On the origin of red and blue shifts of X-H and C-H stretching vibrations in formic acid (formate ion) and proton donor complexes.

Complexes between formic acid or formate anion and various proton donors (HF, H(2)O, NH(3), and CH(4)) are studied by the MP2 and B3LYP methods with the 6-311++G(3df,3pd) basis set. Formation of a complex is characterized by electron-density transfer from electron donor to ligands. This transfer is much larger with the formate anion, for which it exceeds 0.1 e. Electron-density transfer from electron lone pairs of the electron donor is directed into sigma* antibonding orbitals of X--H bonds of the electron acceptor and leads to elongation of the bond and a red shift of the X--H stretching frequency (standard H-bonding). However, pronounced electron-density transfer from electron lone pairs of the electron donor also leads to reorganization of the electron density in the electron donor, which results in changes in geometry and vibrational frequency. These changes are largest for the C--H bonds of formic acid and formate anion, which do not participate in H-bonding. The resulting blue shift of this stretching frequency is substantial and amounts to almost 35 and 170 cm(-1), respectively.     

四氯化苯醌-二苯撑体系的光诱导电子转移研究

用从头算方法对四氯化苯醌-二苯撑体系分子间相互作用进行了理论计算研究.用MP2/6-31G^**方法,分别优化电子给体二苯撑,受体四氯化苯醌的稳定构型,用同样的方法优化配合物的层间距得到其最稳定构型,并计算了BSSE校正后的电子给受体配合物的稳定化能.用CIS/6-31++G^**方法,计算了给体、受体及配合物的电子激发态.理论计算验证了给体和受体间能形成稳定的电子给受体配合物,该配合物受光激发能直接产生电荷转移态.在球孔穴近似和点偶极近似下,对电荷转移吸收的理论计算结果进行了非平衡溶剂化能校正.经非平衡溶剂化能校正的电荷转移跃迁能与实验值符合较好.     

Ab initio study of the complexes of halogen-containing molecules RX (X=Cl, Br, and I) and NH3: towards understanding the nature of halogen bonding and the electron-accepting propensities of covalently bonded halogen atoms

Ab initio calculations have been performed on a series of complexes formed between halogen-containing molecules and ammonia to gain a deeper insight into the nature of halogen bonding. It appears that the dihalogen molecules form the strongest halogen-bonded complexes with ammonia, followed by HOX; the charge-transfer-type contribution has been demonstrated to dominate the halogen bonding in these complexes. For the complexes involving carbon-bound halogen molecules, our calculations clearly indicate that electrostatic interactions are mainly responsible for their binding energies. Whereas the halogen-bond strength is significantly enhanced by progressive fluorine substitution, the substitution of a hydrogen atom by a methyl group in the CH(3)X...NH(3) complex weakened the halogen bonding. Moreover, remote substituent effects have also been noted in the complexes of halobenzenes with different para substituents. The influence of the hybridization state of the carbon atom bonded to the halogen atom has also been examined and the results reveal that halogen-bond strengths decrease in the order HC triple bond CX > H(2)C=CHX approximately O=CHX approximately C(6)H(5)X > CH(3)X. In addition, several excellent linear correlations have been established between the interaction energies and both the amount of charge transfer and the electrostatic potentials corresponding to an electron density of 0.002 au along the R-X axis; these correlations provide good models with which to evaluate the electron-accepting abilities of the covalently bonded halogen atoms. Finally, some positively charged halogen-bonded systems have been investigated and the effect of the charge has been discussed.     

NCO/NCS自由基与XY（X=H,Cl;Y=F,Cl,Br）间σ-型弱作用的理论研究

NCO和NCS是大气化学中非常引人关注的自由基,它们均有三个原子并且两个端基原子均可作为电子给体形成σ-型氢/卤键.本文在MP2/aug-cc-pVDZ水平上研究了NCO/NCS...XY（X=H,Cl;Y=F,Cl,Br）体系中的弱化学键.计算结果表明,氢/卤原子与N原子相连形成的复合物比与O/S原子相连形成的复合物稳定;氢/卤键的稳定性由分子静电势决定,而非原子电负性;对相同的电子给体B（B=N,O/S）和相同的卤原子来说,化学键的强度按Y=F,Cl,Br的顺序逐渐减弱.在氢/卤键形成过程中,自旋电子密度在电子给体和电子受体间的转移较少,但它在自由基内部发生重排,就本文研究的所有复合物而言,自旋电子密度均转移向XY分子的相反位置.     

On differences between hydrogen bonding and improper blue-shifting hydrogen bonding.

Twenty two hydrogen-bonded and improper blue-shifting hydrogen-bonded complexes were studied by means of the HF, MP2 and B3LYP methods using the 6-31G(d,p) and 6--311 ++G(d,p) basis sets. In contrast to the standard H bonding, the origin of the improper blue-shifting H bonding is still not fully understood. Contrary to a frequently presented idea, the electric field of the proton acceptor cannot solely explain the different behavior of the H-bonded and improper blue-shifting H-bonded complexes. Compression of the hydrogen bond due to different attractive forces-dispersion or electrostatics--makes an important contribution as well. The symmetry-adapted perturbation theory (SAPT) has been utilized to decompose the total interaction energy into physically meaningful contributions. In the red-shifting complexes, the induction energy is mostly larger than the dispersion energy while, in the case of blue-shifting complexes, the situation is opposite. Dispersion as an attractive force increases the blue shift in the blue-shifting complexes as it compresses the H bond and, therefore, it increases the Pauli repulsion. On the other hand, dispersion in the red-shifting complexes increases their red shift.     

