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     

Peptide models XXIII. Conformational model for polar side‐chain containing amino acid residues: A comprehensive analysis of RHF,DFT, and MP2 properties of HCO‐L‐SER‐NH2

Geometric and energetic properties of a diamide of serine, HCO‐NH‐L ‐CH(CH₂OH)CO‐NH₂, are investigated by standard methods of computational quantum chemistry. Similarly to other amino acid residues, conformational properties of HCO‐L ‐Ser‐NH₂ can be derived from the analysis of its E=E(ϕ,ψ;χ₁,χ₂) hypersurface. Reoptimization of 44 RHF/3‐21G conformers at the RHF/6‐311++G** level resulted in 36 minima. For all conformers, geometrical properties, including variation of H‐bond parameters and structural shifts in the torsional space, are thoroughly investigated. Results from further single‐point energy calculations at the RHF, DFT, and MP2 levels, performed on the entire conformational data set, form a database of 224 energy values, perhaps the largest set calculated so far for any single amino acid diamide. A comprehensive analysis of this database reveals significant correlation among energies obtained at six levels of ab initio theory. Regression parameters provide an opportunity for extrapolation in order to predict the energy of a conformer at a high level by doing explicit ab initio computations only for a few selected conformers. The computed conformational and relative energy data are compared with structural and occurrence results derived from a nonhomologous protein database incorporating 1135 proteins. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 626–655, 2000     

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 Study on Gas—phase Pyrolytic Reactions of N—Ethyl,Isopropyl and N—t—Butyl Substituted 2—Aminopyrazine

Density functional theory (DFT) and ab initio methods were used to study gas‐phase pyrolytic reaction mechanisms of iV‐ethyl, N‐isopropyl and N‐t‐butyl substituted 2‐aminopyrazine at B3LYP/6–31G* and MP2/6–31G*, respectively. Single‐point energies of all optimized molecular geometries were calculated at B3LYP/6–311 + G(2d,p) level. Results show that the pyrolytic reactions were carried out through a unimolecular first‐order mechanism which were caused by the migration of atom H(17) via a six‐member ring transition state. The activation energies which were verified by vibrational analysis and correlated with zero‐point energies along the reaction channel at B3LYP/6–311 + G(2d,p) level were 252.02 kJ. mo^?1 (N‐ethyl substituted), 235.92 kJ‐mol^?1 (N‐t‐isopropyl substituted) and 234.27 kJ‐mol^?1 (N‐t‐butyl substituted), respectively. The results were in good agreement with available experimental data.     

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     

Multistep conformational interconversion mechanism of cyclododecane. A simple and fast analysis using potential energy curves

An ab initio and Density Functional Theory (DFT) study of the conformational properties of cyclododecane was carried out. The energetically preferred equilibrium structures, their relative stability, and some of the transition state (TS) structures involved in the conformational interconversion pathways were analyzed from RHF/6‐31G(d), B3LYP/6‐31G(d,p) and B3LYP/6311++G(d,p) calculations. Aug‐cc‐pVDZ//B3LYP/6311++G(d,p) single point calculations predict that the multistep conformational interconversion mechanism requires 11.07 kcal/mol, which is in agreement with the available experimental data. These results allow us to form a concise idea about the internal intricacies of the preferred forms of cyclododecane, describing the conformations as well as the conformational interconversion processes in the conformational potential energy hypersurface. Our results indicated that performing an exhaustive analysis of the potential energy curves connecting the most representative conformations is a valid alternate tool to determine the principal conformational interconversion paths for cyclododecane. This methodology represents a satisfactory first approximation for the conformational analysis of medium‐ and large‐size flexible cyclic compounds. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Theoretical studies of uracil–(H2O)n (n = 1–7) clusters by ab initio and ABEEMσπ/MM fluctuating charge model

Uracil–(H₂O)_n (n = 1–7) clusters were systemically investigated by ab initio methods and the newly constructed ABEEMσπ/MM fluctuating charge model. Water molecules have been gradually placed in an average plane containing uracil. The geometries of 38 uracil–water complexes were obtained using B3LYP/6-311++G** level optimizations, and the energies were determined at the MP2/6-311++G** level with BSSE corrections. The ABEEMσπ/MM potential model gives reasonable properties of these clusters when comparing with the present ab initio data. For interaction energies, the root mean square deviation is 0.96 kcal/mol, and the linear coefficient reaches 0.997. Furthermore, the ABEEMσπ charges changed when H₂O interacted with the uracil molecule, especially at the sites where the hydrogen bond form. These results show that the ABEEMσπ/MM model is fine giving the overall characteristic hydration properties of uracil–water systems in good agreement with the high-level ab initio calculations.     

