Solvation dynamics of formamide and N,N-dimethylformamide in aerosol OT reverse micelles

The solvation dynamics of formamide and N,N-dimethylformamide in Aerosol OT reverse micelles has been investigated in this work. The solvation dynamics of formamide and N,N-dimethylformamide in the reverse micelles is more than 100 times slower than that of the pure solvents. The solvation dynamics of formamide in the reverse micelle solution depends strongly on the molar ratio between formamide and Aerosol OT (w = [polar solvent]/[Aerosol OT]), but that of N,N-dimethylformamide in the reverse micelle solution shows a tiny w dependence. We have estimated the interaction energies of the geometry-optimized clusters of a simple model of the Aerosol OT polar headgroup (CH3SO3-) and formamide or N,N-dimethylformamide by ab initio calculations (the second-order M?ller-Plesset perturbation theory) to find their interactions. The interaction energies of the mimic clusters estimated by the ab initio calculations and the features of the slow solvation dynamics and w dependence in formamide and N,N-dimethylformamide reverse micelles are discussed.     

Structure, stability, and hydration of a polypeptide in AOT reverse micelles

In this communication, we provide theoretical evidence that the folded structure of a simple peptide, alanine zwitterionic octapeptide, or A8, unstable in solution, becomes stable in a reverse micelle (RM) of appropriate size. Our molecular dynamics simulations were carried out for realistic models of sodium 2-ethylhexylsulfosuccinate RM in isooctane, simulated for an extended period of time. For the RM of the smaller size, we find that a helical structure is stable for the whole length of the simulation. On the contrary, the peptide very quickly takes an extended structure in larger micelles.     

Protons in non-ionic aqueous reverse micelles

Using molecular dynamics techniques, we investigate the solvation of an excess proton within an aqueous reverse micelle in vacuo, with the neutral surfactant diethylene glycol monodecyl ether [CH3(CH2)11(OC2H4)2OH]. The simulation experiments were performed using a multistate empirical valence bond Hamiltonian model. Our results show that the stable solvation environments for the excess proton are located in the water-surfactant interface and that its first solvation shell is composed exclusively by water molecules. The relative prevalence of Eigen- versus Zundel-like solvation structures is investigated; compared to bulk results, Zundel-like structures in micelles become somewhat more stable. Characteristic times for the proton translocation jumps have been computed using population relaxation time correlation functions. The micellar rate for proton transfer is approximately 40x smaller than that found in bulk water at ambient conditions. Differences in the computed rates are examined in terms of the hydrogen-bond connectivity involving the first solvation shell of the excess charge with the rest of the micellar environment. Simulation results would indicate that proton transfers are correlated with rare episodes during which the HB connectivity between the first and second solvation shells suffers profound modifications.     

Aggregation of polyalanine in a hydrophobic environment

The dimerization of polyalanine peptides in a hydrophobic environment was explored using replica exchange molecular dynamics simulations. A nonpolar solvent (cyclohexane) was used to mimic, among other hydrophobic environments, the hydrophobic interior of a membrane in which the peptides are fully embedded. Our simulations reveal that while the polyalanine monomer preferentially adopts a beta-hairpin conformation, dimeric phases exist in an equilibrium between random coil, alpha-helical, beta-sheet, and beta-hairpin states. A thermodynamic characterization of the dimeric phases reveals that electric dipole-dipole interactions and optimal side-chain packing stabilize alpha-helical conformations, while hydrogen bond interactions favor beta-sheet conformations. Possible pathways leading to the formation of alpha-helical and beta-sheet dimers are discussed.     

Interaction of a tripeptide with cesium perfluorooctanoate micelles

The interaction of alanyl-phenylalanyl-alanine (Ala-Phe-Ala) with the micelles formed by cesium perfluorooctanoate (CsPFO) in water was studied in the isotropic phase by means of 1H NMR and by molecular dynamics (MD) simulations. Information on the location of the peptide was experimentally obtained from selective variations in Ala-Phe-Ala chemical shifts and from differential line broadening in the presence of the paramagnetic ion Mn2+. The peptide-micelle association constant was estimated analyzing the chemical shift variations of the most sensitive Ala-Phe-Ala resonances with the peptide concentration. MD simulations of Ala-Phe-Ala in the micellar environment confirmed the experimental observations, identifying the hydrogen bonding interactions of the different peptide moieties with the micelle, yielding a binding constant close to the experimental one. NOESY experiments suggest that the peptide in the micellar environment does not adopt a preferred conformation but is mainly unstructured. Details on the conformational behavior of the peptide in the micellar solution observed through MD were consistent with a different conformational equilibrium in the proximity of the micelle. Information on Ala-Phe-Ala dynamics was obtained from 1H T1 data and compared to MD simulation results on the overall tumbling motion.     

