Influence of the Greater Protein Environment on the Electrostatic Potential in Metalloenzyme Active Sites: The Case of Formate Dehydrogenase

The Mo/W-containing metalloenzyme formate dehydrogenase (FDH) is an efficient and selective natural catalyst that reversibly converts CO₂ to formate under ambient conditions. In this study, we investigate the impact of the greater protein environment on the electrostatic potential (ESP) of the active site. To model the enzyme environment, we used a combination of classical molecular dynamics and multiscale quantum-mechanical (QM)/molecular-mechanical (MM) simulations. We leverage charge shift analysis to systematically construct QM regions and analyze the electronic environment of the active site by evaluating the degree of charge transfer between the core active site and the protein environment. The contribution of the terminal chalcogen ligand to the ESP of the metal center is substantial and dependent on the chalcogen identity, with similar, less negative ESPs for Se and S terminal chalcogens in comparison to O regardless of whether the metal is Mo or W. The orientation of the side chains and conformations of the cofactor also affect the ESP, highlighting the importance of sampling dynamic fluctuations in the protein. Overall, our observations suggest that the terminal chalcogen ligand identity plays an important role in the enzymatic activity of FDH, suggesting opportunities for a rational bioinspired catalyst design.

Computational Discovery of Transition-metal Complexes: From High-throughput Screening to Machine Learning

Transition-metal complexes are attractive targets for the design of catalysts and functional materials. The behavior of the metal-organic bond, while very tunable for achieving target properties, is challenging to predict and necessitates searching a wide and complex space to identify needles in haystacks for target applications. This review will focus on the techniques that make high-throughput search of transition-metal chemical space feasible for the discovery of complexes with desirable properties. The review will cover the development, promise, and limitations of "traditional" computational chemistry (i.e., force field, semiempirical, and density functional theory methods) as it pertains to data generation for inorganic molecular discovery. The review will also discuss the opportunities and limitations in leveraging experimental data sources. We will focus on how advances in statistical modeling, artificial intelligence, multiobjective optimization, and automation accelerate discovery of lead compounds and design rules. The overall objective of this review is to showcase how bringing together advances from diverse areas of computational chemistry and computer science have enabled the rapid uncovering of structure-property relationships in transition-metal chemistry. We aim to highlight how unique considerations in motifs of metal-organic bonding (e.g., variable spin and oxidation state, and bonding strength/nature) set them and their discovery apart from more commonly considered organic molecules. We will also highlight how uncertainty and relative data scarcity in transition-metal chemistry motivate specific developments in machine learning representations, model training, and in computational chemistry. Finally, we will conclude with an outlook of areas of opportunity for the accelerated discovery of transition-metal complexes.

Quantum Mechanical Description of Electrostatics Provides a Unified Picture of Catalytic Action Across Methyltransferases

Methyl transferases (MTases) are a well-studied class of enzymes for which competing enzymatic enhancement mechanisms have been suggested, ranging from structural methyl group CH···X hydrogen bonds (HBs) to electrostatic- and charge-transfer-driven stabilization of the transition state (TS). We identified all Class I MTases for which reasonable resolution (<2.0 Å) crystal structures could be used to form catalytically competent ternary complexes for multiscale (i.e., quantum-mechanical/molecular-mechanical or QM/MM) simulation of the S_N2 methyl transfer reaction coordinate. The four Class I MTases studied have both distinct functions (e.g., protein repair or biosynthesis) and substrate nucleophiles (i.e., C, N, or O). While CH···X HBs stabilize all reactant complexes, no universal TS stabilization role is found for these interactions in MTases. A consistent picture is instead obtained through analysis of charge transfer and electrostatics, wherein much of cofactor-substrate charge separation is maintained in the TS region, and electrostatic potential is correlated with substrate nucleophilicity (i.e., intrinsic reactivity).

