Influence of hydrodynamic coupling on the electric linear dichroism of DNA fragments

In the present work, we study the effect of translational-rotational hydrodynamic coupling on the stationary electric linear dichroism of DNA fragments. The theoretical resolution of the problem has, so far, been dealt with analytic methods valid only in the limit of low electric fields. In this work, we apply numerical methods that allow us to study the problem and also consider electric fields of arbitrary strength. We use the bent rod molecules model to describe DNA fragments with physical properties characterized by their electric charge, electric polarizability tensor, rotational diffusion tensor, and translation-rotation coupling diffusion tensor. The necessary orientational distribution function to calculate electric dichroism is obtained by solving the Fokker-Planck equation through the finite difference method. We analyze the different contributions due to electric polarizability and translational-rotational coupling to the electric dichroism.     

The nature of "unusual" electro-optical transients observed for DNA

Unusual electro-optical transients have been observed for many different polymers and colloidal systems. These effects provoked serious confusion, because a simple-minded interpretation can be completely misleading. The case of double helical DNA is of particular interest, because DNA has been studied in more detail than other systems and because of its biological function. DNA is subject to bending, which implies a loss of symmetry. Due to its high charge density, non-symmetric conformations must have a non-symmetric distribution of charges leading to a torque of considerable magnitude in the presence of external electric fields. The dipole moment describing this torque must be calculated in a coordinate system with its origin at the center of diffusion. The resulting dipole values are in the range of thousands of Debye units. Because the new dipole type is analogous to but not identical with permanent dipoles, the notation “quasi-permanent” dipole is suggested. Application of this concept, using commonly accepted parameters for DNA and established procedures for calculation of electro-optical transients, leads to “unusual” transients. Thus, these transients must be expected from well-known parameters of DNA double helices. The influence of the quasi-permanent dipole moment may be amplified considerably by hydrodynamic coupling. This effect has been demonstrated for the case of smoothly bent rods.

Both model calculations and experiments illustrate the danger of getting data that may be completely misleading. For example, depending on pulse amplitudes and/or pulse lengths, electro-optical decays may be accelerated artificially due to superposition of decay components with opposite amplitudes. Experiments show that unusual transients and apparent acceleration effects disappear, when high frequency sine pulses are used for the electro-optical analysis of DNA.

Electro-optical effects depend upon the internal dynamics of the object under investigation. In general, the dynamics of DNA bending was assumed to be fast compared to rotational diffusion. Because stacking rearrangements in single stranded nucleic acids are relatively slow and recently the dynamics of the B–A transition was observed in the time range >1 μs, it is likely that there are also relatively slow rearrangements between bending conformers. Bending transitions are expected to be relatively fast, when there are no activation barriers in the bending pathway, and may be slow, when activation barriers must be passed between bending conformers.     

Unique physical signature of DNA curvature and its implications for structure and dynamics

A particularly sensitive birefringence technique is used to analyze a curved DNA fragment with 118 bp and a standard DNA with 119 bp. At salt concentrations from 0.5 to 10 mM, both fragments show the usual negative stationary birefringence and monotonic transients - differences are relatively small. At 100 mM salt the curved DNA shows a positive stationary birefringence and non-monotonic transients with processes having amplitudes of opposite sign, whereas signals of the standard DNA remain as usual. Transients induced by reversal of the field vector indicate the existence of a permanent dipole for the curved DNA. 2-MHz-ac pulses induce a negative stationary birefringence in both DNAs. These results are consistent with calculations on models for curved DNA predicting a quasi-permanent dipole and a positive dichroism/birefringence. The quasi-permanent dipole results from the loss of symmetry in the charge distribution of the curved polyelectrolyte. The appearance of the unique signature of curvature at high salt is mainly due to a strong decrease of the polarizability by about 2 orders of magnitude. The special mode of orientation resulting from the quasi-permanent dipole is expected to contribute to the gel migration anomaly. The time constants of birefringence decay for the curved fragment are shorter than those of the 119 bp fragment by a factor of approximately 1.10 at 0.6 mM salt, whereas this factor is approximately 1.20 at 100 mM Na+. If both fragments were normal DNA with 3.4 A rise per base pair, the factor would be approximately 1.02. At high salt and high electric field strengths the factor increases up to 1.37. The implications for the bending dynamics and the potential to distinguish static from dynamic persistence by field reversal experiments are discussed. The dependence of the curvature on the salt concentration indicated by the time constants is consistent with a clear decrease of the electrophoretic anomaly at decreasing salt concentration.     

