Vibrational Stark Effect Research Articles

Electric Field Asymmetry in the Photosynthetic Reaction Center?

The initial charge-separation steps of photosynthesis occur in the photosynthetic reaction center, which is a membrane-integral protein-pigment complex. The photosynthetic pigments comprise four bacteriochlorophylls, two bacteriopheophytins, two quinones, one carotenoid and one non-heme iron. Although these pigments are arranged in a pseudo C2-symmetry (L- and M-branch), electron transfer occurs almost exclusively along the L-branch. One possible explanation for this unidirectionality is based on the asymmetry of the protein electrostatic fields, which leads to a better stabilization of the charge-separated intermediates in the active L-branch. The vibrational Stark effect provides a way to measure electrostatic fields in proteins and we exploit this effect to compare electric fields between the L- and M-branch by using the carbonyl groups of the pigments involved in the electron transfer reaction.

Electric field effects on the excited properties of Si2N2 molecule with special configuration：a density-functional study

In order to understand in depth the electroluminescence mechanism, the influences of the external electric field on the geometric and electronic structure in ground state, the molecular vibrational spectra of Si2N2 molecule with Cs special symmetry are studied by density functional theory with B3LYP exchange-correlation prescription at the aug-cc-pVTZ basis set level. Following each optimization, the vibrational frequencies are calculated and all optimized structures are stable. The results show that the molecular vibrational Stark effect, i.e., red-shift for the low-frequency modes and blue-shift for the high-frequency modes are observed with the increase of the applied field strength. The energies of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO), the energy gap between HOMO and LUMO of Si2N2 molecule diminish with the increase of external field. A time-dependent density functional theory is used to investigate the excited properties of Si2N2 (Cs) molecule. The calculated absorption spectra of Si2N2 molecule with Cs symmetry are in agreement with the experiment values. The analysis reveals that the absorption spectrum wavelength increases in the visible region with a concomitant increase in the electronic transition oscillator strengths in the course of the increase of the external electric field strength. The results reveal that the excited properties of Si2N2 molecule can be easily tuned by the external electric field, which indicates that the silicon nitride is an interesting optoelectronic functional material. These investigations on the various properties of Si2N2 molecule with Cs symmetry under an external electric field are useful to understand the electroluminescence mechanism for silicon nitride used in molecular electronics.

Calculations of the Electric Fields in Liquid Solutions

The electric field created by a condensed-phase environment is a powerful and convenient descriptor for intermolecular interactions. Not only does it provide a unifying language to compare many different types of interactions, but it also possesses clear connections to experimental observables, such as vibrational Stark effects. We calculate here the electric fields experienced by a vibrational chromophore (the carbonyl group of acetophenone) in an array of solvents of diverse polarities using molecular dynamics simulations with the AMOEBA polarizable force field. The mean and variance of the calculated electric fields correlate well with solvent-induced frequency shifts and band broadening, suggesting Stark effects as the underlying mechanism of these key solution-phase spectral effects. Compared to fixed-charge and continuum models, AMOEBA was the only model examined that could describe nonpolar, polar, and hydrogen bonding environments in a consistent fashion. Nevertheless, we found that fixed-charge force fields and continuum models were able to replicate some results of the polarizable simulations accurately, allowing us to clearly identify which properties and situations require explicit polarization and/or atomistic representations to be modeled properly, and to identify for which properties and situations simpler models are sufficient. We also discuss the ramifications of these results for modeling electrostatics in complex environments, such as proteins.

Imaging Electric Fields in SERS and TERS Using the Vibrational Stark Effect

Electric fields associated with Raman enhancements are typically inferred from changes in the observed scattering intensity. Here we use the vibrational Stark effect from a nitrile reporter to determine the electric field dependent frequency shift of cyanide (CN) on a gold (Au) surface. Electroplated Au surfaces with surface enhanced Raman (SERS) activity exhibit larger Stark shifts near the edge and in areas with large roughness. The Stark shift is observed to correlate with intensity of a co-adsorbed thiophenol molecule. Gap-mode Tip enhanced Raman scattering (TERS), using a Au nanoparticle tip, show dramatic shifts in the CN stretch that correlate to enhancement factors of 1013 in the gap region. The observed peak widths indicate the largest fields are highly localized. Changes in the nitrile stretch frequency provide a direct measurement of the electric fields in SERS and TERS experiments.

