Ab initio base-pairing energies of uracil and 5-hydroxyuracil with standard DNA bases at the BSSE-free DFT and MP2 theory levels

Oxidized cytosine product 5-hydroxyuracil has been shown to be the major chemical precursor for the GC to AT transition, the most frequent substitution mutation observed in aerobic organisms. We have calculated the interaction energy of base-pair formation involving uracil or 5-hydroxyuracil, which is formed in cells by oxidative deamination of cytosine, bound to any of the natural DNA bases, A, C, G, and T, and discuss the effects of the hydroxyl group in this respect. The base-pair geometries and energies were calculated using the 6-311G(dp) basis set under four conditions: using density functional theory (DFT) without out basis set super-position error (BSSE) correction, using DFT with BSSE correction of geometries and energies, using M?ller-Plesset second order perturbation theory (MP2) without BSSE correction, and using MP2 with BSSE geometry and energy correction. We find that the hydroxyl group of 5-HO-U (relative to U) has little effect on the base-pairs with A, C or one conformation of T, while making a substantial energy difference in base-pairs involving G or a different conformation of T. For most of the complexes studied, the BSSE-corrected energies at the DFT and MP2 levels of theory agreed to within 0.5 kcal.     

MP2 study on the hydrogen bonding interaction between 5-hydroxy-5-methylhydantoin and DNA bases: A,C, G,T

The 5-hydroxy-5-methylhydantoin (5-OH-5-Me-dHyd) is a nucleobase lesion induced by the action of ionizing radiation on thymine residue in DNA. In this study, we present the hydrogen bonding base pairs involving 5-OH-5-Me-dHyd bound to the four bases in DNA: adenine (A), cytosine (C), guanine (G), and thymine (T). Full geometry optimizations have been performed for the studied complexes by MP2 method. The interaction energies were corrected for the basis-set superposition error (BSSE), using the full Boys–Bernardi counterpoise correction scheme. Hydrogen bonding patterns of these base pairs were characterized using NBO analysis and AIM analysis. According to the calculated binding energies and structural parameters, the stability of the base pairs decrease in the following order: 5-OH-5-Me-dHyd:G>5-OH-5-Me-dHyd:A>5-OH-5-Me -dHyd:C~5-OH-5-Me-dHyd:T.     

MP2 study on the hydrogen-bonding interaction between 5-hydroxymethyl-uracil and DNA bases: A,C, G,T

The 5-hydroxymethyl-uracil (HmU) is a product of oxidative attack on the methyl group of thymine in DNA. In this work, we present the hydrogen bonding complexes formation involving HmU bound to the four bases in DNA: adenine (A), cytosine (C), guanine (G), and thymine (T). Full geometry optimizations have been performed for the studied complexes by MP2 method. The interaction energies were corrected for the basis-set superposition error (BSSE), using the full Boys-Bernardi counterpoise correction scheme. Hydrogen bonding patterns of these base pairs were characterized using NBO analysis and AIM analysis. According to the calculated binding energies and structural parameters, the stability of the base pairs decrease in the following order: HmU:A > HmU:G > HmU:C > HmU:T.     

Pi-pi interaction in pyridine

pi-pi Interaction in pyridine dimer and trimer has been investigated in different geometries and orientations at the ab initio (HF, MP2) and DFT (B3LYP) levels of theory using various basis sets (6-31G, 6-31G, 6-311++G) and corrected for basis set superposition error (BSSE). While the HF and DFT calculations show the pyridine dimer and the trimer to be unstable with respect to the monomer, the MP2 calculations show them to be clearly stable, thus emphasizing the need to include electron correlation while determining stacking interaction in such systems. The calculated MP2/6-311++G binding energy (100% BSSE corrected) of the parallel-sandwich, antiparallel-sandwich, parallel-displaced, antiparallel-displaced, T-up and T-down geometries for pyridine dimer are 1.53, 3.05, 2.39, 3.97, 1.91, 1.47 kcal/mol, respectively. The results show the antiparallel-displaced geometry to be the most stable. The binding energies for the trimer in parallel-sandwich, antiparallel-sandwich, and antiparallel-displaced geometry are found to be 3.18, 6.14, and 8.04 kcal/mol, respectively.     

