A two-directional vibrational probe reveals different electric field orientations in solution and an enzyme active site

Exploring dynamic solvation kinetics at electrocatalyst surfaces

The interface between electrocatalyst and electrolyte is highly dynamic. Even in absence of major structural changes, the intermediate coverage and interfacial solvent are bias and time dependent. This is not accounted for in current kinetic models. Here, we study the kinetics of the hydrogen evolution, ammonia oxidation and oxygen reduction reactions on polycrystalline Pt with distinct intrinsic rates and intermediates (e.g. *H, *OH, *NH2, *N). Despite these differences, we discover shared relationships between the pre-exponential factor and the activation energy that we link to solvation kinetics in the presence of electronic excess charge and charged intermediates. Further, we study dynamic changes of these kinetic parameters with a millisecond time resolution during electrosorption and double layer charging and dynamic *N and *NO poisoning. Finally, we discover a pH-dependent activation entropy that explains non-Nernstian overpotential shifts with pH. In sum, our results demonstrate the importance of accounting for a bias and time-dependent interfacial solvent and catalyst surface.

Enhanced Selectivity in Microdroplet-Mediated Enzyme Catalysis

Natural enzymes with enhanced catalytic activity and selectivity have long been studied by tuning the microenvironment around the active site, but how to modulate the active-site electric field in a simple fashion remains challenging. Here, we demonstrate that microdroplets as a simple yet versatile reactor can enhance the electric field at the active site of an enzyme. By using horseradish peroxidase as a model, improved selectivity in microdroplet-mediated enzyme catalysis can be obtained. Quantum mechanical/molecular dynamics calculations and vibrational Stark spectroscopy reveal that the electric field at the microdroplet interface can influence the electrostatic preorganization and orientation of the enzyme to enhance its internal electric field. As a result, the free energies of the substrate and heme can be tuned by the internal electric field, thereby changing its catalytic reaction pathway for a classical substrate, 3,3',5,5'-tetramethylbenzidine, and enabling selective C-N additions for specific substrates. This finding provides a green, simple, and effective way to modulate enzyme-catalyzed reactions and holds promise for a broad spectrum of biosensing and biosynthesis applications.

Massive acceleration of SN2 reaction using the oriented external electric field

Nucleophilic substitution is one of the most fundamental chemical reactions, and the pursuit of high reaction rates of the reaction is one of the ultimate goals in catalytic and organic chemistry. The reaction barrier of the nucleophilic substitution originates from the highly polar nature of the transition state that can be stabilized under the electric field created by the solvent environment. However, the intensity of the induced solvent-electric field is relatively small due to the random orientation of solvent molecules, which hinders the catalytic effects and restricts the reaction rates. This work shows that oriented external electric fields applied within a confined nanogap between two nanoscopic tips could accelerate the Menshutkin reaction by more than four orders of magnitude (over 39 000 times). The theoretical calculations reveal that the electric field inside the nanogap reduces the energy barrier to increase the reaction rate. Our work suggests the great potential of electrostatic catalysis for green synthesis in the future.

Ultrafast Interfacial Self-Assembly toward Bioderived Polyester COF Membranes with Microstructure Optimization

The precise manipulation of the microstructure (pore size, free volume distribution, and connectivity of the free-volume elements), thickness, and mechanical characteristics of membranes holds paramount significance in facilitating the effective utilization of self-standing membranes. In this contribution, the synthesis of two innovative ester-linked covalent-organic framework (COF) membranes is first reported, which are generated through the selection of plant-derived ellagic acid and quercetin phenolic monomers in conjunction with terephthaloyl chloride as a building block. The optimization of the microstructure of these two COF membranes is systematically achieved through the application of three different interfacial electric field systems: electric neutrality, positive electricity, and negative electricity. It is observed that the positively charged system facilitates a record increase in the rate of membrane formation, resulting in a denser membrane with a uniform pore size and enhanced flexibility. In addition, a correlation is identified wherein an increase in the alkyl chain length of the surfactants leads to a more uniform pore size and a decrease in the molecular weight cutoff of the COF membrane. The resulting COF membrane exhibits an unprecedented combination of high water permeance, superior sieving capability, robust mechanical strength, chemical robustness for promising membrane-based separation science and technology.

