Takehiko Shimanouchi

The Protein Data Bank: a computer-based archival file for macromolecular structures.

The Protein Data Bank is a computer-based archival file for macromolecular structures. The Bank stores in a uniform format atomic co-ordinates and partial bond connectivities, as derived from crystallographic studies. Text included in each data entry gives pertinent information for the structure at hand (e.g. species from which the molecule has been obtained, resolution of diffraction data, literature citations and specifications of secondary structure). In addition to atomic co-ordinates and connectivities, the Protein Data Bank stores structure factors and phases, although these latter data are not placed in any uniform format. Input of data to the Bank and general maintenance functions are carried out at Brookhaven National Laboratory. All data stored in the Bank are available on magnetic tape for public distribution, from Brookhaven (to laboratories in the Americas), Tokyo (Japan), and Cambridge (Europe and worldwide). A master file is maintained at Brookhaven and duplicate copies are stored in Cambridge and Tokyo. In the future, it is hoped to expand the scope of the Protein Data Bank to make available co-ordinates for standard structural types (e.g. alpha-helix, RNA double-stranded helix) and representative computer programs of utility in the study and interpretation of macromolecular structures.

Tables of molecular vibrational frequencies. Consolidated volume II

The compilations of fundamental vibrational frequencies of molecules previously published as Tables of Molecular Vibrational Frequencies Part 5, Part 6, Part 7, and Part 8, which appeared in the Journal of Physical and Chemical Reference Data in 1972, 1973, and 1974, have been revised. This Consolidated Volume II includes data on a total of 212 molecules in addition to those on 223 molecules included in Volume 1 (NSRDS‐NBS 39). Selected values of the fundamental vibrational frequencies are given for each molecule, together with observed infrared and Raman spectral data and citations to the original literature. The selection of vibrational fundamentals has been based on careful studies of the spectral data and comprehensive normal‐coordinate analyses. An estimate of the accuracy of the selected values is included. The tables provide a convenient source of information for those who require vibrational energy levels and related properties in molecular spectroscopy, thermodynamics, analytical chemistry, and o...

Normal Vibrations of N‐Methylacetamide

The in‐plane normal vibrations of N‐methylacetamide and its deuterated compound were calculated as a six‐body problem. The force constants were transferred from diformylhydrazine and other molecules with similar structures. The normal modes as well as the distributions of the potential energy among symmetry coordinates were also calculated. The result of these calculations allows quantitative discussions concerning the nature of the amide I, II, II′, III, III′, and IV vibrations and other normal vibrations of N‐methylacetamide.

Infrared absorption spectra of aquo complexes and the nature of co-ordination bonds

Abstract The infrared spectra of aquo complexes, MSiF 6 .6H 2 O (M = Ni, Mn and Fe), NiCl 2 .6H 2 O, MnCl 2 .4H 2 O, MSO 4 .7H 2 O (M = Zn and Mg), CuSO 4 .5H 2 O and CrCl 3 .6H 2 O, and some of their deuterium compounds have been reported for the frequency range from 4000 to 270 cm −1 . In addition to the OH stretching and OH 2 scissors frequencies of the co-ordinated water, there have been observed two or three absorption bands in the low-frequency range 1000-270 cm −1 . The band of weak intensity observed in the range 900-600 cm −1 and that of medium intensity observed in the range 650-450 cm −1 have been assigned to the OH 2 rocking and wagging modes, respectively, because of the isotopic shift of their frequencies. The broad band observed in the range 500-300 cm −1 has been assigned to the metal—oxygen stretching vibration. A normal co-ordinate treatment has been made for one complex ion of T h symmetry and for D 4 h symmetry on the basis of Urey—Bradley type potential and the bond stretching force constants for the various metal—oxygen bonds have been calculated. The values for the force constants vary in the order Cr(III) > Ni(II) > Mn(II) ≈ Fe(II) > Cu(II) ≈ Zn(II) > Mg(II), showing that the degree of covalent character of the metal—oxygen bonds decreases in the same order. The largest value of bond stretching force constants K(CrO) is 1·3 md/A, which is still smaller than those for the metal—nitrogen bonds of amine and nitro complexes and those for the metal-carbon bonds of cyanide complexes.

Characteristic Infrared Bands of Monosubstituted Amides

Infrared spectra of various monosubstituted amides and the corresponding deuterated compounds have been measured in the gaseous, liquid, and crystalline states and in solutions. From the experimental results, the bands characteristic of the amide structure have been determined. Furthermore, from the comparison with the spectra of related substances and by the application of the product rule, the assignments of these characteristic bands have been made. The observed change of frequencies of these characteristic bands with change of state confirms this assignment.

OPTICALLY ACTIVE LATTICE VIBRATIONS AS TREATED BY THE GF-MATRIX METHOD.

A general description has been given of an application of the Wilsons GF‐matrix method to the treatment of optically active lattice vibrations. As examples, formulas are derived for the calculation of the frequencies of the lattice vibrations of a one‐dimensional, the diamond, and CaF2 lattices.

Crystal Vibrations and Intermolecular Forces of Polymethylene Crystals

Normal frequencies of crystalline polymethylene have been calculated for various phase differences along the c axis of the crystal. Intermolecular hydrogen—hydrogen force constants have been evaluated from the splitting of the spectroscopically active modes. The results of the calculations explain almost satisfactorily the splitting of the progression bands in the infrared spectra of long‐chain n‐paraffins as well as one lattice vibration band in the far‐infrared spectrum of polyethylene.

Longitudinal Acoustical Vibrations of Finite Polymethylene Chains

The low‐frequency Raman scattering spectra of finite polymethylene chains, observed utilizing laser excitation, show a band progression whose frequencies vary inversely and continuously as a function of chain length. It was established that these transitions arise from the longitudinal acoustical vibration of the chain skeleton and its overtones. These results are related to recent theoretical calculations for crystal vibrations of the infinite chain and are found to be in excellent quantitative agreement. An accurate spectroscopic value is derived for the elastic modulus of polyethylene.

Normal vibrations and force constants of polymethylene chain

Abstract Normal vibrations of an infinite polymethylene chain in the extended conformation have been treated. The G and F matrices of infinite order may be reduced to the G(δ) and F(δ) matrices of finite order corresponding to the phase difference (δ) between two adjacent methylene groups. The observed vibrational frequencies of long-chain n-paraffins and of polyethylene are compared with the frequencies of polymethylene chain calculated for various phase differences and their assignments have been discussed. A modification of the Urey-Bradley force field has been made in accordance with the present vibrational assignments.

Far infra-red spectra and metal—ligand force constants of acetylacetonates of transition metals

Abstract The infra-red spectra of Cu(acac)2, Pd(acac)2, Pt(acac)2, Mn(acac)2, Cd(acac)2, Fe(acac)3, Cr(acac)3, Co(acac)3, Rh(acac)3 and Mn(acac)3 have been measured in the region from 4000 to 60 cm−1. Vibrational assignments have been made on the basis of isotope shifts, infra-red dichroism and frequency shifts due to the change of the central ion. Normal co-ordinate treatments have been made for the 1:2 complex and the 1:3 complex in order to clarify the assignments and the normal modes of vibration quantitatively. The values of the force constants for the metal—oxygen stretching mode vary in the order: Pt(II) > Pd(II) > Cu(II) for the 1:2 complex and Co(III) > Cr(III) > Fe(III) for the 1:3 complex.