Person:

Sherrill, C. David

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https://hdl.handle.net/1853/71694

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Organizational Unit

School of Computational Science and Engineering

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Now showing 1 - 10 of 28

Basis set convergence of the coupled-cluster correction, delta(CCSD(T))(MP2): Best practices for benchmarking non-covalent interactions and the attendant revision of the S22, NBC10, HBC6, and HSG databases

(Georgia Institute of Technology, 2011-11) Marshall, Michael S. ; Burns, Lori A. ; Sherrill, C. David

In benchmark-quality studies of non-covalent interactions, it is common to estimate interaction energies at the complete basis set (CBS) coupled-cluster through perturbative triples [CCSD(T)] level of theory by adding to CBS second-order perturbation theo
Large-scale symmetry-adapted perturbation theory computations via density fitting and Laplace transformation techniques: Investigating the fundamental forces of DNA-intercalator interactions

(Georgia Institute of Technology, 2011-11) Hohenstein, Edward G. ; Parrish, Robert M. ; Sherrill, C. David ; Turney, Justin M. ; Schaefer, Henry F., III

Symmetry-adapted perturbation theory (SAPT) provides a means of probing the fundamental nature of intermolecular interactions. Low-orders of SAPT (here, SAPT0) are especially attractive since they provide qualitative (sometimes quantitative) results while remaining tractable for large systems. The application of density fitting and Laplace transformation techniques to SAPT0 can significantly reduce the expense associated with these computations and make even larger systems accessible. We present new factorizations of the SAPT0 equations with density-fitted two-electron integrals and the first application of Laplace transformations of energy denominators to SAPT. The improved scalability of the DF-SAPT0 implementation allows it to be applied to systems with more than 200 atoms and 2800 basis functions. The Laplace-transformed energy denominators are compared to analogous partial Cholesky decompositions of the energy denominator tensor. Application of our new DF-SAPT0 program to the intercalation of DNA by proflavine has allowed us to determine the nature of the proflavine-DNA interaction. Overall, the proflavine-DNA interaction contains important contributions from both electrostatics and dispersion. The energetics of the intercalator interaction are are dominated by the stacking interactions (two-thirds of the total), but contain important contributions from the intercalator-backbone interactions. It is hypothesized that the geometry of the complex will be determined by the interactions of the intercalator with the backbone, because by shifting toward one side of the backbone, the intercalator can form two long hydrogen-bonding type interactions. The long-range interactions between the intercalator and the next-nearest base pairs appear to be negligible, justifying the use of truncated DNA models in computational studies of intercalation interaction energies.
Quadratically convergent algorithm for orbital optimization in the orbital-optimized coupled-cluster doubles method and in orbital-optimized second-order Møller-Plesset perturbation theory

(Georgia Institute of Technology, 2011-09) Bozkaya, Uğur ; Turney, Justin M. ; Yamaguchi, Yukio ; Schaefer, Henry F., III ; Sherrill, C. David

Using a Lagrangian-based approach, we present a more elegant derivation of the equations necessary for the variational optimization of the molecular orbitals (MOs) for the coupled-cluster doubles (CCD) method and second-order Møller-Plesset perturbation theory (MP2). These orbital-optimized theories are referred to as OO-CCD and OO-MP2 (or simply “OD” and “OMP2” for short), respectively. We also present an improved algorithm for orbital optimization in these methods. Explicit equations for response density matrices, the MO gradient, and the MO Hessian are reported both in spin-orbital and closed-shell spin-adapted forms. The Newton-Raphson algorithm is used for the optimization procedure using the MO gradient and Hessian. Further, orbital stability analyses are also carried out at correlated levels. The OD and OMP2 approaches are compared with the standard MP2, CCD, CCSD, and CCSD(T) methods. All these methods are applied to H₂O, three diatomics, and the O₄⁺ molecule. Results demonstrate that the CCSD and OD methods give nearly identical results for H₂O and diatomics; however, in symmetry-breaking problems as exemplified by O₄⁺, the OD method provides better results for vibrational frequencies. The OD method has further advantagesover CCSD: its analytic gradients are easier to compute since there is no need to solve the coupledperturbed equations for the orbital response, the computation of one-electron properties are easier because there is no response contribution to the particle density matrices, the variational optimized orbitals can be readily extended to allow inactive orbitals, it avoids spurious second-order poles in its response function, and its transition dipole moments are gauge invariant. The OMP2 has these same advantages over canonical MP2, making it promising for excited state properties via linear response theory. The quadratically convergent orbital-optimization procedure converges quickly for OMP2, and provides molecular properties that are somewhat different than those of MP2 for most of the test cases considered (although they are similar for H₂O). Bond lengths are somewhat longer, and vibrational frequencies somewhat smaller, for OMP2 compared to MP2. In the difficult case of O₄⁺, results for several vibrational frequencies are significantly improved in going from MP2 to OMP2.
Challenges of laser-cooling molecular ions

