Peptide models XXVII. An exploratory ab initio study on the 21st amino acid side-chain conformations of N-formyl-L-selenocysteinamide (For-L-Sec-NH2) and N-acetyl-L-selenocysteine-N-methylamide (Ac-L-Sec-NHMe) in their γL backbone conformation

2000 ◽  
Vol 78 (3) ◽  
pp. 395-408 ◽  
Author(s):  
Judith C Vank ◽  
Carlos P Sosa ◽  
Andras Perczel ◽  
Imre G Csizmadia
Keyword(s):  
Ab Initio ◽  
Electron Density ◽  
Single Point ◽  
Topological Analysis ◽  
Side Chain ◽  
Amino Acid Side Chain ◽  
Backbone Conformation ◽  
Density Analysis ◽  
Peptide Models ◽  
Chain Conformations

Selenocysteine is expected to have 9 × 9 = 81 conformations [3 × 3 = 9 backbone: ψ (g+,a,g-) × ϕ (g+,a,g-) and 3 × 3 = 9 side-chain: χ1 (g+,a,g-) × χ2 (g+,a,g-)]. In the present study, all the torsional modes of the side-chain (χ1: rotation about the Cα-Cβ and χ2: rotation about the Cβ-Se bonds) were investigated in the relaxed γL backbone [(ϕ,ψ); (g-,g+)] conformation. Seven out of the nine expected minima were found at the RHF/3-21G level of theory for N-formyl-L-selenocysteinamide (For-L-Sec-NH2) and N-acetyl-L-selenocysteine-N-methylamide (Ac-L-Sec-NHMe). The stabilization energy exerted by the -CH2-SeH side-chain has been compared with that of -CH2-SH and -CH2-OH. Relative energies of the various conformers were also obtained via single point calculations at the B3LYP/6-31G(d,p) level of theory. Topological analysis of the electron density has been performed by Bader's Atoms in Molecule (AIM) approach using the results. The structures were also optimized at the B3LYP/6-31+G(d,p) level of theory.Key words: selenocysteine side-chain conformations, ab initio MO study, Multidimensional Conformational Analysis (MDCA), Atoms in Molecules (AIM), Bader's electron density analysis.

scholarly journals Peptide models XX. Aromatic side-chain–backbone interaction in phenylalanine-containing diamide model system. A systematic search for the identification of all the ab initio conformers of N-formyl-L-phenylalanine-amide

1997 ◽  
Vol 75 (8) ◽  
pp. 1120-1130 ◽  
Author(s):  
András Perczel ◽  
Ödön Farkas ◽  
Imre G. Csizmadia ◽  
Attila G. Császar
Keyword(s):  
Conformational Analysis ◽  
Ab Initio ◽  
Single Point ◽  
Model System ◽  
Stationary Points ◽  
Side Chain ◽  
Aromatic Side Chain ◽  
Point Energy ◽  
Polyproline Ii ◽  
Peptide Models

Phenylalanine is the simplest among the four natural amino acid residues that have aromatic side chains. The ab initio conformational analysis performed at the RHF/3-21G level on a phenylalanine-containing diamide model system (N-Formyl-L-Phe-NH2) revealed 19 different structures. Single-point energy calculations were performed using RHF/6-31+G* and DFT(B3LYP)/6-311++G** levels for all conformers. The inverse (γL) and the normal (γD) gamma turn, the extended (βL), the left-handed helical [Formula: see text], and the inverse polyproline II [Formula: see text] backbone conformers each have three (g+, a, and g−) side-chain (χ1,) rotamers. The [Formula: see text] and the [Formula: see text] type main-chain conformers have only two side-chain orientations, respectively. No minima have been found for the conformational building unit of the right-handed helical [Formula: see text] and for the polyproline II [Formula: see text] structures. The present ab initio conformational analysis for For-L-Phe-NH2 is a unique example in which a systematic and complete conformational set was established for a diamide system with an aromatic side chain. Analytic vibrational frequency calculations were established for all stationary points found as minima on the potential energy surface. These data may be used in the future as reference conformers in more detailed vibrational and (or) chemical shielding calculations or during the structural analysis of peptides and proteins by X-ray or NMR techniques. Keywords: ab initio peptide conformers, all RHF/3-21G structures of For-L-Phe-NH2, backbone – side-chain interaction in phenylalanine-containing peptide models.

