Spectra-structure Correlations Research Articles

Accurate determination of double bond position in mono-unsaturated straight-chain fatty acid ethyl esters from conventional electron impact mass spectra by quantitative spectrum—structure modelling

Brakstad, F., 1993. Accurate determination of double bond position in mono-unsaturated straight-chain fatty acid ethyl esters from conventional electron impact mass spectra by quantitative spectrum—structure modelling. Chemometrics and Intelligent Laboratory Systems, 19: 87–100. An objective approach is given for selecting the most significant fragments for mass spectrum—structure correlation. The method is based on partial least-squares regression (PLSR) on normalised spectral intensities as independent variables, and the carbon—carbon double bond position as response. Such a correlation between a structural descriptor and the mass spectra of pure compounds has not hitherto been reported in the literature. The procedure is demonstrated using conventional electron impact (70 eV)mass spectra of twelve straight-chain mono-unsaturated fatty acid ethyl esters, ranging in carbon—carbon double bond positions from 5 to 11 (except 7), incorporating both cis- and trans-isomers and chain lengths from C 16 to C 20. On the basis of the relative intensity of thirteen fragments, a quantitative model relating these to the response was developed. At a 95% confidence interval, all the residuals from the cross-validation fall within the confidence interval given by [true value ± 0.46] carbon position units. Thus, the model practically always gives an unambiguous estimate of the carbon—carbon double bond position. Possible further developments of this method are discussed for the use of gas chromatography—mass spectrometry and gas chromatography—Fourier transform infrared spectroscopy in combination.

FTIR - spectroscopy study of the three-dimensional structure of 1,3,5-diaza-phosphorinane complexes with transitional metals

The present study deals with the problem of heterocycle three-dimensional structure, its conformational flexibility and especially concerns the influence of complexation with transitional metals on heteroatomic ligand conformational station. IR spectra-structure correlations were also under consideration during the study. The 4000-100 cm −1 spectral range was analyzed.

Investigation of basic relationships in spectral manifestations of vibrations of indanthrone molecule

The experimental spectrum of the indanthrone molecule has been interpreted theoretically. The calculation of vibration frequencies and intensities and the construction of the theoretical spectral curve were performed by means of a gragment method. The set of parameters obtained for the model of the indanthrone molecule provides an adequate reflection of features of spectral manifestations of the experiment, and also intramolecular interactions in the real molecular structure. A clear-cut spectrum-structure correlation is revealed.

Generation of a substructure library for the description and classification of protein secondary structure. II. Application to spectra–structure correlations in fourier transform infrared spectroscopy

Fourier transform infrared spectroscopy has become well known as a sensitive and informative tool for studying secondary structure in proteins. Present analysis of the conformation-sensitive amide I region in protein infrared spectra, when combined with band narrowing techniques, provides more information concerning protein secondary structure than can be meaningfully interpreted. This is due in part to limited models for secondary structure. Using the algorithm described in the previous paper of this series, we have generated a library of substructures for several trypsin-like serine proteases. This library was used as a basis for spectra-structure correlations with infrared spectra in the amide I' region, for five homologous proteins for which spectra were collected. Use of the substructure library has allowed correlations not previously possible with template-based methods of protein conformational analysis.

Infrared Spectra of Protiated and Deuterated Lead(II) Saccharinate Monohydrate : Spectra-Structure Correlations

Abstract The infrared spectra of protiated and deuterated lead(II) saccharinate monohydrate, Pb(C7H4NO3S)2·H2O were studied in the OH, OD, CO and SO2 stretching regions. The spectral characteristics of the HOH and HOD stretching fundamentals were correlated with the structural data on the geometry of the water molecules. Also correlated were the appearance of the spectrum in the CO stretching region, on the one hand, and the number of non-equivalent carbonyl groups in the structure, on the other. An attempt was made to assign the bands which are mainly due to the antisymmetric and the symmetric SO2 stretching vibrations.

