Vibrational Stark Spectroscopy in Proteins: A Probe and Calibration for Electrostatic Fields

Understanding the role of negative charge in the scaffold of an artificial enzyme for CO2 hydrogenation on catalysis

We have approached the construction of an artificial enzyme by employing a robust protein scaffold, lactococcal multidrug resistance regulator, LmrR, providing a structured secondary and outer coordination spheres around a molecular rhodium complex, [RhI(PEt2NglyPEt2)2]-. Previously, we demonstrated a 2-3 fold increase in activity for one Rh-LmrR construct by introducing positive charge in the secondary coordination sphere. In this study, a series of variants was made through site-directed mutagenesis where the negative charge is located in the secondary sphere or outer coordination sphere, with additional variants made with increasingly negative charge in the outer coordination sphere while keeping a positive charge in the secondary sphere. Placing a negative charge in the secondary or outer coordination sphere demonstrates decreased activity by a factor of two compared to the wild-type Rh-LmrR. Interestingly, addition of positive charge in the secondary sphere, with the negatively charged outer coordination sphere restores activity. Vibrational and NMR spectroscopy suggest minimal changes to the electronic density at the rhodium center, regardless of inclusion of a negative or positive charge in the secondary sphere, suggesting another mechanism is impacting catalytic activity, explored in the discussion.

Anionic Effects on Concentrated Aqueous Lithium Ion Dynamics

The dynamics, orientational anisotropy, diffusivity, viscosity, and density were measured for concentrated lithium salt solutions, including lithium chloride (LiCl), lithium bromide (LiBr), lithium nitrite (LiNO2), and lithium nitrate (LiNO3), with methyl thiocyanate as an infrared vibrational probe molecule, using two-dimensional infrared spectroscopy (2D IR), nuclear magnetic resonance (NMR) spectroscopy, and viscometry. The 2D IR, NMR, and viscosity results show that LiNO2 exhibits longer correlation times, lower diffusivity, and nearly 4 times greater viscosity compared to those of the other lithium salt solutions of the same concentration, suggesting that nitrite anions may strongly facilitate structure formation via strengthening water-ion network interactions, directly impacting bulk solution properties at sufficiently high concentrations. Additionally, the LiNO2 and LiNO3 solutions show significantly weakened chemical interactions between the lithium cations and the methyl thiocyanate when compared with those of the lithium halide salts.

Understanding Cysteine Reactivity in Protein Environments with Electric Fields

The role cysteine residues play in proteins is mediated by their protonation state, whereby the thiolate form of the side chain is highly reactive while the thiol form is more inert. However, the pKa of cysteine residues is hard to predict as it can differ widely from its reference value in solution, an effect that is accentuated by local effects in the heterogeneous protein environment. Here, we present a new approach to the prediction of cysteine reactivity based on electric field calculations at the thiol/thiolate group. We validated our approach by predicting the protonation state of cysteine residues in different protein environments (in the active site, at the protein surface, and buried within the protein interior), including Cys-25 in papaya protease omega, which was proven problematic for the more traditional constant pH molecular dynamics (MD) technique. We predict pKa shifts consistent with experimental observations, and the decomposition of the electric fields into contributions from molecular fragments provides a direct handle to rationalize local pH and pKa effects in proteins without introducing parameters other than those of the force field used for MD simulations.

Dioxygen and glucose force motion of the electron-transfer switch in the iron(III) flavohemoglobin-type nitric oxide dioxygenase

Kinetic and structural investigations of the flavohemoglobin-type NO dioxygenase have suggested critical roles for transient Fe(III)O2 complex formation and O2-forced movements affecting hydride transfer to the FAD cofactor and electron-transfer to the Fe(III)O2 complex. Stark-effect theory together with structural models and dipole and internal electrostatic field determinations provided a semi-quantitative spectroscopic method for investigating the proposed Fe(III)O2 complex and O2-forced movements. Deoxygenation of the enzyme causes Stark effects on the ferric heme Soret and charge-transfer bands revealing the Fe(III)O2 complex. Deoxygenation also elicits Stark effects on the FAD that expose forces and motions that create a more restricted NADH access to FAD for hydride transfer and switch electron-transfer off. Glucose also forces the enzyme toward an off state. Amino acid substitutions at the B10, E7, E11, G8, D5, and F7 positions influence the Stark effects of O2 on resting heme spin states and FAD consistent with the proposed roles of the side chains in the enzyme mechanism. Deoxygenation of ferric myoglobin and hemoglobin A also induces Stark effects on the hemes suggesting a common 'oxy-met' state. The ferric myoglobin and hemoglobin heme spectra are also glucose-responsive. A conserved glucose or glucose-6-phosphate binding site is found bridging the BC-corner and G-helix in flavohemoglobin and myoglobin suggesting novel allosteric effector roles for glucose or glucose-6-phosphate in the NO dioxygenase and O2 storage functions. The results support the proposed roles of a ferric O2 intermediate and protein motions in regulating electron-transfer during NO dioxygenase turnover.

