Self-consistent microscopic treatment of the effects of self-motion of the probe on ionic and dipolar solvation dynamics

A simple but self-consistent microscopic theory for the time dependent solvation energy of both ions and dipoles is presented which includes, for the first time, the details of the self-motion of the probe on its own solvation dynamics. The theory leads to several interesting predictions. The most important of them is that, for dipolar solvation, both the rotational and the translational motions of the dipolar solute probe can significantly accelerate the rate of solvation. In addition, the rotational self-motion of the solute can also give rise to an additional mechanism of nonexponentiality in solvation time correlation functions in otherwise slow liquids. A comparison between the present theoretical predictions and the recent experimental studies of Maroncelli et al. on solvation dynamics of aniline in l-propanol seems to indicate that the said experiments have missed the initial solvent response up to about 45 ps. After mapping the experimental results on the redefined time scale, the theoretical results can explain the experimental results for solvation of aniline in 1-propanol very well. For ionic solvation, the translational motion is significant for light solutes only. For example, for Li+ in water, translational motion speeds up the solvation by about 20%. The present theory demonstrates that in dipolar solvation the partial quenching of the self-motion due to the presence of specific solute-solvent interactions (such as H-bonding) may lead to a much slower solvation than that when the self-motion is present. This point has been discussed. In addition, we present the theoretical results for solvation of aniline in propylene carbonate, Here, the solvation is predicted to be complete within 15-20 ps.

Solvation dynamics in slow, viscous liquids: Application to amides

As the viscosity of a liquid increases rapidly in the supercooled regime, the nature of molecular relaxation can exhibit dynamics rather different from the fast dynamics observed in the normal regime. In this article, we present theoretical studies of solvation dynamics and orientational relaxation in slow liquids. As the local short-range correlations are important in the slow liquids, we have extended our previous theory to take into account the shea-range pair correlations between the polar solute and the dipolar solvent molecules. Application of the generalized theory To the study of solvation dynamics of amide systems gives nice agreement with the experimental results of Maroncelli and co-workers (J. Phys. Chem. 1990, 94, 4929). The theory also provides valuable insight into the orientational relaxation precesses in the viscous liquids.

Diffusion Anomaly in Silicalite and VPI-5 from Molecular Dynamics Simulations

Molecular dynamics (MD) simulations on rigid and flexible framework models of silicalite and a rigid framework model of the aluminophosphate VPI-5 for different sorbate diameters are reported. The sorbate-host interactions are modeled in terms of simple atom-atom Lennard-Jones interactions. The results suggest that the diffusion coefficient exhibits an anomaly as gamma approaches unity. The MD results confirm the existence of a linear regime for sorbate diameters significantly smaller than the channel diameter and an anomalous regime observed for sorbate diameters comparable to the channel diameter. The power spectra obtained by Fourier transformation of the velocity autocorrelation function indicate that there is an increase in the intensity of the low-frequency component for the velocity component parallel to the direction of motion for the sorbate diameter in the anomalous regime. The present results suggest that the diffusion anomaly is observed irrespective of (1) the geometry and topology of the pore structure and (2) the nature of the host material. The results are compared with the work of Derouane and co-workers, who have suggested the existence of ''floating molecules'' on the basis of earlier theoretical and computational approaches.

Synthesis of chiral bicyclo[2.2.2]oct-5-en-2-ones via an intramolecular alkylation reaction

Generation of the thermodynamic dienolate of 9-bromocarvone derivatives 5, 7 and 11 furnished the chiral bicycle[2.2.2] octenones 6, 8 and 9 and 12 and 13 containing a bridgehead methyl group via an intramolecular alkylation reaction. In an analogous manner intramolecular alkylation reaction of the bromo enones 15a-e, obtained from carvone 2 by 1,3-alkylative enone transposition (-->14) followed by a regiospecific bromoetherification reaction, furnished the bicyclo[2.2.2]oct-5-en-2-ones 16a-e and 17a-e.