(Georgia Institute of Technology, 2011-06) Nguyen, Jason H.V. ; Viteri, C. Ricardo ; Hohenstein, Edward G. ; Sherrill, C. David ; Brown, Kenneth R. ; Odom, Brian

The direct laser cooling of neutral diatomic molecules in molecular beams suggests that trapped molecular ions can also be laser cooled. The long storage time and spatial localization of trapped molecular ions provides an opportunity for multi-step cooling strategies, but also requires careful consideration of rare molecular transitions. We briefly summarize the requirements that a diatomic molecule must meet for laser cooling, and we identify a few potential molecular ion candidates. We then carry out a detailed computational study of the candidates BH+ and AlH+, including improved ab initio calculations of the electronic state potential energy surfaces and transition rates for rare dissociation events. On the basis of an analysis of the population dynamics, we determine which transitions must be addressed for laser cooling, and compare experimental schemes using continuous-wave and pulsed lasers.
Density-functional approaches to noncovalent interactions: A comparison of dispersion corrections (DFT-D), exchange-hole dipole moment (XDM) theory, and specialized functionals

(Georgia Institute of Technology, 2011-06) Burns, Lori A. ; Vazquez-Mayagoitia, Alvaro ; Sumpter, Bobby G. ; Sherrill, C. David

A systematic study of techniques for treating noncovalent interactions within the computationally efficient density functional theory (DFT) framework is presented through comparison to benchmarkquality evaluations of binding strength compiled for molecular complexes of diverse size and nature. In particular, the efficacy of functionals deliberately crafted to encompass long-range forces, a posteriori DFT+dispersion corrections (DFT-D2 and DFT-D3), and exchange-hole dipole moment (XDM) theory is assessed against a large collection (469 energy points) of reference interaction energies at the CCSD(T) level of theory extrapolated to the estimated complete basis set limit. The established S22 [revised in J. Chem. Phys. 132, 144104 (2010)] and JSCH test sets of minimum-energy structures, as well as collections of dispersion-bound (NBC10) and hydrogenbonded (HBC6) dissociation curves and a pairwise decomposition of a protein–ligand reaction site (HSG), comprise the chemical systems for this work. From evaluations of accuracy, consistency, and efficiency for PBE-D, BP86-D, B97-D, PBE0-D, B3LYP-D, B970-D, M05-2X,M06-2X, ωB97X-D, B2PLYP-D, XYG3, and B3LYP-XDM methodologies, it is concluded that distinct, often contrasting, groups of these elicit the best performance within the accessible double-ζ or robust triple-ζ basis set regimes and among hydrogen-bonded or dispersion-dominated complexes. For overall results, M05-2X, B97-D3, and B970-D2 yield superior values in conjunction with aug-cc-pVDZ, for a mean absolute deviation of 0.41 – 0.49 kcal/mol, and B3LYP-D3, B97-D3, ωB97X-D, and B2PLYP-D3 dominate with aug-cc-pVTZ, affording, together with XYG3/6-311+G(3df,2p), a mean absolute deviation of 0.33 – 0.38 kcal/mol.
The energy computation paradox and ab initio protein folding

(Georgia Institute of Technology, 2011-04) Faver, John C. ; Benson, Mark L. ; He, Xiao ; Roberts, Benjamin P. ; Wang, Bing ; Marshall, Michael S. ; Sherrill, C. David ; Merz, Kenneth M., Jr.

