Induced Dipole Mechanism Research Articles

Electrostatic origin of the cooperative effect on the C[dbnd6]O bond lengths and the amide I vibrational frequencies of the N-methylacetamide oligomers

The electric fields operating among the molecules in the oligomers of N-methylacetamide are analyzed to see the reasons for the cooperative effect on the CO bond lengths and the diagonal force constants in the vibrational subspace of the amide I mode. It is suggested that the following three factors are important for the enhancement of the electric field that gives rise to the cooperative effect: (1) the changes in the intermolecular distances (arising from the changes in the hydrogen-bond lengths); (2) the existence of the electric field directly operating between distant molecules, and (3) the polarization of the intervening molecule(s) between distant molecules. It is shown that the third factor is reasonably explained by the dipole–induced dipole mechanism. Some requirements for the correct representation of the electrostatic effects on the structures and the vibrational modes of polypeptides and proteins are proposed on the basis of this result.

The use of transient electric birefringence to characterize the conformation of DNA in solution, the mechanism of DNA gel electrophoresis, and the structure of agarose gels

Abstract Two small, 153 base-pair (bp) DNA restriction fragments, one of which migrates anomalously slowly during electrophoresis in polyacrylamide gels, have been characterized by transient electric birefringence (TEB). The decay of the birefringence of the anomalously slowly migrating fragment is faster than that of the normal fragment under a variety of buffer conditions, suggesting that the anomalous fragment is stably bent or curved in free solution. Reversing field experiments suggest that both the anomalous and normal DNA fragments orient in the electric field by a slow induced dipole mechanism. Birefringence relaxation times have also been measured for three DNA molecules embedded in agarose gels of various concentrations. The embedded DNA molecules become oriented in the electric field, just as in free solution. If the median pore diameter of the gel is approximately twice as large as the apparent end-to-end length of the DNA in solution, the relaxation times of the embedded DNA molecules are unaffected by the presence of the gel, indicating that the DNA retains its usual wormlike coil conformation in the gel matrix. However, as the end-to-end length of the DNA approaches the median pore diameter of the gel, the DNA molecules become stretched out and elongated in the electric field, leading to a repetitive, or end-on, mode of migration during electrophoresis. The relaxation times of the stretched DNA molecules scale as the 2.8 power of molecular weight, in reasonable agreement with reptation theories. The structure of agarose gels has also been characterized by TEB. The long, low voltage electric fields used for pulsed field gel electrophoresis (PFGE) cause extensive orientation of the agarose gel fibers. A wide range of relaxation times is observed after the field is removed, corresponding to the orientation of gel fibers up to 22 μm in length. The sign of the birefringence is variable, indicating that the gel fibers can be oriented in different directions in different parts of the gel. Surprisingly, the sign of the birefringence reverses upon field reversal, suggesting that the gel fibers change their direction of orientation in reversing electric fields. This anomalous orientation behavior is not observed for chemically crosslinked polyacrylamide gels. The apparent orientation and reorientation of agarose gel fibers in rapidly reversing electric fields may lead to ‘dynamic pores’ in the gel matrix, facilitating the migration of very large DNA molecules during PFGE.

A Selective Receptor for Arginine Derivatives in Aqueous Media. Energetic Consequences of Salt Bridges That Are Highly Exposed to Water

Quantitative measures of salt-bridge-type interactions in a highly exposed aqueous environment have been obtained by modifying the well-studied cyclophane platform 1 to include carboxylates in close proximity to bound, cationic guests, producing hosts 2 and 3. Many guests show significantly enhanced binding to 2 and 3, but cations of the RNMe3+ type show little or no enhancement. We propose that the latter observations result from the fact that RNMe3+ compounds have very diffuse positive charges. Guests that show enhanced binding have focused regions of large, positive electrostatic potential. The highly charged 3 is able to bind very polar, very well-solvated guests, including a series of arginine-based dipeptides. Neutral, water-soluble host 4 was prepared and found to show a decreased affinity for cationic guests. We propose a novel induced dipole mechanism to rationalize these results.

A theory for electric dichroism and birefringence decays and depolarized dynamic light scattering of weakly bending rods

When a weakly bending rod consisting of discrete subunits is partially oriented in a weak electric field by an independent induced dipole mechanism, the off-field decay of its dichroism or birefringence reflects the same mutual-rotational correlation function that is manifested in its forward depolarized dynamic light scattering. An analytical theory of that mutual-rotational correlation function is developed by extending a previous theory for self-rotational correlation functions of subunits in macromolecules with mean local cylindrical symmetry, and the result is formulated in terms of a previous normal mode theory for discrete weakly bending rods. Results from this analytical theory are compared with those of Brownian dynamics simulations with generally good agreement. By dissecting the analytical theory, explanations are found both for the unexpectedly small fraction of total relaxing amplitude that appears in the rapid initial transient due to bending and for the absence of the relaxation time of the longest bending mode from that initial relaxation.

