A semi-empirical and ab initio combined approach for the full conformational searches of gaseous lysine and lysine–H2O complex

A full structural search of the canonical, zwitterionic, protonated and deprotonated lysine conformers in gas phase is presented. A total of 17,496 canonical, 972 zwitterionic, 11,664 protonated and 1458 trial deprotonated structures were generated by allowing for all combinations of internal single-bond rotamers. All the trial structures were initially optimized at the AM1 level, and the resulting structures were determined at the B3LYP/6-311G^* level. A total of 927 canonical, 730 protonated and 193 deprotonated conformers were found, but there were no stable zwitterionic structures in the gas phase. The most stable conformers of the canonical, protonated and deprotonated lysine were further optimized at the B3LYP/6-311++G^** level. The energies of the most stable structures were determined at the MP2/6-311G(2df,p) level and the vibrational frequencies were calculated at the B3LYP/6-311++G^** level. The rotational constants, dipole moments, zero-point vibrational energies, harmonic frequencies, vertical ionization energies, enthalpies, Gibbs free energies and conformational distributions of gaseous lysine were presented. Numerous new structures are found and the lowest-energy lysine conformer is more stable than the existing one by 1.1 kcal/mol. Hydrogen bonds are classified and may cause significant red-shifts to the associated vibrational frequencies. The calculated proton affinity/dissociation energy and gas-phase basicity/acidity are in good agreement with the experiments. Calculations are also presented for the canonical lysine–H₂O and zwitterionic lysine–H₂O clusters. Interaction between lysine and H₂O significantly affects the relative conformational stabilities. Only one water molecule is sufficient to produce the stable zwitterionic structures in gas phase. The lowest-energy structure is found to be zwitterions when applying the conductor-like polarized continuum solvent model (CPCM) to the lysine–H₂O complexes.     

Conformational search for zwitterionic leucine and hydrated conformers of both the canonical and zwitterionic leucine using the DFT-CPCM model

The stable conformations for zwitterionic leucine have been searched for in solution as well as in gas phase. A total of 54 trial structures were generated by considering possible combinations of single bond rotamers. It is observed that zwitterions are not stable in gas phase. In order to investigate the zwitterions of leucine in solution, the calculations for all trial structures of zwitterions were performed initially at the PM3 level and 14 the lowest energy structures were reoptimized at the B3LYP/6-311G(d) level using the CPCM model. Seven of these conformers of zwitterionic leucine were found to be stable in solution. The five most stable conformers were then reoptimized at the B3LYP/6-311++G(d, p) level. The energy ordering of the canonical leucine(neutral) conformers were also considered on the basis of single point energy calculations at the B3LYP/6-311++G(d, p) level using the CPCM model. The chemical hardness, chemical potential, vertical ionization energy and vertical electron affinity were calculated for a few of the most stable canonical leucine and its zwitterions in solution. The effects of explicit addition of water molecules (microsolvation) on the structure and the energy of both canonical and zwitterionic conformers of leucine were investigated. It is noted that in gas phase, the singly and doubly hydrated canonical (neutral) forms are more stable than their zwitterionic counterparts. The solvated zwitterions and canonical structures of leucine were further investigated using the discrete/SCRF model with zero, one and two water molecules. In solution, the continuum solvent model shows that the bare zwitterionic form is more stable than the bare canonical form by 1.6 kcal/mol. This energy separation is increased to 3.8 and 4.8 kcal/mol with inclusion of one and two water molecules, respectively. The optimized structural parameters for the most stable zwitterionic leucine with zero, one and two water molecules in solution were compared with those reported for l-leucine crystal, which shows a close agreement between the optimized geometrical parameters of the zwitterionic leucine with two water molecules in solution with the experimental geometrical parameters for l-leucine crystal. It is also observed that when the structures of zwitterions with one and two explicit water molecules are optimized in solution, the geometrical parameters and their relative energies are found to be appreciably modified. We have also calculated the vibrational spectra of the most stable solvated zwitterionic leucine as well as for the most stable structure of zwitterionic leucine with one and two water molecules in solution.     

