First principles studies of the graphene-phenol interactions.

abstract：:The double-histone fold is a rare protein fold in which two consecutive regions characterized by the typical structure of histones assemble together, thus giving a histone pseudodimer. Previously, this fold was found in a few prokaryotic histones and in the regulatory region of guanine-nucleotide exchange factors of t...

journal_title：Journal of molecular modeling

authors： Greco C,Sacco E,Vanoni M,De Gioia L

更新日期：2005-12-01 00:00:00

abstract：:Beta-lactamase (ampC) in general causes the onset of antibiotic resistance in pathogenic bacteria against the β-lactam antibiotics. Morganella morganii which belongs to the Proteae tribe of the Enterobacteriaceae family is a Gram-negative bacillus. Gram-negative bacteria are the key problematic agents among the human ...

journal_title：Journal of molecular modeling

authors： Alazmi M

更新日期：2020-07-07 00:00:00

abstract：:In the present work, conformational analysis of lignin models was accomplished by considering four cross-link types (3-5', β-5', α-O-4 and β-O-4) and three monomer units [guaiacyl (G), p-hydroxyphenyl (H) and syringyl (S)]. Analysis involving the 3-5' and β-5' dimers was conducted following the standard procedure, i.e...

journal_title：Journal of molecular modeling

authors： Castilho-Almeida EW,De Almeida WB,Dos Santos HF

更新日期：2013-05-01 00:00:00

abstract：:Recent ab initio investigations of some complexes formed between carbon dioxide and its analogues carbonyl sulfide, carbonyl selenide, carbon disulfide, and thiocarbonyl selenide and the common bases ammonia, water, phosphine, and hydrogen sulfide have revealed significant differences between the properties of those c...

journal_title：Journal of molecular modeling

authors： Ramasami P,Ford TA

更新日期：2015-02-01 00:00:00

abstract：:Several noble-gas-containing molecules XNgY were observed experimentally. However, the bonding in such systems is still not understood. Using natural bond orbital and natural resonance theory (NBO/NRT) methods, the present work investigated bonding of the title molecules. The results show that each of the studied XNgY...

journal_title：Journal of molecular modeling

authors： Song J,Su Y,Jia Y,Chen L,Zhang G

更新日期：2018-05-07 00:00:00

abstract：:The virtual combinatorial chemistry approach as a methodology for generating chemical libraries of structurally-similar analogs in a virtual environment was employed for building a general mixed virtual combinatorial library with a total of 53.871 6-FQ structural analogs, introducing the real synthetic pathways of thr...

journal_title：Journal of molecular modeling

authors： Minovski N,Perdih A,Solmajer T

更新日期：2012-05-01 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：:Quantum chemical calculations using density functional theory BP86/def2-TZVPP and ab initio methods at CCSD(T)/def2-TZVPP have been carried for the telluroketones H2A=Te (A = C, Si, Ge). DFT calculations have also been carried out for the ketones H2C=E (E = O, S, Se, Te) and for the complexes NHC → [H2A=Te] → B(C6F5)3...

journal_title：Journal of molecular modeling

authors： Jaufeerally NB,Ramasami P,Jerabek P,Frenking G

更新日期：2014-10-01 00:00:00

abstract：:The structures and stabilities of eleven N13+ and N13- isomers have been investigated with second-order Moller-Plesset (MP2) and density functional theory (DFT) methods. Five N13+ isomers and six N13- isomers are all reasonable local minima on their potential energy hypersurfaces. The most stable N13+ cation is struct...

journal_title：Journal of molecular modeling

authors： Yin PG,Li QS

更新日期：2004-02-01 00:00:00

abstract：:The heme-AB binding energies (AB = CO, O2) in a wild-type myoglobin (Mb) and two mutants (H64L, V68N) of Mb have been investigated in detail with both DFT and dispersion-corrected DFT methods, where H64L and V68N represent two different, opposite situations. Several dispersion correction approaches were tested in the ...

journal_title：Journal of molecular modeling

authors： Liao MS,Huang MJ,Watts JD

更新日期：2013-08-01 00:00:00

abstract：:Nanosecond molecular dynamics using the Ewald summation method have been performed to elucidate the structural and energetic role of the closing base pair in loop-loop RNA duplexes neutralized by Mg2+ counterions in aqueous phases. Mismatches GA, CU and Watson-Crick GC base pairs have been considered for closing the l...

journal_title：Journal of molecular modeling

authors： Golebiowski J,Antonczak S,Fernandez-Carmona J,Condom R,Cabrol-Bass D

更新日期：2004-12-01 00:00:00

abstract：:The quinolinol derivatives clioquinol (5-chloro-7-iodo-8-quinolinol, Quinoform) and cloxiquine (5-chloro-8-quinolinol) were studied experimentally in the solid state via ³⁵Cl NQR, ¹H-¹⁷O and ¹H-¹⁴N NQDR spectroscopies, and theoretically by density functional theory (DFT). The supramolecular synthon pattern of O-H···N ...

journal_title：Journal of molecular modeling

authors： Latosińska JN,Latosińska M,Tomczak MA,Seliger J,Zagar V

更新日期：2011-07-01 00:00:00

abstract：:A systematic investigation of the thermal conductivity of zigzag graphene nanoribbons (ZGNRs) doped with nitrogen and containing a vacancy defect was performed using reverse nonequilibrium molecular dynamics (RNEMD). The investigation showed that the thermal conductivity of the ZGNRs was significantly reduced by nitro...

