Measuring electric fields and noncovalent interactions using the vibrational stark effect

Pick and Choose the Spectroscopic Method to Calibrate the Local Electric Field inside Proteins

Electrostatic interactions in proteins play a crucial role in determining the structure-function relation in biomolecules. In recent years, fluorescent probes have been extensively employed to interrogate the polarity in biological cavities through dielectric constants or semiempirical polarity scales. A choice of multiple spectroscopic methods, not limited by fluorophores, along with a molecular level description of electrostatics involving solute-solvent interactions, would allow more flexibility to pick and choose the experimental technique to determine the local electrostatics within protein interiors. In this work we report that ultraviolet/visible-absorption, infrared-absorption, or (13)C NMR can be used to calibrate the local electric field in both hydrogen bonded and non-hydrogen bonded protein environments. The local electric field at the binding site of a serum protein has been determined using the absorption wavelength as well as the carbonyl stretching frequency of its natural steroid substrate, testosterone. Excellent agreement is observed in the results obtained from two independent spectroscopic techniques.

The Hydrated Excess Proton in the Zundel Cation H5 O2 (+) : The Role of Ultrafast Solvent Fluctuations

The nature of the excess proton in liquid water has remained elusive after decades of extensive research. In view of ultrafast structural fluctuations of bulk water scrambling the structural motifs of excess protons in water, we selectively probe prototypical protonated water solvates in acetonitrile on the femtosecond time scale. Focusing on the Zundel cation H5 O2 (+) prepared in room-temperature acetonitrile, we unravel the distinct character of its vibrational absorption continuum and separate it from OH stretching and bending excitations in transient pump-probe spectra. The infrared absorption continuum originates from a strong ultrafast frequency modulation of the H(+) transfer vibration and its combination and overtones. Vibrational lifetimes of H5 O2 (+) are found to be in the sub-100 fs range, much shorter than those of unprotonated water. Theoretical results support a picture of proton hydration where fluctuating electrical interactions with the solvent and stochastic thermal excitations of low-frequency modes continuously modify the proton binding site while affecting its motions.

Internal electric fields in small water clusters [(H2O)n; n = 2-6]

The electric field experienced by a water molecule within a water cluster depends on its position relative to the rest of the water molecules. The stabilization energies and the red-shifts in the donor O-H stretching vibrations in the water clusters increase with the cluster size concomitant with the increase in the electric field experienced by the donor O-H of a particular water molecule due to the hydrogen bonding network. The red-shifts in O-H stretching frequencies show a spread of about ±100 cm(-1) against the corresponding electric fields. Deviations from linearity were marked in the region of 100-160 MV cm(-1), which can be attributed to the strain in the hydrogen bonding network, especially for structures with DDAA and DDA motifs. The linear Stark effect holds up to 200 MV cm(-1) of internal electric field for the average red-shifts in the O-H stretching frequencies, with a Stark tuning rate of 2.4 cm(-1) (MV cm(-1))(-1), suggesting the validity of the classical model in small water clusters.

Electrostatic Interactions Are Key to C═O n-π* Shifts: An Experimental Proof

Carbonyl n-π* transitions are known to undergo blue shift in polar and hydrogen-bonding solvents. Using semiempirical expressions, previous studies hypothesized several factors like change in dipole moment and hydrogen-bond strength upon excitation to cause the blue shift. Theoretically, ground-state electrostatics has been predicted to be the key to the observed shifts, however, an experimental proof has been lacking. Our experimental results demonstrate a consistent linear correlation between IR (ground-state phenomenon) and n-π* frequency shifts (involves both ground and excited electronic-states) of carbonyls in hydrogen-bonded and non-hydrogen-bonded environments. The carbonyl hydrogen-bonding status is experimentally verified from deviation in n-π*/fluorescence correlation. The IR/n-π* correlation validates the key role of electrostatic stabilization of the ground state toward n-π* shifts and demonstrates the electrostatic nature of carbonyl hydrogen bonds. n-π* shifts show linear sensitivity to calculated electrostatic fields on carbonyls. Our results portray the potential for n-π* absorption to estimate local polarity in biomolecules and to probe chemical reactions involving carbonyl activation/stabilization.

