C_4H_4Y(Y=O,S,Se)与BX_3(X=H,F,Cl)作用的计算化学研究

采用量子化学的密度泛函B3LYP和二阶微扰MP2(full)方法对C4H4Y(Y=O,S,Se)与BX3(X=H,F,Cl)形成的电子授受型复合物进行了研究,所得18个复合物的构型包括BX3位于C=C双键上方的π-p作用型和B与O,S,Se直接作用的n-p作用型.体系C4H4Y-BH3以n-p作用型较为稳定,体系C4H4Y-BF3,C4H4Y-BCl3的π-p和n-p作用型复合物稳定性相当.对各复合物的几何构型、振动频率和自然键轨道分析表明,复合物的形成过程中均存在几何构型的改变、电荷的转移和振动频率的变化,它们的变化规律与复合物稳定性的变化规律基本一致,即按H,F,Cl的顺序依次降低.     

Study of pi halogen bonds in complexes C2H(4-n)Fn-ClF (n = 0-2)

The pi-halogen bond may be considered, in a broad sense, essentially a pi-hydrogen bond. Using the counterpoise-corrected potential energy surface method (interaction energy optimization), the stationary structures of the C2H(4-n)Fn-ClF (n = 0-2) complexes with all real frequencies have been obtained at the MP2/aug-cc-pVDZ level. For C2H(4-n)Fn-ClF (n = 0-2), the pi-halogen bond has a long distance and is elongated by the F substituent effect. The pi-halogen bond length order is 2.661 A for C2H4-ClF < 2.745 A for C2H3F-ClF < 2.766 A for g-C2H2F2-ClF < 2.8076 A for trans-C2H2F2-ClF < 2.8079 A for cis-C2H2F2-ClF. For three complexes C2H3F-ClF, g-C2H2F2-ClF, and cis-C2H2F2-ClF, the pi-halogen bonds are further shifted and sloped by the F substituent effect. The F substituent effect reduces also the interaction energy of the pi-halogen bond. The interaction energies are respectively -3.7 for C2H4-ClF, -2.8 for C2H3F-ClF, -2.3 for g-C2H2F2-ClF, -1.9 for cis-C2H2F2-ClF, and -1.8 kcal/mol for trans-C2H2F2-ClF, at the CCSD(T)/aug-cc-pVDZ level. The electron correlation contribution of the interaction energy is large for C2H(4-n)Fn-ClF (n = 0-2), which shows that the stabilities of the pi-halogen bond systems results primarily from the dispersion interaction. In the double F substituent systems, the interaction energy of the pi-halogen bond structure with a longer interaction distance is larger than that of the corresponding pi-hydrogen bond structure with a shorter interaction distance. This may be because there are the large electron correlation contributions of the interaction energy, and a secondary interaction between lone pairs of Cl atom and some atoms (H, C) with positive charges in the pi-halogen bond structure.     

Ring complexes of S-nitrosothiols with CU+: a density functional theory study

The density functional theory (DFT) method B3P86/6-311+G(2df,p) has been employed to investigate the complexes formed upon interaction of Cu(+) with nitrosylated cysteine (CysNO) and its decarboxylated (H(2)NCH(2)CH(2)SNO) and deaminated (HOOCCH(2)CH(2)SNO) derivatives. Optimized structures, relative enthalpies and relative free energies have been calculated and compared. In addition, the effects of binding an H(2)O molecule to the Cu(+) centre in the resulting complexes have also been considered. It is found that the most stable complexes are formed when Cu(+) coordinates to the S-nitrosothiol via S of the SNO group. This results in dramatic lengthenings of the SN bond with concomitant shortening of the NO bond. In contrast, when Cu(+) coordinates via the nitrogen of the SNO group, a shortening of the SN bond with lengthening of the NO bond is observed. These effects are tempered by the electron donating ability of other functional groups also coordinated with the Cu(+) centre in the complexes and on the coordination state of the Cu(+) ion.     

Photodissociation of diiodomethane in acetonitrile solution and fragment recombination into iso-diiodomethane studied with ab initio molecular dynamics simulations

