Ab initio photoionization dynamics of beta-alanine

Photoionization dynamics of beta-alanine is studied by the trajectory simulations using the ab initio potential energy surface. Vertical photoionization in the spirit of the Franck-Condon principle is assumed both for the adiabatic and thermostatic simulations. Both intramolecular proton transfer and fragmentation while only the proton transfer are found in the thermostatic and adiabatic simulations, respectively, for the conformer having the intramolecular hydrogen bond N...H-O. The theoretical predictions are in line with the experimental observations available in the literatures. It is reported for the first time that the thermostatic temperatures strongly affect the fragmentation processes induced by photoionization.     

Conformation effects on the electronic structures of beta-alanine

Ten low-lying conformers of beta-alanine have been studied by the hybrid density functional B3LYP/aug-cc-pVDZ method. Energetic extrapolation calculations at the MP3 and MP4(SDQ) levels of theory and the theoretical photoelectron spectra simulated with the electron propagation theory demonstrate that there are at least three gauche conformers (G1, G2, and G3) in gas-phase experiments. The calculated ionization potentials are in good agreement with the experimental data available in the literature. Natural bond orbital and atoms-in-molecules analyses exhibit a remarkable influence on the molecular electronic structures by the strong intramolecular hydrogen bonding O-H...N in the neutral conformer G2. Remarkable internal rotations of the COOH group are found in the cationic G1+ and G3+ with respect to the neutral conformers. A distonic [NH3+-(CH2)2-COO*] radical can be formed through the spontaneous intramolecular proton transfer in G2+. A novel intramolecular hydrogen bonding, C-H...O, is found in the anti A1+ cation.     

Dipole-bound anions of beta-alanine: canonical and zwitterionic conformers

The remarkable stabilities of the dipole-bound anions of the canonical and zwitterionic conformers of beta-alanine are predicted at the high level of theories, in which the former is the global minimum and the latter, the anti zwitterionic anion, is the local minimum. In contrast to the dipole-bound anions of glycine, the gauche zwitterionic anion of beta-alanine is an unstable conformer. The vertical electron detachment energies for the canonical and anti zwitterionic anions are 58 and 1145 meV, respectively. The photodetachment electron spectrum of the canonical anion is theoretically simulated on the basis of the Franck-Condon factor calculations.     

The shape of molecules

The two most important molecular shape models are the Valence-Shell-Electron-Pair-Repulsion scheme and the Walsh-Mulliken Diagrams. These models, with illustrative examples, are described and a rigorous quantum mechanical definition of each is stated. A physical-mathematical proof ot their equivalence and of their origin is given along with an analysis of the failures to be expected. The theoretical prediction of bond angles is contrasted with the corresponding prediction of bond lengths, and the low information content inherent to the specification of bond angles shows their determination to be considerably easier than bond lengths.

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Zusammenfassung Die beiden wichtigsten Modelle zur Molekülgeometrie sind das Modell der Valenzelektronen-Paar-Abstoßung und das Walsh-Mulliken-Diagramm. Beide Modelle werden anhand illustrativer Beispiele vorgestellt, eine quantenchemische Definition beider wird gegeben. Ihre physikalische Äquivalenz wird bewiesen; diese Analyse zeigt auch die Grenzen der Modelle. Die theoretische Voraussage von Winkeln wird der von Bindungslängen gegenübergestellt. Da der Informationsgehalt der Winkelspezifikation niedriger ist, ist diese Angabe wesentlich leichter als die der Bindungslängen.

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Résumé Les deux modèles de forme moléculaire les plus importants sont le schéma de répulsion électronique des paires d'électrons des couches de valence et les diagrammes de Walsh-Mulliken. Ces modèles sont décrits, avec des examples illustratifs, et l'on donne une définition quantique rigoureuse de chacun d'entre eux. Une preuve physicomathématique de leur équivalence et de leur origine est fournie avec une analyse des échecs à attendre. La prédiction théorique des angles de valence est opposée aux prédictions théoriques des longueurs de liaison; le faible contenu informationnel inhérent à la spécification des angles de liaison montre que leur détermination est considérablement plus aisée que celle des longueurs de liaison.

     

Hairpin versus extended DNA binding of a substituted beta-alanine linked polyamide

A series of alpha-substituted beta-alanine (beta) linked polyamides (DbaPyPyPy-beta*-PyPyPy) were prepared and examined. This resulted in the observation that while most substituents disrupt DNA binding, (R)-alpha-methoxy-beta-alanine (beta((R)-OMe)) maintains strong binding affinity and preferentially adopts a hairpin versus extended binding mode, providing an alternative hairpin linker to gamma-aminobutyric acid (gamma). A generalized variant of a fluorescent intercalator displacement assay conducted on a series of hairpin deoxyoligonucleotides containing a systematically varied A/T-rich binding site size was developed to distinguish between the extended binding of the parent beta-alanine 1 (DbaPyPyPy-beta-PyPyPy) and the hairpin binding of 3 (DbaPyPyPy-beta((R)-OMe)-PyPyPy).     