Transient electric birefringence of wormlike macromolecules in electric fields of arbitrary strength: a computer simulation study

We have studied the birefringence decay of linear models of macromolecules for two different types of flexibility, the broken-rod chain and the wormlike chain, using a computer simulation of a transient electric birefringence experiment. We have paid particular attention to the influence of the intensity of the orienting field, including two orienting mechanisms, the induced dipole, and the permanent dipole. We have compared wormlike and broken-rod models of the same radius of gyration, finding that they present a different decay curve under the influence of the same intensity of the field. We have seen that these differences are due to the faster relaxation times (smaller in the wormlike chain model) and amplitudes, because, regardless of the type of flexibility, the overall size of a molecule (measured by the radius of gyration) essentially determines the longest relaxation time. We have also analyzed how the relaxation process is affected by the degree of flexibility, the orientation mechanisms, and the intensity of the field. Studying a different aspect, we have paid attention to the deformation of a molecule in a transient electric birefringence experiment as a source of information. In this work we have developed equations to characterize this deformation in terms of one of the components of the gyration tensor, if a dynamic light scattering experiment under the influence of an electric field could be performed. To develop this work we have simulated the Brownian dynamics of the different models, relaxing after the removal of an orienting external electric field of arbitrary strength. A comparison with other methods such a the rigid body treatment or the correlation analysis of Brownian trajectories has also been included. We have seen that differences between the two Brownian dynamics methods are small and that the rigid-body treatment is only an acceptable approximation to obtain the longest relaxation time.     

MECHANISM OF ORIENTATION AND LINEAR DICHROISM OF PHOTOSYNTHETIC PARTICLES IN ELECTRIC FIELDS: CHLOROPLASTS AND CHLOROPHYLL-PROTEIN COMPLEXES

Abstract— The mechanisms of orientation in pulsed and alternating electric fields of thylakoids (derived from the sonication of spinach chloroplasts) and of light-harvesting chlorophyll a/b-protein complexes (CPII) were investigated by utilizing linear dichroism techniques. Comparisons of the linear dichroism spectra of thylakoids and CPII particles suggest that the latter are oriented with their directions of largest electronic polarizabilities (and thus probably their largest dimensions) within the thylakoid membrane planes. At low electric field strengths (< 12 V cm^?1), and at low frequencies of alternating electric fields (< 0.25 Hz), thylakoid membranes tend to align with their normals parallel to the direction of the applied electric field; the mechanism of orientation involves a permanent dipole moment of the thylakoids which is oriented perpendicular to the planes of the membranes. However, at high field strengths and high frequencies of the applied alternating electric fields, the thylakoids tend to orient with their planes parallel to the applied field, thus exhibiting an inversion of the sign of the linear dichroism as the electric field strength is increased. At the higher frequencies and at higher field strengths, the orientation mechanisms of the thylakoids involve induced dipole moments related to anisotropies in the electronic polarizabilities. The polarizability is higher within the plane than along a normal to the plane, thus accounting for the inversion of the dichroism as the electric field strength is increased. The CPII particles align with their largest dimension parallel to the applied field at all field strength, indicating that the induced dipole moment dominates the orientation mechanisms in pulsed electric fields. The magnitude of the absolute linear dichroism of CPII suspensions increases with increasing dilution, indicating that aggregates of lower symmetry are formed at higher concentrations of the CPII complexes.     

