Biomedical subjects

Theresa L Windus

Publications and source records attributed to Theresa L Windus.

6 recordsLinked to original sources

PubMed2006

Ab initio and analytic intermolecular potentials for Ar-CH(3)OH.

Ab initio calculations at the CCSD(T)/aug-cc-pVTZ level of theory were used to characterize the Ar-CH(3)OH intermolecular potential energy surface (PES). Potential energy curves were calculated for four different Ar + CH(3)OH orientations and used to derive an analytic function for the intermolecular PES. A sum of Ar-C, Ar-O, Ar-H(C), and Ar-H(O) two-body potentials gives an excellent fit to these potential energy curves up to 100 kcal mol(-1), and adding an additional r(-n) term to the Buckingham two-body potential results in only a minor improvement in the fit. Three Ar-CH(3)OH van der Waals minima were found from the CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pVTZ calculations. The structure of the global minimum is in overall good agreement with experiment (X.-C. Tan, L. Sun and R. L. Kuczkowski, J. Mol. Spectrosc., 1995, 171, 248). It is T-shaped with the hydroxyl H-atom syn with respect to Ar. Extrapolated to the complete basis set (CBS) limit, the global minimum has a well depth of 0.72 kcal mol(-1) with basis set superposition error (BSSE) correction. The aug-cc-pVTZ basis set gives a well depth only 0.10 kcal mol(-1) smaller than this value. The well depths of the other two minima are within 0.16 kcal mol(-1) of the global minimum. The analytic Ar-CH(3)OH intermolecular potential also identifies these three minima as the only van der Waals minima and the structures predicted by the analytic potential are similar to the ab initio structures. The analytic potential identifies the same global minimum and the predicted well depths for the minima are within 0.05 kcal mol(-1) of the ab initio values. Combining this Ar-CH(3)OH intermolecular potential with a potential for a OH-terminated alkylthiolate self-assembled monolayer surface (i.e., HO-SAM) provides a potential to model Ar + HO-SAM collisions.

Argon↗

PubMed2006

Ab initio and analytic intermolecular potentials for Ar-CF4.

Ab initio calculations at the CCSD(T) level of theory were performed to characterize the Ar + CF4 intermolecular potential. Potential energy curves were calculated with the aug-cc-pVTZ basis set, and with and without a correction for basis set superposition error (BSSE). Additional calculations were performed with other correlation consistent basis sets to extrapolate the Ar-CF4 potential energy minimum to the complete basis set (CBS) limit. Both the size of the basis set and BSSE have substantial effects on the Ar + CF4 potential. Calculations with the aug-cc-pVTZ basis set, and with a BSSE correction, appear to give a good representation of the BSSE corrected potential at the CBS limit. In addition, MP2 theory is found to give potential energies in very good agreement with those determined by the much higher level CCSD(T) theory. Two model analytic potential energy functions were determined for Ar + CF4. One is a fit to the aug-cc-pVTZ calculations with a BSSE correction. The second was derived by fitting an average BSSE corrected potential, which is an average of the CCSD(T)/aug-cc-pVTZ potentials with and without a BSSE correction. These analytic functions are written as a sum of two-body potentials and excellent fits to the ab initio potentials are obtained by representing each two-body interaction as a Buckingham potential.

Journal Article↗

PubMed2005

Complexation of the carbonate, nitrate, and acetate anions with the uranyl dication: density functional studies with relativistic effective core potentials.

