Rotational Diffusion Constants Research Articles

The influence of molecular geometries and experimental errors on rotational diffusion constants, methyl jumping rates, and activation parameters as calculated from 13C relaxation data

The influence of molecular geometries and experimental errors on rotational diffusion constants, methyl jumping rates, and activation parameters as calculated from 13C relaxation data

Measurement of the rotational behaviour of virus particles during adsorption to the host cell surface

The rotational diffusion of bacteriophage ϵ15 was measured before and after virus adsorption to outermembrane vesicles of the host Salmonella anatum. The virus capsid was labeled with eosin isothiocyanate, and the decay of transient dichroism following dye excitation by pulses of plane-polarized light was measured. From the data, the rotational diffusion constant of the unadsorbed virion and its hydrodynamic diameter were estimated and found to be consistent with electron microscopic measurements of the capsid dimensions. Addition of outer membrane vesicles of S. anatum to the virus suspension revealed the immobilization of the virus particles on the membrane surface.

Etude des propriétés électro‐optiques de i' ADN par biréfringence électrique à faible champ, 1. Théorie, appareillage et exploitation des résultats

AbstractElectric birefringence (or Kerr effect) measurements can give, in principle, important informations on the optical, electrical and hydrodynamical properties of macromolecules. The theoretical basis of the Kerr effect is reviewed here so as to be applied to the determination of some molecular parameters of DNA such as optical and electrical polarizability anisotropies, permanent dipole moment, and rotatory diffusion constant. It is necessary to conduct the measurements at very low electric fields. The original device used and the methods for the analysis of the experimental data are described.

Dynamics of non-rigid molecules. - I. — 13C T 1 NMR study of the reorientational and ring-puckering motions of cyclopentene in the liquid state

The 13 C NMR spin-lattice relaxation time T 1 and Nuclear Overhauser Effect (NOE) of the three distinct carbons of cyclopentene have been measured between 220 and 300 K in order to obtain some information about the ring-puckering motion in the liquid state. The data are first analysed under the hypothesis that the rotational diffusion of cyclopentene resembles that of a rigid asymmetric top. The slower rotation is then calculated to occur around the pseudo-C 5 axis and large differences are found between the three rotational diffusion constants D xx , D yy , D zz . These results seem to have little physical meaning. Furthermore they do not agree with those obtained by infrared, Raman and quasielastic neutron scattering. Therefore the ring-puckering motion has to be considered as an efficient 13 C relaxation mechanism. Although parameters needed to describe both external and internal motions cannot all be determined from the information available one can qualitatively show that at 300 K the molecule executes about (5±4), 10 12 jumps s −1 between its two equivalent bent conformations characterized by a puckering angle of 25 to 30°. The activation energy associated with this process seems to be low since the jump rate is still about (1±0.5).10 12 s −1 at 220 K. On the other hand, the whole molecule rotation is found to be nearly isotropic in agreement with the conclusions of the optical and neutron spectroscopies D r =(0.22±0.02)•10 12 s −1 at 300 K with an activation energy of 5.1 kJ.mole −1 Mesure du temps de relaxation spin reseau et de l'effet nucleaire Overhauser afin d'etudier la dynamique d'inversion du cyclopentene en phase liquide. Le mouvement d'inversion du cycle est considere comme un mecanisme efficace de relaxation de 13 C. La molecule execute environ (S±4).10 12 sauts par seconde a 300 K entre ses deux conformations equivalentes, pliees selon un angle de 25 a 30°

Molecular dynamics study of the dynamical properties of an assembly of infinitely thin hard rods

We present molecular dynamics (MD) simulations of a system of N (N=100–500) infinitely thin hard rods of length L (‘hard needles’). An algorithm is described which is reasonably fast and yet is guaranteed not to overlook any collision. Under the assumption that successive binary collisions are uncorrelated (the ‘Enskog’ assumption), we derive expressions for the time correlation functions of linear and angular momentum and rotational energy. We also obtain an exact expression for the collision frequency in a hard needle fluid. The MD results indicate that the Enskog approach works well at reduced densities below ρ*=8. At higher densities (8<ρ*<48) large deviations from the Enskog predictions are observed. However, at these densities the MD data conform to scaling predictions of the kind first put forward by Doi and Edwards. In particular, we find that the rotational diffusion constant D R scales as ρ*-2. One of the surprising consequences of the scaling arguments is that the longitudinal self-diffusion co...