Direct observation by time-resolved infrared spectroscopy of the bright and the dark excited states of the [Ru(phen)2(dppz)]2+ light-switch compound in solution and when bound to DNA

The [Ru(phen)2(dppz)]2+ complex (1) is non-emissive in water but is highly luminescent in organic solvents or when bound to DNA, making it a useful probe for DNA binding. To date, a complete mechanistic explanation for this "light-switch" effect is still lacking. With this in mind we have undertaken an ultrafast time resolved infrared (TRIR) study of 1 and directly observe marker bands between 1280-1450 cm-1, which characterise both the emissive "bright" and the non-emissive "dark" excited states of the complex, in CD3CN and D2O respectively. These characteristic spectral features are present in the [Ru(dppz)3]2+ solvent light-switch complex but absent in [Ru(phen)3]2+, which is luminescent in both solvents. DFT calculations show that the vibrational modes responsible for these characteristic bands are predominantly localised on the dppz ligand. Moreover, they reveal that certain vibrational modes of the "dark" excited state couple with vibrational modes of two coordinating water molecules, and through these to the bulk solvent, thus providing a new insight into the mechanism of the light-switch effect. We also demonstrate that the marker bands for the "bright" state are observed for both Λ- and Δ-enantiomers of 1 when bound to DNA and that photo-excitation of the complex induces perturbation of the guanine and cytosine carbonyl bands. This perturbation is shown to be stronger for the Λ-enantiomer, demonstrating the different binding site properties of the two enantiomers and the ability of this technique to determine the identity and nature of the binding site of such intercalators.

Local electric fields and molecular properties in heterogeneous environments through polarizable embedding

In spectroscopies, the local field experienced by a molecule embedded in an environment will be different from the externally applied electromagnetic field, and this difference may significantly alter the response and transition properties of the molecule. The polarizable embedding (PE) model has previously been developed to model the local field contribution stemming from the direct molecule-environment coupling of the electromagnetic response properties of molecules in solution as well as in heterogeneous environments, such as proteins. Here we present an extension of this approach to address the additional effective external field effect, i.e., the manifestations of the environment polarization induced by the external field, which allows for the calculation of properties defined in terms of the external field. Within a response framework, we report calculations of the one- and two-photon absorption (1PA and 2PA, respectively) properties of PRODAN-methanol clusters as well as the fluorescent protein DsRed. Our results demonstrate the necessity of accounting for both the dynamical reaction field and effective external field contributions to the local field in order to reproduce full quantum chemical reference calculations. For the lowest π→π* transition in DsRed, inclusion of effective external field effects gives rise to a 1.9- and 3.5-fold reduction in the 1PA and 2PA cross-sections, respectively. The effective external field is, however, strongly influenced by the heterogeneity of the protein matrix, and the resulting effect can lead to either screening or enhancement depending on the nature of the transition under consideration.

Identification of Ion-Pair Structures in Solution by Vibrational Stark Effects

Ion pairing is a fundamental consideration in many areas of chemistry and has implications in a wide range of sciences and technologies that include batteries and organic photovoltaics. Ions in solution are known to inhabit multiple possible states, including free ions (FI), contact ion pairs (CIP), and solvent-separated ion pairs (SSIP). However, in solutions of organic radicals and nonmetal electrolytes, it is often difficult to distinguish between these states. In the first part of this work, we report evidence for the formation of SSIPs in low-polarity solvents and distinct measurements of CIP, SSIP, and FI, by using the ν(C≡N) infrared (IR) band of a nitrile-substituted fluorene radical anion. Use of time-resolved IR detection following pulse radiolysis allowed us to unambiguously assign the peak of the FI. In the presence of nonmetal electrolytes, two distinct red-shifted peaks were observed and assigned to the CIP and SSIP. The assignments are interpreted in the framework of the vibrational Stark effect (VSE) and are supported by (1) the solvent dependence of ion-pair populations, (2) the observation of a cryptand-separated sodium ion pair that mimics the formation of SSIPs, and (3) electronic structure calculations. In the second part of this work, we show that a blue-shift of the ν(C≡N) IR band due to the VSE can be induced in a nitrile-substituted fluorene radical anion by covalently tethering it to a metal-chelating ligand that forms an intramolecular ion pair upon reduction and complexation with sodium ion. This adds support to the conclusion that the shift in IR absorptions by ion pairing originates from the VSE. These results combined show that we can identify ion-pair structures by using the VSE, including the existence of SSIPs in a low-polarity solvent.

Vibrational solvatochromism of nitrile infrared probes: beyond the vibrational Stark dipole approach

Systematic probing of local environments around biopolymers is important for understanding their functions.

Excited states in large molecular systems through polarizable embedding

Using the polarizable embedding model enables rational design of light-sensitive functional biological materials.

