Psi4 1.4: Open-source software for high-throughput quantum chemistry

PSI4 is a free and open-source ab initio electronic structure program providing implementations of Hartree-Fock, density functional theory, many-body perturbation theory, configuration interaction, density cumulant theory, symmetry-adapted perturbation theory, and coupled-cluster theory. Most of the methods are quite efficient, thanks to density fitting and multi-core parallelism. The program is a hybrid of C++ and Python, and calculations may be run with very simple text files or using the Python API, facilitating post-processing and complex workflows; method developers also have access to most of PSI4's core functionalities via Python. Job specification may be passed using The Molecular Sciences Software Institute (MolSSI) QCSCHEMA data format, facilitating interoperability. A rewrite of our top-level computation driver, and concomitant adoption of the MolSSI QCARCHIVE INFRASTRUCTURE project, makes the latest version of PSI4 well suited to distributed computation of large numbers of independent tasks. The project has fostered the development of independent software components that may be reused in other quantum chemistry programs.

The water trimer reaction OH + (H2O)3→ (H2O)2OH + H2O

All important stationary points on the potential energy surface (PES) for the reaction OH + (H₂O)₃→ (H₂O)₂OH + H₂O have been fully optimized using the "gold standard" CCSD(T) method with the large Dunning correlation-consistent cc-pVQZ basis sets. Three types of pathways were found. For the pathway without hydrogen abstraction, the barrier height of the transition state (TS1) is predicted to lie 5.9 kcal mol^-1 below the reactants. The two major complexes (H₂O)₃OH (CP1 and CP2a) are found to lie 6.3 and 11.0 kcal mol^-1, respectively, below the reactants [OH + (H₂O)₃]. For one of the H-abstraction pathways the lowest classical barrier height is predicted to be much higher, 6.1 kcal mol^-1 (TS2a) above the reactants. For the other H-abstraction pathway the barrier height is even higher, 15.0 (TS3) kcal mol^-1. Vibrational frequencies and the zero-point vibrational energies connected to the PES are also reported. The energy barriers for the H-abstraction pathways are compared with those for the OH + (H₂O)₂ and OH + H₂O reactions, and the effects of the third water on the energetics are usually minor (0.2 kcal mol^-1).

Perfluoroolefin complexes versus perfluorometallacycles and perfluorocarbene complexes in cyclopentadienylcobalt chemistry

Fluorocarbons have been shown experimentally by Baker and coworkers to combine with the cyclopentadienylcobalt (CpCo) moiety to form fluoroolefin and fluorocarbene complexes as well as fluorinated cobaltacyclic rings. In this connection density functional theory (DFT) studies on the cyclopentadienylcobalt fluorocarbon complexes CpCo(L)(C_nF_2n) (L = CO, PMe₃; n = 3 and 4) indicate structures with perfluoroolefin ligands to be the lowest energy structures followed by perfluorometallacycle structures and finally by structures with perfluorocarbene ligands. Thus, for the CpCo(L)(C₃F₆) (L = CO, PMe₃) complexes, the perfluoropropene structure has the lowest energy, followed by the perfluorocobaltacyclobutane structure and the perfluoroisopropylidene structure less stable by 8 to 11 kcal mol^-1, and the highest energy perfluoropropylidene structure less stable by more than 12 kcal mol^-1. For the two metal carbene structures Cp(L)Co[double bond, length as m-dash]C(CF₃)₂ and Cp(L)Co[double bond, length as m-dash]CF(C₂F₅), the former is more stable than the latter, even though the latter has Fischer carbene character. For the CpCo(L)(C₄F₈) (L = CO, PMe₃) complexes, the perfluoroolefin complex structures have the lowest energies, followed by the perfluorometallacycle structures at 10 to 20 kcal mol^-1, and the structures with perfluorocarbene ligands at yet higher energies more than 20 kcal mol^-1 above the lowest energy structure. This is consistent with the experimentally observed isomerization of the perfluorinated cobaltacyclobutane complexes CpCo(PPh₂Me)(-CFR-CF₂-CF₂-) (R = F, CF₃) to the perfluoroolefin complexes CpCo(PPh₂Me)(RCF[double bond, length as m-dash]CF₂) in the presence of catalytic quantities of HN(SO₂CF₃)₂. Further refinement of the relative energies by the state-of-the-art DLPNO-CCSD(T) method gives results essentially consistent with the DFT results summarized above.

