Transforming a Stable Amide into a Highly Reactive One: Capturing the Essence of Enzymatic Catalysis

Overreact, an in silico lab: Automative quantum chemical microkinetic simulations for complex chemical reactions

Today's demand for precisely predicting chemical reactions from first principles requires research to go beyond Gibbs' free energy diagrams and consider other effects such as concentrations and quantum tunneling. The present work introduces overreact, a novel Python package for propagating chemical reactions over time using data from computational chemistry only. The overreact code infers all differential equations and parameters from a simple input that consists of a set of chemical equations and quantum chemistry package outputs for each chemical species. We evaluate some applications from the literature: gas-phase eclipsed-staggered isomerization of ethane, gas-phase umbrella inversion of ammonia, gas-phase degradation of methane by chlorine radical, and three solvation-phase reactions. Furthermore, we comment on a simple solvation-phase acid-base equilibrium. We show how it is possible to achieve reaction profiles and information matching experiments.

Room temperature synthesis of perylene diimides facilitated by high amic acid solubility

A novel protocol for the synthesis of perylene diimides (PDIs), by reacting perylene dianhydride (PDA) with aliphatic amines is reported. Full conversions were obtained at temperatures between 20 and 60 °C, using DBU as the base in DMF or DMSO. A “green” synthesis of PDIs, that runs at higher temperatures, was developed using K₂CO₃ in DMSO. The reaction sequence for the imidization process, via perylene amic acid intermediates (PAAs), has been confirmed experimentally aided by the synthesis and full characterization of stable model amic acid salts and amic esters. Kinetic studies, using absorption spectroscopy, have established that PDI formation proceeds via fast amic acid formation, followed by a slow conversion to imides. Solubility of the intermediate PAA salts is found to be low and rate-limiting. Based on this finding, quantitative PDI synthesis at room temperature was achieved by diluting the reaction mixture with water, the solvent in which PAA salts have better solubility. Thus, the otherwise harsh synthesis of PDIs has been transformed into an extremely convenient functional group tolerant and highly efficient reaction that runs at room temperature.

Perylene diimides (PDIs) are synthesised at room temperature and obtained in quantitative yields after a single filtration. High solubility of the intermediate amic acid salts 5 and 9 is key to the success of this novel synthesis.

Enzyme Models-From Catalysis to Prodrugs

Enzymes are highly specific biological catalysts that accelerate the rate of chemical reactions within the cell. Our knowledge of how enzymes work remains incomplete. Computational methodologies such as molecular mechanics (MM) and quantum mechanical (QM) methods play an important role in elucidating the detailed mechanisms of enzymatic reactions where experimental research measurements are not possible. Theories invoked by a variety of scientists indicate that enzymes work as structural scaffolds that serve to bring together and orient the reactants so that the reaction can proceed with minimum energy. Enzyme models can be utilized for mimicking enzyme catalysis and the development of novel prodrugs. Prodrugs are used to enhance the pharmacokinetics of drugs; classical prodrug approaches focus on alternating the physicochemical properties, while chemical modern approaches are based on the knowledge gained from the chemistry of enzyme models and correlations between experimental and calculated rate values of intramolecular processes (enzyme models). A large number of prodrugs have been designed and developed to improve the effectiveness and pharmacokinetics of commonly used drugs, such as anti-Parkinson (dopamine), antiviral (acyclovir), antimalarial (atovaquone), anticancer (azanucleosides), antifibrinolytic (tranexamic acid), antihyperlipidemia (statins), vasoconstrictors (phenylephrine), antihypertension (atenolol), antibacterial agents (amoxicillin, cephalexin, and cefuroxime axetil), paracetamol, and guaifenesin. This article describes the works done on enzyme models and the computational methods used to understand enzyme catalysis and to help in the development of efficient prodrugs.

