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Nonmonotonic composition dependence is often observed for numerous properties in the aqueous mixtures of small amphiphilic molecules. The molecular picture underlying this structure-activity relationship, however, remains largely elusive. We herein studied water reorientation dynamics in the aqueous mixture of dimethyl sulfoxide (DMSO), which has a significant nonmonotonic composition dependence, using molecular dynamic simulation and an extended molecular jump model. The analysis indicates that this nonideal behavior is driven by the collective frame diffusion component of water reorientation, which decelerates in the water-rich regime because of the strengthened hydrogen bonds and accelerates in the water-poor regime as the hydrogen bonding network is broken into smaller aggregates. The current work therefore connects the microheterogeneity in the solvation structure of DMSO-water with its nonmonotonic hydration dynamics and sheds new light on how microsegregation leads to the multiscale hydration nonideality in general.

We demonstrate that electron-vibration-vibration two-dimensional infrared spectroscopy (EVV 2DIR) can be used to detect the binding of a drug to a target protein-active site. The EVV 2DIR spectrum of the FGFR1 kinase target protein is found to have ∼200 detectable cross-peaks in the spectral region 1250-1750 cm -1 /2600-3400 cm -1 , with additional 63 peaks caused by the addition of a drug, SU5402. Of these 63 new peaks, it is shown that only six are due to protein-drug interactions, with the other 57 being due to vibrational coupling within the drug itself. Quantum mechanical calculations employing density functional theory are used to support assignment of the six binding-dependent peaks, with one being assigned to a known interaction between the drug and a backbone carbonyl group which forms part of the binding site. None of the 57 intramolecular coupling peaks associated with the drug molecule change substantially in either intensity or frequency when the drug binds to the target protein. This strongly suggests that the structure of the drug in the target binding site is essentially identical to that when it is not bound.

Two-dimensional transition-metal dichalcogenide semiconductors (TMDCs) such as MoS 2 are attracting increasing interest as thermoelectric materials owing to their abundance, nontoxicity, and promising performance. Recently, we have successfully developed n-type MoS 2 thermoelectric material via oxygen doping. Nevertheless, an efficient thermoelectric module requires both n-type and p-type materials with similar compatibility factors. Here, we present a facile approach to obtain a p-type MoS 2 thermoelectric material with a maximum figure of merit of 0.18 through the introduction of VMo 2 S 4 as a second phase by vanadium doping. VMo 2 S 4 nanoinclusions, confirmed by X-ray powder diffraction (XRD) and transmission electron microscopy (TEM) measurements, not only improve the electrical conductivity by simultaneously increasing the carrier concentration and the mobility but also result in the reduction of lattice thermal conductivity by enhancing the interface phonon scattering. Our studies not only shed new light toward improving thermoelectric performance of TMDCs by a facile elemental doping strategy but also pave the way toward thermoelectric devices based on TMDCs.

Synthetic additives are widely used in lubricants nowadays to upgrade lubrication properties. The potential of integrating sustainable components in modern lubricants has rarely been studied yet. In this work, two sustainable resources lignin and gelatin have been synergistically incorporated into ethylene glycol (EG), and their tribological properties were systematically investigated. The abundant hydrogen bonding sites in lignin and gelatin as well as their interchain interaction via hydrogen bonding play the dominating roles in tuning the physicochemical properties of the mixture and improving lubricating properties. Moreover, the synergistic combination of lignin and gelatin induces charge separation of gelatin that enables its preferable adsorption on the friction surface through electrostatic force and forms a robust lubrication layer. This layer will be strengthened by lignin through the interpolymer chain hydrogen bonding. At an optimized lignin:gelatin mass ratio of 1:1 and 19 wt % loading of each in EG, the friction coefficient can be greatly stabilized and the wear loss was reduced by 89% compared to pure EG. This work presents a unique synergistic phenomenon between gelatin and lignin, where hydrogen bonding and change separation are revealed as the key factor that bridges the individual components and improves overall lubricating properties.