Anisotropy and asymmetry of diamagnetic susceptibility, quadrupole coupling constants and molecular motion of fluorene and the fluorenyl carbanion

Fluorene and the fluorenyl carbanion, both perdeuterated, have been studied by 2H N.M.R. at 11·7 Tesla. From deuteron splittings and spin-spin relaxation times, information is obtained about the anisotropy and asymmetry of the diamagnetic susceptibility, the quadrupole coupling constants of the different deuterium nuclei and the rotational diffusion constants of the two species.

Fluorescence depolarization by anisotropic rotational diffusion of a luminophore and its carrier molecule

The analytical expression for the polarization anisotropy is derived for a luminophore undergoing rotational diffusion about a single axis while attached to a nonluminescing, rotationally diffusing, symmetrical carrier molecule. In contrast to previous related calculations, the rotation axis of the luminophore is assumed to have an arbitrary orientation relative to the carrier. Additionally, the polarization anisotropy is measured for bovine serum albumin (BSA) labeled with dansyl, NBD, rhodamine, or eosin that is: (a) surface adsorbed to a glass/buffer interface, using a variation of the technique of total internal reflection fluorescence spectroscopy (TIRFS), or (b) bulk dissolved, using conventional transmitted illumination fluorescence spectroscopy. With this theory, using previously published values for the rotational diffusion constants of BSA and the fluorescence lifetimes of the fluorophores, the rotational diffusion constant of the covalently bound probes is estimated from the measured anisotropy values. The results indicate a wide variability in the rotational diffusion constant of the probes (from ∼107 s−1 for dansyl to ∼109 s−1 for eosin) attached to both the surface adsorbed and bulk dissolved forms of BSA. Contrasting the rotational diffusion constant for each probe for surface adsorbed BSA vs bulk dissolved BSA indicates surface adsorption of the BSA molecule inhibits the rotational motion of the probe. These results have important implications in the application of other fluorescence techniques, such as singlet–singlet energy transfer, where the rotational mobility of the probe is important.

Nuclear spin relaxation in paramagnetic systems

A theory of nuclear spin relaxation in paramagnetic systems, allowing for the electron spin relaxation to be in the slow motion regime, is presented. The formulation is general and can, for example, be used to derive formally the modified Solomon-Bloembergen equations. The theory is applied to the specific problem of nuclear spin lattice relaxation caused by the dipole-dipole interaction between the nuclear spin and an electron spin (S = 1). The lattice is described in terms of the electron Zeeman interaction, a zero field splitting of cylindrical symmetry and isotropic rotational diffusion. The resulting equations are solved numerically for a range of parameter values of practical interest and limiting cases are discussed. In the slow motion regime for the electron spin relaxation (that is, where the zero field splitting is larger than the rotational diffusion constant), the behaviour of the nuclear spin-lattice relaxation rate predicted using the present formalism differs qualitatively from the predicti...

13C chemical shifts and spin-lattice relaxation in the nematic liquid crystal 4-cyano-4′-n-pentylbiphenyl

The 13C chemical shifts and spin-lattice relaxation times were obtained for all the resolved resonances in the isotropic and nematic phases of 5CB. NOE measurements were also obtained for the isotropic phase. A study of these data indicates that a flexibility gradient exists along the n-pentyl chain and that D⊥, the rotational diffusion constant for the entire molecule, can be estimated. A study of the chemical shifts of 5CB shows that a single average shielding tensor is inadequate for a proper description of the chemical shifts of this liquid crystal molecule. These results are compared with those previously obtained for MBBA and PAA.

Non-linear least squares program for the analysis of13C spin–lattice relaxation data based on a symmetric top model. Description of the method and application

A non-linear least squares program has been developed to analyse data for the dipole–dipole relaxation time of carbon (T1DD) based on the symmetric top model of molecular rotational diffusion. The program employs four parameters in the simulation, i.e. two rotational diffusion constants and two angles related to the axis of molecular motion. The internal rotation of methyl groups is also incorporated. The application of the program to methylbenzofurans indicated the reliability and wide applicability of the method. The factors affecting the methyl rotation barrier are also examined with the aid of MNDO MO calculations, and a novel inter-relation is found with the bond length of C–CH3.

