Theoretical studies of structure, energetics and properties of Ca²⁺ complexes with alizarin glucoside.

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 title compound, C(6)H(4)N(4)S(2)·C(3)H(7)NO, crystallizes in the monoclinic space group C 2/c with a = 26.673(5), b = 5.397(1), c = 16.522(3) Å, β = 95.49(3)°, Z = 8, R = 0.0461 for 1891 reflections with I > 2σ(I) and 174 parameters (4 restraints). Single pteridine-2,4(1 H,3 H)-dithione and dimethylformamide molec...

journal_title：Journal of molecular modeling

authors： Illán-Cabeza NA,Peña-Ruiz T,Moreno-Carretero MN

更新日期：2012-02-01 00:00:00

abstract：:Theoretical adiabatic electron affinities are often considered inaccurate because they are referenced to only a single value. Ground state electron affinities for all the main group elements and homonuclear diatomics were identified recently using the normalized binding energy of the hydrogen atom: [0.75420375(3)/2 = ...

journal_title：Journal of molecular modeling

authors： Chen ES,Keith H,Lim T,Pham D,Rosenthal R,Herder C,Pai S,Flores RA,Chen EC

更新日期：2015-04-01 00:00:00

abstract：:The incidence of tuberculosis infections that are resistant to conventional drug therapy has risen steadily in the last decade. Several of the quinolone antibacterials have been examined as inhibitors of M. tuberculosis infection as well as other mycobacterial infections. However, not much has been done to examine spe...

journal_title：Journal of molecular modeling

authors： Bagchi MC,Mills D,Basak SC

更新日期：2007-01-01 00:00:00

abstract：:The impact of a variety of modern computational methods on the structure of biologically relevant zinc complexes is studied. Different density functionals and a Hartree-Fock-based method, scalar-relativistic effects, and basis set integration grid choices, among others, are assessed for set of high-resolution crystall...

journal_title：Journal of molecular modeling

authors： Savasci G,Borges-Martínez M,Berger RJF,Ochsenfeld C,Mera-Adasme R

更新日期：2019-08-09 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：:A novel method for in silico selection of fluckicidal drugs is introduced. Two QSARs that permit us to discriminate between fasciolicide and non-fasciolicide drugs (the first) and to outline some conclusions about the possible mechanism of action of a chemical (the second) are performed. The first model correctly clas...

journal_title：Journal of molecular modeling

authors： González Díaz H,Olazabal E,Castañedo N,Sánchez IH,Morales A,Serrano HS,González J,de Armas RR

更新日期：2002-08-01 00:00:00

abstract：:The addition of C2 to HCN is of relevant interest in astrochemistry. We studied the pathways of this addition to produce CCCN and estimated its reaction rate using the Master Equation in the circumstellar environment. From the results of this study, it was possible to show that a different pathway in the Surface Poten...

journal_title：Journal of molecular modeling

authors： da Silva WB,Albernaz AF,Barreto PR,Correa E

更新日期：2017-04-01 00:00:00

abstract：:To date, no suitable vaccine or specific antiviral drug is available to treat Chikungunya viral (CHIKV) fever. Hence, it is essential to identify drug candidates that could potentially impede CHIKV infection. Here, we present the development of a homology model of nsP2 protein based on the crystal structure of the nsP...

journal_title：Journal of molecular modeling

authors： Singh KhD,Kirubakaran P,Nagarajan S,Sakkiah S,Muthusamy K,Velmurgan D,Jeyakanthan J

更新日期：2012-01-01 00:00:00

abstract：:In quantum chemical calculations, there are two facts of particular relevance: the position-dependent mass Schrödinger equation (PDMSE) and the exponential-type potentials used in the theoretical study of vibrational properties for diatomic molecules. Accordingly, in this work, the treatment of exactly solvable PDMSE ...

journal_title：Journal of molecular modeling

authors： Ovando G,Peña JJ,Morales J,López-Bonilla J

更新日期：2019-08-31 00:00:00

abstract：:ET(A) subtype selective antagonists constitute a novel and potentially important class of agents for the treatment of pulmonary hypertension, heart failure, and other pathological conditions. In this paper, 60 benzodiazepine derivatives displaying potent activities against ET(A) and ET(B) subtypes of endothelin recept...