MP2 study on the hydrogen-bonding interaction between 5-fluorocytosine and DNA bases: A,C, G,T

The 5-fluorocytosine (5-FC) is a fluorinated cytosine analog that is used as an antifungal agent. In this work, we present the hydrogen-bonding base pairs involving 5-FC bound to the four bases in DNA: adenine (A), cytosine (C), guanine (G), and thymine (T). Full geometry optimizations have been performed for the studied complexes by MP2 method. The interaction energies were corrected for the basis set superposition error, using the full Boys–Bernardi counterpoise correction scheme. Hydrogen-bonding patterns of these base pairs were characterized using NBO analysis and AIM analysis. According to the calculated binding energies and structural parameters, the stability of the base pairs decreases in the following order: 5-FC:G > 5-FC:C > 5-FC:A > 5-FC:T.     

The Weak Interaction on CO2 …CO van der Waals Complex : A Theoretical Study

The geometries of van der Waals complex CO2…CO were optimized at DFT and second-order Moller-Plesset perturbation(MP2) levels with the large basis set,three stable structures were found.The most stable structure has a T-shape geometry in which the CO lies along the C2 axis of CO2,with the two C atoms direct contact and R(C…C)=0.3227nm.The corresponding energies of the most stable structure were calculated by means of MP2,MP4D,MP4DQ,MP4SDTQ,MP4SDQ,CCSD and CCSD(T) methods,The BSSE (basis set superposition error) wads eliminated by the Boys-Bernardi counterpoise correction(CP) method.According to thermodynamics data.van der Waals complex CO2…CO can found at a low temperature and or a high pressure,There is a little charge transferred between the two interacted subunits.In the most stable structure,CO2 is the acceptor and CO is the donor.     

Hydrogen bonding in the urea dimers and adenine–thymine DNA base pair: anharmonic effects in the intermolecular H-bond and intramolecular H-stretching vibrations

The equilibrium structures, binding energies, vibrational harmonic frequencies, and the anharmonic corrections for two different (cyclic and asymmetric) urea dimers and for the adenine–thymine DNA base pair system have been studied using the second-order Møller–Plesset perturbation theory (MP2) method and different density functional theory (DFT) exchange–correlation (XC) functionals (BLYP, B3LYP, PBE, HCTH407, KMLYP, and BH and HLYP) with the D95V, D95V**, and D95V++** basis sets. The widely used a posteriori Boys–Bernardi or counterpoise correction scheme for basis set superposition error (BSSE) has been included in the calculations to take into account the BSSE effects during geometry optimization (on structure), on binding energies and on the different levels of approximation used for calculating the vibrational frequencies. The results obtained with the ab initio MP2 method are compared with those calculated with different DFT XC functionals; and finally the suitability of these DFT XC functionals to describe intermolecular hydrogen bonds as well as harmonic frequencies and the anharmonic corrections is assessed and discussed.     

Accurate ab initio binding energies of alkaline earth metal clusters

The effects of basis set superposition error (BSSE) and core-correlation on the electronic binding energies of alkaline earth metal clusters Y(n) (Y = Be, Mg, Ca; n = 2-4) at the Moller-Plesset second-order perturbation theory (MP2) and the single and double coupled cluster method with perturbative triples correction (CCSD(T)) levels are examined using the correlation consistent basis sets cc-pVXZ and cc-pCVXZ (X = D, T, Q, 5). It is found that, while BSSE has a negligible effect for valence-electron-only-correlated calculations for most basis sets, its magnitude becomes more pronounced for all-electron-correlated calculations, including core electrons. By utilizing the negligible effect of BSSE on the binding energies for valence-electron-only-correlated calculations, in combination with the negligible core-correlation effect at the CCSD(T) level, accurate binding energies of these clusters up to pentamers (octamers in the case of the Be clusters) are estimated via the basis set extrapolation of ab initio CCSD(T) correlation energies of the monomer and cluster with only the cc-pVDZ and cc-pVTZ sets, using the basis set and correlation-dependent extrapolation formula recently devised. A comparison between the CCSD(T) and density functional theory (DFT) binding energies is made to identify the most appropriate DFT method for the study of these clusters.     

