The Mechanics of the Bicycle Pedal Photoisomerization in Crystalline cis,cis-1,4-Diphenyl-1,3-butadiene

Direct irradiation of crystalline cis,cis-1,4-diphenyl-1,3-butadiene (cc-DPB) forms trans,trans-1,4-diphenyl-1,3,-butadiene via a concerted two-bond isomerization called the bicycle pedal (BP) mechanism. However, little is known about photoisomerization pathways in the solid state and there has been much debate surrounding the interpretation of volume-conserving isomerization mechanisms. The bicycle pedal photoisomerization is investigated using the quantum mechanics/molecular mechanics complete active space self-consistent field/Amber force-field method. Important details about how the steric environment influences isomerization mechanisms are revealed including how the one-bond flip and hula-twist mechanisms are suppressed by the crystal cavity, the nature of the seam space in steric environments, and the features of the bicycle pedal mechanism. Specifically, in the bicycle pedal, the phenyl rings of cc-DPB are locked in place and the intermolecular packing allows a passageway for rotation of the central diene in a volume-conserving manner. In contrast, the bicycle pedal rotation in the gas phase is not a stable pathway, so single-bond rotation mechanisms become operative instead. Furthermore, the crystal BP mechanism is an activated process that occurs completely on the excited state; the photoproduct can decay to the ground state through radiative and non-radiative pathways. The present models, however, do not capture the quantitative activation barriers, and more work is needed to better model reactions in crystals. Last, the reaction barriers of the different crystalline conformations within the unit cell of cc-DPB are compared to investigate the possibility for conformation-dependent isomerization. Although some difference in reaction barriers is observed, the difference is most likely not responsible for the experimentally observed periods of fast and slow conversion.

Exploring the Mechanism of Catalysis with the Unified Reaction Valley Approach (URVA)—A Review

The unified reaction valley approach (URVA) differs from mainstream mechanistic studies, as it describes a chemical reaction via the reaction path and the surrounding reaction valley on the potential energy surface from the van der Waals region to the transition state and far out into the exit channel, where the products are located. The key feature of URVA is the focus on the curving of the reaction path. Moving along the reaction path, any electronic structure change of the reacting molecules is registered by a change in their normal vibrational modes and their coupling with the path, which recovers the curvature of the reaction path. This leads to a unique curvature profile for each chemical reaction with curvature minima reflecting minimal change and curvature maxima, the location of important chemical events such as bond breaking/forming, charge polarization and transfer, rehybridization, etc. A unique decomposition of the path curvature into internal coordinate components provides comprehensive insights into the origins of the chemical changes taking place. After presenting the theoretical background of URVA, we discuss its application to four diverse catalytic processes: (i) the Rh catalyzed methanol carbonylation—the Monsanto process; (ii) the Sharpless epoxidation of allylic alcohols—transition to heterogenous catalysis; (iii) Au(I) assisted [3,3]-sigmatropic rearrangement of allyl acetate; and (iv) the Bacillus subtilis chorismate mutase catalyzed Claisen rearrangement—and show how URVA leads to a new protocol for fine-tuning of existing catalysts and the design of new efficient and eco-friendly catalysts. At the end of this article the pURVA software is introduced. The overall goal of this article is to introduce to the chemical community a new protocol for fine-tuning existing catalytic reactions while aiding in the design of modern and environmentally friendly catalysts.

Toward Simple, Predictive Understanding of Protein-Ligand Interactions: Electronic Structure Calculations on Torpedo Californica Acetylcholinesterase Join Forces with the Chemist's Intuition

Contemporary efforts for empirically-unbiased modeling of protein-ligand interactions entail a painful tradeoff - as reliable information on both noncovalent binding factors and the dynamic behavior of a protein-ligand complex is often beyond practical limits. We demonstrate that information drawn exclusively from static molecular structures can be used for reproducing and predicting experimentally-measured binding affinities for protein-ligand complexes. In particular, inhibition constants (Ki) were calculated for seven different competitive inhibitors of Torpedo californica acetylcholinesterase using a multiple-linear-regression-based model. The latter, incorporating five independent variables - drawn from QM cluster, DLPNO-CCSD(T) calculations and LED analyses on the seven complexes, each containing active amino-acid residues found within interacting distance (3.5 Å) from the corresponding ligand - is shown to recover 99.9% of the sum of squares for measured Ki values, while having no statistically-significant residual errors. Despite being fitted to a small number of data points, leave-one-out cross-validation statistics suggest that it possesses surprising predictive value (Q2LOO=0.78, or 0.91 upon removal of a single outlier). This thus challenges ligand-invariant definitions of active sites, such as implied in the lock-key binding theory, as well as in alternatives highlighting shape-complementarity without taking electronic effects into account. Broader implications of the current work are discussed in dedicated appendices.

