The opsin shift and mechanism of spectral tuning in rhodopsin

Molecular dynamics simulations and combined quantum mechanical and molecular mechanical calculations have been performed to investigate the mechanism of the opsin shift and spectral tuning in rhodopsin. A red shift of -980 cm(-1) was estimated in the transfer of the chromophore from methanol solution environment to the protonated Schiff base (PSB)-binding site of the opsin. The conformational change from a 6-s-cis-all-trans configuration in solution to the 6-s-cis-11-cis conformer contributes additional -200 cm(-1), and the remaining effects were attributed to dispersion interactions with the aromatic residues in the binding site. An opsin shift of 2100 cm(-1) was obtained, in reasonable accord with experiment (2730 cm(-1)). Dynamics simulations revealed that the 6-s-cis bond can occupy two main conformations for the β-ionone ring, resulting in a weighted average dihedral angle of about -50°, which may be compared with the experimental estimate of -28° from solid-state NMR and Raman data. We investigated a series of four single mutations, including E113D, A292S, T118A, and A269T, which are located near the PSB, along the polyene chain of retinal and close to the ionone ring. The computational results on absorption energy shift provided insights into the mechanism of spectral tuning, which involves all means of electronic structural effects, including the stabilization or destabilization of either the ground or the electronically excited state of the retinal PSB.     

Vibrational polarization and opsin shift of retinal schiff bases: theoretical study

The changes in the electronic excitation energy arising from molecular structural displacement induced by external electric field (so-called vibrational polarization) are examined theoretically for the protonated and neutral 11-cis retinal Schiff bases. It is shown that the magnitude of the field-induced structural displacement is significantly large for the protonated species, so that the change in the electronic excitation energy arising from this structural displacement is of the same order of magnitude as that arising from the direct effect of electric field on the electronic wave function. These two effects contribute additively to the field-induced spectral shift. The intensity-carrying mode (ICM) theory is employed to extract a single vibrational mode (called primary infrared ICM) that is most important for the field-induced structural displacement. A simple one-dimensional model is constructed, and the extent to which we can interpret the field-induced spectral shift by such a model is examined. In the case of the neutral species, only a small change in the electronic excitation energy is induced by external electric field, mainly because the vibrational polarizability of this species is small. The meaning of these results in the spectral tuning of visual pigments is discussed.     

Vibronic structure in the S1-S0 transition of jet-cooled dibenzofuran

Fluorescence excitation spectra of dibenzofuran in a supersonic jet are observed and the vibronic structure is analyzed for the S(1) (1)A(1) (pipi) and S(0) states. An observation of the rotational envelopes reveals that the band is a B-type band. However, it is shown that most of the strong vibronic bands are A-type bands. The intensity arises from vibronic coupling with the S(2) (1)B(2) state. We find a broad emission in the dispersed fluorescence spectrum for the excitation of the high vibrational levels in the S(1) state. This indicates that intramolecular vibrational redistribution (IVR) occurs efficiently in the isolated dibenzofuran molecule.     

A direct comparison of protein structure in the gas and solution phase: the Trp-cage

Molecular dynamics simulations of zwitterions of the Trp-cage protein in the gas phase show that the most stable ion in vacuo has preserved the charge locations acquired in solution. A direct comparison of the gas and solution-phase structures reveals that, despite the similarity in charge location, there is significant difference in the structures, with a substantial increase in hydrogen bonds and exposure of hydrophobic parts in the gas phase. The structure of the salt bridge in the gas phase is also much more stable than in the (experimental) solution structure.     

Theoretical prediction of the S1-S0 internal conversion of 6-cyanoazulene

Ab initio complete active-space self-consistent field (CASSCF) and second-order Multireference M?ller-Plesset perturbation (MRMP2) calculations were performed to examine the S1-S0 internal conversion of 6-cyanoazulene (6CNAZ). The azulene skeletons of 6CNAZ in S0 and S1 have features that resemble those of azulene. The stable geometry in S0 is characterized by (i) a C2v structure, (ii) an aromatic bond-equalized structure in which all the peripheral skeletal bond distances resemble an aromatic CC bond distance, and (iii) a single bond character of the transannular bond. The stable geometry in S1 is characterized by a nonaromatic C2v structure. Contrary to similarities of the stable geometries in S0 and S1 between 6CNAZ and azulene, the conical intersection (S1/S0-CIX) of 6CNAZ is different from that of azulene. The S1/S0-CIX of 6CNAZ takes a planar structure, whereas that of azulene takes a nonplanar structure in the seven-membered ring (Amatatsu, Y.; Komura, K. J. Chem. Phys. 2006, 125, 174311/1-8). On the basis of those computational findings, we predict the photochemical behavior of 6CNAZ in the S1-S0 internal conversion.     

