Ab initio calculations on sulfur-containing compounds. II. One-electron properties of H2S

Closed-shell RHF one-electron properties are calculated for H₂S using a total of 41 different s, p basis sets and two polarized basis sets (6–31G* and 6–31G**). Total energies and geometries alone are not a comprehensive criteria for selecting the best basis sets. It is shown here that the comparison of a number of one-electron properties can serve as an excellent criteria for testing basis sets. The quality or reliability of a basis set is taken as being its agreement with a large uncontracted s, p basis set (s, p limit).     

Uniform quality gaussian basis sets for molecular calculations. II. C2 hydrocarbons

This investigation is a continuation of a study on the optimality of MO basis sets of Gaussian functions, when constructed from AO basis sets optimized for the neutral atom or for ions. A formal charge parameter Q is used to adjust AO basis sets to the molecular environment, by virtue of a simple quadratic equation. Calculations are performed on a series of seven C₂ hydrocarbons (C₂H₂, C₂H₄, C₂H₆, C₂H₃⁺ (open), C₂H₃⁺ (bridged), C₂H₅⁺ (bridged), and C₂H₄^? radical anion). A simple rule is formulated to give approximate values of the charge parameter Q.     

Uniform quality gaussian basis sets for molecular calculations. III. Charge optimized basis sets

Gradient optimized constrained (2s ≠ 2p) and unconstrained (2s ≠ 2p) Gaussian 3G basis sets are reported for the first-row atoms and ions X^O, for Q = ?2 to +4. Analytic equations have been fitted to the logarithm of the exponents as a function of the nuclear charge Z and formal charge Q. Consequently only two parameters Z and Q have to be specified in order to completely define a basis set.     

First principle computational study on the full conformational space of L-proline diamides

Ab initio molecular orbital computations were carried out at three levels of theory: RHF/3-21G, RHF/6-31G(d), and B3LYP/6-31G(d), on four model systems of the amino acid proline, HCO-Pro-NH2 [I], HCO-Pro-NH-Me [II], MeCO-Pro-NH2 [III], and MeCO-Pro-NH-Me [IV], representing a systematic variation in the protecting N- and C-terminal groups. Three previously located backbone conformations, gammaL, epsilonL, and alphaL, were characterized together with two ring-puckered forms syn (gauche+ = g+) or "DOWN" and anti (gauche- = g-) or "UP", as well as trans-trans, trans-cis, cis-trans, and cis-cis peptide bond isomers. The topologies of the conformational potential energy cross-sections (PECS) of the potential energy hypersurfaces (PEHS) for compounds [I]-[IV] were explored and analyzed in terms of potential energy curves (PEC), and HCO-Pro-NH2 [I] was also analyzed in terms of potential energy surfaces (PESs). Thermodynamic functions were also calculated for HCO-Pro-NH2 [I] at the CBS-4M and G3MP2 levels of theory. The study confirms that the use of the simplest model, compound [I] with P(N) = P(C) = H, along with the RHF/3-21G level of theory, is an acceptable practice for the analysis of peptide models because only minor differences in geometry and stability are observed.     

Relaxation in torsional motion of triplet oxirane

The rotational barrier height E_rot in the lowest triplet state oxirane molecule was calculated to be 26.3 kcal/mole using a double zeta basis set with partial geometry optimization. This suggest ldrelaxedrd rotation and the computed e(T₁- E(S_o) + E_rot value is commensurate with the enthalpy change for the oxirane-forming O(³P) + C₂H₄ reaction, thus providing a rationale for the stereochemical features of the reaction.     

