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At least 19 records
All sourcesNASA NTRSDOE OSTI
NASA NTRS1982

The display of molecular models with the Ames Interactive Modeling System (AIMS)

A visualization of molecular models can lead to a clearer understanding of the models. Sophisticated graphics devices supported by minicomputers make it possible for the chemist to interact with the display of a very large model, altering its structure. In addition to user interaction, the need arises also for other ways of displaying information. These include the production of viewgraphs, film presentation, as well as publication quality prints of various models. To satisfy these needs, the display capability of the Ames Interactive Modeling System (AIMS) has been enhanced to provide a wide range of graphics and plotting capabilities. Attention is given to an overview of the AIMS system, graphics hardware used by the AIMS display subsystem, a comparison of graphics hardware, the representation of molecular models, graphics software used by the AIMS display subsystem, the display of a model obtained from data stored in molecule data base, a graphics feature for obtaining single frame permanent copy displays, and a feature for producing multiple frame displays.

Egan, J. T.↗
NASA NTRS1989

Molecular modeling of calmodulin: a comparison with crystallographic data

Two methods of side-chain placement on a modeled protein have been examined. Two molecular models of calmodulin were constructed that differ in the treatment of side chains prior to optimization of the molecule. A virtual bond analysis program developed by Purisima and Scheraga was used to determine the backbone conformation based on 2.2 angstroms resolution C alpha coordinates for the molecules. In the first model, side chains were initially constructed in an extended conformation. In the second model, a conformational grid search technique was employed. Calcium ions were treated explicitly during energy optimization using CHARMM. The models are compared to a recently published refined crystal structure of calmodulin. The results indicate that the initial choices for side-chains, but also significant effects on the main-chain conformation and supersecondary structure. The conformational differences are discussed. Analysis of these and other methods makes possible the formulation of a methodology for more appropriate side-chain placement in modeled proteins.

NASA Discipline Exobiology↗
NASA NTRS1981

A molecular model for ice nucleation and growth

The semi-empirical quantum mechanical approach and the central field empirical pair potential model are applied to the development of molecular models for ice nucleation and growth.

Source record↗
NASA NTRS1999

Molecular Modeling and Experimental Investigations of Nonlinear Optical Compounds Monosubstituted Derivatives of Dicyanovinylbenzene

A search for potential nonlinear optical compounds was performed using the Cambridge Structure Database and molecular modeling. We investigated a series of monosubstituted derivatives of dicyanovinylbenzene, since the nonlinear optical (NLO) properties of such derivatives (o-methoxy-dicyanovinylbenzene, DIVA) were studied earlier. The molecular geometry of these compounds was investigated with x-ray analysis and discussed along with the results of molecular mechanics and ab initio quantum chemical calculations. The influence of crystal packing on the planarity of the molecules of this series has been revealed. Two new compounds from the series studied, ortho-F and para-Cl-dicyanovinylbenzene, according to powder measurements, were found to be NLO compounds in the crystal state about 10 times more active than urea. The peculiarities of crystal structure formation in the framework of balance between van der Waals and electrostatic interactions have been discussed. The crystal shape of DIVA and two new NLO compounds have been calculated on the basis of the known crystal structure.

Timofeeva, Tatiana V.↗
NASA NTRS1980

Interactive display of molecular models using a microcomputer system

A simple, microcomputer-based, interactive graphics display system has been developed for the presentation of perspective views of wire frame molecular models. The display system is based on a TERAK 8510a graphics computer system with a display unit consisting of microprocessor, television display and keyboard subsystems. The operating system includes a screen editor, file manager, PASCAL and BASIC compilers and command options for linking and executing programs. The graphics program, written in USCD PASCAL, involves the centering of the coordinate system, the transformation of centered model coordinates into homogeneous coordinates, the construction of a viewing transformation matrix to operate on the coordinates, clipping invisible points, perspective transformation and scaling to screen coordinates; commands available include ZOOM, ROTATE, RESET, and CHANGEVIEW. Data file structure was chosen to minimize the amount of disk storage space. Despite the inherent slowness of the system, its low cost and flexibility suggests general applicability.

Egan, J. T.↗
NASA NTRS1978

Ames interactive molecular model building system - A 3-D computer modelling system applied to the study of the origin of life

The investigation of specific interactions among biological molecules must take into consideration the stereochemistry of the structures. Thus, models of the molecules are essential for describing the spatial organization of potentially interacting groups, and estimations of conformation are required for a description of spatial organization. Both the function of visualizing molecules, and that of estimating conformation through calculations of energy, are part of the molecular modeling system described in the present paper. The potential uses of the system in investigating some aspects of the origin of life rest on the assumption that translation of conformation from genetic elements to catalytic elements would have been required for the development of the first replicating systems subject to the process of biological evolution.

Coeckelenbergh, Y.↗
NASA NTRS1998

Molecular Modeling of the Compounds with Nonlinear Optical Properties

The molecular polarizability characteristics for a large series of naphthoquinone and quinoline derivatives have been calculated. The dependence of calculated hyperpolarizability on the positions and the number of donor and acceptor substituents is discussed.

Timofeeva, Tatiana V.↗
NASA NTRS1981

A molecular model for ice nucleation and growth, attachment 2

The central field empirical pair potential model is applied to studying the effects of kinks, ledges, and vacancies on the absorption of water molecules from the vapor. Molecular dynamics simulations indicate that cluster and/or surface modes play a primary role in the absorption process, the flexibility of the hydrogen bond serves to decrease the energy required for structural interconversion, and the rapid distribution of added energy in a hydrogen bonded system lead to aggregate stability which greatly exceeds that predicted by static energy calculations.