Stacking of the mutagenic DNA base analog 5-bromouracil

The potential energy surface of the stacked 5-bromouracil/uracil (BrU/U) dimer has been investigated in the gas phase and in solution (water and 1,4-dioxane), modeled by a continuum solvent using the polarizable continuum model. Minima and transition states were optimized using DFT (the M06-2X density functional and the 6-31+G(d) basis set). Six stacked gas-phase BrU/U minima were located: four in the face-to-back orientation and two face-to-face. The global minimum in the gas phase is a face-to-face structure with a twist angle of 60° and a zero-point energy-corrected interaction energy of ?10.7 kcal/mol. The BrU/U potential energy surface is geometrically and energetically similar to that of U/U (Hunter and Van Mourik in J Comput Chem 33:2161, 2012). Energy calculations were also performed on experimental geometries of stacked dimers (47 containing BrU stacking with either adenine, cytosine, guanine or thymine and 51 containing thymine also stacking with one of those four bases) taken from DNA structures in the Protein Data Bank. Single-point interaction energies were computed at different levels of theory including MP2, CCSD(T) and DFT using the mPW2PLYP-D double-hybrid functional augmented with an empirical dispersion term, using basis sets ranging from aug-cc-pVDZ to aug-cc-pVQZ. No strong evidence was found for the suggestion that the mutagenicity of BrU is due to enhanced stacking of BrU compared to the corresponding stacked dimers involving thymine.     

羰基镍簇Ni(CO)n(n=1-4)的结构和Ni-CO键解离性质的密度泛函理论研究

在密度泛函理论框架下, 应用不同泛函计算了配合物Ni(CO)n(n=1~4)的平衡几何构型和振动频率. 考察了泛函和基组重叠误差对预测Ni—CO键解离能的影响. 计算结果表明, 用杂化泛函能得到与实验一致的优化几何构型和较合理的振动频率. 对Ni(CO)n(n=2~4)体系, 用“纯”泛函, 如BP86和BPW91, 可得到与CCSD(T)更符合、 并与实验值接近的解离能. 当解离产物出现单个金属原子或离子(如金属羰基配合物的完全解离)时, BSSE校正项的计算中应保持金属部分的电子结构一致. 只有考虑配体基组和不考虑配体基组两种情况下金属的电子构型与配合物中金属的构型一致时, 才能得到合理的BSSE校正, 从而预测合理的解离能.     

Comparison of aromatic NH···π, OH···π, and CH···π interactions of alanine using MP2, CCSD, and DFT methods

A comparison of the performance of various density functional methods including long‐range corrected and dispersion corrected methods [MPW1PW91, B3LYP, B3PW91, B97‐D, B1B95, MPWB1K, M06‐2X, SVWN5, ωB97XD, long‐range correction (LC)‐ωPBE, and CAM‐B3LYP using 6‐31+G(d,p) basis set] in the study of CH···π, OH···π, and NH···π interactions were done using weak complexes of neutral (A) and cationic (A⁺) forms of alanine with benzene by taking the Møller–Plesset (MP2)/6‐31+G(d,p) results as the reference. Further, the binding energies of the neutral alanine–benzene complexes were assessed at coupled cluster (CCSD)/6‐31G(d,p) method. Analysis of the molecular geometries and interaction energies at density functional theory (DFT), MP2, CCSD methods and CCSD(T) single point level reveal that MP2 is the best overall performer for noncovalent interactions giving accuracy close to CCSD method. MPWB1K fared better in interaction energy calculations than other DFT methods. In the case of M06‐2X, SVWN5, and the dispersion corrected B97‐D, the interaction energies are significantly overrated for neutral systems compared to other methods. However, for cationic systems, B97‐D yields structures and interaction energies similar to MP2 and MPWB1K methods. Among the long‐range corrected methods, LC‐ωPBE and CAM‐B3LYP methods show close agreement with MP2 values while ωB97XD energies are notably higher than MP2 values. © 2010 Wiley Periodicals, Inc. J Comput Chem 2010     

