Benchmarking coupled cluster methods on singlet excited states of nucleobases.

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：:We have performed a multivariate logistic regression analysis to establish a statistical correlation between the structural properties of water molecules in the binding site of a free protein crystal structure, with the probability of observing the water molecules in the same location in the crystal structure of the l...

journal_title：Journal of molecular modeling

authors： García-Sosa AT,Mancera RL,Dean PM

更新日期：2003-06-01 00:00:00

abstract：:Checkpoint kinase 1 (Chk1), a member of the serine/threonine kinase family, is an attractive therapeutic target for anticancer combination therapy. A structure-based modeling approach complemented with shape components was pursued to develop a reliable pharmacophore model for ATP-competitive Chk1 inhibitors. Common ch...

journal_title：Journal of molecular modeling

authors： Chen XM,Lu T,Lu S,Li HF,Yuan HL,Ran T,Liu HC,Chen YD

更新日期：2010-07-01 00:00:00

abstract：:Some recent papers clearly indicate that the cytoplasmic domain of KcsA plays a role in pH sensing. We have performed, for the first time, a targeted molecular dynamics (TMD) simulation of the opening of full-length KcsA at pH 4 and pH 7, with a special interest for the cytoplasmic domain. Association energy calculati...

journal_title：Journal of molecular modeling

authors： Li Y,Barbault F,Delamar M,Zhang R,Hu R

更新日期：2013-04-01 00:00:00

abstract：:A high-throughput screen against Aurora A kinase revealed several promising submicromolar pyrimidine-aniline leads. The bioactive conformation found by docking these leads into the Aurora A ATP-binding site had a semicircular shape. Macrocycle formation was proposed to achieve novelty and selectivity via ring-closing ...

journal_title：Journal of molecular modeling

authors： Poulsen A,William A,Blanchard S,Nagaraj H,Williams M,Wang H,Lee A,Sun E,Teo EL,Tan E,Goh KC,Dymock B

更新日期：2013-01-01 00:00:00

abstract：:The UV absorption spectra of ten N,N'-bisarylmalonamides have been recorded in the range 200-400 nm in a set of selected solvents. The solute-solvent interactions have been analyzed on the basis of the linear solvation energy relationship (LSER) concept proposed by Kamlet and Taft. The effects of substituents on the a...

journal_title：Journal of molecular modeling

authors： Arsovski VM,Božić BĐ,Mirković JM,Vitnik VD,Vitnik ZJ,Fabian WM,Petrović SD,Mijin DZ

更新日期：2014-08-01 00:00:00

abstract：:The effect of CO2 and H2O on the behavior of shale gas confined in calcite [104] slit-like nanopore is investigated using molecular dynamics simulation technique. The study is relevant as the advancement of enhance gas recovery (EGR) technologies requires in-depth atomistic understanding of the hydrocarbons, water, ca...

journal_title：Journal of molecular modeling

authors： Berghe G,Kline S,Burket S,Bivens L,Johnson D,Singh R

更新日期：2019-09-02 00:00:00

abstract：:Molecular-dynamics (MD) simulations of urea crystals of different shapes (cubic, rectangular prismatic, and sheet) have been performed using our previously published force field for urea. This force field has been validated by calculating values for the cohesive energy, sublimation temperature, and melting point from ...

journal_title：Journal of molecular modeling

authors： Özpınar GA,Beierlein FR,Peukert W,Zahn D,Clark T

更新日期：2012-08-01 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：:Several cellular disorders have been related to the overexpression of the cysteine protease cathepsin B (CatB), such as rheumatic arthritis, muscular dystrophy, osteoporosis, Alzheimer's disease, and tumor metastasis. Therefore, inhibiting CatB may be a way to control unregulated cellular functions and prevent tissue ...

journal_title：Journal of molecular modeling

authors： Vega-Teijido MA,El Chamy Maluf S,Bonturi CR,Sambrano JR,Ventura ON

更新日期：2014-06-01 00:00:00

abstract：:We have used density-functional theory to investigate the neighboring-group stabilization of iodine, arsenic, and phosphorus-centered oxyanion moieties in species such as deprotonated 2-iodoxybenzoic acid (IBX) and its analogs. The magnitudes of different stabilizing effects and further candidates for analogous stabil...

journal_title：Journal of molecular modeling

authors： O'Hair RA,Williams CM,Clark T

更新日期：2010-03-01 00:00:00

abstract：:During thermal transition and variation of pH, structural properties of 35 proteins and their complexes (bound with substrate and co-factor) were analyzed in detail. During pH alteration, these proteins were shown to have substantial differences in conformations. pH conformers were analyzed in detail. Free energy and ...

journal_title：Journal of molecular modeling

authors： Bhattacharya P,Ganeshan T,Nandi S,Srivastava A,Singh P,Rehan M,Rashkush R,Subbarao N,Lynn A

更新日期：2009-09-01 00:00:00

abstract：:Detailed density functional theory (DFT) calculations on the structure and harmonic frequencies of model all-trans and all-cis polyenes were undertaken. For the first time, we report on the convergence of selected B3LYP/6-311++G** and BLYP/6-311++G** calculated structural parameters resulting from a systematic increas...

journal_title：Journal of molecular modeling

authors： Kupka T,Buczek A,Broda MA,Stachów M,Tarnowski P

更新日期：2016-05-01 00:00:00

abstract：:This theoretical study presents a comparative analysis of the molecular properties of heterocyclic (C2H4O...HF and C2H5...HF) and homocyclic (C3H6...HF) hydrogen-bonded complexes. Initially, the equilibrium geometries of these complexes were analyzed in detail at the B3LYP/6-311++G(d,p) level of theory. Subsequently, ...