Noncanonical Amino Acids in Biocatalysis

In recent years, powerful genetic code reprogramming methods have emerged that allow new functional components to be embedded into proteins as noncanonical amino acid (ncAA) side chains. In this review, we will illustrate how the availability of an expanded set of amino acid building blocks has opened a wealth of new opportunities in enzymology and biocatalysis research. Genetic code reprogramming has provided new insights into enzyme mechanisms by allowing introduction of new spectroscopic probes and the targeted replacement of individual atoms or functional groups. NcAAs have also been used to develop engineered biocatalysts with improved activity, selectivity, and stability, as well as enzymes with artificial regulatory elements that are responsive to external stimuli. Perhaps most ambitiously, the combination of genetic code reprogramming and laboratory evolution has given rise to new classes of enzymes that use ncAAs as key catalytic elements. With the framework for developing ncAA-containing biocatalysts now firmly established, we are optimistic that genetic code reprogramming will become a progressively more powerful tool in the armory of enzyme designers and engineers in the coming years.

Evaluating aliphatic CF, CF2, and CF3 groups as vibrational Stark effect reporters

Given the extensive use of fluorination in molecular design, it is imperative to understand the solvation properties of fluorinated compounds and the impact of the C-F bond on electrostatic interactions. Vibrational spectroscopy can provide direct insights into these interactions by using the C-F bond stretching [v(C-F)] as an electric field probe through the vibrational Stark effect (VSE). In this work, we explore the VSE of the three basic patterns of aliphatic fluorination, i.e., mono-, di-, and trifluorination in CF, CF2, and CF3 groups, respectively, and compare their response to the well-studied aromatic v(C-F). Magnitudes (i.e., Stark tuning rates) and orientations of the difference dipole vectors of the v(C-F)-containing normal modes were determined using density functional theory and a molecular dynamics (MD)-assisted solvatochromic analysis of model compounds in solvents of varying polarity. We obtain Stark tuning rates of 0.2-0.8 cm-1/(MV/cm), with smallest and largest electric field sensitivities for CFaliphatic and CF3,aliphatic, respectively. While average electric fields of solvation were oriented along the main symmetry axis of the CFn, and thus along its static dipole, the Stark tuning rate vectors were tilted by up to 87° potentially enabling to map electrostatics in multiple dimensions. We discuss the influence of conformational heterogeneity on spectral shifts and point out the importance of multipolar and/or polarizable MD force fields to describe the electrostatics of fluorinated molecules. The implications of this work are of direct relevance for studies of fluorinated molecules as found in pharmaceuticals, fluorinated peptides, and proteins.

Unnatural Amino Acids for Biological Spectroscopy and Microscopy

Due to advances in methods for site-specific incorporation of unnatural amino acids (UAAs) into proteins, a large number of UAAs with tailored chemical and/or physical properties have been developed and used in a wide array of biological applications. In particular, UAAs with specific spectroscopic characteristics can be used as external reporters to produce additional signals, hence increasing the information content obtainable in protein spectroscopic and/or imaging measurements. In this Review, we summarize the progress in the past two decades in the development of such UAAs and their applications in biological spectroscopy and microscopy, with a focus on UAAs that can be used as site-specific vibrational, fluorescence, electron paramagnetic resonance (EPR), or nuclear magnetic resonance (NMR) probes. Wherever applicable, we also discuss future directions.

Substitution of both histidines in the active site of yeast alcohol dehydrogenase 1 exposes underlying pH dependencies

Histidine residues 44 and 48 in yeast alcohol dehydrogenase (ADH) bind to the coenzymes NAD(H) and contribute to catalysis. The individual H44R and H48Q substitutions alter the kinetics and pH dependencies, and now the roles of other ionizable groups in the enzyme were studied in the doubly substituted H44R/H48Q ADH. The substitutions make the enzyme more resistant to inactivation by diethyl pyrocarbonate, modestly improve affinity for coenzymes, and substantially decrease catalytic efficiencies for ethanol oxidation and acetaldehyde reduction. The pH dependencies for several kinetic parameters are shifted from pK values for wild-type ADH of 7.3-8.1 to values for H44R/H48Q ADH of 8.0-9.6, and are assigned to the water or alcohol bound to the catalytic zinc. It appears that the rate of binding of NAD+ is electrostatically favored with zinc-hydroxide whereas binding of NADH is faster with neutral zinc-water. The pH dependencies of catalytic efficiencies (V/EtKm) for ethanol oxidation and acetaldehyde reduction are similarly controlled by deprotonation and protonation, respectively. The substitutions make an enzyme that resembles the homologous horse liver H51Q ADH, which has Arg-47 and Gln-51 and exhibits similar pK values. In the wild-type ADHs, it appears that His-48 (or His-51) in the proton relay systems linked to the catalytic zinc ligands modulate catalytic efficiencies.

