An ab initio study on the geometries and vibrational frequencies of hydrazoic acid and methyl azide

The geometric parameters for hydrazoic acid and methyl azide were optimized at the HF/6-31G^** and MP2/6-31G^** levels and the vibrational frequencies of the compounds were calculated by use of these optimized geometries. The experimental frequencies are assigned on the basis of the calculated results. The effects of deutero-substitution and substitution of hydrogen in HN₃ by a methyl group are also discussed.     

Comparison of calculated DFT/B3LYP and experimental C and O NMR chemical shifts, ab initio HF/6-31G* optimised structures, and single crystal X-ray structures of some substituted methyl 5β-cholan-24-oates

Single crystal X-ray structures (monoclinic space group P2₁) for methyl 3-oxo-5β-cholan-24-oate and methyl 3,12-dioxo-5β-cholan-24-oate have been solved and compared with HF/6-31G* optimised structures. In the crystalline packings the side chains are connected with weak OC(sp³)HO-type of interactions between C25–H and C24–O–C25 and the keto ends with weak C(sp³)HO=C-type of interactions between C4–H and O=C3. The orientations of the side chains, which steric configurations are of great importance to the biological activity of the molecules, are compared with the experimental structure of methyl 3-hydroxy-5β-cholan-24-oate. Probable reasons for the observed differences are discussed. In addition, ¹³C and ¹⁷O NMR chemical shifts of methyl 3-oxo-5β-cholan-24-oate and methyl 3,12-dioxo-5β-cholan-24-oate as well as the epimeric methyl 3-hydroxy-5β-cholan-24-oate and methyl 3β-hydroxy-5β-cholan-24-oate have been calculated (DFT/B3LYP/6-311G*) and compared with the experimental values by linear regression analyses. In general, the correspondence between the theoretical and experimental parameters is good or excellent.     

Tautomeric and conformational equilibrium of 2-nitrosophenol and 9,10-phenanthrenequinonemonooxime: ab initio and NMR study

The tautomeric and conformational equilibrium of 2-nitrosophenol and 9,10-phenanthrenequinonemonooxime was studied by ab initio methods. The geometry optimizations of the structures investigated were done without any geometrical restrictions at HF/6-31G** and MP2/6-31G** levels of theory. The transition structures for tautomeric and rotameric conversions were located. To correct for electron correlation, single-point calculations were carried out up to MP4/6-311G*//MP2/6-31G* level of theory.

Ab initio calculations for 2-nitrosophenol in agreement with the available experimental data define the nitroso form as more stable. It was found that the influence of the correlation energy on the relative stabilities is smaller for the rotamers of the nitroso tautomer but substantially (4–6 kcal/mol) for the oxime forms. It was found that the barrier height of tautomerization reaction is 10.24 kcal/mol.

The structure of the 9,10-phenanthrenequinonemonooxime was studied by solid and liquid state NMR spectroscopy. Ab initio calculations in agreement with our experimental data predict that the compound exists as oxime tautomer and the syn-oxime is most stable. It was found that the solvent influence on the relative stabilities of both isomers: syn- and anti-oxime. While in chloroform solution the syn-oxime is preferred but in DMSO anti-oxime is more stable in energy.

At the MP4/6-311G*//MP2/6-31G**+ZPE level of theory the barrier of tautomerization was predicted to be 10.96 kcal/mol and the rotational barrier around the single C–O bond in the syn-oxime was found to be 7.57 kcal/mol. The rotation is facile and this explains the absence of nitroso tautomers in solution.     