An exploration of conformational search of leucine molecule and their vibrational spectra in gas phase using ab initio methods

An extensive exploration of the conformational space has been carried out to characterize all possible gas phase structures of leucine. A total of 324 unique trial structures for canonical leucine were generated by considering all possible combinations of single bond rotamers. All trial structures were optimized at the B3LYP/6-311G* level of the DFT method. A total of 77 unique and stationary canonical conformers were found. Further, 15 most stable conformers were reoptimized at B3LYP/6-311++G** level and their respective relative energies, vertical ionization energies, hydrogen bonding patterns, rotational constants and dipole moments were calculated. A single point energy calculations for leucine conformers have also been done at both B3LYP/6-311++G(2df, p) and MP2/6-311++G(2df, p) levels. The good agreement between our estimates of rotational constants for two most stable conformers and available experimental measurements supports the reliability of the B3LYP/6-311++G** level of theory for describing the conformational behavior of leucine molecule. The proton affinity and gas phase basicity were also determined. Using the statistical approach, conformational distributions at various temperatures have also been performed and analyzed. Vibrational spectra were also calculated. It is also observed that zwitterions of leucine are not stable in gas phase.     

Ab initio studies of the conformers and conformational distribution of the gaseous hydroxyamino acid threonine

Systematic and extensive conformational search has been performed to characterize the gas-phase threonine structures. A total of 1296 unique trial structures were generated by allowing for all combinations of internal single-bond rotamers. All the trial structures were optimized at the B3LYP/6-311G* level of the theory and then subjected to further optimization at the B3LYP/6-311++G** level. A total of 71 conformers were found and their rotational constants, dipole moments, zero-point vibrational energies, harmonic frequencies and vertical ionization energies of all the conformers were determined. Single-point energies were also calculated at the MP2/6-311G(2df,p) and B3LYP/6-311G(2df,p) levels. Characteristic H-bonding types were classified and listed for all the conformers. The conformational distributions of gaseous threonine at various temperatures were calculated.     

Systematic ab initio studies of the conformers and conformational distribution of gas-phase tyrosine

A full structural assignment of the conformers of gaseous tyrosine is presented. A total of 1296 unique trial structures were generated by allowing for all combinations of internal single-bond rotamers and optimized at the B3LYP6-311G* level of theory and then subjected to further optimization at the B3LYP6-311++G** level. A total of 76 conformers are found and their dipole moments, rotational constants, and harmonic frequencies are determined. Accurate relative energies are given at the MP26-311G(2df,p)B3LYP6-311++G** level of theory. Characteristic H-bonding types are classified and listed for all the conformers. The four most stable conformers display an intramolecular H bond, COOH...NH(2), and an additional H-bonding interaction between the amino group and pi electron of the aromatic ring. The results further confirm that the global minimum conformations of the aromatic amino acids have the same H-bonding type. Combined with statistical mechanics principles, conformational distributions at various temperatures are computed and the temperatures with which the theoretical results match that of experiments are indicated.     

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.     

Gaseous arginine conformers and their unique intramolecular interactions

Extensive ab initio calculations were employed to characterize stable conformers of gaseous arginine, both the canonical and zwitterionic tautomers. Step-by-step geometry optimizations of possible single-bond rotamers at the B3LYP/6-31G(d), B3LYP/6-31++G(d,p), and MP2/6-31++G(d,p) levels yield numerous structures that are more stable than any known ones. The final electronic energies of the conformers were determined at the CCSD/6-31++G(d,p) level. The lowest energies of the canonical and zwitterionic structures are lower than the existing values by 2.0 and 2.3 kcal/mol, respectively. The relative energies, rotational constants, dipole moments, and harmonic frequencies of the stable conformers remain for future experimental verification. The conformational distributions at various temperatures, estimated according to thermodynamic principles, consist almost exclusively of the newly found structures. One striking feature is the occurrence of blue-shifting hydrogen bonds in all six of the most stable conformers. A unique feature of important conformations is the coexistence of dihydrogen and blue- and red-shifting hydrogen bonds. In addition to the hydrogen bonds, the stereoelectronic effects were also found to be important stabilization factors. The calculated and measured proton affinities agree within the theoretical and experimental uncertainties, affirming the high quality of our conformational search. The theoretical gas-phase basicity of 245.9 kcal/mol is also in good agreement with the experimental value of 240.6 kcal/mol. The extensive searches establish firmly that gaseous arginine exists primarily in the canonical and not the zwitterionic form.     

