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1.
2.
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 is a C≡N and C=C bond center in the TCNE and, –NH2 and π-electrons of aniline. The N atom of aniline is oriented toward the TCNE molecule. The charge transfer transition energy,
estimated by calculating the ground-to-excited state transition electric dipole moments of the complex, agree well with the
reported experimental value in chloroform medium.
TCNE-aniline at ground state. TCNE-aniline at excited state 相似文献
3.
Aminophosphine oxides and aminophosphonates are, in general, very stable compounds. However, following phosphorus–carbon bond
cleavage in aqueous acidic media these compounds sometimes decompose to phosphonic acids derivatives (PIII). Despite some controversy in the literature, careful analysis supported by theoretical studies leads to the conclusion that
decomposition to PIII derivatives proceeds via an elimination reaction.
Figure The decomposition of α-aminophosphine oxides to phosphonic acid derivatives (PIII) 相似文献
4.
The electrode potential of 2-(4,5-dihydroxy-2-methylphenyl)-2-phenyl-2H-indene-1,3-dione (DMPID) in acetonitrile has been calculated. The calculations were performed using ab initio molecular orbital
calculations (HF), and density functional theory (DFT) with the inclusion of entropic and thermochemical corrections to yield
free energies of redox reactions. The electrode potential of DMPID was also obtained experimentally with the aid of an electrochemical
technique (cyclic voltammetry). The values for geometric parameters and the vibrational frequencies of DMPID and 2-(6-methyl-3,4-dioxocyclohexa-1,5-dienyl)-2-phenyl-2H-indene-1,3-dione
(MDPID) were also computed using the same levels with the basis set of 6-31G(d). The calculated IR spectrum of DMPID used
for the assignment of IR frequencies was observed in the experimental FT-IR spectrum and the calculated IR and FT-IR observed
spectra of DMPID were compared with correlation factor of 0.996. It should be mentioned that the present work is the first
research on coagulant derivative molecules in which the electrode potential of a molecule is calculated.
Optimized structures of 2-(6-methyl-3,4-dioxocyclohexa-1,5-dienyl)-2-phenyl-2H-indene-1,3-dione (MDPID) 相似文献
5.
Hadj-Kali MK Gerbaud V Joulia X Lacaze-Dufaure C Mijoule C Ungerer P 《Journal of molecular modeling》2008,14(7):571-580
An extension of the anisotropic united atoms intermolecular potential model is proposed for nitriles. The electrostatic part
of the intermolecular potential is calculated using atomic charges obtained by a simple Mulliken population analysis. The
repulsion-dispersion interaction parameters for methyl and methylene groups are taken from transferable AUA4 literature parameters
[Ungerer et al., J. Chem. Phys., 2000, 112, 5499]. Non-bonding Lennard-Jones intermolecular potential parameters are regressed
for the carbon and nitrogen atoms of the nitrile group (–C≡N) from experimental vapor-liquid equilibrium data of acetonitrile.
Gibbs Ensemble Monte Carlo simulations and experimental data agreement is very good for acetonitrile, and better than previous
molecular potential proposed by Hloucha et al. [J. Chem. Phys., 2000, 113, 5401]. The transferability of the resulting potential
is then successfully tested, without any further readjustment, to predict vapor-liquid phase equilibrium of propionitrile
and n-butyronitrile.
Figure Saturated vapour pressure of nitriles calculated in this work by molecular simulation compared to experimental data: a) for
acetonitrile and b) for both propionitrile and butyronitrile 相似文献
6.
Chun-Fang Huo Ralf Jackstell Matthias Beller Haijun Jiao 《Journal of molecular modeling》2010,16(3):431-436
The Pd-catalyzed telomerization in the presence of phosphine and carbene ligands has been computed. It is shown that the C–C
coupling of the less stable complex A with one trans- and one cis-butadiene in syn orientation forms the most stable intermediate B and is favorable both kinetically and thermodynamically. Protonation of B leads to equilibrium of the two most stable isomers of intermediate C. The overall regioselectivity is favored thermodynamically.
相似文献
7.
Nemukhin AV Lushchekina SV Bochenkova AV Golubeva AA Varfolomeev SD 《Journal of molecular modeling》2008,14(5):409-416
The reaction mechanism of acetylcholine hydrolysis by acetylcholinesterase, including both acylation and deacylation stages
from the enzyme-substrate (ES) to the enzyme-product (EP) molecular complexes, is examined by using an ab initio type quantum mechanical – molecular mechanical (QM/MM) approach. The density functional theory PBE0/aug-6–31+G* method for
a fairly large quantum part trapped inside the native protein environment, and the AMBER force field parameters in the molecular
mechanical part are employed in computations. All reaction steps, including the formation of the first tetrahedral intermediate
(TI1), the acylenzyme (EA) complex, the second tetrahedral intermediate (TI2), and the EP complex, are modeled at the same
theoretical level. In agreement with the experimental rate constants, the estimated activation energy barrier of the deacylation
stage is slightly higher than that for the acylation phase. The critical role of the non-triad Glu202 amino acid residue in
orienting lytic water molecule and in stabilizing the second tetrahedral intermediate at the deacylation stage of the enzymatic
process is demonstrated.
