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.     

Interaction between RNA segment (adenine‐uracil) and model of protein unit (formamide): A density‐functional theory study

Various possible structures of adenine‐uracil‐formamide hydrogen‐bond complexes were optimized at 6‐311++G(d,p) level, and the binding energies of these complexes were also calculated at DFT B3LYP/6‐311++G(d,p) level. Eight stable cyclic structures being involved in the interaction are found on the potential energy surface. By analyzing the structure, NPA charge and interaction energy of complexes, we obtain the most stable geometry structure. The results show that the interactions between formamide and adenine‐uracil (A‐U) base pair affect the stabilities of the base pairs. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

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.     

NMR spectra of salicylohydroxamic acid in DMSO-d6 solution: a DFT study

The ¹H, ¹³C and ¹H, ¹³C COSY NMR spectra of salicylohydroxamic acid (sha) were measured in DMSO-d₆ solution. The B3LYP GIAO method with the 6-311++G(d,p) basis set was chosen to reproduce the experimental spectra. All possible zusammen and entgegen conformers of monomeric sha were computed. After geometry optimisation (B3LYP/6-311++G(d,p)) only nine independent models of the molecule were shown to be stable. Additionally, the NMR chemical shifts of the Onsager model of the most stable monomer were calculated. The computed chemical shifts for the labile protons for all aforementioned geometries meaningfully underestimated experimental results suggesting the existence of the H-bonded structure of sha in DMSO solution. The most probable two dimeric structures along with two solvent-bounded aggregates were subsequently calculated at the same level of theory. The best agreement was obtained for sha H-bonded with two DMSO molecules (confirmed by the absence of concentration effect). The relative error not exceeding 10 and 4% for chemical shifts in ¹H and ¹³C NMR spectra of sha–(DMSO)₂, respectively, showed that the applied method with the B3LYP/6-311++G(d,p) basis set was efficient to predict the NMR shifts of a compound with strong H-bonds. Thus, this allows to assign properly NMR resonances to specific structure formed in DMSO solution.     

FT-IR, FT-Raman spectra and quantum chemical calculations of some chloro substituted phenoxy acetic acids

In this work, we will report a combined experimental and theoretical study on molecular and vibrational structure of o-chlorophenoxy acetic acid (OCPAA) and p-chlorophenoxy acetic acids (PCPAA). The FT-IR and Fourier transform-Raman spectra of both the compounds was recorded in the solid phase. The optimized geometry was calculated by HF and B3LYP methods with 6-311++G(d,p) basis set and harmonic vibrational frequencies, infrared intensities and Raman scattering activities were calculated by density functional B3LYP method with the 6-311++G(d,p) basis set. The scaled theoretical wavenumbers showed very good agreement with the experimental values. The thermodynamic functions of the title compounds were also performed at B3LYP/6-311++G(d,p) level of theory. A detailed interpretation of the infrared and Raman spectra of o-chloro and p-chlorophenoxy acetic acid is reported. The theoretical FT-IR spectrograms for the title molecules have been constructed.     

A density functional theory study of interaction between formamide and guanine

Hydrogen bonding in complexes formed between formamide and guanine molecules was completely investigated using density functional theory (DFT) at the 6-311++G(d, p) level. For comparison, the HF and MP2 methods were also used. Nine stable cyclic structures stabilized by two hydrogen bonds were found. One of these was a six-membered ring, five were seven-membered rings, and the others were eight-membered rings. The eight-membered ring is preferable to the seven-and six-membered ones as follows from H-bond lengths and interaction energies. The FG4 structure was calculated to be the most stable, and another cyclic structure, FG5, was least stable because of the six-membered ring and the weakest interaction. The infrared spectrum frequencies, intensities, and vibrational frequency shifts are also reported. The text was submitted by the authors in English.     

A computational study of microsolvation effect on ethylene glycol by density functional method

This study focuses on the conformational analysis of ethylene glycol-(water)n (n=1-3) complex by using density functional theory method and the basis set 6-311++G*. Different conformers are reported and the basis set superposition error corrected total energy is -306.767 5171, -383.221 3135, and -459.694 1528 for lowest energy conformer with 1, 2, and 3 water molecules, respectively, with corresponding binding energy -7.75, -15.43, and -36.28 kcal/mol. On applying many-body analysis it has been found that relaxation energy, two-body, three-body energy have significant contribution to the binding energy for ethylene glycol-(water)3 complex whereas four-body energies are negligible. The most stable conformers of ethylene glycol-(water)n complex are the cyclic structures in which water molecules bridge between the two hydroxyl group of ethylene glycol.     

