dSH扭曲程序的建立以及在两种基组(NBO, LFMO)下对扭曲分子的能量分解

介绍了d_SH 扭曲法产生的背景, 为d_SH扭曲法研究Mills-Nixon效应提供了一个自动化程序和方法. 通过在程序中引入随机函数模拟并代替了人工调节构型参数的过程, 提高了效率并拓宽了程序的应用范围. 利用此程序算得三元苯并分子C₆B₃H₃ 和C₆O₃的一系列的扭曲结构, 并利用自然键轨道(NBO)和定域片断分子轨道(LFMO)两种基组分别进行了NBO能量分析和Morokuma SCF能量分解, 并以动态的方式分析了扭曲过程中垂直共振能及其各分量的变化趋势, 比较了不同基组和不同分析方法下的扭曲的驱动力和阻力. 由分析知, 由于NBO基组的非绝对定域性和NBO能量分析方法的一次性对角化直接导致NBO基组及其能量分析方法在d_SH扭曲能量分析中的不合理.     

LFMO和NBO的定域性和作用能解析

为分析苯并分子C12H6的垂直共振能(VRE), 建立了定域片断分子轨道(LFMO)和自然键轨道(NBO)两种基组, 并在两种基组之上进行NBO能量分析和Morokuma能量分解. 在NBO能量分析中, 两种基组的VRE都是稳定的; 而在Morokuma能量分解中, VRE的稳定性取决于基组. 在NBO能量分析中, Fock矩阵的一次性对角化忽视了σ体系和π体系之间的电子耦合作用. 故NBO基组和NBO能量分析方法在计算VRE时似乎都不合理.     

DFT能量分解和氮苄叉基苯胺分子π电子离域能的研究

为了探索密度泛函理论(DFT)方法中氮苄叉基苯胺分子π电子离域的本质, 介绍了将非平面分子氮苄叉基苯胺分子的DFT能量分成π和σ的方法, 并将π和σ电子能量分成单电子能部分: 动能ΔEπK(θ), ΔEσK(θ)和位能ΔEπP(θ), ΔEσP(θ); 双电子相互作用部分: 库仑作用ΔEππJ(θ), ΔEσσJ(θ), ΔEπσJ(θ)和交换相关作用ΔEππXC(θ), ΔEσσXC(Δ)以及ΔEπσXC(θ), 分析了垂直离域能ΔEV的稳定性及π电子离域对π和σ体系的影响. 在B3LYP/6-31G*, 6-311G*, 6-31G(2d), 6-311G(2d)水平下的计算结果表明, 与经典观点不同, π电子的离域是失稳定的, 且平面时失稳定性最强; 分析各个能量分量表明, 在π电子的离域过程中, π和σ体系均对基组较敏感, π体系本身单电子能的影响大于σ体系, π电子离域对双电子部分作用的影响主要体现在π-σ的耦合作用上.     

Substituent Effect on N-Benzylideneanilines by DFT Energy Partition

To investigate the substituent effect on x-electron delocalization of the N-benzylideneaniline （NBA）, the vertical resonance energies △E^V（θ） of eleven substituted NBAs were separated into n and a parts at the B3LYP/6-311G（d） level of the Density Functional Theory （DFT）. When substituted with an electron-releasing group --OH, the calculated △E^V（θ） of NBA was increased, indicative of more resonance destabilization than the mother molecule. However, when substituted with an electron-withdrawing group -NO2, the calculated △E^V（θ） values indicated less resonance destabilization. The most destabilizing effect was observed especially when the -OH group located at the ortho-position of the aromatic ring in the fragment -N=CH-Ar. For most of the substituted NBA molecules, it was the destabilized a framework that determined the destabilizing feature of the vertical resonance energy, instead of the stabilized n system. When the -NO2 substituent at the para-position of the aromatic ring of the -N=CH-Ar group, the π system had the highest stabilizing effect while the σ framework exhibited the highest destabilizing effect. While the -NO2 substituent was at the para-position of the left aromatic ring （At-）, the NBA had the least vertical resonance energy value.     

