H_2O与NO,CN,OH自由基及负离子相互作用的CP研究

采用量子化学从头算方法在均衡 (Counterpoise)校正和非校正势能面上研究了H2 O与NO ,NO-,CN ,CN-,OH ,OH-之间的相互作用 .比较了CP 梯度优化和非校正梯度优化以及基组的选择对超分子结构和能量的影响 .研究表明 ,6 311++g 基组对于这些体系的研究有很高的效率 .这些自由基和负离子均能与H2 O形成强弱不同的氢键 .按相互作用的强弱次序依次为OH-,CN-,NO-,OH ,CN ,NO ,由相互作用能ΔECP,成键临界点电荷密度 ρ ,二阶稳定化相互作用能E( 2 )分析均得到同样结果 .CP 梯度优化和非校正梯度优化所得能量及BSSE相差不大     

甲醛与乙腈相互作用的理论研究

在HF/6-311G(d,p)、 MP2/6-311G(d,p)和B3LYP/6-311G(d,p)水平上,对H2CO和CH3CN以及设计的4种结构H2CO…CH3CN复合物等进行几何全优化和振动频率计算,排除振动频率为负值的非局域极小点结构,并对稳定的环状构型复合物结合能进行基组重叠误差校正和零点振动能校正.分子间相互作用的能量分解分析显示,静电能在H2CO...CH3CN相互作用能量中占主导地位,电荷转移能居第二位.     

叠氮化氢二聚体的分子间相互作用

通过ａｂ ｉｎｉｔｉｏＨＦ／６－３１Ｇ＊计算求得叠氮化氢二聚体（ＨＮ３）２势能面上四种优化结构型,经ＭＰ４ＳＤＴＱ电子相关校正和基组叠加误差２校正求得这些构型下的分子间相互作用能。结果表明,在四种优化构型中Ｎ３Ｈ．．．ＮＨＮ２最稳定,其分子间相互作用能为－１６．０７ＫＪ．ｍｏｌ＾－１。     

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.     

(CH2)2O, (CH2)2S与双卤分子间卤键的理论研究

运用量子化学密度泛函B3LYP方法, 采用6-311＋＋G(d,p)及aug-cc-pVDZ基组, 通过CP校正的几何梯度优化对(CH2)2O和(CH2)2S与双卤分子XY (XY＝Cl2, Br2, ClF, BrF, BrCl)形成的卤键复合物的几何构型、振动频率和相互作用能等进行了研究. 利用电子密度拓扑分析理论方法对卤键复合物的拓扑性质进行了分析研究, 探讨了该类分子间卤键的作用本质. 结果表明, (CH2)2O和(CH2)2S与双卤分子间的卤键介于共价键与离子键之间, 偏于静电作用成分为主. 形成卤键后, 双卤分子的键长增加, 振动频率减小, 原子积分性质发生改变. 卤键键长的变化、键能的强弱、键鞍点处的电子密度值与双卤分子的电负性有关.     

HCN(HNC)与NH3, H2O和HF分子间相互作用的理论研究

在MP2/aug-cc-pVTZ水平上, 对HCN(HNC)与NH3, H2O和HF分子间可能存在的氢键型复合物进行了全自由度能量梯度优化, 通过在相同水平上的频率验证分析发现了稳定的分子间相互作用形式是HCN(HNC)作为质子供体或作为质子受体形成的复合物. 基组重叠误差对总相互作用能的影响均小于3.34 kJ/mol. 通过自然键轨道(NBO)分析, 研究了单体和复合物中的原子电荷和电荷转移对分子间相互作用的影响. 对称性匹配微扰理论(SAPT, Symmetry Adapted Perturbation Theory)能量分解结果表明, 在分子间相互作用中, 静电作用与诱导作用占主导地位, 而诱导作用与复合物的电荷转移之间具有良好的正相关性.     

O2、CO2和H2O在UN（001）表面化学吸附的密度泛函理论研究

采用广义梯度近似GGA,修正Perdew—Burke—Ernzerhof交换-关联泛函,以及周期性切片模型对O2、CO2和H2O在UN（001）表面的化学吸附行为进行非白旋极化水平的密度泛函理论计算．在四个对称性化学位置条件下,对化学吸附能与分子和UN（001）表面之间距离的关系曲线进行优化．结果表明O2、CO2和H2O分子的最稳定吸附位置分别为桥式平行、空心平行和桥式H向上,化学吸附能分别为14．127、4．421和5．736kJ／mol．从吸附物UN（001）表面角度考虑,O2与UN（001）表面之间的相互作用最高,然后为CO2和H2O,表明这些相互作用与吸附物的晶体结构相关．O2化学吸附导致UN（001）表面的N原子向基体内部迁移,而CO2和H2O化学吸附对UN（001）表面分别具有中等和忽略不计的效应．计算获得的态密度显示了化学吸附分子S、P轨道和U6d、U5f轨道之间的电子电荷转移行为．     