Series of hydrates of the most stable glycine-H+/2H2+ in the gas phase are presented at the B3LYP level. The results show that only the amino hydrogens and hydroxyl hydrogens can be monohydrated for the glycine-H+, and the amino hydrogens are preferred. The H6(O4) of glycine-2H2+ is the best site for a water molecule to attach, i.e., the corresponding hydrate is the most stable one among its isomers. Calculations reveal that the binding energies of hydrated hydrogens decrease relative to their counterparts in the isolated glycine-H+/2H2+ complexes and they are positive values and without proton transfer except those of monohydrated glycine-2H2+ complexes with the combination modes of H3O+...(glycine-H+). The complex H3O+...(glycine-H+) is formed by the combination of a H2O molecule and one hydroxyl-site proton of glycine-2H2+, and with the proton transfer to H2O. Here the interaction between the proton of H3O+ and the glycine-H+ mainly depends on an electronic one instead of an initial covalent one of the isolated glycine-2H2+. The generation of the bond between the H3O+ and the glycine-H+ makes the energy of the complex higher than the energy sum of its two separated species (or two reactants of the complex), just like the case of M+...(glycine-H+) bond (M = Li,Na). The observation can explain satisfactorily why the combinations of both a proton and an alkali ion or two alkali ions to a glycine molecule can make the corresponding complex hold reservation energy bond(s), while the combination of two protons and a glycine in our previous work cannot [H. Ai et al., J. Chem. Phys. 117, 7593 (2002)]. For the glycine-2H2+, monohydration at the any site of its amino hydrogens can make the binding strength of any other neighboring proton (hydrogens) stronger relative to its counterpart in the isolated glycine-2H2+. Further hydration, especially at the site of either of hydroxyl hydrogens, would disfavor the reservation energy of the system.     

A challenge to chemical intuition: donor-acceptor interactions in H3B-L and H2B+-L (L=CO; EC5H5, E=N-Bi)

The equilibrium geometries and bond energies of the complexes H(3)B-L and H(2)B(+)-L (L=CO; EC(5)H(5): E=N, P, As, Sb, Bi) have been calculated at the BP86/TZ2P level of theory. The nature of the donor-acceptor bonds was investigated by energy decomposition analysis (EDA). The bond strengths of H(3)B-L have the order CO>N>P>As>Sb>Bi. The calculated values are between D(e)=37.1 kcal mol(-1) for H(3)B-CO and D(e)=6.9 kcal mol(-1) for H(3)B-BiC(5)H(5). The bond dissociation energies of the cations H(2)B(+)-CO and H(2)B(+)-EC(5)H(5) are larger than for H(3)B--L, particularly for complexes of the heterobenzene ligands. The calculated values are between D(e)=51.9 kcal mol(-1) for H(2)B(+)-CO and D(e)=122.1 kcal mol(-1) for H(2)B(+)-NC(5)H(5). The trend of the BDE of H(2)B(+)-CO and H(2)B(+)-EC(5)H(5) is N>P>As>Sb>Bi>CO. A surprising result is found for H(2)B(+)-CO, which has a significantly stronger and yet substantially longer bond than H(3)B-CO. The reason for the longer but stronger bond in H(2)B(+)-CO compared with that in H(3)B-CO comes mainly from the change in electrostatic attraction and pi bonding at shorter distances, which increases more in the neutral system than in the cation, and to a lesser extent from the deformation energy of the fragments. The H(2)B(+)<--NC(5)H(5) pi( perpendicular) donation plays an important role for the stronger interactions at shorter distances compared with those in H(3)B-NC(5)H(5). The attractive interaction in H(2)B(+)--CO further increases at bond lengths that are shorter than the equilibrium value, but this is compensated by the energy which is necessary to deform BH(2) (+) from its linear equilibrium geometry to the bent form in the complex. The EDA shows that the contributions of the orbital interactions to the donor-acceptor bonds are always larger than the classical electrostatic contributions, but the latter term plays an important role for the trend in bond strength. The largest contributions to the orbital interactions come from the sigma orbitals. The EDA calculations suggest that heterobenzene ligands may become moderately strong pi donors in complexes with strong Lewis acids, while CO is only a weak pi donor. The much stronger interaction energies in H(2)B(+)-EC(5)H(5) compared with those in H(3)B-EC(5)H(5) are caused by the significantly larger contribution of the pi(perpendicular) orbitals in H(2)B(+)-EC(5)H(5) and by the increase of the binding interactions of the sigma+pi( parallel) orbitals.     

1,2,3-三氮杂苯-水复合物氢键相互作用

Density functional theory B3LYP method with 6-31++G** basis was used to optimize the geometries of the ground states for 1,2,3-triazine-(H2O)n (n=1,2,3) complexes. All calculations indicate that the 1,2,3-triazine-water complexes in the ground states have strong hydrogen-bonding interaction, and the complex having a N…H-O hydrogen bond and a chain of water molecules which is terminated by a O…H-C hydrogen bond is the most stable. The H-O stretching modes of complexes are red-shifted relative to that of the monomer. In addition, the Natural bond orbit (NBO) analysis indicates that the intermolecular charge transfer between 1,2,3-triazine and water is 0.0222e, 0.0261e and 0.0273e for the most stable 1:1, 1:2 and 1:3 complexes, respectively. The first singlet (n, π*) vertical excitation energy of the monomer 1,2,3-triazine and the hydrogen-bonding complexes of 1,2,3-triazine-(H2O)n were investigated by time-dependent density functional theory.     

