Michael Ramek

The case of glycine continued: some contradictory SCF results

Abstract The energies of five conformations of glycine were determined by ab initio HF/SCF gradient geometry optimization using 13 different basis sets. The conformations considered are the stretched form ( I ), a heavy-atom framework planar ( II ) and non-planar ( III ) cyclic form, and a planar ( IV ) and non-planar ( V ) bifurcated structure. Form I is the global energy minimum in all calculations, but contradictory results are obtained for the stabilities of the other forms. Of the cyclic forms, II is a local energy minimum at the 4-31G, 6-31G, 6-31+G, and (10s,5p/4s) levels, but a saddle point in calculations with both smaller and larger basis sets (including 6-31G ∗∗ , 6-31 + G ∗∗ , and 6-31 + + G ∗∗ ). Similarly contradictory results are obtained for IV . There is considerable scatter in calculated energy differences and in the optimized values of the non-planar N-C-CO torsions. Form I and the planar cyclic form II were previously found in the microwave spectrum of glycine. The significance of the new calculations for interpretations of the microwave data is discussed. It is concluded that assumption of slight non-planarity of the cyclic form, with a minimum at III and a low lying transition state at II is not necessarily in conflict with the available microwave data. In addition it is possible to conclude that a third conformer, IV or V , hitherto not observed, may exist in glycine vapors in amounts which are similar to those of the observed conformer II .

Ab initio SCF investigation of β-alanine

Abstract The potential-energy surface of the neutral form of β-alanine was investigated with ab initio 4-31G SCF calculations. Geometries, energies and wavenumbers for all 20 symmetry unique local minima are reported together with the potential barriers of the reactions, which interconnect these minima. Intramolecular interactions involving the groups CO, OH and NH 2 were deduced from these informations.

Intramolecular hydrogen bonding in 2-aminoethanol, 3-aminopropanol and 4-aminobutanol

Abstract Two different intramolecular hydrogen-bonds are formed by 2-aminoethanol, 3-aminopropanol and 4-aminobutanol, both of which lead to cyclic conformations. Results based on ab initio self-consistent field (SCF) calculations for the stronger interaction -N⋯H-O-are presented. The influence of ring size on this interaction is discussed.

Ab initio conformational analysis of N-formyl l-alanine amide including electron correlation

Abstract The conformational properties of N -formyl l -alanine amide (ALA) were investigated using RMP2/6-311G ∗∗ ab initio gradient geometry optimization. One hundred forty four structures of ALA were optimized at 30° grid points in its φ (N–C(α)), ψ (C(α)–C′) conformational space. Using cubic spline functions, the grid structures were then used to construct analytical representations of complete surfaces, in φ , ψ -space, of bond lengths, bond angles, torsional sensitivity and electrostatic atomic charges. Analyses show that, in agreement with previous studies, the right-handed helical conformation, α R , is not a local energy minimum of the potential energy surface of ALA. Comparisons with protein crystallographic data show that the characteristic differences between geometrical trends in dipeptides and proteins, previously found for ab initio dipeptide structures obtained without electron correlation, are also found in the electron-correlated geometries. In contrast to generally accepted features of force fields used in empirical molecular modeling, partial atomic charges obtained by the CHELPG method are found to be not constant, but to vary significantly throughout the φ , ψ -space. By comparing RHF and MP2 structures, the effects of dispersion forces on ALA were studied, revealing molecular contractions for those conformations, in which small adjustments of torsional angles entail large changes in non-bonded distances.

Intramolecular interactions in β-alanine, 3-aminopropanal and 3-aminopropanol

Abstract The intramolecular interactions in the local minima on the potential energy surfaces of β-alanine, 3-aminopropanal and 3-aminopropanol are discussed on the basis of electron density maps. The resulting characterization is in agreement with criteria using bond lengths and vibration frequencies. The CO group is found to be the most important structural feature in these compounds.

Comment on “Is N6 an open-chain molecule?”

