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An attempt has been made to predict the beta-regions in 16 globular proteins by applying the one-dimensional Ising model theory of Lifson & Roig (8). The parameters for the theory have been derived from the statistical data on globular proteins given by Chou & Fasman (5). Comparison of our results with the data available from the X-ray crystallographic studies indicates a prediction accuracy which is comparable to those of several other methods, especially in view of the limitations in our method for considering the other secondary structures. It is pointed out that not considering the long-range interactions in our and other methods based on short-range interactions would make these methods incomplete and incapable of being uniformly applicable to all proteins.

The normal modes have been calculated for three kinds of low energy gamma-turn structures resulting from recent conformational energy calculations by Némethy. Frequencies have been computed for a gamma-turn, a mirror-related gamma-turn, and an inverse gamma-turn of CH3-CO-(L-Ala)n-NH-CH3, with n = 3 and n = 5, and for certain 14C and 15N derivatives of the n = 3 molecule. Correlations are evident between amide frequencies and gamma-turn structures, and it is found that only amide I modes of peptide groups in the turn are relatively insensitive to the lengths of attached chains.

Infrared and Raman spectra of the Mg2+ salt of poly(U) in D2O were recorded in the 1600-1800 cm−1 region and between 1 and 20C. The ir spectra showed a melting curve similar to the uv melting curves with a temperature of transition of about 6.5°C. This spectral change is assumed to be associated with the formation of the secondary structure of Mg2+-poly(U) in D2O at this temperature. Three double-helical and two triple-helical structures were used as inputs to compute the normal modes of vibration. A double-helical structure was found to give the best agreement with the observations. Knowledge of the C=0 eigenvectors, and of the expression for transition probability from quantum mechanics, was used to explain the so far unanswered question of H. T. Miles [(1964) Proc. Natl. Acad. Sci. USA 51, 1104–1109; (1980) Biomolecular Structure, Conformation, Function and Evolution, Pergamon, Oxford, pp. 251–264] as to why there is an increase in the ir vibrational wave number of a carbonyl band when that group is H-bonded to another polynucleotide chain in a helix. Such considerations also explain why a predicted band at about 1648 cm−1 is not to be seen in the ir spectra but is present in the Raman spectra. The model incorporating the CO transition dipole-dipole coupling interaction is able to explain also the observed higher intensity of the higher wave-number ir band. The experimental results demonstrate that the complete picture of vibrational dynamics of Mg2+-poly(U) in D2O is obtained only by looking simultaneously at ir and Raman spectra and not at only one of them. Weak ir bands were found to be as useful as the strong ones in understanding structure and vibrational dynamics. On the bases of our ir and Raman spectra, of the normal-mode analyses, and of the literature data, it is concluded that Mg2+-poly(U) in D2O is present in a double-helical structure at temperatures below the temperature of transition, whereby the uracil residues are paired according to arrangement (a) (see Fig. 1). This structure is rodlike and arises by refolding of one poly(U) chain. The computations show that no normal mode is associated with a single CO group vibration; all CO group vibrations are heavily mixed motions of various CO groups.

The Circle® cell has made possible the quantitative analysis of samples by infrared spectroscopy in aqueous solutions. With the use of this technique, which makes use of an FT-IR spectrometer, a novel analytical method is presented for the quantitative determination of sulfur oxide anions in white liquor. The method is appropriate only for oxidized sulfur species. However, it is shown that when Na2S concentrations are determined by another technique (e.g., ion chromatography or ion-selective electrode), the results can be used to carry out material/species balance on the unoxidized as well as oxidized samples of white liquor. The method is fast, straightforward, and convenient to use, and it does not require further treatments of white liquor solutions. Another advantage of this method is that it lends itself to in situ analysis. It is also general enough to be used for the quantitative analysis of other aqueous solutions. Linear regressions carried out on the SO=4, S20=3, and SO=3 species (in concentration ranges of 0–70, 0–45, and 0–42 g/L as salts, respectively) led to correlation coefficients of higher than 0.99; respective minimum detection limits of 0.01, 0.02, and 0.02 g/L were obtained. The latter can be further improved upon by employing longer-pathlength crystals. The method provides a way of carrying out material species balances, and studying reactions and their kinetics. The process does not use any toxic materials or environmentally unfriendly bleaching agents; it makes use of a combination of temperature, pressure, and molecular oxygen to oxidize white liquor to sulfate.

