Systematic QM Region Construction in QM/MM Calculations Based on Uncertainty Quantification

While QM/MM studies of enzymatic reactions are widely used in computational chemistry, the results of such studies are subject to numerous sources of uncertainty, and the effect of different choices by the simulation scientist that are required when setting up QM/MM calculations is often unclear. In particular, the selection of the QM region is crucial for obtaining accurate and reliable results. Simply including amino acids by their distance to the active site is mostly not sufficient as necessary residues are missing or unimportant residues are included without evidence. Here, we take a first step towards quantifying uncertainties in QM/MM calculations by assessing the sensitivity of QM/MM reaction energies with respect to variations of the MM point charges. We show that such a point charge variation analysis (PCVA) can be employed to judge the accuracy of QM/MM reaction energies obtained with a selected QM region, and devise a protocol to systematically construct QM regions that minimize this uncertainty. We apply such a PCVA to the example of catechol \textit{O}-methyltransferase, and demonstrate that it provides a simple and reliable approach for the construction of the QM region. Our PCVA-based scheme is computationally efficient and requires only calculations for a system with a minimal QM region. Our work highlights the promise of applying methods of uncertainty quantification in computational chemistry.

Fast and automated identification of reactions with low barriers using meta-MD simulations

We test our meta-molecular dynamics (MD) based approach for finding low-barrier (<30 kcal/mol) reactions (SciPost Chem. 2021, 1, 003) on uni- and bimolecular reactions extracted from the barrier dataset developed by Grambow et al. (Scientific Data 2020, 7, 137). For unimolecular reactions the meta-MD simulations identify 25 of the 26 products found by Grambow et al., while the subsequent semiempirical screening eliminates an additional four reactions due to at an overestimation of the reaction energies or estimated barrier heights relative to DFT. In addition, our approach identifies an additional 36 reactions not found by Grambow et al., 10 of which are <30 kcal/mol. For bimolecular reactions the meta-MD simulations identify 19 of the 20 reactions found by Grambow et al., while the subsequent semiempirical screening eliminates an additional reaction. In addition, we find 34 new low-barrier reactions. For bimolecular reactions we found that it is necessary to ”encourage” the reactants to go to previously undiscovered products, by including products found by other MD simulations when computing the biasing potential as well as decreasing the size of the molecular cavity in which the MD occurs, until a reaction is observed. We also show that our methodology can find the correct products for two reactions that are more representative of those encountered in synthetic organic chemistry. The meta-MD hyperparameters used in this study thus appears to be generally applicable to finding low-barrier reactions.

Spin-component-scaled and dispersion-corrected second-order Møller-Plesset perturbation theory: A path toward chemical accuracy

Second-order Møller-Plesset perturbation theory (MP2) provides a valuable alternative to density functional theory for modeing problems in organic and biological chemistry. However, MP2 suffers from known lim- itations in the description of van der Waals dispersion interactions and reaction thermochemistry. Here, a spin-component-scaled, dispersion-corrected MP2 model (SCS-MP2D) is proposed that addresses these weaknesses. The dispersion correction, which is based on Grimme’s D3 formalism, replaces the uncoupled Hartree-Fock dispersion inherent in MP2 with a more robust coupled Kohn-Sham treatment. The spin- component scaling of the residual MP2 correlation energy then reduces the remaining errors in the model. This two-part correction strategy solves the problem found in earlier spin-component-scaled MP2 models where completely different spin-scaling parameters were needed for describing reaction energies versus in- termolecular interactions. Results on 18 benchmark data sets and two challenging potential energy curves demonstrate that SCS-MP2D considerably improves upon the accuracy of MP2 for intermolecular interac- tions, conformational energies, and reaction energies. Its accuracy and computational cost are competitive with state-of-the-art density functionals such as DSD-BLYP-D3(BJ), revDSD-PBEP86-D3(BJ), ωB97X-V, and ωB97M-V for systems with ∼100 atoms.

