Dynamics Of Aqueous Solutions Research Articles

TMAO perturbs intermolecular vibrational motions of water revealed by low-frequency modes.

Trimethylamine N-oxide (TMAO) as a representative natural osmolyte has received much attention because of its unique properties, including enhancement of hydrogen bonding networks in liquid water and stabilization of three-dimensional structures of proteins in living organisms. As a hydrogen bond maker and/or a protein stabilizer, its hydrated structures and orientation dynamics in aqueous solutions have been investigated by various spectroscopic methods. Particularly, distinct from other natural osmolytes, it has been found that TMAO molecules form complexes with water molecules even at low concentrations, showing extraordinarily long lifetimes and much larger effective dipole moments. In this study, we demonstrated that collective motions of water molecules are closely correlated to TMAO molecules, as revealed by the changes of the librational modes observed in hyper-Raman (HR) spectra in the low-frequency region (<1000 cm-1) for the first time. Based on HR spectra of the TMAO solutions at submolar concentrations, we observed that the librational bands originating from water apparently upshift (∼15 cm-1) upon the addition of TMAO molecules. Compared to the OH stretching band of water showing a negligible downshift (<5 cm-1), the librational bands of water are more sensitive to reflect changes in the hydrogen bonding networks in the TMAO solutions, suggesting formation of transient TMAO-water complexes plays an essential role toward surrounding water molecules in perturbing their librational motions. We expect to provide a supplementary approach to understand that water molecules in TMAO aqueous solutions are strongly affected by TMAO molecules, different from other osmolytes.

Theoretical models of staurosporine and analogs uncover detailed structural information in biological solution

Staurosporine and its analogs (STA-analogs) are indolocarbazoles (ICZs) compounds able to inhibit kinase proteins in a non-specific way, while present antimicrobial and cytostatic properties. The knowledge of molecular features associated to the complexation, including the ligand shape in solution and thermodynamics of complexation, is substantial to the development of new bioactive ICZs with improved therapeutic properties. In this context, the empirical approach of GROMOS force field is able to accurately reproduce condensed phase physicochemical properties of molecular systems after parameterization. Hence, through parameterization under GROMOS force field and molecular simulations, we assessed STA-analogs dynamics in aqueous solution, as well as its interaction with water to probe conformational and structural features involved in complexation to therapeutic targets. The coexistence of multiple conformers observed in simulations, and confirmed by metadynamics calculations, expanding the conformational space knowledge of these ligands with potential implications in understanding the ligand conformational selection during complexation. Also, changes in availability to H-bonding concerning the different substituents and water can reflect on effects at complexation free energy due to variation at the desolvation energetic costs. Based on these results, we expect the obtained structural data provide systemic framework for rational chemical modification of STA-analogs.

Explicit solvent machine-learned coarse-grained model of sodium polystyrene sulfonate to capture polymer structure and dynamics.

Strongly charged polyelectrolytes (PEs) demonstrate complex solution behavior as a function of chain length, concentrations, and ionic strength. The viscosity behavior is important to understand and is a core quantity for many applications, but aspects remain a challenge. Molecular dynamics simulations using implicit solvent coarse-grained (CG) models successfully reproduce structure, but are often inappropriate for calculating viscosities. To address the need for CG models which reproduce viscoelastic properties of one of the most studied PEs, sodium polystyrene sulfonate (NaPSS), we report our recent efforts in using Bayesian optimization to develop CG models of NaPSS which capture both polymer structure and dynamics in aqueous solutions with explicit solvent. We demonstrate that our explicit solvent CG NaPSS model with the ML-BOP water model [Chan et al. Nat Commun 10, 379 (2019)] quantitatively reproduces NaPSS chain statistics and solution structure. The new explicit solvent CG model is benchmarked against diffusivities from atomistic simulations and experimental specific viscosities for short chains. We also show that our Bayesian-optimized CG model is transferable to larger chain lengths across a range of concentrations. Overall, this work provides a machine-learned model to probe the structural, dynamic, and rheological properties of polyelectrolytes such as NaPSS and aids in the design of novel, strongly charged polymers with tunable structural and viscoelastic properties.

