Ab Initio Molecular Dynamics Simulations of the SN1/SN2 Mechanistic Continuum in Glycosylation Reactions

"Marriage" of Inorganic to Organic Chemistry as Motivation for a Theoretical Study of Chloroform Hydrolysis Mechanisms

Incorporation of chlorides in coordination complexes, prepared by reactions in CHCl3, stimulated MP2 and DFT studies of its complete hydrolysis mechanisms. In excellent agreement with previous experimental results, the most important mechanism for CHCl3 basic hydrolysis at room temperature is the radical one producing :CCl2. The latter inserts into the H-O bond of H2O yielding dichloromethanol (1). The hydrolysis mechanism of α-H-lacking PhCCl3 to the corresponding dichloro(phenyl)methanol (3) was also studied. 1 decomposes by H2O to formyl chloride (2) and HCl. 2, following a variety of pathways, leads to known CHCl3 hydrolysis products, such as CO (4) and formic acid (6), via the intermediates chloromethanediol (5), s-cis, s-trans-dihydroxycarbene (ct-7), and s-trans, s-trans-dihydroxycarbene (tt-7). Interestingly, both ct-7 and tt-7 intermediates have recently been implicated in the reduction of CO2 with H2 to 6. The conversion of CO to HCOOH was studied. Most of the reactions studied are asynchronous concerted processes, the radical mechanism being a multistep one. The synthetic utility of this mechanism is briefly mentioned. To avoid chloride ions when performing reactions in CHCl3, we should use the solvent at room temperature even in the presence of water. This has been verified further by coordination chemistry reactions in progress.

Unveiling the Role of Solvent in Solution Phase Chemical Reactions using Deep Potential-Based Enhanced Sampling Simulations

We have used a deep learning-based active learning strategy to develop ab initio level accurate machine-learned (ML) potential for a solution-phase reactive system. Using this ML potential, we carried out enhanced sampling simulations to sample the reaction process efficiently. Multiple transitions between the reactant and product states allowed us to calculate the converged free energy surface for the reaction. As a prototypical example, we have investigated the Menshutkin reaction, a classic bimolecular nucleophilic substitution reaction (SN2) in aqueous medium. Our analyses revealed that water stabilizes the ionic product state by enhanced solvation, facilitating the reaction and making it more spontaneous. Our approach expands the scope of studying the chemical reaction under realistic conditions, such as explicit solvents at finite temperatures, closely mimicking experiments.

Role of ion pairs in model glycosylation reactions of permethylated glucosyl and xylosyl triflates

Elucidating the molecular mechanisms of chemical O-glycosylation remains a significant challenge in glycochemistry. This study examines the mechanism of the nucleophilic substitution reaction between glycosyl triflates, which are extensively used in studies of glycosylation mechanisms, and several acceptor alcohols. The investigation was conducted through a comparative analysis of permethylated glucosyl triflate GTf and its xylosyl counterpart XTf. The glycosylation reactions, conducted in dichloromethane using GTf and XTf with EtOH, tBuOH, and CF3CH2OH, exhibited diverse α/β selectivities depending on the types of donor and acceptor molecules used. Identifying a unified mechanism to explain this range of selectivities proved challenging. Notably, we observed a distinct trend wherein the addition of excess triflate salt (Bu4NOTf) had a more pronounced effect on the α/β selectivity in glycosylation reactions utilizing XTf compared to those using GTf. Quantum chemical calculations performed at the SCS-MP2//DFT(M06-2X) level, with explicit inclusion of five solvent molecules, showed that contact ion pairs arising from XTf were significantly more stable than those from GTf. These experimental and computational results strongly suggest that ion pairs play a more crucial role in the glycosylation process involving XTf than GTf. Additionally, our quantum chemical analyses clarified that the enhanced stability of the ion pairs from XTf was attributed not to the strength of the C-1-OTf bond within XTf but to the flexibility in the conformational changes of XTf's pyranosyl ring.

