甘氨酸二肽分子酰胺-Ⅰ带光谱与结构相关性

系统探索了蛋白质二肽模型分子——甘氨酸二肽(GLYD)在气相与水溶液中的结构与光谱特性。从分子动力学轨迹中提取具有代表性结构的GLYD-D₂O聚集体的瞬态结构开展简正模式分析,获取了对蛋白质二级结构敏感的酰胺-Ⅰ带的振动光谱参数,建立起振动光谱与特征基团结构间的相关性。将溶剂作用以静电势场的形式投影至二肽分子骨架中,与酰胺-Ⅰ带在气/液相中的频率差相关联,并引入酰胺-Ⅰ带简正模式随二级结构变化的规律,将各个构象态可能存在的振动耦合包含在内,构建具有二级结构敏感性的静电频率转换图,实现溶液相中多肽骨架酰胺-Ⅰ带的快速准确预测。     

C30卡宾三叶结分子结构与稳定性的理论研究

三叶结分子是最简单的非平凡纽结分子, C₃₀卡宾三叶结分子是由一条闭合的(C≡C—)₁₅ sp杂化碳链组成的, 是具有D₃对称性的拓扑手性分子. 本文用密度泛函方法[DFT/RB3LYP/6-31G(D)]对分子结构和光谱性质进行了研究, 在优化构型的基础上通过自然键轨道(NBO)方法和轨道能级研究了它的共轭性、成键情况和稳定性, 并与平面型C₃₀卡宾环分子进行了比较. 计算结果表明三叶结分子的三叶弧上形成了非平面的C≡C共轭和扭曲的内螺旋结构, 交叉处具有弱成键作用, 且分子轨道也发生了扭曲; 三叶结分子比卡宾环的共轭性和赝Jahn-Teller效应都明显小, 而总能量高. 因此, 分子打结是一个能量升高的过程.     

堆积的腺嘌呤体系新失活通道的动力学模拟

采用半经典动力学方法模拟了激光诱导下π堆积的腺嘌呤体系最低激发态的失活过程. 模拟激光脉冲仅作用于一个腺嘌呤分子. 发现随着激发态腺嘌呤分子(A)与基态腺嘌呤分子(A′)之间距离的缩短, 它们的相互作用显著增强. 分子间的相互作用导致了一条新的失活通道, 即C₂原子与C₂′原子靠拢成键, 形成“成键的激基复合体”的中间体. 中间体的寿命约为390 fs. C₂原子的畸变和H₂′原子的环面外振动导致中间体失活. 失活后C₂－C₂′断裂, 释放的键能转化为分子动能, 腺嘌呤分子恢复基态的平面结构.     

苯硫酚各种形态在金上的拉曼光谱研究

用Gaussian 98程序在B3LYP/6-311＋G**(C, H, S)水平上计算得到苯硫酚(TP)的一套校正因子, 对苯硫酚各频率进行了势能分布(PEDs)分析, 并对各振动模式进行了详细的指认. 同时, 在B3LYP/6-311＋G**(C, H, S)/LANL2DZ(Au)水平上优化得到苯硫酚的各种形态与金结合, 即C₆H₅SH-Au, C₆H₅SAu, C₆H₅S^－-Au的平衡构型, 且在此基础上得到了C₆H₅SH-Au, C₆H₅SAu, C₆H₅S^－-Au三种形态的计算拉曼谱图. 其中苯硫酚金盐(C₆H₅SAu)的拉曼谱图与实验得到的苯硫酚在金溶胶中的谱图是一致的, 由此很好地证明了TP与金形成苯硫酚金盐.     

