Conformational analysis of short polar side-chain amino-acids through umbrella sampling and DFT calculations.

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：:Recent experiments have confirmed the importance of nuclear quantum effects even in large biomolecules at physiological temperature. Here we describe how the path integral formalism can be used to describe rigorously the nuclear quantum effects on equilibrium and kinetic properties of molecules. Specifically, we expla...

journal_title：Journal of molecular modeling

authors： Zimmermann T,Vaníček J

更新日期：2010-11-01 00:00:00

abstract：:Abnormal expression of cyclin-dependent kinase 2 (CDK2)/cyclin-E is detected in colorectal, ovarian, breast and prostate cancers. The study of CDK2 with a bound inhibitor revealed CDK2 as a potential therapeutic target for several proliferative diseases. Several highly selective inhibitors of CDK2 are currently underg...

journal_title：Journal of molecular modeling

authors： Pasha FA,Neaz MM

更新日期：2013-02-01 00:00:00

abstract：:Present theoretical study involves the delta shape complexes of beryllium, magnesium, and calcium where the metal atom interacts perpendicularly with disubstituted acetylene. Most of the complexes are found to be fairly stable. The dependence of second-hyperpolarizability on the basis set with increasing polarization ...

journal_title：Journal of molecular modeling

authors： Hatua K,Nandi PK

更新日期：2015-10-01 00:00:00

abstract：:By the use of ellipsoidal coordinates, the two-center Coulomb and hybrid integrals over complete orthonormal sets of Ψα-ETO exponential type orbitals arising in ab initio calculations of molecules are evaluated, where α = 1,0, -1, -2, ...,. These integrals are expressed through the auxiliary functions Q(ns)(q) and G(-...

journal_title：Journal of molecular modeling

authors： Guseinov II,Sahin E

更新日期：2011-04-01 00:00:00

abstract：:High-level quantum chemical techniques have been utilized to accurately describe the geometrical parameters, vibrational frequencies and dissociation pathways of the X (2)A″, 1 (2)A', 2 (2)A', 2 (2)A″ states of S(2)Cl; X (1)A', 1 (3)A″, 1 (1)A″, 1 (3)A' states of S(2)Cl(+); X (1)A', 1 (3)A', (1)A″ states of S(2)Cl(-),...

journal_title：Journal of molecular modeling

authors： Czernek J,Zivný O

更新日期：2012-09-01 00:00:00

abstract：:Meta-hybrid density functional theory calculations using M06-2X/6-31+G(d,p) and M06-2X/6-311+G(d,p) levels of theory have been performed to understand the strength of C-H(…)π interactions of two possible types for benzene-acetylene, 1,3,5-trifluorobenzene-acetylene and coronene-acetylene complexes. Our study reveals t...

journal_title：Journal of molecular modeling

authors： Dinadayalane TC,Paytakov G,Leszczynski J

更新日期：2013-07-01 00:00:00

abstract：:Monoamine oxidase (MAO) is an enzyme of major importance in neurochemistry, because it catalyzes the inactivation pathway for the catecholamine neurotransmitters, noradrenaline, adrenaline and dopamine. In the last decade it was demonstrated that imidazoline derivatives were able to inhibit MAO activity. Furthermore, ...

journal_title：Journal of molecular modeling

authors： Moraes FP,de Azevedo WF Jr

更新日期：2012-08-01 00:00:00

abstract：:In this work we report the atomic partial charges evaluated on dodecyltrimethylammonium ion. The values obtained from 17 quantum methods [CHELP, CHELPG, MK, NPA at (HF, LDA, PBE, B3LYP)//6-31G++(d,p) level and APT at B3LYP//6-31G++(d,p)] on the molecule optimised at B3LYP/6-31G++(d,p) level were compared to two semiem...