DNA甲基化-非甲基化碱基间堆积作用的理论研究

运用二级Mфller-Plesset(MP2)理论方法和cc-pVDZ基组优化了6-甲基鸟嘌呤(O6-MethylG),4-甲基胸腺嘧啶(O4-MethylT)以及5-甲基胞嘧啶(C5-MethylC)与DNA碱基鸟嘌呤(G),腺嘌呤(A),胞嘧啶(C),胸腺嘧啶(T)之间的堆积构型.在MP2/aug-cc-pVXZ//MP2/cc-pVDZ(X=D,T)水平上,采用完全基组外推方法校正了堆积碱基对间的相互作用能,并用完全均衡校正法(CP)校正了基组重叠误差(BSSE).MP2计算结果表明,DNA碱基甲基化使得嘧啶-嘧啶、嘧啶-嘌呤堆积碱基间的平行旋转角发生明显改变,并使堆积碱基间的相互作用能增大.在MP2/cc-pVDZ计算级别上得到了各堆积碱基对的全电子波函数,并用分子中的原子理论(AIM)分析了堆积碱基对间的弱相互作用.AIM分析结果显示,甲基化增强了堆积碱基间的π-π作用,且甲基氢与相邻碱基间形成H2CH…X(X=O,N,CH3,NH2)等类型的氢键.甲基化损伤使碱基间重叠程度增大、π-π作用增强以及堆积碱基间形成多个氢键,是堆积作用能增加的主要原因.     

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.     

A theoretical study of nonlinearity in heterocyclic hydrogen-bonded complexes

Ab initio calculations are performed at the MP2/6-311++G(d,p) and DFT/B3LYP/6-311++G(d,p) theoretical levels to obtain geometries, H-bond energies and harmonic infrared vibrational properties for the Cs symmetry structures of heterocyclic hydrogen-bonded complexes, CnHmY-HX. The H-bond lengths in DFT/B3LYP calculation level are in better agreement with the experimental values than the MP2 results. The geometry optimization are interpreted in terms of hydrogen bond nonlinearity represented by theta; and phi angles, once the hydrogen bond is formed among n-electrons pairs of the heteroatom in heterocyclic and the hydrogen atom in HX. The hydrogen bond energy after of the zero-point vibrational energy (ZPE) and basis set superposition error (BSSE) corrections are overestimated at DFT/B3LYP, whereas the MP2 BSSE corrections are very large than corresponding DFT/B3LYP. For example, the BSSE corrections for the C2H4S-HNC complex are 7.60 and 0.09 kJ mol(-1) in MP2 and DFT/B3LYP calculations levels, respectively. The new vibrational modes in infrared harmonic spectrum arising from complexation show several interesting features, especially the intermolecular stretching mode.     