CnBδ(δ=0, ±1; n =1～6)团簇的结构、稳定性和光谱

采用密度泛函理论(DFT)的B3LYP方法,在6-31G*和6-311＋G(3df)水平上对C_nB(n=1～6)团簇及其阴离子和阳离子的几何构型和电子结构进行了优化和振动频率计算.得到了C_nB(n=1～6)团簇的电离能,绝热电子亲合势以及C_nB^δ(δ=0,±1)团簇的能隙.结果表明C_nB^－(n=1～6)团簇的基态构型均为线形,这与等电子的C_n簇合物的结构是一致的; C_nB(n=1～6)团簇的基态构型中,除C₂B为不对称的三角形,C₆B为具有C_2v对称性的环状结构外,其余均为线形结构.阳离子团簇中n=2、3、6的基态结构具有C_2v对称性外,其它几个均为线形结构.从几何参数和振动频率上发现,采用密度泛函B3LYP方法在6-311＋G(3df)和6-31G*两种基组上计算得到的键长参数和振动频率非常接近,说明B3LYP方法在计算C_nB簇合物结构参数上对于基组的选择是不太敏感的.通过对C_nB(n=1～6)的光电子能谱性质的研究发现,C₄B容易获得一个电子形成阴离子团簇,但失去一个电子是很困难的,这与实验上观测到的结果非常吻合.     

(+)-儿茶素金属配合物的结构、红外光谱和反应活性

用密度泛函理论(DFT)B3LYP方法, 对非金属原子和金属原子分别采用6-311+G(d,p)基组和LANL2DZ基组, 计算并分析了(+)-儿茶素(Cc, C₁₅H₁₄O₆)及其与金属形成的配合物分子(M-Cc, M=Ca, Zn, Cd, Cu, Al, Cr)的几何构型、红外光谱和反应活性的异同. 计算结果表明, M-Cc的分子结构、红外光谱与反应活性均不同于其前体Cc. 形成金属配合物后, 取代基团及结构的改变使得红外光谱有所差异. 前线分子轨道及概念DFT指数计算结果显示, 一些M-Cc体系的反应活性要强于Cc单体. 金属离子的不同使得配合物的各指数有所差异. 这些结果将为进一步认识(+)-儿茶素及其相关化合物的结构、红外光谱和反应活性提供有益启示.     

C30卡宾三叶结分子结构与稳定性的理论研究

三叶结分子是最简单的非平凡纽结分子, C₃₀卡宾三叶结分子是由一条闭合的(C≡C—)₁₅ sp杂化碳链组成的, 是具有D₃对称性的拓扑手性分子. 本文用密度泛函方法[DFT/RB3LYP/6-31G(D)]对分子结构和光谱性质进行了研究, 在优化构型的基础上通过自然键轨道(NBO)方法和轨道能级研究了它的共轭性、成键情况和稳定性, 并与平面型C₃₀卡宾环分子进行了比较. 计算结果表明三叶结分子的三叶弧上形成了非平面的C≡C共轭和扭曲的内螺旋结构, 交叉处具有弱成键作用, 且分子轨道也发生了扭曲; 三叶结分子比卡宾环的共轭性和赝Jahn-Teller效应都明显小, 而总能量高. 因此, 分子打结是一个能量升高的过程.     

1-甲基胸腺嘧啶A-带结构动力学

获取了1-甲基胸腺嘧啶(MT)涵盖紫外光谱中A带和B带吸收的共5 个激发波长的共振拉曼光谱, 并结合密度泛函理论方法研究了MT的电子激发和Franck-Condon 区域结构动力学. 在TD-B3LYP/6-311++G(d,p)计算水平下, A带和B带吸收被分别指认为π_H→π_L^*/π_H-2→π_L+2^*和π_H→π_L+2^→/π_H-2→π_L^*跃迁. 甲基参与嘧啶环的共轭使MT的A带最大吸收波长λ_max相对于胸腺嘧啶(T)发生明显红移, 并对Franck-Condon区域的动态结构产生一定影响. A带和B带共振拉曼光谱分别被指认为14 个振动模式和11 个振动模式的基频、泛频和组合频. C5＝C6伸缩+C6H12面内弯曲振动v₉, 环变形振动v₁₆和N3C2N1反对称伸缩+C4C5C10反对称伸缩振动v₁₈占据了A带共振拉曼光谱强度的绝大部分. 这表明¹π_Hπ_L^*激发态结构动力学主要沿这些反应坐标展开. 考察了溶剂对共振拉曼光谱的影响, 结果表明, C4＝O9伸缩+N3H11面内弯曲振动v₈的活性与溶剂性质有关, 其激发态位移量随溶剂性质的变化规律与胸腺嘧啶一致.     

