Rapid Route-Finding for Bifurcating Organic Reactions.

A large number of organic reactions feature post-transition-state bifurcations. Selectivities in such reactions are difficult to analyze because they cannot be determined by comparing the energies of competing transition states. Molecular dynamics approaches can provide answers but are computationally very expensive. We present an algorithm that predicts the major products in bifurcating organic reactions with negligible computational cost. The method requires two transition states, two product geometries, and no additional information. The algorithm correctly predicts the major product for about 90% of the organic reactions investigated. For the remaining 10% of the reactions, the algorithm returns a warning indication that the conclusion may be uncertain. The method also reproduces the experimental and the molecular dynamics product ratios within 15% for more than 80% of the reactions. We have successfully applied the method to a trifurcating organic reaction, a carbocation rearrangement, and solvent-dependent Pummerer-like reactions, demonstrating the power of the algorithm to simplify and to help understand highly complex reactions.Trinity College, University of Cambridge Cambridge Service for Data Driven Discovery (CSD3) operated by the University of Cambridge Research Computing Service (www.csd3.cam.ac.uk), provided by Dell EMC and Intel using Tier-2 funding from the Engineering and Physical Sciences Research Council (capital grant EP/P020259/1

Asymmetric boronate addition to o-quinone methides: ligand exchange, solvent effects, and Lewis acid catalysis.

Density functional theory calculations suggest that asymmetric boronate addition to o-quinone methides proceeds via a Lewis acid catalyzed process through a closed six-membered transition structure. The BINOL-derived catalyst undergoes an exchange process with the original ethoxide boronate ligands. This activation mode successfully accounts for the sense and level of enantioselectivity observed experimentally. A qualitative model which accurately predicts the observed enantioselectivity has been developed and is consistent with results from our study of ketone propargylation demonstrating the reaction model's generality. The effects of replacing the BINOL framework with H8-BINOL have been rationalized.We thank Girton College, Cambridge (Research Fellowship to M.N.G.), the EPSRC (studentship to M.N.G.), and Unilever for support.This is the final published version. It first appeared at http://pubs.acs.org/doi/abs/10.1021/jo502616a

Goldilocks Catalysts: Computational Insights into the Role of the 3,3' Substituents on the Selectivity of BINOL-Derived Phosphoric Acid Catalysts.

BINOL-derived phosphoric acids provide effective asymmetric catalysis for many organic reactions. Catalysts based on this scaffold show a large structural diversity, especially in the 3,3' substituents, and little is known about the molecular requirements for high selectivity. As a result, selection of the best catalyst for a particular transformation requires a trial and error screening process, as the size of the 3,3' substituents is not simply related to their efficacy: the right choice is neither too large nor too small. We have developed an approach to identify and quantify structural features on the catalyst that determine selectivity. We show that the application of quantitative steric parameters (a new measure, AREA(θ), and rotation barrier) to an imine hydrogenation reaction allows the identification of catalyst features necessary for efficient stereoinduction, validated by QM/MM hybrid calculations.We thank EPSRC for funding.This is the final version of the article. It first appeared from the American Chemical Society via https://doi.org/ 10.1021/jacs.6b0282

A Practical Guide for Predicting the Stereochemistry of Bifunctional Phosphoric Acid Catalyzed Reactions of Imines.

Chiral phosphoric acids have become powerful catalysts for the stereocontrolled synthesis of a diverse array of organic compounds. Since the initial report, the development of phosphoric acids as catalysts has been rapid, demonstrating the tremendous generality of this catalyst system and advancing the use of phosphoric acids to catalyze a broad range of asymmetric transformations ranging from Mannich reactions to hydrogenations through complementary modes of activation. These powerful applications have been developed without a clear mechanistic understanding of the reasons for the high level of stereocontrol. This Account describes investigations into the mechanism of the phosphoric acid catalyzed addition of nucleophiles to imines, focusing on binaphthol-based systems. In many cases, the hydroxyl phosphoric acid can form a hydrogen bond to the imine while the P═O interacts with the nucleophile. The single catalyst, therefore, activates both the electrophile and the nucleophile, while holding both in the chiral pocket created by the binaphthol and constrained by substituents at the 3 and 3' positions. Detailed geometric and energetic information about the transition states can be gained from calculations using ONIOM methods that combine the advantages of DFT with some of the speed of force fields. These high-level calculations give a quantitative account of the selectivity in many cases, but require substantial computational resources. A simple qualitative model is a useful complement to this complex quantitative model. We summarize our calculations into a working model that can readily be sketched by hand and used to work out the likely sense of selectivity for each reaction. The steric demands of the different parts of the reactants determine how they fit into the chiral cavity and which of the competing pathways is favored. The preferred pathway can be found by considering the size of the substituents on the nitrogen and carbon atoms of the imine electrophile, and the position of the nucleophilic site on the nucleophile in relation to the hydrogen-bond which holds it in the catalyst active site. We present a guide to defining the pathway in operation allowing the fast and easy prediction of the stereochemical outcome and provide an overview of the breadth of reactions that can be explained by these models including the latest examples.We are grateful to the EPSRC for a DTA award (J.P.R.).This is the author final version of the article. It first appeared from the American Chemical Society via http://dx.doi.org/10.1021/acs.accounts.6b0005

International chemical identifier for reactions (RInChI).