A computational study of the reaction mechanism involved in the fast cleavage of an unconstrained amide bond assisted by an amine intramolecular nucleophilic attack

In the present work, the fast amide bond cleavage of [3-((1R,5S,7s)-3-azabicyclo[3.3.1]nonane-7-carbonyl)-3-azabicyclo[3.3.1]nonane-7-carboxylic acid (bi-ATDO)], through an intramolecular nucleophilic attack of an amine group is evaluated. First, six possible peptide bond cleavage mechanisms, two of them including a water molecule, are described at the ωB97XD/6-311 + G(d,p)//MP2/6-311 + G(d,p) level of theory. The reaction consisting of an intramolecular nitrogen nucleophilic attack followed by a proton transfer and the amide bond cleavage is determined as the most favorable mechanism. The activation free energy computed for the latter is 20.5 kcal mol^-1 , which agrees with the reported experimental result of 24.8 kcal mol^-1 . Inclusion of a water molecule to assist the first step of the reaction results in an activation free energy increase of about 17 kcal mol^-1 . All the steps in the most favorable mechanism are studied more in detail employing intrinsic reaction coordinate as well as the reaction force and reaction electronic flux analysis.

Supramolecular kinetic effects by pillararenes: the synergism between spatiotemporal and preorganization concepts in decarboxylation reactions

Spatiotemporal and preorganization factors were both responsible for the catalytic and inhibitory supramolecular effects in decarboxylation reactions.

Coordination among Bond Formation/Cleavage in a Bifunctional-Catalyzed Fast Amide Hydrolysis: Evidence for an Optimized Intramolecular N-Protonation Event

A density functional theory (DFT) computational analysis, using the ωB97X-D functional, of a rapid amide cleavage in 2-carboxyphthalanilic acid (2CPA), where the amide group is flanked by two catalytic carboxyls, reveals key mechanistic information: (a) General base catalysis by a carboxylate coupled to general acid catalysis by a carboxyl is not operative. (b) Nucleophilic attack by a carboxylate on the amide carbonyl coupled to general acid catalysis at the amide oxygen can also be ruled out. (c) A mechanistic pathway that remains viable involves general acid proton delivery to the amide nitrogen by a carboxyl, while the other carboxylate engages in nucleophilic attack upon the amide carbonyl; a substantially unchanged amide carbonyl in the transition state; two concurrent bond-forming events; and a spatiotemporal-base rate acceleration. This mechanism is supported by molecular dynamic simulations which confirm a persistent key intramolecular hydrogen bonding. These theoretical conclusions, although not easily verified by experiment, are consistent with a bell-shaped pH/rate profile but are at odds with hydrolysis mechanisms in the classic literature.

From the Shelf to the Particle: Preparation of Highly Organic-Functionalized Magnetic Composites via 4-Nitrophenyl Reactive Ester

Preparation of chemically tunable magnetic nanoparticles (MNPs) is of great interest in many technological fields. Although numerous methods have been developed to prepare MNPs coated with functional organic moieties, most of them are complex, multistep, and involve the preparation of a specific ligand to be inserted on the particle surface. Herein, we describe the preparation of MNPs covered with reactive polymer poly(4-nitrophenyl methacrylate). The composite was prepared by the dispersion polymerization of 4-nitrophenyl methacrylate in the presence of magnetite nanoparticles stabilized by oleic acid. The novel material can be easily modified with amines to give chemically stable amide bonds without installation of pH-dependent features in the link. The extent of particle modification is readily monitored by the release of 4-nitrophenol from the polymer using UV-vis spectrophotometry. Good agreement between the degree of functionalization assessed by colorimetry and elemental analysis was obtained, and functionalization up to 3 mmol g^-1 is easily attained. To illustrate the applicability of the method for catalyst development, we prepared imidazole-covered MNPs that accelerate the hydrolysis of a model organophosphate, with rate constants approximately 10⁵-fold higher than the spontaneous hydrolysis. The catalyst can be recovered by a magnet and recycled without appreciable loss of catalytic activity.

Interaction vs Preorganization in Enzyme Catalysis. A Dispute That Calls for Resolution

