Abstract:
:We have used density-functional theory to investigate the neighboring-group stabilization of iodine, arsenic, and phosphorus-centered oxyanion moieties in species such as deprotonated 2-iodoxybenzoic acid (IBX) and its analogs. The magnitudes of different stabilizing effects and further candidates for analogous stabilization are analyzed.
journal_name
J Mol Modeljournal_title
Journal of molecular modelingauthors
O'Hair RA,Williams CM,Clark Tdoi
10.1007/s00894-009-0567-1subject
Has Abstractpub_date
2010-03-01 00:00:00pages
559-65issue
3eissn
1610-2940issn
0948-5023journal_volume
16pub_type
杂志文章abstract::The ONIOM2 (B3LYP/6-31G (d, p): PM3) and B3LYP/6-31G (d, p) methods were applied to investigate the interaction between STI-571 and abelson tyrosine kinase binding site. The complex of N-[4-methyl-3-(4-pyridin-3-yl-pyrimidin-2-ylamino)- phenyl]-benzamide (part of STI-571) and related 16 amino acid residues were found ...
journal_title:Journal of molecular modeling
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abstract::Leishmaniasis is an endemic disease caused by infection with one of several different species of protozoan parasite Leishmania. Oligopeptidase B (OPB) is a serine peptidase which plays a vital role in survival of the Leishmania parasite in the host (human) macrophage and help in attaining complete virulence. Inhibitio...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-014-2099-6
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abstract::Human dihydrofolate reductase-like 1 (DHFRL1) has been identified as a second human dihydrofolate reductase (DHFR) enzyme. Although DHFRL1 have high sequence homology with human DHFR, dihydrofolate (DHF) exhibits a lowered binding affinity to DHFRL1 and the corresponding molecular mechanism is still unknown. To addres...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-013-2018-2
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更新日期:2020-04-03 00:00:00
abstract::Molecular-dynamics simulations have been used to study the diffusion of a short single model carbonic chain on the graphite (001) surface. The calculated diffusion coefficient (D) first increases, then decreases with increasing chain length (N). This abnormal behavior is similar to polymer lateral diffusion at the sol...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-005-0064-0
更新日期:2006-03-01 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
pub_type: 杂志文章
doi:10.1007/s00894-003-0150-0
更新日期:2003-12-01 00:00:00
abstract::Aminoglycoside-arginine conjugates (AAC and APAC) are multi-target inhibitors of human immunodeficiency virus type-1 (HIV-1). Here, we predict new conjugates of neomycin with two arginine peptide chains binding at specific sites on neomycin [poly-arginine-neomycin-poly-arginine (PA-Neo-PA)]. The rationale for the desi...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-008-0401-1
更新日期:2009-03-01 00:00:00
abstract::Nearly all RNA viruses produce double-stranded RNA (dsRNA) during their replication cycles--an important pathogen-associated molecular pattern recognized by the RNA interference (RNAi) pathway in invertebrates and plants. Nodamura virus (NoV) encodes a suppressor of RNA silencing termed B2, which binds to dsRNA and pr...
journal_title:Journal of molecular modeling
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更新日期:2014-03-01 00:00:00
abstract::Compound P131 has been established to inhibit Cryptosporidium parvum's inosine monophosphate dehydrogenase (CpIMPDH). Its inhibitory activity supersedes that of paromomycin, which is extensively used in treating cryptosporidiosis. Through the per-residue energy decomposition approach, crucial moieties of P131 were ide...
journal_title:Journal of molecular modeling
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更新日期:2021-01-09 00:00:00
abstract::Understanding how temperature affects the electronic transitions of BFO is important for design of BiFeO3 (BFO)-based temperature-sensitive device. Hitherto, however, there have been only very limited reports of the quantitative simulation. Here, we used density functional theory (DFT) and two-dimensional correlation ...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-015-2583-7
更新日期:2015-04-01 00:00:00
abstract::The effects of different monoterpenes and 2-cyclohexen-1-one on the antibacterial activity of nitrofurantoin against resistant Enterobacter cloacae, were compared and the minimal structural component of monoterpene required for the highest level of resistance-modulating activity was determined. Subinhibitory concentra...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-015-2741-y
更新日期:2015-08-01 00:00:00
abstract::The Grand Canonical Monte Carlo method was used to analyse the phenomenon of adsorption of aromatic compounds (i.e. phenol, toluene, benzoic acid and salicylic acid) on the surface of the titania-silica (TiO2/SiO2) catalyst. We found that different types of interactions play important roles in the adsorption of molecu...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-007-0189-4
更新日期:2007-07-01 00:00:00
abstract::We examine a short way to reach an exceptional point that corresponds to a coalescence of two resonance energies. The application concerns the photodissociation of the Na2 molecule exposed to a laser field. In this case, the resonances can be correlated with the field-free vibrational states of the diatomic species. T...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-012-1556-3
更新日期:2013-05-01 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
pub_type: 杂志文章
doi:10.1007/s00894-015-2645-x
更新日期:2015-04-01 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::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
pub_type: 杂志文章
doi:10.1007/s00894-015-2621-5
更新日期:2015-04-01 00:00:00
abstract::The substituted effect on excited-state intramolecular proton transfer (ESIPT) of o-LHBDI derivatives (4R-o-LHBDI) was investigated by DFT and TD-DFT methods. The structures of 4R-o-LHBDI (R: OH, NH2, CN, NO2, CF3) were fully optimized, and the H-bond distances, bond angles, and infrared spectra of the atoms involved ...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-020-04378-5
更新日期:2020-04-23 00:00:00
abstract::A novel mechanism for switching a molecular junction based on a proton transfer reaction triggered by an external electrostatic field is proposed. As a specific example to demonstrate the feasibility of the mechanism, the tautomers [2,5-(4-hydroxypyridine)] and {2,5-[4(1H)-pyridone]} are considered. Employing a combin...