The shape of metallosupramolecular assemblies

Despite original doubts on its feasibility, the control of the stereochemistry in ligand-bridged oligonuclear assemblies based on tris(bidentate) components has seen considerable progress in the last two decades, and differences have been observed in the physical characteristics of stereoisomers of such species. This retrospective review examines the background to this "stereochemical problem" and shows how the control of the stereochemical integrity of dinuclear and trinuclear ligand-bridged complexes has been utilised in studies of intramolecular electron transfer within the oligonuclear assemblies, and in probing the sequence- and structure-selectivity of the interaction of these species with nucleic acids.     

Fragmentation of alpha- and beta-alanine molecules by ions at Bragg-peak energies

The interaction of keV He(+), He(2+), and O(5+) ions with isolated alpha and beta isomers of the amino acid alanine was studied by means of high resolution coincidence time-of-flight mass spectrometry. We observed a strong isomer dependence of characteristic fragmentation channels which manifests in strongly altered branching ratios. Despite the ultrashort initial perturbation by the incoming ion, evidence for molecular rearrangement leading to the formation of H(3)(+) was found. The measured kinetic energies of ionic alanine fragments can be sufficient to induce secondary damage to DNA in a biological environment.     

The size and shape of silica particles

Negatively charged silica particles were investigated at pH 10.0. They were found to be rod-shaped (cylinder) with a diameter of 5–5.5 nm and a full length of 44–67 nm depending on the rod model used. Moreover, the particles were found to be stable against aggregation in the region 0.4–50 mM NaCl. Received: 2 December 1998 Accepted in revised form: 2 February 1999     

Theoretical study of alpha/beta-alanine and their protonated/alkali metal cationized complexes

Density functional theory has been employed to model the structure and the relative stabilities of alpha/beta-alanine conformers and their protonated and alkali metal cationized complexes. In general, we find that the behavior of the beta-alanine (beta-Ala) system is quite similar to that of alpha-alanine (alpha-Ala). However, the presence of the methylene group (-CH2-) at the beta position in beta-Ala leads to a few key differences. First, the intramolecular hydrogen bonding patterns are different between free alpha- and beta-Ala. Second, the stability of zwitterionic species (in either the free ligand or alkali metal cationized complexes) is often enhanced in beta-Ala. Third, the preferred mode of alkali metal cation (M+) binding may also differ in alpha- and beta-Ala. Natural energy decomposition analysis has been applied here to gain further insight into the effects of the ligand, cation size, and mode of binding on the nature of interaction in these M+-Ala complexes.     

The shape of hexadecyloctyldimethylammoniumbromide micelles in aqueous solutions

By means of small-angle neutron and X-ray scattering the shape of hexadecyloctyldimethylammoniumbromide micelles in aqueous solution was studied in a temperature range from 25 to 60°C. The micelles were found to be of rod-like shape. The solutions had concentrations between 10 and 108 mM. Typical lengths and radii of the micelles are around 15 nm and 1.9 nm respectively. With X-rays we were able to determine the position of the Br⁻ ions.     

Molecular analysis of the kirromycin biosynthetic gene cluster revealed beta-alanine as precursor of the pyridone moiety

Kirromycin is a complex linear polyketide that acts as a protein biosynthesis inhibitor by binding to the bacterial elongation factor Tu. The kirromycin biosynthetic gene cluster was isolated from the producer, Streptomyces collinus Tü 365, and confirmed by targeted disruption of essential biosynthesis genes. Kirromycin is synthesized by a large hybrid polyketide synthase (PKS)/nonribosomal peptide synthetase (NRPS) encoded by the genes kirAI-kirAVI. This complex involves some very unusual features, including the absence of internal acyltransferase (AT) domains in KirAI-KirAV, multiple split-ups of PKS modules on separate genes, and swapping in the domain organization. Interestingly, one PKS enzyme, KirAVI, contains internal AT domains. Based on in silico analysis, a route to pyridone formation involving PKS and NRPS steps was postulated. This hypothesis was experimentally proven by feeding studies with [U-13C3(15)N]beta-alanine and NMR and MS analyses of the isolated pure kirromycin.     

The influence of microcrystalline cellulose grade on shape and shape distributions of pellets produced by extrusion-spheronization.

In this study, five microcrystalline cellulose (MCC) grades were physically characterized and their extrusion-spheronization behaviours were characterized in terms of water requirements and pellet shape profiles. It was found that the MCC grades differed significantly in the physical properties investigated. Physical properties of MCC were found to influence the water requirement for extrusion-spheronization. MCC grades of higher bulk densities, lower porosities and water retentive capacities required less water to produce pellets of equivalent size. These MCC grades were also found to produce pellets of lower sphericity and wider shape distributions. Packing of MCC particles within the agglomerate played a role in determining amount of water retention and pellet rounding during spheronization. However, there was a limit to the influence of packing density on the rate of pellet rounding because poor packing resulted in higher water retentive capacity, which also limited the rate of rounding.     