journal_title：Journal of molecular modeling

authors： Xia J,Li J,Sun H

更新日期：2012-04-01 00:00:00

abstract：:Effects of substituents on anion binding in different urea based receptors have been examined using density functional (B3LYP/6-311+G**) level of theory. The complexes formed by a variety of substituted urea with a halide anion (fluoride) and an oxy-anion (acetate) have been calculated. The stronger complexes were pre...

journal_title：Journal of molecular modeling

authors： Ghosh A,Jose DA,Das A,Ganguly B

更新日期：2010-09-01 00:00:00

abstract：:The efficiency and high specificity of tobacco etch virus protease (TEVp) has made it widely used for cleavage of recombinant fusion proteins. However, TEVp suffers from a few intrinsic defects such as self-cleavage, poorly expressed in E. coli and less soluble. So some mutants were designed to improve it, such as S21...

journal_title：Journal of molecular modeling

authors： Wang Y,Zhu GF,Ren SY,Han YG,Luo Y,Du LF

更新日期：2013-11-01 00:00:00

abstract：:The nuclear magnetic shieldings of Si, Ge, and Sn in MH(4-n) Y(n) (M = Si, Ge, Sn; Y = F, Cl, Br, I and n = 1-4) molecular systems are highly influenced by the substitution of one or more hydrogens by heavy-halogen atoms. We applied the linear response elimination of small components (LRESC) formalism to calculate tho...

journal_title：Journal of molecular modeling

authors： Maldonado AF,Aucar GA,Melo JI

更新日期：2014-09-01 00:00:00

abstract：:D222G mutation of the hemagglutinin (HA) is of special interest because of its close association with the enhanced virulence of 2009 pandemic influenza A (H1N1) virus through the increased binding affinity to α2,3-linked sialylated glycan receptors. However, there is still a lack of detailed understanding about the mo...

journal_title：Journal of molecular modeling

authors： Pan D,Xue W,Wang X,Guo J,Liu H,Yao X

更新日期：2012-09-01 00:00:00

abstract：:The nature and strength of intermolecular Se⋯N interaction between selenium-containing compounds HSeX (X = CH3, NH2, CF3, OCH3, CN, OH, NO2, Cl, F), and NH3 have been investigated at the MP2/aug-cc-pVDZ level. The Se⋯N interaction is found to be dependent on the substituent groups, which greatly affect the positive el...

journal_title：Journal of molecular modeling

authors： Zhou F,Liu R,Tang J,Li P,Cui Y,Zhang H

更新日期：2016-01-01 00:00:00

abstract：:The complementarity plot (CP) is an established validation tool for protein structures, applicable to both globular proteins (folding) as well as protein-protein complexes (binding). It computes the shape and electrostatic complementarities (Sm, Em) for amino acid side-chains buried within the protein interior or inte...

journal_title：Journal of molecular modeling

authors： Basu S

更新日期：2017-12-07 00:00:00

abstract：:The crystal structure of the human cystatin C (hCC) dimer revealed that a stable twofold-symmetric dimer was formed via 3D domain swapping. Domain swapping with the need for near-complete unfolding has been proposed as a possible route for amyloid fibril initiation. Thus, the interesting interactions that occur betwee...

journal_title：Journal of molecular modeling

authors： He J,Xu L,Zhang S,Guan J,Shen M,Li H,Song Y

更新日期：2013-02-01 00:00:00

abstract：:The hydration free energies, structures, and dynamics of open- and closed-shell trivalent lanthanide and actinide metal cations are studied using molecular dynamics simulations (MD) based on a polarizable force field. Parameters for the metal cations are derived from an ab initio bottom-up strategy. MD simulations of ...

journal_title：Journal of molecular modeling

authors： Marjolin A,Gourlaouen C,Clavaguéra C,Ren PY,Piquemal JP,Dognon JP

更新日期：2014-10-01 00:00:00

abstract：:Theoretical studies on 1H-indole-3-acetic acid (IAA) were performed to investigate the conformational properties of dimeric species and vibrational spectra. Experimental infrared spectra at 100 K and 297 K and Raman spectrum at 297 K were analyzed and compared against calculations performed at B3LYP/6-31G** level. A e...

