Addition theorems for Slater-type orbitals in momentum space and their application to three-center overlap integrals.

abstract：:The Solanum lycopersicum aspartic protease inhibitor (SLAPI), which belongs to the STI-Kunitz family, is an effective inhibitor of the aspartic proteases human cathepsin D and Saccharomyces proteinase A. However, in contrast with the large number of studies on the inhibition mechanism of the serine proteases by the ST...

journal_title：Journal of molecular modeling

authors： Guerra Y,Valiente PA,Berry C,Pons T

更新日期：2012-06-01 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：:In this paper, we assessed the quantum mechanical level of theory for prediction of linear and nonlinear optical (NLO) properties of push-pull organic molecules. The electric dipole moment (μ), mean polarizability ([Symbol: see text]α[Symbol: see text]) and total static first hyperpolarizability (βt) were calculated f...

journal_title：Journal of molecular modeling

authors： Paschoal D,Santos HF

更新日期：2013-05-01 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：: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：:Nitrogen (N)-doped carbons reportedly exhibit good electrocatalytic activity for the oxygen reduction reaction (ORR) of fuel cells. This work provides theoretical insights into the ORR mechanism of N-doped graphene by using density functional theory calculations. All possible reaction pathways were investigated, and t...

journal_title：Journal of molecular modeling

authors： Zhang J,Wang Z,Zhu Z

更新日期：2013-12-01 00:00:00

abstract：:Chemokine receptor 2 (CCR2) is a G-protein coupled receptor (GPCR) and a crucial target for various inflammatory and autoimmune diseases. The structure based antagonists design for many GPCRs, including CCR2, is restricted by the lack of an experimental three dimensional structure. Homology modeling is widely used for...

journal_title：Journal of molecular modeling

authors： Kim JH,Lim JW,Lee SW,Kim K,No KT

更新日期：2011-10-01 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：:Here, we report a structure-based virtual screening of the ZINC database (containing about five million compounds) by computational docking and the analysis of docking energy calculations followed by in vitro screening against H. pylori urease enzyme. One of the compounds selected showed urease inhibition in the low m...

journal_title：Journal of molecular modeling

authors： Azizian H,Nabati F,Sharifi A,Siavoshi F,Mahdavi M,Amanlou M

更新日期：2012-07-01 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：:A comparative theoretical investigation into the change in strength of the trigger-bond upon formation of the Na(+), Mg(2+) and HF complexes involving the nitro group of RNO₂ (R = -CH₃, -NH₂, -OCH₃) or the C = C bond of (E)-O₂N-CH = CH-NO₂ was carried out using the B3LYP and MP2(full) methods with the 6-311++G**, 6-31...

journal_title：Journal of molecular modeling

authors： Zhang L,Ren FD,Cao DL,Wang JL,Gao JF

更新日期：2013-06-01 00:00:00

abstract：:In erythrocytes, actively multiplying Plasmodium falciparum parasites exhibit a unique signature of virulence associated histone modifications, thereby epigenetically regulating the expression of the majority of genes. Histone acetylation is one such modification, effectuated and maintained by the dynamic interplay of...

journal_title：Journal of molecular modeling

authors： Kumar A,Dhar SK,Subbarao N

更新日期：2018-08-14 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：:Theoretical and spectroscopic studies of a series of monomeric and dimeric complexes formed through the modification of a zirconium butoxide precursor with acetylacetone and subsequent hydrolysis and/or condensation have been performed by applying DFT/B3LYP/6-31++G(d) and highly accurate RI-ADC(2) methods as well as I...

journal_title：Journal of molecular modeling

authors： Georgieva I,Danchova N,Gutzov S,Trendafilova N

更新日期：2012-06-01 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：:The internal rotation in ammonia borane (AB) was studied on the basis of natural orbitals for chemical valence (NOCV) and eigenvectors for Pauli repulsion (NOPR). We found that the total hyperconjugation stabilization (ca. 5 kcal mol(-1)), based on the charge transfer from the occupied σ (B-H) orbitals into the empty ...

journal_title：Journal of molecular modeling

authors： Parafiniuk M,Mitoraj MP

更新日期：2014-06-01 00:00:00

abstract：:Through comparison with ab initio reference data, we have evaluated the performance of various density functionals for describing pi-pi interactions as a function of the geometry between two stacked benzenes or benzene analogs, between two stacked DNA bases, and between two stacked Watson-Crick pairs. Our main purpose...

journal_title：Journal of molecular modeling

authors： Swart M,van der Wijst T,Fonseca Guerra C,Bickelhaupt FM

更新日期：2007-12-01 00:00:00

abstract：:The total energies, growth patterns, equilibrium geometries, relative stabilities, hardnesses, intramolecular charge transfer, and magnetic moments of HoSi n (n = 12-20) clusters have been reexamined theoretically using two different density functional schemes in combination with relativistic small-core Stuttgart effe...

