AB INITIO MOLECULAR ORBITAL STUDY OF 1,2-DITHIANE AND 1,2,4,5-TETRATHIANE

Ab initio calculations at HF/6-31+G? level of theory for geometry optimization, and MP2/6-31+G?//HF/6-31+G? and B3LYP/6-31+G?//HF/6-31+G? levels for a single-point total energy calculation, are reported for the chair and twist conformations of 1,2-dithiane (1), 3,3,6,6-tetramethyl-1,2-dithiane (2), 1,2,4,5-tetrathiane (3), and 3,3,6,6-tetramethyl-1,2,4,5-tetrathiane (4). The C₂ symmetric chair conformations of 1 and 2 are calculated to be 21.9 and 8.6 kJ mol^?1 more stable than the corresponding twist forms. The calculated energy barriers for chair-to-twist processes in 1 and 2 are 56.3 and 72.8 kJ mol^?1, respectively. The C_2h symmetric chair conformation of 3 is 10.7 kJ mol^?1 more stable than the twist form. Interconversion of these forms takes place via a C₂ symmetric transition state, which is 67.5 kJ mol^?1 less stable than 3-Chair. The D₂ symmetric twist-boat conformation of 4 is calculated to be 4.0 kJ mol^?1 more stable than the C_2h symmetric chair form. The calculated strain energy for twist to chair process is 61.1 kJ mol^?1.     

Conformational analysis of cycloheptane,oxacycloheptane, 1,2‐dioxacycloheptane, 1,3‐dioxacycloheptane,and 1,4‐dioxacycloheptane

The conformational analysis of cycloheptane (1), oxacycloheptane (2), 1,2‐dioxacycloheptane (3), 1,3‐dioxacycloheptane (4), and 1,4‐dioxacycloheptane (5) has been carried out using B3LYP, CCD, CCSD, and QCISD with the 6‐311+G(d,p) and cc‐pVDZ basis sets. The twist chair conformers are predicted to be lower in energy than their corresponding boat and chair conformations. All levels of theory predict (4) to be lower in energy than (3) and (5). CCSD predicts remarkably similar activation barriers for the conformational interconversion of the twist chair conformers to their corresponding boat conformers. Small barriers to pseudorotation are also predicted. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Ab initio molecular orbital study of energies and conformers of 3,4-dihydro-1,2-dithiin, 3,6-dihydro-1,2-dithiin, 4H-1,3-dithiin,and 2,3-dihydro-1,4-dithiin

Optimized geometries and energies for 3,4-dihydro-1,2-dithiin ( 1 ), 3,6-dihydro-1,2-dithiin ( 2 ), 4H-1,3-dithiin ( 3 ), and 2,3-dihydro-1,4-dithiin ( 4 ) were calculated using ab initio 6-31G* and MP2/6-31G*//6-31G* methods. At the MP2/6-31G*//6-31G* level, the half-chair conformer of 4 is more stable than those of 1 , 2 , and 3 by 2.5, 3.5, and 3.6 kcal/mol, respectively. The half-chair conformers of 1 , 2 , 3 , and 4 are 2.9, 7.1, 2.0, and 5.6 kcal/mol, respectively, more stable than their boat conformers. The calculated half-chair structures of 1 – 4 are compared with the calculated chair conformer of cyclohexane and the half-chair structures for cyclohexene, 3,4-dihydro-1,2-dioxin ( 5 ), 3,6-dihydro-1,2-dioxin ( 6 ), 4H-1,3-dioxin ( 7 ), and 2,3-dihydro-1,4-dioxin ( 8 ). © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1064–1071, 1998     

Gas-phase structure and conformational properties of 3,3,6,6-tetramethyl-1,2,4,5-tetroxane