氮苄叉基苯胺分子的平面扭曲驱动力的DFT研究

为了探索DFT方法中氮苄叉基苯胺分子的扭曲驱动力, 通过把非平面氮苄叉基苯胺(NBA)分子的DFT能量分成π和σ的方法, 分析了垂直离域能ΔE^V(θ)及σ-π轨道作用能ΔE^σπ(θ)的失稳定性, 并讨论了在扭曲过程中它们所起的作用. 在B3LYP/6-31G*, 6-311G*, 6-31G(2d), 6-311G(2d)水平下的计算结果显示: 与经典观点不同, π电子的离域是失稳定的, 且平面时失稳定性最强, 是分子扭曲的动力; 但σ-π轨道作用也是失稳定的, 随着扭角的增大其失稳定性增强, 是分子扭曲的阻力. NBA分子的大扭角构象, 是包含π-π, σ-π轨道作用在内的各种电子相互作用共同作用的结果.     

Origin of rotational barriers of the N-N bond in hydrazine: NBO analysis

Hydrazine passes through two transition states, TS1 (phi = 0 degrees ) and TS2 (phi = 180 degrees ), in the course of internal rotation around its N-N bond. The origin of the corresponding rotational barriers in hydrazine has been extensively studied by experimental and theoretical methods. Here, we used natural bond orbital (NBO) analysis and energy decomposition of rotational barrier energy (DeltaE(barrier)) to understand the origin of the torsional potential energy profile of this molecule. DeltaE(barrier) was dissected into structural (DeltaE(struc)), steric exchange (DeltaE(steric)), and hyperconjugative (DeltaE(deloc)) energy contributions. In both transition states, the major barrier-forming contribution is DeltaE(deloc). The TS2 barrier is lowered by pyramidalization of nitrogen atoms through lowering DeltaE(struc), not by N-N bond lengthening through lowering DeltaE(steric). Higher pyramidality of nitrogen atoms of TS2 than that of TS1 explains well why the N-N bond of TS2 is longer than that of TS1. Finally, the steric repulsion between nitrogen lone pairs does not determine the rotational barrier; nuclear-nuclear Coulombic repulsion between outer H/H atoms in TS1 plays an important role in increasing DeltaE(struc). Taken together, we explain the reason for the different TS1 and TS2 barriers. We show that NBO analysis is a useful tool for understanding structures and potential energy surfaces of compounds containing the N-N bond.     

Conformation-specific Raman bands and electronic conjugation in substituted thioanisoles

Nonresonant Raman spectra and conformational stability are studied for thioanisole (TA) and substituted analogues [4-XTA, X = NO(2) (1), CN (2), H (3), CH(3) (4), and NH(2) (5)] at the 4-position. The ring-substituent (SCH(3)) vibrational modes of out-of-plane bending and torsional types are calculated to have strong Raman scattering activities only for the vertical conformers. Agreement between observed and calculated Raman spectra is analyzed numerically. The conformational stability of the SCH(3) rotation changes systematically to the electron-withdrawing character of the substituents. The rotational barrier is calculated satisfactorily by B3LYP/6-31++G(d,p) calculations, whereas the second- to fourth-order M?ller-Presset perturbation theory and coupled-cluster with single- and double-excitation calculations tend to overestimate conformational energy barriers with respect to coplanar forms. The coplanar form is obtained for 1 and 2, whereas the vertical conformer is favorable for 4 and 5. The origin of the conformational energy difference, DeltaE, is demonstrated on the basis of canonical molecular orbitals and natural bond orbitals (NBOs) of the ground state. The natural bond orbital interaction between a nonbonding n(S) orbital of the S atom and a pi orbital of the benzene ring is shown to stabilize the coplanar form predominantly. A linear relationship is obtained between the energy of the highest occupied molecular orbitals and DeltaE. The n(S)-pi interaction energy, E(2), based on the NBO representation and the Hammet constants also change linearly with respect to DeltaE.     

