Click-together azobenzene dendrons: Synthesis and characterization

We synthesized 1,2,3-triazole-linked azobenzene dendrons of four generations. No protection-deprotection approach was needed during the generation development via click reaction. The photoisomerization of azobenzene dendrons was Studied using UV-vis spectra. The cis isomers of these dendrons were more stable than trans isomers in the dark; however, the cis isomers could be quickly converted to trans forms under visible light exposure in seconds. The trans form could change to cis form reversibly by UV irradiation as well.

Orientational relaxation in a random dipolar lattice: Wave-number and frequency dependence

In order to understand the role of translational modes in the orientational relaxation in dense dipolar liquids, we have carried out a computer ''experiment'' where a random dipolar lattice was generated by quenching only the translational motion of the molecules of an equilibrated dipolar liquid. The lattice so generated was orientationally disordered and positionally random. The detailed study of orientational relaxation in this random dipolar lattice revealed interesting differences from those of the corresponding dipolar liquid. In particular, we found that the relaxation of the collective orientational correlation functions at the intermediate wave numbers was markedly slower at the long times for the random lattice than that of the liquid. This verified the important role of the translational modes in this regime, as predicted recently by the molecular theories. The single-particle orientational correlation functions of the random lattice also decayed significantly slowly at long times, compared to those of the dipolar liquid.

Dipolar reorientation and phase-transition in mixed alkali-halide crystals

We show that the results of Lüty and Ortiz-Lopez relating the cyanide reorientation rates to the high-temperature phase diagrams of alkali-halide-alkali-cyanide mixed crystals can be understood within simple mean-field theory.

Adsorption isotherms for neutral organic compounds - A hierarchy in modelling: Part V. Models for the inner layer potential difference in the presence of dipolar adsorption

The relations for the inner layer potential &fference (E) in the presence of adsorbed orgamc molecules are derived for three hterarchlcal models, m terms of molecular constants like permanent &pole moments, polarlzablhtles, etc It is shown how the experimentally observed patterns of the E vs 0 plots (hnear m all ranges of $\sigma^M$, non-linear in one or both regions of o M, etc ) can be understood in a serm-quantltatlve manner from the simplest model in our hierarchy, viz the two-state site panty version Two-state multi-site and three-state (sxte panty) models are also analysed and the slope (3E/80),,M tabulated for these also The results for the Esm-Markov effect are denved for all the models and compared with the earlier result of Parsons. A comparison with the GSL phenomenologlcal equation is presented and its molecular basis, as well as the hmltatlons, is analysed. In partxcular, two-state multa-slte and three-state (site panty) models yield E-o M relations that are more general than the "umfied" GSL equation The posslblhty of vaewlng the compact layer as a "composite medium" with an "effective dlelectnc constant" and obtaimng novel phenomenological descnptions IS also indicated.

Direct estimation of an element of order matrix from H-1 NMR spectra of strongly dipolar coupled spins

NMR spectra of molecules oriented in thermotropic liquid crystalline media provide information on the molecular structure and order. The spins are generally strongly dipolar coupled and the spectral analyse require the tedious and time consuming numerical iterative calculations. The present study demonstrates the application of multiple quantum spin state selective detection of single quantum transitions for mimicking the homonuclear decoupling and the direct estimation of an element of ordering matrix. This information is utilized to estimate the nearly accurate starting dipolar couplings for iterative calculations. The studies on the spectra of strongly dipolar coupled five and six interacting spin systems are reported.

Structure and Dynamics of Coil-like Molecules by Residual Dipolar Couplings

Nuclear magnetic resonance (NMR) spectroscopy provides us with many means to study biological macromolecules in solution. Proteins in particular are the most intriguing targets for NMR studies. Protein functions are usually ascribed to specific three-dimensional structures but more recently tails, long loops and non-structural polypeptides have also been shown to be biologically active. Examples include prions, -synuclein, amylin and the NEF HIV-protein. However, conformational preferences in coil-like molecules are difficult to study by traditional methods. Residual dipolar couplings (RDCs) have opened up new opportunities; however their analysis is not trivial. Here we show how to interpret RDCs from these weakly structured molecules. The most notable residual dipolar couplings arise from steric obstruction effects. In dilute liquid crystalline media as well as in anisotropic gels polypeptides encounter nematogens. The shape of a polypeptide conformation limits the encounter with the nematogen. The most elongated conformations may come closest whereas the most compact remain furthest away. As a result there is slightly more room in the solution for the extended than for the compact conformations. This conformation-dependent concentration effect leads to a bias in the measured data. The measured values are not arithmetic averages but essentially weighted averages over conformations. The overall effect can be calculated for random flight chains and simulated for more realistic molecular models. Earlier there was an implicit thought that weakly structured or non-structural molecules would not yield to any observable residual dipolar couplings. However, in the pioneering study by Shortle and Ackerman RDCs were clearly observed. We repeated the study for urea-denatured protein at high temperature and also observed indisputably RDCs. This was very convincing to us but we could not possibly accept the proposed reason for the non-zero RDCs, namely that there would be some residual structure left in the protein that to our understanding was fully denatured. We proceeded to gain understanding via simulations and elementary experiments. In measurements we used simple homopolymers with only two labelled residues and we simulated the data to learn more about the origin of RDCs. We realized that RDCs depend on the position of the residue as well as on the length of the polypeptide. Investigations resulted in a theoretical model for RDCs from coil-like molecules. Later we extended the studies by molecular dynamics. Somewhat surprisingly the effects are small for non-structured molecules whereas the bias may be large for a small compact protein. All in all the work gave clear and unambiguous results on how to interpret RDCs as structural and dynamic parameters of weakly structured proteins.