OPLS all-atom force field for carbohydrates

The OPLS all-atom (AA) force field for organic and biomolecular systems has been expanded to include carbohydrates. Starting with reported nonbonded parameters of alcohols, ethers, and diols, torsional parameters were fit to reproduce results from ab initio calculations on the hexopyranoses, α,β-d -glucopyranose, α,β-d -mannopyranose, α,β-d -galactopyranose, methyl α,β-d -glucopyranoside, and methyl α,β-d -mannopyranoside. In all, geometry optimizations were carried out for 144 conformers at the restricted Hartree–Fock (RHF)/6–31G* level. For the conformers with a relative energy within 3 kcal/mol of the global minima, the effects of electron correlation and basis-set extension were considered by performing single-point calculations with density functional theory at the B3LYP/6–311+G** level. The torsional parameters for the OPLS-AA force field were parameterized to reproduce the energies and structures of these 44 conformers. The resultant force field reproduces the ab initio calculated energies with an average unsigned error of 0.41 kcal/mol. The α/β ratios as well as the relative energies between the isomeric hexopyranoses are in good accord with the ab initio results. The predictive abilities of the force field were also tested against RHF/6–31G* results for d -allopyranose with excellent success; a surprising discovery is that the lowest energy conformer of d -allopyranose is a β anomer. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 1955–1970, 1997     

Theoretical study of light-metal tetrahydroborates

Ab initio calculations of the structural, energetic, vibrational, and magnetic characteristics of the lowest-lying structures for isolated molecules and ions of light-metal tetrahydroborates (Li, Na, Be, Mg, and Al) have been performed by the perturbation theory (MP2), quadratic configuration interaction (QCISD(T)), coupled cluster (CCSD(T)), and density functional theory (B3LYP) methods using the 6-31G*, 6-31G**, 6-311+G**, and 6-311++G** basis sets. The trends in the behavior of the structural parameters, the energies of different decomposition pathways, barriers to internal rotation of BH₄ groups, normal mode frequencies, magnetic shielding constants, and spin density distribution (in radicals) have been analyzed in various related series of these compounds. The results obtained by ab initio methods and at the DFT level are compared. The economical approximation B3LYP/6-311++G**//B3LYP/6-311+G** adequately reproduces the results obtained at the higher level of theory CCSD(T)/6-311++G*s*//MP2/6-31G* even though it requires considerably shorter CPU times and smaller amounts of memory.     

Intramolecular hydrogen bonding in 3‐imino‐propenylamine: Theoretical investigations

Intramolecular H‐bonds existing for derivatives of 3‐imino‐propenylamine have been studied using the B3LYP/6‐311++G** level of theory. The nature of these interactions, known as resonance‐assisted hydrogen bonds, has been discussed. Vibrational frequencies for α‐derivatives were calculated at the same level of theory. The topological properties of the electron density distributions for N? H···N intramolecular bridges have been analyzed in terms of the Bader theory of atoms in molecules (AIM). Calculation for 3‐imino‐propenylamine derivatives in water solution were also carried out at B3LYP/6‐311++G** level of theory. Finally, the analysis of hydrogen bond in this molecule and their derivatives by quantum theory of natural bond orbital methods fairly support the ab initio results. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Kinetic Study and NBO Analysis of the Dehydrogenation Mechanism of Five‐membered Ring Heterocyclic 2,5‐Dihydro‐[furan,thiophene, selenophene