Solvation dynamics in aqueous anionic and cationic micelle solutions: sodium alkyl sulfate and alkyltrimethylammonium bromide

Solvation dynamics of the fluorescence probe, coumarin 102, in anionic surfactant, sodium alkyl sulfate (C(n)H(2n+1)SO(4)Na; n = 8, 10, 12, and 14), and cationic surfactant, alkyltrimethylammonium bromide (C(n)H(2n+1)N(CH(3))(3)Br; n = 10, 12, 14, and 16), micelle solutions have been investigated by a picosecond streak camera system. The solvation dynamics in the time range of 10(-10)-10(-8) s is characterized by a biexponential function. The faster solvation time constants are about 110-160 ps for both anionic and cationic micelle solutions, and the slower solvation time constants for sodium alkyl sulfate and alkyltrimethylammonium bromide micelle solutions are about 1.2-2.6 ns and 450-740 ps, respectively. Both the faster and the slower solvation times become slower with longer alkyl chain surfactant micelles. The alkyl-chain-length dependence of the solvation dynamics in both sodium alkyl sulfate and alkyltrimethylammonium bromide micelles can be attributed to the variation of the micellar surface density of the polar headgroup by the change of the alkyl chain length. The slower solvation time constants of sodium alkyl sulfate micelle solutions are about 3.5 times slower than those of alkyltrimethylammonium bromide micelle solutions for the same alkyl-chain-length surfactants. The interaction energies of the geometry optimized mimic clusters (H(2)O-C(2)H(5)SO(4)(-) and H(2)O-C(2)H(5)N(CH(3))(3)(+)) have been estimated by the density functional theory calculations to understand the interaction strengths between water and alkyl sulfate and alkyltrimethylammonium headgroups. The difference of the slower solvation time constants between sodium alkyl sulfate and alkyltrimethylammonium bromide micelle solutions arises likely from their different specific interactions.     

How does the urea dynamics differ from water dynamics inside the reverse micelle?

In this study, the urea dynamics inside AOT reverse micelle (RM) has been monitored without intervention of water using time-resolved fluorescence techniques from the picosecond to nanosecond time regime. It has been observed that urea dynamics inside the reverse micelle is severely retarded compared to water RM due to the formation of highly networked urea cluster inside the RM. Time-resolved fluorescence anisotropy study also confirms the existence of a confined environment around the dye at higher concentrations of urea inside the reverse micelle. The dynamics of urea-water mixtures inside AOT reverse micelle has also been monitored with increasing urea concentration to get insight about the effect of urea on the overall solvation dynamics feature. It has been observed that with the increase in urea concentration, the overall dynamics becomes slower, and it infers the presence of few water or urea molecules, those strongly associated with surrounding urea and (or) water by hydrogen bonds.     

Molecular dynamics study of the solvation of an alpha-helical transmembrane peptide by DMSO

A 10-ns molecular dynamics study of the solvation of a hydrophobic transmembrane helical peptide in dimethyl sulfoxide (DMSO) is presented. The objective is to analyze how this aprotic polar solvent is able to solvate three groups of amino acid residues (i.e., polar, apolar, and charged) that are located in a stable helical region of a transmembrane peptide. The 25-residue peptide (sMTM7) used mimics the cytoplasmic proton hemichannel domain of the seventh transmembrane segment (TM7) from subunit a of H(+)-V-ATPase from Saccharomyces cerevisiae. The three-dimensional structure of peptide sMTM7 in DMSO has been previously solved by NMR spectroscopy. The radial and spatial distributions of the DMSO molecules surrounding the peptide as well as the number of hydrogen bonds between DMSO and the side chains of the amino acid residues involved are extracted from the molecular dynamics simulations. Analysis of the molecular dynamics trajectories shows that the amino acid side chains are fully embedded in DMSO. Polar and positively charged amino acid side chains have dipole-dipole interactions with the oxygen atom of DMSO and form hydrogen bonds. Apolar residues become solvated by DMSO through the formation of a hydrophobic pocket in which the methyl groups of DMSO are pointing toward the hydrophobic side chains of the residues involved. The dual solvation properties of DMSO cause it to be a good membrane-mimicking solvent for transmembrane peptides that do not unfold due to the presence of DMSO.     

