Insight into the dynamic interaction between different flavonoids and bovine serum albumin using molecular dynamics simulations and free energy calculations.

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：:The USFDA has approved pramlintide, commercially named Symlin (sIAPP), as adjunctive therapy for type 2 diabetes (T2D). This analogue of the human amylin peptide (hIAPP) has triple proline substitutions typical of the rat isoform (rIAPP). Recently, it was proposed that pramlintide solubility and aggregation resistance...

journal_title：Journal of molecular modeling

authors： Alves NA,Dias LG,Frigori RB

更新日期：2019-08-19 00:00:00

abstract：:The Fbw7-Skp1 complex is an essential component in the formation and development of the mammalian cardiovascular system; the complex interaction is mediated through binding of Skp1 C-terminal peptide (qGlu-peptide) to the F-box domain of Fbw7. By visually examining the crystal structure, we identified a typical cation...

journal_title：Journal of molecular modeling

authors： Zhou J,Wang YS

更新日期：2017-09-26 00:00:00

abstract：:Various kinetic studies of the addition of hydrogen halides to alkenes were carried out in the 1930s, 1940s, and 1970s. Since then, there have been theoretical analyses of several aspects of alkene reactivity and regioselectivity during hydrohalogenation. A few works have studied the influence of the hydrogen halide w...

journal_title：Journal of molecular modeling

authors： Firme CL

更新日期：2019-04-25 00:00:00

abstract：:Corynebacterium pseudotuberculosis is a facultatively intracellular Gram-positive bacterium that causes caseous lymphadenitis, principally in sheep and goats, though sometimes in other species of animals, leading to considerable economic losses. This pathogen has a TCS known as PhoPR, which consists of a sensory histi...

journal_title：Journal of molecular modeling

authors： Moraes G,Azevedo V,Costa M,Miyoshi A,Silva A,da Silva V,de Oliveira D,Teixeira MF,Lameira J,Alves CN

更新日期：2012-03-01 00:00:00

abstract：:Orvinols are potent analgesics that target opioid receptors. However, their analgesic mechanism remains unclear and no significant preference for subtype opioid receptor has been achieved. In order to find new orvinols that target the kappa-receptor, comparative 3D-QSAR studies were performed on 26 orvinol analogs usi...

journal_title：Journal of molecular modeling

authors： Li W,Tang Y,Xie Q,Sheng W,Qiu ZB

更新日期：2006-09-01 00:00:00

abstract：:The CO and O2 adsorption as well as CO oxidation on cationic, neutral, and anionic AuM dimers (M = Pd, Ag) are studied by density functional calculations. Our results show that CO and O2 are adsorbed more stably on AuPd dimers than on AuAg dimers with corresponding charge state. O2 is favorable to be adsorbed on Pd at...

journal_title：Journal of molecular modeling

authors： Chen X,Lu RF,Kan EJ,Liu YZ,Xiao CY,Deng KM

更新日期：2014-06-01 00:00:00

abstract：:The average pull-out force and interaction energy of polyethylene (PE) cross-linked functionalized carbon nanotubes (cfCNTs) embedded in polymer matrices (PE-cfCNTs@polymers) was studied using molecular dynamics (MD) simulations. Accordingly, the pull-out process of PE-cfCNTs from inside polymer matrices, i.e., Aramid...

journal_title：Journal of molecular modeling

authors： Haghighi S,Ansari R,Ajori S

更新日期：2019-03-29 00:00:00

abstract：:The C-terminus tail (G144-T149) of the hyperthermophile Sulfolobus tokodaii (Sto-RNase HI) plays an important role in this protein's hyperstabilization and may therefore be a good protein stability tag. Detailed understanding of the structural and dynamic effects of C-terminus tail deletion is required for gaining ins...

journal_title：Journal of molecular modeling

authors： Chen L,Zhang JL,Zheng QC,Chu WT,Xue Q,Zhang HX,Sun CC

更新日期：2013-06-01 00:00:00

abstract：:In this paper, coupled cluster methods CC2, CCSD, CCSDR(3) and EOM-CCSD(T) have been benchmarked against CC3 for the transition energies of nucleobases. Beside presenting vertical excitation energies for about 30 singlet transitions of four molecules, the results are analyzed statistically and problematic cases have b...

journal_title：Journal of molecular modeling

authors： Kánnár D,Szalay PG

更新日期：2014-11-01 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 structural, elastic and electronic properties of lutatium-pnictides (LuN, LuP, LuAs, LuSb, and LuBi) were analyzed by using full-potential linearized augmented plane wave within generalized gradient approximation in the stable rock-salt structure (B1 phase) with space group Fm-3m and high-pressure CsCl structure (...

journal_title：Journal of molecular modeling

authors： Gupta DC,Bhat IH

更新日期：2013-12-01 00:00:00

abstract：:Bacillus anthracis has been employed as an agent of bioterrorism, with high mortality, despite anti-microbial treatment, which strongly indicates the need of new drugs to treat anthrax. Shikimate pathway is a seven step biosynthetic route which generates chorismic acid from phosphoenol pyruvate and erythrose-4-phospha...

journal_title：Journal of molecular modeling

authors： Barcellos GB,Caceres RA,de Azevedo WF Jr

更新日期：2009-02-01 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：:Isothiocyanates (ITC) are well-known chemopreventive agents extracted from vegetables. This activity results from the activation of human oxidoreductase. In this letter, the uncompetitive activatory mechanism of ITC was investigated using docking and molecular dynamics simulations. This indicates that NAD(P)H:quinone ...

journal_title：Journal of molecular modeling

authors： Mazur P,Magdziarz T,Bak A,Chilmonczyk Z,Kasprzycka-Guttman T,Misiewicz-Krzemińska I,Skupińska K,Polanski J