State of myosin in solution: Electric birefringence and dynamic light-scattering studies

Myosin and heavy meromyosin solutions have been studied at high ionic strengths by means of relaxation techniques such as polarized dynamic light-scattering and electric birefringence. Contrary to translational parameters, rotary diffusion constants were found to be independent of protein concentration and depend only slightly on buffer phosphate concentration; the electrical polarizability of both molecules is mainly due to a permanent dipole moment. Considering the results, five of the six association models proposed by Harrington & Burke (1972) have been excluded. Thus, the only remaining possibilities are either a side-to-side parallel dimeric form, which it was not possible to exclude formally, or the quasi-exclusive presence of the monomeric species. On the basis of the hydrodynamic parameters, the dimensions and flexibility of myosin and heavy meromyosin molecules are discussed, particularly in relation to the model proposed by Garcia de la Torre & Bloomfield (1980), which best fits our results.

Raman linewidth study of rotational motion of chloroform in aqueous solution

AbstractIsotropic and anisotropic Raman linewidths of the CD stretching mode of chloroform‐d have been measured in water and other solvents, and rotational diffusion constants for the rocking motion of chloroform molecules around their perpendicular to the symmetry axis have been determined from linewidths. The correlation of experimental rotational diffusion constants in solutions, with fluidities of solvents, is examined, and the effect of iceberg structures formed around chloroform molecules in aqueous solution on the rotational motion of chloroform is discussed.

Physicochemical characterization of soluble complexes of human serum low density lipoprotein with heparin

Soluble complexes of low density lipoproteins (LDL) with heparin (HEP) and chondroitin sulphate (CS) in the absence of divalent cations have been studied by means of a micro-rolling-ball ciscometer to obtain information about molecular size and structure of the aggregates. The rheological results were supplied and corroborated by light scattering measurements, electrophoresis and analytical ultracentrifugation. Molar binding ratios were measured using gel filtration assays and ultracentrifugation. At a certain weight ratio of LD To HEP the solutions showed a significant viscosity maximum. At this weight ratio 2–3 LDL particles are held together 1–2 HEP chains. The hydrodynamic radius R H of this complex is about 16.3 ± 0.90 nm and the rotational diffusion constant is > 7.1 × 10 3 s −1. With excess HEP the radius of the aggregates is almost the same as that of free LDL ( R H = 11.9 ± 0.70 nm). Quantitative binding studies revealed that in this case 1–2 HEP molecules are bound to a single LDL particle. An interaction was also found with CS and LDL but complex formation in this case showed different characteristics. Very low density lipoproteins (VLDL) and high density lipoproteins (HDL) gave no rheologically effective aggregates with HEP.

Raman linewidth study of molecular interactions in mixtures of hexafluorobenzene with benzene and with mesitylene

AbstractRaman linewidths have been measured at room temperature for the 560 cm−1 band of hexafluorobenzene, for the 991 cm−1 band of benzene, and for the 576 cm−1 band of mesitylene, in the pure liquids and in binary solutions. Linewidths have also been measured for the 799 cm−1 band of cyclohexane as a reference. Rotational diffusion constants for the tumbling motion of the molecular planes have been evaluated from the Raman linewidths. Experimental diffusion constants are compared with theoretical values calculated on the basis of the semi‐slip rotational diffusion model. Effects of molecular interactions of hexafluorobenzene with benzene or mesitylene on the rotational motion of molecules in solution are discussed.

Structural analysis of self-replicating RNA synthesized by Qβ replicase

Self-replication of the RNA variant MNV-11 (86 base-pairs) by Qβ replicase leads, in the presence of salt, to stepwise selection of the more salt-resistant variants SV-11 (113 base-pairs) and MDV-1 (220 base-pairs). The structures of these and two other unrelated salt-resistant variants are compared. All variants can exist as double-stranded or as single-stranded RNA. The co-operative thermal denaturation of double-stranded RNAs requires high temperatures, around or even above 100°C. Double-stranded RNA molecules have high negative electric dichroisms and their polarizabilities and rotational diffusion constants show the same length dependences as double-stranded DNAs if RNA is assumed to be in the A-form and DNA in the B-form. The single-stranded RNAs also have sharp melting points at high temperatures and rather high hyperchromicities, revealing strong secondary structuring of the single-stranded RNA. The more salt-resistant variants have still higher melting points and hyperchromicities. Single-stranded RNAs melt a few degrees lower than double-strands of the same species, except for single-stranded MDV-1, which melts at the same temperature as its double-stranded form. Concomitant with increasing secondary structure of the single-stranded RNA is a decrease in their rates of annealing to form double strands. Single-stranded variants are both the immediate products of replication (replicas) and the preferred templates. SV-11 has two single-stranded RNA forms, only one of which is able to serve as an active template for Qβ replicase. Its inactive single-stranded form is more stable and apparently has a hairpin structure. The single-stranded RNAs active in replication have vanishing electric dichroisms, indicating defined tertiary structures that do not allow an independent orientation of stems and loops in the electrical field.

