Justin T. Fermann

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.

PSI3: An open‐source Ab Initio electronic structure package

PSI3 is a program system and development platform for ab initio molecular electronic structure computations. The package includes mature programming interfaces for parsing user input, accessing commonly used data such as basis‐set information or molecular orbital coefficients, and retrieving and storing binary data (with no software limitations on file sizes or file‐system‐sizes), especially multi‐index quantities such as electron repulsion integrals. This platform is useful for the rapid implementation of both standard quantum chemical methods, as well as the development of new models. Features that have already been implemented include Hartree‐Fock, multiconfigurational self‐consistent‐field, second‐order Møller‐Plesset perturbation theory, coupled cluster, and configuration interaction wave functions. Distinctive capabilities include the ability to employ Gaussian basis functions with arbitrary angular momentum levels; linear R12 second‐order perturbation theory; coupled cluster frequency‐dependent response properties, including dipole polarizabilities and optical rotation; and diagonal Born‐Oppenheimer corrections with correlated wave functions. This article describes the programming infrastructure and main features of the package. PSI3 is available free of charge through the open‐source, GNU General Public License.

The torsional conformations of butane: Definitive energetics from ab initio methods

The torsional potential function for butane was probed theoretically using increasingly complete basis sets (up to 840 functions) and treatments of electron correlation [up to the CCSD(T) method] until it was shown that the sequence of relative energies approached convergence. The Schrodinger limit in the Born–Oppenheimer approximation was thus estimated. The equilibrium energies relative to the anti conformation (ΔEe) as obtained by this focal-point extrapolation were 0.62, 3.31, and 5.51 kcal mol−1 for the geometrically optimized stationary points having carbon backbone torsion angles of 64.8°, 119.6°, and 0°, respectively. The final prediction of the anti–syn difference is 5.40±0.15 kcal mol−1. Some consequences of this result are discussed.

Structures, thermochemistry, and electron affinities of the PFn and PF−n series, n=1–6

A quantum mechanical study of the phosphorus fluorides and their singly charged anions was carried out. A range of density functional methods was used. Optimized geometries, adiabatic electron affinities, vertical electron affinities, vertical detachment energies, and stabilities toward the loss of a single fluorine atom or fluorine ion are reported. These properties were evaluated exhaustively using four exchange‐correlation functionals: Becke’s 1988 exchange functional with the correlation functional of Lee, Yang, and Parr, Becke’s 1988 exchange functional with the 1986 correlation functional of Perdew, Becke’s three parameter Hartree–Fock/density functional hybrid exchange functional with the correlation functional of Lee, Yang, and Parr and Becke’s half‐and‐half Hartree–Fock/density functional hybrid exchange functional with the correlation functional of Lee, Yang, and Parr (BHLYP). These exchange‐correlation functionals were used in conjunction with a double‐ζ plus polarization basis and a double‐ζ p...

Modeling proton mobility in acidic zeolite clusters. II. Room temperature tunneling effects from semiclassical rate theory

We have developed a novel semiclassical transition state theory (SC-TST) for truncated parabolic barriers, based on the formulation of Hernandez and Miller [Chem. Phys. Lett. 214, 129 (1993)]. Our SC-TST rate coefficient has the form kSC-TST=kTST⋅Γ, where Γ depends on the zero point corrected barrier, ΔE0, and the barrier curvature, |ωF‡|. Our rate expression is stable to arbitrarily low temperatures, as opposed to purely harmonic SC-TST, because we identify the maximum possible semiclassical action in the reaction coordinate. For low temperatures, we derive an analytical approximation for Γ that is proportional to eβ ΔE0. We develop a theory for the tunneling crossover temperature, Tx, yielding kBTx≅ℏ|ωF‡|ΔE0/(2π ΔE0−ℏ|ωF‡|ln 2), which generalizes the harmonic theory for systems with large but finite barriers. We have calculated rate coefficients and crossover temperatures for the O(1)→O(4) jump in H–Y and D–Y zeolites, yielding Tx=368 K and 264 K, respectively. These results suggest that tunneling domin...

Modeling Proton Transfer in Zeolites: Convergence Behavior of Embedded and Constrained Cluster Calculations.

We have studied the convergence properties of embedded and constrained cluster models of proton transfer in zeolites. We applied density functional theory to describe clusters and ONIOM to perform the embedding. We focused on converging the reaction energy and barrier of the O(1) to O(4) jump in H-Y zeolite as well as vibrational and structural aspects of this jump. We found that using successively larger clusters in vacuo gives convergence of this reaction energy to 14 ± 2 kJ mol(-)(1) and the barrier to 135 ± 5 kJ mol(-)(1) at a cluster size of 5 Å, which contains 11 tetrahedral (Si or Al) atoms. We embedded quantum clusters of various sizes in larger clusters with total radii in the range 7-20 Å, using the universal force field as the lower level of theory in ONIOM. We found convergence to the same values as the constrained clusters, without the use of reactive force fields or periodic boundary conditions in the embedding procedure. For the reaction energy, embedded cluster calculations required smaller clusters than in vacuo calculations, reaching converged reaction energies for quantum systems containing at least 8 tetrahedral atoms. In addition, optimizations on embedded clusters required many fewer cycles, and hence much less CPU time, than did optimizations on comparable constrained clusters.

