Biman Bagchi

Collapse of stiff conjugated polymers with chemical defects into ordered, cylindrical conformations

The optical, electronic and mechanical properties of synthetic and biological materials consisting of polymer chains depend sensitively on the conformation adopted by these chains. The range of conformations available to such systems has accordingly been of intense fundamental as well as practical interest, and distinct conformational classes have been predicted, depending on the stiffness of the polymer chains and the strength of attractive interactions between segments within a chain. For example, flexible polymers should adopt highly disordered conformations resembling either a random coil or, in the presence of strong intrachain attractions, a so-called ‘molten globule’. Stiff polymers with strong intrachain interactions, in contrast, are expected to collapse into conformations with long-range order, in the shape of toroids or rod-like structures. Here we use computer simulations to show that the anisotropy distribution obtained from polarization spectroscopy measurements on individual poly[2-methoxy-5-(2′-ethylhexyl)oxy-1,4-phenylenevinylene] polymer molecules is consistent with this prototypical stiff conjugated polymer adopting a highly ordered, collapsed conformation that cannot be correlated with ideal toroid or rod structures. We find that the presence of so-called ‘tetrahedral chemical defects’, where conjugated carbon–carbon links are replaced by tetrahedral links, divides the polymer chain into structurally identifiable quasi-straight segments that allow the molecule to adopt cylindrical conformations. Indeed, highly ordered, cylindrical conformations may be a critical factor in dictating the extraordinary photophysical properties of conjugated polymers, including highly efficient intramolecular energy transfer and significant local optical anisotropy in thin films.

Theory of the time development of the stokes shift in polar media

Abstract We present a theory for the time evolution of the Stokes shift of a polar molecule in a polar solvent. The time-dependent solute—solvent interaction is calculated in a continuum model by replacing the surrounding solvent by a frequency-dependent dielectric continuum. An expression for the time dependence of the fluorescence maximum is derived. This expression can be considered a direct generalization of the well-known Ooshika—Lippert—Mataga equation to the time domain. We also present an approximate expression for the wavelength dependence of the dynamics of the Stokes shift, and find it to be consistent with recent experimental results. We have investigated the effect of polarizability of the solute molecule and found that for many molecules this effect is not negligible.

Theory of electronic relaxation in solution in the absence of an activation barrier

We present a theory which describes the effects of viscosity on those electronic relaxation processes in solution in which the intramolecular potential surface does not present a barrier to the motion leading to the decay of the initially formed excited state. We model the reactive motion as the motion of a solute particle on the excited state potential surface with a position dependent sink which gives rise to the decay of the excited state population. Three different types of sinks are considered: (A) a pinhole sink at the minimum of the potential surface; this models the situation when the molecule decays to ground state as soon as it reaches the potential minimum; (B) a Gaussian sink with probability of decay maximum at the potential minimum; (C) a Lorentzian sink with maximum decay at the potential minimum. For case (A) an explicit analytic solution is obtained for the decay rate, but for cases (B) and (C) we obtained the decay rate numerically. Model (A) predicts nonexponential decay at all viscosit...

Nonspecifically bound proteins spin while diffusing along DNA

It is known that DNA-binding proteins can slide along the DNA helix while searching for specific binding sites, but their path of motion remains obscure. Do these proteins undergo simple one-dimensional (1D) translational diffusion, or do they rotate to maintain a specific orientation with respect to the DNA helix? We measured 1D diffusion constants as a function of protein size while maintaining the DNA-protein interface. Using bootstrap analysis of single-molecule diffusion data, we compared the results to theoretical predictions for pure translational motion and rotation-coupled sliding along the DNA. The data indicate that DNA-binding proteins undergo rotation-coupled sliding along the DNA helix and can be described by a model of diffusion along the DNA helix on a rugged free-energy landscape. A similar analysis including the 1D diffusion constants of eight proteins of varying size shows that rotation-coupled sliding is a general phenomenon. The average free-energy barrier for sliding along the DNA was 1.1 ± 0.2 kBT. Such small barriers facilitate rapid search for binding sites.

