Abstract:
:The structural characteristics involving thermal stabilities of liquid nitromethane (NM)—one of the simplest energetic materials—confined within a graphene (GRA) bilayer were investigated by means of all-atom molecular dynamics simulations and density functional theory calculations. The results show that ordered and layered structures are formed at the confinement of the GRA bilayer induced by the van der Waals attractions of NM with GRA and the dipole-dipole interactions of NM, which is strongly dependent on the confinement size, i.e., the GRA bilayer distance. These unique intermolecular arrangements and preferred orientations of confined NM lead to higher stabilities than bulk NM revealed by bond dissociation energy calculations.
journal_name
J Mol Modeljournal_title
Journal of molecular modelingauthors
Liu Y,Yu T,Lai W,Kang Y,Ge Zdoi
10.1007/s00894-015-2588-2subject
Has Abstractpub_date
2015-03-01 00:00:00pages
40issue
3eissn
1610-2940issn
0948-5023journal_volume
21pub_type
杂志文章abstract::Quantum chemical calculations are performed to study the interplay between halogen⋯nitrogen and halogen⋯carbene interactions in NCX⋯NCX⋯CH2 complexes, where X = F, Cl, Br and I. Molecular geometries and interaction energies of dyads and triads are investigated at the MP2/aug-cc-pVTZ level of theory. It is found that t...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-013-1983-9
更新日期:2013-11-01 00:00:00
abstract::The molecular geometry, vibrational frequencies, gauge including atomic orbital (GIAO) (1)H and (13)C chemical shift values and several thermodynamic parameters of 5-(2-Hydroxyphenyl)-4-(p-tolyl)-2,4-dihydro-1,2,4-triazole-3-thione in the ground state have been calculated by using the Hartree-Fock (HF) and density fun...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-008-0324-x
更新日期:2008-09-01 00:00:00
abstract::Hepatic fibrosis is a common complication of the infection by the parasite, Clonorchis sinensis. There is a high incidence of this disease in the Asian countries with an increased risk of conversion to cancer. A secretory phospholipase A(2) (PLA(2)) enzyme from the parasite is implicated in the pathology. This is an a...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-011-1333-8
更新日期:2012-07-01 00:00:00
abstract::The aim of this study was to perform an in silico analysis of the interaction of the human beta(2) adrenergic receptor with Galpha(s). In a first step, a systematic surface-interaction-scan between the inactive or active human beta(2) adrenergic receptor and Galpha(s) was performed in order to gain knowledge about ene...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-010-0646-3
更新日期:2010-08-01 00:00:00
abstract::In this work, we investigate the ground- and excited-state structures as well as the optical properties of a series of five formazanate dyes using state-of-the-art density-based and wavefunction-based methods. The present work is the first to evaluate the properties of formazanate-BF2 dyes with wavefunction-correlated...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-016-3126-6
更新日期:2016-11-01 00:00:00
abstract::Extremely extensive calculations of potential energy surfaces for the parallel-displaced configuration of pyridine dimer systems have been carried out using a dispersion-corrected density functional. Instead of focusing on stationary geometries these calculations provide much deeper insight into the "landscape" of the...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-017-3496-4
更新日期:2017-11-09 00:00:00
abstract::The dopamine (DAT), serotontin (SERT) and noradrenalin (NET) transporters are molecular targets for different classes of psychotropic drugs. The crystal structure of Aquifex aeolicus LeuT(Aa) was used as a template for molecular modeling of DAT, SERT and NET, and two putative drug binding sites (pocket 1 and 2) in eac...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-009-0478-1
更新日期:2009-10-01 00:00:00
abstract::Based on the unique advantages of terahertz (THz) spectrum on the detection of energetic cocrystals, the low-temperature dependent THz spectra of CL-20/TNT cocrystal were investigated by using molecular dynamics (MD) simulations from 5 to 296 K, as well as three different crystal faces, (001), (120), and (010). When t...
