Cosolvent Effects on Solute–Solvent Hydrogen-Bond Dynamics: Ultrafast 2D IR Investigations

Perturbation of Fermi Resonance on Hydrogen-Bonded > C═O: 2D IR Studies of Small Ester Probes

We utilized linear and 2D infrared spectroscopy to analyze the carbonyl stretching modes of small esters in different solvents. Particularly noteworthy were the distinct carbonyl spectral line shapes in aqueous solutions, prompting our investigation of the underlying factors responsible for these differences. Through our experimental and theoretical calculations, we identified the presence of the hydrogen-bond-induced Fermi resonance as the primary contributor to the varied line shapes of small esters in aqueous solutions. Furthermore, our findings revealed that the skeletal deformation mode plays a crucial role in the Fermi resonance for all small esters. Specifically, the first overtone band of the skeletal deformation mode intensifies when hydrogen bonds form with the carbonyl group of esters, whereas such coupling is rare in aprotic organic solvents. These spectral insights carry significant implications for the utilization of esters as infrared probes in both biological and chemical systems.

Bridging the Gap in Cryopreservation Mechanism: Unraveling the Interplay between Structure, Dynamics, and Thermodynamics in Cryoprotectant Aqueous Solutions

Cryoprotectants play a crucial role in preserving biological material, ensuring their viability during storage and facilitating crucial applications such as the conservation of medical compounds, tissues, and organs for transplantation. However, the precise mechanism by which cryoprotectants modulate the thermodynamic properties of water to impede the formation and growth of ice crystals, thus preventing long-term damage, remains elusive. This is evident in the use of empirically optimized recipes for mixtures that typically contain DMSO, glycerol, and various sugar constituents. Here, we use terahertz calorimetry, Overhauser nuclear polarization, and molecular dynamics simulations to show that DMSO exhibits a robust structuring effect on water around its methyl groups, reaching a maximum at a DMSO mole fraction of XDMSO = 0.33. In contrast, glycerol exerts a smaller water-structuring effect, even at higher concentrations (Scheme 1). These results potentially suggest that the wrapped water around DMSO's methyl group, which can be evicted upon ligand binding, may render DMSO a more surface-active cryoprotectant than glycerol, while glycerol may participate more as a viscogen that acts on the entire sample. These findings shed light on the molecular intricacies of cryoprotectant solvation behavior and have potentially significant implications for optimizing cryopreservation protocols.

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

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

Effects of External Perturbations on Protein Systems: A Microscopic View

Protein folding can be viewed as the origami engineering of biology resulting from the long process of evolution. Even decades after its recognition, research efforts worldwide focus on demystifying molecular factors that underlie protein structure-function relationships; this is particularly relevant in the era of proteopathic disease. A complex co-occurrence of different physicochemical factors such as temperature, pressure, solvent, cosolvent, macromolecular crowding, confinement, and mutations that represent realistic biological environments are known to modulate the folding process and protein stability in unique ways. In the current review, we have contextually summarized the substantial efforts in unveiling individual effects of these perturbative factors, with major attention toward bottom-up approaches. Moreover, we briefly present some of the biotechnological applications of the insights derived from these studies over various applications including pharmaceuticals, biofuels, cryopreservation, and novel materials. Finally, we conclude by summarizing the challenges in studying the combined effects of multifactorial perturbations in protein folding and refer to complementary advances in experiment and computational techniques that lend insights to the emergent challenges.

On-Off Infrared Absorption of the S═O Vibrational Probe of Dimethyl Sulfoxide

Dimethyl sulfoxide (DMSO), a polar solvent molecule, is used in a wide range of therapeutic and pharmacological applications. Different intermolecular interactions, such as dimerization and hydrogen bonding with water, are crucial to understanding the role of DMSO in applications. Herein, we study DMSO in various solvation environments to decipher the environment-dependent dimerization and hydrogen-bonding propensity. We use a combination of infrared spectroscopy, quantum mechanical calculations, and molecular dynamics simulations to reach our conclusions. Although DMSO can exist in a dynamic equilibrium between monomers and dimers, our results show that the relative intensity of the S═O stretch and the CH₃ rocking modes is a spectroscopic indicator of the extent of DMSO dimerization in solution. The dimerization (self-association) is seen to be maximum in neat DMSO. When dissolved in different solvents, the dimerization propensity decreases with increasing solvent polarity. In the presence of a protic solvent, such as water, DMSO forms a hydrogen bond with the solvent molecules, thereby reducing the extent of dimerization. Further, we estimate the hydrogen-bond occupancy of DMSO. Our results show that DMSO predominantly exists as doubly hydrogen-bonded in water.

