The probable conformation of substrates recognized by dipeptidyl-peptidase IV and some aspects of the catalytic mechanism derived from theoretical investigations

Summary By theoretical conformational investigations of substrates and nonsubstrates of the enzyme dipeptidyl-peptidase IV (DP IV) as well as dipeptide-esters using the ECEPP83 method we determined the structure of peptides recognized and cleaved by the enzyme. From a comparison of all possible structures for the substrates with conformations not possible in nonsubstrates we concluded that a single conformation explains substrate specificities of DP IV. This conformation is characterized by the following dihedral angles: {ie159-1}, {ie159-2}, {ie159-3}, {ie159-4}, and {ie159-5}. The conclusions were supported by comparisons of molecular electrostatic potentials calculated with the molecular graphics program HAMOG.     

Quantum chemical studies on structures and spectra of 2,5-distyrylpyrazine (DSP) laser dye

Semiempirical (MNDO and PM3) molecular orbital calculations have been undertaken to study the structures of the ground and excited states of 2,5-distrylpyrazine dye to assess its activity as a laser dye. In the ground and first excited singlet states, the trans-trans structure of C_2h symmetry is the most stable structure in the gas phase and in DMSO, which agrees with the experimental findings. Upon excitation, the flexibility of the molecule decreases, leading to a subsequent decrease in the radiationless deactivation pathway and this increases the fluorescence efficiency of DSP. The absorption, excitation, and emission spectra have been calculated at the MNDO level using the PM3 optimized geometries in DMSO. At this level the agreement between theory and experiment is quite good. An estimated absorption band at 377 nm (expt 380 nm) is assigned to the S₀→S₁ transition. The excited state absorption band at 457 nm (expt 460 nm) is assigned to the S₁→S₁₂ transition. The emission band at 458 nm (expt 460 nm) is assigned to the S′₁→S′₀ transition. The overlap between the emission and the excited-state absorption spectra is presumably the main reason behind the reduced laser activity of the investigated dye. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 585–592, 1998     

Conformers of gaseous protonated glycine

Ab initio geometry optimizations were performed on gaseous protonated glycine using the second-order Møller–Plesset perturbation theory with the 6-31G*, 6-31G**, 6-31+G**, and 6-311+G** basis sets. Eight energy minima and 12 saddle points in the low-energy region of the electronic potential energy surface were characterized. The global minimum was an amino N-protonated conformer containing an ionic H bond between the (SINGLE BOND)NH₃⁺ and O(DOUBLE BOND)C(DIAGONAL BOND)(DIAGONAL BOND) groups. The lowest energy O-protonated conformer was stabilized by a conjugative attraction between the nitrogen lone-pair electrons and the positively charged planar fragment (SINGLE BOND)C(OH)₂⁺. Relative electronic energies of the nine N- and 11 O-protonated species fall in the ranges of 0–10 and 30–40 kcal mol⁻¹. At room temperature the equilibrium distribution contained the most stable N-protonated conformer almost exclusively. Additional subjects for investigation include the effects of basis set and electron correlation on the predicted structures, nonbonded interactions that influence the relative stability of protonated conformers, conformational interconversions based on intrinsic reaction coordinate calculations, and kinetic pathways for protonation and associated changes in Gibbs free energy. The work provides geometric, energetic, and thermodynamic data pertinent to the study of gas-phase ion chemistry of amino acids and peptides. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1862–1876, 1998     

IR spectra,conformational lability,and intermolecular interactions in long-chain aliphatic compounds