HArF和HNO二聚体相互作用氢键的理论研究

The hydrogen bonding interaction of 1:1 dimer formed between HNO and HArF molecule has been completely investigated in the present study using Second-order M?ller-Plesset Perturbation (MP2) method in conjunction with 6-311+G**, 6-311++G** and 6-311++G(2d,2p) basis sets. The standard and CP-corrected calculations have been employed to determine the equilibrium structures, the vibrational frequencies and interaction energies. The interaction energies of the dimers were also calculated at G2MP2 level. Two stable structures are found as the minima. Dimer I(H···F)is a five-membered cyclic hydrogen bonded structure and is more stable than the Dimer II(H···O). The blue-shifted N-H···F hydrogen bond is confirmed with standard and CP-corrected calculations by the MP2 and DFT methods in conjunction with different basis sets. The results obtained at MP2 in conjunction with different basis sets show there is a red-shifted hydrogen bond (Ar-H···O) in the Dimer II(H···O). The topological and electronic properties, the origin of red- and blue-shifted hydrogen bonds were investigated at MP2/6-311++G(2d,2p) with CP corrected calculations. From the NBO analysis, the reasonable explanations for the red- and blue-shifted hydrogen bonds were proposed.     

A comparison of the AMBER*, OPLSAA and HF potential energy surfaces for a series of diastereomeric cyclic urea HIV-1 inhibitors

The LM:MC conformational search method was used to identify the low energy structures on the OPLS-AA/GBSA(water) and AMBER*/GBSA(water) surfaces for a diastereomeric series of cyclic urea molecules that have been shown to be potent inhibitors of the HIV-1 protease enzyme. The lowest energy structures from each search were then subjected to geometry optimization and frequency analysis using the HF/6-311G** method in conjunction with the self-consistent reaction field (SCRF) treatment for water. A comparison of the diastereomeric energies and structures indicates that the OPLSAA/GBSA(water) surface is in good agreement with the HF/6-311G**/SCRF(water) surface.     

Microhydration of NO3(-): a theoretical study on structure, stability and IR spectra

A systematic study on the structure and stability of nitrate anion hydrated clusters, NO3(-) x n H2O (n = 1-8) are carried out by applying first principle electronic structure methods. Several possible initial structures are considered for each size cluster to locate equilibrium geometry by applying a correlated hybrid density functional with 6-311++G(d,p) basis function. Three different types of arrangements, namely, symmetrical double hydrogen bonding, single hydrogen bonding and inter-water hydrogen bonding are obtained in these hydrated clusters. A structure having inter-water hydrogen bonding is more stable compared to other arrangements. Surface structures are predicted to be more stable over interior structures. Up to five solvent H2O molecules can stay around solute NO3(-) anion in structures having an inter-water hydrogen-bonded cyclic network. A linear correlation is obtained for weighted average solvent stabilization energy with the size (n) of the hydrated cluster. Distinctly different shifts of IR bands are observed in these hydrated clusters for different kinds of bonding environments of O-H and N=O stretching modes compared to isolated H2O and NO3(-) anion. Weighted average IR spectra are calculated on the basis of statistical population of individual configurations of each size cluster at 150 K.     

Conformational stability, the spectroscopic (FT-IR and UV), first order hyperpolarizability, NBO analysis, HOMO and LUMO analysis of 6,8-diphenylimidazo[1,2-α]pyrazine molecule by ab initio HF and density functional methods