Rapid evaluation of the binding energies in hydrogen-bonded amide-thymine and amide-uracil dimers in gas phase

The binding energies and the equilibrium hydrogen bond distances as well as the potential energy curves of 48 hydrogen‐bonded amide–thymine and amide–uracil dimers are evaluated from the analytic potential energy function established in our lab recently. The calculation results show that the potential energy curves obtained from the analytic potential energy function are in good agreement with those obtained from MP2/6‐311+G** calculations by including the BSSE correction. For all the 48 dimers, the analytic potential energy function yields the binding energies of the MP2/6‐311+G** with BSSE correction within the error limits of 0.50 kcal/mol for 46 dimers, only two differences are larger than 0.50 kcal/mol and the largest one is only 0.60 kcal/mol. The analytic potential energy function produces the equilibrium hydrogen bond distances of the MP2/6‐311+G** with BSSE correction within the error limits of 0.050 Å for all the 48 dimers. The analytic potential energy function is further applied to four more complicated hydrogen‐bonded amide–base systems involving amino acid side chain and β‐sheet. The values of the binding energies and equilibrium hydrogen bond distances obtained from the analytic potential energy function are also in good agreement with those obtained from MP2 calculations with the BSSE correction. These results demonstrate that the analytic potential energy function can be used to evaluate the binding energies in hydrogen‐bonded amide–base dimers quickly and accurately. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

Rapid evaluation of the binding energies between peptide amide and DNA base

The binding energies and the equilibrium hydrogen bond distances as well as the potential energy curves of 20 hydrogen‐bonded amide–base dimers are evaluated from the analytic potential energy function established in our laboratory recently. The analytic potential energy function is used to calculate the N? H···N, N? H···O?C, C? H···N, and C? H···O?C dipole–dipole attractive interaction energies and C?O···O?C, N? H···H? N, and N? H···H? C dipole–dipole repulsive interaction energies in the 20 dimers composed of DNA bases adenine, guanine, cytosine, or thymine and peptide amide. The calculation results show that the potential energy curves obtained from the analytic potential energy function are in good agreement with those obtained from MP2/6‐311+G** calculations by including the basis set superposition error (BSSE) correction. For all the 20 dimers, the analytic potential energy function yields the binding energies of the MP2/6‐311+G** with BSSE correction within the error limits of 0.50 kcal/mol for 19 dimers, only one difference is larger than 0.50 kcal/mol and the difference is only 0.61 kcal/mol. The analytic potential energy function produces the equilibrium hydrogen bond distances of the MP2/6‐311+G** with BSSE correction within the error limits of 0.030 Å for all the 20 dimers. The analytic potential energy function is further applied to four more complicated DNA base‐peptide amide systems involving amino acid side chain and β‐sheet. The values of the binding energies and equilibrium hydrogen bond distances obtained from the analytic potential energy function are also in good agreement with those obtained from MP2 calculations with the BSSE correction. These results demonstrate that the analytic potential energy function can be used to evaluate the binding energies in hydrogen‐bonded peptide amide–DNA base dimers quickly and accurately. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

BSSE‐corrected geometry and harmonic and anharmonic vibrational frequencies of formamide–water and formamide–formamide dimers

The basis set superposition error (BSSE) influence in the geometry structure, interaction energies, and intermolecular harmonic and anharmonic vibrational frequencies of cyclic formamide–formamide and formamide–water dimers have been studied using different basis sets (6‐31G, 6‐31G**, 6‐31++G**, D95V, D95V**, and D95V++**). The a posteriori “counterpoise” (CP) correction scheme has been compared with the a priori “chemical Hamiltonian approach” (CHA) both at the Hartree–Fock (HF) and second‐order Møller–Plesset many‐body perturbation (MP2) levels of theory. The effect of BSSE on geometrical parameters, interaction energies, and intermolecular harmonic vibrational frequencies are discussed and compared with the existing experimental data. As expected, the BSSE‐free CP and CHA interaction energies usually show less deep minima than those obtained from the uncorrected methods at both the HF and MP2 levels. Focusing on the correlated level, the amount of BSSE in the intermolecular interaction energies is much larger than that at the HF level, and this effect is also conserved in the values of the force constants and harmonic vibrational frequencies. All these results clearly indicate the importance of the proper BSSE‐free correlation treatment with the well‐defined basis functions. At the same time, the results show a good agreement between the a priori CHA and a posteriori CP correction scheme; this agreement is remarkable in the case of large and well‐balanced basis sets. The anharmonic frequency correction values also show an important BSSE dependence, especially for hydrogen bond stretching and for low frequencies belonging to the intermolecular normal modes. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Coordination of methanol clusters to benzene: a computational study

