Ab Initio Study of Conformational Properties of ( Z, Z)-, ( E, Z)-, and ( E, E)-Cyclonona-1,5-dienes

Ab initio calculations at the HF/6-31G^* level of theory for geometry optimization and MP2/6-31G^*//HF/6-31G^* for a single point total energy calculation are reported for the important energy-minimum conformations and transition-state geometries of (Z,Z)-, (E,Z)-, and (E,E)-cyclonona-1,5-dienes. The C₂ symmetric chair conformation of (Z,Z)-cyclonona-1,5-diene is calculated to be the most stable form; the calculated energy barrier for ring inversion of the chair conformation via the C_s symmetric boat-chair geometry is 58.3kJmol^–1. Interconversion between chair and twist-boat-chair (C₁) conformations takes place via the twist (C₁) as intermediate. The unsymmetrical twist conformation of (E,Z)-cyclonona-1,5-diene is the most stable form. Ring inversion of this conformation takes place via the unsymmetrical chair and boat-chair geometries. The calculated strain energy for this process is 63.5kJmol^–1. The interconversion between twist and the boat-chair conformations can take place by swiveling of the trans double bond with respect to the cis double bond and requires 115.6kJmol^–1. The most stable conformation of (E,E)-cyclonona-1,5-diene is the C₂ symmetric twist-boat conformation of the crossed family, which is 5.3kJmol^–1 more stable than the C_s symmetric chair–chair geometry of the parallel family. Interconversion of the crossed and parallel families can take place by swiveling of one of the double bonds and requires 142.0kJmol^–1.     

Conformational Properties of (Z,Z)-, (E,Z)-, and (E,E)-Cycloocta-1,4-dienes

Summary.  Ab initio calculations at the HF/6-31G^* level of theory for geometry optimization and the MP2/6-31G^*//HF/6-31G^* level for a single point total energy calculation are reported for (Z,Z)-, (E,Z)-, and (E,E)-cycloocta-1,4-dienes. The C ₂-symmetric twist-boat conformation of (Z,Z)-cycloocta-1,4-diene was calculated to be by 3.6 kJ·mol⁻¹ more stable than the C _S-symmetric boat-chair form; the calculated energy barrier for ring inversion of the twist-boat conformation via the C _S-symmetric boat-boat geometry is 19.1 kJ·mol⁻¹. Interconversion between twist-boat and boat-chair conformations takes place via a half-chair (C ₁) transition state which is 43.5 kJ·mol⁻¹ above the twist-boat form. The unsymmetrical twist-boat-chair conformation of (E,Z)-cycloocta-1,4-diene was calculated to be by 18.7 kJ·mol⁻¹ more stable than the unsymmetrical boat-chair form. The calculated energy barrier for the interconversion of twist-boat-chair and boat-chair is 69.5 kJ·mol⁻¹, whereas the barrier for swiveling of the trans-double bond through the bridge is 172.6 kJ·mol⁻¹. The C _S symmetric crown conformation of the parallel family of (E,E)-cycloocta-1,4-diene was calculated to be by 16.5 kJ·mol⁻¹ more stable than the C _S-symmetric boat-chair form. Interconversion of crown and boat-chair takes place via a chair (C _S) transition state which is 37.2 kJ·mol⁻¹ above the crown conformation. The axial- symmetrical twist geometry of the crossed family of (E,E)-cycloocta-1,4-diene is 5.9 kJ·mol⁻¹ less stable than the crown conformation. Corresponding author. E-mail: isayavar@yahoo.com Received March 25, 2002; accepted April 3, 2002     

An ab initio Molecular Orbital Study of the Conformational Properties of all-(Z)-Cyclododeca-1,4,7,10-tetraene

Summary.  Ab initio HF/6-31G^* and MP2/6-31G^*//HF/6-31G^* methods were used to calculate the structure optimization and conformational interconversion pathways for all-(Z )-cyclododeca-1,4,7,10-tetraene. This compound adopts the symmetrical crown (C _4v) conformation. Ring inversion takes place via symmetrical intermediates, such as boat-chair (BC, C _s) and twist (C _2h) conformers and requires about 22.3 kJ · mol⁻¹. The calculated strain energies for BC and twist conformers are 5.9 and 13.5 kJ · mol⁻¹. The results of semiempirical AM1 calculations for structural parameters and relative energies of the important geometries of the title compound are in good agreement with the results of ab initio methods. Received July 9, 2001. Accepted September 26, 2001     

