DFT studies of the adsorption and dissociation of H₂O on the Al₁₃ cluster: origins of this reactivity and the mechanism for H₂ release.

abstract：:B3LYP, PBE, M06-2X, B2PLYP, BN2PLYP-D, ωB97X-D, and MP2 levels of theory, in combination with the 6-311++G(d,p) and cc-pVTZ basis sets were comprehensively assessed for their ability to reproduce experimental FOX-7 structural and detonation data. ωB97X-D/cc-pVTZ, B3LYP/cc-pVTZ, and M06-2X/cc-pVTZ provided highly accur...

journal_title：Journal of molecular modeling

authors： Jeong K,Jeon Y,Kwon S

更新日期：2017-09-01 00:00:00

abstract：:The heats of formation (HOFs), electronic structure, energetic properties, and thermal stabilities for a series of 1,4-bis(1-azo-2,4-dinitrobenzene)-iminotetrazole derivatives with different substituents and substitution positions and numbers of nitrogen atoms in the nitrobenzene rings were studied using the DFT-B3LYP...

journal_title：Journal of molecular modeling

authors： Wu Q,Pan Y,Zhu W,Xiao H

更新日期：2013-04-01 00:00:00

abstract：:We perform density functional theory studies to investigate structural and electronic properties of the (5,5) boron nitride nanotubes (BNNTs) with surfaces and ends functionalized by thiol (SH) and hydroxyl (OH) groups. The exchange-correlation energies are treated according to the functional of Hamprecht-Cohen-Tozer-...

journal_title：Journal of molecular modeling

authors： Chigo Anota E,Cocoletzi GH

更新日期：2013-06-01 00:00:00

abstract：:The structures and stabilities of eleven N13+ and N13- isomers have been investigated with second-order Moller-Plesset (MP2) and density functional theory (DFT) methods. Five N13+ isomers and six N13- isomers are all reasonable local minima on their potential energy hypersurfaces. The most stable N13+ cation is struct...

journal_title：Journal of molecular modeling

authors： Yin PG,Li QS

更新日期：2004-02-01 00:00:00

abstract：:In this work, the spectroscopic information, stability and aromaticity of the boron-nitrogen azulene and naphthalene molecules are provided by the use of CC2 (geometry optimization, dipole moment, UV-vis spectrum calculations) and DFT (vibrational spectrum and NMR calculations) methodologies. One isomer of the investi...

journal_title：Journal of molecular modeling

authors： Catão AJ,López-Castillo A

更新日期：2017-04-01 00:00:00

abstract：:Cathepsin S has been demonstrated to play a crucial role in the remodeling of extracellular matrix proteins such as elastin and collagen, which in turn contribute to the structural integrity of the cardiovascular wall. Atherosclerotic lesions, aneurysm formation, plaque rupture, thrombosis, and calcification are some ...

journal_title：Journal of molecular modeling

authors： Ahmad S,Siddiqi MI

更新日期：2017-03-01 00:00:00

abstract：:The substituted effect on excited-state intramolecular proton transfer (ESIPT) of o-LHBDI derivatives (4R-o-LHBDI) was investigated by DFT and TD-DFT methods. The structures of 4R-o-LHBDI (R: OH, NH2, CN, NO2, CF3) were fully optimized, and the H-bond distances, bond angles, and infrared spectra of the atoms involved ...

journal_title：Journal of molecular modeling

authors： Ni M,Su S,Fang H

更新日期：2020-04-23 00:00:00

abstract：:To date, no suitable vaccine or specific antiviral drug is available to treat Chikungunya viral (CHIKV) fever. Hence, it is essential to identify drug candidates that could potentially impede CHIKV infection. Here, we present the development of a homology model of nsP2 protein based on the crystal structure of the nsP...

journal_title：Journal of molecular modeling

authors： Singh KhD,Kirubakaran P,Nagarajan S,Sakkiah S,Muthusamy K,Velmurgan D,Jeyakanthan J

更新日期：2012-01-01 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 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

authors： Dinçer M,Avci D,Sekerci M,Atalay Y

更新日期：2008-09-01 00:00:00

abstract：:The character of the bridged hydrogen atom (Hb) of B2H6 has become a hot issue in recent years. In this work, the complexes B2H6 · · · NH3, B2H2X4 · · · nNH3 (n = 1, 2) and 2HF · · · B2H2X4 · · · 2NH3 (X = Cl, Br, I) were constructed and studied based on the M06-2X calculations to investigate how to enhance the Hb · ·...

journal_title：Journal of molecular modeling

authors： Gao L,Zhang X,Meng L,Zeng Y

更新日期：2015-09-01 00:00:00

abstract：:The reaction mechanism of Ru-catalyzed cycloisomerization of 2-alkynylanilides to 3-substituted indole or 2-substituted indole was analyzed at the B3LYP level of density functional theory. The solvation effect of the system was also considered by SMD model. The calculation results show that the reaction system first f...

journal_title：Journal of molecular modeling

authors： Zhang X,Li S,Wei X,Lei Y

更新日期：2018-06-14 00:00:00

abstract：:Fully atomistic molecular dynamics simulation studies of thermotropic bilayers were performed using a set of glycosides namely n-octyl-β-D-glucopyranoside (β-C8Glc), n-octyl-α-D-glucopyranoside (α-C8Glc), n-octyl-β-D-galactopyranoside (β-C8Gal), and n-octyl-α-D-galactopyranoside (α-C8Gal) to investigate the stereochem...