Operation and charge dynamics of organic–inorganic hybrid halide C6H4NH2CuBr2I photoelectrode in aqueous solution

The application of halide perovskites containing organic and inorganic lead is hindered by their toxicity and chemical instability in solution. In this study, an organic–inorganic hybrid halide C6H4NH2CuBr2I photoelectrode was fabricated, and its photoelectrochemical properties and charge dynamics in aqueous solution were analyzed. The C6H4NH2CuBr2I photoelectrode provided stable photocurrent output in aqueous solution. The charge diffuse length was lower than that of Pb-based perovskite star materials by 3–4 orders of magnitude, thereby causing the photocurrent to be considerably lower than that in the CH3NH3PbI3 halide perovskite.

Probing the effect of NEK7 and cofactor interactions on dynamics of NLRP3 monomer using molecular simulation.

The NLRP3 inflammasome is a cytoplasmic complex that regulates the activation of inflammatory cytokines and, given its implication in a range of diseases, is an important therapeutic target. The cofactor ATP and the centrosomal kinase NEK7 are important for NLRP3 activation. Here we have constructed and simulated computational models of full‐length monomeric NLRP3 to shed light on the importance of NEK7 and cofactor interactions for its conformation and dynamics in aqueous solution. We find that molecular dynamics simulation reproduces well the features of the recently published cryo‐EM structure of the ADP‐bound NLRP3–NEK7 complex; on the removal of NEK7, the NLRP3 molecule adopts a more compact closed form during simulations. Replacement of ADP by ATP promotes a rearrangement of hydrogen‐bonding interactions, domain interfaces, and a degree of opening of the NLRP3 conformation. We also examine the dynamics of an acidic loop of the LRR domain of NLRP3, which samples in a region observed in the NEK7‐bound cryo‐EM structure but not in an oligomeric form of inactive NLRP3. During the molecular dynamics simulations of NLRP3, we find some plasticity in its topology that suggests access routes for ATP to the cofactor pocket not immediately evident from the existing NEK7‐bound cryo‐EM structure. These computed dynamical trajectories of NLRP3 provide insight into coordinates of deformation that may be key for cofactor binding and inflammasome activation.

Molecular dynamics simulations of structure and dynamics in aqueous solution of neutral and ionized derivatives of poly(vinyl amine): methyl, n-propyl, and iso-propyl substitutions

Molecular dynamics simulations of structure and dynamics in aqueous solution of neutral and ionized derivatives of poly(vinyl amine): methyl, n-propyl, and iso-propyl substitutions

Concentration dependence of dynamics and hydrogen bonding in aqueous solutions of urea, methyl-substituted ureas, and trimethylamine N-oxide

Organic cosolutes can have profound effects on protein stability, and their behavior in aqueous solutions can provide a molecular understanding of these effects. Urea denatures proteins while methyl-substituted ureas are stronger denaturants and the similar cosolute trimethylamine N-oxide (TMAO) is a protein stabilizer. Here, differences between aqueous solutions of urea, dimethylurea (DMU), tetramethylurea (TMU), and TMAO are explored via molecular dynamics simulations. A consistent force field for urea and the methylureas is first developed that reproduces their experimental structure and dynamics in aqueous solution. Simulations show that the cosolutes generally diffuse more slowly with increasing concentration up to ∼ 4 M and that since the cosolutes are hydrogen bonded to water, bulk water also diffuses slower. However, the diffusion of TMU shows a dramatic increase at higher molar concentrations because due to the very small mole fraction of water in the TMU solutions so that it behaves more like pure liquid TMU. The cosolutes also generally diffuse more slowly with increasing size, although the diffusion of TMAO is even slower than DMU because of greater hydration of its oxygen. The slower diffusion of TMAO leads to larger viscosities, which further increases hydrogen bond lifetimes and leads to even slower diffusion in a feedback loop. Ultimately, this strengthens hydrogen bonds within TMAO solutions relative to urea and methylurea solutions.

