Femtosecond Study of Partially Folded States of Cytochrome C by Solvation Dynamics

Dodecahedron CsPbBr3 Perovskite Nanocrystals Enable Facile Harvesting of Hot Electrons and Holes

This Letter reports the facile harvesting of hot carriers (HCs) in a composite of 12-faceted dodecahedron CsPbBr₃ nanocrystal (NC) and a scavenger molecule. We recorded ∼3.3 × 10¹¹ s^-1 HC cooling rate in NC when excited with ∼1.4 times the band gap energy (E_g), increasing to >3 × 10¹² s^-1 in the presence of scavengers at high concentration due to the HC extractions. Since the observed intrinsic charge transfer rate (∼1.7 × 10¹² s^-1) in our NC-scavenger complex is about an order of magnitude higher than the HC cooling rate (∼3.3 × 10¹¹ s^-1), carriers are harvested before their cooling. Further, a fluorescence correlation spectroscopy study reveals NC tends to form a quasi-stable complex with a scavenger molecule, ensuring charge transfer completed (τ_ct ≈ 0.6 ps) much before the complex breaks apart (>600 μs). The overall results of our study highlight the promise shown by 12-faceted NCs and their implications in modern applications, including hot carrier solar cells.

Facet Engineering for Decelerated Carrier Cooling in Polyhedral Perovskite Nanocrystals

We report here the hot carrier (HC) cooling time scales within polyhedral CsPbBr₃ nanocrystals (NCs) characterized by different numbers of facets (6 to 26) utilizing a femtosecond upconversion setup. Interestingly, the observed cooling time scale slows many-fold (>10 times) upon opening the new facets on the NC surface. Furthermore, a temperature-dependent study reveals that cooling in multifaceted NCs is polaron mediated, where newly opened polar facets and the soft lattice of CsPbBr₃ NCs play pivotal roles. Our hallmark result of slow cooling in polyhedral NCs renders an excellent opportunity for harvesting high-energy carriers by a carefully chosen molecular system. To this end, employing the hole scavenger molecule aniline, we successfully extracted hot holes from optically pumped NCs. We believe that several intriguing properties of the polyhedral NCs, including rapid polaron formation, defect-tolerant nature, and the capability of soft lattice to support slow diffusion of charge carriers, resulted in decelerated cooling.

Subpicosecond Hot Hole Transfer in a Graphene Quantum Dot Composite with High Efficiency

Extraction of hot carriers is of prime importance because of its potential to overcome the energy loss that limits the efficiency of an optoelectronic device. Employing a femtosecond upconversion setup, herein we report a few picoseconds carrier cooling time of colloidal graphene quantum dots (GQDs) is at least an order of magnitude slower compared to that in its bulk form. A slower carrier cooling time of GQDs compared to that of the other semiconductor quantum dots and their bulk materials is indeed a coveted property of GQDs that would allow one easy harvesting of high energy species employing a suitable molecular system as shown in this study. A subpicosecond hot hole transfer time scale has been achieved in a GQD-molecular system composite with high transfer efficiency. Our finding suggests a dramatic enhancement of the efficiency of GQD based optoelectronic devices can possibly be a reality.

Microscopic dynamics of water around unfolded structures of barstar at room temperature

The breaking of the native structure of a protein and its influences on the dynamic response of the surrounding solvent is an important issue in protein folding. In this work, we have carried out atomistic molecular dynamics simulations to unfold the protein barstar at two different temperatures (400 K and 450 K). The two unfolded forms obtained at such high temperatures are further studied at room temperature to explore the effects of nonuniform unfolding of the protein secondary structures along two different pathways on the microscopic dynamical properties of the surface water molecules. It is demonstrated that though the structural transition of the protein in general results in less restricted water motions around its segments, but there are evidences of formation of new conformational motifs upon unfolding with increasingly confined environment around them, thereby resulting in further restricted water mobility in their hydration layers. Moreover, it is noticed that the effects of nonuniform unfolding of the protein segments on the relaxation times of the protein-water (PW) and the water-water (WW) hydrogen bonds are correlated with hindered hydration water motions. However, the kinetics of breaking and reformation of such hydrogen bonds are found to be influenced differently at the interface. It is observed that while the effects of unfolding on the PW hydrogen bond kinetics seem to be minimum, but the kinetics involving the WW hydrogen bonds around the protein segments exhibit noticeably heterogeneous characteristics. We believe that this is an important observation, which can provide valuable insights on the origin of heterogeneous influence of unfolding of a protein on the microscopic properties of its hydration water.

