Role of Enzyme and Active Site Conformational Dynamics in the Catalysis by α-Amylase Explored with QM/MM Molecular Dynamics
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Rational design of heterogeneous single-site catalysts via surface organometallic chemistry
Single-site heterogeneous catalysts offer an attractive route to unite the molecular precision of homogeneous catalysis with the durability and practical advantages of solids. Surface organometallic chemistry (SOMC) provides a particularly powerful strategy for this purpose by grafting molecular precursors onto tailored surfaces and converting support functionalities into ligand environments for isolated metal centers. As a result, SOMC brings the language and logic of coordination chemistry to heterogeneous catalysis, where the support becomes an integral part of the active site coordination sphere. This Review surveys recent progress in the rational design of SOMC-derived single-site catalysts, with emphasis on synthetic routes, post synthetic transformations, and the deliberate tuning of catalytic behavior through metal-support interactions. Discussions are made on how support identity, hydroxyl topology, acidity, and redox activity shape the geometry, electronic structure, and oxidation state of supported metal sites, as well as how these factors determine activity, selectivity, and stability. We also examine a central limitation of these systems: despite their molecularly informed design, supported single sites often exist as structurally distributed ensembles rather than uniform species, particularly on amorphous supports. This site heterogeneity, along with catalyst dynamics under operating conditions, remains a major barrier to definitive structure-activity relationships. Therefore, emerging approaches that combine advanced characterization, first-principles modeling, ensemble kinetics, and machine learning to resolve active-site structure and guide catalyst development are highlighted. Together, these advances position SOMC as a versatile coordination chemistry framework for the predictive design of heterogeneous catalysts with well-defined molecularly tailored active sites.
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Oriented Electrostatic Effects on O 2 and CO 2 Reduction by a Polycationic Iron Porphyrin
Next-generation energy technologies require improved methods for rapid and efficient chemical-to-electrical energy transformations. One new approach has been to include atomically-positioned, electrostatic motifs in molecular catalysts to stabilize high-energy, charged intermediates. For example, an iron porphyrin bearing four cationic, ortho-N,N,N-trimethylanilinium groups (o-[N(CH 3 ) 3 ] + ) has recently been used to catalyze the complex, multi-step O 2 and CO 2 reduction reactions (ORR and CO 2 RR) with fast rates and at low overpotentials. The success of this catalyst is attributed, at least in part, to specific charge-charge interactions between the atomically-positioned o-[N(CH 3 ) 3 ] + groups and the bound substrate. However, by nature of the mono-ortho substitution pattern, there are four possible atropisomers of this metalloporphyrin and thus four unique electrostatic environments. This work reports that each of the four individual atropisomers catalyzes both the ORR and CO 2 RR with fast rates and low overpotentials. The maximum turnover frequencies (TOF max ) vary among the atropisomers, by a factor of 60 for the ORR and a factor of 5 for CO 2 RR. For the ORR, the αβαβ isomer is the fastest and has the highest overpotential, while for the CO 2 RR, the order is reversed and the αααα isomer is the fastest and has the highest overpotential. The role of charge-positioning is complex and can affect more than a single step such as CO 2 binding. These data offer a first-of-a-kind perspective on atomically positioned charge and highlight the significance of high charge density, rather than orientation, on the thermodynamics and kinetics of multistep molecular electrochemical transformations.