journal_title：Journal of molecular modeling

authors： Yang H,Tang Y,Gong J,Liu Y,Wang X,Zhao Y,Yang P,Wang S

更新日期：2013-11-01 00:00:00

abstract：:The geometrical parameters and static electric properties of several metal porphyrin halides, including Fe(III) porphine chloride (FePCl), Fe(III) porphine bromide (FePBr), Fe(III) tetraphenylporphine chloride (FeTPPCl), aluminum phthalocyanine chloride (AlPcCl), gallium(III) phthalocyanine chloride (GaPcCl), and mang...

journal_title：Journal of molecular modeling

authors： Asghari-Khiavi M,Safinejad F

更新日期：2010-03-01 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：:Four clusters of ZnO, O-Zn-SR (-SR = ligand) and doping ZnO structures (with Cr, Cu, Al atoms) were investigated using density functional theory at theB3LYP/Lanl2dz level. The characteristics of Zn(3)O(3) and Zn(4)O(4) structures, which are the units of experimental wurtzite and zinc blende structures, were found to b...

journal_title：Journal of molecular modeling

authors： Wang C,Xu S,Ye L,Lei W,Cui Y

更新日期：2011-05-01 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：:Bacillus anthracis has been employed as an agent of bioterrorism, with high mortality, despite anti-microbial treatment, which strongly indicates the need of new drugs to treat anthrax. Shikimate pathway is a seven step biosynthetic route which generates chorismic acid from phosphoenol pyruvate and erythrose-4-phospha...

journal_title：Journal of molecular modeling

authors： Barcellos GB,Caceres RA,de Azevedo WF Jr

更新日期：2009-02-01 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：:Two important classes of organic molecules, perylene diimide (PDI) and pyrene derivatives have been found to possess relatively excellent photophysical and photochemical properties and especially high two-photon absorption cross sections (δ(T)(max)). Herein, one-photon absorption (OPA) and two-photon absorption (TPA) ...

journal_title：Journal of molecular modeling

authors： Liu XT,Zhao Y,Ren AM,Feng JK

更新日期：2011-06-01 00:00:00

abstract：:The stratum corneum, the outer layer of the epidermis, serves as a protective barrier to isolate the skin from the external environment. Keratinocyte transglutaminase 1 (TGase 1) catalyzes amide crosslinking between glutamine and lysine residues on precursor proteins forming the impermeable layers of the epidermal cel...

journal_title：Journal of molecular modeling

authors： Boeshans KM,Mueser TC,Ahvazi B

更新日期：2007-01-01 00:00:00

abstract：:The interpretation of mass spectra (ms) of molecules containing poly-isotopic elements (e.g. Ge, Se, W, Os, Sn, Te, Zn, Yb) can be difficult due to the occurrence of fragments resulting from isotopomeric composition. MS-clusters located in the range lower than or equal to M/2 are very difficult to interpret. In this a...

journal_title：Journal of molecular modeling

authors： Goraczko AJ,Szewczykowska K

更新日期：2009-06-01 00:00:00

abstract：:A molecular dynamics method was employed to study the binding energies associated with the cocrystallization (at selected crystal planes) of either 1,3,5-triamino-2,4,6-trinitro-benzene (TATB), 1,1-diamino-2,2-dinitroethylene, 3-nitro-1,2,4-triazol-5-one (TATB, FOX-7, and NTO, respectively, all of which are explosives...

journal_title：Journal of molecular modeling

authors： Song KP,Ren FD,Zhang SH,Shi WJ

更新日期：2016-10-01 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 stability of cyclic peptide assemblies (CPs) forming a macromolecular nanotube structure was investigated in solvents of different polarity using computational methods. The stability and structure of the complexes were studied using traditional molecular dynamics (MD). Energy of dissociation was estimated from ste...

journal_title：Journal of molecular modeling

authors： Vijayakumar V,Vijayaraj R,Peters GH

更新日期：2016-11-01 00:00:00

abstract：:The CO and O2 adsorption as well as CO oxidation on cationic, neutral, and anionic AuM dimers (M = Pd, Ag) are studied by density functional calculations. Our results show that CO and O2 are adsorbed more stably on AuPd dimers than on AuAg dimers with corresponding charge state. O2 is favorable to be adsorbed on Pd at...

journal_title：Journal of molecular modeling

authors： Chen X,Lu RF,Kan EJ,Liu YZ,Xiao CY,Deng KM

更新日期：2014-06-01 00:00:00

abstract：:Conjugate peak refinement (CPR) is a powerful and robust method to search transition states on a molecular potential energy surface. Nevertheless, the method was to the best of our knowledge so far only implemented in CHARMM. In this paper, we present PyCPR, a new Python-based implementation of the CPR algorithm withi...

journal_title：Journal of molecular modeling

authors： Gisdon FJ,Culka M,Ullmann GM

更新日期：2016-10-01 00:00:00

abstract：:Functionalized carbon nanotubes (CNTs) can be used for improving the mechanical properties and load transfer in nanocomposites. In this research, the buckling behavior of perfect and defective cross-linked functionalized CNTs with polyethylene (PE) chains is studied employing molecular dynamics (MD) simulations. Two d...

journal_title：Journal of molecular modeling

authors： Ajori S,Ansari R,Parsapour H

更新日期：2016-12-01 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：: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