Dynamic electro-optic properties of macromolecules and nanoparticles in solution: a review of computational and simulation methodologies

This paper reviews some theories, and computational and simulation procedures available for the calculation of the time-course of electro-optic properties of particles in solution. For rigid particles, the time evolution of the properties is directly related to their rotational diffusion; therefore, the computational procedures for the calculation of hydrodynamic properties find a direct application in electro-optics. Several of such computational procedures, based on bead models, are reviewed. For flexible particles, the simultaneous effects the external field and the flexibility can be treated with Brownian dynamics simulation. We illustrate the various procedures, with applications to rigid bent rods and flexible, wormlike or hinged rods, trying to show how the absence or presence of flexibility, and its kind, influences the dynamic electro-optic properties, which are therefore valuable sources of information about the conformation of macromolecules and nanoparticles.     

Ab initio study of the two-photon circular dichroism in chiral natural amino acids

Two-photon circular dichroism spectra calculated within an origin-invariant density functional theory approximation in the absorption region where the lowest electronic excited states appear are presented for all 19 essential amino acids in the gas phase. A comparison of intensities and characteristic features is made with the corresponding two-photon absorption and one-photon circular dichroism spectra for each species. Also, the contributions of the electric dipole, magnetic dipole, and electric quadrupole transitions to the rotational strengths are analyzed in some detail. The remarkable fingerprinting capabilities of the two-photon circular dichroism spectroscopy are highlighted.     

Intermolecular electrostatic interactions and Brownian tumbling in protein solutions

It is often implicitly assumed that the long-range intermolecular electrostatic interactions in homogeneous protein solutions either are negligible for affecting protein Brownian tumbling or cause its deceleration without changing the shape of rotational auto-correlation function. This review presents a wide set of experimental data (NMR relaxation, dielectric spectroscopy and Brownian dynamics simulations) demonstrating that the interprotein electrostatic steering leads to a complication of the rotational correlation function. The key point of this effect is the rotational anisotropy caused by the interaction of the electric dipole moment of a protein with the external electric field produced by charges of neighboring proteins. Taking this effect into account in some cases might be of critical importance for the correct interpretation of various experimental data.     

Computer simulations of diffusion and dynamics of short-chain polyelectrolytes

Brownian dynamics simulations are conducted to investigate the diffusional and dynamic properties of polyelectrolytes in dilute salt-free solutions. The polyelectrolyte molecule is represented by a bead-spring chain in a primitive model. The long-range hydrodynamic and Coulomb interactions are both taken into consideration through the Ewald summations for the first time. The major finding of our simulations is that the dependence of the long-time chain diffusivity on the Coulomb interaction strength is very different from that of the Kirkwood short-time diffusivity, which simply shows a trend nearly opposite to the chain size. When ignoring the hydrodynamic interaction (HI), the coupling effect between the chain and its counterions gives rise to a noticeable increase in the long-time diffusivity at intermediate electrostatic interaction strengths. However, the incorporation of HI suppresses this effect to a degree that one can no longer discern it. Moreover, the rotational relaxation is found to show a dependence opposite to that of the gyration radius relaxation.     

Analytical solutions for rotational diffusion in the mean field potential: application to the theory of dielectric relaxation in nematic liquid crystals

A theory of dielectric relaxation in nematics is developed for a molecular dipole moment directed at an arbitrary angle to the molecular long axis. Both exact and simple approximate analytical formulae for the longitudinal and transverse components of the complex dielectric permittivity tensor are obtained for the non-inertial rotational Brownian motion of a molecule in the mean field potential of Maier and Saupe. It appears that both longitudinal and transverse relaxation processes are effectively described by two Debye type mechanisms with corresponding relaxation times and dielectric strengths expressed in terms of the order parameter. The generalization of the theory for an arbitrary axially symmetric mean field potential is given.     

On the electric polarizability of purple membrane

The permanent dipole moment and electric polarizability of purple membrane have been found using electrooptic methods. Comparison of the results with those for other inorganic or biological disperse particles as well as the observed effects and dynamics for a large range of applied electric field strengths support the proposal of a surface origin for the electric polarizability of purple membrane.     

