A comparative study of the vibrational and thermodynamic properties of α-RDX and γ-RDX under ambient conditions.

abstract：:The incidence of tuberculosis infections that are resistant to conventional drug therapy has risen steadily in the last decade. Several of the quinolone antibacterials have been examined as inhibitors of M. tuberculosis infection as well as other mycobacterial infections. However, not much has been done to examine spe...

journal_title：Journal of molecular modeling

authors： Bagchi MC,Mills D,Basak SC

更新日期：2007-01-01 00:00:00

abstract：:The mechanism of the thermal rearrangement of substituted N-acyl-2,2-dimethylaziridines 1 has been studied using quantum chemistry methods. Geometries of reactants, transition states and products have been optimized at the B3LYP/6-311++G(2d,2p) level. Relative energies for various stationary points have been determine...

journal_title：Journal of molecular modeling

authors： Arfaoui Y,Efrit ML,Besbes N

更新日期：2013-10-01 00:00:00

abstract：:The influences of the temperature and the BDNPA/BDNPF (A3) content on the mechanical properties of and the binding energies between hexanitrohexaazaisowurtzitane (HNIW) and cellulose acetate butyrate (CAB)/A3 were studied via molecular dynamics simulations. The morphology of HNIW in acetone was simulated using an atta...

journal_title：Journal of molecular modeling

authors： Lan G,Jin S,Wang D,Li J,Lu Z,Jing B,Li L

更新日期：2018-07-02 00:00:00

abstract：:Iridium (III) 2-phenylpyridine (ppy) complexes with two suitable monodentate L ligands [Ir(ppy)₂(L)₂]⁺ (ppy = 2-phenylpyridine, py = pyridine, L = 4-pyCN 1, 4-pyCHO 2, 4-pyCl 3, py 4, 4-pyNH₂ 5) were studied by density functional theory (DFT) and time-dependent DFT methods. The influences of ligands L on the electroni...

journal_title：Journal of molecular modeling

authors： Zhang TT,Qi XX,Jia J,Wu HS

更新日期：2012-10-01 00:00:00

abstract：:The CO and O2 adsorption as well as CO oxidation on cationic, neutral, and anionic AuM dimers (M = Pd, Ag) are studied by density functional calculations. Our results show that CO and O2 are adsorbed more stably on AuPd dimers than on AuAg dimers with corresponding charge state. O2 is favorable to be adsorbed on Pd at...

journal_title：Journal of molecular modeling

authors： Chen X,Lu RF,Kan EJ,Liu YZ,Xiao CY,Deng KM

更新日期：2014-06-01 00:00:00

abstract：:Ergothioneine (2-mercaptohistidine trimethylbetaine) is a very stable natural compound largely present in cells and tissues of plants and mammals. The biological role of ET is still incompletely understood but its antioxidant properties are well assessed experimentally. However, no theoretical study had been performed...

journal_title：Journal of molecular modeling

authors： Lespade L

更新日期：2019-10-26 00:00:00

abstract：:The treatment of bacterial infections is currently threatened by the emergence of pathogenic bacteria producing β-lactamase, which catalyzes the hydrolysis of β-lactams. Although the hydrolysis of the substrate nitrocefin by a metallo-β-lactamase, namely β-lactamase N1 from USA300 (a typical methicillin-resistant Stap...

journal_title：Journal of molecular modeling

authors： Yu Y,Wang X,Gao Y,Yang Y,Sun L,Wang G,Deng X,Niu X

更新日期：2019-04-13 00:00:00

abstract：:The hydrogen bonding interactions between noradrenaline (NA) and DMSO were studied with density functional theory (DFT) regarding their geometries, energies, vibrational frequencies, and topological features of the electron density. The quantum theory of atoms in molecules (QTAIM) and the natural bond orbital (NBO) an...

