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Abstract In the last several years, there has been a surge in the development of machine learning potential (MLP) models for describing molecular systems. We are interested in a particular area of this field — the training of system‐specific MLPs for reactive systems — with the goal of using these MLPs to accelerate free energy simulations of chemical and enzyme reactions. To help new members in our labs become familiar with the basic techniques, we have put together a self‐guided Colab tutorial (https://cc-ats.github.io/mlp_tutorial/), which we expect to be also useful to other young researchers in the community. Our tutorial begins with the introduction of simple feedforward neural network (FNN) and kernel‐based (using Gaussian process regression, GPR) models by fitting the two‐dimensional Müller‐Brown potential. Subsequently, two simple descriptors are presented for extracting features of molecular systems: symmetry functions (including the ANI variant) and embedding neural networks (such as DeepPot‐SE). Lastly, these features will be fed into FNN and GPR models to reproduce the energies and forces for the molecular configurations in a Claisen rearrangement reaction. 

Abstract Catalysis ofO‐atom transfer (OAT) reactions is a characteristic of both natural (enzymatic) and synthetic molybdenum‐oxo and ‐peroxo complexes. These reactions can employ a variety of terminal oxidants, e. g. DMSO,N‐oxides, and peroxides, etc., but rarely molecular oxygen. Here we demonstrate the ability of a set of Schiff‐base‐MoO₂complexes (cy‐salen)MoO₂(cy‐salen=N,N’‐cyclohexyl‐1,2‐bis‐salicylimine) to catalyze the aerobic oxidation of PPh₃. We also report the results of a DFT computational investigation of the catalytic pathway, including the identification of energetically accessible intermediates and transition states, for the aerobic oxidation of PMe₃. Starting from the dioxo species, (cy‐salen)Mo(VI)O₂(1), key reaction steps include: 1) associative addition of PMe₃to an oxo‐O to give LMo(IV)(O)(OPMe₃) (2); 2) OPMe₃dissociation from2to produce mono‐oxo complex (cy‐salen)Mo(IV)O (3); 3) stepwise O₂association with3via superoxo species (cy‐salen)Mo(V)(O)(η¹‐O₂) (4) to form the oxo‐peroxo intermediate (cy‐salen)Mo(VI)(O)(η²‐O₂) (5); 4) theO‐transfer reaction of PMe₃with oxo‐peroxo species5at the oxo‐group, rather than the peroxo unit leading, after OPMe₃dissociation, to a monoperoxo species, (cy‐salen)Mo(IV)(η²‐O₂) (7); and 5) regeneration of the dioxo complex (cy‐salen)Mo(VI)O₂(1) from the monoperoxo triplet³7or singlet¹7by a concerted, asynchronous electronic isomerization. An alternative pathway for recycling of the oxo‐peroxo species5to the dioxo‐Mo1via a bimetallic peroxo complex LMo(O)‐O−O‐Mo(O)L8is determined to be energetically viable, but is unlikely to be competitive with the primary pathway for aerobic phosphine oxidation catalyzed by1. 

1,2-cis-Furanosides are present in various biomedically relevant glycosides, and their stereoselective synthesis remains a significant challenge. In this vein, we have developed a stereoselective approach to 1,2-cis-furanosylations using earth-abundant copper catalysis. This protocol proceeds under mild conditions at room temperature and employs readily accessible benchtop stable enynalderived furanose donors. This chemistry accommodates a variety of alcohols, including primary, secondary, and tertiary, as well as mannosyl alcohol acceptors, which have been incompatible with most known methods of furanosylation. The resulting 1,2-cisfuranoside products exhibit high yields and anomeric selectivity with both the ribose and arabinose series. Furthermore, the anomeric selectivity is independent of the C2 oxygen-protecting group and the anomeric configuration of the starting donor. Experimental evidence and computational studies support our hypothesis that copper chelation between the C2 oxygen of the furanose donor and an incoming alcohol nucleophile is responsible for the observed 1,2-cisstereoselectivity. 

We derive and implement analytic gradients and derivative couplings for time-dependent density functional theory plus one double (TDDFT-1D) which is a semiempirical configuration interaction method whereby the Hamiltonian is diagonalized in a basis of all singly excited configurations and one doubly excited configuration as constructed from a set of reference Kohn–Sham orbitals. We validate the implementation by comparing against finite difference values. Furthermore, we show that our implementation can locate both optimized geometries and minimum-energy crossing points along conical seams of S1/S0 surfaces for a set of test cases. 

This work is devoted to deriving and implementing analytic second- and third-order energy derivatives with respect to the nuclear coordinates and external electric field within the framework of the hybrid quantum mechanics/molecular mechanics method with induced charges and dipoles (QM/DIM). Using these analytic energy derivatives, one can efficiently compute the harmonic vibrational frequencies, infrared (IR) and Raman scattering (RS) spectra of the molecule in the proximity of noble metal clusters/nanoparticles. The validity and accuracy of these analytic implementations are demonstrated by the comparison of results obtained by the finite-difference method and the analytic approaches and by the full QM and QM/DIM calculations. The complexes formed by pyridine and two sizes of gold clusters (Au18 and Au32) at varying intersystem distances of 3, 4, and 5 Å are used as the test systems, and Raman spectra of 4,4′-bipyridine in the proximity of Au2057 and Ag2057 metal nanoparticles (MNP) are calculated by the QM/DIM method and compared with experimental results as well. We find that the QM/DIM model can well reproduce the IR spectra obtained from full QM calculations for all the configurations, while although it properly enhances some of the vibrational modes, it artificially overestimates RS spectral intensities of several modes for the systems with very short intersystem distance. We show that this could be improved, however, by incorporating the hyperpolarizability of the gold metal cluster in the evaluation of RS intensities. Additionally, we address the potential impact of charge migration between the adsorbate and MNPs.