Molecular and electronic structure of disiloxane,an ab initio MO study

The bond lengths and angels obtained by means of a 4–31G basis agree with electron diffraction data. The calculated SiOSi bending potential, showing a minimum for the linear arrangement, is discussed with regard to available experimental information. Calculated dipole moments and ionization potentials are also in reasonable agreement with experimental data. Comparison is made with STO-3G and INDO results which both overestimate the stability of cyclic structures.     

Thioformaldehyde S-methylide and thioacetone S-methylide: an ab initio MO study of structure and cycloaddition reactivity

The mechanisms of cycloaddition of thioformaldehyde S-methylide and thioacetone S-methylide, as models for an alkyl-substituted ylide, to thioformaldehyde and thioacetone, as well as to ethene as a model for a C=C double bond have been studied by ab initio calculations. Restricted and unrestricted B3LYP/6-31G* calculations were performed for the geometries of ground states, transition structures, and intermediates. Although basis sets with more polarization functions were tested, the 6-31G* basis set was applied throughout. Single-point CASPT2 calculations are reported for analysis of the unsubstituted system. The stabilities of structures with high biradical character seem to be overestimated by DFT methods in comparison to CASPT2. The general trends of the results are independent of the level of theory. Thioformaldehyde adds to thioformaldehyde S-methylide without activation energy, and the activation energies for two-step biradical pathways to 1,3-dithiolane are low. C,S biradicals are more stable than C,C biradicals. The two-step cycloaddition is not competitive with the concerted cycloaddition. Methyl substitution in the 1,3-dipole and the dipolarophile does not change the mechanistic relationships. TSs for the concerted formation of the regioisomeric cycloadducts of thioacetone Smethylide and thioacetone were located. Concerted addition remains the preferred reaction. The reactivity of the C=S double bond is high relative to that of the C=C double bond.     

Electronic and transport properties of silicene-based ammonia nanosensors: an ab initio study

Structural Chemistry - Using density functional theory (DFT) and non-equilibrium Green’s function (NEGF) formalism, the electronic and transport properties of ammonia (NH3) molecule adsorbed...     

An ab initio MO study of allene episulfide, cyclopropanethione and thioxyallyl

The electronic structures of allene episulfide, cyclopropanethione and thioxyallyl were examined by ab initio MO calculations and were compared with those of the corresponding oxygen compounds, allene oxide, cyclopropanone and oxyallyl. The difference in reactivities of allene episulfide and allene oxide was also speculatively estimated from the calculated electronic structures. The lowest singlet state of thioxyallyl was predicted to be the B₂ state, which corresponds to the σ, π-diradical. A small activation energy is required for the cyclization of the B₂ state to give allene episulfide. The A₁ singlet state lies 11 kcal mol⁻¹ higher than the B₂ singlet state and undergoes the disrotatory rotation of methylene groups to give cyclopropanethione with no activation energy.     

Solvent-dependent stereoselectivity in a Still-Wittig rearrangement: an experimental and ab initio study

[see reaction]. The Still-Wittig rearrangement gave opposite selectivities for (Z:E)-alkenes in THF (3:1) vs toluene (1:3) in the synthesis of serine-proline dipeptide amide isosteres. Four transition states leading to (Z)-and (E)-alkenes with THF and without (representing toluene) were identified by ab initio calculations at the 3-21G* level. The calculated (Z:E)-ratios with THF (4.7:1) and without THF (1:3.2) suggested that the transition state geometries and energies were well-represented by the calculations.     

Protonation and deprotonation of hydroxamic acids. An MO ab initio study

Ab initio molecular orbital calculations with 4-31G//4-31G, 6-31G^*//4-31G and 6-31+G//4-31G basis sets have been used to examine the structure, relative energy, protonation and deprotonation of a series of seven hydroxamic acids in the gas phase. The results show that hydroxamic acids are predominantly in the E-TS form and that the most probable protonation site is the carbonyl oxygen atom, while deprotonation proceeds by loss of NH hydrogen.     

In-plane vibrational modes of cytosine from an ab initio MO calculation

Harmonic force constants, in-plane vibrational frequencies, and in-plane vibrational modes of cytosine were calculated by an ab initio Hartree—Fock SCF MO method. The force contants were calculated by the use of an energy gardient method with the STO-3G basis set, and then they were corrected into “4-31G force constants” by the scaling factors given by us previously for the case of uracil. The corrected set of force constants can produce a calculated vibrational spectra of cytosine and cytosine-1,amino-d₃, that can be well corrected with the observed Raman and infrared spectra of these compounds, with little ambiguity. Thus, the assignments of all the in-plane vibrations are now practically established. The calculated vibrational modes, in addition, can account for the recently published resonance Raman effects of cytosine residue.     

