A Benchmark Test Suite for Proton Transfer Energies and its Use to Test Electronic Structure Model Chemistries

Combined DFT and Kinetic Monte Carlo Study of UiO-66 Catalysts for γ-Valerolactone Production

Zr-based metal-organic frameworks (MOFs) are excellent heterogeneous porous catalysts due to their thermal stability. Their tunability via node and linker modifications makes them amenable for theoretical studies on catalyst design. However, detailed benchmarks on MOF-based reaction mechanisms combined with kinetics analysis are still scarce. Thus, we here evaluate different computational models and density functional theory (DFT) methods followed by kinetic Monte Carlo studies for a case reaction relevant in biomass upgrading, i.e., the conversion of methyl levulinate to γ-valerolactone catalyzed by UiO-66. We show the impact of cluster versus periodic models, the importance of the DF of choice, and the direct comparison to experimental data via simulated kinetics data. Overall, we found that Perdew-Burke-Ernzerhof (PBE), a widely employed method in plane-wave periodic calculations, greatly overestimates reaction rates, while M06 with cluster models better fits the available experimental data and is recommended whenever possible.

Concerted versus stepwise proton transfer reactions in the [2, 2'-bipyridyl]-3-3'-diol molecule: A static and dynamic ab-initio investigation

The double proton transfer (PT) reaction has been investigated in the [2,2'-bipyridyl]-3-3'-diol, a complex molecule where the proton movements is coupled to significant rearrangement of the electronic structure. Moreover, the reaction could be concerted, that is the two protons are exchanged simultaneously, or stepwise, where the two protons are transferred sequentially. To this end, a static exploration of the potential energy surface (PES) was carried together with the analysis of the free-energy surface (FES), both surfaces being evaluated at density functional theory level and different exchange-correlation functionals. While the concerted mechanism has been clearly discharged, the characteristics of the stepwise PT significantly depends on the chosen functionals, some suggesting a clear stepwise mechanism characterized by a stable reaction intermediates and two transitions states, whereas other approaches propend for a asynchronous PT, with a single TS. These features appear on both PES and FES, albeit some differences appears due to their different nature.

Free Energy Profiles of Proton Transfer Reactions: Density Functional Benchmark from Biased Ab Initio Dynamics

By coupling an enhanced sampling algorithm with an orbital-localized variant of Car-Parrinello molecular dynamics, the so-called atomic centered density matrix propagation model, we reconstruct the free energy profiles along reaction pathways using different density functional approximations (DFAs) ranging from locals to hybrids. In particular, we compare the computed free energy barrier height of proton transfer (PT) reactions to those obtained by a more traditional static approach, based on the intrinsic reaction coordinate (IRC), for two case systems, namely malonaldehyde and formic acid dimer. The obtained results show that both the IRC profiles and the potentials of mean force, derived from biased dynamic trajectories, are very sensitive to the density functional approximation applied. More precisely, we observe that, with the notable exception of M06-L, local density functionals always strongly underestimate the reaction barrier heights. More generally, we find that also the shape of the free energy profile is very sensitive to the density functional choice, thus highlighting the effect, often neglected, that the choice of DFA has also in the case of dynamics simulations.

BENCHMARKS OF THE DENSITY FUNCTIONAL TIGHT-BINDING METHOD FOR REDOX, PROTONATION AND ELECTRONIC PROPERTIES OF QUINONES

Organic materials with controllable molecular design and sustainable resources are promising electrode materials. Crystalline quinones have been investigated in a variety of rechargeable battery chemistries due to their ubiquitous nature,...

