Bond Character (bond + character)

Distribution by Scientific Domains

Selected Abstracts

Escherichia coli cyclophilin B binds a highly distorted form of trans -prolyl peptide isomer

FEBS JOURNAL, Issue 18 2004
Michiko Konno
Cyclophilins facilitate the peptidyl-prolyl isomerization of a trans -isomer to a cis -isomer in the refolding process of unfolded proteins to recover the natural folding state with cis -proline conformation. To date, only short peptides with a cis -form proline have been observed in complexes of human and Escherichia coli proteins of cyclophilin A, which is present in cytoplasm. The crystal structures analyzed in this study show two complexes in which peptides having a trans -form proline, i.e. succinyl-Ala- trans -Pro-Ala- p -nitroanilide and acetyl-Ala-Ala- trans -Pro-Ala-amidomethylcoumarin, are bound on a K163T mutant of Escherichia coli cyclophilin B, the preprotein of which has a signal sequence. Comparison with cis -form peptides bound to cyclophilin A reveals that in any case the proline ring is inserted into the hydrophobic pocket and a hydrogen bond between CO of Pro and N,2 of Arg is formed to fix the peptide. On the other hand, in the cis -isomer, the formation of two hydrogen bonds of NH and CO of Ala preceding Pro with the protein fixes the peptide, whereas in the trans -isomer formation of a hydrogen bond between CO preceding Ala-Pro and His47 N,2 via a mediating water molecule allows the large distortion in the orientation of Ala of Ala-Pro. Although loss of double bond character of the amide bond of Ala-Pro is essential to the isomerization pathway occurring by rotating around its bond, these peptides have forms impossible to undergo proton transfer from the guanidyl group of Arg to the prolyl N atom, which induces loss of double bond character. [source]

Planarity of acetamides, thioacetamides, and selenoacetamides: Crystal structure of N,N -dimethylselenoacetamide

Shuqiang Niu
The planarity of acetamides 1a,3a, thioacetamides 4a,6a, and selenoacetamides 7a,9a, R1R2NC(=E)CH3 where E = O, S, Se, and R1, R2 = H or CH3, was investigated using theoretical calculations at the density functional theory (DFT) level. The calculations showed that the methyl substitution on nitrogen and the change from the amide moiety (NCO) to NCS or NCSe group increased the double bond character of the NC bond. In other words, the planarity of these compounds (1a,9a) increases in the order NH2 < NHCH3 < N(CH3)2 and O < S < Se. The calculations of bending energy suggest that the planar geometry represents the lowest energy conformation for all compounds investigated in this work. N,N-Dimethyl-selenoacetamide (9a), (CH3)2NC(Se) CH3, has the largest bending energy of 10.37 kcal/mol, which suggests that it possesses the greatest planarity among the compounds 1a,9a. However, the solid phase molecular structure of 9a was found to be slightly nonplanar by X-ray crystallography. The slight nonplanarity observed experimentally is very likely the consequence of intermolecular interactions arising within the crystal packing. 2002 Wiley Periodicals, Inc. Heteroatom Chem 13:380,386, 2002; Published online in Wiley Interscience ( DOI 10.1002/hc.10056 [source]

Theoretical studies on high-valent manganese porphyrins: Toward a deeper understanding of the energetics, electron distributions, and structural features of the reactive intermediates of enzymatic and synthetic manganese-catalyzed oxidative processes

Abhik Ghosh
We present here a relatively comprehensive theoretical study, based on nonlocal density functional theory calculations, of the energetics, electron distributions, and structural features of the low-lying electronic states of various high-valent intermediates of manganese porphyrins. Two classes of molecules have been examined: (a) compounds with the general formula [(P)MnX2]0 (P = porphyrin; X = F, Cl, PF6) and (b) high-valent manganese-oxo species. For [(P)Mn(PF6)2]0, the calculations reveal a number of nearly equienergetic quartet and sextet states as the lowest states, consistent with experimental results on a comparable species, [(TMP)Mn(ClO4)2]0 (TMP = tetramesitylporphyrin). In contrast, [(P)MnCl2]0 and [(P)MnF2]0 have a single well-defined S = 3/2 Mn(IV) ground state, again in agreement with experiment, with the three unpaired spins largely concentrated (>90%) on the manganese atom. Manganese(IV)-oxo porphyrins have an S = 3/2 ground state, with the three unpaired spins distributed approximately 2.3:0.7 between the manganese and oxygen atoms. The metal-to-oxygen spin delocalization, as measured by the oxygen spin population, for MnIV = O porphyrins is less than, but still qualitatively similar to, that in analogous iron(IV)-oxo intermediates, indicating that the MnIV = O bond is significantly weaker than the FeIV = O bond in an analogous molecule. Thus, the optimized metal,oxygen bond distances are 1.654 and 1.674 for (P)FeIV(O)(Py) and (P)MnIV(O)(Py), respectively (Py = pyridine). This is consistent with the experimental observation that MnIV = O stretching frequencies are over 10% lower than FeIV = O stretching frequencies for analogous compounds. For [(P)Mn(O)(PF6)]0, [(P)Mn(O)(Py)]+, and [(P)Mn(O)(F)]0, the ground states clearly correspond to a (dxy)2 Mn(V) configuration and the short Mn,O distances of 1.541, 1.546, and 1.561 for the three compounds, respectively, reflect the formal triple bond character of the Mn,O interaction. Interestingly, the corresponding Mn(IV)-oxo porphyrin cation radical states are calculated to be a few tenths of an electrovolt higher than the Mn(V) ground states, suggesting that the Mn(IV)-oxo porphyrin cation radicals are not likely to exist as ground-state species. [source]

Spectroscopic investigations and computational study of 2-[acetyl(4-bromophenyl)carbamoyl]-4-chlorophenyl acetate

C. Yohannan Panicker
Abstract The Fourier transform Raman (FT-Raman) and Fourier transform infrared (FT-IR) spectra of 2-[acetyl(4-bromophenyl)carbamoyl]-4-chlorophenyl acetate were studied. The vibrational wavenumbers were examined theoretically using the Gaussian03 set of quantum chemistry codes, and the normal modes were assigned by potential energy distribution (PED) calculations. The simultaneous Raman and infrared (IR) activations of the CO stretching mode in the carbamoyl moiety show a charge transfer interaction through a ,-conjugated path. From the optimized structure, it is clear that the hydrogen bonding decreases the double bond character of the CO bond and increases the double bond character of the CN bonds. The first hyperpolarizability and predicted IR intensities are reported. The calculated first hyperpolarizability is comparable with the reported values of similar structures, which makes this compound an attractive object for future studies of nonlinear optics. Optimized geometrical parameters of the compound are in agreement with similar reported structures. Copyright 2009 John Wiley & Sons, Ltd. [source]