Insights into the structural properties of SARS-CoV-2 main protease.

SARS-CoV-2 is the infectious agent responsible for the coronavirus disease since 2019, which is the viral pneumonia pandemic worldwide. The structural knowledge on SARS-CoV-2 is rather limited. These limitations are also applicable to one of the most attractive drug targets of SARS-CoV-2 proteins - namely, main protease Mpro, also known as 3C-like protease (3CLpro). This protein is crucial for the processing of the viral polyproteins and plays crucial roles in interfering viral replication and transcription. In fact, although the crystal structure of this protein with an inhibitor was solved, Mpro conformational dynamics in aqueous solution is usually studied by molecular dynamics simulations without special sampling techniques. We conducted replica exchange molecular dynamics simulations on Mpro in water and report the dynamic structures of Mpro in an aqueous environment including root mean square fluctuations, secondary structure properties, radius of gyration, and end-to-end distances, chemical shift values, intrinsic disorder characteristics of Mpro and its active sites with a set of computational tools. The active sites we found coincide with the currently known sites and include a new interface for interaction with a protein partner.

Solution and Interface Structure and Dynamics in Geochemistry: Gateway to Link Elementary Processes to Mineral Nucleation and Growth

Our understanding of the process of mineral nucleation is starting to evolve from the solely thermodynamical aspects in classical nucleation theory toward a mechanistic study of reactions influenced by solvation structures of ions and their dynamics. A knowledge of how these atomic and molecular interactions respond to changing solution composition and/or the nature of an interface will form a fundamental foundation to understand rate-limiting reactions and processes for nucleation and growth. Here, we review recent advances from multidisciplinary experimental and computational approaches of the structure and dynamics of aqueous solutions and mineral–liquid interfaces that will influence rates of nucleation (and growth behavior) both homogeneously in aqueous solutions and heterogeneously at mineral–liquid interfaces. These processes include structure (and extent) of solute clustering, solvent degrees of freedom, and the presence of noninnocent charge-balancing ions, all of which can drive the selectivity and exert control over nucleation mechanisms. Similar controlling reactions can also occur at interfaces with the added complexities of how solute ions interact with and assemble on surface sites and use different mechanisms from bulk solutes, such as lateral solvent exchanges between distinct surface sites. To gain a predictive understanding of nucleation chemistry, we emphasize several key knowledge gaps that will need to be addressed in this field and highlight the importance of combining computations and experiments.

Double Hydrogen Bonding Dimerization Propensity of Aqueous Hydroxy Acids Investigated Using Vibrational Optical Activity.

Lactic and malic acids are key substances in a number of biochemical processes in living cells and are also utilized in industry. Vibrational spectroscopy represents an efficient and sensitive way to study their structure and interactions. Since water is the natural environment, proper understanding of their molecular dynamics in aqueous solutions is of critical importance. To this end, we employed Raman spectroscopy and Raman optical activity (ROA) to study the conformation of l-lactic and l-malic acids in water (while varying pH, temperature, and concentration), with special emphasis on their double hydrogen bonding dimerization propensity. Raman and ROA experimental data were supported by extensive theoretical calculations of the vibrational properties and by additional experiments (IR absorption, vibrational circular dichroism, and NMR). Conformational behavior of the acids in water was described by molecular dynamics simulations. Reliability of the results was verified by calculating the vibrational properties of populated conformers and by comparing thus obtained spectral features with the experimental data. Calculations estimated the incidence of H-bonded dimers in water to be low in lactic acid and comparable to monomers in malic acid. The "hybrid" approach presented here reveals limitations of relying on the experimental spectra alone to study dimer formation.

Interactions and Dynamics in Aqueous Solutions of pH-Responsive Polymers: A Combined Fluorescence and Dielectric Relaxation Study.