Electric-field-assisted proton coupling enhanced oxygen evolution reaction

The discovery of Mn-Ca complex in photosystem II stimulates research of manganese-based catalysts for oxygen evolution reaction (OER). However, conventional chemical strategies face challenges in regulating the four electron-proton processes of OER. Herein, we investigate alpha-manganese dioxide (α-MnO2) with typical MnIV-O-MnIII-HxO motifs as a model for adjusting proton coupling. We reveal that pre-equilibrium proton-coupled redox transition provides an adjustable energy profile for OER, paving the way for in-situ enhancing proton coupling through a new "reagent"- external electric field. Based on the α-MnO2 single-nanowire device, gate voltage induces a 4-fold increase in OER current density at 1.7 V versus reversible hydrogen electrode. Moreover, the proof-of-principle external electric field-assisted flow cell for water splitting demonstrates a 34% increase in current density and a 44.7 mW/cm² increase in net output power. These findings indicate an in-depth understanding of the role of proton-incorporated redox transition and develop practical approach for high-efficiency electrocatalysis.

Perspectives on Computational Enzyme Modeling: From Mechanisms to Design and Drug Development

Understanding enzyme mechanisms is essential for unraveling the complex molecular machinery of life. In this review, we survey the field of computational enzymology, highlighting key principles governing enzyme mechanisms and discussing ongoing challenges and promising advances. Over the years, computer simulations have become indispensable in the study of enzyme mechanisms, with the integration of experimental and computational exploration now established as a holistic approach to gain deep insights into enzymatic catalysis. Numerous studies have demonstrated the power of computer simulations in characterizing reaction pathways, transition states, substrate selectivity, product distribution, and dynamic conformational changes for various enzymes. Nevertheless, significant challenges remain in investigating the mechanisms of complex multistep reactions, large-scale conformational changes, and allosteric regulation. Beyond mechanistic studies, computational enzyme modeling has emerged as an essential tool for computer-aided enzyme design and the rational discovery of covalent drugs for targeted therapies. Overall, enzyme design/engineering and covalent drug development can greatly benefit from our understanding of the detailed mechanisms of enzymes, such as protein dynamics, entropy contributions, and allostery, as revealed by computational studies. Such a convergence of different research approaches is expected to continue, creating synergies in enzyme research. This review, by outlining the ever-expanding field of enzyme research, aims to provide guidance for future research directions and facilitate new developments in this important and evolving field.

Electrically driven proton transfer promotes Brønsted acid catalysis by orders of magnitude

Electric fields play a key role in enzymatic catalysis and can enhance reaction rates by 100,000-fold, but the same rate enhancements have yet to be achieved in thermochemical heterogeneous catalysis. In this work, we probe the influence of catalyst potential and interfacial electric fields on heterogeneous Brønsted acid catalysis. We observed that variations in applied potential of ~380 mV led to a 100,000-fold rate enhancement for 1-methylcyclopentanol dehydration, which was catalyzed by carbon-supported phosphotungstic acid. Mechanistic studies support a model in which the interfacial electrostatic potential drop drives quasi-equilibrated proton transfer to the adsorbed substrate prior to rate-limiting C-O bond cleavage. Large increases in rate with potential were also observed for the same reaction catalyzed by Ti/TiOyHx and for the Friedel Crafts acylation of anisole with acetic anhydride by carbon-supported phosphotungstic acid.

