Resolving apparent conflicts between theoretical and experimental models of phosphate monoester hydrolysis

Simulation-Guided Conformational Space Exploration to Assess Reactive Conformations of a Ribozyme

Self-splicing ribozymes are small ribonucleic acid (RNA) enzymes that catalyze their own cleavage through a transphosphoesterification reaction. While this process is involved in some specific steps of viral RNA replication and splicing, it is also of importance in the context of the (putative) first autocatalytic RNA-based systems that could have preceded the emergence of modern life. The uncatalyzed phosphoester bond formation is thermodynamically very unfavorable, and many experimental studies have focused on understanding the molecular features of catalysis in these ribozymes. However, chemical reaction paths are short-lived and not easily characterized by experimental approaches, so molecular simulation approaches appear as an ideal tool to unveil the molecular details of the reaction. Here, we focus on the model hairpin ribozyme. We show that identifying a relevant initial conformation for reactivity studies, which is frequently overlooked in mixed quantum-classical studies that predominantly concentrate on the chemical reaction itself, can be highly challenging. These challenges stem from limitations in both available experimental structures (which are chemically altered to prevent self-cleavage) and the accuracy of force fields, together with the necessity for comprehensive sampling. We show that molecular dynamics simulations, combined with extensive conformational phase space exploration with Hamiltonian replica-exchange simulations, enable us to characterize the relevant conformational basins of the minimal hairpin ribozyme in the ligated state prior to self-cleavage. We find that what is usually considered a canonical reactive conformation with active site geometries and hydrogen-bond patterns that are optimal for the addition-elimination reaction with general acid/general base catalysis is metastable and only marginally populated. The thermodynamically stable conformation appears to be consistent with the expectations of a mechanism that does not require the direct participation of ribozyme residues in the reaction. While these observations may suffer from forcefield inaccuracies, all investigated forcefields lead to the same conclusions upon proper sampling, contrasting with previous investigations on shorter timescales suggesting that at least one reparametrization of the Amber99 forcefield allowed to stabilize aligned active site conformations. Our study demonstrates that identifying the most pertinent reactant state conformation holds equal importance alongside the accurate determination of the thermodynamics and kinetics of the chemical steps of the reaction.

Unveiling the Cleavage Mechanism of an RNA Model Compound on the whole pH Scale: Computations Meet Experiments in the Determination of Reaction Rates

The knowledge of the mechanism of reactions occurring in solution is a primary research line both in the context of theoretical-computational chemistry and in the field of organic and bio-organic chemistry. Given the importance of the hydrolysis of nucleic acids in life-related phenomena, here we present a combined experimental and computational study on the cleavage of an RNA model compound. This phosphodiester features a cleavage rate strictly dependent on the pH with three different dependence domains. Such experimental evidence, highlighted by an in-depth kinetic investigation, unequivocally suggests a change in the reaction mechanism along the pH scale. In order to interpret the data and to explain the experimental behavior, we have applied a theoretical-computational procedure, involving a hybrid quantum/classical approach, able to model chemical reactions in complex environments, i. e. in solution. This study turns out to quantitatively reproduce the experimental data with accuracy and, in addition, provides useful mechanistic insight into the transesterification process of the investigated compound. The study indicates that the cleavage can occur through anA N D N ${A_N D_N }$ , anA N + D N ${A_N + D_N }$ , and aD N A N ${D_N A_N }$ mechanism depending on the pH values.

Prebiotic chemical reactivity in solution with quantum accuracy and microsecond sampling using neural network potentials

While RNA appears as a good candidate for the first autocatalytic systems preceding the emergence of modern life, the synthesis of RNA oligonucleotides without enzymes remains challenging. Because the uncatalyzed reaction is extremely slow, experimental studies bring limited and indirect information on the reaction mechanism, the nature of which remains debated. Here, we develop neural network potentials (NNPs) to study the phosphoester bond formation in water. While NNPs are becoming routinely applied to nonreactive systems or simple reactions, we demonstrate how they can systematically be trained to explore the reaction phase space for complex reactions involving several proton transfers and exchanges of heavy atoms. We then propagate at moderate computational cost hundreds of nanoseconds of a variety of enhanced sampling simulations with quantum accuracy in explicit solvent conditions. The thermodynamically preferred reaction pathway is a concerted, dissociative mechanism, with the transient formation of a metaphosphate transition state and direct participation of water solvent molecules that facilitate the exchange of protons through the nonbridging phosphate oxygens. Associative-dissociative pathways, characterized by a much tighter pentacoordinated phosphate, are higher in free energy. Our simulations also suggest that diprotonated phosphate, whose reactivity is never directly assessed in the experiments, is significantly less reactive than the monoprotonated species, suggesting that it is probably never the reactive species in normal pH conditions. These observations rationalize unexplained experimental results and the temperature dependence of the reaction rate, and they pave the way for the design of more efficient abiotic catalysts and activating groups.

Prediction model on hydrolysis kinetics of phthalate monoester: A density functional theory study

As primary degradation products of phthalate esters, phthalate monoesters (MPEs) have been widely detected in various aquatic environments and drawn growing toxicological concerns. Hydrolysis kinetics that is of importance for assessing environmental persistence of chemicals remain elusive for MPEs. Herein, kinetics of base-catalyzed and neutral hydrolysis for 18 MPEs with different leaving groups was investigated by density functional theory calculation. Results indicate that MPEs with leaving groups having pKa of <10 prefer dissociative transition states. MPEs are more persistent than their parents, and their hydrolysis half-lives were calculated to vary from 3.4 min to 79.2 years (pH = 7-9). A quantitative structure-activity relationship model was developed for predicting the hydrolysis kinetics parameters. It was found that pKa of the leaving groups and electronegativity of the MPEs are key factors determining the hydrolysis kinetics. This work may lay a theoretical foundation for better understanding the chemical process that governs MPE persistence in aquatic environments.

Aqueous degradation of 6-APA by hydroxyl radical: a theoretical study

CONTEXT

Degradation reactions of micropollutants such as antibiotics with OH radicals are very important in terms of environmental pollution. Therefore, in this study, the degradation kinetic mechanism of 6-aminopenicillanic acid (6-APA) with OH radical was investigated by density functional theory (DFT) methods.