基态N2O－的势能函数研究

以6-311＋＋G(3df, 3pd)为基函数, 采用密度泛函理论的B3LYP方法对N₂O^－分子体系的结构进行了优化计算. 结果表明N₂O^－分子最稳态为C_s构型, 电子组态为²A', 平衡核间距R_N—N＝0.11873 nm, R_N—O＝0.13012 nm, 键角∠NNO＝133.94448°, 离解能D_e＝10.3857 eV, 基态简正振动频率: 弯曲振动频率ν₁＝656.7488 cm^－1, 对称伸缩振动频率ν₂＝998.1562 cm^－1, 反对称伸缩振动频率ν₃＝1684.3093 cm^－1. 并用多体展式理论方法推导出了基态N₂O^－分子的分析势能函数, 其等值势能图准确地再现了N₂O^－分子的结构特征和离解能.     

杂硼原子簇XB6+ (X=C,Si, Ge,Sn, Pb)的稳定性和芳香性

利用从头算MP2方法和密度泛函理论B3LYP和B3PW91方法, 研究了杂硼原子簇XB₆⁺ (X=C, Si, Ge, Sn, Pb)的结构、稳定性及化学键合情况. 对C, Si, Ge, B使用6-311+G(d)基组, 对Sn和Pb使用LANL2DZ赝势基组. 研究结果表明, 具有C_s对称性的假平面XB₆⁺ (X=C, Si, Ge, Sn, Pb)结构是势能面上的全域极小点, 其稳定性要高于C_6v对称性的锥形结构和C₂对称性的假锥形结构. 在B3LYP水平上, 对这些异构体的势能面的极小点进行了自然键轨道(NBO)的分析; 对最稳定构型的最高占据分子轨道(HOMO)和最低空轨道(LUMO)能级差、分子轨道(MO)和核独立化学位移(NICS)进行了计算和讨论. 分析了杂原子和硼原子间、相邻硼原子间的键合情况, 讨论了最稳定构型的芳香性质.     

Calculations of intermode coupling constants and simulations of amide I,II, and III vibrational spectra of dipeptides

Amide I, II, and III vibrations of polypeptides are important marker modes whose vibrational spectra can provide critical information on structure and dynamics of proteins in solution. The extent of delocalization and vibrational properties of amide normal mode can be described by the amide local mode frequencies and intermode coupling constants between a pair of amide local modes. To determine these fundamental quantities, the previous Hessian matrix reconstruction method has been generalized here and applied to the density functional theory results for various dipeptide conformers. The calculation results are then used to simulate IR absorption, vibrational circular dichroism, and 2D IR spectra of dipeptides. The relationships between dipeptide backbone conformations and these vibrational spectra are discussed. It is believed that the present computational method and results will be of use to quantitatively simulate vibrational spectra of complicated polypeptides beyond simple dipeptides     

Anharmonicity of amide modes

The principal contributions to the anharmonic coupling of amide vibrations are explored with the objective of comparing recent experiments with density functional theory and evaluating simple models of mode coupling. Experimental information obtained by means of two-dimensional infrared spectroscopy (2D IR) is reasonably well predicted by the computed one- and two-quantum anharmonic modes of amide-A, -I, and -II types in mono-, di- and tripeptides. The expansion of the vibrational energy up to the cubic and quartic coupling of harmonic modes suggested criteria to assess how localized are the forces determining the anharmonicity. The off-diagonal anharmonicity between an amide-A and one other amide mode was shown to be mainly determined by forces involving only these two modes, whereas the off-diagonal anharmonicity of two amide-I modes in peptides depended significantly on forces due to motions other than those of the amide-I type. Both the diagonal and off-diagonal anharmonicities exhibit sensitivity to peptide structures. These results should prove useful in linking 2D IR experimental results to secondary structure. Further, the results are used to evaluate the vibrational exciton model for the mixed-mode anharmonicities of the amide-I transitions.     

