Open carbon frameworks - a search for optimal geometry for hydrogen storage.

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 this work, the structural, electronic, and optical features of quinoline derivatives were carried out by experiment and density functional theory (DFT). Our results show that a change in the substitution position of methyl group (CH3) gives rise to a decrease in the bandgap of quinoline derivatives from 2.75 to 2.5...

journal_title：Journal of molecular modeling

authors： Kurban M,Sertbakan TR,Gündüz B

更新日期：2020-05-11 00:00:00

abstract：:The interaction of a model Lys flanked α-helical peptides K2-X24-K2, (X = A,I,L,L+A,V) with lipid bilayers composed of dimyristoylphosphatidylcholine (DMPC) and dipalmitoylphosphatidylcholine (DPPC) both, in a gel and in a liquid-crystalline state, has been studied by molecular dynamics simulations. It has been shown ...

journal_title：Journal of molecular modeling

authors： Melicherčík M,Holúbeková A,Hianik T,Urban J

更新日期：2013-11-01 00:00:00

abstract：:In this work we report the atomic partial charges evaluated on dodecyltrimethylammonium ion. The values obtained from 17 quantum methods [CHELP, CHELPG, MK, NPA at (HF, LDA, PBE, B3LYP)//6-31G++(d,p) level and APT at B3LYP//6-31G++(d,p)] on the molecule optimised at B3LYP/6-31G++(d,p) level were compared to two semiem...

journal_title：Journal of molecular modeling

authors： Minisini B,Chavand S,Barthelery R,Tsobnang F

更新日期：2010-06-01 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：:Nanosecond molecular dynamics using the Ewald summation method have been performed to elucidate the structural and energetic role of the closing base pair in loop-loop RNA duplexes neutralized by Mg2+ counterions in aqueous phases. Mismatches GA, CU and Watson-Crick GC base pairs have been considered for closing the l...

journal_title：Journal of molecular modeling

authors： Golebiowski J,Antonczak S,Fernandez-Carmona J,Condom R,Cabrol-Bass D

更新日期：2004-12-01 00:00:00

abstract：:The intercalation process and the structure of montmorillonite intercalated with [rhodamine B]+ cations have been investigated using molecular modeling (molecular mechanics and molecular dynamics simulations), X-ray powder diffraction and IR spectroscopy. The structure of the intercalate depends strongly on the concen...

journal_title：Journal of molecular modeling

authors： Pospísil M,Capková P,Weissmannová H,Klika Z,Trchová M,Chmielová M,Weiss Z

更新日期：2003-02-01 00:00:00

abstract：:Ab initio and molecular simulation methods were used in calculations of the neutral individual betulin molecule, and molecular simulations were used to optimize the betulin molecule immersed in various amounts of water. Individual betulin was optimized in different force fields to find the one exhibiting best agreemen...

journal_title：Journal of molecular modeling

authors： Pospíšil M,Kovář P,Vácha R,Svoboda M

更新日期：2012-01-01 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 efficiency and high specificity of tobacco etch virus protease (TEVp) has made it widely used for cleavage of recombinant fusion proteins. However, TEVp suffers from a few intrinsic defects such as self-cleavage, poorly expressed in E. coli and less soluble. So some mutants were designed to improve it, such as S21...

journal_title：Journal of molecular modeling

authors： Wang Y,Zhu GF,Ren SY,Han YG,Luo Y,Du LF

更新日期：2013-11-01 00:00:00

abstract：:The present study deals with the decomposition of CF(3)OCF(2)O radical formed from a hydrofluoroether, CF(3)OCHF(2) (HFE-125), in the atmosphere. The study is performed using ab initio quantum mechanical methods. Two plausible pathways of decomposition of the titled species have been considered, one involving C-O bond...

journal_title：Journal of molecular modeling

authors： Singh HJ,Mishra BK

更新日期：2011-03-01 00:00:00

abstract：:In erythrocytes, actively multiplying Plasmodium falciparum parasites exhibit a unique signature of virulence associated histone modifications, thereby epigenetically regulating the expression of the majority of genes. Histone acetylation is one such modification, effectuated and maintained by the dynamic interplay of...

journal_title：Journal of molecular modeling

authors： Kumar A,Dhar SK,Subbarao N

更新日期：2018-08-14 00:00:00

abstract：:Structural-functional divergence is responsible for the preservation of highly homologous genes. Protein functions affected by mutagenesis in divergent sequences require investigation on an individual basis. In the present study, comparative homology modeling and predictive bioinformatics analysis were used to reveal ...

journal_title：Journal of molecular modeling

authors： Tokmakov AA

更新日期：2012-06-01 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：:Zeolites are a group of microporous aluminosilicate frameworks with numerous applications in, for example, catalysis and ion-exchange and sorption processes. One of the most important tools for analyzing the properties of zeolite structures is vibrational spectroscopy. However, the complexity of these structures often...

