Ribonuclease S dynamics measured using a nitrile label with 2D IR vibrational echo spectroscopy

Early Aggregation Mechanism of SOD128-38 Based on Force Field Parameter of 5-Cyano-Tryptophan

The aggregation of superoxide dismutase 1 (SOD1) results in amyloid deposition and is involved in familial amyotrophic lateral sclerosis, a fatal motor neuron disease. There have been extensive studies of its aggregation mechanism. Noncanonical amino acid 5-cyano-tryptophan (5-CN-Trp), which has been incorporated into the amyloid segments of SOD1 as infrared probes to increase the structural sensitivity of IR spectroscopy, is found to accelerate the overall aggregation rate and potentially modulate the aggregation process. Despite these observations, the underlying mechanism remains elusive. Here, we optimized the force field parameters of 5-CN-Trp and then used molecular dynamics simulation along with the Markov state model on the SOD128-38 dimer to explore the kinetics of key intermediates in the presence and absence of 5-CN-Trp. Our findings indicate a significantly increased probability of protein aggregate formation in 5CN-Trp-modified ensembles compared to wildtype. Dimeric β-sheets of different natures were observed exclusively in the 5CN-Trp-modified peptides, contrasting with wildtype simulations. Free-energy calculations and detailed analyses of the dimer structure revealed augmented interstrand interactions attributed to 5-CN-Trp, which contributed more to peptide affinity than any other residues. These results explored the key events critical for the early nucleation of amyloid-prone proteins and also shed light on the practice of using noncanonical derivatives to study the aggregation mechanism.

Anionic Effects on Concentrated Aqueous Lithium Ion Dynamics

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

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.

Nitrile Substituents at the Conjugated Dipyridophenazine Moiety as Infrared Redox Markers in Electrochemically Reduced Heteroleptic Ru(II) Polypyridyl Complexes

Ruthenium(II) complexes [Ru(tap)2(NN)]2+ (tap = 1,4,5,8-tetraazaphenanthrene, NN = 11-cyano-dipyrido[3,2-a:2',3'-c]phenazine (11-CN-dppz) and 11,12-dicyano-dipyrido[3,2-a:2',3'-c]phenazine (11,12-CN-dppz)) feature the C≡N groups as infrared (IR)-active redox markers. They were studied by cyclic voltammetry, UV-vis, and IR spectroelectrochemistry (SEC), and density functional theory calculations to assign the four 1e- reduction waves R1-R4 observed in dichloromethane. Generally, the NN ligands are reduced first (R1). For [Ru(tap)2(11,12-CN-dppz)]2+, R1 is sufficiently separated from R2 and delocalized over both tap ligands. Accordingly, IR SEC conducted at R1 shows a large red shift of the νs,as(C≡N) modes by -18/-28 cm-1, accompanied by a 4-fold enhancement of the νs(C≡N) intensity, comparably with reference data for free 11,12-CN-dppz. The first tap-based reduction of spin-doublet [Ru(tap)2(11,12-CN-dppz)]+ to spin-triplet [Ru(tap)2(11,12-CN-dppz)] at R2 decreased ν(C≡N) by merely -2 cm-1, while the intensity enhancement reached an overall factor of 8. Comparably, a red shift of ν(C≡N) by -27 cm-1 resulted from the 1e- reduction of [Ru(tap)2(11-CN-dppz)]2+ at R1 (poorly resolved from R2), and the intensity enhancement was roughly 3-fold. Concomitant 1e- reductions of the tap ligands (R2 and R3) caused only minor ν(C≡N) shifts of -3 cm-1 and increased the absorbance by overall factors of 6.5 and 8, respectively.

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.

