Induced circular dichroism of the interaction between pinacyanol and algal alginates.

The interaction between pinacyanol chloride and sodium alginate or guluronate-rich alginate is found to effect profound changes in the visible absorbance and circular dichroism spectra. Two different types of aggregates are observed depending on the relative dye/alginate concentrations. With a dye/alginate ratio at 1:1, a complex is deduced based on an analysis of Job's method and conductometric titrations. Another complex forms at 1:10 dye/alginate ratio and only in the presence of alginate or guluronate-rich alginate. The two aggregates are in dynamic equilibrium according to the presence of isosbestic points in the visible spectra. The effects of pH and divalent cations on the spectra are studied. The 1:10 complex is damaged by addition of hydrochloric acid and divalent cations; however, at low concentration of these agents the spectra indicate conversion of the complex into the 1:1 aggregate. Models for the two complexes are proposed taking into account the preference of guluronate binding sites for chelating ions.

Bicycle-pedal isomerization in a rhodopsin chromophore model.

Probing the isomerization of a retinal chromophore model we have found the first ab initio realization of the so-called "bicycle-pedal mechanism". In an ensemble of 47 starting geometries generated by ground-state zero-point-energy sampling one single trajectory followed the aforementioned reaction mode which was proposed by Warshel in 1976. Furthermore restrained optimization of synchronous rotation mode shows that two-double-bond isomerization is barrierless for the conrotatory and disrotatory pathway.

9-Demethylrhodopsin: theoretical evidence for a relaxed batho intermediate.

The 9-methyl group of retinal is crucial for the photoreaction of rhodopsin. On the basis of the results of QM/MM simulations, we propose that the primary function of the methyl group is not to properly align the chromophore in the ground state, but that it is a prerequisite for the peculiarly twisted and strained chromophore observed in the batho state. With the methyl group firmly anchored in the protein binding pocket the protein, at the cost of the incipient photon energy, manages to increase the strain energy stored in the chromophore by 25%, which may be crucial for driving the subsequent transformations.

Glutamic acid 181 is uncharged in dark-adapted visual rhodopsin.

We have performed a high-level quantum chemical analysis to study the chromophore-protein interaction involving the charged (B) and/or uncharged (C) form of E181 and also a mutant E181Q model in the presence of the primary counterion E113 (A). As the magnitude of the calculated spectral shifts on either side remains within +/-10 nm, we show that the orientation of the dipole moment vector is the key to unlocking the puzzle on this contentious issue. We find that E181 is present in the uncharged (or) protonated form in the dark-adapted visual Rhodopsin, and therefore an electrostatically neutral environment is envisaged.

Binding of bivalent cations by hyaluronate in aqueous solution.

The interaction between sodium hyaluronate and bivalent cations was investigated by conductometry, viscosimetry, circular dichroism and nuclear magnetic resonance spectroscopy. It is shown that the hyaluronate chains (Mn approximately 4.0 x 10(5)-1.7 x 10(6)g/mol) bind various bivalent cations (Ca2+, Mg2+, Mn2+, Fe2+, Cu2+, Zn2+, Cd2+ and Pb2+) at pH 6 in aqueous solutions. Hyaluronate deriving from Streptococcus equi was studied in comparison with dextran from Leuconostoc mesenteroides which was shown to develop no specific interactions with the bivalent cations. The molar relation between the bivalent cations and the disaccharide units of the resulting complex was determined with the result that one bivalent cation is bound by approximately five disaccharide units. Heavy metal ions (Cd2+, Pb2+) seem to bind stronger to the hyaluronate chain than their lighter counterparts (Ca2+, Mg2+). Circular dichroism spectra of the hyaluronate exhibit a cation-induced change in the n-pi* transition, indicating that the acetamide group of the aminoglucane unit is involved during the complexation. NMR spectra of hyaluronic acid in presence of paramagnetic manganese cations show strong interactions between the acetamide as well as the carboxylate groups and the cations. Based on these data, a structure of the binding complex is proposed which involves two disaccharide units.

Photoisomerization mechanism of rhodopsin and 9-cis-rhodopsin revealed by x-ray crystallography.

The primary photochemical process of the visual function has been investigated using the three crystallographic models, 11-cis-rhodopsin, all-trans-bathorhodopsin, and the artificial isomeric 9-cis-rhodopsin. Detailed examination of the atomic displacements and dihedral angle changes of the retinal chromophore involved in the interconversion among these isomers suggests the mechanism of isomerization efficiency.

Photochemistry of visual pigment chromophore models by ab initio molecular dynamics.