Far infrared interaction induced absorption spectra of CS2−C6H6 liquid mixtures. A low concentration study

Abstract We report the statis and dynamic interaction induced properties of CS 2 −C 6 H 6 liquid mixtures, particularly at low benzene concentrations, as studied by far infrared absorption spectroscopy. The experimental effective dipole moments are compared with the calculated one, obtained from a simplified approach based on a quadrupole induced dipole mechanism. The dynamic functions are quantified with the Gaussian cage model. The results reinforce the evidence of stronger intermolecular interactions and the formation of ‘transient clusters’ in the mixtures, as found in our previous study.

DNA double helices with positive electric dichroism and permanent dipole moments: Non-symmetric charge distributions and “frozen” configurations

The stationary electric dichroism of DNA restriction fragments with chain lengths of 399, 587 and 859 base pairs (bp) is shown to be positive at low electric field strengths in the range up to about 1 kV/cm; the dichroism is changed to values with the usual negative sign at higher electric field strengths. A positive dichroism at low field strengths has been observed in buffers with Na +-cations of various ionic strengths from 1 to 11 m M. Experiments with reversal of the electric field vector indicate that the alignment is induced by a permanent electric moment at low field strengths; when the field strength is increased, the contribution from an induced dipole moment increases and becomes dominant at high field strengths. Thus, the permanent dipole mechanism is prevailing in the range with positive values of the dichroism found at low electric fields, whereas the induced dipole mechanism is dominant in the range with negative values of the stationary dichroism found at high electric fields. In contrast to these results obtained in buffers containing only monovalent ions, the electric dichroism is negative in the whole accessible range of electric field strengths, when the buffer contained 100 μ M Mg 2+. The stationary values of the dichroism are negative under all tested conditions of buffer concentrations and electric field strengths for DNA double helices with 95, 179, 256, 4361 and 48502 bp. The positive dichroism found in the intermediate range of chain lengths is reduced and finally changed to the standard negative dichroism by UV irradiation. Positive values of the linear dichroism are predicted by Monte Carlo simulations for ensembles of wormlike chains with the charge density and optical parameters of DNA double helices, when the polarizability along the chain axis is negligible and when the internal mobility is frozen. The positive dichroism is due to the fact that virtually all DNA fragments are bent by thermal agitation; most of these bent DNA's are asymmetric and, thus, are associated with permanent dipole moments; the majority of dipole vectors in a given range of chain lengths is perpendicular to the end-to-end vector and, thus, leads to positive values of the linear dichroism at low degrees of bending. The model predicts a chain length dependence consistent with the experimental one due to a superposition of chain length dependences of the dipole moment and of the dichroism. The change from positive to negative values of the linear dichroism at increasing field strengths suggests some increase of the polarizability with the field strength, but may also be partly due to field induced stretching. The absence of the special effect in the presence of Mg 2+ indicates a particularly high compensation of the phosphate charges by this ion. The time constants of electrooptical rise curves observed in the range with the positive stationary dichroism are rather close to those of the decay curves. It is shown by Brownian dynamics simulations that this result is consistent with the existence of a permanent dipole moment. The deviation from the standard expected for permanent dipoles is due to the fact that in the present case the dipole vectors are mainly perpendicular to the long axis of the molecules. The decrease of the positive dichroism by UV irradiation is consistent with the interpretation of the data by a frozen ensemble of configurations and indicates that photoproducts introduce flexible joints into the DNA chains.

Molecules in helium clusters: SF6HeN

Variational and diffusion Monte Carlo results are presented for the ground states of several SF6HeN clusters in the range N=1–499. The diffusion Monte Carlo computations are well converged, yielding an expected accuracy in the energy well under 1%. Computations are performed employing both an isotropic and an anisotropic He–SF6 interaction potential. Novel trial wave functions are used to describe both the shell structure of these clusters and the anisotropy arising from the potential. The ground state helium densities show the SF6 located at the cluster center, inducing a large degree of localization and a shell-like structure in the surrounding helium. Although the full potential causes a large degree of anisotropy in the helium density, general characteristics such as the energy and size are not greatly affected by the potential anisotropy. Finally, we compute spectral shifts for the ν3 SF6 vibration due to the instantaneous dipole–induced dipole mechanism and compare with recent experiments. We find a red shift which for N≤111 increases with N to a maximum value of 0.93 cm−1, with a width of 0.25 cm−1, at N=111.