Many types of polymers have been used for medical devices for blood contacting application. Polyurethanes have been determined to be one of the more blood‐compatible. However, there is variability within types of polyurethanes and even within the same type of polyurethane as far as hemocompatibility. This variability stems in part from differences in processing aids, including waxes, which manufacturers add. An understanding of the surface chemical properties is essential for the determination of the hemocompatibility of polyurethanes. For this presentation, we describe analysis of the wax component of the surface of a polyurethane commonly used for extruded medical devices, Pellethane 2363 (Dow), by Fourier‐transform infrared‐attenuated total reflection (FTIR‐ATR) and x‐ray photoelectron spectroscopy (XPS), and the effect of its presence on the hemocompatibility of Pellethane. Solvent cleaned samples, demonstrating reduced amide processing wax component by the two techniques, are also evaluated for blood...

This review article discusses the amide modes associated with the reverse turns in peptides and proteins. Applications of the normal mode analysis treatment to different types of β-turns in peptides and in proteins like insulin, metallothioneins, phosvitin, and glycoproteins are presented. Similar analysis is carried out on γ-turns in peptides and proteins. The article attempts to bring to notice the so far neglected reverse turn, namely, cross-β conformation. Possible models for further physicochemical studies of this conformation are presented. Applications of cross-β conformation to insulin fibrils, bacteriophage T4, prebiotic polypeptides, DNA—protein interactions, and the Alzheimer's disease are presented and discussed. This article concludes with a critical assessment, a discussion of power and limitations of vibrational spectroscopy in study protein conformation, and a discussion on perspectives for the future.

Ab initio quantum chemical computations were carried out on (a) methyl carbamate, (b) N-methyl methyl carbamate, and (c) the N-methyl methyl carbamate dimers: (i) to determine the optimized parameters, the relative strengths of cis versus trans conformations, and the dipole moment of the carbamate group; (ii) to determine the optimized bond parameters of the N-methyl methyl carbamate (a model for the urethane C-O-C group) and the relative energies of the cis and trans conformations; (iii) to determine the relative strengths of the C-O-C and CO H-bonds. The basis set used was the 3-21G set of the gaussian 80 program obtained from QCPE, Bloomington, IN. Variations in the strengths of these two H-bonds with the Nctdot;O distance (where O is either the carbonyl or the urethane alkoxy oxygen atom) were studied and found to be similar in behavior. The cis carbamate group was found to be energetically more stable than the trans one by 10.74 kcal mol−1. The strength of the urethane C-O-C H-bond was computed to be 5.95 kcal mol−1, which is quite significant compared to the value of 8.25 kcal mol−1 for the more accepted “carbonyl” H-bond. The urethane C-O-C H-bond is found to be directional, specific and non-negligible. Computed dipole moments are in very good agreement with experimental results. Work with two more basis sets has indicated that the results so obtained are not dependent on the choice of the basis set.

This review article discusses the amide modes associated with the reverse turns in peptides and proteins. Applications of the normal mode analysis treatment to different types of β-turns in peptides and in proteins like insulin, metallothioneins, phosvitin, and glycoproteins are presented. Similar analysis is carried out on γ-turns in peptides and proteins. The article attempts to bring to notice the so far neglected reverse turn, namely, cross-β conformation. Possible models for further physicochemical studies of this conformation are presented. Applications of cross-β conformation to insulin fibrils, bacteriophage T4, prebiotic polypeptides, DNA—protein interactions, and the Alzheimer's disease are presented and discussed. This article concludes with a critical assessment, a discussion of power and limitations of vibrational spectroscopy in study protein conformation, and a discussion on perspectives for the future.