Quantification of the (anti)aromaticity of fulvalenes subjected to pi-electron cross-delocalization

Fulvalenes 3-12 were theoretically studied at the ab initio level of theory. For the global minima structures, the occupation of the bonding (pi)C=C orbital of the interring C=C double bond obtained by NBO analysis quantitatively proves pi-electron cross-delocalization resulting in, at least partially, 2- or 6pi-electron aromaticity and 8pi-electron antiaromaticity for appropriate moieties. The cross-conjugation was quantified by the corresponding occupation numbers and lengths of the interring C=C double bonds, while the aromaticity or antiaromaticity due to cross-delocalization of the pi-electrons was visualized and quantified by through-space NMR shielding surfaces.     

Origin of threefold symmetric torsional potential of methyl group in 4-methylstyrene

To understand the effect of the para position vinyl group substitution in toluene on methyl torsion, we investigated 4-methylstyrene, a benchmark molecule with an extended pi conjugation. The assignment for a 33 cm(-1) band in the excitation spectrum to the 3a(2) torsional transition, in addition to the assignments suggested previously for the other bands in the excitation spectrum, leads to the model potentials for the ground as well as excited states with V(3) (")=19.6 cm(-1), V(6) (")=-16.4 cm(-1) and V(3) (')=25.6 cm(-1), V(6) (')=-30.1 cm(-1), respectively. These potentials reveal that both in ground and excited states, the methyl group conformations are staggered with a 60 degrees phase shift between them. MP2 ab initio calculations support the ground state conformations determined from experiments, whereas Hartree-Fock calculations fail to do so. The origin of the modified ground state potential has been investigated by partitioning the barrier energy using the natural bond orbital (NBO) theoretical framework. The NBO analysis shows that the local delocalization (bond-antibond hyperconjugation) interactions of the methyl group with the parent molecule is sixfold symmetric. The threefold symmetric potential, on the other hand, stems from the interaction of the vinyl group and the adjacent ring pi bond. The threefold symmetric structural energy arising predominantly from the pi electron contribution is the barrier forming term that overwhelms the antibarrier contribution of the delocalization energy. The observed 60 degrees phase shift of the excited state potential is attributed to the pi(*)-sigma(*) hyperconjugation between out of plane hydrogens of the methyl group and the benzene ring.     

Vibrational spectra and ab initio molecular orbital calculations of the novel anti-cancer drug combretastatin A-4 prodrug

The NIR-FT Raman and FT-IR spectral studies of the novel antineoplastic and antiangiogenesis substance comprestatin A-4 prodrug (CA4P) were carried out. The equilibrium geometry, various bonding features and harmonic vibrational frequencies of CA4P have been investigated with the help of B3LYP density functional theory (DFT) method. The most preferred cis-configuration for its bioactivity has been demonstrated on the basis of torsional potential energy surface (PES) scan studies. Stability of the molecule arising from hyperconjugative interactions leading to its bioactivity, charge delocalization and mesomeric effects have been analyzed using natural bond orbital (NBO) analysis. Detailed assignments of the vibrational spectra have been made with the aid of theoretically predicted vibrational frequencies. The optimized geometry shows near-planarity of phenyl rings and perpendicular conformation of meta substituted methoxy group. The vibrational analysis confirms the differently acting ring modes, steric repulsion, pi conjugation and back-donation.     

Thermochemistry and NBO analysis of peptide bond: Investigation of basis sets and binding energy

