Adsorption into the MFI zeolite of aromatic molecule of biological relevance. Investigations by Monte Carlo simulations.

abstract：:The structural parameters, Raman/IR spectra, and vibrational and thermodynamic properties of α-RDX and γ-RDX were investigated by performing first-principles calculations using the CASTEP program. The obtained structural parameters and vibrational frequencies of the internal modes of α-RDX are consistent with previous...

journal_title：Journal of molecular modeling

authors： Zhu SH,Qin H,Zeng W,Cai YM,Jin XY,Wang YH,Liu FS,Tang B,Liu QJ

更新日期：2019-06-07 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：: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：: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：:Remarkable advances have been made in the drug therapy of tuberculosis. However much remains to be learned about the molecular and structural basis of drug resistance in Mycobacterium tuberculosis. It is known that, activation of Isoniazid (INH) is mediated by Mycobacterium tuberculosis catalase-peroxidase (MtBKatG) a...

journal_title：Journal of molecular modeling

authors： Purohit R,Rajendran V,Sethumadhavan R

更新日期：2011-04-01 00:00:00

abstract：:The complexes formed between TX3-ZX2 (T = C, Si, Ge; Z = P, As, Sb; X = F, Cl) and NH3 were studied at the MP2/aug-cc-pVTZ(PP) level. For each TX3-ZX2, two types of complex were obtained. For CX3-ZX2, NH3 is inclined to approach the σ-hole on the Z atom, forming a pnicogen bond. For TX3-ZX2 (T = Si and Ge), however, t...

journal_title：Journal of molecular modeling

authors： Li Y,Xu Z

更新日期：2018-08-20 00:00:00

abstract：:We have used density-functional theory to investigate the neighboring-group stabilization of iodine, arsenic, and phosphorus-centered oxyanion moieties in species such as deprotonated 2-iodoxybenzoic acid (IBX) and its analogs. The magnitudes of different stabilizing effects and further candidates for analogous stabil...

journal_title：Journal of molecular modeling

authors： O'Hair RA,Williams CM,Clark T

更新日期：2010-03-01 00:00:00

abstract：:Computational methods are rapidly gaining importance in the field of structural biology, mostly due to the explosive progress in genome sequencing projects and the large disparity between the number of sequences and the number of structures. There has been an exponential growth in the number of available protein seque...

journal_title：Journal of molecular modeling

authors： Saraswathi S,Fernández-Martínez JL,Kolinski A,Jernigan RL,Kloczkowski A

更新日期：2012-09-01 00:00:00

abstract：:The design of stable and inexpensive artificial enzymes with potent catalytic activity is a growing field in peptide science. The first step in this design process is to understand the key factors that can affect the conformational preference of an enzyme and correlate them with its catalytic activity. In this work, m...

journal_title：Journal of molecular modeling

authors： Honarparvar B,Skelton AA

更新日期：2015-04-01 00:00:00

abstract：:In this work, the molecular modeling method was performed to study adsorption interaction between PAMAM molecules of different generations and silicic acid molecules, and the inhibition effect on silica scale were discussed. The results show that adsorption energies of PAMAM molecule of generation 1.0 with amine-termi...

journal_title：Journal of molecular modeling

authors： Chen C,Bai N,Zhang Y,Jiao L,Xia M,Chen G

更新日期：2017-01-01 00:00:00

abstract：:There is evidence that Tetracyclines are potentially useful drugs to treat prion disease, the fatal neurodegenerative disease in which cellular prion proteins change in conformation to become a disease-specific species (PrP(Sc)). Based on an in vitro anti-fibrillogenesis test, and using the peptide PrP106-126 in the p...

journal_title：Journal of molecular modeling

authors： Cosentino U,Pitea D,Moro G,Saracino GA,Caria P,Varì RM,Colombo L,Forloni G,Tagliavini F,Salmona M

更新日期：2008-10-01 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：:The structures of non-ionic [Ag(Tu)(CN)] (1) and ionic [Ag(Dmtu)2]+[Ag(CN)2]- (2) and [Ag(Imt)2]+[Ag(CN)2]- (3) silver(I) complexes, where Tu = thiourea, Dmtu = N,N'-dimethylthiourea and Imt = imidazoline-2-thione), were modeled by periodic DFT/PAW-PBE calculations; results were in good agreement with experiments. The...

journal_title：Journal of molecular modeling

authors： Ahmad S,Georgieva I,Hanif M,Monim-Ul-Mehboob M,Munir S,Sohail A,Isab AA

更新日期：2019-03-08 00:00:00

abstract：:A mechanical molecular rotation model for liquid crystal (LC) systems is employed to evaluate phase transition temperature of fluorinated phenylbicyclohexane isomeric LC compounds. Results show that when a fluorine atom is substituted along the molecular long axis, an LC molecule acquires high rotational speed and its...

journal_title：Journal of molecular modeling

authors： Ma H,Li ZX,Shi DH,Liu YF

更新日期：2008-11-01 00:00:00

abstract：:We studied the structure and dynamics of star-shaped polymers by means of coarse-grained molecular dynamics simulations and analysis of structural transitions of semi-flexible macromolecules confined in nano-channels. The conformation of star arms in narrow channels is given by the channel width, arm flexibility and n...

journal_title：Journal of molecular modeling

authors： Račko D,Cifra P

更新日期：2015-07-01 00:00:00

abstract：:The geometries of three isomers of the C2H4O...2HF tri-molecular heterocyclic hydrogen-bonded complex were examined through B3LYP/aug-cc-pVDZ calculations. Analysis of structural parameters, determination of CHELPG (charge electrostatic potential grid) intermolecular charge transfer, interpretation of infrared stretch...