Prediction of the Reverse Micellar Extraction of Papain Using Dissipative Particle Dynamics Simulation

Reverse micellar extraction is a promising technology for large-scale protein purification, but its molecular interaction mechanisms have not been thoroughly characterized. In this study, a dissipative particle dynamics (DPD) molecular simulation method was employed to study the interactions among the surfactant, organic phase, water, and proteins on the mesoscopic scale. This study simulated the self-assembly process of the reverse micelle extraction of papain. The results showed that the papain could be extracted by a CTAB/isooctane/n-hexanol system, which was validated by extraction experiments. The optimized extraction recovery was 76.9 %. This study elucidates the molecular process of the reverse micellar extraction of proteins and provides a method to predict its efficacy.     

Exploring the inter-molecular interactions in amyloid-β protofibril with molecular dynamics simulations and molecular mechanics Poisson-Boltzmann surface area free energy calculations

Aggregation of amyloid-β (Aβ) peptides correlates with the pathology of Alzheimer's disease. However, the inter-molecular interactions between Aβ protofibril remain elusive. Herein, molecular mechanics Poisson-Boltzmann surface area analysis based on all-atom molecular dynamics simulations was performed to study the inter-molecular interactions in Aβ(17-42) protofibril. It is found that the nonpolar interactions are the important forces to stabilize the Aβ(17-42) protofibril, while electrostatic interactions play a minor role. Through free energy decomposition, 18 residues of the Aβ(17-42) are identified to provide interaction energy lower than -2.5 kcal/mol. The nonpolar interactions are mainly provided by the main chain of the peptide and the side chains of nine hydrophobic residues (Leu17, Phe19, Phe20, Leu32, Leu34, Met35, Val36, Val40, and Ile41). However, the electrostatic interactions are mainly supplied by the main chains of six hydrophobic residues (Phe19, Phe20, Val24, Met35, Val36, and Val40) and the side chains of the charged residues (Glu22, Asp23, and Lys28). In the electrostatic interactions, the overwhelming majority of hydrogen bonds involve the main chains of Aβ as well as the guanidinium group of the charged side chain of Lys28. The work has thus elucidated the molecular mechanism of the inter-molecular interactions between Aβ monomers in Aβ(17-42) protofibril, and the findings are considered critical for exploring effective agents for the inhibition of Aβ aggregation.     

Cation-pi interactions stabilize the structure of the antimicrobial peptide indolicidin near membranes: molecular dynamics simulations

We implemented molecular dynamics simulations of the 13-residue antimicrobial peptide indolicidin (ILPWKWPWWPWRR-NH2) in dodecylphosphocholine (DPC) and sodium dodecyl sulfate (SDS) micelles. In DPC, a persistent cation-pi interaction between TRP11 and ARG13 defined the structure of the peptide near the interface. A transient cation-pi interaction was also observed between TRP4 and the choline group on DPC lipids. We also implemented simulation of a mutant of indolicidin in the DPC micelle where TRP11 was replaced by ALA11. As a result of the mutation, the boat-shaped conformation is lost and the structure becomes significantly less defined. On the basis of this evidence, we argue that cation-pi interactions determine the experimentally measured, well-defined boat-shaped structure of indolicidin. In SDS, the lack of such interactions and the electrostatic binding of the terminal arginine residues to the sulfate groups leads to an extended peptide structure. To the best of our knowledge, this is the first time that a cation-pi interaction between peptide side chains has been shown to stabilize the structure of a small antimicrobial peptide. The simulations are in excellent agreement with available experimental measurements: the backbone of the peptide is more ordered in DPC than in SDS; the tryptophan side chains pack against the backbone in DPC and point away from the backbone in SDS; the rms fluctuation of the peptide backbone and peptide side chains is greater in SDS than in DPC; and the peptide backbone order parameters are higher in DPC than in SDS.     

