Nitrile and thiocyanate IR probes: Molecular dynamics simulation studies

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.

Critical Evaluation of Polarizable and Nonpolarizable Force Fields for Proteins Using Experimentally Derived Nitrile Electric Fields

Molecular dynamics (MD) simulations are frequently carried out for proteins to investigate the role of electrostatics in their biological function. The choice of force field (FF) can significantly alter the MD results, as the simulated local electrostatic interactions lack benchmarking in the absence of appropriate experimental methods. We recently reported that the transition dipole moment (TDM) of the popular nitrile vibrational probe varies linearly with the environmental electric field, overcoming well-known hydrogen bonding (H-bonding) issues for the nitrile frequency and, thus, enabling the unambiguous measurement of electric fields in proteins (J. Am. Chem. Soc. 2022, 144 (17), 7562-7567). Herein, we utilize this new strategy to enable comparisons of experimental and simulated electric fields in protein environments. Specifically, previously determined TDM electric fields exerted onto nitrile-containing o-cyanophenylalanine residues in photoactive yellow protein are compared with MD electric fields from the fixed-charge AMBER FF and the polarizable AMOEBA FF. We observe that the electric field distributions for H-bonding nitriles are substantially affected by the choice of FF. As such, AMBER underestimates electric fields for nitriles experiencing moderate field strengths; in contrast, AMOEBA robustly recapitulates the TDM electric fields. The FF dependence of the electric fields can be partly explained by the presence of additional negative charge density along the nitrile bond axis in AMOEBA, which is due to the inclusion of higher-order multipole parameters; this, in turn, begets more head-on nitrile H-bonds. We conclude by discussing the implications of the FF dependence for the simulation of nitriles and proteins in general.

Molecular dynamics simulation study of water structure and dynamics on the gold electrode surface with adsorbed 4-mercaptobenzonitrile

Understanding water dynamics at charged interfaces is of great importance in various fields, such as catalysis, biomedical processes, and solar cell materials. In this study, we implemented molecular dynamics simulations of a system of pure water interfaced with Au electrodes, on one side of which 4-mercaptobenzonitrile (4-MBN) molecules are adsorbed. We calculated time correlation functions of various dynamic quantities, such as the hydrogen bond status of the N atom of the adsorbed 4-MBN molecules, the rotational motion of the water OH bond, hydrogen bonds between 4-MBN and water, and hydrogen bonds between water molecules in the interface region. Using the Luzar-Chandler model, we analyzed the hydrogen bond dynamics between a 4-MBN and a water molecule. The dynamic quantities we calculated can be divided into two categories: those related to the collective behavior of interfacial water molecules and the H-bond interaction between a water molecule and the CN group of 4-MBN. We found that these two categories of dynamic quantities exhibit opposite trends in response to applied potentials on the Au electrode. We anticipate that the present work will help improve our understanding of the interfacial dynamics of water in various electrolyte systems.

Effects of the Intramolecular Group and Solvent on Vibrational Coupling Modes and Strengths of Fermi Resonances in Aryl Azides: A DFT Study of 4-Azidotoluene and 4-Azido-N-phenylmaleimide

The high transition dipole strength of the azide asymmetric stretch makes aryl azides good candidates as vibrational probes (VPs). However, aryl azides have complex absorption profiles due to Fermi resonances (FRs). Understanding the origin and the vibrational modes involved in FRs of aryl azides is critically important toward developing them as VPs for studies of protein structures and structural changes in response to their surroundings. As such, we studied vibrational couplings in 4-azidotoluene and 4-azido-N-phenylmaleimide in two solvents, N,N-dimethylacetamide and tetrahydrofuran, to explore the origin and the effects of intramolecular group and solvent on the FRs of aryl azides using density functional theory (DFT) calculations with the B3LYP functional and seven basis sets, 6-31G(d,p), 6-31+G(d,p), 6-31++G(d,p), 6-311G(d,p), 6-311+G(d,p), 6-311++G(d,p), and 6-311++G(df,pd). Two combination bands consisting of the azide symmetric stretch and another mode form strong FRs with the azide asymmetric stretch for both molecules. The FR profile was altered by replacing the methyl group with maleimide. Solvents change the relative peak position and intensity more significantly for 4-azido-N-phenylmaleimide, which makes it a more sensitive VP. Furthermore, the DFT results indicate that a comparison among the results from different basis sets can be used as a means to predict more reliable vibrational spectra.

