Unsaturated trinuclear iron fluoroborylene complexes.

abstract：:The effects of different monoterpenes and 2-cyclohexen-1-one on the antibacterial activity of nitrofurantoin against resistant Enterobacter cloacae, were compared and the minimal structural component of monoterpene required for the highest level of resistance-modulating activity was determined. Subinhibitory concentra...

journal_title：Journal of molecular modeling

authors： Shahverdi AR,Mirzaie S,Rafii F,Kakavand M,Foroumadi A

更新日期：2015-08-01 00:00:00

abstract：:Mechanisms for the activation of water, ammonia, and other small molecules by the PCcarbeneP nickel pincer complex were studied computationally with the aid of density functional theory. The calculation results indicate that the strongly donating, nucleophilic carbene center can engage in a variety of heterolytic spli...

journal_title：Journal of molecular modeling

authors： Liu CC,Liu QL,Wu ZY,Chen YC,Xie HJ,Lei QF,Fang WJ

更新日期：2015-09-01 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：:Drug resistance is a very important factor contributing to the failure of current HIV therapies. The ability to understand the resistance mechanism of HIV-protease mutants may be useful in developing more effective and longer lasting treatment regimens. In this paper, we report the first computational study of the cli...

journal_title：Journal of molecular modeling

authors： Meiselbach H,Horn AH,Harrer T,Sticht H

更新日期：2007-02-01 00:00:00

abstract：:In advanced oxidation processes (AOPs), the detailed degradation mechanisms of a typical explosive of 2,4-dinitrotoluene (DNT) can be investigated by the density function theory (DFT) method at the SMD/M062X/6-311+G(d) level. Several possible degradation routes for DNT were explored in the current study. The results s...

journal_title：Journal of molecular modeling

authors： Zhou Y,Yang Z,Yang H,Zhang C,Liu X

更新日期：2017-04-01 00:00:00

abstract：:The deregulated breakpoint cluster region (Bcr)-Abelson tyrosine kinase (Abl) fusion protein represents an attractive pharmacological target for the treatment of chronic myeloid leukemia (CML). The high affinity of monobody AS25 was designed to target the Src homology 2 (SH2) domain of Bcr-Abl, leading to allosteric i...

journal_title：Journal of molecular modeling

authors： Ji M,Zheng G,Li X,Zhang Z,Jv G,Wang X,Wang J

更新日期：2017-06-01 00:00:00

abstract：:Functionalized carbon nanotubes (CNTs) can be used for improving the mechanical properties and load transfer in nanocomposites. In this research, the buckling behavior of perfect and defective cross-linked functionalized CNTs with polyethylene (PE) chains is studied employing molecular dynamics (MD) simulations. Two d...

journal_title：Journal of molecular modeling

authors： Ajori S,Ansari R,Parsapour H

更新日期：2016-12-01 00:00:00

abstract：:PcFK1 is a member of the cysteine knot inhibitor family that displays anti-malarial properties. The naturally occurring molecule is ∼ 40 amino acids in length and forms a highly constrained 3D structure due to the presence of 3 disulfide and multiple intra-molecular H-bonds. Recent experimental studies on PcFK1 wild-t...

journal_title：Journal of molecular modeling

authors： Gleeson MP,Deechongkit S,Ruchirawat S

更新日期：2011-04-01 00:00:00

abstract：:Natural hIFNγ is a glycoprotein with two N-glycosylation sites in each monomer chain, which are independently and differentially glycosylated. Although glycosylation is not necessary for the activity of the cytokine, it was proposed that it protects the cytokine from proteolytic degradation and thus extends its circul...

journal_title：Journal of molecular modeling

authors： Lilkova E,Petkov P,Ilieva N,Krachmarova E,Nacheva G,Litov L

更新日期：2019-04-25 00:00:00

abstract：:We report a DFT, TDDFT and DFTB investigation of the performance of two donor-π-acceptor (D-π-A)-type organic dyes bearing different electron-withdrawing groups (EWG) for dye-sensitized solar cells (DSSCs) to evaluate which EWG is better for an acrylic acid acceptor, i.e., Cyano (-CN) or o-nitrophenyl (o-NO2-Ph). A se...

journal_title：Journal of molecular modeling

authors： Zhang J,Kan YH,Li HB,Geng Y,Wu Y,Duan YA,Su ZM

更新日期：2013-04-01 00:00:00

abstract：:The effects of L-serine amino acid functionalization on a graphene plane were investigated through density functional theory calculations compared with those of oxygen functionalization. Three systems of 4 × 4 graphene supercells were created and functionalized by an epoxy group, a hydroxyl group, and an L-serine mole...

journal_title：Journal of molecular modeling

authors： Prasert K,Sutthibutpong T

更新日期：2020-07-13 00:00:00

abstract：:Studies of the the three-dimensional quantitative structure-activity relationships for ninety-five c-kit tyrosine kinase inhibitors were performed. Based on a co-crystallized compound (1 T46), known inhibitors were aligned with c-kit by induced-fit docking, and multiple training/test set splitting was performed to val...

journal_title：Journal of molecular modeling

authors： Almerico AM,Tutone M,Lauria A

更新日期：2012-07-01 00:00:00

abstract：:In this work, the effect of the external electric field (EF) on the drug delivery performance of peptide-based metal-organic framework (MPF) for 6-mercaptopurine (6-MP) drug is investigated by means of the molecular dynamics (MD) simulations. It is found that the strength interaction of drug molecule with MPF is decre...