Structure and diffusive dynamics of aspartate α-decarboxylase (ADC) liganded with D-serine in aqueous solution

Incoherent neutron spectroscopy, in combination with dynamic light scattering, was used to investigate the effect of ligand binding on the center-of-mass self-diffusion and internal diffusive dynamics of Escherichia coli aspartate α-decarboxylase (ADC). The X-ray crystal structure of ADC in complex with the d-serine inhibitor was also determined, and molecular dynamics simulations were used to further probe the structural rearrangements that occur as a result of ligand binding. These experiments reveal that d-serine forms hydrogen bonds with some of the active site residues, that higher order oligomers of the ADC tetramer exist on ns–ms time-scales, and also show that ligand binding both affects the ADC internal diffusive dynamics and appears to further increase the size of the higher order oligomers.

Neutron spectroscopy, dynamic light scattering, X-ray diffraction, and MD-simulations were used to investigate the effect of ligand binding on the structure and diffusive dynamics of Escherichia coli aspartate alpha-decarboxylase.

Water Dynamics and Structure of Highly Concentrated LiCl Solutions Investigated Using Ultrafast Infrared Spectroscopy

In highly concentrated salt solutions, the water hydrogen bond (H-bond) network is completely disrupted by the presence of ions. Water is forced to restructure as dictated by the water-ion and ion-ion interactions. Using ultrafast polarization-selective pump-probe (PSPP) spectroscopy measurements of the OD stretch of dilute HOD, we demonstrate that the limited water-water H-bonding present in concentrated lithium chloride solutions (up to four waters per ion pair) is, on average, stronger than that occurring in bulk water. Furthermore, information on the orientational dynamics and the angular restriction of water H-bonded to both water oxygens and chloride anions was obtained through analysis of the frequency-dependent anisotropy decays. It was found that, when the salt concentration increased, the water showed increasing restriction and slowing at frequencies correlated with strong H-bonding. The angular restriction of the water molecules and strengthening of water-water H-bonds are due to the formation of a water-ion network not present in bulk water and dilute salt solutions. The structural evolution of the ionic medium was also observed through spectral diffusion of the OD stretch using 2D IR spectroscopy. Compared to bulk water, there is significant slowing of the biexponential spectral diffusion dynamics. The slowest component of the spectral diffusion (13 ps) is virtually identical to the time for complete reorientation of HOD measured with the PSPP experiments. This result suggests that the slowest component of the spectral diffusion reflects rearrangement of water molecules in the water-ion network.

Cross-Correlated Motions in Azidolysozyme

The changes in the local and global dynamics of azide-labelled lysozyme compared with that of the wild type protein are quantitatively assessed for all alanine residues along the polypeptide chain. Although attaching -N3 to alanine residues has been considered to be a minimally invasive change in the protein it is found that depending on the location of the alanine residue, the local and global changes in the dynamics differ. For Ala92, the change in the cross-correlated motions are minimal, whereas attaching -N3 to Ala90 leads to pronounced differences in the local and global correlations as quantified by the cross-correlation coefficients of the Cα atoms. We also demonstrate that the spectral region of the asymmetric azide stretch distinguishes between alanine attachment sites, whereas changes in the low frequency, far-infrared region are less characteristic.

Probing Ligand Effects on the Ultrafast Dynamics of Copper Complexes via Midinfrared Pump-Probe and 2DIR Spectroscopies

The effects of ligand structural variation on the ultrafast dynamics of a series of copper coordination complexes were investigated using polarization-dependent mid-IR pump-probe spectroscopy and two-dimensional infrared (2DIR) spectroscopy. The series consists of three copper complexes [(^R3P₃tren)Cu^IIN₃]BAr₄^F (1^PR3, ^R3P₃tren = tris[2-(phosphiniminato)ethyl]amine, BAr₄^F = tetrakis(pentafluorophenyl)borate) where the number of methyl and phenyl groups in the PR₃ ligand are systematically varied across the series (PR₃ = PMe₃, PMe₂Ph, PMePh₂). The asymmetric stretching mode of azide in the 1^PR3 series is used as a vibrational probe of the small-molecule binding site. The results of the pump-probe measurements indicate that the vibrational energy of azide dissipates through intramolecular pathways and that the bulkier phenyl groups lead to an increase in the spatial restriction of the diffusive reorientation of bound azide. From 2DIR experiments, we characterize the spectral diffusion of the azide group and find that an increase in the number of phenyl groups maps to a broader inhomogeneous frequency distribution (Δ₂). This indicates that an increase in the steric bulk of the secondary coordination sphere acts to create more distinct configurations in the local environment that are accessible to the azide group. This work demonstrates how ligand structural variation affects the ultrafast dynamics of a small molecular group bound to the metal center, which could provide insight into the structure-function relationship of the copper coordination complexes and transition-metal coordination complexes in general.