AMOEBA Force Field Predicts Accurate Hydrogen Bond Counts of Nitriles in SNase by Revealing Water-Protein Interaction in Vibrational Absorption Frequencies

Precisely quantifying the magnitude and direction of electric fields in proteins has long been an outstanding challenge in understanding biological functions. Nitrile vibrational Stark effect probes have been shown to be minimally disruptive to the protein structure and can be better direct reporters of local electrostatic field in the native state of a protein than other measures such as pKa shifts of titratable residues. However, interpretations of the connection between measured vibrational energy and electric field rely on the accurate molecular understanding of interactions of the nitrile group and its environment, particularly from hydrogen bonding. In this work, we compared the extent of hydrogen bonding calculated in two common force fields, the fixed charge force field Amber03 and polarizable force field AMOEBA, at 10 locations of cyanocysteine (CNC) in staphylococcal nuclease (SNase) against the experimental nitrile absorption frequency in terms of full width at half-maximum (FWHM) and frequency temperature line slope (FTLS). We observed that the number of hydrogen bonds correlated well in AMOEBA trajectories with respect to both the FWHM (r = 0.88) and the FTLS (r = -0.85), whereas the correlation of Amber03 trajectories was less reliable because the Amber03 force field predicted more hydrogen bonds in some mutants. Moreover, we demonstrated that contributions from the interactions between CNC and nearby water molecules were significant in AMOEBA trajectories but were not predicted by Amber03. We conclude that although the nitrile absorption peak shape could be qualitatively predicted by the fixed charge Amber03 force field, the detailed electrostatic environment measured by the nitrile probe in terms of the extent of hydrogen bonding could only be accurately observed in the AMOEBA trajectories, where the permanent dipole, quadrupole, and dipole-induced-dipole polarizable interactions were all taken into account. The significance of this finding to the goal of accurately predicting electric fields in complex biomolecular environments is discussed.

Spectroscopic Characterization of the Divalent Metal Docking Motif to Isolated Cyanobenzoate: Direct Observation of Tridentate Binding to ortho-Cyanobenzoate and Implications for the CN Response

Cryogenic ion vibrational spectra of D₂-tagged cyanobenzoate (CBA) derivatives are obtained and analyzed to characterize the intrinsic spectroscopic responses of the -CO₂^- headgroup to its location on the ring in both the isolated anions and the cationic complexes with divalent metal ions, M²⁺ (M = Mg, Ca, Sr). The benzonitrile functionality establishes the different ring isomers (para, meta, ortho) according to the location of the carboxylate and provides an additional reporter on the molecular response to the proximal charge center. The aromatic carboxylates display shifts slightly smaller than those observed for a related aliphatic system upon metal ion complexation. Although the CBA anions display very similar band patterns for all three ring positions, upon complexation with metal ions, the ortho isomer yields dramatically different spectral responses in both the -CO₂^- moiety and the CN group. This behavior is traced to the emergence of a tridentate binding motif unique to the ortho isomer in which the metal ions bind to both the oxygen atoms of the carboxylate group and the N atom of the cyano group. In that configuration, the -CO₂^- moiety is oriented perpendicular to the phenyl ring, and the CN stretching fundamental is both strong and red-shifted relative to its behavior in the isolated neutral. The behaviors of the metal-bound ortho complexes occur in contrast to the usual blue shifts associated with "Lewis" type binding of metal ions end-on to -CN. The origins of these spectroscopic features are analyzed with the aid of electronic structure calculations, which also explore differences expected for complexation of monovalent cations to the ortho carboxylate. The resulting insights have implications for understanding the balance between electrostatic and steric interactions at metal binding sites in chemical and biological systems.

Molecular Simulation-Guided Spectroscopy of Imidazolium-Based Ionic Liquids and Effects of Methylation on Ion-Cage and -Pair Dynamics

Classical molecular dynamics simulations were performed to assess an atomistic interpretation of the ion-probe structural interactions in two typical ionic liquids (ILs), 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide [BMIm][NTf₂] and 1-butyl-2,3-dimethylimidazolium bis(trifluoromethylsulfonyl)imide [BDimIm][NTf₂] through computational ultrafast spectroscopy. The nitrile stretching vibrations of the thiocyanate anion, [SCN]^-, serve as the local mode of the ultrafast system dynamics within the imidazolium-based ionic liquid environment. The wavelet transform of classical trajectories determines the time-varying fluctuating frequencies and the stretch spectral signatures of SCN^- in the normalized distribution. However, computational modeling of the two-dimensional (2D) spectra from the wavelet-derived vibrational frequencies yields time evolution of the local molecular structure along with the varied time-dependent dynamics of the spectral diffusion process. We calculated the frequency-frequency correlation functions (FFCFs), time correlations associated with the ion-pair and -cage dynamics, and mean square displacements as a function of time, depicting diffusive dynamics. The calculated results based on the pair correlation functions and the distribution of atomic density suggest that the hydrogen and methylated carbon at the two-position of the imidazolium ring of [BMIm] and [BDimIm] cations, respectively, strongly interact with the probe through the N of the thiocyanate anion rather than the S atom. The center-of-mass center-of-mass (COM-COM) cation-probe radial distribution functions (RDFs) in conjunction with the site-specific structural analysis further reveal well-structured interactions of the thiocyanate ion and [BMIm]⁺ cation rather than the [BDimIm] cation. In contrast, the anion-probe COM-COM RDFs depict weak interactive associations within the vibrational probe [SCN]^- and [NTf₂]^- ions. Methylation at the two-position of the imidazolium ring predicts slower structural reorganization and breaking and reformation dynamics of the ion pairs and cages within the ionic liquid framework.

