Basis set dependence of the vibrational wavenumbers of the out-of-plane modes of conjugated π-electron ring systems

Basis set dependence of the vibrational wavenumbers of out-of-plane modes calculated at the MP2 level of ab initio molecular orbital theory is examined for benzene, p-benzoquinodimethane, p-benzoquinone, furan, and thiophene. Various polarization functions up to (3df,p) are used in combination with the 6-31G and 6-311G basis sets. It is shown that, especially in the case of normal modes with alternate out-of-plane motions of the carbon atoms (such as the ν₄ (b_2g) mode of benzene), the calculated wavenumbers depend strongly on the exponents (_d) of the d functions on the carbon atoms. It is therefore necessary to include d functions with an optimum exponent (_d0.4) on the carbon atoms to obtain reasonable out-of-plane vibrational force fields. In a few cases (such as the ν₁₆ (a₂) mode of furan), inclusion of a set of f functions on the carbon atoms has some effects on the calculated wavenumbers of out-of-plane modes. However, unless the basis set contains an optimum set of d functions, inclusion of a set of f functions does not improve the agreement between the observed and calculated vibrational wavenumbers. As a case with an exaggerated effect of basis set, it is shown that the wavenumber of the ν₄₁ (b_2g) mode of the planar optimized structure of p-benzoquinodimethane is calculated to be imaginary by using the 6-311G(d,p) or 6-311G(df,p) basis set at the MP2 level. For all the molecules treated in the present study, reasonable out-of-plane vibrational force fields are obtained by using the 6-31G(2df,p) and 6-311G(2df,p) basis sets.     

An ab initio (RHF) and DFT-B3LYP level spectroscopic studies of BrCCCN and the analysis of atomic polar tensors

Conventional ab initio (RHF) and DFT-B3LYP level calculations in conjunction with a variety of basis sets have been used to investigate the variations in the bond lengths, dipole moment, rotational constant, quadruple coupling constants, infrared frequencies, IR intensities and rotational invariants of BrCCCN. Satisfactory agreements between the B3LYP and experimental values were found for bond lengths, rotational constant, dipole moment and all other parameters. All the calculated bond lengths are in good agreement with each other for a given method having the average standard deviations varying between ±0.005 Å at the B3LYP level. Harmonic vibrational frequencies obtained from the B3LYP calculations show good agreement with the available experimental data. The global atomic polar tensor charges, used for interpreting the IR intensities, of all the atoms of BrCCCN have been calculated at the RHF and B3LYP levels in conjunction with the 6-311g(d) and 6-311++g(d,p) basis sets. Linear regression analysis between calculated and experimental infrared frequencies as well as between IR intensities in a series of 15 similar type of nitrile compounds have been achieved at the B3LYP/6-311++g(d,p) level and gives linear regression coefficients 0.983 and 0.970 respectively. Finally, a number of linear relations were found between r(CN) bond lengths and GAPT charges, and GAPT charges on CHELPG and MK charges at the nitrogen atom for these molecules and proved to be producing satisfactory results at the B3LYP/6-311++g(d,p) level of calculations.     

Effects of the residues on the excitation energies of protonated Schiff base of retinal (PSBR) in bR: a TD-DFT study

Effects of the residues on the excitation energies of protonated Schiff base of retinal (PSBR) in bacteriorhodopsin have been investigated by means of time-dependent density functional theory. The residues around PSBR are replaced by the point charges on atoms. The structures of PSBR and residues are referred from X-ray data. The atomic charges on the each residue were calculated the B3LYP/6-311G(d,p) level. The excitation energy of PSBR perturbed by the point charges on atoms of each residue was calculated at the B3LYP/6-31G(d,p) level. A total of 23 residues and five water molecules around PSBR were considered in the calculations. The large spectral shifts were caused by the Asp212 and Asp85. The origin of the spectral shifts was discussed on the basis of theoretical results.     