Generation of strong electric fields in an ice film capacitor

We present a capacitor-type device that can generate strong electrostatic field in condensed phase. The device comprises an ice film grown on a cold metal substrate in vacuum, and the film is charged by trapping Cs(+) ions on the ice surface with thermodynamic surface energy. Electric field within the charged film was monitored through measuring the film voltage using a Kelvin work function probe and the vibrational Stark effect of acetonitrile using IR spectroscopy. These measurements show that the electric field can be increased to ∼4 × 10(8) V m(-1), higher than that achievable by conventional metal plate capacitors. In addition, the present device may provide several advantages in studying the effects of electric field on molecules in condensed phase, such as the ability to control the sample composition and structure at molecular scale and the spectroscopic monitoring of the sample under electric field.

Solvation of fluoroform and fluoroform–dimethylether dimer in liquid krypton: A theoretical cryospectroscopic study

A hybrid, sequential statistical physics-quantum mechanical electronic-quantum mechanical nuclei approach has been applied to study the C-H stretching frequencies of bare fluoroform dissolved in liquid krypton under cryogenic conditions (at ~130 K), as well as upon blue shifting hydrogen bonding interactions with dimethylether in the same solvent. The structure of the liquid at 130 K was generated by Monte Carlo simulations of cryogenic Kr solutions containing either fluoroform or fluoroform and dimethylether molecules. Statistically uncorrelated configurations were appropriately chosen from the equilibrated MC runs and supermolecular clusters containing solute and solvent molecules (either standalone or embedded in the "bulk" part of the solvent treated as a polarizable continuum) were subjected to quantum mechanical electronic (QMel) and subsequent quantum mechanical nuclei (QMnuc) calculations. QMel calculations were implemented to generate the in-liquid 1D intramolecular C-H stretching vibrational potential of the fluoroform moiety and subsequently in the QMnuc phase the corresponding anharmonic C-H stretching frequency was computed by diagonalization techniques. Finally, the constructed vibrational density of states histograms were compared to the experimental Raman bands. The calculated anharmonic vibrational frequency shifts of the fluoroform C-H stretching mode upon interaction with dimethylether in liquid Kr are in very good agreement with the experimental data (20.3 at MP2 level vs. 16.6 cm(-1) experimentally). Most of this relatively large frequency blue shift is governed by configurations characterized by a direct C-H···O contact between monomers. The second population detected during MC simulations, characterized by reversed orientation of the monomers, has a minor contribution to the spectral appearance. The experimentally observed trend in the corresponding bandwidths is also correctly reproduced by our theoretical approach. Solvation of the fluoroform monomer, according to experiment, results in small C-H stretching frequency red shift (~-2 cm(-1)), while our approach predicts a blue shift of about 10 cm(-1). By a detailed analysis of the anharmonic C-H stretching frequency dependence on the position of the nearest solvent krypton atom and also by analyzing the vibrational Stark effect induced by the local fluctuating field component parallel to the C-H axis, we have derived several conclusions related to these observations. The frequency vs. C···Kr distance dependence shows appreciable fluctuations and even changes in sign at R values close to the maximum of the C···Kr radial distribution function, so that most of the first-shell Kr atoms are located at positions at which the CH frequency shifts acquire either small negative or small positive values. It so happens, therefore, that even the actual sign of the frequency shift is strongly dependent on the correct description of the first solvation shell around CF3H by the Monte Carlo method, much more than the other in-liquid properties calculated by similar approaches.

Solvatochromism and the solvation structure of benzophenone

Many complex molecular phenomena, including macromolecular association, protein folding, and chemical reactivity, are determined by the nuances of their electrostatic landscapes. The measurement of such electrostatic effects is nonetheless difficult, and is typically accomplished by exploiting a spectroscopic probe within the system of interest, such as through the vibrational Stark effect. Raman spectroscopy and solvatochromism afford an alternative to this method, circumventing the limitations of infrared spectroscopy, providing a lower detection limit, and permitting measurement in a native chemical environment. To explore this possibility, the solvatochromism of the C=O and aromatic C-H stretching modes of benzophenone are investigated using Raman spectroscopy. In conjunction with density functional theory calculations, these observations are sufficient to determine the probe electrostatic environment as well as contributions from halogen and hydrogen bonding. Further analysis using a detailed Kubo-Anderson lineshape model permits the detailed assignment of distinct hydrogen bonding configurations for water in the benzophenone solvation shell. These observations reinforce the use of benzophenone as an effective electrostatic probe for complex chemical systems.