更新日期：2010-07-01 00:00:00

abstract：:The B3LYP/6-31G (d) method of density functional theory (DFT) was used to study molecular geometry, electronic structure, infrared spectrum (IR) and thermodynamic properties. The heat of formation (HOF) and calculated density were estimated to evaluate the detonation properties using Kamlet-Jacobs equations. Thermal s...

journal_title：Journal of molecular modeling

authors： Zhao GZ,Lu M

更新日期：2013-01-01 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：: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：:In the present work, we applied density functional theory and temperature-dependent Gibbs free energy calculations to wurtzoid structures to explain the sensitivity of ZnO nanocrystals towards chlorine molecules. In agreement with experimental findings, our results revealed that chlorine sensing under ambient conditio...

journal_title：Journal of molecular modeling

authors： Abdulsattar MA

更新日期：2017-04-01 00:00:00

abstract：:The burial of hydrophobic amino acids in the protein core is a driving force in protein folding. The extent to which an amino acid interacts with the solvent and the protein core is naturally proportional to the surface area exposed to these environments. However, an accurate calculation of the solvent-accessible surf...

journal_title：Journal of molecular modeling

authors： Durham E,Dorr B,Woetzel N,Staritzbichler R,Meiler J

更新日期：2009-09-01 00:00:00

abstract：:The mechanism of the copper(I)-catalyzed cyclopropanation reaction for methyl diazoacetate with both (Z)- and (E)-but-2-ene stereoisomers has been studied using the 6-311++G(d,p) basis set by means of M06-2X and O3LYP functionals. According to both methods, the rate-limiting step is the formation of a copper-carbene i...

journal_title：Journal of molecular modeling

authors： Angulo B,Herrerías CI,Hormigón Z,Mayoral JA,Salvatella L

更新日期：2018-07-05 00:00:00

abstract：:Aminoglycoside-arginine conjugates (AAC and APAC) are multi-target inhibitors of human immunodeficiency virus type-1 (HIV-1). Here, we predict new conjugates of neomycin with two arginine peptide chains binding at specific sites on neomycin [poly-arginine-neomycin-poly-arginine (PA-Neo-PA)]. The rationale for the desi...

journal_title：Journal of molecular modeling

authors： Berchanski A,Lapidot A

更新日期：2009-03-01 00:00:00

abstract：:In the present study, we analyze the interactions of NAD+-dependent deacetylase (Sir2 homolog yeast Hst2) with carba-nicotinamide-adenine-dinucleotide (ADP-HPD). For the Sir2 homolog, a yeast Hst2 docking procedure was applied. The structure of the protein-ADP-HPD complex obtained during the docking procedure was used...

journal_title：Journal of molecular modeling

authors： Czeleń P,Czyżnikowska Ż

更新日期：2016-06-01 00:00:00

abstract：:Trinitromethyl-substituted aminotetrazoles with -NH₂, -NO₂, -N₃, and -NHC(NO₂)₃ groups were investigated at the B3LYP/6-31G(d) level of density functional theory. Their sublimation enthalpies, thermodynamic properties, and heats of formation were calculated. The thermodynamic properties of these compounds increase wit...

journal_title：Journal of molecular modeling

authors： Lin H,Chen PY,Zhu SG,Zhang L,Peng XH,Li K,Li HZ

更新日期：2013-06-01 00:00:00

abstract：:An azo bridge (-N=N-) can not only desensitize explosives but also dramatically increase their heats of formation and explosive properties. Amino and nitro are two important high energy density functional groups. Here, we present calculations on 1-nitro-1-triazene (NH2-N=N-NO2). Thermal stability and detonation parame...

journal_title：Journal of molecular modeling

authors： Chi W,Yan T,Li B

更新日期：2014-08-01 00:00:00

abstract：:In this work we present the results of a study of the X-ray structure of 2-[(2,4-dimethoxyphenyl)amino]-1,3-thiazolidin-4-one. Using the FTIR spectra in solid state and results of ab initio calculations we explain the issue of the tautomerism of this molecule. The compound is shown to exist as the 2-amino tautomer rat...

journal_title：Journal of molecular modeling

authors： Nowaczyk A,Kowiel M,Gzella A,Fijałkowski L,Horishny V,Lesyk R

更新日期：2014-08-01 00:00:00

abstract：:Ab initio calculations were performed to study the quantum chemistry reactions mechanisms among Hg(0), elemental halogen and O3. The geometry of reactions, transition states (TS), intermediates (M) and products were optimized using the MP2 method at the SDD basis function level for Hg, and using 6-311++G (3df, 3pd) fo...

journal_title：Journal of molecular modeling

authors： Gao Z,Lv S,Yang W,Yang P,Ji S,Meng X

更新日期：2015-06-01 00:00:00

abstract：:Understanding the interaction between graphene and polymers is of essential interest when designing novel nanocomposites with reinforced mechanical and electrical properties. In this computational study, the interaction of pristine graphene (PG) and graphene oxide (GO) with a series of functional groups, representativ...

journal_title：Journal of molecular modeling

authors： Güryel S,Alonso M,Hajgató B,Dauphin Y,Van Lier G,Geerlings P,De Proft F

更新日期：2017-02-01 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：:We report thermodynamic, geometric, and electronic parameters for the interaction between neutral ligands and the [Hg(H2O)]2+ dication, using the B3LYP/6-311 + G(d,p) approach. Gibbs free energies for the interaction were employed to rank the affinity order of the several neutral ligands. To identify the parameters th...

journal_title：Journal of molecular modeling

authors： da Silva VHM,de Mesquita Carneiro JW,da Costa LM,Ferreira GB

更新日期：2020-05-20 00:00:00