Energetics and mechanisms for the acetonyl radical + O2 reaction: An important system for atmospheric and combustion chemistry

The acetonyl radical (^•CH₂COCH₃) is relevant to atmospheric and combustion chemistry due to its prevalence in many important reaction mechanisms. One such reaction mechanism is the decomposition of Criegee intermediates in the atmosphere that can produce acetonyl radical and OH. In order to understand the fate of the acetonyl radical in these environments and to create more accurate kinetics models, we have examined the reaction system of the acetonyl radical with O₂ using highly reliable theoretical methods. Structures were optimized using coupled cluster theory with singles, doubles, and perturbative triples [CCSD(T)] with an atomic natural orbital (ANO0) basis set. Energetics were computed to chemical accuracy using the focal point approach involving perturbative treatment of quadruple excitations [CCSDT(Q)] and basis sets as large as cc-pV5Z. The addition of O₂ to the acetonyl radical produces the acetonylperoxy radical, and multireference computations on this reaction suggest it to be barrierless. No submerged pathways were found for the unimolecular isomerization of the acetonylperoxy radical. Besides dissociation to reactants, the lowest energy pathway available for the acetonylperoxy radical is a 1-5 H shift from the methyl group to the peroxy group through a transition state that is 3.3 kcal mol^-1 higher in energy than acetonyl radical + O₂. The ultimate products from this pathway are the enol tautomer of the acetonyl radical along with O₂. Multiple pathways that lead to OH formation are considered; however, all of these pathways are predicted to be energetically inaccessible, except at high temperatures.

Formation of Formic Acid Derivatives through Activation and Hydroboration of CO2 by Low-Valent Group 14 (Si, Ge, Sn, Pb) Catalysts

The chemistry of low-valent main group elements has attracted much attention in the past decade. These species are relevant because they have been able to mimic transition metal behavior in catalytic applications, with decreased material costs and diminished toxicity. In this contribution, we study the L¹EH catalysts (E = Si(II), Ge(II), Sn(II), and Pb(II); L¹ = [ArNC(Me)CHC(Me)NAr] with Ar = 2,6-iPr₂C₆H₃) for the formation of formic acid derivatives through hydroboration of CO₂. Detailed characterization of relevant structures on the potential energy surface enabled us to rationalize different paths for the hydroboration of CO₂. Interestingly, it was found that according to the activation energies for the whole catalytic cycle, the process of transformation of CO₂ becomes more favored going down group 14. However, an effective energetic decrease for the process (taking as the reference the uncatalyzed reaction between CO₂ and HBpin) is evidenced just from the germanium analogue. The trend in reactivity found in the present study is a direct consequence of the change in the central main group element, enabling enhanced polar character of the E-H (L¹EH in the CO₂ activation step) and E-O (metal formates in the hydroboration step) bonds as the atomic radius increases. The transient stabilization of reaction intermediates found in the hydroboration step was rationalized through the non-covalent interaction index (NCI) and symmetry-adapted perturbation theory (SAPT). This computational study highlights the reactivity trends in group-14-based hydride catalysts in hydrometalation and posterior hydroboration to form formic acid intermediates. We hope that this study will motivate further experimental work in low-valent lead chemistry.

Is silver a mere terminal oxidant in palladium catalyzed C-H bond activation reactions?

In the contemporary practice of palladium catalysis, a molecular understanding of the role of vital additives used in such reactions continues to remain rather vague. Herein, we disclose an intriguing and a potentially general role for one of the most commonly used silver salt additives, discovered through rigorous computational investigations on four diverse Pd-catalyzed C-H bond activation reactions involving sp2 aryl C-H bonds. The catalytic pathways of different reactions such as phosphorylation, arylation, alkynylation, and oxidative cycloaddition are analyzed, with and without the explicit inclusion of the silver additive in the respective transition states and intermediates. Our results indicate that the pivotal role of silver salts is likely to manifest in the form of a Pd-Ag heterobimetallic species that facilitates intermetallic electronic communication. The Pd-Ag interaction is found to provide a consistently lower energetic span as compared to an analogous pathway devoid of such interaction. Identification of a lower energy pathway as well as enhanced catalytic efficiency due to Pd-Ag interaction could have broad practical implications in the mechanism of transition metal catalysis and the current perceptions on the same.