N-甲硝胺二聚体分子间相互作用的理论研究

用ab initio方法，在HF／6－31G水平下求得N－甲硝胺二聚体势能面上3种优化构型，经MP4和MP2校正电子相关能及校正基组叠加误差（BSSE），求得分子间最大相互作用能为－18．81kJ.mol^-1，甲基内旋转对相互作用能影响较大，在标准状态下，由单体形成最稳定二聚体的自由能变化为10．02kJ.mol^-1，同时还讨论了温度对过程的影响。     

(N_2…CO)~+体系相互作用的密度泛函理论研究

在2种密度泛函方法和适宜基组水平上,对(N2…CO)+体系可能存在的相互作用复合物进行了全自由度能量梯度优化,发现势能面上存在2个能量极小点,均为共平面型。 比较了它们之间的相对稳定性,并对其进行了轨道成键分析,同时探讨了最稳定结构A的正则振动模式。 通过消除基函数引起的重叠误差(BSSE)和零点振动能(ZPVE)的校正,精确求算出复合物结构A、B的相互作用能DE分别为125.0和61.0 kJ/mol, 同等电子体(CO…CO)+相比,二者存在较大的差异。     

CO2与HCN,NH3,H2O分子络合物的从头计算研究

用ab initio能量梯度法(3-21G基组)分别优化CO_2与HCN、NH_3、H_2O_3个分子络合物的平衡几何构型。结果表明HCN、NH_3和H_2O中的N或O原子与CO_2中的C原子之间形成较弱的范德华键,三者的范德华键键长分别为0.2865、0.2775、0.2543nm,稳定化能分别为14.8、27.0、31.2kJ·mol~(-1),3个分子络合物的构型都呈T型,对3个分子络合物的稳定化能的能量分解研究表明它们的形成主要靠静电作用能。     

On the Importance of CP-corrected Gradient Optimization in the Study of Hydrogen Bonded Systems

Geometries, harmonic vibrational frequencies and interaction energies of the water-hydrogen sulfide dimer, hydrogen fluoride dimer and glycine zwitterion-water dimer were determined by the counterpoise-corrected (CP-corrected) gradient optimization that explicitly corrects for the basis set superpusition error (BSSE) and CP-uncorrected (normal) gradient opfimization respectively at the B3LYP and MP2 levels of theory, employing the popular Pople‘s standard 6-31G(d), 6-31G(d,p) and 6-311 G(d,p) basis sets in order to assess the importance of CP-corrected gradient optimiTation in the study of hydrogen bonded systems. The normal optimization of these three H-bonded systems obtained using these popular basis sets all yielded erratic results, whereas use of CP-corrected gradient optimization led to consistent results with those from larger basis sets. So this CP receipt becomes useful and necessary to correctly describe large systems, where the use of small basis sets may be necessary.     

Counterpoise-corrected potential energy surfaces of simple H-bonded systems

Geometries and stabilization energies of various simple H-bonded complexes (water dimer, hydrogen fluoride dimer, formamide dimer, formic acid dimer) have been determined by a gradient optimization that eliminates the basis set superposition error (BSSE) by the counterpoise (CP) method in each gradient cycle as well as by the standard gradient optimization. Both optimization methods lead to different potential energy surfaces (PES). The difference depends on the theoretical level used and is larger if correlation energy is considered. Intermolecular distances from the CP-corrected PES are consistently longer, and this difference might be significant (∼0.1 ?); also angular characteristics determined from both surfaces differ significantly. Different geometries were obtained even when passing to larger basis sets (aug-cc-pVDZ). The standard optimization procedure can result in a completely wrong structure. For example, the “quasi-linear” structure of the (HF)₂ (global minimum) does not exist at the standard MP2/ 6-31G** PES (where only cyclic structure was detected) and is found only at the CP-corrected PES. Stabilization energies obtained from the CP-corrected PES are always larger than these from the standard PES where the BSSE is added only a posteriori for the final optimized structure; both energies converge only when passing to a larger basis set (aug-cc-pVDZ). Received: 11 March 1998 / Accepted: 19 June 1998 / Published online: 4 September 1998 RID=" ID=" <E6>Acknowledgements.</E6> The project was supported by the Grant Agency of the Czech Republic (Grant No. 203/98/1166). RID=" ID=" <E5>Correspondence to</E5>: P. Hobza     

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     

Ab initio study on adsorption of hydrated Na+ and Cu+ cations on the Cu(111) surface