Reactants, products, and transition states of elementary chemical reactions based on quantum chemistry

Reaction times, activation energies, branching ratios, yields, and many other quantitative attributes are important for precise organic syntheses and generating detailed reaction mechanisms. Often, it would be useful to be able to classify proposed reactions as fast or slow. However, quantitative chemical reaction data, especially for atom-mapped reactions, are difficult to find in existing databases. Therefore, we used automated potential energy surface exploration to generate 12,000 organic reactions involving H, C, N, and O atoms calculated at the ωB97X-D3/def2-TZVP quantum chemistry level. We report the results of geometry optimizations and frequency calculations for reactants, products, and transition states of all reactions. Additionally, we extracted atom-mapped reaction SMILES, activation energies, and enthalpies of reaction. We believe that this data will accelerate progress in automated methods for organic synthesis and reaction mechanism generation—for example, by enabling the development of novel machine learning models for quantitative reaction prediction.

Measurement(s)	activation energy • Standard Transformed Enthalpy Change • transition state • reactant • reaction product • chemical reaction • SMILES string
Technology Type(s)	quantum chemistry computational method

Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.12047193

The Exploration of Chemical Reaction Networks

Modern computational chemistry has reached a stage at which massive exploration into chemical reaction space with unprecedented resolution with respect to the number of potentially relevant molecular structures has become possible. Various algorithmic advances have shown that such structural screenings must and can be automated and routinely carried out. This will replace the standard approach of manually studying a selected and restricted number of molecular structures for a chemical mechanism. The complexity of the task has led to many different approaches. However, all of them address the same general target, namely to produce a complete atomistic picture of the kinetics of a chemical process. It is the purpose of this overview to categorize the problems that should be targeted and to identify the principal components and challenges of automated exploration machines so that the various existing approaches and future developments can be compared based on well-defined conceptual principles.

What Does the Machine Learn? Knowledge Representations of Chemical Reactivity

In a departure from conventional chemical approaches, data-driven models of chemical reactions have recently been shown to be statistically successful using machine learning. These models, however, are largely black box in character and have not provided the kind of chemical insights that historically advanced the field of chemistry. To examine the knowledgebase of machine-learning models-what does the machine learn-this article deconstructs black-box machine-learning models of a diverse chemical reaction data set. Through experimentation with chemical representations and modeling techniques, the analysis provides insights into the nature of how statistical accuracy can arise, even when the model lacks informative physical principles. By peeling back the layers of these complicated models we arrive at a minimal, chemically intuitive model (and no machine learning involved). This model is based on systematic reaction-type classification and Evans-Polanyi relationships within reaction types which are easily visualized and interpreted. Through exploring this simple model, we gain deeper understanding of the data set and uncover a means for expert interactions to improve the model's reliability.

Systematic microsolvation approach with a cluster-continuum scheme and conformational sampling

Solvation is a notoriously difficult and nagging problem for the rigorous theoretical description of chemistry in the liquid phase. Successes and failures of various approaches ranging from implicit solvation modeling through dielectric continuum embedding and microsolvated quantum chemical modeling to explicit molecular dynamics highlight this situation. Here, we focus on quantum chemical microsolvation and discuss an explicit conformational sampling ansatz to make this approach systematic. For this purpose, we introduce an algorithm for rolling and automated microsolvation of solutes. Our protocol takes conformational sampling and rearrangements in the solvent shell into account. Its reliability is assessed by monitoring the evolution of the spread and average of the observables of interest.

Photoinduced Phase Transitions in Ferroelectrics

Ferroic materials naturally exhibit a rich number of functionalities, which often arise from thermally, chemically, or mechanically induced symmetry breakings or phase transitions. Based on density functional calculations, we demonstrate here that light can drive phase transitions as well in ferroelectric materials such as the perovskite oxides lead titanate and barium titanate. Phonon analysis and total energy calculations reveal that the polarization tends to vanish under illumination, to favor the emergence of nonpolar phases, potentially antiferroelectric, and exhibiting a tilt of the oxygen octahedra. Strategies to tailor photoinduced phases based on phonon instabilities in the electronic ground state are also discussed.