Dehydroxylation of Glycerol on Pt Surfaces: Ab Initio Molecular Dynamics Study

Glycerol is an important raw material in the chemical industry, and dehydroxylation of glycerol would produce 1, 2-propanediol and 1, 3-propanediol. Here we studied glycerol dehydroxylation with ab initio molecular dynamics simulations on Pt(111) and Pt(211) surfaces at 453 K. The free energies obtained on Pt show that dehydroxylation is more likely to occur at the terminal carbon than the central carbon, and 1, 2-propanediol would be produced preferentially, which is consistent with the selectivity observed experimentally. We found a linear relationship between the free energy barrier and the difference of average distances between O atoms at the initial state and transition state. Although a high correlation between the stability of gaseous glycerol and the number of formed hydrogen bonds is determined from density functional theory calculations, the hydrogen bonds formed within surface structures play a negligible role in determining the free energy barriers of dehydroxylation.     

A Conformational Study on Silacyclohexane. Comparison of ab initio (HF,MP2), DFT,and Molecular Mechanics Calculations. Conformational Energy Surface of Silacyclohexane

The structures and relative energies for the basic conformations of silacyclohexane 1 have been calculated using HF, RI‐MP2, RI‐DFT and MM3 methods. All methods predict the chair form to be the dominant conformation and all of them predict structures which are in good agreement with experimental data. The conformational energy surface of 1 has been calculated using MM3. It is found that there are two symmetric lowest energy pathways for the chair‐to‐chair inversion. Each of them consists of two sofa‐like transition states, two twist forms with C₁ symmetry (twist‐C₁), two boat forms with Si in a gunnel position (C₁ symmetry), and one twist form with C₂ symmetry (twist‐C₂). All methods calculate the relative energy to increase in the order chair < twist‐C₂ < twist‐C₁ < boat. At the MP2 level of theory and using TZVP and TZVPP (Si atoms) basis sets the relative energies are calculated to be 3.76, 4.80, and 5.47 kcal mol^–1 for the twist‐C₂, twist‐C₁, and boat conformations, respectively. The energy barrier from the chair to the twisted conformations of 1 is found to be 6.6 and 5.7 kcal mol^–1 from MM3 and RI‐DFT calculations, respectively. The boat form with Si at the prow (C_s symmetry) does not correspond to a local minimum nor a saddle point on the MM3 energy surface, whereas a RI‐DFT optimization under C_s symmetry constraint resulted in a local minimum. In both cases its energy is above that of the chair‐to‐twist‐C₁ transition state, however, and it is clearly not a part of the chair‐to‐chair inversion.     

Ab Initio Calculations on Halogen Bond Between N——Br and Electron-donating Groups

Ab initio calculations of complexes formed between N-bromosuccinimide and a series of electron-donating groups were performed at the level of MP2/Lanl2DZ to gain a deeper insight into the nature of the N—Br halogen bonding. For the small complexes, H3C—Br…NH3 and H2N—Br…NH3, the primary calculation has demonstrated that the N—Br in H2N—Br…NH3 can form a much stronger halogen-bonding complex than the C—Br. A comparison of neutral hydrogen bond complex series reveals that the electron-donating capacities of the atoms decrease in the order, N>O>S; O(sp3)>O(sp2), which is adequate for the C—Br halogen bonding. Interaction energies, in conjunction with the geometrical parameters show that the affinitive capacity of trihalide anions X-3 with N-bromosuccinimide are markedly lower than that of the corresponding X- with N-bromosuccinimide, even lower than those of neutral molecules with N-bromosuccinimide. AIM analyses further confirmed the above results.     

Syntheses of (E)- and (Z)-volkendousin

The first syntheses of the antitumor agents (E)-volkendousin (1) and acetonide 3 have been accomplished by efficient routes from readily available dehydroisoandrosterone (7) using allylic oxidation with SeO₂ to introduce the 4/gb-hydroxy group and 16-ketone. This sequence should make these compounds readily available for further biological evaluation.     

Ab initio and DFT calculations for the structure and vibrational spectra of cyclopentene and its isotopomers

Ab initio calculations using the MP2/cc-pVTZ basis set do an excellent job of predicting the inversion barrier (247 vs. 232 cm⁻¹) and dihedral angle (26°) of cyclopentene. DFT calculations also do an excellent job of predicting the vibrational frequencies of the d₀, d₁, d₄, and d₈ isotopomers. They have also allowed the reassignments of several of the vibrational frequencies.     