QTAIM charge-charge flux-dipole flux interpretation of electronegativity and potential models of the fluorochloromethane mean dipole moment derivatives

Infrared fundamental vibrational intensities and quantum theory atoms in molecules (QTAIM) charge-charge flux-dipole flux (CCFDF) contributions to the polar tensors of the fluorochloromethanes have been calculated at the QCISD/cc-pVTZ level. A root-mean-square error of 20.0 km mol(-1) has been found compared to an experimental error estimate of 14.4 and 21.1 km mol(-1) for MP2/6-311++G(3d,3p) results. The errors in the QCISD polar tensor elements and mean dipole moment derivatives are 0.059 e when compared with the experimental values. Both theoretical levels provide results showing that the dynamical charge and dipole fluxes provide significant contributions to the mean dipole moment derivatives and tend to be of opposite signs canceling one another. Although the experimental mean dipole moment derivative values suggest that all the fluorochloromethane molecules have electronic structures consistent with a simple electronegativity model with transferable atomic charges for their terminal atoms, the QTAIM/CCFDF models confirm this only for the fluoromethanes. Whereas the fluorine atom does not suffer a saturation effect in its capacity to drain electronic charge from carbon atoms that are attached to other fluorine and chlorine atoms, the zero flux electronic charge of the chlorine atom depends on the number and kind of the other substituent atoms. Both the QTAIM carbon charges (r = 0.990) and mean dipole moment derivatives (r = 0.996) are found to obey Siegbahn's potential model for carbon 1s electron ionization energies at the QCISD/cc-pVTZ level. The latter is a consequence of the carbon mean derivatives obeying the electronegativity model and not necessarily to their similarities with atomic charges. Atomic dipole contributions to the neighboring atom electrostatic potentials of the fluorochloromethanes are found to be of comparable size to the atomic charge contributions and increase the accuracy of Siegbahn's model for the QTAIM charge model results. Substitution effects of the hydrogen, fluorine, and chlorine atoms on the charge and dipole flux QTAIM contributions are found to be additive for the mean dipole derivatives of the fluorochloromethanes.     

Theoretical study of the bonding in Fe---M dimers

The electronic structures of Fe₂, FeMn, FeCo, FeCu and FeNi have been calculated using Gaussian-76 SCF techniques. Gaussian basis sets contracted to [4s, 2p, 1d] functions are used on each atom resulting in sets of near double zeta accuracy in the valence region. The calculated UHF electronic ground state configurations for these Fe---M dimers are comparable with those experimentally determined. By examining the Mulliken atomic overlap population analysis, a correlation is found between the Mössbauer spectrum and calculated binding strengths in these dimers. Our calculations, fixed at r_e of 2.3 Å, show that the binding strengths decrease from FeCu, FeMn, Fe₂, FeCo, FeNi.     

基于电负性均衡理论快速计算多肽分子中原子电荷的新方法

Atomic charges play a crucial role in the understanding and modeling of the chemical behavior of proteins. Fast assessment of atomic charge distributions in larger molecules can be performed by implementing the electronegativity equalization method (EEM). To further improve the accuracy of the EEM approach, a novel and efficient method based on Bader's concept of high degree fragment transferability of atomic charges has been proposed for the parameterization of atoms-in-molecules (AIM) charges of polypeptides or proteins. The EEM parameterization method considers both the factors of connectivity and hybridized states, and the effect of the local chemical environment in fragments or groups. The types of atoms were defined on the basis of the local chemical environments of the fragments or functional groups of these atoms. The fragment transferability feature of QTAIM indicates that the atomic properties for the contributing atoms can be reproduced if the chemical environment is comparable. The constituent fragments or functional groups of macromolecules such as polypeptides and proteins can be utilized as building blocks for the additive generation of their electronic densities. The main peptide group (NH―HαCα―C＝O) of the polypeptide in the backbone was used as a building block to model the EEM parameters for reproducing the atomic charges in the polypeptides. A training set of 20 terminally blocked amino acids (Ac-X-NHMe, X = any neutral residue), which recreated the immediate local environment of the main chain fragments or functional groups of the polypeptides, were chosen for the calibration of AIM charges using the differential evolution (DE) algorithm. The effects of the optimized methods on the results were discussed and it was found that the DE algorithm showed a better performance for the objective function. The quality of the AIM charges obtained from the EEM method presented in this study was evaluated by comparison with those obtained from B3LYP/6-31G+(d, p) calculations for the two test tetrapeptides not contained in the training set. It was found that a remarkable improvement was achieved using the EEM model developed in this study as compared to the previous studies. The introduction of Bader's high fragment charge transfer model into the EEM provided a new scheme for its calibration and parameterization for larger systems such as polypeptides or polynucleotides, which possess highly repetitive segments. Among all types of atomic charges, only the AIM charges showed a significant meaning in experiments and could be obtained by X-ray diffraction experiments. Rapidly reproducing the accurate AIM charge for large systems seems to be more meaningful, especially for the prediction of protein-protein, protein-DNA, and drug-receptor recognition and interactions.     