METHODS

For the calculations, different functionals such as B3LYP, MPW1PW91, and M06-2X were used with a 6-31 g(d,p) basis set. The aquatic effect on the reaction mechanism was investigated by conductor-like polarizable continuum model (CPCM). For the degradation kinetics in aqueous media, the addition of explicit water molecules was also calculated. Subsequent reaction mechanism for the most probable reaction product was briefly discussed.

RESULTS

Among the functionals used, B3LYP results were consistent with the experimental results. Calculated kinetic parameters indicated that the OH-addition path was more dominant than the H-abstraction paths. With the increase of explicit water molecules in the models, the energy required for the formation of transition state complexes decreased. The overall rate constant is calculated as 2.28 × 10¹¹ M^-1 s^-1 at 298 K for the titled reaction.

Distinct chemical factors in hydrolytic reactions catalyzed by metalloenzymes and metal complexes

The selective hydrolysis of the extremely stable phosphoester, peptide and ester bonds of molecules by bio-inspired metal-based catalysts (metallohydrolases) is required in a wide range of biological, biotechnological and industrial applications. Despite the impressive advances made in the field, the ultimate goal of designing efficient enzyme mimics for these reactions is still elusive. Its realization will require a deeper understanding of the diverse chemical factors that influence the activities of both natural and synthetic catalysts. They include catalyst-substrate complexation, non-covalent interactions and the electronic nature of the metal ion, ligand environment and nucleophile. Based on our computational studies, their roles are discussed for several mono- and binuclear metallohydrolases and their synthetic analogues. Hydrolysis by natural metallohydrolases is found to be promoted by a ligand environment with low basicity, a metal bound water and a heterobinuclear metal center (in binuclear enzymes). Additionally, peptide and phosphoester hydrolysis is dominated by two competing effects, i.e. nucleophilicity and Lewis acid activation, respectively. In synthetic analogues, hydrolysis is facilitated by the inclusion of a second metal center, hydrophobic effects, a biological metal (Zn, Cu and Co) and a terminal hydroxyl nucleophile. Due to the absence of the protein environment, hydrolysis by these small molecules is exclusively influenced by nucleophile activation. The results gleaned from these studies will enhance the understanding of fundamental principles of multiple hydrolytic reactions. They will also advance the development of computational methods as a predictive tool to design more efficient catalysts for hydrolysis, Diels-Alder reaction, Michael addition, epoxide opening and aldol condensation.

The Impact of DFT Functional, Cluster Model Size, and Implicit Solvation on the Structural Description of Single-Metal-Mediated DNA Phosphodiester Bond Cleavage: The Case Study of APE1

Phosphodiester bond hydrolysis in nucleic acids is a ubiquitous reaction that can be facilitated by enzymes called nucleases, which often use metal ions to achieve catalytic function. While a two-metal-mediated pathway has been well established for many enzymes, there is growing support that some enzymes require only one metal for the catalytic step. Using human apurinic/apyrimidinic endonuclease (APE1) as a prototypical example and cluster models, this study clarifies the impact of DFT functional, cluster model size, and implicit solvation on single-metal-mediated phosphodiester bond cleavage and provides insight into how to efficiently model this chemistry. Initially, a model containing 69 atoms built from a high-resolution X-ray crystal structure is used to explore the reaction pathway mapped by a range of DFT functionals and basis sets, which provides support for the use of standard functionals (M06-2X and B3LYP-D3) to study this reaction. Subsequently, systematically increasing the model size to 185 atoms by including additional amino acids and altering residue truncation points highlights that small models containing only a few amino acids or β carbon truncation points introduce model strains and lead to incorrect metal coordination. Indeed, a model that contains all key residues (general base and acid, residues that stabilize the substrate, and amino acids that maintain the metal coordination) is required for an accurate structural depiction of the one-metal-mediated phosphodiester bond hydrolysis by APE1, which results in 185 atoms. The additional inclusion of the broader enzyme environment through continuum solvation models has negligible effects. The insights gained in the present work can be used to direct future computational studies of other one-metal-dependent nucleases to provide a greater understanding of how nature achieves this difficult chemistry.

Molecular Mechanisms of Phosphoester Bond Formation in Water Using Tight-Binding Ab Initio Molecular Dynamics

Phosphate groups are ubiquitous in biomolecules and are usually incorporated through phosphoester bonds between alcohol groups and orthophosphate. The formation of this bond is exceptionally difficult, with associated barriers of 30-45 kcal/mol in the absence of catalysts. In abiotic conditions, polymerizing nucleic acids without enzymes remains very challenging and is still a partly unsolved problem that severely questions the RNA World hypothesis for the origins of life. Offering a solution to this problem would involve a detailed knowledge of the reaction energetics and mechanisms, yet these remain not fully understood at a molecular level, especially because of the very slow reaction rates that represent a significant challenge for the experiments. The number of involved reaction coordinates and the possible role of the solvent in assisting the reaction are challenging for computational studies. Here, we use extensive ab initio molecular dynamics simulations using semiempirical tight-binding methods and enhanced sampling to address these issues. We first show that the choice of the tight-binding method is greatly limited by the instability of the water liquid phase for most DFTB generations and parameter sets that are widely available. We then focus on a model reaction involving methanol and orthophosphate, for which the two protonation states (mono- and dianionic) that are dominant around neutral pH are considered. We compare different proton coordinates that enable (or not) the participation of solvent water molecules. Our simulations suggest that in all cases, a dissociative associative mechanism, with an intermediate metaphosphate, is favored. The main difference between the two phosphate species is that reaction with the monoanion is assisted by the substrate, while that with the dianion involves solvent water molecules. Our results are in agreement with early experimental measurements, but the reaction barriers are underestimated in our framework. We believe that our approach provides an interesting perspective on how to sample the reaction phase space efficiently, but it calls for future studies using more accurate descriptions of chemical reactivity.