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Molecular-Level Design of Heterogeneous Chiral Catalysts
A recent major focus of catalyst research has been on improving the selectivity or atom efficiency of catalytic processes. Perhaps the most subtle and difficult form of selectivity to control is enantioselectivity, a catalyst’s ability to preferentially yield one enantiomer of a chiral product. Since two enantiomers are identical in all respects except for their mirror reflection symmetry, both are formed in non-chiral environments at exactly equal rates; only by introducing some type of chiral modification to the system can the rate of formation of one enantiomer be favored over the other. This has been successfully achieved for homogeneous-phase, organometallic catalysts, but the empirical development of heterogeneous-phase analogs has proven elusive. The design of such heterogeneous-phase catalysts would obviate the need for inefficient purification steps to remove the heavy-metal catalysts. The goal of the proposed research by the Chiral Catalysis Group is to understand the interactions of prochiral reactants on chirally modified surfaces that lead to the preferential formation of one enantiomer over the other. There are two general concepts for designing heterogeneous-phase enantioselective catalysts. The first adopts the strategy used in homogeneous phase, by adding a chiral modifier to the surface. This approach, while conceptually simple has challenges associated with modifying an extended surface. The second concept, which is unique to extended surfaces, is the idea of creating surfaces that are themselves naturally chiral. A fundamental understanding of the interactions that control enantioselectivity will enable the Chiral Catalysis Group to develop the concepts necessary to design novel, heterogenous catalytic materials. Enantioselectivity is also central to catalytic processes that underpin the pharmaceutical and agrochemical industries. With funding from the Department of Energy, the Chiral Catalysis Group has played a leading role in developing a fundamental understanding of chiral catalysis and of the adsorbate structures, interactions and kinetic effects that control heterogenous-phase enantioselectivity. The proposed research program is organized conceptually around three types of enantiospecific interactions: interactions with naturally chiral surfaces; those with modified surfaces categorized as chirally templated surfaces; and one-to-one interactions of prochiral molecules with chiral surface modifiers. Our specific goals are to: (1) determine the structures of chiral surfaces, prochiral reactants, chiral products and chiral modifiers; (2) understand the enantiospecific interactions that occur between prochiral reactants and chiral products with chirally modified surfaces; (3) develop methods for detection of enantiospecific surface phenomena; and (4) elucidate enantioselective reaction pathways and the interactions that control them. The range of expertise within the Chiral Catalysis Group includes molecular-scale theory, surface science experiments, state-of-the-art spectroscopic, kinetic and atomic-scale imaging capabilities carried out in vacuum and under more-realistic liquid- and gas-phase environments complemented by catalytic measurements. By fully integrating such a breadth of approaches and extensive expertise, the Chiral Catalysis Group will, for the first time, be able to understand, rationally design and then control active sites for optimal enantioselectivity. In addition to having a significant impact on the field of chiral catalysis, the proposed research program will further our general understanding of the molecular-scale origins of catalytic selectivity.
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Conformational ensembles reveal the origins of serine protease catalysis
Enzymes exist in ensembles of states that encode the energetics underlying their catalysis. Conformational ensembles built from 1231 structures of 17 serine proteases revealed atomic-level changes across their reaction states. By comparing the enzymatic and solution reaction, we identified molecular features that provide catalysis and quantified their energetic contributions to catalysis. Serine proteases precisely position their reactants in destabilized conformers, creating a downhill energetic gradient that selectively favors the motions required for reaction while limiting off-pathway conformational states. The same catalytic features have repeatedly evolved in proteases and additional enzymes across multiple distinct structural folds. In conclusion, our ensemble-function analyses revealed previously unknown catalytic features, provided quantitative models based on simple physical and chemical principles, and identified motifs recurrent in nature that may inspire enzyme design.
Du, Siyuan [Stanford Univ., CA (United States)] (O↗
Fast product release requires active-site water dynamics in carbonic anhydrase
Water plays an essential role in enzyme structure, stability, and the substantial rate enhancement of enzyme catalysis. However, direct observations linking enzyme catalysis and active-site water dynamics pose a significant challenge due to experimental difficulties. By integrating an ultraviolet (UV) photolysis technique with temperature-controlled X-ray crystallography, we track the catalytic pathway of carbonic anhydrase II (CAII) at 1.2 Å resolution. This approach enables us to construct molecular movies of CAII catalysis, encompassing substrate (CO 2 ) binding, conversion from substrate to product (bicarbonate), and product release. In the catalytic pathway, we identify an unexpected configuration in product binding and correlate it with sub-nanosecond rearrangement of active-site water. Based on these experimental observations, we propose a comprehensive mechanism of CAII and describe the detailed structure and dynamics of active-site water in CAII. Our findings suggest that CAII has evolved to utilize the structure and fast dynamics of the active-site waters for its diffusion-limited catalytic efficiency.
