Importance of oligomerisation on Pseudomonas aeruginosaLectin-II binding affinity. In silico and in vitro mutagenesis.

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：:The ternary complexes ML∙∙∙PyZX2∙∙∙NH3 (ML = CuCl, CuCN, AgCN, and AuCN; Z = P, As, and Sb; X = H and F) have been investigated with quantum chemical calculations. The results showed that the existence of coordination interaction has a prominent enhancing effect on the strength of pnicogen bonding. Even in ML∙∙∙PySbH2...

journal_title：Journal of molecular modeling

authors： Tang Q,Li Q

更新日期：2016-03-01 00:00:00

abstract：:Based on the unique advantages of terahertz (THz) spectrum on the detection of energetic cocrystals, the low-temperature dependent THz spectra of CL-20/TNT cocrystal were investigated by using molecular dynamics (MD) simulations from 5 to 296 K, as well as three different crystal faces, (001), (120), and (010). When t...

journal_title：Journal of molecular modeling

authors： Shi L,Duan XH,Zhu LG,Pei CH

更新日期：2020-01-11 00:00:00

abstract：:Compound P131 has been established to inhibit Cryptosporidium parvum's inosine monophosphate dehydrogenase (CpIMPDH). Its inhibitory activity supersedes that of paromomycin, which is extensively used in treating cryptosporidiosis. Through the per-residue energy decomposition approach, crucial moieties of P131 were ide...

journal_title：Journal of molecular modeling

authors： Omolabi KF,Iwuchukwu EA,Agoni C,Olotu FA,Soliman MES

更新日期：2021-01-09 00:00:00

abstract：:A theoretical study of a series of five glucose based glycolipid crown ethers and their complexes with Na(+) and K(+) was performed using the density functional theory with B3LYP/6-31 G* to obtain the optimized geometrical structures and electronic properties. The local nucleophilicity of the five molecules was invest...

journal_title：Journal of molecular modeling

authors： Nguan H,Ahmadi S,Hashim R

更新日期：2012-12-01 00:00:00

abstract：:A density functional theory investigation of adsorption of monomer, dimer and trimer forms of pyrrole on the outer surface of zigzag (7,0) single-walled carbon nanotube (SWCNT) has been reported. Geometries of the complexes were optimized using the M06-2X functional and the 6-31G(d,p) basis set. Moreover, 6-311G(d,p),...

journal_title：Journal of molecular modeling

authors： Shukla MK,Boddu V,Hill F

更新日期：2014-09-01 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

authors： Swart M,van der Wijst T,Fonseca Guerra C,Bickelhaupt FM

更新日期：2007-12-01 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 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：:In order to introduce effectively the external electric fields into the explosive systems, the change trends of the strengths of trigger linkages, nitro group charges, and explosive sensitivities of 1,4-dinitroimidazole-N-oxide (1,4-DNIO) were investigated in the external electric fields at the B3LYP/6-311++G(2d,p) an...

journal_title：Journal of molecular modeling

authors： Wang BG,Ren FD,Wang Y

更新日期：2019-11-28 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 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：: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：:The binding geometry of fluorouracil/cucurbit[n]urils (CB[n]s) complexes with n = 5-8 is investigated using the first-principles van der Waals density functional (vdW-DF) method, involving full geometry optimization. Such host-guest complexes are typically calculated using conventional DFT method, which significantly ...

journal_title：Journal of molecular modeling

authors： Sabet M,Ganji MD

更新日期：2013-09-01 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：: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：:Aluminum enriched 1, 1-diamino-2, 2-dinitroethylene (Al-FOX-7) crystal, as a new high energy density material (HEDM), was designed and investigated using grand canonical monte carlo (GCMC), NVT+NPT-molecular dynamics (MD) and GGA-PBE-density functional theory (DFT) methods. The results show that, Al atoms break out H-...

journal_title：Journal of molecular modeling

authors： Bian L,Shu Y,Xu J,Wang L

更新日期：2013-01-01 00:00:00

abstract：:The stability of cyclic peptide assemblies (CPs) forming a macromolecular nanotube structure was investigated in solvents of different polarity using computational methods. The stability and structure of the complexes were studied using traditional molecular dynamics (MD). Energy of dissociation was estimated from ste...

journal_title：Journal of molecular modeling

authors： Vijayakumar V,Vijayaraj R,Peters GH

更新日期：2016-11-01 00:00:00

abstract：:Quantum chemical calculations of the structures and stabilities of the title series at the CCSD(T) theoretical level are performed. Laplacian, electron density deformation, electron localization function and reduced density gradient analysis are investigated to explore the nature of the interaction. The results show t...