journal_title：Journal of molecular modeling

authors： Shahabi M,Raissi H

更新日期：2019-09-06 00:00:00

abstract：:The structure of a two-dimensional film formed by adsorbed polymer chains was studied by means of Monte Carlo simulations. The polymer chains were represented by linear sequences of lattice beads and positions of these beads were restricted to vertices of a two-dimensional square lattice. Two different Monte Carlo met...

journal_title：Journal of molecular modeling

authors： Pawłowska M,Sikorski A

更新日期：2013-10-01 00:00:00

abstract：:Ethanol and water are the solvents most commonly used to extract flavonoids from propolis. Do hydrogen-bonding interactions exist between flavonoids and ethanol/water? In this work, this question was addressed by using density functional theory (DFT) to provide information on the hydrogen-bonding interactions between ...

journal_title：Journal of molecular modeling

authors： Zheng YZ,Zhou Y,Liang Q,Chen DF,Guo R

更新日期：2016-04-01 00:00:00

abstract：:Comprehensive molecular dynamics simulations are conducted to identify material modifications which can improve strength and reduce hysteresis losses at the nanointerfaces formed between silica, silane coupling agent (SCA) and styrene-butadiene rubber (SBR), all of which are important ingredients of green tyres. Impro...

journal_title：Journal of molecular modeling

authors： Joseph E,Swaminathan N,Kannan K

更新日期：2020-08-17 00:00:00

abstract：:The complementarity plot (CP) is an established validation tool for protein structures, applicable to both globular proteins (folding) as well as protein-protein complexes (binding). It computes the shape and electrostatic complementarities (Sm, Em) for amino acid side-chains buried within the protein interior or inte...

journal_title：Journal of molecular modeling

authors： Basu S

更新日期：2017-12-07 00:00:00

abstract：:The present study reports the geometry, electronic structure and properties of neutral and anionic transition metal (TM = Ti, Zr and Hf)) doped germanium clusters containing 1 to 20 germanium atoms within the framework of linear combination of atomic orbitals density functional theory under spin polarized generalized ...

journal_title：Journal of molecular modeling

authors： Kumar M,Bhattacharyya N,Bandyopadhyay D

更新日期：2012-01-01 00:00:00

abstract：:Uracil has long been known as the main product of nitrosative cytosine deamination in aqueous solution. Recent mechanistic studies of cytosinediazonium ion suggest that the cation formed by its dediazoniation can ring-open to N-protonated (Z,s-cis)-3-isocyanatoacrylonitrile 7. Stereochemical preferences are discussed ...

journal_title：Journal of molecular modeling

authors： Glaser R,Wu H,von Saint Paul F

更新日期：2006-07-01 00:00:00

abstract：:In the past several years, halogen bonds have been shown to be relevant in crystal engineering and biomedical applications. One of the reasons for the utility of these types of noncovalent interactions in the development of, for example, pharmaceutical ligands is that their strengths and geometric properties are very ...

journal_title：Journal of molecular modeling

authors： Riley KE,Murray JS,Fanfrlík J,Rezáč J,Solá RJ,Concha MC,Ramos FM,Politzer P

更新日期：2011-12-01 00:00:00

abstract：:The structures of the N-(hydroxymethyl)acetamide (model molecule of ceramide) dimers have been fully optimized at B3LYP/6-311++G** level. The intermolecular hydrogen bonding interaction energies have been calculated using the B3LYP/6-311++G**, B3LYP/6-311++G(2df,2p), MP2(full)/6-311++G** and MP2(full)/6-311++G(2df,2p)...

journal_title：Journal of molecular modeling

authors： Tang HF,Zhong H,Zhang LL,Gong MX,Song SQ,Tian QP

更新日期：2018-05-31 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：: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

authors： Czeleń P

更新日期：2017-08-01 00:00:00

abstract：:A theoretical investigation of the adsorption of CO₂ onto ZrO₂ is presented. Various cluster models were used to mimic different basic and acidic sites on the surface. The method used was the density functional theory with the generalized gradient approximation and including Grimme's empirical model in order to proper...

journal_title：Journal of molecular modeling

authors： Boulet P,Knöfel C,Kuchta B,Hornebecq V,Llewellyn PL

更新日期：2012-11-01 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：:Periodic DFT method has been firstly used to calculate the bulk structure, electronic structure, electrical transferring and thermodynamic properties of crystalline 5-azido-1H-tetrazole (HCN₇) and its four different salts. The anion CN₇(-) was included in all of the salts such as ammonium 5-azidotetrazolate ([NH₄](+)[...

journal_title：Journal of molecular modeling

authors： Wang K,Zhang J,Shang J,Zhang T

更新日期：2013-06-01 00:00:00

abstract：:Trocarin belongs to group D of prothrombin activators derived from snake venom of Tropidechis carinatus and is a rich non-hepatic source of Xa, the only known hepatic prothrombin activator. The structural and functional similarity with Xa makes trocarin an interesting target for exploring the structure-functional rela...

journal_title：Journal of molecular modeling

authors： Venkateswarlu D,Krishnaswamy S,Darden TA,Pedersen LG

更新日期：2002-10-01 00:00:00

abstract：:Tautomerism in monomers/dimers and association of 2,5-dihydroxy-1,8-naphthyridine was studied at the DFT level recently recommended for studies of non-covalent interactions. Studied dimers are stabilized by double and triple hydrogen-bonding. In some associates the intermolecular proton transfer may take place. Transi...

journal_title：Journal of molecular modeling

authors： Ośmiałowski B

更新日期：2012-04-01 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：: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

authors： Jiang C,Chen Y,Wang X,You Q

更新日期：2007-09-01 00:00:00