Reaction coordinate analysis of the S1-S0 internal conversion of azulene

The reaction coordinate of the S(1)-S(0) internal conversion of azulene has been analyzed using ab initio complete active space self-consistent field method. The stable geometry in S(0) (S(0) geometry) takes a bond-equalized structure where all the peripheral skeletal bond distances are similar to an aromatic CC bond distance. The transannular bond is similar to a normal C-C single bond. The first event upon electronic excitation into S(1) at S(0) geometry is characterized by the following two simultaneous changes in the skeletal bonds; the transannular bond in S(1) increases its double bond character and the aromaticity of the peripheral bonds disappears. In consequence, the most stable azulene in S(1) (S(1) geometry) has a biradical character. To reach the conical intersection between S(1) and S(0) (S(1)S(0)-CIX) where radiationless relaxation takes place, the seven-membered ring greatly deviates from a planar structure. After a transition into S(0) at S(1)S(0)-CIX, the bond-equalized structure is recovered immediately and then the nonplanarity decreases so that azulene again takes the stable planar S(0) geometry. In order to deepen the understanding of the S(1)-S(0) internal conversion, the dipole moments along the reaction coordinate have been analyzed.     

Fluorescence probe of Trp-cage protein conformation in solution and in gas phase

Measurements of protein unfolding in the absence of solvent, when combined with unfolding studies in solution, offer a unique opportunity to measure the effects of solvent on protein structure and dynamics. The experiments presented here rely on the fluorescence of an attached dye to probe the local conformational dynamics through interactions with a Trp residue and fields originating on charge sites. We present fluorescence measurements of thermal fluctuations accompanying conformational change of a miniprotein, Trp-cage, in solution and in gas phase. Molecular dynamics (MD) simulations are performed as a function of temperature, charge state, and charge location to elucidate the dye-protein conformational dynamics leading to the changes in measured fluorescence. The results indicate that the stability of the unsolvated protein is dominated by hydrogen bonds. Substituting asparagine for aspartic acid at position 9 results in a dramatic alteration of the solution unfolding curve, indicating that the salt bridge involving Lys8, Asp9, and Arg16 (+ - +) is essential for Trp-cage stability in solution. In contrast, this substitution results in minor changes in the unfolding curve of the unsolvated protein, showing that hydrogen bonds are the major contributor to the stability of Trp-cage in gas phase. Consistent with this hypothesis, the decrease in the number of hydrogen bonds with increasing temperature indicated by MD simulations agrees reasonably well with the experimentally derived enthalpies of conformational change. The simulation results display relatively compact conformations compared with NMR structures that are generally consistent with experimental results. The measured unfolding curves of unsolvated Trp-cage ions are invariant with the acetonitrile content of the solution from which they are formed, possibly as a result of conformational relaxation during or after desolvation. This work demonstrates the power of combined solution and gas-phase studies and of single-point mutations to identify specific noncovalent interactions which contribute to protein-fold stability. The combination of experiment and simulation is particularly useful because these approaches yield complementary information which can be used to deduce the details of structural changes of proteins in the gas phase.     

Density functional theory study of 1:1 glycine-water complexes in the gas phase and in solution

We present a systematic study of 1:1 glycine-water complexes involving all possible glycine conformers. The complex geometries are fully optimized for the first time both in the gas phase and in solution using three DFT methods (B3LYP, PBE1PBE, X3LYP) and the MP2 method. We calculate the G3 energies and use them as the reference data to gauge hydrogen bond strength in the gas phase. The solvent effects are treated via the integral equation formalism-polarizable continuum model (IEF-PCM). Altogether, we locate fifty-two unique nonionized (N) structures and six zwitterionic (Z) structures in the gas phase, and fifty-five N structures and thirteen Z structures in solution. Both correlation and solvation are shown to be important in geometry determination. We found that in the gas phase, a water molecule binds more strongly to the carboxylic acid group of glycine than to its amine group, whereas in solution phase the reverse is true. The most stable Z structure is isoenergetic with the most stable N structure.     