Figure The computed energy diagram for the reaction path from the enzyme – substrate complex (ES) to the enzyme-product complex (EP). 相似文献
8.
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 at B3LYP/6–31G (d, p) level to have hydrogen bonds and π....π stacking interaction,
their binding energy via HAF optimization was −20.4 kcal mol−1. The results derived from this study agreed well with the reported observation.
Figure Optimized structure of STI-571 and Thr315 in abelson tyrosine kinase based on ONIOM2 method 相似文献
9.
Setzer WN 《Journal of molecular modeling》2008,14(5):335-342
The energetics of the Cope rearrangement of 17 germacrane sesquiterpenoids to their respective elemane forms have been calculated
using both density functional theory (B3LYP/6-31G*) and post Hartee-Fock (MP2/6-31G**) ab initio methods. The calculations are in qualitative agreement with experimentally observed Cope rearrangements, but the two methods
give slightly different results. MP2 calculations generally show more favorable elemene energies compared to the respective
germacrenes (by around 3–4 kcal mol−1) and smaller activation energies (by 2–3 kcal mol−1). Additionally, neither method is accurate enough to consistently reproduce the germacrene/elemene equilibrium. Apparently,
the generally small energy differences between the two forms in these sesquiterpenoids cannot be adequately reproduced at
these levels of calculation.
Figure The Cope rearrangement of the germacrane sesquiterpenoid bacchascandon to the elemane shyobunone 相似文献
10.
Following our recent studies of the thermodynamic properties of azaspiropentane and borospiropentane, in consideration of
their usefulness as new potential high energy materials, we follow up with ab initio calculations on the thermodynamic properties
of azaborospiropentanes. Properties reported in this study include optimized structural parameters, vibrational frequencies,
enthalpies of formation, specific enthalpies of combustion, proton affinities, and hydride affinities. Our results indicate
that azatriborospiropentane gives off most energy when combusted, as evidenced by its specific enthalpy of combustion of about
−52 kJ per gram.
Figure Optimized geometry for R-azatriborospiropentane (10)
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
11.
Eight H-bonded complexes between serotonin (5-hydroxy-tryptamine) and water/hydrogen peroxide were studied at the B3LYP and
HF levels of theory, using the 6-31+G(d) basis set. A thermodynamic analysis was performed in order to find the most stable
complex. The calculated bonding parameters showed that the most stable H-bonded complex is formed between serotonin and hydrogen
peroxide by means of the intermolecular H-bond –H2N...H–OOH.
Fig. a Theoretical study of the hydrogen-bonded supersystems serotonin-water/hydrogen peroxide 相似文献
12.
Karhánek D Kacer P Kuzma M Splíchalová J Cervený L 《Journal of molecular modeling》2007,13(9):1009-1016
Theoretical investigation of Pt(0)-olefin organometallic complexes containing tertiary phosphine ligands was focused on the
strength of platinum-olefin electronic interaction. DFT theoretical study of electronic effects in a substantial number of
ethylene derivatives was evaluated in terms of the Pt-olefin binding energy using MP2 correlation theory. Organometallics
bearing coordinated olefins with general formula (R1R2C = CR3R4)Pt(PH3)2 [R = various substituents] had been selected, including olefins containing both electron-donor substituents as well as electron-withdrawing
groups. The stability of the corresponding complexes increases with a strengthening electron-withdrawal ability of the olefin
substituents.
Figure Representation of (CH2 = CHR)Pt(PPh3)2 and the stability chart 相似文献
13.
de Oliveira BG Araújo RC Chagas FF Carvalho AB Ramos MN 《Journal of molecular modeling》2008,14(10):949-955
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 stretching modes, and Bader’s atoms in molecules (AIM) theory calculations was carried out in order to characterize
the hydrogen bonds in each isomer of the C2H4O···2HF complex. The most stable structure was determined through the identification of hydrogen bonds between C2H4O and HF, (O···H), as well as in the hydrofluoric acid dimer, (HFD–R···HFD). However, the existence of a tertiary interaction (Fλ···Hα) between the fluoride of the second hydrofluoric acid and the axial hydrogen atoms of C2H4O was decisive in the identification of the preferred configuration of the C2H4O···2HF system.
Figure Geometries of three isomers of the C2H4O···2HF tri-molecular heterocyclic hydrogen-bonded complex 相似文献
14.
Rotational strengths in the far-UV of TEM-1 β-lactamase have been investigated with two theoretical models based on the matrix
method. The first model excludes, and a second includes, effects of the local electrostatic interactions on the chromophore
energies. Special attention is given to the contributions of the aromatic side-chain chromophores, and the mechanisms of generation
of rotational strengths are analyzed. The sensitivity of the computational models with respect to the structural changes of
the protein are discussed.
