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     

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     

Density functional theory study on molecular structure and vibrational IR spectra of isocytosine

Density functional theory with the combined Becke3-LYP exchange-correlation energy functional [DFT(B3-LYP) method] using the 6-31G(d, p) basis set is applied to predict molecular parameters (geometries, rotational constants, dipole moments) and vibrational IR spectra (harmonic wavenumbers, absolute intensities) of six tautomers of the isocytosine molecule. The results are compared with the corresponding data calculated at the conventional ab initio Hartree-Fock (HF) level using the same basis set and with available experimental data. Calculations show that (a) three amino tautomers are slightly nonplanar species with, evidently, a distorted amino group, (b) the DFT (B3-LYP)/6-31G(d, p) method predicts better molecular parameters, than do the HF calculations, and (c) the DFT(B3-LYP)-calculated vibrational IR spectra of isocytosine agree well with the available recorded IR spectra, and they show marked improvement over the IR spectra predicted at the HF/6-31G(d, p) level. Tautomeric stabilities of isocytosine are discussed on the basis of computed electronic energies by the DFT(B3-LYP) and ab initio approaches [including the MP2 and MP4(SDQ) calculations of electronic energies] and predicted zero-point vibrational energies by DFT(B3-LYP) and HF methods. This relative energies at 0 K of the tautomeric forms of isocytosine predicted by both conventional ab initio and DFT(B3-LYP) methods correlate well with the experimental data, showing the predominance of the aminohydroxy tautomer of isocytosine for an isolated molecule. © 1997 John Wiley & Sons, Inc.     

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.     

Theoretical study of chiral discrimination in the hydrogen bonding complexes of the hydrazine dimer

In this work, the discrimination of different chiral forms of the hydrazine dimer were investigated using Density Functional Theory (DFT) and second‐order Moller–Plesset Perturbation (MP2) theory at basis set levels from 6‐31g to 6‐31++g(d,p). Four chiral structures were studied. The optimized geometric parameters, interaction energies, and chirodiastatic energy for various isomers at different levels were estimated. Finally, the solvent effects on the geometries of the hydrazine dimers were also investigated using self‐consistent reaction‐field (SCRF) calculations at the B3LYP/6‐31++g(d,p) level. The results indicate that the polarity of the solvent has played an important role in the structures and relative stabilities of different isomers. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Density functional study of HO(H2O)n (n = 1–3) clusters

The hydrogen bonding complexes HO(H₂O)_n (n = 1–3) were completely investigated in the present study using DFT and MP2 methods at varied basis set levels from 6‐31++G(d,p) to 6‐311++G(2d,2p). For n = 1 two, for n = 2 two, and for n = 3 five reasonable geometries are considered. The optimized geometric parameters and interaction energies for various complexes at different levels are estimated. The infrared spectrum frequencies and IR intensities of the most stable structures are reported. Finally, thermochemistry studies are also carried out. The results indicate that the formation and the number of hydrogen bonding have played an important role in the structures and relative stabilities of different complexes. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Evaluation of density functional theory methods for the electronic interactions between indole and substituted benzene: Applications to horseradish peroxidase

In an effort to evaluate and design fast, accurate density functional theory (DFT) methods for calculating electrostatic and dispersion interactions between proteins and ligands, we have set up a model system examining interactions between mono‐substituted benzene and indole in seven different stable conformations. We first optimized the geometries of the monomers at the B3LYP/6‐31G level, and then scanned the potential curves with MP2, HF, B3LYP, SVWN, and HCTH407 [all at the 6‐311++G(d,p) level] to find the optimum separation. We used the approximate counterpoise method to calculate the basis set superposition error‐corrected interaction energies at the optimum geometries. We then applied these methods to the interactions between aromatic active site residues of horseradish peroxidase C with indole‐3‐propionic acid at two different binding sites. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Chiral discrimination in hydrogen‐bonded complexes of hydrogen peroxide with methyl hydroperoxide: Theoretical study

