Picosecond Solvation Dynamics in Nanoconfinement - ACS Publications

Subscriber access provided by AUSTRALIAN NATIONAL UNIV

B: Liquids; Chemical and Dynamical Processes in Solution

Picosecond Solvation Dynamics in Nanoconfinement : Role of Water and Host-Guest Complexation Suman Biswas, Santanu Santra, Semen Yesylevskyy, Jyotirmay Maiti, Madhurima Jana, and RANJAN DAS J. Phys. Chem. B, Just Accepted Manuscript • DOI: 10.1021/acs.jpcb.7b10376 • Publication Date (Web): 12 Mar 2018 Downloaded from http://pubs.acs.org on March 12, 2018

Just Accepted “Just Accepted” manuscripts have been peer-reviewed and accepted for publication. They are posted online prior to technical editing, formatting for publication and author proofing. The American Chemical Society provides “Just Accepted” as a service to the research community to expedite the dissemination of scientific material as soon as possible after acceptance. “Just Accepted” manuscripts appear in full in PDF format accompanied by an HTML abstract. “Just Accepted” manuscripts have been fully peer reviewed, but should not be considered the official version of record. They are citable by the Digital Object Identifier (DOI®). “Just Accepted” is an optional service offered to authors. Therefore, the “Just Accepted” Web site may not include all articles that will be published in the journal. After a manuscript is technically edited and formatted, it will be removed from the “Just Accepted” Web site and published as an ASAP article. Note that technical editing may introduce minor changes to the manuscript text and/or graphics which could affect content, and all legal disclaimers and ethical guidelines that apply to the journal pertain. ACS cannot be held responsible for errors or consequences arising from the use of information contained in these “Just Accepted” manuscripts.

is published by the American Chemical Society. 1155 Sixteenth Street N.W., Washington, DC 20036 Published by American Chemical Society. Copyright © American Chemical Society. However, no copyright claim is made to original U.S. Government works, or works produced by employees of any Commonwealth realm Crown government in the course of their duties.

Page 1 of 36 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

The Journal of Physical Chemistry

Picosecond Solvation Dynamics in Nanoconfinement : Role of Water and Host-Guest Complexation

Suman Biswas#, Santanu Santra±, Semen Yesylevskyy┴, Jyotirmay Maiti#, Madhurima ±* #* Jana and Ranjan Das

# Department of Chemistry, West Bengal State University, Barasat, Kolkata - 700126, India ±Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela, PIN - 769008, Orissa, India ┴

Institute of Physics, National Academy of Sciences of Ukraine, Ukraine, 03028, Kyiv

Corresponding author phone number: 91 0 98361 54202

1 ACS Paragon Plus Environment

The Journal of Physical Chemistry 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Abstract. The dynamics of solvation of an excited chromophore 5-(4//-dimethylaminophenyl)-2(4/-sulfophenyl) oxazole, sodium salt (DMO) have been explored in confined nanoscopic environments of β-cyclodextrin (βCD) and heptakis(2,6-di-O-methyl)-β-cyclodextrin (DIMEB). Solvation occurs on a distinctly slower timescale (τS3 ~ 47 ps, τS4 ~ 517 ps) in the host cavity of DIMEB than that of βCD (τS3 ~ 20 ps, τS4 ~ 174 ps). The calculated equilibrium solvation response of DMO were characterized by four relaxation components (τS1~0.46-0.48 ps, τS2~3.23.4 ps, τS3~32.3-37.7 ps and τS4~232-485 ps) of which the longer ones (τS3,τS4) are nicely consistent with experiments, whereas, the ultrafast components (τS1, τS2) are unresolved.The observed time constant (τS3) within ~20-47 ps range arises from slow water molecules in the primary hydration layers of the host CDs, and is slower for DIMEB than βCD presumably due to longer lived and stronger hydrogen bonds that water forms with the former host relative to the latter. Decomposition of the calculated solvation response of DMO has revealed that conformational fluctuations of the macrocyclic hosts give rise to the observed long-time relaxation component (τS4), which is much slower for the inclusion complexes with DIMEB than βCD due to slower conformational dyamics of the former host than the latter.


