The structure of the gas-phase tyrosine–glycine dipeptide

The structural preferences of the neutral dipeptide Tyr–Gly have been investigated using a hierarchical selection scheme. This scheme consists of a hierarchy of increasingly more accurate electronic structure methods (single-point HF/3-21G* energy calculation, HF/3-21G* geometry optimization, B3LYP/6-31+G* geometry optimization, MP2/6-31+G* single-point energy calculation, and MP2/6-31+G* geometry optimization). The conformers are sorted according to their single-point or optimized energy, and only the most stable conformers according to one level are taken through to the next level of calculation. The defining structural characteristics in the 20 most stable Tyr–Gly conformers are the presence or absence of a folded arrangement of the peptide backbone (‘book’) and an OH···O hydrogen bond between the C-terminal hydroxyl group and the carbonyl oxygen of tyrosine (‘OHO’). The most stable conformer is of the book/OHO type. MP2 geometry optimization significantly alters the structure of the book-type conformers, increasing their degree of foldedness. Thus, care has to be taken when applying standard density functionals like B3LYP in structural studies of peptides with aromatic side chains.     

Potential use of small basis set on the calculations of electronic properties of some four-membered heterocycles: a conformational study

The potential use of small basis sets upon a low level of theory was studied on the calculations of electronic properties (dipole moment, static polarisability and static hyperpolarisabilities) of a series of 16 four-membered heterocycles with an exocyclic double bond at the position 3 (1–16). First, the calculations were performed within the Hartree–Fock (HF) approximation using 6-31G, 6-31G(d,p) and 6-31+G(d,p) as basis sets for the different conformational states of each molecule, and the results obtained were compared with the MP2/6-31+G(d,p) results reported. In the second place, in order to know the real potential of HF calculations, these were compared with those calculated using larger approaches such as MP2/6-311+G(d,p), MP2/aug-cc-pVDZ, CCS/6-311+G(d,p), CCS/aug-cc-pVDZ, CCS/aug-cc-pVTZ, CCSD/6-31+G(d) and CCSD/cc-pVDZ, taken into account only the planar and equilibrium geometries of each molecules. The HF approaches permit us to obtain a good qualitative representation of the dipole moment as a function of puckering angle in comparison with MP2, CCS and CCSD levels for all tested molecules. However, only HF/6-31+G(d,p) provides quantitative values of dipole moment for the heterocycles 1, 5 and 13 in comparison with MP2, CCS and CCSD levels. On the other hand, the polarisability and hyperpolarisabilities were quite sensitive to the quality of level of theory and basis sets. In particular, HF/6-31+G(d,p) predicted a representative approximation of alpha for the molecule 16 in comparison with larger methods as MP2/aug-cc-pVDZ, CCS/aug-cc-pVDZ and CCS/aug-cc-pVTZ, while a detailed analysis showed that HF can be used in the calculation of alpha for the molecules 3, 7, 11 and 15, but it requires the use of extended basis sets. Also, HF/6-31+G(d,p) predicted values of beta very similar to those calculated at the MP2 and CCSD levels used, for the planar and equilibrium geometry of the molecules 10 and 14. Furthermore, HF/6-31+G(d,p) described a representative dependence of this property with the puckering angle for the heterocycles 9, 10 and 14, compared with the MP2 curves.     

Intramolecular BSSE and dispersion affect the structure of a dipeptide conformer

B3LYP and MP2 calculations with the commonly-used 6-31+G(d) basis set predict qualitatively different structures for the Tyr–Gly conformer book1, which is the most stable conformer identified in a previous study. The structures differ mainly in the ψ_tyr Ramachandran angle (138° in the B3LYP structure and 120° in the MP2 structure). The causes for the discrepant structures are attributed to missing dispersion in the B3LYP calculations and large intramolecular BSSE in the MP2 calculations. The correct ψ_tyr value is estimated to be 130°. The MP2/6-31+G(d) profile identified an additional conformer, not present on the B3LYP surface, with a ψ_tyr value of 96° and a more folded structure. This minimum is, however, likely an artefact of large intramolecular BSSE values. We recommend the use of basis sets of at least quadruple-zeta quality in density functional theory (DFT), DFTaugmented with an empirical dispersion term (DFT-D) and second-order Møller-Plesset perturbation theory (MP2 ) calculations in cases where intramolecular BSSE is expected to be large.     

