pi-H...O hydrogen bonds: multicenter covalent pi-H interaction acts as the proton-donating system

The MP2 method and the Pople-style basis sets 6-311++G(d,p), 6-311++G(2df,2pd), and 6-311++G(3df,3pd) were used to perform calculations on H3O+...C2H2 and C2H3+...C2H2 complexes and related species. Hydrogen bonds existing for the analyzed complexes were investigated as well as related pi-H...O --> pi...H-O and pi-H...pi --> pi...H-pi proton-transfer processes. For some of the complexes analyzed the multicenter pi-H interaction possessing the properties of a covalent bond acts as a proton donor; more generally it is classified as the Lewis acid. The quantum theory of "atoms in molecules" (QTAIM) was also applied to deepen the nature of these interactions in terms of characteristics of bond critical points. The pi-H...O, O-H...pi, and pi-H...pi interactions analyzed here may be classified as hydrogen bonds since their characteristics are the same as or at least similar to those of typical hydrogen bonds. H...pi interactions are common in crystal structures of organic and organometallic compounds. The analyses performed here show a continuum of such interactions since there are H...pi contacts possessing the characteristics of weak intermolecular interactions on the one hand and pi-H multicenter covalent bonds on the other. Ab initio and QTAIM results support the latter statements.     

DFT-GIAO calculations of 19F NMR chemical shifts for perfluoro compounds

The (19)F NMR shieldings for 53 kinds of perfluoro compounds were calculated by the B3LYP-GIAO method using the 6-31G(d), 6-31+G(d), 6-31G(d,p), 6-31++G(d,p), 6-311G(d,p), 6-311++G(d,p), 6-311G(2d,2p), 6-311++G(2d,2p), 6-311++G(2df,2p), 6-311++G(3d,2p), and 6-311++G(3df,2p) basis sets. The diffuse functions markedly reduce the difference between the calculated and experimental chemical shifts. The calculations using the 6-31++G(d,p) basis set give the chemical shifts within 10 ppm deviations from experimental values except for the fluorine nuclei attached to an oxygen atom, a four- and a six-coordinated sulfur atom, and FC(CF(3))(2) attached to a sulfur atom.     

一种新型包含平面四配位碳二硼有机化合物的理论研究

采用B3LYP/6-311+G**方法, 研究了一种新型的包含平面四配位碳(ptC)二硼有机化合物C9B2H6的结构、稳定性和振动频率. 计算结果表明, C9B2H6结构的稳定性和两个硼原子的位置有很大关系, 硼原子起给予σ电子和接受π电子的作用. 在C9B2H6的15个异构体中, 最稳定的结构是具有C2v对称性的异构体(1,5), 在异构体(1,5)中, 两个硼原子位于同一个六元环中且与ptC相邻. 而且占据的π轨道说明异构体(1,5)具有10个π电子, 满足4n+2规则. 计算的核独立化学位移(NICS)值显示异构体(1,5)强的芳香性位于C9B2H6的两个三元环而不是两个六元环上.     

A microwave spectroscopic and quantum chemical study of 3-butyne-1-selenol (HSeCH2CH2C[triple bond]CH)

The microwave spectrum of 3-butyne-1-selenol has been studied by means of Stark-modulation microwave spectroscopy and quantum chemical calculations employing the B3LYP/aug-cc-pVTZ and MP2/6-311++G(3df,3pd) methods. Rotational transitions attributable to the H80SeCH2CH2C[triple bond]CH and H78SeCH2CH2C[triple bond]CH isotopologues of two conformers of this molecule were assigned. One of these conformers possesses an antiperiplanar arrangement for the atoms Se-C-C-C, while the other is synclinal and seems to be stabilized by the formation of a weak intramolecular hydrogen bond between the hydrogen atom of the selenol group and the pi electrons of the CC triple bond. The energy difference between these conformers was determined to be 0.2(5) kJ/mol by relative intensity measurements, and the hydrogen-bonded form was slightly lower in energy.     

BeH2与HX(X=F,Cl, Br,I)形成的二氢键复合物的结构特征与本质

对BeH2与HX(X=F, Cl, Br, I)形成的二氢键复合物的结构特征及本质进行了探讨. 在MP2/6-311++G(3d,3p)水平优化、频率验证, 得到复合物的分子结构, 用分子间距离及电子密度拓扑理论确认BeH2与卤化氢已形成了二氢键型复合物. 在MP2/6-311++G(3d, 3p)水平下进行基函数重叠误差(BSSE)校正后的结合能在-14.468 kJ·mol-1到-5.464 kJ·mol-1之间.用对称匹配微扰理论(SAPT)对复合物的结合能进行分解, 结果表明, BeH2…HX二氢键复合物中静电能对总吸引能的贡献都是最主要的, 但交换排斥能、诱导能、色散能对总结合能的贡献也很重要. 从BeH2…HF到BeH2…HI, 诱导能对总吸引能的贡献从37.8%逐渐减小到24.0%. 而色散能对总吸引能的贡献从BeH2…HF体系中的16.0%逐渐增加到BeH2…HI体系中的33.8%.     

