Abstract：
:Carbon monoxide (CO) and oxygen (O2) catalyzed by small neutral iron oxide clusters (FeO(1-3)) was investigated at the density functional level of theory using the Becke-Perdew-Wang functional (BPW91). Three reaction pathways along with singlet, triplet and quintet states were calculated for ascertaining the presence of some spin inversion during the catalytic cycle. The catalytic cycle was found to be "two state reactivity" resulting from the crossing among the multistate energetic profiles. The Landau-Zener equation was used to calculate the thermally-averaged spin transition probabilities for the non-adiabatic surface crossing reaction. In order to predict the efficiency of catalyst the energetic span model developed by Kozuch was implemented, whereas this model is not suitable for handling the diabatic reaction, this feature we must take into consideration. To this end, a kinetic assessment is carried out with an expansion of the energetic span model, including the spin-crossing effects. This approximation enables one to measure the efficiency of catalytic cycle including spin-crossing effects by quantum mechanical computation.
journal_name
J Mol Modeljournal_title
Journal of molecular modelingauthors
Wang HJ,Wang YCdoi
10.1007/s00894-014-2301-xsubject
Has Abstractpub_date
2014-06-01 00:00:00pages
2301issue
6eissn
1610-2940issn
0948-5023journal_volume
20pub_type
杂志文章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
pub_type： 杂志文章
doi：10.1007/s00894-007-0219-2
更新日期：2007-09-01 00:00:00
abstract：:In this work a molecular modeling study was carried out based on a series of organotin(IV) derivatives which were complexed with ONO-Donor type Schiff base ligands to build up a statistical data pool for researchers. For this purpose, various properties of the selected complexes such as energies, band gaps, chemical r...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-015-2764-4
更新日期：2015-09-01 00:00:00
abstract：:The effect of terminal GLY114* deletion on the binding affinity of the PA-IIL lectin toward L: -fucose was investigated. Both experimental (isothermal titration calorimetry) and computational (molecular dynamics simulations) methods have shown that the deletion mutation decreases the L-fucose affinity. It implies that...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-009-0464-7
更新日期：2009-06-01 00:00:00
abstract：:The unsaturated trinuclear iron fluoroborylene complexes Fe3(BF)3(CO) n (n = 7, 6) have been studied using density functional theory (DFT). Relatively complicated potential energy surfaces are found with nine and eight structures within 15 kcal mol-1 of the lowest energy structures for the Fe3(BF)3(CO)7 and Fe3(BF)3(C...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-017-3301-4
更新日期：2017-04-01 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
pub_type： 杂志文章
doi：10.1007/s00894-015-2735-9
更新日期：2015-07-01 00:00:00
abstract：:There is a wide variety of ion channel types with various types of blockers, making research in this field very complicated. To reduce this complexity, it is essential to study ion channels and their blockers independently. Scorpion toxins, a major class of blockers, are charged short peptides with high affinities for...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-015-2822-y
更新日期：2015-11-01 00:00:00
abstract：:In this work molecular modeling was applied to generate homology models of the pore region of the Na(v)1.2 and Na(v)1.8 isoforms of human voltage-gated sodium channels. The models represent the channels in the resting, open, and fast-inactivated states. The transmembrane portions of the channels were based on the equi...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-005-0066-y
更新日期：2006-09-01 00:00:00
abstract：:Properties of a new class of hypothetical high-surface-area porous carbons (open carbon frameworks) have been discussed. The limits of hydrogen adsorption in these carbon porous structures have been analyzed in terms of competition between increasing surface accessible for adsorption and the lowering energy of adsorpt...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-012-1700-0
更新日期：2013-10-01 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
pub_type： 杂志文章
doi：10.1007/s00894-007-0239-y
更新日期：2007-12-01 00:00:00
abstract：:Artemisinin and some derivatives with activity against D-6 strains of Plasmodium falciparum were studied. Molecular electrostatic potential (MEP) maps were used in an attempt to identify key features of the compounds that are necessary for their activities, and then use those to propose new artemisinin derivatives. Th...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-007-0249-9
更新日期：2008-01-01 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
pub_type： 杂志文章
doi：10.1007/s00894-019-4085-5
更新日期：2019-06-15 00:00:00
abstract：:In this theoretical study we used density functional theory to calculate the molecular and crystalline structures of sodium selenite. Our structural results were compared with experimental data. From the molecular structure we determined the ionization potential, electronic affinity, and global reactivity parameters l...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-010-0766-9
更新日期：2011-04-01 00:00:00
abstract：:The double-histone fold is a rare protein fold in which two consecutive regions characterized by the typical structure of histones assemble together, thus giving a histone pseudodimer. Previously, this fold was found in a few prokaryotic histones and in the regulatory region of guanine-nucleotide exchange factors of t...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-005-0008-8
更新日期：2005-12-01 00:00:00