Figure Structure of TEM-1 β-lactamase. Both domains—α and αβ, the secondary structural elements and the aromatic and disulfide chromophores
are shown 相似文献
15.
Luo Y Barbault F Gourmala C Zhang Y Maurel F Hu Y Fan BT 《Journal of molecular modeling》2008,14(10):901-910
It is well known that cell surface carbohydrates play a role in cell–cell adhesion and communication. LewisX glycosphingolipids
form microdomains on cell surfaces. Homotypic and calcium-mediated LewisX–LewisX (LeX-LeX) interactions were proposed to be
responsible for the initial steps of cell adhesion, and to mediate embryogenesis and metastasis. Various techniques have been
used to investigate such interactions, but little information is available on the geometry and the mechanism of dimerisation.
To better understand these interactions, a new molecular model was developed to simulate homotypic interactions in explicit
solvent with and without calcium ions. Accurate analysis of both trajectories yielded valuable information about the energetics
of LeX-LeX dimerisation. Detailed interpretation of the hydrogen bond network and the presence of calcium ions along the trajectory
provide valuable insights into the role of calcium ions in this carbohydrate–carbohydrate interaction.
Figure Calcium population density around the LewisX carbohydrate (after the trajectory has been fitted to the primary unit cell).
All central dimer coordinates are fitted along the time axis, whereas calcium ion positions are recorded and represented as
points. The clouds of points indicate that the ions are not randomly placed around the dimer but take up preferred positions 相似文献
16.
Maciej Szaleniec Renata Tokarz-Sobieraj Wacław Witko 《Journal of molecular modeling》2009,15(8):935-943
The mesogenic species 4-(4-hexylcyclohexyl) isothiocyanatobenzene (6CHBT) was studied with density functional theory and molecular
mechanics in order to investigate the molecular properties, interactions between dimers and to interpret the IR spectrum.
Two types of calculations were performed for model systems containing single and double molecules of 6CHBT. Calculations (involving
conformation analysis) for isolated species indicated that the trans isomer, in the equatorial–equatorial conformation, is
the most energetically stable. The 6CHBT molecule is polar, with a rather high (4.43 D) dipole moment with negatively charged
isothiocyanato (NCS) ligand. The dimer–dimer interaction energies show that the head-to-head configuration (where van der
Waals attraction forces play the major role) is the most energetically stable. Vibrational analysis provided detailed assignment
of the experimental infra-red (IR) spectrum.
Figure Most favorite 6CHBT head to head interaction - ESP mapped to electron density surface
Dedication This paper is dedicated to the memory of Dr. Wacław Witko, who introduced us to research on mesogenic systems. 相似文献
17.
The possibility that stable complexes may be formed between alpha particles (He2+) and small molecules is investigated using QCISD quantum mechanical calculations. Implications for their presence in the
terrestrial atmosphere and/or in interstellar space are discussed.
Figure Optimized structure of a stable H2OHe2+ complex 相似文献
18.
Vuk Micovic Milovan D. Ivanovic Ljiljana Dosen-Micovic 《Journal of molecular modeling》2009,15(3):267-280
An automated docking procedure was used to study binding of a series of δ-selective ligands to three models of the δ-opioid
receptor. These models are thought to represent the three ligand-specific receptor conformations. Docking results are in agreement
with point mutation studies and suggest that different ligands—agonists and antagonists—may bind to the same binding site
under different receptor conformations. Docking to different receptor models (conformations) also suggests that by changing
to a receptor-specific conformation, the receptor may open or close different binding sites to other ligands.
Figure Ligands 5 (green) and 6 (orange) in bindingpocket BP1 of the R1 δ-opioid receptor model 相似文献
19.
20.
σ-Hole bonding is a noncovalent interaction between a region of positive electrostatic potential on the outer surface of a
Group V, VI, or VII covalently-bonded atom (a σ-hole) and a region of negative potential on another molecule, e.g., a lone
pair of a Lewis base. We have investigated computationally the occurrence of increased vibration frequencies (blue shifts)
and bond shortening vs decreased frequencies (red shifts) and bond lengthening for the covalent bonds to the atoms having the σ-holes (the σ-hole
donors). Both are possible, depending upon the properties of the donor and the acceptor. Our results are consistent with models
that were developed earlier by Hermansson and by Qian and Krimm in relation to blue vs red shifting in hydrogen bond formation. These models invoke the derivatives of the permanent and the induced dipole moments
of the donor molecule.
Figure Computed electrostatic potential on the molecular surface of Cl-NO2. Color ranges, in kcal mol−1, are: red, greater than 25; yellow, between 10 and 25; green, between 0 and 10; blue, between −4 and 0; purple, more negative
than −4. The chlorine is facing the viewer, to the right. Note the yellow region of positive potential on the outer side of
the chlorine, along the extension of the N–Cl bond. The blue region shows the sides of the chlorine to have negative potentials.
The calculations were at the B3PW91/6–31G(d,p) level. 相似文献