Application of Nanosecond Pulsed Electric Field and Autofluorescence Lifetime Microscopy of FAD in Lung Cells

Exposure of nanosecond pulsed electric fields (nsPEFs) to live cells is an increasing research interest in biology and medicine. Despite extensive studies, a question still remains as to how effects of application of nsPEF on intracellular functions are different between cancerous cells and normal cells and how the difference can be detected. Herein, we have presented an approach of autofluorescence lifetime (AFL) microscopy of flavin adenine dinucleotide (FAD) to detect effects of application of nsPEF having 50 ns of a pulse width, nsPEF(50), on intracellular function in lung cancerous cells, A549 and H661, which show nsPEF(50)-induced apoptosis, and normal cells, MRC-5, in which the field effect is less or not induced. Then, the application of nsPEF(50) is shown to increase the lifetime of FAD autofluorescence in lung cancerous cells, whereas the electric field effects on the autofluorescence of FAD was not significant in normal healthy cells, which indicates that the lifetime measurements of FAD autofluorescence are applicable to detect the field-induced change in intracellular functions. Lifetime and intensity microscopic images of FAD autofluorescence in these lung cells were also acquired after exposure to the apoptosis-inducer staurosporine (STS). Then, it was found that the AFL of FAD became longer after exposure not only in the cancerous cells but also in the normal cells. These results indicate that nsPEF(50) applied to lung cells induced apoptotic cell death only in lung cancerous cells (H661 and A549) but not in lung normal cells (MRC-5), whereas STS induced apoptotic cell death both in lung cancerous cells and in lung normal cells. The lifetime microscopy of FAD autofluorescence is suggested to be very useful as a sensitive detection method of nsPEF-induced apoptotic cell death.

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.

Distinguishing between the Electrostatic Effects and Explicit Ion Interactions in a Stark Probe

Vibrational Stark probes are incisive tools for measuring local electric fields in a wide range of chemical environments. The interpretation of the frequency shift often gets complicated due to the specific interactions of the probe, such as hydrogen bonding and Lewis bonding. Therefore, it is important to distinguish between the pure electrostatic response and the response due to such specific interactions. Here we report a molecular system that is sensitive to both the Stark effect from a single ion and the explicit Lewis bonding of ions with the probe. The molecule consists of a crown ether with an appended benzonitrile. The crown captures cations of various charges, and the electric field from the ions is sensed by the benzonitrile probe. Additionally, the lone pair of the benzonitrile can engage in Lewis interactions with some of the ions by donating partial charge density to the ions. Our system exhibits both of these effects and therefore is a suitable test bed for distinguishing between the pure electrostatic and the Lewis interactions. Our computational results show that the electrostatic influence of the ion is operative at large distances, while the Lewis interaction becomes important only within distances that permit orbital overlap. Our results may be useful for using the nitrile probe for measuring electrostatic and coordination effects in complex ionic environments such as the electrode-electrolyte interfaces.

Theoretical Investigation of the X-ray Stark Effect in Small Molecules

We have studied the Stark effect in the soft x-ray region for various small molecules by calculating the field-dependent x-ray absorption spectra. This effect is explained in terms of the response of molecular orbitals (core and valence), the molecular dipole moment, and the molecular geometry to the applied electric field. A number of consistent trends are observed linking the computed shifts in absorption energies and intensities with specific features of the molecular electronic structure. We find that both the virtual molecular orbitals (valence and/or Rydberg) as well as the core orbitals contribute to observed trends in a complementary fashion. This initial study highlights the potential impact of x-ray Stark spectroscopy as a tool to study electronic structure and environmental perturbations at a submolecular scale.

4-Cyanotryptophan as a Sensitive Fluorescence Probe of Local Electric Field of Proteins

Electrostatic interactions are key determinants of protein structure, dynamics, and function. Since protein electrostatics are nonuniform, assessment of the internal electric fields (EFs) of proteins requires spatial resolution at the amino acid residue level. In this regard, vibrational Stark spectroscopy, in conjunction with various unnatural amino acid-based vibrational probes, has become a common method for site-specific interrogation of protein EFs. However, application of this method is often limited to proteins with relatively high solubility, due to the intrinsically low oscillator strength of vibrational transitions. Therefore, it would be useful to develop an alternative method that can overcome this limitation. To this end, we show that, using solvatochromic study and molecular dynamics simulations, the frequency of maximum emission intensity of the fluorophore of 4-cyanotryptophan (4CN-Trp), 3-methyl-1H-indole-4-carbonitrile, exhibits a linear dependence on the local EF. Since the absorption and emission spectra of 4CN-Trp are easily distinguishable from those of naturally occurring aromatic amino acids, we believe that this linear relationship provides an easier and more sensitive means to determine the local EF of proteins.

Modulation of Metal Carbonyl Stretching Frequencies in the Second Coordination Sphere through the Internal Stark Effect

Spectroscopic and computational examination of a homologous series of rhodium(I) pybox carbonyl complexes has revealed a correlation between the conformation of the flanking aryl-substituted oxazoline donors and the carbonyl stretching frequency. This relationship is also observed experimentally for octahedral rhodium(III) and ruthenium(II) variants and cannot be explained through the classical, Dewar-Chatt-Duncanson, interpretation of metal-carbonyl bonding. Instead, these findings are reconciled by local changes in the magnitude of the electric field that is projected along the metal-carbonyl vector: the internal Stark effect.