Ab initio methods were used to analyze the structure, energetic and binding energy of the five began dipeptides with methionine, Met-Gly, Met-Ala, Met-Ser, Met-Cys, and Met-Thr dipeptides, in gas phase. The structures of the dipetides and involved amino acids in them were optimized by using Hartree-Fock and DFT methods and 3-21G(d), 6-31G(d), 6-311G, 6-311G(d), and 6-311+G(d) basis sets. The effect of basis sets and electron correlations were analyzed with special emphasis on the calculated binding energies and thermodynamic functions. All used methods revealed that Met-Thr has the highest binding energy among all of the five dipeptide molecules. These numerical results suggest that Thr donates the proton easier than other four amino acids and it has the most tendency to join with methionine and it forms the most strong bond with methionine. This fact may be the reason behind the obtained high binding energies for Met-Thr at all levels. From comparison of the values of binding energy for dipeptides in different levels of theory, we could identify that the order of tendency for joint with methionine is Thr > Gly > Ala > Cys > Ser. Also, these data represented that the highest binding energy provide in HF/6-311G level for all of the dipeptides (14.4202, 11.2387, 8.3267, 9.8853, 17.3362 kcal mol⁻¹ for dipeptides 1–5, respectively). Moreover, natural bond orbital (NBO) analysis demonstrated that the effect of basis sets and electron correlations on σ_N1-C2 bonding orbital occupancy is the same as the basis set and electron correlation effects on binding energy of dipeptides in all cases. The obtained results from studying the effect of basis sets and electron correlations on binding energy, NMR and NBO properties showed that the effect of basis sets is almost independent of molecular structure and computational method, while electron correlation effects are relatively dependent to molecular structure and basis set type. In investigating the effect of basis sets and electron correlations on binding properties, the NBO results are in good agreement with the energetic and thermochemistry data at all levels of calculations. The article is published in the original.     

Vibrational spectra and natural bond orbital analysis of the herbicidal molecule 2(4-chlorophenoxy)-2-methyl propionic acid

The herbicide 2(4-chlorophenoxy)-2-methyl propionic acid (MCPP) has been subjected to NIR FT-Raman and infrared spectral studies. The optimized molecular structure, vibrational wavenumbers, IR intensities and Raman activities have been calculated by using density functional method (B3LYP) with the standard 6-31G(d) basis set. The calculated molecular geometry has been compared with the XRD data. The detailed assignments of the normal modes have been performed based on the potential energy distribution (PED) following the scaled quantum mechanical force field (SQMFF) methodology. The IR and Raman spectra have been plotted for the calculated wavenumbers. The simulated spectra satisfactorily coincide with the experimental spectra. The strong hyperconjugative interaction and charge delocalization that leads to the stability of the molecule have been investigated with the aid of natural bond orbital (NBO) analysis.     

FT-Raman and FTIR spectra, normal coordinate analysis and ab initio computations of (2-methylphenoxy)acetic acid dimer

The Fourier Transform Raman and infrared spectra of the crystallized herbicide (2-methylphenoxy)acetic acid (MPA) have been recorded in the region 4000–400 cm⁻¹. The geometry, intermolecular hydrogen bond, and harmonic vibrational frequencies of MPA have been investigated with the help of B3LYP density functional theory (DFT) methods. The calculated molecular geometry has been compared with the experimental data obtained from XRD data. The assignments of the vibrational spectra have been carried out with the aid of normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology (SQMFF). The strong doubly hydrogen bonded interface of the dimerized system is well demonstrated by the red shift in OH stretching frequency concomitant with the elongation of bond length. The most stable structure of the dimer possesses center of symmetry and interaction energy of −83.642 kJ mol⁻¹ after the basis set superposition error (BSSE) correction by the counterpoise (CP) method. The natural bond orbital analysis (NBO) ascertains that the delocalization of unpaired electron of oxygen atom onto the CO bond causes double bond character.     

New procedure to evaluate aromaticity at the density functional theory,Hartree–Fock,and post‐self‐consistent field levels