Reaction pathways and kinetics study on a syngas combustion system: CO + HO2 in an H2O environment

The reaction between CO and HO2 plays a significant role in syngas combustion. In this work, the catalytic effect of single-molecule water on this reaction is theoretically investigated at the CCSD(T)/aug-cc-pV(D,T,Q)Z and CCSD(T)-F12a/jun-cc-pVTZ levels in combination with the M062X/aug-cc-pVTZ level. Firstly, the potential energy surface (PES) of CO + HO2 (water-free) is revisited. The major products CO2 + OH are formed via a cis- or a trans-transition state (TS) channel and the formation of HCO + O2 is minor. In the presence of water, the title reaction has three different pre-reactive complexes (i.e., RC2: COHO2 + H2O, RC3: COH2O + HO2, and RC4: HO2H2O + CO), depending on the initial hydrogen bond formation. Compared to the water-free process, the reaction barriers of the water-assisted process are reduced considerably, due to more stable cyclic TSs and complexes. The rate constants for the bimolecular reaction pathways CO + HO2, RC2, RC3, and RC4 are further calculated using conventional transition state theory (TST) with Eckart asymmetric tunneling correction. For reaction CO + HO2, our calculations are in good agreement with the literature. In addition, the effective rate constants for the water-assisted process decrease by 1-2 orders of magnitude compared to the water-free one at a temperature below 600 K. In particular, the effective rate constants for the water-assisted and water-free processes are 1.55 × 10-28 and 3.86 × 10-26 cm3 molecule-1 s-1 at 300 K, respectively. This implies that the contribution of a single molecule water-assisted process is small and cannot accelerate the title reaction.

Introducing a closed system approach for the investigation of chemical steps involving proton and electron transfer; as illustrated by a copper-based water oxidation catalyst

We present an ab initio molecular dynamics approach to characterize proton-coupled electron transfer catalytic steps and identify the preferred reaction mechanism.

Exploring the Accuracy Limits of Local Pair Natural Orbital Coupled-Cluster Theory

The domain based local pair natural orbital coupled cluster method with single-, double-, and perturbative triple excitations (DLPNO–CCSD(T)) is an efficient quantum chemical method that allows for coupled cluster calculations on molecules with hundreds of atoms. Because coupled-cluster theory is the method of choice if high-accuracy is needed, DLPNO–CCSD(T) is very promising for large-scale chemical application. However, the various approximations that have to be introduced in order to reach near linear scaling also introduce limited deviations from the canonical results. In the present work, we investigate how far the accuracy of the DLPNO–CCSD(T) method can be pushed for chemical applications. We also address the question at which additional computational cost improvements, relative to the previously established default scheme, come. To answer these questions, a series of benchmark sets covering a broad range of quantum chemical applications including reaction energies, hydrogen bonds, and other noncovalent interactions, conformer energies, and a prototype organometallic problem were selected. An accuracy of 1 kcal/mol or better can readily be obtained for all data sets using the default truncation scheme, which corresponds to the stated goal of the original implementation. Tightening of the three thresholds that control DLPNO leads to mean absolute errors and standard deviations from the canonical results of less than 0.25 kcal/mol (<1 kJ/mol). The price one has then to pay is an increased computational time by a factor close to 3. The applicability of the method is shown to be independent of the nature of the reaction. On the basis of the careful analysis of the results, three different sets of truncation thresholds (termed “LoosePNO”, “NormalPNO”, and “TightPNO”) have been chosen for “black box” use of DLPNO–CCSD(T). This will allow users of the method to optimally balance performance and accuracy.

Molecular Theory of Detonation Initiation: Insight from First Principles Modeling of the Decomposition Mechanisms of Organic Nitro Energetic Materials

This review presents a concept, which assumes that thermal decomposition processes play a major role in defining the sensitivity of organic energetic materials to detonation initiation. As a science and engineering community we are still far away from having a comprehensive molecular detonation initiation theory in a widely agreed upon form. However, recent advances in experimental and theoretical methods allow for a constructive and rigorous approach to design and test the theory or at least some of its fundamental building blocks. In this review, we analyzed a set of select experimental and theoretical articles, which were augmented by our own first principles modeling and simulations, to reveal new trends in energetic materials and to refine known existing correlations between their structures, properties, and functions. Our consideration is intentionally limited to the processes of thermally stimulated chemical reactions at the earliest stage of decomposition of molecules and materials containing defects.

