Biomedical subjects

C David Sherrill

Publications and source records attributed to C David Sherrill.

17 recordsLinked to original sources

PubMed2006

High-level ab initio studies of hydrogen abstraction from prototype hydrocarbon systems.

Symmetric and nonsymmetric hydrogen abstraction reactions are studied using state-of-the-art ab initio electronic structure methods. Second-order Møller-Plesset perturbation theory (MP2) and the coupled-cluster singles, doubles, and perturbative triples [CCSD(T)] methods with large correlation consistent basis sets (cc-pVXZ, where X = D,T,Q) are used in determining the transition-state geometries, activation barriers, and thermodynamic properties of several representative hydrogen abstraction reactions. The importance of basis set, electron correlation, and choice of zeroth-order reference wave function in the accurate prediction of activation barriers and reaction enthalpies are also investigated. The ethynyl radical (*CCH), which has a very high affinity for hydrogen atoms, is studied as a prototype hydrogen abstraction agent. Our high-level quantum mechanical computations indicate that hydrogen abstraction using the ethynyl radical has an activation energy of less than 3 kcal mol(-1) for hydrogens bonded to an sp(2) or sp(3) carbon. These low activation barriers further corroborate previous studies suggesting that ethynyl-type radicals would make good tooltips for abstracting hydrogens from diamondoid surfaces during mechanosynthesis. Modeling the diamond C(111) surface with isobutane and treating the ethynyl radical as a tooltip, hydrogen abstraction in this reaction is predicted to be barrierless.

Computer Simulation↗

PubMed2006

High-accuracy quantum mechanical studies of pi-pi interactions in benzene dimers.

Although supramolecular chemistry and noncovalent interactions are playing an increasingly important role in modern chemical research, a detailed understanding of prototype noncovalent interactions remains lacking. In particular, pi-pi interactions, which are ubiquitous in biological systems, are not fully understood in terms of their strength, geometrical dependence, substituent effects, or fundamental physical nature. However, state-of-the-art quantum chemical methods are beginning to provide answers to these questions. Coupled-cluster theory through perturbative triple excitations in conjunction with large basis sets and extrapolations to the complete basis set limit have provided definitive results for the binding energy of several configurations of the benzene dimer, and benchmark-quality ab initio potential curves are being used to calibrate new density functional and force-field models for pi-pi interactions. Studies of substituted benzene dimers indicate flaws in the conventional wisdom about substituent effects in pi-pi interactions. Three-body and four-body interactions in benzene clusters have also been examined.

Journal Article↗

PubMed2006

Aliphatic C-H/pi interactions: Methane-benzene, methane-phenol, and methane-indole complexes.

Noncovalent C-H/pi interactions are prevalent in biochemistry and are important in molecular recognition. In this work, we present potential energy curves for methane-benzene, methane-phenol, and methane-indole complexes as prototypes for interactions between C-H bonds and the aromatic components of phenylalanine, tyrosine, and tryptophan. Second-order perturbation theory (MP2) is used in conjunction with the aug-cc-pVDZ and aug-cc-pVTZ basis sets to determine the counterpoise-corrected interaction energy for selected complex configurations. Using corrections for higher-order electron correlation determined with coupled-cluster theory through perturbative triples [CCSD(T)] in the aug-cc-pVDZ basis set, we estimate, through an additive approximation, results at the very accurate CCSD(T)/aug-cc-pVTZ level of theory. Symmetry-adapted perturbation theory (SAPT) is employed to determine the physically significant components of the total interaction energy for each complex.

Benzene↗

PubMed2006

Hybrid correlation models based on active-space partitioning: seeking accurate O(N5) ab initio methods for bond breaking.

Moller-Plesset second-order (MP2) perturbation theory remains the least expensive standard ab initio method that includes electron correlation, scaling as O(N5) with the number of molecular orbitals N. Unfortunately, when restricted Hartree-Fock orbitals are employed, the potential energy curves calculated with this method are of little use at large interatomic separations because of the divergent behavior of MP2 in these regions. In our previous study [J. Chem. Phys. 122, 234110 (2005)] we combined the MP2 method with the singles and doubles coupled cluster (CCSD) method to produce a hybrid method that retains the computational scaling of MP2 and improves dramatically the shape of the MP2 curves. In this work we expand the hybrid methodology to several other schemes. We investigate a new, improved MP2-CCSD method as well as a few other O(N5) methods related to the Epstein-Nesbet pair correlation theory. Nonparallelity errors across the dissociation curve as well as several spectroscopic constants are computed for BH, HF, H2O, CH+, CH4, and Li2 molecules with the 6-31G* basis set and compared with the corresponding full configuration interaction results. We show that among the O(N5) methods considered, our new hybrid MP2-CCSD method is the most accurate and significantly outperforms MP2 not only at large interatomic separations, but also near equilibrium geometries.