How cryoprotectants work: hydrogen-bonding in low-temperature vitrified solutions

Dimethyl sulfoxide (DMSO) increases cell and tissue viability at low temperatures and is commonly used as a cryoprotectant for cryogenic storage of biological materials. DMSO disorders the water hydrogen-bond networks and inhibits ice-crystal growth, though the specific DMSO interactions with water are difficult to characterize. In this study, we use a combination of Fourier Transform infrared spectroscopy (FTIR), molecular dynamics simulations, and vibrational frequency maps to characterize the temperature-dependent hydrogen bonding interactions of DMSO with water from 30 °C to −80 °C. Specifically, broad peaks in O–D stretch vibrational spectra of DMSO and deuterated water (HDO) cosolvent systems show that the hydrogen bond networks become increasingly disrupted compared to pure water. Simulations demonstrated that these disrupted hydrogen bond networks remain largely localized to the first hydration shell of DMSO, which explains the high DMSO concentrations needed to prevent ice crystal formation in cryopreservation applications.

Dimethyl sulfoxide (DMSO) increases cell and tissue viability at low temperatures and is commonly used as a cryoprotectant for cryogenic storage of biological materials.

Association-Dissociation Dynamics of Ionic Electrolytes in Low Dielectric Medium

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

Molecular heterogeneity in aqueous cosolvent systems

Aqueous cosolvent systems (ACoSs) are mixtures of small polar molecules such as amides, alcohols, dimethyl sulfoxide, or ions in water. These liquids have been the focus of fundamental studies due to their complex intermolecular interactions as well as their broad applications in chemistry, medicine, and materials science. ACoSs are fully miscible at the macroscopic level but exhibit nanometer-scale spatial heterogeneity. ACoSs have recently received renewed attention within the chemical physics community as model systems to explore the relationship between intermolecular interactions and microscopic liquid-liquid phase separation. In this perspective, we provide an overview of ACoS spatial segregation, dynamic heterogeneity, and multiscale relaxation dynamics. We describe emerging approaches to characterize liquid microstructure, H-bond networks, and dynamics using modern experimental tools combined with molecular dynamics simulations and network-based analysis techniques.

Liquid-Liquid Phase Separation Produces Fast H-Bond Dynamics in DMSO-Water Mixtures

Liquid-liquid phase separation is common in complex mixtures, but the behavior of nanoconfined liquids is poorly understood from a physical perspective. Dimethyl sulfoxide (DMSO) is an amphiphilic molecule with unique concentration-dependent bulk properties in mixtures with water. Here, we use ultrafast two-dimensional infrared (2D IR) spectroscopy to measure the H-bond dynamics of two probe molecules with different polarities: formamide (FA) and dimethylformamide (DMF). Picosecond H-bond dynamics are fastest in the intermediate concentration regime (20-50 mol % DMSO), because such confined water exhibits bulk-like dynamics. Each vibrational probe experiences a unique microscopic environment as a result of nanoscale phase separation. Molecular dynamics simulations show that the dynamics span multiple time scales, from femtoseconds to nanoseconds. Our studies suggest a previously unknown liquid environment, which we label "local bulk", in which despite the local heterogeneity, the ultrafast H-bond dynamics are similar to bulk water.

Arresting an Unusual Amide Tautomer Using Divalent Cations

Ion-specific effects on peptides and proteins are key to biomolecular structure and stability. The subtle roles of the cations are far less understood, compared to the pronounced effects of the anions on proteins. Most importantly, divalent cations such as Ca²⁺ and Mg²⁺ are crucial to several biological functions. Herein, we demonstrate that an amide-iminolate equilibrium is triggered by the binding of the divalent cations to the amide oxygen in aqueous solution. The excellent agreement between the experimental and theoretical results confirms the arrest of an unusual amide tautomer by the divalent cations, which is a rarely known phenomenon that might open up an array of applications in chemistry and biology.