The stability of transmembrane helices: A molecular dynamics study on the isolated helices of bacteriorhodopsin

Bacteriorhodopsin (bR) continues to be a proven testing ground for the study of integral membrane proteins (IMPs). It is important to study the stability of the individual helices of bR, as they are postulated to exist as independently stable transmembmne helices (TMHs) and also for their utility as templates for modeling other IMPs with the postulated seven-helix bundle topology. Toward this purpose, the seven helices of bR have been studied by molecular dynamics simulation in this study. The suitability of using the backbone-dependent rotamer library of side-chain conformations arrived at from the data base of globular protein structures in the case TMHs has been tested by another set of ? helix simulations with the side-chain orientations taken from this library. The influence of the residue's net charge oil the helix stability was examined by simulating the helices III, IV, and VI (from both of the above sets of helices) with zero net charge on the side chains. The results of these 20 simulations demonstrate in general the stability of the isolated helices of bR in conformity with the two-stage hypothesis of IMP folding. However, the helices I, II, V, and VII are more stable than the other three helices. The helical nature of certain regions of III, IV, and VI are influenced by factors such as the net charge and orientation of several residues. It is seen that the residues Arg, Lys, Asp, and Glu (charged residues), and Ser, Thr, Gly, and Pro, play a crucial role in the stability of the helices of bR. The backbone-dependent rotamer library for the side chains is found to be suitable for the study of TMHs in IMP. (C) 1996 John Wiley & Sons, Inc.

Effect of Alkyl Chain Arrangement on Conformation and Dynamics in a Surfactant Intercalated Layered Double Hydroxide: Spectroscopic Measurements and MD Simulations

The anionic surfactant dodecyl sulfate (DDS) has been intercalated in an Mg-Al layered double hydroxide (LDH). Monolayer and bilayer arrangements of the alkyl chains of the intercalated surfactant can be engineered by tuning the Al/Mg ratio of the LDH. In both arrangements the anionic headgroup of the surfactant is tethered to the LDH sheets, and consequently translational mobility of the chains is absent. The degrees of freedom of the confined alkyl chains are restricted to changes in conformation. The effects of the arrangement of the intercalated surfactant chains on conformational order and dynamics have been,investigated by spectroscopic measurements and molecular dynamics simulations. Infrared, Raman, and C-13 NMR spectroscopies were used to investigate conformation of the alkyl chains in the monolayer and bilayer arrangements and variable contact time cross-polarization magic angle spinning (VCT CPMAS) NMR measurements to probe molecular motion. The alkyl chains in the monolayer arrangement of the intercalated DDS chains showed considerably greater conformational disorder and faster dynamics as compared to chains in the bilayer arrangement, in spite of the fact that the volume available per chain in the monolayer is smaller than that in the bilayer. Atomistic MD simulations of the two arrangements of the intercalated surfactant were carried out using an isothermal-isobaric ensemble. The simulations are able to reproduce the essential results of the experiment-greater conformational disorder and faster dynamics for the alkyl chains in the monolayer arrangement of the intercalated surfactant. The MD simulations show that these results are a consequence of the fact that the nature of conformational disorder in the two arrangements is different. In the monolayer arrangement the alkyl chains can sustain isolated gauche defects, whereas in the bilayer arrangement gauche conformers occur only as part of a kink a gauche(+) trans gauche(-) sequence.

Synthesis, properties and crystal structures of diastereomeric areneruthenium(II) chiral Schiff-base complexes