Electron-proton effect and the structure of excited molecular complexes

The essence of the electron-proton effect is clarified by the example of donor-acceptor complexes. It is shown that this effect plays a universal role in accelerating dark and photochemical processes due to interaction between electron and proton excitations.     

Computational studies of σ-type weak interactions between NCO/NCS radicals and XY(X = H,Cl;Y = F,Cl,and Br)

The triatomic radicals NCO and NCS are of interest in atmospheric chemistry,and both the ends of these radicals can potentially serve as electron donors during the formation of σ-type hydrogen/halogen bonds with electron acceptors XY(X = H,Cl;Y = F,Cl,and Br).The geometries of the weakly bonded systems NCO/NCS···XY were determined at the MP2/aug-cc-pVDZ level of calculation.The results obtained indicate that the geometries in which the hydrogen/halogen atom is bonded at the N atom are more stable than those where it is bonded at the O/S atom,and that it is the molecular electrostatic potential(MEP)-not the electronegativity-that determines the stability of the hydrogen/halogen bond.For the same electron donor(N or O/S) in the triatomic radical and the same X atom in XY,the bond strength decreases in the order Y = F > Cl > Br.In the hydrogen/halogen bond formation process for all of the complexes studied in this work,transfer of spin electron density from the electron donor to the electron acceptor is negligible,but spin density rearranges within the triatomic radicals,being transferred to the terminal atom not interacting with XY.     

Electronic structures and long‐range electron transfer through DNA molecules

Quantum chemical calculation on an entire molecule of segments of native DNA was performed in an ab initio scheme with a simulated aqueous solution environment by overlapping dimer approximation and negative factor counting method. The hopping conductivity was worked out by random walk theory and compared with recent experiment. We conclude that electronic transport in native DNA molecules should be caused by hopping among different bases as well as phosphates and sugar rings. Bloch type transport through the delocalized molecular orbitals on the whole molecular system also takes part in the electronic transport, but should be much weaker than hopping. The complementary strand of the double helix could raise the hopping conductivity for more than 2 orders of magnitudes, while the phosphate and sugar ring backbone could increase the hopping conductivity through the base stacks for about 1 order of magnitude. DNA could transport electrons easily through the base stacks of its double helix but not its single strand. Therefore, the dominate factor that influences the electronic transfer through DNA molecules is the π stack itself instead of the backbone. The final conclusion is that DNA can function as a molecular wire in its double helix form with the conditions that it should be doped, the transfer should be a multistep hopping process, and the time period of the transfer should be comparable with that of an elementary chemical reaction. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 78: 112–130, 2000     

Directional hydrogen bonding in the MM3 force field: II

Extensive calculations on hydrogen bonded systems were carried out using the improved MM3 directional hydrogen bond potential. The resulting total function was reoptimized. Comparisons of the hydrogen bonding potential function from ab initio calculations (MP2/6-31G**); the original MM3(89); and the reoptimized MM3 force field MM3(96), for a variety of C, N, O, and Cl systems including the formamide dimer and formamide–water complex, are described herein. Hydrogen bonding is shown to be a far more complicated and ubiquitous phenomenon than is generally recognized. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1001–1016, 1998     

7,8-二氢-8-氧鸟嘌呤碱基对的量子化学研究

遗传信息的完整性不断受氧化基因的威胁,7,8-二氢-8-氧鸟嘌呤（8-oxo-G）是氧化DNA损伤最常见的产物. 氧化碱基会引起基因突变、癌变及衰老等. 应用量子化学方法分析得出：鸟嘌呤（G）被氧化为8-oxo-G后,其电荷分布、氢键的供体和受体位点的数目和位置随之改变,N7和O6原子所带的电荷变得更负,使得它们作为氢键供体的能力增强. 从而G被误认为其他碱基,与正常碱基形成多种氢键复合物. 可将8-oxo-G划分为3个作用位点与正常碱基相互作用. 与正常的单体相比,碱基对中形成氢键的受体原子上所带电荷平均变负0.05e,占原电荷的8%; 供体H原子所带电荷平均变正0.02e,占原电荷的4%. 1位点与正常碱基作用形成的氢键复合物更稳定,2位点和3位点性质相似,水溶剂使碱基对的结合能力减弱,其中与C作用形成氢键复合物的结合能减弱程度最大,且使碱基对结合能力的次序改变. 在8-oxo-G导致的GC→TA突变中,亲核反应位点从G所在链转到A（C）所在链,影响酶对碱基的识别,从而产生基因突变.     

