Characterization of peroxo reaction intermediates in the water oxidation process on hematite surfaces.

abstract：:The nitrogen doping and phenyl substitution effects on the geometries, molecular stacking character, electronic, and charge transport properties of tetrabenzoheptacene (TTBH) have been investigated by means of density functional theory (DFT) calculation and incoherent charge hopping model. Our results indicate that th...

journal_title：Journal of molecular modeling

authors： Guan L,Wang W,Shao R,Liu F,Yin S

更新日期：2015-05-01 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...

journal_title：Journal of molecular modeling

authors： Kulczycka-Mierzejewska K,Sadlej J,Trylska J

更新日期：2018-07-03 00:00:00

abstract：:In this study, eight oxytocin (OT) antagonists were subjected to conformational analysis. By means of simulated annealing, 2,000 structures were generated to sample the conformational space. The preferred main-chain and side-chain dihedral angles, intramolecular H-bond interactions (types 1<--4 and 1<--3), and seconda...

journal_title：Journal of molecular modeling

authors： Jójárt B,Márki A

更新日期：2006-09-01 00:00:00

abstract：:The shuttling motion of a macrocycle in rotaxane-based molecular switching devices has been studied by computational density functional methods. In the test case, energy profiles corresponding to the dethreading process of different types of guest molecules in a cyclobis(paraquat-p-phenylene) host verified the experim...

journal_title：Journal of molecular modeling

authors： Hirva P,Haukka M,Pakkanen TA

更新日期：2008-10-01 00:00:00

abstract：:We here report a combined quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) study on the binding interactions between the α(V)β₃ integrin and eight cyclic arginine-glycine-aspartate (RGD) containing peptides. The initial conformation of each peptide within the binding site of the integrin was det...

journal_title：Journal of molecular modeling

authors： Xiang M,Lin Y,He G,Chen L,Yang M,Yang S,Mo Y

更新日期：2012-11-01 00:00:00

abstract：:With the help of quantum mechanical calculations, we have examined the series of central system X(ML)(3) (+)(X = O, S, Se; M = Au, Ag, Cu). Using a scalar-relativistic density functional approach, we studied the geometry structures, Mulliken populations and charges of the systems. Structure parameters of the experimen...

journal_title：Journal of molecular modeling

authors： Fang H,Wang SG

更新日期：2007-01-01 00:00:00

abstract：:Solar-assisted water splitting using photoelectrochemical cells (PECs) is one of the promising ways for the production of hydrogen to store renewable energy. Semiconducting materials are used as a key factor which controls the overall energy conversion efficiency in PECs. However, finding new semiconductors with appro...

journal_title：Journal of molecular modeling

authors： Uğur Ş,Akbudak S,Kushwaha AK,Bayrak G

更新日期：2020-05-15 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

authors： Zheng S,Xiong Y,Wang J

更新日期：2010-12-01 00:00:00

abstract：:The functionalization of pristine and Stone-Wales defected BC3 nanosheets with a pyrene molecule was investigated using density functional theory. Frontier molecular analysis shows that the main interaction is π-π stacking, releasing energies in the range of 143.6 to 169.1 kJ mol(-1). We predicted that after the funct...

journal_title：Journal of molecular modeling

authors： Peyghan AA,Noei M,Bagheri Z

更新日期：2014-12-01 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：:The concepts of polarization (induction), charge transfer and covalent bonding contributions are discussed in terms of weak interactions. They are shown to be different incarnations of the same phenomenon, so that using polarization to describe them is most consistent as it is the only real, measurable and uniquely de...

journal_title：Journal of molecular modeling

authors： Clark T

更新日期：2017-09-27 00:00:00

abstract：:By the use of ellipsoidal coordinates, the two-center Coulomb and hybrid integrals over complete orthonormal sets of Ψα-ETO exponential type orbitals arising in ab initio calculations of molecules are evaluated, where α = 1,0, -1, -2, ...,. These integrals are expressed through the auxiliary functions Q(ns)(q) and G(-...

journal_title：Journal of molecular modeling

authors： Guseinov II,Sahin E

更新日期：2011-04-01 00:00:00

abstract：:Faced with the worldwide spread of multidrug-resistant (MDR) bacterial strains, together with a lack of any appropriate treatment, urgent steps to combat infectious diseases should be taken. Usually, bacterial components are studied to understand, by analogy, the functioning of human proteins. However, molecular data ...

journal_title：Journal of molecular modeling

authors： Wiczew D,Borowska A,Szkaradek K,Biegus T,Wozniak K,Pyclik M,Sitarska M,Jaszewski L,Radosinski L,Hanus-Lorenz B,Kraszewski S

更新日期：2019-06-11 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：:ET(A) subtype selective antagonists constitute a novel and potentially important class of agents for the treatment of pulmonary hypertension, heart failure, and other pathological conditions. In this paper, 60 benzodiazepine derivatives displaying potent activities against ET(A) and ET(B) subtypes of endothelin recept...