journal_title：Journal of molecular modeling

authors： Hou L,Yang J,Liu Y

更新日期：2016-08-01 00:00:00

abstract：:A density functional theory augmented by the long-range corrected hybrid density functional ωB97XD and 6-31G(d,p) basis set has been applied to generate sandwich structures consist of nanocomposites between graphene oxide and polyvinyl alcohol. We predicted the interaction energies and discuss the contribution of elec...

journal_title：Journal of molecular modeling

authors： Gorb L,Ilchenko M,Leszczynski J

更新日期：2020-06-25 00:00:00

abstract：:In this work, hybrid functional and G4 methods were employed in the rational design of carbonitrile-carboxaldehyde receptor models for cation recognition. Electron-sharing and ionic interactions between the models and the cations were analyzed utilizing the concepts of overlap population, atomic valence, electrostatic...

journal_title：Journal of molecular modeling

authors： Rosli AN,Abu Bakar MA,Lee VS,Zain SM,Ahmad MR,Abdul Manan NS,Alias Y,Woi PM

更新日期：2014-09-01 00:00:00

abstract：:ORF 3a of human severe acute respiratory syndrome corona virus (SARS-CoV) has been identified as a 274 amino acid membrane protein. When expressed in Xenopus oocytes the protein forms channels. Based on bioinformatics approaches the topology has been identified to include three transmembrane domains (TMDs). Since stru...

journal_title：Journal of molecular modeling

authors： Hsu HJ,Fischer WB

更新日期：2012-02-01 00:00:00

abstract：:Given the increasing complexity of simulated molecular systems, and the fact that simulation times have now reached milliseconds to seconds, immense amounts of data (in the gigabyte to terabyte range) are produced in current molecular dynamics simulations. Manual analysis of these data is a very time-consuming task, a...

journal_title：Journal of molecular modeling

authors： Victor Paul Raj FR,Exner TE

更新日期：2014-04-01 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：:A density functional theory investigation of adsorption of monomer, dimer and trimer forms of pyrrole on the outer surface of zigzag (7,0) single-walled carbon nanotube (SWCNT) has been reported. Geometries of the complexes were optimized using the M06-2X functional and the 6-31G(d,p) basis set. Moreover, 6-311G(d,p),...

journal_title：Journal of molecular modeling

authors： Shukla MK,Boddu V,Hill F

更新日期：2014-09-01 00:00:00

abstract：:The preferential selectivity of dicyclohexano-18-crown-6 (DCH18C6) for bivalent Sr(+2) ion over tetravalent Th(+4) ion was investigated using generalized gradient approximated (GGA) BP86 and the hybrid B3LYP density functional, employing split valence plus polarization (SV(P)) and triple-zeta valence plus polarization...

journal_title：Journal of molecular modeling

authors： Boda A,Joshi JM,Ali SM,Shenoy KT,Ghosh SK

更新日期：2013-12-01 00:00:00

abstract：:HP1γ, a non-histone chromatin protein, has elicited significant attention because of its role in gene silencing, elongation, splicing, DNA repair, cell growth, differentiation, and many other cancer-associated processes, including therapy resistance. These characteristics make it an ideal target for developing small d...

journal_title：Journal of molecular modeling

authors： Velez G,Lin M,Christensen T,Faubion WA,Lomberk G,Urrutia R

更新日期：2016-01-01 00:00:00

abstract：:Conjugated organic polymers represent an important class of materials for varied technological applications including in active layers of chemical sensors. In this context, polyaniline (PANI) derivatives are promising candidates, mainly due to their high chemical stability, good processability, versatility of synthesi...

journal_title：Journal of molecular modeling

authors： Mandú LO,Batagin-Neto A

更新日期：2018-06-09 00:00:00

abstract：:The structures of non-ionic [Ag(Tu)(CN)] (1) and ionic [Ag(Dmtu)2]+[Ag(CN)2]- (2) and [Ag(Imt)2]+[Ag(CN)2]- (3) silver(I) complexes, where Tu = thiourea, Dmtu = N,N'-dimethylthiourea and Imt = imidazoline-2-thione), were modeled by periodic DFT/PAW-PBE calculations; results were in good agreement with experiments. The...

journal_title：Journal of molecular modeling

authors： Ahmad S,Georgieva I,Hanif M,Monim-Ul-Mehboob M,Munir S,Sohail A,Isab AA

更新日期：2019-03-08 00:00:00

abstract：:Fifteen KSP inhibitors were docked into the receptor and the binding mode was analyzed for the first time. It was considered that in addition to the main binding pocket all the inhibitors merged in, there exists a cooperative minor binding pocket, which could be explored for significantly increased binding affinity. I...

journal_title：Journal of molecular modeling

authors： Jiang C,Chen Y,Wang X,You Q

更新日期：2007-09-01 00:00:00

abstract：:Eleven 1,4-naphthoquinone analogues with different amino substitutions at position 3 of the quinone ring earlier reported for macrofilaricidal activity were selected and screened against purified cytosolic GST isolated from the bovine filarial worm Setaria digitata and IC(50) values were determined. Of the 11 compound...

journal_title：Journal of molecular modeling

authors： Mathew N,Srinivasan L,Karunan T,Ayyanar E,Muthuswamy K

更新日期：2011-10-01 00:00:00