Abstract：
:The first and second moment operators are used to define the origin invariant shape and size of a molecule or functional group, as well as expressions for the distance between two electrons and the distance between an electron and a nucleus. The measure of molecular size correlates quite well with an existing theoretical measure of molecular volume calculated from isodensity contours. Also, the measure of size is effective in predicting steric effects of substituents which have been measured experimentally. The electron-electron and electron-nuclear distances are related to components of the Hartree-Fock energy. The average distance between two-electrons can model the Coulomb energy quite well, especially in the case of localized molecular orbitals. The average distance between an electron and a nucleus is closely related to the electron-nuclear attraction energy of a molecule.
journal_name
J Mol Modeljournal_title
Journal of molecular modelingauthors
Hollett JW,Poirier RAdoi
10.1007/s00894-008-0391-zsubject
Has Abstractpub_date
2009-06-01 00:00:00pages
739-45issue
6eissn
1610-2940issn
0948-5023journal_volume
15pub_type
杂志文章abstract：:The reaction pathways of several Friedel-Crafts acylations involving phenyl aromatic compounds were studied using density functional theory. The reactions were related to the Friedel-Crafts polycondensation of polyaryletherketones. In particular, the acylation of benzene with benzoyl chloride to form benzophenone and ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-013-1984-8
更新日期：2013-11-01 00:00:00
abstract：:The electric field induced within a molecule by its electrons determines a whole series of important physical properties of the molecule. In particular, the values of the gradient of this field at the nuclei determine the interaction of their quadrupole moments with the electrons. Using unsymmetrical one-range additio...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-010-0851-0
更新日期：2011-06-01 00:00:00
abstract：:The unsaturated trinuclear iron fluoroborylene complexes Fe3(BF)3(CO) n (n = 7, 6) have been studied using density functional theory (DFT). Relatively complicated potential energy surfaces are found with nine and eight structures within 15 kcal mol-1 of the lowest energy structures for the Fe3(BF)3(CO)7 and Fe3(BF)3(C...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-017-3301-4
更新日期：2017-04-01 00:00:00
abstract：:Models of the hydrogenoxalate (bioxalate, charge -1) and oxalate (charge -2) anions were developed for classical molecular dynamics (CMD) simulations and parametrized against ab initio molecular dynamics (AIMD) data from our previous study (Kroutil et al. (2016) J Mol Model 22:210). The interactions of the anions with...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-017-3490-x
更新日期：2017-10-28 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
pub_type： 杂志文章
doi：10.1007/s00894-014-2196-6
更新日期：2014-04-01 00:00:00
abstract：:Density functional calculations have been used to investigate the interactions of 1-(2-hydroxyethyl)-3-methylimidazolium ([C2OHmim](+))-based ionic liquids (hydroxyl ILs) with water (H2O), methanol (CH3OH), and dimethyl sulfoxide (DMSO). It was found that the cosolvent molecules interact with the anion and cation of e...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-016-3063-4
更新日期：2016-08-01 00:00:00
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
pub_type： 杂志文章
doi：10.1007/s00894-008-0441-6
更新日期：2009-07-01 00:00:00
abstract：:The average pull-out force and interaction energy of polyethylene (PE) cross-linked functionalized carbon nanotubes (cfCNTs) embedded in polymer matrices (PE-cfCNTs@polymers) was studied using molecular dynamics (MD) simulations. Accordingly, the pull-out process of PE-cfCNTs from inside polymer matrices, i.e., Aramid...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-019-3983-x
更新日期：2019-03-29 00:00:00
abstract：:Ab initio and molecular simulation methods were used in calculations of the neutral individual betulin molecule, and molecular simulations were used to optimize the betulin molecule immersed in various amounts of water. Individual betulin was optimized in different force fields to find the one exhibiting best agreemen...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-011-1055-y
更新日期：2012-01-01 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
pub_type： 杂志文章
doi：10.1007/s00894-013-1845-5
更新日期：2013-08-01 00:00:00
abstract：:We design four high performance non-fullerene acceptor materials by applying strong electron withdrawing groups at the end of A-D-A-D-A type organic solar cells molecules and compute their different opto-electronic and photovoltaic properties, including absorption spectrum, electron density, solubility strength, charg...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-019-3932-8
更新日期：2019-01-31 00:00:00
abstract：:Selective poly (ADP-ribose) polymerase (PARP)-1 inhibitor represents promising therapy against cancers with a good balance between efficacy and safety. Owing to the conserved structure between PARP-1 and PARP-2, most of the clinical and experimental drugs show equivalent inhibition against both targets. Most recently,...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-016-2952-x
更新日期：2016-04-01 00:00:00
abstract：:In this paper, we theoretically studied the geometries, stabilities, and the electronic and thermodynamic properties of 4H-cyclopenta[2,1-b,3;4-b']dithiopene S-oxide derivatives (BTO-X, with X = BH(2), SiH(2), S, S=O, or O) using semi-empirical methods, ab initio methods, and density functional theory. The geometries ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-011-1291-1