The spatial exchange interaction, arising from the exchange‐type two‐electron integrals ( ) between two different groups P and Q, is another driving force for the delocalization of π‐electrons besides orbital charge‐transfer and exchange interactions. We have developed a new combination program for restricted geometry optimization, in which all of the orbital and spatial interactions among isolated groups were excluded from the localized geometry of a conjugated molecule. This was achieved by deleting particular Fock elements and the 15 types of exchange‐type two‐electron integrals, ensuring that the corresponding π‐electrons are completely localized within their respective groups and the π‐orbitals are fully localized. The extra stabilization energy (ESE) of benzene is ?36.3 kcal/mol (B3LYP/6‐31G*), and the level of density functional theory, Hartree–Fock, and post‐self‐consistent field (Møller–Plesset 2, configuration interaction singles and doubles, and singles and doubles coupled‐cluster) and the basis sets have slight effect on the ESE. Based on the comparisons between our procedure, Morokuma's energy decomposition analysis and the block‐localized wave function method, it was confirmed that our program calculates reliable results. The nonaromaticity of acyclic polyenes and antiaromaticity of cyclobutadiene and planar cyclooctatetraene were also estimated. Comparison of the C? C single bond lengths in the ground state with its π‐localized geometries showed that shortening of the single bonds in acyclic polyenes and butadiyne should be attributed to different hybridization, demonstrating that the effect of π‐delocalization on single bonds is so small as to be negligible. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

Evaluating the Free Energies of Solvation and Electronic Structures of Lithium‐Ion Battery Electrolytes

Adaptive biasing force molecular dynamics simulations and density functional theory calculations were performed to understand the interaction of Li⁺ with pure carbonates and ethylene carbonate (EC)‐based binary mixtures. The most favorable Li carbonate cluster configurations obtained from molecular dynamics simulations were subjected to detailed structural and thermochemistry calculations on the basis of the M06‐2X/6‐311++G(d,p) level of theory. We report the ranking of these electrolytes on the basis of the free energies of Li‐ion solvation in carbonates and EC‐based mixtures. A strong local tetrahedral order involving four carbonates around the Li⁺ was seen in the first solvation shell. Thermochemistry calculations revealed that the enthalpy of solvation and the Gibbs free energy of solvation of the Li⁺ ion with carbonates are negative and suggested the ion–carbonate complexation process to be exothermic and spontaneous. Natural bond orbital analysis indicated that Li⁺ interacts with the lone pairs of electrons on the carbonyl oxygen atom in the primary solvation sphere. These interactions lead to an increase in the carbonyl (C=O) bond lengths, as evidenced by a redshift in the vibrational frequencies [ν(C=O)] and a decrease in the electron density values at the C=O bond critical points in the primary solvation sphere. Quantum theory of atoms in molecules, localized molecular orbital energy decomposition analysis (LMO‐EDA), and noncovalent interaction plots revealed the electrostatic nature of the Li⁺ ion interactions with the carbonyl oxygen atoms in these complexes. On the basis of LMO‐EDA, the strongest attractive interaction in these complexes was found to be the electrostatic interaction followed by polarization, dispersion, and exchange interactions. Overall, our calculations predicted EC and a binary mixture of EC/dimethyl carbonate to be appropriate electrolytes for Li‐ion batteries, which complies with experiments and other theoretical results.     

Steric repulsions, rotation barriers, and stereoelectronic effects: a real space perspective

Widely used chemical concepts like Pauli repulsion or hyperconjugation, and their role in determining rotation barriers or stereoelectronic effects, are analyzed from the real space perspective of the interacting quantum atoms approach (IQA). IQA emerges from the quantum theory of atoms in molecules (QTAIM), but is free from the equilibrium geometry constraint of the former. A framework with both electronically unrelaxed and relaxed wavefunctions is presented that leads to an approximate correspondence between the IQA concepts and those used in the EDA (energy decomposition analysis) or NBO (natural bond orbital) procedures. We show that no net force acts upon the electrons in an electronically relaxed system, so that any reasonable definition of Pauli repulsion must involve unrelaxed state functions. Using antisymmetrized fragments clarifies that Pauli repulsions are energetically connected to the IQA deformation energies, leaving footprints in the finally relaxed states. Similarly, EDA or NBO hyperconjugative stabilizations are found to be naturally related to the IQA electron delocalization patterns. Applications to the rotation barrier of ethane and other simple systems are presented, and the very often forgotten role of electrostatic contributions in determining preferred conformations is highlighted.     

