Ion Transport and Inhibitor Binding by Human NHE1: Insights from Molecular Dynamics Simulations and Free Energy Calculations.

The human Na+/H+ exchanger (NHE1) plays a crucial role in maintaining intracellular pH by regulating the electroneutral exchange of a single intracellular H+ for one extracellular Na+ across the plasma membrane. Understanding the molecular mechanisms governing ion transport and the binding of inhibitors is of importance in the development of anticancer therapeutics targeting NHE1. In this context, we performed molecular dynamics (MD) simulations based on the recent cryo-electron microscopy (cryo-EM) structures of outward- and inward-facing conformations of NHE1. These simulations allowed us to explore the dynamics of the protein, examine the ion-translocation pore, and confirm that Asp267 is the ion-binding residue. Our free energy calculations did not show a significant difference between Na+ and K+ binding at the ion-binding site. Consequently, Na+ over K+ selectivity cannot be solely explained by differences in ion binding. Our MD simulations involving NHE1 inhibitors (cariporide and amiloride analogues) maintained stable interactions with Asp267 and Glu346. Our study highlights the importance of the salt bridge between the positively charged acylguanidine moiety and Asp267, which appears to play a role in the competitive inhibitory mechanism for this class of inhibitors. Our computational study provides a detailed mechanistic interpretation of experimental data and serves the basis of future structure-based inhibitor design.

Electrostatic Contribution to 19F Chemical Shifts in Fluorotryptophans in Proteins.

DFT calculations indicate that the 19F chemical shifts of aromatic rings containing single fluorine substituents are sensitive to the electric fields and electric field gradients at the position of the fluorine atom. The present work explores whether long-range structure restraints can be gained from changes in 19F chemical shifts following mutations of charged to uncharged residues. 19F chemical shifts of fluorotryptophan residues were measured in two different proteins, GB1 and the NT* domain, following mutations of single asparagine residues to aspartic acid. Four different versions of fluorotryptophan were investigated, including 4-, 5-, 6-, and 7-fluorotryptophan, which were simultaneously installed by cell-free protein synthesis using 4-, 5-, 6-, and 7-fluoroindole as precursors for the tryptophan synthase present in the S30 extract. For comparison, the 1H chemical shifts of the corresponding nonfluorinated protein mutants produced with 13C-labeled tryptophan were also measured. The results show that the 19F chemical shifts respond more sensitively to the charge mutations than the 1H chemical shifts in the nonfluorinated references, but the chemical shift changes were much smaller than predicted by DFT calculations of fluoroindoles in the electric field of a partial charge in vacuum, indicating comprehensive dielectric shielding by water and protein. No straightforward correlation with the location of the charge mutation could be established.

DFT Mechanistic Insights into the Ni(II)-Catalyzed Enantioselective Arylative Cyclization of Tethered Allene-Ketones.

Density functional theory (DFT) has provided a detailed mechanistic picture for the redox neutral nickel(II)-catalyzed arylative cyclization reactions of a tethered allene-ketone with arylboronic acids. A mechanistic rationale for the high diastereo- and enantioselectivity achieved experimentally at high reaction temperature was uncovered through modeling the reaction with a chiral ligand and the predicted stereochemical outcome corroborates with experimental results. An unprecedented mechanism for the base-free organoboron transmetalation was revealed and the regioselectivity of migratory insertion of tethered allene-ketones as well as the stability of the possible allylnickel isomers (σ-allyl vs π-allyl) were clarified. The multifaceted nature of the reaction is revealed with certain elementary steps preferring cationic compared to the neutral state.

Diastereoselective Petasis-Borono-Mannich Crotylation Reactions of Chiral α-Heteroatom (F, OBz, OH) Aldehydes: Rapid Access to Valuable Mono and Bicyclic Heterocyclic Scaffolds.

The crotylation reactions of chiral α-F, α-OBz and α-OH aldehydes under Petasis-borono-Mannich conditions using (E)- or (Z)-crotylboronates and primary amines resulted in γ-addition products in high dr and high er. α-F and α-OBz aldehydes gave 1,2-anti-2,3-syn and 1,2-anti-2,3-anti, products, respectively while an α-OH aldehyde gave 1,2-syn-2,3-syn products. The stereochemical outcomes of reactions of the former aldehydes can be explained using a six-membered ring transition state (TS) model in which a Cornforth-like conformation around the imine intermediate is favoured resulting in 1,2-anti products. The 2,3-stereochemical outcome is dependent upon the geometry of the crotylboronate. These TS models were also supported by DFT calculations. The stereochemical outcomes of reactions employing an α-OH aldehyde can be rationalised as occurring via an open-TS involving H-bonding in the imine intermediate between the α-OH group and the imine N atom. Representative products were converted to highly functionalized 1,2,3,6-tetrahydropyridines and 3H-oxazolo[3,4-a]pyridine-3-ones which will be valuable scaffolds in synthesis.

