Theoretical study of the N-H…O red-shifted and blue-shifted hydrogen bonds

Theoretical calculations are performed to study the nature of the hydrogen bonds in complexes HCHO…HNO, HCOOH…HNO, HCHO…NH3, HCOOH…NH3, HCHO…NH2F and HCOOH…NH2F. The geometric structures and vibrational frequencies of these six complexes at the MP2/6-31+G(d,p), MP2/6-311++G(d,p), B3LYP/6-31+G(d,p) and B3LYP/6-311++G(d,p) levels are calculated by standard and counterpoise-corrected methods, respectively. The results indicate that in complexes HCHO…HNO and HCOOH…HNO the N-H bond is strongly contracted and N-H…O blue-shifted hydrogen bonds are observed. While in complexes HCHO…NH3, HCOOH…NH3, HCHO…NH2F and HCOOH…NH2F, the N-H bond is elongated and N-H…O red-shifted hydrogen bonds are found. From the natural bond orbital analysis it can be seen that the X-H bond length in the X-H…Y hydrogen bond is controlled by a balance of four main factors in the opposite directions: hyperconjugation, electron density redistribution, rehybridization and structural reorganization. Among them hyperconjugation has the effect of elongating the X-H bond, and the other three factors belong to the bond shortening effects. In complexes HCHO…HNO and HCOOH…HNO, the shortening effects dominate which lead to the blue shift of the N-H stretching frequencies. In complexes HCHO…NH3, HCOOH…NH3, HCHO…NH2F and HCOOH…NH2F where elongating effects are dominant, the N-H…O hydrogen bonds are red-shifted.     

Intramolecular hydrogen bond in the push–pull CF3-aminoenones: DFT and FTIR study,NBO analysis

Postulated conformers of trifluoromethylated β-aminoenones stabilized by intramolecular NH?O and N?HO bonds were studied by IR and NMR spectroscopy and evaluated with quantum chemical calculations (B3LYP/6-311+G(d,p), MP2/6-311+G(d,p)//B3LYP/6-311+G(d,p) and MP2/6-31G(d,p)) and NBO analysis. The influence of the nature of EWG, substituents at the nitrogen atom and double bond, and of orbital interactions of heteroatoms and double bonds in these structures on the proton affinity of basic and acid centers, strength of hydrogen bonds, and the energy of tautomeric transfers is discussed. The theoretical results agree satisfactorily with the experimental observations.     

优化几何构型对高级别从头算能量的影响

对《ＣＲＣ物理与化学手册》（第７７版）中第三周期以前的无机双原子分子,当其理论优化构型的相对误差大于２％时,分别在实验构型和最大偏差的理论构型下,计算了ＱＣＩＳＤ（Ｔ）／６－３１１＋Ｇ（３ｄｆ,２ｐ）能量并作了比较。结果表明,大多数能量的差别在４．２ｋＪ．ｍｏｌ＾－１以内。由此说明,目前一般采用的构型优化理论方法,多数情况下不至于明显影响单点高级别从头算的计算精度。同时还发现,Ｇ２（ＱＣＩ）的高级     

HArF和HNO二聚体相互作用氢键的理论研究

The hydrogen bonding interaction of 1:1 dimer formed between HNO and HArF molecule has been completely investigated in the present study using Second-order M?ller-Plesset Perturbation (MP2) method in conjunction with 6-311+G**, 6-311++G** and 6-311++G(2d,2p) basis sets. The standard and CP-corrected calculations have been employed to determine the equilibrium structures, the vibrational frequencies and interaction energies. The interaction energies of the dimers were also calculated at G2MP2 level. Two stable structures are found as the minima. Dimer I(H···F)is a five-membered cyclic hydrogen bonded structure and is more stable than the Dimer II(H···O). The blue-shifted N-H···F hydrogen bond is confirmed with standard and CP-corrected calculations by the MP2 and DFT methods in conjunction with different basis sets. The results obtained at MP2 in conjunction with different basis sets show there is a red-shifted hydrogen bond (Ar-H···O) in the Dimer II(H···O). The topological and electronic properties, the origin of red- and blue-shifted hydrogen bonds were investigated at MP2/6-311++G(2d,2p) with CP corrected calculations. From the NBO analysis, the reasonable explanations for the red- and blue-shifted hydrogen bonds were proposed.     