Conversion of amyloid fibrils of cytochrome c to mature nanorods through a honeycomb morphology

Amyloid species with various morphologies have been found for different proteins and disease systems. In this article, we aim to ask if these morphologies are unique to a particular protein or if they convert from one to another. Using a heme protein containing iron as the transition-metal activator of aggregation and a negatively charged surfactant, partial unfolding of the protein and its aggregation have been induced. In the pathway of aggregation, we have observed the formation of several morphological structures of a single protein, which were visualized directly using atomic force microscopy (AFM). These structures have been found to appear and disappear with time, and their formation could be monitored under normal buffer conditions and at room temperature without requiring any sophisticated chemical or biological methodologies. In addition, we have observed the formation of honeycomb-shaped morphology, which may serve as an intermediate. These amyloid-based nanostructures may have the potential to be explored in therapeutics delivery and other biomedical applications.

Modulation of ultrafast photoinduced electron transfer in H-bonding environment: PET from aniline to coumarin 153 in the presence of an inert co-solvent cyclohexane

A passive component is found to boost H-bond assisted PET in a mixture using femtosecond fluorescence measurements and MD simulation.

Probing protein multidimensional conformational fluctuations by single-molecule multiparameter photon stamping spectroscopy

Conformational motions of proteins are highly dynamic and intrinsically complex. To capture the temporal and spatial complexity of conformational motions and further to understand their roles in protein functions, an attempt is made to probe multidimensional conformational dynamics of proteins besides the typical one-dimensional FRET coordinate or the projected conformational motions on the one-dimensional FRET coordinate. T4 lysozyme hinge-bending motions between two domains along α-helix have been probed by single-molecule FRET. Nevertheless, the domain motions of T4 lysozyme are rather complex involving multiple coupled nuclear coordinates and most likely contain motions besides hinge-bending. It is highly likely that the multiple dimensional protein conformational motions beyond the typical enzymatic hinged-bending motions have profound impact on overall enzymatic functions. In this report, we have developed a single-molecule multiparameter photon stamping spectroscopy integrating fluorescence anisotropy, FRET, and fluorescence lifetime. This spectroscopic approach enables simultaneous observations of both FRET-related site-to-site conformational dynamics and molecular rotational (or orientational) motions of individual Cy3-Cy5 labeled T4 lysozyme molecules. We have further observed wide-distributed rotational flexibility along orientation coordinates by recording fluorescence anisotropy and simultaneously identified multiple intermediate conformational states along FRET coordinate by monitoring time-dependent donor lifetime, presenting a whole picture of multidimensional conformational dynamics in the process of T4 lysozyme open-close hinge-bending enzymatic turnover motions under enzymatic reaction conditions. By analyzing the autocorrelation functions of both lifetime and anisotropy trajectories, we have also observed the dynamic and static inhomogeneity of T4 lysozyme multidimensional conformational fluctuation dynamics, providing a fundamental understanding of the enzymatic reaction turnover dynamics associated with overall enzyme as well as the specific active-site conformational fluctuations that are not identifiable and resolvable in the conventional ensemble-averaged experiment.

Probing deuterium isotope effect on structure and solvation dynamics of human serum albumin

The deuterium isotopic effect on the structure and solvation dynamics of the protein, human serum albumin (HSA), has been studied by using circular dichroism (CD), femtosecond up-conversion, FRET, and single-molecule spectroscopy. The CD spectra suggest that D(2)O affects the structure of HSA, leading to a 20% decrease in the helical structure. The FRET study indicates that the distance of C153 from the lone tryptophan residue of HSA is quite similar (≈21 Å) in H(2)O and D(2)O, and hence, the location of the probe in the protein remains the same in the two solvents. The single-molecule study suggests that coumarin 153 (C153) binds almost exclusively (>96%) to one site of HSA. Solvation dynamics of C153 in HSA is found to be markedly retarded in D(2)O compared with H(2)O. In H(2)O, the solvation of C153 bound to HSA is found to be biexponential with one component of 7 ps (30%) and a long component of 350 ps (70%). In D(2)O, we detected a short component of 4 ps (41%) and a long component of 950 ps (59%). Thus, the ultraslow component of the solvation dynamics of C153 bound to HSA in D(2)O (950 ps) is 2.5-fold slower than that in H(2)O (350 ps). The marked deuterium isotope effect has been ascribed to water molecules confined in the protein environment and to a lesser extent to the structural modification of protein by D(2)O.