Origins of Temperature-Dependent Anomeric Selectivity in Glycosylations with an L-Idose Thioglycoside

L-Idose thioglycosides are useful glycosyl donors for the construction of glycosaminoglycan oligosaccharides. When activated with NIS and catalytic TMSOTf in the presence of methanol, the stereoselectivity of O-glycosylation displays an intriguing dependence on the reaction temperature, with an increased preference for formation of the α-glycoside at higher temperatures. Using a combination of vt-NMR spectroscopy and DFT calculations, we show how a simple mechanistic model, based on competing reactions of the iodinated thioglycoside, can explain the main features of the temperature dependence. In this model, the increased selectivity at high temperature is attributed to differences among the entropy and energy terms of the competing reaction pathways. Neighbouring-group participation (giving an intermediate acyloxonium ion) plays an increasingly dominant role as temperature is raised. The general features of this kinetic regime may also apply more broadly to other glycosylations that likewise favour α-glycoside formation at high temperature.

Stereospecific alkenylidene homologation of organoboronates by SNV reaction

Concerted nucleophilic substitution, known as SN2 reaction, is a fundamental organic transformation used in synthesis to introduce new functional groups and construct carbon-carbon and carbon-heteroatom bonds1. SN2 reactions typically involve backside attack of a nucleophile to the σ* orbital of a C(sp3)-X bond (X = halogen or other leaving group), resulting in complete inversion of a stereocentre2. By contrast, the corresponding stereoinvertive nucleophilic substitution on electronically unbiased sp2 vinyl electrophiles, namely concerted SNV(σ) reaction, is much rarer, and so far limited to carefully designed substrates mostly in ring-forming processes3,4. Here we show that concerted SNV reactions can be accelerated by a proposed strain-release mechanism in metallated complexes, leading to the development of a general and stereospecific alkenylidene homologation of diverse organoboronates. This method enables the iterative incorporation of multiple alkenylidene units, giving cross-conjugated polyenes that are challenging to prepare otherwise. Further application to the synthesis of bioactive compounds containing multi-substituted alkenes is also demonstrated. Computational studies suggest an unusual SN2-like concerted pathway promoted by diminishing steric strain in the square planar transition state, which explains the high efficiency and stereoinversive feature of this metallate SNV reaction.

Open-Framework Vanadate as Efficient Ion Exchanger for Uranyl Removal

The elimination of uranium from radioactive wastewater is crucial for the safe management and operation of environmental remediation. Here, we present a layered vanadate with high acid/base stability, [Me2NH2]V3O7, as an excellent ion exchanger capturing uranyl from highly complex aqueous solutions. The material possesses an indirect band gap, ferromagnetic characteristic and a flower-like morphology comprising parallel nanosheets. The layered structure of [Me2NH2]V3O7 is predominantly upheld by the H-bond interaction between anionic framework [V3O7]nn- and intercalated [Me2NH2]+. The [Me2NH2]+ within [Me2NH2]V3O7 can be readily exchanged with UO22+. [Me2NH2]V3O7 exhibits high exchange capacity (qm = 176.19 mg/g), fast kinetics (within 15 min), high removal efficiencies (>99%), and good selectivity against an excess of interfering ions. It also displays activity for UO22+ ion exchange over a wide pH range (2.00-7.12). More importantly, [Me2NH2]V3O7 has the capability to effectively remove low-concentration uranium, yielding a residual U concentration of 13 ppb, which falls below the EPA-defined acceptable limit of 30 ppb in typical drinking water. [Me2NH2]V3O7 can also efficiently separate UO22+ from Cs+ or Sr2+ achieving the highest separation factors (SFU/Cs of 589 and SFU/Sr of 227) to date. The BOMD and DFT calculations reveal that the driving force of ion exchange is dominated by the interaction between UO22+ and [V3O7]nn-, whereas the ion exchange rate is influenced by the mobility of UO22+ and [Me2NH2]+. Our experimental findings indicate that [Me2NH2]V3O7 can be considered as a promising uranium scavenger for environmental remediation. Additionally, the simulation results provide valuable mechanistic interpretations for ion exchange and serve as a reference for designing novel ion exchangers.

