The anti-fibrillogenic activity of tetracyclines on PrP 106-126: a 3D-QSAR study.

abstract：:A computational chemistry investigation was undertaken to shed light on the facilitatory role played by Fe3+ and Al3+ cations in the adsorption of anionic As(V) species by humic acids through the formation of so-called cationic bridges. Geometric and energetic parameters were obtained using density functional theory a...

journal_title：Journal of molecular modeling

authors： Gorb L,Shukla MK

更新日期：2017-03-01 00:00:00

abstract：:The prediction of the series of complexes [Au(3)Cl(3)M(2)] with M = Li, Na, K, Rb and Cs, has been achieved at the ab initio level of theory. All geometries were fully optimized at the MP2 level of theory; the central Au(3) cluster is capped by chlorine atoms and the alkaline metals lie above and below the plane of th...

journal_title：Journal of molecular modeling

authors： Muñiz J,Sansores LE,Pyykkö P,Martínez A,Salcedo R

更新日期：2009-10-01 00:00:00

abstract：:The adsorption of the molecules CO, CO2, and H2 on several ceria and zinc oxide surfaces was studied by means of periodical DFT calculations and compared with infrared frequency data. The stable CeO2(111), CeO2(331), and ZnO(0001) perfect faces were the first substrates considered. Afterwards, the same surfaces with o...

journal_title：Journal of molecular modeling

authors： Reimers WG,Baltanás MA,Branda MM

更新日期：2014-06-01 00:00:00

abstract：:The mechanism and kinetics of 2,2,3,3,3-pentafluoropropanol (CF₃CF₂CH₂OH) reaction with Chlorine atom (Cl) is investigated in this work. Two hydrogen abstraction channels of the title reaction are identified. The geometries of all the stationary points in the potential energy surface are obtained at the BHandHLYP/6-31...

journal_title：Journal of molecular modeling

authors： Yu AY,Zhang HX

更新日期：2013-10-01 00:00:00

abstract：:In this study, the complete orthonormal sets of phi(alpha)-momentum space orbitals (where alpha = 1, 0, -1, -2, ...) obtained from the psi(alpha)-ETO in coordinate representation (I.I. Guseinov, J. Mol. Model., 9 (2003) 135) are reduced to the complete orthonormal sets of hyperspherical harmonics (HSH) by means of a F...

journal_title：Journal of molecular modeling

authors： Guseinov II

更新日期：2006-09-01 00:00:00

abstract：:Hyaluronan lyase from Streptococcus pneumoniae can degrade hyaluronic acid, which is one of the major components in the extracellular matrix. Hyaluronan can regulate water balance, osmotic pressure, and act as an ion exchange resin. Followed by our recent work on the catalytic reaction mechanism and substrate binding ...

journal_title：Journal of molecular modeling

authors： Li F,Xu D

更新日期：2015-08-01 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：: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：: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：:We examine a short way to reach an exceptional point that corresponds to a coalescence of two resonance energies. The application concerns the photodissociation of the Na2 molecule exposed to a laser field. In this case, the resonances can be correlated with the field-free vibrational states of the diatomic species. T...

journal_title：Journal of molecular modeling

authors： Lefebvre R,Atabek O

更新日期：2013-05-01 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：: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 geometries, relative stabilities of some 4(7) and 5(6) substituted 2-hydroxybenzimidazole derivatives were calculated with full geometry optimization using AM1 and PM3 in aqueous phase. With the exception of molecules 4, 6 and 7 for all the 4(7) and 5(6) substituted 2-hydroxybenzimidazole derivatives the 3H and ke...

journal_title：Journal of molecular modeling

authors： Oğretir C,Yarligan S,Berber H,Arslan T,Topal S

更新日期：2003-12-01 00:00:00

abstract：:Following our recent study on triazane, we present a follow-up study on the thermodynamic properties of triazane's unsaturated analog, triazene. We predict optimized structural parameters, vibrational frequencies, enthalpies of formation, enthalpies of combustion, specific enthalpies of combustion, and proton affiniti...

