Biomedical subjects

A Bagno

Publications and source records attributed to A Bagno.

6 recordsLinked to original sources

PubMed2001

Complete prediction of the 1H NMR spectrum of organic molecules by DFT calculations of chemical shifts and spin-spin coupling constants.

1H NMR chemical shifts and coupling constants for several aromatic and aliphatic organic molecules have been calculated with DFT methods. In some test cases (furan, o-dichlorobenzene and n-butyl chloride) the performance of several functionals and basis sets has been analyzed, and the various contributions to spin-spin coupling (Fermi-contact, diamagnetic and paramagnetic spin-orbit) have been evaluated. The latter two components cancel each other, so that the calculation of the contact term only is sufficient for an accurate evaluation of proton-proton couplings. Such calculated values are used to simulate the 1H NMR spectra of organic molecules with complicated spin systems (e.g. naphthalene, o-bromochlorobenzene), obtaining a generally very good agreement with experimental spectra with no prior knowledge of the involved parameters.

Journal Article↗

PubMed2000

Detecting hydrogen bonding by NMR relaxation of the acceptor nuclei

The formation of hydrogen bonds (HB) between phenol or N-methyltrifluoroacetamide and several acceptors (pyridine, carbonyl compounds, nitriles, amides) in CCl4 or CHCl3 been investigated through the analysis of NMR relaxation times (T1) of the heteronuclei (14N and 17O) directly involved in the HB interaction. Thus, a comparison is made between such T1 values (corrected for changes in molecular dynamics and motional anisotropy) and electric field gradients calculated by ab initio methods for the acceptor molecules, both isolated and in 1:1 or 2:1 hydrogen-bonded complexes. When other effects are properly accounted for, there is a good agreement between theoretical and experimental electric field gradient (efg) changes. The noticeable difference found between CCl4 or CHCl3 as solvents is discussed in relation to the presence of phenol oligomers, and the non-negligible HB donor power of CHCl3.

Journal Article↗

PubMed2000

Quantum chemical modeling of through-hydrogen bond spin-spin coupling in amides and ubiquitin.

Through-hydrogen bond spin-spin coupling has been investigated computationally in the formamide dimer and in fragments of the protein ubiquitin. The Fermi-contact term was calculated by finite perturbation theory with the B3LYP DFT method with several basis sets. The distance and angular dependence of the 3J(N,C') coupling constant (N-H--O=C) in the hydrogen-bonded formamide dimer was firstly examined for a wide range of mutual arrangements, also in relation to the stability of the dimer. The magnitude of 3J(N,C') is relatively insensitive to the dihedral angle between the two amide planes, whereas values between 1-2 Hz are calculated for a variety of arrangements, including non-linear hydrogen bonds, in agreement with the shape of some occupied, low-lying molecular orbitals which connect donor and acceptor. Then, fragments of the ubiquitin protein (for which such coupling constants are experimentally available) were generated by removing from the experimental structure all amino acids except those involved in hydrogen bonding, and coupling constants were calculated for such fragments. Although calculated 3J(N,C') values are sometimes overestimated, they generally correlate with the corresponding experimental values.

Amides↗

PubMed2000

Selectivity in proton transfer, hydrogen bonding, and solvation.

The site of protonation (or deprotonation) of polyfunctional bases and acids can be determined through the comparison of experimental NMR properties (chemical shift and relaxation rates) with the corresponding data calculated by quantum chemical methods. The results can be interpreted in terms of the competition between intrinsic base strengths and solvation. Qualitatively similar criteria are found to hold for hydrogen bonding. The selective enrichment in a cosolvent in the solvation shell of a solute dissolved in a solvent mixture (preferential solvation) can be determined through the analysis of intermolecular cross-peak intensities in NOESY spectra.

Chemistry, Organic↗

PubMed1997

A novel algorithm for the coupling control in solid-phase peptide synthesis.

This paper describes a new method for the evaluation of conductimetric data collected during the in-line monitoring of the coupling step in solid-phase peptide synthesis. The control scheme relies on a feed-forward artificial neural network algorithm which can predict the final yield of the reaction within its initial 5 min by analyzing the conductivity signal profile. The yield values predicted by the artificial neural network algorithm result in good accordance with the data obtained by the commonly used ninhydrin test.

Algorithms↗

PubMed1997

SPPS of difficult sequences. A comparison of chemical conditions, synthetic strategies and on-line monitoring.

The H-Ala-Arg-(Ala)6-Lys-OH sequence is a biologically interesting 'difficult sequence' presenting N alpha-Fmoc deprotection and coupling problems. Different chemical conditions and synthetic strategies have been tested in order to overcome the problems due to sequence-dependent interactions. In particular, it was confirmed that different solvents in the deprotection step did not provide any significant improvement, but the use of a more efficient base in the deprotection mixture avoided insufficient unblocking of N alpha-protecting group; problems due to partial coupling in the last steps of the synthesis were solved by double coupling techniques. Moreover, the synthesis of the model peptide was carried out using both "continuous flow' and "batch' techniques. The present results demonstrate that on-line monitoring of the deprotection step by absorbance measurements represents a very effective tool to detect the onset of internal aggregations during the synthesis.

Chromatography, High Pressure Liquid↗