Syntheses of (E)- and (Z)-3-styrylchromones

Several (E)- and (Z)-3-styrylchromones were prepared by two different methodologies, the Wittig reaction of chromone-3-carboxaldehyde with benzylic ylides and the Knoevenagel condensation of chromone-3-carboxaldehyde with phenylacetic acids in the presence of potassium tert-butoxide under microwave irradiation. The Knoevenagel reaction followed by a decarboxylation offered an efficient and diastereoselective method for preparing (E)-3-styrylchromones in a shorter reaction time. It was also demonstrated that phenylacetic acid can also be substituted with success by phenylmalonic acid. The stereochemistry of all products was assigned by NMR experiments.     

Conformational Analysis of 2,2′-bifuran: Correlated High-level Ab initio and DFT Results

The torsional potential for inter-ring rotation in 2,2′-bifuran has been systematically tackled using highly accurate ab initio calculations as well as cost-effective DFT methods. The successful convergence of the ab initio results allowed to confirm the presence of a shallow gauche minimum in the torsional potential curve. The standard DFT methods failed to capture such a tiny energy barrier but, interestingly, the results could be remarkably improved by a mixture of wavefunction and DFT energies in a multi-coefficient fashion; thus, accurate DFT-based and ab initio reference data also become available. Since the experimental evaluation of torsional potentials faces quantitative problems, the outcome of high-level theoretical calculations is expected to be reliably used in further investigation on structure and conformational distribution of this system.     

NBO,NMR Analysis,and Hybrid DFT Study of Structural and Configurational Properties of Di-tert-butyl-, bis(trimethysilyl)-, Bis(trimethgermyl)-, and Bis(trimethylstannyl)- cyclopenta-1,3-dienes

Abstract

The alkyl 1,2-shift in di-tert-butylcyclopenta-1,3-diene (1) and the metallotropic 1,2-shifts in bis(trimethylsilyl)cyclopenta-1,3-diene (2), bis(trimethylgermyl)cyclopenta-1,3-diene (3), and bis(trimethylstannyl)cyclopenta-1,3-diene (4) have been investigated by means of natural bond orbital (NBO), nuclear magnetic resonance (NMR) analysis, and hybrid density functional theory based methods. The B3LYP/DZVP results showed that the M(CH₃)₃ group [M = C (1), Si (2), Ge (3), and Sn (4)] migration barrier heights around cyclopentadienyl rings decrease from di-tert-butylcyclopenta-1,3-diene to its stannane derivative. Also, based on the results obtained, the stabilities of the 5,5-isomers in comparison to the 1,5- and 2,5-isomers increase from di-tert-butylcyclopenta-1,3-diene to its stannane derivative. The results suggest that in these compounds the metallotropic shifts are controlled by the stabilization energies associated with σ→π* electron delocalizations and the increase of the σ_C5-M→π*_C1-C2 electron delocalizations facilitates the M(CH₃)₃ group migrations around cyclopentadienyl rings. Based on the aromatic stabilization energy (ASE) values calculated, the aromaticity increases from the 5,5-isomers of di-tert-butylcyclopenta-1,3-diene to its stannane derivative but the variation of the nucleus-independent chemical shift, NICS(0) and NICS(1), values calculated are not in accordance with the ASE values calculated and the σ_C5-M→π*_C1-C2

electron delocalizations. The correlations between the sigmatropic shift barrier heights, σ→π* electron delocalizations, ASE, and NICS values were investigated.

GRAPHICAL ABSTRACT     

Conformational analysis of methyl 2-methyl-2-(1-naphthyl)propionate

(S)-2-Methoxy-2-(1-naphthyl)propionic acid (MαNP acid 1) is used for enantioseparation of many secondary alcohols and for determining the stereogenic centers. In the liquid state, based on the ¹H NMR anisotropy effect and reported results, it was shown that the MαNP ester preferred a coplanar relation between the methyl and naphthyl groups and a synperiplanar relation between the Cα-OMe and CO groups. In the case of 1,2,3,4-tetrahydro-4-phenanthrenol, which is a secondary alcohol, the stereogenic center was determined by X-ray analysis. It was shown that MαNP ester adopted similar arrangements in the solid state. However, it was presumed that the strong repulsion between oxygen atoms may be disadvantageous in the solid state. Therefore, we carried out conformational analysis using the simplest MαNP methyl ester to clarify this unique relationship. From detailed results based on the energy surface determined using the RHF/STO-3G basis set, the synperiplanar positional relation was the most stable, and the calculated results agreed with many reported experimental results. At the same time, all conformational isomers of the MαNP methyl ester were used to clarify the internal conversion pathways.     

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.     

