A comparison of computational methodologies for the structural modelling of biologically relevant zinc complexes.

abstract：:The mechanism of transformation of two radicals (R1p and R1i) obtained by addition of a hydrogen atom to an external and internal carbon atom of dicyclopenta[de,mn]anthracene (P1) was investigated. Two pathways were revealed. The first mechanism is a one-step process, whereas the second mechanism includes two transiti...

journal_title：Journal of molecular modeling

authors： Stanković S,Marković S,Gutman I,Sretenović S

更新日期：2010-09-01 00:00:00

abstract：:We propose a scheme to estimate hydrogen isotope effects on molecular polarizabilities. This approach combines the any-particle molecular orbital method, in which both electrons and H/D nuclei are described as quantum waves, with the auxiliary density perturbation theory, to calculate analytically the polarizability t...

journal_title：Journal of molecular modeling

authors： Moncada F,Flores-Moreno R,Reyes A

更新日期：2017-03-01 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...

journal_title：Journal of molecular modeling

authors： Chaban VV,Fileti EE

更新日期：2015-09-01 00:00:00

abstract：:The unusual π-halogen bond interactions are investigated between (BNN)₃⁺ and X1X2 (X1, X2 = F, Cl, Br) employing MP2 at 6-311 + G(2d) and aug-cc-pVDZ levels according to the "CP (counterpoise) corrected potential energy surface (PES)" method. The order of the π-halogen bond interactions and stabilities of the complexe...

journal_title：Journal of molecular modeling

authors： Qi HT,Ren FD,Zhang JL,Wang JY

更新日期：2011-05-01 00:00:00

abstract：:The structural features, spectroscopic properties, and interaction energies of the linear proton-bound complexes of OCH(+) and its sulfur analog SCH(+) with N2 were investigated using the high-level ab initio methods MP2 and CCSD(T) as well as density functional theory with the aug-cc-pVXZ (X = D, T) basis sets. The r...

journal_title：Journal of molecular modeling

authors： Begum S,Subramanian R

更新日期：2016-01-01 00:00:00

abstract：:We present a theoretical study of the adsorption of 2,2,6,6-tetramethylpiperidine-1-oxoammonium cation (TEMPO) onto the TiO₂(110) surface rutile, investigating its bonding nature, electron properties and structural stability. Based on the results obtained with the PBE0/def2-SVP method, natural bond orbital (NBO) analy...

journal_title：Journal of molecular modeling

authors： Nieto-López I,Hernández-García L,Bonilla-Cruz J,Sanchez M

更新日期：2014-03-01 00:00:00

abstract：:Nearly all RNA viruses produce double-stranded RNA (dsRNA) during their replication cycles--an important pathogen-associated molecular pattern recognized by the RNA interference (RNAi) pathway in invertebrates and plants. Nodamura virus (NoV) encodes a suppressor of RNA silencing termed B2, which binds to dsRNA and pr...

journal_title：Journal of molecular modeling

authors： Allen WJ,Wiley MR,Myles KM,Adelman ZN,Bevan DR

更新日期：2014-03-01 00:00:00

abstract：:The chain tacticity of a polymer is a key influence on its structure and dynamics, which ultimately determine its properties. While they have great potential to elucidate the influence of chain tacticity, all-atom molecular simulations are often restricted to short chains and small systems. In this work, two typical s...

journal_title：Journal of molecular modeling

authors： Wu C

更新日期：2014-08-01 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

authors： Faragi S,Hamedani A,Alahyarizadeh G,Minuchehr A,Aghaie M,Arab B

更新日期：2019-06-15 00:00:00

abstract：:Paracetamol is a relatively safe analgesia/antipyretic drug without the risks of addiction, dependence, tolerance, and withdrawal when used alone. However, when administrated in an opioid/paracetamol combination product, which often contains a large quantity of paracetamol, it can be potentially dangerous due to the r...

journal_title：Journal of molecular modeling

authors： Wang Y,Lin W,Wu N,He X,Wang J,Feng Z,Xie XQ

更新日期：2018-08-18 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：:The geometries, stabilities, and electronic properties of ScBn (n = 1-12) clusters have been systematically investigated by using density functional theory B3LYP method and coupled-cluster theory CCSD(T) method. It is found that the ground state isomers of ScBn have planar or quasi-planar structure when n ≤ 6, which c...