Journal Article↗

PubMed2006

Advances in methods and algorithms in a modern quantum chemistry program package.

Advances in theory and algorithms for electronic structure calculations must be incorporated into program packages to enable them to become routinely used by the broader chemical community. This work reviews advances made over the past five years or so that constitute the major improvements contained in a new release of the Q-Chem quantum chemistry package, together with illustrative timings and applications. Specific developments discussed include fast methods for density functional theory calculations, linear scaling evaluation of energies, NMR chemical shifts and electric properties, fast auxiliary basis function methods for correlated energies and gradients, equation-of-motion coupled cluster methods for ground and excited states, geminal wavefunctions, embedding methods and techniques for exploring potential energy surfaces.

Algorithms↗

PubMed2006

The effect of multiple substituents on sandwich and T-shaped pi-pi interactions.

Sandwich and T-shaped configurations of substituted benzene dimers were studied by second-order perturbation theory to determine how substituents tune pi-pi interactions. Remarkably, multiple substituents have an additive effect on the binding energy of sandwich dimers, except in some cases when substituents are aligned on top of each other. The energetics of substituted T-shaped configurations are more complex, but nevertheless a simple model that accounts for electrostatic and dispersion interactions (and direct contacts between substituents on one ring and hydrogen atoms on the other), provides a good match to the quantum mechanical results. These results provide insight into the manner by which substituents csan be utilized in supramolecular design.

Benzene↗

PubMed2006

The electronic structure of oxo-Mn(salen): single-reference and multireference approaches.

Using single- and multireference approaches we have examined many of the low-lying electronic states of oxo-Mn(salen), several of which have not been explored previously. Large complete-active-space self-consistent-field (CASSCF) computations have been performed in pursuit of an accurate ordering for the lowest several electronic states. Basis set and relativistic effects have also been considered. For the geometry considered, our best results indicate the ground spin state to be a closed-shell singlet, followed by a pair of low-lying triplet states, with additional singlet states and the lowest quintet state lying significantly higher in energy. Hartree-Fock and density functional theory (DFT) results are obtained and are compared to the more robust CASSCF results. The Hartree-Fock results are qualitatively incorrect for the relative energies of the states considered. Popular density functionals such as BP86 and B3LYP are superior to Hartree-Fock for this problem, but they give inconsistent answers regarding the ordering of the lowest singlet and triplet states and they greatly underestimate the singlet-quintet gap. We obtained multiple Hartree-Fock and DFT solutions within a given spin multiplicity, and these solutions have been subjected to wave function stability analysis.

Journal Article↗

PubMed2005

Beyond the benzene dimer: an investigation of the additivity of pi-pi interactions.

The benzene dimer is the simplest prototype of pi-pi interactions and has been used to understand the fundamental physics of these interactions as they are observed in more complex systems. In biological systems, however, aromatic rings are rarely found in isolated pairs; thus, it is important to understand whether aromatic pairs remain a good model of pi-pi interactions in clusters. In this study, ab initio methods are used to compute the binding energies of several benzene trimers and tetramers, most of them in 1D stacked configurations. The two-body terms change only slightly relative to the dimer, and except for the cyclic trimer, the three- and four-body terms are negligible. This indicates that aromatic clusters do not feature any large nonadditive effects in their binding energies, and polarization effects in benzene clusters do not greatly change the binding that would be anticipated from unperturbed benzene-benzene interactions, at least for the 1D stacked systems considered. Three-body effects are larger for the cyclic trimer, but for all systems considered, the computed binding energies are within 10% of what would be estimated from benzene dimer energies at the same geometries.

Algorithms↗

PubMed2005

Hybrid correlation models based on active-space partitioning: correcting second-order Moller-Plesset perturbation theory for bond-breaking reactions.

Moller-Plesset second-order (MP2) perturbation theory breaks down at molecular geometries which are far away from equilibrium. We decompose the MP2 energy into contributions from different orbital subspaces and show that the divergent behavior of the MP2 energy comes from the excitations located within a small (or sometimes even the minimal) active space. The divergent behavior of the MP2 energy at large interfragment distances may be corrected by replacing a small number of terms by their more robust counterparts from coupled-cluster (CCSD) theory. We investigated several schemes of such a substitution, and we find that a coupling between the active-space CCSD and the remaining MP2 amplitudes is necessary to obtain the best results. This naturally leads us to an approach which has previously been examined in the context of cost-saving approximations to CCSD for equilibrium properties by Nooijen [J. Chem. Phys. 111, 10815 (1999)]. The hybrid MP2-CCSD approach, which has the same formal scaling as conventional MP2 theory, provides potential curves with a correct shape for bond-breaking reactions of BH, CH(4), and HF. The error of the MP2-CCSD method (measured against full configuration-interaction data) is smaller than that of MP2 at all interfragment separations and is qualitatively similar to that of full CCSD.

