Retention Of Configuration Research Articles

Efficient quantum mechanical minimum free energy path calculation by combining path integral hybrid Monte Carlo and climbing image nudged elastic band methods, and its application to the addition reaction of hydrogen isocyanide to formaldehyde.

We propose an efficient algorithm for a minimum free energy path calculation based on the path integral hybrid Monte Carlo (PIHMC) method by combining the climbing image-nudged elastic band (CI-NEB) and the thermodynamic integration (TI) methods. Here, the CI-NEB and the TI methods are used to find a transition state along the reaction path and evaluate the free energy path, respectively. Our algorithm is applied to the Walden inversion reaction of the hydronium ions (H3O+). The numerical results show that the computational effort by our algorithm is significantly reduced compared to that of the previously proposed algorithm combining PIHMC without losing accuracy. We also demonstrate the importance of temperature and isotope effects on the addition reaction of hydrogen isocyanide to formaldehyde. In this reaction, the nuclear quantum effect causes the structural change at the TS and decreases the energy barrier.

On the Origin of Enantioselectivity in Chiral Zeolite Asymmetric Catalyst GTM-3: Host-Guest Transfer of Chirality.

Knowledge of how extra-large-pore chiral zeolite asymmetric catalysts based on the -ITV framework imprint their chirality during a catalytic reaction is crucial in order to spread the scope for the catalytic enantioselective production of chiral compounds of interest. In this work, we have carried out a combined experimental and computational study on the catalytic activity of antipode GTM-3 catalysts during the ring-opening of trans-stilbene oxide with 1-butanol. Identification of the enantiomers of all the chiral species unraveled a surprising catalytic behavior: these chiral catalysts promote the transformation of one enantiomer of trans-stilbene oxide in the corresponding unlike product (with inversion of configuration of the attacked C) via an SN2 mechanism, and at the same time, the transformation of the other enantiomer of trans-stilbene oxide via an SN1-like mechanism into the like (with retention of configuration) and secondary products (diphenylacetaldehyde via Meinwald rearrangement and derived products). A computational study based on DFT + D methods suggested a potential explanation for this catalytic behavior, associated with a different orientation of trans-stilbene oxide enantiomers bound on the Ge(T7) positions in d4r units, which is stabilized by the development of intraframework H-bonds between the interrupted T7OH adjacent positions characteristic of this framework. Calculations suggest that each enantiomer of trans-stilbene oxide follows a different reaction pathway, one favoring the SN2 route by addition of butanol from the opposite side to form unlike-products, while the different orientation of the antipode enantiomer disfavors such SN2 route mainly by steric repulsions and at the same time favors the reaction toward the SN1 mechanism to give like- and secondary-products. Our study suggests that the strong enantioselectivity of GTM-3 catalysts for this reaction is associated with the particular orientation adopted by the chiral reactants within the chiral nanospace provided by the -ITV framework, similarly to what occurs with enzymes, and such preferential orientation is directly controlled by the asymmetric cavities where the reaction takes place, by the particular features of the Ge active sites in adjacent interrupted positions and by the presence of several framework OH groups in the nearby nanospace that interact with guest species. The experimental observations and the reaction mechanism proposed suggest that GTM-3 catalysts prepared from the (1S,2S) enantiomer of the N,N-ethyl-methyl-pseudoephedrinium organic agent should be enriched in the P4332 enantiomorphic space group of the -ITV framework and GTM-3 prepared from the (1R,2R) enantiomer in the antipode P4132. Interestingly, resolution of the absolute configuration of GTM-3 materials from 3D-electron diffraction data has been accomplished and confirms such an assignment, giving an average 82% enantio-enrichment in the corresponding chiral polymorph. Structure-solution of the location of the chiral structure-directing agents indicates that the transfer of chirality from the molecular component to the zeolite polymorph is governed by the development of strong H-bonds between the molecular hydroxyl group and the interrupted T(7)OH framework positions.

A Convenient Synthesis of Short α-/β-Mixed Peptides as Potential α-Amylase Inhibitors.