Page 2 of 36

Page 3 of 36 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


1.Introduction. In nanoscale confinement water plays an essential role in a multitude of chemical and biological processes, and its unique properties stem from an extended hydrogen bonding network1 which evolves continuously on a picosecond time scale facilitating processes ranging from proton diffusion to protein folding.2,3 It was experimentally demonstrated that the structural and dynamical features of confined water are different from those exhibited by bulk water.4-11 Cyclodextrins (CDs) are used as model host systems for studying water in confined nanoscopic environments.12-14 Fleming et al.12 studied the dynamics of water in restricted environments by comparing the spectral dynamics of an optically excited probe molecule coumarin 480 (C480) embedded in γ-cyclodextrin (γCD) with the spectral dynamics of the same probe molecule in bulk water. The spectral dynamics reflect the collective rearrangement of the solvating water, and were found to be much slower within the cavity of γCD than in bulk water. Bhattacharayya et al.13 studied the solvation dynamics of coumarin 153 (C153) encapsulated within two β-cyclodextrins (βCD) of similar sizes, albeit different functionalization, and observed ultraslow relaxation components of few nanoseconds. Recently, extensive molecular dynamics (MD) simulations14 were carried out to explore the origin of these nanosecond relaxation components13 in the solvation response of C153 entrapped within the hydrophobic cavities of β-cyclodextrins (βCD) in water. In this study Laria et al.14 were unable to detect any slow dynamic modes of water in the solvation response, and ascribed the ultraslow dynamics of solvation of C153 to the gauche-trans interconversions in the primary hydroxyl chains of the βCDs, which is not directly connected to the optical excitation of the probe. This intramolecular motions in the βCD as the new source of ultraslow solvation dynamics has never been contemplated in the previous analyses.12,13 Recently, Corcelli et al.15,16 used MD simulations to calculate the equilibrium and non-equilibrium solvation response to excitation of Hoechst 33258



(H33258) bound to DNA, and showed that DNA motion was responsible for the long-time relaxtion component (~20 ps) in the solvation dynamics. Therefore, study of solvation dynamics in host-guest inclusion complexes provides a particularly intriguing avenue of exploration of the origin of slower relaxation component of few hundreds of picoseconds to few nanoseconds. In the present study we have used picosecond resolved emission spectroscopy in conjunction with MD simulations to probe the solvation response of an optically excited fluorophore 5-(4//dimethylaminophenyl)-2-(4/-sulfophenyl) oxazole, sodium salt (DMO) in the cavities of pure βcyclodextrin (βCD) and heptakis(2,6-di-O-methyl)-β-cyclodextrin (DIMEB), (Scheme 1) with a limited number of co-included water molecules. The CDs are toroidal-shaped molecules containing seven glucopyranose units (Scheme 1) with a hydrophobic cavity surrounded by a hydrophilic exterior comprising primary and secondary hydroxyl (OH) groups.17-19 These hydroxyl groups on the rims of a CD cavity may strongly perturb the structure and dynamics of water molecules surrounding the inclusion complex.20-22 The goals of the present study are to investigate the effects of increased confinement on the dynamics of solvation to the optical excitation of a chromophore in the nanoscopic domains of the CD cavities, and to explore the origin of the slower relaxation which have remained elusive, so far.


Page 4 of 36

Page 5 of 36 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


5-(4//-dimethylaminophenyl)-2-(4/-sulfophenyl)oxazole, sodium salt (DMO)

Scheme 1. Molecular structures of DMO, (a) βCD, and (b) DIMEB 5 ACS Paragon Plus Environment


Page 6 of 36

2. EXPERIMENTAL SECTION a. Materials. 5-(4//-dimethylaminophenyl)-2-(4/-sulfophenyl)oxazole, sodium salt was purchased from Molecular Probes Inc. Heptakis(2,6-di-O-methyl)-β-cyclodextrin (DIMEB) and βcyclodextrin (βCD) were obtained from Sigma-Aldrich and used as received. The stock solutions of the CDs were prepared in deionized water (from Millipore Milli-Q nanopure water system). For the measurements of UV-Vis, steady state and time-resolved fluorescence decays the final concentration of DMO was maintained at 5 µM, and the concentration of βCD and DIMEB were maintained at 750 µM and 250 µM, respectively. Quantum yields (Φ) of the dye were determined with respect to its solution in ethanol (Φ = 0.72) as a reference.23 All of the spectroscopic measurements were performed at 25◦C in cuvettes of 1 cm optical path. Steady-state absorption and fluorescence spectra were recorded on a Perkin Elmer Lambda 35 UV-Vis spectrometer and a Perkin Elmer LS 55 spectrofluorimeter, respectively. Time-resolved fluorescence measurements were recorded with a commercial time-correlated single-photon counting (TCSPC) set up from Edinburgh Instruments (LifeSpec-ps) described elsewhere.23 The system is equipped with a 375 nm diode laser as the excitation source (PicoQuant LDH-P-C-375, 80 ps fwhm) and a microchannel plate photomultiplier (Hamamatsu R3809U-50) as detector. The decays were analyzed using FAST software of Edinburgh Instruments. The time resolution of the equipment is ∼16 ps after IRF reconvolution. Timeresolved fluorescence intensity decays were fitted with the following multi-exponential function,