By applying molecular dynamics (MD) simulations and quantum chemical calculations, we have characterized the states and processes involved in the excited-state proton transfer (ESPT) of LSSmKate1. MD simulations identify two stable structures in the electronic ground state of LSSmKate1, one with a protonated chromophore and the other with a deprotonated chromophore, thus leading to two separate low-energy absorption maxima with a large energy spacing, as observed in the calculated and experimentally measured absorption spectra. Proton transfer is induced by electronic excitation. When LSSmKate1 is excited, the electrons in the chromophore are transferred from the phenol ring to the N-acylimine moiety; the acidity of a phenolic hydroxyl group is thus enhanced. The calculated potential energy curves (PECs) exhibit energetic feasibility in the generation of the fluorescent species in LSSmKate1, and the exact agreement between the calculated and experimentally measured values of the large Stokes shift further provides solid theoretical evidence for the ESPT process taking place in photoexcited LSSmKate1. The molecular environments play a significant role in the geometries and absorption/emission energies of the chromophores. Overall, TD-ωB97X-D/molecular mechanics (MM) provides a better description of the optical properties of LSSmKate1 than TD-B3LYP/MM, although it always overestimates the excitation energies.

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.

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.

The methodology and principle using vibrational energy transfer to measure molecular distances in liquids are introduced. The application of the method to the studies of ion pairing and clustering in strong electrolyte aqueous solutions is demonstrated with MSCN aqueous solutions where M = Li, Na, K, Cs, and NH4. Experiments suggest that ions in the concentrated aqueous solutions can form substantial quantities of ion clusters in which both cations and anions are involved. More and larger clusters form in solutions that are relatively more concentrated and which include a larger cation. In KSCN solutions, the shortest anionic distance in the ion clusters is the same as that in the KSCN crystal. The rotational time of the anion and the nonresonant vibrational energy transfer time with a gap of 75 cm(-1) in the KSCN saturated solution are very similar to those in the KSCN crystal. However, the KSCN ion clusters are closer in structure to the melt. The clusters form an interconnected network with random ionic orientations. Because of ion clustering, the anion and water dynamics behave distinctly in the same solutions. At high concentrations, the anion rotation significantly slows down because of the increase in the size of the ion clusters, but the slowdown amplitude of water rotation is very modest because many of the water molecules still remain in the "bulk" state due to ion clustering. The rotational dynamics of both water and anions are slower in a solution with a smaller cation, primarily because a smaller cation has a stronger cation/anion interaction and a cation/water interaction that leads to more water molecules confined in the ion clusters. Adding ions or molecules into the KSCN solutions can perturb the ion clusters. Weakly hydrated anions can participate in clustering and form mixed ion clusters with KSCN, and strongly hydrated anions can reduce the effective water molecules solvating KSCN and facilitate the formation of more and larger KSCN ion clusters. Similarly, molecules which can strongly bind to SCN(-) prefer to participate in the KSCN ion clusters. Molecules which are strongly hydrated prefer to remain hydrated and facilitate the ion clustering of KSCN.

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.

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.

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.

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.

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.

The infrared optical response of amyloid fibrils Aβ(1-40) is investigated. Simulations of two models corresponding to different protonation states are compared with experiment. The simulations reveal that vibrational frequency distributions inside the fibrils are dominated by side chain fluctuations. We further confirm earlier suggestions based on 2D-IR measurements that water molecules can be trapped inside the fibrils., (© 2012 American Chemical Society)

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.

We have investigated the sensitivity of two-dimensional infrared (2D IR) spectroscopy to peptide helicity with an experimental and theoretical study of Z-[l-(alphaMe)Val](8)-OtBu in CDCl(3). 2D IR experiments were carried out in the amide-I region under the parallel and the double-crossed polarization configurations. In the latter polarization configuration, the 2D spectra taken with the rephasing and nonrephasing pulse sequences exhibit a doublet feature and a single peak, respectively. These cross-peak patterns are highly sensitive to the underlying peptide structure. Spectral calculations were performed on the basis of a vibrational exciton model, with the local mode frequencies and couplings calculated from snapshots of molecular dynamics (MD) simulation trajectories using six different models for the Hamiltonian. Conformationally variant segments of the MD trajectory, while reproducing the main features of the experimental spectra, are characterized by extraneous features, suggesting that the structural ensembles sampled by the simulation are too broad. By imposing periodic restraints on the peptide dihedral angles with the crystal structure as a reference, much better agreement between the measured and the calculated spectra was achieved. The result indicates that the structure of Z-[l-(alphaMe)Val](8)-OtBu in CDCl(3) is a fully developed 3(10)-helix with only a small fraction of alpha-helical or nonhelical conformations in the middle of the peptide. Of the four different combinations of pulse sequences and polarization configurations, the nonrephasing double-crossed polarization 2D IR spectrum exhibits the highest sensitivity in detecting conformational variation. Of the six local mode frequency models tested, the electrostatic maps of Mukamel and Cho perform the best. Our results show that the high sensitivity of 2D IR spectroscopy can provide a useful basis for developing methods to improve the sampling accuracy of force fields and for characterizing the relative merits of the different protocols for the Hamiltonian calculation.