Sub-Nanometer Mapping of the Interfacial Electric Field Profile Using a Vibrational Stark Shift Ruler

The characterization of electrical double layers is important since the interfacial electric field and electrolyte environment directly affect the reaction mechanisms and catalytic rates of electrochemical processes. In this work, we introduce a spectroscopic method based on a Stark shift ruler that enables mapping the electric field strength across the electric double layer of electrode/electrolyte interfaces. We use the tungsten-pentacarbonyl(1,4-phenelenediisocyanide) complex attached to the gold surface as a molecular ruler. The carbonyl (CO) and isocyanide (NC) groups of the self-assembled monolayer (SAM) provide multiple vibrational reporters situated at different distances from the electrode. Measurements of Stark shifts under operando electrochemical conditions and direct comparisons to density functional theory (DFT) simulations reveal distance-dependent electric field strength from the electrode surface. This electric field profile can be described by the Gouy-Chapman-Stern model with Stern layer thickness of ∼4.5 Å, indicating substantial solvent and electrolyte penetration within the SAM. Significant electro-induction effect is observed on the W center that is ∼1.2 nm away from the surface despite rapid decay of the electric field (∼90%) within 1 nm. The applied methodology and reported findings should be particularly valuable for the characterization of a wide range of microenvironments surrounding molecular electrocatalysts at electrode interfaces and the positioning of electrocatalysts at specific distances from the electrode surface for optimal functionality.

Structural dynamics support electrostatic interactions in the active site of Adenylate Kinase

Electrostatic preorganization as well as structural and dynamic heterogeneity are often used to rationalize the remarkable catalytic efficiency of enzymes. However, they are often presented as incompatible because the generation of permanent electrostatic effects implies that the protein structure remains rigid. Here, we use a metric, electric fields, that can treat electrostatic contributions and dynamics effects on equal footing, for a unique perspective on enzymatic catalysis. We find that the residues that contribute the most to electrostatic interactions with the substrate in the active site of Adenylate Kinase (our working example) are also the most flexible residues. Further, entropy-tuning mutations raise flexibility at the picosecond timescale where more conformations can be visited on short time periods, thereby softening the sharp heterogeneity normally visible at the microsecond timescale.

A fixed multi-site interaction charge model for an accurate prediction of the QM/MM interactions

A fixed multi-site interaction charge (FMIC) model was proposed for the accurate prediction of intermolecular electrostatic interactions based on the quantum mechanical linear response of a molecule to an external electric field. In such a model, some additional off-center interaction sites were added for capturing multipole interactions for a given molecule. By multivariate least-square fitting analysis of the calculated QM/MM interactions of a given molecule with the electrostatic environment and the electrostatic potentials of the environment at the pre-defined distributed interaction sites, the FMIC of the molecule was obtained. The model system of CO in myoglobin (Mb) was utilized to demonstrate the derivation of the FMIC. The accuracy of FMIC in predicting the electrostatic interactions between CO and the Mb environment was investigated using 10 000 different Mb-CO configurations generated from the 400 ps QM/MM MD simulation. In comparison to the QM/MM calculations at the B3LYP/aug-cc-pVTZ/ff99SB level, the mean unsigned error (MUE) of the results based on the FMIC model was merely 0.10 kcal mol^-1, and the root mean square error (RMSE) was only 0.13 kcal mol^-1, which are significantly lower than the results predicted by the ESP charge model (MUE = 1.45 kcal mol^-1, and RMSE = 1.7 kcal mol^-1, respectively). The transferability of FMIC was tested by applying the obtained FMIC in the wild type Mb-CO system to the mutants of V68F and H64L Mb-CO systems. The MUEs of the obtained results for 10 000 different configurations are both smaller than 0.2 kcal mol^-1 for the V68F and H64L Mb-CO systems in comparison to the B3LYP/aug-cc-pVTZ/ff99SB calculations, and the RMSEs are also lower than 0.2 kcal mol^-1 for both mutants. The applications of FMIC were extended to model the electrostatic interactions between a hydrogen fluoride molecule and 492 waters in a truncated octahedron box; our study showed that the FMIC could give satisfactory results with a MUE of 0.12 kcal mol^-1 and a RMSE of 0.16 kcal mol^-1 in comparison to the B3LYP/aug-cc-pVDZ/TIP3P calculations for 10 000 different configurations generated using the 10 ns classical MD simulation. Therefore, the FMIC method provides an accurate and efficient tool for predicting intermolecular electrostatic interactions, which can be utilized in the future development of molecular force fields.

Electric Fields Influence Intramolecular Vibrational Energy Relaxation and Line Widths

Intramolecular vibrational energy relaxation (IVR) is fundamentally important to chemical dynamics. We show that externally applied electric fields affect IVR and vibrational line widths by changing the anharmonic couplings and frequency detunings between modes. We demonstrate this effect in benzonitrile for which prior experimental results show a decrease in vibrational line width as a function of applied electric field. We identify three major channels for IVR that depend on electric field. In the dominant channel, the electric field affects the frequency detuning, while in the other two channels, variation of anharmonic couplings as a function of field is the underlying mechanism. Consistent with experimental results, we show that the combination of all channels gives rise to reduced line widths with increasing electric field in benzonitrile. Our results are relevant for controlling IVR with external or internal fields and for gaining a more complete interpretation of line widths of vibrational Stark probes.