Computational estimates of the gas-phase basicities,proton affinities and ionization potentials of the six isomers of dihydroxybenzoic acid

The gas-phase basicities (GBs), gas-phase proton affinities (PAs) and ionization potentials (IPs) of all six isomers of dihydroxybenzoic acid have been calculated using density functional theory at the B3LYP/6-311++G(2df,p)//B3LYP/6-31+G** level. A detailed conformational analysis of each isomer was performed, and the calculated thermodynamic properties were Boltzmann averaged over all conformations. Respectively, the GBs and the gas-phase PAs vary from 803.8 and 832.5?kJ?mol^?1 for the least basic species (3,5-DHB) to 830.1 and 861.4?kJ?mol^?1 for the most basic isomer (2,4-DHB). The reported GBs and gas-phase PAs of 2,3-DHB and 2,4-DHB, are in excellent agreement with previous experimental measurements. Agreement for the 2,5-DHB and 3,4-DHB isomers are not as good, but still close to or within the experimental error estimates. The calculated values for the GB and gas-phase PA of 2,6-DHB and especially 3,5-DHB are significantly outside the experimental error brackets. Repeating these calculations on the lowest energy conformation of each isomer at the MP2/6-311++G(2df,p)//MP2/6-31+G** level yielded significantly worse results. Our results indicate that protonation in all isomers takes place on the carboxylic sites. The vertical IPs vary from 8.14 eV for 2,5-DHB to 8.56 eV for 2,4-DHB.     

硝酸丙酯结构、振动频率和热力学性质的密度泛函理论研究

用密度泛函理论(DFT)研究硝酸丙酯化合物的分子结构、振动光谱和热力学等基本性质.取BLYP、B3LYP方法和6-31G*、6-31G**、6-311G*、6-311G**基组,对硝酸丙酯分子的几何构型进行全优化计算并分析其电子结构性质.和考虑了二级相关能校正的MP2/6-311G*计算结果比较表明,B3LYP/6-31G*是研究许多较大体系化合物卓有成效和颇有前途的方法.在B3LYP/6-31G*的水平上对优化后的结构进行了正则振动频率分析,用因子0.95校正后的振动光谱和实验结果比较,符合较好.进一步     

在小硅化物SiXm（X—H，F，Cl；m＝1─4）中平衡几何和振动频率的从头算研究

本文使用分子轨道从头算方法，在ＨＦ／６—３１Ｇ和ＭＰ２／６—３１Ｇ“水平下，计算了小硅化物ＳｉＸｍ的平衡几何和谐振子振动频率。理论值和实验值的比较表明，对于ＳｉＨｍ分子，实验的键长位于ＨＦ键长和ＭＰ２键长之间，而ＭＰ２振动频率更接近于实验的振动；率。对于ＳｉＣｌｍ分子，无论是键长还是振动频率ＨＦ值和ＭＰ２值都比较接近。对于ＳｉＦｍ分子，处于这两类的中间情况。关联作用随着Ｘ原子的原子序数的增加而减弱。     

Hydrogen bonded rings,chains and lassos: the case of t-butyl alcohol clusters

Infrared OH stretching spectra of hydrogen bonded 2-methyl-propan-2-01 (t-butyl alcohol) clusters are investigated by ragout-jet FTIR spectroscopy. A spectral difference technique is used to discriminate approximately between neighbouring cluster sizes. Dimers, trimers and cyclic tetramers can be detected along with larger clusters, which exhibit a surprisingly structured vibrational fingerprint. Comparison is made to the spectra of related alcohols and to energetic and harmonic vibrational predictions from electronic structure calculations. The experimentally observed 32% increase in OH stretching wavenumber shift from methanol dimer to t-butyl alcohol dimer is reproduced at the HF/3-21G level (+ 33%). It is also qualitatively correct at the MP2/6-31 +G* level (+ l5%), whereas it has the wrong sign at the B3LYP/6-31+ G* level (5%) and is negligible at the HF/6-31+ G* level, disregarding anharmonic effects. The cyclic tetramer of t-butyl alcohol is found to be particularly stable due to a favourable updown alternation of the bulky t-butyl groups. Beyond the t-butyl alcohol tetramer, lasso structures are found to be energetically competitive with simple ring structures. A many-body decomposition shows that this is due to a reduced cooperativity in the sterically hindered pentamer ring. The resulting thermodynamic and kinetic relevance of cyclic tetramers is discussed.     

