A valence force field for the amide group

Jakeš, J.; Krimm, Samuel

doi:10.1016/0584-8539(71)80004-1

Cited by 153 publications

(80 citation statements)

References 22 publications

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“…A normal vibration calculation of the system below, using the force constants of Suzuki and Shimanouchi (24), with and without a F(C'==O str, C'==O str) term, shows that A;, _ 130.F(C'==O str, C'==O str) [11] For a A,;…”

Section: Modified Perturbation Treatment Of Amide I Vibrationsmentioning

confidence: 99%

“…Such variations can give rise to errors in the interaction constants Do and Do, that are of the same order as the constants themselves. This objection to taking vo from nylon 66 as applicable to polypeptides has a general validity, since it should not be expected that the unperturbed frequency associated with the peptide group is completely independent of the local chemical environment of this group: This is amply established by detailed normal coordinate analyses of N-methyl acetamides and nylons (11), as well as of related molecules (12).…”

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confidence: 99%

“…Similar results are found with the Raman spectra of other polypeptides (17,18 (19) and alanine (20) does not indicate this to be the case, the splittings being essentially independent of chain length. But the most serious problem is that a normal vibration analysis of the exact structure of crystalline polyglycine I (13), based on a detailed general valence force field containing 78 force constants [and refined from a comparably complete force field for the peptide group in nylons and Nmethylacetamides (11)], fails to reproduce a large value for Do: from such an anaiysis Dio is typically of the order of a few cm-,. We feel, therefore, that the representation of Amide I frequencies given by Eq.…”

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confidence: 99%

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Intermolecular Interaction Effects in the Amide I Vibrations of β Polypeptides

Krimm

Abe

1972

Proc. Natl. Acad. Sci. U.S.A.

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320

242

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Previous perturbation treatments of the Amide I vibrations of 8 polypeptides are inconsistent with a detailed normal coordinate analysis of crystalline polyglycine I. This analysis indicates that the Do interaction constant is essentially zero, rather than the large value (about 20 cm-') required by the earlier application of the perturbation theory. It is suggested that the previously neglected Di, term should be included in the perturbation expression, and it is shown that the physical origin of such a term can be accounted for by transition dipole coupling. This mechanism is shown to give a reasonable explanation of splittings of the C=O stretching vibrations in hydrogenbonded carboxylic acid dimers. Its application to , polypeptides provides a satisfactory interpretation of splittings in the Amide I modes.The useof vibrational spectra to identify different polypeptidechain conformations dates from the work of Elliott and Ambrose (1), who observed that the frequency of the infrared-active Amide I vibration of a polypeptides was about 20 cm-' higher than that of # polypeptides. Further studies on synthetic polypeptides (2) established this observation as a firm empirical rule.Early attempts (3, 4) to account for this difference were not fruitful. A significant advance in understanding the theoretical basis for the above observation was achieved by Miyazawa (5), who developed a perturbation treatment for the interaction of amide-group vibrations in various polypeptide-chain structures. He also noted that, in addition to the strong Amide I band at about 1630 cm-' in the # polypeptides, a weak band at about 1690 cm-' could be assigned to the antiparallel-chain pleated-sheet structure. This treatment has formed the basis for interpretation of the vibrational spectra of polypeptides and proteins (6, 7).In the Miyazawa theory, the frequency of an Amide I mode (which is the only one that we will be concerned with in this paper) is given by p(B,V') = vo + E D,, cos(s8) cos(t') [1] In applications of Eq.[2] to the antiparallel-chain pleatedsheet structure, v(O,Tr) and v(r,O) were taken from the spectrum of polyglycine I, and the frequency of nylon 66 was The above procedure has been criticized (9, 10), primarily on the grounds of the assumed constancy of vo. This criticism was based on studies of a series of polyamides (10) that indicated that jo varied by 6 cm-I between nylon 10 and nylon 2. Such variations can give rise to errors in the interaction constants Do and Do, that are of the same order as the constants themselves. This objection to taking vo from nylon 66 as applicable to polypeptides has a general validity, since it should not be expected that the unperturbed frequency associated with the peptide group is completely independent of the local chemical environment of this group: This is amply established by detailed normal coordinate analyses of N-methyl acetamides and nylons (11), as well as of related molecules (12).It is also confirmed by an extension of these calculations to polyglycines I (13) ...

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Section: Modified Perturbation Treatment Of Amide I Vibrationsmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

See 1 more Smart Citation

Intermolecular Interaction Effects in the Amide I Vibrations of β Polypeptides

Krimm

Abe

1972

Proc. Natl. Acad. Sci. U.S.A.

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320

242

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“…These force fields were used to test our program. All predicted frequencies were within 1 cm-l of values previously obtained for pyrrole, N-methylpyrrole, and N-methylacetamide using the Schactschneider normal coordinate analysis program (14,15). The predicted frequencies and normal modes of N-methylpyrrole-2-carboxaldehyde were calculated by interfacing force constant sets for N-methylpyrrole and the carboxaldehyde group (16).…”

mentioning

confidence: 99%

“…Our imental frequencies is minimized. Partial valence force fields determined in this way were available for pyrrole, N-methylpyrrole, and the peptide group (14,15). These force fields were used to test our program.…”

mentioning

confidence: 99%

Conformational features of distamycin-DNA and netropsin-DNA complexes by Raman spectroscopy.

Martin¹,

Wartell²,

O’Shea³

1978

Proc. Natl. Acad. Sci. U.S.A.

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The binding of distamycin and netropsin to duplex DNA has been studied by Raman spectroscopy. Several changes occur in the Raman spectra of these drugs upon binding DNA. These changes were analyzed by assigning specific motions to the observed Raman bands through the use of molecular subunits of the drugs and normal mode calculations. Our Fig. 1.) Netropsin samples, available in both sulfate and hydrochloride forms, were purified by repeated recrystallization into the sulfate form. Various concentrations of the drug were used up to its solubility limit. At room temperature this was about 0.7 mg/ml. The distamycin A samples required no purification to obtain high-quality spectra. Because the solubility of distamycin A is much greater than that of netropsin, concentrations up to 2.5 mg/ml could be used. Spectra were obtained from 100 to 2000 cm-l. Care was taken to minimize the length of time the samples were irradiated by the laser. Raman spectra obtained at 250 and 10C were not significantly different. Laser irradiation had no effect on the ultraviolet absorbance spectra of the samples. The drugs were dissolved in a 3-4 mM NaCl solution at pH 6.0-7.0. Calf thymus DNA, obtained from Sigma, was extracted with chloroform and sonicated, then extensively dialyzed with 1.0 mM NaCI. It was rotoevaporated to dryness and redissolved with double-distilled water to a final concentration of 6.0 mg/ml. The

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Dynamic rheo-optical characterization of uniaxially oriented polyamide 11

Wang

Lehmann

1998

J. Polym. Sci. B Polym. Phys.

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A valence force field for the amide group

Cited by 153 publications

References 22 publications

Intermolecular Interaction Effects in the Amide I Vibrations of β Polypeptides

Intermolecular Interaction Effects in the Amide I Vibrations of β Polypeptides

Conformational features of distamycin-DNA and netropsin-DNA complexes by Raman spectroscopy.

Dynamic rheo-optical characterization of uniaxially oriented polyamide 11

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