Origin of iodine preferential attack at sulfur in phosphorothioate and subsequent P-O or P-S bond dissociation

Iodine-induced cleavage at phosphorothioate DNA (PT-DNA) is characterized by extremely high sensitivity (∼1 phosphorothioate link per 106 nucleotides), which has been used for detecting and sequencing PT-DNA in bacteria. Despite its foreseeable potential for wide applications, the cleavage mechanism at the PT-modified site has not been well established, and it remains unknown as to whether or not cleavage of the bridging P-O occurs at every PT-modified site. In this work, we conducted accurate ωB97X-D calculations and high-performance liquid chromatography-mass spectrometry to investigate the process of PT-DNA cleavage at the atomic and molecular levels. We have found that iodine chemoselectively binds to the sulfur atom of the phosphorothioate link via a strong halogen-chalcogen interaction (a type of halogen bond, with binding affinity as high as 14.9 kcal/mol) and thus triggers P-O bond cleavage via phosphotriester-like hydrolysis. Additionally, aside from cleavage of the bridging P-O bond, the downstream hydrolyses lead to unwanted P-S/P-O conversions and a loss of the phosphorothioate handle. The mechanism we outline helps to explain specific selectivity at the PT-modified site but also predicts the dynamic stoichiometry of P-S and P-O bond breaking. For instance, Tris is involved in the cascade derivation of S-iodo-phosphorothioate to S-amino-phosphorothioate, suppressing the S-iodo-phosphorothioate hydrolysis to a phosphate diester. However, hydrolysis of one-third of the Tris-O-grafting phosphotriester results in unwanted P-S/P-O conversions. Our study suggests that bacterial DNA phosphorothioation may more frequently occur than previous bioinformatic estimations have predicted from iodine-induced deep sequencing data.

Promiscuous Catalytic Activity of a Binuclear Metallohydrolase: Peptide and Phosphoester Hydrolyses

In this study, chemical promiscuity of a binuclear metallohydrolase Streptomyces griseus aminopeptidase (SgAP) has been investigated using DFT calculations. SgAP catalyzes two diverse reactions, peptide and phosphoester hydrolyses, using its binuclear (Zn-Zn) core. On the basis of the experimental information, mechanisms of these reactions have been investigated utilizing leucine p-nitro aniline (Leu-pNA) and bis(4-nitrophenyl) phosphate (BNPP) as the substrates. The computed barriers of 16.5 and 16.8 kcal/mol for the most plausible mechanisms proposed by the DFT calculations are in good agreement with the measured values of 13.9 and 18.3 kcal/mol for the Leu-pNA and BNPP hydrolyses, respectively. The former was found to occur through the transfer of two protons, while the latter with only one proton transfer. They are in line with the experimental observations. The cleavage of the peptide bond was the rate-determining process for the Leu-pNA hydrolysis. However, the creation of the nucleophile and its attack on the electrophile phosphorus atom was the rate-determining step for the BNPP hydrolysis. These calculations showed that the chemical nature of the substrate and its binding mode influence the nucleophilicity of the metal bound hydroxyl nucleophile. Additionally, the nucleophilicity was found to be critical for the Leu-pNA hydrolysis, whereas double Lewis acid activation was needed for the BNPP hydrolysis. That could be one of the reasons why peptide hydrolysis can be catalyzed by both mononuclear and binuclear metal cofactors containing hydrolases, while phosphoester hydrolysis is almost exclusively by binuclear metallohydrolases. These results will be helpful in the development of versatile catalysts for chemically distinct hydrolytic reactions.

Computational Modelling of the Interactions Between Polyoxometalates and Biological Systems

Polyoxometalates (POMs) structures have raised considerable interest for the last years in their application to biological processes and medicine. Within this area, our mini-review shows that computational modelling is an emerging tool, which can play an important role in understanding the interaction of POMs with biological systems and the mechanisms responsible of their activity, otherwise difficult to achieve experimentally. During recent years, computational studies have mainly focused on the analysis of POM binding to proteins and other systems such as lipid bilayers and nucleic acids, and on the characterization of reaction mechanisms of POMs acting as artificial metalloproteases and phosphoesterases. From early docking studies locating binding sites, molecular dynamics (MD) simulations have allowed to characterize the nature of POM···protein interactions, and to evaluate the effect of the charge, size, and shape of the POM on protein affinity, including also, the atomistic description of chaotropic character of POM anions. Although these studies rely on the interaction with proteins and nucleic acid models, the results could be extrapolated to other biomolecules such as carbohydrates, triglycerides, steroids, terpenes, etc. Combining MD simulations with quantum mechanics/molecular mechanics (QM/MM) methods and DFT calculations on cluster models, computational studies are starting to shed light on the factors governing the activity and selectivity for the hydrolysis of peptide and phosphoester bonds catalysed by POMs.

Atomistic Simulations for Reactions and Vibrational Spectroscopy in the Era of Machine Learning─Quo Vadis?

Atomistic simulations using accurate energy functions can provide molecular-level insight into functional motions of molecules in the gas and in the condensed phase. This Perspective delineates the present status of the field from the efforts of others and some of our own work and discusses open questions and future prospects. The combination of physics-based long-range representations using multipolar charge distributions and kernel representations for the bonded interactions is shown to provide realistic models for the exploration of the infrared spectroscopy of molecules in solution. For reactions, empirical models connecting dedicated energy functions for the reactant and product states allow statistically meaningful sampling of conformational space whereas machine-learned energy functions are superior in accuracy. The future combination of physics-based models with machine-learning techniques and integration into all-purpose molecular simulation software provides a unique opportunity to bring such dynamics simulations closer to reality.

Heavy-Atom Kinetic Isotope Effects: Primary Interest or Zero Point?

Chemists have many options for elucidating reaction mechanisms. Global kinetic analysis and classic transition-state probes (e.g., LFERs, Eyring) inevitably form the cornerstone of any strategy, yet their application to increasingly sophisticated synthetic methodologies often leads to a wide range of indistinguishable mechanistic proposals. Computational chemistry provides powerful tools for narrowing the field in such cases, yet wholly simulated mechanisms must be interpreted with great caution. Heavy-atom kinetic isotope effects (KIEs) offer an exquisite but underutilized method for reconciling the two approaches, anchoring the theoretician in the world of calculable observables and providing the experimentalist with atomistic insights. This Perspective provides a personal outlook on this synergy. It surveys the computation of heavy-atom KIEs and their measurement by NMR spectroscopy, discusses recent case studies, highlights the intellectual reward that lies in alignment of experiment and theory, and reflects on the changes required in chemical education in the area.

