Correlating Nitrile IR Frequencies to Local Electrostatics Quantifies Noncovalent Interactions of Peptides and Proteins

Evaluating aliphatic CF, CF2, and CF3 groups as vibrational Stark effect reporters

Given the extensive use of fluorination in molecular design, it is imperative to understand the solvation properties of fluorinated compounds and the impact of the C-F bond on electrostatic interactions. Vibrational spectroscopy can provide direct insights into these interactions by using the C-F bond stretching [v(C-F)] as an electric field probe through the vibrational Stark effect (VSE). In this work, we explore the VSE of the three basic patterns of aliphatic fluorination, i.e., mono-, di-, and trifluorination in CF, CF2, and CF3 groups, respectively, and compare their response to the well-studied aromatic v(C-F). Magnitudes (i.e., Stark tuning rates) and orientations of the difference dipole vectors of the v(C-F)-containing normal modes were determined using density functional theory and a molecular dynamics (MD)-assisted solvatochromic analysis of model compounds in solvents of varying polarity. We obtain Stark tuning rates of 0.2-0.8 cm-1/(MV/cm), with smallest and largest electric field sensitivities for CFaliphatic and CF3,aliphatic, respectively. While average electric fields of solvation were oriented along the main symmetry axis of the CFn, and thus along its static dipole, the Stark tuning rate vectors were tilted by up to 87° potentially enabling to map electrostatics in multiple dimensions. We discuss the influence of conformational heterogeneity on spectral shifts and point out the importance of multipolar and/or polarizable MD force fields to describe the electrostatics of fluorinated molecules. The implications of this work are of direct relevance for studies of fluorinated molecules as found in pharmaceuticals, fluorinated peptides, and proteins.

Unnatural Amino Acids for Biological Spectroscopy and Microscopy

Due to advances in methods for site-specific incorporation of unnatural amino acids (UAAs) into proteins, a large number of UAAs with tailored chemical and/or physical properties have been developed and used in a wide array of biological applications. In particular, UAAs with specific spectroscopic characteristics can be used as external reporters to produce additional signals, hence increasing the information content obtainable in protein spectroscopic and/or imaging measurements. In this Review, we summarize the progress in the past two decades in the development of such UAAs and their applications in biological spectroscopy and microscopy, with a focus on UAAs that can be used as site-specific vibrational, fluorescence, electron paramagnetic resonance (EPR), or nuclear magnetic resonance (NMR) probes. Wherever applicable, we also discuss future directions.

Good Vibrations Report on the DNA Quadruplex Binding of an Excited State Amplified Ruthenium Polypyridyl IR Probe

The nitrile containing Ru(II)polypyridyl complex [Ru(phen)2(11,12-dCN-dppz)]2+ (1) is shown to act as a sensitive infrared probe of G-quadruplex (G4) structures. UV-visible absorption spectroscopy reveals enantiomer sensitive binding for the hybrid htel(K) and antiparallel htel(Na) G4s formed by the human telomer sequence d[AG3(TTAG3)3]. Time-resolved infrared (TRIR) of 1 upon 400 nm excitation indicates dominant interactions with the guanine bases in the case of Λ-1/htel(K), Δ-1/htel(K), and Λ-1/htel(Na) binding, whereas Δ-1/htel(Na) binding is associated with interactions with thymine and adenine bases in the loop. The intense nitrile transient at 2232 cm-1 undergoes a linear shift to lower frequency as the solution hydrogen bonding environment decreases in DMSO/water mixtures. This shift is used as a sensitive reporter of the nitrile environment within the binding pocket. The lifetime of 1 in D2O (ca. 100 ps) is found to increase upon DNA binding, and monitoring of the nitrile and ligand transients as well as the diagnostic DNA bleach bands shows that this increase is related to greater protection from the solvent environment. Molecular dynamics simulations together with binding energy calculations identify the most favorable binding site for each system, which are in excellent agreement with the observed TRIR solution study. This study shows the power of combining the environmental sensitivity of an infrared (IR) probe in its excited state with the TRIR DNA "site effect" to gain important information about the binding site of photoactive agents and points to the potential of such amplified IR probes as sensitive reporters of biological environments.

A Systematic Study on the Role of Hydrogen Bond Donors in Dictating the Dynamics of Choline-Based Deep Eutectic Solvents

Deep eutectic solvents, promising green alternatives to conventional solvents, consist of a hydrogen bond donor and a hydrogen bond acceptor. The hydrogen bonding components in deep eutectic solvents form an extended hydrogen bonding network, which can be tuned to specific applications by changing the hydrogen bond donors. In this work, we have changed the hydrogen bond donor from a diol to a dicarboxylic acid by systematically replacing a hydroxyl group with an acid group one at a time to investigate the solvation structure and dynamics of the deep eutectic systems. Using a combination of ultrafast vibrational spectroscopy and molecular dynamics simulations, we compared the spectral diffusion and orientational relaxation dynamics of three deep eutectic systems using the vibrational responses of a dissolved anion. Our results indicate that although the solvation structures are marginally different across the systems, distinct differences are present in the solvent fluctuation and solute reorientation dynamics. This work provides a detailed molecular understanding of carboxylic-acid-based deep eutectic systems and how they differ from alcohol-based deep eutectic systems.

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.

Does variation in composition affect dynamics when approaching the eutectic composition?