Slow solvent relaxation dynamics of nanometer sized reverse micellar systems through tryptophan metabolite, kynurenine

Exploration of environmental dynamics using intrinsic biological probe tryptophan is very important; however, it suffers from various difficulties. An alternative probe, kynurenine (KN), has been found to be an efficient probe for the ultrafast dynamics in the biological environment ( 1 ] J. Phys. Chem. B., 114, 15236–15243). In the present study, we have investigated the efficacy of KN for the exploration of relatively slower dynamics of biologically relevant environments. A detailed investigation involving UV–Vis, steady‐state/time‐resolved fluorescence spectroscopy and Förster resonance energy transfer (FRET) studies on KN compared to a well‐known solvation probe, H33258, a DNA‐minor groove binder in a model nonionic reverse micelle reveals that ultrafast internal conversion associated with the hydrogen‐bonding dynamics masks KN to become a dynamical reporter of the immediate environments of the probe.     

Free energy decomposition analysis of bonding and nonbonding interactions in solution

A free energy decomposition analysis algorithm for bonding and nonbonding interactions in various solvated environments, named energy decomposition analysis-polarizable continuum model (EDA-PCM), is implemented based on the localized molecular orbital-energy decomposition analysis (LMO-EDA) method, which is recently developed for interaction analysis in gas phase [P. F. Su and H. Li, J. Chem. Phys. 130, 074109 (2009)]. For single determinant wave functions, the EDA-PCM method divides the interaction energy into electrostatic, exchange, repulsion, polarization, desolvation, and dispersion terms. In the EDA-PCM scheme, the homogeneous solvated environment can be treated by the integral equation formulation of PCM (IEFPCM) or conductor-like polarizable continuum model (CPCM) method, while the heterogeneous solvated environment is handled by the Het-CPCM method. The EDA-PCM is able to obtain physically meaningful interaction analysis in different dielectric environments along the whole potential energy surfaces. Test calculations by MP2 and DFT functionals with homogeneous and heterogeneous solvation, involving hydrogen bonding, vdW interaction, metal-ligand binding, cation-π, and ionic interaction, show the robustness and adaptability of the EDA-PCM method. The computational results stress the importance of solvation effects to the intermolecular interactions in solvated environments.     

Computer Simulation of Luminophore Solubilization in Reverse Micelles

The solubilization of ionic (sodium naphthalene-2,6-disulfonate) and nonionic (diethyl 2,5-dihydroxyterephthalate) organic luminophores in water–isooctane–NaАОТ (sodium 1,4-bis[(2-ethylhexyl) oxy]-1,4-dioxybutane-2-sulfonate) reverse micelles is simulated by the molecular dynamics method. In a stationary state, the localization of luminophore molecules in a micelle appears to be the same irrespective of their initial positions in the system. The position and orientation of solubilized luminophores relative to a reverse micelle depend on the hydrophobicity and the capability for dissociation of the functional groups of their molecules, the size of the reverse micelle, and the structure of its electrical double layer.     

Application of the level-set method to the implicit solvation of nonpolar molecules

A level-set method is developed for numerically capturing the equilibrium solute-solvent interface that is defined by the recently proposed variational implicit solvent model [Dzubiella, Swanson, and McCammon, Phys. Rev. Lett. 104, 527 (2006); J. Chem. Phys. 124, 084905 (2006)]. In the level-set method, a possible solute-solvent interface is represented by the zero level set (i.e., the zero level surface) of a level-set function and is eventually evolved into the equilibrium solute-solvent interface. The evolution law is determined by minimization of a solvation free energy functional that couples both the interfacial energy and the van der Waals type solute-solvent interaction energy. The surface evolution is thus an energy minimizing process, and the equilibrium solute-solvent interface is an output of this process. The method is implemented and applied to the solvation of nonpolar molecules such as two xenon atoms, two parallel paraffin plates, helical alkane chains, and a single fullerence C(60). The level-set solutions show good agreement for the solvation energies when compared to available molecular dynamics simulations. In particular, the method captures solvent dewetting (nanobubble formation) and quantitatively describes the interaction in the strongly hydrophobic plate system.     