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Understanding dynamic properties of materials using neutron spectroscopy and atomistic simulation
Recent developments in first-principles lattice dynamics and classical force field based molecular dynamics are revolutionising the field of neutron spectroscopy. Herein we present a short review of these methods, their critical role in the supporting of cutting-edge experiments, and how they are improved by matching experimental data. We begin with a brief overview of how lattice dynamics calculations can be compared to inelastic neutron scattering (INS) and molecular dynamics simulations to both INS and quasi-elastic neutron scattering (QENS). We then provide a series of exemplar applications where lattice dynamics and molecular dynamics have been used in conjunction with neutron spectroscopy to bring significant understanding to topical areas of materials science namely: (i) lattice dynamics and INS for the study of hybrid organic-inorganic perovskites (ii) lattice dynamics and INS for the study of flexible porous solids and (iii) molecular dynamics and QENS for probing molecular behaviour in zeolite catalysis. In all three cases, the understanding gained through the synergy of experiment and computation would have been significantly reduced using either in isolation. Finally, we consider the current state of the art, describing outstanding challenges and suggesting future directions in this exciting and fertile area of physical science.
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Molecular Functionalization of Semiconductor Surfaces
The presence of molecules on semiconductor surfaces can have a profound impact on their properties and applications in solar energy conversion. In this chapter we discuss the methods used to effect functionalization of semiconductor surfaces with molecular dipoles and catalysts. A major focus is the energetic impacts such molecules have to the fields at the semiconductor|contact interface. These field modulations are strongly dependent on the nature of the surface-bound molecule including its dipole moment and orientation as well as the distance of the dipole from the semiconductor surface. The contacting phase also has a strong impact on the energetics, since ions in the liquid electrolytes relevant to inorganic photochemistry partially screen dipolar effects at the surface. In addition to detailed description of these fundamentals, we present the history of this field as well as state-of-the-art chemistries that leverage the preceding decades of knowledge to impart the molecular interfacial layer with dynamic properties such as light absorption and catalysis. The challenges of establishing stable molecular attachment schemes at semiconductor|electrolyte interfaces are interwoven throughout the chapter. We conclude with a prognosis and future outlook that we hope will be a useful guide to those interested in developing the next generation of molecular chemistries at photoelectrode interfaces.
CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS,I↗
Electron transfer in polysaccharide monooxygenase catalysis
Polysaccharide monooxygenase (PMO) catalysis involves the chemically difficult hydroxylation of unactivated C–H bonds in carbohydrates. The reaction requires reducing equivalents and will utilize either oxygen or hydrogen peroxide as a cosubstrate. Two key mechanistic questions are addressed here: 1) How does the enzyme regulate the timely and tightly controlled electron delivery to the mononuclear copper active site, especially when bound substrate occludes the active site? and 2) How does this electron delivery differ when utilizing oxygen or hydrogen peroxide as a cosubstrate? Using a computational approach, potential paths of electron transfer (ET) to the active site copper ion were identified in a representative AA9 family PMO from Myceliophthora thermophila ( Mt PMO9E). When Y62, a buried residue 12 Å from the active site, is mutated to F, lower activity is observed with O 2 . However, a WT-level activity is observed with H 2 O 2 as a cosubstrate indicating an important role in ET for O 2 activation. To better understand the structural effects of mutations to Y62 and axial copper ligand Y168, crystal structures were solved of the wild type Mt PMO9E and the variants Y62W, Y62F, and Y168F. A bioinformatic analysis revealed that position 62 is conserved as either Y or W in the AA9 family. The Mt PMO9E Y62W variant has restored activity with O 2 . Overall, the use of redox-active residues to supply electrons for the reaction with O 2 appears to be widespread in the AA9 family. Furthermore, the results provide a molecular framework to understand catalysis with O 2 versus H 2 O 2 .