journal_title：Journal of molecular modeling

authors： Huang Z,Dai Y,Yu L,Wang H

更新日期：2011-10-01 00:00:00

abstract：:Fruit softening is associated to cell wall modifications produced by a set of hydrolytic enzymes and proteins. Expansins are proteins with no catalytic activity, which have been associated with several processes during plant growth and development. A role for expansins has been proposed during softening of fruits, and...

journal_title：Journal of molecular modeling

authors： Gaete-Eastman C,Morales-Quintana L,Herrera R,Moya-León MA

更新日期：2015-05-01 00:00:00

abstract：:An accurate comparison of the interaction of furan, pyrrole, and thiophene with different gaseous analytes is vital not only for understanding the sensing mechanism of corresponding polymers but also for rational design of new materials. In the present study, DFT calculations at (M05-2X/Aug-cc-PVDZ) have been performe...

journal_title：Journal of molecular modeling

authors： Sajid H,Mahmood T,Ayub K

更新日期：2017-09-26 00:00:00

abstract：:Mechanical properties of graphene- and carbon nanotube-reinforced Araldite LY 5052/Aradur HY 5052 epoxy resins were investigated by molecular dynamics simulations. The COMPASS II force field was implemented in the simulations. Mechanical properties of the reinforced araldite/aradur resin epoxy system with CNT reveal t...

journal_title：Journal of molecular modeling

authors： Faragi S,Hamedani A,Alahyarizadeh G,Minuchehr A,Aghaie M,Arab B

更新日期：2019-06-15 00:00:00

abstract：:The generation of the highly reactive ylide in thiamin diphosphate catalysis is analyzed in terms of the nucleophilicity of key atoms, by means of density functional calculations at X3LYP/6-31++G(d,p) level of theory. The Fukui functions of all tautomeric/ionization forms are calculated in order to assess their reacti...

journal_title：Journal of molecular modeling

authors： Jaña GA,Delgado EJ

更新日期：2013-09-01 00:00:00

abstract：:In this work, the poly(ethylene oxide) bulk as one example has been iteratively heated and cooled back using MD simulations to examine the effects of thermal history on the resulting Tg. It is demonstrated that, after the system is equilibrated once at the high temperatures, the simulated Tg does not exhibit a systema...

journal_title：Journal of molecular modeling

authors： Wu C

更新日期：2017-08-22 00:00:00

abstract：:In order to introduce effectively the external electric fields into the explosive systems, the change trends of the strengths of trigger linkages, nitro group charges, and explosive sensitivities of 1,4-dinitroimidazole-N-oxide (1,4-DNIO) were investigated in the external electric fields at the B3LYP/6-311++G(2d,p) an...

journal_title：Journal of molecular modeling

authors： Wang BG,Ren FD,Wang Y

更新日期：2019-11-28 00:00:00

abstract：:The addition of C2 to HCN is of relevant interest in astrochemistry. We studied the pathways of this addition to produce CCCN and estimated its reaction rate using the Master Equation in the circumstellar environment. From the results of this study, it was possible to show that a different pathway in the Surface Poten...

journal_title：Journal of molecular modeling

authors： da Silva WB,Albernaz AF,Barreto PR,Correa E

更新日期：2017-04-01 00:00:00

abstract：:The nature of non-covalent interactions in self-assembling systems is a topic that has aroused great attention in literature. In this field, the 1,3,5-triazinane-2,4,6-trione or cyanuric acid (CA) is one of the most widely used molecules to formulate self-assembled materials or monolayers. In the present work, a varie...

journal_title：Journal of molecular modeling

authors： Petelski AN,Peruchena NM,Pamies SC,Sosa GL

更新日期：2017-08-14 00:00:00

abstract：:Aluminum enriched 1, 1-diamino-2, 2-dinitroethylene (Al-FOX-7) crystal, as a new high energy density material (HEDM), was designed and investigated using grand canonical monte carlo (GCMC), NVT+NPT-molecular dynamics (MD) and GGA-PBE-density functional theory (DFT) methods. The results show that, Al atoms break out H-...