Multipolar Force Fields for Amide-I Spectroscopy from Conformational Dynamics of the Alanine Trimer

The dynamics and spectroscopy of N-methyl-acetamide (NMA) and trialanine in solution are characterized from molecular dynamics simulations using different energy functions, including a conventional point charge (PC)-based force field, one based on a multipolar (MTP) representation of the electrostatics, and a semiempirical DFT method. For the 1D infrared spectra, the frequency splitting between the two amide-I groups is 10 cm^-1 from the PC, 13 cm^-1 from the MTP, and 47 cm^-1 from self-consistent charge density functional tight-binding (SCC-DFTB) simulations, compared with 25 cm^-1 from experiment. The frequency trajectory required for the frequency fluctuation correlation function (FFCF) is determined from individual normal mode (INM) and full normal mode (FNM) analyses of the amide-I vibrations. The spectroscopy, time-zero magnitude of the FFCF C(t = 0), and the static component Δ₀² from simulations using MTP and analysis based on FNM are all consistent with experiments for (Ala)₃. Contrary to this, for the analysis excluding mode-mode coupling (INM), the FFCF decays to zero too rapidly and for simulations with a PC-based force field, the Δ₀² is too small by a factor of two compared with experiments. Simulations with SCC-DFTB agree better with experiment for these observables than those from PC-based simulations. The conformational ensemble sampled from simulations using PCs is consistent with the literature (including P_II, β, α_R, and α_L), whereas that covered by the MTP-based simulations is dominated by P_II with some contributions from β and α_R. This agrees with and confirms recently reported Bayesian-refined populations based on 1D infrared experiments. FNM analysis together with a MTP representation provides a meaningful model to correctly describe the dynamics of hydrated trialanine.

Protein Dynamics by Two-Dimensional Infrared Spectroscopy

Proteins function as ensembles of interconverting structures. The motions span from picosecond bond rotations to millisecond and longer subunit displacements. Characterization of functional dynamics on all spatial and temporal scales remains challenging experimentally. Two-dimensional infrared spectroscopy (2D IR) is maturing as a powerful approach for investigating proteins and their dynamics. We outline the advantages of IR spectroscopy, describe 2D IR and the information it provides, and introduce vibrational groups for protein analysis. We highlight example studies that illustrate the power and versatility of 2D IR for characterizing protein dynamics and conclude with a brief discussion of the outlook for biomolecular 2D IR.

Vibrational Stark shift spectroscopy of catalysts under the influence of electric fields at electrode-solution interfaces

External control of chemical processes is a subject of widespread interest in chemical research, including control of electrocatalytic processes with significant promise in energy research. The electrochemical double-layer is the nanoscale region next to the electrode/electrolyte interface where chemical reactions typically occur. Understanding the effects of electric fields within the electrochemical double layer requires a combination of synthesis, electrochemistry, spectroscopy, and theory. In particular, vibrational sum frequency generation (VSFG) spectroscopy is a powerful technique to probe the response of molecular catalysts at the electrode interface under bias. Fundamental understanding can be obtained via synthetic tuning of the adsorbed molecular catalysts on the electrode surface and by combining experimental VSFG data with theoretical modelling of the Stark shift response. The resulting insights at the molecular level are particularly valuable for the development of new methodologies to control and characterize catalysts confined to electrode surfaces. This Perspective article is focused on how systematic modifications of molecules anchored to surfaces report information concerning the geometric, energetic, and electronic parameters of catalysts under bias attached to electrode surfaces.

Heterogeneous electrocatalysis: characterization of interfacial electric field within the electrochemical double layer.