Interfacial H-Bond Dynamics in Reverse Micelles: The Role of Surfactant Heterogeneity

Characterizing the hydrogen bond structure and dynamics at surfactant interfaces is essential for understanding how microscopic interactions translate to bulk microemulsion properties. Heterogeneous blends containing tens or hundreds of surfactants are common in the industry, but the most fundamental studies have been carried out on micelles composed of a single surfactant species. Therefore, the effect of surfactant heterogeneity on the interfacial structure and dynamics remains poorly understood. Here, we use ultrafast two-dimensional infrared spectroscopy and molecular dynamics simulations to characterize sub-picosecond solvation dynamics as a function of the surfactant composition in ∼120 nm water-in-oil reverse micelles. We probe the ester carbonyl vibrations of nonionic sorbitan surfactants, which are located precisely at the interface between the polar and nonpolar regions, and as such, report on the interfacial water dynamics. We show a 7% increase in hydrogen bond populations together with a 37% slowdown of interfacial hydrogen bond dynamics in heterogeneous mixtures containing hundreds of species, compared to more uniform compositions. Simulations, which are in semiquantitative agreement with experiments, indicate that structural diversity leads to decreased packing efficiency, which in turn drives water further into the otherwise hydrophobic region. Interestingly, this increase in hydration is accompanied by a slowdown of dynamics, indicating that water molecules solvating surfactants are conformationally constrained. These studies demonstrate that the composition and heterogeneity are key factors in determining interfacial properties.

Linear and Nonlinear Infrared Spectroscopies Reveal Detailed Solute-Solvent Dynamic Interactions of a Nitrosyl Ruthenium Complex in Solution

In this work, the solvation of a nitrosyl ruthenium complex, [(CH₃)₄N][RuCl₃(qn)(NO)] (with qn = deprotonated 8-hydroxyquinoline), which is a potential NO-releasing molecule in the bio-environment, was studied in two bio-friendly solvents, namely deuterated dimethyl sulfoxide (dDMSO) and water (D₂O). A blue-shifted NO stretching frequency was observed in water with respect to that in dDMSO, which was believed to be due to ligand-solvent hydrogen-bonding interactions, one N═O···D and particularly three Ru-Cl···D, that show competing effects on the NO bond length. The dynamic differences of the NO stretch in these two solvents were further revealed by transient pump-probe IR and two-dimensional IR results: faster vibrational relaxation and faster spectral diffusion (SD) were observed in D₂O, confirming stronger solvent-solute interaction and also faster solvent structural dynamics in D₂O than in DMSO. Further, a significant non-decaying residual in the SD dynamics was observed in D₂O but not in DMSO, suggesting the formation of a stable solvation shell in water due to strong multi-site ligand-solvent hydrogen-bonding interactions, which is in agreement with the observed blue-shifted NO stretching frequency. This work demonstrates that small solvent molecules such as water can form a relatively rigid solvation shell for certain transition metal complexes due to cooperative ligand-solvent interactions and show slower dynamics.

Interconverting Hydrogen-Bonding and Weak n → π* Interactions in Aqueous Solution: A Direct Spectroscopic Evidence

Molecular structure and function depend on myriad noncovalent interactions. However, the weak and transient nature of noncovalent interactions in solution makes them challenging to study. Information on weak interactions is typically derived from theory and indirect structural data. Solvent fluctuations, not revealed by structure analysis, further complicate the study of these interactions. Using 2D infrared spectroscopy, we show that the strong hydrogen bond and the weak n → π* interaction coexist and interconvert in aqueous solution. We found that the kinetics of these interconverting interactions becomes faster with increasing water content. This experimental observation provides a new perspective on the existence of weak noncovalent interactions in aqueous solution.

Micellar and bicontinuous microemulsion structures show different solute–solvent interactions: a case study using ultrafast nonlinear infrared spectroscopy

Using aqueous and organic probes to simultaneously explore the structural dynamics of reverse micellar and bicontinuous microemulsion structures.