Rotationally resolved S1-S0 electronic spectra of 2,6-diaminopyridine: a four-fold barrier problem

A comparison of the electronic properties of the nitrogen-containing rings aniline, 2-aminopyridine, and 2,6-diaminopyridine (26DAP) shows that the potential energy surface of the molecule is significantly affected as more nitrogen atoms are added to the system. High resolution, rotationally resolved spectra of four vibrational bands in the S(1)-S(0) electronic transition of 26DAP were obtained in order to explain these changes. The zig-zagging inertial defects point to a double minimum excited state potential energy surface along the coupled amino group inversion vibrational mode, which becomes a four-fold well (and barrier) problem when the existence of two nearly degenerate isomers is taken into account. Assuming that the molecules are in the lower energy, opposite-side configuration, ab initio calculations were performed using the MP2/6-31G** level of theory to create a potential energy surface modeling the simultaneous antisymmetric NH(2)-inversion mode. The calculated potential energy surface shows a ground electronic state barrier to simultaneous NH(2) inversion of ~220 cm(-1), and a fit to experimental vibrational energy level spacings and relative intensities produces an excited electronic state barrier of ~400 cm(-1). The ground state barrier is less than that in aniline, but the excited state barrier is larger.     

Effect of polarization on the opsin shift in rhodopsins. 1. A combined QM/QM/MM model for bacteriorhodopsin and pharaonis sensory rhodopsin II

The optical and IR-spectroscopic properties of the protonated Schiff base of retinal are highly sensitive to the electrostatic environment. This feature makes retinal a useful probe to study structural differences and changes in rhodopsins. It also raises an interest to theoretically predict the spectroscopic response to mutation and structural evolution. Computational models appropriate for this purpose usually combine sophisticated quantum mechanical (QM) methods with molecular mechanics (MM) force fields. In an effort to test and improve the accuracy of these QM/MM models, we consider in this article the effects of polarization and inter-residual charge transfer within the binding pocket of bacteriorhodopsin (bR) and pharaonis sensory rhodopsin II (psRII, also called pharaonis phoborhodopsin, ppR) on the excitation energy using an ab initio QM/QM/MM approach. The results will serve as reference for assessing empirical polarization models in a consecutive article.     

Effects of stepwise excitation on fragmentation of gas phase ions: An especially striking case

Dramatically different fragmentation patterns are obtained for 4-ethyl-2,6,7-trioxa-1-phosphabicyclo-[2.2.2]octane-1-oxide upon electron ionization (EI) and for the corresponding molecular ion on collision-induced dissociation (CID). Two reasons for this behaviour have been discovered. (i) Irreversible multistep isomerization of the molecular ions occurs prior to collisional activation in mass spectrometry/mass spectrometry (MS/MS). Isomerization reactions have been characterized by isotopic labelling and by examining structures of relevant unlabelled and labelled fragment ions by MS/MS. The extent of isomerization can be controlled by varying the amount of internal energy of the molecular ions. This has been done by changing the number of thermalizing collisions which the ions undergo with neutral molecules in the ion source. (ii) When multiple collisions are used to dissociate the molecular ions, the initially stable fragmentation products undergo extensive further decomposition. As a result, abundant phosphorus-containing fragment ions are obtained for the bicyclic phosphate in high-pressure CID, whereas electron ionization leads to predominant hydrocarbon ions. A minor change in the structure of this molecule has major effects on the fragmentation behaviour: high- and low-energy collisional activation spectra of the molecular ion of the corresponding phosphite are identical with the 12 e V EI mass spectrum of the neutral.     