Quantum chemical computations and Fourier transform infrared spectral studies of a nonlinear food dye E110

Fourier transform infrared (FTIR) spectrum of a well-known food dye sunset yellow FCF (E110) has been recorded and analysed. Assignments of the vibrational spectrum has been facilitated by density functional theory (DFT) calculations. The results of the optimized molecular structure obtained on the basis of B3LYP with 6-31G(d) along with the 'LANL2DZ' basis sets give clear evidence for the intramolecular charge transfer (ICT) and strong hydrogen bonding enhancing the optical nonlinearity of the molecule. The first hyperpolarizability of the acidic monoazo dye 'E110' is computed. Azo stretching frequencies have been lowered due to conjugation and pi-electron delocalization. Hydroxyl vibrations with intramolecular H-bonding are analyzed, supported by the computed results. The natural bond orbitals (NBO) analysis confirms this strong hydrogen bond between the hydrogen of the hydroxyl group and nitrogen of the azo group of the molecule. Assignments of benzene and naphthalene ring vibrations are found to agree well with the theoretical wave numbers.     

DFT study of the monomers and dimers of 2-pyrrolidone: equilibrium structures, vibrational, orbital, topological, and NBO analysis of hydrogen-bonded interactions

A computational study of the monomers and hydrogen-bonded dimers of 2-pyrrolidone was executed at different DFT levels and basis sets. The above dimeric complexes were treated theoretically to elucidate the nature of the intermolecular hydrogen bonds, geometry, thermodynamic parameters, interaction energies, and charge transfer. The processes of dimer formation from monomers and concerted reactions of double proton transfer were considered. The evolution of geometry, vibrational frequencies, charge distribution, and AIM properties in going from monomers to dimers was systematically followed. The solvent effects upon dimer formation were investigated in terms of the self-consistent reaction field (SCRF Onsager model). For the monomers and three dimers, vibrational frequencies were calculated and the changes in frequencies of the vibrations most sensitive to complexation were discussed. The orbital interactions were shown to lengthen the X-H (X = N, O) bond and lower its vibrational frequency (a red shift). To better understand the nature of the corresponding intermolecular interactions, we performed natural bond orbital (NBO) analysis. Topological analysis of electron density at bond critical points (BCP) was executed for complex molecules using the Bader's atoms in molecules (AIM) theory. The interaction energies were calculated, and the basis set superposition errors (BSSE) were estimated systematically. Satisfactory correlations between the structural parameters, interaction energies, and electron density characteristics at BCP were found.     

Molecular structure, vibrational spectroscopic, first hyperpolarizability, NBO and HOMO, LUMO studies of P-Iodobenzene sulfonyl chloride

In this work, the experimental and theoretical vibrational spectra of P-Iodobenzene sulfonyl chloride (P-IBSC) were studied. P-IBSC and its derivatives present in many biologically active compounds. Because of their spectroscopic properties and chemical significance in particular, sulfonyl chloride and its derivatives have been studied extensively by spectroscopic (FTIR and FT-Raman spectra) and theoretical methods. The infrared spectra of these compounds were recorded in condensed states, while the Raman spectra were measured without polarization using both parallel and perpendicular polarizations of scattered light. The molecular geometry, highest occupied molecular orbital (HOMO), lowest unoccupied molecular orbital (LUMO), first order hyperpolarizability and thermodynamic properties of P-IBSC have been computed with the help of density functional theory (B3LYP) and ab initio (HF) methods with the LanL2DZ basis set. The HOMO and LUMO energy gap explains the charge transfer interactions taking place within the molecule. NBO study explains charge delocalization of the molecule. The contributions of the different modes to each wave number were determined using potential energy distributions (PEDs). The experimental and calculated results were consistent with each other.     

TiHx(x=2,3,4)的从头计算研究

过渡金属氢化物分子与诸多催化过程密切相关[1].而过渡金属氢化物本身是一种颇有潜力的能源材料,即贮氢材料,如钛系、钒系贮氢材料在工业上已得到了广泛的应用 [2].但对于金属与氢的相互作用的机理研究的报道甚少.