Detailed ab initio studies of the conformers and conformational distributions of gaseous tryptophan

A systematic and extensive conformational search has been performed to characterize the gas-phase tryptophan structures. A total of 648 unique trial structures were generated by allowing for all combinations of internal single-bond rotamers and were optimized at the DFT/B3LYP/6-311G* level of theory. A total of 45 local minima conformers were found. Further optimization of the 45 conformers with B3LYP and MP2/6-311++G** did not produce meaningful structural change, and accurate geometries, dipole moments, rotational constants, harmonic frequencies, and relative energies were then determined. Combined with statistical mechanics principles, the conformational distributions of gas-phase tryptophan at different temperatures are shown. The results clearly support the conclusion drawn by Compagnon et al. that only one dominant isomer existed in the molecular beam at 85 K and add further evidence that the supersonic jet expansion or embedding helium droplets did not produce an equilibrium distribution.     

An ab initio study of water clusters in gas phase and bulk aqueous media: (H2O)n,n=1–12

Geometries of several clusters of water molecules including single minimum energy structures of n‐mers (n=1–5), several hexamers and two structures of each of heptamer to decamer derived from hexamer cage and hexamer prism were optimized. One structural form of each of 11‐mer and 12‐mer were also studied. The geometry optimization calculations were performed at the RHF/6‐311G* level for all the cases and at the MP2/6‐311++G** level for some selected cases. The optimized cluster geometries were used to calculate total energies of the clusters in gas phase employing the B3LYP density functional method and the 6‐311G* basis set. Frequency analysis was carried out in all the cases to ensure that the optimized geometries corresponded to total energy minima. Zero‐point and thermal free energy corrections were applied for comparison of energies of certain hexamers. The optimized cluster geometries were used to solvate the clusters in bulk water using the polarized continuum model (PCM) of the self‐consistent reaction field (SCRF) theory, the 6‐311G* basis set, and the B3LYP density functional method. For the cases for which MP2/6‐311++G** geometry optimization was performed, solvation calculations in water were also carried out using the B3LYP density functional method, the 6‐311++G** basis set, and the PCM model of SCRF theory, besides the corresponding gas‐phase calculations. It is found that the cage form of water hexamer cluster is most stable in gas phase among the different hexamers, which is in agreement with the earlier theoretical and experimental results. Further, use of a newly defined relative population index (RPI) in terms of successive total energy differences per water molecule for different cluster sizes suggests that stabilities of trimers, hexamers, and nonamers in gas phase and those of hexamers and nonamers in bulk water would be favored while those of pentamer and decamer in both the phases would be relatively disfavored. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 81: 90–104, 2001     

Theoretical determinations of ionization potentials of dopamine

Adiabatic and vertical ionization potentials (IPs) of nine conformers of dopamine in the gas phase are determined using density functional theory (DFT) B3LYP, B3P86, B3PW91 methods and high level ab initio HF method with 6-311++G** basis set, respectively. And the nine stable cationic states have been found in the ionization process of dopamine. Vertical ionization potentials of nine conformers of dopamine are calculated using the older outer-valence Green’s function (OVGF) calculations at 6-311++G** basis set. Vibrational frequencies and infrared spectrum intensities of G1b and G1b⁺ at B3LYP/6-311++G** level are discussed.     