Multiple Ensembles of the Hydrogen-bonded Network in Ethylammonium Nitrate versus Water from Vibrational Spectral Dynamics of SCN- Probe

We performed classical molecular dynamics simulations to monitor the structural interactions and ultrafast dynamical and spectral response in the protic ionic liquid, ethylammonium nitrate (EAN) and water using the nitrile stretching mode of thiocyanate ion (SCN-) as the vibrational probe. The normalized stretch frequency distribution of nitrile stretch of SCN- attains an asymmetric shape in EAN, indicating the existence of more than one hydrogen-bonding environment in EAN. We computed the 2D IR spectrum from classical trajectories, applying the response function formalism. Spectral diffusion dynamics in EAN undergo an initial rattling of the SCN - inside the local ion-cage occurring at a timescale of 0.10 ps, followed by the breakup of the ion-cage activating molecular diffusion at 7.86 ps timescale. In contrast, the dynamics of structural reorganization occur at a timescale of 0.58 ps in H 2 O. Hence, the time dependence of the frequency-frequency correlation function decay hints at the local molecular structure and ultrafast ion dynamics of the SCN - probe. The loss of frequency correlation read from the peak shape changes in the 2D correlation spectrum as a function of waiting time is faster in H 2 O than in EAN due to the enhanced structural ordering and higher viscosity of the latter. We provide an atomic-level interpretation of the solvation environment around SCN - in EAN and water, which indicates the multiple ensembles of the hydrogen bond network in EAN.

Importance of Hydrogen Bonding in Crowded Environments: A Physical Chemistry Perspective

Cells are heterogeneous on every length and time scale; cytosol contains thousands of proteins, lipids, nucleic acids, and small molecules, and molecular interactions within this crowded environment determine the structure, dynamics, and stability of biomolecules. For decades, the effects of crowding at the atomistic scale have been overlooked in favor of more tractable models largely based on thermodynamics. Crowding can affect the conformations and stability of biomolecules by modulating water structure and dynamics within the cell, and these effects are nonlocal and environment dependent. Thus, characterizing water's hydrogen-bond (H-bond) networks is a critical step toward a complete microscopic crowding model. This perspective provides an overview of molecular crowding and describes recent time-resolved spectroscopy approaches investigating H-bond networks and dynamics in crowded or otherwise complex aqueous environments. Ultrafast spectroscopy combined with atomistic simulations has emerged as a powerful combination for studying H-bond structure and dynamics in heterogeneous multicomponent systems. We discuss the ongoing challenges toward developing a complete atomistic description of macromolecular crowding from an experimental as well as a theoretical perspective.

Origin of thiocyanate spectral shifts in water and organic solvents

Vibrational spectroscopy is a useful technique for probing chemical environments. The development of models that can reproduce the spectra of nitriles and azides is valuable because these probes are uniquely suited for investigating complex systems. Empirical vibrational spectroscopic maps are commonly employed to obtain the instantaneous vibrational frequencies during molecular dynamics simulations but often fail to adequately describe the behavior of these probes, especially in its transferability to a diverse range of environments. In this paper, we demonstrate several reasons for the difficulty in constructing a general-purpose vibrational map for methyl thiocyanate (MeSCN), a model for cyanylated biological probes. In particular, we found that electrostatics alone are not a sufficient metric to categorize the environments of different solvents, and the dominant features in intermolecular interactions in the energy landscape vary from solvent to solvent. Consequently, common vibrational mapping schemes do not cover all essential interaction terms adequately, especially in the treatment of van der Waals interactions. Quantum vibrational perturbation (QVP) theory, along with a combined quantum mechanical and molecular mechanical potential for solute-solvent interactions, is an alternative and efficient modeling technique, which is compared in this paper, to yield spectroscopic results in good agreement with experimental FTIR. QVP has been used to analyze the computational data, revealing the shortcomings of the vibrational maps for MeSCN in different solvents. The results indicate that insights from QVP analysis can be used to enhance the transferability of vibrational maps in future studies.