Interfacial Acid-Base Equilibria and Electric Fields Concurrently Probed by In Situ Surface-Enhanced Infrared Spectroscopy

Understanding how applied potentials and electrolyte solution conditions affect interfacial proton (charge) transfers at electrode surfaces is critical for electrochemical technologies. Herein, we examine mixed self-assembled monolayers (SAMs) of 4-mercaptobenzoic acid (4-MBA) and 4-mercaptobenzonitrile (4-MBN) on gold using in situ surface-enhanced infrared absorption spectroscopy (SEIRAS). Measurements as a function of the applied potential, the electrolyte pD, and the electrolyte concentration determined both the relative surface populations of acidic and basic forms of 4-MBA, as well as the local electric fields at the SAM-solution interface by following the Stark shifts of 4-MBN. The effective acidity of the SAM varied with the applied potential, requiring a 600 mV change to move the pK_a by one unit. Since this is ca. 10× the Nernstian value of 59 mV/pK_a, ∼90% of the applied potential dropped across the SAM layer. This emphasizes the importance of distinguishing applied potentials from the potential experienced at the interface. We use the measured interfacial electric fields to estimate the experienced potential at the SAM edge. The SAM pK_a showed a roughly Nernstian dependence on this estimated experienced potential. An analysis of the combined acid-base equilibria and Stark shifts reveals that the interfacial charge density has significant contributions from both SAM carboxylate headgroups and electrolyte components. Ion pairing and ion penetration into the SAM also influence the observed surface acidity. To our knowledge, this study is the first concurrent examination of both effective acidity and electric fields, and highlights the relevance of experienced potentials and specific ion effects at functionalized electrode surfaces.

Quantification of Local Electric Field Changes at the Active Site of Cytochrome c Oxidase by Fourier Transform Infrared Spectroelectrochemical Titrations

Cytochrome c oxidase (CcO) is a transmembrane protein complex that reduces molecular oxygen to water while translocating protons across the mitochondrial membrane. Changes in the redox states of its cofactors trigger both O₂ reduction and vectorial proton transfer, which includes a proton-loading site, yet unidentified. In this work, we exploited carbon monoxide (CO) as a vibrational Stark effect (VSE) probe at the binuclear center of CcO from Rhodobacter sphaeroides. The CO stretching frequency was monitored as a function of the electrical potential, using Fourier transform infrared (FTIR) absorption spectroelectrochemistry. We observed three different redox states (R₄CO, R₂CO, and O), determined their midpoint potential, and compared the resulting electric field to electrostatic calculations. A change in the local electric field strength of +2.9 MV/cm was derived, which was induced by the redox transition from R₄CO to R₂CO. We performed potential jump experiments to accumulate the R₂CO and R₄CO species and studied the FTIR difference spectra in the protein fingerprint region. The comparison of the experimental and computational results reveals that the key glutamic acid residue E286 is protonated in the observed states, and that its hydrogen-bonding environment is disturbed upon the redox transition of heme a₃. Our experiments also suggest propionate A of heme a₃ changing its protonation state in concert with the redox state of a second cofactor, heme a. This supports the role of propionic acid side chains as part of the proton-loading site.

Quasi-Static Two-Dimensional Infrared Spectra of the Carboxyhemoglobin Subsystem under Electric Fields: A Theoretical Study

There is no doubt that electric fields of a specific frequency and intensity could excite certain vibrational modes of a macromolecule, which alters its mode coupling and conformation. Motivated by recent experiments and theories, we study the mode coupling between the Fe-CO mode and CO-stretch mode and vibration energy transfer among the active site and proteins in carboxyhemoglobin (HbCO) under different electric fields using the quasi-static two-dimensional infrared spectra. This study uses iron-porphyrin-imidazole-CO and two distal histidines in HbCO as the subsystem. The potential energy and dipole moment surfaces of the subsystem are calculated using an all-electron ab initio (B3LYP-D3(BJ)) method with the basis set Lanl2dz for the Fe atom and 6-31G(d,p) for C, H, O, and N atoms. Although the subsystem is reduced dimensionally, the anharmonic frequency and anharmonicity of the CO-stretch mode show excellent agreement with experimental values. We use the revealing noncovalent interaction method to confirm the hydrogen bond between the H_ε atom of the His63 and the CO molecule. Our study confirms that the mode coupling between the Fe-CO mode and CO-stretch mode does not exist when the subsystem is free of electric field perturbation, which is coupled when the electric field is -0.5142 V/nm. In addition, with the increases of distance between the active site and the His92, there is no vibrational energy transfer between them when the electric field is 1.028 V/nm. We believe that our work could provide new ideas for increasing the dissociation efficiency of the Fe-CO bond and theoretical references for experimental research.

Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction

Vibrational spectroscopy is an essential tool in chemical analyses, biological assays, and studies of functional materials. Over the past decade, various coherent nonlinear vibrational spectroscopic techniques have been developed and enabled researchers to study time-correlations of the fluctuating frequencies that are directly related to solute-solvent dynamics, dynamical changes in molecular conformations and local electrostatic environments, chemical and biochemical reactions, protein structural dynamics and functions, characteristic processes of functional materials, and so on. In order to gain incisive and quantitative information on the local electrostatic environment, molecular conformation, protein structure and interprotein contacts, ligand binding kinetics, and electric and optical properties of functional materials, a variety of vibrational probes have been developed and site-specifically incorporated into molecular, biological, and material systems for time-resolved vibrational spectroscopic investigation. However, still, an all-encompassing theory that describes the vibrational solvatochromism, electrochromism, and dynamic fluctuation of vibrational frequencies has not been completely established mainly due to the intrinsic complexity of intermolecular interactions in condensed phases. In particular, the amount of data obtained from the linear and nonlinear vibrational spectroscopic experiments has been rapidly increasing, but the lack of a quantitative method to interpret these measurements has been one major obstacle in broadening the applications of these methods. Among various theoretical models, one of the most successful approaches is a semiempirical model generally referred to as the vibrational spectroscopic map that is based on a rigorous theory of intermolecular interactions. Recently, genetic algorithm, neural network, and machine learning approaches have been applied to the development of vibrational solvatochromism theory. In this review, we provide comprehensive descriptions of the theoretical foundation and various examples showing its extraordinary successes in the interpretations of experimental observations. In addition, a brief introduction to a newly created repository Web site (http://frequencymap.org) for vibrational spectroscopic maps is presented. We anticipate that a combination of the vibrational frequency map approach and state-of-the-art multidimensional vibrational spectroscopy will be one of the most fruitful ways to study the structure and dynamics of chemical, biological, and functional molecular systems in the future.