Characterization of the ultrafast spectral diffusion and vibronic coherence of TIPS-pentacene using 2D electronic spectroscopy

TIPS-pentacene is a small-molecule organic semiconductor that is widely used in optoelectronic devices. It has been studied intensely owing to its ability to undergo singlet fission. In this study, we aim to develop further understanding of the coupling between the electronic and nuclear degrees of freedom of TIPS-pentacene (TIPS-Pn). We measured and analyzed the 2D electronic spectra of TIPS-Pn in solutions. Using center line slope (CLS) analysis, we characterized the frequency-fluctuation correlation function of the 0-0 vibronic transition. Strong oscillations in the CLS values were observed for up to 5 ps with a frequency of 264 cm^-1, which are attributable to a large vibronic coupling with the TIPS-Pn ring-breathing vibrational mode. In addition, detailed analysis of the CLS values allowed us to retrieve two spectral diffusion lifetimes, which are attributed to the inertial and diffusive dynamics of solvent molecules. Amplitude beating analysis also uncovered couplings with another vibrational mode at 1173 cm^-1. The experimental results can be described using the displaced harmonic oscillator model. By comparing the CLS values of the simulated data with the experimental CLS values, we estimated a Huang-Rhys factor of 0.1 for the ring-breathing vibrational mode. The results demonstrated how CLS analysis can be a useful method for characterizing the strength of vibronic coupling.

Coupling chemical biology and vibrational spectroscopy for studies of amyloids in vitro and in cells

Amyloid diseases are characterized by the aggregation of various proteins to form insoluble β-sheet-rich fibrils leading to cell death. Vibrational spectroscopies have emerged as attractive methods to study this process because of the rich structural information that can be extracted without large, perturbative probes. Importantly, specific vibrations such as the amide-I band directly report on secondary structure changes, which are key features of amyloid formation. Beyond intrinsic vibrations, the incorporation of unnatural vibrational probes can improve sensitivity for secondary structure determination (e.g. isotopic labeling), can provide residue-specific information of the surrounding polarity (e.g. unnatural amino acid), and are translatable into cellular studies. Here, we review the latest studies that have leveraged tools from chemical biology for the incorporation of novel vibrational probes into amyloidogenic proteins for both mechanistic and cellular studies.

Site-selective dynamics of azidolysozyme

The spectroscopic response of and structural dynamics around all azido-modified alanine residues (AlaN₃) in lysozyme are characterized. It is found that AlaN₃ is a positionally sensitive probe for the local dynamics, covering a frequency range of ∼15 cm^-1 for the center frequency of the line shape. This is consistent with findings from selective replacements of amino acids in PDZ2, which reported a frequency span of ∼10 cm^-1 for replacements of Val, Ala, or Glu by azidohomoalanine. For the frequency fluctuation correlation functions, the long-time decay constants τ₂ range from ∼1 to ∼10 ps, which compares with experimentally measured correlation times of 3 ps. Attaching azide to alanine residues can yield dynamics that decays to zero on the few ps time scale (i.e., static component Δ₀ ∼ 0 ps^-1) or to a remaining, static contribution of ∼0.5 ps^-1 (corresponding to 2.5 cm^-1), depending on the local environment on the 10 ps time scale. The magnitude of the static component correlates qualitatively with the degree of hydration of the spectroscopic probe. Although attaching azide to alanine residues is found to be structurally minimally invasive with respect to the overall protein structure, analysis of the local hydrophobicity indicates that the hydration around the modification site differs for modified and unmodified alanine residues, respectively.

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.