Modern valence-bond description of chemical reaction mechanisms: the 1,3-dipolar addition of diazomethane to ethene

The electronic mechanism for the gas-phase concerted 1,3-dipolar cycloaddition of diazomethane (CH2N2) to ethene (C2H4) is described through spin-coupled (SC) calculations at a sequence of geometries along the intrinsic reaction coordinate obtained at the MP2/6-31G(d) level of theory. It is shown that the bonding rearrangements occurring during the course of this reaction follow a heterolytic pattern, characterized by the movement of three well-identifiable orbital pairs, which are initially responsible for the pi bond in ethene and the C-N pi bond and one of the N-N pi bonds in diazomethane and are retained throughout the entire reaction path from reactants to product. Taken together with our previous SC study of the electronic mechanism of the 1,3-dipolar cycloaddition of fulminic acid (HCNO) to ethyne (C2H2) (Theor. Chim. Acc. 1998, 100, 222), the results of the present work suggest strongly that most gas-phase concerted 1,3-dipolar cycloaddition reactions can be expected to follow a heterolytic mechanism of this type, which does not involve an aromatic transition state. The more conventional aspects of the gas-phase concerted 1,3-dipolar cycloaddition of diazomethane to ethene, including optimized transition structure geometry, electronic activation energy, activation barrier corrected for zero-point energies, standard enthalpy, entropy and Gibbs free energy of activation, have been calculated at the HF/6-31G(d), B3LYP/6-31G(d), MP2/6-31G(d), MP2/6-31G(d,p), QCISD/6-31G(d) and CCD/6-31G(d) levels of theory. We also report the CCD/6-311++G(2d, 2p)//CCD/6-31G(d), MP4(SDTQ)/6-311++G(2d,2p)//CCD/6-31G(d) and CCSD(T)/6-311++G(2d, 2p)//CCD/6-31G(d) electronic activation energies.     

A new scheme for determining the intramolecular seven-membered ring N-H...O=C hydrogen-bonding energies of glycine and alanine peptides

In this paper a new scheme was proposed to calculate the intramolecular hydrogen-bonding energies in peptides and was applied to calculate the intramolecular seven-membered ring N-H...O=C hydrogen-bonding energies of the glycine and alanine peptides. The density-functional theory B3LYP6-31G(d) and B3LYP6-311G(d,p) methods and the second-order Moller-Plesset perturbation theory MP26-31G(d) method were used to calculate the optimal geometries and frequencies of glycine and alanine peptides and related structures. MP26-311++G(d,p), MP26-311++G(3df,2p), and MP2/aug-cc-pVTZ methods were then used to evaluate the single-point energies. It was found that the B3LYP6-31G(d), MP26-31G(d), and B3LYP6-311G(d,p) methods yield almost similar structural parameters for the conformers of the glycine and alanine dipeptides. MP2/aug-cc-pVTZ predicts that the intramolecular seven-membered ring N-H...O=C hydrogen-bonding strength has a value of 5.54 kcal/mol in glycine dipeptide and 5.73 and 5.19 kcal/mol in alanine dipeptides, while the steric repulsive interactions of the seven-membered ring conformers are 4.13 kcal/mol in glycine dipeptide and 6.62 and 3.71 kcal/mol in alanine dipeptides. It was also found that MP26-311++G(3df,2p) gives as accurate intramolecular N-H...O=C hydrogen-bonding energies and steric repulsive interactions as the much more costly MP2/aug-cc-pVTZ does.     

An exploration of conformational search of leucine molecule and their vibrational spectra in gas phase using ab initio methods

An extensive exploration of the conformational space has been carried out to characterize all possible gas phase structures of leucine. A total of 324 unique trial structures for canonical leucine were generated by considering all possible combinations of single bond rotamers. All trial structures were optimized at the B3LYP/6-311G* level of the DFT method. A total of 77 unique and stationary canonical conformers were found. Further, 15 most stable conformers were reoptimized at B3LYP/6-311++G** level and their respective relative energies, vertical ionization energies, hydrogen bonding patterns, rotational constants and dipole moments were calculated. A single point energy calculations for leucine conformers have also been done at both B3LYP/6-311++G(2df, p) and MP2/6-311++G(2df, p) levels. The good agreement between our estimates of rotational constants for two most stable conformers and available experimental measurements supports the reliability of the B3LYP/6-311++G** level of theory for describing the conformational behavior of leucine molecule. The proton affinity and gas phase basicity were also determined. Using the statistical approach, conformational distributions at various temperatures have also been performed and analyzed. Vibrational spectra were also calculated. It is also observed that zwitterions of leucine are not stable in gas phase.     

