Insights into the self-assembly steps of cyanuric acid toward rosette motifs: a DFT study.

abstract：:Three-dimensional pharmacophore models of human adenosine receptor A(₂A) antagonists were developed based on 23 diverse compounds selected from a large number of A(₂A) antagonists. The best pharmacophore model, Hypo1, contained five features: one hydrogen bond donor , three hydrophobic points and one ring aromatic. It...

journal_title：Journal of molecular modeling

authors： Xu Z,Cheng F,Da C,Liu G,Tang Y

更新日期：2010-12-01 00:00:00

abstract：:DFT computations were carried out to characterize the (17)Oand (2)H electric field gradient, EFG, in various bisphosphonate derivatives. The computations were performed at the B3LYP level with 6-311++G (d,P) standard basis set. Calculated EFG tensors were used to determine the (17)O and (2)H nuclear quadrupole couplin...

journal_title：Journal of molecular modeling

authors： Aghabozorg H,Sohrabi B,Mashkouri S,Aghabozorg HR

更新日期：2012-03-01 00:00:00

abstract：:The interactions between chemosensors, donor-π-acceptor (D-π-A) dipolar organoboron derivatives, and different (CN⁻, F⁻, Cl⁻, and Br⁻) anions have been theoretically investigated using DFT approaches. Theoretical investigations have been performed to explore the optical, electronic, charge transport, and stability pro...

journal_title：Journal of molecular modeling

authors： Jin R,Tang S,Luo D

更新日期：2014-03-01 00:00:00

abstract：:Our recent molecular dynamics (MD) simulation of an insertion/duplication mutant 'L20' of bacteriophage T4 lysozyme demonstrated a solvent induced α→β transition in a loosely held duplicate helical region, while α-helical conformation in the parent region was relatively stabilized by its tertiary interactions with the...

journal_title：Journal of molecular modeling

authors： Kaur H,Sasidhar YU

更新日期：2015-04-01 00:00:00

abstract：:DFT calculations were carried out on the homo- and hetero-bimetallic model wires [(η(5)-C5H5)(dpe)Fe-C≡C-C6H4-C≡C-Fe(dpe)(η(5)-C5H5)] (1'), [(η(7)-C7H7)(dpe)Mo-C≡C-C6H4-C≡C-Mo(dpe)(η(7)-C7H7)] (2'), and [(η(5)-C5H5)(dpe)Fe-C≡C-C6H4-C≡C-Mo(dpe)(η(7)-C7H7)] (3') used to tentatively mimic [(η(5)-C5Me5)(dppe)Fe-C≡C-C6H4-C...

journal_title：Journal of molecular modeling

authors： Ladjarafi A,Costuas K,Meghezzi H,Halet JF

更新日期：2015-04-01 00:00:00

abstract：:Epidermal growth factor receptors (EGFR) are associated with a number of biological processes and are becoming increasingly recognized as important therapeutic targets against cancer. In this work, we provide models based on homology for the extracellular domains (ECD) of ErbB3 and ErbB4 in their active conformations,...

journal_title：Journal of molecular modeling

authors： Franco-Gonzalez JF,Ramos J,Cruz VL,Martínez-Salazar J

更新日期：2013-02-01 00:00:00

abstract：:The design of stable and inexpensive artificial enzymes with potent catalytic activity is a growing field in peptide science. The first step in this design process is to understand the key factors that can affect the conformational preference of an enzyme and correlate them with its catalytic activity. In this work, m...

journal_title：Journal of molecular modeling

authors： Honarparvar B,Skelton AA

更新日期：2015-04-01 00:00:00

abstract：:In recent years, several new chelating reagents have been synthesized and tested for their collecting power in sulfide and non-sulfide minerals flotation. Many researchers have indicated that chelating reagents have the advantage of offering better selectivity and specificity as flotation collectors. Therefore, densit...

journal_title：Journal of molecular modeling

authors： Yekeler H,Yekeler M

更新日期：2006-09-01 00:00:00

abstract：:The nature of E-M bonds in CpE-MCp (E = B, Al, Ga; M = Li, Na, K; Cp = η (5)-C5H5) donor-acceptor sandwiches was studied using the atoms in molecules (AIM) theory, electron localization function (ELF), energy decomposition analysis (EDA), and natural bond orbital analysis (NBO) methods. Both topological and orbital an...

journal_title：Journal of molecular modeling

authors： Huo S,Meng D,Zhang X,Meng L,Li X

更新日期：2014-10-01 00:00:00

abstract：:The aquatic leech, Theromyzon tessulatum, secretes a proteinaceous cocoon with extraordinary physical properties (e.g., proteolytic, thermal resiliency). The deduced amino acid sequence of a major protein (Tcp-Theromyzon cocoon protein) from the T. tessulatum cocoon wall has been used to model the endogenous structure...

journal_title：Journal of molecular modeling

authors： Mason TA,McIlroy PJ,Shain DH

更新日期：2006-09-01 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：:With the help of quantum mechanical calculations, we have examined the series of central system X(ML)(3) (+)(X = O, S, Se; M = Au, Ag, Cu). Using a scalar-relativistic density functional approach, we studied the geometry structures, Mulliken populations and charges of the systems. Structure parameters of the experimen...

journal_title：Journal of molecular modeling

authors： Fang H,Wang SG

更新日期：2007-01-01 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 electron transport of the 4-(3-nitro-4-tetrafluorophenylthiolate-ethynyl, phenylethynyl) benzenethiolate (S-FNPPB-o) molecule assembled in two Au (111) electrodes, was studied using two approaches: in the first approximate approach an electric field was applied to the pure molecule attached to two thiolate ends fi...