Benzonitrile as a Probe of Local Environment in Ionic Liquids

Because of its sensitivity to chemical and electrostatic characteristics, nitrile group as an infrared (IR) probe to monitor the local structure, folding kinetics, and electrostatic environment of protein, or solvation of molecular solvents, has attracted increasing attention. Herein, by choosing benzonitrile and imidazolium ionic liquids (ILs) as the IR probe and model ILs, respectively, we report that the nitrile stretching vibration (νCN) could be utilized as a simple and substantial IR probe to monitor the local environment of ILs such as hydrogen bonding (H-bonding) as well as intrinsic electric field. In 1-alkyl-3-methylimidazolium-based non-hydroxyl ILs, the νCN is in a "free" state, and is less affected by the alkyl chain, while it significantly decreases with the effective anion charge. In 1-(2-hydroxyethyl)-3-methylimidazolium-based hydroxyl ILs, however, a distinct anion-dependent νCN forming H-bonding with the hydroxyl is also observed besides the "free" νCN band. The "free" component of νCN can be further employed to determine the intrinsic electric field in both non-hydroxyl (directly) and hydroxyl (indirectly by subtracting H-bonding contribution) ILs by using vibrational Stark effect. Moreover, the result suggests that benzonitrile is preferentially located in the charge domain in ILs and it could be a more suitable probe to report the ionic network rather than the nonpolar domain in ILs.

Vibrational Stark Effects in the Active Site of Ketosteroid Isomerase Point to Large Electric Fields Driving Chemical Catalysis

Enzymes are extraordinary catalysts that actuate nearly all biomolecular processes with speed and specificity. Nevertheless, the physical origins of enzymes’ catalytic power remain elusive despite investigations of many enzymes’ mechanisms over the last half-century. Ketosteroid isomerase (KSI) is a small and proficient enzyme - accelerating an isomerization reaction ∼1 trillion-fold over its intrinsic rate in water - that has been employed as a test system to examine the catalytic strategies at Nature's disposal. Electrostatic interactions are broadly purported to play an essential role in catalysis, but this proposal has yet to be experimentally tested in a quantitative fashion. Toward this end, vibrational Stark effect spectroscopy provides a toolkit to measure electric fields in biomolecular environments. By measuring the vibrational Stark effect of an intrinsic probe that mimics the reactive species of KSI's catalytic cycle, we found that KSI's active site focuses an extremely large electric field onto the scissile bond, potentially enabling its speedy chemical conversion through electrostatic interactions. Moreover, we observed a strong correlation between active site electric field and catalytic power across several KSI mutants. These studies are building toward a highly reductionist picture of KSI's catalysis and possibly enzyme catalysis in general.

Vibrational Stark effect spectroscopy reveals complementary electrostatic fields created by protein–protein binding at the interface of Ras and Ral

Electrostatic fields at the interface of the GTPase H-Ras (Ras) docked with the Ras binding domain of the protein Ral guanine nucleoside dissociation stimulator (Ral) were measured with vibrational Stark effect (VSE) spectroscopy. Nine residues on the surface of Ras that participate in the protein-protein interface were systematically mutated to cysteine and subsequently converted to cyanocysteine in order to introduce a nitrile VSE probe into the protein-protein interface. The absorption energy of the nitrile was measured both on the surface of Ras in its monomeric state, then after incubation with the Ras binding domain of Ral to form the docked complex. Boltzmann-weighted structural snapshots of the nitrile-labeled Ras protein were generated both in monomeric and docked configurations from molecular dynamics simulations using enhanced sampling of the cyanocysteine side chain's χ2 dihedral angle. These snapshots were used to determine that on average, most of the nitrile probes were aligned along the Ras surface, parallel to the Ras-Ral interface. The average solvent-accessible surface areas (SASA) of the cyanocysteine side chain were found to be <60 Å(2) for all measured residues, and was not significantly different whether the nitrile was on the surface of the Ras monomer or immersed in the docked complex. Changes in the absorption energy of the nitrile probe at nine positions along the Ras-Ral interface were compared to results of a previous study examining this interface with Ral-based probes, and found a pattern of low electrostatic field in the core of the interface surrounded by a ring of high electrostatic field around the perimeter of the interface. These data are used to rationalize several puzzling features of the Ras-Ral interface.