Interaction of bovine serum albumin with dipolar molecules: fluorescence and molecular docking studies

Interaction of bovine serum albumin (BSA) with two series of dipolar molecules having both rigid and flexible structures has been studied by monitoring the spectral and temporal behavior of the intramolecular charge transfer fluorescence of the systems. The binding sites of the molecular systems in BSA have been located with the help of docking studies. Three different sites of varying hydrophobicity have been identified where these molecules are located. Binding in the hydrophobic domains of BSA leads to a blue shift of the fluorescence spectra and an enhancement of fluorescence intensity and lifetime. This enhancement is found to be the largest for flexible systems in which internal motion serves as a nonradiative decay route. In the BSA-bound condition, some of the dipolar molecules exhibit not-so-common "dip-rise-dip" time-resolved fluorescence anisotropy profiles. It is shown that a large difference of the fluorescence lifetimes of the protein-bound and unbound molecules is one of the factors that contributes to this kind of anisotropy profiles. As internal motion is often responsible for the short fluorescence lifetime of the flexible dipolar molecules, a large increase in the fluorescence lifetime of these systems occurs if binding to BSA leads to disruption/prevention of this motion. It thus appears that it might be possible to obtain information on the prevention/disruption of nonradiative pathway on protein binding from the anisotropy profiles of the kind discussed above. However, since the present study reveals cases where a large change in fluorescence lifetime also occurs due to other reasons, one needs to be careful prior to making any conclusion.

Nanosecond time-dependent Stokes shift at the tunnel mouth of haloalkane dehalogenases

The tunnel mouths are evolutionally the most variable regions in the structures of haloalkane dehalogenases originating from different bacterial species, suggesting their importance for adaptation of enzymes to various substrates. We decided to monitor the dynamics of this particular region by means of time-resolved fluorescence spectroscopy and molecular dynamic simulations. To label the enzyme specifically, we adapted a novel procedure that utilizes a coumarin dye containing a halide-hydrocarbon linker, which serves as a substrate for enzymatic reaction. The procedure leads to a coumarin dye covalently attached and specifically located in the tunnel mouth of the enzyme. In this manner, we stained two haloalkane dehalogenase mutants, DbjA-H280F and DhaA-H272F. The measurements of time-resolved fluorescence anisotropy, acrylamide quenching, and time-resolved emission spectra reveal differences in the polarity, accessibility and mobility of the dye and its microenvironment for both of the mutants. The obtained experimental data are consistent with the results obtained by molecular dynamics calculations and correlate with the anatomy of the tunnel mouths, which were proposed to have a strong impact on the catalytic activity and specificity of the examined mutants. Interestingly, the kinetics of the recorded time-dependent Stokes shift is unusual slow; it occurs on the nanosecond time-scale, suggesting that the protein dynamics is extremely slowed down at the region involved in the exchange of ligands between the active-site cavity and bulk solvent.

Thickness of the hydration layer of a protein from molecular dynamics simulation

Water molecules around a protein exhibit slow dynamics with respect to that of pure bulk water. One important issue in protein hydration is the thickness of the hydration layer (i.e., the distance from the protein surface up to which the water dynamics is influenced by the protein). Estimation of thickness is crucial to understand better the properties of "biological water" and the role that it plays in guiding the protein's function. We have performed an atomistic molecular dynamics simulation of an aqueous solution of the protein villin headpiece subdomain or HP-36 to estimate the thickness of its hydration water. In particular, several dynamical properties of water around different segments (three alpha-helices) of the protein have been calculated by varying the thickness of the hydration layers. It is found that in general the influence of the helices on water properties extends beyond the first hydration layer. However, the heterogeneous nature of water among the first hydration layers of the three helices diminishes as the thickness is increased. It indicates that, for a small protein such as HP-36, the thickness of "biological water" is uniform for different segments of the protein.

Dynamics of water in the hydration layer of a partially unfolded structure of the protein HP-36

Atomistic molecular dynamics simulations of the folded native structure and a partially unfolded molten globule structure of the protein villin headpiece subdomain or HP-36 have been carried out with explicit solvent to explore the effects of unfolding on the dynamical behavior of water present in the hydration layers of different segments (three alpha-helices) of the protein. The calculations revealed that the unfolding of helix-2 influences the translational and rotational motions of water present in the hydration layers of the three helices in a heterogeneous manner. It is observed that a correlation exists between the unfolding of helix-2 and the microscopic kinetics of protein-water hydrogen bonds formed by its residues. This in turn has an influence on the rigidity of the hydration layers of the helices in the unfolded structure versus that in the folded native structure. These results should provide a microscopic explanation to recent solvation dynamics experiments on folded native and unfolded structures of proteins.