Facilitating Proton Coupled Electron Transfer Reaction through the Interfacial Micro Electric Field with Fe─N4 ─C in FeMOFs Glass

The proton-coupled electron transfer(PCET) reaction plays a crucial role in the chemical transformation process andhas become one of the most concerned elementary reactions. However, the complex kinetics of PCET reaction, which requires the simultaneous transfer of protons and electrons, leads to the dilemma that thermodynamics and kinetics cannot bebalanced and restricts its further development. In this, an interface micro-electric field (IMEF) basedon Fe─N4 in FeMOFs (Fe-Based Metal-Organic Frameworks) glass is designed tosynchronize proton/electron interface behavior for the first time to realizeefficient PCET reaction and optimize reaction thermodynamics and kinetics. The IMEF facilitates the separation of photogenerated electrons and holes, and accelerates Fe(III)/Fe(II) cycle. Driven by near-surface electric field force, the protons near surfacemigrate to Fe sites and participate in Fe(IV)═O formation and reaction, lowering the reaction energy barrier. Based on the interface regulation ofIMEF, a high-efficiency PCET reaction is realized, and kinetic reactionrate constant of photocatalytic oxidation of emerging contaminants is increasedby 3.7 times. This study highlights a strategy for IMEFs to modulate PEC Treactions for a wide range of potential applications, including environmental and ecological applications.

Molecular mechanisms and evolutionary robustness of a color switch in proteorhodopsins

Proteorhodopsins are widely distributed photoreceptors from marine bacteria. Their discovery revealed a high degree of evolutionary adaptation to ambient light, resulting in blue- and green-absorbing variants that correlate with a conserved glutamine/leucine at position 105. On the basis of an integrated approach combining sensitivity-enhanced solid-state nuclear magnetic resonance (ssNMR) spectroscopy and linear-scaling quantum mechanics/molecular mechanics (QM/MM) methods, this single residue is shown to be responsible for a variety of synergistically coupled structural and electrostatic changes along the retinal polyene chain, ionone ring, and within the binding pocket. They collectively explain the observed color shift. Furthermore, analysis of the differences in chemical shift between nuclei within the same residues in green and blue proteorhodopsins also reveals a correlation with the respective degree of conservation. Our data show that the highly conserved color change mainly affects other highly conserved residues, illustrating a high degree of robustness of the color phenotype to sequence variation.

Electrostatic catalysis of a click reaction in a microfluidic cell

Electric fields have been highlighted as a smart reagent in nature's enzymatic machinery, as they can directly trigger or accelerate chemical processes with stereo- and regio-specificity. In enzymatic catalysis, controlled mass transport of chemical species is also key in facilitating the availability of reactants in the active reaction site. However, recent progress in developing a clean catalysis that profits from oriented electric fields is limited to theoretical and experimental studies at the single molecule level, where both the control over mass transport and scalability cannot be tested. Here, we quantify the electrostatic catalysis of a prototypical Huisgen cycloaddition in a large-area electrode surface and directly compare its performance to the conventional Cu(I) catalysis. Our custom-built microfluidic cell enhances reagent transport towards the electrified reactive interface. This continuous-flow microfluidic electrostatic reactor is an example of an electric-field driven platform where clean large-scale electrostatic catalytic processes can be efficiently implemented and regulated.

Triple-Bond Vibrations: Emerging Applications in Energy and Biological Sciences

Triple bonds, such as that formed between two carbon atoms (i.e., C≡C) or that formed between one carbon atom and one nitrogen atom (i.e., C≡N), afford unique chemical bonding and hence vibrational characteristics. As such, they are not only frequently used to construct molecules with tailored chemical and/or physical properties but also employed as vibrational probes to provide site-specific chemical and/or physical information at the molecular level. Herein, we offer our perspective on the emerging applications of various triple-bond vibrations in energy and biological sciences with a focus on C≡C and C≡N triple bonds.

Enhanced active-site electric field accelerates enzyme catalysis

The design and improvement of enzymes based on physical principles remain challenging. Here we demonstrate that the principle of electrostatic catalysis can be leveraged to substantially improve a natural enzyme's activity. We enhanced the active-site electric field in horse liver alcohol dehydrogenase by replacing the serine hydrogen-bond donor with threonine and replacing the catalytic Zn2+ with Co2+. Based on the electric field enhancement, we make a quantitative prediction of rate acceleration-50-fold faster than the wild-type enzyme-which was in close agreement with experimental measurements. The effects of the hydrogen bonding and metal coordination, two distinct chemical forces, are described by a unified physical quantity-electric field, which is quantitative, and shown here to be additive and predictive. These results suggest a new design paradigm for both biological and non-biological catalysts.