Shot-to-shot 2D IR spectroscopy at 100 kHz using a Yb laser and custom-designed electronics

The majority of 2D IR spectrometers operate at 1-10 kHz using Ti:Sapphire laser technology. We report a 2D IR spectrometer designed around Yb:KGW laser technology that operates shot-to-shot at 100 kHz. It includes a home-built OPA, a mid-IR pulse shaper, and custom-designed electronics with optional on-chip processing. We report a direct comparison between Yb:KGW and Ti:Sapphire based 2D IR spectrometers. Even though the mid-IR pulse energy is much lower for the Yb:KGW driven system, there is an 8x improvement in signal-to-noise over the 1 kHz Ti:Sapphire driven spectrometer to which it is compared. Experimental data is shown for sub-millimolar concentrations of amides. Advantages and disadvantages of the design are discussed, including thermal background that arises at high repetition rates. This fundamental spectrometer design takes advantage of newly available Yb laser technology in a new way, providing a straightforward means of enhancing sensitivity.

Exploring the 2D-IR repertoire of the -SCN label to study site-resolved dynamics and solvation in the calcium sensor protein calmodulin

The calcium sensor protein calmodulin is ubiquitous among eukaryotes. It translates intracellular Ca2+ influx (by a decrease of conformational flexibility) into increased target recognition affinity. Here we demonstrate that by using the IR reporter -SCN in combination with 2D-IR spectroscopy, global structure changes and local dynamics, degree of solvent exposure and protein-ligand interaction can be characterised in great detail. The long vibrational lifetime of the -SCN label allows for centerline slope analysis of the 2D-IR line shape up to 120 ps to deduce the frequency-frequency correlation function (FFCF) of the -SCN label in various states and label positions in the protein. Based on that we show clear differences between a solvent exposed site, the environment close to the Ca2+ binding motif and three highly conserved positions for ligand binding. Furthermore, we demonstrate how these dynamics are affected by conformational change induced by the addition of Ca2+ ions and by interaction with a short helical peptide mimicking protein binding. We show that the binding mode is strongly heterogeneous among the probed key binding methionine residues. SCN's vibrational relaxation is dominated by intermolecular contributions. Changes in the vibrational lifetime upon changing between H2O and D2O buffer therefore provide a robust measure for water accessibility of the label. Characterising -SCN's extinction coefficient, vibrational lifetime in light and heavy water and its FFCF we demonstrate the vast potential it has as a label especially for nonlinear spectroscopies, such as 2D-IR spectroscopy.

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.

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.

Towards the critical understanding of selected vibrational features in biologically important dicyano aromatic conjugated molecules: Importance of electron donating/withdrawal groups and geometry associated with dicyano group

The Raman spectra of a series of synthesized DC molecules (benzylidene malononitrile derivatives) with different electron donating (EDG) and electron withdrawing (EWG) group have been presented and analyzed with DFT calculated spectra. In particular, different functional groups effect on cyano stretching (∼2200 cm^-1), phenyl ring breathing and alkenic double bond stretch which often appears mixed up (1475-1650 cm^-1) are studied systematically for several aromatic conjugated DC derivatives. Interestingly, symmetric stretching frequency of the DC compounds having two CN groups at geminal position appears at higher wavenumber (by 11-15 cm^-1) compared to their corresponding asymmetric stretch frequency. Angle (between dicyano group) dependent theoretical study indicates that the relative appearance of cyano symmetric/anti-symmetric stretching frequency depends on whether dicyano groups are at the geminal or vicinal position and the angle between them. Complete band assignments of observed Raman frequencies have been performed by potential energy distributions (PEDs) available in GAR2PED software. Our results will help to understand the vibrational feature of this important class of compounds in biological medium when used as probe.

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.

Following local light-induced structure changes and dynamics of the photoreceptor PYP with the thiocyanate IR label