Neutron spectroscopic study of hydrogen bonding dynamics in L-serine

Inelastic incoherent neutron scattering (IINS) spectra were obtained at 10 K for normal and deuterated L-serine. The geometry of L-serine molecule was optimized for the zwitterion form using ab initio HF, MP2 and DFT (B3LYP) levels with 6-31G* and 6-311 + +G4** basis sets. The theoretical frequencies of normal and d4-L-serine were compared with IINS spectra. Normal coordinate analysis and band assignments based on ab initio calculations and experimental data were presented. IINS frequencies due to the out-of-plane gamma(N-H...O) hydrogen bond motions were observed and identified.     

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.     

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.     

Infrared and Raman spectra, conformational stability, ab initio calculations and vibrational assignments for trans-3-chloropropenoyl chloride

The infrared (3500-30 cm(-1)) spectra of gaseous and solid and the Raman (3500-200 cm(-1)) spectra of the liquid with quantitative depolarization ratios and solid trans-3-chloropropenoyl chloride (trans-ClCHCHCClO) have been recorded. These data indicate that both the anti (carbonyl bond trans to the carbon-carbon double bond) and syn conformers are present in the fluid states but only the anti conformer is present in the crystalline state. The mid-infrared spectra of the sample dissolved in liquid xenon as a function of temperature (-55 to -100 degrees C) have been recorded. Utilizing conformer pairs at 870 and 725 cm(-1), 1215 and 1029 cm(-1), and 1215 and 1228 cm(-1), the enthalpy difference has been determined to be 136+/-5 cm(-1) (389+/-14 cal mol(-1)) with the anti conformer the more stable form. Optimized geometries and conformational stabilities were obtained from ab initio calculations at the levels of RHF/6-31G(d), MP2/6-31G(d), MP2/6-311 + + G(d,p), MP2/6-311 + + G(2d,2p) and MP2/6-311 + + G(2df,2pd) with only the latter two calculations predicting the anti rotamer to be the more stable form. The vibrational frequencies, harmonic force constants and infrared intensities were obtained from the MP2/6-31G(d) calculations, whereas the Raman activities and depolarization values were obtained from the RHF/6-31G(d) calculations. The spectra are interpreted in detail and the results are compared with those obtained for some related molecules.     

Spectra and structure of small ring compounds. LXVII vibrational spectra, variable temperature FT-IR spectra of krypton solutions, conformational stability and ab initio calculations of 1-bromosilacyclobutane

The infrared (3,200-30 cm(-1) spectra of gaseous and solid 1-bromosilacyclobutane, c-C3H6SiBrH, have been recorded. Additionally, the Raman spectra of the liquid (3,200- 30 cm(-1) with quantitative depolarization values and the solid have been recorded. Both the equatorial and the axial conformers have been identified in the fluid phases, Variable temperature ( - 105 to - 150 degrees C) studies of the infrared spectra of the sample dissolved in liquid krypton have been carried out. From these data the enthalpy difference has been determined to be 182 +/- 18 cm(-1) (2.18 +/- 0.22 kJ/mol) with the equatorial conformer the more stable rotamer and only conformer remaining in the annealing solid. At ambient temperature there is approximately 22% of the axial conformer present in the vapor phase. A complete vibrational assignment is proposed for both conformers based on infrared contours, relative intensities, depolarization values and group frequencies. The vibrational assignments are supported by normal coordinate calculations utilizing the force constants from ab initio MP2/6-31G(d) calculations. From the frequencies of the Si-H stretch, the Si-H bond distance of 1.483 A has been determined for both the equatorial and the axial conformers. Complete equilibrium geometries have been determined for both rotamers by ab initio calculations employing the 6-31G(d) and 6-311 +/- G(d,p) basis sets at levels of Hartree Fock (RHF) and/or Moller- Plesset with full electron correlation by the perturbation method to the second order (MP2). The results are discussed and compared to those obtained for some similar molecules.     

Unexpected conformational properties of 1-trifluoromethyl-1-silacyclohexane, C5H10SiHCF3: gas electron diffraction, low-temperature NMR spectropic studies, and quantum chemical calculations