Trinitromethyl anion. An ab initio MO study of its structure

Several conformers of nitroform anion are studied with ab initio MO methods.     

Tautomerism and infrared spectra of 2-thiopurine: an experimental matrix isolation and theoretical ab initio and density functional theory study

Infrared spectra of 2-thiopurine (2-mercaptopurine, 2-purinethiol ) isolated in low-temperature Ar and N2 matrixes are reported. These spectra indicate that the compound adopts exclusively the thiol N9H tautomeric form. The theoretical calculations of relative energies of 2-thiopurine tautomers have been carried out at the MP4(SDTQ)//HF level using the 6-31G(d,p) basis set. The thiol N9H tautomer was predicted to be the most stable of all isomers of 2-thiopurine. The infrared spectra of the tautomers of 2-thiopurine have been calculated at the DFT(B3LYP)/6-31G(d,p) level. Good agreement between the experimental spectra and the spectra calculated for thiol N9H tautomer supported the identification of the dominant tautomer. It has also allowed for the reliable assignment of the bands observed in the experimental IR spectrum.     

Electronic structure of NH+: An ab initio study

We report ab initio self‐consistent field MRSD‐CI electronic structure calculations of the NH⁺ cation. A basis set of DZ + POL quality augmented with Rydberg and bond functions was employed together with an extensive treatment of electron correlation. More than 50 electronic states of NH⁺ are reported, including doublets, quartets, and sextets. Leading configurations, vertical ionization energies of NH, vertical excitation energies of NH⁺, and potential energy curves are reported. Spectroscopic properties calculated for the known bound electronic states of NH⁺ are found in good agreement with experiment. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Structure-property relationship in py-hexahydrocinchonidine diastereomers: ab initio and NMR study

Two py-hexahydrocinchonidine diastereomers were selectively obtained in the heterogeneous catalytic hydrogenation of cinchonidine over supported Pt catalyst. The two isolated compounds when used as chiral base catalysts in the Michael addition of a beta-keto ester to methyl vinyl ketone gave products of opposite configuration in excess. To trace the reason of this behavior, in the present study, the structures of the two diastereomers were fully optimized by ab initio quantum chemical calculation. These results were then compared with several nuclear Overhauser enhancement spectroscopy (NOESY) signal intensities from the spectra of the two compounds. Further we performed a conformational search on all the optimized geometries independently for the two flexible torsional angles, which are linking the quinuclidine and tetrahydroquinoline moieties present in these molecules. This study allowed us to propose the configuration of the C(4)(') chiral center. Thus, the product mixture resulted in the hydrogenation of cinchonidine containing the 4'-(S)-diastereomer in excess (de = 20%). According to the computation results the 4'-(S)-diastereomer is more stable than the 4'-(R)-diastereomer. The 4'-(S)-conformer obtained by computation has lower electronic energy than the structures obtained for the 4'-(R)-diastereomer, which may explain the excess formation of the first one. The results of the Michael addition catalyzed by these diastereomers were interpreted on the basis of these conclusions.     

The thermal decomposition of thiirane: a mechanistic study by ab initio MO theory

Using high-level ab initio MO methods, we have identified two reaction pathways with different thermodynamic and kinetic properties for the thermal decomposition of the three-membered heterocycle thiirane (C2H4S) and related derivatives. A homolytic ring opening, followed by attack of the generated diradical on another thiirane molecule, and subsequent elimination of ethene in a fast radical chain reaction results in the formation of disulfur molecules in their triplet ground state (3S2) and requires activation enthalpies of deltaH#(298) = 222 kJ mol(-1) and deltaG#(298) = 212 kJ mol(-1). This reaction mechanism would result in a first-order rate law in agreement with one reported gas-phase experiment but does neither match the experimental activation energy nor does it explain the observed retention of the stereochemical configuration in the thermal decomposition of certain substituted thiiranes. Alternatively, sulfur atoms can be transferred from one thiirane moleculeto another with the intermediate formation of thiirane 1-sulfide (C2H4S2). This molecule can either decompose unimolecularly to ethene and disulfur in its excited singlet state (1S2) or, by means of spin crossover, S2 in its triplet ground state may be formed. On the other hand, the thiirane 1-sulfide may react with itself and transfer one sulfur atom from one molecule to another with formation of thiirane 1,1-disulfide (C2H4S3), which is an analogue of thiirane sulfone; thiirane is formed as the second product. The 1,1-disulfide may then decompose to ethene and S3. In still another bimolecular reaction, the thiirane 1-sulfide may react with itself in a strongly exothermic reaction to give S4 and two equivalents of ethene. This series of reactions results in a second-order rate law and requires activation enthalpies of deltaH#(298) = 109 kJ mol(-1) and deltaG#(298) = 144 kJ mol(-1) for the formation of thiirane 1-sulfide, while the consecutive reactions require less activation enthalpy. Elemental sulfur (S8) is eventually formed by oligomerization of either S2, S3, or S4 in spin-allowed reactions. These findings are in agreement with most experimental data on the thermal desulfurization of thiirane and its substituted derivatives. Thiirane 1-persulfide (C2H4S3) with a linear arrangement of the three sulfur atoms as well as zwitterions and radicals derived from thiirane are not likely to be intermediates in the thermal decomposition of episulfides.     