Thermal decomposition of 1,3,3-trinitroazetidine in the gas phase, solution, and melt

1,3,3-Trinitroazetidine (TNAZ) was synthesized using the alternative approach based on the transformation of 3-oximino-1-(p-toluenesulfonyl)azetidine in the reaction with nitric acid through intermediate pseudonitrol. The thermal decomposition of TNAZ in the gas phase, melt and m-dinitrobenzene solution in a wide concentration range (5–80%) was studied by manometry, volumetry, thermogravimetry, IR spectroscopy, and mass spectrometry. In the gas phase in the temperature range from 170 to 220°C the thermal decomposition proceeds according to the first-order kinetic law with the activation energy 40.5 kcal mol^?1 and pre-exponential factor 10^15.0 s^?1. The major gaseous reaction products are N₂, NO, NO₂, CO₂, H₂O, and nitroacetaldehyde, and trace amounts of CO and HCN are formed. The rate-determining step of the process is the homolytic cleavage of the N-NO₂ bond in the TNAZ molecule. In melt at 170–210 °C the thermal decomposition proceeds with the pronounced self-acceleration and the maximum reaction rates are observed at conversions 53.9–67.4%. The solid decomposition products accelerate the reaction. It is most likely that the autocatalysis of TNAZ decomposition in the liquid phase is due to the autocatalytic decomposition of 1-nitroso-3,3-dinitroazetidine, which is formed by the thermal decomposition of TNAZ. In m-dinitrobenzene TNAZ also decomposes with self-acceleration. The higher the concentration in the solution, the more pronounced the self-acceleration. Additives of picric acid moderately accelerate the thermal decomposition of TNAZ, whereas hexamethylenetetraamine additives exert a strong acceleration.     

Photoisomerization dynamics of azobenzene in solution with S1 excitation: a femtosecond fluorescence anisotropy study

Measurements of anisotropy of femtosecond fluorescence after direct excitation of the S1(n,pi*) state of azobenzene in hexane and ethylene glycol solutions have been carried out to address the controversy about inversion and rotation in the mechanism of photoisomerization. The observed anisotropies in hexane decay to a nonzero asymptotic level with a relaxation period the same as that for slow decay of the corresponding biexponential transient; this effect is attributed to involvement of the out-of-plane CNNC-torsional motion on approach to a twisted conical intersection along the "rotation channel" that depolarizes the original in-plane transition moment. In contrast, when the rotational channel becomes substantially hindered in ethylene glycol, the anisotropies show no discernible decay feature, but the corresponding transients show prominent decays attributed to involvement of in-plane symmetric motions; the latter approach a planar-sloped conical intersection along a "concerted inversion channel" for efficient internal conversion through vibronic coupling. The proposed mechanism is consistent with theoretical calculations and rationalizes both results on quantum yields and ultrafast observations.     

Pendular-state spectroscopy of the S(1)-S(0) electronic transition of 9-cyanoanthracene

Fluorescence excitation spectra of the S(1)-S(0) origin band of 9-cyanoanthracene have been observed under a uniform electric field up to 200 kV/cm to explore pendular-state spectrum of an asymmetric-top molecule close to the strong field limit. The observed spectra exhibit distinct evolution of the band contour as a function of the applied electric field, which are much different from each other for different excitation configurations. An approximate method suitable for spectrum simulations of large asymmetric-top molecules in a pendular condition is developed for the analysis of the experimental results. The comparison of the observed and simulated spectra shows that the spectra are well ascribed in terms of the pendular-state selection rules, which have recently been derived from theoretical consideration of the pendular-limit representation of energy levels and spectra.     

Ionization of imidazole in the gas phase, microhydrated environments, and in aqueous solution

Hydration of neutral and cationic imidazole is studied by means of ab initio and molecular dynamics calculations, and by photoelectron spectroscopy of the neutral species in a liquid microjet. The calculations show the importance of long range solvent polarization and of the difference between the structure of water molecules in the first shell around the neutral vs cationic species for determining vertical and adiabatic ionization potentials. The vertical ionization potential of neutral imidazole of 8.06 eV calculated using a nonequilibrium polarizable continuum model agrees well with the value of 8.26 eV obtained experimentally for an aqueous solution at pH 10.6.     