The weakly bound dinitrogen tetroxide molecule: High level single reference wavefunctions are good enough

Ab initio studies of dinitrogen tetroxide (N2O4) have been performed to predict the equilibrium geometry, harmonic vibrational frequencies, and fragmentation energy (N2O4→2 NO2). The structure was optimized at the self-consistent field, configuration interaction, and coupled-cluster levels of theory with large basis sets. At the highest level of theory, the N–N bond distance was 1.752 A, in excellent agreement with the experimental value of 1.756±0.01 A. In addition, the harmonic vibrational frequencies were predicted with an average absolute error of 51 cm−1 relative to experimental fundamental values with differences largely attributed to anharmonic effects. The fragmentation energy corrected for zero point vibrational energy and basis set superposition error was 7.2 kcal/mol, in fair agreement with the experimental value of 12.7 kcal/mol. Despite the suggestion that a multireference wavefunction may be necessary to accurately describe the biradical nature of N2O4, single reference treatments with large...

Modeling proton mobility in acidic zeolite clusters. I. Convergence of transition state parameters from quantum chemistry

We have applied electronic structure methods to the calculation of transition state parameters for the O(1)→O(4) proton transfer in H-Y zeolite. We arrive at a set of recommendations for calculating these transition state parameters accurately and efficiently. Density functional theory using the B3LYP functional and basis sets of triple-ζ quality in the valence space, and including polarization functions on all atoms, is the most efficient method for converging structures and vibrational frequencies. For converging classical barrier heights, we find it necessary to augment MP2 barrier heights calculated using large basis sets with MP4 energies obtained in more limited basis sets. We obtain an O(1)→O(4) barrier height of 86.1 kJ mol−1, and find the curvature of the barrier at the transition state to be 1570 cm−1. Including long range effects from the work of Sauer et al. [ACS Symp. Ser. 721, 358 (1999)] results in a higher barrier, which we estimate to be 97.1 kJ mol−1. We attribute the fact that our barri...

Modeling energy landscapes of proton motion in nonaqueous, tethered proton wires.

We have modeled structures and energetics of anhydrous proton-conducting wires: tethered hydrogen-bonded chains of the form ···HX···HX···HX···, with functional groups HX = imidazole, triazole, and formamidine; formic, sulfonic, and phosphonic acids. We have applied density functional theory (DFT) to model proton wires up to 19 units long, where each proton carrier is linked to an effective backbone to mimic polymer tethering. This approach allows the direct calculation of hydrogen bond strengths. The proton wires were found to be stabilized by strong hydrogen bonds (up to 50 kJ/mol) whose strength correlates with the proton affinity of HX [related to pK(b)(HX)] and not to pK(a)(HX) as is often assumed. Geometry optimizations and ab initio molecular dynamics near 400 K on imidazole-based proton wires both predict that adding a proton to the end of such wires causes the excess charge to embed into the interior segments of these wires. Proton translocation energy landscapes for imidazole-based wires are sensitive to the imidazole attachment point (head or feet) and to wire architecture (linear or interdigitated). Linear imidazole wires with head-attachment exhibit low barriers for intrawire proton motion, rivaling proton diffusion in liquid imidazole. Excess charge relaxation from the edge of wires is found to be dominated by long-range Grotthuss shuttling for distances as long as 42 Å, especially for interdigitated wires. For imidazole, we predict that proton translocation is controlled by the energetics of desorption from the proton wire, even for relatively long wires (600 imidazole units). Proton desorption energies show no correlation with functional group properties, suggesting that proton desorption is a collective process in proton wires.

The hydroperoxyl radical dimer: Triplet ring or singlet string?

In order to determine the lowest energy isomer of the hydroperoxyl radical dimer, H2O4, ab initio quantum mechanical methods were employed to predict the geometrical structures, relative energies, harmonic vibrational frequencies, and associated IR intensities of both open chain and cyclic isomers. Two minima were located on the open chain potential energy surface, one of C2 symmetry and one of C1 symmetry. The relative energies of the different H2O4 structures vary strongly with level of theory. The most reliable treatment used in the present study predicted that the global minimum is the closed-shell C1 chain isomer which is lower in energy than the planar C2h triplet cyclic isomer by 1.6 kcal mol−1 including zero point vibrational energy corrections. It is argued that both structures should be observable, depending on the method of preparation.