Interaction and dynamics of aqueous solutions of pH-responsive smart polymers are investigated via steady-state, time-resolved fluorescence emission spectroscopy with the help of external local reporter coumarin 153 (C153), while MHz to GHz dielectric relaxation spectroscopic (DRS) measurement reports the intrinsic medium relaxation features. A series of pH-responsive random copolymers (DPL-DP60) comprising of a pH-responsive moiety 2-((leucinyl)oxy)ethyl methacrylate (l-Leu-HEMA) and hydrophobic methyl methacrylate (MMA) are synthesized and characterized. A balance between the pH-responsive (l-Leu-HEMA) and the hydrophobic (MMA) content dictates the phase transition pH, which is found to be ∼5-7 for these aqueous copolymer solutions (1 mg/mL). Dynamic light scattering measurements in aqueous solutions of these polymers reflect a small particle size (∼2-8 nm) at solution pH below their individual phase transition pH, while a large particle size (∼140-340 nm) forms beyond their phase transition pH. No signature of a phase transition pH-driven abrupt change in static and dynamic properties of aqueous polymer solutions has been registered from pH-dependent dielectric relaxation as well as solute (C153)-centric fluorescence measurements. A significant impact of varying the l-Leu-HEMA/MMA segment ratio on steady-state fluorescence emission and rotational anisotropy decay of the fluorophore solute (C153) has been observed. MHz to GHz DRS in aqueous solutions of these pH-responsive polymers reflects bulk water-like dielectric features.

Phase separation dynamics in aqueous solutions of thermoresponsive polymers

Phase transition kinetics of aqueous hydroxypropyl cellulose solution was studied by using turbidimetric monitoring and mathematical modelling techniques. Based on the nonlinear Cahn-Hilliard equation with a mobility depending on the component concentration, the phase separation has been modeled on a simple one-dimensional Flory lattice. For value set of the interfacial energy parameter, data were obtained on the changing of the average values of the cluster sizes, their mass and concentration. The simulation results allow us to distinguish three stages of the spinodal decomposition: early, intermediate and final. It was found that for the intermediate stage, the kinetics of the cluster mass growth is described by a dependence that is characteristic of the usual diffusion mass transfer; the change in the average cluster size can be represented by a scaling function with an exponent close to 1/3, typical of the systems with a conserved scalar order parameter. It is shown that the concentration of clusters at the final stage is determined by the temperature dependence of the interfacial energy.

Polymer Knot in Solution near the θ Point.

We study knot effects on polymer dynamics in aqueous solution by dissipative particle dynamics. A methodology to identify the θ point is developed by combining simulation data and analytical methods. Polymer internal motions are investigated systematically by gradually changing solvent quality from a good to poor case. In a good solvent, the knot length grows with fluctuations (breathing stage) and then moves to chain ends (moving stage) to release. Nearby the θ point from the good solvent side, the breathing effect becomes stronger with a weak moving effect. As a result, it is easy for the knot to release because of strong fluctuations in chain conformation. In a poor solvent, both breathing and moving effects are weak. A knot is confined in the chain and suppresses polymer condensation because of the excluded volume effect. Our results are useful for the interpretation of relevant experiments and industrial applications of polymer knots.

Water dynamics and self-assembly of single-chain nanoparticles in concentrated solutions.

