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     

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 analysis of vibrational spectra and scaling‐factor of 2‐aryl‐1,3,4‐oxadiazole derivatives

In this study, the direct molecular structure implementations for calculating vibrational spectra and scaling factors, and infrared intensities at both the Hartree–Fock (HF) and density functional (B3LYP) levels of theory with 6‐31G(d), 6‐311G(d), 6‐31++G(d,p), and 6‐311++G(d,p) basis sets are presented. Also, vibrational frequencies have been investigated as dependence on the choice of method and basis set. The parameters of molecular geometry and vibrational frequencies values of 2‐aryl‐1,3,4‐oxadiazoles 5a–g in the ground state have been calculated. Theoretical determination of vibrational frequencies is quite useful both in understanding the relationship between the molecular structures and scaling factor. The data of 2‐aryl‐1,3,4‐oxadiazoles 5a–g display significant electronic properties provide the basis for future design of efficient materials having the oxadiazole core and theoretical IR studies. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

The influence of formamide (model of protein unit) on the intramolecular proton transfer in the DNA simple base guanine: A density functional theory study

For the purpose of investigating the influence of protein unit on the intramolecular proton transfer (IPT) reactions in the simple base guanine, a simple model (formamide) of peptides is designed to biological system investigations, and five complexes of formamide–guanine (FG1, FG2, FG3, FG4, and FG5) are determined at the B3LYP/6‐311++G(d,p) level of theory. For comparison, HF and MP2 methods are also used in this paper. The proton transfer (PT) reaction processes of guanine and FGs have been investigated employing the B3LYP/6‐311++G(d,p) level of theory. The selected thermodynamic and kinetic parameters, such as the activation energies (E_a), changes of enthalpy (ΔH) and changes of free energies (ΔG), as well as the equilibrium constants (K_p) for those reaction processes, have also been obtained by calculational means. The calculated results indicate that the assisted and protected effects of formamide on IPT in guanine are site‐dependent. CH1 is the lowest activation energy needed PT process no matter where the formamide molecule is located in. The activation energy of CH1 with formamide in S2 is the lowest one (153.3 KJ/mol), whereas the one of CH5 with formamide in S5 is the highest (318.3 KJ/mol). © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Contemplation on Some Prismatic Polynitrogen Structures – A DFT Treatment

Polynitrogen compounds, are rare molecules having only nitrogen atoms. In recent years, they have been considered as promising candidates of clean (green) high energy density materials. They possess high energy content and their sole decomposition product is N₂. Presently some prismatic polynitrogen structures (N₆ – N₁₄) are considered within the limitations of density functional theory at the levels of B3LYP/6‐311++G(d,p) and B3LYP/cc‐PVTZ. The calculations reveal that they are all highly endothermic but stable. Certain quantum chemical properties, IR and UV/Vis spectra are reported. Homolytic bond cleavage of top rings are considered. Then, the transition state and activation energies, and also homolytic bond dissociation energies for the top rings have been calculated at the level of UB3LYP/6‐311++G(d,p). Also NICS(0) values have been calculated at the level of B3LYP/6‐311++G(d,p). The results indicate that N₆ and N₁₀ have aromatic and nonaromatic top (and also base) rings, respectively. All the rest of the structures have antiaromatic rings (all the structures have antiaromatic N₄ rings).     

Effect of metal cations [Li+, Na+, K+, Be2+, Mg2+, and Ca2+] on the structure of 2‐(3′‐hydroxy‐2′‐pyridyl)benzoxazole: A theoretical investigation

Density functional theory calculations were performed at the B3LYP/6‐311++G(d,p) level to systematically explore the geometrical multiplicity and binding strength for the complexes formed by alkaline and alkaline earth metal cations, viz. Li⁺, Na⁺, K⁺, Be²⁺, Mg²⁺, and Ca²⁺ (Mⁿ⁺, hereinafter), with 2‐(3′‐hydroxy‐2′‐pyridyl)benzoxazole. A total of 60 initial structures were designed and optimized, of which 51 optimized structures were found, which could be divided into two different types: monodentate complexes and bidentate complexes. In the cation‐heteroatom complex, bidentate binding is generally stronger than monodentate binding, and of which the bidentate binding with five‐membered ring structure has the strongest interaction. Energy decomposition revealed that the total binding energies mainly come from electrostatic interaction for alkaline metal ion complexes and orbital interaction energy for alkaline earth metal ion complex. In addition, the electron localization function analysis show that only the Be? O and Be? N bond are covalent character, and others are ionic character. © 2012 Wiley Periodicals, Inc.     