Structure of the boronic acid dimer and the relative stabilities of its conformers

Despite the widespread use of boronic acids in materials science and as pharmaceutical agents, many aspects of their structure and reactivity are not well understood. In this research the boronic acid dimer, [HB(OH)(2)](2), was studied by second-order M?ller-Plesset (MP2) perturbation theory and coupled cluster methodology with single and double excitations (CCSD). Pople split-valence 6-31+G*, 6-311G**, and 6-311++G** and Dunning-Woon correlation-consistent cc-pVDZ, aug-cc-pVDZ, cc-pVTZ, and aug-cc-pVTZ basis sets were employed for the calculations. A doubly hydrogen-bonded conformer (1) of the dimer was consistently found to be lowest in energy; the structure of 1 was planar (C(2h)) at most computational levels employed but was significantly nonplanar (C(2)) at the MP2/6-311++G** and CCSD/6-311++G** levels, the result of an intrinsic problem with Pople-type sp-diffuse basis functions on heavy atoms. The dimerization energy, enthalpy, and free energy for the formation of (1) from the exo-endo conformer of the monomer were -10.8, -9.2, and +1.2 kcal/mol, respectively, at the MP2/aug-cc-pVTZ level. Several other hydrogen-bonded conformers of the dimer were local minima on the potential energy surface (PES) and ranged from 2 to 5 kcal/mol higher in energy than 1. Nine doubly OH-bridged conformers, in which the boron atoms were tetracoordinated, were also local minima on the PES, but they were all greater than 13 kcal/mol higher in energy than 1; doubly H-bridged structures proved to be transition states. MP2 and CCSD results were compared to those from the BLYP, B3LYP, OLYP, O3LYP, PBE1PBE, and TPSS functionals with the 6-311++G** and aug-cc-pVTZ basis sets; the PBE1PBE functional performed best relative to the MP2 and CCSD results. Self-consistent reaction field (SCRF) calculations predict that boronic acid dimerization is less favorable in solution than in vacuo.     

气相中O3与HSO自由基间的氢键复合物

气相中O3与HSO自由基之间的相互作用及其反应在大气化学中非常重要.在DFT-B3LYP/6-311++G**和MP2/6-311++G**水平上求得O3+HSO复合物势能面上的稳定构型,B3LYP方法得到了三种构型(复合物Ⅰ,Ⅱ和Ⅲ),而MP2方法只能得到一种构犁(复合物Ⅱ).在复合物Ⅰ和Ⅲ中,HSO单元中的1H原子作为质子供体.与O3分子中的端基O原子作为质子受体相互作用,形成红移氢键复合物;而在复合物Ⅱ中,虽与复合物Ⅰ和Ⅲ中具有相间的质子供体和质子受体,却形成了蓝移氢键复合物.B3LYP/6-311++G**水平上计算的单体间相互作用能的计算考虑了基组重甍误差(BSSE)和零点振动能(ZPVE)校正,其值在-3.37到-4.55 kJ·mol-1之间.采用自然键轨道理论(NBO)对单体间相互作用的本质进行了考查,并通过分子中原子理论(AIM)分析了三种复合物中氢键的电子密度拓扑性质.     

Computational treatment of the microsolvation of neutral and zwitterionic forms of alanine

B3LYP/6-31++G** and MP2/6-31++G**//B3LYP/6-31++G** calculations are reported for the structures of neutral alanine–(H₂O)_n and zwitterionic alanine–(H₂O)_n clusters where n = 2–10. Optimized geometries and energies were obtained. In general, with an increasing number of water molecules, the hydrated zwitterionic form becomes more thermodynamically stable. In the presence of six or seven water molecules, the energetics indicate that the two forms may coexist. Eight water molecules are sufficient to computationally guarantee the reported experimental observation of zwitterionic dominance in solution.     