This essay focuses on the debate between Warshel et al. (proponents of preorganization) and Menger and Nome (proponents of spatiotemporal effects) over the source of fast enzyme catalysis. The Warshel model proposes that the main function of enzymes is to push the solvent coordinate toward the transition state. Other physical-organic factors (e.g., desolvation, entropic effects, ground state destabilization, etc.) do not, ostensibly, contribute substantially to the rate. Indeed, physical organic chemistry in its entirety was claimed to be "irrelevant to an enzyme's active site". Preorganization had been applied by Warshel to his "flagship" enzyme, ketosteroid isomerase, but we discuss troubling issues with their ensuing analysis. For example, the concepts of "general acid" and "general base", known to play a role in this enzyme's mechanism, are ignored in the text. In contrast, the spatiotemporal theory postulates that enzyme-like rates (i.e., accelerations >10⁸) occur when two functionalities are held rigidly at contact distances less than ca. 3 Å. Numerous diverse organic systems are shown to bear this out experimentally. Many of these are intramolecular systems where distances between functionalities are known. Among them are fast intramolecular systems where strain is actually generated during the reaction, thereby excluding steric compression as a source of the observed enzyme-like rates. Finally, the account ends with structural data from four active sites of enzymes, obtained by others, all showing contact distances between substrate analogues and enzyme. To our knowledge, contact distances less than the diameter of water are found universally among enzymes, and it is to this fact that we attribute their extremely fast rates given the assumption that enzymes, whatever their particular mechanism, obey elementary chemical principles.

Theoretical Study of the Adsorption Process of Antimalarial Drugs into Acrylamide-Base Hydrogel Model Using DFT Methods: The First Approach to the Rational Design of a Controlled Drug Delivery System

The interaction between three widely used antimalarial drugs chloroquine, primaquine and amodiaquine with acrylamide dimer and trimer as a hydrogel model, were studied by means of density functional theory calculation in both vacuum and water environments, using the functional wb97xd with 6-31++G(d,p) basis set and polarizable continuum model (C-PCM) of solvent. According to binding energy, around −3.15 to −11.91 kJ/mol, the interaction between antimalarial compounds and hydrogel model are exothermic in nature. The extent of interaction found is primaquine > amodiaquine > chloroquine. The natural bond orbital (NBO) calculation and application of second-order perturbation theory show strong charge transfer between the antimalarial and hydrogel model. In addition, the results suggest these interactions are polar in nature, where hydrogen bonds play a principal role in stabilization of the complex. Comparing with the gas-phase, the complexes in the water environment are also stable, with suitable values of Log P (Partition coefficient), and dipolar momentum. Consequently, these results encourage to test acrylamide hydrogels as antimalarial delivery systems.

Fast Amide Bond Cleavage Assisted by a Secondary Amino and a Carboxyl Group-A Model for yet Unknown Peptidases?

Unconstrained amides that undergo fast hydrolysis under mild conditions are valuable sources of information about how amide bonds may be activated in enzymatic transformations. We report a compound possessing an unconstrained amide bond surrounded by an amino and a carboxyl group, each mounted in close proximity on a bicyclic scaffold. Fast amide hydrolysis of this model compound was found to depend on the presence of both the amino and carboxyl functions, and to involve a proton transfer in the rate-limiting step. Possible mechanisms for the hydrolytic cleavage and their relevance to peptide bond cleavage catalyzed by natural enzymes are discussed. Experimental observations suggest that the most probable mechanisms of the model compound hydrolysis might include a twisted amide intermediate and a rate-determining proton transfer.

Misunderstanding the preorganization concept can lead to confusions about the origin of enzyme catalysis

Understanding the origin of the catalytic power of enzymes has both conceptual and practical importance. One of the most important finding from computational studies of enzyme catalysis is that a major part of the catalytic power is due to the preorganization of the enzyme active site. Unfortunately, misunderstanding of the nontrivial preorganization idea lead some to assume that it does not consider the effect of the protein residues. This major confusion reflects a misunderstanding of the statement that the interaction energy of the enzyme group and the transition state (TS) is similar to the corresponding interaction between the water molecules (in the reference system) and the TS, and that the catalysis is due to the reorganization free energy of the water molecules. Obviously, this finding does not mean that we do not consider the enzyme groups. Another problem is the idea that catalysis is due to substrate preorganization. This more traditional idea is based in some cases on inconsistent interpretation of the action of model compounds, which unfortunately, do not reflect the actual situation in the enzyme active site. The present article addresses the above problems, clarifying first the enzyme polar preorganization idea and the current misunderstandings. Next we take a specific model compound that was used to promote the substrate preorganization proposal and establish its irrelevance to enzyme catalysis. Overall, we show that the origin of the catalytic power of enzymes cannot be assessed uniquely without computer simulations, since at present this is the only way of relating structure and energetics.