Investigations of the conformational lability and intermolecular interactions in long-chain aliphatic compounds (LACs), namely, in carboxylic acid derivatives (alkyl- and alkoxybenzoic acids; alkylcyclohexanecarboxylic acids and their completely or partially fluoroalkyl-substituted derivatives), 4-cyano-4-p-alkoxybiphenyls, 4-cyano-4-p-alkylbiphenyls, and cholesterol p-n-butyloxybenzoate are reviewed. Major attention is paid to experimental and theoretical IR spectroscopy data. Differential thermal analysis, polarization microscopy, and X-ray diffraction data are also taken into account. A more detailed treatment is presented on IR spectrum simulation based on data about the conformational lability of molecules and their specific (H-bonding) intermolecular interactions. The first mechanism is responsible for the conformational type of polymorphism in LACs and for the structure of the latter in solid crystal (SC) and liquid crystal (LC) states and in isotropic liquids (ILs). The second mechanism complements the structure-forming aspect of polymorphism in carboxylates, which is due to a rearrangement of hydrogen bond systems in H-complexes during polymorphic transitions to the LC and IL states. Both mechanisms are reflected in IR absorption spectra. A more adequate interpretation is possible in order to explain the many spectral features associated with the structure of LAC polymorphs and their H-complexes if these mechanisms are taken into account.Original Russian Text Copyright © 2004 by L.M. BabkovTranslated from Zhurnal Strukturnoi Khimii, Vol. 45, No. 3, pp. 389–397, May–June, 2004.     

IR spectroscopic study of the conformational lability of 4′-ethyl-4-cyanobiphenyl

The conformational lability of 4-ethyl-4-cyanobiphenyl molecules in solid crystal (SC) and isotropic liquid (IL) states was investigated by IR spectroscopic techniques (experiment and theory). IR absorption spectra were measured at 28°C–95°C in the frequency range 400 cm^–1–4000 cm^–1. Spectrum simulation was performed using the fragment method with allowance for the conformational fluctuations of molecules. The experimental and calculated spectra were compared and analyzed, and it was shown that in the IL, the samples are mixtures of conformers. The temperature changes in the spectra in the stated range are caused by the conformational lability of molecules.Original Russian Text Copyright © 2004 by L. M. Babkov, I. I. Gnatyuk, G. A. Puchkovskaya, and S. V. TrukhachevTranslated from Zhurnal Strukturnoi Khimii, Vol. 45, No. 3, pp. 398–405, May–June, 2004.     

Interactions of D-Maltose and Sucrose with Some Amino Acids in Aqueous Solutions

Calorimetric titrations have been performed at 298.15 K in aqueous solutions to derive the stability constants and thermodynamic parameters of the interactions of D-maltose and sucrose with some amino acids (glycine, DL-alanine, DL-leucine, and L-serine). The apparent molal volumes of the disaccharides in dilute aqueous solutions of the amino acids have been determined from density measurements at 298.15 K. In contrast to D-maltose, sucrose was found to associate with the amino acids and these associated species are preferentially entropy stabilized. These results are interpreted in terms of the influence of the nature of the solutes, their specific conformations, and hydration, on the ability of the disaccharides to form associated complexes with the amino acids.     

Theoretical study of structure,vibrational and electronic spectra of isomers of methyl-3-methoxy-2-propenoate

A systematic quantum mechanical study of the possible conformations, their relative stabilities, vibrational and electronic spectra and thermodynamic parameters of methyl-3-methoxy-2-propenoate has been reported for the electronic ground (S₀) and first excited (S₁) states using time-dependent and time-independent Density Functional Theory (DFT) and RHF methods in extended basis sets. Detailed studies have been restricted to the E-isomer, which is found to be substantially more stable than the Z-isomer. Four possible conformers c′Cc, c′Tc, t′Cc, t′Tc, of which the first two are most stable, have been identified in the S₀ and S₁ states. Electronic excitation to S₁ state is accompanied with a reversal in the relative stability of the c′Cc and c′Tc conformers and a substantial reduction in the rotational barrier between them, as compared with the S₀ state. Optimized geometries of these conformers in the S₀ and S₁ states are being reported. Based on suitably scaled RHF/6-31G^** and DFT/6-311G^** calculations, assignments have been provided to the fundamental vibrational bands of both these conformers in terms of frequency, form and intensity of vibrations and potential energy distribution across the symmetry coordinates in the S₀ state. A complete interpretation of the electronic spectra of the conformers has been provided.