Conformation dependence of the SH and CS stretch frequencies of the cysteine residue

SYNOPSIS In order to relate the observed SH and CS stretch frequencies of the cysteine residue in proteins more closely to its conformation, we have done normal mode calculations on a model for this structure, viz., (CCONH) (CNHCO)CHCH2SH. A range of x' and x2 were studied, combined with the $,$ of the a-helix, P-sheet, glutathione, and extended-helix conformations. The force field was a combination of a scaled ab initio force field of the -CH2SH group, obtained from ethanethiol and tested on 1-propanethiol and 3-thiol-Nmethylpropionamide, and our empirical force field for the peptide group. The results provide more detailed structure-spectra correlations than are possible from experimental studies of model compounds. 0 1992 John Wiley & Sons, Inc. I NTRODU CTl ON The cysteine residue side chain, -CH2SH, is an important one in proteins, both because of its inherent properties as well as its ability to react with similar groups to form a disulfide bridge, -CH2SSCH2-, between polypeptide chains. It is therefore important to develop detailed spectroscopic correlations for characterizing its conformation. It has long been known that the SH stretch (s) mode, v(SH), is generally found in the range of 2500-2600 cm-' , being weak in the ir and strong in the Raman spectrum. Since v(SH) is sensitive to the presence of SH groups and to their environment, particularly hydrogen bonding, it has been studied in various proteins, such as hemoglobin, 122 eye lens proteins, 3-5 0-lactoglobulin, and virus protein^.^,' Conformational information with respect to the CCs-S-H dihedral angle ( x2) has been sought through experimental studies of model alkanethiolsg- as well as normal mode calculations on such molecule~.'~~~~ Low-frequency torsional modes have also been studied14-16 in order to obtain information on rotational barriers. The v(CS) mode has been known to give rise to Raman bands in the 600-800-cm-' region. Confor

Resonance Raman spectroscopic and kinetic consequences of a nitrogen ... sulphur enzyme-substrate contact in a series of dithioacylpapains

The resonance Raman (RR) spectroscopic, conformational, and kinetic properties of six dithioacylpapain intermediates have been examined. Five of the intermediates are of the form N-(methyloxycarbonyl)-X-glycine-C(= S)S-papain, where X is L-phenyl-alanine, D-phenylalanine, glycine, L-phenylglycine, or D-phenylglycine. The sixth intermediate is N-phenylacetyl-glycine-C(= S)S-papain. Throughout the series there is an approximately 50-fold variation in kcat, the rate constant for deacylation, and a 1750-fold variation in kcat/KM. Existing RR spectra structure correlations allow us to define the torsional angles in the NH-CH2-C(= S)-S-CH2-CH fragment of the functioning intermediates. The values of these angles for each bound substrate appear to be very similar, with the substrates assuming a B-type conformer such that the nitrogen atom of the P1 glycine residue is cis to the thiol sulphur atom of cysteine-25. For each intermediate, the C(= S)S-CH2CH torsional angle is approximately -90 degrees, whereas for the SCH2-CH torisonal angle the cysteine-25 thiol sulphur (S) and cysteine-25 C alpha hydrogen (H) atoms are approximately trans. The three acyl-enzymes with the lowest catalytic rate constants, viz. N-(methyloxycarbonyl)-glycine-glycine-, N-(methyloxycarbonyl)-L-phenylglycine-glycine-, or N-(phenylacetyl)-glycine-dithioacylpapains, have atypical RR spectra in that they show a feature of medium intensity in the 1,085-cm-1 region. This band is sensitive to NH to ND exchange of the P1 glycine residues' (-NH-) function and, thus, the corresponding mode involves an excursion of the NH hydrogen. It is hypothesized that the high intensity is due to a particularly strong interaction between the P1 glycine nitrogen atom and the thiol sulphur of cysteine-25, which also has the effect of retarding deacylation, because the nitrogen . . . sulphur contact has to be broken in the rate-determining step.

Monohydrates of the thiosaccharinates of sodium and potassium: spectra-structure correlations

The infrared spectra of the monohydrates of sodium and potassium thiosaccharinates and of some of their partially deuterated analogues were recorded at room and liquid-nitrogen temperatures. The spectral features in the OH and OD stretching regions were correlated with the crystallographic data on the geometry of the water molecules and their nearest neighbours. In an attempt to assign the bands due to the SO 2 stretching modes, the spectra of the thiosaccharinates were compared with those of the hydrate of sodium saccharinate, Na 3(C 7H 4NO 3S) 3 · 2H 2O.

Description of molecular distortions. VI. spectra-structure correlations in orthophosphate compounds

Second rank tensors were used to describe the distortions in a number of ortophosphate compounds, by a method introduced previously [1]. The results are compared with results obtained by other methods. A significant correlation was found between the principal values of the tensor of distortion and the frequencies of the components of the antisymmetric PO 4 stretching vibrations.