Deep eutectic solvent is a mixture of two or more components, mixed in a certain molar ratio, such that the mixture melts at a temperature lower than individual substances. In this work, we have used a combination of ultrafast vibrational spectroscopy and molecular dynamics simulations to investigate the microscopic structure and dynamics of a deep eutectic solvent (1:2 choline chloride: ethylene glycol) at and around the eutectic composition. In particular, we have compared the spectral diffusion and orientational relaxation dynamics of these systems with varying compositions. Our results show that although the time-averaged solvent structures around a dissolved solute are comparable across compositions, both the solvent fluctuations and solute reorientation dynamics show distinct differences. We show that these subtle changes in solute and solvent dynamics with changing compositions arise from the variations in the fluctuations of the different intercomponent hydrogen bonds.

Dicyanamide Anion Reports on Water Induced Local Structural and Dynamic Heterogeneity in Ionic Liquid Mixtures

The effects of limited amounts (under 21.6% χ_Water) of water on 1-butyl-3-methylimidazolium tetrafluoroborate (BmimBF₄) and 1-butyl-3-methylimidazolium dicyanamide (BmimDCA) room-temperature ionic liquid (RTIL) mixtures were characterized by tracking changes in the linear and two-dimensional infrared (2D IR) vibrational features of the dicyanamide anion (DCA). Peak shifts with increasing water suggest the formation of water-associated and nonwater-associated DCA populations. Further results showed clear differences in the dynamic behavior of these different populations of DCA at low (defined here as below 2.5% χ_Water), mid (defined here as between 2.5% χ_Water and 9.6% χ_Water), and high (defined here as between 11.6% χ_Water and 21.6% χ_Water) range water concentrations. Vibrational relaxation is accelerated with increasing water content for water-associated populations of DCA, indicating water facilitates population relaxation, possibly through the provision of additional bath modes. Conversely, spectral diffusion of water-associated populations slowed dramatically with increasing water, suggesting that water drives the formation of distinct and noninterchangeable or very slowly interchangeable local solvent environments.

Blue Fluorescence of Cyano-tryptophan Predicts Local Electrostatics and Hydrogen Bonding in Biomolecules

Cyano-tryptophan is an unnatural fluorescent amino acid that emits in the visible region. Along with the structural similarity with tryptophan, the unique photophysical properties of this fluorophore make it an ideal probe for biophysical research. Herein, combining fluorescence spectroscopy, infrared spectroscopy, and molecular dynamics simulations, we show that the cyano-tryptophan's emission energy quantifies the underlying bond-specific noncovalent interactions in terms of the electric field. We further report the use of fluorophore's emission energy to predict its hydrogen bond characteristics. We demonstrate that combining experiments with molecular dynamics simulations can provide the hydrogen bonding status of the nitrile moiety. In addition, we report a method to differentiate between aqueous and nonaqueous hydrogen-bonding partners. Using a phenomenological approach, we demonstrate that the presence of the cyano-indole moiety is responsible for the distinct correlations between the fluorophore's emission and the electrostatic forces on the nitrile bond. As indole is a privileged scaffold for both native amino acids and nucleobases, cyano-indoles will have many multifaceted applications.

Probing the local structure and dynamics of nucleotides using vibrationally enhanced alkynyl stretching

Monitoring the site-specific local structure and dynamics of polynucleotides and DNA is important for understanding their biological functions. However, structurally characterizing these biomolecules with high time resolution has been known to be experimentally challenging. In this work, several 5-silylethynyl-2'-deoxynucleosides and 5-substituted phenylethynyl-2'-deoxynucleosides on the basis of deoxycytidine (dC) and deoxythymidine (dT) were synthesized, in which the alkynyl group shows intensified CC stretching vibration with infrared transition dipole moment magnitude close to that of typical CO stretching, and exhibits structural sensitivities in both vibrational frequency and spectral width. In particular, 5-trimethylsilylethynyl-2'-dC (^TMSEdC, molecule 1a) was examined in detail using femtosecond nonlinear IR spectroscopy. The solvent dependent CC stretching frequency of 1a can be reasonably interpreted mainly as the hydrogen-bonding effect between the solvent and cytosine base ring structure. Transient 2D IR and pump-probe IR measurements of 1a carried out comparatively in two aprotic solvents (DMSO and THF) and one protic solvent (MeOH) further reveal solvent dependent ultrafast vibrational properties, including diagonal anharmonicity, spectral diffusion, vibrational relaxation and anisotropy dynamics. These observed sensitivities are rooted in an extended π-conjugation of the base ring structure in which the CC group is actively involved. Our results show that the intensified CC stretching vibration can potentially provide a site-specific IR probe for monitoring the equilibrium and ultrafast structural dynamics of polynucleotides.