Confirmation de la geometrie acyclique de N 6 par des calculs 6-21 G. Etat de transition pour la reaction (N 2 ) 3 →3N 2

Symmetries in Science IX

Classical vs Quantum Groups as Symmetries of Quantized Systems M. Arik, G. Unel. Algebraic Model of an Oblate Top R.Bijker, A. Leviatan. The Mass-Squared Operator and the Einstein-Hilbert Action for Rescaled Lorentz Metrics E. Binz, P. Oellers. Multichannel Dynamic Symmetry J. Cseh. Kazhdan-Lusztig Polynomials, Subsingular Vectors and Conditionally Invariant q-Deformed Equations V.K. Dobrev. On a Path to Nonlinear Quantum Mechanics H.-D. Doebner, J.-D. Hennig. Quantum Mechanical Problems with q-Deformations and over the p-Adic Number Fields I.H. Duru. A Symmetry Adapted Algebraic Approach to Molecular Spectroscopy A. Frank, et al. Dyson Boson-Fermion Realization of Lie (Super)Algebras D.V. Fursa, et al. Formal Languages for Quasicrystals J.G. Escudero. On Quadratic and Nonquadratic Forms: Applications to R2m -> R2m-n Nonbijective Transformations M. Kibler. Quantization of Systems with Constraints J.R. Klauder. Automorphisms and Discrete Fiber Bundles P. Kramer, et al. Algebraic Approach to Baryon Structure A. Leviatan, R. Bijker. Discrete Reflection Groups and Induced Representations of Poincare Group on the Lattice M. Lorente. 10 Additional Articles. Index.

Theoretical structure investigations of N-acetyl-l-proline amide

Abstract The potential energy surface of N -acetyl-l-proline amide has been investigated via RHF, AM1, and PM3 calculations. The results show significant differences between these methods: seven local minima can be found with RHF, three with AM1, 17 with PM3. The conformation of the RHF/6-31G∗ global minimum corresponds to the γ-turn structure of polypeptides. In contrast to this, the proline conformer that participates in the formation of ten-membered β-turns in peptide chains has a relatively high energy in the dipeptide.

Ab initio SCF investigation of 3-aminopropanol and 3-aminopropanal

Abstract Results of ab initio SCF (4-31G) studies of the potential energy surfaces of 3-aminopropanol and 3-aminopropanal are reported. Geometry data of all local minima are given and various intramolecular interactions are deduced from these data. All reaction paths in the potential energy surface of 3-aminopropanal and selected reaction paths in the potential energy surface of 3-aminopropanol are discussed.

Dke1—structure, dynamics, and function: a theoretical and experimental study elucidating the role of the binding site shape and the hydrogen-bonding network in catalysis

This study elucidates the role of the protein structure in the catalysis of β-diketone cleavage at the three-histidine metal center of diketone cleaving enzyme (Dke1) by computational methods in correlation with kinetic and mutational analyses. Molecular dynamics simulations, using quantum mechanically deduced parameters for the nonheme Fe(II) cofactor, were performed and showed a distinct organization of the hydrophilic triad in the free and substrate-ligated wild-type enzyme. It is shown that in the free species, the Fe(II) center is coordinated to three histidines and one glutamate, whereas the substrate-ligated, catalytically competent enzyme–substrate complex has an Fe(II) center with three-histidine coordination, with a small fraction of three-histidine, one-glutamate coordination. The substrate binding modes and channels for the traffic of water and ligands (2,4-pentandionyl anion, methylglyoxal, and acetate) were identified. To characterize the impact of the hydrophobic protein environment around the metal center on catalysis, a set of hydrophobic residues close to the active site were targeted. The variations resulted in an up to tenfold decrease of the O2 reduction rates for the mutants. Molecular dynamics studies revealed an impact of the hydrophobic residues on the substrate stabilization in the active site as well as on the orientations of Glu98 and Arg80, which have previously been shown to be crucial for catalysis. Consequently, the Glu98–His104 interaction in the variants is weaker than in the wild-type complex. The role of protein structure in stabilizing the primary O2 reduction step in Dke1 is discussed on the basis of our results.