Structural and dynamical changes observed when transitioning from an ionic liquid to a deep eutectic solvent

The microscopic molecular structure and dynamics of a new deep eutectic solvent (DES) composed of an ionic liquid (1-hexyl-3-methylimidazolium chloride) and an amide (trifluoroacetamide) at various molar ratios were investigated using linear and non-linear infrared spectroscopy with a vibrational probe. The use of the ionic liquid allows us to investigate the changes that the system undergoes with the addition of the amide or, equivalently, the changes from an ionic liquid to a DES. Our studies revealed that the vibrational probe in the DES senses a very similar local environment irrespective of the cation chemical structure. In addition, the amide also appears to perceive the same molecular environment. The concentration dependence studies also showed that the amide changes from being isolated from other amides in the ionic liquid environment to an environment where the amide-amide interactions are favored. In the case of the vibrational probe, the addition of the amide produced significant changes in the slow dynamics associated with the making and breaking of the ionic cages but did not affect the rattling-in-cage motions perceived by it. Furthermore, the concentration dependence of slow dynamics showed two regimes which are linked to the changes in the overall structure of the solution. These observations are interpreted in the context of a nanoscopic heterogeneous environment in the DES which, according to the observed dynamical regimes, appears at very large concentrations of the amide (molar ratio of greater than 1:1) since for lower amide molar ratios, the amide appears to be not segregated from the ionic liquid. This proposed molecular picture is supported by small angle x-ray scattering experiments.

Local Electric Fields in Aqueous Electrolytes

Vibrational Stark shifts were explored in aqueous solutions of organic molecules with carbonyl- and nitrile-containing constituents. In many cases, the vibrational resonances from these moieties shifted toward lower frequency as salt was introduced into solution. This is in contrast to the blue-shift that would be expected based upon Onsager's reaction field theory. Salts containing well-hydrated cations like Mg²⁺ or Li⁺ led to the most pronounced Stark shift for the carbonyl group, while poorly hydrated cations like Cs⁺ had the greatest impact on nitriles. Moreover, salts containing I^- gave rise to larger Stark shifts than those containing Cl^-. Molecular dynamics simulations indicated that cations and anions both accumulate around the probe in an ion- and probe-dependent manner. An electric field was generated by the ion pair, which pointed from the cation to the anion through the vibrational chromophore. This resulted from solvent-shared binding of the ions to the probes, consistent with their positions in the Hofmeister series. The "anti-Onsager" Stark shifts occur in both vibrational spectroscopy and fluorescence measurements.

Substituent Effects on the Vibrational Properties of the CN Stretch Mode of Aromatic Nitriles: IR Probes Useful for Time-resolved IR Spectroscopy

Developing ideal IR probes is essential to understand the structure and dynamics of biomolecules with time-resolved IR spectroscopies and imaging techniques. Especially, nitrile (CN) group has recently been proposed to serve as IR probes of the local environment of proteins. Herein, we investigated the effect of a substituent on the vibrational properties of the benzonitrile. The electron-donating and withdrawing character of p-substituent on benzonitrile are expected to modulate the vibrational frequency, molar extinction coefficient, and vibrational lifetime of CN probe. FT-IR revealed the positive correlation between electron-donating character and the molar extinction coefficient of CN stretch mode. Infrared pump-probe (IR-PP) measurements showed that the vibrational lifetime of CN stretch mode exhibits a relatively weak correlation with the electron-donating strength. Among the investigated samples, 4-dimethylamino benzonitrile with the strongest electron-donating strength shows enhanced absorption and extended vibrational lifetime. Utilizing substituent effects will be a practical strategy to improve the performance of the IR probe.

Structures of (NaSCN)2(H2O)n -/0 (n = 0-7) and solvation induced ion pair separation: Gas phase anion photoelectron spectroscopy and theoretical calculations

We studied (NaSCN)₂(H₂O)_n ^- clusters in the gas phase using size-selected anion photoelectron spectroscopy. The photoelectron spectra and vertical detachment energies of (NaSCN)₂(H₂O)_n ^- (n = 0-5) were obtained in the experiment. The structures of (NaSCN)₂(H₂O)_n ^-/0 up to n = 7 were investigated with density functional theory calculations. Two series of peaks are observed in the spectra, indicating that two types of structures coexist, the high electron binding energy peaks correspond to the chain style structures, and the low electron binding energy peaks correspond to the Na-N-Na-N rhombic structures or their derivatives. For the (NaSCN)₂(H₂O)_n ^- clusters at n = 3-5, the Na-N-Na-N rhombic structures are the dominant structures, the rhombic four-membered rings start to open at n = 4, and the solvent separated ion pair (SSIP) type of structures start to appear at n = 6. For the neutral (NaSCN)₂(H₂O)_n clusters, the Na-N-Na-N rhombic isomers become the dominant starting at n = 3, and the SSIP type of structures start to appear at n = 5 and become dominant at n = 6. The structural evolution of (NaSCN)₂(H₂O)_n ^-/0 (n = 0-7) confirms the possible existence of ionic clusters such as Na(SCN)₂ ^- and Na₂(SCN)⁺ in NaSCN aqueous solutions.