Unraveling Complex Local Protein Environments with 4-Cyano-l-phenylalanine

We present a multifaceted approach to effectively probe complex local protein environments utilizing the vibrational reporter unnatural amino acid (UAA) 4-cyano-l-phenylalanine (pCNPhe) in the model system superfolder green fluorescent protein (sfGFP). This approach combines temperature-dependent infrared (IR) spectroscopy, X-ray crystallography, and molecular dynamics (MD) simulations to provide a molecular interpretation of the local environment of the nitrile group in the protein. Specifically, a two-step enantioselective synthesis was developed that provided an 87% overall yield of pCNPhe in high purity without the need for chromatography. It was then genetically incorporated individually at three unique sites (74, 133, and 149) in sfGFP to probe these local protein environments. The incorporation of the UAA site-specifically in sfGFP utilized an engineered, orthogonal tRNA synthetase in E. coli using the Amber codon suppression protocol, and the resulting UAA-containing sfGFP constructs were then explored with this approach. This methodology was effectively utilized to further probe the local environments of two surface sites (sites 133 and 149) that we previously explored with room temperature IR spectroscopy and X-ray crystallography and a new interior site (site 74) featuring a complex local environment around the nitrile group of pCNPhe. Site 133 was found to be solvent-exposed, while site 149 was partially buried. Site 74 was found to consist of three distinct local environments around the nitrile group including nonspecific van der Waals interactions, hydrogen-bonding to a structural water, and hydrogen-bonding to a histidine side chain.

Photoenhancement of the C≡N Stretching Vibration Intensity of Aromatic Nitriles

The C≡N stretching vibration is a versatile infrared (IR) reporter that is useful for a wide range of applications. Aiming to further expand its spectroscopic utility, herein, we show that, using 4-cyanoindole and 4-cyano-7-azaindole as examples, photoexcitation can significantly shift the frequency (ν_CN) and enhance the molar extinction coefficient (ε_CN) of this vibrational mode of aromatic nitriles and that, for these indole derivatives, the enhancement factor can reach 13. Moreover, we find that while solvent relaxation at the excited electronic state(s) always leads to an increase in ε_CN, its effect on ν_CN depends on the solute and the solvent. Taken together, these results demonstrate that solvent relaxation can differently affect the local environment of the nitrile group and its conjugation with the indole ring and, more importantly, that the C≡N stretching vibration can serve as a sensitive IR probe of charge and electron transfer processes in which an aromatic nitrile is involved.

Potential Distribution across Model Membranes

Membrane models assembled on electrodes are widely used tools to study potential-dependent molecular processes at or in membranes. However, the relationship between the electrode potential and the potential across the membrane is not known. Here we studied lipid bilayers immobilized on mixed self-assembled monolayers (SAM) on Au electrodes. The mixed SAM was composed of thiol derivatives of different chain lengths such that between the islands of the short one, mercaptobenzonitrile (MBN), and the tethered lipid bilayer an aqueous compartment was formed. The nitrile function of MBN, which served as a reporter group for the vibrational Stark effect (VSE), was probed by surface-enhanced infrared absorption spectroscopy to determine the local electric field as a function of the electrode potential for pure MBN, mixed SAM, and the bilayer system. In parallel, we calculated electric fields at the VSE probe by molecular dynamics (MD) simulations for different charge densities on the metal, thereby mimicking electrode potential changes. The agreement with the experiments was very good for the calculations of the pure MBN SAM and only slightly worse for the mixed SAM. The comparison with the experiments also guided the design of the bilayer system in the MD setups, which were selected to calculate the electrode potential dependence of the transmembrane potential, a quantity that is not directly accessible by the experiments. The results agree very well with estimates in previous studies and thus demonstrate that the present combined experimental-theoretical approach is a promising tool for describing potential-dependent processes at biomimetic interfaces.

Versatile Vibrational Energy Sensors for Proteins

Vibrational energy transfer (VET) is emerging as key mechanism for protein functions, possibly playing an important role for energy dissipation, allosteric regulation, and enzyme catalysis. A deep understanding of VET is required to elucidate its role in such processes. Ultrafast VIS-pump/IR-probe spectroscopy can detect pathways of VET in proteins. However, the requirement of having a VET donor and a VET sensor installed simultaneously limits the possible target proteins and sites; to increase their number we compare six IR labels regarding their utility as VET sensors. We compare these labels in terms of their FTIR, and VET signature in VET donor-sensor dipeptides in different solvents. Furthermore, we incorporated four of these labels in PDZ3 to assess their capabilities in more complex systems. Our results show that different IR labels can be used interchangeably, allowing for free choice of the right label depending on the system under investigation and the methods available.

Nitrile Infrared Intensities Characterize Electric Fields and Hydrogen Bonding in Protic, Aprotic, and Protein Environments

Nitriles are widely used vibrational probes; however, the interpretation of their IR frequencies is complicated by hydrogen bonding (H-bonding) in protic environments. We report a new vibrational Stark effect (VSE) that correlates the electric field projected on the -C≡N bond to the transition dipole moment and, by extension, the nitrile peak area or integrated intensity. This linear VSE applies to both H-bonding and non-H-bonding interactions. It can therefore be generally applied to determine electric fields in all environments. Additionally, it allows for semiempirical extraction of the H-bonding contribution to the blueshift of the nitrile frequency. Nitriles were incorporated at H-bonding and non-H-bonding protein sites using amber suppression, and each nitrile variant was structurally characterized at high resolution. We exploited the combined information available from variations in frequency and integrated intensity and demonstrate that nitriles are a generally useful probe for electric fields.