The Impact of Electron Correlation on Describing QM/MM Interactions in the Attendant Molecular Dynamics Simulations of CO in Myoglobin

The impact of the dispersion and electron correlation effects on describing quantum mechanics/molecular mechanics (QM/MM) interactions in QM/MM molecular dynamics (MD) simulations was explored by performing a series of up to 2 ns QM/MM MD simulations on the B states of the myoglobin-carbon monoxide (MbCO) system. The results indicate that both dispersion and electron correlations play significant roles in the simulation of the ratios of two B states (B₁/B₂), which suggests that the inclusion of the electron correlation effects is essential for accurately modeling the interactions between QM and MM subsystems. We found that the QM/MM interaction energies between the CO and the surroundings statistically present a linear correlation with the electric fields along the CO bond. This indicates that QM/MM interactions can be described by a simple physical model of a dipole with constant moment under the action of the electric fields. The treatment provides us with an accurate and effective approach to account for the electron correlation effects in QM/MM MD simulations.

Characterization of endogenous fluorescence in nonsmall lung cancerous cells: A comparison with nonmalignant lung normal cells

Monitoring fluorescence properties of endogenous fluorophores such as nicotinamide adenine dinucleotide (NADH) and flavin adenine dinucleotide (FAD) in normal and cancerous cells provide substantial information noninvasively on biochemical and biophysical aspects of metabolic dysfunction of cancerous cells. Time-resolved spectral profiles and fluorescence lifetime images of NADH and FAD were obtained in human lung nonsmall carcinomas (H661 and A549) and normal lung cells (MRC-5). Both fluorophores show the fast and slowly decaying emission components upon pulsed excitation, and fluorescence spectra of NADH and FAD show blue- and red-shifts, respectively, during their decay. All identified lifetime components of NADH and FAD were found to be shorter in cancerous cells than in normal cells, no matter how they were measured under different extra-cellular conditions (cells suspended in cuvette and cells attached on glass substrate), indicating that the changes in metabolism likely altered the subcellular milieu and potentially also affected the interaction of NADH and FAD with enzymes to which these cofactors were bound. The intensity ratio of NADH and FAD of cancerous cells was also shown to be larger than that of normal cells.

A Critical Evaluation of Vibrational Stark Effect (VSE) Probes with the Local Vibrational Mode Theory

Over the past two decades, the vibrational Stark effect has become an important tool to measure and analyze the in situ electric field strength in various chemical environments with infrared spectroscopy. The underlying assumption of this effect is that the normal stretching mode of a target bond such as CO or CN of a reporter molecule (termed vibrational Stark effect probe) is localized and free from mass-coupling from other internal coordinates, so that its frequency shift directly reflects the influence of the vicinal electric field. However, the validity of this essential assumption has never been assessed. Given the fact that normal modes are generally delocalized because of mass-coupling, this analysis was overdue. Therefore, we carried out a comprehensive evaluation of 68 vibrational Stark effect probes and candidates to quantify the degree to which their target normal vibration of probe bond stretching is decoupled from local vibrations driven by other internal coordinates. The unique tool we used is the local mode analysis originally introduced by Konkoli and Cremer, in particular the decomposition of normal modes into local mode contributions. Based on our results, we recommend 31 polyatomic molecules with localized target bonds as ideal vibrational Stark effect probe candidates.

Vibrational Stark Spectroscopy of Fluorobenzene Using Quantum Cascade Laser Dual Frequency Combs

We demonstrate the performance of a dual frequency comb quantum cascade laser (QCL) spectrometer for the application of vibrational Stark spectroscopy. Measurements performed on fluorobenzene with the dual-comb spectrometer (DCS) were compared to results obtained using a conventional Fourier transform infrared (FT-IR) instrument in terms of spectral response, parameter estimation, and signal-to-noise ratio (S/N). The dual-comb spectrometer provided similar qualitative and quantitative data as the FT-IR setup in 250 times shorter acquisition time. For fluorobenzene, the DCS measurement resulted in a more precise estimation of the fluorobenzene Stark tuning rate ((0.81 ± 0.09) cm^-1/(MV/cm)) than with the FT-IR system ((0.89 ± 0.15) cm^-1/(MV/cm)). Both values are in accordance with the previously reported value of 0.84 cm^-1/(MV/cm). We also point to an improvement of signal-to-noise ratio in the DCS configuration. Additional characteristics of the dual-comb spectrometer applicable to vibrational Stark spectroscopy and their scaling properties for future applications are discussed.

