Rebecca Jacob

Infrared absorption spectra and structures of zwitterions of glycyl-L-alanine and its N-deuterated isotopomer in a KBr matrix

Abstract The IR absorption spectra of zwitterions of glycyl- l -alanine and its N -deuterated isotopomer isolated in a KBr matrix have been measured using a novel sampling technique involving dissolution, spray and deposition. In a parallel theoretical study the number of conformers, their IR absorption spectra and structures have been determined by ab initio molecular orbital calculations. The calculations were carried out at both the density functional theory and Hartree–Fock levels, and were of the non-aqueous self-consistent reaction field type, using the Onsager dipole-sphere model. Four conformers were identified. The trans conformer was found to have the lowest energy at all levels of theory and for the range of cavity radii studied. Its structure was found to be closely similar to that of glycyl- l -alanine in the crystal. Comparison of the predicted spectra of the four conformers with the measured spectra showed that both the trans and/or cis conformers could be present in the KBr matrix. Good agreement between measured and calculated spectra, both cis and trans , has been obtained for the majority of the prominent bands in the spectrum.

The infrared spectra and structures of the valyl-glycine zwitterion isolated in a KBr matrix

Abstract The IR absorption spectrum of zwitterions of l -valyl-glycine isolated in a KBr matrix has been measured using a novel dissolution, spray and deposition technique. The number of conformers, their molecular structures and their vibrational spectra have been determined by ab initio molecular orbital calculations of the non-aqueous self-consistent reaction field type, using the Onsager dipole-sphere model at both the density functional theory and Hartree–Fock levels. Six conformers were determined. Although differences in their relative energies were found to be small, one conformer Tg2 was consistently the lowest for a range of cavity radii and for both levels of theory. From comparison of the observed and predicted spectra it is concluded that one or more of the trans group of conformers is present in the KBr matrix. Good agreement between measured and calculated spectra has been obtained for the majority of the prominent bands in the spectrum.

H and D Attachment to Naphthalene: Spectra and Thermochemistry of Cold Gas-Phase 1-C10H9 and 1-C10H8D Radicals and Cations

Excitation spectra of the 1H-naphthalene (1-C10H9) and 1D-naphthalene (1-C10H8D) radicals, and their cations, are obtained by laser spectroscopy and mass spectrometry of a skimmed free-jet expansion following an electrical discharge. The spectra are assigned on the basis of density functional theory calculations. Isotopic shifts in origin transitions, vibrational frequencies and ionization energies were found to be well reproduced by (time-dependent) density functional theory. Absolute bond dissociation energies, ionization energies and proton affinities were calculated using high-level quantum chemical methods.

The role of lysine-41 in RNase A catalysis: a quantum chemical study on the active site-ligand complex

Abstract Several mechanisms have been proposed to explain the action of enzymes at the atomic level. Among them, the recent proposals involving short hydrogen bonds as a step in catalysis by Gerlt and Gassman [1] and proton transfer through low barrier hydrogen bonds (LBHBs) 2 , 3 have attracted attention. There are several limitations to experimentally testing such hypotheses. Recent developments in computational methods facilitate the study of active site–ligand complexes to high levels of accuracy. Our previous studies, which involved the docking of the dinucleotide substrate UpA to the active site of RNase A 4 , 5 , enabled us to obtain a realistic model of the ligand-bound active site of RNase A. From these studies, based on empirical potential functions, we were able to obtain the molecular dynamics averaged coordinates of RNase A, bound to the ligand UpA. A quantum mechanical study is required to investigate the catalytic process which involves the cleavage and formation of covalent bonds. In the present study, we have investigated the strengths of some of the hydrogen bonds between the active site residues of RNase A and UpA at the ab initio quantum chemical level using the molecular dynamics averaged coordinates as the starting point. The 49 atom system and other model systems were optimized at the 3-21G level and the energies of the optimized systems were obtained at the 6-31G* level. The results clearly indicate the strengthening of hydrogen bonds between neutral residues due to the presence of charged species at appropriate positions. Such a strengthening manifests itself in the form of short hydrogen bonds and a low barrier for proton transfer. In the present study, the proton transfer between the 2′-OH of ribose (from the substrate) and the imidazole group from the H12 of RNase A is influenced by K41, which plays a crucial role in strengthening the neutral hydrogen bond, reducing the barrier for proton transfer.

The mechanism of the dissolution, spray and deposition technique - a novel infrared sampling method

The dissolution, spray and deposition (DSD) technique, a novel infrared (IR) sampling technique, gives very sharp spectra for amino acids and peptides. The mechanism of this unique technique has been established by scanning electron microscopy (SEM) studies and found to be due to the formation of several layers of fairly large KBr crystals in situ on an IR transparent window. The zwitterions of the amino acids and dipeptides are adsorbed on the surface of these large KBr crystals, which ensures the isolation of monomers of the amino acid or dipeptide zwitterions in the KBr matrix, thereby leading to sharp and well-resolved IR spectra. This methodology provides a powerful IR sampling technique, akin to matrix isolation, with the added advantage of being extremely cost effective as it does not require low-temperatures or a sophisticated experimental set up.