Quantum chemical analysis of the unfolding of a penta-glycyl 3(10)-helix initiated by HO(●), HO2(●), and O2(-●)

In this study, the thermodynamic functions of hydrogen abstraction from the C(α) and amide nitrogen of Gly(3) in a homo-pentapeptide (N-Ac-GGGGG-NH(2); G5) by HO(●), HO(2)(●), and O(2)(-●) were computed using the Becke three-parameter Lee-Yang-Parr (B3LYP) density functional. The thermodynamic functions, standard enthalpy (ΔH°), Gibbs free energy (ΔG°), and entropy (ΔS°), of these reactions were computed with G5 in the 3(10)-helical (G5(Hel)) and fully-extended (G5(Ext)) conformations at the B3LYP/6-31G(d) and B3LYP/6-311+G(d,p) levels of theory, both in the gas phase and using the conductor-like polarizable continuum model implicit water model. H abstraction is more favorable at the C(α) than at the amide nitrogen. The secondary structure of G5 affects the bond dissociation energy of the H-C(α), but has a negligible effect on the dissociation energy of the H-N bond. The HO(●) radical is the strongest hydrogen abstractor, followed by HO(2)(●), and finally O(2)(-●). The secondary structure elements, such as H-bonds in the 3(10)-helix, protect the peptide from radical attack by disabling the potential electron delocalization at the C(α), which is possible when G5 is in the extended conformation. The unfolding of the peptide radicals is more favorable than the unfolding of G5(Hel); however, only the HO(●) can initiate the unfolding of G5(Hel) and the formation of G5(Ext)(●). These results are relevant to peptides that are prone to undergoing transitions from helical structures to β-sheets in the cellular condition known as "oxidative stress" and the results are discussed in this context.     

Polystyrene models. II. Ab initio study of isobutylbenzene

The structure and stability of the various conformations of isobutylbenzene are studied using ab initio molecular orbital theory. The calculations show that coupling between the structural units is important. The results indicate that complete geometry optimization of the stable and transition structures of isobutylbenzene produce significant changes in geometrical parameters and charge distributions of this molecule when compared with the corresponding results obtained using the rigid-rotor approximation. These changes are particularly noticeable in one of the gauche conformations and in transition structures of isobutylbenzene generated by the phenyl group rotation. For polystyrene, these results present evidence that there is a strong coupling between the chain-backbone folding and the rotation of the phenyl group. Multidimensional potential energy surfaces are displayed using a topological representation. © 1992 John Wiley & Sons, Inc.     

Furthest neighbours in space

A finite subset of the union of the polar axis and the equator of a sphere is called a suspension. We prove that if n points in 3-space determine the maximum number of furthest neighbours then they form a suspension. The exact maximum and the optimal arrangement are also given. This sharpens a result of Avis, Erdös and Pach.     

A note on a non-empirical molecular orbital study of some cytosine and thymine tautomers

The relative stabilities of a series of cytosine and thymine tautomers have been investigated by means of non-empirical (ab initio) LCAO-MO-SCF Hartree-Fock-Roothaan calculations employing a small contracted Gaussian basis set (STO-3G) in all cases. The relative stabilities of the various tautomeric forms agree in general with the results of earlier empirical and semi-empirical calculations on these molecules. In particular, the “enol forms” of cytosine and thymine, within the isolated molecule approximation inherent in these MO calculations, are predicted to possess greater stability than the forms commonly assigned to these molecules in aqueous solution and found in the solid state by X-ray crystallographic studies.     

N-acetyl-L-aspartic acid-N'-methylamide with side-chain orientation capable of external hydrogen bonding

In this study, we generated and analyzed the side-chain conformational potential energy hypersurfaces for each of the nine possible backbone conformers for N-acetyl-L-aspartic acid-N' methylamide. We found a total of 27 out of the 81 possible conformers optimized at the B3LYP/6-31G(d) level of theory. The relative energies, as well as the stabilization energies exerted by the side-chain on the backbone, have been calculated for each of the 27 optimized conformers at this level of theory. Various backbone-backbone (N-H ^{. . .} O=C) and backbone-side-chain (N-H ^{. . .} O=C; N-H ^{. . .} OH) hydrogen bonds were analyzed. The appearance of the notoriously absent backbone conformer may be attributed to such side-chain-backbone (SC/BB) and backbone-backbone (BB/BB) hydrogen bonds. Received 10 February 2002 Published online 13 September 2002     

Chemical evolution of biomolecule building blocks. Can thermodynamics explain the accumulation of glycine in the prebiotic ocean?