Over the last decades, the increased incidence of metabolic disorders, such as type two diabetes and obesity, has motivated researchers to investigate new enzyme inhibitors. Inhibition of the α-amylase enzyme is one therapeutic approach in lowering glucose levels in the blood to manage diabetes mellitus. The objective of this study was to synthesize short α-/β-mixed peptides in the solution phase. The Boc-protected α-L-leucine was converted to β-analogue by using Arndt-Eistert synthesis with the advantage of no racemization and retention of configuration. Three novel short peptides were successfully synthesized: N(Boc)-Gly-β-Leu-OCH3(14), N(Boc)-O(Bz)α-Ser-β-Leu-OCH3(16), and N(Boc)-O(Bz)-α-Tyr-α-Gly-β-Leu-OCH3(17), characterized by FTIR and 1H NMR analysis. The synthesized peptide 16 showed highest inhibitory activity (45.22%) followed by peptide 14 (18.51%) and peptide 17 (17.05%), respectively. Intriguingly, peptide 16 showed higher inhibition on α-amylase compared with other α-/β-mixed peptides.

Molecular Mechanism of Double-Displacement Retaining β-Kdo Glycosyltransferase WbbB.

Glycosyltransferases (GTs) are pivotal enzymes involved in glycosidic bond synthesis, which can lead to either retention or inversion of the glycosyl moiety's anomeric configuration. However, the catalytic mechanism for retaining GTs remains a subject of controversy. In this study, we employ MD and QM/MM metadynamics to investigate the double-displacement catalytic mechanism of the retaining β-Kdo transferase WbbB. Our findings demonstrate that the nucleophile Asp232 initiates the reaction by attacking the sugar ring containing a carboxylate at the anomeric position, forming a covalent adduct. Subsequently, the adduct undergoes a rotational rearrangement, ensuring proper orientation of the anomeric carbon for the acceptor substrate. In the second step, Glu158 acts as the catalytic base to abstract the proton of the acceptor substrate to complete the transglycosylation reaction. Notably, His265 does not function as the anticipated catalytic acid; instead, it stabilizes the phosphate group through H-bonding interactions. Our simulations support the double-displacement mechanism implicated from the crystallographic studies of WbbB. This mechanism deviates from the common SNi-type and retaining glycoside hydrolase mechanisms, thereby expanding our understanding of GT catalytic mechanisms.

Stereoinvertive SN1 Through Neighboring Group Participation.

Neighboring group participation, the assistance of non-conjugated electrons to a reaction center, is a fundamental phenomenon in chemistry. In the framework of nucleophilic substitution reactions, neighboring group participation is known to cause rate acceleration, first order kinetics (SN1), and retention of configuration. The latter phenomenon is a result of double inversion: the first one when the neighboring group displaces the leaving group, and the second when a nucleophile substitutes the neighboring group. This powerful control of stereoretention has been widely used in organic synthesis for more than a century. However, neighboring group participation may also lead to inversion of configuration, a phenomenon which is often overlooked. Herein, we review this unique mode of stereoinversion, dividing the relevant reactions into three classes with the aim to introduce a fresh perspective on the different modes of stereoinversion via neighboring group participation as well as the factors that control this stereochemical outcome.

Stereoinvertive SN1 Through Neighboring Group Participation

AbstractNeighboring group participation, the assistance of non‐conjugated electrons to a reaction center, is a fundamental phenomenon in chemistry. In the framework of nucleophilic substitution reactions, neighboring group participation is known to cause rate acceleration, first order kinetics (SN1), and retention of configuration. The latter phenomenon is a result of double inversion: the first one when the neighboring group displaces the leaving group, and the second when a nucleophile substitutes the neighboring group. This powerful control of stereoretention has been widely used in organic synthesis for more than a century. However, neighboring group participation may also lead to inversion of configuration, a phenomenon which is often overlooked. Herein, we review this unique mode of stereoinversion, dividing the relevant reactions into three classes with the aim to introduce a fresh perspective on the different modes of stereoinversion via neighboring group participation as well as the factors that control this stereochemical outcome.

Chemical Synthesis of a Densely Functionalized Aminodisaccharide from Fusobacterium nucleatum ATCC 23726 O-Antigen.

