Lori A. Burns

Psi4: an open-source ab initio electronic structure program

The Psi4 program is a new approach to modern quantum chemistry, encompassing Hartree–Fock and density‐functional theory to configuration interaction and coupled cluster. The program is written entirely in C++ and relies on a new infrastructure that has been designed to permit high‐efficiency computations of both standard and emerging electronic structure methods on conventional and high‐performance parallel computer architectures. Psi4 offers flexible user input built on the Python scripting language that enables both new and experienced users to make full use of the programs capabilities, and even to implement new functionality with moderate effort. To maximize its impact and usefulness, Psi4 is available through an open‐source license to the entire scientific community.

Density-functional approaches to noncovalent interactions: A comparison of dispersion corrections (DFT-D), exchange-hole dipole moment (XDM) theory, and specialized functionals

A systematic study of techniques for treating noncovalent interactions within the computationally efficient density functional theory (DFT) framework is presented through comparison to benchmark-quality 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 hydrogen-bonded (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.

Assessment of the Performance of DFT and DFT-D Methods for Describing Distance Dependence of Hydrogen-Bonded Interactions.

Noncovalent interactions such as hydrogen bonds, van der Waals forces, and π-π interactions play important roles influencing the structure, stability, and dynamic properties of biomolecules including DNA and RNA base pairs. In an effort to better understand the fundamental physics of hydrogen bonding (H-bonding), we investigate the distance dependence of interaction energies in the prototype bimolecular complexes of formic acid, formamide, and formamidine. Potential energy curves along the H-bonding dissociation coordinate are examined both by establishing reference CCSD(T) interaction energies extrapolated to the complete basis set limit and by assessing the performance of the density functional methods B3LYP, PBE, PBE0, B970, PB86, M05-2X, and M06-2X and empirical dispersion corrected methods B3LYP-D3, PBE-D3, PBE0-D3, B970-D2, BP86-D3, and ωB97X-D, with basis sets 6-311++G(3df,3pd), aug-cc-pVDZ, and aug-cc-pVTZ. Although H-bonding interactions are dominated by electrostatics, it is necessary to properly account for dispersion interactions to obtain accurate energetics. In order to quantitatively probe the nature of hydrogen bonding interactions as a function of distance, we decompose the interaction energy curves into physically meaningful components with symmetry-adapted perturbation theory (SAPT). The SAPT results confirm that the contribution of dispersion and induction are significant at and near equilibrium, although electrostatics dominate. Among the DFT/DFT-D techniques, the best overall results are obtained utilizing counterpoise-corrected ωB97X-D with the aug-cc-pVDZ basis set.

Comparing Counterpoise-Corrected, Uncorrected, and Averaged Binding Energies for Benchmarking Noncovalent Interactions

High-quality benchmark computations are critical for the development and assessment of approximate methods to describe noncovalent interactions. Recent advances in the treatment of dispersion by density functional theory and also the development of more efficient wave function techniques to reliably address noncovalent interactions motivate new benchmark computations of increasing accuracy. This work considers focal point approximations to estimate the complete basis set limit of coupled-cluster theory through perturbative triples [CCSD(T)/CBS] and evaluates how this approach is affected by the use or absence of counterpoise (CP) correction or, as has recently gained traction, the average of those values. Current benchmark protocols for interaction energies are computed with all CP procedures and assessed against the A24 and S22B databases and also to highly converged results for formic acid, cyanogen, and benzene dimers. Whether CP correction, no correction, or the average is favored depends upon the the...

Buckyplates and buckybowls: examining the effects of curvature on π-π interactions.

π-π interactions are integral to many areas of chemistry, biochemistry, and materials science. Here we use electronic structure theory to analyze how π-π interactions change as the π-systems are curved in model complexes based on coronene and corannulene dimers. Curvature redistributes electronic charge in the π-cloud and creates a dipole moment in these systems, leading to enhanced intermolecular electrostatic interactions in the concave-convex (nested) geometries that are the focus of this work. Curvature of both monomers also has a geometric effect on the interaction by decreasing the average C-C distance between monomers and by increasing the magnitude of both favorable London dispersion interactions and unfavorable exchange-repulsion interactions. Overall, increasing curvature in nested π-π interactions leads to more favorable interaction energies regardless of the native state of the monomers, except at short distances where the most highly curved systems are less favorable as exchange repulsion terms begin to dominate the interaction.