It has always been a question of considerable scientific interest why amino acids (and other biomolecule building blocks) formed and accumulated in the prebiotic ocean. In this study, we suggest an answer to this question for the simplest amino acid, glycine. We have shown for the first time that classical equilibrium thermodynamics can explain the most likely selection of glycine (and the derivative of its dipeptide) in aqueous media, although glycine is not the lowest free energy structure among all (404) possible constitutional isomers. Species preceding glycine in the free energy order are either supramolecular complexes of small molecules or such molecules likely to dissociate and thus get back to the gas phase. Then, 2-hydroxyacetamide condensates yielding a thermodynamically favored derivative of glycine dipeptide providing an alternative way for peptide formation. It is remarkable that a simple equilibrium thermodynamic model can explain the accumulation of glycine and provide a reason for the importance of water in the formation process.     

Density Functional Theory Investigation of the Alkyl–Alkyl Negishi Cross‐Coupling Reaction Catalyzed by N‐Heterocyclic Carbene (NHC)–Pd Complexes

Why bigger is better : A “steric wall” created by the N‐(2,6‐diisopropylphenyl) substituent on the bulky NHC ligand IPr (1,3‐bis(2,6‐diisopropylphenyl)imidazol‐2‐ylidene) guides the reactants to and from the Pd center through weak, fleeting (IPr)H–Pd interactions that help the oxidative addition intermediate escape “the anti‐trap”. The alternative “side” approach leads to transmetalation (the rate‐limiting step) for which a novel Pd–Zn interaction was identified.

     

The structure and fragmentation of B n (n≥3) ions in peptide spectra

The unimolecular and low energy collision-induced fragmentation reactions of the MH⁺ ions of N-acetyl-tri-alanine, N-acetyl-tri-alanine methyl ester, N-acetyl-tetra-alanine, tetra-alanine, penta-alanine, hexa-glycine, and Leu-enkephalin have been studied with a particular emphasis on the formation and fragmentation of B _n (n=3,4,5) ions. In addition, the metastable ion fragmentation reactions of protonated tetra-glycine, penta-glycine, and Leu-enkephalin amide have been studied. B _n ions are prominent stable species in all spectra. The B _n ions fragment, in part, by elimination of CO to form A _n ions; this reaction occurs on the metastable ion time scale with a substantial release of kinetic energy (T _1/2=0. 3–0. 5 eV) that indicates that a stable configuration of the B _n ion fragments by way of a reacting configuration that is higher in energy than the fragmentation products, A _n + CO. Ab initio calculations strongly suggest that the stable configuration of the B₃ and B₄ ions is a protonated oxazolone formed by interaction of the developing charge with the next-nearest carbonyl group as HX is lost from the protonated species H-(Yyy) _n -X · H⁺. The higher B _n ions also fragment, in part, to form the next-lower B ion, presumably in its stable protonated oxazolone form. This reaction is rationalized in terms of the three-dimensional structure of the B _n ions and it is proposed that the neutral eliminated is an α-lactam.     

A comparative quantum chemical study of ethylcarbonium ion and hydroxymethylcarbonium ion

Nonempirical molecular orbital calculations of the energies of CH₃CH (ethylcarbonium ion) and HOCH (hydroxymethylcarbonium ion) as a function of rotation about the C? C or C? O bonds and deviation from coplanarity at the carbonium ion center are reported. As expected, and in agreement with previous work, both carbonium centers are planar and there is no barrier to rotation in the planar ethylcarbonium ion. However, for the planar configuration at carbon, the conjugative interaction between oxygen and carbon produces a barrier to rotation about the C? O bond of HOCH of 19.6 Kcal/mole. When a pyramidal geometry is imposed upon the carbonium ion center of CH₃CH, a typical three-fold barrier results. As the deviation from coplanarity increases there is a regular increase in the barrier height (1.72 Kcal/mole at the tetrahedral geometry), but the energy minimum remains at the same position in each case (60°). For HOCH, imposition of a pyramidal geometry on the carbonium ion center causes a change in both rotational barriers. One decreases slightly (from 19.6 to 15.4 Kcal/mole) and the other increases to 30.5 Kcal/mole. There is an accompanying change in the position of the minimum of the rotational potential, from 90° towards the gauche structure.