Association-Dissociation Dynamics of Ionic Electrolytes in Low Dielectric Medium

Ionic electrolytes are known to form various complexes which exist in dynamic equilibrium in a low dielectric medium. However, structural characterization of these complexes has always posed a great challenge to the scientific community. An additional challenge is the estimation of the dynamic association-dissociation time scales (lifetime of the complexes), which are key to the fundamental understanding of ion transport. In this work, we have used a combination of infrared absorption spectroscopy, two-dimensional infrared spectroscopy, molecular dynamics simulations, and density functional theory calculations to characterize the various ion complexes formed by the thiocyanate-based ionic electrolytes as a function of different cations in a low dielectric medium. Our results demonstrate that thiocyanate is an excellent vibrational reporter of the heterogeneous ion complexes undergoing association-dissociation dynamics. We find that the ionic electrolytes exist as contact ion pairs, dimers, and clusters in a low dielectric medium. The relative ratios of the various ion complexes are sensitive to the cations. In addition to the interactions between the thiocyanate anion and the countercation, the solute-solvent interactions drive the dynamic equilibrium. We have estimated the association-dissociation dynamics time scales from two-dimensional infrared spectroscopy. The exchange time scale involving the cluster is faster than that between a dimer and an ion pair. Moreover, we find that the dynamic equilibrium between the cluster and another ion complex is correlated to the solvent fluctuations.

Local Electric Field Changes during the Photoconversion of the Bathy Phytochrome Agp2

Phytochromes switch between a physiologically inactive and active state via a light-induced reaction cascade, which is initiated by isomerization of the tetrapyrrole chromophore and leads to the functionally relevant secondary structure transition of a protein segment (tongue). Although details of the underlying cause-effect relationships are not known, electrostatic fields are likely to play a crucial role in coupling chromophores and protein structural changes. Here, we studied local electric field changes during the photoconversion of the dark state Pfr to the photoactivated state Pr of the bathy phytochrome Agp2. Substituting Tyr165 and Phe192 in the chromophore pocket by para-cyanophenylalanine (pCNF), we monitored the respective nitrile stretching modes in the various states of photoconversion (vibrational Stark effect). Resonance Raman and IR spectroscopic analyses revealed that both pCNF-substituted variants undergo the same photoinduced structural changes as wild-type Agp2. Based on a structural model for the Pfr state of F192pCNF, a molecular mechanical-quantum mechanical approach was employed to calculate the electric field at the nitrile group and the respective stretching frequency, in excellent agreement with the experiment. These calculations serve as a reference for determining the electric field changes in the photoinduced states of F192pCNF. Unlike F192pCNF, the nitrile group in Y165pCNF is strongly hydrogen bonded such that the theoretical approach is not applicable. However, in both variants, the largest changes of the nitrile stretching modes occur in the last step of the photoconversion, supporting the view that the proton-coupled restructuring of the tongue is accompanied by a change of the electric field.

Transition of a Deep Eutectic Solution to Aqueous Solution: A Dynamical Perspective of the Dissolved Solute

Disruption of the deep eutectic solvent (DES) nanostructure around the dissolved solute upon addition of water is investigated by polarization-selective two-dimensional infrared spectroscopy and molecular dynamics simulations. The heterogeneous DES nanostructure around the solute is partially retained up to 41 wt % of added water, although water molecules are gradually incorporated in the solute's solvation shell even at lower hydration levels. Beyond 41 wt %, the solute is observed to be preferentially solvated by water. This composition denotes the upper hydration limit of the deep eutectic solvent above which the solute senses an aqueous solvation environment. Interestingly, our results indicate that the transition from a deep eutectic solvation environment to an aqueous one around the dissolved solute can happen at a hydration level lower than that reported for the "water in DES" to "DES in water" transition.

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.

Testing the Limitations of MD-Based Local Electric Fields Using the Vibrational Stark Effect in Solution: Penicillin G as a Test Case

Noncovalent interactions underlie nearly all molecular processes in the condensed phase from solvation to catalysis. Their quantification within a physically consistent framework remains challenging. Experimental vibrational Stark effect (VSE)-based solvatochromism can be combined with molecular dynamics (MD) simulations to quantify the electrostatic forces in solute-solvent interactions for small rigid molecules and, by extension, when these solutes bind in enzyme active sites. While generalizing this approach toward more complex (bio)molecules, such as the conformationally flexible and charged penicillin G (PenG), we were surprised to observe inconsistencies in MD-based electric fields. Combining synthesis, VSE spectroscopy, and computational methods, we provide an intimate view on the origins of these discrepancies. We observe that the electric fields are correlated to conformation-dependent effects of the flexible PenG side chain, including both the local solvation structure and solute conformational sampling in MD. Additionally, we identified that MD-based electric fields are consistently overestimated in three-point water models in the vicinity of charged groups; this cannot be entirely ameliorated using polarizable force fields (AMOEBA) or advanced water models. This work demonstrates the value of the VSE as a direct method for experiment-guided refinements of MD force fields and establishes a general reductionist approach to calibrating vibrational probes for complex (bio)molecules.

Photochemistry using a host-guest charge transfer paradigm: DMABN as a dynamical probe of ground and excited states

Photoexciting charge transfer (CT) transitions arising from host-guest interactions in a confined environment can efficiently yield kinetically trapped radicals. In order to predispose these photogenerated radicals for diffusion limited reactions it becomes imperative to understand the nature of the host-guest CT interactions in the ground and excited states. Here we probe the heterogeneity of guest orientations and the ensuing excited state charge transfer dynamics of an electron-rich molecular probe N,N-dimethylaminobenzonitrile (DMABN) incarcerated inside an electron deficient water-soluble cationic Pd6L412+ nanohost. Using a combination of 1H-NMR, resonance Raman spectrosocopy, and pump-probe spectroscopy we highlight the necessary challenges that need to be addressed in order to use molecular cages as photocatalytic reaction vessels.

