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The conformational minima of a series of chiral ethers have been studied by means of DFT (B3LYP/6-31+G**) and ab initio (MP2/6-311+G**) methods. The protonation of these compounds results in diasteromeric systems depending on the protonated lone pair. The relative energy of the conformers has been analyzed using the QTAIM and NBO methods. © 2007 Elsevier B.V. All rights reserved.

Formic, acetic, trichloroacetic, benzoic and salicylic acids were studied with density functional theory in the explicit presence of six or seven water molecules, comparing the relative energies of the solvated acid and dissociated forms. Six water molecules are found to be sufficient to stabilize the dissociated ion pair of these weak acids at the B3LYP/6-31++G** level of theory. The H13O6+ ion appears as a common (six water molecule) structural unit for the dissociated carboxylic acids as studied here. The relative energy differences between the non-dissociated and dissociated clusters for each acid are in accordance with pKa data.

Free radical-induced aggregation of amyloid beta (Aβ) peptide is a recently proposed mechanism in which C α -centered radicals can form on either Gly33 or Gly29 of Aβ(1-42). Limited structural data for the glycyl radical are available. In this study, the structure of N -Ac-Gly-NHMe and N -Ac-Gly -NHMe was determined using ab initio and DFT calculations. E = f (ϕ,ψ) potential energy surfaces (PES) were constructed by independently constraining the ϕ and ψ angles, 30° apart from 0 to 360°. The structure of each conformer was subsequently optimized using Hartree–Fock and DFT calculations, and the relative energy was calculated using B3LYP/6-31G(d,p). The Poisson–Boltzmann (PB) solver was used to simulate an aqueous environment. The PES of N -Ac-Gly-NHMe was flat, displaying the ability of Gly to sample conformations in both the L and D configurations. Conversely, the N -Ac-Gly -NHMe had a global minimum in the β L conformation, with a high-energy barrier preventing transitions to other minima. The restricted β conformation of N -Ac-Gly -NHMe corresponds to the anti-parallel β-sheets observed in Aβ aggregates. The β conformation permits inter-strand H-bonding that could stabilize the aggregates.

The effect of substituents on the enone–dienol tautomerism of but-2-enal by [1,5]-H shift has been investigated systematically. All stationary point structures and energies of substituted but-2-enal are obtained at the levels of B3LYP/6-31G* and B3LYP/6-311++G(d,p). It is shown that the substituents in the 2-substituted series exert more significant effects on the relative energies of dienol with respect to enone and the energy barriers for enolization than those in the 3- or 4-substituted series. In general, the relative energies and energy barriers could be reduced by the electron-withdrawing substituents BH2, CN, NO, since the structure of dienol and the corresponding transition state could be stabilized more than those of enone, but increased by the electron-donating substituents in the order NH2

Twenty-four individual geometric structures of the 20-carbon system are investigated using hybrid Hartree–Fock/density functional theory (DFT-B3LYP) in combination with the 6-31G and 6-311G* basis sets. These computations are carried out in order to evaluate the relative energies of the various C20 isomers utilizing both geometry optimization and single-point energy calculations. The relative energies of the three most widely studied C20 isomers (ring, bowl, and cage) are compared to the energies of other cyclic, bowl-like, and miscellaneous isomers. Although the ring and the bowl isomers are predicted to be the two most stable species, we have identified three to four additional cyclic structures that are predicted to be energetically competitive with the fullerene structure.

The calculated energies of alanine model conformers correlate with the natural abundance of alanine conformers in proteins. However, the observed conformational distribution of alaine in proteins cannot be described solely on the basis of quantum chemical calculations of the corresponding diamide. We suggest that amino acid residue conformation in a folded protein is the result of multiple factors, among which the relative energy of the residue is one of the most important ones. In this study, we investigate the possible role of a second factor, namely atom–atom contacts. We found that natural conformer abundance correlates well with the atom–atom contacts of the respective conformers. Additionally, contacts can also be responsible for the deviations form the conformer distribution expected on the basis of the calculated energies. However, the observed correlations are much more robust for surface than for internal residues in proteins, suggesting that residue conformation is influenced by other interactions to a greater extent in the core of proteins.

A variety of ab initio molecular orbital methods, RHF, MP2 and B3LYP, have been applied to N-methyl-N-nitrosourea (1), N-methyl-N-nitrosoacetamide (2) and N-methyl-N-nitrosomethylcarbamate (3) and the anti and syn structures and the transition state (TS) structures connecting them have been examined. In each of these compounds, the anti structure was predicted to be more stable than the syn structure and the relative energy of the TS structure was considerably higher than those of the anti and syn structures. The energy difference between anti and syn of 1 is slightly smaller than those of 2 and 3 owing to the existence of hydrogen bonding between O in the nitroso group and H in the NH2 group.

The stereoisomers of 7-acetyl-benzo[b]naphtho[1,8-f,g]thiazocin-8(7H)-one 13-oxide (1) were studied by ab initio MO method at the HF/3–21G level of theory, and the results were compared with those obtained at the semiempirical MO (AM1) level of theory. Of the eight energy-minimum structures optimized by the semiempirical methods two were rather distorted in their molecular geometries. These two structures were annihilated at the ab initio level of theory. The relative order of stability obtained by the two methods was qualitatively the same. Quantitatively, however, the corresponding structures differed somewhat from each other both in their geometry data and relative energy values. Bader-type electron density analysis suggested that the transannular S…N interactions in some stereoisomers of 1,5-thiazocine derivative 1 may be regarded in the vicinity of 10% of a single bond.

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.

A 4-21G conformational analysis with complete geometry optimization was carried out for isobutylamine and diisopropylamine. The results are compared with available geometrical data for similar amines in order to establish general conformational trends.

Conformational energies of the title peptide calculated by the empirical program packages GROMOS, CHARMM and DISCOVER (the latter two also with the AMBER force field), semiempirical MO scheme AMI, and the ab initio STO-3G basis set are compared. The lowest energies were obtained for either of the C7C7 (axial and equatorial) conformations except by CHARMM with incorporated AMBER force field, by which the βII conformation is preferred. The relative energy differences of these three conformations are within 3–5 kcal mol −1 . Energy minimizations of the peptide surrounded by 121 SPC type water molecules give the lowest energy of hydration for the βII bend. The calculated energies are compared with the results of experimental conformational analysis.

The geometries of the lowest energy gauche and trans conformers of 2-fluoroethanol (2FE) and 2-chloroethanol (2CE) have been calculated at the 6-31G* level, and the energies calculated with several basis sets and the inclusion of electron correlation. The global minimum for both compounds is found to be the gauche conformer, in agreement with experiment. At the MP3/6-31G* level, trans 2CE is 1.66 kcal mol−1 higher in energy than gauche, while trans 2FE is 2.34 kcal mol−1 higher than gauche. Geometries were also optimized for various fixed values of the HOCC dihedral angle, from which the barrier to OH rotation was derived. Further calculations at the MP3/6-311+ +G** level lowered the relative energy of trans 2FE by only 0.3 kcal mol−1 to 2.03, but had a much larger effect on the HOCC rotational barrier. Calculations at the MP3/6-311++G** level were also done for ethanol, and a comparison of the ethanol and 2FE rotational profiles indicates a strongly attractive HF interaction which, after elimination of non-bonding and bending contributions, may be most simply modelled as a coulombic term. Vibrational frequencies were estimated for 2FE and 2CE at the 6-31G* level, and do not support the idea that a small HF separation is responsible for the frequency differences between trans and gauche.