Free Energy Profile Decomposition Analysis for QM/MM Simulations of Enzymatic Reactions

In enzyme mechanistic studies and mutant design, it is highly desirable to know the individual residue contributions to the reaction free energy and barrier. In this work, we show that such free energy contributions from each residue can be readily obtained by postprocessing ab initio quantum mechanical molecular mechanical (ai-QM/MM) free energy simulation trajectories. Specifically, through a mean force integration along the minimum free energy pathway, one can obtain the electrostatic, polarization, and van der Waals contributions from each residue to the free energy barrier. Separately, a similar analysis procedure allows us to assess the contribution from different collective variables along the reaction coordinate. The chorismate mutase reaction is used to demonstrate the utilization of these two trajectory analysis tools.

Electro-inductive Effect Dominates Vibrational Frequency Shifts of Conjugated Probes on Gold Electrodes

Interfacial electric fields play a critical role in electrocatalysis and are often characterized by using vibrational probes attached to an electrode surface. Understanding the physical principles dictating the impact of the applied electrode potential on the vibrational probe frequency is important. Herein, a comparative study is performed for two molecular probes attached to a gold electrode. Both probes contain a nitrile (CN) group, but 4-mercaptobenzonitrile (4-MBN) exhibits continuous conjugation from the electrode through the nitrile group, whereas this conjugation is interrupted for 2-(4-mercaptophenyl)acetonitrile (4-MPCN). Periodic density functional theory calculations predict that the CN vibrational frequency shift of the 4-MBN system is dominated by induction, which is a through-bond polarization effect, leading to a strong potential dependence that does not depend significantly on the orientation of the CN bond relative to the surface. In contrast, the CN vibrational frequency shift of the 4-MPCN system is influenced less by induction and more by through-space electric field effects, leading to a weaker potential dependence and a greater orientation dependence. These theoretical predictions were confirmed by surface-enhanced Raman spectroscopy experiments. Balancing through-bond and through-space electrostatic effects may assist in the fundamental understanding and design of electrocatalytic systems.

Direct measurements of biomolecular electrostatics through experiments

Biomolecular electrostatics has been a subject of computational investigations based on 3D structures. This situation is changing because emerging experimental tools allow us to quantitatively investigate biomolecular electrostatics without any use of structure information. Now, electrostatic potentials around biomolecules can directly be measured for many residues simultaneously by nuclear magnetic resonance (NMR) spectroscopy. This NMR method can be used to study electrostatic aspects of various processes, including macromolecular association and liquid-liquid phase separation. Applications to structurally flexible biomolecules such as intrinsically disordered proteins are particularly useful. The new tools also facilitate examination of theoretical models and methods for biomolecular electrostatics.

A closed-loop catalytic nanoreactor system on a transistor

Precision chemistry demands miniaturized catalytic systems for sophisticated reactions with well-defined pathways. An ideal solution is to construct a nanoreactor system functioning as a chemistry laboratory to execute a full chemical process with molecular precision. However, existing nanoscale catalytic systems fail to in situ control reaction kinetics in a closed-loop manner, lacking the precision toward ultimate reaction efficiency. We find an inter-electrochemical gating effect when operating DNA framework-constructed enzyme cascade nanoreactors on a transistor, enabling in situ closed-loop reaction monitoring and modulation electrically. Therefore, a comprehensive system is developed, encapsulating nanoreactors, analyzers, and modulators, where the gate potential modulates enzyme activity and switches cascade reaction "ON" or "OFF." Such electric field-effect property enhances catalytic efficiency of enzyme by 343.4-fold and enables sensitive sarcosine assay for prostate cancer diagnoses, with a limit of detection five orders of magnitude lower than methodologies in clinical laboratory. By coupling with solid-state electronics, this work provides a perspective to construct intelligent nano-systems for precision chemistry.