journal_title：Journal of molecular modeling

authors： Minisini B,Chavand S,Barthelery R,Tsobnang F

更新日期：2010-06-01 00:00:00

abstract：:The thermally allowed electrocyclic reaction syn-cyclophanediene (CPD) to dihydropyrene (DHP) was compared with the disallowed thermal electrocyclic reaction in anti CPD through density functional theory (DFT) calculations at the B3LYP/6-31 + G(d) level. Moreover, the results were also compared with the electrocycliza...

journal_title：Journal of molecular modeling

authors： Saima B,Khan A,Nisa RU,Mahmood T,Ayub K

更新日期：2016-04-01 00:00:00

abstract：:Herbicides targeting grass plastidic acetyl-CoA carboxylase (ACCase, EC 6.4.1.2) are selectively effective against graminicides. The intensive worldwide use of this herbicide family has selected for resistance genes in a number of grass weed species. Recently, the active-site W374C mutation was found to confer multi-d...

journal_title：Journal of molecular modeling

authors： Zhu XL,Yang WC,Yu NX,Yang SG,Yang GF

更新日期：2011-03-01 00:00:00

abstract：:A computational study was carried out to characterize the hydrogen-bonded dimers of Zoledronate (ZOL), which is used widely in treating skeletal diseases. The stable conformations, hydrogen bonding interactions, IR spectra, thermodynamic properties, and electronic characteristics of nine possible ZOL dimers were studi...

journal_title：Journal of molecular modeling

authors： Liu Q,Li K,Lv G,Li X,Peng Y,Lin J,Qiu L

更新日期：2018-10-09 00:00:00

abstract：:A coarse-grained Brownian dynamics model was used to simulate two proteins of similar sizes inside model membrane pores of varying size and hydrophobicity. The two proteins, which have radii of gyration of approximately 9.5 Å in their native states, are a 36-residue hydrophilic villin head piece (HP-36) and a 40-resid...

journal_title：Journal of molecular modeling

authors： Zhang Y,Zhang Y,McCready MJ,Maginn EJ

更新日期：2019-04-25 00:00:00

abstract：:Hepatic fibrosis is a common complication of the infection by the parasite, Clonorchis sinensis. There is a high incidence of this disease in the Asian countries with an increased risk of conversion to cancer. A secretory phospholipase A(2) (PLA(2)) enzyme from the parasite is implicated in the pathology. This is an a...

journal_title：Journal of molecular modeling

authors： Hariprasad G,Kaur P,Srinivasan A,Singh TP,Kumar M

更新日期：2012-07-01 00:00:00

abstract：:Extremely extensive calculations of potential energy surfaces for the parallel-displaced configuration of pyridine dimer systems have been carried out using a dispersion-corrected density functional. Instead of focusing on stationary geometries these calculations provide much deeper insight into the "landscape" of the...

journal_title：Journal of molecular modeling

authors： Sierański T

更新日期：2017-11-09 00:00:00

abstract：:Amorphous molecular simulation to model the reaction species in the synthesis of chemically inert and energetic 1,1-diamino-2,2-dinitroethene (DADNE) explosive material was performed in this work. Nitromethane was selected as the starting reactant to undergo halogenation, nitration, deprotonation, intermolecular conde...

journal_title：Journal of molecular modeling

authors： Liu MH,Liu CW

更新日期：2017-01-01 00:00:00

abstract：:The cold shock protein from the hyperthermophile Thermotoga maritima (Tm-Csp) exhibits significantly higher thermostability than its homologue from the thermophile Bacillus caldolyticus (Bc-Csp). Experimental studies have shown that the electrostatic interactions unique to Tm-Csp are responsible for improving its ther...

journal_title：Journal of molecular modeling

authors： Su JG,Han XM,Zhao SX,Hou YX,Li XY,Qi LS,Wang JH

更新日期：2016-04-01 00:00:00

abstract：:In this work molecular modeling was applied to generate homology models of the pore region of the Na(v)1.2 and Na(v)1.8 isoforms of human voltage-gated sodium channels. The models represent the channels in the resting, open, and fast-inactivated states. The transmembrane portions of the channels were based on the equi...