Dynamic solvation in phosphonium ionic liquids: comparison of bulk and micellar systems and considerations for the construction of the solvation correlation function, C(t)

Dynamic solvation of the dye coumarin 153 is studied in a phosphonium ionic liquid: hexadecyltributylphosphonium bromide, [(C4)3C16P+][Br-]. It forms micelles in water, and the bulk also exists as a liquid under our experimental conditions. This system permits a comparison with an imidazolium ionic liquid studied earlier, which also formed micelles in water (J. Phys. Chem. A 2006, 110, 10725-10730). We conclude that our analysis of the comparable situation in a phosphonium liquid is not as definitive as we had proposed earlier, i.e., that the majority of the early-time solvation arises from the organic cation. Part of the difficulty in performing this analysis is most likely due to the amount of water that is associated with the micelle. In the course of this work, we have focused on the calculation of the solvation correlation function, C(t), and investigated how it depends upon the methods with which the "zero-time" spectrum is constructed.

Solvation dynamics in protein environments: Comparison of fluorescence upconversion measurements of coumarin 153 in monomeric hemeproteins with molecular dynamics simulations

The complexes of the fluorescence probe coumarin 153 with apomyoglobin and apoleghemoglobin are used as model systems to study solvation dynamics in proteins. Time-resolved Stokes shift experiments are compared with molecular dynamics simulations, and very good agreement is obtained. The solvation of the coumarin probe is very rapid with approximately 60% occurring within 300 fs and is attributed to interactions with water (or possibly to the protein itself). Differences in the solvation relaxation (or correlation) function C(t) for the two proteins are attributed to differences in their hemepockets.

Temperature-dependent hydration at micellar surface: activation energy barrier crossing model revisited

In recent years, the validity of the activation energy barrier crossing model at the micellar surface brings notable controversy (Sen, P.; Mukherjee, S.; Halder, A.; Bhattacharyya, K. Chem. Phys. Lett. 2004, 385, 357-361. Kumbhakar, M.; Goel, T.; Mukherjee, T.; Pal, H. J. Phys. Chem. B 2004, 108, 19246-19254.) in the literature. In order to check the validity of the model by time-resolved solvation of a probe fluorophore, a wider range of temperature must be considered. At the same time, spatial heterogeneity (solubilization) of the probe and structural perturbation of the host micelle should carefully be avoided, which was not strictly maintained in the earlier studies. We report here the solvation dynamics of 4-(dicyanomethylene)-2-methyl-6(p-dimethylamino-styryl) 4H-pyran (DCM) in the SDS micelle at 298, 323, and 348 K. The probe DCM is completely insoluble in bulk water in this wide range of temperature. The size of the micelle at different temperatures using the dynamic light scattering (DLS) technique is found to have insignificant change. The hydration number of the micelle, determined by sound velocity measurements, decreases with increasing temperature. Time-resolved fluorescence anisotropy reveals the retention of the probe in the micellar interface within the temperature range. The average solvation time decreases with increasing temperature. The result of the solvation study has been analyzed in the light of energetics of bound to free water conversion at a constant size and decreasing hydration number at the micellar surface. The solvation process at the micellar surface has been found to be the activation energy barrier crossing type, in which interfacially bound type water molecules get converted into free type molecules. We have calculated Ea to be 3.5 kcal mol-1, which is in good agreement with that obtained by molecular dynamics simulation studies.

Correlation between the Dynamics of Hydrogen Bonds and the Local Density Reorganization in the Protein Hydration Layer

An atomistic molecular dynamics simulation of the protein villin headpiece subdomain or HP-36 has been carried out with explicit water to explore the microscopic inhomogeneity of local density reorganization of the hydration layers of the three alpha-helical segments of the protein. The density reorganization of the hydration layer of helix-3 is found to occur faster than that for the hydration layers of the other two helices. It is noticed that such inhomogeneous density reorganization at the surface of different secondary structures exhibits excellent correlation with the microscopic dynamics of hydrogen bonds between the protein residues and the hydration water. Further, it is observed that the reorientation of water molecules involved in the formation and breaking of protein-water or water-water hydrogen bonds plays an important role in determining the dynamics of local density of the hydration layer. The faster density reorganization of the hydration layer of helix-3 is also consistent with the functionality of HP-36, as helix-3 contains several active site residues.

