A new charge distribution is proposed for the amino acids where each atom is associated with two point charges while each
bond center is associated with one point charge. Centroids of charges arising due to atomic orbital hybridization called hybridization-displaced
charges (HDC) and those located at the atomic sites and bond centers obtained by a modified form of the Mulliken scheme were
combined. The density matrix calculations required for this analysis were performed at the B3LYP/6-31G** level of density
functional theory. The combination of HDC centroids with the modified Mulliken charges was found to yield dipole moments and
surface molecular electrostatic potentials (MEP) of the amino acids in good agreement with those obtained by rigorous DFT
calculations or those obtained using the MEP-fitted CHelpG charges. This study shows that the combination of HDC centroids
with the modified Mulliken charges is significantly superior to the conventional Mulliken charges. 相似文献
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
Covalently bonded atoms, at least in Groups V–VII, may have regions of both positive and negative electrostatic potentials
on their surfaces. The positive regions tend to be along the extensions of the bonds to these atoms; the origin of this can
be explained in terms of the σ-hole concept. It is thus possible for such an atom in one molecule to interact electrostatically
with its counterpart in a second, identical molecule, forming a highly directional noncovalent bond. Several examples are
presented and discussed. Such “like-like” interactions could not be understood in terms of atomic charges assigned by any
of the usual procedures, which view a bonded atom as being entirely positive or negative.
Figure Calculated electrostatic potential on the surface of SCl2. The sulfur is in the foreground, the chlorines are at the back. Color ranges (kcal mol−1): purple negative, blue between 0 and 8, green between 8 and 15, yellow between 15 and 20, red more positive than 20. Note that the sulfur has regions of both positive (red) and negative (purple) electrostatic potential 相似文献
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
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
This work presents new developments of the moving-domain QM/MM (MoD-QM/MM) method for modeling protein electrostatic potentials.
The underlying goal of the method is to map the electronic density of a specific protein configuration into a point-charge
distribution. Important modifications of the general strategy of the MoD-QM/MM method involve new partitioning and fitting
schemes and the incorporation of dynamic effects via a single-step free energy perturbation approach (FEP). Selection of moderately
sized QM domains partitioned between and C (from C=O), with incorporation of delocalization of electrons over neighboring domains, results in a marked improvement
of the calculated molecular electrostatic potential (MEP). More importantly, we show that the evaluation of the electrostatic
potential can be carried out on a dynamic framework by evaluating the free energy difference between a non-polarized MEP and
a polarized MEP. A simplified form of the potassium ion channel protein Gramicidin-A from Bacillus brevis is used as the model system for the calculation of MEP.
Figure Schematic representation of the Moving Domain QM/MM method 相似文献
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
We report a consistent set of AMBER force-field parameters for the most common phosphorylated amino acids, phosphoserine,
phosphothreonine, phosphotyrosine, and phosphohistidine in different protonation states. The calculation of atomic charges
followed the original restrained electrostatic potential fitting procedure used to determine the charges for the parm94/99
parameter set, taking α-helical and β-strand conformations of the corresponding ACE-/NME-capped model peptide backbone into
account. Missing force-field parameters were taken directly from the general AMBER force field (gaff) and the parm99 data
set with minor modifications, or were newly generated based on ab initio calculations for model systems. Final parameters
were validated by geometry optimizations and molecular-dynamics simulations. Template libraries for the phosphorylated amino
acids in Leap format and corresponding frcmod parameter files are made available.
Figure Schematic illustration of the systems used for parameter generation. Acid hydrogens are shown in red
Electronic Supplementary Material Supplementary material is available for this article at 相似文献
An organic molecule, designed in this study, is proposed as a candidate molecular switch and characterized using the B3LYP/6-31G*
computational method. Structural and electronic properties of this molecular switch (M) and its singly charged (M+ and M−) species in their lowest and the first higher spin states are calculated and analyzed. Molecular volume and electronic spatial
extent (ESE) of this nanoswitch undergo negligibly small changes (<2%) upon charging. Furthermore, the small difference between
the calculated dipole moments of the M+ and M− species shows that switching between negative and positive poles does not significantly affect the charge transfer performance
of this molecular switch. Natural bond orbital (NBO) and spin density distributions are also calculated and analyzed. A preliminary
study on the response of the proposed molecular switch to the external electric field approves its function as a multi-pole
nanoswitch controlled by a bias voltage.