Single-chain polymer nanoparticles (SCNPs) are soft nano-objects consisting of uni-macromolecular chains collapsed to a certain degree by intramolecular crosslinking. The similarities between the behaviour of SCNPs and that of intrinsically disordered proteins suggest that SCNPs in concentrated solutions can be used as models to design artificial micro-environments, which mimic many of the general aspects of cellular environments. In this work, the self-assembly into SCNPs of an amphiphilic random copolymer, composed by oligo(ethylene glycol)methyl ether methacrylate (OEGMA) and 2-acetoacetoxy ethyl methacrylate (AEMA), has been investigated by means of the dielectric relaxation of water. Direct evidence of segregation of the AEMA repeating units is provided by comparison with the dielectric relaxation of water in similar solutions of the linear hydrophilic polymer, P(OEGMA). Furthermore, the results of comparative studies with similar water solutions of an amphiphilic block copolymer forming multi-chain micelles support the single-chain character of the self-assembly of the random copolymer. The overall obtained results highlight the suitability of the dielectric spectroscopy to confirm the self-assembly of the amphiphilic random copolymers into globular like core-shell single-chain nanoparticles at a concentration well above the overlap concentration.

Cloud Point Driven Dynamics in Aqueous Solutions of Thermoresponsive Copolymers: Are They Akin to Criticality Driven Solution Dynamics?

Cloud point driven interaction and relaxation dynamics of aqueous solutions of amphiphilic thermoresponsive copolymers were explored through picosecond resolved and steady state fluorescence measurements employing hydrophilic (coumarin 343, C343) and hydrophobic (coumarin 153, C153) solute probes of comparable sizes. These thermoresponsive random copolymers, with tunable cloud point temperatures (Tcp's) between 298 and 323 K, were rationally designed first and then synthesized via reversible addition-fragmentation chain transfer (RAFT) copolymerization of methyl methacrylate (MMA) and poly(ethylene glycol) monomethyl ether methacrylate (PEGMA). Subsequently, copolymers were characterized by NMR spectroscopy and size exclusion chromatography (SEC). A balance between the hydrophilic (PEGMA) and the hydrophobic (MMA) content dictates the critical aggregation concentration (CAC), with CAC ∼ 2-14 mg/L for these copolymers in aqueous media. No abrupt changes in the steady state spectral features of both C153 and C343 in the aqueous solutions of these polymers near but below the cloud point temperatures were observed. Interestingly, spectral properties of C153 in these solutions show the impact of hydrophobic/hydrophilic interaction balance but not by those of C343. More specifically, C153 reported a blue shift (relative to that in neat water) and heterogeneity in its local environment. This suggested different locations for the hydrophilic (C343) and the hydrophobic (C153) probes. In addition, the excited state fluorescence lifetime (⟨τlife⟩) of C153 increased with the increase of hydrophobic (MMA) content in these copolymers. However, C343 reported no such variations, although fluorescence anisotropy decays for both solutes were significantly slowed down in these aqueous solutions compared to neat water. Anisotropy decays indicated bimodal time-dependent friction for these solutes in aqueous solutions of these copolymers but monomodal in neat water. A linear dependence of the average rotational relaxation rates (⟨krot⟩ = ⟨τrot⟩-1) of the type ⟨krot⟩ ∝ (|T - Tcp|/Tcp)γ with negative values for the exponent γ was observed for both solutes. No slowing down of the solute rotation with temperature approaching the Tcp was detected; rather, rotation became faster upon increasing the solution temperature, suggesting domination of the local friction.

Ultrafast photoelectron spectroscopy of aqueous solutions.

Chemical reaction dynamics in liquids and at interfaces are central themes in the materials, energy, and environmental sciences. Ultrafast photoelectron spectroscopy of liquids enables unprecedented access to the electronic dynamics of transient chemical species, providing deeper insights into nonadiabatic reaction dynamics in aqueous solutions, which are strongly coupled with solvation dynamics.

Model-free description of polymer-coated gold nanoparticle dynamics in aqueous solutions obtained by Bayesian analysis of neutron spin echo data.