journal_title：Journal of molecular modeling

authors： Richard RM,Ball DW

更新日期：2008-01-01 00:00:00

abstract：:PB1-F2 is a recently described influenza A viral protein that induces apoptosis by binding with two mitochondrial membrane proteins, i.e. VDAC1 (outer membrane) and ANT3 (inner membrane). Knowledge of this binding mechanism could provide insights that would aid in the design of novel inhibitors against this protein. T...

journal_title：Journal of molecular modeling

authors： Danishuddin M,Khan SN,Khan AU

更新日期：2010-03-01 00:00:00

abstract：:The ability to accurately predict the oxidation and reduction potentials of molecules is very useful in various fields and applications. Quantum mechanical calculations can be used to access this information, yet sometimes the usefulness of these calculations can be limited because of the computational requirements fo...

journal_title：Journal of molecular modeling

authors： Méndez-Hernández DD,Tarakeshwar P,Gust D,Moore TA,Moore AL,Mujica V

更新日期：2013-07-01 00:00:00

abstract：:Understanding the interactions of the cage molecules with a variety of invited molecules is getting very important. But, the hydrogen bonds can also play a crucial role in the interaction phenomenon. In this work, natural population analysis (NPA), chemical shifts, and atom in molecules (AIM) analysis have been used t...

journal_title：Journal of molecular modeling

authors： Gassoumi B,Chaabene M,Ghalla H,Chaabane RB

更新日期：2019-12-13 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 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：: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：:The performances of quantum chemistry methods (i.e., DFT and ab initio) in calculating the structural and vibrational properties of phosphates and phosphorylated compounds have been evaluated. Diethyl-phosphate, phosphonic acid, dihydrogen phosphate anion, phosphoric acid dimer and protonated glycylphosphotyrosine dip...

journal_title：Journal of molecular modeling

authors： Sharma A,Ohanessian G,Clavaguéra C

更新日期：2014-09-01 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：:A series of no-chlorine and oxygen-rich hydrazine derivatives (hydrazine modified with -NO₂ and NO₃(-) groups) was designed and optimized to obtain molecular geometries and electronic structures at density functional theory-B3PW91/6-311++G(3df,3pd) level. Some important properties such as bond dissociation enthalpy, d...

journal_title：Journal of molecular modeling

authors： Wang PC,Zhu ZS,Xu J,Zhao XJ,Lu M

更新日期：2013-06-01 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：:Recently inulinase has regained interest due to its usage in the production of fructooligosaccharides, biofuels, and in pharmaceutical industries. Inulinases properties are experimentally reported by nomerous studies but their characteristics are just partially explained by only a few computational investigations. In ...

journal_title：Journal of molecular modeling

authors： Singh PK,Joseph J,Goyal S,Grover A,Shukla P

更新日期：2016-04-01 00:00:00

abstract：:Studies of the interaction between phenol and intrinsic graphene, as well as phenol and aluminum doped graphene layer are performed using first principles total energy calculations within the periodic density functional theory. A 4x4 periodic structure is used to explore the adsorption of a phenol molecule on the intr...

journal_title：Journal of molecular modeling

authors： Hernández JM,Anota EC,de la Cruz MT,Melchor MG,Cocoletzi GH

更新日期：2012-08-01 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：:An electronic study of nimesulide was performed by using density functional theory calculations. The activities of the six different derivatives were related with electron donating or accepting capacities. All compounds which had nitro moiety had low electron donating and high electron accepting capacities. However, t...

journal_title：Journal of molecular modeling

authors： Borges RS,Oliveira JP,Matos RF,Chaves Neto AM,Carneiro AS,Monteiro MC

更新日期：2015-07-01 00:00:00

abstract：:Acylthiocarbamates (ATCs) have been identified as a class of potent non-nucleoside HIV-1 reverse transcriptase (RT) inhibitors. A computational strategy based on molecular docking studies followed by comparative molecular fields analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) was used t...

journal_title：Journal of molecular modeling

authors： Cichero E,Cesarini S,Spallarossa A,Mosti L,Fossa P

更新日期：2009-07-01 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