Figure Electron transfer scheme and arrangement of the π-electrons in the turn-on state of the candidate multi-pole molecular switch. 相似文献
Halogen bonding refers to the non-covalent interactions of halogen atoms X in some molecules, RX, with negative sites on others.
It can be explained by the presence of a region of positive electrostatic potential, the σ-hole, on the outermost portion
of the halogen’s surface, centered on the R–X axis. We have carried out a natural bond order B3LYP analysis of the molecules
CF3X, with X = F, Cl, Br and I. It shows that the Cl, Br and I atoms in these molecules closely approximate the configuration, where the z-axis is along the R–X bond. The three unshared pairs of electrons produce a belt of negative electrostatic potential around
the central part of X, leaving the outermost region positive, the σ-hole. This is not found in the case of fluorine, for which
the combination of its high electronegativity plus significant sp-hybridization causes an influx of electronic charge that neutralizes the σ-hole. These factors become progressively less
important in proceeding to Cl, Br and I, and their effects are also counteracted by the presence of electron-withdrawing substituents
in the remainder of the molecule. Thus a σ-hole is observed for the Cl in CF3Cl, but not in CH3Cl.
Figure Schematic representation of the atomic charge generation. The molecular electrostatic potential (MEP) is calculated using
the AM1* Hamiltonian. The semiempirical MEP is then scaled to DFT or ab initio level and atomic charges are generated from it by the restrained electrostatic potential (RESP) fit method. 相似文献
Quantum chemical calculations at the B3LYP/6-31G* level of theory have been carried out on 20 celastroid triterpenoids to
obtain a set of molecular electronic properties and to correlate these with cytotoxic activities. The cytotoxic activities
of these compounds can be roughly correlated with electronic effects related to nucleophilic addition to C(6) of the compounds:
The energies of the frontier molecular orbitals (EHOMO and ELUMO), the HOMO-LUMO energy gap, the dipole moment, the charge on C(6), and the electrophilicity on C(6).
Figure LUMO of Pristimerin. 相似文献
A few different theoretical methods for assigning the partial atomic charges were benchmarked for calculation of the hydrophilic/lipophilic index (HLI). The coefficients were selected to produce the best correlation of the HLI values with the experimental octanol-water partition. Different parameters were checked in calculations of partial charges to get the best performance of the HLI values obtained. Thus, four partitioning schemes (Coulson, Mulliken, Merz-Kollman, Ford-Wang) were benchmarked for calculations of atomic charges with six semiempirical methods (AM1, PM3, RM1, PM6, PM6-D3H4, PM7). Moreover, five distinct types of partial atomic charges (Mulliken, Hirshfeld, Löwdin, CHELPG, NPA), obtained at the Hartree–Fock and DFT levels of theory with three basis sets, were tested for their ability to produce the HLI values with the best correlation to experimental logP coefficients of 50 mono-charged organic anions. In the case of the semiempirical methods, the best correlation between the HLI and logP values (the correlation coefficient r?=?0.9216) was obtained with the AM1 Ford–Wang parametric electrostatic potential charges. The Mulliken and Coulson charges calculated with the PM7 method can be used as an alternative to AM1, with the r values of 0.9107 and 0.8984, respectively. In the case of the DFT, the PBE/def2-TZVP natural population analysis charges produce the best correlation (r?=?0.9220). Nevertheless, in spite of a marginally lower performance (r?=?0.9159), the NPA charges computed at the PBE/def2-SVP level are more robust and can be regarded as the optimum choice for calculating the HLI values.