Algorithms↗

PubMed2005

The X1Sigmag+, B1Deltag, and B' 1Sigmag+ states of C2: a comparison of renormalized coupled-cluster and multireference methods with full configuration interaction benchmarks.

Unusual bonding and electronic near degeneracies make the lowest-lying singlet states of the C2 molecule particularly challenging for electronic structure theory. Here we compare two alternative approaches to modeling bond-breaking reactions and excited states: sophisticated multireference configuration interaction and multireference perturbation theory methods, and a more "black box," single-reference approach, the completely renormalized coupled-cluster method. These approximate methods are assessed in light of their ability to reproduce the full configuration interaction potential energy curves for the X1Sigmag+, B1Deltag, and B' 1Sigmag+ states of C2, which are numerically exact solutions of the electronic Schrodinger equation within the space spanned by a 6-31G* basis set. Both the multireference methods and the completely renormalized coupled-cluster approach provide dramatic improvements over the standard single-reference methods. The multireference methods are nearly as reliable for this challenging test case as for simpler reactions which break only single bonds. The completely renormalized coupled-cluster approach has difficulty for large internuclear separations R in this case, but over the wide range of R=1.0-2.0 A, it compares favorably with the more complicated multireference methods.

Journal Article↗

PubMed2005

High accuracy ab initio studies of Li6+, Li6-, and three isomers of Li6.

The structures and energetics of Li(6) (+), Li(6) (-) and three isomers of Li(6) are investigated using the coupled-cluster singles, doubles and perturbative triples [CCSD(T)] method with valence and core-valence correlation consistent basis sets of double- to quadruple-zeta quality (cc-pVXZ and cc-pCVXZ, where X=D-Q). These results are compared with qualitatively different predictions by less reliable methods. Our results conclusively show that the D(4h) isomer is the global minimum structure for Li(6). It is energetically favored over the C(5v) and D(3h) structures by about 5.1 and 7.1 kcal mol(-1), respectively, after the inclusion of the zero-point vibrational energy (ZPVE) correction. Our most accurate total atomization energies are 123.2, 117.6, and 115.7 kcal mol(-1) for the D(4h), C(5v), and D(3h) isomers, respectively. Comparison of experimental optical absorption spectra with our computed electronic spectra also indicate that the D(4h) isomer is indeed the most stable structure. The cation, anion, and some higher spin states are investigated using the less expensive cc-pCVDZ basis set. Adiabatic ionization energies and electron affinities are reported and compared with experimental values. Predictions of molecular properties are found to be sensitive to the basis set used and to the treatment of electron correlation.

Journal Article↗

PubMed2005

Estimates of the ab initio limit for sulfur-pi interactions: the H2S-benzene dimer.

The interaction between aromatic rings and sulfur atoms in the side chains of amino acids is a factor in the formation and stabilization of alpha-helices in proteins. We studied the H(2)S-benzene dimer as the simplest possible prototype of sulfur-pi interactions. High-quality potential energy curves were obtained using coupled-cluster theory with single, double, and perturbative triple substitutions (CCSD(T)) and a large, augmented quadruple-zeta basis set (aug-cc-pVQZ). The equilibrium intermonomer distance for the hydrogens-down C(2)(v) configuration is 3.8 A with an interaction energy of -2.74 kcal mol(-1). Extrapolating the binding energy to the complete basis set limit gives -2.81 kcal mol(-1). This binding energy is comparable to that of H(2)O-benzene or of the benzene dimer, and the equilibrium distance is in close agreement with experiment. Other orientations of the dimer were also considered at less complete levels of theory. A considerable reduction in binding for the sulfur-down configuration, together with an energy decomposition analysis, indicates that the attraction in H(2)S-benzene is best thought of as arising from a favorable electrostatic interaction between partially positive hydrogens in H(2)S with the negatively charged pi-cloud of the benzene.

Benzene Derivatives↗

PubMed2004

Full configuration interaction potential energy curves for the X (1)Sigma(g) (+), B (1)Delta(g), and B(') (1)Sigma(g) (+) states of C(2): a challenge for approximate methods.

