Abstract:
:Structure-olfactive threshold relationships for 40 pyrazine derivatives have been studied by multivariate statistical analysis. Variable descriptors used to describe the molecules studied were obtained using molecular-mechanics software. A correlation coefficient of 0.82 was obtained when all the molecules were included in the model. When the model was established for closely related subsets of molecules, the correlation coefficients obtained were higher and the established models were bilinear. Such models allow the identification of optimal structures corresponding to low olfactive thresholds for the subsets studied. Surprisingly, we find that the optimum structures are included in the set of 40 molecules. The efficiency of the models was supported by the cross-validation technique, where the correlation coefficients were found to be good with respect to the precision of the values of the olfactive thresholds.
journal_name
J Mol Modeljournal_title
Journal of molecular modelingauthors
Zakarya D,Farhaoui L,Hamidi M,Bouachrine Mdoi
10.1007/s00894-006-0115-1subject
Has Abstractpub_date
2006-09-01 00:00:00pages
985-9issue
6eissn
1610-2940issn
0948-5023journal_volume
12pub_type
杂志文章abstract::Corynebacterium pseudotuberculosis is a facultatively intracellular Gram-positive bacterium that causes caseous lymphadenitis, principally in sheep and goats, though sometimes in other species of animals, leading to considerable economic losses. This pathogen has a TCS known as PhoPR, which consists of a sensory histi...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-011-1145-x
更新日期:2012-03-01 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
pub_type: 杂志文章
doi:10.1007/s00894-015-2621-5
更新日期:2015-04-01 00:00:00
abstract::Solar-assisted water splitting using photoelectrochemical cells (PECs) is one of the promising ways for the production of hydrogen to store renewable energy. Semiconducting materials are used as a key factor which controls the overall energy conversion efficiency in PECs. However, finding new semiconductors with appro...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-020-04397-2
更新日期:2020-05-15 00:00:00
abstract::The adsorption behavior of sulfur-based toxic gases (H2S and SO2) on armchair silicene nanoribbons (ASiNRs) was investigated using first-principles density functional theory (DFT). Being a zero band gap material, application of bulk silicene is limited in nanoelectronics, despite its high carrier mobility. By restrict...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-018-3631-x
更新日期:2018-03-16 00:00:00
abstract::The interactions between the template molecule paclitaxel (PTX) and seven functional monomers containing methacrylic acid (MA), acrolein (AC), 4-vinylbenzoic acid (4VA), acrylonitrile (AN), 2-vinylpyridine (2VP), 2,6-bisacrylamide pyridine (BAP) and methyl methacrylate (MM) were systematically investigated adopting th...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-019-4277-z
更新日期:2020-01-11 00:00:00
abstract::Matrix metalloproteinase-8 (MMP-8) is the key mediator in initiating type I collagen degradation and is associated with rheumatoid arthritis. In the present study, a pharmacophore hypothesis was developed based on selective non zinc binding inhibitors of MMP-8. The pharmacophore hypothesis was refined manually and val...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-014-2191-y
更新日期:2014-05-01 00:00:00
abstract::The analysis of the electronic-structure changes along IRC paths for double-proton-transfer reactions in the formamide dimer (R1), formamide-thioformamide system (R2), and the thioformamide dimer (R3) was performed based on the extended-transition-state natural orbitals for chemical valence (ETS-NOCV) partitioning of ...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-017-3564-9
更新日期:2017-12-22 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
pub_type: 杂志文章
doi:10.1007/s00894-008-0380-2
更新日期:2009-02-01 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
pub_type: 杂志文章
doi:10.1007/s00894-018-3665-0
更新日期:2018-05-07 00:00:00
abstract::The B3LYP/6-31G (d) method of density functional theory (DFT) was used to study molecular geometry, electronic structure, infrared spectrum (IR) and thermodynamic properties. The heat of formation (HOF) and calculated density were estimated to evaluate the detonation properties using Kamlet-Jacobs equations. Thermal s...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-012-1522-0
更新日期:2013-01-01 00:00:00