Fusobacterium nucleatum, a colorectal-cancer-associated oncomicrobe, can trigger or accelerate numerous pathologies. We report the first synthesis of a conjugation-ready disaccharide containing six amino groups from F. nucleatum ATCC 23726 O-antigen. Rare 2,3-diamido-d-glucuronic acid amide and 2-acetamido-4-amino-d-fucose were synthesized from d-glucosamine through configuration inversion, nucleophilic substitution, C6 oxidation, and C6 deoxygenation. A judicious choice of protecting groups and reaction conditions enabled the selective installation of N-acetyl, N-propanoyl, N-formyl, and carboxamido groups.

Synthesis of Quillaic Acid through Sustainable C-H Bond Activations.

To meet the demand for quillaic acid, a multigram synthesis of quillaic acid was accomplished in 14 steps, starting from oleanolic acid, leading to an overall yield of 3.4%. Key features include C-H activation at C-16 and C-23. Through Pd-catalyzed C-H acetoxylation, the oxidation at C-23 was observed as the major product, as opposed to at C-24. A copper-mediated C-H hydroxylation using O2 successfully afforded the single isomer, 16β-ol triterpenoid, followed by configuration inversion to the desired 16α-ol compound. In summary, with steps optimized and conducted on a multigram scale, quillaic acid could be feasibly acquired through C-H activation with inexpensive copper catalysts, promoting a more sustainable approach.

Editing Tetrasubstituted Carbon: Dual C-O Bond Functionalization of Tertiary Alcohols Enabled by Palladium-Based Dyotropic Rearrangement.

Many elegant asymmetric syntheses of enantioenriched tertiary alcohols have been developed, and both the transition metal-catalyzed and the radical-based peripheral functionalization of tertiary alcohols have attracted intensive research interest in recent years. However, directly editing tetrasubstituted carbons remains challenging. Herein, we report a Pd-catalyzed migratory fluoroarylation reaction that converts tertiary alcohols to α-fluorinated tertiary alkyl ethers in good to excellent yields. An unprecedented 1,2-aryl/PdIV dyotropic rearrangement along the C-O bond, integrated in a PdII-catalyzed domino process, is key to the dual functionalization of both the hydroxyl group and the tetrasubstituted carbon. This reaction, which is compatible with a broad range of functional groups, generates a tertiary alkyl fluoride and an alkyl-aryl ether functional group with inversion of the absolute configuration at the tetrasubstituted stereocenter.

Exploitation of Mechanistic Product Selectivity for the Two‐Step Synthesis of Optically Active Bio‐Derived Cyclic Carbonates Incorporating Amino Acids

AbstractThe synthesis of bio‐derived cyclic carbonates is attracting a lot of attention as the incorporation of bio‐derived functionality into these compounds provides the opportunity to prepare previously unknown structures, whilst also improving their sustainability profiles. This study presents a facile preparation of diastereomerically pure bio‐derived cyclic carbonates displaying a range of optical rotation values. These compounds are obtained from glycidol, amino acids and CO2 in a facile two‐step approach. Initially, the diastereomerically pure amino acid functionalised epoxides are prepared through a robust Steglich esterification of enantiopure glycidol (R or S) and an amino acid (D or L). Thereafter, in a second step, cycloaddition of the epoxide with CO2 results in the retention of the initial stereochemistry of the epoxide, furnishing novel diastereomerically pure and optically active cyclic carbonate products. A DFT study has explained the basis of this observed retention of configuration for these compounds. Further, results from this DFT study also provide new mechanistic information concerning a co‐catalyst‐free cycloaddition reaction starting from glycidol when using the gallium‐catalyst, which is found to operate through metal‐ligand cooperativity.

Unusual N[sbnd]H/O[sbnd]H Activation Mechanism for Au-Catalyzed N,O-Functionalization of 1,4-diyn-3-ols with N-hydroxyanilines

Au-catalyzed N,O-functionalization of 1,4-diyn-3-ols with N-hydroxyanilines provides a short and efficient approach to construct versatile pyrrole frameworks. Using DFT calculations, we systematically investigated the detailed mechanisms involved in this reaction. It was found that, the commonly asserted NH/OH activation mechanism was unfavoured due to a high energy barrier. The main reason was believed to be associated with the inversion of configuration on the sp3-hybrid C atom (generated after the H(N)-shift) which results in significant energy consumption for the subsequent H(O)-shift. Therefore, here we present a unique “1,4-elimination/1,4-syn-protodeauration” catalytic mechanism, in which (i) the charge delocalization on the carbon cation is conductive to the stability of the 1,4-elimination TS; (ii) the high exergonicity of the 1,4-elimination decreases the potential energy surface of the subsequent reaction; and (iii) the sp2-C site ensures energy-efficient retention of configuration during the 1,4-syn-protodeauration, in contrast to the energy-consuming inversion of configuration during the classical anti-protodeauration.