Ab initio excited-state molecular dynamics calculations have been performed to study the effect of methyl substitution and chromophore distortion on the photoreaction of different four-double-bond retinal model chromophores. Randomly distributed starting geometries were generated by zero-point energy sampling; after Franck-Condon excitation the reaction was followed on the S1 surface. For determining the photoproduct and its configuration, a simplified approach--torsion angle following--is discussed and applied. We find that chromophore distortion significantly affects the outcome of the photoreaction: with dihedral angles taken from the rhodopsin-embedded 11-cis-retinal chromophore, the reaction rate of the model chromophore is increased by a factor of 3 compared to that of the relaxed chromophore. Also, the reaction proceeds in a completely stereoselective manner involving only the cis double bond and with a minimum quantum yield of 72%. Bond torsion is more effective than methyl substitution for fast and selective photochemistry, which is in agreement with photophysical measurements on rhodopsin analogues. We conclude that apart from the geometric distortions caused by the protein pocket it is not necessary to postulate other specific interactions between the protein and the chromophore to effect the selective and ultrafast photoreaction in rhodopsin.

Bis-ortho-substitution by methyl groups dramatically increases the racemization barrier of Tröger bases.

We have shown through racemization kinetics studies that the enantiomerization barriers of the bis-ortho-methyl substituted Tröger bases 2 and 3 in acidic media are raised by 30 kJ mol(-1) relative to the parent compound 1, that is 130.4(4) and 131.6(4) kJ mol(-1), respectively (105 degrees C, pH 1, ethylene glycol). The enantiomerization barrier of para-methoxy-para-nitro substituted Tröger base 4 was determined by dynamic capillary electrophoresis to 96.3(2) kJ mol(-1) (25 degrees C, pH 2.2, H(2)O), which is lower by 5 kJ mol(-1) relative to 1. The influence of deutero-substitution on the racemization rates was also studied. The influence of steric and electronic factors on the enantiomerization barrier was investigated by quantum-mechanical (DFT) calculations. It is shown that enantiomerization takes place in two steps: ring-opening and further interconversion of the monocyclic intermediate. For the interconversion to occur a transition state has to be passed which is sensitive to steric effects. Ortho-substitution by methyl groups significantly increases the energy of this state. Thus, compounds 2 and 3 are the simplest Tröger bases which are configurationally stable in acidic media.

Ground and excited states of retinal schiff base chromophores by multiconfigurational perturbation theory.

We have studied the wavelength dependence of retinal Schiff base absorbencies on the protonation state of the chromophore at the multiconfigurational level of theory using second order perturbation theory (CASPT2) within an atomic natural orbital basis set on MP2 optimized geometries. Quantitative agreement between calculated and experimental absorption maxima was obtained for protonated and deprotonated Schiff bases of all-trans- and 11-cis-retinal and intermediate states covering a wavelength range from 610 to 353 nm. These data will be useful as reference points for the calibration of more approximate schemes.

Origin and consequences of steric strain in the rhodopsin binding pocket.

To study the origin and the effects of steric strain on the chromophore conformation in rhodopsin, we have performed quantum-mechanical calculations on the wild-type retinal chromophore and four retinal derivatives, 13-demethyl-, 10-methyl-13-demethyl-, 10-methyl-, and 9-demethylretinal. For the dynamics of the whole protein, a combined quantum mechanics/molecular mechanics method (DFTB/CHARMM) was used and for the calculation of excited-state properties the nonempirical CASSCF/CASPT2 method. After relaxation inside the protein, all chromophores show significant nonplanar distortions from C10 to C13, most strongly for 10-methylretinal and least pronounced for 9-demethylretinal. In all five cases, the dihedral angle of the C10-C11=C12-C13 bond is negative which attests to the strong chiral discrimination exerted by the protein pocket. The calculations show that the nonplanar distortion of the chromophore, including the sense of rotation, is caused by a combination of two effects: the fitting of both ends to the protein matrix which imposes a distance constraint and the bonding arrangement at the Schiff base terminus. With both the counterion Glu113 and Lys296 displaced off the plane of the chromophore, their binding to N16 exerts a torque on the chromophore. As a result, the polyene chain, from N16 to C13, is twisted in a clockwise manner against the remaining part of the chromophore, leading to a C11=C12 bond with the observed negative dihedral angle. Shifts of the absorption maxima are reproduced correctly, in particular, the red shift of the 10-methyl and the strong blue shift of the 9-demethyl analogue relative to the wild type. Calculated positive rotatory strengths of the alpha-CD bands are in agreement with the calculated absolute conformation of the mutant chromophores.

Bond torsion affects the product distribution in the photoreaction of retinal model chromophores.

