Computational Exploration of Conformations of Glycine-Arginine and a Deduced Model on Global Minimum Configurations of Dipeptides in Gas Phase

An extensive computational study on the conformations of gaseous dipeptide glycinearginine, GlyArg, has been performed. A large number of trail structures were generated by systematically sampling the potential energy surface (PES) of GlyArg. The trial structures were successively optimized with the methods of PM3, HF/3-21G^*, BHandHLYP/6-31G^*, and BHandHLYP/6-311++G^** in order to reliably find the low energy conformations. The conformational energies were finally determined with the methods of BHandHLYP, camB3LYP, B97D, and MP2 using the basis set of 6-311++G(3df,3pd). The results establish firmly that gaseous GlyArg exists primarily in its canonical form, in sharp contrast with ArgGly that adopts the zwitterionic form. Important data such as the rotational constants, dipole moments, vertical ionization energies, temperature distributions and IR spectra of the low energy conformers are represented for the understanding of the future experiments. Moreover, considering the global minima of all amino acids and many dipeptides, combined with the hydrophobicities of amino acids, a model predicting whether the global minimum configuration of a dipeptide is canonical or zwitterionic is developed.     

Gas Phase Conformations of Tetrapeptide Glycine-Phenylalanine-Glycine-Glycine

Systematic search of the potential energy surface of tetrapeptide glycine-phenylalanine-glycine-glycine (GFGG) in gas phase is conducted by a combination of PM3, HF and BHandHLYP methods. The conformational search method is described in detail. The rela-tive electronic energies, zero point vibrational energies, dipole moments, rotational constants, vertical ionization energies and the temperature dependent conformational distributions for a number of important conformers are obtained. The structural characteristics of these conformers are analyzed and it is found that the entropic effect is a dominating factor in determining the relative stabilities of the conformers. The measurements of dipole moments and some characteristic IR mode are shown to be effective approaches to verify the theoreti-cal prediction. The structures of the low energy GFGG conformers are also analyzed in their connection with the secondary structures of proteins. Similarity between the local structures of low energy GFGG conformers and the α-helix is discussed and many β- and γ-turn local structures in GFGG conformers are found.     

Theoretical Studies on Complexes of Calcium Ion with Amino Acids

The complexes formed by calcium ion and 12 common amino acids were investigated systematically in the gas phase at the level of MP2/6-311＋＋G（d,p）//MP2/6-3 1G（d,p）.The results show that the salt-bridge structure is the most preferred motif for Ca2＋ binding aliphatic amino acids without heteroatom in the side chain,while charge-solvated（CS） structure is the most preferred motif for Ca2＋ binding other amino acids except for glutamine and lysine.IR spectra of Gln-Ca2＋ and Asn-Ca2＋ complexes were calculated and compared well with the available experiments.From the study in aqueous solution,the bidentate salt-bridge structure was determined to be the most favorable for all the twenty kinds of amino acids to chelate Ca2＋ to both the oxygen atoms of the negatively carboxylate group in the backbone.     

The influence of hydration on the rotational barriers of glycine

The influence of a full first hydration shell on the energy barriers related to conformational changes of glycine has been studied by means of molecular orbital calculations. The energy optimized pathway is discussed and compared with that of the isolated molecule, evaluating the possibility of corotation of the hydration shell during conformational changes.

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Der Einfluß der Hydratation auf die Rotationsbarrieren von Glycin

Zusammenfassung Es wurde mit Hilfe einer Molekülorbitalrechnung der Einfluß der vollen ersten Hydrathülle auf Rotationsbarrieren bei Konformationsänderungen im Glycinmolekül untersucht. Es wird ein energieoptimierter Rotationsverlauf diskutiert und mit dem des freien Moleküls verglichen, wobei insbesondere die Möglichkeit einer Korotation der Hydrathülle beachtet wird.

     

Theoretical Study on Dissociation Potential Energy Surface of Peroxynitric Acid

The lowest energy structures of peroxynitric acid have been studied with B3LYP/6-311+ G(2d,2p) method. The potential energy surfaces (PES) along the O-N and O-Obonds have been scanned at CCSD(T)/aug-cc-pVDZ level, respectively. The calculated results show that on the O-N PES, the O3-N4 bond length of the loose transition state is 2.82 ? and the corresponding energy barrier is 25.6 kcal/mol, while on the O-O PES, the loose transition state with of O2-O3 bond length of 2.35 ? has the energy barrier of 37.4 kcal/mol. Thus the primary reaction path for peroxynitric acid is the dissociation into HO₂ and NO₂.     

