Theoretical study of the red‐ and blue‐shifted hydrogen bonds of nitroxyl and acetylene dimers

Ab initio molecular orbital and density functional theory (DFT) in conjunction with different basis sets calculations were performed to study the C? H…O red‐shifted and N? H…π blue‐shifted hydrogen bonds in HNO? C₂H₂ dimers. The geometric structures, vibrational frequencies and interaction energies were calculated by both standard and counterpoise (CP)‐corrected methods. In addition, the G3B3 method was employed to calculate the interaction energies. The topological and natural bond orbital (NBO) analysis were investigated the origin of N? H…π blue‐shifted hydrogen bond. From the NBO analysis, the electron density decrease in the σ* (N? H) is due to the significant electron density redistribution effect. The blue shifts of the N? H stretching frequency are attributed to a cooperative effect between the rehybridization and electron density redistribution. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

An analytic potential energy function for the amide–amide and amide–water intermolecular hydrogen bonds in peptides

An analytic potential energy function is proposed and applied to evaluate the amide–amide and amide–water hydrogen‐bonding interaction energies in peptides. The parameters in the analytic function are derived from fitting to the potential energy curves of 10 hydrogen‐bonded training dimers. The analytic potential energy function is then employed to calculate the N? H…O?C, C? H…O?C, N? H…OH₂, and C?O…HOH hydrogen‐bonding interaction energies in amide–amide and amide–water dimers containing N‐methylacetamide, acetamide, glycine dipeptide, alanine dipeptide, N‐methylformamide, N‐methylpropanamide, N‐ethylacetamide and/or water molecules. The potential energy curves of these systems are therefore obtained, including the equilibrium hydrogen bond distances R(O…H) and the hydrogen‐bonding energies. The function is also applied to calculate the binding energies in models of β‐sheets. The calculation results show that the potential energy curves obtained from the analytic function are in good agreement with those obtained from MP2/6‐31+G** calculations by including the BSSE correction, which demonstrate that the analytic function proposed in this work can be used to predict the hydrogen‐bonding interaction energies in peptides quickly and accurately. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

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     

TATB二聚体分子间作用力及其气相几何构型研究

采用对称性匹配微扰理论(SAPT)定量地求得TATB分子间的静电、交换排斥、诱导和色散等分子间作用能项, 从理论上揭示了TATB分子间作用本质; 在此基础上, 阐明了密度泛函在研究TATB二聚体时的适合性问题. 结果表明: (1)在有分子间氢键的TATB二聚体中, 库仑力足以与交换排斥力相抗衡, 起主导作用. (2)含分子间氢键的气相TATB二聚体的合理几何构型为平面型结构, 此结构的产生与色散力无关, 因此不管泛函是否含有近程色散作用, 均应预测到这种强极性的平面型结构. (3)在无分子间氢键的TATB二聚体中, 库仑力难以与交换排斥力相抗衡, 色散作用起到了关键作用; (4)在这种情况下, 未含有近程色散作用的密度泛函不可能给出合理构型. 恰好相反, 含有近程色散作用的密度泛函PBE0却能正确地预测到具有“平行重叠”结构且呈微弱极性的TATB二聚体, 色散力是导致这种构型产生的根本原因. “平行重叠”TATB二聚体是典型的色散体系, 其色散力占绝对主导地位并极有可能起源于两个TATB分子上π电子的相互作用. (5)对于所有TATB二聚体, 色散力或很显著或起主导作用. 由于密度泛函或未含有近程色散, 或只能部分地把近程色散表达出来, 这样使得当前所有密度泛函不可能精确求得这些二聚体的作用能.     

DFT study of the monomers and dimers of 2-pyrrolidone: equilibrium structures, vibrational, orbital, topological, and NBO analysis of hydrogen-bonded interactions

A computational study of the monomers and hydrogen-bonded dimers of 2-pyrrolidone was executed at different DFT levels and basis sets. The above dimeric complexes were treated theoretically to elucidate the nature of the intermolecular hydrogen bonds, geometry, thermodynamic parameters, interaction energies, and charge transfer. The processes of dimer formation from monomers and concerted reactions of double proton transfer were considered. The evolution of geometry, vibrational frequencies, charge distribution, and AIM properties in going from monomers to dimers was systematically followed. The solvent effects upon dimer formation were investigated in terms of the self-consistent reaction field (SCRF Onsager model). For the monomers and three dimers, vibrational frequencies were calculated and the changes in frequencies of the vibrations most sensitive to complexation were discussed. The orbital interactions were shown to lengthen the X-H (X = N, O) bond and lower its vibrational frequency (a red shift). To better understand the nature of the corresponding intermolecular interactions, we performed natural bond orbital (NBO) analysis. Topological analysis of electron density at bond critical points (BCP) was executed for complex molecules using the Bader's atoms in molecules (AIM) theory. The interaction energies were calculated, and the basis set superposition errors (BSSE) were estimated systematically. Satisfactory correlations between the structural parameters, interaction energies, and electron density characteristics at BCP were found.     