Guanidine-based biomimetic hydrides for carbon dioxide reduction.

The feasibility of various bespoke guanidine-based compounds as biomimetic hydrides were assessed by Density Functional Theory (DFT). The results predicted that tricyclic pentanidine hydrides are viable candidates to reduce CO2 to HCOO- and be regenerated electrochemically, demonstrating a recyclable and sustainable method to achieve metal-free electrochemical reduction of CO2.

Direct SN2 or SN2X Manifold─Mechanistic Study of Ion-Pair-Catalyzed Carbon(sp3)-Carbon(sp3) Bond Formation.

Density functional theory (DFT) is used in this work to predict the mechanism for constructing congested quaternary-quaternary carbon(sp3)-carbon(sp3) bonds in a pentanidium-catalyzed substitution reaction. Computational mechanistic studies were carried out to investigate the proposed SN2X manifold, which consists of two primary elementary steps: halogen atom transfer (XAT) and subsequent SN2. For the first calculated model on original experimental substrates, XAT reaction barriers were more kinetically competitive than an SN2 pathway and connect to thermodynamically stable intermediates. Extensive computational screening modeling was then done on various substrate combinations designed to study the steric influence and to understand the mechanistic rationale, and calculations reveal that sterically congested substrates prefer the SN2X manifold over SN2. Different halides as leaving groups were also screened, and it was found that the reactivity increases in the order of I > Br > Cl > F, in agreement with the strength of C-X bonds. However, DFT modeling suggests that chlorides can be a viable substrate for the SN2X process, which should be further explored experimentally. ONIOM calculations on the full catalyst model predicted the correct stereochemical outcome, and further catalyst screening with cationic Me4N+ and K+ predicted that pentanidium is still the choice for SN2X C-C bond formation.

Postsynthetic Modification of Half-Sandwich Ruthenium Complexes by Mechanochemical Synthesis.

A mild and environmentally friendly method to synthesize half-sandwich ruthenium complexes through the Wittig reaction between an aldehyde-tagged half-sandwich ruthenium complex and phosphorus ylide mechanochemically is reported herein. The mechanochemical synthesis of valuable half-sandwich ruthenium complexes resulted in a fast reaction, good yield with simple workup, and the avoidance of harsh reaction conditions and organic solvents. The synthesized half-sandwich ruthenium complexes exhibited high catalytic activity for transfer hydrogenation of ketones using 2-propanol as the hydrogen source and solvent. Density functional theory was carried out to propose a mechanism for the transfer hydrogenation process. The modeling suggests the importance of the labile p-cymene ligand in modulating the reactivity of the catalyst.

Enantioselective Addition-Alkylation of α,ß-Unsaturated Carbonyls via Bisguanidinium Silicate Ion Pair Catalysis.

Silicon hydrides, alkynylsilanes, and alkoxylsilanes were activated by fluoride in the presence of bisguanidinium catalyst to form hypervalent silicate ion pairs. These activated silicates undergo 1,4-additions with chromones, coumarins, and α-cyanocinnamic esters generating enolsilicate intermediates, for a consequent stereoselective alkylation reaction. The reduction-alkylation reaction proceeded under mild conditions using polymethylhydrosiloxane, a cheap and environmentally friendly hydride source. The addition-alkylation reactions with alkynylsilanes and alkoxylsilanes resulted in the construction of two vicinal chiral carbon centers with excellent enantioselectivities and diastereoselectivities (up to 99% ee, >99:1 dr). Density functional theory calculations and experimental NMR studies revealed that penta-coordinated silicates are crucial intermediates.

Kinetic and Dynamic Kinetic Resolution of Racemic Tertiary Bromides by Pentanidium-Catalyzed Phase-Transfer Azidation.

We have developed a method to afford enantiomerically enriched tertiary azides and bromides through pentanidium-catalyzed kinetic resolution (KR) of racemic tertiary bromides under base-free conditions. We found that the absence of water is crucial to attain a high selectivity factor (s). On the other hand, new experimental observations and DFT modeling led us to propose that enantioconvergent azidation of tertiary bromides proceeded through dynamic kinetic resolution (DKR). The investigations particularly identified the crucial roles of base and water in the enantioconvergent process, thus supporting the proposal that the tertiary bromide isomerizes in the presence of base and water through a SN 2X pathway.