A study of ortho- and para-siloxyanilines for the synthesis of mono-, bi-, and tetra-nuclear early transition metal–imido complexes

The siloxyanilines o-Me₃SiOC₆H₄NH₂ (1) and p-RMe₂SiOC₆H₄NH₂ (R=H (2); R=Me (3)), and their N-silylated derivatives p-Me₃SiOC₆H₄NHSiMe₃ (4) and p-Me₃SiOC₆H₄N(SiMe₃)₂ (5) have been prepared from ortho- or para-aminophenol and used in the synthesis of imido complexes. Thus, binuclear [{Ti(η⁵-C₅H₅)Cl}{μ-NC₆H₄(p-OSiMe₃)}]₂ (6) and mononuclear [TiCl₂{NC₆H₄(p-OSiMe₃)}(py)₃] (7) imido complexes have been obtained from the reaction of 3 and [Ti(η⁵-C₅H₅)Cl₃] or [TiCl₂(N^tBu)(py)₃], respectively. In contrast, the reaction of 1 with TiCl₄ and ^tBupy affords the titanocycle [TiCl₂{OC₆H₄(o-NH)---N,O}(^tBupy)₂] (8). Compound 5 has also been used to prepare the niobium imide complex [NbCl₃{NC₆H₄(p-OSiMe₃)}(MeCN)₂] (9), by its reaction with NbCl₅ in CH₃CN. These findings have been applied to the synthesis of polynuclear systems. Thus, chlorocarbosilane Si[CH₂CH₂CH₂Si(Me)₂Cl]₄ (CS–Cl) has been functionalized with the ortho- and para-aminophenoxy groups to give 10 and 11, respectively. The use of 11 has allowed the formation of the tetranuclear compound 12. Attempts to synthesize terminal imido titanium complexes from 10 and TiCl₄ in the presence of ^tBupy and Et₃N, give complex 8 and carbosilane CS–Cl.     

On the charge distribution in ethanes and disilanes and correlations with equilibrium bond lengths; an ab initio study

The equilibrium electronic wave-functions for a series of fluoro- and chloro-ethanes and disilanes of general formula M₂H_6−nX_n, (M=C, Si; X=F, Cl), were analysed by the most commonly used methods for electron distribution, using the Mulliken and Löwdin populations, natural atomic orbital (NAO) populations and atoms in molecules (AIM) electron densities. Although the numerical values for local atomic charges vary greatly, all the methods correlate, but in markedly differing ways. The Mulliken charges seem the most selective in relation to systematic change of substituents in the current type of molecular structure. A number of examples occur where the AIM charges at C, Si centres are effectively identical in different molecules, where some differences might have been anticipated. These are often distinguished by Mulliken populations. The fluoroethanes exemplify this, since a plot of the AIM charges (for example on either the F or H centres) against the Mulliken charges for all members of the series, shows three nearly parallel lines, corresponding to those centres with 0, 1 or 2 fluorine atoms on the centre under study. The bond critical points at which the AIM charges are determined seem to be counter to intuition in some cases. This is a density rather than atomic orbital size issue however. The Mulliken and NAO charges seem more reasonable than those from the AIM method. There is an unexpected correlation of the local bond dipoles from the Mulliken analyses, with the calculated equilibrium bond lengths. These correlations lead to bond length values for the non-polarised bonds MX, which agree with data based on covalent radii for some bonds.     

