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The acid-base behavior of amino acids plays critical roles in several biochemical processes. Depending on the interactions with the protein environment, the pKa values of these amino acids shift from their respective solution values. As the side chains interact with the polypeptide backbone, a pH-induced change in the protonation state of aspartic and glutamic acids might significantly influence the structure and stability of a protein. In this work, we have combined two-dimensional infrared spectroscopy and molecular dynamics simulations to elucidate the pH-induced structural changes in an antimicrobial enzyme, lysozyme, over a wide range of pH. Simultaneous measurements of the carbonyl signals arising from the backbone and the acidic side chains provide detailed information about the pH dependence of the local and global structural features. An excellent agreement between the experimental and the computational results allowed us to obtain a residue-specific molecular understanding. Although lysozyme retains the helical structure for the entire pH range, one distinct loop region (residues 65-75) undergoes local structural deformation at low pH. Interestingly, combining our experiments and simulations, we have identified the aspartic acid residues in lysozyme, which are influenced the most/least by pH modulation.
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Muramidase , Proteínas , Concentração de Íons de Hidrogênio , Proteínas/química , Aminoácidos , Ácido Aspártico/químicaRESUMO
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.
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The mechanism of cold denaturation in proteins is often incompletely understood due to limitations in accessing the denatured states at extremely low temperatures. Using atomistic molecular dynamics simulations, we have compared early (nanosecond timescale) structural and solvation properties of yeast frataxin (Yfh1) at its temperature of maximum stability, 292 K (Ts), and the experimentally observed temperature of complete unfolding, 268 K (Tc). Within the simulated timescales, discernible "global" level structural loss at Tc is correlated with a distinct increase in surface hydration. However, the hydration and the unfolding events do not occur uniformly over the entire protein surface, but are sensitive to local structural propensity and hydrophobicity. Calculated infrared absorption spectra in the amide-I region of the whole protein show a distinct red shift at Tc in comparison to Ts. Domain specific calculations of IR spectra indicate that the red shift primarily arises from the beta strands. This is commensurate with a marked increase in solvent accessible surface area per residue for the beta-sheets at Tc. Detailed analyses of structure and dynamics of hydration water around the hydrophobic residues of the beta-sheets show a more bulk water like behavior at Tc due to preferential disruption of the hydrophobic effects around these domains. Our results indicate that in this protein, the surface exposed beta-sheet domains are more susceptible to cold denaturing conditions, in qualitative agreement with solution NMR experimental results.
Assuntos
Temperatura Baixa , Proteínas de Ligação ao Ferro/química , Modelos Moleculares , Leveduras , Simulação de Dinâmica Molecular , Desnaturação Proteica , FrataxinaRESUMO
Diols, characterized by the presence of two hydroxyl groups, form extended hydrogen-bonded networks. Increasing hydrocarbon chain length is known to elevate the viscosity of diols. Given the established influence of viscosity on solvent dynamics, it becomes imperative to comprehend the impact of viscosity on the fluctuation dynamics within diols and establish connections with hydrogen bond formation and breaking dynamics. In this study, we employ two-dimensional infrared spectroscopy to investigate the viscosity dependence of the structural evolution dynamics in three diols with varying chain lengths. Complementing our experimental approach, molecular dynamics simulations are conducted to extract hydrogen bond lifetimes. Our findings reveal a linear correlation between bulk viscosity, solvent fluctuation timescales, and hydrogen bond lifetimes. Notably, the selected diols exhibit the capability to form deep eutectic solvents upon mixing with choline chloride at specific molar ratios. In contrast to molecular solvents like diols, deep eutectic solvents are characterized by the formation of heterogeneous nanodomains, comprising various intercomponent hydrogen-bonded networks. Interestingly, our observations indicate that while the fluctuation dynamics decelerate with increasing bulk viscosity in diol-based deep eutectic solvents, the relationship between viscosity and dynamics is not linear, in contrast to the observed linearity in diols. This nuanced understanding contributes to the broader comprehension of the interplay between viscosity and dynamics in both molecular and deep eutectic solvents.