Influence of Isotope Effects on Product Polarizations of N(2D)+D2, N(2D)+H2 and N(2D)+HD Reactive Systems

To figure out the influence of isotope effect on product polarizations of the N(²D)+D₂ reactive system and its isotope variants, quasi-classical trajectory(QCT) calculation was performed on Ho’s potential energy surface(PES) of ²A″ state. Product polarizations such as product distributions of P(θ_r), P(φ_r) and P(θ_r,φ_r), as well as the generalized polarization-dependent differential cross sections(PDDCSs) were discussed and compared in detail among the four product channels of the title reactions. Both the intermolecular and intramolecular isotope effects were proved to be influential on product polarizations.     

基于三辛胺缔合作用的草酸及柠檬酸电极的制备

草酸、柠檬酸可分别与三辛胺(TOA)生成稳定的缔合物,化学分析和红外光谱表明缔合比为1∶1。以此缔合物为活性物质制作的PVC膜电极,测定溶液中的草酸盐、柠檬酸盐的线性范围分别为1.0×10-4~1.0×10-1mol.L-1和1.0×10-5~1.0×10-2mol.L-1。该电极用于简单模拟体系中草酸和柠檬酸浓度的测定,效果良好。     

Surface,Size and Thermal Effects in Alkali Metal with Core-Electron Binding-Energy Shifts

Consistency between density functional theory calculations and X-ray photoelectron spectroscopy measurements confirms our predications on the undercoordination-induced local bond relaxation and core level shift of alkali metal, which determine the surface, size and thermal properties of materials. Zone-resolved photoelectron spectroscopy analysis method and bond order-length-strength theory can be utilized to quantify the physical parameters regarding bonding identities and electronic property of metal surfaces, which allows for the study of the core-electron binding-energy shifts in alkali metals. By employing these methods and first principle calculation in this work, we can obtain the information of bond and atomic cohesive energy of under-coordinated atoms at the alkali metal surface. In addition, the effect of size and temperature towards the binding-energy in the surface region can be seen from the view point of Hamiltonian perturbation by atomic relaxation with atomic bonding.     

谷氨酰胺与碱金属及碱土金属离子络合物的构象和金属离子亲和势：第一性原理研究

Conformations and reaction energetics are important for understanding the interactions be-tween biomolecules and metal ions. In this work, we report a systematic ab initio study on the conformations and metal ion affinities of glutamine (Gln) binding with alkali and alkaline earth metal ions. An efficient and reliable method of searching low energy conformations of metalated Gln is proposed and applied to the complexes of Gln.M^+/++ (M^+/++=Li⁺、Na⁺、K⁺、Rb⁺、Cs⁺、Be⁺⁺、Mg⁺⁺、Ca⁺⁺、Sr⁺⁺和Ba⁺⁺). In addition to all conformers known in literatures, many new important conformations are located, demonstrating the power of the new method and the necessity of the conformational search performed here. The metal coordination modes, relative energies, dipole moments, and equilibrium distribu-tions of all important conformations of Gln.M^+/++ are calculated by the methods of B3LYP, BHandHLYP, and MP2. IR spectra and metalation enthalpies and free energies are also pre-sented and compared with the available experiments. The results form an extensive database for systematic examination of the metalation properties of Gln.     

Theoretical study on infrared vibrational spectra of boric-acid in gas-phase using density functional methods

Density functional theory (DFT) methods with various exchange-correlation functionals such as SVWN, BVWN, BVWN5, BLYP, B1LYP, B3LYP, B3PW91, and BH and H are employed in a theoretical study of molecular boric-acid in gas-phase. In the calculations, the split valence 6-311++G** and 6-31G* basis sets were used. The geometry, zero-point vibrational energies (ZPVEs), and harmonic infrared vibrational (IR) frequencies are predicted. The calculated C_3h-symmetry geometrical parameters are compared with Hartree–Fock (HF) calculation results and experimental data. IR frequencies predicted by the BLYP, B3LYP, and B3PW91 calculations are in good agreement with experimental data. The frequency calculations presented here also suggest that the C_3h-symmetrical structure corresponds to a minimum in the potential energy surface, but neither is D_3h- or C₃-symmetrical structure.     

