Consistent porphyrin force field. 1. Normal-mode analysis for nickel porphine and nickel tetraphenylporphine from resonance Raman and infrared spectra and isotope shifts

1990 ◽  
Vol 94 (1) ◽  
pp. 31-47 ◽  
Author(s):  
Xiao Yuan. Li ◽  
Roman S. Czernuszewicz ◽  
James R. Kincaid ◽  
Y. Oliver. Su ◽  
Thomas G. Spiro
Keyword(s):  
Force Field ◽  
Normal Mode ◽  
Infrared Spectra ◽  
Normal Mode Analysis ◽  
Resonance Raman ◽  
Mode Analysis ◽  
Isotope Shifts

Modeling the heme vibrational spectrum: Normal-mode analysis of nickel (II) etioporphyrin-I from resonance raman, ft-raman, and infrared spectra of multiple isotopomers

1995 ◽  
Vol 1 (6) ◽  
pp. 395-412 ◽  
Author(s):  
Songzhou Hu ◽  
Arka Mukherjee ◽  
Christine Piffat ◽  
Ronald S. W. Mak ◽  
Xiao-Yuan Li ◽  
...  
Keyword(s):  
Vibrational Spectrum ◽  
Normal Mode ◽  
Infrared Spectra ◽  
Normal Mode Analysis ◽  
Resonance Raman ◽  
Mode Analysis ◽  
Ft Raman

Scaled Hartree-Fock force field calculations for organothallium compounds: normal-mode analysis for TlCH3, Tl(CH3)2+, Tl(CH3)3, Tl(CH3)2Br, and Tl(CH3)4-

1990 ◽  
Vol 9 (2) ◽  
pp. 504-508 ◽  
Author(s):  
Peter Schwerdtfeger ◽  
Graham A. Bowmaker ◽  
Peter D. W. Boyd ◽  
David C. Ware ◽  
Penelope J. Brothers ◽  
...  
Keyword(s):  
Force Field ◽  
Normal Mode ◽  
Normal Mode Analysis ◽  
Mode Analysis ◽  
Force Field Calculations ◽  
Hartree Fock ◽  
Organothallium Compounds

scholarly journals A force field for virtual atom molecular mechanics of proteins

2009 ◽  
Vol 106 (37) ◽  
pp. 15667-15672 ◽  
Author(s):  
Anil Korkut ◽  
Wayne A. Hendrickson
Keyword(s):  
Force Field ◽  
Molecular Mechanics ◽  
Normal Mode ◽  
Conformational Changes ◽  
Normal Mode Analysis ◽  
Coarse Grained ◽  
Mode Analysis ◽  
Biological Macromolecules ◽  
Molecular Mechanics Calculations ◽  
Low Degrees

Activities of many biological macromolecules involve large conformational transitions for which crystallography can specify atomic details of alternative end states, but the course of transitions is often beyond the reach of computations based on full-atomic potential functions. We have developed a coarse-grained force field for molecular mechanics calculations based on the virtual interactions of Cα atoms in protein molecules. This force field is parameterized based on the statistical distribution of the energy terms extracted from crystallographic data, and it is formulated to capture features dependent on secondary structure and on residue-specific contact information. The resulting force field is applied to energy minimization and normal mode analysis of several proteins. We find robust convergence in minimizations to low energies and energy gradients with low degrees of structural distortion, and atomic fluctuations calculated from the normal mode analyses correlate well with the experimental B-factors obtained from high-resolution crystal structures. These findings suggest that the virtual atom force field is a suitable tool for various molecular mechanics applications on large macromolecular systems undergoing large conformational changes.

Genetic refinement of the molecular force field: Normal mode analysis of purine vibrations

1997 ◽  
Vol 3 (1) ◽  
pp. 61-71 ◽  
Author(s):  
B. Brutovský ◽  
J. Uličný ◽  
P. Miškovský ◽  
V. Lisý ◽  
L. Chinsky
Keyword(s):  
Force Field ◽  
Normal Mode ◽  
Normal Mode Analysis ◽  
Mode Analysis ◽  
Molecular Force ◽  
Molecular Force Field

Vibrational Dynamics of 2-[3-(p-flourobenzoyl) Propyl]-1,2,3,4,6,7,12,12, a-octahydropyrazino[2′,1&prime:6,1] Pyrido [3,4-b] Indole [centbutindole]: A Potent Nuroleptic Drug

2015 ◽  
Vol 3 (1) ◽  
Author(s):  
D. B. Singh ◽  
Abadur-Rahman   ◽  
V. N. Shukla ◽  
Vikash Kumar ◽  
Pragya Gupta
Keyword(s):  
Force Field ◽  
Normal Mode ◽  
Title Compound ◽  
Normal Mode Analysis ◽  
Mode Analysis ◽  
X Ray Diffraction ◽  
Vibrational Dynamics ◽  
5Ht2 Receptors ◽  
Gross Behavior ◽  
Good Agreement

FITR spectra and normal mode analysis of compound 2-[3-(p-flourobenzoyl)propyl]-1,2,3,4,6,7,12,12, a-octahydropyrazino[2′,1′:6,1] pyrido [3,4-b] indole [centbutindole], which is a potent nuroleptic drug and belong to a series of 2-substituted pyrazino-pyrido indoles. It also blind with 5HT2 receptors. It has shown good antihypotensive activity. The well known Wilson’s G-F matrix method with Urey-Bradely force field has been used to evaluate the normal mode frequencies of vibration. Good agreement has been obtain between them and a set of 29 force field constants is established. The vibrational dynamics of the title compound is being reported using Urey Bradley force field. It has shown acute toxicity, gross behavior and central effects like anti convulsant activity, anti reserpine activity and stereo specificity of action. The conformation of the title compound was determined by X-ray diffraction. It is planned to determine the conformation in such cases by the application of Fourier Transform Infrared (FITR) spectroscopy and normal mode analysis. As a first step in this direction the FITR spectrum of the title compound has been recorded and its normal mode analysis is carried out. The assignments of the frequencies are based on the theoretically calculated frequencies have also been given their best assignment.

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