journal_title：Journal of molecular modeling

authors： de Oliveira BG,Araújo RC,Chagas FF,Carvalho AB,Ramos MN

更新日期：2008-10-01 00:00:00

abstract：:Periplasmic binding proteins are the initial receptors for the transport of various substrates over the inner membrane of gram-negative bacteria. The binding proteins are composed of two domains, and the substrate is entrapped between these domains. For several of the binding proteins it has been established that a cl...

journal_title：Journal of molecular modeling

authors： Siuda I,Thøgersen L

更新日期：2013-11-01 00:00:00

abstract：:In the present work, we applied density functional theory and temperature-dependent Gibbs free energy calculations to wurtzoid structures to explain the sensitivity of ZnO nanocrystals towards chlorine molecules. In agreement with experimental findings, our results revealed that chlorine sensing under ambient conditio...

journal_title：Journal of molecular modeling

authors： Abdulsattar MA

更新日期：2017-04-01 00:00:00

abstract：:D222G mutation of the hemagglutinin (HA) is of special interest because of its close association with the enhanced virulence of 2009 pandemic influenza A (H1N1) virus through the increased binding affinity to α2,3-linked sialylated glycan receptors. However, there is still a lack of detailed understanding about the mo...

journal_title：Journal of molecular modeling

authors： Pan D,Xue W,Wang X,Guo J,Liu H,Yao X

更新日期：2012-09-01 00:00:00

abstract：:The structures and intramolecular interactions of complexes (FeCNT-CO, FeCNT-NO, NiCNT-CO, and NiCNT-NO) formed by the Fe or Ni doped single-wall carbon nanotube (FeCNT or NiCNT) and gas CO or NO were studied using density functional theory, quantum theory of atom in molecule (QTAIM), and natural bond orbital methods....

journal_title：Journal of molecular modeling

authors： Zhang X,Gong X

更新日期：2015-09-01 00:00:00

abstract：:Nowadays, scientists are trying to develop low-cost fullerene free acceptors for small organic photovoltaic cells in order to overcome the limitations of fullerene derivatives. Current research work deals with theoretical study on three non-fullerene acceptors based on indaceno, dithiophene core, and thiophene bridge ...

journal_title：Journal of molecular modeling

authors： Ajmal M,Ali U,Javed A,Tariq A,Arif Z,Iqbal J,Shoaib M,Ahmed T

更新日期：2019-09-11 00:00:00

abstract：:Modulation of γ-aminobutyric acid (GABA) levels has been required in various disorders. GABA itself cannot be directly introduced into central nervous system (CNS) because of the blood brain barrier; inhibition of GABA aminotransferase (GABA-AT), which degrades GABA in CNS, has been the target for the modulation of GA...

journal_title：Journal of molecular modeling

authors： Park JY,Lee Y,Lee HJ,Kwon YS,Chun W

更新日期：2020-08-11 00:00:00

abstract：:The pathogen Legionella longbeachae is a causative agent of legionellosis. The antibiotic resistance is the major problem of this modern world. Thus, selective pressure warrants the need for identification of newer drug target. In current study, subtractive proteomics approach screen out SIS (sugar isomerase) domain p...

journal_title：Journal of molecular modeling

authors： Ahmad F,Shabaz Z,Azam SS

更新日期：2020-08-03 00:00:00

abstract：:Density functional theory investigations at the DFT-B3LYP/6-311++G** theoretical level employed to determine the tautomerism, substituent effects of 4-substituted 4-amino-5-methyl-2,4-dihydro-3H-1,2,4-triazole-3-thione, and its derivatives (4-R-H, 4-R-CH3, 4-R-F, 4-R-NO2) in the selected solvent (acetone, acetonitrile...

journal_title：Journal of molecular modeling

authors： Shiroudi A,Safaei Z,Kazeminejad Z,Repo E,Pourshamsian K

更新日期：2020-02-13 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：:We present a theoretical study of the adsorption of 2,2,6,6-tetramethylpiperidine-1-oxoammonium cation (TEMPO) onto the TiO₂(110) surface rutile, investigating its bonding nature, electron properties and structural stability. Based on the results obtained with the PBE0/def2-SVP method, natural bond orbital (NBO) analy...

journal_title：Journal of molecular modeling

authors： Nieto-López I,Hernández-García L,Bonilla-Cruz J,Sanchez M

更新日期：2014-03-01 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：:The internal rotation in ammonia borane (AB) was studied on the basis of natural orbitals for chemical valence (NOCV) and eigenvectors for Pauli repulsion (NOPR). We found that the total hyperconjugation stabilization (ca. 5 kcal mol(-1)), based on the charge transfer from the occupied σ (B-H) orbitals into the empty ...

journal_title：Journal of molecular modeling

authors： Parafiniuk M,Mitoraj MP

更新日期：2014-06-01 00:00:00

abstract：:Theoretical adiabatic electron affinities are often considered inaccurate because they are referenced to only a single value. Ground state electron affinities for all the main group elements and homonuclear diatomics were identified recently using the normalized binding energy of the hydrogen atom: [0.75420375(3)/2 = ...

journal_title：Journal of molecular modeling

authors： Chen ES,Keith H,Lim T,Pham D,Rosenthal R,Herder C,Pai S,Flores RA,Chen EC

更新日期：2015-04-01 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