确定蛋白质-短肽复合物结构的新方法

大部分蛋白质 -蛋白质复合物的三维结构在接触表面都显示出很好的几何匹配 .由于蛋白质的表面几何形状和其它的一些物理化学性质在分子的专一性相互作用中起了主要作用 ,所以 ,接触表面几何形状的互补常常被认为是蛋白质分子识别的基础 .一般来说 ,蛋白质接触表面的几何匹配只涉及 5到 1 0几个紧密堆积的氨基酸残基 ,因此 ,蛋白质与蛋白质配体之间的识别计算可以通过蛋白质与突变周围的或与蛋白质表面紧密接触的配体肽段的识别计算来实现 . Stoddard等 [1] 已经利用从 MBP上选取的八肽成功地计算出接近晶体结构的 MBP-受体复合物 .许多研…     

Theoretical Study on Mechanism of Cycloadditional Reaction Between Dichloro-Germylidene and Formaldehyde

Mechanism of the cycloadditional reaction between singlet dichloro-germylidene and formaldehyde has been investigated with MP2/6-31G^* method, including geometry opti-mization, vibrational analysis and energies for the involved stationary points on the poten-tial energy surface. From the potential energy profile, we predict that the cycloaddition reaction between singlet dichloro-germylidene and formaldehyde has two competitive dom-inant reaction pathways, going with the formation of two side products (INT3 and INT4), simultaneously. Both of the two competitive reactions consist of two steps, two reactants firstly form a three-membered ring intermediate INT1 and a twisted four-membered ring intermediate INT2, respectively, both of which are barrier-free exothermic reactions of 41.5 and 72.3 kJ/mol; then INT1 isomerizes to a four-membered ring product P1 via transition state TS1, and INT2 isomerizes to a chlorine-transfer product P2 via transition state TS2,with the barriers of 2.9 and 0.3 kJ/mol, respectively. Simultaneously, P1 and INT2 further react with formaldehyde to form INT3 and INT4, respectively, which are also barrier-free exothermic reaction of 74.9 and 88.1 kJ/mol.     

Cl+HD反应产物的极化与态分布

利用准经典轨线理论,在BW2和G3两个势能面上,研究了Cl+HD反应的动力学.计算结果表明,产物的转动取向对势能面及反应体系的质量因子非常敏感.在BW2势能面上,计算的两个产物的转动取向强于在G3势能面上计算的结果,而无论是在BW2势能面上还是在G3势能面上,DCl产物的取向都强于HCl产物的取向.计算结果还表明,在不同的势能面上反应物的转动激发对反应的影响有着显著的不同.在BW2势能面上,反应物的初始转动激发有利于Cl+HD反应的进行;而在G3势能面上,反应物的初始转动激发消弱了反应的反应性.     

Ab initio Study on Mechanism of Forming a Silicic Bis-Heterocyclic Compound Between Dimethylmethylenesilylene and Ethene

The mechanism of the cycloaddition reaction of forming a silicic bis-heterocyclic compound between singlet dimethylmethylenesilylene (Me₂C=Si:) and ethene has been investigated with the CCSD(T)//MP2/6-31G^* method. From the potential energy profile, it can be predicted that, this reaction has one dominant channel. The presented rule of this dominant channel: the 3p unoccupied orbital of Si in dimethylmethylenesilylene and the π orbital of ethene forming the π→p donor-acceptor bond, resulting in the formation of three-membered ring intermediate (INT1); INT1 then isomerizes to a four-membered ring silylene (P2), which is driven by ring-enlargement effect; due to sp³ hybridization of Si atom in P2, P2 further combines with ethene to form a silicic bis-heterocyclic compound.     