journal_title：Journal of molecular modeling

authors： Li X

更新日期：2012-03-01 00:00:00

abstract：:This paper used numerical and experimental methods to investigate the mechanical properties of amorphous NiAl alloys during the nanoindentation process. A simulation was performed using the many-body tight-binding potential method. Temperature, plastic deformation, elastic recovery, and hardness were evaluated. The ex...

journal_title：Journal of molecular modeling

authors： Wang CH,Fang TH,Cheng PC,Chiang CC,Chao KC

更新日期：2015-06-01 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：:The optical properties of polymer/solvent systems composed by the polymers P3HT and PolyeraActivInk N2200 under the present of chloroform as solvent are experimentally and theoretically investigated using UV-Vis spectroscopy, molecular dynamics (MD), and density functional theory (DFT) calculations. The study is focus...

journal_title：Journal of molecular modeling

authors： Dias Ledo RM,Leal LA,de Brito Silva PP,da Cunha WF,de Souza LE,Almeida Fonseca AL,Ceschin AM,da Silva Filho DA,Ribeiro Junior LA

更新日期：2017-02-01 00:00:00

abstract：:The dopamine (DAT), serotontin (SERT) and noradrenalin (NET) transporters are molecular targets for different classes of psychotropic drugs. The crystal structure of Aquifex aeolicus LeuT(Aa) was used as a template for molecular modeling of DAT, SERT and NET, and two putative drug binding sites (pocket 1 and 2) in eac...

journal_title：Journal of molecular modeling

authors： Ravna AW,Sylte I,Dahl SG

更新日期：2009-10-01 00:00:00

abstract：:The geometrical structure and electronic properties of bis(10-hydroxybenzo[h]quinolinato)beryllium (Bebq2) molecule and its dimer both in the neutral and in the positively and negatively charged states were studied using quantum-chemical calculations. It is found that the excess charge in the charged systems is locali...

journal_title：Journal of molecular modeling

authors： Safonov AA,Bagaturyants AA

更新日期：2014-08-01 00:00:00

abstract：:A molecular modeling strategy is proposed to describe the temperature (T) dependence of solubility parameter (δ) for the amorphous polymers which exhibit glass-rubber transition behavior. The commercial forcefield "COMPASS" is used to support the atomistic simulations of the polymer. The temperature dependence behavio...

journal_title：Journal of molecular modeling

authors： Chen X,Yuan C,Wong CK,Zhang G

更新日期：2012-06-01 00:00:00

abstract：:Cyclic nucleotide binding domain (CNBD) is a ubiquitous domain of effector proteins involved in signalling cascades of prokaryota and eukaryota. CNBD activation by cyclic nucleotide monophosphate (cNMP) is studied well in the case of several proteins. However, this knowledge is hardly applicable to cNMP-modulated cati...

journal_title：Journal of molecular modeling

authors： Gushchin IY,Gordeliy VI,Grudinin S

更新日期：2012-09-01 00:00:00

abstract：:We present the synthesis and structure determination for two thiohydantoin compounds (5-benzylidene-2-sulfanylideneimidazolidin-4-one and 5-cinnamylidene-2-sulfanylideneimidazolidin-4-one), proposed as potential novel fungicides. The exact chemical structure of these molecules has not yet been determined since they ca...

journal_title：Journal of molecular modeling

authors： Kobyłka K,Żuchowski G,Tejchman W,Zborowski KK

更新日期：2019-08-24 00:00:00

abstract：:In this work, a computational framework is proposed by utilizing molecular dynamics simulation to explore the existing relation between molecular structure and ionic conductivity of the electrolyte system [LiPF6+(EC+DMC 1:1)] consisting of a mixture of cyclic ethylene carbonate (EC) and acyclic dimethyl carbonate (DMC...

journal_title：Journal of molecular modeling

authors： Haghkhah H,Ghalami Choobar B,Amjad-Iranagh S

更新日期：2020-08-01 00:00:00

abstract：:The Z-DNA-binding domain of human double-stranded RNA adenosine deaminase I (hZαADAR1) can specifically recognize the left-handed Z-DNA which preferentially occurs at alternating purine-pyrimidine repeats, especially the CG-repeats. The interactions of hZαADAR1 and Z-DNAs in different sequence contexts can affect many...

journal_title：Journal of molecular modeling

authors： Wang Q,Li L,Wang X,Liu H,Yao X

更新日期：2014-11-01 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

authors： Devi A,Deswal S,Dharavath S,Ghule VD

更新日期：2015-11-01 00:00:00