Optical and Infrared Spectroelectrochemical Studies of CN-Substituted Bipyridyl Complexes of Ruthenium(II)

Ruthenium(II) polypyridyl complexes [Ru(CN-Me-bpy)_x(bpy)_3-x]²⁺ (CN-Me-bpy = 4,4'-dicyano-5,5'-dimethyl-2,2'-bipyridine, bpy = 2,2'-bipyridine, and x = 1-3, abbreviated as 1²⁺, 2²⁺, and 3²⁺) undergo four (1²⁺) or five (2²⁺ and 3²⁺) successive one-electron reduction steps between -1.3 and -2.75 V versus ferrocenium/ferrocene (Fc⁺/Fc) in tetrahydrofuran. The CN-Me-bpy ligands are reduced first, with successive one-electron reductions in 2²⁺ and 3²⁺ being separated by 150-210 mV; reduction of the unsubstituted bpy ligand in 1²⁺ and 2²⁺ occurs only when all CN-Me-bpy ligands have been converted to their radical anions. Absorption spectra of the first three reduction products of each complex were measured across the UV, visible, near-IR (NIR), and mid-IR regions and interpreted with the help of density functional theory calculations. Reduction of the CN-Me-bpy ligand shifts the ν(C≡N) IR band by ca. -45 cm^-1, enhances its intensity ∼35 times, and splits the symmetrical and antisymmetrical modes. Semireduced complexes containing two and three CN-derivatized ligands 2⁺, 3⁺, and 3⁰ show distinct ν(C≡N) features due to the presence of both CN-Me-bpy and CN-Me-bpy^•-, confirming that each reduction is localized on a single ligand. NIR spectra of 1⁰, 1^-, and 2^- exhibit a prominent band attributable to the CN-Me-bpy^•- moiety between 6000 and 7500 cm^-1, whereas bpy^•--based absorption occurs between 4500 and 6000 cm^-1; complexes 2⁺, 3⁺, and 3⁰ also exhibit a band at ca. 3300 cm^-1 due to a CN-Me-bpy^•- → CN-Me-bpy interligand charge-transfer transition. In the UV-vis region, the decrease of π → π* intraligand bands of the neutral ligands and the emergence of the corresponding bands of the radical anions are most diagnostic. The first reduction product of 1²⁺ is spectroscopically similar to the lowest triplet metal-to-ligand charge-transfer excited state, which shows pronounced NIR absorption, and its ν(C≡N) IR band is shifted by -38 cm^-1 and 5-7-fold-enhanced relative to the ground state.

Mapping solvation heterogeneity in live cells by hyperspectral stimulated Raman scattering microscopy

Water provides a dynamic matrix in which all biochemical processes occur in living organisms. The structure and dynamics of intracellular water constitute the cornerstone for understanding all aspects of cellular function. Fundamentally, direct visualization of subcellular solvation heterogeneity is essential but remains challenging with commonly used nuclear magnetic resonance methods due to poor spatial resolution. To explore this question, we demonstrate a vibrational-shift imaging approach by combining the spectral-focusing hyperspectral stimulated Raman scattering technique with an environmentally sensitive nitrile probe. The sensing ability of a near-infrared nitrile-containing molecule is validated in the solution phase, microscopic droplets, and cellular environments. Finally, we quantitatively measure the subcellular solvation variance between the cytoplasm (29.5%, S.E. 1.8%) and the nucleus (57.3%, S.E. 1.0%), which is in good agreement with previous studies. This work sheds light on heterogeneous solvation in live systems using coherent Raman microscopy and opens up new avenues to explore environmental variance in complex systems with high spatiotemporal resolution.

Assessing the Effect of Hofmeister Anions on the Hydrogen-Bonding Strength of Water via Nitrile Stretching Frequency Shift

The temperature dependence of the peak frequency (ν_max) of the C≡N stretching vibrational spectrum of a hydrogen-bonded C≡N species is known to be a qualitative measure of its hydrogen-bonding strength. Herein, we show that within a two-state framework, this dependence can be analyzed in a more quantitative manner to yield the enthalpy and entropy changes (ΔH_HB and ΔS_HB) for the corresponding hydrogen-bonding interactions. Using this method, we examine the effect of ten common anions on the strength of the hydrogen-bond(s) formed between water and the C≡N group of an unnatural amino acid, p-cyanophenylalanine (Phe_CN). We find that based on the ΔH_HB values, these anions can be arranged in the following order: HPO₄^2- > OAc^- > F^- > SO₄^2- ≈ Cl^- ≈ (H₂O) ≈ ClO₄^- ≈ NO₃^- > Br^- > SCN^- ≈ I^-, which differs from the corresponding Hofmeister series. Because Phe_CN has a relatively small size, the finding that anions having very different charge densities (e.g., SO₄^2- and ClO₄^-) act similarly suggests that this ranking order is likely the result of specific ion effects. Since proteins contain different backbone and side-chain units, our results highlight the need to assess their individual contributions toward the overall Hofmeister effect in order to achieve a microscopic understanding of how ions affect the physical and chemical properties of such macromolecules. In addition, the analytical method described in the present study is applicable for analyzing the spectral evolution of any vibrational spectra composed of two highly overlapping bands.

