Unified Electrostatic Understanding on the Solvation-Induced Changes in the CN Stretching Frequency and the NMR Chemical Shifts of a Nitrile

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

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

Asymmetry of the Electrostatic Environment as the Origin of the Symmetry Breaking Effect of the Nitrate Ion in Aqueous Solution

Elucidating the mechanism of how vibrational modes are affected by intermolecular interactions is important for a better understanding of the nature of the former as probes of the latter. Here, such an analysis is carried out for the N-O stretching modes of the nitrate ion interacting with water, with an emphasis on the symmetry breaking effect. On the basis of theoretical calculations on the structural, vibrational, and electrostatic properties of molecular clusters and spectral simulations for an aqueous solution, a transparent view is demonstrated on the mechanism that modulations of spatially local electrostatic environment give rise to structural and spectroscopic symmetry breaking effect. The electrostatic interaction model constructed here is a seven-parameter model; the use of a single electrostatic parameter, such as the electric field on a single atomic site, is found to be insufficient for quantitative evaluation. It is also shown that the frequency modulations of the N-O stretching modes in aqueous solution occur on a time scale much shorter than 0.1 ps.

Theoretical Understanding of the Nonlinear Raman Shift of C≡N Stretching Vibration of p-Aminobenzonitrile in Supercritical Water

Subcritical and supercritical fluids (SCF) have attracted significant attention in the past few decades because of their unique properties. In a previous study, a nonlinear Raman shift of the C≡N stretching vibration of p-aminobenzonitrile (p-ABN) with respect to the supercritical water (SCW) density was observed [K. Osawa et al., J. Phys. Chem. A 2009, 113, 3143-3154]. Although a plausible mechanism of the nonlinear Raman shift was proposed in the study, the discussion at the atomistic level was inadequate. To elucidate the nonlinear Raman shift mechanism of the C≡N stretching vibration of p-ABN in SCW from a theoretical viewpoint, we employed RISM-SCF-cSED, which is the hybrid method between quantum mechanics and statistical mechanics. We discovered that the hydrogen-bonding effect is dominant at low- and middle-density regions, while the packing effect is dominant at the high-density region. The balances of these effects determine the Raman shift of p-ABN in SCF.

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

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

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

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

Hidden Halogen-Bonding Ability of Fluorine Manifesting in the Hydrogen-Bond Configurations of Hydrogen Fluoride

Elucidating how the intermolecular interactions of a covalently bonded fluorine atom are similar to and different from those of the other halogen atoms will be helpful for a better unified understanding of them. In the present study, the case of hydrogen fluoride is theoretically studied from this viewpoint by using the techniques of electron density analysis, molecular dynamics of liquid, and others. It is shown that the extra-point model, which locates an additional charge site on the line extended from (not within) the covalent bond and has been adopted for halogen-bonding systems as a key to the generation of proper stability and directionality, works well also in this case. A significantly bent hydrogen-bond configuration, which is characteristic of the intermolecular interactions of hydrogen fluoride, is reasonably well reproduced, meaning that it is a manifestation of the latent halogen-bonding ability, which is hidden by the strongly electronegative nature.

Dissecting the electric quadrupolar and polarization effects operating in halogen bonding through electron density analysis with a focus on bromine

The form of the electron density change (or difference) is usable as a kind of fingerprint of the electronic structural origin or mechanism that gives rise to intermolecular interactions. Here, this method is applied to halogen-bonding brominated systems to dissect the electric quadrupolar effect (arising from the anisotropic distribution of the valence electrons and intrinsic to the s²p_x ²p_y ²p_z electronic configuration) and the polarization effect (induced by a partial negative charge of the halogen-bond accepting atom). It is shown that a suitable location of the "extra point" for placing a partial positive charge to represent the former is crucial and is clearly found from the electron density difference from the spherically isotropic Br^- ion, while the latter consists of the dipolar polarization of the Br atom and the delocalized polarization of the whole molecule. A practical way for application to molecular dynamics simulations, etc., to represent these two factors is discussed.

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.

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.

Correlation of the partial charge-transfer and covalent nature of halogen bonding with the THz and IR spectral changes

Changes in the spectral intensities in the THz region are good probes for the non-electrostatic aspect of halogen bonding.

Strategy for Modeling the Electrostatic Responses of the Spectroscopic Properties of Proteins

For better understanding and more efficient use of the spectroscopic probes (vibrational and NMR) of the local electrostatic situations inside proteins, appropriate modeling of the properties of those probes is essential. The present study is devoted to examining the strategy for constructing such models. A more well-founded derivation than the ones in previous studies is given in constructing the models. Theoretical analyses are conducted on two representative example cases related to proteins, i.e., the peptide group of the main chains and the CO and NO ligands to the Fe²⁺ ion of heme, with careful treatment of the behavior of electrons in the electrostatic responses and with verification of consistency with observable quantities. It is shown that, for the stretching frequencies and NMR chemical shifts, it is possible to construct reasonable electrostatic interaction models that encompass the situations of hydration and uniform electric field environment and thus are applicable also to the cases of nonuniform electrostatic situations, which are highly expected for inside of proteins.