For the first time, the discrimination of different chiral forms of 1:1 complexes with hydrogen peroxide and methyl hydroperoxide have been investigated using density functional theory (DFT) and Møller–Plesset type 2 (MP2) methods at varied basis set levels from 6‐31+G(d,p) to 6‐31++G(2d,2p). Three pairs of chiral enantiomers were considered. The optimized geometric parameters, interaction energies, and chirodiastatic energies for various isomers at different levels are estimated. To take into account the water solvation effect, the polarized continuum model (PCM) method has been used to evaluate the ΔG_solv. The gas phase results show that the heterochiral six‐membered ring complex (structure I) and homochiral five‐membered ring complexes (structures IV and V) are preferred configurations for the three pairs of chiral enantiomers. The solvation effect on six‐membered ring complexes (structures I and II) shows nonsignificant changes in the configurations preferred, but on five‐membered ring complexes, the homo‐/heterochiral preference is found to be inverse in the polar solvent. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Hydrogen bonding interaction in sarcosine–water complex using ab initio and DFT method

The hydrogen bonding interaction in the Sarcosine (N‐methylglycine)–water complex is studied using ab initio, MP2, and density functional theory (DFT/B3LYP). For this complex, binding energies, dipole–dipole interactions, chemical hardness, and chemical potential have been calculated. Three different basis sets, viz. 6‐311+G, 6‐311++G, and 6‐311++G*, have been used to optimize the geometries by all three methods. The basis set superposition errors are also calculated, and the corrected binding energies are reported for this complex. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Comparative study on formamide–water complex

The hydrogen bonding of 1:1 complexes formed between formamide and water molecule have been investigated systematically using Hartree–Fock (HF), hybrid density functional theory (B3LYP), and post‐Hartree–Fock (MP2 and CCSD(T)) methods with range of basis sets 6‐31G(d), cc‐pVXZ (X = D, T, Q) and aug‐cc‐pVYZ (Y = D, T). Three stable structures are considered on the potential energy surface of formamide and water system. The optimized geometric parameters and interaction energies for various isomers at different levels are estimated. The IR frequencies, intensities, and frequency shifts are reported. This study shows that B3LYP/aug‐cc‐pVDZ method gives better performance for formamide‐water complexes. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010.     

水和甲醇混合溶剂氢键相互作用及对高分子链溶解能力的理论研究

用密度泛函理论对水和甲醇混合溶剂体系的氢键结构进行了详细研究.通过构象和频率分析发现在水团簇中五聚体和六聚体环状结构最为稳定,同时发现一个全新的特征,即甲醇分子能与水五聚体和六聚体形成双氢键.根据各相互作用的稳定化能,分析了水和甲醇混合溶剂对PNIPAM溶解能力的影响,并对实验现象给予了合理解释.     

Theoretical study of molecular interaction between tirapazamine enzymatic catalysis metabolites and water

The weakly hydrogen‐bonded complexes, between tirapazamine enzymatic catalysis metabolites and water, have been investigated by density functional theory (DFT), using the B3LYP hybrid functional. The geometries of these complexes have been fully optimized at the B3LYP/6‐31G(d) and B3LYP/6‐311+G(d) levels. The stabilization energies and charge changes of some atoms have been calculated and analyzed. The results indicate that the catalysis metabolites and water can form stable hydrogen‐bonded complexes. Nine complexes are identified. It is important and necessary to add zero‐point vibrational energy (ZPVE) and basis set superposition error (BSSE) corrections for calculating stabilization energy. The results also reveal an important relationship between the relative stabilities of hydrogen‐bonded complexes and the final products of tirapazamine medication. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Systematic study of the performance of density functional theory methods for prediction of energies and geometries of organoselenium compounds

A variety of density functional theory (DFT) methods are paired with Pople basis sets of varying sizes and evaluated for use with organoselenium compounds. The ability of each method to predict reliable geometries and energies is determined through comparison with quadratic configuration interaction with single and double excitations (QCISD) results. The recommended procedure for accurate prediction of energies and geometries is to use the B3PW91 functional with the 6-311G(2df,p) basis set. The B3PW91/6-31G(d,p) level of theory gives almost identical geometries as larger basis sets, so geometries can be predicted at this level for computational efficiency.     