Microwave spectrum of 3-butyne-1-thiol: evidence for intramolecular S-H...pi hydrogen bonding

The microwave spectrum of 3-butyne-1-thiol has been studied by means of Stark-modulation microwave spectroscopy and quantum-chemical calculations employing the B3LYP/6-311++G(3df,2pd), MP2/aug-cc-pVTZ, MP2/6-311++G(3df,2pd), and G3 methods. Rotational transitions attributable to two conformers of this molecule were assigned. One of these conformers possesses an antiperiplanar arrangement of the atoms S-C1-C2-C3, while the other is synclinal and stabilized by the formation of an intramolecular hydrogen bond between the H-atom of the thiol group and the pi-electrons of the C[triple bond]C triple bond. The energy difference between these conformers was estimated to be 1.7(4) kJ mol(-1) by relative intensity measurements, with the hydrogen-bonded conformer being lower in energy. The spectra of five vibrationally excited states of the synclinal conformer were observed, and an assignment of these states to particular vibrational modes was made with the aid of a density functional theory (DFT) calculation of the vibrational frequencies at the B3LYP/6-311++G(3df,2pd) level of theory.     

Thermochemical properties of molecules and cations of MgNnHm (n=1,2 and m=1–6): enthalpies of formation, proton affinities and ionization energies

Ab initio molecular orbital calculations are reported for small neutral molecules and cations containing magnesium, nitrogen and hydrogen. Structures have been optimized using gradient techniques at B3LYP/6-31+G(d) and at MP2(full)/6-311++G(d,p). Single-point calculations are reported at QCISD(T)(full)/6-311++G(2df,p) and at CCSD(T)(full)/6-311++G(2df,p) levels using geometries optimized at MP2(full)/6-311++G(d,p). Standard enthalpies of formation at 298 K have been calculated at these two higher levels of theory. Other thermochemical properties calculated include ionization energies and proton affinities. The binding enthalpies of ammonia to Mg⁺, MgNH₂⁺ and MgNH₃⁺ are also reported.     

NMR spectra, GIAO and charge density calculations of five-membered aromatic heterocycles

The B3LYP/6-31+G(d) molecular geometry optimized structures of 17 five-membered heterocycles were employed together with the gauge including atomic orbitals (GIAO) density functional theory (DFT) method at the B3LYP/6-31+G(d,p), B3LYP/6-311++G(d,p) and B3LYP/6-311+G(2d,p) levels of theory for the calculation of proton and carbon chemicals shifts and coupling constants. The method of geometry optimization for pyrrole (1), N-methylpyrrole (2) and thiophene (7) using the larger 6-311++G(d,p) basis sets at the B3LYP/6-31+G(d,p), B3LYP/6-311++G(d,p), B3LYP/6-31+G(2d,p) and B3LYP/cc-pVTZ levels of theory gave little difference between calculated and experimental values of coupling constants. In general, the (1)H and 13C chemical shifts for all compounds are in good agreement with theoretical calculations using the smaller 6-31 basis set. The values of nJHH(n=3, 4, 5) and rmnJ(CH)(n=1, 2, 3, 4) were predicted well using the larger 6-31+G(d,p) and 6-311++G(d,p) basis sets and at the B3LYP/6-31+G(d,p), B3LYP/6-311++G(d,p), B3LYP/6-31+G(2d,2p) levels of theory. The computed atomic charges [Mülliken; Natural Bond Orbital Analysis (NBO); Merz-Kollman (MK); CHELP and CHELPG] for the B3LYP/6-311++G(d,p) geometry optimized structures of 1-17 were used to explore correlations with the experimental proton and carbon chemical shifts.     

