) methodology is the most accu...

journal_title：Journal of molecular modeling

authors： Reddy RN,Mutyala RR,Aparoy P,Reddanna P,Reddy MR

更新日期：2010-02-01 00:00:00

abstract：:The treatment of neuropathic pain is very complex and there are few drugs approved for this purpose. Among the studied compounds in the literature, sigma-1 receptor antagonists have shown to be promising. In order to develop QSAR studies applied to the compounds of 1-arylpyrazole derivatives, multivariate analyses hav...

journal_title：Journal of molecular modeling

authors： Oliveira AA,Lipinski CF,Pereira EB,Honorio KM,Oliveira PR,Weber KC,Romero RAF,de Sousa AG,da Silva ABF

更新日期：2017-10-02 00:00:00

abstract：:Herbicides targeting grass plastidic acetyl-CoA carboxylase (ACCase, EC 6.4.1.2) are selectively effective against graminicides. The intensive worldwide use of this herbicide family has selected for resistance genes in a number of grass weed species. Recently, the active-site W374C mutation was found to confer multi-d...

journal_title：Journal of molecular modeling

authors： Zhu XL,Yang WC,Yu NX,Yang SG,Yang GF

更新日期：2011-03-01 00:00:00

abstract：:In this article, we explore, both theoretically and experimentally, the general reactivity of alkyl hydrogeno-phenylphosphinates with alcohols. We show that alcohol molecules act exclusively as nucleophilic species, and add to alkyl hydrogeno-phenylphosphinates, leading to pentacoordinated intermediates. These interme...

journal_title：Journal of molecular modeling

authors： Javierre G,Fortrie R,Jean M,Moraleda D,Naubron JV,Fotiadu F

更新日期：2017-05-01 00:00:00

abstract：:Classification of pharmacologic activity of a chemical compound is an essential step in any drug discovery process. We develop two new atom-centered fragment descriptors (vertex indices)--one based solely on topological considerations without discriminating atom or bond types, and another based on topological and elec...

journal_title：Journal of molecular modeling

authors： Kandel DD,Raychaudhury C,Pal D

更新日期：2014-04-01 00:00:00

abstract：:Drug resistance is a very important factor contributing to the failure of current HIV therapies. The ability to understand the resistance mechanism of HIV-protease mutants may be useful in developing more effective and longer lasting treatment regimens. In this paper, we report the first computational study of the cli...

journal_title：Journal of molecular modeling

authors： Meiselbach H,Horn AH,Harrer T,Sticht H

更新日期：2007-02-01 00:00:00

abstract：:With the help of quantum chemical calculations, S(AuPH3)2, [HS(AuPH3)2]+ and their dimers have been examined by using scalar-relativistic theory. In agreement with experimental data, [HS(AuPH3)2 +]2 is a C(2h) structure. However, [S(AuPH3)2]2 is predicted to favor a D(2d) structure. Experimental structure parameters o...

journal_title：Journal of molecular modeling

authors： Fang H,Zhang XG,Wang SG

更新日期：2009-05-01 00:00:00

abstract：:The binding properties of the protein-inhibitor complex of human immunodeficiency virus type 1 (HIV-1) protease with the inhibitor TMC-126 are investigated by combining computational alanine scanning (CAS) mutagenesis with binding free-energy decomposition (BFED). The calculated results demonstrate that the flap regio...

journal_title：Journal of molecular modeling

authors： Li D,Han JG,Chen H,Li L,Zhao RN,Liu G,Duan Y

更新日期：2012-05-01 00:00:00

abstract：:The mechanism of the copper(I)-catalyzed cyclopropanation reaction for methyl diazoacetate with both (Z)- and (E)-but-2-ene stereoisomers has been studied using the 6-311++G(d,p) basis set by means of M06-2X and O3LYP functionals. According to both methods, the rate-limiting step is the formation of a copper-carbene i...

journal_title：Journal of molecular modeling

authors： Angulo B,Herrerías CI,Hormigón Z,Mayoral JA,Salvatella L

更新日期：2018-07-05 00:00:00

abstract：:This work is focused in three topical subjects: intermolecular interactions, metal ions, and aromaticity. A comprehensive MP2/6-31 + G and B3LYP/6-31 + G study of the influence of cation-π interactions on the aromatic character of phosphole was conducted. For this purpose, the structures of complexes were optimized at...

journal_title：Journal of molecular modeling

authors： Peña-Gallego A,Rodríguez-Otero J,Cabaleiro-Lago EM

更新日期：2012-02-01 00:00:00

abstract：:This paper used numerical and experimental methods to investigate the mechanical properties of amorphous NiAl alloys during the nanoindentation process. A simulation was performed using the many-body tight-binding potential method. Temperature, plastic deformation, elastic recovery, and hardness were evaluated. The ex...

journal_title：Journal of molecular modeling

authors： Wang CH,Fang TH,Cheng PC,Chiang CC,Chao KC

更新日期：2015-06-01 00:00:00

abstract：:Density functional theory and its time-dependent extension (DFT, TDDFT) were employed to establish the feasibility of using a series of 4,4-difluoro-4-bora-3a,4a-diaza-s-indacenes (BODIPYs) in photodynamic therapy. Their absorption electronic spectra, singlet-triplet energy gaps, and spin-orbit matrix elements were co...