Theoretical Studies on the Interactions of Cations with Diazine

1 INTRODUCTION Interaction between cations and π electron systems is a kind of common and important non-covalent inter- action[1～21]. It could be observed in many systems, such as gas ion-molecule complexes and biological macromolecular proteins. Especially, in biological macromolecular systems, this interaction is signi- ficant for revealing the structures and functions of proteins or disclosing the atomic essence of protein- ligand effect. Interaction between benzene and metal ions h…     

HOCl…HCOCl复合物的结构和电子性质

在DFT-B3LYP/6-311++G**水平上求得HOCl+HCOCl复合物势能面上的四种稳定构型(S1,S2,S3和S4).其中,在复合物S1和S3中,HOCl单体的5H原子作为质子供体,与HCOCl单体中作为质子受体的10原子相互作用,形成红移氢键复合物;在复合物S4中,HOCl单体的7Cl原子作为质子供体,与HCOCl单体中作为质子受体的IO原子相互作用,形成红移卤键复合物;而在复合物S2中,同时存在2C-3H…6O蓝移氢键和4Cl…5O相互作用.在MP2/6-311++G**水平上计算的单体间的相互作用能考虑了基组重叠误差(BSSE)和零点振动能(ZPVE)校正,其值在-5.05与-14.76 kJ·mol-1之间.采用自然键轨道理论(NBO)对两种单体间相互作用的本质进行了考查,并通过分子中原子理论(AIM)分析了复合物中氢键和卤键键鞍点处的电子密度拓扑性质.     

Co-crystals of ethenzamide with 2-nitrobenzoic acid - Conformational analysis,MD simulations and DFT investigations

In crystal engineering and pharmaceutical chemistry, co-crystals have a wide range of applications. Ethenzamide (EA) is found to form co-crystal with 2-nitrobenzoic acid (NBA). Geometry properties like stability energy, charge distribution, bond length, electronic properties and thermodynamic characteristics have been analyzed. The C–H?O hydrogen bond involves C–H of EA and oxygen of NBA. Configuration with the angle, N3–C4–C5–C6 gives the lowest energy conformation. Partition coefficient value suggests that EA-NBA has pharmaceutics behavior. RMSD values show the simulation's relative stability and the complexes, remained stable throughout.     

Interaction between NH2NO and H2O2: A quantum chemistry study

The H‐bonded complexes formed from interaction between NH₂NO (NA) and H₂O₂ (HP) have been investigated by using B3LYP and MP2 methods with a wide range of basis sets. We found six H‐bonded complexes in which three of them have cyclic structure. Calculations carried out at various levels show that the seven‐membered cyclic structure with O···HO and O···HN hydrogen bonding interactions is the most stable complex. The large binding energy obtained for A1 complex probably results from a more linear arrangement of the O···H N and O H···OH‐bonds in the seven‐membered structure A1. The natural bond orbital (NBO) analysis and the Bader's quantum theory of atoms in molecules have been used to elucidate the interaction characteristics of the NA‐HP complexes. The NBO results reveal that the charge transfer energy corresponds to the H‐bond interactions for A1 complex is grater than other complexes. The electrostatic nature of H‐bond interactions is predicted from QTAIM analysis. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

DFT study of H--H activation by Cp(2) LnH d(0) complexes.

The energy required to activate the H--H bond in the entire series of Cp(2)LnH complexes has been calculated by DFT (B3PW91) methods. The activation energies have been calculated to vary from 0.5 to 8.0 kcal x mol(-1), indicating an overall facile reaction. The electronegativity of the lanthanide in its most stable oxidation state is suggested to be a leading factor for interpreting the trends in activation energy. The geometry of the transition state is best viewed as an almost linear H(3)(-) ligand with short H--H distances and strong M--H interaction, through the wingtip H centers, with Ln. The exchange reaction is thus established to be a sigma bond metathesis reaction.     

