Biomedical subjects

Angela K Wilson

Publications and source records attributed to Angela K Wilson.

13 recordsLinked to original sources

PubMed2006

The correlation-consistent composite approach: application to the G3/99 test set.

The correlation-consistent composite approach (ccCA), an ab initio composite technique for computing atomic and molecular energies, recently has been shown to successfully reproduce experimental data for a number of systems. The ccCA is applied to the G3/99 test set, which includes 223 enthalpies of formation, 88 adiabatic ionization potentials, 58 adiabatic electron affinities, and 8 adiabatic proton affinities. Improvements on the original ccCA formalism include replacing the small basis set quadratic configuration interaction computation with a coupled cluster computation, employing a correction for scalar relativistic effects, utilizing the tight-d forms of the second-row correlation-consistent basis sets, and revisiting the basis set chosen for geometry optimization. With two types of complete basis set extrapolation of MP2 energies, ccCA results in an almost zero mean deviation for the G3/99 set (with a best value of -0.10 kcal mol(-1)), and a 0.96 kcal mol(-1) mean absolute deviation, which is equivalent to the accuracy of the G3X model chemistry. There are no optimized or empirical parameters included in the computation of ccCA energies. Except for a few systems to be discussed, ccCA performs as well as or better than Gn methods for most systems containing first-row atoms, while for systems containing second-row atoms, ccCA is an improvement over Gn model chemistries.

Journal Article↗

PubMed2006

Accurate enthalpies of formation of alkali and alkaline earth metal oxides and hydroxides: assessment of the correlation consistent composite approach (ccCA).

Computing the enthalpies of formation for alkali metal and alkaline earth metal oxides (M(x)O) and hydroxides [M(OH)(n)] using the Gaussian-n (Gn) and Weismann-n (Wn) ab initio model chemistries is difficult due to an improper treatment of core-valence electron correlation effects. Using a new model chemistry called the correlation consistent Composite Approach (ccCA), enthalpies of formation were determined for eight different alkali/alkaline earth metal oxides and hydroxides. Unlike the Gn and Wn model chemistries, which must be modified to properly account for core-valence electron correlation, the standard implementations of the ccCA provide acceptable results, and all enthalpies of formation obtained with the ccCA are within the accepted range of recommended values.

Computer Simulation↗

PubMed2006

The correlation consistent composite approach (ccCA): an alternative to the Gaussian-n methods.

An alternative to the Gaussian-n (G1, G2, and G3) composite methods of computing molecular energies is proposed and is named the "correlation consistent composite approach" (ccCA, ccCA-CBS-1, ccCA-CBS-2). This approach uses the correlation consistent polarized valence (cc-pVXZ) basis sets. The G2-1 test set of 48 enthalpies of formation (DeltaHf), 38 adiabatic ionization potentials (IPs), 25 adiabatic electron affinities (EAs), and 8 adiabatic proton affinities (PAs) are computed using this approach, as well as the DeltaHf values of 30 more systems. Equilibrium molecular geometries and vibrational frequencies are obtained using B3LYP density functional theory. When applying the ccCA-CBS method with the cc-pVXZ series of basis sets augmented with diffuse functions, mean absolute deviations within the G2-1 test set compared to experiment are 1.33 kcal mol(-1) for DeltaHf,0.81 kcal mol(-1) for IPs, 1.02 kcal mol(-1) for EAs, and 1.51 kcal mol(-1) for PAs, without including the "high-level correction" (HLC) contained in the original Gn methods. Whereas the HLC originated in the Gaussian-1 method as an isogyric correction, it evolved into a fitted parameter that minimized the error of the composite methods, eliminating its physical meaning. Recomputing the G1 and G3 enthalpies of formation without the HLC reveals a systematic trend where most DeltaHf values are significantly higher than experimental values. By extrapolating electronic energies to the complete basis set (CBS) limit and adding G3-like corrections for the core-valence and infinite-order electron correlation effects, ccCA-CBS-2 often underestimates the experimental DeltaHf, especially for larger systems. This is desired as inclusion of relativistic and atomic spin-orbit effects subsequently improves theoretical DeltaHf values to give a 0.81 kcal mol(-1) mean absolute deviation with ccCA-CBS-2. The ccCA-CBS method is a viable "black box" method that can be used on systems with at least 10-15 heavy atoms.

Journal Article↗

PubMed2006

Behavior of density functionals with respect to basis set. 3. Basis set superposition error.

The impact of basis set superposition error (BSSE) upon molecular properties determined using the density functionals B3LYP, B3PW91, B3P86, BLYP, BPW91, and BP86 in combination with the correlation consistent basis sets [cc-pVnZ, where n = D(2), T(3), Q(4), and 5] for a set of first-row closed-shell molecules has been examined. Correcting for BSSE enables the irregular convergence behavior in molecular properties such as dissociation energies with respect to increasing basis set size, noted in earlier studies, to be improved. However, for some molecules and functional combinations, BSSE correction alone does not improve the irregular convergence behavior.