From groove binding to intercalation: unravelling the weak interactions and other factors modulating the modes of interaction between methylated phenanthroline-based drugs and duplex DNA

Several antitumor drugs base their cytotoxicity on their capacity to intercalate between base pairs of DNA. Nevertheless, it has been established that the mechanism of intercalation of drugs in DNA starts with the prior groove binding mode of interaction of the drug with DNA. Sometimes, for some kind of flat small molecules, groove binding does not produce any cytotoxic effect and the fast transition of such flat small molecules to the cytotoxic intercalation mode is desirable. This is the case of methylated phenanthroline (phen) derivatives, where, changes in the substitution in the position and number of methyl groups determine their capability as cytotoxic compounds and, therefore, it is a way for the modulation of cytotoxic effects. In this work, we studied this modulation by means of the interaction of the [Pt(en)(phen)]²⁺ complex and several derivatives by methylation of phen in different number and position and the d(GTCGAC)₂ DNA hexamer via groove binding using PM6-DH2 and DFT-D methods. The analysis of the geometries, electronic structure and energetics of the studied systems was compared to experimental works to gain insight into the relation structure-interaction for the studied systems with cytotoxicity. The trends are explained by means of the Non-Covalent Interaction (NCI) index, the Energy Decomposition Analysis (EDA) and solvation contributions. Our results are in agreement with the experiments, in which the methylation of position 4 of phen seems to favour the interaction via groove binding thus making the transition to the intercalation cytotoxic mode difficult. Looking at the NCI results, these interactions come not only from the CH/π and CH/n interactions of the methyl group in position 4 but also from the ethylenediamine (en) ligand, whose orientation in the Pt complex was found in such a way that it produces a high number of weak interactions with DNA, especially with the sugar and phosphate backbone.

Structure and Reactivity of Alloxan Monohydrate in the Liquid Phase

Alloxan is an important toxic glucose analogue used to induce diabetes in lab test animals. Once regarded as a "problem structure," the condensed-phase structure of anhydrous alloxan has largely been settled, but literature inconsistencies remain for the structure of the typically employed reagent alloxan monohydrate. Due to the criticality of structure-function relationships, we have used ¹H/¹³C{¹H} NMR, IR spectroscopy, as well as quantum mechanical (QM) calculations to probe the liquid-phase structure and reactivity of alloxan monohydrate. In protic solvents (D₂O and acetic acid-d₄), hydration at the C5 carbonyl of alloxan monohydrate occurs quantitatively to form the C5 gem-diol (5,5'-dihydroxybarbituric acid). In the aprotic solvent dimethyl sulfoxide (DMSO)-d₆, there exists a mixture of the C5 gem-diol and planar tetraketo form of alloxan monohydrate. QM calculations explain the solvent-dependent hydration reactivity, where a solvent-assisted H-atom transfer mechanism lowers the activation energy of water addition at the C5 carbonyl by ∼16 or 27 kcal/mol in water or acetic acid, respectively, compared to the unassisted hydration reaction. Prompt recrystallization of alloxan monohydrate from boiling water does not alter the structure of the reagent. These findings probe the exact structure of alloxan monohydrate to guide future research efforts in biological sciences and in organic synthesis.

Synthesis, Stability, and Kinetics of Hydrogen Sulfide Release of Dithiophosphates

The development of chemicals to slowly release hydrogen sulfide would aid the survival of plants under environmental stressors as well as increase harvest yields. We report a series of dialkyldithiophosphates and disulfidedithiophosphates that slowly degrade to release hydrogen sulfide in the presence of water. Kinetics of the degradation of these chemicals were obtained at 85 °C and room temperature, and it was shown that the identity of the alkyl or sulfide group had a large impact on the rate of hydrolysis, and the rate constant varied by more than 10⁴×. For example, using tert-butanol as the nucleophile yielded a dithiophosphate (8) that hydrolyzed 13,750× faster than the dithiophosphate synthesized from n-butanol (1), indicating that the rate of hydrolysis is structure-dependent. The rates of hydrolysis at 85 °C varied from a low value of 6.9 × 10^-4 h^-1 to a high value of 14.1 h^-1. Hydrogen sulfide release in water was also quantified using a hydrogen sulfide-sensitive electrode. Corn was grown on an industrial scale and dosed with dibutyldithiophosphate to show that these dithiophosphates have potential applications in agriculture. At a loading of 2 kg per acre, a 6.4% increase in the harvest yield of corn was observed.

New Insights on the Interaction of Phenanthroline Based Ligands and Metal Complexes and Polyoxometalates with Duplex DNA and G-Quadruplexes

This work provides new insights from our team regarding advances in targeting canonical and non-canonical nucleic acid structures. This modality of medical treatment is used as a form of molecular medicine specifically against the growth of cancer cells. Nevertheless, because of increasing concerns about bacterial antibiotic resistance, this medical strategy is also being explored in this field. Up to three strategies for the use of DNA as target have been studied in our research lines during the last few years: (1) the intercalation of phenanthroline derivatives with duplex DNA; (2) the interaction of metal complexes containing phenanthroline with G-quadruplexes; and (3) the activity of Mo polyoxometalates and other Mo-oxo species as artificial phosphoesterases to catalyze the hydrolysis of phosphoester bonds in DNA. We demonstrate some promising computational results concerning the favorable interaction of these small molecules with DNA that could correspond to cytotoxic effects against tumoral cells and microorganisms. Therefore, our results open the door for the pharmaceutical and medical applications of the compounds we propose.