The conformational analysis of 6,8-diphenylimidazo[1,2-α]pyrazine molecule (abbreviated as 68DIP) was performed by using B3LYP/6-31G(d) level of theory to find the most stable form. Two staggered stable conformers were observed on the torsional potential energy surface. The equilibrium geometry, bonding features and vibrational frequencies of 68DIP have been investigated by using the DFT (B3LYP) and HF methods for the lowest energy conformer. The first order hyperpolarizability (β(total)) of this molecular system and related properties (β, μ, <α> and Δα) are calculated using HF/6-311++G(d,p) and B3LYP/6-311++G(d,p) methods based on the finite-field approach. Stability of the molecule arising from hyperconjugative interactions, charge delocalization and C-H?N intramolecular hydrogen-bond-like weak interaction has been analyzed using natural bond orbital (NBO) analysis by using B3LYP/6-311++G(d,p) method. The results show that electron density (ED) in the σ* and π* antibonding orbitals and second order delocalization energies E((2)) confirm the occurrence of intramolecular charge transfer (ICT) within the molecule. UV-vis spectrum of the compound was recorded and electronic properties, such as HOMO, LUMO energies, excitation energies and wavelength were performed by TD-DFT/B3LYP, CIS and TD-HF methods by using 6-311++G(d,p) basis set. Finally, the calculation results were applied to simulated infrared spectra of the title compound which show good agreement with observed spectra.     

Ab initio study of hydrogen-bond formation between cyclic ethers and selected amino acid side chains

Binding energies for hydrogen-bonded complexes of six cyclic ethers with five hydrogen-bond donor molecules that mimic selected amino acid side chains have been calculated at the MP2/6-31G*, MP2/6-31+G*, MP2/6-311++G**(single point), and MP2/aug-cc-pvtz levels, using geometries obtained with or without counterpoise corrections throughout the geometry optimization. The calculated basis set superposition error (BSSE) amounts to 10-20% and 5-10% of the uncorrected binding energies for the neutral and ionic species, respectively, at the MP2/aug-cc-pvtz level. The authors conclude that the O...H distances in the hydrogen bonds and binding energies for the studied systems may be determined with uncertainties of up to 0.08 A and 1-2 kcal/mol, respectively, in comparison with the MP2/aug-cc-pvtz values at a reasonable computational cost by performing standard geometry optimization at the MP2/6-31+G* level. Hydrogen-bond formation energies are more negative for cyclic ethers compared to their counterparts with a C=C double bond in the ring next to the oxygen atom. The less negative hydrogen-bonding energy and the increased O...H separation have been attributed to the reduced basicity of the ether oxygen when the lone pairs can enter conjugation with the pi-electrons of the Calpha=Cbeta double bond. The present study is the first step toward the development of an affordable computational level for estimating the binding energies of natural product, fused ring ether systems to the human estrogen receptor.     

Hydrogen bonding interaction between 1,4‐dioxane and water

This work reports an interaction of 1,4‐dioxane with one, two, and three water molecules using the density functional theory method at B3LYP/6‐311++G* level. Different conformers were studied and the most stable conformer of 1,4‐dioxane‐(water)_n (n = 1–3) complex has total energies ?384.1964038, ?460.6570694, and ?537.1032381 hartrees with one, two, and three water molecules, respectively. Corresponding binding energy (BE) for these three most stable structures is 6.23, 16.73, and 18.11 kcal/mol. The hydrogen bonding results in red shift in O? O stretching and C? C stretching modes of 1,4‐dioxane for the most stable conformer of 1,4‐dioxane with one, two, and three water molecules whereas there was a blue shift in C? O symmetric stretching and C? O asymmetric stretching modes of 1,4‐dioxane. The hydrogen bonding results in large red shift in bending mode of water and large blue shift in symmetric stretching and asymmetric stretching mode of water. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Density functional theory study of the hydrogen bonding interaction of 1:1 complexes of serine with water

The hydrogen bonding of 1:1 complexes formed between serine and water molecules were completely investigated in the present study employing ab initio and Density Functional Theory (DFT) methods at varied basis set levels from 6‐31g to 6‐311++g (2d,2p). For comparison, we also used the second‐order Moller–Plesset Perturbation (MP2) method at the 6‐31+g(d) level. Twelve reasonable geometries on the potential energy hypersurface of serine and water system were considered with the global minimum, 10 of which are cyclic double‐hydrogen bonded structures and the other two are one‐hydrogen bonded structures. The optimized geometric parameters and interaction energies for various isomers at different levels were estimated. The infrared spectrum frequencies, IR intensities, and the vibrational frequency shifts are reported. Finally, the solvent effects on the geometries of the serine–water complexes were also investigated using self‐consistent reaction‐field (SCRF) calculations at the B3LYP/6‐311++g(d,p) level. The results indicate that the polarity of the solvent played an important role in the structures and relative stabilities of different isomers. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Theoretical study on intermolecular interactions in BrF/HnX adducts