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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.
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Surface chemistry dictates the optoelectronic properties of semiconductor quantum dots (QDs). Tailoring these properties relies on the meticulous selection of surface ligands for efficient passivation. While long-chain organic ligands boast a well-understood passivation mechanism, the intricacies of short inorganic ionic ligands remain largely unexplored. This study sheds light on the surface-passivation mechanism of short inorganic ligands, particularly focusing on SCN- ions on CdSe QDs. Employing steady-state and time-resolved infrared spectroscopic techniques, we elucidated the surface-ligand interactions and coordination modes of SCN--capped CdSe QDs. Comparative analysis with studies on CdS QDs unveils intriguing insights into the coordination behavior and passivation efficacy of SCN- ions on Cd2+ rich QD surfaces. Our results reveal the requirement of both surface-bound (strong binding) and weakly-interacting interfacial SCN- ions for effective CdSe QD passivation. Beyond fostering a deeper understanding of surface-ligand interactions and highlighting the importance of a comprehensive exploration of ligand chemistries, this study holds implications for optimizing QD performance across diverse applications.
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Vibrational probes can provide a direct readout of the local electrostatic field in complex molecular environments, such as protein binding sites and enzyme active sites. This information provides an experimental method to explore the underlying physical causes of important biomolecular processes such as binding and catalysis. However, specific chemical interactions such as hydrogen bonds can have complicated effects on vibrational probes and confound simple electrostatic interpretations of their frequency shifts. We employ vibrational Stark spectroscopy along with infrared spectroscopy of carbonyl probes in different solvent environments and in ribonuclease S to understand the sensitivity of carbonyl frequencies to electrostatic fields, including those due to hydrogen bonds. Additionally, we carried out molecular dynamics simulations to calculate ensemble-averaged electric fields in solvents and in ribonuclease S and found excellent correlation between calculated fields and vibrational frequencies. These data enabled the construction of a robust field-frequency calibration curve for the CâO vibration. The present results suggest that carbonyl probes are capable of quantitatively assessing the electrostatics of hydrogen bonding, making them promising for future study of protein function.
Assuntos
Acetofenonas/química , Sondas Moleculares/química , Eletricidade Estática , Vibração , Ligação de Hidrogênio , Simulação de Dinâmica Molecular , Conformação Proteica , Ribonucleases/química , Ribonucleases/metabolismo , Solventes/químicaRESUMO
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.
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Electrostatic interactions provide a primary connection between a protein's three-dimensional structure and its function. Infrared probes are useful because vibrational frequencies of certain chemical groups, such as nitriles, are linearly sensitive to local electrostatic field and can serve as a molecular electric field meter. IR spectroscopy has been used to study electrostatic changes or fluctuations in proteins, but measured peak frequencies have not been previously mapped to total electric fields, because of the absence of a field-frequency calibration and the complication of local chemical effects such as H-bonds. We report a solvatochromic model that provides a means to assess the H-bonding status of aromatic nitrile vibrational probes and calibrates their vibrational frequencies to electrostatic field. The analysis involves correlations between the nitrile's IR frequency and its (13)C chemical shift, whose observation is facilitated by a robust method for introducing isotopes into aromatic nitriles. The method is tested on the model protein ribonuclease S (RNase S) containing a labeled p-CN-Phe near the active site. Comparison of the measurements in RNase S against solvatochromic data gives an estimate of the average total electrostatic field at this location. The value determined agrees quantitatively with molecular dynamics simulations, suggesting broader potential for the use of IR probes in the study of protein electrostatics.