t It a exp 1 τ

where ai’s are amplitudes of the decay components with time constants of τi. The average excited-state fluorescence lifetime is given by the equation τ = 6 ACS Paragon Plus Environment

, where

.

Page 7 of 36 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


The time-resolved fluorescence anisotropy decays (r(t)) were determined by measuring the parallel (IVV(t)) and perpendicularly polarized (IVH(t)) fluorescence transients using eq 2 as shown below. rt

I t GI t 2 I t + 2GI t

The magnitude of G, the grating factor of emission monochromator of the TCSPC system, is found using a long-tail matching technique.24 Time-resolved anisotropy decays, r(t), were fitted reasonably well with a mono-exponential decay function (3) both in water and the βCDs. rt r . exp

t 3 θ

where r0 is the initial anisotropy and θ1 is the rotational correlation time. Time-resolved emission spectra (TRES) were generated from a set of emission decays (at least 16 wavelengths) recorded at 10 nm intervals spanning the fluorescence spectrum using the “spectral reconstruction” method as described elsewhere.25 The time evolution of the peak wavenumbers ν(t) in the TRES were fitted using a log-normal line-shape function: I(ν,t) = A exp{-ln 2 (ln[1+2bi(ν-νi)/∆i]/bi)2} α > 1 = 0, for α ≤ 1

(4)

where α = 2bi(ν-νi)/∆i

where A,νi, bi and ∆i are the peak height, peak wavenumber, asymmetry parameter and width parameter, respectively. The normalized spectral shift correlation function or the solvent response function, C(t), was calculated according to:



C(t) =

ν (t ) − ν (∞) ν ( 0) − ν ( ∞ )

(5)

where ν(0), ν(t), and ν(∞) are the wave numbers of the emission maxima at time 0, t, and ∞, respectively. The decay of C(t) is satisfactorily fitted by the following bi-exponential function: C(t) = a3exp (-t/τS3) + a4.exp (-t/τS4)

(6)

where τS3, τS4 and a3, a4 are the solvent relaxation components and their corresponding amplitudes, respectively. MOLECULAR DYNAMICS SIMULATIONS The initial configurations of the 1:1 inclusion complexes of βCD/DMO (complex-1) and DIMEB/DMO (complex-2) in aqueous medium were prepared as following. The coordinates of the βCD molecule were taken from the corresponding crystal structure.26 The coordinates of the DIMEB were obtained by replacing the hydroxyl (OH) groups of βCD by methoxy (OCH3) groups. The initial coordinates of the DMO and the topologies of DMO, BCD and DIMEB were generated by CHARMM-GUI.27 The structures of DMO probe in ground and the first excited states were optimized using Gaussian 09 at B3LYP/6-31G level of theory.28 After that the ESP atomic charges were computed on optimized structures using the same level of theory. The charges of structurally equivalent atoms were averaged. Obtained charges were assigned to the draft topology of DMO leading to two different topologies for ground and excited states of the probe. This approach where the topologies for ground and excited state differ only by atomic charges, while all bonded