journal_title：Journal of molecular modeling

authors： Bian L,Shu Y,Xu J,Wang L

更新日期：2013-01-01 00:00:00

abstract：:Some recent papers clearly indicate that the cytoplasmic domain of KcsA plays a role in pH sensing. We have performed, for the first time, a targeted molecular dynamics (TMD) simulation of the opening of full-length KcsA at pH 4 and pH 7, with a special interest for the cytoplasmic domain. Association energy calculati...

journal_title：Journal of molecular modeling

authors： Li Y,Barbault F,Delamar M,Zhang R,Hu R

更新日期：2013-04-01 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：: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：: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：:The structure and electronic properties of the complexes formed by the interaction of imidazole and pyrazole with different BeXH(BeX2) (X = H, Me, F, Cl) derivatives have been investigated via B3LYP/6-311+G(3df,2p)//B3LYP/6-31+G(d,p) calculations. The formation of these azole:BeXH(BeX2) complexes is accompanied by a d...

journal_title：Journal of molecular modeling

authors： Mó O,Yáñez M,Alkorta I,Elguero J

更新日期：2013-10-01 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 binding of the reductase inhibitor drug fluvastatin, hydroxy-3-methylglutaryl coenzyme A, with the hydrophilic ι- or λ-carrageenan polymers, serving as potential controllers of the drug's release rate, have been studied at the density functional level of theory with the B3LYP exchange correlation functional. Three...

journal_title：Journal of molecular modeling

authors： Papadopoulos AG,Sigalas MP

更新日期：2011-07-01 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：:We report a DFT, TDDFT and DFTB investigation of the performance of two donor-π-acceptor (D-π-A)-type organic dyes bearing different electron-withdrawing groups (EWG) for dye-sensitized solar cells (DSSCs) to evaluate which EWG is better for an acrylic acid acceptor, i.e., Cyano (-CN) or o-nitrophenyl (o-NO2-Ph). A se...

journal_title：Journal of molecular modeling

authors： Zhang J,Kan YH,Li HB,Geng Y,Wu Y,Duan YA,Su ZM

更新日期：2013-04-01 00:00:00

abstract：:Three potential anticancer agents {trans-[PtCl(2)(NH(3))(thiazole)], cis-[PtCl(2)(NH(3))(piperidine)], and PtCl(2)(NH(3))(cyclohexylamine) (JM118)} were explored and compared with cisplatin and the inactive [PtCl(dien)](+) complex. Basic electronic properties, bonding and stabilization energies were determined, and th...

journal_title：Journal of molecular modeling

authors： Bradác O,Zimmermann T,Burda JV

更新日期：2008-08-01 00:00:00

abstract：:Human gonadotropin hormone receptor, a G-protein coupled receptor, is the target of many medications used in fertility disorders. Obtaining more structural information about the receptor could be useful in many studies related to drug design. In this study, the structure of human gonadotropin receptor was subjected to...

journal_title：Journal of molecular modeling

authors： Sakhteman A,Khoddami M,Negahdaripour M,Mehdizadeh A,Tatar M,Ghasemi Y

更新日期：2016-09-01 00:00:00

abstract：:Studying the electrochemical characteristics is an important step for determining interactions between molecules and the chemical environment. Moreover, the electrochemical evaluation of dyes is highly needed to establish the behavior of electro-active chemical species inside dye-sensitized solar cells (DSSCs). Four c...

journal_title：Journal of molecular modeling

authors： Ortega E,Bernède JC,Ramírez AMR,Louarn G,Díaz FR,Cattin L,Del Valle MA

更新日期：2019-02-27 00:00:00

abstract：:In quantum chemical calculations, there are two facts of particular relevance: the position-dependent mass Schrödinger equation (PDMSE) and the exponential-type potentials used in the theoretical study of vibrational properties for diatomic molecules. Accordingly, in this work, the treatment of exactly solvable PDMSE ...

journal_title：Journal of molecular modeling

authors： Ovando G,Peña JJ,Morales J,López-Bonilla J

更新日期：2019-08-31 00:00:00