Revisiting Textbook Azide-Clock Reactions: A "Propeller-Crawling" Mechanism Explains Differences in Rates

An ongoing challenge to chemists is the analysis of pathways and kinetics for chemical reactions in solution, including transient structures between the reactants and products that are difficult to resolve using laboratory experiments. Here, we enabled direct molecular dynamics simulations of a textbook series of chemical reactions on the hundreds of ns to μs time scale using the weighted ensemble (WE) path sampling strategy with hybrid quantum mechanical/molecular mechanical (QM/MM) models. We focused on azide-clock reactions involving addition of an azide anion to each of three long-lived trityl cations in an acetonitrile-water solvent mixture. Results reveal a two-step mechanism: (1) diffusional collision of reactants to form an ion-pair intermediate; (2) "activation" or rearrangement of the intermediate to the product. Our simulations yield not only reaction rates that are within error of experiment but also rates for individual steps, indicating the activation step as rate-limiting for all three cations. Further, the trend in reaction rates is due to dynamical effects, i.e., differing extents of the azide anion "crawling" along the cation's phenyl-ring "propellers" during the activation step. Our study demonstrates the power of analyzing pathways and kinetics to gain insights on reaction mechanisms, underscoring the value of including WE and other related path sampling strategies in the modern toolbox for chemists.

Backside versus Frontside SN2 Reactions of Alkyl Triflates and Alcohols

Nucleophilic substitution reactions are elementary reactions in organic chemistry that are used in many synthetic routes. By quantum chemical methods, we have investigated the intrinsic competition between the backside SN2 (SN2-b) and frontside SN2 (SN2-f) pathways using a set of simple alkyl triflates as the electrophile in combination with a systematic series of phenols and partially fluorinated ethanol nucleophiles. It is revealed how and why the well-established mechanistic preference for the SN2-b pathway slowly erodes and can even be overruled by the unusual SN2-f substitution mechanism going from strong to weak alcohol nucleophiles. Activation strain analyses disclose that the SN2-b pathway is favored for strong alcohol nucleophiles because of the well-known intrinsically more efficient approach to the electrophile resulting in a more stabilizing nucleophile-electrophile interaction. In contrast, the preference of weaker alcohol nucleophiles shifts to the SN2-f pathway, benefiting from a stabilizing hydrogen bond interaction between the incoming alcohol and the leaving group. This hydrogen bond interaction is strengthened by the increased acidity of the weaker alcohol nucleophiles, thereby steering the mechanistic preference toward the frontside SN2 pathway.

Reprogramming the Transition States to Enhance C-N Cleavage Efficiency of Rhodococcus opacusl-Amino Acid Oxidase

l-Amino acid oxidase (LAAO) is an important biocatalyst used for synthesizing α-keto acids. LAAO from Rhodococcus opacus (RoLAAO) has a broad substrate spectrum; however, its low total turnover number limits its industrial use. To overcome this, we aimed to employ crystal structure-guided density functional theory calculations and molecular dynamic simulations to investigate the catalytic mechanism. Two key steps were identified: S → [TS1] in step 1 and Int1 → [TS2] in step 2. We reprogrammed the transition states [TS1] and [TS2] to reduce the identified energy barrier and obtain a RoLAAO variant capable of catalyzing 19 kinds of l-amino acids to the corresponding high-value α-keto acids with a high total turnover number, yield (≥95.1 g/L), conversion rate (≥95%), and space-time yields ≥142.7 g/L/d in 12-24 h, in a 5 L reactor. Our results indicated the promising potential of the developed RoLAAO variant for use in the industrial production of α-keto acids while providing a potential catalytic-mechanism-guided protein design strategy to achieve the desired physical and catalytic properties of enzymes.