Cooperativity between two types of hydrogen bond in H(3)C-HCN-HCN and H(3)C-HNC-HNC complexes

Hydrogen-bonded clusters, H(3)C-HCN, HCN-HCN, H(3)C-HCN-HCN, H(3)C-HNC, HNC-HNC, and H(3)C-HNC-HNC, have been studied by using ab initio calculations. The optimized structures, harmonic vibrational frequencies, and interaction energies are calculated at the MP2 level with aug-cc-pVTZ basis set. The cooperative effects in the properties of these complexes are investigated quantitatively. A cooperativity contribution of around 10% relative to the total interaction energy was found in the H(3)C-HCN-HCN complex. In the case of H(3)C-HNC-HNC complex, the cooperativity contribution is about 15%. The cooperativity contribution in the single-electron hydrogen bond is larger than that in the hydrogen bond of HCN-HCN and HNC-HNC complexes. NMR chemical shifts, charge transfers, and topological parameters also support such conclusions.     

CH3SH…HOO开壳型氢键复合物的结构及其电子密度拓扑性质

在DFT-B3LYP/6-311++G**水平下求得CH3SH…HOO复合物势能面上的稳定构型. 计算结果表明, 在HOO以其O8—H7作为质子供体与CH3SH分子中的S5原子为质子受体形成的氢键复合物1和2中, O8—H7明显被“拉长”, 且其伸缩振动频率发生显著的红移, 红移值分别为330.1和320.4 cm-1; 在CH3SH分子以其S5—H6作为质子供体与HOO的端基O9原子为质子受体形成的氢键复合物3和4中, 也存在类似的情况, 但S5—H6伸缩振动频率红移不大. 经MP2/6-311++G**水平计算的4种复合物含BSSE校正的相互作用能分别为-20.81, -20.10, -4.46和-4.52 kJ/mol. 自然键轨道理论(NBO)分析表明, 在CH3SH…HOO复合物1和2中, 引起H7—O8键长增加的因素包括两种电荷转移, 即孤对电子n1(S5)→σ*(H7—O8)和孤对电子n2(S5)→σ*(H7—O8), 其中后者为主要作用. 在复合物3和4中也有相似的电荷转移情况, 但轨道间的相互作用要弱一些. AIM理论分析结果表明, 4个复合物中的S5…H7间和O9…H6间都存在键鞍点, 且其Laplacian量▽2ρ(r)都是很小的正值, 说明这种相互作用介于共价键和离子键之间, 偏静电作用为主.     

1,2,4-三氮杂苯-(H2O)n复合物氢键相互作用的密度泛函理论研究

用密度泛函理论方法在B3LYP/6-31++G**水平上对1,2,4-三氮杂苯-(H₂O)_n (n＝1, 2, 3)氢键复合物的基态进行了结构优化和能量计算, 结果表明复合物之间存在较强的氢键作用, 所有稳定复合物结构中形成一个N…H—O氢键并终止于弱O…H—C氢键的氢键水链的构型最稳定. 同时, 用含时密度泛函理论方法(TD-DFT)在TD-B3LYP/6-31++G**水平上计算了1,2,4-三氮杂苯单体及其氢键复合物的单重态第一¹(n, π^*)垂直激发能.     

Does the molecular structure of CaH2 affect the dihydrogen bonding in CaH2 … HY (Y = CH3, C2H3, C2H, CN, and NC) complexes? A quantum chemistry study using MP2 and B3LYP methods

Second-order M ller-Plesset(MP2) and density functional theory(DFT) calculations have been carried out in order to investigate the structures and properties of dihydrogen-bonded CaH 2 HY(Y = CH 3,C 2 H 3,C 2 H,CN,and NC) complexes.Our calculations revealed two possible structures for CaH 2 in CaH 2 HY complexes:linear(I) and bent(II).The bond lengths,interaction energies,and strengths for H H interactions obtained by both MP2 and B3LYP methods are quite close to each other.It was found that the interaction energy decreases with increasing electron density at the Ca-H bond critical point.Atom-in-molecule(AIM) results show that for all of Ca-H H-Y interactions considered here,the Laplacian of the electron density at the H H bond critical point is positive,indicating the electrostatic nature of these Ca-H H-Y dihydrogen bonded systems.     