Experimental and Theoretical Study on p-Chlorofluorobenzene in the S0, S1 and D0 States

The geometric structures and vibration frequencies of \begin{document}$ para $\end{document}-chlorofluorobenzene (\begin{document}$ p $\end{document}-ClFPh) in the first excited state of neutral and ground state of cation were investigated by resonance-enhanced multiphoton ionization and slow electron velocity-map imaging. The infrared spectrum of S\begin{document}$ _0 $\end{document} state and absorption spectrum for S\begin{document}$ _1 $\end{document}\begin{document}$ \leftarrow $\end{document}S\begin{document}$ _0 $\end{document} transition in \begin{document}$ p $\end{document}-ClFPh were also recorded. Based on the one-color resonant two-photon ionization spectrum and two-color resonant two-photon ionization spectrum, we obtained the adiabatic excited-state energy of \begin{document}$ p $\end{document}-ClFPh as 36302\begin{document}$ \pm $\end{document}4 cm\begin{document}$ ^{-1} $\end{document}. In the two-color resonant two-photon ionization slow electron velocity-map imagin spectra, the accurate adiabatic ionization potential of \begin{document}$ p $\end{document}-ClFPh was extrapolated as 72937\begin{document}$ \pm $\end{document}8 cm\begin{document}$ ^{-1} $\end{document} via threshold ionization measurement. In addition, Franck-Condon simulation was performed to help us confidently ascertain the main vibrational modes in the S\begin{document}$ _1 $\end{document} and D\begin{document}$ _0 $\end{document} states. Furthermore, the mixing of vibrational modes between S\begin{document}$ _0 $\end{document}\begin{document}$ \rightarrow $\end{document}S\begin{document}$ _1 $\end{document} and S\begin{document}$ _1 $\end{document}\begin{document}$ \rightarrow $\end{document}D\begin{document}$ _0 $\end{document} has been analyzed.     

Crossing the phase boundary to study protein dynamics and function: combination of amide hydrogen exchange in solution and ion fragmentation in the gas phase

Protein dynamics are the key to understanding their behavior. The static protein structure alone in most cases is insufficient to describe the vast array of complex functions they perform in vivo. Until recently there were relatively few techniques available to investigate the dynamic nature of these proteins. Mass spectrometry has recently emerged as a powerful biophysical method, capable of providing both structural and dynamic information. By utilizing the labile nature of amide hydrogens as a marker of the backbone dynamics in solution, combined with gas-phase dissociation techniques, we now have a high-resolution tool to locate these exchanging hydrogens within the sequence of the protein and to probe the functional importance of its structural elements. In this paper we describe several applications of these methodologies to illustrate the importance of dynamics to the biological functions of proteins.     

Doppler-free two-photon excitation spectroscopy and the Zeeman effects. Perturbations in the 14(0)1 and 1(0)(1)14(0)1 bands of the S1 <-- S0 transition of C6D6

Doppler-free two-photon excitation spectra and the Zeeman effects for the 1 band of the S1 1B2u <-- S0 1A1g transition in gaseous benzene-d6 were measured. Although the spectral lines were strongly perturbed, almost all of the lines near the band origin could be assigned. From a deperturbation analysis, the perturbation near the band origin was identified as originating from an anharmonic resonance interaction. Perturbation centered at K = 28-29 in the 14(0)1 band was analyzed, and it was identified as originating from a perpendicular Coriolis interaction. The symmetry and the assignment of the perturbing state proposed by Schubert et al. (Schubert, U.; Riedle, E.; Neusser, H. J. J. Chem. Phys. 1989, 90, 5994.) were confirmed. No perturbation originating from an interaction with a triplet state was observed in both bands. From the Zeeman spectra and the analysis, it is demonstrated that rotationally resolved levels are not mixed with a triplet state. The intersystem mixing is not likely to occur at levels of low excess energy in the S1 state of an isolated benzene. Nonradiative decay of an isolated benzene in the low vibronic levels of the S1 state will occur through the internal mixing followed by the rotational and vibrational relaxation in the S0 state.     

Competing S(N)2 and E2 reaction pathways for hexachlorocyclohexane degradation in the gas phase, solution and enzymes

Quantum chemistry calculations have been used alongside experimental kinetic analysis to investigate the competition between S(N)2 and E2 mechanisms for the dechlorination of hexachlorocyclohexane isomers, revealing that enzyme specificity reflects the intrinsic reactivity of the various isomers.