Model calculations on the amide-I infrared bands of globular proteins

Model calculations are performed on the amide-I infrared (ir) bands of globular proteins by assigning one oscillator with a transition dipole to each peptide group. Coupling between these oscillators is introduced through the transition dipole coupling mechanism. As examples of application of the model, the ir spectra in the amide-I region of eight representative proteins, viz., carbonmonoxy myoglobin, ribonuclease A, α-lactalbumin, lysozyme, flavodoxin, carboxypeptidase A, concanavalin A, and β-trypsin are calculated. Good agreement is obtained between the calculated and observed amide-I band envelopes. Some structure-spectrum correlations are discussed on the basis of the model calculations. The presence of bands with significant ir intensities for myoglobin in the region below 1640 cm−1 is consistent with its x-ray structure having no β sheet. Analysis of the contributions of β sheets to the amide-I band envelopes shows that parallel, antiparallel, and mixed parallel/antiparallel β sheets give rise to strong ir bands at a similar position in the wave number region below 1650 cm−1, and that no band in the region above 1650 cm−1 can be regarded as a reliable marker of antiparallel β sheets. The contributions of non-α-non-β parts spread over a wide wave number region. The differences in the amide-I band envelopes between α-lactalbumin and lysozyme originate most probably from the structural differences between the α-helical parts near the N termini of these proteins.

Infrared and Nuclear Magnetic Resonance Spectra-Structure Correlations for Anisoles

Spectra-structure correlations are presented for anisoles using IR, NMR, and chemical parameter values which aid in the spectra-structure identification of unknown materials. Spectra-structure correlations also aid in assigning carbon-13 chemical shifts to the correct carbon atom in anisoles.

Circular dichroism spectrum of gadolinium diglycolate single crystal

One-photon absorption (OPA) and circular dichroism (CD) spectra of gadolinium diglycolate single crystal at room temperature are examined and analysed. Observed dipole strengths, rotational strengths and dissymmetry factors for 6P J and 6D J groups are compared with the calculated values and a satisfactory spectra-structure correlation between the observed and the simulated spectrum is achieved.

Conformation-sensitive infrared bands of uridine-5′-monophosphate

Infrared spectra are presented for six compounds containing ribose residues with various conformations. The assignments are based chiefly on comparison of the vibrational data observed for these compounds with those for uracil and d-ribose-5-phosphate and on a previous normal coordinate calculation. A spectral feature in the 1300−1260 cm −1 region seems to be sensitive to the ribofuranose conformation, and the usefulness of these structure-spectrum correlations in the conformation studies of polynucleotides is also discussed.

Comparison of various molecular forms of bovine trypsin: correlation of infrared spectra with x-ray crystal structures

Fourier-transform infrared spectroscopy is a valuable method for the study of protein conformation in solution primarily because of the sensitivity to conformation of the amide I band (1700-1620 cm-1) which arises from the backbone C = O stretching vibration. Combined with resolution-enhancement techniques such as derivative spectroscopy and self-deconvolution, plus the application of iterative curve-fitting techniques, this method provides a wealth of information concerning protein secondary structure. Further extraction of conformational information from the amide I band is dependent upon discerning the correlations between specific conformational types and component bands in the amide I region. In this paper, we report spectra-structure correlations derived from conformational perturbations in bovine trypsin which arise from autolytic processing, zymogen activation, and active-site inhibition. IR spectra were collected for the single-chain (beta-trypsin) and once-cleaved, double-chain (alpha-trypsin) forms as well as at various times during the course of autolysis and also for zymogen, trypsinogen, and beta-trypsin inhibited with diisopropyl fluorophosphate. Spectral differences among the various molecular forms were interpreted in light of previous biochemical studies of autolysis and the known three-dimensional structures of the zymogen, the active enzyme, and the DIP-inhibited form. Our spectroscopic results from these proteins in D2O imply that certain loop structures may absorb in the region of 1655 cm-1. Previously, amide I' infrared bands near 1655 cm-1 have been interpreted as arising solely from alpha-helices. These new data suggest caution in interpreting this band. We have also proposed that regions of protein molecules which are known from crystallographic experiments to be disordered absorb in the 1645 cm-1 region and that type II beta-turns absorb in the region of 1672-1685 cm-1. Our results also corroborate assignment of the low-frequency component of extended strands to bands below 1636 cm-1. Additionally, the results of multiple measurements have allowed us to estimate the variability present in component band areas calculated by curve fitting the resolution-enhanced IR spectra. We estimate that this approach to data analysis and interpretation is sensitive to changes of 0.01 unit or less in the relative integrated intensities of component bands in spectra whose peaks are well resolved.