The molecular structure of axial and equatorial conformers of 1-trifluoromethyl-1-silacyclohexane, (C5H10SiHCF3), as well as the thermodynamic equilibrium between these species was investigated by means of gas electron diffraction (GED), dynamic nuclear magnetic resonance (DNMR) spectroscopy, and quantum chemical calculations (B3LYP, MP2, and CBS-QB3). According to GED, the compound exists as a mixture of two Cs symmetry conformers possessing the chair conformation of the six-membered ring and differing in the axial or equatorial position of the CF3 group (axial=58(12) mol%/equatorial=42(12) mol%) at T=293 K. This result is in a good agreement with the theoretical prediction. This is, however, in sharp contrast to the conformational properties of the cyclohexane analogue. The main structural feature for both conformers is the unusually long exocyclic bond length Si--C 1.934(10) A. A low-temperature 19F NMR experiment results in an axial/equatorial ratio of 17(2) mol%:83(2) mol% at 113 K and a DeltaG (not equal) of 5.5(2) kcal mol-1. CBS-QB3 calculations in the gas-phase and solvation effect calculations using the PCM(B3LYP/6-311G*) and IPCM(B3LYP/6-311G*) models were applied to estimate the axial/equatorial ratio in the 100-300 K temperature range, which showed excellent agreement with the experimental results. The minimum energy pathways for the chair-to-chair inversion of trifluoromethylsilacyclohexane and methylsilacyclohexane were also calculated using the STQN(Path) method.     

Origin of the axial-alkyl preference of (R)-α-phellandrene and related compounds investigated by high-level ab initio MO calculations. Importance of the CH/π hydrogen bond

Ab initio MO calculations were carried out, at the MP2/6-311++G(d,p)//MP2/6-311G(d,p) level, to investigate the Gibbs energy of conformational isomers of (R)-α-phellandrene and related 5-alkyl-1,3-cyclohexadienes. It has been found that the conformer bearing the 5-alkyl group in axial orientation is more stable than the equatorial congener. The result is consistent with experimental evidence that the axial-isopropyl conformer prevails in the conformational equilibrium of α-phellandrene. The reason for the stability of the folded conformer has been sought in the context of the CH/π hydrogen bond. A number of short non-bond distances have been disclosed in the axial conformers, between CHs in the 5-alkyl group and sp²-carbons of the cyclohexadiene ring. We suggest that the stability of the folded conformation often observed in conjugated diene compounds of natural origin, such as α-phellandrene and levopimaric acid, is attributed to an attractive molecular force, the CH/π hydrogen bond.     

Molecular structure of the octatetranyl anion, C8H-: a computational study

The equilibrium molecular structure of the octatetranyl anion, C8H(-), which has been recently detected in two astronomical environments, is investigated with the aid of both ab initio post-Hartree-Fock and density functional theory (DFT) calculations. The model chemistry adopted in this study was selected after a series of benchmark calculations performed on molecular acetylene for which accurate gas-phase structural data are available. Geometry optimizations performed at the CCSD/6-311+G(2d,p), QCISD/6-311+G(2d,p), and MP4(SDQ)/6-311+G(2d,p) levels of theory yield for C8H(-) an interesting polyyne-type structure that defies the chemical formula displaying a simple alternation of triple and single carbon-carbon bonds, [:C[triple bond]C-C[triple bond]C-C[triple bond]C-C[triple bond]CH](1-). In the optimized geometry of C8H(-), as one proceeds from the naked carbon atom on one side of the chain to the CH unit on the opposite side of the chain, the short (formally triple) carbon-carbon bonds decrease in length from 1.255 to 1.213 A whereas the long (formally single) carbon-carbon bonds increase (albeit only slightly) in length from 1.362 to 1.378 A (CCSD results). In striking contrast, both MP2 and DFT (B3LYP and PBE0) calculations fail in reproducing the pattern of the carbon-carbon bond lengths obtained with the CCSD, QCISD, and MP4 methods. The structures of three shorter n-even chains, C(n)H(-) (n = 2, 4, and 6), along with those of four n-odd compounds (n = 3, 5, 7, and 9) are also investigated at the CCSD/6-311+G(2d,p) level of theory.     