Mechanistic Insights into Promoted Hydrolysis of Phosphoester Bonds by MoO2Cl2(DMF)2

A phosphoester bond is a crucial structural block in biological systems, whose occurrence is regulated by phosphatases. Molybdenum compounds have been reported to be active in phosphate ester hydrolysis of model phosphates. Specifically, MoO₂Cl₂(DMF)₂ is active in the hydrolysis of para-nitrophenyl phosphate (pNPP), leading to heteropolyoxometalate structures. We use density functional theory (DFT) to clarify the mechanism by which these species promote the hydrolysis of the phosphoester bond. The present calculations give insight into several key aspects of this reaction: (i) the speciation of this complex prior to interaction with the phosphate (DMF release, Mo-Cl hydrolysis, and pH influence on the speciation), (ii) the competition between phosphate addition and the molybdate nucleation process, (iii) and the mechanisms by which some plausible active species promote this hydrolysis in different conditions. We described thoroughly two different pathways depending on the nucleation possibilities of the molybdenum complex: one mononuclear mechanism, which is preferred in conditions in which very low complex concentrations are used, and another dinuclear mechanism, which is preferred at higher concentrations.

Mechanisms of a Cyclobutane-Fused Lactone Hydrolysis in Alkaline and Acidic Conditions

Searching for functional polyesters with stability and degradability is important due to their potential applications in biomedical supplies, biomass fuel, and environmental protection. Recently, a cyclobutane-fused lactone (CBL) polymer was experimentally found to have superior stability and controllable degradability through hydrolysis reactions after activation by mechanical force. In order to provide a theoretical basis for developing new functional degradable polyesters, in this work, we performed a detailed quantum chemical study of the alkaline and acidic hydrolysis of CBL using dispersion-corrected density functional theory (DFT-D3) and mixed implicit/explicit solvent models. Various possible hydrolysis mechanisms were found: B_AC2 and B_AL2 in the alkaline condition and A_AC2, A_AL2, and A_AL1 in the acidic condition. Our calculations indicated that CBL favors the B_AC2 and A_AC2 mechanisms in alkaline and acidic conditions, respectively. In addition, we found that incorporating explicit water solvent molecules is highly necessary because of their strong hydrogen-bonding with reactant/intermediate/product molecules.

Dual-Selective Catalysis in Dephosphorylation Tuned by Hf6-Containing Metal-Organic Frameworks Mimicking Phosphatase

Selective dephosphorylation is full of great challenges in the field of biomimetic catalysis. To mimic the active sites of protein phosphatase, Hf-OH-Hf motif-containing metal-organic frameworks (MOFs) were obtained and structurally characterized, which are assembled from [Hf48Ni6] cubic nanocages and exhibit good stability in various solvents and acid/base solutions. Catalytic investigations suggest as-synthesized Hf-Ni and Hf-Ni-NH 2 display accurate type-selectivity (selectively catalyzed P-O rather than S-O or C-O bonds) and position-selectivity (selectively catalyzed phosphomonoesters over phosphodiesters) for the hydrolysis of phosphoesters. Reaction kinetic studies further revealed the high activity of the catalytic sites in these catalysts, and the unique catalytic selectivity and high activity are comparable to phosphatase. Additionally, these MOF catalysts possess good recursivity and hypotoxicity. Control experiments (including Hf- and Zr-based isomorphous MOFs) and theoretical calculations indicate that both triplet nickel and Hf6 clusters play significant roles in the unique binding site and favorable binding energy. To our knowledge, this is the first example of selective dephosphorylation through MOF catalysts as mimic enzymes, which paves a potential way for the development of specific therapeutic MOFs.

Phosphorus Compounds of Natural Origin: Prebiotic, Stereochemistry, Application

Organophosphorus compounds play a vital role as nucleic acids, nucleotide coenzymes, metabolic intermediates and are involved in many biochemical processes. They are part of DNA, RNA, ATP and a number of important biological elements of living organisms. Synthetic compounds of this class have found practical application as agrochemicals, pharmaceuticals, bioregulators, and othrs. In recent years, a large number of phosphorus compounds containing P-O, P-N, P-C bonds have been isolated from natural sources. Many of them have shown interesting biological properties and have become the objects of intensive scientific research. Most of these compounds contain asymmetric centers, the absolute configurations of which have a significant effect on the biological properties of the products of their transformations. This area of research on natural phosphorus compounds is still little-studied, that prompted us to analyze and discuss it in our review. Moreover natural organophosphorus compounds represent interesting models for the development of new biologically active compounds, and a number of promising drugs and agrochemicals have already been obtained on their basis. The review also discusses the history of the development of ideas about the role of organophosphorus compounds and stereochemistry in the origin of life on Earth, starting from the prebiotic period, that allows us in a new way to consider this most important problem of fundamental science.

Reactions of aryl dimethylphosphinothioate esters with anionic oxygen nucleophiles: transition state structure in 70% water-30% ethanol

Aryl dimethylphosphinates, 2, react with anionic oxygen nucleophiles in water via a concerted (ANDN) mechanism. With EtO- in anhydrous ethanol, the mechanism is associative (AN + DN), with rate-limiting pentacoordinate intermediate formation. This change in mechanism with solvent change has been ascribed to changes in the nucleophile and leaving group basicities accompanying solvent change. This paper reports on a kinetic analysis of the reactions of the aryl dimethylphosphinothioates, 3a-g, with oxygen nucleophiles in 70% water-30% ethanol (v/v) solvent at 25 °C, reactions known to proceed by a concerted mechanism in water, to test the rationalization stated above, since the nucleophiles and LGs of interest are more basic in aqueous ethanol than in water. The change in solvent causes an ca. 14 to 320-fold decrease in rate. Hammett and Brønsted-type correlations characterize a concerted TS with less P-LG bonding in aqueous ethanol than in water. Two opposing consequences are associated with the solvent change: (a) increased basicity of nucleophiles and LGs, which lead to a modest tightening of the TS; and (b) better stabilization of the IS relative to the TS in aqueous ethanol, which results in a slower reaction with a more product-like TS. Hammond and anti-Hammond effects on the TS arising from better stabilization of the IS over the TS dominate over the effects of increased nucleophile and LG basicity in determining the looser TS structure in aqueous ethanol. An altered TS structure is consistent with an altered reaction potential energy surface, in this case caused by a change in solvent polarity.

Biomolecular QM/MM Simulations: What Are Some of the "Burning Issues"?

QM/MM simulations have become an indispensable tool in many chemical and biochemical investigations. Considering the tremendous degree of success, including recognition by a 2013 Nobel Prize in Chemistry, are there still "burning challenges" in QM/MM methods, especially for biomolecular systems? In this short Perspective, we discuss several issues that we believe greatly impact the robustness and quantitative applicability of QM/MM simulations to many, if not all, biomolecules. We highlight these issues with observations and relevant advances from recent studies in our group and others in the field. Despite such limited scope, we hope the discussions are of general interest and will stimulate additional developments that help push the field forward in meaningful directions.