Complementary C-H Functionalization Mode of Benzoylacetonitriles: Computer-Augmented Study of a Regio- and Stereoselective Synthesis of Functionalized Benzofulvenes.

A highly regio- and stereoselective synthesis of functionalized benzofulvenes via Rh(III)-catalyzed cascade reactions of benzoyl acetonitrile/methylsulfone/acetate with propargyl alcohols is presented herein. Mechanistic modeling performed with density functional theory (DFT) calculations suggested that the hydroxyl group and CsOAc played important roles in mediating the 5-membered ring cyclization by forming a very thermodynamically stable Rh(III) intermediate. Another remarkable feature of this transformation is its excellent stereoselectivity in that only E-isomers are obtained.

A ruthenium bisoxazoline complex as a photoredox catalyst for nitro compound reduction under visible light.

An unreported ruthenium(ii) complex containing bisoxazoline ligands has been synthesized and characterized. To test the catalytic ability of the ruthenium complex, the synthesis of anilines from nitro compounds in the presence of a mild reducing agent sodium borohydride and visible light has been developed. Mechanistic studies involving the experiment and DFT calculations suggest that the reaction could involve a radical pathway with the assistance of a photoredox catalyst.

Chiral acid-catalysed enantioselective C-H functionalization of toluene and its derivatives driven by visible light.

Toluene and its derivatives are petroleum-derived raw materials produced from gasoline by catalytic reformation. These abundant chemical feedstocks are commonly used as solvents in organic synthesis. The C(sp3)-H functionalization of these unactivated substrates has been widely used to directly introduce benzylic motifs into diverse molecules to furnish important compounds. Despite these advances, progress in asymmetric catalysis remains underdeveloped. Here, we report photoinduced radical-based enantioselective C(sp3)-C(sp3) coupling reactions of activated ketones with toluene and its derivatives by means of chiral acid catalysis. With a La(OTf)3/pybox complex catalyst, a variety of chiral 3-hydroxy-3-benzyl-substituted 2-oxindoles, including many conventionally difficult-to-access variants, are obtained directly from isatins in high yields with good to excellent enantioselectivities. Acenaphthoquinone is also compatible with the use of a chiral phosphoric acid (CPA) catalyst, leading to another series of important enantioenriched tertiary alcohols.

Catalytic Enantioselective Addition of Prochiral Radicals to Vinylpyridines.

Pyridine, one of the most important azaarenes, is ubiquitous in functional molecules. The electronic properties of pyridine have been exploited to trigger asymmetric transformations of prochiral species as a direct approach for accessing chiral pyridine derivatives. However, the full potential of this synthetic strategy for the construction of enantioenriched γ-functionalized pyridines remains untapped. Here, we describe the first enantioselective addition of prochiral radicals to vinylpyridines under cooperative photoredox and asymmetric catalysis mediated by visible light. The enantioselective reductive couplings of vinylpyridines with aldehydes, ketones, and imines were achieved by employing a chiral Brønsted acid to activate the reaction partners and provide stereocontrol via H-bonding interactions. Valuable chiral γ-secondary/tertiary hydroxyl- and amino-substituted pyridines were obtained in high yields with good to excellent enantioselectivities.

A Photoexcitation-Induced Twisted Intramolecular Charge Shuttle.

Charge transfer and separation are important processes governing numerous chemical reactions. Fundamental understanding of these processes and the underlying mechanisms is critical for photochemistry. Herein, we report the discovery of a new charge-transfer and separation process, namely the twisted intramolecular charge shuttle (TICS). In TICS systems, the donor and acceptor moieties dynamically switch roles in the excited state because of an approximately 90° intramolecular rotation. TICS systems thus exhibit charge shuttling. TICSs exist in several chemical families of fluorophores (such as coumarin, BODIPY, and oxygen/carbon/silicon-rhodamine), and could be utilized to construct functional fluorescent probes (i.e., viscosity- or biomolecule-sensing probes). The discovery of the TICS process expands the current perspectives of charge-transfer processes and will inspire future applications.

An enantioconvergent halogenophilic nucleophilic substitution (SN2X) reaction.