We have carried out B3PW91 and MP2-FC computational studies of dimethyl sulfoxide, (CH3)2SO, and dimethyl sulfone, (CH3)2SO2. The objective was to establish quantitatively the basis for their high polarities and boiling points, and their strong solvent
powers for a variety of solutes. Natural bond order analyses show that the sulfur–oxygen linkages are not double bonds, as
widely believed, but rather are coordinate covalent single S+→O− bonds. The calculated electrostatic potentials on the molecular surfaces reveal several strongly positive and negative sites
(the former including σ-holes on the sulfurs) through which a variety of simultaneous intermolecular electrostatic interactions
can occur. A series of examples is given. In terms of these features the striking properties of dimethyl sulfoxide and dimethyl
sulfone, their large dipole moments and dielectric constants, their high boiling points and why they are such good solvents,
can readily be understood.
Figure Dimers of dimethyl sulfoxide (DMSO; left) and dimethyl sulfone (DMSO2; right) showing O S—O -hole bonding and C H—O hydrogen bonding. Sulfur atoms are yellow, oxygens are red, carbons are gray and hydrogens are white相似文献
A 3D QSAR analysis has been performed on a series of 67 benzodiazepine analogues reported as γ-secretase inhibitors using
molecular field analysis (MFA), with G/PLS to predict steric and electrostatic molecular field interaction for the activity.
The MFA study was carried out using a training set of 54 compounds. The predictive ability of model developed was assessed
using a test set of 13 compounds ( as high as 0.729). The analyzed MFA model has demonstrated a good fit, having r2 value of 0.858 and cross validated coefficient, value as 0.790. The analysis of the best MFA model provided insight into possible modification of the molecules for better
activity.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
The structural and electronic properties of a three-state molecular switch—an active device in a nano-electronic circuit—were
studied using the B3LYP/6-31G* method. Due to its chemical stability, high conductivity upon doping, and non-linear optical
properties, polythiophene is among the most widely studied conjugated organic polymers, both experimentally and theoretically.
The aim of the present work was to theoretically study a very complex case: a three-state switch synthesized and experimentally
investigated by Nishida et al. (Org Lett 6:2523–2526, 2004). An initial set of test calculations showed B3LYP level of theory
and 6-31G* basis set to be the most appropriate for our purpose, i.e., the study of the structure, charge and spin distributions,
as well as electrical characteristics such as electric polarizability, HOMO-LUMO gap (HLG) and electric dipole moment, for
one of the 1,2-dithienylcyclopentene derivatives. Also, natural bond orbital analyses were performed to calculate local charges
and charge transfers in order to study the capability of the molecule as a molecular switch. The results reported here are
of general significance, and demonstrate that it is possible to use certain structural and electrical properties to understand
and design electro-photochromic compounds showing a switching function in cases where stable forms can be exchanged by light
or electron transfer.
Figure Model of a thiophene wire incorporating a redox active unit 相似文献
A global electrophilicity parameter and the aromaticity of some heterocyclic polyaromatic hydrocarbons were evaluated on the
basis of DFT calculations. The substitution of carbon atoms by nitrogen atoms dramatically changes the global electrophilicity
of the molecules, with the fully substituted molecule being the most electrophilic with a reactivity very close to that of
fullerene.
Figure Fully substituted heterohexabenzocoronene
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
Effective force fields for Ni-C interactions developed by Yamaguchi and Maruyama for the formation of metallofullerenes are
modified to simulate the catalyzed growth of single-wall carbon nanotubes on Nin clusters with n >20, and the reactive empirical bond order Brenner potential for C-C interactions is also revised to include the effect of
the metal atoms on such interactions.
Figure Force field parameters for carbon-metal interactions obtained from DFT calculations in small clusters. 相似文献
A mechanical molecular rotation model for liquid crystal (LC) systems is employed to evaluate phase transition temperature
of fluorinated phenylbicyclohexane isomeric LC compounds. Results show that when a fluorine atom is substituted along the
molecular long axis, an LC molecule acquires high rotational speed and its rotation becomes stable, thereby resulting in a
better thermal stability of the nematic phase. A novel explanation is proposed for the behavior of the nematic-isotropic phase
of the LC system when a heavy atom is substituted along the molecular long axis.
Figure Molecular conformation of fluorinated bicyclohexylphenyl compounds. . The fluorine atoms are substituted in different positions 2, 3, 4, and 5 of the phenyl ring, respectively. The axis expresses
molecular long rotation axis. 相似文献