Journal Article↗

PubMed2005

Structures and thermochemistry of calcium-containing molecules.

A variety of theoretical procedures, including the high-level ab initio methods G3, G3[CC](dir,full), and W2C//ACQ, have been used to predict the structures and heats of formation of several small calcium-containing molecules (CaH, CaH2, CaO, CaOH, Ca(OH)2, CaF, CaF2, CaS, CaCl, and CaCl2). B3-LYP and CCSD(T) with both the (aug-)cc-pWCVQZ and (aug-)cc-pWCVQ+dZ basis sets are found to give molecular geometries that agree well with the experimental results. The CCSD(T)(riv)/(aug-)cc-pWCVQ+dZ results are found to be the most accurate, with a mean absolute deviation from experiment of just 0.008 angstroms. Zero-point vibrational energies (ZPVEs) and thermochemical corrections are found to be relatively insensitive to the level of theory, except in the case of molecules with highly anharmonic calcium-centered bending modes (CaH2, Ca(OH)2, CaF2, CaCl2), where special procedures need to be employed in order to obtain satisfactory results. Several potential improvements to the W2C method were investigated, most of which do not produce significant changes in the heats of formation. It was observed, however, that for CaO and CaS the scalar relativistic corrections are unexpectedly large and highly basis set dependent. In these cases, Douglas-Kroll CCSD(T)/(aug-)cc-pWCV5Z calculations appear to give a converged result. The G3[CC](dir,full) and best W2C-type heats of formation are both found generally to agree well with experimental values recommended in recent critical compendia. However, in some cases (CaO, Ca(OH)2, and CaF2), they differ from one another by more than their predicted error margins. The available experimental data are not sufficiently precise to distinguish definitively between the two sets of results although, in general, when discrepancies exist the W2C heats of formation are lower in energy and tend to be in better agreement with experiment. In the case of CaO, the W2C heat of formation (20.7 kJ mol(-1)) is approximately 20 kJ mol(-1) lower than the G3[CC](dir, full) result and most of the experimental data. Extensive investigation of possible refinements of the W2C method has failed to reveal any weaknesses that could account for this discrepancy. We therefore believe that the heat of formation of CaO is likely to lie closer to the more recent direct experimental determination of 27 kJ mol(-1) than to the value of approximately 40 kJ mol(-1) recommended in recent thermochemical reviews.

Journal Article↗

PubMed2005

Beyond a T-shape.

Varying the steric bulk of either the phosphine or the halide in Au(PR3)2X complexes allows intuitive tuning of the phosphorescence energy to multiple visible colors, including the coveted blue for LED applications. The excited-state structure involves distortion of the trigonal coordination sphere beyond a T-shape. The [Au(TPA)2]Cl complex exhibits orange phosphorescence due to exciplex formation with the counterion to form the same type of excited state, representing the first example of a luminescent two-coordinate Au(I) complex in absence of both Au...Au interactions and aromatic moieties.

Crystallography, X-Ray↗

PubMed2005

Density functional theory and the correlation consistent basis sets: the tight d effect on HSO and HOS.

The HSO and HOS isomers have been revisited using the DFT functionals, B3LYP, B3PW91, and PBE, in combination with tight d-augmented correlation consistent basis sets, cc-pV(x+d)Z and aug-cc-pV(x+d)Z for second-row atoms. Structures, vibrationally averaged structures, relative energies, harmonic and anharmonic frequencies, enthalpies of formation of HSO and HOS, and the barrier for the HSO/HOS isomerization have been determined. These results were compared with results from previous DFT and ab initio studies in which the standard correlation consistent basis sets were used. The relative energies of the two isomers converge more rapidly and smoothly with respect to increasing basis set size for the tight d-augmented sets than for the standard basis sets. Our best calculations, B3PW91/aug-cc-pV(5+d)Z, for the relative energy of the isomers are in excellent agreement with previous CCSD(T) results given by Wilson and Dunning.

Journal Article↗

PubMed2005

Relativistic effects determined using the Douglas-Kroll contracted basis sets and correlation consistent basis sets with small-core relativistic pseudopotentials.

The coupled cluster approximation with single, double, and quasiperturbative triple excitations [CCSD(T)] was used in combination with the Douglas-Kroll contracted correlation consistent basis sets [cc-pVnZ-DK, where n = D(2), T(3), Q(4), and 5] and small-core relativistic pseudopotentials (PP) with correlation consistent polarized valence basis sets (cc-pVnZ-PP and aug-cc-pVnZ-PP) to investigate the impact of scalar relativistic corrections on energetic and structural properties of small molecules containing third-row (Ga-Kr) atoms. These molecules were taken from the Gaussian-2 extended test set for third-row atoms. Atomization energies, ionization energies, electron affinities, and proton affinities for molecules in the test set were determined and compared with nonrelativistic results which were obtained in a recent study in which the standard and augmented correlation consistent basis sets were used in combination with CCSD(T). Several schemes were used to extrapolate the energies to the complete basis set limit.