Development of Semiempirical Models for Proton Transfer Reactions in Water

This letter presents a method for the parametrization of semiempirical models for proton transfer reactions in water clusters. Two new models are developed: AM1-W, which is a reparameterization of the classic AM1 model, and AM1PG-W, which is a modified AM1-like model including a pairwise correction to the core repulsion function. Both models show good performance on hydrogen-bonding energies and on proton transfer energy profiles, which are of great importance for proton transfer reactions in large water clusters and in proteins. The parametrization method introduced is general and can be used to develop any other system-specific semiempirical models.

A computational mechanistic study of pH-dependent alcohol dehydrogenation catalyzed by a novel [C,N] or [C,C] cyclometalated Cp*Ir complex in aqueous solution

Our results have elucidated the impressive performance of a catalyst in alcohol dehydrogenation in aqueous solution by tuning the pH value.

Quantum mechanical force field for water with explicit electronic polarization

A quantum mechanical force field (QMFF) for water is described. Unlike traditional approaches that use quantum mechanical results and experimental data to parameterize empirical potential energy functions, the present QMFF uses a quantum mechanical framework to represent intramolecular and intermolecular interactions in an entire condensed-phase system. In particular, the internal energy terms used in molecular mechanics are replaced by a quantum mechanical formalism that naturally includes electronic polarization due to intermolecular interactions and its effects on the force constants of the intramolecular force field. As a quantum mechanical force field, both intermolecular interactions and the Hamiltonian describing the individual molecular fragments can be parameterized to strive for accuracy and computational efficiency. In this work, we introduce a polarizable molecular orbital model Hamiltonian for water and for oxygen- and hydrogen-containing compounds, whereas the electrostatic potential responsible for intermolecular interactions in the liquid and in solution is modeled by a three-point charge representation that realistically reproduces the total molecular dipole moment and the local hybridization contributions. The present QMFF for water, which is called the XP3P (explicit polarization with three-point-charge potential) model, is suitable for modeling both gas-phase clusters and liquid water. The paper demonstrates the performance of the XP3P model for water and proton clusters and the properties of the pure liquid from about 900 × 10(6) self-consistent-field calculations on a periodic system consisting of 267 water molecules. The unusual dipole derivative behavior of water, which is incorrectly modeled in molecular mechanics, is naturally reproduced as a result of an electronic structural treatment of chemical bonding by XP3P. We anticipate that the XP3P model will be useful for studying proton transport in solution and solid phases as well as across biological ion channels through membranes.

Investigation of simple and water assisted tautomerism in a derivative of 1,3,4-oxadiazole: a DFT study

Investigation of tautomerism and transition states in a derivative of 1,3,4-oxadiazole (A, B, C and D) in the gas phase and in solution and in a micro hydrated environment with 1-3 water molecules was performed by calculations at the DFT-B3LYP/6-311++G(d,p) level of theory. The solvent effect is taken into account via the self-consistent reaction field (SCRF) method. The geometries of four possible tautomers of 5-amino-1,3,4-oxadiazole-2(3H)-one were optimized in the gas phase and solution with polarized continuum model (PCM). It was found that in the gas phase and different solvents, A and C tautomers are the most stable and unstable forms, respectively. The results show that the tautomeric interconversion C to D has the lowest Gibbs free energy changes and so the highest equilibrium constant in the gas phase and solution. The equilibrium and rate constants of intermolecular tautomerism in the absence and presence of 1-3 molecules of water were also calculated. The calculated results show that the presence of water molecules considerably reduces the barrier energy of the various reactions. Therefore, this water-assisted tautomerism can be performed fast, especially, with the assistance of two molecules of water.