Exploration of Chemical Compound, Conformer, and Reaction Space with Meta-Dynamics Simulations Based on Tight-Binding Quantum Chemical Calculations

The semiempirical tight-binding based quantum chemistry method GFN2-xTB is used in the framework of meta-dynamics (MTD) to globally explore chemical compound, conformer, and reaction space. The biasing potential given as a sum of Gaussian functions is expressed with the root-mean-square-deviation (RMSD) in Cartesian space as a metric for the collective variables. This choice makes the approach robust and generally applicable to three common problems (i.e., conformer search, chemical reaction space exploration in a virtual nanoreactor, and for guessing reaction paths). Because of the inherent locality of the atomic RMSD, functional group or fragment selective treatments are possible facilitating the investigation of catalytic processes where, for example, only the substrate is thermally activated. Due to the approximate character of the GFN2-xTB method, the resulting structure ensembles require further refinement with more sophisticated, for example, density functional or wave function theory methods. However, the approach is extremely efficient running routinely on common laptop computers in minutes to hours of computation time even for realistically sized molecules with a few hundred atoms. Furthermore, the underlying potential energy surface for molecules containing almost all elements ( Z = 1-86) is globally consistent including the covalent dissociation process and electronically complicated situations in, for example, transition metal systems. As examples, thermal decomposition, ethyne oligomerization, the oxidation of hydrocarbons (by oxygen and a P450 enzyme model), a Miller-Urey model system, a thermally forbidden dimerization, and a multistep intramolecular cyclization reaction are shown. For typical conformational search problems of organic drug molecules, the new MTD(RMSD) algorithm yields lower energy structures and more complete conformer ensembles at reduced computational effort compared with its already well performing predecessor.

Computational Approach to Molecular Catalysis by 3d Transition Metals: Challenges and Opportunities

Computational chemistry provides a versatile toolbox for studying mechanistic details of catalytic reactions and holds promise to deliver practical strategies to enable the rational in silico catalyst design. The versatile reactivity and nontrivial electronic structure effects, common for systems based on 3d transition metals, introduce additional complexity that may represent a particular challenge to the standard computational strategies. In this review, we discuss the challenges and capabilities of modern electronic structure methods for studying the reaction mechanisms promoted by 3d transition metal molecular catalysts. Particular focus will be placed on the ways of addressing the multiconfigurational problem in electronic structure calculations and the role of expert bias in the practical utilization of the available methods. The development of density functionals designed to address transition metals is also discussed. Special emphasis is placed on the methods that account for solvation effects and the multicomponent nature of practical catalytic systems. This is followed by an overview of recent computational studies addressing the mechanistic complexity of catalytic processes by molecular catalysts based on 3d metals. Cases that involve noninnocent ligands, multicomponent reaction systems, metal-ligand and metal-metal cooperativity, as well as modeling complex catalytic systems such as metal-organic frameworks are presented. Conventionally, computational studies on catalytic mechanisms are heavily dependent on the chemical intuition and expert input of the researcher. Recent developments in advanced automated methods for reaction path analysis hold promise for eliminating such human-bias from computational catalysis studies. A brief overview of these approaches is presented in the final section of the review. The paper is closed with general concluding remarks.

A Trajectory-Based Method to Explore Reaction Mechanisms

The tsscds method, recently developed in our group, discovers chemical reaction mechanisms with minimal human intervention. It employs accelerated molecular dynamics, spectral graph theory, statistical rate theory and stochastic simulations to uncover chemical reaction paths and to solve the kinetics at the experimental conditions. In the present review, its application to solve mechanistic/kinetics problems in different research areas will be presented. Examples will be given of reactions involved in photodissociation dynamics, mass spectrometry, combustion chemistry and organometallic catalysis. Some planned improvements will also be described.

Globally Optimal Catalytic Fields - Inverse Design of Abstract Embeddings for Maximum Reaction Rate Acceleration

The search for, and understanding of, good catalysts for chemical reactions is a central issue for chemists. Here, we present first steps toward developing a general computational framework to better support this task. This framework combines efficient, unbiased global optimization techniques with an abstract representation of the catalytic environment, to shrink the search space. To analyze the resulting catalytic embeddings, we employ dimensionality reduction and clustering techniques. This not only provides an inverse design approach to new catalytic embeddings but also illuminates the actual interactions behind catalytic effects. All this is illustrated here with a strictly electrostatic model for the environment and with two versions of a selected example reaction. We close with detailed discussions of future improvements of our framework.

Automated reaction path searches for spin-forbidden reactions

Many catalytic and biomolecular reactions containing transition metals involve changes in the electronic spin state. These processes are referred to as "spin-forbidden" reactions within nonrelativistic quantum mechanics framework. To understand detailed reaction mechanisms of spin-forbidden reactions, one must characterize reaction pathways on potential energy surfaces with different spin states and then identify crossing points. Here we propose a practical computational scheme, where only the lowest mixed-spin eigenstate obtained from the diagonalization of the spin-coupled Hamiltonian matrix is used in reaction path search calculations. We applied this method to the ^6,4 FeO⁺  + H₂ → ^6,4 Fe⁺  + H₂ O, ^6,4 FeO⁺  + CH₄ → ^6,4 Fe⁺  + CH₃ OH, and ⁷ Mn⁺  + OCS → ⁵ MnS⁺  + CO reactions, for which crossings between the different spin states are known to play essential roles in the overall reaction kinetics. © 2018 Wiley Periodicals, Inc.