The Retaining Pse5Ac7Ac Pseudaminyltransferase KpsS1 Defines a Previously Unreported glycosyltransferase family (GT118).

Cell surface sugar 5,7-diacetyl pseudaminic acid (Pse5Ac7Ac) is a bacterial analogue of the ubiquitous sialic acid, Neu5Ac, and contributes to the virulence of a number of multidrug resistant bacteria, including ESKAPE pathogens Pseudomonas aeruginosa, and Acinetobacter baumannii. Despite its discovery in the surface glycans of bacteria over thirty years ago, to date no glycosyltransferase enzymes (GTs) dedicated to the synthesis of a pseudaminic acid glycosidic linkage have been unequivocally characterised in vitro. Herein we demonstrate that A. baumannii KpsS1 is a dedicated pseudaminyltransferase enzyme (PseT) which constructs a Pse5Ac7Ac-α(2,6)-Glcp linkage, and proceeds with retention of anomeric configuration. We utilise this PseT activity in tandem with the biosynthetic enzymes required for CMP-Pse5Ac7Ac assembly, in a two-pot, seven enzyme synthesis of an α-linked Pse5Ac7Ac glycoside. Due to its unique activity and protein sequence, we also assign KpsS1 as the prototypical member of a previously unreported GT family (GT118).

The Retaining Pse5Ac7Ac Pseudaminyltransferase KpsS1 Defines a Previously Unreported glycosyltransferase family (GT118)

AbstractCell surface sugar 5,7‐diacetyl pseudaminic acid (Pse5Ac7Ac) is a bacterial analogue of the ubiquitous sialic acid, Neu5Ac, and contributes to the virulence of a number of multidrug resistant bacteria, including ESKAPE pathogens Pseudomonas aeruginosa, and Acinetobacter baumannii. Despite its discovery in the surface glycans of bacteria over thirty years ago, to date no glycosyltransferase enzymes (GTs) dedicated to the synthesis of a pseudaminic acid glycosidic linkage have been unequivocally characterised in vitro. Herein we demonstrate that A. baumannii KpsS1 is a dedicated pseudaminyltransferase enzyme (PseT) which constructs a Pse5Ac7Ac‐α(2,6)‐Glcp linkage, and proceeds with retention of anomeric configuration. We utilise this PseT activity in tandem with the biosynthetic enzymes required for CMP‐Pse5Ac7Ac assembly, in a two‐pot, seven enzyme synthesis of an α‐linked Pse5Ac7Ac glycoside. Due to its unique activity and protein sequence, we also assign KpsS1 as the prototypical member of a previously unreported GT family (GT118).

Enantioselective Intramolecular ortho Photocycloaddition Reactions of 2-Acetonaphthones.

2-Acetonaphthones, which bear an alkenyl group tethered to its C1 carbon atom via an oxygen atom, were found to undergo an enantioselective intramolecular ortho photocycloaddition reaction. A chiral oxazaborolidine Lewis acid leads to a bathochromic absorption shift of the substrate and enables an efficient enantioface differentiation. Visible light irradiation (λ=450 nm) triggers the reaction which is tolerant of various groups at almost any position except carbon atom C8 (16 examples, 53-99 % yield, 80-97 % ee). Consecutive reactions were explored including a sensitized rearrangement to tetrahydrobiphenylenes, which occurred with full retention of configuration. Evidence was collected that the catalytic photocycloaddition occurs via triplet intermediates, and the binding mode of the acetonaphthone to the chiral Lewis acid was elucidated by DFT calculations.