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     

Polarizable model potential function for nucleic acid bases

A polarizable model potential (PMP) function for adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U) is developed on the basis of ab initio molecular orbital calculations at the MP2/6-31+G* level. The PMP function consists of Coulomb, van der Waals, and polarization terms. The permanent atomic charges of the Coulomb term are determined by using electrostatic potential (ESP) optimization. The multicenter polarizabilities of the polarization term are determined by using polarized one-electron potential (POP) optimization in which the electron density changes induced by a test charge are target. Isotropic and anisotropic polarizabilities are adopted as the multicenter polarizabilities. In the PMP calculations using the optimized parameters, the interaction energies of Watson-Crick type A-T and C-G base pairs were -15.6 and -29.4 kcal/mol, respectively. The interaction energy of Hoogsteen type A-T base pair was -17.8 kcal/mol. These results reproduce well the quantum chemistry calculations at the MP2/6-311++G(3df,2pd) level within the differences of 0.6 kcal/mol. The stacking energies of A-T and C-G were -9.7 and -10.9 kcal/mol. These reproduce well the calculation results at the MP2/6-311++G (2d,2p) level within the differences of 1.3 kcal/mol. The potential energy surfaces of the system in which a sodium ion or a chloride ion is adjacent to the nucleic acid base are calculated. The interaction energies of the PMP function reproduced well the calculation results at the MP2/6-31+G* or MP2/6-311++G(2d,2p) level. The reason why the PMP function reproduces well the high-level quantum mechanical interaction energies is addressed from the viewpoint of each energy terms.     

乙烯、乙炔和苯与氨基锂间的π型锂键相互作用

分别在DFT-B3LYP和MP2/6-311++G**水平上求得乙烯、乙炔和苯与氨基锂锂键复合物势能面上的3个几何构型. 频率分析表明,3个构型均为稳定构型. 计算结果表明,形成锂键复合物后,质子供体N(2)- Li(4)的键长明显增大,且其伸缩振动的频率发生了不同程度的红移. 分别在乙烯…氨基锂、乙炔…氨基锂和苯…氨基锂三种复合物中,经MP2/6-311++G**水平计算的同时含基组重叠误差(BSSE)和零点振动能校正的单体间锂键相互作用能分别为-26.04、-24.86 和 -30.02 kJ·mol-1. 自然键轨道理论（NBO）分析表明单体间的弱相互作用属于π-s型锂键.     

Quantum-chemical Study on the Structures and Properties of Uracil-BX3 （X = F, Cl） Complexes

1 INTRODUCTION The intermolecular interaction of bases in DNA or RNA is of immense interest and significance to che- mists and biologists alike. The interactions of these bases with metal cations, solvent molecules and other small molecules or ions would affect the struc- ture and biological properties or recognition process,which has been investigated widely[1～8]. Boron contained compounds are electron deficient com- pounds and have been extensively used as catalysts in chemical react…     

An ab initio MO study on the structures and electronic states of hydrogen-bonded O3- HF and SO2-HF complexes

Ab initio molecular orbital (MO) calculations have been carried out for base-hydrogen fluoride (HF) complexes (base = O3 and SO2) in order to elucidate the structures and energetics of the complexes. The ab initio calculations were performed up to the QCISD(T)/6-311++G(d,p) level of theory. In both complexes, hydrogen-bonded structures where the hydrogen of HF orients toward one of the oxygen atoms of bases were obtained as stable forms. The calculations showed that cis and trans isomers exist in both complexes. All calculations for the SO2-HF complex indicated that the cis form is more stable in energy than the trans form. On the other hand, in O3-HF complexes, the stable structures are changed by the ab initio levels of theory used, and the energies of the cis and trans forms are close to each other. From the most sophisticated calculations (QCISD(T)/6-311++G(d,p)//QCISD/6-311+G(d) level), it was predicted that the complex formation energies for cis SO2-HF, trans SO2-HF, cis O3-HF, and trans O3-HF are 6.1, 5.7, 3.4, and 3.6 kcal/mol, respectively, indicating that the binding energy of HF to SO2 is larger than that of O3. The harmonic vibrational frequencies calculated for cis O3-HF and cis SO2-HF complexes were in good agreement with the experimental values measured by Andrews et al. Also, the calculated rotation constants for cis SO2-HF agreed with the experiment.     