HO3、HO+3、HO-3光谱和结构的MP2和DFT理论研究

用B3LYP和MP2量子化学理论 ,详细地计算了HO3 、HO+ 3 、HO-3 可能的平衡构型、能量和光谱参数 ,分析了它们可能的解离通道和稳定性 .还分析了HO3 的电离势 (IE)及电子亲和势 (Ea) ,讨论了HO3 、HO3 -自由基的光电子能谱的特征 ,及用光电子能谱去探测HO3 的可能性     

Interaction studies of cysteine with Li+, Na+, K+, Be2+, Mg2+, and Ca2+ metal cation complexes

The coordination geometries, electronic features, metal ion affinities, entropies, and the energetics of Li⁺, Na⁺, K⁺, Be²⁺, Mg²⁺, and Ca²⁺ metal cations with different possible conformations of cysteine complexes were studied. The complexes were optimized using density functional theory (B3LYP) and second order Moller–Plesset Perturbation (MP2) theory methods using 6‐311 + +G** basis set. The interactions of the metal cations at different nucleophilic sites of cysteine conformations were considered after a careful selection among several binding sites. All the metal cations coordinate with cysteine in a tridentate manner and also the most preferred position for the interaction. It is found that, the overall structural parameters of cysteine are not altered by metal ion substitution, but, the metal ion‐binding site has undergone a noticeable change. All the complexes were characterized by an electrostatic interaction between ligand and metal ions that appears slightly more pronounced for lithium and beryllium metal complexes. The metal ion affinity (MIA) and basis set superposition error (BSSE) corrected interaction energy were also computed for all the complexes. The effect of metal cations on the infrared (IR) stretching vibrational modes of amino N? H bond, side chain thiol group S? H bond, hydroxyl O? H bond, and Carbonyl C?O bond in cysteine molecules have also been studied. The nature of the metal ion‐ligand bond and the coordination properties were examined using natural bond order (NBO) at bond critical point (electron density and their Laplacian of electron density) through Atoms in Molecules (AIM) analyses. Copyright © 2010 John Wiley & Sons, Ltd.     

Rotational spectra, conformational structures, and dipole moments of thiodiglycol by jet-cooled FTMW and ab initio calculations

The rotational spectra of three low-energy conformers of thiodiglycol (TDG) (HOCH₂CH₂SCH₂CH₂OH) have been measured in a molecular beam using a pulsed-nozzle Fourier-transform microwave spectrometer. To determine the likely conformational structures with ab initio approach, conformational structures of 2-(ethylthio)ethanol (HOEES) (CH₃CH₂SCH₂CH₂OH) were used as starting points together with the consideration of possible intramolecular hydrogen bonding in TDG. Three lower-energy conformers have been found for TDG at the MP2=Full/6311G** level and ab initio results agree nicely with experimentally determined rotational constants. In addition, Stark measurements were performed for two of the three conformers for dipole moment determinations, adding to our confidence of the conformational structure matches between experimental observations and ab initio calculations. Of the three lower-energy conformers, one displays a compact folded-like structure with strong hydrogen bonding between the two hydroxyl groups and the central sulfide atom. Two other conformers have relatively open chain-like structures with hydrogen bonding between each of the hydroxyl groups to the central sulfur atom, of which one has pure b-type dipole moment according to the ab initio results.     

The mechanism of alkaline hydrolysis of amides: a comparative computational and experimental study of the hydrolysis of N‐methylacetamide,N‐methylbenzamide,and acetanilide

Theoretical computations and experimental kinetic measurements were applied in studying the mechanistic pathways for the alkaline hydrolysis of three secondary amides: N‐methylbenzamide, N‐methylacetamide, and acetanilide. Electronic structure methods at the HF/6‐31+G(d,p) and B3LYP/6‐31+G(d,p) levels of theory are employed. The energies of the stationary points along the reaction coordinate were further refined via single point computations at the MP2/6‐31+G(d,p) and MP2/6‐311++G(2d,2p) levels of theory. The role of water in the reaction mechanisms is examined. The theoretical results show that in the cases of N‐methylbenzamide and N‐methylacetamide the process is catalyzed by an ancillary water molecule. The influence of water is further assessed by predicting its role as bulk solvent. The alkaline hydrolysis process in aqueous solution is characterized by two distinct free energy barriers: the formation of a tetrahedral adduct and its breaking to products. The results show that the rate‐determining stage of the process is associated with the second transition state. The entropy terms evaluated from theoretical computations referring to gas‐phase processes are significantly overestimated. The activation barriers for the alkaline hydrolysis of N‐methylbenzamide and acetanilide were experimentally determined. Quite satisfactory agreement between experimental values and computed activation enthalpies was obtained. Copyright © 2008 John Wiley & Sons, Ltd.     