Ultrafast Relaxation Dynamics of the Excited States of Michler's Thione

Ultrafast relaxation dynamics of the S2 and S1 states of 4,4'-bis(N,N-dimethylamino)thiobenzophenone (Michler's thione, MT) have been investigated in different kinds of solvents, using steady-state absorption and emission as well as femtosecond transient absorption and fluorescence up-conversion spectroscopic techniques. Steady-state fluorescence measurements, following photoexcitation to the S2 state of MT, reveal weak fluorescence from the S2 state (phi F approximately 10(-3) in nonpolar and 10(-4) in polar solvents) but much weaker fluorescence from the S1 state. Yield of fluorescence from the S2 state is reduced in polar solvents because of reduced energy gap between the S2 and S1 states, Delta E(S2-S1), as well as interaction with the solvent molecules. Occurrence of S2-fluorescence in polar solvents, despite small energy gap, suggests that symmetry allowed S2(1A1) --> S0 (1A1) radiative and symmetry forbidden S2(1A1) --> S1 (1A2) nonradiative transitions are the factors responsible for the S2 fluorescence in MT. Lifetime of the S2 state is shorter (varying in the range 0.28-3.5 ps in different solvents) than that predicted from the Delta E(S2-S1) value and this can be attributed to its flexible molecular structure, which promotes an efficient intramolecular radiationless deactivation pathways. The lifetime of the S1 state (approximately 1.9-6.5 ps) is also very short because of small energy difference between the S1 and T1 states (Delta E(S1-T1) approximately 300 cm(-1)) in cyclohexane and hydrogen-bonding interaction as well as the presence of the isoenergetic T1(pipi*) state to enhance the rate of the intersystem crossing process from the S1(npi*) state in protic solvents.

Exploration of the Secondary Structure Specific Differential Solvation Dynamics between the Native and Molten Globule States of the Protein HP-36

Recent experiments have shown that the time dependence of fluorescence Stokes shift of a chromophore is substantially different when the chromophore is located in a molten globule (MG) state and in the native state of the same protein. To understand the origin of this difference, particularly the role of water in the differential solvation of the protein in the native and the MG states, we have carried out fully atomistic molecular dynamics simulations with explicit water of a partially unfolded MG state of the protein HP-36 and compared the results with the solvation dynamics of the protein in the folded native state. It is observed that the polar solvation dynamics of the three helical segments of the protein is influenced in a nonuniform heterogeneous manner in the MG state. While the equilibrium solvation time correlation function for helix-3 has been found to relax faster in the MG state as compared to that in the native state, the decay of the corresponding function for the other two helices slows down in the MG state. A careful analysis shows that the origin of such heterogeneous relative solvation behavior lies in the differential location of the polar probe residues and their exposure to bulk solvent. We find a significant negative cross-correlation between the contribution (to the solvation energy of a tagged amino acid residue) of water and the other groups of the protein, indicating a competing role in solvation. The sensitivity of solvation dynamics to the secondary structure and the immediate environment can be used to discriminate the partially unfolded and folded states. These results therefore should be useful in explaining recent solvation dynamics experiments on native and MG states of proteins.

Solvation Dynamics of a Protein in the Pre Molten Globule State

The nature of solvent molecules around proteins in native and different non-native states is crucial for understanding the protein folding problem. We have characterized two compact denatured states of glutaminyl-tRNA synthetase (GlnRS) under equilibrium conditions in the presence of a naturally occurring osmolyte, l-glutamate. The solvation dynamics of the compact denatured states and the fully unfolded state has been studied using a covalently attached probe, acrylodan, near the active site. The solvation dynamics progressively becomes faster as the protein goes from the native to the molten globule to the pre molten globule to the fully unfolded state. Anisotropy decay measurements suggest that the pre-molten-globule intermediate is more flexible than the molten globule although the secondary structure is largely similar. Dynamic light scattering studies reveal that both the compact denatured states are aggregated under the measurement conditions. The implications of solvation dynamics in aggregated compact denatured states have been discussed.

Ultrafast fluorescence resonance energy transfer in a micelle

Ultrafast fluorescence resonance energy transfer (FRET) from coumarin 153 (C153) to rhodamine 6G (R6G) is studied in a neutral PEO(20)-PPO(70)-PEO(20) triblock copolymer (P123) micelle and an anionic micelle (sodium dodecyl sulfate, SDS) using a femtosecond up-conversion setup. Time constants of FRET were determined from the rise time of the acceptor emission. It is shown that a micelle increases efficiency of FRET by holding the donor and the acceptor at a close distance (intramicellar FRET) and also by tuning the donor and acceptor energies. It is demonstrated that in the P123 micelle, intramicellar FRET (i.e., donor and acceptor in same micelle) occurs in 1.2 and 24 ps. In SDS micelle, there are two ultrafast components (0.7 and 13 ps) corresponding to intramicellar FRET. The role of diffusion is found to be minor in the ultrafast components of FRET. We also detected a much longer component (1000 ps) for intramicellar FRET in the larger P123 micelle.