Combined experimental and computational modeling studies on 3,5‐dimethyl‐pyrazole‐1‐carbodithioic acid benzyl ester

The title compound, 3,5‐Dimethyl‐pyrazole‐1‐carbodithioic acid benzyl ester, has been synthesized and structurally characterized by X‐ray single crystal diffraction, elemental analysis, IR spectra, and UV‐Vis spectrum. The crystal belongs to orthorhombic, space group P212121, with a = 5.3829(15), b = 11.193(3), c = 21.824(6) Å, V = 1315.0(6) ų, and Z = 4. The molecules are connected via intermolecular C–H···N hydrogen bonds into 1D infinite chains. The crystal structure is consolidated by the intramolecular C–H···S hydrogen bonds. Furthermore, Density functional theory (DFT) calculations of the structure, stabilities, orbital energies, composition characteristics of some frontier molecular orbitals and Mulliken charge distributions of the title compound were performed by means of Gaussian 03W package and taking B3LYP/6‐31G(d) basis set. The time‐dependent DFT (TD‐DFT) calculations have been employed to calculate the electronic spectrum of the title compound, and the UV‐Vis spectra has been discussed on this basis. The results show that DFT method at B3LYP/6‐31G(d) level can well reproduce the structure of the title compound. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Density Functional Theory Study on Hydrogen Bonding Interaction of Catechin-(H2O)n

Density functional theory B3LYP method with 6‐31G* basis set has been used to optimize the geometries of the catechin, water and catechin‐(H₂O)_n complexes. The vibrational frequencies have been studied at the same level to analyze these complexes. Six and eleven stable structures for the catechin‐H₂O and catechin‐(H₂O)₂ have been found, respectively. Theories of atoms in molecules (AIM) and natural bond orbital (NBO) have been utilized to investigate the hydrogen bonds involved in all the systems. The interaction energies of all the complexes corrected by basis set superposition error, are from ?13.27 to ?83.56 kJ/mol. All calculations also indicate that there are strong hydrogen‐bonding interactions in catechin‐water complexes. The strong hydrogen‐bonding contributes to the interaction energies dominantly. The O–H stretching motions in all the complexes are red‐shifted relative to that of the monomer.     

Theoretical studies on the effects of methods and parameterization on the calculated free energy of hydration for small molecules

Free energies of hydration (FEH) have been computed for 13 neutral and nine ionic species as a difference of theoretically calculated Gibbs free energies in solution and in the gas phase. In‐solution calculations have been performed using both SCIPCM and PCM polarizable continuum models at the density functional theory (DFT)/B3LYP and ab initio Hartree–Fock levels with two basis sets (6‐31G* and 6‐311++G**). Good linear correlation has been obtained for calculated and experimental gas‐phase dipole moments, with an increase by ～30% upon solvation due to solute polarization. The geometry distortion in solution turns out to be small, whereas solute polarization energies are up to 3 kcal/mol for neutral molecules. Calculation of free energies of hydration with PCM provides a balanced set of values with 6‐31G* and 6‐311++G** basis sets for neutral molecules and ionic species, respectively. Explicit solvent calculations within Monte Carlo simulations applying free energy perturbation methods have been considered for 12 neutral molecules. Four different partial atomic charge sets have been studied, obtained by a fit to the gas‐phase and in‐solution molecular electrostatic potentials at in‐solution optimized geometries. Calculated FEH values depend on the charge set and the atom model used. Results indicate a preference for the all‐atom model and partial charges obtained by a fit to the molecular electrostatic potential of the solute computed at the SCIPCM/B3LYP/6‐31G* level. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

Electron and Geometry Structure of Hydrogen-Bonded Complexes of Guanine with One Molecule Methanol. A DFT Level Study

Summary. The geometries, harmonic vibrational frequencies, and energies of eight hydrogen-bonded complexes of guanine with one molecule methanol are computed using the DFT (B3LYP) method together with the 6-31+G* basis functions. In the investigation two stable tautomers of guanine (oxo-amino N9H and oxo-amino N7H) were chosen. They were included in a variety of H-bonded complexes with one molecule methanol. In order to investigate the nature of the intermolecular bonds, the bonding energies and thermodynamic properties of the complexes were calculated.     