Ab initio quantum chemical computations were carried out on (a) dimethyl ether, (b) N-methyl formamide, (c) dimethyl ether-N-methyl formamide complex, and (d) N-methyl formamide dimer to compute the strengths of hydrogen bonds (H-bonds) between the NH groups and CO and ether COC groups. The basis set used was the 3-21G set of the GAUSSIAN 80 program obtained from QCPE, Bloomington, IN. Variations in the strengths of these two H-bonds with the N . . O distance (where O is either carbonyl or ether group oxygen) were studied and found to be similar in behavior. The strength of the “ether” hydrogen bond is computed to be 10.32 kcal mol−1, which is quite significant compared to the value of 10.11 kcal mol−1 for the more accepted “carbonyl” hydrogen bond. The “ether” hydrogen bond is found to be directional, specific and non-negligible. Work with two more basis sets has indicated that the results so obtained are not dependent on their choice. Possible importance of such a hydrogen bond in polyurethanes, inhalation anesthetics, and depsi-peptides is indicated.

Fourier-transform-infrared-attenuated total internal reflectance (FT-IR-ATR) has been used to study polyurethanes containing different hard segments but the same soft segment. The spectra of a series of blended polyurethanes have been systematically studied. The changes in the urethane COC regions of the polyurethanes with respect to the hard segments make a strong case for the existence of hydrogen-bonding interactions between the urethane COC groups and the NH groups. The decreases in the relative intensities of carbonyl bands and shifts of NH stretching bands (as the urethane COC bonding with NH groups increases) are in support of this proposal. The urethane COC region is shown to be a useful region in interpreting ATR spectra of polyurethanes. The implications of these results to the present methods of estimating phase separations in polyurethanes are discussed. Results obtained from ab initio quantum chemical computational methods show this hydrogen bond to be directional and to have an energy of 6.32 kcal mol −1 (compared with carbonyl hydrogen bond energy of 8.37 kcal mol −1 ) which is surprisingly high.

We have found that tri-L-alanine (Ala3) can crystallize in a parallel-chain beta structure in addition to the previously known antiparallel-chain beta structure. Although the chain conformations in each structure are essentially similar, the ir and Raman spectra are distinctively different. We have calculated the normal modes of each structure, and can account in significant detail for these differences. This demonstrates the essential validity of our empirically refined force fields, as well as showing that deeper insights into polypeptide and protein structure can be achieved through the rigorous analyses of normal mode calculations.

We have obtained a simplified ab initio force field for diethyl disulfide, based on our previous scaled ab initio force field, which can be used in normal coordinate analysis of proteins containing the disulfide bridge. A normal coordinate analysis has been performed for diisobutyl disulfide in all possible conformations. The correlations thus obtained between the SS and CS stretch frequencies and the conformation are useful in understanding similar correlations in proteins containing the disulfide bridge. A simple way is presented to identify local C2 symmetry in a disulfide bridge through Raman polarization studies.

Many types of proprietary processing aids are used by the manufacturers of polymer medical devices, which are difficult to completely eliminate from the end product. In such cases, it is important to investigate how such processing aids affect the properties of the materials. One such material is Pellethane and a most commonly found processing aid is wax. We investigated the effect of the presence of such wax on hecompatibility properties, particularly on the adhesion and activation of human platelets, on a group of Pellethane samples with varying amounts of wax. The effectiveness of cleaning agents, like Freon, was examined for wax removal. The type and quantity of wax present within the near-surface regions of the Pellethane tubings was estimated by using the FT-IR-ATR technique. The presence of bis amide processing wax was found to affect the hemocompatibility properties of the Pellethane samples. Correlation between hemocompatibility and the amount of wax was made; platelet activation, as well as amount and density of fibrin formation, showed a linear correlation.