Page 8 of 36

Page 9 of 36 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


and Van der Waals parameters remain the same, is commonly employed for solvation response simulations.15 The initial configurations of the complexes were prepared by fitting the centre of the dye at the centre of the CD molecules. The two complexes were then solvated in the cubic simulation boxes containing ~1300 water molecules. A single Na+ ion was inserted randomly into the simulation box to balance the negative charge of DMO. System preparation was facilitated by Pteros molecular modeling library.29,30 All simulations were performed in Gromacs 2016.1 package31 using CHARMM36 force field. TIP3P water model was used. All simulations were performed in NPT conditions with the temperature 300 K and the isotropic pressure of 1 bar maintained by v-rescale thermostat and Berendsen barostat respectively. The time step of 1 fs was used. The parameters for cut-offs recommended for CHARMM36 force field were used as suggested in CHARMM GUI output. The minimum image convention32 was employed to calculate the short range Lennard Jones interactions using a spherical cut-off distance of 12 Å with a switch distance of 10 Å. The long range electrostatic interactions were calculated using the Particle-Mesh-Ewald (PME) method.33 Four systems were simulated: βCD/DMO in ground and excited states and DIMEB/DMO in ground and excited states. All systems were initially equilibrated for 20 ns. After that the production simulations of 200 ns were performed on each system. The trajectories were saved each 20 fs. After that the electrostatic interaction energies between the DMO and the rest of the system were computed for each trajectory frame using ground and excited state topologies of DMO. The solvation response functions C0(t) and C1(t) are defined below and were computed using the equilibrium time correlation function of fluctuations from the solvation energy differences as described elsewhere.15



C, t

〈!∆#0!∆#%〉, 〈|!∆#|( 〉,

where !∆#% ∆#% 〈∆#〉, . ∆#% #)*+,-). % #/0123. % is the difference of electrostatic energies of the dye in excited and ground states for the same system configuration observed at time t in the MD trajectory. The angular brackets represent an ensemble average over equilibrium MD trajectory computed in either the ground (subscript 0) or the excited (subscript 1) state of the dye. GROMACS tools were used to compute the autocorrelation functions. The calculated solvation response functions exhibit multiexponential behavior and the number of their exponential components was not known in advance. One of the most successful techniques of decomposing such complex signals into exponential components is the Maximum Entropy Method (MEM).34,35 In this work we used MEMfit software, which was previously used with great success in the analysis of multi-exponential relaxation in non-equilibrium MD simulations.36 It allows finding the spectrum of exponential components of the signal automatically in completely model-free manner. RMSD of βCD and DIMEB were computed over first 50 ns of production trajectories using all atoms including hydrogens. Cyclodextrin molecules were structurally aligned to the conformation from the first frame and the RMSD was computed using Gromacs “msd” tool. Autocorrelation of RMSD was computed using standard Gromacs analysis tool over the time window of 20 ns. Although RMSD is not the most precise method of comparing conformational mobility it is known to work well in most cases where rough estimate of conformational changes is sufficient.37 In our case conformational changes are not too large to produce redundant results


Page 10 of 36

Page 11 of 36 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


in RMSD measurements. We use this method only to visualize an existence of conformational changes in βCD and DIMEB in the nanosecond time scale. 3. RESULTS AND DISCUSSION. 3.1. Steady State Emission Spectra DMO is known to display strong polarity sensitive fluorescence. For example, the steady state emission peak maximum of the dye is significantly red shifted from 420 nm in n-hexane to 582 nm in water, which is attributable to a highly polar excited state originating from an intramolecular charge transfer (ICT) process.38 Addition of βCD and DIMEB to an aqueous solution of DMO causes a blue shift of the emission peak maximum by 25 nm and 38 nm, respectively (Figure 1, Table 1.) along with the significant enhancement of the fluorescence quantum yield in comparison to water. These observations are in good agreement with those in the bile salt aggregates39 and confirms the encapsulation of the probe molecules into the cavities of βCD and DIMEB, where the local environments of DMO are less polar and more hydrophobic than water. Furthermore, the larger blue shift and higher quantum yield in DIMEB is indicative of a less polar and more hydrophobic nature of the cavity of DIMEB relative to βCD. 3.2. Formation of Dye/CD inclusion complexes The encapsulation of DMO into the cavities of βCD and DIMEB leads to the formation of host (CD)/guest (dye) inclusion complexes. Because of the lower concentrations of CD used (≤ 0.75 mM) in the present study, it is reasonable to assume the formation of 1:1 CD/dye complexes.40,41 This is well corroborated from the excellent fitting (correlation coefficients R2 ≥ 0.996) of the experimental data of emission intensity at different CD concentrations (Figure 2.) by the following equation based on the formation of 1:1 CD/dye complexes.42 11 ACS Paragon Plus Environment


I

45 647 87 9:;< 687 9:;
/=@,A ∑IA CD EF>⁄GH ; ∑MA KL A, τSn and an are correlation times, and their amplitudes, obtained from multiexponential fitting. Statistical errors of the measured timescales are shown within parentheses. a solvent response function, C(t), constructed from time-resolved data.