We present a neutron spin echo study of the nanosecond dynamics of polyethylene glycol (PEG) functionalized nanosized gold particles dissolved in D_{2}O at two temperatures and two different PEG molecular weights (400D and 2000D). The analysis of the neutron spin echo data was performed by applying a Bayesian approach to the description of time correlation function decays in terms of exponential terms, recently proved to be theoretically rigorous. This approach, which addresses in a direct way the fundamental issue of model choice in any dynamical analysis, provides here a guide to the most statistically supported way to follow the decay of the intermediate scattering functions I(Q,t) by basing on statistical grounds the choice of the number of terms required for the description of the nanosecond dynamics of the studied systems. Then, the presented analysis avoids from the start resorting to a preselected framework and can be considered as model free. By comparing the results of PEG-coated nanoparticles with those obtained in PEG2000 solutions, we were able to disentangle the translational diffusion of the nanoparticles from the internal dynamics of the polymer grafted to them, and to show that the polymer corona relaxation follows a pure exponential decay in agreement with the behavior predicted by coarse grained molecular dynamics simulations and theoretical models. This methodology has one further advantage: in the presence of a complex dynamical scenario, I(Q,t) is often described in terms of the Kohlrausch-Williams-Watts function that can implicitly represent a distribution of relaxation times. By choosing to describe the I(Q,t) as a sum of exponential functions and with the support of the Bayesian approach, we can explicitly determine when a finer-structure analysis of the dynamical complexity of the system exists according to the available data without the risk of overparametrization. The approach presented here is an effective tool that can be used in general to provide an unbiased interpretation of neutron spin echo data or whenever spectroscopy techniques yield time relaxation data curves.

Unraveling RNA dynamical behavior of TPP riboswitches: a comparison between Escherichia coli and Arabidopsis thaliana

Riboswitches are RNA sensors that affect post-transcriptional processes through their ability to bind to small molecules. Thiamine pyrophosphate (TPP) riboswitch class is the most widespread riboswitch occurring in all three domains of life. Even though it controls different genes involved in the synthesis or transport of thiamine and its phosphorylated derivatives in bacteria, archaea, fungi, and plants, the TPP aptamer has a conserved structure. In this study, we aimed at understanding differences in the structural dynamics of TPP riboswitches from Escherichia coli and Arabidopsis thaliana, based on their crystallographic structures (TPPswec and TPPswat, respectively) and dynamics in aqueous solution, both in apo and holo states. A combination of Molecular Dynamics Simulations and Network Analysis empowered to find out slight differences in the dynamical behavior of TPP riboswitches, although relevant for their dynamics in bacteria and plants species. Our results suggest that distinct interactions in the microenvironment surrounding nucleotide U36 of TPPswec (and U35 in TPPswat) are related to different responses to TPP. The network analysis showed that minor structural differences in the aptamer enable enhanced intramolecular communication in the presence of TPP in TPPswec, but not in TPPswat. TPP riboswitches of plants present subtler and slower regulation mechanisms than bacteria do.

Applicability of photofluorescent techniques for research of protein structure dynamics in aqueous solutions

Applicability of photofluorescent techniques for research of protein structure dynamics in aqueous solutions

Hydrophobic pattern of alkylated ureas markedly affects water rotation and hydrogen bond dynamics in aqueous solution.

Alkylated ureas are frequently used amphiphiles to mediate biomolecule water interactions, yet their hydrophobic substitution pattern critically affects their function. These differences can be traced back to their hydration, which is poorly understood. Here, we investigate subtle effects of the hydrophobic pattern of ureas on hydration dynamics using a combination of linear and non-linear infrared spectroscopies on the OD stretching vibration of HDO. Isomeric 1,3-dimethylurea (1,3-DMU), 1,1-dimethylurea (1,1-DMU) and 1-ethylurea (1-EU) exhibit very similar and rather weak modulation of the water hydrogen-bond strength distribution. Yet, only 1,3-DMU and 1,1-DMU enhance the hydrogen-bond heterogeneity and slow-down its fluctuation dynamics. In turn, rotational dynamics of water molecules, which is dominated by hydrogen bond switches, is significantly impeded in the presence of 1,3-DMU and only weakly by 1,1-DMU and 1-EU. These marked differences can be explained by both excluded volume effects in hydration and self-aggregation, which may be the key to their biotechnological function.