Measurement of Electric Fields Experienced by Urea Guest Molecules in the 18-Crown-6/Urea (1:5) Host-Guest Complex: An Experimental Reference Point for Electric-Field-Assisted Catalysis

High-resolution synchrotron and neutron single-crystal diffraction data of 18-crown-6/(pentakis)urea measured at 30 K are combined, with the aim of better appreciating the electrostatics associated with intermolecular interactions in condensed matter. With two 18-crown-6 molecules and five different urea molecules in the crystal, this represents the most ambitious combined X-ray/synchrotron and neutron experimental charge density analysis to date on a cocrystal or host-guest system incorporating such a large number of unique molecules. The dipole moments of the five urea guest molecules in the crystal are enhanced considerably compared to values determined for isolated molecules, and 2D maps of the electrostatic potential and electric field show clearly how the urea molecules are oriented with dipole moments aligned along the electric field exerted by their molecular neighbors. Experimental electric fields in the range of 10-19 GV m^-1, obtained for the five different urea environments, corroborate independent measurements of electric fields in the active sites of enzymes and provide an important experimental reference point for recent discussions focused on electric-field-assisted catalysis.

An Ab Initio QM/MM Study of the Electrostatic Contribution to Catalysis in the Active Site of Ketosteroid Isomerase

The electric field in the hydrogen-bond network of the active site of ketosteroid isomerase (KSI) has been experimentally measured using vibrational Stark effect (VSE) spectroscopy, and utilized to study the electrostatic contribution to catalysis. A large gap was found in the electric field between the computational simulation based on the Amber force field and the experimental measurement. In this work, quantum mechanical (QM) calculations of the electric field were performed using an ab initio QM/MM molecular dynamics (MD) simulation and electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method. Our results demonstrate that the QM-derived electric field based on the snapshots from QM/MM MD simulation could give quantitative agreement with the experiment. The accurate calculation of the electric field inside the protein requires both the rigorous sampling of configurations, and a QM description of the electrostatic field. Based on the direct QM calculation of the electric field, we theoretically confirmed that there is a linear correlation relationship between the activation free energy and the electric field in the active site of wild-type KSI and its mutants (namely, D103N, Y16S, and D103L). Our study presents a computational protocol for the accurate simulation of the electric field in the active site of the protein, and provides a theoretical foundation that supports the link between electric fields and enzyme catalysis.

Strategy for Modeling the Electrostatic Responses of the Spectroscopic Properties of Proteins

For better understanding and more efficient use of the spectroscopic probes (vibrational and NMR) of the local electrostatic situations inside proteins, appropriate modeling of the properties of those probes is essential. The present study is devoted to examining the strategy for constructing such models. A more well-founded derivation than the ones in previous studies is given in constructing the models. Theoretical analyses are conducted on two representative example cases related to proteins, i.e., the peptide group of the main chains and the CO and NO ligands to the Fe²⁺ ion of heme, with careful treatment of the behavior of electrons in the electrostatic responses and with verification of consistency with observable quantities. It is shown that, for the stretching frequencies and NMR chemical shifts, it is possible to construct reasonable electrostatic interaction models that encompass the situations of hydration and uniform electric field environment and thus are applicable also to the cases of nonuniform electrostatic situations, which are highly expected for inside of proteins.

Ultrafast dynamics induced by the interaction of molecules with electromagnetic fields: Several quantum, semiclassical, and classical approaches

Several strategies for simulating the ultrafast dynamics of molecules induced by interactions with electromagnetic fields are presented. After a brief overview of the theory of molecule-field interaction, we present several representative examples of quantum, semiclassical, and classical approaches to describe the ultrafast molecular dynamics, including the multiconfiguration time-dependent Hartree method, Bohmian dynamics, local control theory, semiclassical thawed Gaussian approximation, phase averaging, dephasing representation, molecular mechanics with proton transfer, and multipolar force fields. In addition to the general overview, some focus is given to the description of nuclear quantum effects and to the direct dynamics, in which the ab initio energies and forces acting on the nuclei are evaluated on the fly. Several practical applications, performed within the framework of the Swiss National Center of Competence in Research "Molecular Ultrafast Science and Technology," are presented: These include Bohmian dynamics description of the collision of H with H2, local control theory applied to the photoinduced ultrafast intramolecular proton transfer, semiclassical evaluation of vibrationally resolved electronic absorption, emission, photoelectron, and time-resolved stimulated emission spectra, infrared spectroscopy of H-bonding systems, and multipolar force fields applications in the condensed phase.

The reductive phase of Rhodobacter sphaeroides cytochrome c oxidase disentangled by CO ligation

Cytochrome c oxidase (CcO) is a membrane protein of the respiratory chain that catalytically reduces molecular oxygen (O2) to water while translocating protons across the membrane. The enzyme hosts two copper and two heme iron moieties (heme a/heme a3). The atomic details of the sequential steps that go along with this redox-driven proton translocation are a matter of debate. Particularly for the reductive phase of CcO that precedes oxygen binding experimental data are scarce. Here, we use CcO under anaerobic conditions where carbon monoxide (CO) is bound to heme a3 which in tandem with CuB forms the binuclear center (BNC). Fourier-transform infrared (FTIR) absorption spectroscopy is combined with electro-chemistry to probe different redox and protonation states populated by variation of the external electrostatic potential. With this approach, the redox behavior of heme a and the BNC could be separated and the corresponding redox potentials were determined. We also infer the protonation of one of the propionate side chains of heme a3 to correlate with the oxidation of heme a. Experimental changes in the local electric field surrounding CO bound to heme a3 are determined by their vibrational Stark effect and agree well with electrostatic computations. The comparison of experimental and computational results indicates that changes of the heme a3/CuB redox state are coupled to proton transfer towards heme a3. The latter supports the role of the heme a3 propionate D as proton loading site.