To visualize the existence of conformational dynamics of CDs we have also computed the RMSDs of the host-guest inclusion complexes (Figure 9), and the time evolution of their autocorrelations (Figure 10). The fluctuations of the structures of CDs which occur on the time scale of hundreds of picoseconds and nanoseconds are evident. The autocorrelation of RMSD fluctuations converge to zero (Figure 10) on a time scale of few nanoseconds confirming the existence of long-time dynamics of both βCD and DIMEB. Moreover, the decay of the autocorrelation is much slower for DIMEB relative to βCD, which is consistent with the slower dynamics of conformational fluctuation of the former host than the latter. The slower dynamics of conformational fluctuation of DIMEB relative to βCD gives rise to much slower collective solvation response of DMO in its inclusion complex with the former than the latter.



Figure 8. Ground-state equilibrium correlation functions, C0(t), calculated for the fluorescent probe DMO encapsulated in inclusion complexes with βCD (black), DIMEB (grey) and free in water (green). Decomposition of C0(t) into individual contributions from water and Na+ ion for both complexes (─, ─), βCD (─), DIMEB(─).


Page 24 of 36

Page 25 of 36 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


Figure 9: Time evolution of the RMSDs for all the atoms of the complex with βCD and DIMEB with respect to their initial structures

Figure 10: Time evolution of autocorrelation of RMSDs for the complexes with βCD and DIMEB, respectively. 25 ACS Paragon Plus Environment


4. CONCLUSIONS. Time-resolved Stokes shift experiments have revealed that the collective solvation response to excitation of the fluorescent probe DMO is bimodal and remarkably slower in inclusion complexes with DIMEB (τS3 ~ 47 ps, τS4 ~ 517 ps) than with βCD (τS3 ~ 20 ps, τS4 ~ 174 ps).These observations are nicely consistent with the equilibrium solvation response calculated from MD simulations. However, due to limited time resolution ultrafast relaxation components (τS1~0.46 ps, τS2~3.2 ps) could not be resolved as predicted from the equilibrium solvation response calculations. These time constants likely originate from relatively mobile waters that solvate the probe itself as well as the host CDs.15,16 The relaxation component of few tens of picoseconds (τS3~20-47 ps) is ascribed to slow orientational and translational motion of water molecules in the primary hydration layers of βCD and DIMEB on the basis of recent MD simulations.46,47 This component is slower for DIMEB than βCD presumably due to long lived and stronger hydrogen bonds that water forms with the former host relative to the latter in the primary hydration layer.47 The equilibrium solvation response calculations demonstrate clearly that the long-time relaxation dynamics (τS4~174-517 ps) on the time scale of hundreds of picoseconds are associated with the conformational dynamics of the host CDs. Furthermore, time evolution of the autocorrelation of RMSD fluctuations display slower dynamics of conformational fluctuations of DIMEB than βCD, which is consistent with the much slower relaxation component (τS3~517 ps) observed for the inclusion complexes with DIMEB than that with βCD (τS3~174 ps). In the present study, host CDs effectively “solvates” the probe along with water, and exhibits a distinctly different time dependence of reorganization compared to water.