Unusual effects of the bulky 1-norbornyl group in cobalt carbonyl chemistry: low-energy structures with agostic hydrogen atoms

Low-energy (nor)Co(CO)_n (n = 3, 2) and (nor)₂Co₂(CO)_n (nor = 1-norbornyl; n = 6, 5) structures are found to have agostic hydrogen atoms from a CH₂ group adjacent to the Co–C bond forming C–H–Co bridges. In addition, low-energy structures are found with (nor)CO acyl ligands resulting from carbonyl migration.

The atmospheric importance of methylamine additions to Criegee intermediates

The methylamine addition to Criegee intermediates is investigated using high level ab initio methods.

Relatives of cyanomethylene: replacement of the divalent carbon by B-, N+, Al-, Si, P+, Ga-, Ge, and As. Phys Chem Chem Phys 2019;21:26438-26452. [PMID: 31774089 DOI: 10.1039/c9cp05777c]

The lowest lying singlet and triplet states of HBCN-, HCCN, HNCN+, HAlCN-, HSiCN, HPCN+, HGaCN-, HGeCN, and HAsCN+ were studied using the CCSDT(Q)/CBS//CCSD(T)/aug-cc-pVQZ level of theory. Periodic trends in geometries, singlet-triplet gaps, and barriers to linearity were established and analyzed. The first row increasingly favors the triplet state, with a singlet-triplet gap (ΔEST = Esinglet - Etriplet) of 3.5 kcal mol-1, 11.9 kcal mol-1, and 22.6 kcal mol-1, respectively, for HBCN-, HCCN, and HNCN+. The second row increasing favors the singlet state, with singlet-triplet gaps of -20.4 kcal mol-1 (HAlCN-), -26.6 kcal mol-1 (HSiCN), and -26.8 kcal mol-1 (HPCN+). The third row also favors the singlet state, with singlet-triplet gaps of -26.8 kcal mol-1 (HGaCN-), -33.5 kcal mol-1 (HGeCN), and -33.1 kcal mol-1 (HAsCN+). The HXCN species have larger absolute singlet-triplet energy gaps compared to their parent species XH2 except for the case of X = N+. The effect of the substitution of hydrogen with a cyano group was analyzed with isodesmic bond separation analysis and NBO.

Important features of the potential energy surface of the methylamine plus O(1D) reaction

This research presents an ab initio characterization of the potential energy surface for the methylamine plus ¹D oxygen atom reaction, which may be relevant to interstellar chemistry. Geometries and harmonic vibrational frequencies were determined for all stationary points at the CCSD(T)/aug-cc-pVTZ level of theory. The focal point method along with several additive corrections was used to obtain reliable CCSDT(Q)/CBS potential energy surface features. Extensive conformational analysis and intrinsic reaction coordinate computations were performed to ensure accurate chemical connectivity of the stationary points. Five minima were determined to be possible products of this reaction and three novel transition states were found that were previously unreported or mislabeled in the literature. The pathways we present can be used to guide further searches for NH₂ containing species in the interstellar medium.

Dispersion Effects in Stabilizing Organometallic Compounds: Tetra-1-norbornyl Derivatives of the First-Row Transition Metals as Exceptional Examples

In 1972 Bower and Tennett first synthesized a series of tetra-1-norbornyl derivatives, (nor)₄M, of the first-row transition metals from titanium to cobalt. These were found to be exceptionally stable for homoleptic metal alkyls containing only metal-carbon σ-bonds. The theoretical energies for the dissociation of 1-norbornyl ligands from these unusually high oxidation state organometallics through the reactions (nor)₄M → (nor)₃M + nor^• and (nor)₄M → (nor)₂M + nor-nor indicate that dispersion effects play an important role in determining their exceptional stability. Thus, all of the (nor)₄M (M = Ti to Cu) derivatives are viable with respect to 1-norbornyl radical dissociation when the London dispersion effect is considered. However, (nor)₄Cu becomes disfavored if the dispersion correction is ignored. Thus, the stability of the (nor)₄M molecules is seen to arise from the favorable combination of steric and dispersion force effects of the four 1-norbornyl groups tetrahedrally disposed around the metal atom and maximizing the dispersion attraction between them in a spherical hydrocarbon structure with a central metal atom. The tri-1-norbornyl derivatives (nor)₃M appear be disfavored with respect to disproportionation into (nor)₄M + (nor)₂M. This is consistent with the experimental syntheses of the (nor)₄M (M = Cr to Co) derivatives with the metal in the +4 oxidation by reactions with 1-norbornyllithium with metal halides in the +2 or +3 metal oxidation states. Both the OPBE method and the BPW91 method predict high-spin states for the d² and d³ complexes (nor)₄Cr and (nor)₄Mn but low-spin states for (nor)₄Fe and (nor)₄Co, consistent with experiment.