Monitoring one-electron photo-oxidation of guanine in DNA crystals using ultrafast infrared spectroscopy

To understand the molecular origins of diseases caused by ultraviolet and visible light, and also to develop photodynamic therapy, it is important to resolve the mechanism of photoinduced DNA damage. Damage to DNA bound to a photosensitizer molecule frequently proceeds by one-electron photo-oxidation of guanine, but the precise dynamics of this process are sensitive to the location and the orientation of the photosensitizer, which are very difficult to define in solution. To overcome this, ultrafast time-resolved infrared (TRIR) spectroscopy was performed on photoexcited ruthenium polypyridyl-DNA crystals, the atomic structure of which was determined by X-ray crystallography. By combining the X-ray and TRIR data we are able to define both the geometry of the reaction site and the rates of individual steps in a reversible photoinduced electron-transfer process. This allows us to propose an individual guanine as the reaction site and, intriguingly, reveals that the dynamics in the crystal state are quite similar to those observed in the solvent medium.

Understanding and Manipulating Electrostatic Fields at the Protein-Protein Interface Using Vibrational Spectroscopy and Continuum Electrostatics Calculations

Biological function emerges in large part from the interactions of biomacromolecules in the complex and dynamic environment of the living cell. For this reason, macromolecular interactions in biological systems are now a major focus of interest throughout the biochemical and biophysical communities. The affinity and specificity of macromolecular interactions are the result of both structural and electrostatic factors. Significant advances have been made in characterizing structural features of stable protein-protein interfaces through the techniques of modern structural biology, but much less is understood about how electrostatic factors promote and stabilize specific functional macromolecular interactions over all possible choices presented to a given molecule in a crowded environment. In this Feature Article, we describe how vibrational Stark effect (VSE) spectroscopy is being applied to measure electrostatic fields at protein-protein interfaces, focusing on measurements of guanosine triphosphate (GTP)-binding proteins of the Ras superfamily binding with structurally related but functionally distinct downstream effector proteins. In VSE spectroscopy, spectral shifts of a probe oscillator's energy are related directly to that probe's local electrostatic environment. By performing this experiment repeatedly throughout a protein-protein interface, an experimental map of measured electrostatic fields generated at that interface is determined. These data can be used to rationalize selective binding of similarly structured proteins in both in vitro and in vivo environments. Furthermore, these data can be used to compare to computational predictions of electrostatic fields to explore the level of simulation detail that is necessary to accurately predict our experimental findings.

Ionizable Nitroxides for Studying Local Electrostatic Properties of Lipid Bilayers and Protein Systems by EPR

Electrostatic interactions are known to play a major role in the myriad of biochemical and biophysical processes. Here, we describe biophysical methods to probe local electrostatic potentials of proteins and lipid bilayer systems that are based on an observation of reversible protonation of nitroxides by electron paramagnetic resonance (EPR). Two types of probes are described: (1) methanethiosulfonate derivatives of protonatable nitroxides for highly specific covalent modification of the cysteine's sulfhydryl groups and (2) spin-labeled phospholipids with a protonatable nitroxide tethered to the polar head group. The probes of both types report on their ionization state through changes in magnetic parameters and degree of rotational averaging, thus, allowing the electrostatic contribution to the interfacial pKa of the nitroxide, and, therefore, the local electrostatic potential to be determined. Due to their small molecular volume, these probes cause a minimal perturbation to the protein or lipid system. Covalent attachment secures the position of the reporter nitroxides. Experimental procedures to characterize and calibrate these probes by EPR, and also the methods to analyze the EPR spectra by simulations are outlined. The ionizable nitroxide labels and the nitroxide-labeled phospholipids described so far cover an exceptionally wide range of ca. 2.5-7.0 pH units, making them suitable to study a broad range of biophysical phenomena, especially at the negatively charged lipid bilayer surfaces. The rationale for selecting proper electrostatically neutral interface for probe calibration, and examples of lipid bilayer surface potential studies, are also described.

BIOPHYSICS. Response to Comments on "Extreme electric fields power catalysis in the active site of ketosteroid isomerase"

Natarajan et al. and Chen and Savidge comment that comparing the electric field in ketosteroid isomerase's (KSI's) active site to zero overestimates the catalytic effect of KSI's electric field because the reference reaction occurs in water, which itself exerts a sizable electrostatic field. To compensate, Natarajan et al. argue that additional catalytic weight arises from positioning of the general base, whereas Chen and Savidge propose a separate contribution from desolvation of the general base. We note that the former claim is not well supported by published results, and the latter claim is intriguing but lacks experimental basis. We also take the opportunity to clarify some of the more conceptually subtle aspects of electrostatic catalysis.

Spontaneously electrical solids in a new light

Reflection–absorption infrared spectroscopy (RAIRS) of nitrous oxide (N₂O) thin films is shown to provide an independent means of observing the spontelectric state; the first new structural phase of matter, with unique electrical properties, to have emerged in decades.