abstract：:Multilayer-shaped compression and slide models were employed to investigate the complex sensitive mechanisms of cocrystal explosives in response to external mechanical stimuli. Here, density functional theory (DFT) calculations implementing the generalized gradient approximation (GGA) of Perdew-Burke-Ernzerhof (PBE) w...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-016-2973-5
更新日期：2016-05-01 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
pub_type： 杂志文章
doi：10.1007/s00894-012-1682-y
更新日期：2013-10-01 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
pub_type： 杂志文章
doi：10.1007/s00894-009-0467-4
更新日期：2009-10-01 00:00:00
abstract：:A good understanding of the inhibition mechanism of enzymes exhibiting high levels of similarity is the first step to the discovery of new drugs with selective potential. Examples of such proteins include glycogen synthase kinase-3 (GSK-3β) and cyclin-dependent kinase 2 (CDK-2). This article reports the mechanism of s...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-017-3395-8
更新日期：2017-08-01 00:00:00
abstract：:Following our recent studies of the thermodynamic properties of azaspiropentane and borospiropentane, in consideration of their usefulness as new potential high energy materials, we follow up with ab initio calculations on the thermodynamic properties of azaborospiropentanes. Properties reported in this study include ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-008-0329-5
更新日期：2008-09-01 00:00:00
abstract：:The nuclear magnetic shieldings of Si, Ge, and Sn in MH(4-n) Y(n) (M = Si, Ge, Sn; Y = F, Cl, Br, I and n = 1-4) molecular systems are highly influenced by the substitution of one or more hydrogens by heavy-halogen atoms. We applied the linear response elimination of small components (LRESC) formalism to calculate tho...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-014-2417-z
更新日期：2014-09-01 00:00:00
abstract：:The geometric and electronic structures, absorption spectra, transporting properties, chemical reactivity indices and electrostatic potentials of the planar three-coordinate organoboron compounds 1-2 and twisted reference compound Mes(3)B, have been investigated by employing density functional theory (DFT) and concept...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-013-1845-5
更新日期：2013-08-01 00:00:00
abstract：:Contact sites between amino acids characterize important structural features of a protein. We investigated characteristics of contact sites in a representative set of proteins and their relations between protein class or topology. For this purpose, we used a non-redundant set of 5872 protein domains, identically categ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-014-2497-9
更新日期：2014-11-01 00:00:00
abstract：:The energetic and electronic structure of various water dimer isomers has been explored through DFT methodology. Six different possible water dimers come in two broad categories, planar and non-planar. In each of the categories, three distinct topologies (i) linear, (ii) ring and (iii) bifurcated, have been obtained. ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-019-4274-2
更新日期：2020-01-06 00:00:00
abstract：:We use density functional theory-based calculations to study structural, electronic, and magnetic properties of two key reaction intermediates on a hematite, [Formula: see text]-Fe2O3, photoanode during the solar-driven water splitting reaction. Both intermediates contain an oxygen atom bonded to a surface iron atom. ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-018-3815-4
更新日期：2018-09-18 00:00:00
abstract：:The ladder-type polyheterofluorenes were investigated theoretically by using density functional theory (DFT) to reveal their optical and electronic properties for applications in organic optoelectronic devices. The incorporation of heteroatoms (B, Si, Ge, N, P, O, and S) into the ladder-type highly fused polyfluorene ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-012-1483-3
更新日期：2012-11-01 00:00:00
abstract：:Selective A(2B) receptor antagonists and agonists may play a role in important pathologies such as gastrointestinal, neurological (i.e., Alzheimer disease and dementia) and hypersensitive disorders (i.e., asthma), diabetes, atherosclerosis, restenosis and cancer. Hence, it is regarded as a good target for the developm...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-012-1427-y
更新日期：2012-09-01 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
pub_type： 杂志文章
doi：10.1007/s00894-014-2313-6
更新日期：2014-06-01 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
pub_type： 杂志文章
doi：10.1007/s00894-011-1079-3
更新日期：2012-01-01 00:00:00
abstract：:Six nitramines (N1-6) were designed with all possible arrangements of N-NO2 groups on a cyclic skeleton and structural optimization was performed using the density functional theory (DFT). We observed that all nitramines have high positive heats of formation proportionate to the number of N-NO2 groups in their molecul...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-015-2846-3
更新日期：2015-11-01 00:00:00
abstract：:Following our recent study on triazane, we present a follow-up study on the thermodynamic properties of triazane's unsaturated analog, triazene. We predict optimized structural parameters, vibrational frequencies, enthalpies of formation, enthalpies of combustion, specific enthalpies of combustion, and proton affiniti...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-007-0248-x
更新日期：2008-01-01 00:00:00
abstract：:Amorphous molecular simulation to model the reaction species in the synthesis of chemically inert and energetic 1,1-diamino-2,2-dinitroethene (DADNE) explosive material was performed in this work. Nitromethane was selected as the starting reactant to undergo halogenation, nitration, deprotonation, intermolecular conde...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-016-3182-y
更新日期：2017-01-01 00:00:00