Computational assessment of the crystallization tendency of 1-ethyl-3-methylimidazolium ionic liquids

A test set of 20 1-ethyl-3-methylimidazolium ionic liquids, differing in their anions, is subjected to a computational study with an aim to interpret the experimental difficulties related to the preparation of crystalline phases of the selected species. Molecular dynamics simulations of the liquid phases, quantum-chemical symmetry-adapted perturbation theory calculations of the interaction energies within the ion pair, and density functional theory calculations of the cohesive energies of the crystal phases are used in this work to obtain the structural, energetic, and diffusion parameters of the materials. Correlations of fusion temperatures and enthalpies and temperatures of the glass transitions with 15 calculated parameters are investigated in order to interpret the trends of the phase behavior of the selected ionic liquids. Correlations of a fair significance are found between the glass transition temperatures and selected energetic, cohesive, and diffusion-related characteristics of the liquids; however, the correlations of calculated transport and some enthalpic properties are blurred by the limited accuracy of the non-polarizable CL&P force field for predicting these properties. 1-Ethyl-3-methylimidazolium acetate is found to have an exclusive position among those in the test set due to several outlying characteristics, such as the short contact distance of its counterions in the liquid, high pair interaction energies, and importance of the dispersion interactions for the collective cohesion, impeding its crystallization significantly.

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.

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.

Experimental observation of nanophase segregation in aqueous salt solutions around the predicted liquid-liquid transition in water

The liquid-liquid transition in supercooled liquid water, predicted to occur around 220 K, is controversial due to the difficulty of studying it caused by competition from ice crystallization (the so-called "no man's land"). In aqueous solutions, it has been predicted to give rise to phase separation on a nanometer scale between a solute-rich high-density phase and a water-rich low-density phase. Here we report direct experimental evidence for the formation of a nanosegregated phase in eutectic aqueous solutions of LiCl and LiSCN where the presence of crystalline water can be experimentally excluded. Femtosecond infrared and Raman spectroscopies are used to determine the temperature-dependent structuring of water, the solvation of the SCN^- anion, and the size of the phase segregated domains.

2D-IR studies of cyanamides (NCN) as spectroscopic reporters of dynamics in biomolecules: Uncovering the origin of mysterious peaks

Cyanamides (NCN) have been shown to have a larger transition dipole strength than cyano-probes. In addition, they have similar structural characteristics and vibrational lifetimes to the azido-group, suggesting their utility as infrared (IR) spectroscopic reporters for structural dynamics in biomolecules. To access the efficacy of NCN as an IR probe to capture the changes in the local environment, several model systems were evaluated via 2D IR spectroscopy. Previous work by Cho [G. Lee, D. Kossowska, J. Lim, S. Kim, H. Han, K. Kwak, and M. Cho, J. Phys. Chem. B 122(14), 4035-4044 (2018)] showed that phenylalanine analogues containing NCN show strong anharmonic coupling that can complicate the interpretation of structural dynamics. However, when NCN is embedded in 5-membered ring scaffolds, as in N-cyanomaleimide and N-cyanosuccinimide, a unique band structure is observed in the 2D IR spectrum that is not predicted by simple anharmonic frequency calculations. Further investigation indicated that electron delocalization plays a role in the origins of the band structure. In particular, the origin of the lower frequency transitions is likely a result of direct interaction with the solvent.

Application of a transparent window vibrational probe (azido probe) to the structural dynamics of model dipeptides and amyloid β-peptide