Resonance Raman spectroscopic studies of enzymesubstrate intermediates at 5 K

A simple and versatile system for resonance Raman (RR) spectroscopic analysis of enzymesubstrate complexes at liquid helium temperatures is described. The system allows us to record high-quality RR spectra for dithioacyl papain intermediates (MeO-Phe-Gly- and MeO-Gly-Gly-Phe-Gly-C (S)S-papain) in ice matrices at 5 K. Based on established structure-spectra correlations, it is concluded that the active-site conformation of the intermediates about the φ′, ψ′ glycinic linkages and cysteine-25 side chain is B-G+-PH both in ice matrices at 5 K and in solution at room temperature.

Infrared Spectra-Structure Correlations and Adsorption Behavior for Helix Proteins

A vibrational assignment has been made for most of the observed bands of aqueous solutions of albumin. This assignment is based not only on past assignments, but on experimental justifications and the use of both the infrared and Raman spectra. With the use of these assignments, changes in the secondary structure of both myoglobin and albumin with adsorption can be followed. Changes in the adsorbed protein films indicate that both reversible and irreversible protein adsorption takes place under certain conditions. The presence of reversibly adsorbed proteins can affect the extent of unfolding of the irreversibly adsorbed protein film.

Infrared and Raman Group Frequencies of Cyclic Imides

Infrared and Raman spectra of several examples of each of three classes of cyclic imides have been examined. Spectra-structure correlations have been sought for each of the classes, with particular emphasis being placed on the 1600–1800 cm−1 region. The spectra in this region are often complex, reflecting subtle structural features in the condensed phases. Group frequencies for substituted succinimides, phthalimides, and maleimides are proposed.

A neural network approach to infrared spectrum interpretation

The simple linear neural network model was investigated as a method for automated interpretation of infrared spectra. The model was trained using a database of infrared spectra of organic compounds of known structure. The model was able to learn, without any prior input of spectrum-structure correlations, to recognize and identify 76 functional groupings with accuracies ranging from fair to excellent. The effect of network input parameters and of training set composition were studied, and several sources of spurious correlations were identified and corrected.

The OH and O-D stretching vibrations in the hydrates of sodium and potassium saccharinate : spectra-structure correlations

The infrared spectra of the two hydrates of sodium saccharinate in the region of the OH and O-D stretching vibrations of protiated and partially deuterated samples are considerably different. The less stable monoclinic form is obviously a higher hydrate which is easily converted into the more stable triclinic one. The observed infrared frequencies for the triclinic crystals are correlated with the crystallographically determined Ow⋯O and Ow⋯N distances. The infrared spectra of the sodium compounds in the region of the OH and O-D stretching vibrations are compared with those of potassium saccharinate.

Hydrogen bonding Part 30. New IR spectra-structure correlations for tetraethylammonium, tetramethylammonium, and N, N-dimethyl-pyrrolidinium fluoride monohydrates, tetraethylammonium chloride monohydrate, and tetramethylammonium hydroxide dihydrate; evidence for a planar (H 2O·F −) 2 cluster

Tetraethylammonium chloride is not dimorphous, as we had once suspected; material recrystallized from hot acetone is identical to that prepared by Loehlin and Kvick by a different route, and contains a planar (H 2O·Cl −) 2 cluster of C 2h symmetry. Since the IR spectra of the water-fluoride cluster in tetraethylammonium and tetramethylammonium fluoride monohydrates are very similar to that of the water-chloride cluster in tetraethylammonium chloride monohydrate, we conclude that these hydrates contain a planar (H 2O·F −) 2 cluster, rather than the tetrahedral model previously proposed. IR spectra of N, N-dimethylpyrrolidinium fluoride monohydrate and monohydrate- d 2, demonstrate that they contain similar clusters. The crystal structure of tetramethylammonium hydroxide dihydrate has recently been reported, which allows a final correlation of the IR spectrum and the structure of this hydrate.