What Does the Brønsted Slope Measure in the Phosphoryl Transfer Transition State?

The structural and energetic features of phosphate and phosphonate hydrolysis in Protein Phosphatase-1 (PP1) and water are studied using quantum mechanical (QM) cluster models. The calculations are able to reproduce observed kinetic isotope effects and capture several key trends in the experimental Brønsted plots: the β l g values are rather different for phosphate and phosphonate ester hydrolysis in solution but are similar in PP1. Detailed analyses of structure, charge distribution and bond order of computed transition states support the general conclusion from experimental study that phosphoryl transfer transition states are different for the two classes of substrates in solution but similar in PP1. On the other hand, the microscopic models also highlight notable differences between the phosphate and phosphonate transition states, which are manifested in not only structure but also kinetic isotope effects. Overall, we find that while β l g / β E Q , l g generally correlates with the partial charge on leaving group oxygen and the fractional bond order of the breaking P- O l g bond, the precise mapping between β l g / β E Q , l g and P- O l g bond order in the transition state is difficult due largely to the cross talk between breaking and forming P-O bonds. Therefore, further supporting previous analyses of limitations of free energy relations, our results suggest that while free energy relation is a valuable tool for probing the nature of transition state, a quantitative mapping of β l g and β l g / β E Q , l g values to structure or charge in the transition state should be conducted with great care.

Modeling the Alkaline Hydrolysis of Diaryl Sulfate Diesters: A Mechanistic Study

Phosphate and sulfate esters have important roles in regulating cellular processes. However, while there has been substantial experimental and computational investigation of the mechanisms and the transition states involved in phosphate ester hydrolysis, there is far less work on sulfate ester hydrolysis. Here, we report a detailed computational study of the alkaline hydrolysis of diaryl sulfate diesters, using different DFT functionals as well as mixed implicit/explicit solvation with varying numbers of explicit water molecules. We consider the impact of the computational model on computed linear free-energy relationships (LFER) and the nature of the transition states (TS) involved. We obtain good qualitative agreement with experimental LFER data when using a pure implicit solvent model and excellent agreement with experimental kinetic isotope effects for all models used. Our calculations suggest that sulfate diester hydrolysis proceeds through loose transition states, with minimal bond formation to the nucleophile and bond cleavage to the leaving group already initiated. Comparison to prior work indicates that these TS are similar in nature to those for the alkaline hydrolysis of neutral arylsulfonate monoesters or charged phosphate diesters and fluorophosphates. Obtaining more detailed insights into the transition states involved assists in understanding the selectivity of enzymes that hydrolyze these reactions.

Recent Advances in Understanding Biological GTP Hydrolysis through Molecular Simulation

GTP hydrolysis is central to biology, being involved in regulating a wide range of cellular processes. However, the mechanisms by which GTPases hydrolyze this critical reaction remain controversial, with multiple mechanistic possibilities having been proposed based on analysis of experimental and computational data. In this mini-review, we discuss advances in our understanding of biological GTP hydrolysis based on recent computational studies and argue in favor of solvent-assisted hydrolysis as a conserved mechanism among GTPases. A concrete understanding of the fundamental mechanisms by which these enzymes facilitate GTP hydrolysis will have significant impact both for drug discovery efforts and for unraveling the role of oncogenic mutations.

Examining the Mechanism of Phosphite Dehydrogenase with Quantum Mechanical/Molecular Mechanical Free Energy Simulations

The projected decline of available phosphorus necessitates alternative methods to derive usable phosphate for fertilizer and other applications. Phosphite dehydrogenase oxidizes phosphite to phosphate with the cofactor NAD⁺ serving as the hydride acceptor. In addition to producing phosphate, this enzyme plays an important role in NADH cofactor regeneration processes. Mixed quantum mechanical/molecular mechanical free energy simulations were performed to elucidate the mechanism of this enzyme and to identify the protonation states of the substrate and product. Specifically, the finite temperature string method with umbrella sampling was used to generate the free energy surfaces and determine the minimum free energy paths for six different initial conditions that varied in the protonation state of the substrate and the position of the nucleophilic water molecule. In contrast to previous studies, the mechanism predicted by all six independent strings is a concerted but asynchronous dissociative mechanism in which hydride transfer from the phosphite substrate to NAD⁺ occurs prior to attack by the nucleophilic water molecule. His292 is identified as the most likely general base that deprotonates the attacking water molecule. However, Arg237 could also serve as this base if it were deprotonated and His292 were protonated prior to the main chemical transformation, although this scenario is less probable. The simulations indicate that the phosphite substrate is monoanionic in its active form and that the most likely product is dihydrogen phosphate. These mechanistic insights may be helpful for designing mutant enzymes or artificial constructs that convert phosphite to phosphate and NAD⁺ to NADH more effectively.

Diversity of mechanisms in Ras-GAP catalysis of guanosine triphosphate hydrolysis revealed by molecular modeling

The mechanism of the deceptively simple reaction of guanosine triphosphate (GTP) hydrolysis catalyzed by the cellular protein Ras in complex with the activating protein GAP is an important issue because of the significance of this reaction in cancer research. We show that molecular modeling of GTP hydrolysis in the Ras-GAP active site reveals a diversity of mechanisms of the intrinsic chemical reaction depending on molecular groups at position 61 in Ras occupied by glutamine in the wild-type enzyme. First, a comparison of reaction energy profiles computed at the quantum mechanics/molecular mechanics (QM/MM) level shows that an assignment of the Gln61 side chain in the wild-type Ras either to QM or to MM parts leads to different scenarios corresponding to the glutamine-assisted or the substrate-assisted mechanisms. Second, replacement of Gln61 by the nitro-analog of glutamine (NGln) or by Glu, applied in experimental studies, results in two more scenarios featuring the so-called two-water and the concerted-type mechanisms. The glutamine-assisted mechanism in the wild-type Ras-GAP, in which the conserved Gln61 plays a decisive role, switching between the amide and imide tautomer forms, is consistent with the known experimental results of structural, kinetic and spectroscopy studies. The results emphasize the role of the Ras residue Gln61 in Ras-GAP catalysis and explain the retained catalytic activity of the Ras-GAP complex towards GTP hydrolysis in the Gln61NGln and Gln61Glu mutants of Ras.