Accurate partial atomic charges for high-energy molecules using class IV charge models with the MIDI! basis set

We have recently developed a new class IV charge model for calculating partial atomic charges in molecules. The new model, called charge model 3 (CM3), was parameterized for calculations on molecules containing H, Li, C, N, O, F, Si, S, P, Cl, and Br by Hartree–Fock theory and by hybrid density functional theory (HDFT) based on the modified Perdew–Wang density functional with several basis sets. In the present article, we extend CM3 for calculating partial atomic charges by Hartree–Fock theory with the economical but well balanced MIDI! basis set. Then, using a test set of accurate dipole moments for molecules containing nitramine functional groups (which include many high-energy materials), we demonstrate the utility of several parameters designed to improve the charges in molecules containing both N and O atoms. We also show that one of our most recently developed CM3 models that is designed for use with wave functions calculated at the mPWXPW91/MIDI! level of theory (where X denotes a variable percentage of Hartree–Fock exchange) gives accurate charge distributions in nitramines without additional parameters for N and O. To demonstrate the reliability of partial atomic charges calculated with CM3, we use these atomic charges to calculate polarization free energies for several nitramines, including the commonly used explosives 1,3,5-trinitro-s-triazine (RDX) and 2,4,6,8,10,12-hexanitrohexaazaisowurtzitane (HNIW), in nitromethane. These polarization energies are large and negative, indicating that electrostatic interactions between the charge distribution of the molecule and the solvent make a large contribution to the free energy of solvation of nitramines. By extension, the same conclusion should apply to solid-state condensation. Also, in contrast to some other charge models, CM3 yields atomic charges that are relatively insensitive to the presence of buried atoms and small conformational changes in the molecule, as well as to the level of treatment of electron correlation. This type of charge model should be useful in the future development of solvation models and force fields designed to estimate intramolecular interactions of nitramines in the condensed phase.     

Ab initio cluster calculations of silica surface sites

Silica surface sites, which can be formed in cleavage processes, and their hydrolyzed counterparts are investigated with ab initio cluster calculations. Natural Bond Orbital (NBO) theory is used to characterize bonding around silica surface sites. Higher energy lone pairs of electrons on oxygen atoms either hyperconjugate to vicinal silanol/siloxane antibonding orbitals or backdonate electron density via donor–acceptor π-type bonding with participation of pd or p hybrids on silicon atoms. Upon substitution of hydroxyl groups of orthosilicic acid with silica monomers the strength of siloxane and silanol Si–O bonding increases as energies of bonding orbitals and contributions from p-orbitals decrease. Silanone sites and a complementary pair of silyl/siloxy radical sites are found to be the most stable geminal and single non-hydrolyzed sites, respectively. Atomic charges based on natural wavefunctions and on fitting to electrostatic potential, and characteristic bands of IR spectra associated with siloxane and silanol stretching vibrations of silica surface sites are reported.     

Post Hartree–Fock and density functional theory studies on Di-Protonated Allopurinol

Post Hartree–Fock and density functional theory (DFT) methods have been employed to study the molecular properties of Di-Protonated Allopurinol²⁺ tautomers in gaseous and aqueous phase environments. The tautomers in gaseous phase have been optimized at MP2/6-311G(2d,2p) and B3LYP/6-311G(2d,2p) levels of theory. The self-consistent reaction field theory (SCRF) has been employed to optimize the tautomers in aqueous phase (ε = 78.5) at B3LYP/6-311G(2d,2p) level of theory and the solvent effect has been studied. The structure, energetics and relative stabilities of the tautomers have been analyzed both in gaseous and aqueous phases. The principle of maximum hardness (MHP) has been tested at B3LYP/6-311G(2d,2p) level of theory. The condensed Fukui functions have been calculated using the atomic charges obtained through Natural population analysis to identify the relative change in the most reactive site of the optimized structures. NMR studies have been carried out, on the basis of Cheeseman coworker’s method, to analyze the molecular environment as well as the delocalization activities of electron clouds.     