Detonation Nanodiamonds: A Comparison Study by Photoacoustic, Diffuse Reflectance, and Attenuated Total Reflection FTIR Spectroscopies

The qualitative analysis of nanodiamonds by FTIR spectrometry as photoacoustic (FTIR–PAS), diffuse-reflectance (DRIFT), and attenuated total reflection (ATR) modalities was evaluated for rapid and nondestructive analysis and comparison of nanodiamonds. The reproducibility and signal-gathering depth of spectra was compared. The assignment of characteristic bands showed that only six groups of bands were present in spectra of all the modalities with appropriate sensitivity: 1760 (C=O stretch, isolated carboxyl groups); 1640–1632 (H–O–H bend, liquid water); 1400–1370 (non-carboxyl C–O–H in-plane bend and CH₂ deformation); 1103 (non-carboxyl C–O stretch); 1060 (in-plane C–H bend, non-aromatic hydrocarbons and carbohydrates); 940 cm⁻¹ (out-of-plane carboxyl C–O–H bend). DRIFT provides the maximum number of bands and is capable of measuring hydrogen-bonded bands and CH_x groups. ATR provides the good sensitivity for water and C–H/C–C bands in the range 2000–400 cm⁻¹. FTIR–PAS reveals less bands than DRIFT but more intense bands than ATR–FTIR and shows the maximum sensitivity for absorption bands that do not appear in ATR-IR spectra and are expedient for supporting either DRIFT or FTIR–PAS along with depth-profiling. Thus, all three modalities are required for the full characterization of nanodiamonds surface functional groups.

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.

Electric Field Measurements Reveal the Pivotal Role of Cofactor-Substrate Interaction in Dihydrofolate Reductase Catalysis

The contribution of ligand–ligand electrostatic interaction to transition state formation during enzyme catalysis has remained unexplored, even though electrostatic forces are known to play a major role in protein functions and have been investigated by the vibrational Stark effect (VSE). To monitor electrostatic changes along important steps during catalysis, we used a nitrile probe (T46C-CN) inserted proximal to the reaction center of three dihydrofolate reductases (DHFRs) with different biophysical properties, Escherichia coli DHFR (EcDHFR), its conformationally impaired variant (EcDHFR-S148P), and Geobacillus stearothermophilus DHFR (BsDHFR). Our combined experimental and computational approach revealed that the electric field projected by the substrate toward the probe negates those exerted by the cofactor when both are bound within the enzymes. This indicates that compared to previous models that focus exclusively on subdomain reorganization and protein–ligand contacts, ligand–ligand interactions are the key driving force to generate electrostatic environments conducive for catalysis.

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.

Electric Fields at Metal-Surfactant Interfaces: A Combined Vibrational Spectroscopy and Capacitance Study

Surfactants modulate interfacial processes. In electrochemical CO₂ reduction, cationic surfactants promote carbon product formation and suppress hydrogen evolution. The interfacial field produced by the surfactants affects the energetics of electrochemical intermediates, mandating their detailed understanding. We have used two complementary tools-vibrational Stark shift spectroscopy which probes interfacial fields at molecular length scales and electrochemical impedance spectroscopy (EIS) which probes the entire double layer-to study the electric fields at metal-surfactant interfaces. Using a nitrile as a probe, we found that at open-circuit potentials, cationic surfactants produce larger effective interfacial fields (∼-1.25 V/nm) when compared to anionic surfactants (∼0.4 V/nm). At a high bulk surfactant concentration, the surface field reaches a terminal value, suggesting the formation of a full layer, which is also supported by EIS. We propose an electrostatic model that explains these observations. Our results help in designing tailored surfactants for influencing electrochemical reactions via the interfacial field effect.

Insulin-copper quantum clusters preparation and receptor targeted bioimaging

Protein embedded fluorescence quantum clusters (QCs) have received a great amount of interest among the researchers because of their high aqueous solubility, stability, cost efficiency, and target specificity. Considerable advancement has happened in making functional quantum clusters with target specificity. This work reports the simple synthesis of insulin protected copper quantum clusters (ICuQCs) and its receptor-targeted bioimaging applications. The preparation of copper quantum clusters (CuQCs) was done simply by one-pot synthesis method by changing the pH of the insulin protein firstly to 10.5 basic pH than physiological pH. At physiological pH, the mixture incubated in oven 37 ⁰C at 240 rpm has been developed to process initially polydisperse, non-fluorescent, and unstable CuDs into monodispersed (∼2-3 nm), highly fluorescent, and extremely stable ICuQCs in the same phase (aqueous) using insulin as protein. HRTEM image show uniform distribution of CuDs within the protein matrix. Metal ion binding site prediction and docking server (MIB) results show that chain B of insulin contains 3 templates contains 5 amino acid residues which bind with Cu²⁺ metal ion. Groove 1 contains GLY8 and HIS10 bind has the highest binding potential towards Cu metal ions. The methodology adopted in this study should largely contribute to the practical applications of this new class of QCs. In view of the protein protection, coupled with direct synthesis and easy functionalization, this hybrid QC-protein system is expected to have numerous optical and bioimaging applications in the future.