Page 26 of 36

Page 27 of 36 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


SUPPORTING INFORMATION. Figure S1 shows profile of the calculated excited-state equilibrium correlation functions, C1(t), for the chromophore DMO in water and inclusion complexes with βCD and DIMEB. Decomposition of C1(t) into individual contributions from water, Na+ ion and host CDs are also displayed in the same figure. ACKKNOWLEDGMENTS. Generous financial support to RD from CSIR, Government of India vide CSIR project 01(2445)/10/EMR-II is gratefully acknowledged. MJ acknowledges the Department of Science and Technology, Government of India (SB/FT/CS-065/2012) for grant support for creating high performance computing facility. S.S thanks NIT, Rourkela for providing a scholarship. Sincere thanks are to Priya for her help with TCSPC measurements. S.Y. was supported by the NATO Science for Peace and Security programme under the project SPS 985291. REFERENCES (1) Steinel, T.; Asbury, J. B.; Fayer, M. D. Watching hydrogen bonds break: a transient absorption study of water. J. Phys. Chem. A 2004, 108, 10957-10964. (2) Laage, D.; Hynes, J. T. A molecular jump mechanism of water reorientation. Science 2006, 311, 832–835. (3) Laage, D.; Hynes, J. T. On the molecular mechanism of water reorientation. J. Phys. Chem. B 2008, 112, 14230-14242. (4) Bellissent-Funel, M. C. Status of experiments probing the dynamics of water in confinement. Eur. Phys. J. E 2003, 12, 83-92. (5) Tsukahara, T.; Hibara, A.; Ikeda, Y. Kitamori, T. NMR Study of Water Molecules Confined in Extended Nanospaces. Angew. Chem. Int. Ed. 2007, 46, 1180-1183.



(6) Pal, S. K.; Zhao, L.; Zewail, A. H. Water at DNA surfaces: Ultrafast dynamics in minor groove recognition. Proc. Natl. Acad. Sci. USA 2003, 100, 8113–8118. (7) Moilanen, D. E.; Levinger, N. E.; Spry, D. B.; Fayer, M. D. Confinement or the Nature of the Interface? Dynamics of Nanoscopic Water. J. Am. Chem. Soc. 2007, 129, 14311-14318. (8) Moilanen, D. E.; Piletic, I. R.; Fayer, M. D. Water Dynamics in Nafion Fuel Cell Membranes: The Effects of Confinement and Structural Changes on the Hydrogen Bond Network. J. Phys. Chem. C, 2007, 111, 8884–8891. (9) Moilanen, D. E.; Spry, D. B.; Fayer, M. D. Water Dynamics and Proton Transfer in Nafion Fuel Cell Membranes. Langmuir 2008, 24, 3690–3698. (10)

Moilanen, D. E.; Piletic, I. R.; Fayer, M. D. Tracking Water's Response to Structural

Changes in Nafion Membranes. J. Phys. Chem. A 2006, 110, 9084–9088. (11)

Dokter, A. M.; Woutersen, S.; Bakker, H. J. Inhomogeneous dynamics in confined water

nanodroplets. Proc. Natl. Acad. Sci. USA 2006, 103, 15355–15358. (12)

Vajda, S.; Jimenez, R.; Rosenthal, S. J.; Fidler, V.; Flemimg, G. R.; Castner, E. W., Jr.

Femtosecond to Nanosecond Solvation Dynamics in Pure Water and inside the γCyclodextrin Cavity. J. Chem. Soc., Faraday Trans.1995, 91, 867-873. (13)

Sen, P.; Roy, D.; Mondal, S. K.; Sahu, K.; Ghosh, S.; Bhattacharyya, K. Fluorescence

Anisotropy Decay and Solvation Dynamics in a Nanocavity: Coumarin 153 in Methyl βCyclodextrins. J. Phys. Chem. A 2005, 109, 9716-9722. (14)

Rodriguez, J.; Marti, J.; Guardia, E.; Laria, D. Exploring the Picosecond Time Domain of

the Solvation Dynamics of Coumarin 153 within β-Cyclodextrins. J. Phys. Chem. B 2008, 112, 8990–8998. (15)

Furse, K. E.; Corcelli, S. A. The Dynamics of Water at DNA Interfaces: Computational


Page 28 of 36

Page 29 of 36 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


Studies of Hoechst 33258 Bound to DNA. J. Am. Chem. Soc. 2008, 130, 13103-13109. (16)

Furse, K. E.; Corcelli, S. A.

Molecular Dynamics Simulations of DNA Solvation

Dynamics. J. Phys. Chem. Lett. 2010, 1, 1813–1820. (17)

Uekama, K.; Hirayama, F.; Irie, T. Cyclodextrin Drug Carrier Systems. Chem. Rev.1998,

98, 2045–2076. (18)

Rekharsky, M. V.; Inoue, Y. Complexation Thermodynamics of Cyclodextrins. Chem.

Rev.1998, 98, 1875–1918. (19)

Szejtli, J . Introduction and General Overview of Cyclodextrin Chemistry. Chem. Rev.