Attempts have been made to understand the nature and significance of hydrogen bonds of the type X-H-C (X = 0, N) . These unusual interactions have been discussed recently. Crystallographic studies on 17a-ethynylandrosta- 2,4-dieno[2,3-d]dihydroxazol1-7 8-01 (donazole) provide direct evidence of such an 0-H.0-C interaction. Ab initio computations, IR spectroscopy, and database studies show that these hydrogen bonds, while uncommon, are energetically and structurally significant.

modes are given for the latter three structures. Calculations have been done for structures with standard dihedral angles, as well as for structures whose dihedral angles differ from these by amounts found in protein structures. The force field was that refined in our previous work on polypeptides. Transition dipole coupling was included, and is crucial to predicting frequency splittings in the amide I and amide I1 modes. The results show that in the amide I region, P-turn frequencies can overlap with those of the cu-helix and @-sheet structures, and therefore caution must be exercised in the interpretation of protein bands in this region. The amide I11 modes of 0-turns are predicted at significantly higher frequencies than those of (?-helix and 0-sheet structures, and this region therefore provides the hest possibility of identifying 0-turn structures. Amide V frequencies of fl-turns may also he distinctive for such structures.

We have refined vibrational force fields for polypeptides that permit excellent reproduction of the normal mode frequencies of such molecules. This is demonstrated in the present study, in which 80 IR and Raman bands of crystalline triglycine between 1800 and 200 cm −1 are reproduced with an average error of 6 cm −1 . A deuterated sample is shown by normal mode analysis to have remained protonated at the C-terminal peptide group. Such results show that normal mode analysis can now provide a rigorous base for spectral studies of conformation in peptides and proteins.

The local-structure model of Bryan and Curnutte, which treated a single molecule in a rigid cage, has been extended to include a central water molecule and its four nearest neighbors surrounded by a rigid cage of next-nearest neighbors. The influence of the next-nearest neighbors is accounted for by the average forces they exert on the five-molecule local-structure group. With parameters based on water at 25°C, we give calculations of the spectra of liquid H 2 O and D 2 O at 25°C and for ice I . The results of the calculations are compared with observed spectra and with recent molecular-dynamics calculations.

Using the force fields due to Nishimura et al.[1] and to Harsanyi et al.[2], dipole moment derivatives (DMD's) and their orientations have been computed by ab initio techniques. The values so computed using the above two force fields are surprisingly close to each other. The DMD's corresponding to the C = O stretching (s) and CN s are found to be among the most significant. The DMD values of C2 = O s and C4 = O s are found to be comparable in value, both of them thus expected to contribute to C = O s ir band intensities. The DMD's of NH in-plane bending (ipb) modes are found to be surprisingly small, thus explaining the observed absence of splittings due to the corresponding transition dipole- transition dipole coupling (TDC) interactions. The DMD values obtained here are shown to be crucial in deciding which of the observed bands in solid state or condensed phase samples could be due to Fermi resonance and/or overtone and/or combination bands. They could also be used effectively in studying rela...

Theoretical arguments are presented, based on Davydov's exciton theory, for expecting the presence of coupling between the CO transition dipoles in uracil. In order to observe the effects of these coupling interactions, relevant experiments have been performed and their results discussed. The observed CO band-splittings in uracil seem to be in support of such a coupling between various CO dipoles within the unit cell of uracil. Since this transition dipole—dipole coupling interaction leads to band-splittings in the double-bond region, it is proposed that these splittings might provide a way to distinguish between different conformations in polynucleotides as well as in nucleic acids.