拉曼光谱法确定某些硅聚合物的构象稳定性(英文)

为了比较某些取代乙烯硅烷不同构象的相对稳定性 ,我们进行了一系列波数在 5 0 -35 0 0cm- 1间的拉曼光谱研究。本文所涉及的分子包括一 ,二卤 (F ,Cl,Br)代乙烯硅烷 ,甲基乙烯基二卤 (F ,Cl)代硅烷以及二甲基乙烯基—卤 (F ,Cl)代硅烷。对以上这些分子 ,我们进行了全电子相关Moller -Plesset微扰理论第二阶(MP2 )的从头 (abinitio)计算。我们仅引入两个比率因子 (scalingfactor)用以计算出液相中上述分子两种稳定构象的拉曼光谱。依据计算模拟所得的谱图 ,以及与实验所得的固相拉曼谱图的比较 ,我们便可判定哪种构象存在于固态之中。通过对液态样品拉曼谱峰的温度相关性研究以及对低温下样品的稀有气体溶液红外谱峰的温度相关性研究 ,我们测定了一系列乙烯硅烷分子两种稳定构象间的焓差 ,并将这些实验结果与上至 6-31 1 +G( 2d ,2 p)的一系列基组的微扰理论和密度泛函理论 (DFT)从头计算结果进行比较。     

O-与CH3CN反应机理的密度泛函理论研究

采用G3MP2B3方法研究了氧负离子与乙腈反应的势能剖面.在(U)B3LYP/6-31+G(d,p)理论水平下分别优化了该反应势能面上反应物、产物、中间体和过渡态的分子结构,采用G3MP2B3方法校正了这些关键点的能量. 势能面上的各个反应路径均通过针对过渡态的內禀反应坐标理论计算加以确定. 分别考察了四个可能的热力学产物通道,即质子转移、氢原子转移、H₂⁺转移和双分子亲核取代反应途径. 其中,经H₂⁺转移生成H₂O的反应通道为该反应的主要产物通道.     

A computational characterization of N2@C60

Recent observations of N₂@C₆₀ are supported computationally. The geometry is optimized at the B3LYP/3-21G and PW91/3-21G levels. The lowest-energy structure has the N₂ unit oriented towards a pair of parallel pentagons so that the complex exhibits D_5d symmetry. Single-point energy calculations are further carried out at the B3LYP/6-31G*, PW91/6-31G* and MP2?=?FC/6-31G* levels and corrected for the basis set superposition error (BSSE). The MP2?=?FC/6-31G* treatment with the BSSE correction gives a stabilization energy of -9.3?kcal?mol^?1, whereas DFT approaches mostly fail to produce a stabilization. The entropy term for the encapsulation is also evaluated and leads to a standard Gibbs energy change upon encapsulation at room temperature of -3.3?kcal?mol^?1. The computed structural and vibrational characteristics are also reported.     

20,20-二氯-1,10-二甲氧基三环[5,4,0,012,19]十一碳 -1,5,6-三烯结构和性质的理论研究

在RHF/6-31G、B3LYP/6-31G和MP2/6-31G水平下优化了标题化合物的平均几何构型,用B3LYP/6-31G方法计算了该化合物的红外光谱.并用GIAO分别在B3LYP/6-31G、B3LYP/6-311G和B3LYP/6-311++G水平对该化合物的核磁共振谱进行了研究.计算结果与实验结果吻合很好.同时对在合成过程中发现的两个中间产物进行了理论计算,研究证实了合成标题化合物时中间产物的存在.     

Theoretical Studies on Electronic Structures and Spectroscopy of Fluorescent Arylamino Fumaronitrile

设计了一系列发荧光的芳胺氰化物, 并用密度泛函方法在B3LYP/6-31G*水平上进行几何构型优化．在优化构型基础上,分别用INDO/CIS、AM1、CIS-ZINDO TD和B3LYP/6-31G*方法计算了芳胺氰化物的电子光谱、红外光谱、荧光光谱及核磁共振碳谱．结果表明,与母体相比,由于萘环较大的立体效应使氰化物的能隙变宽,荧光光谱及电子光谱的主要吸收峰发生蓝移．而由于电子被分散到萘环上,氰化物的主要红外频率发生红移．相反,羟基的存在改善了分子的对称性,扩展了共轭体系,使能隙变窄,荧光光谱及电子光谱的主要吸收峰发生红移．同时由于羟基的供电效应,C-H伸缩振动发生蓝移．     

基于密度泛函理论的三聚氰胺结构及振动光谱研究

利用密度泛函(DFT)算法,对三聚氰胺分子的空间结构进行了优化;然后分别用MP2/6-31G和DFT/DGTIVP两种算法计算了它的拉曼光谱与红外光谱,给出光谱强度图;对比了两种算法的拉曼光谱图和其实验光谱图,结果显示了很好的一致性;给出了三聚氰胺分子中的各原子间键长,键角等空间结构参数;并对三聚氰胺分子在550～3 800cm-1区间的振动谱做了指认。上述工作将有助于食品中三聚氰胺含量测量技术的研究。     

