Relative stability of major types of beta-turns as a function of amino acid composition: a study based on Ab initio energetic and natural abundance data

Folding properties of small globular proteins are determined by their amino acid sequence (primary structure). This holds both for local (secondary structure) and for global conformational features of linear polypeptides and proteins composed from natural amino acid derivatives. It thus provides the rational basis of structure prediction algorithms. The shortest secondary structure element, the beta-turn, most typically adopts either a type I or a type II form, depending on the amino acid composition. Herein we investigate the sequence-dependent folding stability of both major types of beta-turns using simple dipeptide models (-Xxx-Yyy-). Gas-phase ab initio properties of 16 carefully selected and suitably protected dipeptide models (for example Val-Ser, Ala-Gly, Ser-Ser) were studied. For each backbone fold most probable side-chain conformers were considered. Fully optimized 321G RHF molecular structures were employed in medium level [B3LYP/6-311++G(d,p)//RHF/3-21G] energy calculations to estimate relative populations of the different backbone conformers. Our results show that the preference for beta-turn forms as calculated by quantum mechanics and observed in Xray determined proteins correlates significantly.     

Non-empirical LCAO-MO-SCF-CI calculations on organic molecules with Gaussian type functions

This paper (Part I) describes the theoretical and computational bases of some non-empirical calculations on small organic molecules to be reported in later papers (Parts II et seq). Approximate solutions for the usual fixed nucleus electronic Hamiltonian, in the term of wave functions composed of Slater determinants, are discussed, with particular emphasis on their computational utility. Possible choices of basis functions, from which to form the determinants are examined, and the advantages of Gaussian type functions (GTF) centered on the component atoms are pointed out. Some of the properties of molecules which can be calculated using such approximate wave functions are outlined. Finally an attempt is made to discuss the current limitations of non-empirical calculations of the type described here, and some guesses are made about their future. Brief outlines as a set of appendices are given of the mathematical formalism and computational details of the calculations.     

Theoretical conformational analysis of a simple sulphilimine model

The topomerization (bond rotation andS-pyramidal inversion) of a simple sulphilimine model, H₂SNH has been studied with the aid ofab initio SCF MO calculations. The highest rotation barrier occurs when the H₂SN moiety is planar, < HSN = 120 °. The maxima of the inversion crossections occur at the planar conformation for all rotation angles α as expected, however, the minima belong to different values when α is varied. The minimum energy path between the two lowest minima of the conformational energy surface consists of a pure inversion section and a section which is mostly rotation. The optimum values of the < HSN bond angles are significantly smaller than the corresponding < RSN bond angles of sulphilimines of bulkierR substituents.     

An ab initio molecular orbital study of the protonation of amines

Ab initio molecular orbital calculations using an 8 ^s , 3 ^p ; 3 ^s Gaussian basis set, with contraction, have been used to study a series of primary amines XNH₂, where X = H, CH₃, OH, F, CN, CHO, and NO₂. The geometries of the corresponding ammonium ions have been optimised and the energy differences have been used to estimate relative proton affinities. The 1 ^s orbital energies for both the amines and ammonium ions, when corrected for the effects of charges on the other atoms in the molecule by use of an ESCA equation, give a good correlation with the computed charge on the nitrogen atom.     

An ab initio study of the structure of the 2-chloroethyl radical

Minimal and split-valence shell basis set calculations, both with and without d orbitais, predict the radical centre to be pyramidal, with the planar radical only 0.3 kcal mol^?1 higher. The barrier to internal rotation is 2 kcal mol^?1. There is no evidence of bridging from chlorine.     

JChem: Java applets and modules supporting chemical database handling from web browsers

A Java based development tool for building portable chemical information systems is presented. The system contains applets for constructing web-based interfaces and classes that add structure handling to relational databases. Custom applications built with JChem can combine SQL and structural queries.     

Quantum chemical studies on electrophilic addition

The geometries of the 2-aminoethyl cation and the isomeric protonated aziridine have been optimized using ab initio molecular orbital calculations employing the split-valence shell 4-31G basis set. The protonated aziridine is computed to be the more stable ion by 46.5 kcal/mole (4-31G level) and 44.9 kcal/mole (double-zeta basis set). The profile to interconversion is found to have a barrier of less than 15 kcal/mole (relative to the 2-aminoethyl cation) and this profile is compared with those computed for the similar ions XCH₂CH ₂ ⁺ where X=OH, F, SH and Cl.     

Quantum chemical studies on electrophilic addition

The geometries of the 2-chloroethyl and ethylenechloronium cations, two possible intermediates in the electrophilic addition of chlorine to ethylene, have been fully optimized using ab initio molecular orbital calculations employing the split valence shell 4-31G basis set.These geometries were then used to compute more accurate wave functions using Dunning's double-zeta basis set. The bridged chloronium ion was found to be more stable by 9.35 kcal/mole, the opposite order of stability from the C₂H₄F⁺ ions. Interconversion of the two C₂H₄Cl⁺ cations was computed to have a barrier of 6.25 kcal/mole.The activation energy for this chlorination reaction, using the ethylenechloronium cation and a chlorine anion at infinite separation as the model for the activated complex, was computed to be 128.7 kcal/mole, showing that this is not a feasible gas phase reaction.     

Vertical proton affinities of CH2O and CH2OH+ in their ground singlet,excited triplet and ionized doublet states

Vertical proton affinities were calculated with closed and open shell direct SCF-MO methods for the ground, excited triplet and ionized doublet states of CH₂O and CH₂OH⁺.The computed gas phase basicity of CH₂O follows the order: CH₂O(¹ A ₁) > CH₂O*(³ A ₁ or ³ A ₂) > CH₂O⁺(² B ₂ or ² B ₁).     

Polymeric (NO)3(N2O) n , (NO)3(N2O) n + , and (NO)3(N2O) n − : an interpretation of experimental observations

Semi-empirical and ab initio calculations are reported which provide a possible explanation for reported experimental results on 2-photon ionization of NO containing a few percent of N₂O, which found (NO)₃(N₂O) _n ^+or? clusters to be significantly more abundant than other (NO) _m (N₂O) _n products. It is found that the observed abundances of (NO)₃(N₂O) _n ionic clusters may be accounted for by the existence of covalent cyclic trimers of nitric oxide attached to oligomers of nitrous oxide. The extra stability of NO trimers in the observed clusters appears to arise from (NO) ₃ ⁺ rather than (NO)₃. Attachment of an (N₂O) _n side chain to (NO) ₃ ⁺ occurs exothermically. It is suggested that the addition of N₂O to cyclic-(NO) ₃ ⁺ might provide a means of making a polymer of nitrous oxide, which could have useful properties.