Bands in the ir and Raman spectra of L-valyl-glycyl-glycine (VGG) and VGG-ND have been assigned on the basis of a normal mode analysis of the known parallel-chain β-structure of this tripeptide. Amide I, II, III, and V mode shifts are obtained by the interactions of dipole derivatives in symmetry coordinates, referred to as dipole derivative coupling. These derivatives, obtained from ab initio studies, are also used to calculate ir intensities of amide I, II, and V modes. The agreement between predicted and observed frequencies and intensities is very good, providing confidence in the application of our force fields to the calculation of the vibrational modes of the general parallel-chain β-sheet structure (following paper).

A normal coordinate analysis has been performed on the unit cell of uracil. Transition dipole—dipole coupling interaction between CO groups within the four molecules in the unit cell was found necessary to explain the observed band splittings in the double-bond region. It has been proposed that this new interaction may be important in our future attempts to distinguish between various conformations in polynucleotides and nucleic acids. Bands due to NH in-plane and out-of-plane bending modes were assigned by means of the spectra of uracil, 1-methyluracil and 3-methyluracil. Spectra of uracil and C 5 -deuterouracil were made use of in assigning bands due to CH deformation modes. Bands due to C 2 O and C 4 O deformation modes were assigned by studying the spectra of uracil, 2-thiouracil and 2,4-dithiouracil. NH in-plane bending mode bands have shown no indications of effects due to interactions through transition dipole—dipole coupling. NH out-of-plane bending mode bands were found to be unusually sensitive to the strengths of hydrogen bonding. Normal mode calculations have shown a mixing of in-plane and out-of-plane bending modes below 1000 cm −1 . It is hoped that the calculations performed here will provide the basis for future studies of polynucleotide as well as nucleic acid conformations by making use of the conformational sensitivity of the CO stretching bands.

Normal vibration calculations have been done for a type I β-turn of CH 3 -CO-(Ala) 4 -NH-CH 3 and a type II β-turn of CH 3 -CO-(Ala) 2 -Gly-Ala-NH-CH 3 . The force field was the one we refined for β-sheet and α-helical structures. A calculation was also done for CH 3 -O-CO-Gly-(Ala) 2 -Gly-O-CH 3 , which is an appropriate model for two tetrapeptides for which infrared data are available. The agreement between observed and calculated frequencies in this case is good, thus supporting the conclusions drawn from the above β-turn calculations. The most important result of the calculations is the prediction of bands near 1690 cm -1 , a region heretofore associated only with the antiparallel-chain pleated sheet structure. This means that bands observed in proteins near 1690 cm -1 should be associated with the presence of β-turns as well as of β-sheets. We also find that a band near 1665 cm -1 is characteristic of type II turns.

Normal mode calculations have been carried out for parallel-chain β-sheet structures. These include the parallel-chain pleated sheet of poly(L-alanine) and the parallel-chain rippled sheet of polyglycine. Dipole derivative coupling has been included for amide I and II modes, and the effects of parallel-sheet and antiparallel-sheet arrangements of varying separation have been examined for the poly(L-alanine) case. Some amide and nonamide modes are distinctly different from their antiparallel-chain counterparts, thus providing a basis for distinguishing between such structures from their ir and Raman spectra. As in our previous studies, these results emphasize the need for both kinds of spectral data in order to draw definitive conclusions about conformation.

Far-i.r. spectra in the region 20–600 cm−1 are reported for solid l -alanine as a function of temperature between 6 and 300 K. Understanding of the temperature-sensitive as well as the temperature-insensitive bands is aided by the normal coordinate analysis of l -alanine. Bands containing contributions from hydrogen bonds, skeletal deformation and NH3+ torsion are found to be highly sensitive to temperature changes. Although the hydrogen bonds are stronger at lower temperatures, no evidence of amide formation is detected even at 6 K. Thus the zwitterion form seems to be more stable than the amide form in the temperature range studied here.