Vibrational Stark Spectroscopy Directly Probes Electric Fields in Proteins

We have developed vibrational Stark effect (VSE) spectroscopy to probe electrostatics and dynamics in organized systems, in particular in proteins where they can report on functionally important electric fields. The strategy involves deploying site-specific vibrational probes (-C≡N, -C-D, -C=O and -C-F) whose sensitivity to an electric field is measured in a calibrated external electric field by VSE spectroscopy. This gives the magnitude of the vibrational frequency shift associated with an electric field change in a protein, e.g. by making a mutation, changing pH, ligand binding, etc., projected along the bond axis, which is typically determined by x-ray crystallography. This concept can also be used to estimate the electrostatic contribution to non-covalent X-H••π interactions that stabilize protein structures. Recent results in which we attempt to calibrate the absolute magnitude of the field will be presented, along with complications that arise from non-electrostatic contributions to the frequency shifts. This requires a substantial development of simulations methods in parallel with experiments. By fully understanding the origins of these effects, they can be applied to obtain information on functionally-relevant fields at the active site of enzymes (see also presentation by Fried, Bagchi and SGB). This approach provides experimental benchmarks for high-level simulations which have suggested a critical role for electric fields and electric field gradients in biological function.

Investigation of the intrinsic electric field of nonhydroxyl and hydroxyl ionic liquids by vibrational Stark effect spectroscopy

Electric fields of ionic liquids (ILs) were investigated by vibrational Stark effect spectroscopy using ethyl thiocyanate as a probe molecule. It was found that the stretching vibration of CN in nonhydroxyl ILs originates exclusively from the intrinsic electric fields, which are on average 3.0 MV cm−1 higher than those of molecular solvents. In contrast, in the case of hydroxyl functional ILs, hydrogen bonding as well as the electric field contribute to the IR shift of CN.

Calculation of Vibrational Shifts of Nitrile Probes in the Active Site of Ketosteroid Isomerase upon Ligand Binding

The vibrational Stark effect provides insight into the roles of hydrogen bonding, electrostatics, and conformational motions in enzyme catalysis. In a recent application of this approach to the enzyme ketosteroid isomerase (KSI), thiocyanate probes were introduced in site-specific positions throughout the active site. This paper implements a quantum mechanical/molecular mechanical (QM/MM) approach for calculating the vibrational shifts of nitrile (CN) probes in proteins. This methodology is shown to reproduce the experimentally measured vibrational shifts upon binding of the intermediate analogue equilinen to KSI for two different nitrile probe positions. Analysis of the molecular dynamics simulations provides atomistic insight into the roles that key residues play in determining the electrostatic environment and hydrogen-bonding interactions experienced by the nitrile probe. For the M116C-CN probe, equilinen binding reorients an active-site water molecule that is directly hydrogen-bonded to the nitrile probe, resulting in a more linear C≡N--H angle and increasing the CN frequency upon binding. For the F86C-CN probe, equilinen binding orients the Asp103 residue, decreasing the hydrogen-bonding distance between the Asp103 backbone and the nitrile probe and slightly increasing the CN frequency. This QM/MM methodology is applicable to a wide range of biological systems and has the potential to assist in the elucidation of the fundamental principles underlying enzyme catalysis.