Electric Fields and Enzyme Catalysis

What happens inside an enzyme's active site to allow slow and difficult chemical reactions to occur so rapidly? This question has occupied biochemists' attention for a long time. Computer models of increasing sophistication have predicted an important role for electrostatic interactions in enzymatic reactions, yet this hypothesis has proved vexingly difficult to test experimentally. Recent experiments utilizing the vibrational Stark effect make it possible to measure the electric field a substrate molecule experiences when bound inside its enzyme's active site. These experiments have provided compelling evidence supporting a major electrostatic contribution to enzymatic catalysis. Here, we review these results and develop a simple model for electrostatic catalysis that enables us to incorporate disparate concepts introduced by many investigators to describe how enzymes work into a more unified framework stressing the importance of electric fields at the active site.

Conformational Heterogeneity and the Affinity of Substrate Molecular Recognition by Cytochrome P450cam

The broad and variable substrate specificity of cytochrome P450 enzymes makes them a model system for studying the determinants of protein molecular recognition. The archetypal cytochrome P450cam (P450cam) is a relatively specific P450, a feature once attributed to the high rigidity of its active site. However, increasingly studies have provided evidence of the importance of conformational changes to P450cam activity. Here we used infrared (IR) spectroscopy to investigate the molecular recognition of P450cam. Toward this goal, and to assess the influence of a hydrogen bond (H-bond) between active site residue Y96 and substrates, two variants in which Y96 is replaced by a cyanophenyl (Y96CNF) or phenyl (Y96F) group were characterized in complexes with the substrates camphor, isoborneol, and camphane. These combinations allow for a comparison of complexes in which the moieties on both the protein and substrate can serve as a H-bond donor, acceptor, or neither. The IR spectra of heme-bound CO and the site-specifically incorporated CN of Y96CNF were analyzed to characterize the number and nature of environments in each protein, both in the free and bound states. Although the IR spectra do not support the idea that protein-substrate H-bonding is central to P450cam recognition, the data altogether suggest that the differing conformational heterogeneity in the active site of the P450cam variants and changes in heterogeneity upon binding of different substrates likely contribute to their variable affinities via a conformational selection mechanism. This study further extends our understanding of the molecular recognition of archetypal P450cam and demonstrates the application of IR spectroscopy combined with selective protein modification to delineate protein-ligand interactions.

Direct Determination of Site-Specific Noncovalent Interaction Strengths of Proteins from NMR-Derived Fast Side Chain Motional Parameters

A novel approach to accurately determine residue-specific noncovalent interaction strengths (ξ) of proteins from NMR-measured fast side chain motional parameters (O_axis²) is presented. By probing the environmental sensitivity of side chain conformational energy surfaces of individual residues of a diverse set of proteins, the microscopic connections between ξ, O_axis², conformational entropy (S_conf), conformational barriers, and rotamer stabilities established here are found to be universal among proteins. The results reveal that side chain flexibility and conformational entropy of each residue decrease with increasing ξ and that for each residue type there exists a critical range of ξ, determined primarily by the mean side chain conformational barriers, within which flexibility of any residue can be reversibly tuned from highly flexible (with O_axis² ∼ 0) to highly restricted (with O_axis² ∼ 1) by increasing ξ by ∼3 kcal/mol. Beyond this critical range of ξ, both side chain flexibility and conformational entropy are insensitive to ξ. The interrelationships between conformational dynamics, conformational entropy, and noncovalent interactions of protein side chains established here open up new avenues to probe perturbation-induced (for example, ligand-binding, temperature, pressure) changes in fast side chain dynamics and thermodynamics of proteins by comparing their conformational energy surfaces in the native and perturbed states.

Solvent-Independent Anharmonicity for Carbonyl Oscillators

The physical origins of vibrational frequency shifts have been extensively studied in order to understand noncovalent intermolecular interactions in the condensed phase. In the case of carbonyls, vibrational solvatochromism, MD simulations, and vibrational Stark spectroscopy suggest that the frequency shifts observed in simple solvents arise predominately from the environment's electric field due to the vibrational Stark effect. This is contrary to many previously invoked descriptions of vibrational frequency shifts, such as bond polarization, whereby the bond's force constant and/or partial nuclear charges are altered due to the environment, often illustrated in terms of favored resonance structures. Here we test these hypotheses using vibrational solvatochromism as measured using 2D IR to assess the solvent dependence of the bond anharmonicity. These results indicate that the carbonyl bond's anharmonicity is independent of solvent as tested using hexanes, DMSO, and D₂O and is supported by simulated 2D spectra. In support of the linear vibrational Stark effect, these 2D IR measurements are consistent with the assertion that the Stark tuning rate is unperturbed by the electric field generated by both hydrogen and non-hydrogen bonding environments and further extends the general applicability of carbonyl probes for studying intermolecular interactions.

