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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Elucidation of Agonist and Antagonist Dynamic Binding Patterns in ER-α by Integration of Molecular Docking, Molecular Dynamics Simulations and Quantum Mechanical Calculations

Estrogen receptor alpha (ERα) is a ligand-dependent transcriptional factor in the nuclear receptor superfamily. Many structures of ERα bound with agonists and antagonists have been determined. However, the dynamic binding patterns of agonists and antagonists in the binding site of ERα remains unclear. Therefore, we performed molecular docking, molecular dynamics (MD) simulations, and quantum mechanical calculations to elucidate agonist and antagonist dynamic binding patterns in ERα. 17β-estradiol (E2) and 4-hydroxytamoxifen (OHT) were docked in the ligand binding pockets of the agonist and antagonist bound ERα. The best complex conformations from molecular docking were subjected to 100 nanosecond MD simulations. Hierarchical clustering was conducted to group the structures in the trajectory from MD simulations. The representative structure from each cluster was selected to calculate the binding interaction energy value for elucidation of the dynamic binding patterns of agonists and antagonists in the binding site of ERα. The binding interaction energy analysis revealed that OHT binds ERα more tightly in the antagonist conformer, while E2 prefers the agonist conformer. The results may help identify ERα antagonists as drug candidates and facilitate risk assessment of chemicals through ER-mediated responses.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1991

Quantum mechanical calculations to chemical accuracy

The accuracy of current molecular-structure calculations is illustrated with examples of quantum mechanical solutions for chemical problems. Two approaches are considered: (1) the coupled-cluster singles and doubles (CCSD) with a perturbational estimate of the contribution of connected triple excitations, or CCDS(T); and (2) the multireference configuration-interaction (MRCI) approach to the correlation problem. The MRCI approach gains greater applicability by means of size-extensive modifications such as the averaged-coupled pair functional approach. The examples of solutions to chemical problems include those for C-H bond energies, the vibrational frequencies of O3, identifying the ground state of Al2 and Si2, and the Lewis-Rayleigh afterglow and the Hermann IR system of N2. Accurate molecular-wave functions can be derived from a combination of basis-set saturation studies and full configuration-interaction calculations.

Bauschlicher, Charles W., Jr.↗
NASA NTRS1988

Quantum mechanical calculations of vibrational population inversion in chemical reactions - Numerically exact L-squared-amplitude-density study of the H2Br reactive system

Numerically exact, fully three-dimensional quantum mechanicl reactive scattering calculations are reported for the H2Br system. Both the exchange (H + H-prime Br to H-prime + HBr) and abstraction (H + HBR to H2 + Br) reaction channels are included in the calculations. The present results are the first completely converged three-dimensional quantum calculations for a system involving a highly exoergic reaction channel (the abstraction process). It is found that the production of vibrationally hot H2 in the abstraction reaction, and hence the extent of population inversion in the products, is a sensitive function of initial HBr rotational state and collision energy.

Zhang, Y. C.↗
NASA NTRS1979

Quantum-mechanical calculation of three-dimensional atom-diatom collisions in the presence of intense laser radiation

A formalism is presented for describing the collision of fluorine with the hydrogen molecule in the presence of intense radiation. For a laser frequency on the order of the spin-orbit splitting of fluorine, the interaction of the molecular system with the radiation occurs at relatively long range where, for this system, the electric dipole is vanishingly small. Hence the interaction occurs due to the magnetic dipole coupling. Even so, at low collision energies a substantial enhancement of the quenching cross section is found for a radiation intensity of 10 to the 11th W/sq cm.

Devries, P. L.↗
NASA NTRS1982

The rotational spectra of HOCO/plus/, HOCN, HN3, and HNCO from quantum mechanical calculations

Ab initio molecular orbital theory has been used to determine the equilibrium geometries, rotational constants, and rotational spectra of four isoelectronic molecules. Two of these, HOCO(plus) and HOCN, are candidate interstellar molecules. The other two, HNCO and HN3, have known rotational constants. Theoretical rotational constants and spectra for the two unknown species were corrected with the mean experimental to theoretical ratios from the two known species. This procedure resulted in predicted frequencies of 83.75 plus or minus 0.2 GHz for the 4(04) to 3(03) transition in HOCN and 85.08 plus or minus 0.2 GHz for the same transition in HOCO(plus). These are the central lines of triplets whose other members are the 4(14) to 3(13) and 4(13) to 3(12) transitions. The triplet splittings were predicted to be 0.36 plus or minus 0.01 GHz for HOCN and 0.33 plus or minus 0.01 GHz for HOCO(plus). These results indicate that HOCO(plus) is a better candidate for the source of a series of lines reported by Thaddeus, Guelin, and Linke than is HOCN.