Rotational diffusion of colloidal particles near confining walls

We study the rotational diffusion of a spherical colloid confined in a narrow channel between parallel plane hard walls. The walls damp translational diffusion much more than rotational diffusion so that there is expected to be little translation-rotation coupling. Using a recent calculation of the nonisotropic rotational mobilities arising from the hydrodynamic interactions with the walls, we set up the rotational Smoluchowski equation for either a particle with a permanent dipole moment or a polarizable particle with axisymmetric polarizabilities subject to an external electric field. Using the Smoluchowski equation dynamics we calculate the time-correlation functions of orientation that are measured in depolarized light scattering for the cases of no external field, external field normal to the walls, and external field parallel to the walls. The decay of correlations is shown to be given by a weighted sum of decaying exponentials and can be characterized by an initial and a mean characteristic decay time. The weights and decay rates of each component and the characteristic decay times are studied numerically for a range of field strengths. The nonisotropic rotational mobilities make these decay times highly sensitive to the distance of the particle from the confining walls. This position dependence can be used as a method of measuring the rotational mobilities or, conversely, the rate of decay of correlations can be used as a probe of particle position between the confining walls.     

Brownian dynamics algorithm for bead-rod semiflexible chain with anisotropic friction

A model of semiflexible bead-rod chain with anisotropic friction can mimic closely the hydrodynamics of a slender filament. We present an efficient algorithm for Brownian dynamics simulations of this model with configuration dependent anisotropic bead friction coefficients. The algorithm is an extension of that given previously for the case of configuration independent isotropic friction coefficients by Grassia and Hinch [J. Fluid Mech. 308, 255 (1996)]. We confirm that the algorithm yields predicted values for various equilibrium properties. We also present a stochastic algorithm for evaluation of the stress tensor, and we show that in the limit of stiff chains the algorithm recovers the results of Kirkwood and Plock [J. Chem. Phys. 24, 665 (1956)] for rigid rods with hydrodynamic interactions.     

Transport properties of the rough hard sphere fluid

Results are presented of a systematic study of the transport properties of the rough hard sphere fluid. The rough hard sphere fluid is a simple model consisting of spherical particles that exchange linear and angular momenta, and energy upon collision. This allows a study of the sole effect of particle rotation upon fluid properties. Molecular dynamics simulations have been used to conduct extensive benchmark calculations of self-diffusion, shear and bulk viscosity, and thermal conductivity coefficients. As well, the validity of several kinetic theory equations have been examined at various levels of approximation as a function of density and translational-rotational coupling. In particular, expressions from Enskog theory using different numbers of basis sets in the representation of the distribution function were tested. Generally Enskog theory performs well at low density but deviates at larger densities, as expected. The dependence of these expressions upon translational-rotational coupling was also examined. Interestingly, even at low densities, the agreement with simulation results was sometimes not even qualitatively correct. Compared with smooth hard sphere behaviour, the transport coefficients can change significantly due to translational-rotational coupling and this effect becomes stronger the greater the coupling. Overall, the rough hard sphere fluid provides an excellent model for understanding the effects of translational-rotational coupling upon transport coefficients.     

Theoretical study of internal field effects on peptide amide I modes

Charged terminal groups or polar side chains of amino acids create spatially nonuniform electrostatic potential around intramolecular peptide bonds and induce amide I mode frequency shifts in polypeptides. By carrying out a series of quantum chemistry calculation studies of various ionic di- and tripeptides as well as dipeptides of 20 different amino acids, these internal field effects on vibrational properties are theoretically investigated. The amide I local and normal mode frequencies and dipole and rotational strengths determining IR and vibrational circular dichroism intensities, respectively, are found to depend on the polar nature of side chains, whereas the vibrational coupling strength weakly does so. The empirical correction and fragment analysis methods were used to theoretically calculate the amide I local mode frequencies and dipole and rotational strengths. These values were directly compared with ab initio and density functional theory calculation results, and the agreements were found to be quantitative.     