Enantioselective Intramolecular ortho Photocycloaddition Reactions of 2‐Acetonaphthones

Abstract2‐Acetonaphthones, which bear an alkenyl group tethered to its C1 carbon atom via an oxygen atom, were found to undergo an enantioselective intramolecular ortho photocycloaddition reaction. A chiral oxazaborolidine Lewis acid leads to a bathochromic absorption shift of the substrate and enables an efficient enantioface differentiation. Visible light irradiation (λ=450 nm) triggers the reaction which is tolerant of various groups at almost any position except carbon atom C8 (16 examples, 53–99 % yield, 80–97 % ee). Consecutive reactions were explored including a sensitized rearrangement to tetrahydrobiphenylenes, which occurred with full retention of configuration. Evidence was collected that the catalytic photocycloaddition occurs via triplet intermediates, and the binding mode of the acetonaphthone to the chiral Lewis acid was elucidated by DFT calculations.

Snapshots of the Reaction Coordinate of a Thermophilic 2'-Deoxyribonucleoside/ribonucleoside Transferase.

Nucleosides are ubiquitous to life and are required for the synthesis of DNA, RNA, and other molecules crucial for cell survival. Despite the notoriously difficult organic synthesis of nucleosides, 2'-deoxynucleoside analogues can interfere with natural DNA replication and repair and are successfully employed as anticancer, antiviral, and antimicrobial compounds. Nucleoside 2'-deoxyribosyltransferase (dNDT) enzymes catalyze transglycosylation via a covalent 2'-deoxyribosylated enzyme intermediate with retention of configuration, having applications in the biocatalytic synthesis of 2'-deoxynucleoside analogues in a single step. Here, we characterize the structure and function of a thermophilic dNDT, the protein from Chroococcidiopsis thermalis (CtNDT). We combined enzyme kinetics with structural and biophysical studies to dissect mechanistic features in the reaction coordinate, leading to product formation. Bell-shaped pH-rate profiles demonstrate activity in a broad pH range of 5.5-9.5, with two very distinct pKa values. A pronounced viscosity effect on the turnover rate indicates a diffusional step, likely product (nucleobase1) release, to be rate-limiting. Temperature studies revealed an extremely curved profile, suggesting a large negative activation heat capacity. We trapped a 2'-fluoro-2'-deoxyarabinosyl-enzyme intermediate by mass spectrometry and determined high-resolution structures of the protein in its unliganded, substrate-bound, ribosylated, 2'-difluoro-2'-deoxyribosylated, and in complex with probable transition-state analogues. We reveal key features underlying (2'-deoxy)ribonucleoside selection, as CtNDT can also use ribonucleosides as substrates, albeit with a lower efficiency. Ribonucleosides are the building blocks of RNA and other key intracellular metabolites participating in energy and metabolism, expanding the scope of use of CtNDT in biocatalysis.

Modifying the Oxidative Potentials of Imines in a Dye Loaded Capsule for Photocatalytic Cyclization with Hydrogen Evolution

AbstractModifying redox potential of substrates and intermediates to balance pairs of redox steps are important stages for multistep photosynthesis but faced marked challenges. Through co‐clathration of iridium photosensitizer and imine substrate within one packet of a metal‐organic capsule to shift the redox potentials of substrate, herein, we reported a multiphoton enzymatic strategy for the generation of heterocycles by intramolecular C−X hydrogen evolution cross‐couplings. The cage facilitated a pre‐equilibrium substrate‐involving clathrate that cathodic shifts the oxidation potential of the substrate‐dye‐host ternary complex and configuration inversion of substrate via spatial constraints in the confined space. The new two photon excitation strategy enabled the precise control of the multistep electron transfer between each pair (photosensitizer, substrate and the capsule), endowing the catalytic system proceeding smoothly with an enzymatic fashion. Three kinds of 2‐subsituted (−OH, −NH2, and −SH) imines and N‐aryl enamines all give the corresponding cyclization products efficiently under visible light irradiation, demonstrating the promising of the microenvironment driven thermodynamic activation in the host‐dye‐substrate ternary for synergistic combination of multistep photocatalytic transformations.

Modifying the Oxidative Potentials of Imines in a Dye Loaded Capsule for Photocatalytic Cyclization with Hydrogen Evolution.