Defrees, D. J.↗
NASA NTRS1982

The rotational spectra of HCNH/+/ and COH/+/ from quantum mechanical calculations

A description is provided of ab initio molecular orbital calculations designed to provide accurate predictions for the J = 1 to 0 rotational line of the candidate interstellar molecules HCNH(+) and COH(+). The former is believed to be important in the formation of both HCN and HNC in the interstellar medium. The latter, a metastable isomer of HCO(+), was first proposed as an interstellar molecule by Herbst et al. (1976). Attention is given to thermochemical arguments that this molecule can be formed in the same reactions which are proposed to form HCO(+), taking into account theoretical data which establish its stability to intramolecular rearrangement. Rotational constants are derived by applying an empirical correction to the ab initio rotational constants.

Defrees, D. J.↗
NASA NTRS1982

Rotational and vibrational spectra of ethynol from quantum-mechanical calculations

It is noted that ethynol (HCCOH), despite the theoretical prediction of its stability to tautomerization to ketene, has thus far not been observed. It is shown here that the identification of this unknown molecule, both in space and in the laboratory, can be aided by an ab initio calculation of spectroscopic parameters. At the HF/3-21G level, harmonic vibrational frequencies are computed by way of analytic second differentiation of the Hartee-Fock (HF) energy with respect to the nuclear coordinates. After applying an empirical scale factor, the resultant frequencies are (per cm) 473, 517, 773, 841, 1003, 1217, 2206, 3285, and 3418. The computed dipole moment at the CISD/DZ+P level is 1.79 D. At the CISD+Q/DZ+P level, the molecule's rotational constants are determined. After scaling by empirical correction factors, they are used in deriving the 4(04) - 3(03) frequency of 76.81 + or - 0.3 GHz with a triplet splitting of 0.30 + or - 0.01 GHz. The triplet splitting involves 4(14) - 3(13) and 4(13) - 3(12) relative to the 4(04) - 3(03) transition as the central line.

Defrees, D. J.↗
NASA NTRS1992

Importance of parametrizing constraints in quantum-mechanical variational calculations

In variational calculations of quantum mechanics, constraints are sometimes imposed explicitly on the wave function. These constraints, which are deduced by physical arguments, are often not uniquely defined. In this work, the advantage of parametrizing constraints and letting the variational principle determine the best possible constraint for the problem is pointed out. Examples are carried out to show the surprising effectiveness of the variational method if constraints are parameterized. It is also shown that misleading results may be obtained if a constraint is not parameterized.

Chung, Kwong T.↗
DOE OSTI2023

Enhancing the accuracy of density functional tight binding models through ChIMES many-body interaction potentials

Semi-empirical quantum models such as Density Functional Tight Binding (DFTB) are attractive methods for obtaining quantum simulation data at longer time and length scales than possible with standard approaches. However, application of these models can require lengthy effort due to the lack of a systematic approach for their development. In this work, we discuss the use of the Chebyshev Interaction Model for Efficient Simulation (ChIMES) to create rapidly parameterized DFTB models, which exhibit strong transferability due to the inclusion of many-body interactions that might otherwise be inaccurate. We apply our modeling approach to silicon polymorphs and review previous work on titanium hydride. We also review the creation of a general purpose DFTB/ChIMES model for organic molecules and compounds that approaches hybrid functional and coupled cluster accuracy with two orders of magnitude fewer parameters than similar neural network approaches. In all cases, DFTB/ChIMES yields similar accuracy to the underlying quantum method with orders of magnitude improvement in computational cost. In conclusion, our developments provide a way to create computationally efficient and highly accurate simulations over varying extreme thermodynamic conditions, where physical and chemical properties can be difficult to interrogate directly, and there is historically a significant reliance on theoretical approaches for interpretation and validation of experimental results.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1995

Nucleosynthesis in AGB stars: Observation of Mg-25 and Mg-26 in IRC+10216 and possible detection of Al-26

We report the detection in the circumstellar envelope IRC+10216 of millimeter lines of the rare isotopomers (25)MgNC and (26)MgNC, as well as of a line at 234433 MHz, which could be the J= 7-6 transition of (26)AlF (an alternate, although less likely identified would be the J= 9-8 transition of NaF). The derived Mg-24:Mg-25:Mg-26 isotopic abundance ratios (78 : 11+/- 1 : 11 +/-1) are consistent with the solar system values (79.0:10.0:11.0), following Anders & Grevesse 1989). According to new calculations of evolutionary models of 3 solar mass and 5 solar mass asymptotic giant branch (AGB) stars, these ratios and the previously measured N, O and Si isotopic ratios imply that the central star had an initial mass 3 solar mass (less than or equal to M(sub *, ini) less than 5 solar mass and has already experienced many 3rd dredge-up events. From this, it can be predicted that the Al-26/Al-27 isotopics ratio lies between 0.01 and 0.08; in fact, the value derived in the case that U234433 arises from (26)AlF is Al-26/Al-27 = 0.04. The identification of the (25)MgNC and (26)MgNC lines was made possible by ab-initio quantum mechanical calculations of the molecule geometrical structure. It was confirmed through millimeter-wave laboratory measurements. The quantum mechanical calculations are briefly described and the laboratory results presented in some detail. The rotation constants B, D, H and the spin-rotation constant gamma of (25)MgNC and (26)MgNC are determined from a fit of laboratory and astronomical data.

Guelin, M.↗