The azido asymmetric stretching motion is widely used for the elucidation of the intrinsic conformational preference and folding mechanism of protein since it has strong vibrational absorbance in the spectral transparent windows. However, the possible secondary structural disturbance induced by the insertion of azido group in the side chain of polypeptides should be carefully evaluated. Here, DFT calculation and enhanced sampling method were employed for model dipeptides with or without azido substitution, and the outcome results show that the lower potential energy basins of isolated model dipeptides are consistent with the preferred structural distributions of model dipeptides in aqueous solution. The azido asymmetric stretching frequency shows its sensitivity to the backbone configurations just like amide-I vibration does, and the azido vibration exhibits great potential as a structural reporter in the transparent window. For the evaluation of the application of azido group in biologically related system, the structural dynamics of Aβ_37-42 and N₃-Aβ_37-42 fragments and the self-assemble process of their protofiliments in aqueous solution were demonstrated. The outcome results show that the structural fluctuations of Aβ_37-42 and its protofilament in aqueous solution are quite similar with or without azido substitution, and the dewetting transitions of Aβ_37-42 and N₃-Aβ_37-42 β-sheet layers are both complete within 30 ns and assemble into stable protofilaments. Therefore, the azido asymmetric vibrational motion is a minimally invasive structural probe and would not introduce much disturbance to the structural dynamics of polypeptides.

Empirical S=O stretch vibrational frequency map

Dimethyl sulfoxide (DMSO) water mixtures have been widely studied due to their unique concentration-dependent bulk properties. Here, we present an empirical spectroscopic map for the sulfinyl (S=O) stretching mode. The model can be used to interpret infrared (IR) absorption and ultrafast two-dimensional infrared (2D IR) spectra and quantify hydrogen bond populations and lifetimes by directly connecting spectroscopic measurements with structures and dynamics from molecular dynamics simulations. The electrostatic map is directly parameterized against experimental absorption spectra in the S=O stretching region (980-1100 cm^-1) of dilute DMSO in water. A comparison of center peak frequencies shows that the map performs well across the entire DMSO concentration range, accurately reproducing the ∼10 cm^-1 red-shift per hydrogen bond observed in the experiments. We further benchmark the map by comparing experimental and simulated 2D IR spectra generated by direct numerical integration of the Schrödinger equation. We expect that this empirical frequency map will provide a quantitative platform for investigating intermolecular interactions, microscopic heterogeneity, and ultrafast dynamics in complex liquid mixtures containing DMSO.

Differential evolution algorithm approach for describing vibrational solvatochromism

We model the solvation-induced vibrational frequency shifts of the amide I and amide II modes of N-methylacetamide in water and the nitrile stretch mode of acetonitrile in water by expressing the frequency shift as a polynomial function expanded by the inverse power of interatomic distances. The coefficients of the polynomial are optimized to minimize the deviation between the predicted frequency shifts and those calculated with quantum chemistry methods. Here, we show that a differential evolution algorithm combined with singular value decomposition is useful to find the optimum set of coefficients of polynomial terms. The differential evolution optimization shows that only a few terms in the polynomial are dominant in the contribution to the vibrational frequency shifts. We anticipate that the present work paves the way for further developing different genetic algorithms and machine learning schemes for their applications to vibrational spectroscopic studies.

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.

Quantitative Measurement of Intrinsic GTP Hydrolysis for Carcinogenic Glutamine 61 Mutants in H-Ras

Mutations of human oncoprotein p²¹H-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 stabilizes the formation of the charged transition state at the γ-phosphate during hydrolysis. However, there is no comprehensive data set of the effects of mutations to Q61 on the protein's intrinsic catalytic rate, structure, or interactions with water at the active site. Here, we present the first comprehensive and quantitative set of initial rates of intrinsic hydrolysis for all stable variants of RasQ61X. We further conducted enhanced molecular dynamics (MD) simulations of each construct to determine the solvent accessible surface area (SASA) of the side chain at position 61 and compared these results to previously measured changes in electric fields caused by RasQ61X mutations. For polar and negatively charged residues, we found that the rates are normally distributed about an optimal electrostatic contribution, close to that of the native Q61 residue, and the rates are strongly correlated to the number of waters in the active site. Together, these results support a mechanism of GTP hydrolysis in which Q61 stabilizes a transient hydronium ion, which then stabilizes the transition state while the γ-phosphate is undergoing nucleophilic attack by a second, catalytically active water molecule. We discuss the implications of such a mechanism on future strategies for combating Ras-based cancers.

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.

Conformational Ensembles of Calmodulin Revealed by Nonperturbing Site-Specific Vibrational Probe Groups