Nonadiabatic effects on peptide vibrational dynamics induced by conformational changes

Quantum dynamical simulations of vibrational spectroscopy have been carried out for glycine dipeptide (CH(3)-CO-NH-CH(2)-CO-NH-CH(3)). Conformational structure and dynamics are modeled in terms of the two Ramachandran dihedral angles of the molecular backbone. Potential energy surfaces and harmonic frequencies are obtained from electronic structure calculations at the density functional theory (DFT) [B3LYP/6-31+G(d)] level. The ordering of the energetically most stable isomers (C(7) and C(5)) is reversed upon inclusion of the quantum mechanical zero point vibrational energy. Vibrational spectra of various isomers show distinct differences, mainly in the region of the amide modes, thereby relating conformational structures and vibrational spectra. Conformational dynamics is modeled by propagation of quantum mechanical wave packets. Assuming a directed energy transfer to the torsional degrees of freedom, transitions between the C(7) and C(5) minimum energy structures occur on a sub-picosecond time scale (700...800 fs). Vibrationally nonadiabatic effects are investigated for the case of the coupled, fundamentally excited amide I states. Using a two state-two mode model, the resulting wave packet dynamics is found to be strongly nonadiabatic due to the presence of a seam of the two potential energy surfaces. Initially prepared adiabatic vibrational states decay upon conformational change on a time scale of 200...500 fs with population transfer of more than 50% between the coupled amide I states. Also the vibrational energy transport between localized (excitonic) amide I vibrational states is strongly influenced by torsional dynamics of the molecular backbone where both enhanced and reduced decay rates are found. All these observations should allow the detection of conformational changes by means of time-dependent vibrational spectroscopy.     

Infrared and Raman spectra, ab initio calculations and vibrational assignment for 3-fluoro-1-butyne

The infrared (3500-80 cm⁻¹) and Raman (3500-20 cm⁻¹) spectra of 3-fluoro-1-butyne, CH₃CHFCCH, have been recorded for the gas and solid. Additionally, the Raman spectrum of the liquid has also been recorded to aid in the vibrational assignment. Ab initio electronic structure calculations of energies, geometrical structures, vibrational frequencies, infrared intensities, Raman activities and the potential energy function for the methyl torsion have been calculated to assist in the interpretation of the spectra. The fundamental torsional mode is observed at 251 cm⁻¹ with a series of sequence peaks falling to lower frequency. The three-fold methyl torsional barrier is calculated to be 1441 ± 20 cm⁻¹ (4.12 ± 0.06 kcal mol⁻¹) where the uncertainty is partly due to the uncertainty in values of the V₆ term. A complete vibrational assignment is proposed based on band contours, relative intensities, and ab initio predicted frequencies. Several fundamentals are significantly shifted in the condensed phases compared to values in the vapor state.     

Dynamics of amide-I modes of the alanine dipeptide in D2O

The equilibrium dynamics of the acetyl and amino amide-I groups of the alanine dipeptide were examined separately using (13)C isotopic selection and 2D IR. The population relaxation times of the amide transitions were measured to be in the range 500 fs by means of heterodyne transient grating methods. The vibrational frequency correlation functions consisted in all cases of a motionally narrowed part, a component near 800 fs, and a constant part representing a distribution of structures that is static on the few ps time scale. The intermediate time scale is attributed to fluctuations in the stretching and bending of hydrogen bonds between the carbonyl and water.     

Tripeptides adopt stable structures in water. A combined polarized visible Raman,FTIR, and VCD spectroscopy study