abstract::We have examined the effects of substituents on the computed electrostatic potentials V(S)(r) and average local ionization energies I(S)(r) on the surfaces of model carbon nanotubes of the types (5,5), (6,1) and (6,0). For the (5,5) and the (6,1), the effects upon both V(S)(r) and I(S)(r) of substituting a hydroxyl gr...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-005-0265-6
更新日期:2005-09-01 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::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::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
pub_type: 杂志文章
doi:10.1007/s00894-012-1644-4
更新日期:2013-05-01 00:00:00
abstract::The ion-pair S(N)2 reaction LiNCS + CH3F with two mechanisms, inversion and retention, was investigated at the MP2(full)/6-311+G**//HF/6-311+G** level in the gas phase and in acetone solution. All HF-optimized structures were confirmed by vibrational frequency analysis. Based on IRC analyses, eight possible reaction p...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-005-0016-8
更新日期:2006-01-01 00:00:00
abstract::Noncovalent interactions in XCN···YO2H (X = F, Cl, Br, I; Y = P, As, Sb) complexes were investigated using ab initio calculations at the MP2/aug-cc-pVDZ level of theory. There are four different configurations of these complexes, and the complexes are formed via hydrogen bonds, halogen bonds, π-hole interactions, or d...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-017-3358-0
更新日期:2017-06-01 00:00:00
abstract::Antihistamines are frequently used pharmaceuticals that treat the symptoms of allergic reactions. Loratadine (LOR) is an active component of the second generation of selective antihistaminic pharmaceutical usually known as Claritin. Frequent usage of this type of pharmaceuticals imposes the need for understanding thei...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-016-3101-2
更新日期:2016-10-01 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
pub_type: 杂志文章
doi:10.1007/s00894-013-1793-0
更新日期:2013-06-01 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::Recently, both lithium (Li) salts and Li electrides formed by one Li atom interacting with ligand complexes, have been widely investigated. An interesting question emerges: is the configuration of one Li atom interacting with ligand complexes a Li salt or electride? In the present work, four configurations n-Li-PNA (n...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-014-2560-6
更新日期:2015-02-01 00:00:00
abstract::Hepatic fibrosis is a common complication of the infection by the parasite, Clonorchis sinensis. There is a high incidence of this disease in the Asian countries with an increased risk of conversion to cancer. A secretory phospholipase A(2) (PLA(2)) enzyme from the parasite is implicated in the pathology. This is an a...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-011-1333-8
更新日期:2012-07-01 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
pub_type: 杂志文章
doi:10.1007/s00894-016-3111-0
更新日期:2016-10-01 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::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
pub_type: 杂志文章
doi:10.1007/s00894-015-2714-1
更新日期:2015-06-01 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
pub_type: 杂志文章
doi:10.1007/s00894-016-3122-x
更新日期:2016-11-01 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::B3LYP, PBE, M06-2X, B2PLYP, BN2PLYP-D, ωB97X-D, and MP2 levels of theory, in combination with the 6-311++G(d,p) and cc-pVTZ basis sets were comprehensively assessed for their ability to reproduce experimental FOX-7 structural and detonation data. ωB97X-D/cc-pVTZ, B3LYP/cc-pVTZ, and M06-2X/cc-pVTZ provided highly accur...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-017-3427-4
更新日期:2017-09-01 00:00:00
abstract::Quantum chemical calculations have been performed to study the all-metal π halogen bonding in Al(4)(2-)···halohydrocarbon complexes. The result shows the existence of the all-metal π halogen bond in the complexes. There are three interaction modes (top, corner, and side) between Al(4)(2-) and halohydrocarbon. The inte...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-011-1252-8
更新日期:2012-06-01 00:00:00
abstract::The effective dissolution of calcium oxalate, the main component of kidney stones, is important in the treatment of nephrolithisis. Polyphenol glycosides constitute compounds supporting dissolution and inhibition of formation of stones. These moieties possess oxygen atoms which can interact with calcium cations. Densi...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-013-1841-9
更新日期:2013-10-01 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
pub_type: 杂志文章
doi:10.1007/s00894-011-1310-2
更新日期:2012-07-01 00:00:00