Exploring borderline SN1-SN2 mechanisms: the role of explicit solvation protocols in the DFT investigation of isopropyl chloride

Nucleophilic substitution at saturated carbon is a crucial class of organic reactions, playing a pivotal role in various chemical transformations that yield valuable compounds for society. Despite the well-established SN1 and SN2 mechanisms, secondary substrates, particularly in solvolysis reactions, often exhibit a borderline pathway. A molecular-level understanding of these processes is fundamental for developing more efficient chemical transformations. Typically, quantum-chemical simulations of the solvent medium combine explicit and implicit solvation methods. The configuration of explicit molecules can be defined through top-down approaches, such as Monte Carlo (MC) calculations for generating initial configurations, and bottom-up methods that involve user-dependent protocols to add solvent molecules around the substrate. Herein, we investigated the borderline mechanism of the hydrolysis of a secondary substrate, isopropyl chloride (iPrCl), at DFT-M06-2X/aug-cc-pVDZ level, employing explicit and explicit + implicit protocols. Top-down and bottom-up approaches were employed to generate substrate-solvent complexes of varying number (n = 1, 3, 5, 7, 9, and 12) and configurations of H2O molecules. Our findings consistently reveal that regardless of the solvation approach, the hydrolysis of iPrCl follows a loose-SN2-like mechanism with nucleophilic solvent assistance. Increasing the water cluster around the substrate in most cases led to reaction barriers of ΔH‡ ≈ 21 kcal mol-1, with nine water molecules from MC configurations sufficient to describe the reaction. The More O'Ferrall-Jencks plot demonstrates an SN1-like character for all transition state structures, showing a clear merged profile. The fragmentation activation strain analyses indicate that energy barriers are predominantly controlled by solvent-substrate interactions, supported by the leaving group stabilization assessed through CHELPG atomic charges.

Energetics of high temperature degradation of fentanyl into primary and secondary products

Fentanyl is a synthetic opioid used for managing chronic pain. Due to its higher potency (50-100×) than morphine, fentanyl is also an abused drug. A sensor that could detect illicit fentanyl by identifying its thermally degraded fragments would be helpful to law enforcement. While experimental studies have probed the thermal degradation of fentanyl, little theoretical work has been done to understand the mechanism. Here, we studied the thermal degradation pathways of fentanyl using extensive ab initio molecular dynamics simulations combined with enhanced sampling via multiple-walker metadynamics. We calculated the free energy profile for each bond suggested earlier as a potential degradation point to map the thermodynamic driving forces. We also estimated the forward attempt rate of each bond degradation reaction to gain information about degradation kinetics.

Unraveling the promoter effect and the roles of counterion exchange in glycosylation reaction

The stereoselectivity of glycosidic bond formation continues to pose a noteworthy hurdle in synthesizing carbohydrates, primarily due to the simultaneous occurrence of SN1 and SN2 processes during the glycosylation reaction. Here, we applied an in-depth analysis of the glycosylation mechanism by using low-temperature nuclear magnetic resonance and statistical approaches. A pathway driven by counterion exchanges and reaction byproducts was first discovered to outline the stereocontributions of intermediates. Moreover, the relative reactivity values, acceptor nucleophilic constants, and Hammett substituent constants (σ values) provided a general index to indicate the mechanistic pathways. These results could allow building block tailoring and reaction condition optimization in carbohydrate synthesis to be greatly facilitated and simplified.

Modulating the Reaction Configuration by Breaking the Structural Symmetry of Active Sites for Efficient Photocatalytic Reduction of Low-concentration CO2

Photocatalytic conversion of low-concentration CO2 is considered as a promising way to simultaneously mitigate the environmental and energy issues. However, the weak CO2 adsorption and tough CO2 activation process seriously compromise the CO production, due to the chemical inertness of CO2 molecule and the formed fragile metal-C/O bond. Herein, we designed and fabricated oxygen vacancy contained Co3 O4 hollow nanoparticles on ordered macroporous N-doped carbon framework (Vo-HCo3 O4 /OMNC) towards photoreduction of low-concentration CO2 . In situ spectra and ab initio molecular dynamics simulations reveal that the constructed oxygen vacancy is able to break the local structural symmetry of Co-O-Co sites. The formation of asymmetric active site switches the CO2 configuration from a single-site linear model to a multiple-sites bending one with a highly stable configuration, enhancing the binding and structural polarization of CO2 molecules. As a result, Vo-HCo3 O4 /OMNC shows unprecedent activity in the photocatalytic conversion of low-concentration CO2 (10 % CO2 /Ar) under laboratory light source or even natural sunlight, affording a syngas yield of 337.8 or 95.2 mmol g-1  h-1 , respectively, with an apparent quantum yield up to 4.2 %.