The interactions of Na+ and Cu+ cations with a Cu(111) surface in the presence and absence of water molecules were investigated using cluster models and ab initio methods. Adsorption in aqueous solution was modeled with one to five water molecules around the adsorbing cation. The Cu surface was described with Cu10 and Cu18 cluster models and the computational method was MP2/RECP/6-31+G. The effect of the basis set superposition error (BSSE) was taken into account with counterpoise (CP) correction, and the accuracy of HF-level results was examined. The interactions between Na+ and the Cu surface were found to be primarily electrostatic, and the energy differences among the different adsorption sites were small. The largest CP-corrected MP2 adsorption energy for the Cu18 cluster was -188 kJ/mol. When water molecules were added around it, Na+ receded from the Cu surface and finally was surrounded totally by the water molecules. The interactions between Cu+ and the Cu surface were dominated by orbital interactions, and Cu+ preferred to adsorb on sites where it could bind to more than one surface atom. The largest CP-corrected MP2 adsorption energy for the Cu18 cluster was -447 kJ/mol. Adding water molecules around it did not cause Cu+ to draw away from the surface, but instead the water molecules began to form hydrogen bonds with one another. The magnitude of BSSE was substantial in most cases. CP corrections did not, however, have a significant impact on the relative trends among the interaction energies.     

On the application of the counterpoise correction for the basis set superposition error in geometry optimization calculations of molecular systems: some inconsistent results

It is shown that the conjecture that the total energy for a given molecular or supermolecular system is affected by basis set superposition error (BSSE) leads to inconsistent results. While the calculations of interaction energies, dissociation energies, or energy barriers depend on the fragments (reactants, products) involved in their definitions and, consequently, are affected by BSSE, the total energies of molecular or supermolecular systems do not depend on any virtual fragment partition and are, therefore, BSSE free. Contribution to the Serafin Fraga Memorial Issue.     

Ab initio study on the adsorption of hydrated Na+ and Ag+ cations on a Ag(111) surface

The interactions of Na(+) and Ag(+) cations with an Ag(111) surface in the presence and absence of water molecules were investigated with cluster models and ab initio methods. The Ag surface was described with two-layered Ag(10) and Ag(18) cluster models, and MP2/RECP/6-31+G(d) was used as the computational method. The effect of the basis set superposition error (BSSE) was taken into account with counterpoise (CP) correction. The interactions between Na(+) and Ag(111) surface were found to be primarily electrostatic, and the interaction energies and equilibrium distances at the different adsorption sites were closely similar. The largest CP-corrected MP2 adsorption energy for Na(+) was -190.2 kJ/mol. Owing to the electrostatic nature of the Na(+)-Ag(111) interaction, Na(+) prefers to be completely surrounded by water molecules rather than directly adsorbed to the surface. Ag(+)-Ag(111) interactions were much stronger than Na(+)-Ag(111) interactions because they were dominated by orbital contributions. The largest CP-corrected MP2 adsorption energy for Ag(+) was -358.9 kJ/mol. Ag(+) prefers to adsorb on sites where it can bind to several surface atoms, and in the presence of water molecules, it remains adsorbed to the surface while the water molecules form hydrogen bonds with one another. The CP correction had an effect on the interaction energies but did not change the relative trends.     

尿素与鸟嘌呤相互作用的DFT研究

采用B3LYP／6—311＋G^＋方法对鸟嘌呤-尿素复合物氢键相互作朋体系进行了研究,并对该复合物的几何构型及结合能（BSSE）进行了计算．此外,采用从静电势导出原子净电荷的chelpg方法分析了体系中的电荷转移和利用分子中的原子理论（AIM）方法对相互作用的本质进行了分析．结果一共得到五个稳定的复合物构型,其中A5是最稳定的,结合能为-73．95kJ／mol．     

First-principles calculations of the electronic and geometrical structures of neutral [Sc,O,H] molecules and the monocations, ScOH(0,+) and HScO(0,+)

Using multireference configuration interaction and coupled-cluster methodologies, with quadruple-ζ basis sets, we explored the potential energy surfaces of the ground and excited states of the neutral and cationic triatomics [Sc,O,H](0,+). In its ground state, the neutral species is trapped into either a linear ScOH or a bent HScO conformation; these two minima are approximately equal in energy and separated by a barrier of 40 kcal/mol. The linear ScOH structure is preferred by the excited states of the neutral species and by all of the electronic states of the charged molecular systems that we studied in this work. Both ScOH and ScOH(+) present ionic characters, Sc(+)OH(-) and Sc(2+)OH(-), similar to those found for the isovalent ScF(0,+) species. The HScO(0,+) structures are obtained by covalent or dative interaction of hydrogen and ScO(0,+). For most of the minima located in this work, we calculated geometries, vibrational frequencies, binding energies, excitation energies, and dipole moments. Our numerical results agree well with existing experimental data.