更新日期：2012-06-01 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
pub_type： 杂志文章
doi：10.1007/s00894-011-1257-3
更新日期：2012-06-01 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
pub_type： 杂志文章
doi：10.1007/s00894-011-1018-3
更新日期：2012-01-01 00:00:00
abstract：:Drug resistance is a very important factor contributing to the failure of current HIV therapies. The ability to understand the resistance mechanism of HIV-protease mutants may be useful in developing more effective and longer lasting treatment regimens. In this paper, we report the first computational study of the cli...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-006-0121-3
更新日期：2007-02-01 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
pub_type： 杂志文章
doi：10.1007/s00894-013-1864-2
更新日期：2013-08-01 00:00:00
abstract：:In this paper, coupled cluster methods CC2, CCSD, CCSDR(3) and EOM-CCSD(T) have been benchmarked against CC3 for the transition energies of nucleobases. Beside presenting vertical excitation energies for about 30 singlet transitions of four molecules, the results are analyzed statistically and problematic cases have b...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-014-2503-2
更新日期：2014-11-01 00:00:00
abstract：:The unusual π-halogen bond interactions are investigated between (BNN)₃⁺ and X1X2 (X1, X2 = F, Cl, Br) employing MP2 at 6-311 + G(2d) and aug-cc-pVDZ levels according to the "CP (counterpoise) corrected potential energy surface (PES)" method. The order of the π-halogen bond interactions and stabilities of the complexe...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-010-0790-9
更新日期：2011-05-01 00:00:00
abstract：:First principles calculations have been performed for C60@C180 carbon double-layer endofullerenes with up to: three diatomic radioiodine molecules (131I2), two potassium radio-iodide (K131I), and three sodium radio-iodide (Na131I) inside. The plane-wave pseudopotential (PP) method within the general gradient approxima...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-017-3538-y
更新日期：2017-12-04 00:00:00
abstract：:In the absence of interlogs, building docking models is a time intensive task, involving generation of a large pool of docking decoys followed by refinement and screening to identify near native docking solutions. This limits the researcher interested in building docking methods with the choice of benchmarking only a ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-010-0758-9
更新日期：2011-03-01 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
pub_type： 杂志文章
doi：10.1007/s00894-003-0172-7
更新日期：2004-04-01 00:00:00
abstract：:The CFIm25 subunit of the heterotetrameric cleavage factor Im (CFIm) is a critical factor in the formation of the poly(A) tail at mRNA 3' end, regulating the recruitment of polyadenylation factors, poly(A) site selection, and cleavage/polyadenylation reactions. We previously reported the homologous protein (EhCFIm25) ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-018-3729-1
更新日期：2018-07-12 00:00:00
abstract：:The interaction between tetramethylcucurbit[6]uril (host) and 5,5'-dimethyl-2,2'-bipyridyl hydrochloride (guest) was studied by 1H NMR, X-ray crystallography, electronic absorption spectroscopy, fluorescence emission spectra and quantum chemistry calculations. This experimental-computational study that indicated the h...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-007-0243-2
更新日期：2007-12-01 00:00:00
abstract：:The geometries of three isomers of the C2H4O...2HF tri-molecular heterocyclic hydrogen-bonded complex were examined through B3LYP/aug-cc-pVDZ calculations. Analysis of structural parameters, determination of CHELPG (charge electrostatic potential grid) intermolecular charge transfer, interpretation of infrared stretch...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-008-0337-5
更新日期：2008-10-01 00:00:00
abstract：:Cation-π interactions are known to be one of the strongest noncovalent forces in the gas phase, but they rarely occur in a fully solvated environment. The present work used two different ab initio molecular dynamics-based approaches to describe the correlation between the strength of the cation-π interactions and the ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-012-1433-0
更新日期：2012-09-01 00:00:00
abstract：:In this work we present the results of a study of the X-ray structure of 2-[(2,4-dimethoxyphenyl)amino]-1,3-thiazolidin-4-one. Using the FTIR spectra in solid state and results of ab initio calculations we explain the issue of the tautomerism of this molecule. The compound is shown to exist as the 2-amino tautomer rat...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-014-2366-6
更新日期：2014-08-01 00:00:00
abstract：:The biological toxicity of uranyl ion (UO (2) (2+) ) lies in interacting with proteins and disrupting their native functions. The structural and functional consequences of UO (2) (2+) interacting with cytochrome b (5) (cyt b (5)), a small membrane heme protein, and its heme axial ligand His39Ser variant, cyt b (5) H39...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-011-1097-1
更新日期：2012-03-01 00:00:00
abstract：:White spot disease caused by the white spot syndrome virus (WSSV) incurs a huge loss to the shrimp farming industry. Since no effective therapeutic measures are available, early detection and prevention of the disease are indispensable. Towards this goal, we previously identified a 12-mer phage displayed peptide (desi...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-020-04524-z
更新日期：2020-09-10 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
pub_type： 杂志文章
doi：10.1007/s00894-019-4028-1
更新日期：2019-08-16 00:00:00