Systematic QM Region Construction in QM/MM Calculations Based on Uncertainty Quantification

While QM/MM studies of enzymatic reactions are widely used in computational chemistry, the results of such studies are subject to numerous sources of uncertainty, and the effect of different choices by the simulation scientist that are required when setting up QM/MM calculations is often unclear. In particular, the selection of the QM region is crucial for obtaining accurate and reliable results. Simply including amino acids by their distance to the active site is mostly not sufficient as necessary residues are missing or unimportant residues are included without evidence. Here, we take a first step towards quantifying uncertainties in QM/MM calculations by assessing the sensitivity of QM/MM reaction energies with respect to variations of the MM point charges. We show that such a point charge variation analysis (PCVA) can be employed to judge the accuracy of QM/MM reaction energies obtained with a selected QM region, and devise a protocol to systematically construct QM regions that minimize this uncertainty. We apply such a PCVA to the example of catechol \textit{O}-methyltransferase, and demonstrate that it provides a simple and reliable approach for the construction of the QM region. Our PCVA-based scheme is computationally efficient and requires only calculations for a system with a minimal QM region. Our work highlights the promise of applying methods of uncertainty quantification in computational chemistry.

Quantum Mechanistic Studies of the Oxidation of Ethylene by Rhenium Oxo Complexes

Transition-metal-mediated oxygen transfer reactions are of importance in both industry and academia; thus, a series of rhenium oxo complexes of the type ReO3L (L = O−, Cl−, F−, OH−, Br−, I−) and their effects as oxidation catalysts on ethylene have been studied. The activation and reaction energies for the addition pathways involving multiple spin states (singlet and triplet) have been computed. In all cases, structures on the singlet potential energy surfaces showed higher stability compared to their counterparts on the triplet potential energy surfaces (PESs). Frontier Molecular Orbital calculations show electrons flow from the HOMO of ethylene to the LUMO of rhenium for all complexes studied except ReO4− where the reverse case occurs. In the reaction between ReO3L (L = O−, Cl−, F−, OH−, Br−, and I−) and ethylene, the concerted [3 + 2] addition pathway on the singlet PES leading to the formation of dioxylate intermediate is favored over the [2 + 2] addition pathway leading to the formation of a metallaoxetane intermediate and subsequent rearrangement to the dioxylate. The activation and the reaction energies for the formation of the dioxylate on the singlet PES for the ligands studied followed the order O− > OH− > I− > F− > Br− > Cl− and O− > OH− > F− > I− > Br− > Cl−, respectively. Furthermore, the activation and the reaction energies for the formation of the metallaoxetane intermediate increase in the order O− > OH− > I− > Br− > Cl− > F− and O− > Br− > I− > Cl− > OH− > F−, respectively. The subsequent rearrangement of the metallaoxetane intermediate to the dioxylate is only feasible in the case of ReO4−. Of all the complexes studied, the best dioxylating catalyst is ReO3Cl (singlet surface) and the best epoxidation catalyst is ReO3F (singlet surface).

Computational Design of New N-Heterocyclic Silyl Pincer Fullerenes

A density functional study was performed to design a new N‑heterocyclic silyl pincer fullerenes based on the reactions of diaminofullerene with chlorosilanes SiHRCl2. Reaction energies of the formation of pincer fullerene ligands increased through the substitution of flanking arms with CH3 and phenyl groups. However, substituting hydrogen of SiH2 with methyl slightly increased the corresponding reaction energies, replacing of hydrogen with phenyl groups decreased the reaction energies of the considered pincer fullerenes. While the calculated electrophilicity values of the pincer fullerenes are larger than the electrophilicity values obtained for the fullerene derivatives, the substitution of hydrogen atoms of central SiH2 and PH2 did not have a noticeable impact on the electrophilicity values of the pincer fullerenes. The only exception was SiHPh(NCH2PH2)2C60. Natural bonding orbital analysis showed that the delocalization of electrons from the lone pairs of flanking arms phosphorous atoms to the n* orbital of transition metal atoms was a key factor for stabilizing the considered complexes. The strongest interaction was due to the delocalization of electrons from lone pairs of phosphorous atoms in the flanking arms to the LP* of transition metals, which was follow by the delocalization of electrons of the Si-H σ* orbitals to the LP* of transition metals.

Mechanistic insights into α-branched amines formation with pivalic acid assisted C−H bond activation catalysed by Cp*Rh complexes

Density functional theory computations revealed a pivalic acid assisted C−H bond activation mechanism for rhodium catalyzed formation of α-branched amines with C−C and C−N bond couplings. The reaction energies of...