Kinetics and mechanism of the beta-alanine + OH gas phase reaction: a quantum mechanical approach

The OH hydrogen abstraction reaction from beta-alanine has been studied using the BHandHLYP hybrid HF-density functional and 6-311G(d,p) basis sets. The energies have been improved by single point calculations at the CCSD(T)/6-311G(d,p) level of theory. The structures of the different stationary points are discussed. Reaction profiles are modeled including the formation of pre-reactive and product complexes. Negative net activation energy is obtained for the overall reaction. A complex mechanism is proposed, and the rate coefficients are calculated using transition state theory over the temperature range of 250-400 K. The rate coefficients are proposed for the first time and it was found that in the gas phase the hydrogen abstraction occurs mainly from the CH(2) group next to the amino end. The following expressions, in cm(3) mol(-1) s(-1), are obtained for the overall rate constants, at 250-400 and 290-310 K, respectively: k(250-400)= 2.36 x 10(-12) exp(340/T), and k(290-310)= 1.296 x 10(-12) exp(743/T). The three parameter expression that best describes the studied reaction is k(250-400)= 1.01 x 10(-21)T(3.09) exp(1374/T). The beta-alanine + OH reaction was found to be 1.5 times faster than the alpha-alanine + OH reaction.     

The shape of leucine in the gas phase.

Two structures of neutral leucine are detected in the jet-cooled rotational spectrum of a laser-ablation molecular-beam Fourier transform microwave (LA-MB-FTMW) experiment. The comparison between the experimental rotational and (14)N nuclear quadrupole coupling constants and those calculated ab initio provides conclusive evidence for the identification of the conformers. The most stable species is stabilized by a N-H...O=C intramolecular hydrogen bond and a cis-COOH interaction, while a higher-energy conformer exhibits a N...H-O intramolecular hydrogen bond and trans-COOH, as in lower aliphatic amino acids. The isobutyl side chain adopts the same configuration in the two conformers of leucine, characterized by a trans arrangement of the C'-C(alpha)-C(beta)-C(gamma)-C(delta) chain. The differences with the preferred side chain configurations observed in valine and isoleucine are discussed.     

The effect of crystallite shape on small-angle X-ray scattering

Summary Diffraction by a linear crystallite system was calculated to explain different shapes of small-angle reflections. The calculations show that various SAXS patterns observed can be obtained theoretically if the shape of certain crystallites are accounted for. Various reflection shapes can be explained chiefly by the changes in the crystallite shape and size. Dash, four-point and two-point reflections are associated with rectangular and oblique crystallite of small lateral dimensions. In the case of radial reflections the crystallite represents a plate and the fibril — a stack of plates. Structural changes in oriented samples with planar crystallite texture caused by shrinkage were studied. The principal process of shrinkage consists in the growth of lateral (with respect to the texture axis) crystallite dimensions and in their transformation into plates. Simultaneously the rotation of the macromolecule axis takes place. At the second stage of the shrinkage the layers twist around an axis perpendicular to the film plane. Then isotropic structure is formed. Transition between the two kinds of reflections are typical of various processes taking place in the course of polymer deformation and shrinkage.

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Zusammenfassung Die Röntgen-Beugung eines Systems aus linearen Kristalliten wurde berechnet, um verschiedene Formen von Kleinwinkelreflexionen zu erklären. Die Berechnungen zeigen, daß die beobachteten verschiedenen SAX-Beugungsbilder theoretisch erhalten werden können, wenn die Form der verschiedenen Kristallite in geeigneter Weise gewählt wird. Verschiedene Beugung kann im wesentlichen mit Änderungen von Kristallitgestalt und -große gedeutet werden. Strich-, 2-Punkt- und 4-Punkt-Beugung sind mit rechteckigen und plättchenförmigen Kristalliten von kleinen lateralen Dimensionen verknüpft. Im Fall von radialen Reflektionen ist der einzelne Kristallit ein Plättchen, und eine Fibrille ist ein Stapel von Plättchen. Strukturänderungen in orientierten Proben mit planarer Kristallittextur, erzeugt durch Schrumpfung, wurden studiert. Der Hauptvorgang bei Schrumpfung besteht im Wachsen der lateralen (mit Hinblick auf die Texturachse) Kristallit-dimensionen und in ihrer Überführung in Plättchen. Gleichzeitig findet eine Drehung der Achsen der Makromoleküle statt. Im 2. Stadium der Schrumpfung schrauben sich die Schichten um eine Achse senkrecht zur Filmebene. Dann bildet sich die isotrope Struktur. Der Übergang zwischen den beiden Arten von Beugungen ist für die verschiedenen Prozesse typisch, die im Laufe einer Deformation und einer Schrumpfung von Polymeren stattfinden.

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Dedicated to Prof.R. Hosemann on the occasion of his 60th birthday