Modifying redox potential of substrates and intermediates to balance pairs of redox steps are important stages for multistep photosynthesis but faced marked challenges. Through co-clathration of iridium photosensitizer and imine substrate within one packet of a metal-organic capsule to shift the redox potentials of substrate, herein, we reported a multiphoton enzymatic strategy for the generation of heterocycles by intramolecular C-X hydrogen evolution cross-couplings. The cage facilitated a pre-equilibrium substrate-involving clathrate that cathodic shifts the oxidation potential of the substrate-dye-host ternary complex and configuration inversion of substrate via spatial constraints in the confined space. The new two photon excitation strategy enabled the precise control of the multistep electron transfer between each pair (photosensitizer, substrate and the capsule), endowing the catalytic system proceeding smoothly with an enzymatic fashion. Three kinds of 2-subsituted (-OH, -NH2 , and -SH) imines and N-aryl enamines all give the corresponding cyclization products efficiently under visible light irradiation, demonstrating the promising of the microenvironment driven thermodynamic activation in the host-dye-substrate ternary for synergistic combination of multistep photocatalytic transformations.

Working Memory Maintenance of Visual and Auditory Spatial Information Relies on Supramodal Neural Codes in the Dorsal Frontoparietal Cortex.

The frontoparietal attention network plays a pivotal role during working memory (WM) maintenance, especially under high-load conditions. Nevertheless, there is ongoing debate regarding whether this network relies on supramodal or modality-specific neural signatures. In this study, we used multi-voxel pattern analysis (MVPA) to evaluate the neural representation of visual versus auditory information during WM maintenance. During fMRI scanning, participants maintained small or large spatial configurations (low- or high-load trials) of either colour shades or sound pitches in WM for later retrieval. Participants were less accurate in retrieving high- vs. low-load trials, demonstrating an effective manipulation of WM load, irrespective of the sensory modality. The frontoparietal regions involved in maintaining high- vs. low-load spatial maps in either sensory modality were highlighted using a conjunction analysis. Widespread activity was found across the dorsal frontoparietal network, peaking on the frontal eye fields and the superior parietal lobule, bilaterally. Within these regions, MVPAs were performed to quantify the pattern of distinctness of visual vs. auditory neural codes during WM maintenance. These analyses failed to reveal distinguishable patterns in the dorsal frontoparietal regions, thus providing support for a common, supramodal neural code associated with the retention of either visual or auditory spatial configurations.

Unusual catalytic strategy by non-heme Fe(ii)/2-oxoglutarate-dependent aspartyl hydroxylase AspH.

Biocatalytic C-H oxidation reactions are of important synthetic utility, provide a sustainable route for selective synthesis of important organic molecules, and are an integral part of fundamental cell processes. The multidomain non-heme Fe(ii)/2-oxoglutarate (2OG) dependent oxygenase AspH catalyzes stereoselective (3R)-hydroxylation of aspartyl- and asparaginyl-residues. Unusually, compared to other 2OG hydroxylases, crystallography has shown that AspH lacks the carboxylate residue of the characteristic two-His-one-Asp/Glu Fe-binding triad. Instead, AspH has a water molecule that coordinates Fe(ii) in the coordination position usually occupied by the Asp/Glu carboxylate. Molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) studies reveal that the iron coordinating water is stabilized by hydrogen bonding with a second coordination sphere (SCS) carboxylate residue Asp721, an arrangement that helps maintain the six coordinated Fe(ii) distorted octahedral coordination geometry and enable catalysis. AspH catalysis follows a dioxygen activation-hydrogen atom transfer (HAT)-rebound hydroxylation mechanism, unusually exhibiting higher activation energy for rebound hydroxylation than for HAT, indicating that the rebound step may be rate-limiting. The HAT step, along with substrate positioning modulated by the non-covalent interactions with SCS residues (Arg688, Arg686, Lys666, Asp721, and Gln664), are essential in determining stereoselectivity, which likely proceeds with retention of configuration. The tetratricopeptide repeat (TPR) domain of AspH influences substrate binding and manifests dynamic motions during catalysis, an observation of interest with respect to other 2OG oxygenases with TPR domains. The results provide unique insights into how non-heme Fe(ii) oxygenases can effectively catalyze stereoselective hydroxylation using only two enzyme-derived Fe-ligating residues, potentially guiding enzyme engineering for stereoselective biocatalysis, thus advancing the development of non-heme Fe(ii) based biomimetic C-H oxidation catalysts, and supporting the proposal that the 2OG oxygenase superfamily may be larger than once perceived.