Density functional calculations of the pseudorotational flexibility of tetrahydrofuran

The flexibility of the five-membered ring in tetrahydrofuran was investigated using quantum mechanical methods involving density functional, Hartree-Fock, and many-body perturbation theory (MP2, MP4) calculations. We found that motion along the pseudorotational path of tetrahydrofuran is nearly free. The 0.1 kcal/mol energy barrier for pseudorotation, calculated at the highest MP4(SDQ)/6-311++G(2d,p)//MP2/6-311++G(2d,p) level of theory, agrees well with the experimental value of 0.16±0.03 kcal/mol. Similar results were obtained with the S-VWN, B3-LYP and B-LYP density functional calculations using the 6-31G(d) set of atomic orbitals. Also the density functional dipole moments and geometries were in good agreement with both the MP2 and experimental benchmarks. However, all density functional methods that utilized the default integration grid in the Gaussian 94 program were found to provide false stationary points of the C ₁ symmetry near the pseudorotational angle of 100°. These stationary points disappeared when a denser spherical-product grid was used. Overall, the hybrid B3-LYP functional was found to be the most promising quantum mechanical method for the modeling of biomolecules containing the furanose ring. Received: 17 June 1997 / Accepted: 20 November 1997     

Density functional calculations of vibrational wavenumbers, ring puckering, and asymmetric CHO potential functions for cyclobutanecarboxaldehyde: comparative study between theoretical and experimental spectra

The structural parameters and energies of the trans-equatorial and gauche-equatorial conformers of cyclobutanecarboxaldehyde c-C₄H₇–CHO were investigated by quantum mechanical DFT-B3LYP (Density Functional Theory-Becke 3 exchange and Lee-Yang–Parr correlation functional) calculations using 6-311G^** basis set. The potential functions for the CHO asymmetric torsion in the equatorial molecule and for the ring puckering inversion were derived. The vibrational wavenumbers were calculated and the potential energy distributions PED among the symmetry coordinates of the normal modes were computed for the two stable conformers of the molecule. The vibrational assignments on the basis of the calculated PED values were compared to the reported ones from experimental data. The vibrational infrared and Raman spectra of the mixture of the trans-equatorial and gauche-equatorial were plotted and the line intensities were compared to the corresponding experimental ones.     

Ab initio fragment molecular orbital (FMO) method applied to analysis of the ligand-protein interaction in a pheromone-binding protein

Full quantum computation of the electronic state of proteins has recently become possible by the advent of the ab initio fragment molecular orbital (FMO) method. We applied this method to the analysis of the interaction between the Bombyx mori pheromone-binding protein and its ligand, bombykol. The protein–ligand interaction of this molecular complex was minutely analyzed by the FMO method, and the analysis revealed several important interactions between the ligand and amino acid residues.     

A Theoretical Study of 1‐D and 2‐D Helium Lattices

One‐ and two‐dimensional (1‐D and 2‐D) helium lattices have been studied using ab initio RHF/6–31G** computations. Structural, physical and thermochemical properties have been calculated and analyzed for the 1‐D and 2‐D He_N lattices respectively up to N = 50 and N = 36. Asymptotic properties of the 1‐D He_N lattices are obtained by extrapolating N‐dependence properties to large values of N. Analysis of the results show that the bulk per‐atom interaction (binding) energies increase while the optimized interatomic distances (bond lengths) slightly decrease with the increase in size of the 1‐D He_N lattices and both reach their asymptotic values of 0.352 cm^?1 and 3.18775 Å, respectively. Between the square and hexagonal (packed) structures of the 2‐D He_N lattices, the latter is more favored. Extrapolated values of the calculated properties, including lattice parameter, binding and zero point energies, heat capacity, and entropy have also been calculated for both 1‐D and 2‐D He_N lattices. The surface densities for monolayer films of helium atoms with square and hexagonal configurations have been calculated to be respectively 9.84 × 10¹⁸ and 1.04 × 10¹⁹ helium atoms/cm² which are comparable to the experimental value of 2.4 × 10¹⁹ helium atom/m² well within the typical large and directional error bars of the experiments. Surface effects have been investigated by comparing the packed He_N2‐D lattices with the same value of N but with different geometries (arrangements). This comparison showed that the He_N lattices prefer arrangements with the smallest surface area.     