Diastereomers (SRu,Sc)-1a and (RRu,Sc)-1b, in a ratio of 85: 15 and formulated as [Ru(η-MeC6H4Pri-p)Cl(L*)], have been prepared by treating [{Ru(η-MeC6H4Pri-p)Cl2}2] with the sodium salt of (S)-α-methylbenzylsalicylaldimine (HL*) in tetrahydrofuran at –70 °C. The reaction of 1(1a+1b) with AgClO4 in acetone followed by an addition of PPh3 or 4-methylpyridine (4Me-py) leads to the formation of adducts [Ru(η-MeC6H4Pri-p)(PPh3)(L*)]ClO42[(SRu,Sc)2a, (FRu,Sc)2b] and [Ru(η-MeC6H4Pri-p)(4Me-py)(L*)]ClO43[(SRu,Sc)3a, (RRu,Sc)3b] in the diastereomeric ratios (SRu,Sc) : (RRu,Sc) of 2 : 98 and 76 : 24, respectively. Complex 1 crystallises with equal numbers of 1a and 1b molecules in an asymmetric unit of monoclinic space group P21 with a= 10.854(1), b= 17.090(1), c= 12.808(4)Å, β= 110.51(1)°, and Z= 4. The structure was refined to R= 0.0552 and R′= 0.0530 with 2893 reflections having I[gt-or-equal] 1.5σ(I). The absolute configurations of the chiral centres in the optically pure single crystal of the PPh3 adduct have been obtained from an X-ray study. Crystals of formulation [Ru(η-MeC6H4Pri-p)-(PPh3)(L*)]2[ClO4][PF6]·1.5 CHCl3, obtained in presence of both ClO4 and PF6 anions, belong to the non-centric triclinic space group P1 with a= 10.852(2), b= 14.028(1), c= 15.950(2)Å, α= 91.51(1), β= 105.97(1), γ= 106.11(1)°, and Z= 2. The final residuals were R= 0.0713, R′= 0.0752 with 7283 reflections having I[gt-or-equal] 2.5σ(I). The crystal structures of 1a,1b, and the PPh3 adduct (2b,2b′) consist of a ruthenium(II) centre bonded to a η-p-cymene, a bidentate chelating Schiff base, and a unidentate ligand (Cl or PPh3). The chirooptical properties of the complexes have been studied using 1H NMR and CD spectral data. The presence of a low-energy barrier for the intermediate involved in these reactions, showing both retention as well as inversion of the metal configuration, is discussed.

Application of selective F-1 decoupled H-1 NMR for enantiomer resolution and accurate measurement of enantiomeric excess at low chiral substrate/auxiliary concentration

The higher substrate and chiral auxiliary concentration is a pre-requisite to obtain efficient separation of H-1 NMR signals of enantiomers. The higher concentration of chiral lanthanide shift reagents provides broadened spectral lines resulting in a severe loss of resolution between the enantiomer resonances. In order to circumvent such difficulties, herein we present the application and the usefulness of a selective F-1 decoupled correlation (COSY) experiment which yields proton decoupled proton spectra in the indirect dimension. The potentiality of the experiment is demonstrated on several chiral compounds possessing different functional groups, employing either a lanthanide shift reagent or a solvating reagent as chiral auxiliaries. (C) 2011 Elsevier B.V. All rights reserved.

Short-bite chiral diphosphazanes derived from (S)-?-methyl benzyl amine and their Pd, Pt and Rh metal complexes

New chiral diphosphazane ligands of the type Ph(2)PN(S-*CHMePh)PYY' {YY'= Ph(2) (2), O2C6H4 (3); Y= Ph, Y'= Cl {4a (SS), 4b (SR)}, N(2)C(3)HMe(2)-3,5 {5a (SR), 5b (SS)} are synthesised starting from a chiral aminophosphine, Ph(2)PNH(S-*CHMePh) (1). The structure of one of the diastereomer 5a has been confirmed by single crystal X-ray diffraction {Orthorhombic system, P2(1)2(1)2(1); a=10.456 (4), b=15.362 (7), c=17.379 (6) Angstrom, Z=4}. Transition metal mononuclear complexes [Rh{eta(2)-(Ph(2)P)(2)N- (S-*CHMePh)}(2)](+)(BF4)(-) (6), [PdCl2{eta(2)-(Ph(2)P)(2)N(S-*CHMePh)}] (7) and [PtCl2{eta(2)-(Ph(2)P)(2)N- (S-*CHMePh)}] (8) have also been synthesised. The structure of the palladium complex 7 is solved by X-ray crystallography {Orthorhombic system, P2(1)2(1)2(1); a=8.746 (2), b=18.086 (2), c=20.811 (3) Angstrom, Z=4}. All these compounds are characterised by micro analyses, IR and NMR spectroscopic data.

Dynamics of Fractional Brownian Walks

We investigate the dynamics of polymers whose solution configurations are represented by fractional Brownian walks. The calculation of the two dynamical quantities considered here, the longest relaxation time tau(r) and the intrinsic viscosity [eta], is formulated in terms of Langevin equations and is carried out within the continuum approach developed in an earlier paper. Our results for tau(r) and [eta] reproduce known scaling relations and provide reasonable numerical estimates of scaling amplitudes. The possible relevance of the work to the study of globular proteins and other compact polymeric phases is discussed.