Ionized state of hydroperoxy radical-water hydrogen-bonded complex: (HO2-H2O)+

Ab initio molecular orbital calculations have been employed to characterize the structure and bonding of the (HO2-H2O)+ radical cation system. Geometry optimization of this system was carried out using unrestricted density functional theory in conjunction with the BHHLYP functional and 6-311++G(2df,2p) as well as 6-311++G(3df,3p) basis sets, the second-order M?ller-Plesset perturbation (MP2) method with the 6-311++G(3df,3p) basis set, and the couple cluster (CCSD) method with the aug-cc-pVTZ basis set. The effect of spin multiplicity on the stability of the (HO2-H2O)+ system has been studied and also compared with that of oxygen. The calculated results suggest a proton-transferred hydrogen bond between HO2 and H2O in H3O3+ wherein a proton is partially transferred to H2O producing the O2...H3O+ structure. The basis set superposition error and zero-point energy corrected results indicate that the H3O3+ system is energetically more stable in the triplet state; however, the singlet state of H3O3+ is more stable with respect to its dissociation into H3O+ and singlet O2. Since the resulting proton-transferred hydrogen-bonded complex (O2...H3O+) consists of weakly bound molecular oxygen, it might have important implications in various chemical processes and aquatic life systems.     

包含平面四配位和五配位碳原子的特殊硼碳化合物

采用密度泛函理论(DFT), 在B3LYP/6-311+G**水平上, 研究了三类包含平面四配位碳原子(ptC)和平面五配位碳原子(ppC)的硼碳化合物. 这三类新型化合物是由C3B2H4(包含ptC)、CB4H2(包含ptC)和CB5H2(包含ppC)三种稳定结构和—CHCH—单元连接起来而得到的. 在理论上探讨了这些新型的硼碳化合物的成键特征, 光谱性质以及芳香性. 研究结果表明: 包含ptC和ppC原子的能量最低的结构, 在不受对称面限制的条件下, 具有C2v对称性的顺式立体构型比具有反式平面构型的化合物稳定. 计算的核独立化学位移(NICS)显示, 这些新型化合物的三元环中心有强的芳香性. 计算最稳定硼碳化合物的ptC和ppC原子的Wiberg键指数(WBIs)表明ptC和ppC的成键遵循八隅规则.     

A combined density functional theory and coupled cluster method investigation of the structural properties and stabilities of radical CH(2)CP and its isomers

The doublet potential energy surface of radical system [C(2), H(2), P] is investigated at the UB3LYP/6-311++G(d,p) and UCCSD(T)/6-311++G(2df,2p) (single-point) levels. Eight chainlike and three-membered ring structures are located as energy minima connected by 10 interconversion transition states. At the final UCCSD(T)/6-311++G(2df,2p)//UB3LYP/6-311++G(d,p) level with zero-point vibrational energy correction, species CH(2)CP is found to be thermodynamically the most stable isomer followed by HCCPH, H-cCPC-H, cPCC-H(H), H-cCCP-H, cis-CC(H)PH, trans-CC(H)PH, and CCPH(2) at 11.01, 12.57, 40.07, 43.63, 50.25, 56.82, and 65.36 kcal/mol, respectively. The computed results indicate that the chainlike isomers CH(2)CP and HCCPH and cyclic radical H-cCPC-H possess considerable kinetic stability at extra low pressures and temperatures. Interestingly, radical CCPH(2), whose energy is the highest in all predicted CH(2)CP isomers, can be also regarded as a kinetically stable species with the smallest isomerization barrier of 22.26 kcal/mol at extra low pressures and temperatures. Therefore, considering higher kinetic stability, in addition to the microwave spectroscopy characterized isomer CH(2)CP in previous experiments, the species HCCPH, H-cCPC-H, and CCPH(2) should be considered as excellent candidates for possible experimental observation. Furthermore, the structural nature of stable radical isomers is discussed based on bonding characteristics, single electron spin distribution, and comparison with their analogues.     

Theoretical studies on dynamics and thermochemistry of the reactions CF(3)CHCl(2)+Cl-->CF(3)CCl(2)+HCl and CF(3)CHFCl+Cl-->CF(3)CFCl+HCl

A dual-level direct dynamics study has been carried out for the two hydrogen abstraction reactions CF(3)CHCl(2)+Cl and CF(3)CHFCl+Cl. The geometries and frequencies of the stationary points are optimized at the BHLYP/6-311G(d,p), B3LYP/6-311G(d,p), and MP2/6-31G(d) levels, respectively, with single-point calculations for energy at the BHLYP/6-311++G(3df,2p), G3(MP2), and QCISD(T)/6-311G(d,p) levels. The enthalpies of formation for the species CF(3)CHCl(2), CF(3)CHFCl, CF(3)CCl(2), and CF(3)CFCl are evaluated at higher levels. With the information of the potential energy surface at BHLYP/6-311++G(3df,2p)//6-311G(d,p) level, we employ canonical variational transition-state theory with small-curvature tunneling correction to calculate the rate constants. The agreement between theoretical and experimental rate constants is good in the measured temperature range 276-382 K. The effect of fluorine substitution on reactivity of the C-H bond is discussed.     