NH0-1+2-3离解能等的高级ab initio计算与评价

A recent experimental determination[1] of the dissociation energies (D0) for H2N-H, H2N+-H and H2N-H+, the ionization energies for NH3 and NH2 resulted in large deviations when compared with those of the earlier values and the QCISD(T)/6-311+G(3df,2p) ab initio calculations. We have performed some higher level ab initio calculations on these data by utilizing the Gaussian 92/DFT and Gaussian 94 pakages of programs and have assessed the available experimental values. Our calculations were carried out at the QCISD (TQ)/aug-cc-pVDZ, G2(QCI), QCISD(T)/6-311 ++G(3df,3pd) and QCISD(T)/aug-cc-pVTZ levels of theory. Geometries were optimized at both of the MP2(full)/6-31G(d) and the MP2(full)/6-31(d,p) levels, and were compared with those of the experiments if available. The MP2(full)/6-31G(d,p) tight-optimized geometries for the neutrals are closer to those of the experiments than those of the MP2 (full)/6-31G(d), and are in excellent agreement with the experimental results as shown in Table 1. In this case, we assumed that the optimized geometries for the cations would be better if p polarization functions are added to the hydrogen atoms. We firstly noted that the symmetry of the NH3+ cation was D3h, other than Cs. as reported in ref.[1]. All of the zero-point energies and the final geometries are calculated at the MP2(full)/6-31G(d,p) level of theory. We have also repeated the QCISD(T )/6-311 + G(3df,2p) calculations of ref. [1], because we could not identify their level of goemetry optimization. It is found that the total energy, -55.244 19 Hartrees, for NH2+(1A1 ) in ref.[1] might be in error. Our result is -55.336 29 Hartrees at the same level of theory. At our highest level [QCISD(T)/aug-cc-pVTZ] of calculations as shown in Table 3, the D0 (temperature at zero Kelvin) values of H2N-H, H2N+-H(3B1for NH2+ ) and H2N- H+ are 4.51, 5.49 and 8.00 eV, respectively. These data reported in re f.[1] were 4.97, 5.59 and 8.41 eV, respectively. Our result on D0(H2N-H) supports the work of ref.[2,3,5,6]. The ionization energies (IE) for NH3 and NH2 (3B1 for NH2+) at our highest level are 10.11 and 11.09 eV while in ref.[1] were 10.16 and 10.78 eV, respectively. For the latter, our result supports the experiment of ref.[3]. Our predicted D0 for HN2+-H and IE for NH2 (1A1 for each NH2+) are 6.80 and 12.39 eV, respectively. These values differ greatly from the predicted values (9.29 and 14.88 eV) of ref.[1] where the total energy of NH2+(1A1) might be in error. The D0 value for HN-H has not been found in ref.[1]. Our result supports the work of ref.[3]. We have also derived all of these values at the temperature of 298K and under the pressure of 101kPa at several levels of thoery as shown in Table 3. On examining the experiment of ref.[1] in detail, it is easy to find that all of the larger deviations might be from a too high value of the appearance potential of proton AP(H+). Indeed, ref.[1] has mentioned that the determintion of AP(H+), due to kinetic shift, would lead to a hihger value for the dissociation energy as has been pointed out by Berkowitz and Ruscic. In this work, we concluded that, besides some mistakes in the theoretical calculations of ref.[1], the dissociation energies for H2N-H and H2N-H+,the IE for NH2 (3B1 for NH2+) might also be unreliable and need to be re-examined.
     

丁烯和丁烷自由基阳离子的分子结构和超精细结构的 理论研究

用密度函数理论B3LYP方法和6-31G(d,p),6-311G(d,p)及6-311+G(d,p)基组，分别对1-C4H^+~8,2-C4H^+~8和C4H^+~10进行了构型优化和频率分析计算，预言1-C4H^+~8具有非平面构型，与以往报道的从头算和密度函数理论计算结果不同。在各自由基阳离子的B3LYP构型上，进行了B3LYP、MP2及MRSDCI方法的超精细偶合常数计算，得到了比以往更好的结果，特别是MP2/B3LYP计算值是至今与实验值符合得最好的理论计算结果。     

CH3 CH2 +N(4S)反应机理的理论研究

The reaction for CH3CH2+N(4S) was studied by ab initio method. The geometries of the reactants, intermediates, transition states and products were optimized at MP2/6-311+G(d,p) level. The corresponding vibration frequencies were calculated at the same level. The single point calculations for all the stationary points were carried out at the QCISD(T)/ 6-311+G(d,p) level using the MP2/6-311+G(d,p) optimized geometries. The results of the theoretical study indicate that the major products are the CH2CH2+3NH and H2CN＋CH3, and the minor products are the CH3CHN+H in the reaction. The majority of the products CH2CH2+3NH are formed via a direct hydrogen abstraction channel. The products H2CN＋CH3 are produced via an addition/dissociation channel. The products CH3CHN+H are produced via an addition/dissociation channel.     