journal_title：Journal of molecular modeling

authors： Lobayan RM,Schmit MC,Jubert AH,Vitale A

更新日期：2011-06-01 00:00:00

abstract：:The structure and electronic properties of the complexes formed by the interaction of imidazole and pyrazole with different BeXH(BeX2) (X = H, Me, F, Cl) derivatives have been investigated via B3LYP/6-311+G(3df,2p)//B3LYP/6-31+G(d,p) calculations. The formation of these azole:BeXH(BeX2) complexes is accompanied by a d...

journal_title：Journal of molecular modeling

authors： Mó O,Yáñez M,Alkorta I,Elguero J

更新日期：2013-10-01 00:00:00

abstract：:The halogen bonding interactions between C6F5I and a series of transition metal monohalides trans-[M(X)(2-C5NF4)-(PR3)2] (M = Ni, Pd, Pt; X = F, Cl, Br; R = Me, Cy) have been studied with quantum chemical calculations. Optimized geometries of the halogen bonding complexes indicate that angles C1-I···X are basically li...

journal_title：Journal of molecular modeling

authors： Cheng N,Liu Y,Zhang C,Liu C

更新日期：2013-09-01 00:00:00

abstract：:To determine the kinase inhibitory potential of natural products that could be utilized in lung cancer therapy in the near future, a pharmacophore-based activity profiling protocol using parallel pharmacophore-based virtual screening of ZINC-a natural product database-was employed. The work presented here is based on ...

journal_title：Journal of molecular modeling

authors： Singh PK,Silakari O

更新日期：2018-10-20 00:00:00

abstract：:We report a DFT, TDDFT and DFTB investigation of the performance of two donor-π-acceptor (D-π-A)-type organic dyes bearing different electron-withdrawing groups (EWG) for dye-sensitized solar cells (DSSCs) to evaluate which EWG is better for an acrylic acid acceptor, i.e., Cyano (-CN) or o-nitrophenyl (o-NO2-Ph). A se...

journal_title：Journal of molecular modeling

authors： Zhang J,Kan YH,Li HB,Geng Y,Wu Y,Duan YA,Su ZM

更新日期：2013-04-01 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：:Quantum chemical calculations were performed for LiNH2-HMgX (X=H, F, Cl, Br, CH3, OH, and NH2) complexes to propose a new interaction mechanism between them. This theoretical survey showed that the complexes are stabilized through the combinative interaction of magnesium and lithium bonds. The binding energies are in ...

journal_title：Journal of molecular modeling

authors： Yang X,Li Q,Cheng J,Li W

更新日期：2013-01-01 00:00:00

abstract：:G-Quadruplex and i-Motif-forming sequences in the promoter regions of several oncogenes show promise as targets for the regulation of oncogenes. In this study, molecular models were created for the c-MYC NHE-III(1) (nuclease hypersensitivity element III(1)) from two 39-base complementary sequences. The NHE modeled her...

journal_title：Journal of molecular modeling

authors： Cashman DJ,Buscaglia R,Freyer MW,Dettler J,Hurley LH,Lewis EA

更新日期：2008-02-01 00:00:00

abstract：:In our work, three kinds of functional monomers were selected to modify polyacrylamide (PAM) or partially hydrolyzed polyacrylamide (HPAM) by molecular dynamics simulation so as to achieve the stronger salt-tolerance of modified HM-HPAM. The radius of gyration (R (g)), the hydrodynamic radius (...

journal_title：Journal of molecular modeling

authors： Yao L,Chen P,Ding B,Luo J,Jiang B,Zhou G

更新日期：2012-09-01 00:00:00

abstract：:Reactions of lithium halide (LiX, X = F, Cl, Br and I) and methyl halide (CH₃X, X = F, Cl, Br and I) have been investigated at the B3LYP/6-31G(d) level of theory using the microhydration model. Beginning with hydrated lithium ion, four or two water molecules have been conveniently introduced to these aqueous-phase hal...

journal_title：Journal of molecular modeling

authors： Zheng S,Xiong Y,Wang J

更新日期：2010-12-01 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