The infrared spectrum of sulphur hexafluoride solvated in large molecular hydrogen clusters

The infrared spectrum of SF 6 and (SF 6) 2 in molecular hydrogen clusters containing approximately 1000 molecules has been measured. Absorptions are observed at 942.0 cm −1 for the monomer and at 928.5 and 949.6 cm −1 for the dimer, indicating that both species are solvated. The location of the impurities and the spectral shifts are analyzed in terms of the instantaneous dipole—induced dipole mechanism previously developed by Eichenauer and Le Roy. The relatively small discrepancy between the calculated and the observed shifts is explained in terms of an increased local density of hydrogen around the SF 6 which is a result of the decrease in the zero-point energy caused by the deeper local potential.

A molecular dynamics study of the far infrared spectrum of liquid water

The far infrared spectrum of liquid water at room temperature is calculated by molecular dynamics simulation over the spectral range 0.5–1000 cm−1. It is shown that the experimental absorption intensity can be reproduced satisfactorily provided that the dipole induced dipole mechanism is conveniently implemented in the calculation and the classical profile corrected for quantum effects. The contribution due to exchange overlap dipoles between O and H atoms is also investigated but its role in the genesis of the far infrared (FIR) spectrum is negligible. Although the dipole induced dipole (DID) mechanism is found to be responsible for the peculiar band shape near 200 cm−1 by revealing the intermolecular oscillations of the hydrogen bond network, no other translational band is detected in the region 10–60 cm−1, a result in contradistinction with data put forward recently. Moreover, it is shown that the absorption spectrum is the seat of various cancellation effects between permanent and induced dipoles, effects which are described in detail.

The Raman spectra of alkali halide melts: A theoretical description

A theoretical description of the light scattering (Raman) spectra of molten salts is presented. Expressions are derived to relate the spectra of the fluctuating polarizability induced by the ion Coulomb field and by the dipole–induced dipole mechanism to the spectra of the mass and charge density fluctuations (i.e., the dynamical structure factors). The theory thereby connects the spectral features seen in light scattering to well known dynamical processes in the ionic melt, such as the charge density wave (plasmon) and the ionic diffusive motion. The validity of this description is confirmed by evaluating the theoretical expression, using dynamical structure factors calculated in computer simulations, and comparing it with spectra calculated directly from the simulations.

Intermolecular coupling of the CO stretching vibrations in electrolyte solutions of carbonyl compounds

The polarized Raman scattering and infrared spectra of perchlorate solutions in acetone have been investigated in the CO stretching band region. The cation-dependent separation between the isotropic and anisotropic maxima of Raman band is interpreted in terms of intermolecular coupling of the CO vibrators in the solvation shell of cation. The linear correlation between the isotropic-anisotropic separation and integral intensities of the IR band indicates that the induced dipole mechanism of the coupling dominates.

Interaction-induced contributions to Rayleigh and allowed Raman bands

Molecular dynamics simulations of a model of CS2 have been analysed to calculate the shapes and intensities of the Rayleigh and allowed Raman bands of the liquid. The calculations are performed using the first order dipole induced dipole mechanism (DID). There is a clear time scale separation between the collision induced and reorientational components of the spectrum which becomes more marked at lower temperatures. The projection factors which determine the effective polarizabilities are large for CS2 at first order DID and second order DID terms calculated for the Raman polarizabilities are also substantial. An empirical renormalization scheme to incorporate higher order DID effects for the Raman intensities is described. A simple model which neglects orientational correlations and orientational translational correlations provides a semi quantitative prediction of the collision induced intensities.

Polarized absorption and magnetic circular dichroism of the FeCl42-ion in a tetragonally distorted tetrahedral site

Pure single crystals of Cs3FeCl5 have been prepared from the melt and characterized by Raman, polarized absorption and Magnetic Circular Dichroism (MCD) spectroscopies. Most of the observed features of the spectra can be understood on the basis of a single ion spin-orbit coupling mechanism. Relative transition probabilities have been derived using that scheme for the various possible 5 E →3Γ transitions. Our spectroscopic data indicate that, as for CoCl4 2- in Cs3CoCl5, the geometry of the FeCl4 2- ion in Cs3FeCl5 is a tetrahedron elongated along one of the C 4 axes. The ground state is 5 Ee with the MS = ± 1 and MS = ± 2 components at 1·2 cm-1 and 4 cm-1 respectively; the 5 Eϑ manifold lies around 25 cm-1. Most of the major bands are assigned on the basis of the sign of the MCD, in the light of a crystal field model which proves reasonably satisfactory. The possible occurrence of an exchange induced dipole mechanism is thought to be responsible for some disagreement between experimental results and our p...