Photoactive Yellow Protein (PYP) is a bacterial blue light receptor that enters a photocycle after excitation. The intermediate states are formed on time scales ranging from femtoseconds up to hundreds of milliseconds, after which the signaling state with a lifetime of about 1 s is reached. To investigate structural changes and dynamics, we incorporated the SCN IR label at distinct positions of the photoreceptor via cysteine mutation and cyanylation. FT-IR measurements of the SCN label at different sites of the well-established dark state structure of PYP characterized the spectral response of the label to differences in the environment. Under constant blue light irradiation, we observed the formation of the signaling state with significant changes of wavenumber and lineshape of the SCN bands. Thereby we deduced light-induced structural changes in the local environment of the labels. These results were supported by molecular dynamics simulations on PYP providing the solvent accessible surface area (SASA) at the different positions. To follow protein dynamics via the SCN label during the photocycle, we performed step-scan FT-IR measurements with a time resolution of 10 μs. Global analysis yielded similar time constants of τ1 = 70 μs, τ2 = 640 μs, and τ3 > 20 ms for the wild type and τ1 = 36 μs, τ2 = 530 μs, and τ3 > 20 ms for the SCN-labeled mutant PYP-A44C*, a mutant which provided a sufficiently large SCN difference signal to measure step-scan FT-IR spectra. In comparison to the protein (amide, E46) and chromophore bands the dynamics of the SCN label show a different behavior. This result indicates that the local kinetics sensed by the label are different from the global protein kinetics.

Multipurpose isothiocyanyl alanine/lysine: Use as solvatochromic IR probes and in site specific labeling/ligation of short peptides

The solvatochromic IR responsivity of small side chain -NCS in two unexplored unnatural amino acids, isothiocyanyl alanine (^NCSAla = Ita) and lysine (^NCSLys = Itl), without perturbing the conformation is demonstrated in two designed short tripeptide (BocAla-^NCSAla-Ala-OMe) and hexapeptide (BocLeu-Val-Phe-Phe-^NCSLys-Gly-OMe). Demonstration of site specific fluorescent labeling in both the peptides and ligation type reaction in ^NCSLys indicates the novelty of these two amino acids as alternative to the available canonical amino acids.

Exploring local solvation environments of a heme protein using the spectroscopic reporter 4-cyano-l-phenylalanine

The vibrational reporter unnatural amino acid (UAA) 4-cyano-l-phenylalanine (pCNF) was genetically incorporated individually at three sites (5, 36, and 78) in the heme protein Caldanaerobacter subterraneus H-NOX to probe local hydration environments. The UAA pCNF was incorporated site-specifically using an engineered, orthogonal tRNA synthetase in E. coli. The ability of all of the pCNF-containing H-NOX proteins to form the ferrous CO, NO, or O₂ ligated and unligated states was confirmed with UV-Vis spectroscopy. The solvation state at each site of the three sites of pCNF incorporation was assessed using temperature-dependent infrared spectroscopy. Specifically, the frequency-temperature line slope (FTLS) method was utilized to show that the nitrile group at site 36 was fully solvated and the nitrile group at site 78 was de-solvated (buried) in the heme pocket. The nitrile group at site 5 was found to be partially solvated suggesting that the nitrile group was involved in moderate strength hydrogen bonds. These results were confirmed by the determination of the X-ray crystal structure of the H-NOX protein construct containing pCNF at site 5.

Vibrational Stark spectroscopy for assessing ligand-binding strengths in a protein

Nitrile groups are potentially useful spectroscopic probes in the infrared to characterize the binding and dynamics of ligands in proteins. This opens the possibility of locating and determining the binding mode of suitably labelled ligands in proteins based on optical spectroscopy, without the need for determining an X-ray structure. However, relating structure and spectroscopy requires means to accurately compute infrared spectra. This is investigated for benzonitrile (PhCN) in water, wild type (WT) and two lysozyme mutants in solution. The force field is validated by comparing with experimental data for benzonitrile in water which is the basis for computing the Stark shift and time scale for spectral diffusion of PhCN in WT and the L99A and L99G mutants of T4 lysozyme. The 1-d spectra for PhCN in WT and the two mutant proteins differ in their maximum absorption by up to 4 cm^-1, which reflects the modified electrostatic environments in the three proteins. It is also tested whether extending from 1-d to 2-d infrared spectroscopy provides further discrimination in the ligand-binding modes. First, for PhCN in solution the frequency fluctuation correlation function (FFCF) decays to zero at short times whereas in the protein a pronounced static inhomogeneous component is found. Secondly, the decay time of the FFCF for the mutant to which PhCN binds most strongly has the longest decay time. It is demonstrated explicitly that the ligand-binding free energy with respect to the three protein variants correlates with the Stark shift. This makes 1-d infrared spectroscopy together with computations a valuable tool for characterizing binding modes and potentially binding locations in proteins.