journal_title:Journal of molecular modeling
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更新日期:2020-01-11 00:00:00
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journal_title:Journal of molecular modeling
pub_type: 杂志文章
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更新日期:2017-04-01 00:00:00
abstract::Quantum chemical calculations of the structures and stabilities of the title series at the CCSD(T) theoretical level are performed. Laplacian, electron density deformation, electron localization function and reduced density gradient analysis are investigated to explore the nature of the interaction. The results show t...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-011-1138-9
更新日期:2012-03-01 00:00:00
abstract::The adsorption of the molecules CO, CO2, and H2 on several ceria and zinc oxide surfaces was studied by means of periodical DFT calculations and compared with infrared frequency data. The stable CeO2(111), CeO2(331), and ZnO(0001) perfect faces were the first substrates considered. Afterwards, the same surfaces with o...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-014-2270-0
更新日期:2014-06-01 00:00:00
abstract::The title compound, C(6)H(4)N(4)S(2)·C(3)H(7)NO, crystallizes in the monoclinic space group C 2/c with a = 26.673(5), b = 5.397(1), c = 16.522(3) Å, β = 95.49(3)°, Z = 8, R = 0.0461 for 1891 reflections with I > 2σ(I) and 174 parameters (4 restraints). Single pteridine-2,4(1 H,3 H)-dithione and dimethylformamide molec...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-011-1109-1
更新日期:2012-02-01 00:00:00
abstract::PB1-F2 is a recently described influenza A viral protein that induces apoptosis by binding with two mitochondrial membrane proteins, i.e. VDAC1 (outer membrane) and ANT3 (inner membrane). Knowledge of this binding mechanism could provide insights that would aid in the design of novel inhibitors against this protein. T...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-009-0555-5
更新日期:2010-03-01 00:00:00
abstract::Ab initio computations are performed to study the structural, elastic, electronic, and vibrational characteristics of the cubic antiperovskite compound PbNCa3 under pressure up to 50 GPa. By using the generalized gradient approximation (GGA), the equilibrium structural parameters, energy band structure, density of sta...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-020-04656-2
更新日期:2021-01-03 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
pub_type: 杂志文章
doi:10.1007/s00894-013-1991-9
更新日期:2013-11-01 00:00:00
abstract::The contribution of folic acid (FA)-tryptophan interactions to FA-protein association was investigated in the context of using FA as a drug carrier in protein delivery systems. Bovine serum albumin (BSA) and indolicidin were used as model proteins in the study. The FA-BSA complex was characterized by using the Bradfor...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-015-2847-2
更新日期:2015-12-01 00:00:00
abstract::The heme-AB binding energies (AB = CO, O2) in a wild-type myoglobin (Mb) and two mutants (H64L, V68N) of Mb have been investigated in detail with both DFT and dispersion-corrected DFT methods, where H64L and V68N represent two different, opposite situations. Several dispersion correction approaches were tested in the ...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-013-1864-2
更新日期:2013-08-01 00:00:00
abstract::Fifteen KSP inhibitors were docked into the receptor and the binding mode was analyzed for the first time. It was considered that in addition to the main binding pocket all the inhibitors merged in, there exists a cooperative minor binding pocket, which could be explored for significantly increased binding affinity. I...
journal_title:Journal of molecular modeling
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更新日期:2007-09-01 00:00:00
abstract::Beta-lactamase (ampC) in general causes the onset of antibiotic resistance in pathogenic bacteria against the β-lactam antibiotics. Morganella morganii which belongs to the Proteae tribe of the Enterobacteriaceae family is a Gram-negative bacillus. Gram-negative bacteria are the key problematic agents among the human ...
journal_title:Journal of molecular modeling
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更新日期:2020-07-07 00:00:00
abstract::Clindamycin, a lincosamide antibiotic, binds to 23S ribosomal RNA and inhibits protein synthesis. The A2058G mutation in 23S RNA results in bacterial resistance to clindamycin. To understand the influence of this mutation on short-range interactions of clindamycin with 23S RNA, we carried out full-atom molecular dynam...
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更新日期:2018-07-03 00:00:00
abstract::Reactions of lithium halide (LiX, X = F, Cl, Br and I) and methyl halide (CH₃X, X = F, Cl, Br and I) have been investigated at the B3LYP/6-31G(d) level of theory using the microhydration model. Beginning with hydrated lithium ion, four or two water molecules have been conveniently introduced to these aqueous-phase hal...
journal_title:Journal of molecular modeling
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更新日期:2010-12-01 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
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更新日期:2019-08-16 00:00:00
abstract::A theoretical study of the sulfur cumulenes SCnS (n = 3-8), CnS ( n = 1-8) and of their protonated forms (SCnS)H(+) and (CnS)H(+) that might exist in the interstellar environment, has been carried out by means of the standard B3LYP/6-311G** method. The geometries and relative energies of singlet and triplet states acc...
journal_title:Journal of molecular modeling
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更新日期:2014-07-01 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
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更新日期:2017-10-02 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
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更新日期:2012-01-01 00:00:00
abstract::New ionic liquids (ILs) involving increasing numbers of organic and inorganic ions are continuously being reported. We recently developed a new force field; in the present work, we applied that force field to investigate the structural properties of a few novel imidazolium-based ILs in aqueous mixtures via molecular d...
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更新日期:2015-09-01 00:00:00
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journal_title:Journal of molecular modeling
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更新日期:2010-03-01 00:00:00
abstract::A computational chemistry investigation was undertaken to shed light on the facilitatory role played by Fe3+ and Al3+ cations in the adsorption of anionic As(V) species by humic acids through the formation of so-called cationic bridges. Geometric and energetic parameters were obtained using density functional theory a...
journal_title:Journal of molecular modeling
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更新日期:2017-03-01 00:00:00
abstract::In order to understand the mechanisms of ligand binding and the interaction between the ligand and the bovine phenol sulfotransferase, (bSULT1A1, EC 2.8.2.1) a three-dimensional (3D) model of the bSULT1A1 is generated based on the crystal structure of the estrogen sulfotransferase (PDB code 1AQU) by using the InsightI...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-004-0225-6
更新日期:2005-03-01 00:00:00
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journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-019-4148-7
更新日期:2019-08-26 00:00:00