We have measured the band profile of amide I in the infrared, isotropic, and anisotropic Raman spectra of L-alanyl-D-alanyl-L-alanine, acetyl-L-alanyl-L-alanine, L-vanyl-L-vanyl-L-valine, L-seryl-L-seryl-L-serine, and L-lysyl-L-lysyl-L-lysine at acid, neutral, and alkaline pD. The respective intensity ratios of the two amide I bands depend on the excitonic coupling between the amide I modes of the peptide group. These intensity ratios were obtained from a self-consistent spectral decomposition and then were used to determine the dihedral angles between the two peptide groups by means of a recently developed algorithm (Schweitzer-Stenner, R. Biophys. J. 2002, 83, 523-532). The validity of the obtained structures were checked by measuring and analyzing the vibrational circular dichroism of the two amide I bands. Thus, we found two solutions for all protonation states of trialanine. Assuming a single conformer, one obtains a very extended beta-helix-like structure. Alternatively, the data can be explained by the coexistence of a 3(1)(PII) and a beta-sheet-like structure. Acetyl-L-alanyl-L-alanine exhibits a structure which is very similar to that obtained for trialanine. The tripeptide with the central D-alanine adopts an extended structure with a negative psi and a positive phi angle. Trivaline and triserine adopt single beta(2)-like structures such as that identified in the energy landscape of the alanine dipeptide. Trilysine appears different from the other investigated homopeptides in that it adopts a left-handed helix which at acid pD is in part stabilized by hydrogen bonding between the protonated carboxylate (donor) and the N-terminal peptide carbonyl. Our result provides compelling evidence for the capability of short peptides to adopt stable structures in an aqueous solution, which at least to some extent reflect the intrinsic structural propensity of the respective amino acids in proteins. Furthermore, this paper convincingly demonstrates that the combination of different vibrational spectroscopies provides a powerful tool for the determination of the secondary structure of peptides in solution.     

Anharmonic vibrational probe for N-methylacetamide in different micro-environments

In the present study, anharmonic vibrational properties of the amide modes in N-methylacetamide (NMA), a model molecule for peptide vibrational spectroscopy, are examined by DFT calculations. The 3N-6 normal mode frequencies, diagonal and off-diagonal anharmonicities are evaluated by means of the second order vibrational perturbation theory (VPT2). Good performance of B3LYP/6-31+G** is found for predicting vibrational frequencies in comparison with gas phase experimental data. The amide vibrational modes are assigned through potential energy distribution analysis (PED). The solvation effect on the amide vibrational modes is modeled within the PCM method. From gas phase to polar solvents, red shifts are observed for both harmonic and anharmonic vibrational frequency of amide I mode while the CO bond length increases upon the solvent polarity. Cubic and quartic force constants are further calculated to evaluate the origin of the anharmonicity for the amide I mode of NMA in different micro-environments.     

Ab initio studies of methylenecarbene and isoelectronic species

Optimum equilibrium geometries, energetics, harmonic vibrational frequencies, and infared intensities within the double harmonic approximation are computed for methylenecarbene, CCH₂, and isoelectronic species involving silicon and germanium at both the SCF level of theory and the level of second-order perturbation theory using a 6-311G(2df, 2p) basis set or its equivalent. Optimum equilibrium geometries and energetics are also computed at both levels of theory using a smaller 6-311G(d, p) basis set or its equivalent. This investigation of these species is the first to include all of the systems with germanium. In addition, this present work is the first study to includef-type polarization functions in a systematic investigation of the molecular structure and properties of all the molecules in the series. Acetylenic structures are also computed for energy comparisons. Of all the linear isomers, only acetylene is found to be a minimum on the potential energy surface. However, all of the C_2v structures are found to be local minima. Both the C_2v and linear structures will serve as a basis for future work involving mapping the entire hyperenergy surfaces of all of the molecular systems in the series.     

Chain-length and mode-delocalization dependent amide-I anharmonicity in peptide oligomers

The diagonal anharmonicities of the amide-I mode in the alanine oligomers are examined in the normal-mode basis by ab initio calculations. The selected oligomers range from dimer to heptamer, in either the α-helical or β-sheet conformations. It is found that the anharmonicity varies from mode to mode within the same oligomer. For a given amide-I mode, the anharmonicity is closely related to the delocalization extent of the mode: the less it delocalizes, the larger the anharmonicity it has. Thus, the single-mode potential energy distribution (PED(max)) can be used as an indicator of the magnitude of the anharmonicity. It is found that as the peptide chain length increases, the averaged diagonal anharmonicity generally decreases; however, the sum of the averaged diagonal and off-diagonal anharmonicities within a peptide roughly remains a constant for all the oligomers examined, indicating the excitonic characteristics of the amide-I modes. Excitonic coupling tends to decrease the diagonal anharmonicities in a coupled system with multiple chromophores, which explains the observed behavior of the anharmonicities. The excitonic nature of the amide-I band in peptide oligomers is thus verified by the anharmonic computations. Isotopic substitution effect on the anharmonicities and mode localizations of the amide-I modes in peptides is also discussed.