In this work, MD simulations with two different force fields, vibrational energy relaxation and resonant energy transfer experiments, and neutron scattering data are used to investigate ion pairing and clustering in a series of GdmSCN aqueous solutions. The MD simulations reproduce the major features of neutron scattering experimental data very well. Although no information about ion pairing or clustering can be obtained from the neutron scattering data, MD calculations clearly demonstrate that substantial amounts of ion pairs and small ion clusters (subnanometers to a few nanometers) do exist in the solutions of concentrations 0.5 M*, 3 M*, and 5 M* (M* denotes mole of GdmSCN per 55.55 mole of water). Vibrational relaxation experiments suggest that significant amounts of ion pairs form in the solutions. Experiments measuring the resonant energy transfers among the thiocyanate anions in the solutions suggest that the ions form clusters and in the clusters the average anion distance is 5.6 Å (5.4 Å) in the 3 M* (5 M*) Gdm–DSCN/D2O solution.

On the basis of molecular dynamics simulation, we model the ester carbonyl stretch FTIR signals of methyl acetate in D2O and DMSO. An ab initio map is constructed at the B3LYP/6-311++G** level to relate the carbonyl stretch frequency to the external electric field. Using this map, fluctuating Hamiltonian of the carbonyl stretch is constructed from the MD simulation trajectory. The IR spectra calculated based on this Hamiltonian are found to be in good agreement with the experiment. For methyl acetate in D2O, hydrogen bonding on alkoxy oxygen causes a blue shift of frequency, while that on carbonyl oxygen causes a red shift. Two peaks observed in FTIR signals originate from the balance of these two effects. Furthermore, in both D2O and DMSO solutions, correlations are found between the instantaneous electric field on C═O and the frequencies. Broader line width of the signal in D2O suggests a more inhomogeneous electric field distribution due to the complicated hydrogen-bonding environment.

Infrared photon dissociation (IRPD) spectra of the NaSO4–(H2O)n clusters with up to five water molecules have been studied using quantum chemical calculations. Our calculation reveals that the splitting of the peaks in the ∼800–1300 cm–1 region of the IRPD spectra, which contains the information on S–O bond stretching of the anion, indicates the deviation of the cation from the C3v axis as well as the asymmetric distribution of the water molecules. The frequency of the H-bonded O–H stretching peak in the ∼2300–3000 cm–1 window, on the other hand, provides information on the position of the newly added water molecule with respect to the cation. The IRPD technique thus provides abundant structural information on the early stage of the microsolvation and has the potential to become a powerful tool complementary to photoelectron spectroscopy.

Using a molecular dynamics simulation technique, we compared several commonly used ion-water models to describe the microscopic structures and dynamics in KSCN aqueous solutions. Results are compared with observations of femtosecond infrared vibrational-energy transfer and anisotropy measurements. The Jorgensen/TIP4P model is found to provide the best reproduction of clustering properties such as percentage of clustered ions, cluster-size distribution, concentration dependence of the water, and ion-rotation time constants.

Molecular dynamics simulations were carried out to investigate the microscopic origin of the deviation from Stokes–Einstein behavior observed in the dynamics of KSCN aqueous solutions. When the solution becomes more concentrated, the rotational mobilities of SCN– and water bifurcate significantly as also observed in the experimental ultrafast infrared measurements. The translational mobilities of different components, on the other hand, have similar concentration dependences. Furthermore, when concentrating the solution, the mobilities increase slightly first and then reduce afterward. Our simulations revealed that these phenomena observed in the dynamics originate from the ion assembling in the solution. The RDF and pair residence time analysis further suggest the ion pairing effect has significant contribution to the ion assembling. Results herein thus provide a microscopic insight on the origin of the ion assembling phenomenon and its connection with various experimentally observable dynamical phenomena in the ionic solutions.

Waiting time dependent rotational anisotropies of SCN– anions and water molecules in alkali thiocyanate (XSCN, X = Li, Na, K, Cs) aqueous solutions at various concentrations were measured with ultrafast infrared spectroscopy. It was found that cations can significantly affect the reorientational motions of both water molecules and SCN– anions. The dynamics are slower in a solution with a smaller cation. The reorientational time constants follow the order of Li+ > Na+ > K+ ≃ Cs+. The changes of rotational time constants of SCN– at various concentrations scale almost linearly with the changes of solution viscosity, but those of water molecules do not. In addition, the concentration-dependent amplitudes of dynamical changes are much more significant in the Li+ and Na+ solutions than those in the K+ and Cs+ solutions. Further investigations on the systems with the ultrafast vibrational energy exchange method and molecular dynamics simulations provide an explanation for the observations: the observed rotational dynamics are the balanced results of ion clustering and cation/anion/water direct interactions. In all the solutions at high concentrations (>5 M), substantial amounts of ions form clusters. The structural inhomogeneity in the solutions leads to distinct rotational dynamics of water and anions. The strong interactions of Li+ and Na+ because of their relatively large charge densities with water molecules and SCN– anions, in addition to the likely geometric confinements because of ion clustering, substantially slow down the rotations of SCN– anions and water molecules inside the ion clusters. The interactions of K+ and Cs+ with water or SCN– are much weaker. The rotations of water molecules inside ion clusters of K+ and Cs+ solutions are not significantly different from those of other water species so that the experimentally observed rotational relaxation dynamics are only slightly affected by the ion concentrations.