journal_title:Journal of molecular modeling
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journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-017-3428-3
更新日期:2017-08-14 00:00:00
abstract::Understanding the interaction between graphene and polymers is of essential interest when designing novel nanocomposites with reinforced mechanical and electrical properties. In this computational study, the interaction of pristine graphene (PG) and graphene oxide (GO) with a series of functional groups, representativ...
journal_title:Journal of molecular modeling
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更新日期:2017-02-01 00:00:00
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journal_title:Journal of molecular modeling
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doi:10.1007/s00894-014-2554-4
更新日期:2015-03-01 00:00:00
abstract::A practical mixed basis set was developed to facilitate accurate calculations of potential energy surfaces for π-stacking interactions. Correlation consistent basis sets (cc-PVXZ) were augmented by p-type Gaussian functions placed above and below the planes of C6 moieties. Møller-Plesset (MP2, SCS-MP2) and coupled clu...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-014-2558-0
更新日期:2015-01-01 00:00:00
abstract::PcFK1 is a member of the cysteine knot inhibitor family that displays anti-malarial properties. The naturally occurring molecule is ∼ 40 amino acids in length and forms a highly constrained 3D structure due to the presence of 3 disulfide and multiple intra-molecular H-bonds. Recent experimental studies on PcFK1 wild-t...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-010-0732-6
更新日期:2011-04-01 00:00:00
abstract::Quantum chemical calculations on the isomerization of 24-methylenecycloartanol are described. An energetically viable mechanism, with a rate-determining protonation step, is proposed. This rearrangement may find applicability in tests for determining if an olive oil has been refined. ...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-015-2652-y
更新日期:2015-05-01 00:00:00
abstract::Natural hIFNγ is a glycoprotein with two N-glycosylation sites in each monomer chain, which are independently and differentially glycosylated. Although glycosylation is not necessary for the activity of the cytokine, it was proposed that it protects the cytokine from proteolytic degradation and thus extends its circul...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-019-4013-8
更新日期:2019-04-25 00:00:00
abstract::A theoretical study of the chemisorption and dissociation pathways of water on the Al₁₃ cluster was performed using the hybrid density functional B3LYP method with the 6-311+G(d, p) basis set. The activation energies, reaction enthalpies, and Gibbs free energy of activation for the reaction were determined. Calculatio...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-012-1730-7
更新日期:2013-04-01 00:00:00
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journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-013-1860-6
更新日期:2013-08-01 00:00:00
abstract::The drug discovery process typically involves target identification and design of suitable drug molecules against these targets. Despite decades of experimental investigations in the drug discovery domain, about 96% overall failure rate has been recorded in drug development due to the "undruggability" of various ident...
journal_title:Journal of molecular modeling
pub_type: 杂志文章,评审
doi:10.1007/s00894-020-04385-6
更新日期:2020-05-08 00:00:00
abstract::In this work, the spectroscopic information, stability and aromaticity of the boron-nitrogen azulene and naphthalene molecules are provided by the use of CC2 (geometry optimization, dipole moment, UV-vis spectrum calculations) and DFT (vibrational spectrum and NMR calculations) methodologies. One isomer of the investi...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-017-3279-y
更新日期:2017-04-01 00:00:00
abstract::Molecular and quantum mechanics calculations were carried out in a series of tripeptides (GXG, where X = D, N and C) as models of the unfolded states of proteins. The selected central amino acids, especially aspartic acid (D) and asparagine (N) are known to present significant average conformations in partially allowe...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-016-3139-1
更新日期:2016-11-01 00:00:00