Birefringence and dielectric relaxation decay transients and anisotropic rotational diffusion of macromolecules in a strong external electric field

The decay transient response of polar and polarizable rigid bodies (macromolecules) diluted in a nonpolar solvent after a sudden switch-off of a strong external dc field is evaluated in the context of the anisotropic noninertial rotational diffusion model. On solving the differential-recurrence equations for the statistical moments (expectation values of Wigner's D functions), the decay transients of the birefringence and dielectric relaxation are obtained. The solutions (valid for arbitrary strengths of an external electric field) are given in a closed form suitable for comparison with experiment and Brownian dynamics simulations.     

Experimental and simulation investigation of ion transfer in different sampling capillaries

Atmospheric pressure interfaces were a fundamental structure for transferring air generated ions into the vacuum manifold of a mass spectrometer. This work is devoted to the characterization of ion transfer in metal capillaries through both experimental and simulated investigations. The impact of capillary configurations on ion transmission efficiency was evaluated using an electrospray mass spectrometer with various bent capillaries as the transfer devices. In addition, a numerical model has been set up by coupling the SIMION 8.0 and the computational flow dynamics for simulation study of ion migration in the complex atmospheric system. The transfer efficiency was found to be highly affected by the variation in electric field and the capillary geometry, revealing that the hydrodynamic and electric force were both dominant and interactional during the transmission process. The consistency of the results from the experimental analysis and simulation modeling proved the validity of the model, which was helpful for understanding ion activity in transfer capillaries. Copyright © 2015 John Wiley & Sons, Ltd.     

Modelling the circularly and linearly polarised spectrum of [Ni(en)3]2+

The relative intensity and band shapes of the low energy spin-allowed transitions in the linearly polarised and circular dichroism spectrum of [Ni(en)(3)](2+) have been calculated using a time-dependent density functional theory approach. The effect of the trigonal ligand-field is minimal and no splitting of the bands is predicted by the simulations or observed experimentally. The 'd-d' transitions of the [Ni(en)(3)](2+) ion are electric dipole allowed but gain much of their intensity through Herzberg-Teller vibronic coupling. Its CD spectrum is dominated by the low energy band, which gains its rotatory strength through the magnetic dipole-allowed character of the parent octahedral transition and the electric dipole character due to the trigonal field. The simulation of the spectrum incorporates the contribution from all inducing vibrational modes with significant involvement of the {NiN(6)} unit. Vibrations which are centred on the chelate rings are not important in generating intensity, reflecting the localised d-d' character of the transitions. Simulated linearly polarised and circular dichroism spectra of such an open-shell system are presented for the first time and predict the essential elements of the experimental spectra.     

Electric circular dichroism

The theory of the circular dichroism induced by a static electric field is derived using quantum electrodynamics. Only terms linear in the electric field are considered, and molecular response is restricted to the dipole approximation. Selection rules and conditions under which the effect may be observed are discussed.     

Deflection and deceleration of hydrogen Rydberg molecules in inhomogeneous electric fields

Hydrogen molecules are excited in a molecular beam to Rydberg states around n=17-18 and are exposed to the inhomogeneous electric field of an electric dipole. The large dipole moment produced in the selected Stark eigenstates leads to strong forces on the H2 molecules in the inhomogeneous electric field. The trajectories of the molecules are monitored using ion-imaging and time of flight measurements. With the dipole rods mounted parallel to the beam direction, the high-field-seeking and low-field-seeking Stark states are deflected towards and away from the dipole, respectively. The magnitude of the deflection is measured as a function of the parabolic quantum number k and of the duration of the applied field. It is also shown that a large deflection is observed when populating the (17d2)1 state at zero field and switching the dipole field on after a delay. With the dipole mounted perpendicular to the beam direction, the molecules are either accelerated or decelerated as they move towards the dipole. The Rydberg states are found to survive for over 100 micros after the dipole field is switched off before being ionized at the detector and the time of flight is measured. A greater percentage change in kinetic energy is achieved by initial seeding of the beam in helium or neon followed by inhomogeneous field deceleration/acceleration. Molecular dynamics trajectory simulations are presented highlighting the extent to which the trajectories can be predicted based on the known Stark map. The spectroscopy of the populated states is discussed in detail and it is established that the N+=2, J=1, MJ=0 states populated here have a special stability with respect to decay by predissociation.