1998, 98,1743–1754. (20)

Starikov, E. B.; Brasicke, K.; Knapp, E. W.; Saenger, W. Negative solubility coefficient

of methylated cyclodextrins in water: A theoretical study. Chem. Phys. Letts. 2001, 336, 504510. (21)

Heine, T.; Dos Santos, H. F.; Patchkovskii, S.; Duarte, H. A. Structure and Dynamics of

β-Cyclodextrin in Aqueous Solution at the Density-Functional Tight Binding Level. J. Phys. Chem. A, 2007, 111, 5648–5654. (22)

Hansen, J. E.; Pines, E.; Fleming, G. R. Excited-state proton transfer of protonated 1-

Aminopyrene complexed with β-cyclodextrin. J. Phys. Chem.1992, 96, 6904–6910. (23)

Maiti, J.; Sarkar, Y.; Parui, P. P.; Chakraborty, S.; Biswas, S.; Das, R. Photophysical

study of a charge transfer oxazole dye in micelles: Role of surfactant headgroups. J. Lumin. 2015, 163, 21-27. (24)

Lakowicz, J. R. Principles of Fluorescence Spectroscopy; Kluwer Academic/ Plenum:

New York, 2006.



(25)

Horng, M. L.; Gardecki, J. A.; Papazyan, A.; Maroncelli, M. Subpicosecond

Measurements of Polar Solvation Dynamics: Coumarin 153 Revisited. J. Phys. Chem. 1995, 99, 17311-17337. (26)

Sharff, A. J.; Rodseth, L. E.; Quiocho, F. A. Refined 1.8-Å Structure Reveals the Mode

of Binding of β-Cyclodextrin to the Maltodextrin Binding Protein. Biochemistry 1993, 32, 10553−10559. (27)

Jo, S.; Kim, T.; Iyer, V.; Im, W. CHARMM-GUI: A web-based graphical user interface

for CHARMM. J. Comp. Chem. 2008, 29, 1859-1865. (28)

Frisch, M.J. Gaussian 09; Gaussian Inc.: Wallingford, CT, USA, 2009.

(29)

Yesylevskyy, S.O. Pteros: Fast and easy to use open-source C++ library for molecular

analysis. J. Comp. Chem. 2012, 33, 1632-1636. (30)

Yesylevskyy, S.O. Pteros 2.0: Evolution of the fast parallel molecular analysis library

for C++ and python. J. Comp. Chem. 2015, 36, 1480-1488. (31)

Abraham, M.J.; Murtola, T.; Schulz, R.; Szilard, P.; Smith, J. C.; Hess, B.; Lindahl, E.

GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 2015, 1–2, 19-25. (32)

Allen, M. P.; Tildesley, D. J. Computer Simulations of Liquids; Clarrendon Press:

Oxford, 1987. (33)

Darden, T.; York, D.; Pedersen, L. Particle Mesh Ewald: An N.log(N) Method for Ewald

Sums in Large Systems. J. Chem. Phys. 1993, 98, 10089−10092. (34)

Skilling J. Classic maximum entropy; Kluwer Academic; Norwell, MA, U.S.A. 1989.


Page 30 of 36

Page 31 of 36 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


(35)

Steinbach P. J.; Ansari A.; Berendzen J.; Braunstein D.; Chu K.; Cowen B. R.; Ehrenstein

D.; Frauenfelder H.; Johnson J. B. Ligand binding to heme proteins: connection between dynamics and function. Biochemistry, 1991, 30, 3988–4001. (36)

Yesylevskyy, S.O. and Hushcha, T.O. Conformational relaxations of human serum

albumin studied by molecular dynamics simulations with pressure jumps. Biopolym. Cell. 2012, 28, 486-492. (37)

Kufareva, I.; Abagyan, R. Methods of protein structure comparison. Methods. Mol. Biol.