α- and β-Lapachone Isomerization in Acidic Media: Insights from Experimental and Implicit/Explicit Solvation Approaches

Combined experimental and mixed implicit/explicit solvation approaches were employed to gain insights into the origin of switchable regioselectivity of acid-catalyzed lapachol cyclization and α-/β-lapachone isomerization. It was found that solvating species under distinct experimental conditions stabilized α- and β-lapachone differently, thus altering the identity of the thermodynamic product. The energy profile for lapachol cyclization revealed that this process can occur with low free-energy barriers (lower than 8.0 kcal mol^-1 ). For α/β isomerization in a dilute medium, the computed enthalpic barriers are 15.1 kcal mol^-1 (α→β) and 14.2 kcal mol^-1 (β→α). These barriers are lowered in concentrated medium to 11.5 and 12.6 kcal mol^-1 , respectively. Experimental determination of isomers ratio was quantified by HPLC and NMR measurements. These findings provide insights into the chemical behavior of lapachol and lapachone derivatives in more complex environments.

Extensive free-energy simulations identify water as the base in nucleotide addition by DNA polymerase

Transphosphorylation of nucleotide triphosphates is the central reaction in DNA replication by DNA polymerase as well as many other biological processes. Despite its importance, the microscopic chemical mechanism of transphosphorylation of nucleotide triphosphates is, in most cases, unknown. Here we use extensive simulations of DNA polymerase η to test mechanistic hypotheses. We systematically survey the reactive space by calculating 2D free-energy surfaces for 10 different plausible mechanisms that have been proposed. We supplement these free-energy surfaces with calculations of pKa for a number of potentially acidic protons in different states relevant to the catalytic cycle. We find that among all of the conditions that we test, the smallest activation barrier occurs for a reaction where a Mg2+-coordinated water deprotonates the nucleophilic 3'-OH, and this deprotonation is concerted with the phosphoryl transfer. The presence of a third Mg2+ in the active site lowers the activation barrier for the water-as-base mechanism, as does protonation of the pyrophosphate leaving group, which is consistent with general acid catalysis. The results demonstrate the value of simulations, when used in conjunction with experimental data, to help establish a microscopic chemical mechanism in a complex environment.

Alkoxide ligand controlled self-assembling of (imido)vanadium(V) compounds having a tetrahedral VO3N geometry

The reaction of (1S,2S)-(-)-1,2-diphenylethylenediamine with VO(OⁱPr)₃ in the presence of NaH was found to afford the binuclear (imido)vanadium(V) triisopropoxide, [(OⁱPr)₃V(N-meso-1,2-DPE-N)V(OⁱPr)₃] (DPE = diphenylethylene), (1a_RS/SS). Using (1R,2R)-(+)-1,2-diphenylethylenediamine as a starting material, one-step reaction also proceeded to form the binuclear (imido)vanadium(V) triisopropoxide, [(OⁱPr)₃V(N-meso-1,2-DPE-N)V(OⁱPr)₃], (1a_RS/RR). The single-crystal X-ray structure determination of 1a_RS/SS revealed the hydrogen-bonded self-assembled structure utilizing the advantage of anti-conformation through the intermolecular hydrogen bonds of C-H···O pattern between phenyl and isopropoxide moieties, wherein each vanadium atom is coordinated in a nearly tetrahedral VO₃N geometry (τ₄ = 0.017 and 0.057). On the contrary, a discrete (imido)vanadium(V) tris(triphenylsiloxide) unit, which possesses a nearly tetrahedral VO₃N arrangement around the vanadium metal center (τ₄ = 0.060), was observed in the crystal structure of the (4-methoxyphenylimido)vanadium(V) tris(triphenylsiloxide), [(p-MeOC₆H₄N)V(OSiPh₃)₃], (1b) with bulky triphenylsiloxide ligands.

GTP Hydrolysis Without an Active Site Base: A Unifying Mechanism for Ras and Related GTPases

GTP hydrolysis is a biologically crucial reaction, being involved in regulating almost all cellular processes. As a result, the enzymes that catalyze this reaction are among the most important drug targets. Despite their vital importance and decades of substantial research effort, the fundamental mechanism of enzyme-catalyzed GTP hydrolysis by GTPases remains highly controversial. Specifically, how do these regulatory proteins hydrolyze GTP without an obvious general base in the active site to activate the water molecule for nucleophilic attack? To answer this question, we perform empirical valence bond simulations of GTPase-catalyzed GTP hydrolysis, comparing solvent- and substrate-assisted pathways in three distinct GTPases, Ras, Rab, and the G_αi subunit of a heterotrimeric G-protein, both in the presence and in the absence of the corresponding GTPase activating proteins. Our results demonstrate that a general base is not needed in the active site, as the preferred mechanism for GTP hydrolysis is a conserved solvent-assisted pathway. This pathway involves the rate-limiting nucleophilic attack of a water molecule, leading to a short-lived intermediate that tautomerizes to form H₂PO₄^- and GDP as the final products. Our fundamental biochemical insight into the enzymatic regulation of GTP hydrolysis not only resolves a decades-old mechanistic controversy but also has high relevance for drug discovery efforts. That is, revisiting the role of oncogenic mutants with respect to our mechanistic findings would pave the way for a new starting point to discover drugs for (so far) "undruggable" GTPases like Ras.