journal_title：Journal of molecular modeling

authors： Xia J,Li J,Sun H

更新日期：2012-04-01 00:00:00

abstract：:Recent experiments have confirmed the importance of nuclear quantum effects even in large biomolecules at physiological temperature. Here we describe how the path integral formalism can be used to describe rigorously the nuclear quantum effects on equilibrium and kinetic properties of molecules. Specifically, we expla...

journal_title：Journal of molecular modeling

authors： Zimmermann T,Vaníček J

更新日期：2010-11-01 00:00:00

abstract：:We investigate the conformational properties of a potent inhibitor of neuropilin-1, a protein involved in cancer processes and macular degeneration. This inhibitor consists of four aromatic/conjugated fragments: a benzimidazole, a methylbenzene, a carboxythiourea, and a benzene-linker dioxane, and these fragments are ...

journal_title：Journal of molecular modeling

authors： Goldwaser E,de Courcy B,Demange L,Garbay C,Raynaud F,Hadj-Slimane R,Piquemal JP,Gresh N

更新日期：2014-11-01 00:00:00

abstract：:Three potential anticancer agents {trans-[PtCl(2)(NH(3))(thiazole)], cis-[PtCl(2)(NH(3))(piperidine)], and PtCl(2)(NH(3))(cyclohexylamine) (JM118)} were explored and compared with cisplatin and the inactive [PtCl(dien)](+) complex. Basic electronic properties, bonding and stabilization energies were determined, and th...

journal_title：Journal of molecular modeling

authors： Bradác O,Zimmermann T,Burda JV

更新日期：2008-08-01 00:00:00

abstract：:Molecular and quantum mechanics calculations were carried out in a series of tripeptides (GXG, where X = D, N and C) as models of the unfolded states of proteins. The selected central amino acids, especially aspartic acid (D) and asparagine (N) are known to present significant average conformations in partially allowe...

journal_title：Journal of molecular modeling

authors： Ramos J,Cruz VL

更新日期：2016-11-01 00:00:00

abstract：:We have systematically explored and investigated the geometrical structures, stability, growth pattern, bonding character, and potential energy surface (PES) of the possible isomers of each cluster for planar B(n)P (n = 1 ∼ 7) at the CCSD(T)/6-311+;G(d)//B3LYP/6-311+G(d) level. A large number of planar structures for ...

journal_title：Journal of molecular modeling

authors： Shi R,Shao J,Wang C,Zhu X,Lu X

更新日期：2011-05-01 00:00:00

abstract：:Bicyclo[3.3.1]nonylidenebicyclo[3.3.1]nonane (1) and adamantylideneadamantane (Ad=Ad) are two caged olefins with closely related structures at the double bond. Both compounds react instantaneously with Br2 in chlorinated hydrocarbon solvents to give mixtures of olefin-Br2 aggregates identified as the 1:1 pi-complex an...

journal_title：Journal of molecular modeling

authors： Chiappe C,Pomelli CS,Lenoir D,Wattenbach C

更新日期：2006-07-01 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：:B-C binary monolayers and fullerenes (borafullerenes) have received considerable attention in recent years. Inspired by the newly reported B4C3 semiconducting boron carbide monolayer isovalent to graphene (Tian et al., Nanoscale, 2019, 11, 11099), we predict herein at density functional theory level a new class of bor...

journal_title：Journal of molecular modeling

authors： Yan M,Tian XX,Pei L,Ma YY,Zan WY,Mu YW,Li SD

更新日期：2020-07-07 00:00:00

abstract：:Nitrogen (N)-doped carbons reportedly exhibit good electrocatalytic activity for the oxygen reduction reaction (ORR) of fuel cells. This work provides theoretical insights into the ORR mechanism of N-doped graphene by using density functional theory calculations. All possible reaction pathways were investigated, and t...

journal_title：Journal of molecular modeling

authors： Zhang J,Wang Z,Zhu Z

更新日期：2013-12-01 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

authors： Alazmi M

更新日期：2020-07-07 00:00:00

abstract：:The behavior of the carbon monoxide (CO) adsorbed on the external surface of H-capped (6,0) zigzag single-walled aluminum nitride nanotube (AlNNT) was studied using parallel and transverse electric field (strengths 0-140 × 10(-4) a.u.) and density functional calculations. The calculated adsorption energies of the CO/A...

journal_title：Journal of molecular modeling

authors： Peyghan AA,Baei MT,Hashemian S,Torabi P

更新日期：2013-02-01 00:00:00

abstract：:The applicability of the newly developed PM6 method for modeling proteins is investigated. In order to allow the geometries of such large systems to be optimized rapidly, three modifications were made to the conventional semiempirical procedure: the matrix algebra method for solving the self-consistent field (SCF) equ...

journal_title：Journal of molecular modeling

authors： Stewart JJ

更新日期：2009-07-01 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：: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 l...

journal_title：Journal of molecular modeling

authors： Liu Y,Yu T,Lai W,Kang Y,Ge Z

更新日期：2015-03-01 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

authors： Xu L,Li QS,King RB

更新日期：2017-04-01 00:00:00