Neighboring-Group Participation by C-2 Acyloxy Groups: Influence of the Nucleophile and Acyl Group on the Stereochemical Outcome of Acetal Substitution Reactions

A single acyloxy group at C-2 can control the outcome of nucleophilic substitution reactions of pyran-derived acetals, but the extent of the neighboring-group participation depends on a number of factors. We show here that neighboring-group participation does not necessarily control the stereochemical outcome of acetal substitution reactions with weak nucleophiles. The 1,2-trans selectivity increased with increasing reactivity of the incoming nucleophile. This trend suggests the intermediacy of both cis-fused dioxolenium ions and oxocarbenium ions in the stereochemistry-determining step. In addition, as the electron-donating ability of the neighboring group decreased, the preference for the 1,2-trans products increased. Computational studies show how the barriers for the ring-opening reaction on the dioxolenium ions and the transition states to provide the oxocarbenium ions change with the electron-donating capacity of the C-2-acyloxy group and the reactivity of the nucleophile.

Accelerating explicit solvent models of heterogeneous catalysts with machine learning interatomic potentials

Realistically modelling how solvents affect catalytic reactions is a longstanding challenge due to its prohibitive computational cost. Typically, an explicit atomistic treatment of the solvent molecules is needed together with molecular dynamics (MD) simulations and enhanced sampling methods. Here, we demonstrate the utility of machine learning interatomic potentials (MLIPs), coupled with active learning, to enable fast and accurate explicit solvent modelling of adsorption and reactions on heterogeneous catalysts. MLIPs trained on-the-fly were able to accelerate ab initio MD simulations by up to 4 orders of magnitude while reproducing with high fidelity the geometrical features of water in the bulk and at metal-water interfaces. Using these ML-accelerated simulations, we accurately predicted key catalytic quantities such as the adsorption energies of CO*, OH*, COH*, HCO*, and OCCHO* on Cu surfaces and the free energy barriers of C-H scission of ethylene glycol over Cu and Pd surfaces, as validated with ab initio calculations. We envision that such simulations will pave the way towards detailed and realistic studies of solvated catalysts at large time- and length-scales.

Allylic Carbocyclic Inhibitors Covalently Bind Glycoside Hydrolases

Allylic cyclitols were investigated as covalent inhibitors of glycoside hydrolases by chemical, enzymatic, proteomic, and computational methods. This approach was inspired by the C₇ cyclitol natural product streptol glucoside, which features a potential carbohydrate leaving group in the 4-position (carbohydrate numbering). To test this hypothesis, carbocyclic inhibitors with leaving groups in the 4- and 6- positions were prepared. The results of enzyme kinetics analyses demonstrated that dinitrophenyl ethers covalently inhibit α-glucosidases of the GH13 family without reactivation. The labeled enzyme was studied by proteomics, and the active site residue Asp214 was identified as modified. Additionally, computational studies, including enzyme homology modeling and density functional theory (DFT) calculations, further delineate the electronic and structural requirements for activity. This study demonstrates that previously unexplored 4- and 6-positions can be exploited for successful inhibitor design.

Ab Initio Metadynamics Simulations of Hexafluoroisopropanol Solvent Effects: Synergistic Role of Solvent H-Bonding Networks and Solvent-Solute C-H/π Interactions

The solvent effects in Friedel-Crafts cycloalkylation of epoxides and Cope rearrangement of aldimines were investigated by using ab initio molecular dynamics simulations. Explicit molecular treatments were applied for both reactants and solvents. The reaction mechanisms were elucidated via free energy calculations based on metadynamics simulations. The results reveal that both reactions proceed in a concerted fashion. Key solvent-substrate interactions are identified from the structures of transition states with explicit solvent molecules. The remarkable promotion effect of hexafluoroisopropanol solvent is ascribed to the synergistic effect of H-bonding networks and C-H/π interactions with substrates.