Seven native residues on the regulatory protein calmodulin, including three key methionine residues, were replaced (one by one) by the vibrational probe amino acid cyanylated cysteine, which has a unique CN stretching vibration that reports on its local environment. Almost no perturbation was caused by this probe at any of the seven sites, as reported by CD spectra of calcium-bound and apo calmodulin and binding thermodynamics for the formation of a complex between calmodulin and a canonical target peptide from skeletal muscle myosin light chain kinase measured by isothermal titration. The surprising lack of perturbation suggests that this probe group could be applied directly in many protein–protein binding interfaces. The infrared absorption bands for the probe groups reported many dramatic changes in the probes’ local environments as CaM went from apo- to calcium-saturated to target peptide-bound conditions, including large frequency shifts and a variety of line shapes from narrow (interpreted as a rigid and invariant local environment) to symmetric to broad and asymmetric (likely from multiple coexisting and dynamically exchanging structures). The fast intrinsic time scale of infrared spectroscopy means that the line shapes report directly on site-specific details of calmodulin’s variable structural distribution. Though quantitative interpretation of the probe line shapes depends on a direct connection between simulated ensembles and experimental data that does not yet exist, formation of such a connection to data such as that reported here would provide a new way to evaluate conformational ensembles from data that directly contains the structural distribution. The calmodulin probe sites developed here will also be useful in evaluating the binding mode of calmodulin with many uncharacterized regulatory targets.

Watching Proteins Wiggle: Mapping Structures with Two-Dimensional Infrared Spectroscopy

Proteins exhibit structural fluctuations over decades of time scales. From the picosecond side chain motions to aggregates that form over the course of minutes, characterizing protein structure over these vast lengths of time is important to understanding their function. In the past 15 years, two-dimensional infrared spectroscopy (2D IR) has been established as a versatile tool that can uniquely probe proteins structures on many time scales. In this review, we present some of the basic principles behind 2D IR and show how they have, and can, impact the field of protein biophysics. We highlight experiments in which 2D IR spectroscopy has provided structural and dynamical data that would be difficult to obtain with more standard structural biology techniques. We also highlight technological developments in 2D IR that continue to expand the scope of scientific problems that can be accessed in the biomedical sciences.

Electrostatic frequency maps for amide-I mode of β-peptide: Comparison of molecular mechanics force field and DFT calculations

The spectroscopy of amide-I vibrations has been widely utilized for the understanding of dynamical structure of polypeptides. For the modeling of amide-I spectra, two frequency maps were built for β-peptide analogue (N-ethylpropionamide, NEPA) in a number of solvents within different schemes (molecular mechanics force field based, GM map; DFT calculation based, GD map), respectively. The electrostatic potentials on the amide unit that originated from solvents and peptide backbone were correlated to the amide-I frequency shift from gas phase to solution phase during map parameterization. GM map is easier to construct with negligible computational cost since the frequency calculations for the samples are purely based on force field, while GD map utilizes sophisticated DFT calculations on the representative solute-solvent clusters and brings insight into the electronic structures of solvated NEPA and its chemical environments. The results show that the maps' predicted amide-I frequencies present solvation environmental sensitivities and exhibit their specific characters with respect to the map protocols, and the obtained vibrational parameters are in satisfactory agreement with experimental amide-I spectra of NEPA in solution phase. Although different theoretical schemes based maps have their advantages and disadvantages, the present maps show their potentials in interpreting the amide-I spectra for β-peptides, respectively.

Vibrational Probes: From Small Molecule Solvatochromism Theory and Experiments to Applications in Complex Systems

The vibrational frequency of a chosen normal mode is one of the most accurately measurable spectroscopic properties of molecules in condensed phases. Accordingly, infrared absorption and Raman scattering spectroscopy have provided valuable information on both distributions and ensemble-average values of molecular vibrational frequencies, and these frequencies are now routinely used to investigate structure, conformation, and even absolute configuration of chemical and biological molecules of interest. Recent advancements in coherent time-domain nonlinear vibrational spectroscopy have allowed the study of heterogeneous distributions of local structures and thermally driven ultrafast fluctuations of vibrational frequencies. To fully utilize IR probe functional groups for quantitative bioassays, a variety of biological and chemical techniques have been developed to site-specifically introduce vibrational probe groups into proteins and nucleic acids. These IR-probe-labeled biomolecules and chemically reactive systems are subject to linear and nonlinear vibrational spectroscopic investigations and provide information on the local electric field, conformational changes, site-site protein contacts, and/or function-defining features of biomolecules. A rapidly expanding library of data from such experiments requires an interpretive method with atom-level chemical accuracy. However, despite prolonged efforts to develop an all-encompassing theory for describing vibrational solvatochromism and electrochromism as well as dynamic fluctuations of instantaneous vibrational frequencies, purely empirical and highly approximate theoretical models have often been used to interpret experimental results. They are, in many cases, based on the simple assumption that the vibrational frequency of an IR reporter is solely dictated by electric potential or field distribution around the vibrational chromophore. Such simplified description of vibrational solvatochromism generally referred to as vibrational Stark effect theory has been considered to be quite appealing and, even in some cases, e.g., carbonyl stretch modes in amide, ester, ketone, and carbonate compounds or proteins, it works quantitatively well, which makes it highly useful in determining the strength of local electric field around the IR chromophore. However, noting that the vibrational frequency shift results from changes of solute-solvent intermolecular interaction potential along its normal coordinate, Pauli exclusion repulsion, polarization, charge transfer, and dispersion interactions, in addition to the electrostatic interaction between distributed charges of both vibrational chromophore and solvent molecules, are to be properly included in the theoretical description of vibrational solvatochromism. Since the electrostatic and nonelectrostatic intermolecular interaction components have distinctively different distance and orientation dependences, they affect the solvatochromic vibrational properties in a completely different manner. Over the past few years, we have developed a systematic approach to simulating vibrational solvatochromic data based on the effective fragment potential approach, one of the most accurate and rigorous theories on intermolecular interactions. We have further elucidated the interplay of local electric field with the general vibrational solvatochromism of small IR probes in either solvents or complicated biological systems, with emphasis on contributions from non-Coulombic intermolecular interactions to vibrational frequency shifts and fluctuations. With its rigorous foundation and close relation to quantitative interpretation of experimental data, this and related theoretical approaches and experiments will be of use in studying and quantifying the structure and dynamics of biomolecules with unprecedented time and spatial resolution when combined with time-resolved vibrational spectroscopy and chemically sensitive vibrational imaging techniques.