Peptide models. XXXIII. Extrapolation of low-level Hartree-Fock data of peptide conformation to large basis set SCF,MP2, DFT,and CCSD(T) results. The Ramachandran surface of alanine dipeptide computed at various levels of theory

At the dawn of the new millenium, new concepts are required for a more profound understanding of protein structures. Together with NMR and X-ray-based 3D-structure determinations in silico methods are now widely accepted. Homology-based modeling studies, molecular dynamics methods, and quantum mechanical approaches are more commonly used. Despite the steady and exponential increase in computational power, high level ab initio methods will not be in common use for studying the structure and dynamics of large peptides and proteins in the near future. We are presenting here a novel approach, in which low- and medium-level ab initio energy results are scaled, thus extrapolating to a higher level of information. This scaling is of special significance, because we observed previously on molecular properties such as energy, chemical shielding data, etc., determined at a higher theoretical level, do correlate better with experimental data, than those originating from lower theoretical treatments. The Ramachandran surface of an alanine dipeptide now determined at six different levels of theory [RHF and B3LYP 3-21G, 6-31+G(d) and 6-311++G(d,p)] serves as a suitable test. Minima, first-order critical points and partially optimized structures, determined at different levels of theory (SCF, DFT), were completed with high level energy calculations such as MP2, MP4D, and CCSD(T). For the first time three different CCSD(T) sets of energies were determined for all stable B3LYP/6-311++G(d,p) minima of an alanine dipeptide. From the simplest ab initio data (e.g., RHF/3-21G) to more complex results [CCSD(T)/6-311+G(d,p)//B3LYP/6-311++G(d,p)] all data sets were compared, analyzed in a comprehensive manner, and evaluated by means of statistics.     

Correlated one‐electron wave functions

Using four basis sets, 6‐311G(d,p), 6‐31+G(d,p), 6‐311++G(2d,2p), and 6‐311++G(3df,3pd), the optimized structures with all real frequencies were obtained at the MP2 level for dimers CH₂O? HF, CH₂O? H₂O, CH₂O? NH₃, and CH₂O? CH₄. The structures of CH₂O? HF, CH₂O? H₂O, and CH₂O? NH₃ are cycle‐shaped, which result from the larger bend of σ‐type hydrogen bonds. The bend of σ‐type H‐bond O…H? Y (Y?F, O, N) is illustrated and interpreted by an attractive interaction of a chemically intuitive π‐type hydrogen bond. The π‐type hydrogen bond is the interaction between one of the acidic H atoms of CH₂O and lone pair(s) on the F atom in HF, the O atom in H₂O, or the N atom in NH₃. By contrast with above the three dimers, for CH₂O? CH₄, because there is not a π‐type hydrogen‐bond to bend its linear hydrogen bond, the structure of CH₂O? CH₄ is a noncyclic shaped. The interaction energy of hydrogen bonds and the π‐type H‐bond are calculated and discussed at the CCSD(T)/6‐311++G(3df,3pd) level. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

1,2,3-三氮杂苯－(水)3复合物多体相互作用

The interaction between 1,2,3-triazine and three water molecules was studied using density functional theory B3LYP method at 6-31-t＋＋G^＊＊ basis set. Various structures for 1,2,3-triazine-（water）n （n= 1, 2, 3） complex were investigated and the different lower energy structures were reported. Many-body analysis was also carded out to obtain relaxation energy and many-body interaction energy （two, three, and four-body）, and the most stable conformer has the basis set superposition error corrected interaction energy of -- 102.61 kJ/mol. The relaxation energy, two- and three-body interactions have significant contribution to the total interaction energy whereas four-body interaction was very small for 1,2,3-triazine-（water）3 complex.     

Hydrogen bonding structure and many‐body interactions in 1,3,5‐triazine–(water)3 and 1,2,4‐triazine–(water)3 complexes

The hydrogen bonding structure and many‐body interactions between 1,3,5‐triazine (1,2,4‐triazine) and three water molecules are studied using the density functional theory (DFT) B3LYP method and 6‐31++G** basis set. Various structures of 1,3,5‐triazine–(water)₃ and 1,2,4‐triazine–(water)₃ complexes are investigated, and the seven and eight stable structures are reported for 1,3,5‐triazine–(water)₃ and 1,2,4‐triazine–(water)₃, respectively. Many‐body analysis is also carried out to obtain relaxation energy and many‐body interaction energy (two‐, three‐, and four‐body), and the most stable conformer has the basis set superposition error corrected interaction energy of ?92.09 and ?99.53 kJ/mol. The two‐ and three‐body interactions have significant contribution to the total interaction energy, whereas the relaxation energy, four‐body interactions are very small for 1,3,5‐triazine–(water)₃ and 1,2,4‐triazine–(water)₃ complexes. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