The IUPAC International Chemical Identifier (InChI) provides a method to generate a unique text descriptor of molecular structures. Building on this work, we report a process to generate a unique text descriptor for reactions, RInChI. By carefully selecting the information that is included and by ordering the data carefully, different scientists studying the same reaction should produce the same RInChI. If differences arise, these are most likely the minor layers of the InChI, and so may be readily handled. RInChI provides a concise description of the key data in a chemical reaction, and will help enable the rapid searching and analysis of reaction databases

BINOPtimal: a web tool for optimal chiral phosphoric acid catalyst selection.

A catalyst selection program, BINOPtimal, has been developed. This interactive web tool selects the best performing chiral phosphoric acid catalysts from analysis of the starting materials, imine and nucleophile, on the basis of rules derived from the transformations within its database. This procedure has been applied to an example transformation demonstrating the potential to assist reaction design. The tool is available at www-mmm.ch.cam.ac.uk.EPSRC Leverhulme Isaac Newton trus

Mechanistic insights into a BINOL-derived phosphoric acid-catalyzed asymmetric Pictet-Spengler reaction.

The reaction of tryptamine and (2-oxocyclohexyl)acetic acid can be catalyzed by 3,3'-bis(triphenylsilyl)-1,1'-bi-2-naphthol phosphoric acid to give an asymmetric β-carboline. This reaction was first studied by Holloway et al. ( Org. Lett. 2010 , 12 , 4720 - 4723 ), but their mechanistic work did not explain the high stereoselectivity achieved. This study uses density functional theory and hybrid quantum mechanics/molecular mechanics calculations to investigate this reaction and provide a model to explain its outcome. The step leading to diastereo- and enantioselectivity is an asymmetric Pictet-Spengler reaction involving an N-acyliminium ion bound to the catalyst in a bidentate fashion. This interaction occurs via hydrogen bonds between the two terminal oxygen atoms of the catalyst phosphate group and the hydrogen atoms at N and C2 of the substrate indole group. These bonds hold the transition structure rigidly and thus allow the catalyst triphenylsilyl groups to influence the enantioselectivity.We thank Girton College, Cambridge (research fellowship to M.N.G.), the EPSRC (studentship to M.N.G.), and Unilever for support.The is the final published version. It first appeared at http://pubs.acs.org/doi/abs/10.1021/jo5028134

International chemical identifier for reactions (RInChI).

The Reaction InChI (RInChI) extends the idea of the InChI, which provides a unique descriptor of molecular structures, towards reactions. Prototype versions of the RInChI have been available since 2011. The first official release (RInChI-V1.00), funded by the InChI Trust, is now available for download ( http://www.inchi-trust.org/downloads/ ). This release defines the format and generates hashed representations (RInChIKeys) suitable for database and web operations. The RInChI provides a concise description of the key data in chemical processes, and facilitates the manipulation and analysis of reaction data

Hunting Galaxies to (and for) Extinction

In studies of star-forming regions, near-infrared excess (NIRX) sources--objects with intrinsic colors redder than normal stars--constitute both signal (young stars) and noise (e.g. background galaxies). We hunt down (identify) galaxies using near-infrared observations in the Perseus star-forming region by combining structural information, colors, and number density estimates. Galaxies at moderate redshifts (z = 0.1 - 0.5) have colors similar to young stellar objects (YSOs) at both near- and mid-infrared (e.g. Spitzer) wavelengths, which limits our ability to identify YSOs from colors alone. Structural information from high-quality near-infrared observations allows us to better separate YSOs from galaxies, rejecting 2/5 of the YSO candidates identified from Spitzer observations of our regions and potentially extending the YSO luminosity function below K of 15 magnitudes where galaxy contamination dominates. Once they are identified we use galaxies as valuable extra signal for making extinction maps of molecular clouds. Our new iterative procedure: the Galaxies Near Infrared Color Excess method Revisited (GNICER), uses the mean colors of galaxies as a function of magnitude to include them in extinction maps in an unbiased way. GNICER increases the number of background sources used to probe the structure of a cloud, decreasing the noise and increasing the resolution of extinction maps made far from the galactic plane.Comment: 16 pages and 16 figures. Accepted for publication in ApJ. Full resolution version at http://www.cfa.harvard.edu/COMPLETE/papers/Foster_HuntingGalaxies.pd

Expanding DP4: application to drug compounds and automation.

The DP4 parameter, which provides a confidence level for NMR assignment, has been widely used to help assign the structures of many stereochemically-rich molecules. We present an improved version of the procedure, which can be downloaded as Python script instead of running within a web-browser, and which analyses output from open-source molecular modelling programs (TINKER and NWChem) in addition to being able to use output from commercial packages (Schrodinger's Macromodel and Jaguar; Gaussian). The new open-source workflow incorporates a method for the automatic generation of diastereomers using InChI strings and has been tested on a range of new structures. This improved workflow permits the rapid and convenient computational elucidation of structure and relative stereochemistry.The authors wish to thank Medivir for the generous financial support.This is the final version of the article. It first appeared from the Royal Society of Chemistry via https://doi.org/10.1039/C6OB00015