2-羟基吡啶与水氢键作用的理论研究

本文采用量子化学的Hatree-Fock方法和密度泛函理论(DFT)的B3LYP方法,在6-31G(d)水平上,研究了2-羟基吡啶分子(Hy)及其酮式互变异构体2(1H)-吡啶酮(Py)与水的相互作用。考察它们之间在形成Hy…H2O,Py…H2O,Hy…Hy,Py…Py和Hy…Py等复合物前后的能量变化和分子结构参数变化特点。计算结果表明,在这些复合物中都形成了较强的氢键作用,在水合物中,Py与水形成复合物时能量降低较多,与实验结果一致。经过零点振动能(ZPVE)和基组叠加误差(BSSE)校正后的复合物离解能分别为38.3,40.8,73.0,82.7和71.1 kJ/mol(B3LYP/6-31G(d)),水合物的离解能远小于二聚体复合物,而酮式结构的二聚体的离解能最大。     

Dissociation energies of deoxyribose nucleotide dimer anions measured using blackbody infrared radiative dissociation

The dissociation kinetics of deprotonated deoxyribose nucleotide dimers were measured using blackbody infrared radiative dissociation. Experiments were performed with noncovalently bound dimers of phosphate, adenosine (dAMP), cytosine (dCMP), guanosine (dGMP), thymidine (dTMP), and the mixed dimers dAMP.dTMP and dGMP.dCMP. The nucleotide dimers fragment through two parallel pathways, resulting in formation of the individual nucleotide or nucleotide + HPO3 ion. Master equation modeling of this kinetic data was used to determine threshold dissociation energies. The dissociation energy of (dGMP.dCMP-H)- is much higher than that for the other nucleotide dimers. This indicates that there is a strong interaction between the nucleobases in this dimer, consistent with the existence of Watson-Crick hydrogen bonding between the base pairs. Molecular mechanics simulations indicate that Watson-Crick hydrogen bonding occurs in the lowest energy structures of (dGMP.dCMP-H)-, but not in (dAMP.dTMP-H)-. The trend in gas phase dissociation energies is similar to the trend in binding energies measured in nonaqueous solutions within experimental error. Finally, the acidity ordering of the nucleotides is determined to be dTMP < dGMP < dCMP < dAMP, where dAMP has the highest acidity (largest delta Gacid).     

SARS冠状病毒主要蛋白酶二聚体静电和疏水效应的研究

从三种冠状病毒主要蛋白酶SARS 3CL, HCoV 3CL和TGEC 3CL蛋白酶结构出发,着重研究了三种蛋白酶二聚体单体之间的静电和疏水相互作用.用连续介质模型有限差分方法计算得到三种蛋白二聚体界面处的静电势,发现三种蛋白酶单体和单体之间静电势分布具有明显的互补性,三种蛋白酶二聚体单体之间具有相同的静电相互作用能.用溶剂可及表面积模型分析了分子表面积及疏水性,发现三种蛋白酶具有相同的疏水分布,其中SARS 3CL蛋白酶疏水率为74%,驱动其单体聚合成二聚体.对三种蛋白酶的去溶剂化能疏水项的计算表明,三种蛋白酶二聚体单体之间具有相似的疏水相互作用能.     

Theoretical study of peptide model dimers. Homo versus heterochiral complexes

The study of possible chiral recognition of a series of peptide models (For-Gly-NH₂, For-Ala-NH₂ and four of their fluoro substituted derivatives) has been carried out by means of DFT calculations. Homo (L,L) and heterochiral (L,D) dimers formed by hydrogen bond (HB) complexation have been considered. Initially, the conformational preferences of the monomers have been calculated and used to generate all the possible homo and heterochiral dimers. The energetic results show that in most cases, the β monomers are the most stable while in the dimers, the γ–γ complexes show the strongest interaction energies. In three of the four chiral cases studied, a heterochiral dimer is the most stable one. In addition, the electron density and nuclear shielding of the complexes have been studied.     