Electric properties and structure of DNA-restriction fragments from measurements of the electric dichroism.

The electric dichroism of 17 homogeneous DNA fragments, ranging in size from 43 to 4362 base-pairs, has been analyzed in high electric fields. The orientation of the small fragments can be described in terms of an induced dipole moment, whereas the large fragments are oriented according to a constant dipole mechanism. In the intermediate size range, DNA orients according to an induced dipole mechanism at low field strengths and according to a constant dipole mechanism at high field strengths. From these observations we propose an orientation mechanism with a saturating induced dipole. The induced dipole observed at low field strengths is saturated at a field strength Eo within a transition range Em to give a constant dipole moment at high field strengths. These parameters together with the polarizability and the limit reduced dichroism are evaluated by a least-squares analysis of the experimental data. Eo and Em are found to decrease with increasing chain length from Eo approximately 40 kV/cm (Em approximately 14 kV/cm) at 65 base-pairs to 10 kV/cm (6 kV/cm) at 194 base-pairs. The polarizability is found to increase with the square of the chain length, whereas the saturated dipole increases with chain length N at low N and goes to a limit value at high N. The temperature dependence of the orientation parameters is found to be very small. The values obtained for the limit dichroism are between -1.0 and -1.3 for chain lengths between 60 and 1000 base-pairs, whereas values around -1.4 are observed at chain lengths greater than 1000 base-pairs. These data indicate that electric fields extend the contour of DNA strands at high chain lengths from a weakly bent to a more linear form. The variations of the limit dichroism observed for short fragments suggest sequence-dependent differences in the secondary structure of the helix. The experimental results are compared with numerical calculations based on simple polyelectrolyte models. For short fragments the magnitude of several electrochemical parameters can be adequately explained by a polarization of the ion cloud around the DNA molecules. However, these polyelectrolyte models do not adequately describe the observed chain length dependence of the orientation phenomena.

A solution to the rotational diffusion equation to describe molecular orientation due to a time dependent torque

When aqueous solutions of macromolecules are placed in a square, pulsed, orienting electric field they frequently become dichroic and birefrigent. By following the rise of the optical anisotropy as a function of time after application of the pulse one can frequently distinguish between permanent and induced dipole orientation modes. Occasionally, molecules which for symmetry or other reasons are known to have no permanent dipole moment mimic permanent moment orientation. A possible explanation for this phenomenon is that the induced dipole is time dependent. Here we present a formal solution to the rotary diffusion equation for a molecule subjected to a time dependent torque due to an induced dipole mechanism. A new method of solution which can have broad application has been employed. The results are seen to be a viable explanation for the subject in question.

Interactions between ortho-H2 molecules in nearly pure para-H2

A comprehensive theory is presented for the interaction of two ortho-H2 molecules in otherwise pure solid para-H2. A general Hamiltonian is constructed, which takes full account of the local environment of the pair of ortho molecules. For the dominant interactions between the pair, the pair axis is an axis of cylindrical symmetry. The various parameters which describe these interactions are then calculated from a microscopic theory. Contributions to these parameters include the 'bare' interaction parameters of the pair, ε00, ε20, and ε40, where ε40 is mainly determined by the quadrupole coupling constant Γ0. In addition, there are renormalizations due to various solid state effects, e.g. zero point motion, three-body polarizations, etc. These cylindrically symmetric interactions split the nine energy levels of the pair into three singlets and three doublets. The doublets are split by smaller interactions which sense the lack of cylindrical symmetry in the local crystalline environment. Among these are (1) the crystalline field whose axis of symmetry, the crystal c-axis, does not coincide with the pair axis, (2) three-body electronic polarizability interactions of order Γ0ρ, where ρ is proportional to the molecular polarizability, (3) three-body 'rotational polarizability' interactions of order Γ02/B, where B is the rotational constant, (4) higher order polarizability interactions, and (5) phonon- and zero point-induced interactions which depend on the anisotropy of motion transverse to the pair axis. The effect of zero point motion and short-range correlations on the three-body polarizability interactions has also been computed. Wave functions and energy levels for the pair are derived from this Hamiltonian, and the coefficients for infrared absorption by the quadrupole – induced dipole mechanism are calculated.