Bimolecular nucleophilic substitution (SN2) plays a central role in organic chemistry. In the conventionally accepted mechanism, the nucleophile displaces a carbon-bound leaving group X, often a halogen, by attacking the carbon face opposite the C-X bond. A less common variant, the halogenophilic SN2X reaction, involves initial nucleophilic attack of the X group from the front and as such is less sensitive to backside steric hindrance. Herein, we report an enantioconvergent substitution reaction of activated tertiary bromides by thiocarboxylates or azides that, on the basis of experimental and computational mechanistic studies, appears to proceed via the unusual SN2X pathway. The proposed electrophilic intermediates, benzoylsulfenyl bromide and bromine azide, were independently synthesized and shown to be effective.

Guanidine-Copper Complex Catalyzed Allylic Borylation for the Enantioconvergent Synthesis of Tertiary Cyclic Allylboronates.

An enantioconvergent synthesis of chiral cyclic allylboronates from racemic allylic bromides was achieved by using a guanidine-copper catalyst. The allylboronates were obtained with high γ/α regioselectivities (up to 99:1) and enantioselectivities (up to 99 % ee), and could be further transformed into diverse functionalized allylic compounds without erosion of optical purity. Experimental and DFT mechanistic studies support an SN 2' borylation process catalyzed by a monodentate guanidine-copper(I) complex that proceeds through a special direct enantioconvergent transformation mechanism.

The evolution of multiple active site configurations in a designed enzyme.

Developments in computational chemistry, bioinformatics, and laboratory evolution have facilitated the de novo design and catalytic optimization of enzymes. Besides creating useful catalysts, the generation and iterative improvement of designed enzymes can provide valuable insight into the interplay between the many phenomena that have been suggested to contribute to catalysis. In this work, we follow changes in conformational sampling, electrostatic preorganization, and quantum tunneling along the evolutionary trajectory of a designed Kemp eliminase. We observe that in the Kemp Eliminase KE07, instability of the designed active site leads to the emergence of two additional active site configurations. Evolutionary conformational selection then gradually stabilizes the most efficient configuration, leading to an improved enzyme. This work exemplifies the link between conformational plasticity and evolvability and demonstrates that residues remote from the active sites of enzymes play crucial roles in controlling and shaping the active site for efficient catalysis.

(Guanidine)copper Complex-Catalyzed Enantioselective Dynamic Kinetic Allylic Alkynylation under Biphasic Condition.

Highly enantioselective allylic alkynylation of racemic bromides under biphasic condition is furnished in this report. This approach employs functionalized terminal alkynes as pro-nucleophiles and provides 6- and 7-membered cyclic 1,4-enynes with high yields and excellent enantioselectivities (up to 96% ee) under mild conditions. Enantioretentive derivatizations highlight the synthetic utility of this transformation. Cold-spray ionization mass spectrometry (CSI-MS) and X-ray crystallography were used to identify some catalytic intermediates, which include guanidinium cuprate ion pairs and a copper-alkynide complex. A linear correlation between the enantiopurity of the catalyst and reaction product indicates the presence of a copper complex bearing a single guanidine ligand at the enantio-determining step. Further experimental and computational studies supported that the alkynylation of allylic bromide underwent an anti-SN2' pathway catalyzed by nucleophilic cuprate species. Moreover, metal-assisted racemization of allylic bromide allowed the reaction to proceed in a dynamic kinetic fashion to afford the major enantiomer in high yield.

Formal enantioconvergent substitution of alkyl halides via catalytic asymmetric photoredox radical coupling.

Classic nucleophilic substitution reactions (SN1 and SN2) are not generally amenable to the enantioselective variants that use simple and racemic alkyl halide electrophiles. The merging of transition metal catalysis and radical chemistry with organometallic nucleophiles is a versatile method for addressing this limitation. Here, we report that visible light-driven catalytic asymmetric photoredox radical coupling can act as a complementary and generic strategy for the enantioconvergent formal substitution of alkyl haldies with readily available and bench-stable organic molecules. Single-electron reductive debrominations of racemic α-bromoketones generate achiral alkyl radicals that can participate in asymmetric Csp3-Csp3 bonds forming cross-coupling reactions with α-amino radicals derived from N-aryl amino acids. A wide range of valuable enantiomerically pure ß2- and ß2,2-amino ketones were obtained in satisfactory yields with good-to-excellent enantioselectivities by using chiral phosphoric acid catalysts to control the stereochemistry and chemoselectivity. Fluoro-hetero-quaternary and full-carbon quaternary stereocenters that are challenging to prepare were successfully constructed.