journal_title：Journal of molecular modeling

authors： Scheib H,McLay I,Guex N,Clare JJ,Blaney FE,Dale TJ,Tate SN,Robertson GM

更新日期：2006-09-01 00:00:00

abstract：:Studying the electrochemical characteristics is an important step for determining interactions between molecules and the chemical environment. Moreover, the electrochemical evaluation of dyes is highly needed to establish the behavior of electro-active chemical species inside dye-sensitized solar cells (DSSCs). Four c...

journal_title：Journal of molecular modeling

authors： Ortega E,Bernède JC,Ramírez AMR,Louarn G,Díaz FR,Cattin L,Del Valle MA

更新日期：2019-02-27 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：:Insulin-like growth factor-binding proteins (IGFBPs) control bioactivity and distribution of insulin-like growth factors (IGFs) through high-affinity complex of IGFBP and IGF. To get more insight into the binding interaction of IGF system, the site-directed mutagenesis and force-driving desorption methods were employe...

journal_title：Journal of molecular modeling

authors： Chen X,Zhu S,Duan D,Wu T,Wang Q

更新日期：2013-12-01 00:00:00

abstract：:Although molecularly targeted therapy with imatinib has improved treatments of chronic myeloid leukemia (CML), clinical resistance gradually develops in patients with accelerated or blast phase CML. The inability of imatinib to cure CML suggests that inactivation of BCR-ABL kinase activity alone is not sufficient to c...

journal_title：Journal of molecular modeling

authors： Shao S,Yu R,Yu Y,Li Y

更新日期：2014-08-01 00:00:00

abstract：:The effective dissolution of calcium oxalate, the main component of kidney stones, is important in the treatment of nephrolithisis. Polyphenol glycosides constitute compounds supporting dissolution and inhibition of formation of stones. These moieties possess oxygen atoms which can interact with calcium cations. Densi...

journal_title：Journal of molecular modeling

authors： Toczek D,Kubas K,Turek M,Roszak S,Gancarz R

更新日期：2013-10-01 00:00:00

abstract：:CO2 reduction has attracted extensive attentions for its wide applications in chemical engineering and green chemistry. As one of major commercial catalysts, Cu have been widely studied considering its low price and high catalytic efficiency. However, previous studies were mostly focused on the Cu(111) surface, while ...

journal_title：Journal of molecular modeling

authors： Wang R,Zhu B,Zhang G,Gao Y

更新日期：2020-07-09 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：:Knowledge-based models for protein folding assume that the early-stage structural form of a polypeptide is determined by the backbone conformation, followed by hydrophobic collapse. Side chain-side chain interactions, mostly of hydrophobic character, lead to the formation of the hydrophobic core, which seems to stabil...

journal_title：Journal of molecular modeling

authors： Brylinski M,Kochanczyk M,Broniatowska E,Roterman I

更新日期：2007-07-01 00:00:00

abstract：:In this work, the molecular modeling method was performed to study adsorption interaction between PAMAM molecules of different generations and silicic acid molecules, and the inhibition effect on silica scale were discussed. The results show that adsorption energies of PAMAM molecule of generation 1.0 with amine-termi...

journal_title：Journal of molecular modeling

authors： Chen C,Bai N,Zhang Y,Jiao L,Xia M,Chen G

更新日期：2017-01-01 00:00:00

abstract：:Temperature dependences of the spontaneous polarization and the dielectric constant are calculated near the paraelectric-ferroelectric (cubic-tetragonal) transition in BaTiO3 using our mean field model. By expanding the free energy in terms of the spontaneous polarization (order parameter), expressions for the tempera...

journal_title：Journal of molecular modeling

authors： Yurtseven H,Kiraci A

更新日期：2013-09-01 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：: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