journal_title：Journal of molecular modeling

authors： Jia J,Ma L,Wang JF,Wu HS

更新日期：2013-08-01 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：:Understanding how temperature affects the electronic transitions of BFO is important for design of BiFeO3 (BFO)-based temperature-sensitive device. Hitherto, however, there have been only very limited reports of the quantitative simulation. Here, we used density functional theory (DFT) and two-dimensional correlation ...

journal_title：Journal of molecular modeling

authors： Bian L,Xu JB,Song MX,Dong FQ,Dong HL,Shi FN,Zhang XY,Duan T

更新日期：2015-04-01 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

authors： Ghosh SR,Debnath B,Jana AD

更新日期：2020-01-06 00:00:00

abstract：:In the absence of interlogs, building docking models is a time intensive task, involving generation of a large pool of docking decoys followed by refinement and screening to identify near native docking solutions. This limits the researcher interested in building docking methods with the choice of benchmarking only a ...

journal_title：Journal of molecular modeling

authors： Mitra P,Pal D

更新日期：2011-03-01 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：: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

authors： Laurent AD,Otten E,Le Guennic B,Jacquemin D

更新日期：2016-11-01 00:00:00

abstract：:The treatment of bacterial infections is currently threatened by the emergence of pathogenic bacteria producing β-lactamase, which catalyzes the hydrolysis of β-lactams. Although the hydrolysis of the substrate nitrocefin by a metallo-β-lactamase, namely β-lactamase N1 from USA300 (a typical methicillin-resistant Stap...

journal_title：Journal of molecular modeling

authors： Yu Y,Wang X,Gao Y,Yang Y,Sun L,Wang G,Deng X,Niu X

更新日期：2019-04-13 00:00:00

abstract：:In the present work, C-F bond cleavage mediated by the super-reduced form of cobalamin (i.e., CoICbl) was theoretically studied at the ONIOM(BP86/6-311++G(d,p):PM6) + SMD level of theory. Dispersion effects were introduced by employing Grimme's empirical dispersion at the ONIOM(BP86-D/6-311++G(d,p):PM6) + SMD level. I...

journal_title：Journal of molecular modeling

authors： Cortés-Arriagada D,Toro-Labbe A,Mora JR,Rincón L,Mereau R,Torres FJ

更新日期：2017-08-17 00:00:00

abstract：:The electric field induced within a molecule by its electrons determines a whole series of important physical properties of the molecule. In particular, the values of the gradient of this field at the nuclei determine the interaction of their quadrupole moments with the electrons. Using unsymmetrical one-range additio...

journal_title：Journal of molecular modeling

authors： Guseinov II,Görgün NS

更新日期：2011-06-01 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：: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：:This article analyzes the interplay between X···N and X···X halogen bonds interactions in NCX···NCX···XCH3 complexes, where X=Cl and Br. To better understand the properties of these systems, the corresponding dyads were also studied. These effects are studied theoretically in terms of geometric and energetic features ...

journal_title：Journal of molecular modeling

authors： Esrafili MD,Vakili M,Solimannejad M

更新日期：2014-02-01 00:00:00

abstract：:The density functional theory method using the B3LYP/6-31G(d,p) level of theory was used to perform isoenergetic maps in order to determine the lower energy conformers of four disaccharides constituting alginic acids, which are based on β-D-mannuronic (M) and α-L-guluronic acid (G), called MM, GG, MG, and GM. The pref...

journal_title：Journal of molecular modeling

authors： Bekri L,Zouaoui-Rabah M,Springborg M,Rahal MS

更新日期：2018-10-10 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

authors： Benmensour MA,Djennane-Bousmaha S,Boucekkine A

更新日期：2014-07-01 00:00:00

abstract：:Low temperature oxidation of CO to CO2 is an important process for the environment. Similarly adsorption of CO from the releasing sources is also of major concern today. Whereas the potential of gold and silver clusters is well proven for the catalysis of the above mentioned reaction, the potential of aluminum (Al) cl...

journal_title：Journal of molecular modeling

authors： Samanta B,Sengupta T,Pal S

更新日期：2018-12-06 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：:DFT computations were carried out to characterize the (17)Oand (2)H electric field gradient, EFG, in various bisphosphonate derivatives. The computations were performed at the B3LYP level with 6-311++G (d,P) standard basis set. Calculated EFG tensors were used to determine the (17)O and (2)H nuclear quadrupole couplin...

journal_title：Journal of molecular modeling

authors： Aghabozorg H,Sohrabi B,Mashkouri S,Aghabozorg HR

更新日期：2012-03-01 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

authors： Greco C,Sacco E,Vanoni M,De Gioia L

更新日期：2005-12-01 00:00:00