Revisiting the charge density analysis of 2,5-dichloro-1,4-benzoquinone at 20 K

2017 ◽  
Vol 73 (4) ◽  
pp. 654-659 ◽  
Author(s):  
Zhijie Chua ◽  
Bartosz Zarychta ◽  
Christopher G. Gianopoulos ◽  
Vladimir V. Zhurov ◽  
A. Alan Pinkerton
Keyword(s):  
Charge Density ◽  
Electron Density ◽  
Topological Analysis ◽  
Diffraction Measurement ◽  
X Ray Diffraction ◽  
Total Electron Density ◽  
Total Electron ◽  
Structure Factors ◽  
Density Analysis ◽  
Experimental Charge Density

A high-resolution X-ray diffraction measurement of 2,5-dichloro-1,4-benzoquinone (DCBQ) at 20 K was carried out. The experimental charge density was modeled using the Hansen–Coppens multipolar expansion and the topology of the electron density was analyzed in terms of the quantum theory of atoms in molecules (QTAIM). Two different multipole models, predominantly differentiated by the treatment of the chlorine atom, were obtained. The experimental results have been compared to theoretical results in the form of a multipolar refinement against theoretical structure factors and through direct topological analysis of the electron density obtained from the optimized periodic wavefunction. The similarity of the properties of the total electron density in all cases demonstrates the robustness of the Hansen–Coppens formalism. All intra- and intermolecular interactions have been characterized.

Atomic interactions in ethylenebis(1-indenyl)zirconium dichloride as derived by experimental electron density analysis

2005 ◽  
Vol 61 (4) ◽  
pp. 418-428 ◽  
Author(s):  
Adam I. Stash ◽  
Kiyoaki Tanaka ◽  
Kazunari Shiozawa ◽  
Hitoshi Makino ◽  
Vladimir G. Tsirelson
Keyword(s):  
Electron Density ◽  
Topological Analysis ◽  
Electronic Energy ◽  
Ligand Interaction ◽  
Atomic Interactions ◽  
Particle Potential ◽  
Density Analysis ◽  
The One ◽  
Electron Density Analysis ◽  
Experimental Electron Density

A topological analysis of the experimental electron density in racemic ethylenebis(1-indenyl)zirconium dichloride, C20H16Cl2Zr, measured at 100 (1) K, has been performed. The atomic charges calculated by the numerical integration of the electron density over the zero-flux atomic basins demonstrate the charge transfer of 2.25 e from the Zr atom to the two indenyl ligands (0.19 e to each) and two Cl atoms (0.93 e to each). All the atomic interactions were quantitatively characterized in terms of the electron density and the electronic energy-density features at the bond critical points. The Zr—C2 bond paths significantly curved towards the C1—C2 bond were found; no other bond paths connecting the Zr atom and indenyl ligand were located. At the same time, the π-electrons of the C1—C2 bond are significantly involved in the metal–ligand interaction. The electron density features indicate that the indenyl coordination can be approximately described as η1 with slippage towards η2. The `ligand-opposed' charge concentrations around the Zr atom were revealed using the Laplacian of the electron density and the one-particle potential; they were linked to the orbital representations. Bonds in the indenyl ligand were characterized using the Cioslowski–Mixon bond-order indices calculated directly from the experimental electron density.

Topological analysis of electron density and the electrostatic properties of isoniazid: an experimental and theoretical study

2014 ◽  
Vol 70 (2) ◽  
pp. 331-341 ◽  
Author(s):  
Gnanasekaran Rajalakshmi ◽  
Venkatesha R. Hathwar ◽  
Poomani Kumaradhas
Keyword(s):  
Hydrogen Bonding ◽  
Charge Density ◽  
Electron Density ◽  
Topological Analysis ◽  
Bond Critical Point ◽  
Potential Region ◽  
Electrostatic Properties ◽  
Structural And Electronic Properties ◽  
Density Analysis ◽  
Mycobacterial Cell Wall

Isoniazid (isonicotinohydrazide) is an important first-line antitubercular drug that targets the InhA enzyme which synthesizes the critical component of the mycobacterial cell wall. An experimental charge-density analysis of isoniazid has been performed to understand its structural and electronic properties in the solid state. A high-resolution single-crystal X-ray intensity data has been collected at 90 K. An aspherical multipole refinement was carried out to explore the topological and electrostatic properties of the isoniazid molecule. The experimental results were compared with the theoretical charge-density calculations performed usingCRYSTAL09with the B3LYP/6-31G** method. A topological analysis of the electron density reveals that the Laplacian of electron density of the N—N bond is significantly less negative, which indicates that the charges at the b.c.p. (bond-critical point) of the bond are least accumulated, and so the bond is considered to be weak. As expected, a strong negative electrostatic potential region is present in the vicinity of the O1, N1 and N3 atoms, which are the reactive locations of the molecule. The C—H...N, C—H...O and N—H...N types of intermolecular hydrogen-bonding interactions stabilize the crystal structure. The topological analysis of the electron density on hydrogen bonding shows the strength of intermolecular interactions.

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