The C7-C10 cycloalkanes revisited

The conformers of cycloheptane through cyclodecane have been examined at the B3LYP/6-311+G* and MP2/6-311+G* theoretical levels, with some additional calculations at the CCD/6-311+G* and CCSD(T)/6-311++G** levels. With cyclooctane, B3LYP predicts that the boat-chair and crown conformers have similar energies, whereas MP2 and CCSD(T) predict that the crown conformer is 2 kcal/mol higher in energy. The latter is in agreement with the electron diffraction data. With cyclononane, B3LYP predicts that two of the higher-energy conformers found in molecular mechanics calculations should convert to one of the lower-energy conformers. However, MP2/6-311+G* optimizations find them to be true minima on the potential energy surface. B3LYP systematically predicts larger C-C-C bond angles for these compounds than either MP2 or CCD. The results of molecular mechanics MM4 calculations are generally in good agreement with those obtained using MP2.     

Redox potentials of dopamine and its supramolecular complex with aspartic acid

Dopamine (DA) can be oxidized to dopamine quinone (DAquinone) through a one-step, two-electron redox reaction. The electron transfer property of DA and its supramolecular complex with aspartic acid (Asp) has been investigated by the theoretical calculations. We calculated the standard redox potentials (E ^o) of DA/DAquinone at the MP2/6-31G(d,p)//B3LYP/6-31G(d,p), MP2/6-31+G(d,p)//B3LYP/6-31+G(d,p), MP2/6-31G(d,p)//B3LYP/6-311G(d,p), and MP2/6-311+G(d,p)//B3LYP/6-311+G(d,p) levels. Comparing the experimental value, the redox potentials of DA/DAquinone obtained at MP2//B3LYP/6-311G(d,p) and MP2//B3LYP/6-311+G(d,p) levels can be considered as the upper and lower estimates. DA can form supramolecular complex (DA-Asp) with Asp through hydrogen bond (H-bond). Therefore, the values of 0.631 and 0.628 V obtained at MP2//B3LYP/6-311G(d,p) and MP2//B3LYP/6-311+G(d,p) levels for DA-Asp/DAquinone-Asp can be proposed as the upper and lower estimates of a probable (about 0.630 V) value of the corresponding redox potential. The calculated E ^o values of DA-Asp/DAquinone-Asp at the four theoretical levels are upper than those of DA/DAquinone, which indicates that the formation of H-bonds weaken the electron-donating ability of DA.     

SiH3+O(3P)反应机理的理论研究

The reaction for SiH3+O(3P) was studied by ab initio method. The geometries of the reactants, intermediates, transition states and products were optimized at MP2/6-311+G(d,p) level. The single point calculations for all the stationary points were carried out at the QCISD(T) /6-311+G(d,p) level using the MP2/6-311+G(d,p) optimized geometries. The results of the theoretical study indicate that the major pathway is the SiH3+O(3P)→IM1→TS3→IM2→TS8→HOSi+H2. The other minor products include the HSiOH+H, H2SiO+H and HSiO+H2. Furthermore, the products HOSi, HSiO and HSiOH(cis) can undergo dissociation into the product SiO. In addition, the calculations provide a possible interpretation for disagreement about the mechanism of the reaction SiH4+O(3P). It suggests that the products HSiOH, H2SiO and SiO observed by Withnall and Andrews are produced from the secondary reaction SiH3+O(3P) and not from the reaction SiH4+O(3P).     

分子几何构型优化方法的系统性比较

对《ＣＲＣ物理化学手册》第７７版中收集的第三周期以前的所有已知实验构型的无机分子的构型,以ＭＰ２、Ｂ３ＬＹＰ、Ｂ３ＰＷ９１级别上进行了构型优化的系统性比较,优化采用基组为６－３１Ｇ（ｄ,ｐ）,６－３１１Ｇ（ｄ,ｐ）,６－３１１Ｇ（２ｄ,ｐ）。对大多数分子另比较了ＱＣＩＳＤ（Ｔ）方法,对多原子分子比较了ＢＰＷ９１方法,对含氢双原子分子也使用ＱＣＩＳＤ方法。结果表明,键长的平均绝对偏差（单位：ｐｐｍ）     

戊烯自由基阳离子的密度泛函理论研究

使用密度泛函理论B3LYP方法和6-31G(d,p)、6-31＋G(d,p)、6-311G(d,p)及6-311＋G(d,p)基组，分别对2-C5H10＋和1-C5H10＋的各种构象进行了几何构型优化，并用B3LYP/6-311G(d,p)进行了频率分析计算.计算预言1-C5H10＋具有非平面构型，与以往报导的从头算计算结论相反.在两个自由基阳离子的各种构象的B3LYP几何构型上，进行了B3LYP和UMP2(full)方法的超精细偶合常数计算，得到了比以往更好的结果.