Synthesis and Evaluation of the Sensitivity and Vibrational Lifetimes of Thiocyanate and Selenocyanate Infrared Reporters

Two novel 2'-deoxyadenosine (dA) analogues, Si₂-dA-SCN and Si₂-dA-SeCN, and two novel phenylalanine (Phe) analogues, Boc-Me-PheCH₂SCN and Boc-Me-PheCH₂SeCN, have been synthesized and the thiocyanate (SCN) and selenocyanate (SeCN) functional groups evaluated as vibrational reporters. The syntheses of Si₂-dA-SCN and Si₂-dA-SeCN were accomplished in three steps in 16% and 32% overall yields, respectively, and the syntheses of Boc-Me-PheCH₂SCN and Boc-Me-PheCH₂SeCN were completed in four steps in 8.9% and 2.3% overall yields, respectively. The SCN and SeCN stretch vibrational modes were shown to be sensitive to the local environment by frequency shifts and full-width half-maximum (fwhm) changes in response to tetrahydrofuran (THF) and THF/water solvent mixtures. The vibrational lifetimes of the Si₂-dA-SeCN (237±12 ps) and Boc-Me-PheCH₂SeCN (295±31 ps) in THF solution were determined by ultrafast infrared pump-probe spectroscopy to be 1.5 to 3 times longer than those for Si₂-dA-SCN (140±6 ps) and Boc-Me-PheCH₂SCN (102±4 ps). The longer lifetimes for the SeCN analogues were attributed to the better insulating effects of the heavier selenium atom compared to the sulfur atom. The solvent sensitivity and longer vibrational lifetimes compared to other vibrational reporters suggest that SCN and SeCN vibrational reporters are well suited to studying several dynamic processes including protein and nucleic acid hydration and conformational changes, however stability issues may require post-synthetic modification methods to incorporate these reporters into biomacromolecules.

C≡N stretching vibration of 5-cyanotryptophan as an infrared probe of protein local environment: what determines its frequency?

Recently it has been suggested that the C≡N stretching vibration of a tryptophan analog, 5-cyanotryptophan, could be used as an infrared probe of the local environment, especially the hydration status, of tryptophan residues in proteins. However, the factors that influence the frequency of this vibrational mode are not understood. To determine these factors, herein we carried out linear and nonlinear infrared measurements on the C≡N stretching vibration of the sidechain of 5-cyanotryptophan, 3-methyl-5-cyanoindole, in a series of protic and aprotic solvents. We found that while the C≡N stretching frequencies obtained in these solvents do not correlate well with any individual Kamlet-Taft solvent parameter, i.e., π* (polarizability), β (hydrogen bond accepting ability), and α (hydrogen bond donating ability), they do however, collapse on a straight line when plotted against σ = π* + β - α. This linear relationship provides a firm indication that both specific interactions, i.e., hydrogen-bonding interactions with the C≡N (through α) and indole N-H (through β) groups, and non-specific interactions with the molecule (through π*) work together to determine the C≡N stretching frequency, thus laying a quantitative framework for applying 5-cyanotryptophan to investigate the microscopic environment of proteins in a site-specific manner. Furthermore, two-dimensional and pump-probe infrared measurements revealed that a significant portion (∼31%) of the ground state bleach signal has a decay time constant of ∼12.3 ps, due to an additional vibrational relaxation channel, making it possible to use 5-cyanotryptophan to probe dynamics occurring on a timescale on the order of tens of picoseconds.