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

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

Sensitivity of core-level spectroscopy to electrostatic environments of nitrile groups: An ab initio study

Ab initio quantum chemistry calculations have been performed to probe the influence of hydrogen bonding on the electronic structure of hydrogen cyanide (HCN). Our calculations determine the origin of nitrogen-specific Raman spectral features from resonant inelastic X-ray scattering occurring in the presence of a water molecule and an electric dipole field. The similarity of the two interactions in altering the electronic structure of the nitrogen atom differs only in the covalent contributions from the water molecule. The CN stretching mode as a structural probe was also investigated to study the electronic origin of the anomalous frequency shift of the nitrile group when subjected to hydrogen bonding and an electrostatic dipole field. The major changes in the electronic structure of HCN are electrostatic in nature and originate from dipole-dipole interactions. The relative shifts of the CN stretching frequency are in good agreement with those experimentally observed.

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.

Effect of ion–ligand binding on ion pairing dynamics studied by two-dimensional infrared spectroscopy

Cation-specific ion pairing dynamics between M⁺ (M = Ag or Cu) and SCN⁻ in N,N-dimethylthioformamide (DMTF) are studied by probing the nitrile (CN) stretching vibration.

Deriving Structural Information from Experimentally Measured Data on Biomolecules

During the past half century, the number and accuracy of experimental techniques that can deliver values of observables for biomolecular systems have been steadily increasing. The conversion of a measured value Q^exp of an observable quantity Q into structural information is, however, a task beset with theoretical and practical problems: 1) insufficient or inaccurate values of Q^exp , 2) inaccuracies in the function Q(r→) used to relate the quantity Q to structure r→ , 3) how to account for the averaging inherent in the measurement of Q^exp , 4) how to handle the possible multiple-valuedness of the inverse r→(Q) of the function Q(r→) , to mention a few. These apply to a variety of observable quantities Q and measurement techniques such as X-ray and neutron diffraction, small-angle and wide-angle X-ray scattering, free-electron laser imaging, cryo-electron microscopy, nuclear magnetic resonance, electron paramagnetic resonance, infrared and Raman spectroscopy, circular dichroism, Förster resonance energy transfer, atomic force microscopy and ion-mobility mass spectrometry. The process of deriving structural information from measured data is reviewed with an eye to non-experts and newcomers in the field using examples from the literature of the effect of the various choices and approximations involved in the process. A list of choices to be avoided is provided.

Minimalist IR and fluorescence probes of protein function

Spectroscopic studies of small proteins and peptides, especially those requiring fine spatial and/or temporal resolution, demand synthetic probes that confer the minimal possible steric and functional change on the native properties. Here we review the recent progress in development of minimally disruptive probes for fluorescence and infrared spectroscopies, as well as the methods to efficiently incorporate them into proteins. Advances in spectroscopy on the one hand result in high specialization of synthetic probes for a particular purpose, but on the other hand allow for the same probes be used for different techniques to gather complementary biochemical information.

Two-Dimensional Infrared Study of Vibrational Coupling between Azide and Nitrile Reporters in a RNA Nucleoside

The vibrations in the azide, N3, asymmetric stretching region and nitrile, CN, symmetric stretching region of 2'-azido-5-cyano-2'-deoxyuridine (N3CNdU) are examined by two-dimensional infrared (2D IR) spectroscopy. At earlier waiting times, the 2D IR spectrum shows the presence of both vibrational transitions along the diagonal and off-diagonal cross peaks indicating vibrational coupling. The coupling strength is determined from the off-diagonal anharmonicity to be 66 cm(-1) for the intramolecular distance of ∼7.9 Å, based on a structural map generated for this model system. In addition, the frequency-frequency correlation decay is detected, monitoring the solvent dynamics around each individual probe position. Overall, these vibrational reporters can be utilized in tandem to simultaneously track global structural information and fast structural fluctuations.