Molecular motion in anisotropic medium. II. The proton relaxation study of CH3CN: The general A3 spin system

The coupled relaxation of an A3 spin system (CH3CN) dissolved in a perdeuterated nematic phase (EBBA-d23) is studied for the first time. The partially averaged dipolar interaction allows one to observe a triplet pattern on which four different spin perturbations have been performed: a selective soft π pulse on either an external or the central transition, and a nonselective π pulse affecting all three transitions with or without spin tickling on one of the external transitions. The last perturbation provides a measure of the time evolution of the doublet components in the central line of the triplet. The relaxation processes are modeled as intramolecular dipole–dipole interactions plus other mechanisms which are treated collectively as external random magnetic fields (RF). A restricted diffusion model is used which takes account of the molecular orientation of the solute molecule. Cross relaxation terms are very important, and RF mechanisms are not negligible even in a perdeuterated nematic phase. The anisotropy of the rotational diffusion is obtained, and R, the rotational diffusion constant of an axis perpendicular to the axis of symmetry of the rotor, is found to be 25 times smaller than in neat liquid. The diffusion constant about the principal axis R∥ is not affected significantly by the liquid crystal. The values of R⊥ and R∥ give correlation times which allow extreme narrowing approximations, but in accordance with theoretical predictions it is demonstrated experimentally that the zeroth, first, and second order projections of the dipolar spectral densities are not equal due to preferential ordering of CH3CN in the liquid crystal. Optimal values of the effective ordering parameter SZZ obtained from dipolar splittings in the spectrum and from the dipolar relaxation parameters differ from each other. This difference may be rationalized on the basis of models which account for the two different physical phenomena.

Transient electric birefringence study of the length and stiffness of short DNA restriction fragments

AbstractTransient electric birefringence measurements of the rotational diffusion constant of five short restriction fragments of the plasmid pBR322 show that the hydrodynamic length is independent of sodium ion concentration in the range of 0.2 to 2.5 mM. The fragments are too stiff to be modeled as wormlike molecules. The rotational relaxation times of the fragments, which range from 64 to 124 base pairs, have been used to calculate the rise per base pair using six different theoretical expressions for the length dependence of the rotational diffusion coefficient of straight cylinder. The best estimate for the rise per base pair of Na‐DNA in solution is 3.3 ± 0.1 Å.

Molecular Dynamics Study of Infinitely Thin Hard Rods: Scaling Behavior of Transport Properties

A molecular dynamics study on a system of infinitely thin hard rods is reported. At low densities, rotational and translational diffusion is adequately described by the Enskog theory, but at high densities (ρ*≫1) large deviations are observed. For ρ*≫1, the rotational diffusion constant (Dr) and the longitudinal translational diffusion constant (D∥) are compared with scaling predictions. The molecular dynamics results confirm that Dr∼ρ*-2, and are consistent with a predicted divergence of D∥∼ρ*1/2.

Determination of anisotropic rotational diffusion constants of cyclohexane from raman linewidths and NMR T1 data

Isotropie and anisotropic Raman linewidths of the v2, v3, v4,v5 and v6 modes of cyclohexane and cyclohexane-d12 are measured in the liquid state. Rotational diffusion constants for rotations around the C2 and C3 axes are determined by combining Raman linewidth and NMR T1 data. The results show slight anisotropy in the rotational motion of liquid cyclohexane.

Hydrodynaimcal Properties of Nucleosomes

AbstractDynamic light scattering and electric birefringence have been used together to measure both translational and rotational diffusion constants of nucleosomes oligomers. Assuming an ellipsoïdic model, the overall size and shape of these oligomers have been calculated; incertitude determinations, carefully carried out, give an idea of the actual validity of this type of results. Monomer and dimer can be considered as weakly elongated ellipsoïds, while trimer to hexamer are better represented by spheres. De la Torre and Bloomfield modelisation has also been applied to interpret our experimental results, leading for the monomer and dimer to dimensions which are reasonnably well in accordance with electron microscopic determinations.