Tautomer Structures in Ketose-Aldose Transformation of 1,3-Dihydroxyacetone Studied by Infrared Electroabsorption Spectroscopy

The acyclic form of monosaccharides exists in a structural equilibrium, with aldose having the aldehyde group and ketose the ketone group (ketose-aldose equilibrium). A basic catalyst facilitates their transformation, which affects the chemical properties of the monosaccharide. In this study, we investigated the ketose-aldose transformation of 1,3-dihydroxyacetone (1,3-DHA), one of the simplest systems of the ketose-aldose equilibrium. We examined the effects of piperidine as the basic catalyst and used IR electroabsorption spectroscopy to study the responses to an external electric field. We analyzed the changes in IR absorption by considering the changes in the molecular orientation and number of molecules in response to the external electric field. The results of the analysis revealed the permanent dipole moment μ_P, an angle η between μ_P and μ_T (the transition moment of the molecular vibration), and the equilibrium constants. The ketose-aldose transformation of 1,3-DHA can be explained in terms of the equilibrium of three states. In the presence of piperidine, a five-state equilibrium was concluded. On the basis of the experimental data, we propose plausible models of dihydroxyacetone, E-enediols, Z-enediol, or glyceraldehyde for each state. The results of our structural analysis of these tautomers provide a detailed understanding of the ketose-aldose transformation of acyclic saccharides and the effects of the basic catalyst.

Optical mapping of biological water in single live cells by stimulated Raman excited fluorescence microscopy

Water is arguably the most common and yet least understood material on Earth. Indeed, the biophysical behavior of water in crowded intracellular milieu is a long-debated issue. Understanding of the spatial and compositional heterogeneity of water inside cells remains elusive, largely due to a lack of proper water-sensing tools with high sensitivity and spatial resolution. Recently, stimulated Raman excited fluorescence (SREF) microscopy was reported as the most sensitive vibrational imaging in the optical far field. Herein we develop SREF into a water-sensing tool by coupling it with vibrational solvatochromism. This technique allows us to directly visualize spatially-resolved distribution of water states inside single mammalian cells. Qualitatively, our result supports the concept of biological water and reveals intracellular water heterogeneity between nucleus and cytoplasm. Quantitatively, we unveil a compositional map of the water pool inside living cells. Hence we hope SREF will be a promising tool to study intracellular water and its relationship with cellular activities.

Visualizing the movement of the amphipathic helix in the respiratory complex I using a nitrile infrared probe and SEIRAS

Conformational movements play an important role in enzyme catalysis. Respiratory complex I, an L-shaped enzyme, connects electron transfer from NADH to ubiquinone in its peripheral arm with proton translocation through its membrane arm by a coupling mechanism still under debate. The amphipathic helix across the membrane arm represents a unique structural feature. Here, we demonstrate a new way to study conformational changes by introducing a small and highly flexible nitrile infrared (IR) label to this helix to visualize movement with surface-enhanced IR absorption spectroscopy. We find that labeled residues K551C^L and Y590C^L move to a more hydrophobic environment upon NADH reduction of the enzyme, likely as a response to the reorganization of the antiporter-like subunits in the membrane arm.

Paired Spectroscopic and Crystallographic Studies of Proteases

The active sites of subtilisin and trypsin have been studied by paired IR spectroscopic and X-ray crystallographic studies. The active site serines of the proteases were reacted with 4-cyanobenzenesulfonyl fluoride (CBSF), an inhibitor that contains a nitrile vibrational reporter. The nitrile stretch vibration of the water-soluble inhibitor model, potassium 4-cyanobenzenesulfonate (KCBSO), and the inhibitor were calibrated by IR solvent studies in H2O/DMSO and the frequency-temperature line-slope (FTLS) method in H2O and THF. The inhibitor complexes were examined by FTLS and the slopes of the best fit lines for subtilisin-CBS and trypsin-CBS in aqueous buffer were both measured to be -3.5×10-2 cm-1/°C. These slopes were intermediate in value between that of KCBSO in aqueous buffer and CBSF in THF, which suggests that the active-site nitriles in both proteases are mostly solvated. The X-ray crystal structures of the subtilisin-CBS and trypsin-CBS complexes were solved at 1.27 and 1.32 Å, respectively. The inhibitor was modelled in two conformations in subtilisin-CBS and in one conformation in the trypsin-CBS. The crystallographic data support the FTLS data that the active-site nitrile groups are mostly solvated and participate in hydrogen bonds with water molecules. The combination of IR spectroscopy utilizing vibrational reporters paired with X-ray crystallography provides a powerful approach to studying protein structure.

The Effect of Solvent on the Seebeck Coefficient and Thermocell Performance of Cobalt Bipyridyl and Iron Ferri/Ferrocyanide Redox Couples

The conversion of thermal energy to electricity using thermoelectrochemical cells (thermocells) is a developing approach to harvesting waste heat. The performance of a thermocell is highly dependent on the solvent used in the electrolyte, but the interplay of the various solvent effects is not yet well understood. Here, using the redox couples [Co(bpy)3][BF4]2/3 (bpy=2,2′-bipyridyl) and (Et4N)3/(NH4)4Fe(CN)6, which have been designed to allow dissolution in different solvent systems (aqueous, non-aqueous, and mixed solvent), the effect of solvent on the Seebeck coefficient (Se) and cell performance was studied. The highest Se for a cobalt-based redox couple measured thus far is reported. Different trends in the Seebeck coefficients of the two redox couples as a function of the ratio of organic solvent to water were observed. The cobalt redox couple produced a more positive Se in organic solvent than in water, whereas addition of water to organic solvent resulted in a more negative Se for Fe(CN)6 3−/4−. UV-vis and IR investigations of the redox couples indicate that Se is affected by changes in solvent–ligand interactions in the different solvent systems.