气相中O3与HSO自由基间的氢键复合物

气相中O3与HSO自由基之间的相互作用及其反应在大气化学中非常重要. 在DFT-B3LYP/6-311++G**和MP2/6-311++G**水平上求得O3+HSO复合物势能面上的稳定构型, B3LYP方法得到了三种构型(复合物I, II和III), 而MP2方法只能得到一种构型(复合物II). 在复合物I和III中, HSO单元中的1H原子作为质子供体, 与O3分子中的端基O原子作为质子受体相互作用, 形成红移氢键复合物; 而在复合物II中, 虽与复合物I和III中具有相同的质子供体和质子受体, 却形成了蓝移氢键复合物. B3LYP/6-311++G**水平上计算的单体间相互作用能的计算考虑了基组重叠误差(BSSE)和零点振动能(ZPVE)校正, 其值在-3.37到-4.55 kJ·mol-1之间. 采用自然键轨道理论(NBO)对单体间相互作用的本质进行了考查, 并通过分子中原子理论(AIM)分析了三种复合物中氢键的电子密度拓扑性质.     

Computational studies on carbohydrates: I. Density functional ab initio geometry optimization on maltose conformations

Ab initio geometry optimization was carried out on 10 selected conformations of maltose and two 2‐methoxytetrahydropyran conformations using the density functional denoted B3LYP combined with two basis sets. The 6‐31G* and 6‐311++G** basis sets make up the B3LYP/6‐31G* and B3LYP/6‐311++G** procedures. Internal coordinates were fully relaxed, and structures were gradient optimized at both levels of theory. Ten conformations were studied at the B3LYP/6‐31G* level, and five of these were continued with full gradient optimization at the B3LYP/6‐311++G** level of theory. The details of the ab initio optimized geometries are presented here, with particular attention given to the positions of the atoms around the anomeric center and the effect of the particular anomer and hydrogen bonding pattern on the maltose ring structures and relative conformational energies. The size and complexity of the hydrogen‐bonding network prevented a rigorous search of conformational space by ab initio calculations. However, using empirical force fields, low‐energy conformers of maltose were found that were subsequently gradient optimized at the two ab initio levels of theory. Three classes of conformations were studied, as defined by the clockwise or counterclockwise direction of the hydroxyl groups, or a flipped conformer in which the ψ‐dihedral is rotated by ∼180°. Different combinations of ω side‐chain rotations gave energy differences of more than 6 kcal/mol above the lowest energy structure found. The lowest energy structures bear remarkably close resemblance to the neutron and X‐ray diffraction crystal structures. © 2000 John Wiley & Sons, Inc. * J Comput Chem 21: 1204–1219, 2000     

苯并咪唑羧酸及其碱土金属配合物电子光谱性质的含时密度泛函及其概念密度泛函研究

用密度泛函理论(DFT)以及B3 LYlP泛函在6-311++G**水平上,对苯并咪唑羧酸(L)及其3种碱土金属配合物ML(M=Mg,Ca,Ba)的基态(S0)结构进行优化,用含时密度泛函理论(TD-DFT)在6-311++G**水平下计算其吸收光谱.用单激发组态相互作用(CIS)法在HF/6-31+G*上优化其最低激发单重态(S1)的几何结构,用ID-DFT B3IYP/6-311++G**计算其发射光谱.结果表明,配体L与M(Ⅱ)结合成ML后,随原子序数的增大(Mg相似文献   

Protonation processes and electronic spectra of histidine and related ions

A full structural assignment of the neutral, protonated, and deprotonated histidine conformers in the gas phase is presented. A total of 3024 unique trial structures were generated by all combinations of internal single-bond rotamers of these species and optimized at the B3LYP/6-311G* level and further optimized at the B3LYP/6-311++G** level. A set of unique conformers is found, and their relative energies, free energies, dipole moments, rotational constants, electron affinities, ionization energies, and harmonic frequencies are determined. The population ratio of histidine and its tautomer is 1:0.16 at 298 K. Massive conformational changes are observed due to protonation and deprotonation, and the intramolecular H-bonds are characterized with the atoms in molecules theory. The calculated proton dissociation energy, gas-phase acidity, proton affinity, and gas-phase basicity are in excellent agreement with the experiments. The deprotonation and protonation of gaseous histidine both occur on the imidazole ring, explaining the versatile biofunctions of histidine in large biomolecules. The UV spectra of neutral and singly and doubly protonated histidine are investigated with the TDDFT/B3LYP/6-311+G(2df,p) calculations. The S0-S1, S0-S2, and S0-S3 excitations of histidine are mixed pipi*/npi* transitions at 5.37, 5.44, and 5.69 eV, respectively. The three excitation energies for histidine tautomer are 4.85, 5.47, and 5.52 eV, respectively. The three excitations for protonated histidine are mainly npi* transitions at 5.45, 5.67, and 5.82 eV, respectively. The S0-S1 excitation of protonated histidine produces ImH-CbetaH2-CalphaH(COOH)-NH2+, while the S0-S2 and S0-S3 transitions produce ImH-CbetaH2-CalphaH(NH2)-(COOH)+. These data may help to understand the mechanisms of the UV fragmentation of biomolecules.     