A normal coordinate treatment of a general bent XYZ molecule and a continuum picture of the liquid state are used to calculate the frequency distribution of intramolecular vibrations of a water molecule in the liquid state. The effect of neighboring molecules on the vibrational frequencies is taken into account by assuming complete tetrahedral hydrogen bonding with a distribution of equilibrium OO distances. The equilibrium OO distance distributions at various temperatures are obtained from X-ray pair correlation functions. The vibrational distributions are converted into spectra by taking the intensity of scattering or absorption of the band at each frequency as being determined by the number of oscillators having that particular frequency at any instant. Of the four adjustable parameters in the potential energy function, the stretching constants are chosen from the Lippincott-Schroeder potential function, while the remaining three are determined from H 2 O, HDO, and D 2 O infrared vapor data.

Placzek [1] was the first to derive general expressions for the intensities of overtones in case of Raman scattering. He assumed electrical anharmonicity. However, he left the expressions for the derivations of the polarizability tensor undetermined. In 1941, a classical and semiempirical theory was developed by Wolkenstein [2]. He assumed the validity of the additivity of bond polarizabilities. However, the expressions derived by him for the intensities of overtones remain yet to be verified. It is the purpose of this paper to derive a formula for Raman polarizability tensor for overtones of (intramolecular) vibrational spectra along the lines of Kondilenko et al. [3,4].

It is shown in this note that the modified form of the Lippincott-Schroeder potential function [1, 2] which has been extensively used by us in theoretical studies of the vibrational spectra of liquid water [3, 4] gives a reasonably good value of the bond energy.

The normal modes have been calculated for structures having the dihedral angles of the four β-turns of insulin. Frequencies are predicted in the amide I region near 1652 and 1680 cm−1. The former overlaps the α-helix band at 1658 cm−1 in the Raman spectrum, while the latter accounts for the hitherto unassignable band at 1681 cm−1. Calculated amide III frequencies extend above 1300 cm−1, providing a compelling assignment of the 1303-cm−1 band in insulin and similar bands in other globular proteins.

Whether proteins denature in all-or-none fashion or in a continuous fashion is as yet an unresolved problem. The all-or-none process implies that while the process of denaturation is going on, only two kinds of protein molecules can exist. One is completely unchanged and the other is altered. The altered protein molecules are indistinguishable. Underlying the 'continuum' models is the assumption that all the chains in a protein globule undergo similar changes so that it is enough to consider a single chain.

Publisher Summary The vibrational spectrum of a molecule is determined by its three-dimensional structure and its vibrational force field. An analysis of this (usually infrared (IR) and Raman) spectrum can therefore provide information on the structure and on intramolecular and intermolecular interactions. The more probing the analysis, the more detailed is the information that can be obtained. Detailed analyses of the vibrational spectra of macromolecules, however, have provided a deeper understanding of structure and interactions in these systems. An important advance in this direction for proteins came with the determination of the normal modes of vibration of the peptide group in N-methylacetamide, and the characterization of several specific amide vibrations in polypeptide systems. Extensive use has been made of spectra-structure correlations based on some of these amide modes, including attempts to determine secondary structure composition in proteins. Polypeptide molecules exhibit many more vibrational frequencies than the amide modes. Over the years, some normal-mode calculations have provided greater insight into the spectra of particular molecules. However, these have often been based on approximate structures or have employed limited force fields. These force fields can now serve as a basis for detailed analyses of spectral and structural questions in other polypeptide molecules. The aim of this chapter is to present these recent developments in the vibrational spectroscopy of peptides, polypeptides, and proteins.

The effect of copper complexation upon the conformational angles in mononucleotides and dinucleotides was studied using classical potential energy expressions. The geometrical parameters were taken from crystallographic reports on the base-metal complexes. It was found that the preferred conformations of the complexes were quite different from the preferred conformations of the corresponding pure nucleotides. Notable among the disallowed conformations in case of Cu(II)-dinucleotide complexes were the regions corresponding to RRNA's, RNA's and the A, B and C forms of DNA. It is proposed that the energetics of a single strand is more important than inter-strand interactions in promoting copper-induced denaturation of DNA.