Observation of Electronic Excitation Transfer Through Light Harvesting Complex II Using Two-Dimensional Electronic-Vibrational Spectroscopy

Light-harvesting complex II (LHCII) serves a central role in light harvesting for oxygenic photosynthesis and is arguably the most important photosynthetic antenna complex. In this work, we present two-dimensional electronic-vibrational (2DEV) spectra of LHCII isolated from spinach, demonstrating the possibility of using this technique to track the transfer of electronic excitation energy between specific pigments within the complex. We assign the spectral bands via comparison with the 2DEV spectra of the isolated chromophores, chlorophyll a and b, and present evidence that excitation energy between the pigments of the complex are observed in these spectra. Finally, we analyze the essential components of the 2DEV spectra using singular value decomposition, which makes it possible to reveal the relaxation pathways within this complex.

Vibrational Stark Effects of Carbonyl Probes Applied to Reinterpret IR and Raman Data for Enzyme Inhibitors in Terms of Electric Fields at the Active Site

IR and Raman frequency shifts have been reported for numerous probes of enzyme transition states, leading to diverse interpretations. In the case of the model enzyme ketosteroid isomerase (KSI), we have argued that IR spectral shifts for a carbonyl probe at the active site can provide a connection between the active site electric field and the activation free energy (Fried et al. Science 2014, 346, 1510-1514). Here we generalize this approach to a much broader set of carbonyl probes (e.g., oxoesters, thioesters, and amides), first establishing the sensitivity of each probe to an electric field using vibrational Stark spectroscopy, vibrational solvatochromism, and MD simulations, and then applying these results to reinterpret data already in the literature for enzymes such as 4-chlorobenzoyl-CoA dehalogenase and serine proteases. These results demonstrate that the vibrational Stark effect provides a general framework for estimating the electrostatic contribution to the catalytic rate and may provide a metric for the design or modification of enzymes. Opportunities and limitations of the approach are also described.

Quantum mechanical calculation of electric fields and vibrational Stark shifts at active site of human aldose reductase

Recent advance in biophysics has made it possible to directly measure site-specific electric field at internal sites of proteins using molecular probes with C = O or C≡N groups in the context of vibrational Stark effect. These measurements directly probe changes of electric field at specific protein sites due to, e.g., mutation and are very useful in protein design. Computational simulation of the Stark effect based on force fields such as AMBER and OPLS, while providing good insight, shows large errors in comparison to experimental measurement due to inherent difficulties associated with point charge based representation of force fields. In this study, quantum mechanical calculation of protein's internal electrostatic properties and vibrational Stark shifts was carried out by using electrostatically embedded generalized molecular fractionation with conjugate caps method. Quantum calculated change of mutation-induced electric field and vibrational Stark shift is reported at the internal probing site of enzyme human aldose reductase. The quantum result is in much better agreement with experimental data than those predicted by force fields, underscoring the deficiency of traditional point charge models describing intra-protein electrostatic properties.

Conformational Heterogeneity in the Michaelis Complex of Lactate Dehydrogenase: An Analysis of Vibrational Spectroscopy Using Markov and Hidden Markov Models

Lactate dehydrogenase (LDH) catalyzes the interconversion of pyruvate and lactate. Recent isotope-edited IR spectroscopy suggests that conformational heterogeneity exists within the Michaelis complex of LDH, and this heterogeneity affects the propensity toward the on-enzyme chemical step for each Michaelis substate. By combining molecular dynamics simulations with Markov and hidden Markov models, we obtained a detailed kinetic network of the substates of the Michaelis complex of LDH. The ensemble-average electric fields exerted onto the vibrational probe were calculated to provide a direct comparison with the vibrational spectroscopy. Structural features of the Michaelis substates were also analyzed on atomistic scales. Our work not only clearly demonstrates the conformational heterogeneity in the Michaelis complex of LDH and its coupling to the reactivities of the substates, but it also suggests a methodology to simultaneously resolve kinetics and structures on atomistic scales, which can be directly compared with the vibrational spectroscopy.

Accurate Calculation of Electric Fields Inside Enzymes

The specific electric field generated by a protease at its active site is considered as an important source of the catalytic power. Accurate calculation of electric field at the active site of an enzyme has both fundamental and practical importance. Measuring site-specific changes of electric field at internal sites of proteins due to, eg, mutation, has been realized by using molecular probes with CO or CN groups in the context of vibrational Stark effect. However, theoretical prediction of change in electric field inside a protein based on a conventional force field, such as AMBER or OPLS, is often inadequate. For such calculation, quantum chemical approach or quantum-based polarizable or polarized force field is highly preferable. Compared with the result from conventional force field, significant improvement is found in predicting experimentally measured mutation-induced electric field change using quantum-based methods, indicating that quantum effect such as polarization plays an important role in accurate description of electric field inside proteins. In comparison, the best theoretical prediction comes from fully quantum mechanical calculation in which both polarization and inter-residue charge transfer effects are included for accurate prediction of electrostatics in proteins.

Interplay of Bias-Driven Charging and the Vibrational Stark Effect in Molecular Junctions

We observe large, reversible, bias driven changes in the vibrational energies of PCBM based on simultaneous transport and surface-enhanced Raman spectroscopy (SERS) measurements on PCBM-gold junctions. A combination of linear and quadratic shifts in vibrational energies with voltage is analyzed and compared with similar measurements involving C60-gold junctions. A theoretical model based on density functional theory (DFT) calculations suggests that both a vibrational Stark effect and bias-induced charging of the junction contribute to the shifts in vibrational energies. In the PCBM case, a linear vibrational Stark effect is observed due to the permanent electric dipole moment of PCBM. The vibrational Stark shifts shown here for PCBM junctions are comparable to or larger than the charging effects that dominate in C60 junctions.