Molecular structures and ab initio molecular orbital calculations of the optically active derivatives of 1-aminocyclopropane-1-carboxylic acid

The novel optically active derivatives of 2,2′-disubstituted-1-aminocyclopropane-1-carboxylic acid (−)-2 and (+)-3 were synthesised from the spiro-azlactone (+)-1. Oxidation of the diol moiety of (+)-3 gave by ring enlargement the racemic mixture of 2,3-dihydrofuran derivative (±)-6. This conversion is explained by stepwise rearrangement of the initially formed tetrasubstituted cyclopropanecarbaldehyde 4 through zwitterionic's reactive intermediate 5. The formation of (±)-6 is preferred energetically as established by ab initio calculations of the ground states and possible intermediates for that rearrangement. The crystal structure and absolute configuration of the compounds (+)-1, (−)-2, (+)-3 and (−)-7 were determined by single-crystal X-ray diffraction method. All four compounds possess Z-configuration of the cyclopropane ring. The dioxolane ring in the structures (+)-1 and (−)-2 adopts half-chair conformation, while the cyclopropane ring and geminally substituted groups in the structures (−)-2, (+)-3 and (−)-7 possess the anticlinal conformation. The molecules of the compound (+)-1 are connected by very weak intermolecular hydrogen bond of C-H?O type. In the compounds (−)-2, (+)-3 and (−)-7inter- and intramolecular hydrogen bonds of N-H?O type were observed. The spiro-compound (+)-1 exhibited a more pronounced inhibitory activity against the proliferation of murine leukemia and human T-lymphocytes cells than other type of tumor cell lines and normal human fibroblast cells.     

Modeling of biliverdin reduction process: regio-specificity and H-bonding

Octa ethyl biliverdin (OEBV) has been employed as a model for natural biliverdin and its geometry has been optimized by using semiempirical (AM1, PM3), DFT, and hybrid ONIOM methods. Geometries and energetics of formation of octa ethyl bilirubin (OEBR) formed by reduction from OEBV via three carbon sites β, γ, and δ have been obtained. It has been shown that γ-OEBR has two configurational isomers (named γ₁ and γ₂), which can convert to each other by internal 1,5-hydrogen shift. The results show that, within the accuracy level of semiempirical methods, all three isomers namely, β, γ₁, and δ-OEBR are of similar stability whereas, at higher level of theory, γ₁-OEBR is less stable than others. Moreover, γ₂-isomer with one more of its pyrrole rings being aromatic can achieve a higher symmetry, and is the most stable among others by at least 5–6 kcal mol⁻¹ based on various methods employed. It is interesting to note that the ridge-tile conformation, which has been confirmed for natural bilirubin was not observed for calculated geometries of γ₁- and γ₂-isomers. A conformational analysis show that an energy barrier of 25 kcal mol⁻¹ must be surmounted for γ₂ to obtain the ridge-tile geometry.

OEBV was synthesized and purified from octa ethyl porphyrin iron (III) chloride, and was reduced to OEBR by sodium borohydride (NaBH₄). Chemical reduction of OEBV with NaBH₄ was followed in CDCl₃ and CD₃OD solutions and the product was characterized by ¹H NMR and UV–Vis spectroscopy. The results show that γ₂-isomer as the major product, forms along with γ₁ via an equilibrium tautomerization reaction.     

Theoretical Studies of Distyrylbenzene and its Optical Properties

The electronic and geometrical properties of distyrylbenzene (DSB) are investigated by using chemistry theoretical calculation methods. Specifically, the excited state properties are studied by performing ab initio correlation interaction singlet (CIS) and time‐dependent density functional theory; the ground state and Raman activities are computed by density functional theory with the B3LYP method. Eight conformers of distyrylbenzene are found and they are derived from three isomers which are cis, cis‐, cis, trans‐, and trans, trans‐, respectively. The relative energy shows that each isomer of three types is separated with a large energy barrier, but a small energy difference of each conformer is found if they are in the same type. The transition state also shows the barrier between conformers is lower than isomers. The computed excited transition energies using ZINDO/S based on the optimized geometries at a DFT/B3LYP level with 6–31+G show an excellent agreement with experimental absorption spectra.