Journal Article↗

PubMed2005

Truncation of the correlation consistent basis sets: extension to third-row (Ga-Kr) molecules.

The systematic reduction of the commonly used correlation consistent basis sets [cc-pVnZ where n=D(2), T(3), Q(4), and 5] as a means to reduce computational cost has been extended to hydrogen-containing third-row (Ga-Kr) molecules of the G2 test suite. Coupled cluster with singles, doubles, and quasiperturbative triple excitations [CCSD(T)] calculations were performed using both the full correlation consistent basis sets and a series of truncated basis sets in order to assess the impact of basis set reduction upon the structures and energies of the species. The impact that truncation of the basis sets for hydrogen has upon extrapolation of energies to the complete basis set limit also has been examined, and the cost savings that can be achieved are discussed. Overall, basis set reduction can be accomplished which preserves the systematic convergence behavior of the full correlation consistent basis sets.

Journal Article↗

PubMed2005

Electronic structure of mercury oligomers and exciplexes: models for long-range/multicenter bonding in phosphorescent transition-metal compounds.

Spectroscopic and bonding properties of Hg(n) oligomers and *Hg(n) exciplexes are determined by rigorous theoretical treatments. Reliable values that agree well with experimental data have been computed for the luminescence energies and other molecular spectroscopic parameters by making a careful selection of theoretical methods and basis sets. The calculations clarified the assignments for several phosphorescence bands in the mercury vapor based on calculated energies and other parameters that quantify the large excited-state distortion in the emitting states. Both the weak ground-state mercurophilic bonding and the stronger covalent bonding in the triplet and quintet excited states studied are found to be cooperative, which is important for fundamental and applied research for luminescent and magnetic materials that have spectral behavior similar to that of Hg(n) systems.

Journal Article↗

PubMed2004

The behavior of density functionals with respect to basis set. I. The correlation consistent basis sets.

The accuracy of density functional theory in the description of geometries and atomization energies has been assessed by comparison to experimental data for a series of first-row closed-shell molecules. Six commonly used functionals (B3LYP, B3PW91, B3P86, BLYP, BPW91, BP86) were investigated in combination with the correlation-consistent basis sets [cc-pVxZ and aug-cc-pVxZ where x=D(2), T(3), Q(4), 5]. The convergence of molecular properties with respect to increasing basis set size has been examined. A full statistical error analysis has been performed, assessing the success of each functional with respect to each basis set in terms of both accuracy and precision. Overall, there is smooth convergence towards the Kohn-Sham limit for the hybrid functionals B3LYP and B3PW91, whereas the nonlocal functionals are relatively insensitive to basis set choice.

Journal Article↗

PubMed2004

Truncation of the correlation consistent basis sets: an effective approach to the reduction of computational cost?

The systematic reduction of commonly used basis sets as a means to reduce computational cost is examined for a small test set of molecules, which includes H(2), CH(4), NH(3), H(2)O, HF, and HCN. Coupled cluster with single, double, and quasiperturbative triple excitations calculations were performed using both the correlation consistent basis sets, and a set of systematically reduced basis sets to examine both the impact of the reduction upon the accuracy of the structures and energies, and the computational cost savings achieved. The effect of several truncation scenarios upon basis set convergence is also examined. Overall, for the systems studied, a reduction can occur which preserves the well-established systematic convergence behavior of the correlation consistent basis sets.

Journal Article↗

PubMed2004

Accurate energetics of small molecules containing third-row atoms Ga-Kr: a comparison of advanced ab initio and density functional theory.

Advanced ab initio [coupled cluster theory through quasiperturbative triple excitations (CCSD(T))] and density functional (B3LYP) computational chemistry approaches were used in combination with the standard and augmented correlation consistent polarized valence basis sets [cc-pVnZ and aug-cc-pVnZ, where n=D(2), T(3), Q(4), and 5] to investigate the energetic and structural properties of small molecules containing third-row (Ga-Kr) atoms. These molecules were taken from the Gaussian-2 (G2) extended test set for third-row atoms. Several different schemes were used to extrapolate the calculated energies to the complete basis set (CBS) limit for CCSD(T) and the Kohn-Sham (KS) limit for B3LYP. Zero point energy and spin orbital corrections were included in the results. Overall, CCSD(T) atomization energies, ionization energies, proton affinities, and electron affinities are in good agreement with experiment, within 1.1 kcal/mol when the CBS limit has been determined using a series of two basis sets of at least triple zeta quality. For B3LYP, the overall mean absolute deviation from experiment for the three properties and the series of molecules is more significant at the KS limit, within 2.3 and 2.6 kcal/mol for the cc-pVnZ and aug-cc-pVnZ basis set series, respectively.

Journal Article↗