The routine prediction of three-dimensional protein structure from sequence remains a challenge in computational biochemistry. It has been intuited that calculated energies from physics-based scoring functions are able to distinguish native from nonnative folds based on previous performance with small proteins and that conformational sampling is the fundamental bottleneck to successful folding. We demonstrate that as protein size increases, errors in the computed energies become a significant problem. We show, by using error probability density functions, that physics-based scores contain significant systematic and random errors relative to accurate reference energies. These errors propagate throughout an entire protein and distort its energy landscape to such an extent that modern scoring functions should have little chance of success in finding the free energy minima of large proteins. Nonetheless, by understanding errors in physics-based score functions, they can be reduced in a post-hoc manner, improving accuracy in energy computation and fold discrimination.
The computational chemistry end station

(Georgia Institute of Technology, 2010-12-31) Sherrill, C. David
Theoretical models for potential energy landscapes of challenging chemical systems

(Georgia Institute of Technology, 2010-12-31) Sherrill, C. David
Density fitting of intramonomer correlation effects in symmetry-adapted perturbation theory

(Georgia Institute of Technology, 2010-07) Hohenstein, Edward G. ; Sherrill, C. David

Symmetry-adapted perturbation theory (SAPT) offers insight into the nature of intermolecular interactions. In addition, accurate energies can be obtained from the wave function-based variant of SAPT provided that intramonomer electron correlation effects are included. We apply density-fitting (DF) approximations to the intramonomer correlation corrections in SAPT. The introduction of this approximation leads to an improvement in the computational cost of SAPT by reducing the scaling of certain SAPT terms, reducing the amount of disk I/O, and avoiding the explicit computation of certain types of MO integrals. We have implemented all the intramonomer correlation corrections to SAPT through second-order under the DF approximation. Additionally, leading third-order terms are also implemented. The accuracy of this truncation of SAPT is tested against the S22 test set of Hobza and co-workers [Phys. Chem. Chem. Phys. 8, 1985 (2006)] . When the intramonomer corrections to dispersion are included in SAPT, a mean absolute deviation of 0.3–0.4 kcal mol⁻¹ is observed for the S22 test set when using an aug-cc-pVDZ basis. The computations on the adenine-thymine complexes in the S22 test set with an aug-cc-pVDZ basis represent the largest SAPT computations to date that include this degree of intramonomer correlation. Computations of this size can now be performed routinely with our newly developed DF-SAPT program.
Density fitting and Cholesky decomposition approximations in symmetry-adapted perturbation theory: Implementation and application to probe the nature of π-π interactions in linear acenes

(Georgia Institute of Technology, 2010-05) Hohenstein, Edward G. ; Sherrill, C. David

Density fitting (DF) approximations have been used to increase the efficiency of several quantum mechanical methods. In this work, we apply DF and a related approach, Cholesky decomposition (CD), to wave function-based symmetry-adapted perturbation theory (SAPT). We also test the one-center approximation to the Cholesky decomposition. The DF and CD approximations lead to a dramatic improvement in the overall computational cost of SAPT, while introducing negligible errors. For typical target accuracies, the Cholesky basis needed is noticeably smaller than the DF basis (although the cost of constructing the Cholesky vectors is slightly greater than that of constructing the three-index DF integrals). The SAPT program developed in this work is applied to the interactions between acenes previously studied by Grimme [Angew. Chem., Int. Ed. 47, 3430 (2008)], expanding the cases studied by adding the pentacene dimer. The SAPT decomposition of the acene interactions provides a more realistic picture of the interactions than that from the energy decomposition analysis previously reported. The data suggest that parallel-displaced and T-shaped acene dimers both feature a special stabilizing π-π interaction arising from electron correlation terms which are significantly more stabilizing than expected on the basis of pairwise −C₆R⁻⁶ estimates. These terms are qualitatively the same in T-shaped as in parallel-displaced geometries, although they are roughly a factor of 2 smaller in T-shaped geometries because of the larger distances between the intermolecular pairs of electrons.