Electron and Geometry Structure of Hydrogen-Bonded Complexes of Guanine with One Molecule Methanol. A DFT Level Study

The geometries, harmonic vibrational frequencies, and energies of eight hydrogen-bonded complexes of guanine with one molecule methanol are computed using the DFT (B3LYP) method together with the 6-31+G* basis functions. In the investigation two stable tautomers of guanine (oxo-amino N9H and oxo-amino N7H) were chosen. They were included in a variety of H-bonded complexes with one molecule methanol. In order to investigate the nature of the intermolecular bonds, the bonding energies and thermodynamic properties of the complexes were calculated.     

A scheme for rapid prediction of cooperativity in hydrogen bond chains of formamides,acetamides, and N‐methylformamides

A scheme is proposed in this article to predict the cooperativity in hydrogen bond chains of formamides, acetamides, and N‐methylformamides. The parameters needed in the scheme are derived from fitting to the hydrogen bonding energies of MP2/6‐31+G** with basis set superposition error (BSSE) correction of the hydrogen bond chains of formamides containing from two to eight monomeric units. The scheme is then used to calculate the individual hydrogen bonding energies in the chains of formamides containing 9 and 12 monomeric units, in the chains of acetamides containing from two to seven monomeric units, in the chains of N‐methylformamides containing from two to seven monomeric units. The calculation results show that the cooperativity predicted by the scheme proposed in this paper is in good agreement with those obtained from MP2/6‐31+G** calculations by including the BSSE correction, demonstrating that the scheme proposed in this article is reasonable. Based on our scheme, a cooperativity effect of almost 240% of the dimer hydrogen bonding energy in long hydrogen bond formamide chains, a cooperativity effect of almost 190% of the dimer hydrogen bonding energy in long hydrogen bond acetamide chains, and a cooperativity effect of almost 210% of the dimer hydrogen bonding energy in long hydrogen bond N‐methylformamide chains are predicted. The scheme is further applied to some heterogeneous chains containing formamide, acetamide, and N‐methylformamide. The individual hydrogen bonding energies in these heterogeneous chains predicted by our scheme are also in good agreement with those obtained from Møller‐Plesset calculations including BSSE correction. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Study of conformational and optical rotation for the alaninamide

Six stationary points of alaninamide have been located on the potential surface energy (PES) at the B3LYP/6‐311++G(2d,2p) level of theory both in the gas phase and in aqueous solution. In the aqueous solution, to take the water solvent effect into account, the polarizable continuum model (PCM) method has been used. Accurate geometric structures and their relative stabilities have been investigated. The results show that the intramolecular hydrogen bond plays a very important role in stabilizing the global minimum of the alaninamide. Moreover, the consistent result in relative energy using high‐level computations, including the MP2 and MP3 methods with the same basis set [6‐311++G(2d,2p)], indicates that the B3LYP/6‐311++G(d,p) level may be applied to the analogue system. More importantly, the optical rotation of the optimized conformers (both in the gas phase and in aqueous solution) of alaninamide have been calculated using the density functional theory (DFT) and Hartree–Fock (HF) method at various basis sets (6‐31+G*, 6‐311++G(d,p), 6‐311++G(2d,2p) and aug‐cc‐pvdz). The results show that the selection of the computation method and the basis set in calculation has great influence on the results of the optical rotations. The reliability of the HF method is less than that of DFT, and selecting the basis set of 6‐311++G(2d,2p) and aug‐cc‐pvDZ produces relative reliable results. Analysis of the computational results of the structure parameters and the optical rotations yields the conclusion that just the helixes in molecules caused the chiral molecules to be optical active. The Boltzmann equilibrium distributions for the six conformers (both in the gas phase and in the aqueous solution) are also carried out. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007