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Simulação de Dinâmica Molecular , Nitrilas/química , Ribonucleases , Eletricidade Estática , Calibragem , Raios Infravermelhos , Espectroscopia de Ressonância Magnética , Modelos Moleculares , Ribonucleases/química , VibraçãoRESUMO
Deep eutectic solvents, consisting of heterogeneous nanodomains of hydrogen-bonded networks, have evolved into a range of viscous fluids that find applications in several fields. As viscosity is known to influence the dynamics of other neoteric solvents like ionic liquids, understanding the effect of viscosity on deep eutectic solvents is crucial to realize their full potential. Herein, we combine polarization-selective pump-probe spectroscopy, two-dimensional infrared spectroscopy, and molecular dynamics simulations to elucidate the impact of viscosity on the dynamics of an alcohol-based deep eutectic solvent, ethaline. We compare the solvent fluctuation and solute reorientation time scales in ethaline with those in ethylene glycol, an ethaline constituent. Interestingly, we find that the solute's reorientation apparently scales the bulk viscosity of the solvent, but the same is not valid for the overall solvation dynamics. Using the variations in the estimated intercomponent hydrogen bond lifetimes, we show that a dissolved solute does not sense the bulk viscosity of the deep eutectic solvent; instead, it senses domain-specific local viscosity determined by the making and breaking of the hydrogen bond network. Our results indicate that understanding the domain-specific local environment experienced by the dissolved solute is of utmost importance in deep eutectic solvents.
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The nanocrystal surface, which acts as an interface between the semiconductor lattice and the capping ligands, plays a significant role in the attractive photophysical properties of semiconductor nanocrystals for use in a wide range of applications. Replacing the long-chain organic ligands with short inorganic variants improves the conductivity and carrier mobility of nanocrystal-based devices. However, our current understanding of the interactions between the inorganic ligands and the nanocrystals is obscure due to the lack of experiments to directly probe the inorganic ligands. Herein, using two-dimensional infrared spectroscopy, we show that the variations in the inorganic ligand dynamics within the heterogeneous nanocrystal ensemble can identify the diversities in the inorganic ligand-nanocrystal interactions. The ligand dynamics time scale in SCN- capped CdS nanocrystals identifies three distinct ligand populations and provides molecular insight into the nanocrystal surface. Our results demonstrate that the SCN- ligands engage in a dynamic equilibrium and stabilize the nanocrystals by neutralizing the surface charges through both direct binding and electrostatic interaction.
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Compostos de Cádmio , Nanopartículas , Compostos de Cádmio/química , Ligantes , Nanopartículas/química , Sulfetos , TiocianatosRESUMO
This study investigates four machine-learning (ML) models to predict the redox potentials of phenazine derivatives in dimethoxyethane using density functional theory (DFT). A small data set of 151 phenazine derivatives having only one type of functional group per molecule (20 unique groups) was used for the training. Prediction accuracy was improved by a combined strategy of feature selection and hyperparameter optimization, using the external validation set. Models were evaluated on the external test set containing new functional groups and diverse molecular structures. High prediction accuracies of R 2 > 0.74 were obtained on the external test set. Despite being trained on the molecules with a single type of functional group, models were able to predict the redox potentials of derivatives containing multiple and different types of functional groups with good accuracies (R 2 > 0.7). This type of performance for predicting redox potential from such a small and simple data set of phenazine derivatives has never been reported before. Redox flow batteries (RFBs) are emerging as promising candidates for energy storage systems. However, new green and efficient materials are required for their widespread usage. We believe that the hybrid DFT-ML approach demonstrated in this report would help in accelerating the virtual screening of phenazine derivatives, thus saving computational and experimental costs. Using this approach, we have identified promising phenazine derivatives for green energy storage systems such as RFBs.
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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.
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Nitrilas , Triptofano , Ligação de Hidrogênio , Triptofano/química , Eletricidade Estática , Espectrofotometria Infravermelho , Nitrilas/química , Espectrometria de FluorescênciaRESUMO
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 SâO 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.