The structures and vibrational frequencies of uranyl carbonates, [UO2(CO3)n](2-2n) and [(UO2)3(CO3)6]6-, uranyl nitrates, [UO2(NO3)n](2-n), and uranyl acetates, [UO2(CH3COO)n](2-n) (n = 1,2,3) have been calculated by using local density functional theory (LDFT). Only bidentate ligand coordination modes to the uranyl dication have been modeled. The calculated structures and frequencies are compared to available experimental data, including IR, Raman, X-ray diffraction, and EXAFS solution and crystal structure data. The energetics of ligand binding have been calculated using the B3LYP hybrid functional. In general, the structural and vibrational results at the LDFT level are in good agreement with experimental results and provide realistic pictures of solution phase and solid-state behavior. For the [UO2(CO3)3]6- anion, calculations suggest that complexity in the CO3(2-) stretching signature upon complexation is due to the formation of C=O and C-O domains, the latter of which can split by as much as 300 cm(-1). Assessment of the binding energies indicate that the [UO2(CO3)2]2- anion is more stable than the [UO2(CO3)3]4- anion due to the accumulation of excess charge, whereas the tri-ligand species are the most stable in the nitrate and acetate anions.

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PubMed2005

Active-space coupled-cluster study of electronic states of Be3.

The active-space coupled-cluster (CC) and equation-of-motion (EOM) CC methods with all single and double excitations with triple excitations defined via active orbitals (CCSDt, EOMCCSDt), as implemented with TENSOR CONTRACTION ENGINE, are applied to the challenging Be3 system, which is characterized by a large number of low-lying excited states dominated by two-electron transitions and significant high-order correlation effects in the ground electronic state. It is demonstrated that the CCSDt and EOMCCSDt methods provide an excellent description of complicated electronic quasidegeneracies present in the Be3 cluster. Different strategies for defining triple excitations within the CCSDtEOMCCSDt approach are discussed.

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PubMed2005

Thermodynamic properties of the C5, C6, and C8 n-alkanes from ab initio electronic structure theory.

The heats of formation for the n-alkanes C(n)H(n+2) for n = 5, 6, and 8 have been calculated using ab initio molecular orbital theory. Coupled-cluster calculations with perturbative triples (CCSD(T)) were employed for the total valence electronic energies. Correlation-consistent basis sets were used, up through the augmented quadruple zeta, to extrapolate to the complete basis set limit. Geometries were optimized at the B3LYP/TZVP and MP2/aug-cc-pVTZ levels. The MP2 geometries were used in the CCSD(T) calculations. Frequencies were determined at the density functional level (B3LYP/TZVP), and scaled zero point energies were calculated from the B3LYP frequencies. Core/valence, scalar relativistic, and spin-orbit corrections were included in an additive fashion to predict the atomization energies. The core/valence corrections are not small, (approximately 1.1 kcal/mol per carbon unit) and cannot be neglected for chemical accuracy. The calculated deltaH(298)f values are -35.0, -40.2, and -50.2 kcal/mol for C5H12, C6H14, and C8H18, respectively, in excellent agreement with the respective experimental values of -35.11 +/- 0.19, -39.89 +/- 0.19, and -49.90 +/- 0.31 kcal/mol. Isodesmic reaction energies are presented for some simple reactions involving C8H18 and are shown not to be strongly method dependent.

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PubMed2004

Component-based integration of chemistry and optimization software.

Typical scientific software designs make rigid assumptions regarding programming language and data structures, frustrating software interoperability and scientific collaboration. Component-based software engineering is an emerging approach to managing the increasing complexity of scientific software. Component technology facilitates code interoperability and reuse. Through the adoption of methodology and tools developed by the Common Component Architecture Forum, we have developed a component architecture for molecular structure optimization. Using the NWChem and Massively Parallel Quantum Chemistry packages, we have produced chemistry components that provide capacity for energy and energy derivative evaluation. We have constructed geometry optimization applications by integrating the Toolkit for Advanced Optimization, Portable Extensible Toolkit for Scientific Computation, and Global Arrays packages, which provide optimization and linear algebra capabilities. We present a brief overview of the component development process and a description of abstract interfaces for chemical optimizations. The components conforming to these abstract interfaces allow the construction of applications using different chemistry and mathematics packages interchangeably. Initial numerical results for the component software demonstrate good performance, and highlight potential research enabled by this platform.

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