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Sherrill, C. David

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Author: Marshall, Michael S. ×

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    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
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    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.
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    Basis set consistent revision of the S22 test set of noncovalent interaction energies
    (Georgia Institute of Technology, 2010-03) Takatani, Tait ; Hohenstein, Edward G. ; Malagoli, Massimo ; Marshall, Michael S. ; Sherrill, C. David
    The S22 test set of interaction energies for small model complexes [ Phys. Chem. Chem. Phys. 8, 1985 (2006) ] has been very valuable for benchmarking new and existing methods for noncovalent interactions. However, the basis sets utilized to compute the CCSD(T) interaction energies for some of the dimers are insufficient to obtain converged results. Here we consistently extrapolate all CCSD(T)/complete basis set (CBS) interaction energies using larger basis sets for the CCSD(T) component of the computation. The revised values, which we designate S22A, represent the most accurate results to date for this set of dimers. The new values appear to be within a few hundredths of 1 kcal mol−1 of the true CCSD(T)/CBS limit at the given geometries, but the former S22 values are off by as much as 0.6 kcal mol−1 compared to the revised values. Because some of the most promising methods for noncovalent interactions are already achieving this level of agreement (or better) compared to the S22 data, more accurate benchmark values would clearly be helpful. The MP2, SCS-MP2, SCS-CCSD, SCS(MI)-MP2, and B2PLYP-D methods have been tested against the more accurate benchmark set. The B2PLYP-D method outperforms all other methods tested here, with a mean average deviation of only 0.12 kcal mol⁻¹. However, the consistent, slight underestimation of the interaction energies computed by the SCS-CCSD method (an overall mean absolute deviation and mean deviation of 0.24 and −0.23 kcal mol⁻¹, respectively) suggests that the SCS-CCSD method has the potential to become even more accurate with a reoptimization of its parameters for noncovalent interactions.