Conformation-specific detection of calmodulin binding using the unnatural amino acid p-azido-phenylalanine (AzF) as an IR-sensor

Calmodulin (CaM) is a very conserved, ubiquitous, eukaryotic protein that binds four Ca²⁺ ions with high affinity. It acts as a calcium sensor by translating Ca²⁺ signals into cellular processes such as metabolism, inflammation, immune response, memory, and muscle contraction. Calcium binding to CaM leads to conformational changes that enable Ca²⁺/CaM to recognize and bind various target proteins with high affinity. The binding mode and binding partners of CaM are very diverse, and a consensus binding sequence is lacking. Here, we describe an elegant system that allows conformation-specific detection of CaM-binding to its binding partners. We incorporate the unnatural amino acid p-azido-phenylalanine (AzF) in different positions of CaM and follow its unique spectral signature by infrared (IR)-spectroscopy of the azido stretching vibration. Our results suggest that the AzF vibrational probe is sensitive to the chemical environment in different CaM/CaM-binding domain (CaMBD) complexes, which allows differentiating between different binding motifs according to the spectral characteristics of the azido stretching mode. We corroborate our results with a crystal structure of AzF-labelled CaM (CaM108AzF) in complex with a binding peptide from calmodulin-dependent protein kinase IIα identifying the structural basis for the observed IR frequency shifts.

Long-Range Modulations of Electric Fields in Proteins

Electrostatic interactions are essential for controlling the protein structure and function. Whereas so far experimental and theoretical efforts focused on the effect of local electrostatics, this work aims at elucidating the long-range modulation of electric fields in proteins upon binding to charged surfaces. The study is based on cytochrome c (Cytc) variants carrying nitrile reporters for the vibrational Stark effect that are incorporated into the protein via genetic engineering and chemical modification. The Cytc variants were thoroughly characterized with respect to possible structural perturbations due to labeling. For the proteins in solution, the relative hydrogen bond occupancy and the calculated electric fields, both obtained from molecular dynamics (MD) simulations, and the experimental nitrile stretching frequencies were used to develop a relationship for separating hydrogen-bonding and non-hydrogen-bonding electric field effects. This relationship provides an excellent description for the stable Cytc variants in solution. For the proteins bound to Au electrodes coated with charged self-assembled monolayers (SAMs), the underlying MD simulations can only account for the electric field changes Δ E_ads due to the formation of the electrostatic SAM-Cytc complexes but not for the additional contribution, Δ E_int, representing the consequences of the potential drops over the electrode/SAM/protein interfaces. Both Δ E_ads and Δ E_int, determined at distances between 20 and 30 Å with respect to the SAM surface, are comparable in magnitude to the non-hydrogen-bonding electric field in the unbound protein. This long-range modulation of the internal electric field may be of functional relevance for proteins in complexes with partner proteins (Δ E_ads) and attached to membranes (Δ E_ads + Δ E_int).

Cyanylated Cysteine Reports Site-Specific Changes at Protein-Protein-Binding Interfaces Without Perturbation

To investigate the cyanylated cysteine vibrational probe group’s ability to report on binding-induced changes along a protein–protein interface, the probe group was incorporated at several sites in a peptide of the calmodulin (CaM)-binding domain of skeletal muscle myosin light chain kinase. Isothermal titration calorimetry was used to determine the binding thermodynamics between calmodulin and each peptide. For all probe positions, the binding affinity was nearly identical to that of the unlabeled peptide. The CN stretching infrared band was collected for each peptide free in solution and bound to calmodulin. Binding-induced shifts in the IR spectral frequencies were correlated with estimated solvent accessibility based on molecular dynamics simulations. This work generally suggests (1) that site-specific incorporation of this vibrational probe group does not cause major perturbations to its local structural environment and (2) that this small probe group might be used quite broadly to map dynamic protein-binding interfaces. However, site-specific perturbations due to artificial labeling groups can be somewhat unpredictable and should be evaluated on a site-by-site basis through complementary measurements. A fully quantitative, simulation-based interpretation of the rich probe IR spectra is still needed but appears to be possible given recent advances in simulation techniques.

A Direct, Quantitative Connection between Molecular Dynamics Simulations and Vibrational Probe Line Shapes

A quantitative connection between molecular dynamics simulations and vibrational spectroscopy of probe-labeled systems would enable direct translation of experimental data into structural and dynamical information. To constitute this connection, all-atom molecular dynamics (MD) simulations were performed for two SCN probe sites (solvent-exposed and buried) in a calmodulin-target peptide complex. Two frequency calculation approaches with substantial nonelectrostatic components, a quantum mechanics/molecular mechanics (QM/MM)-based technique and a solvatochromic fragment potential (SolEFP) approach, were used to simulate the infrared probe line shapes. While QM/MM results disagreed with experiment, SolEFP results matched experimental frequencies and line shapes and revealed the physical and dynamic bases for the observed spectroscopic behavior. The main determinant of the CN probe frequency is the exchange repulsion between the probe and its local structural neighbors, and there is a clear dynamic explanation for the relatively broad probe line shape observed at the "buried" probe site. This methodology should be widely applicable to vibrational probes in many environments.