Molecular-dynamics studies of systems of confined dumbbell molecules

We present the results of molecular-dynamics simulations of systems of dumbbell molecules confined by parallel molecular walls. We have carried out systematic studies of three cases: freezing, steady flows, and stick-slip friction. We find that the molecular orientational degrees of freedom cause the surface layers to deviate from a planar configuration. Nevertheless, steady flows, in a channel as narrow as 15 molecular sizes, display continuum behavior. A range of mechanisms in the dynamics of the freezing of a confined fluid is found, as a function of the wall-fluid interactions and the bond length of the dumbbell molecules. The simple order-disorder transition associated with stick-slip motion in the presence of a layer of monoatomic lubricant molecules is supplanted by more complex behavior due to rotational degrees of freedom of the diatomic molecules.

Ultrafast solvation dynamics in water: Isotope effects and comparison with experimental results

A detailed theoretical study of solvation dynamics in water is presented. The motivation of the present study comes from the recent experimental observation that the dynamics of solvation of an ion in water is ultrafast and the solvation time correlation function decays with a time constant of about 55 fs. The slower decay in the long time can be described by a sum of two exponentials with time constants equal to 126 and 880 fs. The molecular theory (developed earlier) predicts a time constant equal to 52 fs for the initial Gaussian decay and time constants equal to 134 and 886 fs for the two exponential components at the long time. This nearly perfect agreement is obtained by using the most detailed dynamical information available in the literature. The present study emphasizes the importance of the intermolecular vibrational band originating from the O...O stretching mode of the O�H...O units in the initial dynamics and raises several interesting questions regarding the nature of the decay of this mode. We have also studied the effects of isotope substitution on solvation dynamics. It is predicted that a significant isotope effect may be observed in the long time. The experimental results have also been compared with the prediction of the dynamic mean spherical approximation (DMSA); the agreement is not satisfactory at the long time. It is further found that the molecular theory and the DMSA lead to virtually identical results if the translational modes of the solvent molecules are neglected in the former. DMSA has also been used to investigate the dynamics of solvation of a dipolar solute in water. It is found that the dynamics of dipolar solvation exhibit features rather different from those of ion solvation. © 1995 American Institute of Physics.

Ultrafast Solvation Dynamics Of An Ion In A Restricted Environment

The solvation dynamics of an excited coumarin dye molecule (C-480) enclosed within a restricted space have been studied using molecular hydrodynamic theory (MHT) and compared with the recent experimental findings. The solvation dynamics of the dye molecule within the cavity of a toroidal gamma-cyclodextrin molecule have been shown to be explained only in terms of the freezing of the solvent translational modes using MHT. The results of the theoretical calculation are in good agreement with the experimental results. The inertial components of the solvation time correlation function remain the same in both the restricted environment and in the free space. These results are interesting in the light of the simulation studies of Maroncelli and Fleming [J chem Phys, 89 (1988) 5044] which concludes that the participation of the different solvation shells in controlling the dynamics are much different. The earlier studies have been reviewed and the recent findings are discussed.

Model studies directed towards the synthesis of functionalised chiral A-ring derivatives of taxanes

Model studies, starting from the monoterpene R-carvone, directed towards the synthesis of chiral A-ring derivatives of taxanes with oxygen functionalities at C-2, 9 and 13 carbon atoms as in taxol is described.

Monte Carlo and molecular dynamics simulation of argon clusters andn-alkanes in the confined regions of zeolites

Geometry and energy of argon clusters confined in zeolite NaCaA are compared with those of free clusters. Results indicate the possible existence of magic numbers among the confined clusters. Spectra obtained from instantaneous normal mode analysis of free and confined clusters give a larger percentage of imaginary frequencies for the latter indicating that the confined cluster atoms populate the saddle points of the potential energy surface significantly. The variation of the percentage of imaginary frequencies with temperature during melting is akin to the variation of other properties. It is shown that confined clusters might exhibit inverse surface melting, unlike medium-to-large-sized free clusters that exhibit surface melting. Configurational-bias Monte Carte (CBMC) simulations of n-alkanes in zeolites Y and A are reported. CBMC method gives reliable estimates of the properties relating to the conformation of molecules. Changes in the conformational properties of n-butane and other longer n-alkanes such as n-hexane and n-heptane when they are confined in different zeolites are presented. The changes in the conformational properties of n-butane and n-hexane with temperature and concentration is discussed. In general, in zeolite Y as well as A, there is significant enhancement of the gauche population as compared to the pure unconfined fluid.