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  • AERODYNAMICS  (9)
  • Biochemistry  (5)
  • 2020-2022
  • 1990-1994  (14)
  • 1
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 254-265 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab-initio self-consistent-field molecular-orbital (SCF MO) Hartree-Fock (HF) calculations using the STO-3G, 6-31G, and 6-31G* basis sets, were performed to model quasi-tetrahedral silicon species in silicon dioxide. Mostly nine-atom clusters, [Si(OH)4]qt, with charge number qt = 0 or + 1, were studied. The positions of the Si and O atoms were varied to achieve minimum total energies, while the protons were held fixed in the O-(neighboring)Si direction to simulate the rigid crystal surroundings. The α-quartz-type local symmetry C2 was found to be retained for the neutral cluster, but not for the ionic one. The unrestricted HF calculations indicate that the latter paramagnetic centre, (qt = +1), has its spin population almost entirely on one short-bonded oxygen ion bonded weakly to its neighboring Si, and is quite high in energy (9.55 eV with 6-31G) compared to the diamagnetic centre (qt = 0). The ionization energy is much higher than the self-trapping potential of the polaronic hole, a fact which may account for the failure so far to observe a [SiO4]+1 center in quartz by means of continuous-wave electron paramagnetic resonance spectroscopy. Calculations on the [SiO4]+1 center agree well with ultraviolet spectra, and with the [hole portion of a] proposed radiation-induced exciton in quartz. The hole in [Si(OH)4]+1 can be shifted from a short-bonded to a long-bonded oxygen to give the excited state [Si(OH)4]es+1. Conclusions reached with the nine-atom clusters were confirmed by a series of calculations on the extended model [Si(OSiH3)4]qt. Comparisons with the known isoelectronic species [AlO4]0 were carried out.
    Additional Material: 4 Ill.
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  • 2
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 209-214 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In molecular modeling projects which require use of several different computer programs, one encounters problems in sharing data between programs. One difficult problem is the conversion of atom types from one program's definition to another. A second problem is the conversion of a polymer, such as a protein or polynucleotide molecule, from a “general” program, which understands molecules as a collection of atoms, to a “polymer” program, which understands molecules as a collection of molecular fragments stored in some library. We describe here a new method by which atom types are deduced from the environment of each atom. We use the Daylight Chemical Information Systems library of programs to deduce the atom types based only on the atomic symbol, connectivity and formal charge of each atom in the molecule. We also describe a method by which the polypeptide nature and sequence of a molecule can be deduced from minimal information about the atoms in the molecule. We have written a computer program which demonstrates this method. This program deduces atom types for AMBER, GRIN/GRID, CHARMm, and ALOGP. It will also produce input files for the AMBER/PREP fragment library preparation program.
    Additional Material: 2 Ill.
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  • 3
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 446-453 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio SCF-MO Hartree-Fock calculations were performed using the STO-3G, 6-31G, and 6-31G* basis sets to model hypothetical substitutional carbon impurities in silicon dioxide. We utilized nine-atom clusters, [C(OH)4]qt, with charge number qt = 0 and + 1. The positions of the C and O atoms were varied to achieve minimum total energies, while the fixed protons served to simulate the rigid crystal surroundings. In the optimized configuration of the neutral cluster, the C—O bond lengths are appreciably longer than typical C—O bonds, indicating relatively weak bonds for a carbon impurity at a silicon site. For comparison, the relative positions of all nine atoms in the [C(OH)4]0 model were allowed to vary. This unconstrained model yielded more normal bond lengths and was lower in energy than the fixed-proton model by 6.80 eV with the 6-31G* basis set. The free-H model compared favorably with the x-ray diffraction data for an analogous orthocarbonate. Our results are in concert with the lack of reports of any substitutional carbon impurity in α-quartz. In the fixed-H models, the twofold local symmetry was found to be retained when qt is 0 but not when qt is + 1. For the latter ion, the unrestricted H-F calculations indicate that this paramagnetic center has its spin population almost entirely on one oxygen ion and is high in energy (5.31 eV with 6-31G) compared to the diamagnetic neutral one. Conclusions reached with the nine-atom clusters were confirmed by a series of calculations on the extended model [C(OSiH3)4]0.
    Additional Material: 3 Ill.
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  • 4
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1241-1253 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ro 31-8959 is a highly potent inhibitor of HIV-1 proteinase in phase III clinical trials for treatment of AIDS. It is also the first subnanomolar inhibitor that demonstrated reversed stereochemical preference at the central hydroxyl group. Free energy perturbation calculations have been carried out to rationalize the preference for the R-diastereomer by consideration of two models of the (weaker) S-diastereomer. In the first model, the central hydroxyl group makes only one hydrogen bond with the active site aspartates, whereas the hydroxyl group in the second model makes at least three strong hydrogen bonds. Using the first model, the free energy difference in binding of Ro 31-8959 and its S-diastereomer is calculated to be 3.4 kcal/mol, which is in close agreement with the experimental value. Although the second model has a more favorable interaction with the active site aspartates compared to the first model, it has a higher energy N-axial conformation at the decahydroisoquinoline group in P1′. We show here that the two contributions cancel each other and the two models of S-diastereomer are predicted to have equivalent binding. The stereochemical preference in a hydroxyethylamine series of inhibitors appears to be affected by both intermolecular and intramolecular (conformational) energies. The binding data on the proline containing inhibitors are rationalized based on these results. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 8 Ill.