journal_title：Journal of molecular modeling

authors： Oliveira BG,Araújo RC,Carvalho AB,Ramos MN

更新日期：2009-02-01 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：:The energetic and electronic structure of various water dimer isomers has been explored through DFT methodology. Six different possible water dimers come in two broad categories, planar and non-planar. In each of the categories, three distinct topologies (i) linear, (ii) ring and (iii) bifurcated, have been obtained. ...

journal_title：Journal of molecular modeling

authors： Ghosh SR,Debnath B,Jana AD

更新日期：2020-01-06 00:00:00

abstract：:The reactivity of the 5-arylidenerhodanine and 5-arylideneisorhodanine derivatives in reactions with dimethyl maleate was computationally studied at the DFT(M06-2X)/6-311+G(d,p) theory level. Eight stereoisomers of the reaction products were considered. The effect of the solvent was taken into account by means of the ...

journal_title：Journal of molecular modeling

authors： Tejchman W,Michalski M,Zborowski KK,Berski S

更新日期：2019-06-14 00:00:00

abstract：:Dirithromycin is a macrolide antibiotic derived from erythromycin A. Dirithromycin is synthesized by the condensation of 9(S)-erythromycylamine with 2-(2-methoxyethoxy)-acetaldehyde. To gain insight into the synthesis, the condensation mechanism has been analyzed computationally by the AM1 method in the gas phase. Fir...

journal_title：Journal of molecular modeling

authors： Duran D,Aviyente V,Baysal C

更新日期：2004-04-01 00:00:00

abstract：:The geometric and electronic structures, absorption spectra, transporting properties, chemical reactivity indices and electrostatic potentials of the planar three-coordinate organoboron compounds 1-2 and twisted reference compound Mes(3)B, have been investigated by employing density functional theory (DFT) and concept...

journal_title：Journal of molecular modeling

authors： Jin JL,Li HB,Lu T,Duan YA,Geng Y,Wu Y,Su ZM

更新日期：2013-08-01 00:00:00

abstract：:Multilayer-shaped compression and slide models were employed to investigate the complex sensitive mechanisms of cocrystal explosives in response to external mechanical stimuli. Here, density functional theory (DFT) calculations implementing the generalized gradient approximation (GGA) of Perdew-Burke-Ernzerhof (PBE) w...

journal_title：Journal of molecular modeling

authors： Gao HF,Zhang SH,Ren FD,Gou RJ,Han G,Wu JB,Ding X,Zhao WH

更新日期：2016-05-01 00:00:00

abstract：:B3LYP, PBE, M06-2X, B2PLYP, BN2PLYP-D, ωB97X-D, and MP2 levels of theory, in combination with the 6-311++G(d,p) and cc-pVTZ basis sets were comprehensively assessed for their ability to reproduce experimental FOX-7 structural and detonation data. ωB97X-D/cc-pVTZ, B3LYP/cc-pVTZ, and M06-2X/cc-pVTZ provided highly accur...

journal_title：Journal of molecular modeling

authors： Jeong K,Jeon Y,Kwon S

更新日期：2017-09-01 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 ladder-type polyheterofluorenes were investigated theoretically by using density functional theory (DFT) to reveal their optical and electronic properties for applications in organic optoelectronic devices. The incorporation of heteroatoms (B, Si, Ge, N, P, O, and S) into the ladder-type highly fused polyfluorene ...

journal_title：Journal of molecular modeling

authors： Zheng C,Tao Y,Cao JZ,Chen RF,Zhao P,Wu XJ,Huang W

更新日期：2012-11-01 00:00:00

abstract：:A computational study has been performed for studying the characteristics of the interaction of phenol with ammonium and methylammonium cations. The effect of the presence of water molecules has also been considered by microhydrating the clusters with up to three water molecules. Clusters of phenol with ammonium and m...

journal_title：Journal of molecular modeling

authors： Rodríguez-Sanz AA,Carrazana-García J,Cabaleiro-Lago EM,Rodríguez-Otero J

更新日期：2013-05-01 00:00:00

abstract：:In this work, the spectroscopic information, stability and aromaticity of the boron-nitrogen azulene and naphthalene molecules are provided by the use of CC2 (geometry optimization, dipole moment, UV-vis spectrum calculations) and DFT (vibrational spectrum and NMR calculations) methodologies. One isomer of the investi...

journal_title：Journal of molecular modeling

authors： Catão AJ,López-Castillo A

更新日期：2017-04-01 00:00:00

abstract：:Periplasmic binding proteins are the initial receptors for the transport of various substrates over the inner membrane of gram-negative bacteria. The binding proteins are composed of two domains, and the substrate is entrapped between these domains. For several of the binding proteins it has been established that a cl...

journal_title：Journal of molecular modeling

authors： Siuda I,Thøgersen L

更新日期：2013-11-01 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：:The geometrical, conformational, and electronic properties of a series of D-π-A metal-free dyes designed for use as sensitizers in DSSCs were studied using DFT and TD-DFT methods. A substituted triphenylamine moiety was used as the donor group and 2-cyanoacrylic acid as the acceptor group in these dyes. They also cont...

journal_title：Journal of molecular modeling

authors： Hasanein AA,Elmarassi YR,Kassem EN

更新日期：2016-05-01 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：:The structures of the 4,4',4″-tris(N,N-phenyl-3-methylphenylamino)triphenylamine (m-MTDATA) molecule and its dimer in their neutral and positively charged forms were studied by performing quantum-chemical calculations at the Hartree-Fock (HF) and density functional theory (DFT) levels of theory using several exchange-...

journal_title：Journal of molecular modeling

authors： Safonov A,Rykova E,Bagaturyants A

更新日期：2018-11-28 00:00:00