碱土金属与萘啶酸配合物荧光特性的研究及其应用

研究了碱土金属（Ｍｇ，Ｃａ，Ｓｒ和Ｂａ）离子与喹诺酮类药物萘酸配合物的荧光特性，发现在ｐＨ７～９介质中，碱土金属离子与萘啶酸可形成稳定的荧光配合物，其荧光强度随碱土金属离子半径的减小而呈现有规律的增强效应，其中镁离子与萘啶酸配合物的荧光萘啶酸强５８倍，利用此配合反应发展了镁离子增强一份导数荧光激发光谱测定萘啶酸的分析方法，其检出限为０．０１５μｇ／ｍＬ。可直接测定尿液中萘啶酸含量，其回收率为９６．     

A Theoretical Study on the Potential Energy Surface of the C3 + NO Reaction

The reaction of linear form carbon cluster C₃ molecules in their ¹Σ ground state with NO (X²Π) radicals is explored theoretically to investigate the formation of hitherto undetected NCCCO molecules in the interstellar medium via a neutral-neutral reaction. The doublet potential energy surface is worked out by the ab initio MO calculations at the CCSD(T)/cc-pVTZ//B3LYP/6-311G(d,p)+ZPE level of theory. It is shown that the main pathway of the C₃(¹Σ)+NO(X²Π) reaction involves the N-atom of NO attacking the side C-atom of the ¹C₃ molecule first to form the adduct CCCNO, followed by the N-shift to give I6 CCNCO, and then to the main products P₁ (CCN+CO). Alternatively, I6 can be converted via the N-shift again to I9 (CN)CCO, and then it leads to the minor products P₂ (CNC+CO) and P₃ NCCCO. Since the three pathways have zero threshold energy and proceed via strongly bound energized complexes, they should possess the character of negative temperature dependence, and might be quite rapid even at very low temperature. The reaction represents facile neutral-neutral pathways to produce hitherto undetected CCN, CNC and NCCCO molecules in interstellar environments.     

1,3,5,7-四硝基金刚烷结构和性能的理论研究

在DFT-B3LYP/6-31G*水平下求得1,3,5,7-四硝基金刚烷的全优化分子几何和电子结构. 经简谐振动分析求得其IR谱并作归属. 由统计热力学求得其不同温度下的热力学性质. 以非限制性半经验MO方法探讨其热解机理, 求得各反应通道的过渡态和活化能, 发现热解始于侧链C—NO₂键的均裂. 还基于理论计算密度和生成热, 以Kamlet-Jacobs方程估算其爆速和爆压.     

2,4-二氟戊烷的构象与能量的理论研究

在MP2/6-311++G**和G3水平下,对2,4-二氟戊烷异构体的构象进行几何优化和能量计算.氟的强电负效应使构型发生偏转,同时导致了相隔超过3个键的原子间的电子相互作用.     

基于新一代密度泛函和神经网络势能面的量子反应动力学计算

介绍了近年来发展起来的新一代密度泛函XYG3及利用神经网络构造分子体系势能面的最新进展。以H₃和CH₅等体系为实例,表明基于高效准确的密度泛函电子结构计算,与神经网络高精度势能面构造的理想结合,可以得到可靠的化学动力学结果,并有望用于更大更复杂的体系。     

Ab Initio Study on the Potential Energy Surfaces of B4 Cluster

The singlet and triplet potential energy surfaces (PES) for the isomerization and dissociation reactions of B₄ isomers have been investigated using ab initio methods. Ten B4 isomers have been identified and of these 10 species, 4 have not been reported previously. The singlet rhombic structure ¹1 is found to be the most stable on the B₄ surface, in agreement with the results of previous reports. Several isomerization and dissociation pathways have been found. On the singlet PES, the linear ¹3b can rearrange to rhombus ¹1 directly, while ¹3c rearranges to ¹1 through two‐step reactions involving a cyclic intermediate. On the triplet PES, the capped triangle structure ³2 undergoes ring opening to the linear isomer ³3b with a barrier of 34.8 kcal/mol and 44.9 kcal/mol, and the latter undergoes ring closure to the square structure ³1 with a barrier of 30.4 kcal/mol and 33.0 kcal/mol at the MP4/6–311+G(3df)//MP2/6–311G(d) and CCSD/aug‐cc‐pVTZ//MP2/6–311G(d) levels of theory, respectively. The direct decomposition of singlet B₄ yielding to B₃+B is shown to have a large endothermicity of 87.3 kcal/mol (CCSD), and that producing 2B₂ to have activation energy of 133.4 kcal/mol (CCSD).