Glycosidase mechanisms: Sugar conformations and reactivity in endo- and exo-acting enzymes

The enzymatic breakdown of carbohydrates plays a critical role in several biological events and enables the development of sustainable processes to obtain bioproducts and biofuels. In this scenario, the design of efficient inhibitors for glycosidases that can act as drug targets and the engineering of carbohydrate-active enzymes with tailored catalytic properties is of remarkable importance. To guide rational approaches, it is necessary to elucidate enzyme molecular mechanisms, in particular understanding how the microenvironment modulates the conformational space explored by the substrate. Computer simulations, especially those based on ab initio methods, have provided a suitable atomic description of carbohydrate conformations and catalytic reactions in several glycosidase families. In this review, we will focus on how the active-site topology (pocket or cleft) and mode of cleavage (endo or exo) can affect the catalytic mechanisms adopted by glycosidases, in particular the substrate conformations along the reaction coordinate.

Involvement of an Oxonium Ion Intermediate in Controlling the Diastereoselectivity of Nucleophilic Substitution Reactions of Septanoses

The alkoxy substituents at C4 and C2 of septanoses control the stereochemical outcomes of O-glycosylation reactions of these seven-membered-ring intermediates. Isolation of a bicyclic acetal byproduct in some substitution reactions suggests that the C4 benzyloxy substituent engaged in long-range participation, stabilizing intermediates by the formation of an oxonium ion intermediate. Inductive destabilization of the carbocationic intermediate provided by the C2 substituent is crucial to the participation of the remote alkoxy group.

Mimicry of the proton wire mechanism of enzymes inside a supramolecular capsule enables β-selective O-glycosylations

Enzymes achieve high substrate and product selectivities by orientating and activating the substrate(s) appropriately inside a confined and finely optimized binding pocket. Although some basic aspects of enzymes have already been mimicked successfully with man-made catalysts, substrate activation by proton wires inside enzyme pockets has not been recreated with man-made catalysts so far. A proton wire facilitates the dual activation of a nucleophile and an electrophile via a reciprocal proton transfer, enabling highly stereoselective reactions under mild conditions. Here we present evidence for such an activation mode inside the supramolecular resorcin[4]arene capsule and demonstrate that it enables catalytic and highly β-selective glycosylation reactions-still a major challenge in glycosylation chemistry. Extensive control experiments provide very strong evidence that the reactions take place inside the molecular container. We show that this activation strategy is compatible with a broad scope of glycoside donors and nucleophiles, and is only limited by the cavity size.

Recent Advances in Stereoselective Chemical O-Glycosylation Reactions

Carbohydrates involving glycoconjugates play a pivotal role in many life processes. Better understanding toward glycobiological events including the structure–function relationship of these biomolecules and for diagnostic and therapeutic purposes including tailor-made vaccine development and synthesis of structurally well-defined oligosaccharides (OS) become important. Efficient chemical glycosylation in high yield and stereoselectivity is however challenging and depends on the fine tuning of a protection profile to get matching glycosyl donor–acceptor reactivity along with proper use of other important external factors like catalyst, solvent, temperature, activator, and additive. So far, many glycosylation methods have been reported including several reviews also. In the present review, we will concentrate our discussion on the recent trend on α- and β-selective glycosylation reactions reported during the past decade.

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 S_N2X manifold, which consists of two primary elementary steps: halogen atom transfer (XAT) and subsequent S_N2. For the first calculated model on original experimental substrates, XAT reaction barriers were more kinetically competitive than an S_N2 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 S_N2X manifold over S_N2. 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 S_N2X 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 S_N2X C-C bond formation.

Computational discoveries of reaction mechanisms: recent highlights and emerging challenges

This review examines some of the notable advances and trends that have shaped the field of computational elucidation of organic reaction mechanisms over the last 10-15 years. It highlights the types of mechanistic problems that have recently become possible to study and summarizes the methodological developments that have permitted these new advances. Case studies are taken from three representative areas of organic chemistry-asymmetric catalysis, glycosylation reactions, and single electron transfer reactions-which illustrate themes common to the broader field. These include the trend towards modelling systems that are increasingly complex (both structurally and mechanistically), the growing appreciation of the mechanistic roles of non-covalent interactions, and the increasing ability to explore dynamical features of reaction mechanisms. Some interesting new challenges that have emerged in the field are identified.