Revised Damping Parameters for the D3 Dispersion Correction to Density Functional Theory

Since the original fitting of Grimmes DFT-D3 damping parameters, the number and quality of benchmark interaction energies has increased significantly. Here, conventional benchmark sets, which focus on minimum-orientation radial curves at the expense of angular diversity, are augmented by new databases such as side chain-side chain interactions (SSI), which are composed of interactions gleaned from crystal data and contain no such minima-focused bias. Moreover, some existing databases such as S22×5 are extended to shorter intermolecular separations. This improved DFT-D3 training set provides a balanced description of distances, covers the entire range of interaction types, and at 1526 data points is far larger than the original training set of 130. The results are validated against a new collection of 6773 data points and demonstrate that the effect of refitting the damping parameters ranges from no change in accuracy (LC-ωPBE-D3) to an almost 2-fold decrease in average error (PBE-D3).

Comparison of Explicitly Correlated Methods for Computing High-Accuracy Benchmark Energies for Noncovalent Interactions

The reliability of explicitly correlated methods for providing benchmark-quality noncovalent interaction energies was tested at various levels of theory and compared to estimates of the complete basis set (CBS) limit. For all systems of the A24 test set, computations were performed using both aug-cc-pVXZ (aXZ; X = D, T, Q, 5) basis sets and specialized cc-pVXZ-F12 (XZ-F12; X = D, T, Q, 5) basis sets paired with explicitly correlated coupled cluster singles and doubles [CCSD-F12n (n = a, b, c)] with triple excitations treated by the canonical perturbative method and scaled to compensate for their lack of explicit correlation [(T**)]. Results show that aXZ basis sets produce smaller errors versus the CBS limit than XZ-F12 basis sets. The F12b ansatz results in the lowest average errors for aTZ and larger basis sets, while F12a is best for double-ζ basis sets. When using aXZ basis sets (X ≥ 3), convergence is achieved from above for F12b and F12c ansatzë and from below for F12a. The CCSD(T**)-F12b/aXZ approach converges quicker with respect to basis than any other combination, although the performance of CCSD(T**)-F12c/aXZ is very similar. Both CCSD(T**)-F12b/aTZ and focal point schemes employing density-fitted, frozen natural orbital [DF-FNO] CCSD(T)/aTZ exhibit similar accuracy and computational cost, and both are much more computationally efficient than large-basis conventional CCSD(T) computations of similar accuracy.

Redox-Linked Conformational Control of Proton Coupled Electron Transfer: Y122 in the Ribonucleotide Reductase β2 Subunit

Tyrosyl radicals play essential roles in biological proton-coupled electron transfer (PCET) reactions. Ribonucleotide reductase (RNR) catalyzes the reduction of ribonucleotides and is vital in DNA replication in all organisms. Class Ia RNRs consist of α2 and β2 homodimeric subunits. In class Ia RNR, such as the E. coli enzyme, an essential tyrosyl radical (Y122O(•))-diferric cofactor is located in β2. Although Y122O(•) is extremely stable in free β2, Y122O(•) is highly reactive in the quaternary substrate-α2β2 complex and serves as a radical initiator in catalytic PCET between β2 and α2. In this report, we investigate the structural interactions that control the reactivity of Y122O(•) in a model system, isolated E. coli β2. Y122O(•) was reduced with hydroxyurea (HU), a radical scavenger that quenches the radical in a clinically relevant reaction. In the difference FT-IR spectrum, associated with this PCET reaction, amide I (CO) and amide II (CN/NH) bands were observed. Specific (13)C-labeling of the tyrosine C1 carbon assigned a component of these bands to the Y122-T123 amide bond. Comparison to density functional calculations on a model dipeptide, tyrosine-threonine, and structural modeling demonstrated that PCET is associated with a Y122 rotation and a 7.2 Å translation of the Y122 phenolic oxygen. To test for the functional consequences of this structural change, a proton inventory defined the origin of the large solvent isotope effect (SIE = 16.7 ± 1.0 at 25 °C) on this reaction. These data suggest that the one-electron, HU-mediated reduction of Y122O(•) is associated with two, rate-limiting (full or partial) proton transfer reactions. One is attributable to HU oxidation (SIE = 11.9, net H atom transfer), and the other is attributable to coupled, hydrogen-bonding changes in the Y122O(•)-diferric cofactor (SIE = 1.4). These results illustrate the importance of redox-linked changes to backbone and ring dihedral angles in high potential PCET and provide evidence for rate-limiting, redox-linked hydrogen-bonding interactions between Y122O(•) and the iron cluster.