Catalytic efficiency of dehaloperoxidase A is controlled by electrostatics – application of the vibrational Stark effect to understand enzyme kinetics

The vibrational Stark effect is gaining popularity as a method for probing electric fields in proteins. In this work, we employ it to explain the effect of single charge mutations in dehaloperoxidase-hemoglobin A (DHP A) on the kinetics of the enzyme. In a previous communication published in this journal (BBRC 2012, 420, 733–737) it has been shown that an increase in the overall negative charge of DHP A through mutation causes a decrease in its catalytic efficiency. Here, by labeling the protein with 4-mercaptobenzonitrile (MBN), a Stark probe molecule, we provide further evidence that the diffusion control of the catalytic process arises from the electrostatic repulsion between the enzyme and the negatively charged substrate. The linear correlation observed between the nitrile stretching frequency of the protein-bound MBN and the catalytic efficiency of the single-site mutants of the enzyme indicates that electrostatic interactions play a dominant role in determining the catalytic efficiency of DHP A.

Experimental quantification of electrostatics in X-H···π hydrogen bonds.

Hydrogen bonds are ubiquitous in chemistry and biology. The physical forces that govern hydrogen-bonding interactions have been heavily debated, with much of the discussion focused on the relative contributions of electrostatic vs quantum mechanical effects. In principle, the vibrational Stark effect, the response of a vibrational mode to electric field, can provide an experimental method for parsing such interactions into their electrostatic and nonelectrostatic components. In a previous study we showed that, in the case of relatively weak O-H···π hydrogen bonds, the O-H bond displays a linear response to an electric field, and we exploited this response to demonstrate that the interactions are dominated by electrostatics (Saggu, M.; Levinson, N. M.; Boxer, S. G. J. Am. Chem. Soc.2011, 133, 17414-17419). Here we extend this work to other X-H···π interactions. We find that the response of the X-H vibrational probe to electric field appears to become increasingly nonlinear in the order O-H < N-H < S-H. The observed effects are consistent with differences in atomic polarizabilities of the X-H groups. Nonetheless, we find that the X-H stretching vibrations of the model compounds indole and thiophenol report quantitatively on the electric fields they experience when complexed with aromatic hydrogen-bond acceptors. These measurements can be used to estimate the electrostatic binding energies of the interactions, which are found to agree closely with the results of energy calculations. Taken together, these results highlight that with careful calibration vibrational probes can provide direct measurements of the electrostatic components of hydrogen bonds.

Intrinsic Electric Fields in Ionic Liquids Determined by Vibrational Stark Effect Spectroscopy and Molecular Dynamics Simulation

The electric fields of ionic liquids are only slightly higher than those of common molecular solvents, and are strongly structure-dependent; they noticeably decrease with anion size because of increased separation of ions, and slightly decrease as the alkyl chain elongates due to increasing spatial heterogeneity. These were the key results of vibrational Stark effect spectroscopy and molecular dynamics simulations.

Role of Electrostatics in Differential Binding of RalGDS to Rap Mutations E30D and K31E Investigated by Vibrational Spectroscopy of Thiocyanate Probes

The human protein Rap1A (Rap) is a member of the Ras superfamily of GTPases that binds to the downstream effector Ral guanine nucleotide dissociation stimulator (RalGDS). Although Ras and Rap have nearly identical amino acid sequences and structures along the effector binding surface, the charge reversal mutation Rap K31E has previously been shown to increase the dissociation constant of Rap-RalGDS docking to values similar to that of Ras-RalGDS docking. This indicates that the difference in charge at position 31 could provide a mechanism for Ral to distinguish two structurally similar but functionally distinct GTPases, which would be of vital importance for appropriate biological function. In this report, vibrational Stark effect spectroscopy, dissociation constant measurements, and molecular dynamics simulations were used to investigate the role that electrostatic field differences caused by the charge reversal mutation Rap K31E play in determining the binding specificity of RalGDS to Rap versus Ras. To do this, six variants of RalGDS carrying a thiocyanate electrostatic probe were docked with three Rap mutants, E30D, K31E, and E30D/K31E. The change in absorption energy of the thiocyanate probe caused by RalGDS docking to these Rap variants was then compared to that observed with wild-type Ras. Three trends emerged: the expected reversion behavior, an additive behavior of the two single mutations, and cancelation of the effects of each single mutation in the double mutant. These observations are explained with a physical model of the position of the thiocyanate probe with respect to the mutated residue based on molecular dynamics simulations.