Revealing quantum mechanical effects in enzyme catalysis with large-scale electronic structure simulation

Enzymes have evolved to facilitate challenging reactions at ambient conditions with specificity seldom matched by other catalysts. Computational modeling provides valuable insight into catalytic mechanism, and the large size of enzymes mandates multi-scale, quantum mechanical-molecular mechanical (QM/MM) simulations. Although QM/MM plays an essential role in balancing simulation cost to enable sampling with full QM treatment needed to understand electronic structure in enzyme active sites, the relative importance of these two strategies for understanding enzyme mechanism is not well known. We explore challenges in QM/MM for studying the reactivity and stability of three diverse enzymes: i) Mg2+-dependent catechol O-methyltransferase (COMT), ii) radical enzyme choline trimethylamine lyase (CutC), and iii) DNA methyltransferase (DNMT1), which has structural Zn2+ binding sites. In COMT, strong non-covalent interactions lead to long range coupling of electronic structure properties across the active site, but the more isolated nature of the metallocofactor in DNMT1 leads to faster convergence of some properties. We quantify these effects in COMT by computing covariance matrices of by-residue electronic structure properties during dynamics and along the reaction coordinate. In CutC, we observe spontaneous bond cleavage following initiation events, highlighting the importance of sampling and dynamics. We use electronic structure analysis to quantify the relative importance of CHO and OHO non-covalent interactions in imparting reactivity. These three diverse cases enable us to provide some general recommendations regarding QM/MM simulation of enzymes.

Communication: Observation of local-bender eigenstates in acetylene

We report the observation of eigenstates that embody large-amplitude, local-bending vibrational motion in acetylene by stimulated emission pumping spectroscopy via vibrational levels of the S1 state involving excitation in the non-totally symmetric bending modes. The N(b) = 14 level, lying at 8971.69 cm(-1) (J = 0), is assigned on the basis of degeneracy due to dynamical symmetry breaking in the local-mode limit. The level pattern for the N(b) = 16 level, lying at 10 218.9 cm(-1), is consistent with expectations for increased separation of ℓ = 0 and 2 vibrational angular momentum components. Increasingly poor agreement between our observations and the predicted positions of these levels highlights the failure of currently available normal mode effective Hamiltonian models to extrapolate to regions of the potential energy surface involving large-amplitude displacement along the acetylene ⇌ vinylidene isomerization coordinate.

Simplified Cartesian basis model for intrapolyad emission intensities in the bent-to-linear electronic transition of acetylene

The acetylene emission spectrum from the trans-bent electronically excited à state to the linear ground electronic X̃ state has attracted considerable attention because it grants Franck–Condon access to local bending vibrational levels of the X̃ state with large-amplitude motion along the acetylene ⇌ vinylidene isomerization coordinate. For emission from the ground vibrational level of the à state, there is a simplifying set of Franck–Condon propensity rules that gives rise to only one zero-order bright state per conserved vibrational polyad of the X̃ state. Unfortunately, when the upper level involves excitation in the highly admixed ungerade bending modes, ν4′ and ν6′, the simplifying Franck–Condon propensity rule breaks down--as long as the usual polar basis (with v and l quantum numbers) is used to describe the degenerate bending vibrations of the X̃ state--and the intrapolyad intensities result from complicated interference patterns between many zero-order bright states. In this article, we show that, when the degenerate bending levels are instead treated in the Cartesian two-dimensional harmonic oscillator basis (with vx and vy quantum numbers), the propensity for only one zero-order bright state (in the Cartesian basis) is restored, and the intrapolyad intensities are simple to model, as long as corrections are made for anharmonic interactions. As a result of trans ⇌ cis isomerization in the à state, intrapolyad emission patterns from overtones of ν4′ and ν6′ evolve as quanta of trans bend (ν3′) are added, so the emission intensities are not only relevant to the ground-state acetylene ⇌ vinylidene isomerization, they are also a direct reporter of isomerization in the electronically excited state.

Observation of the A1A" state of isocyanogen

The A1A" state of isocyanogen, CNCN, is observed using photofragment fluorescence excitation spectroscopy in a room temperature cell and in a molecular beam. The spectra are highly congested, but progressions that correspond to the Franck-Condon active C-N-C bending vibration in the excited state are evident. Linewidth measurements indicate that the excited state lifetime is <10 ps. These measurements are consistent with previous ab initio calculations, which predicted a bent excited state with a short lifetime due to predissociation. Although we do not believe that we have observed the origin band of the electronic transition, we place an upper limit of 42,523 cm(-1) on the energy of the excited state zero point level.