Sayler, Richard I. (ORCID:000000017252707X)↗
Stereoconvergent Reduction of Activated Alkenes by a Nicotinamide Free Synergistic Photobiocatalytic System
There is a growing interest in developing cooperative chemoenzymatic reactions to harness the reactivity of chemical catalysts and the selectivity of enzymes for the synthesis of nonracemic chiral compounds. However, existing chemoenzymatic systems with more than one chemical reaction and one enzymatic reaction working cooperatively are rare. Moreover, the application of oxidoreductases in cooperative chemoenzymatic reactions is limited by the necessity of using expensive and unstable redox equivalents such as nicotinamide cofactors. Here we report a lightdriven cooperative chemoenzymatic system comprised of a photoinduced electron transfer reaction (PET) and a photosensitized energy transfer reaction (PEnT) with enzymatic reduction in one-pot to synthesize chiral building blocks of bioactive compounds. As a proof of concept, ene-reductase was directly regenerated by PET in the absence of external cofactors. Meanwhile, enzymatic reduction worked cooperatively with photocatalyst-catalyzed energy transfer that continuously replenished the reactive isomer from the less reactive one. The whole system stereoconvergently reduced E/Z mixtures of alkenes to the enantiopure products. Additionally, enantioselective enzymatic reduction worked competitively with photocatalyst-catalyzed racemic background reaction and side reactions to channel the overall electron flow to the single enantiopure product. As a result, such a light-driven cooperative chemoenzymatic system holds great potential for asymmetric synthesis using inexpensive petroleum or biomass derived alkenes.
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Distinct Kinetic Signatures of Photodesorption from Metal Nanoparticles
Visible photon fluxes can influence the rate and selectivity of heterogeneously catalyzed reactions on metal nanoparticle surfaces. Models describing the influence of photon fluxes have typically introduced photon flux dependent apparent thermal kinetic parameters (reaction orders, activation energies, binding energies, etc.). This has relied on empirical fitting of reaction rate data, making mechanistic interpretations of how photon fluxes influence elementary step rates challenging and inconsistent with fundamental descriptions of photochemistry on metal surfaces developed from surface science studies. Using the CO adsorption–desorption quasi-equilibrium reaction on Pt/Al 2 O 3 catalysts as a model system, we measured steady state adsorbed CO (CO*) coverages under isothermal and isobaric (1 mbar CO) conditions as a function of temperature (473–573 K) and of 440 nm photon flux ((0.1–5.2) × 10 3 # hv Pt site –1 s –1 ) using in situ IR spectroscopy. Steady state CO* coverage on Pt was photon flux dependent with increasing photon flux causing decreasing coverage, consistent with photons driving CO* desorption rates faster than thermal CO* desorption rates. However, photon flux dependent CO* coverages were essentially temperature independent, inconsistent with models that describe photon effects using perturbations to apparent thermal kinetic parameters. Instead, 120 steady state CO* coverages as a function of temperature and photon flux are quantitatively described by a kinetic model in which the overall desorption rate is a summation of independent thermal and photon induced CO* desorption rates. Site-resolved analysis reveals distinct kinetic parameters for photon driven desorption of CO* from well-coordinated, under-coordinated, and highly under-coordinated Pt sites, with temperature-dependent apparent quantum efficiencies (AQE) consistent with temperature dependence of vibrational quanta distribution of adsorbed CO. The rigorous kinetic rate laws for independent photon and thermal driven pathways allow for predictive modeling of the influence of photon fluxes on the rates of CO* desorption under catalytic conditions. Further, the analysis provides evidence that steady state continuous wave photon fluxes can drive desorption/adsorption reactions on metal surfaces out of thermal equilibrium, reconciling surface science observations of molecular photodesorption with applied catalysis. The work establishes a general kinetic framework to be considered for photon driven processes on metals, and defines catalyst, reaction, and photon flux characteristic design principles for breaking Sabatier limitations.