Vibrational Stark Effect of the Electric-Field Reporter 4-Mercaptobenzonitrile as a Tool for Investigating Electrostatics at Electrode/SAM/Solution Interfaces

4-mercaptobenzonitrile (MBN) in self-assembled monolayers (SAMs) on Au and Ag electrodes was studied by surface enhanced infrared absorption and Raman spectroscopy, to correlate the nitrile stretching frequency with the local electric field exploiting the vibrational Stark effect (VSE). Using MBN SAMs in different metal/SAM interfaces, we sorted out the main factors controlling the nitrile stretching frequency, which comprise, in addition to external electric fields, the metal-MBN bond, the surface potential, and hydrogen bond interactions. On the basis of the linear relationships between the nitrile stretching and the electrode potential, an electrostatic description of the interfacial potential distribution is presented that allows for determining the electric field strengths on the SAM surface, as well as the effective potential of zero-charge of the SAM-coated metal. Comparing this latter quantity with calculated values derived from literature data, we note a very good agreement for Au/MBN but distinct deviations for Ag/MBN which may reflect either the approximations and simplifications of the model or the uncertainty in reported structural parameters for Ag/MBN. The present electrostatic model consistently explains the electric field strengths for MBN SAMs on Ag and Au as well as for thiophenol and mercaptohexanoic acid SAMs with MBN incorporated as a VSE reporter.

Solvent-induced infrared frequency shifts in aromatic nitriles are quantitatively described by the vibrational Stark effect.

The physical properties of solvents strongly affect the spectra of dissolved solutes, and this phenomenon can be exploited to gain insight into the solvent-solute interaction. The large solvatochromic shifts observed for many dye molecules in polar solvents are due to variations in the solvent reaction field, and these shifts are widely used to estimate the change in the dye's dipole moment upon photoexcitation, which is typically on the order of ∼1-10 D. In contrast, the change in dipole moment for vibrational transitions is approximately 2 orders of magnitude smaller. Nonetheless, vibrational chromophores display significant solvatochromism, and the relative contributions of specific chemical interactions and electrostatic interactions are debated, complicating the interpretation of vibrational frequency shifts in complex systems such as proteins. Here we present a series of substituted benzonitriles that display widely varying degrees of vibrational solvatochromism. In most cases, this variation can be quantitatively described by the experimentally determined Stark tuning rate, coupled with a simple Onsager-like model of solvation, reinforcing the view that vibrational frequency shifts are largely caused by electrostatic interactions. In addition, we discuss specific cases where continuum solvation models fail to predict solvatochromic shifts, revealing the necessity for more advanced theoretical models that capture local aspects of solute-solvent interactions.

Electrostatic Effects of Mutations of Ras Glutamine 61 Measured Using Vibrational Spectroscopy of a Thiocyanate Probe

Mutations of human oncoprotein p21(Ras) (hereafter Ras) at glutamine 61 are known to slow the rate of guanosine triphosphate (GTP) hydrolysis and transform healthy cells into malignant cells. It has been hypothesized that this glutamine plays a role in the intrinsic mechanism of GTP hydrolysis by interacting with an active site water molecule that electrostatically stabilizes the formation of the charged transition state at the γ-phosphate during hydrolysis. We have tested the interactions between amino acids at this position and water by measuring changes in the electrostatic field experienced by a nitrile probe positioned near Ras Q61 using vibrational Stark effect (VSE) spectroscopy. We mutated this glutamine to every amino acid except cysteine and proline and then incubated these mutants with a Ral guanine nucleotide dissociation stimulator (Ral) containing the I18C mutation that was chemically labeled with a thiocyanate vibrational spectroscopic probe. The formation of the docked Ras Q61X-labeled Ral complex was confirmed by measurement of the dissociation constant of the interaction. We measured the absorption energy of this nitrile to determine any differences in electrostatic environment in the immediate vicinity of the thiocyanate probe between wild type and mutants of Ras. For each Ras Q61X mutant, we correlate the change in electrostatic field at position 61 with the solvent accessible surface area of polar components of the mutant side chain determined from a Boltzmann-weighted ensemble of structures, as well as the residue's hydration potential. These results support the hypothesis that the role of Ras Q61 is to stabilize water in or near the active site during GTP hydrolysis. The substantial effect that nonpolar side chains of Ras Q61X have on the absorption energy of the thiocyanate must be investigated with further experiments.