Hydrogen bonding in substituted formic acid dimers

The hydrogen-bonded dimers of formic acid derivatives XCOOH (X = H, F, Cl, and CH3) have been investigated using density functional theory (B3LYP) and second-order M?ller-Plesset perturbation (MP2) methods, with the geometry optimization carried out using 6-311++G(2d,2p) basis set. The dimerization energies calculated using aug-cc-pVXZ (with X = D and T) basis have been extrapolated to infinite basis set limit using the standard methodology. The results indicate that the fluorine-substituted formic acid dimer is the most stable one in comparison to the others. Topological analysis carried out using Bader's atoms in molecules (AIM) theory shows good correlation of the values of electron density and its Laplacian at the bond critical points (BCP) with the hydrogen bond length in the dimers. Natural bond orbital (NBO) analysis carried out to study the charge transfer from the proton acceptor to the antibonding orbital of the X-H bond in the complexes reveals that most of the dimers are associated with conventional H-bonding except a few, where improper blue-shifting hydrogen bonds are found to be present.     

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     

Partition potential for hydrogen bonding in formic acid dimers

The ground-state energy and density of 4 low-energy conformations of the formic acid dimer were calculated via partition density functional theory (PDFT). The differences between isolated and PDFT monomer densities display similar deformation patterns for primary and secondary hydrogen bonds (HBs) among all 4 dimers. In contrast, the partition potential shows no transferable features in the bonding regions. These observations highlight the global character of the partition potential and the cooperative effect that occurs when a dimer is bound via more than 1 HB. We also provide numerical confirmation of the intuitive (but unproven) observation that fragment deformation energies are larger for systems with larger binding energies.     

羟基二酰亚胺二聚体分子间相互作用的量子化学研究

采用从头算MP2方法在6-311++G~**基组水平上讨论了CP梯度校正对两种羟基 二酰亚胺异构体所的相互作用能和几何结构的影响，并利用分子中的原子理论（ Atoms in molecules，AIM）计算了五个拓扑参数：键临荷密度、电荷密度的 Iaplacian值、氢键中氢原子的体积、氢原子集居数、氢原子能量来表征氢键的形 成．种构型氢键体系中还讨论了二聚体的相互作用能与氢键临界点的电荷密度、质 子供体X-H键长的线性相关性问题．表明这种线性相关性的存在有范围限制，复合 物和其中单体的构型能够影响这种关系的存在.     

Proton-bound homodimers involving second-row atoms

High-level ab initio quantum chemical calculations (G4(MP2)//MP2/6-311+G(2df,p)) have been used to examine homodimers of second-row bases, and to compare the results with those obtained previously for the first-row analogs. The relationship between the binding energies of the dimers and the proton affinities (PAs) of the bases follows the same pattern as that for the first-row systems, with the binding energies initially increasing with increasing proton affinity but subsequently decreasing. This may be attributed to the opposing effects of increased PA on the hydrogen-bond donor and hydrogen-bond acceptor. The binding energies are generally smaller for the second-row dimers than for the corresponding first-row dimers. There is an increased tendency for asymmetrical hydrogen bonds in homodimers of the second-row compared with first-row dimers. This may be attributed to the lower electronegativities of second-row atoms relative to their first-row counterparts, and to the longer internuclear separation between the hydrogen-bonded second-row atoms.     

Differences in structure, energy, and spectrum between neutral, protonated, and deprotonated phenol dimers: comparison of various density functionals with ab initio theory

We have carried out extensive calculations for neutral, cationic protonated, anionic deprotonated phenol dimers. The structures and energetics of this system are determined by the delicate competition between H-bonding, H-π interaction and π-π interaction. Thus, the structures, binding energies and frequencies of the dimers are studied by using a variety of functionals of density functional theory (DFT) and M?ller-Plesset second order perturbation theory (MP2) with medium and extended basis sets. The binding energies are compared with those of highly reliable coupled cluster theory with single, double, and perturbative triple excitations (CCSD(T)) at the complete basis set (CBS) limit. The neutral phenol dimer is unique in the sense that its experimental rotational constants have been measured. The geometry of the neutral phenol dimer is governed by the hydrogen bond formed by two hydroxyl groups and the H-π interaction between two aromatic rings, while the structure of the protonated/deprotonated phenol dimers is additionally governed by the electrostatic and induction effects due to the short strong hydrogen bond (SSHB) and the charges populated in the aromatic rings in the ionic systems. Our salient finding is the substantial differences in structure between neutral, protonated, and deprotonated phenol dimers. This is because the neutral dimer involves in both H(π)···O and H(π)···π interactions, the protonated dimer involves in H(π)···π interactions, and the deprotonated dimer involves in a strong H(π)···O interaction. It is important to compare the reliability of diverse computational approaches employed in quantum chemistry on the basis of the calculational results of this system. MP2 calculations using a small cc-pVDZ basis set give reasonable structures, but those using extended basis sets predict wrong π-stacked structures due to the overestimation of the dispersion energies of the π-π interactions. A few new DFT functionals with the empirical dispersion give reliable results consistent with the CCSD(T)/CBS results. The binding energies of the neutral, cationic protonated, and anionic deprotonated phenol dimers are estimated to be more than 28.5, 118.2, and 118.3 kJ mol(-1), respectively. The energy components of the intermolecular interactions for the neutral, protonated and deprotonated dimers are analyzed.     