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Controlled Placement of Trivalent Heteroatoms in MFI Zeolite Frameworks Using Structure-Directing Agents
MFI zeolites contain distinct confining pore environments, either smaller (∼0.55 nm) channels or larger (∼0.70 nm) intersections. The substitution of trivalent heteroatoms generates Brønsted acid sites of varying acid strength, which, together with their location within different pore environments, dictates the stability of transition states via electrostatic (ion-pair) and van der Waals interactions. Here, we report that structure-directing agents (SDAs) that control Al 3+ substitutional patterns during MFI crystallization analogously position other trivalent heteroatoms (Ga 3+ , Fe 3+ , B 3+ ), altering the distribution of acid sites between channels and intersections, as probed by low-temperature (403 K) toluene methylation kinetics. Heteroatom-substituted MFI crystallized with tetrapropylammonium result in low selectivity toward p-xylene (<30%), while those crystallized using (co-)SDAs containing peripheral hydrogen-bonding groups (e.g., ethylenediamine) show high p-xylene selectivity (∼80%). These selectivities are consistent with DFT-calculated Gibbs free energy barriers for intersection-dominant and channel-dominant active site distributions, respectively. Transition states to form each xylene isomer are similar in size and charge; thus, their rate constants decrease with acid strength similarly, causing isomer selectivity to depend strongly on confinement but not on acid strength. These generalizable synthetic strategies enable independently controlling acid site strength and location in MFI zeolites and, in turn, catalytic rates and selectivities.
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A new perspective on lone pair dynamics in halide perovskites
Halide perovskites form the foundation of an emerging class of materials for broad application in renewable and sustainable applications, including photocatalysis and solar energy harvesting. These materials exhibit beneficial photophysical properties, including bandgaps suitable for solar energy harvesting and efficient charge screening that underlies efficient charge carrier separation and resistance to defects. For organic–inorganic hybrid perovskites, these benefits are thought to arise, in part, from dipolar molecular cations that can reorient in response to charged particles and defects. In this work, we provide a similar perspective for inorganic metal halide perovskites, which do not contain molecular species with permanent dipoles. We discuss how lone pair electrons lead to dipolar ions that exhibit dynamics in analogy with traditional molecular plastic crystals and hybrid perovskites. We argue that further understanding these electronic plastic crystal motions with first principles simulations and synchrotron scattering can help create a basic understanding of photophysical properties of metal halide perovskites and inform the design of advanced functional materials.
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A modular and extensible CHARMM-compatible model for all-atom simulation of polypeptoids
Peptoids (N-substituted glycines) are a class of sequence-defined synthetic peptidomimetic polymers with applications including drug delivery, catalysis, and biomimicry. Classical molecular simulations have been used to predict and understand the conformational dynamics of single chains and their self-assembly into morphologies including sheets, tubes, spheres, and fibrils. The CGenFF-NTOID model based on the CHARMM General Force Field has demonstrated success in accurate all-atom molecular modeling of peptoid structure and thermodynamics. Extension of this force field to new peptoid side chains has historically required reparameterization of side chain bonded interactions against ab initio data. This fitting protocol improves the accuracy of the force field but is also burdensome and precludes modular extensibility of the model to arbitrary peptoid sequences. In this work, we develop and demonstrate a Modular Side Chain CGenFF-NTOID (MoSiC-CGenFF-NTOID) as an extension of CGenFF-NTOID employing a modular decomposition of the peptoid backbone and side chain parameterizations, wherein arbitrary side chains within the large family of substituted methyl groups (i.e., –CH 3 , –CH 2 R, –CHRR', and –CRR'R") are directly ported from CGenFF. We validate this approach against ab initio calculations and experimental data to develop a MoSiC-CGenFF-NTOID model for all 20 natural amino acid side chains along with 13 commonly used synthetic side chains and present an extensible paradigm to efficiently determine whether a novel side chain can be directly incorporated into the model or whether refitting of the CGenFF parameters is warranted. We make the model freely available to the community along with a tool to perform automated initial structure generation.