Two-Dimensional Infrared Spectroscopy Reveals Cosolvent-Composition-Dependent Crossover in Intermolecular Hydrogen-Bond Dynamics

Cosolvents have versatile composition-dependent applications in chemistry and biology. The simultaneous presence of hydrophobic and hydrophilic groups in dimethyl sulfoxide (DMSO), an industrially important amphiphilic cosolvent, when combined with the unique properties of water, plays key roles in the diverse fields of pharmacology, cryoprotection, and cell biology. Moreover, molecules dissolved in aqueous DMSO exhibit an anomalous concentration-dependent nonmonotonic behavior in stability and activity near a critical DMSO mole fraction of 0.15. An experimental identification of the origin of this anomaly can lead to newer chemical and biological applications. We report a direct spectroscopic observation of the anomalous behavior using ultrafast two-dimensional infrared spectroscopy experiments. Our results demonstrate the cosolvent-concentration-dependent nonmonotonicity arises from nonidentical mechanisms in ultrafast hydrogen-bond-exchange dynamics of water above and below the critical cosolvent concentration. Comparison of experimental and theoretical results provides a molecular-level mechanistic understanding: a distinct difference in the stabilization of the solute through dynamic solute-solvent interactions is the key to the anomalous behavior.

Solvent-Independent Anharmonicity for Carbonyl Oscillators

The physical origins of vibrational frequency shifts have been extensively studied in order to understand noncovalent intermolecular interactions in the condensed phase. In the case of carbonyls, vibrational solvatochromism, MD simulations, and vibrational Stark spectroscopy suggest that the frequency shifts observed in simple solvents arise predominately from the environment's electric field due to the vibrational Stark effect. This is contrary to many previously invoked descriptions of vibrational frequency shifts, such as bond polarization, whereby the bond's force constant and/or partial nuclear charges are altered due to the environment, often illustrated in terms of favored resonance structures. Here we test these hypotheses using vibrational solvatochromism as measured using 2D IR to assess the solvent dependence of the bond anharmonicity. These results indicate that the carbonyl bond's anharmonicity is independent of solvent as tested using hexanes, DMSO, and D₂O and is supported by simulated 2D spectra. In support of the linear vibrational Stark effect, these 2D IR measurements are consistent with the assertion that the Stark tuning rate is unperturbed by the electric field generated by both hydrogen and non-hydrogen bonding environments and further extends the general applicability of carbonyl probes for studying intermolecular interactions.

Vibrational Stark Effects of Carbonyl Probes Applied to Reinterpret IR and Raman Data for Enzyme Inhibitors in Terms of Electric Fields at the Active Site

IR and Raman frequency shifts have been reported for numerous probes of enzyme transition states, leading to diverse interpretations. In the case of the model enzyme ketosteroid isomerase (KSI), we have argued that IR spectral shifts for a carbonyl probe at the active site can provide a connection between the active site electric field and the activation free energy (Fried et al. Science 2014, 346, 1510-1514). Here we generalize this approach to a much broader set of carbonyl probes (e.g., oxoesters, thioesters, and amides), first establishing the sensitivity of each probe to an electric field using vibrational Stark spectroscopy, vibrational solvatochromism, and MD simulations, and then applying these results to reinterpret data already in the literature for enzymes such as 4-chlorobenzoyl-CoA dehalogenase and serine proteases. These results demonstrate that the vibrational Stark effect provides a general framework for estimating the electrostatic contribution to the catalytic rate and may provide a metric for the design or modification of enzymes. Opportunities and limitations of the approach are also described.

Water Collective Dynamics in Whole Photosynthetic Green Algae as Affected by Protein Single Mutation

In the context of the importance of water molecules for protein function/dynamics relationship, the role of water collective dynamics in Chlamydomonas green algae carrying both native and mutated photosynthetic proteins has been investigated by neutron Brillouin scattering spectroscopy. Results show that single point genetic mutation may notably affect collective density fluctuations in hydrating water providing important insight on the transmission of information possibly correlated to biological functionality. In particular, we highlight that the damping factor of the excitations is larger in the native compared to the mutant algae as a signature of a different plasticity and structure of the hydrogen bond network.

2D-IR spectroscopy of hydrogen-bond-mediated vibrational excitation transfer

Inter-molecular vibrational energy transfer in the hydrogen-bonded complexes of methyl acetate and 4-cyanophenol is studied by dual-frequency 2D-IR spectroscopy.