Quantum mechanical interpretation of the IR Spectrum of 2-deoxy-D-ribose in the oh group stretching vibration region

Within MP2/6-311++G(d,p)//DFT B3LYP/6-31 G(d,p) theory, taking into account the anharmonicity of the vibrations, we have calculated the vibrational spectra of all the conformers of the furanose, pyranose, and linear forms of the 2-deoxy-D-ribose molecule. Based on the calculation, we have interpreted the experimental IR spectrum of this molecule in the region of stretching vibrations of the OH groups. For the α and β anomers of the pyranose form of the molecule, we observe and explain the difference between the populations realized in the experiment and the calculated thermodynamic equilibrium values. We present the structures of the eight isomers of 2-deoxy-D-ribose determining its IR spectrum in a low-temperature inert matrix.     

Mechanism and kinetics of the atmospheric degradation of 2-formylcinnamaldehyde with O3 and hydroxyl OH radicals – a theoretical study

In the present investigation, the reaction mechanism and kinetics of 2-formylcinnamaldehyde (2-FC) with O₃ and hydroxyl OH radicals were studied. The reaction of 2-FC with O₃ radical are initiated by the formation of primary ozonide, whereas the reaction of 2-FC with the hydroxyl OH radical are initiated by two different ways: (1). H-atom abstraction by hydroxyl OH radical from the –CHO and –CH = CHCHO group of 2-FC (2). Hydroxyl OH addition to the –CH = CHCHO group to the ring-opened 2-FC. These reactions lead to the formation of an alkyl radical. The reaction pathways corresponding to the reactions between 2-FC with O₃ and hydroxyl OH radicals have been analysed using density functionals of B3LYP and M06-2X level of methods with the 6-31+G(d,p) basis set. Single-point energy calculations for the most favourable reactive species are determined by B3LYP/6-311++G(d,p) and CCSD(T)/6-31+G(d,p) levels of theory. From the obtained results, the hydroxyl OH addition at C8 position of 2-FC are most favourable than the C9 position of 2-FC. The subsequent reactions of the alkyl radicals, formed from the hydroxyl OH addition at C8 position, are analysed in detail. The individual and overall rate constant for the most favourable reactions are calculated by canonical variational transition theory with small-curvature tunnelling corrections over the temperature range of 278–350 K. The calculated theoretical rate constants are in good agreement with the available experimental data. The Arrhenius plot of the rate constants with the temperature are fitted and the atmospheric lifetimes of the 2-FC with hydroxyl OH radical reaction in the troposphere calculate for the first time, which can be applied to the study on the atmospheric implications. The condensed Fukui function has been verified for the most favourable reaction sites. This study can be regarded as an attempt to investigate the O₃-initiated and hydroxyl OH-initiated reaction mechanisms of 2-FC in the atmosphere.     

Theoretical calculations of the kinetics and mechanisms of the gas phase elimination of primary,secondary, and tertiary 2‐hydroxyalkylbenzenes

Theoretical study of the elimination kinetics of 2‐phenylethanol, 1‐phenyl‐2‐propanol, and 2‐methyl‐1‐phenyl‐2‐propanol in the gas‐phase has been carried out at the MP2/6‐31G(d,p), B3LYP/6‐31G(d,p), B3LYP/6‐31++G(d,p), MPW1PW91/6‐31G(d,p), MPW1PW91/6‐31++G(d,p), PBEPBE/6‐31G(d,p), and PBEPBE/6‐31++G(d,p) levels of theory. The three substrates undergo two parallel elimination reactions. The first elimination appears to proceed through a six‐membered cyclic transition state to give toluene and the corresponding aldehyde or ketone. The second parallel elimination takes place through a four‐membered cyclic transition state producing water and the corresponding unsaturated aromatic hydrocarbon. Results from MP2/6‐31G(d,p) and MPW1PW91/6‐31++G(d,p) methods were found to be in good agreement with the experimental kinetic and thermodynamic parameters in the formation of toluene and the corresponding carbonyl compound. However, the results for PBEPBE/6‐31G(d,p) were in better agreement with the experimental data for the second parallel reaction yielding water and the corresponding unsaturated aromatic hydrocarbon. The charge distribution differences in the TS related to the substitution by methyl groups in the substrates can account for the observed reaction rate coefficients. The synchronicity parameters imply semi‐polar transition states for these elimination reactions. Copyright © 2009 John Wiley & Sons, Ltd.