Unusual Anisotropic Effects from 1,3-Dipolar Cycloadducts of 4-Azidomethyl Coumarins

4-Bromomethylcoumarins (1) reacted with sodium azide in aqueous acetone to give 4-azidomethyl-coumarins (2), which underwent 1,3-dipolar cycloaddition with acetylenic dipolarophiles to give triazoles (3). These triazoles (3) have been found to exhibit interesting variations in the chemical shifts of C-3-H and C-4-methylene protons. Protonation studies indicate that the shielding effect of the C-3-H of coumarin is due to pi-electrons of the triazole ring, further supported by diffraction and computational studies.

Dynamic nature of proteins - interpretation of residual dipolar couplings

Protein conformations and dynamics can be studied by nuclear magnetic resonance spectroscopy using dilute liquid crystalline samples. This work clarifies the interpretation of residual dipolar coupling data yielded by the experiments. It was discovered that unfolded proteins without any additional structure beyond that of a mere polypeptide chain exhibit residual dipolar couplings. Also, it was found that molecular dynamics induce fluctuations in the molecular alignment and doing so affect residual dipolar couplings. The finding clarified the origins of low order parameter values observed earlier. The work required the development of new analytical and computational methods for the prediction of intrinsic residual dipolar coupling profiles for unfolded proteins. The presented characteristic chain model is able to reproduce the general trend of experimental residual dipolar couplings for denatured proteins. The details of experimental residual dipolar coupling profiles are beyond the analytical model, but improvements are proposed to achieve greater accuracy. A computational method for rapid prediction of unfolded protein residual dipolar couplings was also developed. Protein dynamics were shown to modulate the effective molecular alignment in a dilute liquid crystalline medium. The effects were investigated from experimental and molecular dynamics generated conformational ensembles of folded proteins. It was noted that dynamics induced alignment is significant especially for the interpretation of molecular dynamics in small, globular proteins. A method of correction was presented. Residual dipolar couplings offer an attractive possibility for the direct observation of protein conformational preferences and dynamics. The presented models and methods of analysis provide significant advances in the interpretation of residual dipolar coupling data from proteins.

2(n)-SEMA-a robust solid state nuclear magnetic resonance experiment for measuring heteronuclear dipolar couplings in static oriented systems using effective transverse spin-lock

Separated local field (SLF) spectroscopy is a powerful technique to measure heteronuclear dipolar couplings. The method provides site-specific dipolar couplings for oriented samples such as membrane proteins oriented in lipid bilayers and liquid crystals. A majority of the SLF techniques utilize the well-known Polarization Inversion Spin Exchange at Magic Angle (PISEMA) pulse scheme which employs spin exchange at the magic angle under Hartmann-Hahn match. Though PISEMA provides a relatively large scaling factor for the heteronuclear dipolar coupling and a better resolution along the dipolar dimension, it has a few shortcomings. One of the major problems with PISEMA is that the sequence is very much sensitive to proton carrier offset and the measured dipolar coupling changes dramatically with the change in the carrier frequency. The study presented here focuses on modified PISEMA sequences which are relatively insensitive to proton offsets over a large range. In the proposed sequences, the proton magnetization is cycled through two quadrants while the effective field is cycled through either two or four quadrants. The modified sequences have been named as 2(n)-SEMA where n represents the number of quadrants the effective field is cycled through. Experiments carried out on a liquid crystal and a single crystal of a model peptide demonstrate the usefulness of the modified sequences. A systematic study under various offsets and Hartmann-Hahn mismatch conditions has been carried out and the performance is compared with PISEMA under similar conditions.

Solvation dynamics in dipolar liquids

The time dependent response of a polar solvent to a changing charge distribution is studied in solvation dynamics. The change in the energy of the solute is measured by a time domain Stokes shift in the fluorescence spectrum of the solute. Alternatively, one can use sophisticated non-linear optical spectroscopic techniques to measure the energy fluctuation of the solute at equilibrium. In both methods, the measured dynamic response is expressed by the normalized solvation time correlation function, S(t). The latter is found to exhibit uniquefeatures reflecting both the static and dynamic characteristics of each solvent. For water, S(t) consists of a dominant sub-50 fs ultrafast component, followed by a multi-exponential decay. Acetonitrile exhibitsa sub-100 fs ultrafast component, followed by an exponential decay. Alcohols and amides show features unique to each solvent and solvent series. However, understanding and interpretation of these results have proven to be difficult, and often controversial. Theoretical studiesand computer simulations have greatly facilitated the understanding ofS(t) in simple systems. Recently solvation dynamics has been used extensively to explore dynamics of complex systems, like micelles and reverse micelles, protein and DNA hydration layers, sol-gel mixtures and polymers. In each case one observes rich dynamical features, characterized again by multi-exponential decays but the initial and final time constants are now widely separated. In this tutorial review, we discuss the difficulties in interpreting the origin of the observed behaviour in complex systems.