journal_title：Journal of molecular modeling

authors： Serrato-Villegas L,Gallo M,Delgado-Ríos M,Romero MT,Glossman-Mitnik D

更新日期：2012-02-01 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：:We present a theoretical investigation of the electric properties of two kinds of one-dimensional lithium bonded chains: (NC-Li)n and (NC-CC-Li)n (n = 1-8). The resulting (NC-Li)n and (NC-CC-Li)n were found to exhibit enhanced first hyperpolarizabilities (β 0) with increasing n, and a slight change in the absorption m...

journal_title：Journal of molecular modeling

authors： Ma F,Bai D,Xu H

更新日期：2014-12-01 00:00:00

abstract：:The treatment of neuropathic pain is very complex and there are few drugs approved for this purpose. Among the studied compounds in the literature, sigma-1 receptor antagonists have shown to be promising. In order to develop QSAR studies applied to the compounds of 1-arylpyrazole derivatives, multivariate analyses hav...

journal_title：Journal of molecular modeling

authors： Oliveira AA,Lipinski CF,Pereira EB,Honorio KM,Oliveira PR,Weber KC,Romero RAF,de Sousa AG,da Silva ABF

更新日期：2017-10-02 00:00:00

abstract：:Ergothioneine (2-mercaptohistidine trimethylbetaine) is a very stable natural compound largely present in cells and tissues of plants and mammals. The biological role of ET is still incompletely understood but its antioxidant properties are well assessed experimentally. However, no theoretical study had been performed...

journal_title：Journal of molecular modeling

authors： Lespade L

更新日期：2019-10-26 00:00:00

abstract：:The geometric and electronic structure of tetracyanoethylene (TCNE)-aniline (donor-acceptor type) complex has been investigated in gas phase using ab initio and time dependent density functional theory calculations. Both the above calculations predict a composed structure for the complex, in which the interacting site...

journal_title：Journal of molecular modeling

authors： Manna T,Bhattacharya S

更新日期：2009-08-01 00:00:00

abstract：:Density functional theory and its time-dependent extension (DFT, TDDFT) were employed to establish the feasibility of using a series of 4,4-difluoro-4-bora-3a,4a-diaza-s-indacenes (BODIPYs) in photodynamic therapy. Their absorption electronic spectra, singlet-triplet energy gaps, and spin-orbit matrix elements were co...

journal_title：Journal of molecular modeling

authors： Ponte F,Mazzone G,Russo N,Sicilia E

更新日期：2018-06-29 00:00:00

abstract：:The role of resultant gradient-information concept, reflecting the kinetic energy of electrons, in shaping the molecular electronic structure and reactivity preferences of open reactants is examined. This quantum-information descriptor combines contributions due to both the modulus (probability) and phase (current) co...

journal_title：Journal of molecular modeling

authors： Nalewajski RF

更新日期：2019-08-16 00:00:00

abstract：:Comprehensive molecular dynamics simulations are conducted to identify material modifications which can improve strength and reduce hysteresis losses at the nanointerfaces formed between silica, silane coupling agent (SCA) and styrene-butadiene rubber (SBR), all of which are important ingredients of green tyres. Impro...

journal_title：Journal of molecular modeling

authors： Joseph E,Swaminathan N,Kannan K

更新日期：2020-08-17 00:00:00

abstract：:We tested different approaches to including the effect of binding-site water molecules for ligand-binding affinities within the MM/GBSA approach (molecular mechanics combined with generalised Born and surface-area solvation). As a test case, we studied the binding of nine phenol analogues to ferritin. The effect of wa...

journal_title：Journal of molecular modeling

authors： Mikulskis P,Genheden S,Ryde U

更新日期：2014-06-01 00:00:00

abstract：:Faced with the worldwide spread of multidrug-resistant (MDR) bacterial strains, together with a lack of any appropriate treatment, urgent steps to combat infectious diseases should be taken. Usually, bacterial components are studied to understand, by analogy, the functioning of human proteins. However, molecular data ...

journal_title：Journal of molecular modeling

authors： Wiczew D,Borowska A,Szkaradek K,Biegus T,Wozniak K,Pyclik M,Sitarska M,Jaszewski L,Radosinski L,Hanus-Lorenz B,Kraszewski S

更新日期：2019-06-11 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：: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：:49Ti chemical shifts for a total of 20 titanium complexes are reported, and several levels of theory are evaluated in order to identify a reliable approach for the calculation of titanium NMR data. The popular B3LYP/6-31G(d)//B3LYP/6-31G(d) proves to give very good agreement with experimental data over a range from 1,...

journal_title：Journal of molecular modeling

authors： Koch R,Bruhn T

更新日期：2006-07-01 00:00:00

abstract：:The formation of selenium species in some biological processes involves the generation of ionic and radical intermediates such as RSe●, RSe-, RSeO●, and RSeO-, among others. We performed a theoretical study of the possible mechanisms for the reaction of the two simplest Se radicals-the hydroselenyl (HSe●) and seleneni...

journal_title：Journal of molecular modeling

authors： Vega-Teijido MA,Kieninger M,Ventura ON

更新日期：2017-12-05 00:00:00

abstract：:Zeolites are a group of microporous aluminosilicate frameworks with numerous applications in, for example, catalysis and ion-exchange and sorption processes. One of the most important tools for analyzing the properties of zeolite structures is vibrational spectroscopy. However, the complexity of these structures often...

journal_title：Journal of molecular modeling

authors： Mikuła A,Król M,Koleżyński A

更新日期：2015-10-01 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