Intramolecular hydrogen bond in 3‐imino‐propenylamine isomers: AIM and NBO studies

The molecular structure and intramolecular hydrogen bond energy of 18 conformers of 3‐imino‐propenyl‐amine were investigated at MP2 and B3LYP levels of theory using the standard 6‐311++G** basis set. The atom in molecules or AIM theory of Bader, which is based on the topological properties of the electron density (ρ), was used additionally and the natural bond orbital (NBO) analysis was also carried out. Furthermore calculations for all possible conformations of 3‐imino‐propenyl‐amin in water solution were also carried out at B3LYP/6‐311++G** and MP2/6‐311++G** levels of theory. The calculated geometrical parameters and conformational analyses in gas phase and water solution show that the imine–amine conformers of this compound are more stable than the other conformers. B3LYP method predicts the IMA‐1 as global minimum. This stability is mainly due to the formation of a strong N? H···N intramolecular hydrogen bond, which is assisted by π‐electrons resonance, and this π‐electrons are established by NH2 functional group. Hydrogen bond energies for all conformers of 3‐imino‐propenyl‐amine were obtained from the related rotamers methods. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

HOCl…HCOCl复合物的结构和电子性质

在DFT-B3LYP/6-311++G**水平上求得HOCl+HCOCl复合物势能面上的四种稳定构型(S1, S2, S3和S4). 其中, 在复合物S1和S3中, HOCl单体的5H原子作为质子供体, 与HCOCl单体中作为质子受体的1O原子相互作用, 形成红移氢键复合物; 在复合物S4中, HOCl单体的7Cl原子作为质子供体, 与HCOCl单体中作为质子受体的1O原子相互作用, 形成红移卤键复合物; 而在复合物S2中, 同时存在2C—3H…6O蓝移氢键和4Cl…5O相互作用. 在MP2/6-311++G**水平上计算的单体间的相互作用能考虑了基组重叠误差(BSSE)和零点振动能(ZPVE)校正, 其值在-5.05与-14.76 kJ·mol-1之间. 采用自然键轨道理论(NBO)对两种单体间相互作用的本质进行了考查, 并通过分子中原子理论(AIM)分析了复合物中氢键和卤键键鞍点处的电子密度拓扑性质.     

Theoretical Studies on the Intermolecular Interactions of Aza-calix[2]arene[2]-triazines with RDX

Six fully optimized structures of the aza-calix[2]arene[2]-triazines/RDX supramo-lecular complexes have been obtained at the DFT-B3LYP/6-311++G** level,and the corresponding intermolecular interactions have been investigated using the B3LYP,mPWPW91 and MP2 methods at the 6-311++G** level,respectively.The natural bond orbital(NBO) and atoms in molecules(AIM) analyses have been performed to reveal the origin of interactions.To our interest,the result indicates that the strongest interaction is up to -22.34 kJ/mol after basis set superposition error(BSSE) and zero point energy(ZPE) correction at the MP2/6-311++G** level.Furthermore,the intermolecular interactions between aza-calix[2]arene[2]-triazines with the substituted amidos and RDX are stronger than those of other complexes.Thus,the complexes with amidos can be used as the candidates to increase the stability of explosive and eliminate the explosive wastewater.