高级量子化学从头计算法研究N2和H2O分子间相互作用

在MP2/6-311++G(3d,3p)电子相关校正水平上,对N₂和H₂O分子间可能存在的氢键复合物进行全自由度能量梯度优化,发现了一个接近于直线的弱氢键总能量极小结构(1),进一步在高级电子相关校正的MP4SDTQ和CCSD(T)水平,用6-311++G(3d,3p)基组加上(3s3p2d1f)键函数,用MP4和CCSD(T)计算的结构1的结合能分别为-5.061kJ/mol和-4.715kJ/mol.     

Direct dynamics study on mechanism and kinetics of the biradical self‐reaction of HOO

A theoretical study of the mechanism and the kinetics for the hydrogen abstraction reaction of the biradical hydroperoxy radical has been presented at the CCSD(T)/6‐311++G(3d,2p)//CCSD/6‐31+G(d,p) level of theory. Our theoretical calculations suppose a stepwise mechanism involving the formation of a postreactant complex in the triplet and singlet entrance channels. Four transition states of the six‐membered chain complexes (³TS1 and ¹TS1) and six‐membered ring complexes (³TS2 and ¹TS2) are located at the high dual level CCSD(T)/6‐311++G(3d,2p)//CCSD/6‐31+G(d,p) method. The rate constants of Path 1 ～ Path 4 at the CCSD(T)/6‐311++G(3d,2p)//CCSD/6‐31+G (d,p) level are calculated by means of the conventional transition state theory (TST) and canonical variational TST without and with small‐curvature tunneling (SCT) correction within the temperature range of 200–2,500 K. The calculated results show that the triplet channel is the dominating reaction channel and Path 2 is found to be the most favorable pathway. The rate constants of Path 2 are in good agreement with the experimental values at the experimentally measured temperatures. Moreover, the variational effect is not obvious in the low temperature range but is not neglectable in the high temperature range. The SCT plays an important role particularly in the low temperature range. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Can cytosine, thymine and uracil be formed in interstellar regions? A theoretical study

This theoretical study investigates possible synthetic routes to cytosine, uracil and thymine in the gas phase from precursor molecules that have been detected in interstellar media. Studies at the CCSD(T)/6-311++G(d,p)//B3LYP/6-311++G(d,p) level of theory suggest that: The reactions between :CCCNH and :CCCO with monosolvated urea may constitute viable interstellar syntheses of cytosine and uracil. No low energy equilibration between cytosine and uracil has been demonstrated. The interaction of :CH(2) with the 5 C-H bond of uracil may form thymine in an energetically favourable reaction, but competing reactions where :CH(2) reacts with double bonds and other CH and NH bonds of uracil, reduce the effectiveness of this synthesis. The reaction between the hydrated propional enolate anion and isocyanic acid may produce thymine, in a reaction sequence where ΔG(reaction)(298 K) is -22 kJ mol(-1) and the maximum energy requirement (barrier to the first transition state) is only 47 kJ mol(-1).     

Theoretical studies on dynamics and thermochemistry of the reactions CF(3)CHCl(2)+Cl-->CF(3)CCl(2)+HCl and CF(3)CHFCl+Cl-->CF(3)CFCl+HCl

A dual-level direct dynamics study has been carried out for the two hydrogen abstraction reactions CF(3)CHCl(2)+Cl and CF(3)CHFCl+Cl. The geometries and frequencies of the stationary points are optimized at the BHLYP/6-311G(d,p), B3LYP/6-311G(d,p), and MP2/6-31G(d) levels, respectively, with single-point calculations for energy at the BHLYP/6-311++G(3df,2p), G3(MP2), and QCISD(T)/6-311G(d,p) levels. The enthalpies of formation for the species CF(3)CHCl(2), CF(3)CHFCl, CF(3)CCl(2), and CF(3)CFCl are evaluated at higher levels. With the information of the potential energy surface at BHLYP/6-311++G(3df,2p)//6-311G(d,p) level, we employ canonical variational transition-state theory with small-curvature tunneling correction to calculate the rate constants. The agreement between theoretical and experimental rate constants is good in the measured temperature range 276-382 K. The effect of fluorine substitution on reactivity of the C-H bond is discussed.