Highly stable neutral and positively charged dicarbollide sandwich complexes

Novel sandwich metallacarboranes commo-[3,3'-Ni(8-SMe2-1,2-C2B9H10)2] (1), commo-[3,3'-Co(8-SMe2-1,2-C2B9H10)2]+ (2+), commo-[3,3'-Ru(8-SMe2-1,2-C2B9H10)2] (4) and commo-[3,3'-Fe(8-SMe2-1,2-C2B9H10)2] (5) have been prepared by reaction of [10-SMe2-7,8-nido-C2B9H10]- with NiCl2 x 6 H2O, CoCl2, [RuCl2(dmso)4] and [FeCl2(dppe)], respectively. Reduction of 2+ with metallic Zn leads to the neutral and isolable complex commo-[3,3'-Co(8-SMe2-1,2-C2B9H10)2] (3). Theoretical calculations using the ZINDO/1 semiempirical method show three energy minima for complexes 1-3 and 5 that agree with the presence of three different rotamers in solution at low temperature, while four relative energy minima have been found for 4. The calculated rotational energy barriers for complexes 1-5 have been found in the range 5.2+/-0.2 and 11.5+/-0.2 kcal mol(-1). These values are in agreement with the experimental data calculated for complexes 2+ and 5. Only one rotamer is found in the X-ray crystal structure of complexes 1-3, while two are observed for 4. Neutral complexes 1, 3 and 4 exhibit a gauche conformation, whereas a cisoid conformation is found for the 2+ ion. Rotamers evident from X-ray diffraction studies are in agreement with the global energy minimum calculated by the ZINDO/1 method. The electrochemical studies conducted on 1, 3, 4 and 5 support the proposal that the charge-compensated ligand [10-SMe2-7,8-nido-C2B9H10]- stabilises lower oxidation states in metals than the dianionic [7,8-nido-C2B9H11]2- and even the [C5H5]- ligands.     

Sigma bond activation by cooperative interaction with s2 atoms: B+ + nCH4, n = 1, 2

Ab initio investigations at the MP2 and CCSD(T) level with augmented double and triple zeta basis sets have identified various stationary points on the B+/nCH4, n = 1, 2 hypersurfaces. The electrostatic complexes show a strong variation in the sequential binding energy with De for the loss of one CH4 molecule calculated to be 16.5 and 6.8 kcal mol-1 for the n = 1 and n = 2 complexes, respectively. The covalent molecular ion, CH3BH+, is found to have the expected C3 nu geometry and to be strongly bound by 84.0 kcal mol-1 with respect to B+ + CH4. The interaction of CH4 with CH3BH+ is qualitatively very similar to the interaction of CH4 with HBH+, however, the binding is only about 50% as strong due to the electron donating characteristic of the methyl group. Of particular interest are the insertion transition states which adopt geometries allowing the B+ ion to interact with multiple sigma bonds. In the n = 1 case, the interaction with two CH bonds lowers the insertion activation energy by about 25 kcal mol-1 from that expected for a mechanism involving only one sigma bond. For n = 2, B+ interacts with two CH sigma bonds from one CH4 and one CH sigma bond from the other CH4 leading to an additional activation energy decrease of about 15.7 kcal mol-1 relative to B+ + nCH4.     

Theoretical analysis of the hydrogen bond of imidazolium C(2)-H with anions

The intermolecular interaction energies of ion pairs of imidazolium-based ionic liquids were studied by MP2/6-311G level ab initio calculations. Although the hydrogen bond between the C(2) hydrogen atom of an imidazolium cation and anion has been regarded as an important interaction in controlling the structures and physical properties of ionic liquids as in the cases of conventional hydrogen bonds, the calculations show that the nature of the C(2)-H...X interaction is considerably different from that of conventional hydrogen bonds. The interaction energies of the imidazolium cation with neighboring anions in the four crystals of ionic liquids were calculated. The size of the interaction is determined mainly by the distance between the imidazolium ring and anion. The calculated interaction energy is nearly inversely proportional to the distance, which shows that the charge-charge interaction is the dominant interaction in the attraction. The orientation of the anion relative to the C(2)-H bond does not greatly affect the size of the interaction energy. Calculated interaction energy potentials of 1,3-dimethylimidazolium tetrafluoroborate ([dmim][BF(4)]) complexes show that the C(2)-H bond does not prefer to point toward a fluorine atom of the BF(4). This shows that the C(2)-H...X hydrogen bond is not essential for the attraction.     

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.     

C4H4Y (Y＝O, S, Se)与BX3 (X＝H, F, Cl)作用的计算化学研究

采用量子化学的密度泛函B3LYP和二阶微扰MP2(full)方法对C₄H₄Y (Y＝O, S, Se)与BX₃ (X＝H, F, Cl)形成的电子授受型复合物进行了研究, 所得18个复合物的构型包括BX₃位于C＝C双键上方的π-p作用型和B与O, S, Se直接作用的n-p作用型. 体系C₄H₄Y-BH₃以n-p作用型较为稳定, 体系C₄H₄Y-BF₃, C₄H₄Y-BCl₃的π-p和n-p作用型复合物稳定性相当. 对各复合物的几何构型、振动频率和自然键轨道分析表明, 复合物的形成过程中均存在几何构型的改变、电荷的转移和振动频率的变化, 它们的变化规律与复合物稳定性的变化规律基本一致, 即按H, F, Cl的顺序依次降低.