Hale, B. N.↗
NASA NTRS1981

A molecular model for ice nucleation and growth, attachment 1

The quantum mechanical technique is used to study ionic, configurational, and impurity defects in the ice surface. In addition to static calculations of the energetics of the water monomer-ice surface interactions, molecular dynamics studies were initiated. The calculations of the monomer-ice surface interaction, molecular dynamics studies were initiated. The calculations of monomer-ice surface interactions indicate that many adsorption sites exist on the ice surfaces and that the barriers between bonding sites are relatively low. Bonding on the prism face of ice is preferentially above lattice sites.

Plummer, P. L. M.↗
NASA NTRS1999

Molecular Modeling of the Poling of Piezoelectric Polyimides

The computational method described in this paper allows the calculation of the dielectric relaxation strength of an amorphous polymer based solely upon its chemical structure. The 4,4' oxydiphthalic anhydride (ODPA) dianhydride and bis-aminophenoxybenzene (APB) diamine based polyimides, (beta-CN) APB-ODPA and APB-ODPA were studied. Amorphous cells were constructed and then poled using molecular dynamics. Dielectric relaxation strengths of Delta(epsilon) = 17.8 for (beta-CN) APB-ODPA and Delta(epsilon) = 7.7 for APB-ODPA were predicted. These values are in excellent agreement with the experimental values. It was found that both the pendant nitrile dipole and the backbone anhydride residue dipole make significant contributions to the polyimides dielectric response. Specifically, it was shown that the difference in the magnitude of the dielectric relaxations is directly attributable to the nitrile dipole. The size of the relaxations indicate an absence of cooperative dipolar motions, The model was used to explain these results in terms of the average orientation of the nitrile and anhydride dipoles to within 51 deg. and 63 deg., respectively, of the applied electric field.

Young, J. A.↗
NASA NTRS1977

Molecular model of ice nucleation

Two complementary techniques, semi-empirical quantum mechanical calculations and empirical central field pair potential calculations were used in developing a model of the interaction of water with simple surfaces.

Plummer, P. L. M.↗
NASA NTRS1998

Modeling Molecular Opacities Using Galileo Probe Observations

Data from the Net Flux Radiometer (NFR) experiment on the Galileo mission has been successfully collected and analyzed through 1996. As data was received, the best available laboratory spectroscopic data and was used in the reduction procedure. Since then newer and more accurate spectroscopic data has become available. During this agreement, research efforts focused on re-analysis of certain aspects of the data which benefited from recent improvements in spectroscopic databases, and from a more exact treatment of certain aspects of the physical theory of line shape and line broadening. In addition, a brief survey was completed of the available information, both theoretical and observational, of the absorption, reflection and transmission spectra of the atmospheres of the various types of planets that could reasonably be expected to occur in other solar systems.

Freedman, Richard S.↗
NASA NTRS1998

Modeling Molecular Opacities using Galileo Probe Observations

Data from the Net Flux Radiometer (NFR) experiment on the Galileo mission has been successfully collected and analyzed through 1996. As data was received, the best available laboratory spectroscopic data and was used in the reduction procedure. Since then newer and more accurate spectroscopic data has become available. During this agreement, research efforts focused on re-analysis of certain aspects of the data which benefited from recent improvements in spectroscopic databases, and from a more exact treatment of certain aspects of the physical theory of line shape and line broadening. In addition, a brief survey was completed of the available information, both theoretical and observational, of the absorption, reflection and transmission spectra of the atmospheres of the various types of planets that could reasonably be expected to occur in other solar systems.

Freedman, Richard S.↗
NASA NTRS1974

Molecular absorption parameters in atmospheric modelling

Molecular spectroscopic parameters are compiled for a number of infrared-active molecules occurring naturally in the terrestrial atmosphere. The following molecules are included in this compilation: water vapor; carbon dioxide; ozone; nitrous oxide; carbon monoxide; methane; and oxygen. The spectral region covered extends from less than 1 micron to the far infrared, and data are presented on more than 100,000 spectral lines. The parameters included in the compilation for each line are: frequency, intensity, half-width, energy of the lower state of the transition, vibrational and rotational identifications of the upper and lower energy states, an isotopic identification, and a molecular identification. Using this data compilation, band model parameters are presented for water vapor, carbon dioxide, and ozone averaged over 20 wavenumber intervals. Using these parameters in a random model formulation, transmittance spectra are provided and compared with both degraded monochromatic calculations and laboratory data.

Mcclatchey, R. A.↗
NASA NTRS1993

Multipole correction of atomic monopole models of molecular charge distribution. I. Peptides

The defects in atomic monopole models of molecular charge distribution have been analyzed for several model-blocked peptides and compared with accurate quantum chemical values. The results indicate that the angular characteristics of the molecular electrostatic potential around functional groups capable of forming hydrogen bonds can be considerably distorted within various models relying upon isotropic atomic charges only. It is shown that these defects can be corrected by augmenting the atomic point charge models by cumulative atomic multipole moments (CAMMs). Alternatively, sets of off-center atomic point charges could be automatically derived from respective multipoles, providing approximately equivalent corrections. For the first time, correlated atomic multipoles have been calculated for N-acetyl, N'-methylamide-blocked derivatives of glycine, alanine, cysteine, threonine, leucine, lysine, and serine using the MP2 method. The role of the correlation effects in the peptide molecular charge distribution are discussed.

NASA Discipline Exobiology↗