Equilibrium geometries, interaction energies, and charge transfer for the intermolecular interactions between BrF and H_nX (HF, H₂O, and NH₃) were studied at the MP2/6-311++G(3d,3p) level. The halogen-bonded geometry and hydrogen-bonded geometry are observed in these interactions. The calculated interaction energies show that the halogen-bonded structures are more stable than the corresponding hydrogen-bonded structures. To study the nature of the intermolecular interactions, symmetry-adapted perturbation theory (SAPT) calculations were carried out and the results indicate that the halogen bonding interactions are dominantly inductive energy in nature, while electrostatic energy governs the hydrogen bonding interactions.     

Hydrogen peroxide clusters: the role of open book motif in cage and helical structures

Hartree-Fock (HF) calculations using 6-31G*, 6-311++G(d,p), aug-cc-pVDZ, and aug-cc-pVTZ basis sets show that hydrogen peroxide molecular clusters tend to form hydrogen-bonded cyclic and cage structures along the lines expected of a molecule which can act as a proton donor as well as an acceptor. These results are reiterated by density functional theoretic (DFT) calculations with B3LYP parametrization and also by second-order M?ller-Plesset perturbation (MP2) theory using 6-31G* and 6-311++G(d,p) basis sets. Trends in stabilization energies and geometrical parameters obtained at the HF level using 6-311++G(d,p), aug-cc-pVDZ, and aug-cc-pVTZ basis sets are similar to those obtained from HF/6-31G* calculation. In addition, the HF calculations suggest the formation of stable helical structures for larger clusters, provided the neighbors form an open book structure.     

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     

Effect of methyl groups substitution on the strength of intramolecular hydrogen bonding of naphthazarin: DFT and NBO studies

A density functional theory (DFT) study-based method B3LYP/6-311++G** was carried out to investigate the methyl groups substitution effect on the structure and the strength of intramolecular hydrogen bonding in naphthazarin (NZ) (5,8-dihydroxy-1,4-naphthoquinone). The full geometry optimization of molecular structures, the difference between the energies of hydrogen-bonded and non-hydrogen-bonded rotamers, and the proton chemical shift of the hydroxyl groups in NZ and its methyl substituents obtained at the B3LYP/6-311++G** level. The vibrational frequencies of all samples and their deuterated analogues were calculated at the same theoretical level. The ¹H chemical shifts for NZ and its methyl substituents were computed at the B3LYP/6-311++G** level using the gauge-including atomic orbital method. Furthermore, in order to investigate the changes in bond order, electron density, electron delocalization, and steric effects caused by methyl substituents, natural bond orbital analysis were carried out at the B3LYP/6-311++G** level. After comparing these effective parameters in methyl substituents with those of their parent, NZ, we concluded that, in general, intramolecular hydrogen bonding strength increases by substituting methyl groups in the different positions of NZ.     

Calculation of the hydrogen binding energies of complexes between formamide and adenine-thymine pair

The hydrogen bonding of complexes formed between formamide and adenine-thymine base pair has been completely investigated in the present study. In order to gain deeper insight into structure, charge distribution, and energies of complexes, we have investigated them using density functional theory at 6–311++G(d, p), 6–31G, 6–31+G(d), and 6–31++G(d, p) level. Seven stable cyclic structures (ATF1–ATF7) being involved in the interaction has been found on the potential energy surface. In addition, for further correction of interaction energies between adenine—thymine and formamide, the basis set superposition error associated with the hydrogen bond energy has been computed via the counterpoise method using the individual bases as fragments. The infrared spectrum frequencies, IR intensities and the vibrational frequency shifts are reported.     

Density functional theory study of the interaction between formamide and uracil

The hydrogen bonding of complexes formed between the formamide and uracil molecule has been fully investigated in the present study using the density functional theory (DFT) method at varied basis set levels from 6‐31G to 6‐311++G(d,p). Eight stable cyclic structures with two hydrogen bonds involved in the interaction are found on the potential energy surface (PES). The four structures are seven‐membered rings; the others are eight‐membered rings. The eight‐membered ring is preferred over the seven‐membered one by analyzing the hydrogen bond lengths and the interaction energies. The infrared (IR) spectrum frequencies, IR intensities, and the vibrational frequency shifts are reported. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007