Inductive effects in radicals calculated from DFT energies; substituted bicyclo[2.2.2]octan-1-yloxy radicals

Energies of a series of 4-substituted 1-oxybicyclo[2.2.2]octan-1-yloxy radicals with 18 various substituents were calculated within the framework of the DFT theory at the levels UB3LYP/6-311+G(d,p)//UB3LYP/6-311+G(d,p) and UB3LYP/6-311++G(2df,p)//UB3LYP/6-311+G(d,p) and compared with similar series of the parent alcohols, their deprotonated and protonated forms calculated at the levels B3LYP/6-311+G(d,p)//B3LYP/6-311+G(d,p) and B3LYP/6-311++G(2df,p)//B3LYP/6-311+G(d,p). The two levels are of the same performance and both are sufficient for molecules of this type according to comparison with scarce experimental gas-phase acidities and basicities. The substituent effects were analyzed in terms of isodesmic equations. In addition to strong dependence on the substituent inductive effect, a slight dependence on the electronegativity of the first atom of the substituent was proven in certain cases. In all aspects, there is no qualitative difference between the effects on radicals and on similar closed shell species. Radicals behave as slightly electron deficient; the substituent effect is weaker than that on the ions but stronger than on neutral molecules.     

An ab initio correlated study of the potential energy surface for the HOBr.H2O complex

The potential energy surface (PES) for the HOBr.H(2)O complex has been investigated using second- and fourth-order M?ller-Plesset perturbation theory (MP2, MP4) and coupled cluster theory with single and doubles excitations (CCSD), and a perturbative approximation of triple excitations (CCSD-T), correlated ab initio levels of theory employing basis sets of triple zeta quality with polarization and diffuse functions up to the 6-311++G(3dp,3df ) standard Pople's basis set. Six stationary points being three minima, two first-order transition state (TS) structures and one second-order TS were located on the PES. The global minimum syn and the anti equilibrium structure are virtually degenerated [DeltaE(ele-nuc) approximately 0.3 kcal mol(-1), CCSD-T/6-311++G(3df,3pd) value], with the third minima being approximately 4 kcal mol(-1) away. IRC analysis was performed to confirm the correct connectivity of the two first-order TS structures. The CCSD-T/6-311++G(3df,3pd)//MP2/6-311G(d,p) barrier for the syn<-->anti interconversion is 0.3 kcal mol(-1), indicating that a mixture of the syn and anti forms of the HOBr.H(2)O complex is likely to exist.     

Systematic ab initio studies of the conformers and conformational distribution of gas-phase tyrosine

A full structural assignment of the conformers of gaseous tyrosine is presented. A total of 1296 unique trial structures were generated by allowing for all combinations of internal single-bond rotamers and optimized at the B3LYP6-311G* level of theory and then subjected to further optimization at the B3LYP6-311++G** level. A total of 76 conformers are found and their dipole moments, rotational constants, and harmonic frequencies are determined. Accurate relative energies are given at the MP26-311G(2df,p)B3LYP6-311++G** level of theory. Characteristic H-bonding types are classified and listed for all the conformers. The four most stable conformers display an intramolecular H bond, COOH...NH(2), and an additional H-bonding interaction between the amino group and pi electron of the aromatic ring. The results further confirm that the global minimum conformations of the aromatic amino acids have the same H-bonding type. Combined with statistical mechanics principles, conformational distributions at various temperatures are computed and the temperatures with which the theoretical results match that of experiments are indicated.     

Matrix isolation and ab initio study of the hydrogen-bonded H2O2-CO complex

The structure, energetics, and infrared spectrum of the H2O2-CO complex have been studied computationally with the use of ab initio calculations and experimentally by FTIR matrix isolation techniques. Computations predict two stable conformations for the H2O2-CO complex, both of which show almost linear hydrogen bonds between the subunits. The carbon-attached HOOH-CO complex is the lower-energy form, and it has an interaction energy of -9.0 kJmol(-1) at the CCSD(T)/6-311++G(3df,3pd)// MP2/6-311++G(3df,3pd) level. The higher-energy form, HOOH-OC, has an interaction energy of 4.7 kJmol(-1) at the same level of theory. Experimentally, only the lower-energy form, HOOH-CO, was observed in Ar, Kr, and Xe matrices, and the hydrogen bonding results in substantial perturbations of the observed vibrational modes of both complex subunits. UV photolysis of the complex species primarily produces a complex between water and carbon dioxide, but minor amounts of HCO and trans-HOCO were found as well.