On the Correlation between the Blue Shift of Hydrogen Bonding and the Proton Donor-Proton Acceptor Distance

It is demonstrated that in all types of hydrogen bonds (X—H…Y) there is a balance between the long-range attractive orbital interactions and short-range Pauli/nucleus repulsions. When the proton acceptor approaches the proton donor from distance, the hydrogen bonding energy becomes more negative at relatively large distance, goes through a minimum, and then starts to become less negative when the short-range repulsive forces come into effect.Meanwhile, the X--H bond length increases at relatively large distances, goes through a maximum and starts to shorten when the short-range repulsive forces come into effect. Whether the hydrogen bond is red or blue shifted is dictated by the energy minimum position. If at the energy minimum position the X—H bond length is shorter than that for the free monomer, the hydrogen bond is blue shifted and vice versa. Further studies demonstrate that the recent report about the correlation of C—H bond lengths with proton donor-acceptor distance in F3C—H…OH2 and F3C—H…Cl^- is not fully correct because the authors conducted an inappropriate comparison. Furthermore, it is shown for the first time that the Pauli/nucleus repulsion theory is applicable to the blue-shifted hydrogen bonds in the X—H…π complexes and the blue-shifted lithium bonds in the X—Li…Y complexes.     

Hydrogen Bonding Interactions of Radicals

Hydrogen bonding interactions of organic radicals are systematically studied using diverse ab initio and density functional theory (DFT) methods. It is found that open-shell hydrogen bonds with radical proton donors are more difficult to model than those with radical proton acceptors. The DFT methods perform significantly worse than the unrestricted second order Möller-Plesset perturbation (UMP2) method in both geometry optimization and interaction energy calculations for the open-shell hydrogen bonds. The UB3LYP method seriously underestimates the donor-acceptor distances and overestimates interaction energies for the open-shell hydrogen bonds with radical proton donors. Nevertheless, use of the UBH&HLYP functional to study the open-shell hydrogen bonds is still acceptable. Furthermore, it is necessary to use sufficiently flexible basis sets, such as 6-311++G(2df,2p), to get reliable interaction energies for the open-shell hydrogen bonds. The open-shell proton donors are stronger Lewis acids than the corresponding closed-shell proton donors. The open-shell proton acceptors are weaker Lewis bases than the corresponding closed-shell proton acceptors.     

Spectroscopic and theoretical study of vibrational spectra of hydrogen‐bonded tropolone

Theoretical simulation of the bandshape and fine structure of the ν_s stretching band is presented for tropolone‐H and tropolone‐D taking into account an adiabatic coupling between the high‐frequency O–H(D) stretching and the low‐frequency intra‐ and intermolecular OO stretching modes, and linear and quadratic distortions of the potential energies for the low‐frequency vibrations in the excited state of the O–H(D) stretching vibration. In order to determine the low‐frequency vibrations, the experimental spectra of the polycrystalline tropolone in the far‐infrared and the low‐frequency Raman range have been recorded for the first time. The experimental frequencies in the low‐frequency region are compared with the results of the HF/6‐31G** and Becke3LYP/6‐31G** calculations carried out for the tropolone dimer. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 73: 275–282, 1999     

Ab initio studies of electron acceptor-donor interactions with blue- and red-shifted hydrogen bonds.

The features of blue- and red-shifted electron acceptor-donor (ACH/B) hydrogen bonds have been compared by using quantum chemical calculations. The geometry, the interaction energy and the vibrational frequencies of both blue- (ACH=F3CH, Cl3CH with B=FCD3) and red-shifted (ACH=F3CH, Cl3CH with B=NH3 and ACH=CH3CCH with B=FCD3, NH3) complexes were obtained by using ab initio MP2(Full)/6-31+G(d,p) calculations with the a priori basis-set superposition error (BSSE) correction method. One-dimensional potential energy and dipole moment functions of the dimensionless normal coordinate Q1, corresponding to the CH stretching mode of ACH, have been compared for both types of complexes. Contributions of separate components of the interaction energy to the frequency shift and the effect of electron charge transfer were examined for a set of intermolecular distances by using the symmetry-adapted perturbation theory (SAPT) approach and natural bond orbitals (NBO) population analysis.     

Contra-thermodynamic behavior in intermolecular hydrogen transfer of alkylperoxy radicals.

Quantum chemical investigation of bimolecular hydrogen transfer involving alkylperoxy radicals, a key reaction family in the free-radical oxidation of hydrocarbons, was performed to establish structure-reactivity relationships. Eight different reactions were investigated featuring four different alkane substrates (methane, ethane, propane and isobutane) and two different alkylperoxy radicals (methylperoxy and iso-propylperoxy). Including forward and reverse pairs, sixteen different activation energies and enthalpies of reaction were used to formulate structure-reactivity relationships to describe this chemistry. We observed that the enthalpy of formation of loosely bound intermediate states has a strong inverse correlation with the overall heat of reaction and that this results in unique contra-thermodynamic behavior such that more exothermic reactions have higher activation barriers. A new structure-reactivity relationship was proposed that fits the calculated data extremely well: E(A)=E(o)+alphaDeltaH(rxn) where alpha=-0.10 for DeltaH(rxn)<0, and alpha=1.10 for DeltaH(rxn)>0 and E(o)=3.05 kcal mol(-1).