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Dimetil Sulfóxido , Água , Dimetil Sulfóxido/química , Hidrogênio , Ligação de Hidrogênio , Solventes/química , Água/químicaRESUMO
Barbituric acid is believed to be a proto-RNA nucleobase that was used for biological information transfer on prebiotic earth before DNA and RNA in their present forms evolved. Nucleobases have various tautomeric forms and the relative stability of these forms is critical to their biological function. It has been shown that barbituric acid has a tri-keto form in the gas phase and an enol form in the solid state. However, its dominant tautomeric form in aqueous medium that is most relevant for biology has been investigated only to a limited extent and the findings are inconclusive. We have used multiple approaches, namely, molecular dynamics, quantum chemistry, NMR, and IR spectroscopy to determine the most stable tautomer of barbituric acid in solution. We find a delicate balance in the stability of the two tautomers, tri-keto and enol, which is tipped toward the enol as the extent of solvation by water increases.
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Prebióticos , Água , DNA/química , Simulação de Dinâmica Molecular , RNA , Água/químicaRESUMO
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.
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Disruption of the deep eutectic solvent (DES) nanostructure around the dissolved solute upon addition of water is investigated by polarization-selective two-dimensional infrared spectroscopy and molecular dynamics simulations. The heterogeneous DES nanostructure around the solute is partially retained up to 41 wt % of added water, although water molecules are gradually incorporated in the solute's solvation shell even at lower hydration levels. Beyond 41 wt %, the solute is observed to be preferentially solvated by water. This composition denotes the upper hydration limit of the deep eutectic solvent above which the solute senses an aqueous solvation environment. Interestingly, our results indicate that the transition from a deep eutectic solvation environment to an aqueous one around the dissolved solute can happen at a hydration level lower than that reported for the "water in DES" to "DES in water" transition.
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Warfarin is a potent anti-coagulant drug and is on the World Health Organization's List of Essential Medicines. Additionally, it displays fluorescence enhancement upon binding to human serum albumin, making warfarin a prototype fluorescent probe in biology. Despite its biological significance, the current structural assignment of warfarin in aqueous solution is based on indirect evidence in organic solvents. Warfarin is known to exist in different isomeric forms-open-chain, hemiketal, and anionic forms-based on the solvent and pH. Moreover, warfarin displays a dual absorption feature in several solvents, which has been employed to study the ring-chain isomerism between its open-chain and hemiketal isomers. In this study, our pH-dependent experiments on warfarin and structurally constrained warfarin derivatives in aqueous solution demonstrate that the structural assignment of warfarin solely on the basis of its absorption spectrum is erroneous. Using a combination of steady-state and time-resolved spectroscopic experiments, along with quantum chemical calculations, we assign the observed dual absorption to two distinct π â π* transitions in the 4-hydroxycoumarin moiety of warfarin. Furthermore, we unambiguously identify the isomeric form of warfarin that binds to human serum albumin in aqueous buffer.
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Varfarina , Água , Humanos , Isomerismo , Solventes , Espectrometria de Fluorescência , Análise EspectralRESUMO
1,2-Dibenzoyl-1-tert-butylhydrazine (RH-5849) and related N-alkyl-N,N'-diacylhydrazines are environmentally benign insect growth regulators. Herein, we show that an unusual nN(amide) â π*Ar interaction mediated by a hydrazide amide nitrogen atom plays a crucial role in stabilizing their biologically active trans-cis (t-c) rotameric conformations. We provide NMR and IR spectroscopic evidence for the presence of these interactions, which is also supported by X-ray crystallographic and computational studies.
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An unusual Namide···H-Namide hydrogen bond (HB) was previously proposed to stabilize the azapeptide ß-turns. Herein we provide experimental evidence for the Namide···H-Namide HB and show that this HB endows a stabilization of 1-3 kcal·mol-1 and enforces the trans-cis-trans (t-c-t) and cis-cis-trans (c-c-t) amide bond conformations in azapeptides and N-methyl-azapeptides, respectively. Our results indicate that these Namide···H-Namide HBs can have stabilizing contributions even in short azapeptides that cannot fold to form ß-turns.