The theoretical study of the dehydrogenation of 2,5‐dihydro‐[furan ( 1 ), thiophene ( 2 ), and selenophene ( 3 )] was carried out using ab initio molecular orbital (MO) and density functional theory (DFT) methods at the B3LYP/6‐311G**//B3LYP/6‐311G** and MP2/6‐311G**//B3LYP/6‐311G** levels of theory. Among the used methods in this study, the obtained results show that B3LYP/6‐311G** method is in good agreement with the available experimental values. Based on the optimized ground state geometries using B3LYP/6‐311G** method, the natural bond orbital (NBO) analysis of donor‐acceptor (bond‐antibond) interactions revealed that the stabilization energies associated with the electronic delocalization from non‐bonding lone‐pair orbitals [LP(e)_X3] to δ*_{C(1)  H(2)} antibonding orbital, decrease from compounds 1 to 3 . The LP(e)_X3→δ*_{C(1)  H(2)} resonance energies for compounds 1 – 3 are 23.37, 16.05 and 12.46 kJ/mol, respectively. Also, the LP(e)_X3→δ*_{C(1)  H(2)} delocalizations could fairly explain the decrease of occupancies of LP(e)_X3 non‐bonding orbitals in ring of compounds 1 – 3 ( 3 > 2 > 1 ). The electronic delocalization from LP(e)_X3 non‐bonding orbitals to δ*_{C(1)  H(2)} antibonding orbital increases the ground state structure stability, Therefore, the decrease of LP(e)_X3→δ*_{C(1)  H(2)} delocalizations could fairly explain the kinetic of the dehydrogenation reactions of compounds 1 – 3 (k ₁ >k ₂ >k ₃ ). Also, the donor‐acceptor interactions, as obtained from NBO analysis, revealed that the (_C(4)C(7)→δ*_{C(1)  H(2)} resonance energies decrease from compounds 1 to 3 . Further, the results showed that the energy gaps between (_C(4)C(7) bonding and δ*_{C(1)  H(2)} antibonding orbitals decrease from compounds 1 to 3 . The results suggest also that in compounds 1 – 3 , the hydrogen eliminations are controlled by LP(e)→δ* resonance energies. Analysis of bond order, natural bond orbital charges, bond indexes, synchronicity parameters, and IRC calculations indicate that these reactions are occurring through a concerted and synchronous six‐membered cyclic transition state type of mechanism.     

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.     

Kinetic and thermodynamic study of inter‐ and intramolecular proton transfer in N′‐acetyl formohydrazide tautomers

Nine tautomers and eleven possible tautomeric interconversions of N′‐acetyl formohydrazide have been studied at B3LYP/6‐311++G** level of theory. From these calculations, optimized geometries, molecular parameters, IR frequencies, NMR chemical shifts, and energetic results are obtained. In all tautomers except tautomers 4, E isomer is more stable than Z isomer. Energetic data were used to calculate the energy barriers of tautomeric interconversions and very high energy barriers were obtained for all tautomeric interconversions. Moreover, study of solvent effects on relative stabilities of tautomers and transition states showed that they are similar to those in the gas phase. In addition, intermolecular proton transfer with the assistance of one to three water molecules has been studied and the results showed that activation barriers in water‐assisted tautomerism are in general lower than those in the gas phase. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Influence of ionization on the conformational preferences of peptide models. Ramachandran surfaces of N‐formyl‐glycine amide and N‐formyl‐alanine amide radical cations

Ramachandran maps of neutral and ionized HCO–Gly–NH₂ and HCO–Ala–NH₂ peptide models have been built at the B3LYP/6‐31++G(d,p) level of calculation. Direct optimizations using B3LYP and the recently developed MPWB1K functional have also been carried out, as well as single‐point calculations at the CCSD(T) level of theory with the 6‐311++G(2df,2p) basis set. Results indicate that for both peptide models ionization can cause drastic changes in the shape of the PES in such a way that highly disallowed regions in neutral PES become low‐energy regions in the radical cation surface. The structures localized in such regions, and are highly stabilized due to the formation of 2‐centre‐3‐electron interactions between the two carbonyl oxygens. Inclusion of solvent effects by the conductor‐like polarizable continuum model (CPCM) shows that the solute‐solvent interaction energy plays an important role in determining the stability order. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009     

Interaction of anions with perfluoro aromatic compounds

The complexes formed by a variety of anions with perfluoro derivatives of benzene, naphthalene, pyridine, thiophene, and furan have been calculated using DFT (B3LYP/6-31++G**) and MP2 (MP2/6-31++G** and MP2/6-311++G**) ab initio methods. The minimum structures show the anion interacting with the pi-cloud of the aromatic compounds. The interaction energies obtained range between -8 and -19 kcal mol(-1). The results obtained at the MP2/6-31++G** and MP2/6-311++G** levels are similar. However, the B3LYP/6-31++G** results provide longer interaction distances and smaller interaction energies than do the MP2 results. The interaction energies have been partitioned using an electrostatic, polarization, and van der Waals scheme. The AIM analysis of the electron density shows a variety of topologies depending on the aromatic system considered.     