Phenol as a Tethering Group to Gold Surfaces: Stark Response and Comparison to Benzenethiol

Understanding the adsorption of organic molecules on metals is important in numerous areas of surface science, including electrocatalysis, electrosynthesis, and biosensing. While thiols are commonly used to tether organic molecules on metals, it is desirable to broaden the range of anchoring groups. In this study, we use a combined spectroelectrochemical and computational approach to demonstrate the adsorption of 4-cyanophenols (CPs) on polycrystalline gold. Using the nitrile stretching vibration as a marker, we confirm the adsorption of CP on the gold electrode and compare our results with those obtained for the thiol counterpart, 4-mercaptobenzonitirle (MBN). Our results reveal that CP adsorbs on the gold electrode via the OH linker, as evidenced by the similarity in the direction and magnitude of the nitrite Stark shifts for CP and MBN. This finding paves the way for exploring new approaches to modify electrode surfaces for controlled reactivity. Furthermore, it highlights adsorption on metals as an important step in the electroreactivity of phenols.

An algorithm to find the optimal oriented external electrostatic field for annihilating a reaction barrier in a polarizable molecular system

The use of oriented external electric fields (OEEFs) to promote and control chemical reactivity has motivated many theoretical and computational studies in the last decade to model the action of OEEFs on a molecular system and its effects on chemical processes. Given a reaction, a central goal in this research area is to predict the optimal OEEF (oOEEF) required to annihilate the reaction energy barrier with the smallest possible field strength. Here, we present a model rooted in catastrophe and optimum control theories that allows us to find the oOEEF for a given reaction valley in the potential energy surface (PES). In this model, the effective (or perturbed) PES of a polarizable molecular system is constructed by adding to the original, non-perturbed, PES a term accounting for the interaction of the OEEF with the intrinsic electric dipole and polarizability of the molecular system, so called the polarizable molecular electric dipole (PMED) model. We demonstrate that the oOEEF can be established by locating a point in the original PES with unique topological properties: the optimal barrier breakdown or bond-breaking point (oBBP). The essential feature of the oBBP structure is the fact that this point maintains its topological properties for all the applied OEEFs, also for the unperturbed PES, thus becoming much more relevant than the commonly used minima and transition state structures. The PMED model proposed here has been implemented in an open access package and is shown to successfully predict the oOEEF for two processes: an isomerization reaction of a cumulene derivative and the Huisgen cycloaddition reaction.

Structural Characterization of Fluorescent Proteins Using Tunable Femtosecond Stimulated Raman Spectroscopy

The versatile functions of fluorescent proteins (FPs) as fluorescence biomarkers depend on their intrinsic chromophores interacting with the protein environment. Besides X-ray crystallography, vibrational spectroscopy represents a highly valuable tool for characterizing the chromophore structure and revealing the roles of chromophore-environment interactions. In this work, we aim to benchmark the ground-state vibrational signatures of a series of FPs with emission colors spanning from green, yellow, orange, to red, as well as the solvated model chromophores for some of these FPs, using wavelength-tunable femtosecond stimulated Raman spectroscopy (FSRS) in conjunction with quantum calculations. We systematically analyzed and discussed four factors underlying the vibrational properties of FP chromophores: sidechain structure, conjugation structure, chromophore conformation, and the protein environment. A prominent bond-stretching mode characteristic of the quinoidal resonance structure is found to be conserved in most FPs and model chromophores investigated, which can be used as a vibrational marker to interpret chromophore-environment interactions and structural effects on the electronic properties of the chromophore. The fundamental insights gained for these light-sensing units (e.g., protein active sites) substantiate the unique and powerful capability of wavelength-tunable FSRS in delineating FP chromophore properties with high sensitivity and resolution in solution and protein matrices. The comprehensive characterization for various FPs across a colorful palette could also serve as a solid foundation for future spectroscopic studies and the rational engineering of FPs with diverse and improved functions.

High-throughput computational investigation of protein electrostatics and cavity for SAM-dependent methyltransferases

S-adenosyl methionine (SAM)-dependent methyl transferases (MTases) are a ubiquitous class of enzymes catalyzing dozens of essential life processes. Despite targeting a large space of substrates with diverse intrinsic reactivity, SAM MTases have similar catalytic efficiency. While understanding of MTase mechanism has grown tremendously through the integration of structural characterization, kinetic assays, and multiscale simulations, it remains elusive how these enzymes have evolved to fit the diverse chemical needs of their respective substrates. In this work, we performed a high-throughput molecular modeling analysis of 91 SAM MTases to better understand how their properties (i.e., electric field [EF] strength and active site volumes) help achieve similar catalytic efficiency toward substrates of different reactivity. We found that EF strengths have largely adjusted to make the target atom a better methyl acceptor. For MTases that target RNA/DNA and histone proteins, our results suggest that EF strength accommodates formal hybridization state and variation in cavity volume trends with diversity of substrate classes. Metal ions in SAM MTases contribute negatively to EF strength for methyl donation and enzyme scaffolds tend to offset these contributions.