聚偏二氯乙烯构象分布的理论研究

在MP2/6-311++G**水平下, 对2,2,4,4-四氯戊烷与2,2,4,4,6,6-六氯庚烷旋转异构体构象进行几何优化和能量计算. 结果表明, 对于2,2,4,4-四氯戊烷, 采用gauche-gauche排列的旋转异构体的能量较低; 2,2,4,4,6,6-六氯庚烷旋转异构体中, 采用trans-gauche-trans-gauche排列的构象能量较低. 反之, 完全采用trans-trans排列的旋转异构体构象能量较高, 不稳定. 通过比较模型分子不同旋转异构体构象的能量差值可以得到一级和二级特征的相互作用能差, 进而计算统计权重参数. 在此基础上, 应用计算得到的模型分子的几何构型与统计权重参数, 分别构建针对—CH2—和—CCl2—中心的聚偏二氯乙烯的6态旋转异构态模型. 通过旋转异构态模型可以计算聚偏二氯乙烯分子中各种构象的分布.     

An Ab Initio Study and NBO Analysis of the Stability and Conformational Properties of Hexakis(trimethylelementhyl)benzene (Element = C,Si, Ge,and Sn)

Ab initio molecular orbital and density functional theory were used to investigate energetic and structural properties of the various conformations of hexa-tertbutylbenzene (1), hexakis(trimethylsilyl)benzene (2), hexakis (trimethylgermyl)benzene (3), and hexakis(trimethylstannyl)benzene (4). HF/3-21G//HF/3-21G and B3LYP/3-21G//HF/3-21G results revealed that the Twist-Boat (TB) conformer of compound 1 is more stable than the 1-Chair (C), 1-Boat (B), and 1-Planar (P) conformers. B3LYP/3-21G//HF/3-21G results show that the 1- TB conformer is more stable than 1- C, 1- B, and 1- P conformers of about 1.13, 4.34, and 99.94 kcal mol^?1 , respectively. Contrary to the stability order of compound 1 conformers, the C conformer of compounds 2–4 is more stable than TB, B, and P conformations, as calculated by B3LYP/3-21G//HF/3-21G and HF/3-21G//HF/3-21G levels of theory. The energy gap between the C and P conformers in compounds 1–4 is decreased in the following order: ΔE(4: C, P) < ΔE (3: C, P) < ΔE(2: C, P) < ΔE (1: C, P). This fact can be explained in terms of the increase of C _aromatic -M (M═C, Si, Ge, and Sn) bond lengths and the decrease of steric (van der Waals) repulsions in the previously discussed compounds. For compounds 1–3, the calculations were also performed at the B3LYP/ 6-31G*//HF/3-21G level of theory. However, the comparison showed that the results at B3LYP/3-21G//HF/3-21G methods correlated well with those obtained at the B3LYP/6-31G*// HF/6-31G method. Further, NBO analysis revealed that in compounds 1–4, the resonance energy associated with the σ_M-C1 to σ*_C2-C3 delocalization is 5.20, 9.68, 11.15, and 12.27 kcal mol^?1, respectively. These resonance energy values could explain the easiness of the ring flipping processes of C, B, and TB conformers of compounds 4 to 1. Also, the NBO results showed that by an increase of the σ_M-C1 → σ *_C2-C3 resonance energies in compounds 1–4, the σ_M-C1 bonding orbital occupancies decrease. This fact could fairly explain the increase of the C_aryl-M bond length from compound 1 to 4. The NBO results are also in good agreement with the calculated energy barriers for the ring flipping of the chair conformations in compounds 1–4, as calculated by B3LYP and HF methods.     

Predicting Stable Molecular Structures for (RNC)2AuIX Complexes

Calculations have been performed at the MP2 and DFT levels for investigating the reasons for the difficulties in synthesizing bis(isocyanide)gold(I) halide complexes. Three‐coordinated gold(I) complexes of the type (R₃P)₂Au^IX ( 1 ) can be synthesized, whereas the analogous isocyanide complexes (RNC)₂Au^IX ( 2 ) are not experimentally known. The molecular structures of (R₃P)₂Au^IX (X = Cl, Br, and I) and (RNC)₂Au^IX with X = halide, cyanide, nitrite, methylthiolate, and thiocyanate are compared and structural differences are discussed. Calculations of molecular properties elucidate which factors determine the strength of the gold‐ligand interactions in (RNC)₂Au^IX. The linear bonding mode of RNC favors a T‐shaped geometry instead of the planar Y‐shaped trigonal structure of (R₃P)₂Au^IX complexes that have been synthesized. An increased polarity of the Au–X bond in 2 leads to destabilization of the Y‐shaped structure. Chalcogen‐containing ligands or cyanide appear to be good X‐ligand candidates for synthesis of (RNC)₂Au^IX complexes.     