The geometric structure and conformational properties of 3,3,6,6-tetramethyl-1,2,4,5-tetroxane (diacetone diperoxide) have been studied by gas electron diffraction and quantum chemical calculations (MP2 and B3LYP methods with 6-31G(d,p) and 6-311+G(2df,p) basis sets). The molecule possesses a chair conformation with C2h symmetry and the following geometric parameters for the six-membered ring (rh1 values) have been determined: O-O = 1.463(5) A, C-O = 1.432 (4) A, O-C-O = 108.2(7) degrees, C-O-O = 107.7(4) degrees, phi(C-O-O-C) = 63.7(4) degrees, and phi(O-O-C-O) = -63.9(4) degrees. A small contribution of less than 3.5% of a twist conformer with C2 symmetry cannot be excluded. Quantum chemical calculations predict a contribution between 1 and 2%. Additional calculations for the parent compound 1,2,4,5-tetroxane (diformaldehyde diperoxide) demonstrate that methyl substitution at the carbon atoms has a minor effect on the ring geometry but a strong effect on the conformational properties. Methyl substitution reduces the energy difference between twist and chair conformers by more than 5 kcal/mol.     

Quantum chemical studies on structure, conformation and isomerization of nitroso, nitro substituted benzene and 1,3-cyclopentadiene

The molecular structure, conformational stability and isomerization of nitroso, nitro substituted benzene and 1,3-cyclopentadiene in gas phase have been investigated using ab initio and density functional theory methods. The molecular geometries and energetics of possible conformers were obtained by employing MP2, B3LYP and B3PW91 levels of theory implementing 6-31G* basis set. The relative stabilities of the conformations were evaluated from the energy differences of the structure. Chemical hardness (η) and chemical potential (μ) were calculated at HF/6-31G* level of theory for all the positional and geometrical isomers to study the maximum hardness principle. Each optimized structure has been tested against the imaginary frequencies at MP2/6-31G* level of theory in order to be sure they are located at energy minimum.     

A Computational Study of Conformers of 2-Thiaoxacyclohexane (1,2-Oxathiane)

Ab initio molecular orbital theory with the 6-31G(d), 6-31G(2d), 6-31+G(d), 6-31G(d,p), 6-31+G(d,p), and 6-311G(d,p) basis sets and the hybrid density functionals B3LYP, B3P86, and B3PW91 have been used to calculate the optimized geometries and relative energies of the chair, half-chair, sofa, twist, and boat structures of 2-thiaoxacyclohexane (1,2-oxathiane). The values of the energy difference (E, kcal/mol) between the chair and 3,6-twist structures of 1,2-oxathiane were 4.92 (HF), 4.73 (MP2), and 4.66 (DFT). The HF chair–twist energy difference (G _c–t ^o) for 1,2-oxathane was 5.16 kcal/mol. Intrinsic reaction coordinate (IRC) calculations connected a transition state (TS-A) between the chair conformation and the less stable 2,5-twist form and connected two transition states (TS-B, TS-C) between the chair conformation and the more stable 3,6-twist conformer. The DFT energy differences between the chair and TS-A, TS-B, and TS-C were 11.4, 10.8, and 12.6 kcal/mol, respectively. Hyperconjugative stereoelectronic interactions were observed in the chair (n _o and ) and 3,6-twist (n _S and n _O ) conformers of 1,2-oxathiane. The chair conformation of 1,2-oxthiane is 9.6 and 10.0 kcal/mol, respectively, less stable than the chair conformations of 3-thiaoxacyclohexane (1,3-oxathiane) and 4-thiaoxacyclohexane (1,4-oxathiane, thioxane).     

Comparative conformational analysis of 1,3-dioxane and 1,3-dithiane

It was shown by ab initio quantum-chemical approximations HF/6-31G(d) and MP2/6-31G(d)//HF/6-31G(d) that the conformational isomerization of 1,3-dioxane and 1,3-dithiane proceeded along common routes. The potential energy surface of both compounds contains six minima including the chair invertomers and enantiomeric flexible forms. They are separated by several potential barriers. It was established by molecular dynamics method that the flexible conformers at heating and keeping at 295–300 K transformed into each other and in the chair conformer.     