journal_title：Journal of molecular modeling

authors： Ponte F,Mazzone G,Russo N,Sicilia E

更新日期：2018-06-29 00:00:00

abstract：:A theoretical investigation of the adsorption of CO₂ onto ZrO₂ is presented. Various cluster models were used to mimic different basic and acidic sites on the surface. The method used was the density functional theory with the generalized gradient approximation and including Grimme's empirical model in order to proper...

journal_title：Journal of molecular modeling

authors： Boulet P,Knöfel C,Kuchta B,Hornebecq V,Llewellyn PL

更新日期：2012-11-01 00:00:00

abstract：:The stability, geometry and electronic structure of the title nanoclusters were compared by using density functional theory (DFT) calculations. Their electrical property analysis showed that the relative magnitude of the HOMO-LUMO gaps (eV) that are average values from the calculated results with five different DFT fu...

journal_title：Journal of molecular modeling

authors： Beheshtian J,Bagheri Z,Kamfiroozi M,Ahmadi A

更新日期：2012-06-01 00:00:00

abstract：:Ab initio (MP2) and DFT (B3LYP) calculations, using the cc-pVTZ and aug-cc-pVTZ basis sets, have been performed to characterize some stationary points on the ground state potential energy surface of the title molecules. Several properties as, for instance, relative energies, the barriers for NO rotation around the NN ...

journal_title：Journal of molecular modeling

authors： do Monte SA,de Andrade RB,Ventura E,de Santana SR

更新日期：2012-01-01 00:00:00

abstract：:Complexes F2XO∙∙∙HCN (X = C and Si) have been studied by quantum chemical calculations at the MP2/aug-cc-pVTZ level to investigate the competition between π-hole interaction and hydrogen bond. F2XO has a dual role of a Lewis acid and base with the π-hole on the X atom and the O atom to participate in the π-hole intera...

journal_title：Journal of molecular modeling

authors： Guo X,Cao L,Li Q,Li W,Cheng J

更新日期：2014-11-01 00:00:00

abstract：:A high-throughput screen against Aurora A kinase revealed several promising submicromolar pyrimidine-aniline leads. The bioactive conformation found by docking these leads into the Aurora A ATP-binding site had a semicircular shape. Macrocycle formation was proposed to achieve novelty and selectivity via ring-closing ...

journal_title：Journal of molecular modeling

authors： Poulsen A,William A,Blanchard S,Nagaraj H,Williams M,Wang H,Lee A,Sun E,Teo EL,Tan E,Goh KC,Dymock B

更新日期：2013-01-01 00:00:00

abstract：:We report results of numerical simulations of complex fluids, using a combination of discrete-particle methods. Our molecular modeling repertoire comprises three simulation techniques: molecular dynamics (MD), dissipative particle dynamics (DPD), and the fluid particle model (FPM). This type of model can depict multi-...

journal_title：Journal of molecular modeling

authors： Dzwinel W,Yuen DA,Boryczko K

更新日期：2002-01-01 00:00:00

abstract：:Functionalized carbon nanotubes (CNTs) can be used for improving the mechanical properties and load transfer in nanocomposites. In this research, the buckling behavior of perfect and defective cross-linked functionalized CNTs with polyethylene (PE) chains is studied employing molecular dynamics (MD) simulations. Two d...

journal_title：Journal of molecular modeling

authors： Ajori S,Ansari R,Parsapour H

更新日期：2016-12-01 00:00:00

abstract：:A density functional theory augmented by the long-range corrected hybrid density functional ωB97XD and 6-31G(d,p) basis set has been applied to generate sandwich structures consist of nanocomposites between graphene oxide and polyvinyl alcohol. We predicted the interaction energies and discuss the contribution of elec...

journal_title：Journal of molecular modeling

authors： Gorb L,Ilchenko M,Leszczynski J

更新日期：2020-06-25 00:00:00

abstract：:The mechanism and kinetics of 2,2,3,3,3-pentafluoropropanol (CF₃CF₂CH₂OH) reaction with Chlorine atom (Cl) is investigated in this work. Two hydrogen abstraction channels of the title reaction are identified. The geometries of all the stationary points in the potential energy surface are obtained at the BHandHLYP/6-31...

journal_title：Journal of molecular modeling

authors： Yu AY,Zhang HX

更新日期：2013-10-01 00:00:00

abstract：:Ionic liquids (ILs) have been extensively studied and are considered green solvents capable of replacing traditional organic solvents. In this study, seven 1,2,3-triazolium derivative ILs have been synthesized. In order to study the effect of the cation nature on the ILs cytotoxicity, their structures were first ident...

journal_title：Journal of molecular modeling

authors： Glanzmann N,Carmo AML,Antinarelli LMR,Coimbra ES,Costa LAS,da Silva AD

更新日期：2018-06-14 00:00:00