2012, 857, 231−257. (38)

Pal, K.; Chandra, F.; Mallick, S.; Koner, A. L. Effect of solvents and cyclodextrin

complexation on acid–base and photophysical properties of dapoxyl dye. J. Photochem. Photobiol. A: Chemistry 2015, 306, 47–54. (39)

Maiti, J.; Kalyani, V.; Biswas, S.; Rodriguez-Prieto, F.; Mosquera, M.; Das, R. Slow

solvation dynamics in supramolecular systems based on bile salts: Role of structural rigidity of bile salt aggregates. J. Photochem. Photobiol. A: Chemistry 2017, 346, 17–23. (40)

Kusumoto, Y. A. Spectrofluorimetric method for determining the association constants

of pyrene with cyclodextrins based on polarity variation. Chem. Phys. Letts.1987, 136, 535538. (41)

Roberts, E. L.; Chou, P. T.; Alexander, T.A.; Agbaria, R. A.; Warner, I. M. Effects of

Organized Media on

the Excited-State Intramolecular Proton

Transfer of 10-

Hydroxybenzo[h]quinoline. J. Phys. Chem. 1995, 99, 5431–5437. (42)

Nigam, S.; and Durocher, G. Spectral and Photophysical Studies of Inclusion Complexes

of Some Neutral 3H-Indoles and Their Cations and Anions with β-Cyclodextrin. J. Phys. Chem.1996, 100, 7135-7142.



(43)

Page 32 of 36

O’Connor, D. V.; Phillips, D. Time Correlated Single Photon Counting; Academic Press:

New York, 1984. (44)

Shaikh, M.; Mohanty, J.; Sundararajan, M.; Bhasikuttan, A. C.; Pal, H. Supramolecular

Host−Guest Interactions of Oxazine‑1 Dye with β- and γ‑Cyclodextrins: A Photophysical and Quantum Chemical Study. J. Phys. Chem. B 2012, 116, 12450−12459. (45)

Singh, P.; Choudhury, S.; Singha, S.; Jun, Y.; Chakraborty, S.; Sengupta, J.; Das, R.;

Ahn, K-H.; Pal, S. K.

A sensitive fluorescent probe for the polar solvation dynamics at

protein–surfactant interfaces. Phys. Chem. Chem. Phys. 2017, 19, 12237-12245. (46)

Mondal, S.; Mukherjee, S.; Bagchi, B. Origin of diverse time scales in the protein

hydration layer solvation dynamics: A simulation study. J. Chem. Phys. 2017, 147, 15490111. (47)

Mukherjee, S.; Mondal, S.; Bagchi, B.

Distiguishing dynamical features of water inside

protein hydration layer: Distribution reveals what is hidden behind the average.

J. Chem.

Phys. 2017, 147, 024901-12. (48)

Fogarty, A. C.; Laage, D. Water dynamics in protein hydration shells: The molecular

origin of the dynamical perturbation. J. Phys. Chem. B. 2014, 118, 7715−7729. (49)

Sterpone, F.; Stirnemann, G.; Hynes, J. T.; Laage, D.

Water hydrogen-bond dynamics

around amino acids: The key role of hydrophilic hydrogen-bond acceptor groups. J. Phys. Chem. B 2010,114, 2083−2089. (50)

Supporting Information file

(51)

Levenberg, K. A Method for the Solution of Certain Non-Linear Problems in Least

Squares. Quarterly of Applied Mathematics. 1944, 2, 164–168.


Page 33 of 36 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


(52)

Marquardt, D. An Algorithm for Least-Squares Estimation of Nonlinear Parameters.

SIAM Journal on Applied Mathematics. 1963, 11, 431–441. (53)

Jimenez, R.; Fleming, G. R.; Kumar, P. V.; Maroncelli, M. Femtosecond solvation

dynamics of water. Nature 1994, 369, 471-473. (54)

Pal, S. K.; Peon, J.; Zewail, A. H. Biological water at the protein surface: Dynamical

solvation probed directly with femtosecond resolution. Proc. Natl. Acad. Sci. USA 2002, 99, 1763–1768. (55)

Kumar, P. V.; Maroncelli, M.

Polar solvation dynamics of polyatomic solutes:

Simulation studies in acetonitrile and methanol. J. Chem. Phys. 1995, 103, 3038–3060. (56)

Peon, J.; Pal, S. K.; Zewail, A. H. Hydration at the surface of the protein Monellin:

Dynamics with femtosecod resolution. Proc. Natl. Acad. Sci. USA 2002, 99, 10964–10969.



TOC graphic

1.0

DIMEB β CD

0.8

0.6

C(t)

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 34 of 36

0.4

0.2

0.0 0

200 400 600 800 1000 1200 1400 1600 1800

Time/ps


Page 35 of 36 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60





Page 36 of 36

Picosecond Solvation Dynamics in Nanoconfinement - ACS Publications

Recommend Documents