Hydrogen-bond dynamics near a micellar surface: origin of the universal slow relaxation at complex aqueous interfaces

The dynamics of hydrogen bonds among water molecules themselves and with the polar head groups (PHG) at a micellar surface have been investigated by long molecular dynamics simulations. The lifetime of the hydrogen bond between a PHG and a water molecule is found to be much longer than that between any two water molecules, and is likely to be a general feature of hydrophilic surfaces of organized assemblies. Analyses of individual water trajectories suggest that water molecules can remain bound to the micellar surface for more than 100 ps. The activation energy for such a transition from the bound to a free state for the water molecules is estimated to be about 3.5 kcal/mol.

The effect of frequency dependent friction on isomerization dynamics in solution

We investigate the effect of the frequency dependence of friction on the rate of photochemical isomerization in solution. Recent experiments have shown a significantly smaller effect of viscosity on rates at high viscosities than that predicted by Kramers’ theory. We show that this partial saturation of viscosity effects arises from the fact that the effective friction in the barrier region is much smaller than its zero frequency value at high viscosities. The fractional values of the exponent α (where kiso=A (ηs0)−α and ηs0 is the zero frequency shear viscosity) observed in recent experiments naturally arise when the frequency dependence of the friction is taken into account. The physical significance of these results is discussed.

Water inertial reorientation: Hydrogen bond strength and the angular potential

The short-time orientational relaxation of water is studied by ultrafast infrared pump-probe spectroscopy of the hydroxyl stretching mode (OD of dilute HOD in H2O). The anisotropy decay displays a sharp drop at very short times caused by inertial orientational motion, followed by a much slower decay that fully randomizes the orientation. Investigation of temperatures from 1°C to 65°C shows that the amplitude of the inertial component (extent of inertial angular displacement) depends strongly on the stretching frequency of the OD oscillator at higher temperatures, although the slow component is frequency-independent. The inertial component becomes frequency-independent at low temperatures. At high temperatures there is a correlation between the amplitude of the inertial decay and the strength of the O-DO hydrogen bond, but at low temperatures the correlation disappears, showing that a single hydrogen bond (ODO) is no longer a significant determinant of the inertial angular motion. It is suggested that the loss of correlation at lower temperatures is caused by the increased importance of collective effects of the extended hydrogen bonding network. By using a new harmonic cone model, the experimentally measured amplitudes of the inertial decays yield estimates of the characteristic frequencies of the intermolecular angular potential for various strengths of hydrogen bonds. The frequencies are in the range of ≈400 cm−1. A comparison with recent molecular dynamics simulations employing the simple point charge-extended water model at room temperature shows that the simulations qualitatively reflect the correlation between the inertial decay and the OD stretching frequency.

On the molecular mechanism of drug intercalation into DNA: a simulation study of the intercalation pathway, free energy, and DNA structural changes.

Intercalation into DNA (insertion between a pair of base pairs) is a critical step in the function of many anticancer drugs. Despite its importance, a detailed mechanistic understanding of this process at the molecular level is lacking. We have constructed, using extensive atomistic computer simulations and umbrella sampling techniques, a free energy landscape for the intercalation of the anticancer drug daunomycin into a twelve base pair B-DNA. A similar free energy landscape has been constructed for a probable intermediate DNA minor groove-bound state. These allow a molecular level understanding of aspects of the thermodynamics, DNA structural changes, and kinetic pathways of the intercalation process. Key DNA structural changes involve opening the future intercalation site base pairs toward the minor groove (positive roll), followed by an increase in the rise, accompanied by hydrogen bonding changes of the minor groove waters. The calculated intercalation free energy change is -12.3 kcal/mol, in reasonable agreement with the experimental estimate -9.4 kcal/mol. The results point to a mechanism in which the drug first binds to the minor groove and then intercalates into the DNA in an activated process, which is found to be in general agreement with experimental kinetic results.

Anomalous diffusion of small particles in dense liquids

We present here a microscopic and self-consistent calculation of the self-diffusion coefficient of a small tagged particle in a dense liquid of much larger particles. In this calculation the solute motion is coupled to both the collective density fluctuation and the transverse current mode of the liquid. The theoretical results are found to be in good agreement with the known computer simulation studies for a wide range of solute–solvent size ratio. In addition, the theory can explain the anomalous enhancement of the self-diffusion over the Stokes–Einstein value for small solutes, for the first time. Further, we find that for large solutes the crossover to Stokes–Einstein behavior occurs only when the solute is 2–3 times bigger than the solvent molecules. The applicability of the present approach to the study of self-diffusion in supercooled liquids is discussed.

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....