Atomic and molecular absorption spectra of indium in air-acetylene flame

Absorption spectra of both atomic and molecular species in the air-acetylene flame, which are produced when the aqueous solutions of indium dissolved in HNO₃, HF, HCl, HBr and HI were aspirated into the flame, have been investigated in the u.v. region. Numerous atomic absorption lines of indium have been observed in the absorption spectra. Most of these lines were previously listed only as emission lines. Those atomic lines have been ascribed to the electronic transitions from the ground states of 5p ²P_1/2⁰ and 5p ²P_3/2⁰ to the excited states such as ls ²S_1/2, md ²D_3/2, nd ²D_5/2, 4p^{2 4}P_1/2, 4p^{2 4}P_3/2 and 4p^{2 4}P_5/2, respectively, where 13 l 6 and 14 m,n 5. The molecular absorption bands for InF, InCl and InBr in the airacetylene flame have been also observed near 234 nm, 267 nm and 282 nm, respectively, as the electronic transition of ¹Σ⁺ → ¹Π₁ Those absorption bands show fine structures due to the molecular vibrations. The spectral parameters for the molecular vibrations have been obtained from the simulations of the observed spectra. The molecular absorption band for InI was not observed because of the decomposition of the molecule in the flame. In addition, the molecular absorption band for InO has been observed near 273 nm and those for NO near 205 and 215 nm.     

Complexation of trivalent lanthanide cations by inositol in solid state. The crystal structure and Raman spectra study of NdCl3·inositol·9H2O

The crystal structure of NdCl₃·C₆H₁₂O₆·9H₂O has been determined. It crystallizes in the monoclinic system, p2(1)/n space group with cell dimensions: a=15.824(3) Å, b=8.633(2) Å, c=16.219(3) Å, β=107.24°, V=2116.1(7) ų and Z=4. Each Nd ion is coordinated to nine oxygen atoms, two from inositol and seven from water molecules, with an Nd–O distance of 2.449–2.683 Å, the other two water molecules are hydrogen bonded. No direct contacts exist between Nd and Cl. There is an extensive network of hydrogen bonds in hydroxyl groups, water molecules and chloride ions in the crystal structure of the lanthanide complex. The Raman spectra of Pr–, Nd– and Sm–inositol are similar, which show that the three metal ions have the same coordination mode. The Raman spectra are consistent with their structures.     

The performance of the rapid estimation of basis set error and correlation energy from partial charges method on new molecules of the G3/99 test set

Experimental enthalpies of formation have been approximated using single-point Hartree–Fock (HF)–self-consistent-field (SCF) total energies plus the rapid estimation of basis set error and correlation energy from partial charges (REBECEP) energy corrections. The energy corrections are calculated from the HF–SCF partial atomic charges and optimized atomic energy parameters. The performance of the method was tested on 51 closed-shell neutral molecules (50 molecules from the G3/99 thermochemistry database plus urea, composed of H, C, N, O, and F atoms). The predictive force of the method is demonstrated, because these larger molecules were not used for the optimization of the atomic parameters. We used the earlier RECEP-3 [HF/6-311+G(2d,p)] and REBECEP [HF/6-31G(d)] atomic parameter sets obtained from the G2/97 thermochemistry database (containing small molecules) together with natural population analysis and Mulliken partial charges. The best results were obtained using the natural population analysis charges, although the Mulliken charges also provide useful results. The root-mean-square deviations from the experimental enthalpies of formation for the selected 51 molecules are 1.15, 3.96, and 2.92 kcal/mol for Gaussian-3, B3LYP/6-11+G(3df,2p), and REBECEP (natural population analysis) enthalpies of formation, respectively (the corresponding average absolute deviations are 0.94, 7.09, and 2.27 kcal/mol, respectively). The REBECEP method performs considerably better for the 51 test molecules with a moderate 6-31G(d) basis set than the B3LYP method with a large 6-311+G(3df,2p) basis set. Received: 10 March 2001 / Accepted: 5 July 2001 / Published online: 11 October 2001     