The optical Kerr effect (OKE) and dielectric relaxation spectroscopy (DRS) signals of MgCl2 aqueous solutions were modeled based on the same group of molecular dynamics simulation trajectories. Plausible agreement between the simulations and the experiments allows us to analyze the microscopic origin of the different concentration dependences of relaxation times probed by these two techniques. Our simulations suggest that a significant amount of cations and anions associate in the solutions due to the ion pairing effect. These ion assemblies as well as the free cations form suspending clusters together with the water molecules in their cation hydration shells. The dynamics of water molecules in these clusters is significantly hindered, while that of other water molecules remains largely unaffected. The relaxation times measured by OKE and DRS have different concentration dependences because DRS probes only the rotational dynamics of water molecules outside of the cluster while OKE contains the information of dynamics of all of the water molecules in the solutions. Such findings provide us a microscopic picture on how the ion hydration affects the water dynamics in certain ionic solutions in which ion pairing plays an important role.

We simulated the equilibrium isotope-edited FTIR and 2DIR spectra of a β-hairpin peptide trpzip2 at a series of temperatures. The simulation was based on the configuration distributions generated using the GBOBC implicit solvent model and the integrated tempering sampling (ITS) technique. A soaking procedure was adapted to generate the peptide in explicit solvent configurations for the spectroscopy calculations. The nonlinear exciton propagation (NEP) method was then used to calculate the spectra. Agreeing with the experiments, the intensities and ellipticities of the isotope-shifted peaks in our simulated signals have the site-specific temperature dependences, which suggest the inhomogeneous local thermal stabilities along the peptide chain. Our simulation thus proposes a cost-effective means to understand a peptide’s conformational change and related IR spectra across its thermal unfolding transition.

Vibrationally resolved fluorescence spectra of the β-hairpin trpzip2 peptide at two temperatures as well as during a T-jump unfolding process are simulated on the basis of a combination of Markov state models and quantum chemistry schemes. The broad asymmetric spectral line shape feature is reproduced by considering the exciton–phonon couplings. The temperature dependent red shift observed in the experiment has been attributed to the state population changes of specific chromophores. Through further theoretical study, it is found that both the environment's electric field and the chromophores’ geometry distortions are responsible for tryptophan fluorescence shift.

Microscopic structures and dynamics of aqueous salt solutions were investigated with the ultrafast vibrational energy exchange method and anisotropy measurements. In KSCN aqueous solutions of various concentrations, the rotational time constants of SCN– anions are proportional to the viscosities of the solutions. However, the reorientation dynamics of the water molecules are only slightly affected by the solution viscosity. With the addition of strongly hydrated F– anions, the rotations of both SCN– anions and water molecules slow down. With the addition of weakly hydrated I– anions, only the rotation of SCN– anions slows down with that of water molecules unaffected. Vibrational energy exchange measurements show that the separation among SCN– anions decreases with the addition of F– and increases with the addition of I–. The series of experiments clearly demonstrate that both structures and dynamics of ion and water are segregated in the strong electrolyte aqueous solutions.

We proposed a computational protocol of simulating the T-jump peptide unfolding experiments and the related transient IR and two-dimensional IR (2DIR) spectra based on the Markov state model (MSM) and nonlinear exciton propagation (NEP) methods. MSMs partition the conformation space into a set of nonoverlapping metastable states, and we can calculate spectra signal for each of these states using the NEP method. Thus the overall spectroscopic observable for a given system is simply the sum of spectra of different metastable states weighted by their populations. We show that results from MSMs constructed from a large number of simulations have a much better agreement with the equilibrium experimental 2DIR spectra compared to that generated from straightforward MD simulations starting from the folded state. This indicates that a sufficient sampling of important relevant conformational states is critical for calculating the accurate spectroscopic observables. MSMs are also capable of simulating the unfolding relaxation dynamics upon the temperature jump. The agreement of the simulation using MSMs and NEP with the experiment not only provides a justification for our protocol, but also provides the physical insight of the underlying spectroscopic observables. The protocol we developed has the potential to be extended to simulate a wide range of fast triggering plus optical detection experiments for biomolecules.

Elucidating the structural features of the Aβ monomer, the peptide constituent of amyloid fibrils found in Alzheimer’s disease, can enable a direct characterization of aggregation pathways. Recent studies support the view that the ensemble of Aβ42 monomers is a mixture of diverse ordered and disordered conformational species, which can be classified according to the formation of a characteristic β-hairpin conformation in a certain region. Despite the disparity in the structural features of these species, commonly used spectroscopic techniques such as NMR may not directly trace the conformational dynamics in the ensemble due to the limited time resolution and the lack of well-resolved spectral features for different comformers. Here we use molecular dynamics simulations combined with simulations of two-dimensional IR (2DIR) spectra to investigate the structure of these species, their interchange kinetics, and their spectral features. We show that while the discrimination efficiency of the ordinary, nonchiral 2DIR signal is limited due to its intrinsic dependence on common order parameters that are dominated by the generally unstructured part of the sequence, signals with carefully designed chirality-sensitive pulse configurations have the high resolution required for differentiating the various monomer structures. Our combined simulation studies indicate the power of the chirality-induced (CI) 2DIR technique in investigating early events in Aβ42 aggregation and open the possibility for their use as a novel experimental tool.