Development of Prediction Models on Base-Catalyzed Hydrolysis Kinetics of Phthalate Esters with Density Functional Theory Calculation

Many phthalate esters (PAEs) are chemicals of high production volume and of toxicological concern. The second-order rate constant for base-catalyzed hydrolysis ( k_B) is a key parameter for assessing environmental persistence of PAEs. However, the k_B values for most PAEs are lacking, and the experimental determination of k_B encounters various difficulties. Herein, density functional theory (DFT) methods were selected by comparing empirical k_B values of five PAEs and five carboxylic acid esters with the DFT-calculated ones. Results indicate that PAEs with cyclic side chains are more vulnerable to base-catalyzed hydrolysis than PAEs with linear alkyl side chains, followed by PAEs with branched alkyl side chains. By combining experimental and DFT-calculated second-order rate constants for base-catalyzed hydrolysis of one side chain in PAEs ( k_{B_side chain}), quantitative structure-activity relationship models were developed. The models can differentiate PAEs with the departure of the leaving group (or the nucleophilic attack of OH^-) as the rate-determining step in the hydrolysis and estimate k_B values, which provides a promising way to predict hydrolysis kinetics of PAEs. The half-lives of the investigated PAEs were calculated and vary from 0.001 h to 558 years (pH = 7∼9), further illustrating the necessity of prediction models for hydrolysis kinetics in assessing the environmental persistence of chemicals.

Molecular Mechanism of ATP Hydrolysis in an ABC Transporter

Hydrolysis of nucleoside triphosphate (NTP) plays a key role for the function of many biomolecular systems. However, the chemistry of the catalytic reaction in terms of an atomic-level understanding of the structural, dynamic, and free energy changes associated with it often remains unknown. Here, we report the molecular mechanism of adenosine triphosphate (ATP) hydrolysis in the ATP-binding cassette (ABC) transporter BtuCD-F. Free energy profiles obtained from hybrid quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations show that the hydrolysis reaction proceeds in a stepwise manner. First, nucleophilic attack of an activated lytic water molecule at the ATP γ-phosphate yields ADP + HPO₄ ^2- as intermediate product. A conserved glutamate that is located very close to the γ-phosphate transiently accepts a proton and thus acts as catalytic base. In the second step, the proton is transferred back from the catalytic base to the γ-phosphate, yielding ADP + H₂PO₄ ^-. These two chemical reaction steps are followed by rearrangements of the hydrogen bond network and the coordination of the Mg²⁺ ion. The rate constant estimated from the computed free energy barriers is in very good agreement with experiments. The overall free energy change of the reaction is close to zero, suggesting that phosphate bond cleavage itself does not provide a power stroke for conformational changes. Instead, ATP binding is essential for tight dimerization of the nucleotide-binding domains and the transition of the transmembrane domains from inward- to outward-facing, whereas ATP hydrolysis resets the conformational cycle. The mechanism is likely relevant for all ABC transporters and might have implications also for other NTPases, as many residues involved in nucleotide binding and hydrolysis are strictly conserved.

The hydrolysis of 6-phosphogluconolactone in the second step of pentose phosphate pathway occurs via a two-water mechanism

Hydrolysis reaction marks the basis of life yet the mechanism of this crucial biochemical reaction is not completely understood. We recently reported the mechanisms of hydrolysis of nucleoside triphosphate and phosphate monoester. These two reactions hydrolyze P-O-P and P-O-C linkages, respectively. Here, we present the mechanism of hydrolysis of δ-6-phosphogluconolactone, which is an important precursor in the second step of the pentose phosphate pathway. Its hydrolysis requires the cleavage of C-O-C linkage and its mechanism is hitherto unknown. We report three mechanisms of hydrolysis of δ-6-phosphogluconolactone based on density functional computations. In the energetically most favorable mechanism, two water molecules participate in the hydrolysis reaction and the mechanism is sequential, i.e., activation of the attacking water molecule (OH bond breaking) precedes that of the cleavage of the CO bond of the C-O-C linkage. The rate-limiting energy barrier of this mechanism is comparable to the reported experimental free energy barrier. This mechanism has similarities with the mechanism of triphosphate hydrolysis and that of hydrolytic cleavage of DNA in EcoRV enzyme. This two-water sequential hydrolysis mechanism could be the unified mechanism required for the hydrolysis of other hydrolysable species in living cells.

Challenges and advances in the computational modeling of biological phosphate hydrolysis

Phosphate ester hydrolysis is fundamental to many life processes, and has been the topic of substantial experimental and computational research effort. However, even the simplest of phosphate esters can be hydrolyzed through multiple possible pathways that can be difficult to distinguish between, either experimentally, or computationally. Therefore, the mechanisms of both the enzymatic and non-enzymatic reactions have been historically controversial. In the present contribution, we highlight a number of technical issues involved in reliably modeling these computationally challenging reactions, as well as proposing potential solutions. We also showcase examples of our own work in this area, discussing both the non-enzymatic reaction in aqueous solution, as well as insights obtained from the computational modeling of organophosphate hydrolysis and catalytic promiscuity amongst enzymes that catalyze phosphoryl transfer.

Mechanistic Insights on Human Phosphoglucomutase Revealed by Transition Path Sampling and Molecular Dynamics Calculations

Human α-phosphoglucomutase 1 (α-PGM) catalyzes the isomerization of glucose-1-phosphate into glucose-6-phosphate (G6P) through two sequential phosphoryl transfer steps with a glucose-1,6-bisphosphate (G16P) intermediate. Given that the release of G6P in the gluconeogenesis raises the glucose output levels, α-PGM represents a tempting pharmacological target for type 2 diabetes. Here, we provide the first theoretical study of the catalytic mechanism of human α-PGM. We performed transition-path sampling simulations to unveil the atomic details of the two catalytic chemical steps, which could be key for developing transition state (TS) analogue molecules with inhibitory properties. Our calculations revealed that both steps proceed through a concerted S_N 2-like mechanism, with a loose metaphosphate-like TS. Even though experimental data suggests that the two steps are identical, we observed noticeable differences: 1) the transition state ensemble has a well-defined TS region and a late TS for the second step, and 2) larger coordinated protein motions are required to reach the TS of the second step. We have identified key residues (Arg23, Ser117, His118, Lys389), and the Mg²⁺ ion that contribute in different ways to the reaction coordinate. Accelerated molecular dynamics simulations suggest that the G16P intermediate may reorient without leaving the enzymatic binding pocket, through significant conformational rearrangements of the G16P and of specific loop regions of the human α-PGM.

Computer simulations of the catalytic mechanism of wild-type and mutant β-phosphoglucomutase

β-Phosphoglucomutase (β-PGM) has served as an important model system for understanding biological phosphoryl transfer.