Ultrafast relaxation dynamics of a biologically relevant probe dansyl at the micellar surface

We report picosecond-resolved measurement of the fluorescence of a well-known biologically relevant probe, dansyl chromophore at the surface of a cationic micelle (cetyltrimethylammonium bromide, CTAB). The dansyl chromophore has environmentally sensitive fluorescence quantum yields and emission maxima, along with large Stokes shift. In order to study the solvation dynamics of the micellar environment, we measured the fluorescence of dansyl chromophore attached to the micellar surface. The fluorescence transients were observed to decay (with time constant approximately 350 ps) in the blue end and rise with similar timescale in the red end, indicative of solvation dynamics of the environment. The solvation correlation function is measured to decay with time constant 338 ps, which is much slower than that of ordinary bulk water. Time-resolved anisotropy of the dansyl chromophore shows a bi-exponential decay with time constants 413 ps (23%) and 1.3 ns (77%), which is considerably slower than that in free solvents revealing the rigidity of the dansyl-micelle complex. Time-resolved area-normalized emission spectroscopic (TRANES) analysis of the time dependent emission spectra of the dansyl chromophore in the micellar environment shows an isoemissive point at 21066 cm-1. This indicates the fluorescence of the chromophore contains emission from two kinds of excited states namely locally excited state (prior to charge transfer) and charge transfer state. The nature of the solvation dynamics in the micellar environments is therefore explored from the time-resolved anisotropy measurement coupled with the TRANES analysis of the fluorescence transients. The time scale of the solvation is important for the mechanism of molecular recognition.     

New approach to free energy of solvation applying continuum models to molecular dynamics simulation

A new approach to the calculation of the free energy of solvation from trajectories obtained by molecular dynamics simulation is presented. The free energy of solvation is computed as the sum of three contributions originated at the cavitation of the solute by the solvent, the solute-solvent nonpolar (repulsion and dispersion) interactions, and the electrostatic solvation of the solute. The electrostatic term is calculated based on ideas developed for the broadly used continuum models, the cavitational contribution from the excluded volume by the Claverie-Pierotti model, and the Van der Waals term directly from the molecular dynamics simulation. The proposed model is tested for diluted aqueous solutions of simple molecules containing a variety of chemically important functions: methanol, methylamine, water, methanethiol, and dichloromethane. These solutions were treated by molecular dynamics simulations using SPC/E water and the OPLS force field for the organic molecules. Obtained free energies of solvation are in very good agreement with experimental data.     

Examination of the folding of a short alanine-based helical peptide with salt bridges using molecular dynamics simulation

A molecular dynamics simulation of the folding of a short alanine-based helical peptide of 17 residues with three Glu...Lys (i, i + 4) salt bridge pairs, referred to as the AEK17 peptide, was carried out. The simulation gave an estimated simulation folding time of 2.5 ns, shorter than 12 ns for an alanine-based peptide of 16 residues with three Lys residues only, referred to as the AK16 peptide, simulated previously. After folded, the AEK17 peptide had a helical content of 77%, in excellent agreement with the experimentally determined value of 80%. An examination of the folding pathways of AEK17 indicated that the peptide proceeded via three-turn helix conformations more than the helix-turn-helix conformation in the folding pathways. An analysis of interactions indicated that the formation of hydrogen bonds between Lys residue side chains and backbone carbonyls is a major factor in the abundant conformation of the three-turn helix intermediate. The substitution of three Ala with Glu residues reduces the extent of hydrophobic interaction in alanine-based AK peptides with the result that the breaking of the interactions of Lys epsilon-NH3+(side chain)...C=O(backbone) is a major activation action for the AEK17 to achieve a complete fold, in contrast to the AK16 peptide, in which breaking non-native hydrophobic interaction is the rate-determining step.     

Excited-state solvation and proton transfer dynamics of DAPI in biomimetics and genomic DNA

The fluorescent probe DAPI (4',6-diamidino-2-phenylindole) is an efficient DNA binder. Studies on the DAPI-DNA complexes show that the probe exhibits a wide variety of interactions of different strengths and specificities with DNA. Recently the probe has been used to report the environmental dynamics of a DNA minor groove. However, the use of the probe as a solvation reporter in restricted environments is not straightforward. This is due to the presence of two competing relaxation processes (intramolecular proton transfer and solvation stabilization) in the excited state, which can lead to erroneous interpretation of the observed excited-state dynamics. In this study, the possibility of using DAPI to unambiguously report the environmental dynamics in restricted environments including DNA is explored. The dynamics of the probe is studied in bulk solvents, biomimetics like micelles and reverse micelles, and genomic DNA using steady-state and picosecond-resolved fluorescence spectroscopies.