去氢抗坏血酸分子振动光谱的理论研究

采用RHF, MP2, DFT(B3LYP)方法, 以6-311++G**为基组研究了去氢抗坏血酸分子(DHA)的平衡几何构型和振动光谱. 计算结果表明, 采用RHF, B3LYP以及MP2 方法优化得到的几何结构以及频率值是一致的. 采用B3LYP/6-311++G**计算了DHA分子平衡构型下的谐振动力场﹑振动频率和振动强度. 使用Wilson的GF矩阵方法对DHA分子进行了简正坐标分析, 依据所得的势能分布对DHA分子的振动基频进行了合理的理论归属.     

Study of the temperature‐dependent conformational averaging of 1H NMR resonances in vinylcyclopropane through the use of ab initio methodology and Boltzmann statistics

The temperature dependence of the ¹ H NMR resonance of the C‐4 olefinic proton in vinylcyclopropane was investigated through a combination of ab initio calculations and Boltzmann statistics. A torsional energy profile as a function of the 〈?〉 dihedral angle was obtained using HF methodology with a 6–311G** basis set, while the corresponding ¹ H chemical shift profiles for the C‐4 proton were computed using the GIAO approach and either HF, DFT (B3LYP) or MP2 methods at the 6–311G** level of theory. Chemical shifts at different temperatures calculated as canonical ensemble averages in which the different ab initio ¹ H chemical shift profiles and a Boltzmann factor defined by the HF/ 6–311G** energy function are employed reproduce remarkably well the temperature dependence observed experimentally. Attempts to perform a similar study using only the GIAO‐MP2 ¹ H chemical shift profile and 〈?〉 dihedral angle trajectories obtained from molecular dynamics simulations at different temperatures failed to reproduce the experimental trends. This shortcoming was attributed to the inability of the force fields employed, Tripos 6.0 and MMFF94, to reproduce properly the three‐well torsional potential of vinylcyclopropane. The application of both methodologies to the calculation of population‐dependent chemical shifts in other systems is discussed. Copyright © 2002 John Wiley & Sons, Ltd.     

Quantum study on the electrocyclic reactions of CH2CHCHCHX (XH,F, Cl)

The microscopic mechanisms of the electrocyclic reactions for cis‐1,3‐butadiene and its monofluoro‐, monochloroderivatives have been studied by density functional theory (DFT), using the B3LYP method and 6‐311++G** basis sets. We optimized the geometric configurations of reactants, transition states, and products; verified all the probable transition states through vibrational analysis; and calculated the relative single‐point energies at the QCISD(T)/6‐311++G**//B3LYP/6‐311++G**. The results show that the monofluoro‐, monochloroderivatives of cis‐1,3‐butadiene both have two conformers; the reactant favors the electrocyclic reaction when one outboard hydrogen atom of the CH₂ groups is substituted by the fluorine or chlorine atom. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

Ab initio studies of aspartic acid conformers in gas phase and in solution

Systematic and extensive conformational searches of aspartic acid in gas phase and in solution have been performed. For the gaseous aspartic acid, a total of 1296 trial canonical structures and 216 trial zwitterionic 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 and then subjected to further optimization at the B3LYP/6-311++G** level. A total of 139 canonical conformers were found, but no stable zwitterionic structure was found. The rotational constants, dipole moments, zero-point vibrational energies, harmonic frequencies, and vertical ionization energies of the canonical conformers were determined. Single-point energies were also calculated at the MP2/6-311++G** and CCSD/6-311++G** levels. The equilibrium distributions of the gaseous conformers at various temperatures were calculated. The proton affinity and gas phase basicity were calculated and the results are in excellent agreement with the experiments. The conformations in the solution were studied with different solvation models. The 216 trial zwitterionic structures were first optimized at the B3LYP/6-311G* level using the Onsager self-consistent reaction field model (SCRF) and then optimized at the B3LYP/6-311++G** level using the conductorlike polarized continuum model (CPCM) SCRF theory. A total of 22 zwitterions conformers were found. The gaseous canonical conformers were combined with the CPCM model and optimized at the B3LYP/6-311++G** level. The solvated zwitterionic and canonical structures were further examined by the discrete/SCRF model with one and two water molecules. The incremental solvation of the canonical and zwitterionic structures with up to six water molecules in gas phase was systematically examined. The studies show that combining aspartic acid with at least six water molecules in the gas phase or two water molecules and a SCRF solution model is required to provide qualitatively correct results in the solution.