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Structural basis for carotenoid cleavage by an archaeal carotenoid dioxygenase
Abstract not provided
Daruwalla, Anahita↗
Compact Peptoid Molecular Brushes for Nanoparticle Stabilization
Controlling the interfaces and interactions of colloidal nanoparticles (NPs) via tethered molecular moieties is crucial for NP applications in engineered nanomaterials, optics, catalysis, and nanomedicine. Despite a broad range of molecular types explored, there is a need for a flexible approach to rationally vary the chemistry and structure of these interfacial molecules for controlling NP stability in diverse environments, while maintaining a small size of the NP molecular shell. Here, we demonstrate that low-molecular-weight, bifunctional comb-shaped, and sequence-defined peptoids can effectively stabilize gold NPs (AuNPs). The generality of this robust functionalization strategy was also demonstrated by coating of silver, platinum, and iron oxide NPs with designed peptoids. Each peptoid (PE) is designed with varied arrangements of a multivalent AuNP-binding domain and a solvation domain consisting of oligo-ethylene glycol (EG) branches. Among designs, a peptoid (PE5) with a diblock structure is demonstrated to provide a superior nanocolloidal stability in diverse aqueous solutions while forming a compact shell (similar to 1.5 nm) on the AuNP surface. We demonstrate by experiments and molecular dynamics simulations that PE5-coated AuNPs (PE5/AuNPs) are stable in select organic solvents owing to the strong PE5 (amine)-Au binding and solubility of the oligo-EG motifs. At the vapor-aqueous interface, we show that PE5/AuNPs remain stable and can self-assemble into ordered 2D lattices. The NP films exhibit strong near-field plasmonic coupling when transferred to solid substrates.
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Effect of Solvent on the Local Structure, Dynamics, and Vibrational Density of States in Sn-BEA Zeolite
Lewis acid zeolites are attractive catalysts for epoxidation and biomass valorization, as they are highly active and selective in the liquid phase and can operate at or near ambient conditions. While a rich experimental literature exists on liquid-phase Lewis acid zeolite catalysis, our understanding of the molecular organization and solvent dynamics in the vicinity of Lewis acid sites with differing metal site speciation remains limited. In this work, we investigate the molecular coordination and diffusion of two common solvents (methanol and water) around the closed and open Sn-BEA zeolite active sites using molecular dynamics simulations with a machine-learned interatomic potential trained on ab initio molecular dynamics trajectories. Molecular dynamics simulations reveal that introducing active sites significantly enhances local order in the first and second solvation shells compared to the pure silica case. For methanol, both closed and open active sites are singly coordinated, while more than two water molecules coordinate the open site. In contrast to methanol, we observed that water molecules dissociate, leading to the formation of additional Sn-OH and silanol groups away from the active site. The diffusion coefficients of water and methanol are functions of the solvent population in the pore. Here, our work provides insights into how active site speciation in Lewis acid zeolites affects solvent coordination, diffusion, and vibrational signature. This information is foundational for catalyst design and optimization of liquid-phase catalytic processes in zeolites. It also demonstrates the suitability of machine-learned interatomic potentials for modeling reactive systems, enabling sufficiently long trajectories for appropriate statistical averaging.
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Reaction Chemistry at Discrete Organometallic Fragments on Black Phosphorus
Abstract Black phosphorus (bP) is a two‐dimensional van der Waals material unique in its potential to serve as a support for single‐site catalysts due to its similarity to molecular phosphines, ligands quintessential in homogeneous catalysis. However, there is a scarcity of synthetic methods to install single metal centers on the bP lattice. Here, we demonstrate the functionalization of bP nanosheets with molecular Re and Mo complexes. A suite of characterization techniques, including infrared, X‐ray photoelectron and X‐ray absorption spectroscopy as well as scanning transmission electron microscopy corroborate that the functionalized nanosheets contain a high density of discrete metal centers directly bound to the bP surface. Moreover, the supported metal centers are chemically accessible and can undergo ligand exchange transformations without detaching from the surface. The steric and electronic properties of bP as a ligand are estimated with respect to molecular phosphines. Sterically, bP resembles tri(tolyl)phosphine when monodentate to a metal center, and bis(diphenylphosphino)propane when bidentate, whereas electronically bP is a σ‐donor as strong as a trialkyl phosphine. This work is foundational in elucidating the nature of black phosphorus as a ligand and underscores the viability of using bP as a basis for single‐site catalysts.
Mitra, Kendahl L. Walz↗