Evaluating the Transition State Stabilization/Destabilization Effects of the Electric Fields from Scaffold Residues by a QM/MM Approach

The protein scaffolds of enzymes not only provide structural support for the catalytic center but also exert preorganized electric fields for electrostatic catalysis. In recent years, uniform oriented external electric fields (OEEFs) have been widely applied to enzymatic reactions to mimic the electrostatic effects of the environment. However, the electric fields exerted by individual residues in proteins may be quite heterogeneous across the active site, with varying directions and strengths at different positions of the active site. Here, we propose a QM/MM-based approach to evaluate the effects of the electric fields exerted by individual residues in the protein scaffold. In particular, the heterogeneity of the residue electric fields and the effect of the native protein environment can be properly accounted for by this QM/MM approach. A case study of the O-O heterolysis reaction in the catalytic cycle of TyrH shows that (1) for scaffold residues that are relatively far from the active site, the heterogeneity of the residue electric field in the active site is not very significant and the electrostatic stabilization/destabilization due to each residue can be well approximated with the interaction energy between a uniform electric field and the QM region dipole; (2) for scaffold residues near the active site, the residue electric fields can be highly heterogeneous along the breaking O-O bond. In such a case, approximating the residue electric fields as uniform fields may misrepresent the overall electrostatic effect of the residue. The present QM/MM approach can be applied to evaluate the residues' electrostatic impact on enzymatic reactions, which also can be useful in computational optimization of electric fields to boost the enzyme catalysis.

Vibrational Solvatochromism Study of the C-H···O Improper Hydrogen Bond

The improper C-H···O hydrogen bond is an important weak interaction, with broad implications for protein and nucleic acid structure, molecular recognition, enzyme catalysis, and drug interaction. Despite its wide identification in crystal structures, the general existence of C-H···O hydrogen bonds remains elusive especially for natural C-H groups in bulk aqueous solutions at room temperature. Vibrational spectroscopy is a promising methodology to tackle this challenge, as formation of C-H···O hydrogen bonds usually causes shifts of the C-H stretch frequency. Yet, prior observations are inconclusive, as they are all based on a simple blue-shift in aqueous solution and cannot distinguish if it is an effect caused by solvent reorganization or a specific hydrogen-bonding interaction. In this work, we used vibrational solvatochromism as a calibration of the solvent reorganization effect and identified a specific H-bonding interaction. We performed vibrational solvatochromism study of C-H(D) of multiple alcohol molecules including the CH mode of CD₃CH(OH)CD₃ and the CD₃ modes of CD₃OH, CD₃CH₂OH, and CD₃CH(OH)CD₃ in a series of solvents. We found an abnormal blue-shift of the Raman frequency of the C-H and C-D bonds at both the C_α and C_β positions of alcohols in water, which lies in an opposite direction to the expected trend due to vibrational solvatochromism. This experimental evidence supports that the improper C-H···O hydrogen bonds might generally exist between nonpolarized C-H and water in liquid solutions at room temperature.

Protein Dynamics and Enzymatic Catalysis

This Perspective presents a review of our work and that of others in the highly controversial topic of the coupling of protein dynamics to reaction in enzymes. We have been involved in studying this topic for many years. Thus, this perspective will naturally present our own views, but it also is designed to present an overview of the variety of viewpoints of this topic, both experimental and theoretical. This is obviously a large and contentious topic.

A catastrophe theory-based model for optimal control of chemical reactions by means of oriented electric fields

The effect of oriented external electric fields (OEEF) on chemical reactivity has been studied theoretically and computationally in the last decades. A central goal in this research area is to predict the orientation and the smallest amplitude electric field that renders a barrierless chemical process with the smallest possible strength. Recently, a model to find the optimal electric field has been proposed and described (Bofill JM et al., J. Chem. Theory Comput. 18:935, 2022). We here proof that this model is based on catastrophe and optimum control theories. Based on both theories a technical treatment of the model is given and applied to a two-dimensional generic example that provides insight into its nature and capability. Finally, the model is applied to determine the optimal OEEF for the trans-to-cis isomerization of a [3]cumulene derivative.