The two-dimensional infrared photon echo spectrum of Antamanide (- (1)Val- (2)Pro- (3)Pro- (4)Ala- (5)Phe- (6)Phe- (7)Pro- (8)Pro- (9)Phe- (10)Pro-) in chloroform is calculated using an explicit solvent molecular dynamics (MD) simulation combined with a density functional theory (DFT) map for the effective vibrational Hamiltonian. Evidence for a strong intramolecular hydrogen bonding network is found. Comparison with experimental absorption allows the identification of the dominant conformation. Multidimensional spectroscopy reveals intramolecular couplings and gives information on its dynamics. A two-color amide-I and amide-A crosspeak is predicted and analyzed in terms of local structure.

The linear IR and two-dimensional (2D) IR spectra of the amide-I modes of the 12-residue beta-hairpin peptide tryptophan zipper-2 (SWTWENGKWTWK) and its two 13C isotopomers were simulated, with local mode frequencies evaluated by two solution-phase peptide amide-I frequency maps proposed recently: an electrostatic potential map and an electrostatic field map. Both maps predict a set of nondegenerate local amide-I mode transition energies for the hairpin. Spectral simulations using both maps predict the main spectral features of the linear IR and 2D IR experimental results of the (13)C-labeled and -unlabeled hairpin. The radial distribution functions obtained using trajectories from classical molecular dynamics simulations demonstrate different water distributions at different sites of the hairpin. Our results suggest that the observed difference of the (13)C-shifted band, including its peak position and frequency distributions for different isotopomers, in both linear IR and 2D IR spectra, is likely to be due to the difference in the local environment of the solvated peptide. Ab initio density functional theory calculations show a residue-independent (13)C shift of the amide-I mode, further supporting the result. The variations of these shifts are attributed to the residue level heterogeneity of the electrostatic environment of the peptide. Our results show that 2D IR of peptide with single (13)C isotopic labeling can be used to probe the electrostatic environment of the peptide local structure.

The phase behaviors of the binary mixture of an anionic surfactant aerosol OT (AOT) and water are investigated on a mesoscopic level using dissipative particle dynamics (DPD) computer simulations. With a simple surfactant model, various aggregation structures of AOT in water including the lamellar, viscous isotropic, and reverse hexagonal phases are obtained, which agree well with the experimental phase diagram. Special attention is given on the unusual lamellar regions. Water diffusivity shows much useful information to understand how the phase behaviors varied with concentration and temperature. It is proposed that the anomalous lamellar phenomena at intermediate AOT concentration (about 40%) are due to the formation of a defective structure, pseudoreversed hexagonal phase, which evidently decreases the water diffusivity. After increasing temperature above 328 K, the pseudoreversed hexagonal structure will be partly transformed to a normal lamellar phase structure and the system lamellar ordering is therefore enhanced.

Two algorithms for simulating the response of peptides to sequences of IR pulses are developed and applied to N-methyl acetamide (NMA) and a 17 residue alpha-helical peptide (YKKKH17) in D(2)O. A fluctuating vibrational-exciton Hamiltonian for the amide I mode is constructed from molecular dynamics trajectories. Coupling with the environment is described using a density functional theory electrostatic map. The cumulant expansion of Gaussian fluctuation incorporates motional narrowing due to fast frequency fluctuations and is adequate for NMA and for isotopically labeled bands in large peptides. Real-space truncation of the scattering matrix of the nonlinear exciton equations significantly reduces the computational cost, making it particularly attractive for slow fluctuations in large globular proteins.

Single-crystalline gold nano- and microplates with triangular or hexagonal shapes are synthesized by reduction of HAuCl(4) in lyotropic liquid crystal (LLC) mainly made of poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) block copolymers and water after adding a small amount of capping agents, cetyltrimethylammonium bromide (CTAB) or tetrabutylammonium bromide (TBAB). During the growth of such plates, capping agents play the crucial role. It is found that there is an optimal value of CTAB or TBAB concentration for producing microplates. The selective adsorption of CTAB or TBAB on certain crystallographic facets may be the key point of the supposed mechanism. Although LLC does not really act as a template, it provides an ordered structure confining CTAB as well as the nascent metal nuclei, which enhances the oriented attachment of nuclei and thus the consequent growth of single-crystal plates.