外电场对甲醛分子的结构与电子光谱的影响

采用密度泛函理论(DFT)在B3LYP/6-311++G(d,p)基组水平上,计算了不同外加电场(-8.22×10~9~8.22×10~9 V/m)下甲醛分子基态稳定构型、分子键长、电荷分布、能级分布、能隙、红外光谱、拉曼光谱和分子的总能量.在此基础上利用TDDFT/B3LYP/6-311++G(d,p)方法研究了甲醛分子由基态跃迁到前25个激发态的激发能E、谐振强度f、吸收波长λ受外电场的影响.结果表明:随着C=O连线方向外电场的增加,C=O键键长、氢原子电荷、偶极矩和能隙递增;C—H键键长、C,O原子电荷递减,总能量降低.振动频率与红外强度及拉曼强度由于不同振动有不同变化.甲醛分子UV-Vis光谱随外电场的增加,不同的吸收峰发生了不同程度的蓝移或者红移;外电场对甲醛分子的激发能、谐振强度和吸收波长的强度有一定影响,但随电场变化比较复杂.     

Density functional calculation of quinone electrode potentials

Here, we have applied density functional methods, in combination with free energy hydration calculations, to calculate two-electron electrode potentials for quinones and naphthoquinones. While we find that the free-energy perturbation method, implemented within a molecular dynamics framework, is superior to the PM 3—SM 3 continuum method for determining free energies of hydration, the computationally less expensive PM 3—SM 3 method does perform well when there is not an internal hydrogen bond. Generally, all the density functional approaches investigated gave good energetics when applied to this problem, but the Beck '88—Vosko—Wilk—Nusair combination of functionals for the exchange-correlation energy gave the best results. The density functional results are marginally better than the Møller-Plesset second-order perturbation results. Moreover, because the results are obtained using a thermodynamic cycle which involves taking differences in total energies, the results are not too dependent on the quadrature scheme used to calculate the exchange-correlation energy. By using semiempirically optimized geometries and the PM 3—SM 3 method for determining free energies of hydration, it has been possible to calculate electrode potentials for a series of large molecules (naphthoquinones) to within about 30 mV of experiment. This result is extremely encouraging and shows that density functional methods offer great promise in the design of redox-active molecules such as bioreductive anticancer agents. © 1995 John Wiley & Sons, Inc.     

6-甲基-4-羟基嘧啶单体及二聚体质子转移过程的理论研究

应用密度泛函理论的B3LYP/6-311+G(d)方法研究了6-甲基-4-羟基嘧啶单体及二聚体质子转移的异构化反应.对反应势能面的研究发现,该化含物可能存在9种单体异构体,对其最稳定的单体构型进行分析.各单体间异构化反应的过渡态共有9种,反应的活化能最小为22.06 kJ/mol,最大为356.55 kJ/mol,最可能的反应路径在室温下即可进行. 研究了2种二聚体及其异构化反应的过渡态,发现二聚体均比其对应的单体稳定,而且质子转移所需要的活化能仅为20.13 kJ/mol,比单体低很多. 氢键在这种变化中起了主要作用,由单体和二聚体的总能量计算了氢键的键能.     

Furan-formic acid dimers: an ab initio and matrix isolation study

The dimers formed by formic acid (FA) and furan are investigated by ab initio methods and matrix isolation spectroscopy. Nine complexes with binding energies between -3.91 and -0.82 kcal/mol (MP2/6-311++G(d,p) + ZPE + BSSE) are identified. Another five weaker bound complexes are localized at lower level of theory only. The binding in the furan-FA dimers can be described in terms of OH...O, C=O...H, HO...H, CH...O, OH...pi, and CH...pi interactions. Therefore, the furan-FA complexes are classified in two types: (1) the dimers where the OH hydrogen of formic acid interacts with the furan molecule and (2) the dimers where the main interactions of FA with the furan molecule are via the less acidic CH hydrogen. Duning's and Pople's triple and double basis sets were used to study the dependence of the geometries and energies of the complexes from the basis set. BSSE (basis set superposition error) counterpoise corrections (CP) were included during the geometry optimizations of all dimers at the MP2/6-31G(d,p) level of theory. Matrix isolation spectroscopy allowed us to record the IR spectrum of aggregates between FA and furan. By comparison of the experimental IR spectrum with calculated IR spectra of a variety of complexes, it was possible to identify the most stable furan-FA dimer as the major product of the aggregation.