journal_title：Journal of molecular modeling

authors： Ahmadi S,Manickam Achari V,Nguan H,Hashim R

更新日期：2014-03-01 00:00:00

abstract：:The effect of CO2 and H2O on the behavior of shale gas confined in calcite [104] slit-like nanopore is investigated using molecular dynamics simulation technique. The study is relevant as the advancement of enhance gas recovery (EGR) technologies requires in-depth atomistic understanding of the hydrocarbons, water, ca...

journal_title：Journal of molecular modeling

authors： Berghe G,Kline S,Burket S,Bivens L,Johnson D,Singh R

更新日期：2019-09-02 00:00:00

abstract：:The formation of selenium species in some biological processes involves the generation of ionic and radical intermediates such as RSe●, RSe-, RSeO●, and RSeO-, among others. We performed a theoretical study of the possible mechanisms for the reaction of the two simplest Se radicals-the hydroselenyl (HSe●) and seleneni...

journal_title：Journal of molecular modeling

authors： Vega-Teijido MA,Kieninger M,Ventura ON

更新日期：2017-12-05 00:00:00

abstract：:The mechanism and origin of selectivity for [3 + 2]-cycloaddition (32CA) reactions between thioketone and carbohydrate-derived nitrones in THF were investigated by using the density functional theory (DFT) at the M06-2X/6-311+G(d,p)//M06-2X/6-31+G(d,p) level of theory combined with the solvation SMD model. The calcula...

journal_title：Journal of molecular modeling

authors： Yang J,Zhang Y,Yang Y,Xue Y

更新日期：2019-07-02 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 nature of E-M bonds in CpE-MCp (E = B, Al, Ga; M = Li, Na, K; Cp = η (5)-C5H5) donor-acceptor sandwiches was studied using the atoms in molecules (AIM) theory, electron localization function (ELF), energy decomposition analysis (EDA), and natural bond orbital analysis (NBO) methods. Both topological and orbital an...

journal_title：Journal of molecular modeling

authors： Huo S,Meng D,Zhang X,Meng L,Li X

更新日期：2014-10-01 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 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

authors： Oliveira AA,Lipinski CF,Pereira EB,Honorio KM,Oliveira PR,Weber KC,Romero RAF,de Sousa AG,da Silva ABF

更新日期：2017-10-02 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

authors： Kuchta B,Firlej L,Mohammadhosseini A,Beckner M,Romanos J,Pfeifer P

更新日期：2013-10-01 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：: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：:Ten functionals were used to assess their capability to compute a local reactivity descriptor coming from the Conceptual Density Functional Theory on a group of iron-based organometallic compounds that have been synthesized by Zohuri, G.H. et al. in 2010; these compounds bear the following substituent groups: H-, O2N-...

journal_title：Journal of molecular modeling

authors： Martínez-Araya JI,Glossman-Mitnik D

更新日期：2018-01-18 00:00:00

abstract：:First principles calculations have been performed for C60@C180 carbon double-layer endofullerenes with up to: three diatomic radioiodine molecules (131I2), two potassium radio-iodide (K131I), and three sodium radio-iodide (Na131I) inside. The plane-wave pseudopotential (PP) method within the general gradient approxima...

journal_title：Journal of molecular modeling

authors： Valderrama A,Reynoso R,Gómez RW,Quintana M,Romero M

更新日期：2017-12-04 00:00:00

abstract：:In this study, the complete orthonormal sets of phi(alpha)-momentum space orbitals (where alpha = 1, 0, -1, -2, ...) obtained from the psi(alpha)-ETO in coordinate representation (I.I. Guseinov, J. Mol. Model., 9 (2003) 135) are reduced to the complete orthonormal sets of hyperspherical harmonics (HSH) by means of a F...

journal_title：Journal of molecular modeling

authors： Guseinov II

更新日期：2006-09-01 00:00:00

abstract：:This work presents a theoretical study of gallium arsenide (GaAs) nanotubes obtained from the (100), (110) and (111) crystal planes of zincblende structure in order to evaluate the electronic properties. The DFT/B3LYP/6-31G method was used to predict structures and stabilities. It was found that nanotubes from the (11...

journal_title：Journal of molecular modeling

authors： Silva JCF,Dos Santos JD,Taft CA,Martins JBL,Longo E

更新日期：2017-07-01 00:00:00

abstract：:White spot disease is a devastating disease of shrimp Penaeus monodon in which the shrimp receptor protein PmRab7 interacts with viral envelop protein VP28 to form PmRab7-VP28 complex, which causes initiation of the disease. The molecular mechanism implicated in the disease, the dynamic behavior of proteins as well as...

journal_title：Journal of molecular modeling

authors： Verma AK,Gupta S,Verma S,Mishra A,Nagpure NS,Singh SP,Pathak AK,Sarkar UK,Singh SP,Singh M,Seth PK

更新日期：2013-03-01 00:00:00

abstract：:The ability to accurately predict the oxidation and reduction potentials of molecules is very useful in various fields and applications. Quantum mechanical calculations can be used to access this information, yet sometimes the usefulness of these calculations can be limited because of the computational requirements fo...

journal_title：Journal of molecular modeling

authors： Méndez-Hernández DD,Tarakeshwar P,Gust D,Moore TA,Moore AL,Mujica V

更新日期：2013-07-01 00:00:00

abstract：:Both [5]-circulene and [7]-circulene can be selected to design the molecular tweezers theoretically using the DFT method. Leaning on the cyclic polymerization mechanism, we obtain four new tweezer compounds. Theoretical results offer that tweezer compound (I) is additionally stable than other compounds because it has ...

journal_title：Journal of molecular modeling

authors： Issa AA,Obayes HR

更新日期：2020-09-29 00:00:00