Assessing the Accuracy of Density Functional and Semiempirical Wave Function Methods for Water Nanoparticles: Comparing Binding and Relative Energies of (H2O)16 and (H2O)17 to CCSD(T) Results

The binding energies and relative conformational energies of five configurations of the water 16-mer are computed using 61 levels of density functional (DF) theory, 12 methods combining DF theory with molecular mechanics damped dispersion (DF-MM), seven semiempirical-wave function (SWF) methods, and five methods combining SWF theory with molecular mechanics damped dispersion (SWF-MM). The accuracies of the computed energies are assessed by comparing them to recent high-level ab initio results; this assessment is more relevant to bulk water than previous tests on small clusters because a 16-mer is large enough to have water molecules that participate in more than three hydrogen bonds. We find that for water 16-mer binding energies the best DF, DF-MM, SWF, and SWF-MM methods (and their mean unsigned errors in kcal/mol) are respectively M06-2X (1.6), ωB97X-D (2.3), SCC-DFTB-γ(h) (35.2), and PM3-D (3.2). We also mention the good performance of CAM-B3LYP (1.8), M05-2X (1.9), and TPSSLYP (3.0). In contrast, for relative energies of various water nanoparticle 16-mer structures, the best methods (and mean unsigned errors in kcal/mol), in the same order of classes of methods, are SOGGA11-X (0.3), ωB97X-D (0.2), PM6 (0.4), and PMOv1 (0.6). We also mention the good performance of LC-ωPBE-D3 (0.3) and ωB97X (0.4). When both relative and binding energies are taken into consideration, the best methods overall (out of the 85 tested) are M05-2X without molecular mechanics and ωB97X-D when molecular mechanics corrections are included; with considerably higher average errors and considerably lower cost, the best SWF or SWF-MM method is PMOv1. We use six of the best methods for binding energies of the water 16-mers to calculate the binding energies of water hexamers and water 17-mers to test whether these methods are also reliable for binding energy calculations on other types of water clusters.

Optimization of parameters for semiempirical methods VI: more modifications to the NDDO approximations and re-optimization of parameters

Modern semiempirical methods are of sufficient accuracy when used in the modeling of molecules of the same type as used as reference data in the parameterization. Outside that subset, however, there is an abundance of evidence that these methods are of very limited utility. In an attempt to expand the range of applicability, a new method called PM7 has been developed. PM7 was parameterized using experimental and high-level ab initio reference data, augmented by a new type of reference data intended to better define the structure of parameter space. The resulting method was tested by modeling crystal structures and heats of formation of solids. Two changes were made to the set of approximations: a modification was made to improve the description of noncovalent interactions, and two minor errors in the NDDO formalism were rectified. Average unsigned errors (AUEs) in geometry and ΔHf for PM7 were reduced relative to PM6; for simple gas-phase organic systems, the AUE in bond lengths decreased by about 5% and the AUE in ΔHf decreased by about 10%; for organic solids, the AUE in ΔHf dropped by 60% and the reduction was 33.3% for geometries. A two-step process (PM7-TS) for calculating the heights of activation barriers has been developed. Using PM7-TS, the AUE in the barrier heights for simple organic reactions was decreased from values of 12.6 kcal/mol(-1) in PM6 and 10.8 kcal/mol(-1) in PM7 to 3.8 kcal/mol(-1). The origins of the errors in NDDO methods have been examined, and were found to be attributable to inadequate and inaccurate reference data. This conclusion provides insight into how these methods can be improved.

DFT and Proton Transfer Reactions: A Benchmark Study on Structure and Kinetics

A significant number of different exchange correlation functionals, ranging from generalized gradient approximations to double hybrids, has been tested on a difficult playground represented by proton transfer reactions. In order to have a complete picture of their performances, both energetics and structural features have been compared and the obtained ranking compared with those issued from the standard test for kinetics (i.e., the DBH24/08 set). Among all of the functionals, the ωB97X, BMK, B1LYP, and PBE0-DH approaches are those providing a good error balance on all four trials. Beyond these figures, the obtained results allow for some general considerations, such as those on the role of Hartree-Fock exchange in reaction barriers or the relation between structure and energetics.