The C(2) molecule exhibits unusual bonding and several low-lying excited electronic states, making the prediction of its potential energy curves a challenging test for quantum chemical methods. We report full configuration interaction results for the X (1)Sigma(g) (+), B (1)Delta(g), and B(') (1)Sigma(g) (+) states of C(2), which exactly solve the electronic Schrodinger equation within the space spanned by a 6-31G( *) basis set. Within the D(2h) subgroup used by most electronic structure programs, these states all have the same symmetry ((1)A(g)), and all three states become energetically close for interatomic distances beyond 1.5 A. The quality of several single-reference ab initio methods is assessed by comparison to the benchmark results. Unfortunately, even coupled-cluster theory through perturbative triples using an unrestricted Hartree-Fock reference exhibits large nonparallelity errors (>20 kcal mol(-1)) for the ground state. The excited states are not accurately modeled by any commonly used single-reference method, nor by configuration interaction including full quadruple substitutions. The present benchmarks will be helpful in assessing theoretical methods designed to break bonds in ground and excited electronic states.

Algorithms↗

PubMed2004

A general diagrammatic algorithm for contraction and subsequent simplification of second-quantized expressions.

We present a general computer algorithm to contract an arbitrary number of second-quantized expressions and simplify the obtained analytical result. The functions that perform these operations are a part of the program Nostromo which facilitates the handling and analysis of the complicated mathematical formulas which are often encountered in modern quantum-chemical models. In contrast to existing codes of this kind, Nostromo is based solely on the Goldstone-diagrammatic representation of algebraic expressions in Fock space and has capabilities to work with operators as well as scalars. Each Goldstone diagram is internally represented by a line of text which is easy to interpret and transform. The calculation of matrix elements does not exploit Wick's theorem in a direct way, but uses diagrammatic techniques to produce only nonzero terms. The identification of equivalent expressions and their subsequent factorization in the final result is performed easily by analyzing the topological structure of the diagrammatic expressions.

Algorithms↗

PubMed2004

Substituent effects in pi-pi interactions: sandwich and T-shaped configurations.

Sandwich and T-shaped configurations of benzene dimer, benzene-phenol, benzene-toluene, benzene-fluorobenzene, and benzene-benzonitrile are studied by coupled-cluster theory to elucidate how substituents tune pi-pi interactions. All substituted sandwich dimers bind more strongly than benzene dimer, whereas the T-shaped configurations bind more or less favorably depending on the substituent. Symmetry-adapted perturbation theory (SAPT) indicates that electrostatic, dispersion, induction, and exchange-repulsion contributions are all significant to the overall binding energies, and all but induction are important in determining relative energies. Models of pi-pi interactions based solely on electrostatics, such as the Hunter-Sanders rules, do not seem capable of explaining the energetic ordering of the dimers considered.

Journal Article↗

PubMed2003

X-ray structures, photophysical characterization, and computational analysis of geometrically constrained copper(I)--phenanthroline complexes.

A series of three geometrically constrained C(2)-symmetric Cu(I) mono-phenanthroline complexes were characterized by X-ray structural analysis, and their photophysical properties were investigated by absorption and emission spectroscopy. Visible light excitation yielded metal-to-ligand charge-transfer (MLCT) excited states with luminescence lifetimes up to 155 ns. Ultrafast transient absorption spectroscopy provided further insights into the excited-state dynamics and suggests for all three complexes the formation of a phenanthroline radical anion. In agreement with electrochemical measurements, the data further indicate that coordinative rearrangements are involved in nonradiative deactivation of the excited states. According to time-dependent density functional theory calculations (B3LYP/6-31G), the major MLCT transitions are polarized along the C(2) axis of the complex and originate predominantly from the copper d(xz) orbital. The computational analysis identifies an excited-state manifold with a number of close-lying, potentially emissive triplet states and is in agreement with the multiexponential decay kinetics of the MLCT luminescence. The relationship between structural and photophysical data of the studied Cu(I) mono-phenanthroline complexes agrees well with current models describing the photophysics of the related Cu(I) bis-diimine complexes.

Journal Article↗

PubMed2002

Estimates of the ab initio limit for pi-pi interactions: the benzene dimer.

State-of-the-art electronic structure methods have been applied to the simplest prototype of aromatic pi-pi interactions, the benzene dimer. By comparison to results with a large aug-cc-pVTZ basis set, we demonstrate that more modest basis sets such as aug-cc-pVDZ are sufficient for geometry optimizations of intermolecular parameters at the second-order Møller-Plesset perturbation theory (MP2) level. However, basis sets even larger than aug-cc-pVTZ are important for accurate binding energies. The complete basis set MP2 binding energies, estimated by explicitly correlated MP2-R12/A techniques, are significantly larger in magnitude than previous estimates. When corrected for higher-order correlation effects via coupled cluster with singles, doubles, and perturbative triples [CCSD(T)], the binding energies D(e) (D(0)) for the sandwich, T-shaped, and parallel-displaced configurations are found to be 1.8 (2.0), 2.7 (2.4), and 2.8 (2.7) kcal mol(-1), respectively.

Benzene Derivatives↗