Beam Action Spectroscopy via Inelastic Scattering

In this article, a new technique we call Beam Action Spectroscopy via Inelastic Scattering (BASIS) is demonstrated. BASIS takes advantage of the sensitivity of rotational state distributions in a supersonic molecular beam to inelastic scattering within the beam. We exploit BASIS to achieve increased sensitivity in two very different types of experiments. In the first, the UV photodissociation spectrum of OClO is recovered by monitoring intensity changes in the pure rotational transition of a spectator molecule (OCS) downstream from the nozzle, revealing a new vibrational structure in the region between 30,000 and 36,000 cm(-1). In the second, the mid-IR vibrational spectrum of acetylene is recorded simply by monitoring a single pure rotational transition of OCS co-expanded with acetylene. The technique may prove particularly fruitful when an excitation process produces product dark states that are not easily probed by conventional spectroscopy.

Electronic Signatures of Large Amplitude Motions: Dipole Moments of Vibrationally Excited Local-Bend and Local-Stretch States of S0 Acetylene

A one-dimensional local bend model is used to describe the variation of electronic properties of acetylene in vibrational levels that embody large amplitude local motions on the S0 potential energy surface. Calculations performed at the CCSD(T) and MR-AQCC levels of theory predict an approximately linear dependence of the dipole moment on the number of quanta in either the local bending or local stretching excitation. In the local mode limit, one quantum of stretching excitation in one CH bond leads to an increase of 0.025 D in the dipole moment, and one quantum of bending vibration in the CCH angle leads to an increase of 0.068 D. The use of a one-dimensional model for the local bend is justified by comparison to the well-established polyad model which reveals a decoupling of the large amplitude bending from other degrees of freedom in the range of Nbend = 14-22. We find that the same one-dimensional large amplitude bending motion emerges from two profoundly different representations, a one-dimensional cut through an ab initio, seven-dimensional Hamiltonian and the three-dimensional (l = 0) pure-bending experimentally parametrized spectroscopic Hamiltonian.

Millimeter-wave-detected, millimeter-wave optical polarization spectroscopy

We report a new form of microwave optical double-resonance spectroscopy called millimeter-wave-detected, millimeter-wave optical polarization spectroscopy (mmOPS). In contrast to other forms of polarization spectroscopy, in which the polarization rotation of optical beams is detected, the mmOPS technique is based on the polarization rotation of millimeter waves induced by the anisotropy from optical pumping out of the lower or upper levels of the millimeter wave transition. By monitoring ground-state rotational transitions with the millimeter waves, the mmOPS technique is capable of identifying weak or otherwise difficult-to-observe optical transitions in complex chemical environments, where multiple molecular species or vibrational states can lead to spectral congestion. Once a transition is identified, mmOPS can then be used to record pure rotational transitions in vibrationally and electronically excited states, with the resolution limited only by the radiative decay rate. Here, the sensitivity of this nearly-background-free technique is demonstrated by optically pumping the weak, nominally spin-forbidden CS e (3)Sigma(-)-X (1)Sigma(+) (2-0) and d (3)Delta-X (1)Sigma(+) (6-0) electronic transitions while probing the CS X (1)Sigma(+) (v(")=0,J(")=2-1) rotational transition with millimeter waves. The J(')=2,N(')=2<--J(')=1,N(')=1 pure rotational transition of the CS e (3)Sigma(-) (v(')=2) state is then recorded by optically preparing the J(')=1,N(')=1 level of the e (3)Sigma(-) (v(')=2) state via the J(')=1,N(')=1<--J(")=1 transition of the e (3)Sigma(-)-X (1)Sigma(+) (2-0) band.

CH-stretching overtone spectroscopy of 1,1,1,2-tetrafluoroethane

We have recorded the vibrational absorption spectrum of 1,1,1,2-tetrafluoroethane (HFC-134a) in the fundamental and first five CH-stretching overtone regions with the use of Fourier transform infrared, dispersive long-path, intracavity laser photoacoustic, and cavity ringdown spectroscopies. We compare our measured total oscillator strengths in each region with intensities calculated using an anharmonic oscillator local mode model. We calculate intensities with 1D, 2D, and 3D Hamiltonians, including one or two CH stretches and two CH stretches with the HCH bending mode, respectively. The dipole moment function is calculated ab initio with self-consistent-field Hartree-Fock and density functional theories combined with double- and triple-zeta-quality basis sets. We find that the basis set choice affects the total intensity more than the choice of the Hamiltonian. We achieve agreement between the calculated and measured total intensities of approximately a factor of 2 or better for the fundamental and first five overtones.