可乐定分子构象异构和互变异构的理论研究

采用HF/6-31G*方法, 对氨基型和亚胺型可乐定中性分子以及质子化的可乐定分子进行了构象分析. 之后采用B3LYP/6-31G**方法对处于势能面上的能量极小构象异构体进行全自由度几何优化和频率分析. Onsager反应场溶剂模型用于水相的计算. 结果表明, 在气相和水相中可乐定中性分子主要以亚胺型存在, 这同已有实验结果一致. 进一步, 寻找构象异构化过渡态和氨基型亚胺型互变异构化过渡态, 探讨质子化和水溶剂化效应对异构化过程的几何结构和能量的影响. 为了考察氯苯的共轭效应对可乐定互变异构体稳定性的影响, 在B3LYP/6-31G**水平上, 研究了2-氨基-2-咪唑啉的互变异构化反应机理.     

吡啶-BH~3相互作用复合物的理论研究

对吡啶-BH~3复合物分别用MP2/6-31+G^*和B3LYP/6-31+G^*进行理论计算以预测该复合物的构型及解离能，得到四种构型，在MP2优化构型基础上作CCSD/6-31+G^*单点能量计算以验证MP2与B3LYP结果的可靠性，然后用B3LYP作振动频率分析，计算了各构型的垂直电离势，最后用更大基组作单点能量计算和自然键轨道(NBO)分析。结果表明，N-B直接相连的构型最稳定，其解离能为141.50kJ/mol,MP2和B3LYP对N-H接近的构型结果相关较大，另外两种构型稳定性介于二者之间，解离能分别为15.18kJ/mol,14.06kJ/mol(MP2/6-31+G^*)。     

Iminopropadienones R–NCCCO and carbon suboxide, C3O2. Theoretical and experimental C NMR spectra

The ¹³C NMR data of five iminopropadienones R–NCCCO as well as carbon suboxide, C₃O₂, have been examined theoretically and experimentally. The best theoretical results were obtained using the GIAO/B3LYP/6-31+G**//MP2/6-31G* level of theory, which reproduces the chemical shifts of the iminopropadienone substituents extremely well while underestimating those of the cumulenic carbons by 5–10 ppm. The computationally faster GIAO/HF/6-31+G**//B3LYP/6-31G* level is also adequate.     

A computational study of conformational interconversions in 1,4-dithiacyclohexane (1,4-dithiane)

Ab initio molecular orbital theory with the 6-31G(d), 6-31G(d,p), 6-31+G(d), 6-31+G(d,p), 6-31+G(2d,p), 6-311G(d), 6-311G(d,p), and 6-311+G(2d,p) basis sets and density functional theory (BLYP, B3LYP, B3P86, B3PW91) have been used to locate transition states involved in the conformational interconversions of 1,4-dithiacyclohexane (1,4-dithiane) and to calculate the geometry optimized structures, relative energies, enthalpies, entropies, and free energies of the chair and twist conformers. In the chair and 1,4-twist conformers the C-Hax and C-Heq bond lengths are equal at each carbon, which suggest an absence of stereoelectronic hyperconjugative interactions involving carbon-hydrogen bonds. The 1,4-boat transition state structure was 9.53 to 10.5 kcal/mol higher in energy than the chair conformer and 4.75 to 5.82 kcal/mol higher in energy than the 1,4-twist conformer. Intrinsic reaction coordinate (IRC) calculations showed that the 1,4-boat transition state structure was the energy maximum in the interconversion of the enantiomers of the 1,4-twist conformer. The energy difference between the chair conformer and the 1,4-twist conformer was 4.85 kcal/mol and the chair-1,4-twist free energy difference (deltaG degrees (c-t)) was 4.93 kcal/mol at 298.15 K. Intrinsic reaction coordinate (IRC) calculations connected the transition state between the chair conformer and the 1,4-twist conformer. This transition state is 11.7 kcal/mol higher in energy than the chair conformer. The effects of basis sets on the 1,4-dithiane calculations and the relative energies of saturated and unsaturated six-membered dithianes and dioxanes are also discussed.     