Synthesis of novel water-soluble linear and heterocyclic phosphino amino acids from 2-phosphinophenols or 2-phosphinophenolethers, formaldehyde and amino acids

Acyclic and cyclic amino acid derivatives of 2-phosphinophenols have been synthesised by reaction of primary phosphinophenols (4-R-2-H₂PC₆H₃OH; R=H, Me, OMe) 1a–c with formaldehyde and amino acids (o- and p-aminobenzoic acid, -lysine) via in situ formed hydroxymethyl species 2a–c. Condensation reactions with glycine did not afford defined products except when the methoxymethyl and tetrahydropyranyl ethers of 1d,e were used instead of the hydroxy compounds. o-Aminobenzoic acid gives rise to linear bis(o-carboxyphenylaminomethyl)phosphines 3a–e. p-Aminobenzoic acid, dependent on the molar ratio, affords bis(p-carboxyphenylaminomethyl)phosphines 4a,d as well as eight-membered heterocyclic 1,5,3,7-diazadiphosphacyclooctanes 5a–e. The aliphatic amino acids glycine and -lysine form six-membered heterocyclic 1,3,5-diazaphosphorinanes 6d and 7a–e, respectively, in presence of excess formaldehyde. -lysine differs from glycine by reaction at the terminal amino group. The structures of the compounds have been elucidated by multinuclear NMR spectroscopy. The salts of the phosphino amino acids are soluble in water. Water solubility increases with the number of hydrophilic groups, i.e. free phenols are more soluble than their ethers. Ligand concentrations in water from 0.1 to 1 M were observed.     

Multicenter point charge model for high-quality molecular electrostatic potentials from AM1 calculations

The natural atomic orbital/point charge (NAO-PC) model based upon the AM1 wave function has been developed to calculate molecular electrostatic potentials (MEPs). Up to nine point charges (including the core charge) are used to represent heavy atoms. The positions and magnitudes of the eight charges that represent the atomic electron cloud are calculated from the natural atomic orbitals (NAOs) and their occupations. Each hybrid NAO is represented by two point charges situated at the centroid of each lobe. The positions of the centroids and the magnitudes of the charges were obtained by numerical integration of the Slater-type hybrids and the results used to set up polynomials and look-up tables that replace the integration step in the actual MEP calculation. The MEPs calculated using this method are found to be in better agreement with those obtained using RHF/6-31G* than those obtained from the AM1 wave function using Coulson charges or with MOPAC-ESP. The MEP calculations are extremely fast and have, for instance, been incorporated into an interactive graphics package. © 1993 John Wiley & Sons, Inc.     

关于卤化硼的Lewis酸性强度的讨论

众所周知,卤化硼与Lewis强碱相互作用所呈现出的酸性强度顺序为BF3＜ BCl3＜ BBr3.这个顺序和人们所熟知的电负性规律矛盾,因为按照电负性变化规律,似乎BF3的酸性应该最强.为此化学工作者进行了解释,一个流行的说法是因为F含有孤对电子的2p轨道和B的空2p轨道能形成最有效的64键.但是后来的研究表明,Cl含有孤对电子的3p轨道和B的空2p轨道的重叠程度比相应的F含有孤对电子的2p轨道和B的空2p轨道的重叠程度大.为此,化学工作者提出了诸如电荷容量、价电子缺失数、前线轨道理论、锥形化能、最大硬度原理、最小亲电性原理等概念以解释卤化硼的酸性规律,本文对这些解释一一做了评点.