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  • 5
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 1446-1453 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Pipecolic acid derivatives have proven to be effective P′1 groups in a series of highly potent inhibitors of the enzyme HIV protease. One such inhibitor, Ro 31-8959, contains the saturated bicyclic ring system decahydroisoquinoline (DIQ) in the P′1 position. The binding orientation of Ro 31-8959 is known from X-ray crystallography. However, the bound conformation of the S-hydroxy diastereomer has not been studied, and for this molecule there are at least two different possible binding conformations. Specifically, the N-alkyl substituents may be equatorial or axial and the 3-carboxamide may be rotated into several different orientations. To gain a better understanding of the relative energies of these various conformations, ab initio molecular orbital calculations have been carried out on a series of pipecolic acid and DIQ derivatives. The results indicate that the lowest-energy N-equatorial rotamer is always at least 3 kcal/mol more stable than the lowest-energy N-axial rotamer. The presence of the second ring, as in the DIQ system, considerably raises the equatorial-axial difference to nearly 7 kcal/mol. Also, the preferred rotation angle of the amide group is different for the N-equatorial and N-axial cases. When the molecular dynamics-averaged conformation of the bound S-hydroxy inhibitor is considered, the energy difference between the N-equatorial and N-axial conformers drops to 4-5 kcal/mol. The preferred amide rotations in these systems are compared to those found in proline-containing peptides. Finally, some observations are made with respect to the large conformational energy penalty necessary for binding Ro 31-8959. © John Wiley & Sons, Inc.
    Additional Material: 4 Tab.
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  • 6
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    In:  CASI
    Publication Date: 2017-10-02
    Description: The progress of continuing investigations on vortex control techniques is updated. The following topics are briefly discussed: (1) vortex flaps adapted for high-alpha control; (2) alleviation of leading edge extension (LEX) vortex induced twin-tail buffet; (3) controlled decoupling of interactive forebody chine and wing vortices; (4) forebody vortex manipulation by mechanical and pneumatic techniques; and (5) stall-departure alleviation of high aspect-ratio wings. Salient results of exploratory low speed wind tunned experiments are presented. The investigations, primarily aimed at concept validation, were performed on generic configurations utilizing flow visualizations and pressure and balance measurements. Selected results illustrate the efficacy and potential for development of specific vortex control concepts for improved high-alpha configuration aerodynamics.
    Keywords: AERODYNAMICS
    Type: AGARD, Vortex Flow Aerodynamics; 12 p
    Format: text
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  • 7
    Publication Date: 2019-06-28
    Description: A semi-empirical model is described for predicting unsteady aerodynamic forces on arbitrary airfoils under mildly stalled and unstalled conditions. Aerodynamic forces are modeled using second order ordinary differential equations for lift and moment with airfoil motion as the input. This model is simultaneously integrated with structural dynamics equations to determine flutter characteristics for a two degrees-of-freedom system. Results for a number of cases are presented to demonstrate the suitability of this model to predict flutter. Comparison is made to the flutter characteristics determined by a Navier-Stokes solver and also the classical incompressible potential flow theory.
    Keywords: AERODYNAMICS
    Type: NASA-TM-105414 , E-6820 , NAS 1.15:105414
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  • 8
    Publication Date: 2019-06-28
    Description: A proposed concept to alleviate high alpha asymmetry and lateral/directional instability by decoupling of forebody and wing vortices was studied on a generic chine forebody/ 60 deg. delta configuration in the NASA Langley 7 by 10 foot High Speed Tunnel. The decoupling technique involved inboard leading edge flaps of varying span and deflection angle. Six component force/moment characteristics, surface pressure distributions and vapor-screen flow visualizations were acquired, on the basic wing-body configuration and with both single and twin vertical tails at M sub infinity = 0.1 and 0.4, and in the range alpha = 0 to 50 deg and beta = -10 to +10 degs. Results are presented which highlight the potential of vortex decoupling via leading edge flaps for enhanced high alpha lateral/directional characteristics.
    Keywords: AERODYNAMICS
    Type: NASA-CR-189641 , NAS 1.26:189641
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  • 9
    Publication Date: 2019-06-28
    Description: A test program conducted in the LaRC 8-foot Transonic Pressure Tunnel on a blended chine/delta wing model to verify the concept of controlled vortex decoupling via inboard leading-edge flaps for improved high-alpha lateral/directional characteristics is discussed. This test extended the Mach number range of a data base previously generated in a LaRC 7 ft. by 10 ft High Speed Tunnel investigation. Six-component force/moment, forebody surface pressures, and central and twin tall static and dynamic loads were measured at Mach numbers of 0.4 to 1.2; laser light-sheet visualizations were also performed. Selected data are analyzed and discussed, emphasizing lateral/directional improvements and tail environment enhanced attainable by leading-edge flaps in the maximum lift region.
    Keywords: AERODYNAMICS
    Type: NASA-CR-189642 , NAS 1.26:189642
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  • 10
    Publication Date: 2019-06-28
    Description: The three-dimensional, thin-layer Navier-Stokes equations on a body-conforming, overset, multiple-grid topology are solved in the present numerical simulations of the flow around a 60-deg delta-planform wing equipped with two thrust-reverser jets in ground-effect conditions. Such experimentally flow-visualized features as jet-deformation and ground vertex-formation are captured by these simulations; the loss of wing-borne lift due to the 'suck-down' phenomenon, which arises as the delta planform flies at low speeds in close proximity to the ground, is also well simulated.
    Keywords: AERODYNAMICS
    Type: AIAA PAPER 90-0299
    Format: text
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