Understanding selenocysteine through conformational analysis,proton affinities,acidities and bond dissociation energies

Density functional methods have been employed to characterize the gas phase conformations of selenocysteine. The 33 stable conformers of selenocysteine have been located on the potential energy surface using density functional B3LYP/6‐31+G* method. The conformers are analyzed in terms of intramolecular hydrogen bonding interactions. The proton affinity, gas phase acidities, and bond dissociation energies have also been evaluated for different reactive sites of selenocysteine for the five lowest energy conformers at B3LYP/6‐311++G*//B3LYP/6‐31+G* level. Evaluation of these intrinsic properties reflects the antioxidant activity of selenium in selenocysteine. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Calculated gas-phase infrared spectra of imidazo[1,2-a]pyrazinediones derived from alanine

IR spectra of bicyclic and tricyclic amidine derivatives of alanine (2,5,8-trimethylhexahydroimidazo[1,2-a]pyrazine-3,6-dione, 2,5,8-trimethyltetrahydroimidazo[1,2-a]pyrazine-3,6-dione and 2,5,7,10-tetramethylhexahydroimidazo[1,2-a]imidazo[1,2-d]pyrazine-3,8-dione) were computed by the HF, B3LYP, B3P86 and B3PW91 methods in conjunction with the 6-31G(d) basis set. The IR spectra calculated are in a good agreement with the observed FTIR spectra. The correlation between the calculated and experimental vibration frequencies is characterized by the coefficients of 0.9997 for all three DFT methods; for HF it is about 0.9992. The calculated absolute band intensities satisfactory match the observed relative intensities. Optimal uniform scaling factors calculated for this series of compounds are 0.8967, 0.9598, 0.9544 and 0.9555 for HF, B3LYP, B3P86 and B3PW91, respectively. Taking into account small variations of the scaling factors for the derivatives of different amino acids, for future IR spectral predictions for unknown compounds of this class, one can recommend scaling factors of 0.897, 0.959, 0.954 and 0.955 for HF, B3LYP, B3P86 and B3PW91, respectively.     

Ab initio molecular orbital calculations of 3,4-dihydro-1,2-dioxin, 3,6-dihydro-1,2-dioxin, 4H-1,3-dioxin (1,3-diox-4-ene), and 2,3-dihydro-1,4-dioxin (1,4-dioxene)

Optimized geometries and total energies for 3,4-dihydro-1,2-dioxin ( 1 ), 3,6-dihydro-1,2-dioxin ( 2 ), 4H-1,3-dioxin (1,3-diox-4-ene, 3 ), and 2,3-dihydro-1,4-dioxin (1,4-dioxene, 4 ) were calculated using ab initio 3-21G, 6-31G*, and MP2/6-31G*//6-31G* methods. The half-chair conformers of 1 (C₁), 2 (C₂), 3 (C₁), and 4 (C₂) are more stable than their respective planar structures [ 1 (C_s), 2 (C_2v), 3 (C_s), and 4 (C_2v)]. Among the four isomers 1 – 4 , the half-chair conformer of 3 is the most stable. It is 53.1, 54.6, and 3.4 kcal mol⁻¹ more stable than 1 , 2 , and 4 , respectively. The largest energy difference (19.0 kcal mol⁻¹) is observed between the half-chair and planar conformers of 2 . The boat conformers of 2 and 4 are less stable than their respective half-chair conformers, but are more stable than their planar structures. Hyperconjugative orbital interactions (anomeric effects) contribute to the greater stability of 3 (n_O(3) →σ*_C(2)—O(1), n_O(3)→σ*,n _O(3)→σ*) and of 4 (n_O(1)→ σ*). The ab initio calculated structural features of the half-chair conformations of the dihydrodioxins 1 – 4 are compared with the half-chair conformations of cyclohexene and the chair conformations of cyclohexane, oxacyclohexane (tetrahydropyran), 1,2-dioxacyclohexane (1,2-dioxane), 1,3-dioxacyclohexane (1,3-dioxane), and 1,4-dioxacyclohexane (1,4-dioxane) © 1997 by John Wiley & Sons, Inc. J Comput Chem 18 : 1392–1406, 1997     

Theoretical Study on the Optical Properties for 2,7- and 3,6-Linked Carbazole Trimers by Time-dependent Density Functional Theory