Intrinsically stable secondary structure elements of proteins: a comprehensive study of folding units of proteins by computation and by analysis of data determined by X-ray crystallography

Different protein architectures show strong similarities regardless of their amino acid composition: the backbone folds of the different secondary structural elements exhibit nearly identical geometries. To investigate the principles of folding and stability properties, oligopeptide models (that is, HCO-(NH-L-CHR-CO)(n)-NH(2)) have been studied. Previously, ab initio structure determinations have provided a small amount of information on the conformational building units of di- and tripeptides. A maximum of nine differently folded backbone types is available for any natural alpha-amino acid residue, with the exception of proline. All of these conformers have different relative energies. The present study compiles an ab inito database of optimized HCO-(L-Xxx)(n)-NH(2) structures, where 1相似文献   

Simple relationship between total molecular correlation energies and LMO sizes

As an alternative to the density functional approach to estimating total molecular correlation energies, the equation E_corr=?0.06593 ∑ R, where R_i=〈r²〉${}_{\text{i}}^{\text{½}}$ and i runs over the localized molecular orbitals was fitted to 25 STO -3G data points with a root-mean-square error of 0.025 hartree. Other more general equations were tried but no significant improvement was observed in the fit.     

Folded and unfolded conformations of the omega-3 polyunsaturated fatty acid family: ch(3)ch(2)[ch=chch(2)](b)[ch(2)](m)cooh: first principles study

Polyunsaturated fatty acids (PUFA) like stearidonic acid (SDA;18:4 n-3) eicosapentaenoic acid (EPA; 20:5 n-3), and docosahexaenoic acid (DHA; 22:6 n-3) and its chain fragment models were studied at B3LYP/6-31G(d) levels of theory. Significant conformations for the cis and trans isomers were selected to obtained the thermodynamic functions (DeltaH, DeltaS, DeltaG) for the cis-trans isomerization and for folding using the B3LYP/6-311+G(2d,p)//B3LYP/6-31G(d) level of theory. The structural analysis shows that there are significant differences in thermodynamic function of the trans- and cis-PUFAs. The trans-cis isomerization energy values reinforce the consistency and the relative accuracy of theoretical model calculations. The observed flexibility of naturally cis PUFAs could be explained by a very special "smooth basin" PES of the motif of sp(2)-sp(3)-sp(2) hybrid states as reported previously (J. Phys. Chem. A 2005, 109, 520-533). We assumed that intrinsic thermodynamic functions may describe this flexible folding process. The folding enthalpy as well as the folding entropy suggests that there is a new role of the cis-PUFAs in membranes: these cis isomers may have a strong influence on membrane stability and permeability. The average length of the cis helix and beta PUFA was approximated. The difference between the lengths of these two structures is approximately 10 A.     

First-principle computational study on the full conformational space of L-threonine diamide, the energetic stability of cis and trans isomers

First-principle computations were carried out on the conformational space of trans and cis peptide bond isomers of HCO-Thr-NH2. Using the concept of multidimensional conformational analysis (MDCA), geometry optimizations were performed at the B3LYP/6-31G(d) level of theory, and single-point energies as well as thermodynamic functions were calculated at the G3MP2B3 level of theory for the corresponding optimized structures. Two backbone Ramachandran-type potential energy surfaces (PESs) were computed, one each for the cis and trans isomers, keeping the side chain at the fully extended orientation (chi1=chi2=anti). Similarly, two side chain PESs for the cis and trans isomers were generated for the (phi=psi=anti) orientation corresponding to approximately the betaL backbone conformation. Besides correlating the relative Gibbs free energy of the various stable conformations with the number of stabilizing hydrogen bonds, the process of trans-->cis isomerization is discussed in terms of intrinsic stabilities as measured by the computed thermodynamic functions.     

Role of aromacity, ring strain, and stereochemistry of selected disulfides and their congeners in the oxidative linkage of DNA strands at the major groove. A computational study

Three aromatic disulfides and their two selected congeners were studied in order to see if they could be initiators or catalysts in a process that aims to tie together the two strands of a DNA double helix. Thermodynamic functions were calculated from first principle molecular computations on deoxyribose models and the disulfide congener. The gas reaction of one of the disulfides turned out to be the closest to the thermoneutral process. Solvation study caused a relatively minor energetic modification. The disulfides were subjected to docking studies, and the stabilities of the complexes obtained were further analyzed by molecular dynamics simulations. Only one of the two atropic disulfide enantiomers was the matching partner of the chiral DNA double helix, and therefore this remained in the major groove of the DNA. The other enantiomer dissociated from the major groove as it was incapable of forming a stable complex with the chiral double helix. A mechanistic scheme for the reaction has been investigated.