An ab initio MO study on the thymine dimer and its radical cation

Ab initio SCF calculations with the 6-31G basis set for the thymine dimer (cys-syn form) and the thymine dimer radical cation are reported. The fusion of the thymine bases at the C5 and C6 positions involves the formation of a cyclobutane ring with puckering. The puckering causes a notable difference in the electronic structures of the two bases of the thymine dimer. The density of the HOMO orbital of the thymine dimer is localized on the O2, N1, and C6 atoms of both thymine rings, with the higher density on one of the rings. The HOMO orbital has a bonding character on the C6(SINGLEBOND)C6 bond. In the thymine dimer radical cation, the unpaired electron is localized mainly on the lengthened C6(SINGLEBOND)C6 bond with the higher density on one of the C6 atoms and to a lesser extent on the N1 atoms of both rings. © 1996 John Wiley & Sons, Inc.     

Size-expanded yDNA bases: an ab initio study

xDNA and yDNA are new classes of synthetic nucleic acids characterized by having base-pairs with one of the bases larger than the natural congeners. Here these larger bases are called x- and y-bases. We recently investigated and reported the structural and electronic properties of the x-bases (Fuentes-Cabrera et al. J. Phys. Chem. B 2005, 109, 21135-21139). Here we extend this study by investigating the structure and electronic properties of the y-bases. These studies are framed within our interest that xDNA and yDNA could function as nanowires, for they could have smaller HOMO-LUMO gaps than natural DNA. The limited amount of experimental structural data in these synthetic duplexes makes it necessary to first understand smaller models and, subsequently, to use that information to build larger models. In this paper, we report the results on the chemical and electronic structure of the y-bases. In particular, we predict that the y-bases have smaller HOMO-LUMO gaps than their natural congeners, which is an encouraging result for it indicates that yDNA could have a smaller HOMO-LUMO gap than natural DNA. Also, we predict that the y-bases are less planar than the natural ones. Particularly interesting are our results corresponding to yG. Our studies show that yG is unstable because it is less aromatic and has a Coulombic repulsion that involves the amino group, as compared with a more stable tautomer. However, yG has a very small HOMO-LUMO gap, the smallest of all the size-expanded bases we have considered. The results of this study provide useful information that may allow the synthesis of an yG-mimic that is stable and has a small HOMO-LUMO gap.     

An ab initio MO study on the thiol—disulphide exchange reaction

The characteristics of the thiol—disulphide exchange reaction are examined by an ab initio MO method. It is shown that this exchange reaction proceeds via one transition state, with almost no conformational distortion.     

Gas-phase structure of protonated histidine and histidine methyl ester: combined experimental mass spectrometry and theoretical ab initio study

Gas-phase H/D exchange experiments with CD3OD and D2O and quantum chemical ab initio G3(MP2) calculations were carried out on protonated histidine and protonated histidine methyl ester in order to elucidate their bonding and structure. The H/D exchange experiments show that both ions have three equivalent fast hydrogens and one appreciably slower exchangeable hydrogen assigned to the protonated amino group participating in a strong intramolecular hydrogen bond (IHB) with the nearest N(sp2) nitrogen of the imidazole fragment and to the distal ring NH-group, respectively. It is taken for granted that the proton exchange in the IHB is much faster than the H/D exchange. Unlike in other protonated amino acids (glycine, proline, phenylalanine, tyrosine, and tryptophan) studied earlier, the exchange rate of the carboxyl group in protonated histidine is slower than that of the amino group. The most stable conformers and the enthalpies of neutral and protonated histidine and its methyl ester are calculated at the G3(MP2) level of theory. It is shown that strong intramolecular hydrogen bonding between the amino group and the imidazole ring nitrogen sites is responsible for the stability and specific properties of the protonated histidine. It is found that the proton fluctuates between the amino and imidazole groups in the protonated form across an almost vanishing barrier. Proton affinity (PA) of histidine calculated by the G3(MP2) method is 233.2 and 232.4 kcal mol(-1) for protonation at the imidazole ring and at the amino group nitrogens, respectively, which is about 3-5 kcal mol(-1) lower than the reported experimental value.     