Electronic properties, such as HOMO and LUMO energies, band gaps, ionization potential (IP) and electron affinity (EA) of 2,7- and 3,6-linked carbazole trimers, two conjugated oligomers with different linkages of carbazole, were studied by the density functional theory with Becke-Lee-Young-Parr composite exchange correlation functional (B3LYP). The absorption spectra of these compounds were also investigated by time-dependent density functional theory (TD-DFT) with 6-31G* basis set. The calculated results indicated that the HOMO and LUMO of the 2,7- and 3,6-linked carbazole trimers are both slightly destabilized on going from methyl substitution to sec-butyl substitution. Both IP and EA exhibit their good hole-transporting but poor electron- accepting ability. The presence of alkyl groups on the nitrogen atoms does not affect the intra-chain electronic delocalization along the molecular frame. Thus no significant effect on the band gap and absorption spectra of compounds has been found.     

Si~2Cl~6分子的内旋转能垒和振动基频的理论研究

用从头算方法HF/6-31G^*^*和密度函方法B3LYP/6-31G^*^*,对Si~2Cl~6分子的平衡几何构型进行优化,优化的结果与实验结果吻合得较好.并用上述两种不同的方法计算Si~2Cl~6分子的内旋转能垒,结果分别为8.786和6.694kJ/mol,其中DFT方法的计算结果与实验结果4.18kJ/mol吻合得较好.对Si~2Cl~6分子的振动基频进行计算.用HF/6-31G^*^*SQM力场所计算的频率理论值与实验值的平均误差为7.3cm^-^1,用B3LYP/6-31G^*^*未标度的力场所计算的频率理论值与实验值的平均误差为6.0cm^-^1.该密度泛函方法(B3LYP/~6-31G^*^*)的理论计算值比用HF/6-31G^*^*标度后的SQM力场计算的频率与实验值(除Si--Si键扭转振动基频之外的11条振动基频)吻合得更好.并给出了Si--Si键扭转振动基频的预测值。     

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.     

Conformational isomerization of 4-methyl-1,3-dioxane

The whole possible course of conformational isomerization of 4-methyl-1,3-dioxane has been established using empirical (MM+) and nonempirical [STO-3G, 3-21G, 6-31G(d) and 6-31G(d,p)] approximations within the limits of the Hartree-Fock method. It was shown that the potential energy surface of this compound contains a principal (equatorial chair conformer) and local minima corresponding to the axial chair conformer and series flexible forms.     

Salt effects on the conformational behavior of 5-carboxy- and 5-hydroxy-1,3-dioxane

The varied and essential involvement of metal ions and inorganic salts in biological and chemical processes motivated the present study where 5-carboxy- and 5-hydroxy-1,3-dioxanes are used as model frameworks for the evaluation of the conformational behavior of oxygen-containing receptors in the presence of Li(+), Na(+), K(+), Ag(+), Mg(2+), Ca(2+), Ba(2+), and Zn(2+). Thus, the position of equilibria, established by means of BF(3), between diastereomeric cis- and trans-5-substituted-2-phenyl-1,3-dioxanes, in solvent THF and in the presence of 0, 1, and 5 equiv of salt, has been determined. The observed Delta G(o) degrees values for the conformational equilibria of 5-carboxy-1,3-dioxane show that Ag(+), Li(+), and Ca(2+) complexation leads to increased stability of the axial isomer. In the case of the 5-hydroxy-1,3-dioxane, Mg(2+), Ag(+), and Zn(2+) are the metal ions that stabilize the axial conformer of the heterocycle upon association. Interpretation of the experimental observations was based on DFT molecular modeling studies at the Becke3LYP/6-31G* and Becke3LYP/6-31+G** levels of theory. Although gas-phase calculations give Delta E values that are too large when modeling equilibria involving ionic species in polar solution, the computational results confirm the structural and energetic consequences of metal cation coordination to the oxygen atom in carbonyls or ethers. The results derived from the present study contribute to our understanding of the chemical processes involved in molecular recognition and physiological events.