Stereoselective gem-C,B-Glycosylation via 1,2-Boronate Migration

A novel protocol is established for the long-standing challenge of stereoselective geminal bisglycosylations of saccharides. The merger of PPh₃ as a traceless glycosidic leaving group and 1,2-boronate migration enables the simultaneous introduction of C-C and C-B bonds at the anomeric stereogenic center of furanoses and pyranoses. The power of this method is showcased by a set of site-selective modifications of glycosylation products for the construction of bioactive conjugates and skeletons. A scarce metal-free 1,1-difunctionalization process of alkenes is also concomitantly demonstrated.

Effect of solvent motions on the dynamics of the Diels-Alder reaction

How solvent motions affect the dynamics of chemical reactions in which the solute undergoes a substantial shape change is a fundamental but elusive issue. This work utilizes reactive simulation and Grote-Hynes theory to explore the effect of solvent motions on the dynamics of the Diels-Alder reaction (in the reverse direction, this reaction involves very substantial solute expansion) in aprotic solvents. The results reveal that the solvent environment is not sufficiently constraining to influence transition state passage dynamics, with the calculated transmission coefficients being close to unity. Even when solvent motions are suppressed or artificially slowed down, the solvent only affects the reaction dynamics in the transition state region to a very small extent. The only notable effect of solvent occurs far from the transition state region and corresponds to caging of the reactants within the reactant well.

Melding of Experiment and Theory Illuminates Mechanisms of Metal-Catalyzed Rearrangements: Computational Approaches and Caveats

This review summarizes approaches and caveats in computational modeling of transition-metal-catalyzed sigmatropic rearrangements involving carbene transfer. We highlight contemporary examples of combined synthetic and theoretical investigations that showcase the synergy achievable by integrating experiment and theory.

1 Introduction

2 Mechanistic Models

3 Theoretical Approaches and Caveats

3.1 Recommended Computational Tools

3.2 Choice of Functional and Basis Set

3.3 Conformations and Ligand-Binding Modes

3.4 Solvation

4 Synergy of Experiment and Theory – Case Studies

4.1 Metal-Bound or Free Ylides?

4.2 Conformations and Ligand-Binding Modes of Paddlewheel Complexes

4.3 No Metal, Just Light

4.4 How To ‘Cope’ with Nonstatistical Dynamic Effects

5 Outlook

Structural insights into the repair mechanism of AGT for methyl-induced DNA damage

Methylation induced DNA base-pairing damage is one of the major causes of cancer. O6-alkylguanine-DNA alkyltransferase (AGT) is considered a demethylation agent of the methylated DNA. Structural investigations with thermodynamic properties of the AGT-DNA complex are still lacking. In this report, we modeled two catalytic states of AGT-DNA interactions and an AGT-DNA covalent complex and explored structural features using molecular dynamics (MD) simulations. We utilized the umbrella sampling method to investigate the changes in the free energy of the interactions in two different AGT-DNA catalytic states, one with methylated GUA in DNA and the other with methylated CYS145 in AGT. These non-covalent complexes represent the pre- and post-repair complexes. Therefore, our study encompasses the process of recognition, complex formation, and separation of the AGT and the damaged (methylated) DNA base. We believe that the use of parameters for the amino acid and nucleotide modifications and for the protein-DNA covalent bond will allow investigations of the DNA repair mechanism as well as the exploration of cancer therapeutics targeting the AGT-DNA complexes at various functional states as well as explorations via stabilization of the complex.