The effect of immediate environment on bond strength of different bond types-A valence bond study

The ability to design catalysis largely depends on our understanding of the electrostatic effect of the surrounding on the bonds participating in the reaction. Here, we used a simplistic model of point charges (PCs) to determine a set of rules guiding how to construct PC-bond arrangement that can strengthen or weaken different chemical bonds. Using valence bond theory to calculate the in situ bond energies, we show that the effect of the PC mainly depends on the bond's dipole moment irrespective of its type (being covalent or charge shift). That is, polar bonds are getting stronger or weaker depending on the sign and location of the PC, whereas non- or weakly polar bonds become stronger or weaker depending only on the location of the PC and to a smaller extent compared with polar bonds. We also show that for polar bonds, the maximal bond strengthening and weakening effect can be achieved when the PC is placed along the bond axis, as close as possible to the more and less polarizable atom/fragment, respectively. Finally, due to the stabilizing effects of polarizability, we show that, overall, it is easier to cause bond strengthening compared with bond weakening. Particularly, for polar bonds, bond strengthening is larger than bond weakening obtained by an oppositely signed PC. These rules should be useful in the future design of catalysis in, e.g., enzyme active sites.

Protein Electric Fields Enable Faster and Longer-Lasting Covalent Inhibition of β-Lactamases

The widespread design of covalent drugs has focused on crafting reactive groups of proper electrophilicity and positioning toward targeted amino-acid nucleophiles. We found that environmental electric fields projected onto a reactive chemical bond, an overlooked design element, play essential roles in the covalent inhibition of TEM-1 β-lactamase by avibactam. Using the vibrational Stark effect, the magnitudes of the electric fields that are exerted by TEM active sites onto avibactam's reactive C═O were measured and demonstrate an electrostatic gating effect that promotes bond formation yet relatively suppresses the reverse dissociation. These results suggest new principles of covalent drug design and off-target site prediction. Unlike shape and electrostatic complementary which address binding constants, electrostatic catalysis drives reaction rates, essential for covalent inhibition, and deepens our understanding of chemical reactivity, selectivity, and stability in complex systems.

Perspective: Path Sampling Methods Applied to Enzymatic Catalysis

This Perspective reviews the use of Transition Path Sampling methods to study enzymatically catalyzed chemical reactions. First applied by our group to an enzymatic reaction over 15 years ago, the method has uncovered basic principles in enzymatic catalysis such as the protein promoting vibration, and it has also helped harmonize such ideas as electrostatic preorganization with dynamic views of enzyme function. It is now being used to help uncover principles of protein design necessary to artificial enzyme creation.

Solvent Organization and Electrostatics Tuned by Solute Electronic Structure: Amide versus Non-Amide Carbonyls

The ability to exploit carbonyl groups to measure electric fields in enzymes and other complex reactive environments by using the vibrational Stark effect has inspired growing interest in how these fields can be measured, tuned, and ultimately designed. Previous studies have concentrated on the role of the solvent in tuning the fields exerted on the solute. Here, we explore instead the role of the solute electronic structure in modifying the local solvent organization and electric field exerted on the solute. By measuring the infrared absorption spectra of amide-containing molecules, as prototypical peptides, and contrasting them with non-amide carbonyls in a wide range of solvents, we show that these solutes experience notable differences in their frequency shifts in polar solvents. Using vibrational Stark spectroscopy and molecular dynamics simulations, we demonstrate that while some of these differences can be rationalized by using the distinct intrinsic Stark tuning rates of the solutes, the larger frequency shifts for amides and dimethylurea primarily result from the larger solvent electric fields experienced by their carbonyl groups. These larger fields arise due to their stronger p-π conjugation, which results in larger C═O bond dipole moments that further induce substantial solvent organization. Using electronic structure calculations, we decompose the electric fields into contributions from solvent molecules that are in the first solvation shell and those from the bulk and show that both of these contributions are significant and become larger with enhanced conjugation in solutes. These results show that structural modifications of a solute can be used to tune both the solvent organization and electrostatic environment, indicating the importance of a solute-centric paradigm in modulating and designing the electrostatic environment in condensed-phase chemical processes.