journal_title：Journal of molecular modeling

authors： Mikuła A,Król M,Koleżyński A

更新日期：2015-10-01 00:00:00

abstract：:The increasing incidence of bacterial resistance to most available antibiotics has underlined the urgent need for the discovery of novel efficacious antibacterial agents. The biosynthesis of bacterial peptidoglycan, where the MurD enzyme is involved in the intracellular phase of UDP-MurNAc-pentapeptide formation, repr...

journal_title：Journal of molecular modeling

authors： Perdih A,Bren U,Solmajer T

更新日期：2009-08-01 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：: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：:The thermally allowed electrocyclic reaction syn-cyclophanediene (CPD) to dihydropyrene (DHP) was compared with the disallowed thermal electrocyclic reaction in anti CPD through density functional theory (DFT) calculations at the B3LYP/6-31 + G(d) level. Moreover, the results were also compared with the electrocycliza...

journal_title：Journal of molecular modeling

authors： Saima B,Khan A,Nisa RU,Mahmood T,Ayub K

更新日期：2016-04-01 00:00:00

abstract：:The role of resultant gradient-information concept, reflecting the kinetic energy of electrons, in shaping the molecular electronic structure and reactivity preferences of open reactants is examined. This quantum-information descriptor combines contributions due to both the modulus (probability) and phase (current) co...

journal_title：Journal of molecular modeling

authors： Nalewajski RF

更新日期：2019-08-16 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：: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：:The nature and strength of intermolecular Se⋯N interaction between selenium-containing compounds HSeX (X = CH3, NH2, CF3, OCH3, CN, OH, NO2, Cl, F), and NH3 have been investigated at the MP2/aug-cc-pVDZ level. The Se⋯N interaction is found to be dependent on the substituent groups, which greatly affect the positive el...

journal_title：Journal of molecular modeling

authors： Zhou F,Liu R,Tang J,Li P,Cui Y,Zhang H

更新日期：2016-01-01 00:00:00

abstract：:In this work, a computational framework is proposed by utilizing molecular dynamics simulation to explore the existing relation between molecular structure and ionic conductivity of the electrolyte system [LiPF6+(EC+DMC 1:1)] consisting of a mixture of cyclic ethylene carbonate (EC) and acyclic dimethyl carbonate (DMC...

journal_title：Journal of molecular modeling

authors： Haghkhah H,Ghalami Choobar B,Amjad-Iranagh S

更新日期：2020-08-01 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：:The prediction of the series of complexes [Au(3)Cl(3)M(2)] with M = Li, Na, K, Rb and Cs, has been achieved at the ab initio level of theory. All geometries were fully optimized at the MP2 level of theory; the central Au(3) cluster is capped by chlorine atoms and the alkaline metals lie above and below the plane of th...

journal_title：Journal of molecular modeling

authors： Muñiz J,Sansores LE,Pyykkö P,Martínez A,Salcedo R

更新日期：2009-10-01 00:00:00

abstract：:Quantum chemical calculations have been performed to study the all-metal π halogen bonding in Al(4)(2-)···halohydrocarbon complexes. The result shows the existence of the all-metal π halogen bond in the complexes. There are three interaction modes (top, corner, and side) between Al(4)(2-) and halohydrocarbon. The inte...

journal_title：Journal of molecular modeling

authors： Li R,Li Q,Cheng J,Li W

更新日期：2012-06-01 00:00:00

abstract：:Cystic fibrosis (CF), the most common lethal genetic disease among Caucasians, is caused by mutations in cystic fibrosis transmembrane conductance regulator (CFTR). CFTR's main role is to transport chloride ions across epithelial cell membranes. It also regulates many cell functions. However, the exact role of CFTR in...

journal_title：Journal of molecular modeling

authors： Siwiak M,Edelman A,Zielenkiewicz P

更新日期：2012-01-01 00:00:00

abstract：:Using density functional theory (DFT) and molecular dynamics (MD), we studied the interaction of a titanium atom with a half of a C60 fullerene (i.e., C30), formed from the corannulene structure with a pentagonal base. We considered atmospheric pressure and 300 K. We found that the most stable adsorption of the titani...

journal_title：Journal of molecular modeling

authors： Canales M,Ramírez-de-Arellano JM,Magana LF

更新日期：2016-09-01 00:00:00

abstract：:Molecular-dynamics (MD) simulations of urea crystals of different shapes (cubic, rectangular prismatic, and sheet) have been performed using our previously published force field for urea. This force field has been validated by calculating values for the cohesive energy, sublimation temperature, and melting point from ...

journal_title：Journal of molecular modeling

authors： Özpınar GA,Beierlein FR,Peukert W,Zahn D,Clark T

更新日期：2012-08-01 00:00:00