Benzene-methanol cluster structures were investigated with theoretical chemistry methods to describe the microsolvation of benzene and the benzene-methanol azeotrope. Benzene-methanol (MeOH) clusters containing up to six methanol molecules have been calculated by ab initio [MP2/6-311++G(d,p)//MP2/6-31+G(d,p) + BSSE correction] method. The BSSE was found quite large with this basis set, hence, different extrapolation schemes in combination with the aug-cc-pVxZ basis sets have been used to estimate the complete basis set limit of the MP2 interaction energy [ΔE(MP2/CBS)]. For smaller clusters, n ≤ 3, DFT procedures (DFTB+, MPWB1K, M06-2X) have also been applied. Geometries obtained for these clusters by M06-2X and MP2 calculations are quite similar. Based on the MP2/CBS results, the most stable C(6)H(6)(MeOH)(3) cluster is characterized by a hydrogen bonded MeOH trimer chain interacting with benzene via π···H-O and O···H-C(benzene) hydrogen bonds. Larger benzene-MeOH clusters with n ≥ 4 consist of cyclic (MeOH)(n) subclusters interacting with benzene by dispersive forces, to be denoted by C(6)H(6) + (MeOH)(n). Interaction energies and cooperativity effects are discussed in comparison with methanol clusters. Besides MP2/CBS calculations, for selected larger clusters the M06-2X/6-311++G(d,p)//M06-2X/6-31+G(d,p) procedure including the BSSE correction was also used. Interaction energies obtained thereby are usually close to the MP2/CBS limit. To model the benzene-MeOH azeotrope, several structures for (C(6)H(6))(2)(MeOH)(3) clusters have been calculated. The most stable structures contain a tilted T-shaped benzene dimer interacting by π···H-O and O···H-C (benzene) hydrogen bonds with a (MeOH)(3) chain. A slightly less negative interaction energy results for a parallel displaced benzene sandwich dimer with a (MeOH)(3) chain atop of one of the benzene molecules.     

硝酸甲酯分子间相互作用的DFT和ab initio比较

用密度泛函理论(DFT)和从头算(ab initio)方法,分别在B3LYP/6 31G和HF/6 31G水平上求得硝酸甲酯三种二聚体的全优化几何构型和电子结构,并用6 311G和6 311＋＋G基组进行总能量计算.对HF/6 31G计算结果进行MP4SDTQ电子相关校正.在各基组下均进行基组叠加误差(BSSE)和零点能(ZPE)校正求得结合能.对6 31G优化构型作振动分析并基于统计热力学求得200～600 K温度下单体和二聚体的热力学性质.详细比较两种方法的相应计算结果,发现DFT求得的分子间距离较短,分子内键长较长,所得结合能均小于相应ab initio计算值.     

Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs

MP2 and CCSD(T) complete basis set (CBS) limit interaction energies and geometries for more than 100 DNA base pairs, amino acid pairs and model complexes are for the first time presented together. Extrapolation to the CBS limit is done by using two-point extrapolation methods and different basis sets (aug-cc-pVDZ - aug-cc-pVTZ, aug-cc-pVTZ - aug-cc-pVQZ, cc-pVTZ - cc-pVQZ) are utilized. The CCSD(T) correction term, determined as a difference between CCSD(T) and MP2 interaction energies, is evaluated with smaller basis sets (6-31G** and cc-pVDZ). Two sets of complex geometries were used, optimized or experimental ones. The JSCH-2005 benchmark set, which is now available to the chemical community, can be used for testing lower-level computational methods. For the first screening the smaller training set (S22) containing 22 model complexes can be recommended. In this case larger basis sets were used for extrapolation to the CBS limit and also CCSD(T) and counterpoise-corrected MP2 optimized geometries were sometimes adopted.