Riddles of the structure and vibrational dynamics of HO3 resolved near the ab initio limit

The hydridotrioxygen (HO₃) radical has been investigated in many previous theoretical and experimental studies over several decades, originally because of its possible relevance to the tropospheric HO_x cycle but more recently because of its fascinating chemical bonding, geometric structure, and vibrational dynamics. We have executed new, comprehensive research on this vexing molecule via focal point analyses (FPA) to approach the ab initio limit of optimized geometric structures, relative energies, complete quartic force fields, and the entire reaction path for cis-trans isomerization. High-order coupled cluster theory was applied through the CCSDT(Q) and even CCSDTQ(P) levels, and CBS extrapolations were performed using cc-pVXZ (X = 2-6) basis sets. The cis isomer proves to be higher than trans by 0.52 kcal mol^-1, but this energetic ordering is achieved only after the CCSDT(Q) milestone is reached; the barrier for cis → trans isomerization is a minute 0.27 kcal mol^-1. The FPA central r_e(O-O) bond length of trans-HO₃ is astonishingly long (1.670 Å), consistent with the semiexperimental r_e distance we extracted from microwave rotational constants of 10 isotopologues using FPA vibration-rotation interaction constants (α_i). The D₀(HO-O₂) dissociation energy converges to a mere 2.80 ± 0.25 kcal mol^-1. Contrary to expectation for such a weakly bound system, vibrational perturbation theory performs remarkably well with the FPA anharmonic force fields, even for the torsional fundamental near 130 cm^-1. Exact numerical procedures are applied to the potential energy function for the torsional reaction path to obtain energy levels, tunneling rates, and radiative lifetimes. The cis → trans isomerization occurs via tunneling with an inherent half-life of 1.4 × 10^-11 s and 8.6 × 10^-10 s for HO₃ and DO₃, respectively, thus resolving the mystery of why the cis species has not been observed in previous experiments executed in dissipative environments that allow collisional cooling of the trans-HO₃ product. In contrast, the pure ground eigenstate of the cis species in a vacuum is predicted to have a spontaneous radiative lifetime of about 1 h and 5 days for HO₃ and DO₃, respectively.

Lewis base-complexed magnesium dithiolenes

The first magnesium-based dithiolene, 2, was prepared by reaction of the lithium dithiolene radical, 1˙, with 2-mesitylmagnesium bromide. Reaction of 2 with N-heterocyclic carbenes (in toluene) gave a carbene-stabilized magnesium monodithiolene complex, 3. Complex 3, in turn, is readily converted to a THF-solvated magnesium bis-dithiolene dianion, 4, via partial hydrolysis in polar solvents (i.e., THF/CH3CN). Compounds 2, 3 and 4 have been spectroscopically and structurally characterized and probed by DFT computations.

Tris(butadiene) Metal Complexes of the First-Row Transition Metals versus Coupling of Butadiene to Eight- and Twelve-Carbon Hydrocarbon Chains

The role that zerovalent nickel plays in catalyzing the trimerization of butadiene to 1,5,9-cyclododecatriene conveys interest in the properties of the tris(butadiene)metal complexes (C₄H₆)₃M. In this connection the complexes (C₄H₆)₃M (M = Ti-Ni) of the first-row transition metals have been investigated by density functional theory. The intermediate C₁₂H₁₈Ni which has been isolated in the nickel-catalyzed trimerization of butadiene but is too unstable for X-ray crystallography is suggested here to have an open-chain hexahapto η^3,3-C₁₂H₁₈ ligand rather than the octahapto such ligand suggested by some investigators. The lowest energy (C₄H₆)₃M structures of the other first-row transition metals from vanadium to cobalt are found to have related structures with open-chain C₁₂H₁₈ ligands having hapticities ranging from four to eight with hexahapto structures being most common. The nickel and cobalt (C₁₂H₁₈)M derivatives favor low-spin singlet and doublet spin states, respectively, whereas the manganese derivative (C₁₂H₁₈)Mn favors the high-spin sextet state corresponding to the half-filled d⁵ shell of Mn(II). A (C₄H₆)₃Cr structure with three separate tetrahapto butadiene ligands analogous to the very stable (η⁴-C₄H₆)₃M (M = Mo, W) with the favored 18-electron metal configuration is found to be a very high energy structure relative to isomers containing an open-chain C₁₂H₁₈ ligand.