An ab initio theoretical study of the stereoisomers of tetrahydrocannabinols

An extensive theoretical study of the stereoisomers of tetrahydrocannabinols has been performed at the ab initio HF/6-31G^* and B3LYP/6-31G^* levels. Effects of solvation were calculated with the Onsager model (with full geometry optimization), SCRF with Tomasi's PCM, and isodensity polarization continuum models. Single-point MP2//HF/6-31G^* calculations were carried out. Frequency calculations for all the isomers at the HF/6-31G^* level and for two natural isomers ¹-THC-RR and ⁶-THC-RR at the B3LYP/6-31G^* level were performed. Our results support the findings of the previous AM1 studies that the orientation of the carbocyclic ring and its C1 substituent with respect to the phenyl group hydroxyl oxygen play the major role in the activity. The calculated values of the LUMO energy (lowest unoccupied molecular orbital) and the hardness of the stereoisomers show that for the trans isomers it is easier to remove one electron from its HOMO (highest occupied molecular orbital) to the LUMO and easier to accept an electron from the receptor binding site than for the cis isomers. Combining geometric features (the orientation of the carbocyclic ring and its C1 substituent with respect to the phenyl group hydroxyl oxygen) with electronic features (LUMO and hardness), we explain the activity differences among the stereoisomers.     

Stereochemistry and tautomerism of silicon-containing 1,2,3-triazole: ab initio and NMR study

Structural Chemistry - In this paper, an approach is proposed for determining the ratio of prototropic annular tautomers of organosilicon 1,2,3-triazoles, which are hardly experimentally determined...     

Structural NMR and ab initio study of salicylhydroxamic and p-hydroxybenzohydroxamic acids: evidence for an extended aggregation

The acid-base behavior and self-aggregation of salicylhydroxamic (SHA) and p-hydroxybenzohydroxamic acids (PHBHA)have been investigated by UV and 1HNMR spectroscopy, respectively. The acid-base parameters, measured in H2O at 25 degrees C and I=0.1 M, were pK1=7.56, pK2=9.85 for SHA and pK1=8.4, pK2=9.4 for PHBHA. The 1H NMR signals for salicylhydroxamic and p-hydroxybenzohydroxamic acids measured in acetone indicate that both acids self-aggregate according to a mechanism where two monomers produce planar E-E dimers stabilized by horizontal H-bonds. Further dimer aggregation yields sandwich-like tetramer structures stabilized by vertical H-bonds and pi-pi interactions. The p-hydroxybenzohydroxamic tetramers, less stable than those of salicylhydroxamic, contain two water molecules in their structures. The gas-phase structures of salicylhydroxamic acid and its anions were investigated by ab initio calculations using the density functional theory at the B3LYP/AUG-cc-pVDZ level. The SHA most stable gas-phase conformer is the A-Z amide, a structure with all three phenolate (OP), carboxylate (OC), and hydroxamate (OH) oxygen atoms in the cis position. The B-Z amide, with the OP oxygen trans to OC, lies 5.4 kcal above the A-Z amide. The most stable monoanion is the N-deprotonated A-Z amide.     

Interaction energy anisotropy of the pyrrole dimer: ab initio theoretical study

The van der Waals pyrrole dimer is studied using supermolecular and perturbation ab initio treatment with inclusion of correlation energy. The influence of selected geometry variations on the interaction energy components is investigated. Our calculations verified the minimum on the potential energy surface deduced from microwave spectra. Its stability is possibly related not to the extremal values of the selected interaction energy contributions but its physical origin is connected with the delicate equilibrium between the repulsive and attractive forces. Any structure variation connected with the extremal attraction energy is more than compensated for by the repulsion energy. Received: 11 June 1998 / Accepted: 6 October 1998 / Published online: 1 February 1999