Molecular theory of solvation and solvation dynamics of a classical ion in a dipolar liquid

A microscopic theory of equilibrium solvation and solvation dynamics of a classical, polar, solute molecule in dipolar solvent is presented. Density functional theory is used to explicitly calculate the polarization structure around a solvated ion. The calculated solvent polarization structure is different from the continuum model prediction in several respects. The value of the polarization at the surface of the ion is less than the continuum value. The solvent polarization also exhibits small oscillations in space near the ion. We show that, under certain approximations, our linear equilibrium theory reduces to the nonlocal electrostatic theory, with the dielectric function (c(k)) of the liquid now wave vector (k) dependent. It is further shown that the nonlocal electrostatic estimate of solvation energy, with a microscopic c(k), is close to the estimate of linearized equilibrium theories of polar liquids. The study of solvation dynamics is based on a generalized Smoluchowski equation with a mean-field force term to take into account the effects of intermolecular interactions. This study incorporates the local distortion of the solvent structure near the ion and also the effects of the translational modes of the solvent molecules.The latter contribution, if significant, can considerably accelerate the relaxation of solvent polarization and can even give rise to a long time decay that agrees with the continuum model prediction. The significance of these results is discussed.

A molecular theory of collective orientational relaxation in pure and binary dipolar liquids

A molecular theory of collective orientational relaxation of dipolar molecules in a dense liquid is presented. Our work is based on a generalized, nonlinear, Smoluchowski equation (GSE) that includes the effects of intermolecular interactions through a mean‐field force term. The effects of translational motion of the liquid molecules on the orientational relaxation is also included self‐consistently in the GSE. Analytic expressions for the wave‐vector‐dependent orientational correlation functions are obtained for one component, pure liquid and also for binary mixtures. We find that for a dipolar liquid of spherical molecules, the correlation function ϕ(k,t) for l=1, where l is the rank of the spherical harmonics, is biexponential. At zero wave‐vector, one time constant becomes identical with the dielectric relaxation time of the polar liquid. The second time constant is the longitudinal relaxation time, but the contribution of this second component is small. We find that polar forces do not affect the higher order correlation functions (l>1) of spherical dipolar molecules in a linearized theory. The expression of ϕ(k,t) for a binary liquid is a sum of four exponential terms. We also find that the wave‐vector‐dependent relaxation times depend strongly on the microscopic structure of the dense liquid. At intermediate wave vectors, the translational diffusion greatly accelerates the rate of orientational relaxation. The present study indicates that one must pay proper attention to the microscopic structure of the liquid while treating the translational effects. An analysis of the nonlinear terms of the GSE is also presented. An interesting coupling between the number density fluctuation and the orientational fluctuation is uncovered.

Polarization relaxation, dielectric dispersion, and solvation dynamics in dense dipolar liquid

A unified treatment of polarization relaxation, dielectric dispersion and solvation dynamics in a dense, dipolar liquid is presented. It is shown that the information of solvent polarization relaxation that is obtained by macroscopic dielectric dispersion experiments is not sufficient to understand dynamics of solvation of a newly created ion or dipole. In solvation, a significant contribution comes from intermediate wave vector processes which depend critically on the short range (nearest‐neighbor) spatial and orientational order that are present in a dense, dipolar liquid. An analytic expression is obtained for the time dependent solvation energy that depends, in addition to the translational and rotational diffusion coefficients of the liquid, on the ratio of solute–solvent molecular sizes and on the microscopic structure of the polar liquid. Mean spherical approximation (MSA) theory is used to obtain numerical results for polarization relaxation, for wave vector and frequency dependent dielectric function and for time dependent solvation energy. We find that in the absence of translational contribution, the solvation of an ion is, in general, nonexponential. In this case, the short time decay is dominated by the longitudinal relaxation time but the long time decay is dominated by much slower large wave vector processes involving nearest‐neighbor molecules. The presence of a significant translational contribution drastically alters the decay behavior. Now, the long‐time behavior is given by the longitudinal relaxation time constant and the short time dynamics is controlled by the large wave vector processes. Thus, although the continuum model itself is conceptually wrong, a continuum model like result is recovered in the presence of a sizeable translational contribution. The continuum model result is also recovered in the limit of large solute to solvent size ratio. In the opposite limit of small solute size, the decay is markedly nonexponential (if the translational contribution is not very large) and a complete breakdown of the continuum model takes place. The significance of these results is discussed.