Ab initio molecular dynamics (MD) calculations have been performed to study the photoisomerization of a 3-double-bond retinal model chromophore, the all-trans-4, 6-dimethylpenta-3, 5-dieniminium cation, and the possible influence of non-planar distortions on the product distribution. In total, 171 trajectories have been generated for four different conformations of the structure, a planar one and three in which the C4-C5 and the C5=C6 bonds were increasingly twisted out of plane. Starting geometries randomly distributed about the equilibrium geometry were generated by zero-point energy sampling; trajectories were calculated using CASSCF-BOMD methodology and were followed until the photoproduct and its configuration could be assigned. For the latter, two different approaches were applied, one involving the CASSCF configuration vectors, the other an analysis of the MD at the first possible hopping event. Isomerization was found to occur almost exclusively about the central C3=C4 double bond in the case of the planar model compound. Twisting the conjugated pi-system shifts the isomerization site from the central double bond to the terminal C5=C6 double bond. With both the C4-C5 and the C5=C6 bonds twisted by 20 degrees, about 35% of the trajectories lead to the configurationally inverted 5-cis product. The results are discussed with reference to the highly selective and efficient photo-induced isomerization of the retinal chromophore in rhodopsin.

The retinal conformation and its environment in rhodopsin in light of a new 2.2 A crystal structure.

A new high-resolution structure is reported for bovine rhodopsin, the visual pigment in rod photoreceptor cells. Substantial improvement of the resolution limit to 2.2 A has been achieved by new crystallization conditions, which also reduce significantly the probability of merohedral twinning in the crystals. The new structure completely resolves the polypeptide chain and provides further details of the chromophore binding site including the configuration about the C6-C7 single bond of the 11-cis-retinal Schiff base. Based on both an earlier structure and the new improved model of the protein, a theoretical study of the chromophore geometry has been carried out using combined quantum mechanics/force field molecular dynamics. The consistency between the experimental and calculated chromophore structures is found to be significantly improved for the 2.2 A model, including the angle of the negatively twisted 6-s-cis-bond. Importantly, the new crystal structure refinement reveals significant negative pre-twist of the C11-C12 double bond and this is also supported by the theoretical calculation although the latter converges to a smaller value. Bond alternation along the unsaturated chain is significant, but weaker in the calculated structure than the one obtained from the X-ray data. Other differences between the experimental and theoretical structures in the chromophore binding site are discussed with respect to the unique spectral properties and excited state reactivity of the chromophore.

11-cis-retinal protonated Schiff base: influence of the protein environment on the geometry of the rhodopsin chromophore.

Density functional theory (DFT) calculations based on the self-consistent-charge tight-binding approximation have been performed to study the influence of the protein pocket on the 3-dimensional structure of the 11-cis-retinal Schiff base (SB) chromophore. Starting with an effectively planar chromophore embedded in a protein pocket consisting of the 27 next-nearest amino acids, the relaxed chromophore geometry resulting from energy optimization and molecular dynamics (MD) simulations has yielded novel insights with respect to the following questions: (i) The conformation of the beta-ionone ring. The protein pocket tolerates both conformations, 6-s-cis and 6-s-trans, with a total energy difference of 0.7 kcal/mol in favor of the former. Of the two possible 6-s-cis conformations, the one with a negative twist angle (optimized value: -35 degrees ) is strongly favored, by 3.6 kcal/mol, relative to the one in which the dihedral is positive. (ii) Out-of-plane twist of the chromophore. The environment induces a nonplanar helical deformation of the chromophore, with the distortions concentrated in the central region of the chromophore, from C10 to C13. The dihedral angle between the planes formed by the bonds from C7 to C10 and from C13 to C15 is 42 degrees. (iii) The absolute configuration of the chromophore. The dihedral angle about the C12-C13 bond is +170 degrees from planar s-cis, which imparts a positive helicity on the chromophore, in agreement with earlier considerations based on theoretical and spectroscopic evidence.

Nonempirical Calculation of Polymethine Excited States.

Sometimes the simplest systems need the most sophisticated treatment! Only with multiconfigurational SCF methodology including second-order correction (CASPT2) is it possible to quantitatively reproduce the position of the high-intensity methine band of streptocyanine dyes such as the one shown.

Structural, Chemical, and Theoretical Evidence for the Electrophilicity of the [C(6)F(5)Xe](+) Cation in [C(6)F(5)Xe][AsF(6)].

[C(6)F(5)Xe][AsF(6)] was prepared by metathesis from [C(6)F(5)Xe][(C(6)F(5))(2)BF(2)]. The thermal stability of the melt (