Conformational Study of Glycal-Type Neuraminidase Inhibitors

The conformational flexibility of two glycal-type neuraminidase inhibitors has been studied, using several molecular modeling techniques. In agreement with the experimental data available, an intramolecular hydrogen bond, representing a key structural feature that controls the conformer distribution in solution, has been identified. The contribution of each substituent to the overall equilibrium was evaluated using simplified derivatives. Additionally, four methods for estimating NMR coupling constants from dihedral angles were evaluated and the Haasnoot method was found to be appropriate for this class of sugars. These results should allow a better understanding of the structural parameters governing physico-chemical properties of glycal-like compounds. Supplemental materials are available for this article. Go to the publisher's online edition of Journal of Carbohydrate Chemistry to view the free supplemental file.     

Synthesis of (E)- and (Z)-3(5)-(2-hydroxyphenyl)-4-styrylpyrazoles

Abstract  

An efficient synthesis method for the preparation of a series of new (Z)- and (E)-3(5)-(2-hydroxyphenyl)-4-styrylpyrazoles was developed. The reaction of (Z)- and (E)-3-styrylchromones with hydrazine hydrate afforded the corresponding (Z)- and (E)-3(5)-(2-hydroxyphenyl)-4-styrylpyrazoles, except for nitro derivatives, where both (Z)- and (E)-4′-nitro-3-styrylchromones afforded (E)-3(5)-(2-hydroxyphenyl)-4-(4-nitrostyryl)pyrazoles. The reaction mechanism for these transformations is discussed and the stereochemistries of all products were established by NMR experiments.     

Configurational and Conformational Properties of 1,3,7,9-Tetraphospha-Cyclododeca-1,2,7,8-tetraene: An Ab Initio Study and NBO Analysis

An investigation employing the ab initio molecular orbital (MO) and density functional theory (DFT) methods to calculate structural optimization and conformational interconversion pathways for the two diastereoisomeric forms, (±) and meso configurations of 1,3,7,9-tetraphospha-cyclododeca-1,2,7,8-tetraene (1) was undertaken. Two axial symmetrical conformations are found for (±)-1 configuration. (±)-1-TB axial symmetrical form is found to be about 0.35 and 0.99 kcal mol^?1 more stable than (±)-1-Crown axial symmetrical conformation, as calculated by HF/6-31G*//HF/6-31G* and B3LYP/6-31G*//HF/6-31G* levels of theory, respectively. The unsymmetrical meso-1-TBCC form is found to be the most stable geometry, among the various conformations of meso-1 configuration. HF/6-31G*//HF/6-31G* and B3LYP/6-31G*//HF/6-31G* results showed that between the two most stable conformations of (±) and meso configurations, (±)-1-TB is more stable than meso-1-TBCC by about 3.35 and 2.43 kcal mol^?1, respectively. In addition, MP2/6-31G* and B3LYP/6-311+G** results showed that the (±)-1-TB form is about 1.10 and 2.36 kcal mol^?1 more stable than the meso-1-TBCC form. Further, NBO results revealed that in the most stable form of meso configuration (meso-1-TBCC), the sum of the π* allenic antibonding orbital occupancies (Σ π *_occupancy) is greater than dl configuration ((±)-1-TB). Also, NBO results indicated that in the (±)-1-TB conformer, the sum of σ and π allenic moieties bonding orbital deviations (Σ σ _dev+Σ π _dev) from their normal values, is lower than in the meso-1-TBCC form.     

Synthesis of (Z)- and (E)-3-(2-chloropyridin-5-ylmethyl) oximino-(22E,24R)-ergosta-4,7,22-trienes and their oxidative transformations

(Z)- and (E)-3-(2-chloropyridin-5-ylmethyl)oximino-(22E,24R)-ergosta-4,7,22-trienes (5–6) were synthesized by chemical transformation of ergosterol. Several oxidative transformations of them were studied. It was found that oxidation of these compounds by chromium(VI) oxide formed the corresponding O-substituted 3-ketoximes of the mycosteroid (22E,24R)-ergosta-4,7,22-trien-3,6-dione (7) and (8), which contained α-chloropyridine fragments characteristic of biologically active neonicotinoids. It was shown that oxidation of 5 and 6 by selenium dioxide occurred with formation of the corresponding 9α-hydroxy derivatives 9 and 10.