Electronic Structure and Proton Transfer in Ground-State Hexafluoroacetylacetone

The ground electronic state (X(1)A(1)) of hexafluoroacetylacetone (HFAA) has been subjected to synergistic experimental and theoretical investigations designed to resolve controversies surrounding the nature of intramolecular hydrogen bonding for the enol tautomer. Cryogenic (93K) X-ray diffraction studies were conducted on single HFAA crystals grown in situ by means of the zone-melting technique, with the resulting electron density maps affording clear evidence for distinguishable O(1)-H and H...O(2) bonds that span an interoxygen distance of 2.680 +/- 0.003 A. Such laboratory findings have been corroborated by a variety of quantum chemical methods including Hartree-Fock (HF), density functional [DFT (B3LYP)], Møller-Plesset perturbation (MPn), and coupled cluster [CCSD, CCSD(T)] treatments built upon extensive sets of correlation-consistent basis functions. Geometry optimizations performed at the CCSD(T)/aug-cc-pVDZ level of theory predict an asymmetric (C(s)) equilibrium configuration characterized by an O...O donor-acceptor separation of 2.628 A. Similar analyses of the transition state for proton transfer reveal a symmetric (C(2v)) structure that presents a potential barrier of 21.29 kJ/mol (1779.7 cm(-1)) height. The emerging computational description of HFAA is in reasonable accord with crystallographic measurements and suggests a weakening of hydrogen-bond strength relative to that of the analogous acetylacetone molecule.

Dissection of rovibronic structure by polarization-resolved two-color resonant four-wave mixing spectroscopy.

A synergistic theoretical and experimental investigation of stimulated emission pumping (SEP) as implemented in the coherent framework of two-color resonant four-wave mixing (TC-RFWM) spectroscopy is presented, with special emphasis directed toward the identification of polarization geometries that can distinguish spectral features according to their attendant changes in rotational quantum numbers. A vector-recoupling formalism built upon a perturbative treatment of matter-field interactions and a state-multipole expansion of the density operator allowed the weak-field signal intensity to be cast in terms of a TC-RFWM response tensor, RQ(K)(epsilon4*epsilon3epsilon2*epsilon1;Jg,Je,Jh,Jf), which separates the transverse characteristics of the incident and generated electromagnetic waves (epsilon4*epsilon3epsilon2*epsilon1) from the angular momentum properties of the PUMP and DUMP resonances (Jg,Je,Jh,Jf). For an isolated SEP process induced in an isotropic medium, the criteria needed to discriminate against subsets of rovibronic structure were encoded in the roots of a single tensor element, R0(0)(epsilon4*epsilon3epsilon2*epsilon1;Jg,Je,Jh,Je). By assuming all optical fields to be polarized linearly and invoking the limit of high quantum numbers, specific angles of polarization for the detected signal field were found to suppress DUMP resonances selectively according to the nature of their rotational branch and the rotational branch of the meshing PUMP line. These predictions were corroborated by performing SEP measurements on the ground electronic potential energy surface of tropolone in two distinct regimes of vibrational excitation, with the near-ultraviolet 1B2-1A1 (pi*<--pi) absorption system affording the requisite PUMP and DUMP transitions.