Influence of Configuration at the 4- and 6-Positions on the Conformation and Anomeric Reactivity and Selectivity of 7-Deoxyheptopyranosyl Donors: Discovery of a Highly Equatorially Selective l-glycero-d-gluco-Heptopyranosyl Donor

The preparation of four per-O-benzyl-d- or l-glycero-d-galacto and d- or l-glycero-d-gluco heptopyranosyl sulfoxides and the influence of their side-chain conformations on reactivity and stereoselectivity in glycosylation reactions are described. The side-chain conformation in these donors is determined by the relative configuration of its point of attachment to the pyranoside ring and the two flanking centers in agreement with a recent model. In the d- and l-glycero-d-galacto glycosyl donors, the d-glycero-d-galacto isomer with the more electron-withdrawing trans,gauche conformation of its side chain was the more equatorially selective isomer. In the d- and l-glycero-d-gluco glycosyl donors, the l-glycero-d-gluco isomer with the least disarming gauche,gauche side-chain conformation was the most equatorially selective donor. Variable temperature NMR studies, while supporting the formation of intermediate glycosyl triflates at -80 °C in all cases, were inconclusive owing to a change in the decomposition mechanism with the change in configuration. It is suggested that the equatorial selectivity of the l-glycero-d-gluco isomer arises from H-bonding between the glycosyl acceptor and O6 of the donor, which is poised to deliver the acceptor antiperiplanar to the glycosyl triflate, resulting in a high degree of S_N2 character in the displacement reaction.

Self-Promoted Stereoselective Glycosylations - Past, Present, Future

Self-promoted glycosylations have generally not received much attention, despite having the advantages of being easy to perform and often highly stereoselective. This account covers the work done in this field and the mechanistic aspects of self-promoted glycosylations are discussed, with a main focus on the stereoselectivity of the reactions. Most self-promoted glycosylations utilize trichloroacetimidate donors, but examples of self-promoted reactions with other donors have been described and will be discussed. Self-promoted glycosylation strategies can provide a basis for new stereoselective glycosylation methodologies.

A dynamic picture of the halolactonization reaction through a combination of ab initio metadynamics and experimental investigations

The halolactonization reaction is one of the most common electrophilic addition reactions to alkenes. The mechanism is generally viewed as a two-step pathway, which involves the formation of an ionic intermediate, in most cases a haliranium ion. Recently, an alternative concerted mechanism was proposed, in which the nucleophile of the reaction played a key role in the rate determining step by forming a pre-polarized complex with the alkene. This pathway was coined the nucleophile-assisted alkene activation (NAAA) mechanism. Metadynamics simulations on a series of model halolactonization reactions were used to obtain the full dynamic trajectory from reactant to product and investigate the explicit role of the halogen source and solvent molecules in the mechanism. The results in this work ratify the occasional preference of a concerted mechanism over the classic two-step transformation under specific reaction conditions. Nevertheless, as the stability of both the generated substrate cation and counter-anion increase, a transition towards the classic two-step mechanism was observed. NCI analyses on the transition states revealed that the activating role of the nucleophile is independent of the formation and stability of the intermediate. Additionally, the dynamic insights obtained from the metadynamics simulations and NCI analyses employed in this work, unveiled the presence of syn-directing noncovalent interactions, such as hydrogen bonding, between the alkenoic acid and the halogen source, which rationalized the experimentally observed diastereoselectivities. Explicit noncovalent interactions between the reactants and a protic solvent or basic additive are able to disrupt these syn-directing noncovalent interactions, affecting the diastereoselective outcome of the reaction.

Automated Quantification of Hydroxyl Reactivities: Prediction of Glycosylation Reactions

The stereoselectivity and yield in glycosylation reactions are paramount but unpredictable. We have developed a database of acceptor nucleophilic constants (Aka) to quantify the nucleophilicity of hydroxyl groups in glycosylation influenced by the steric, electronic and structural effects, providing a connection between experiments and computer algorithms. The subtle reactivity differences among the hydroxyl groups on various carbohydrate molecules can be defined by Aka, which is easily accessible by a simple and convenient automation system to assure high reproducibility and accuracy. A diverse range of glycosylation donors and acceptors with well-defined reactivity and promoters were organized and processed by the designed software program "GlycoComputer" for prediction of glycosylation reactions without involving sophisticated computational processing. The importance of Aka was further verified by random forest algorithm, and the applicability was tested by the synthesis of a Lewis A skeleton to show that the stereoselectivity and yield can be accurately estimated.