Constraints of opsin structure on the ligand-binding site: studies with ring-fused retinals

Ring-fused retinal analogs were designed to examine the hula-twist mode of the photoisomerization of the 9-cis retinylidene chromophore. Two 9-cis retinal analogs, the C11-C13 five-membered ring-fused and the C12-C14 five-membered ring-fused retinal derivatives, formed the pigments with opsin. The C11-C13 ring-fused analog was isomerized to a relaxed all-trans chromophore (lambda(max) > 400 nm) at even -269 degrees C and the Schiff base was kept protonated at 0 degrees C. The C12-C14 ring-fused analog was converted photochemically to a bathorhodopsin-like chromophore (lambda(max) = 583 nm) at -196 degrees C, which was further converted to the deprotonated Schiff base at 0 degrees C. The model-building study suggested that the analogs do not form pigments in the retinal-binding site of rhodopsin but form pigments with opsin structures, which have larger binding space generated by the movement of transmembrane helices. The molecular dynamics simulation of the isomerization of the analog chromophores provided a twisted C11-C12 double bond for the C12-C14 ring-fused analog and all relaxed double bonds with a highly twisted C10-C11 bond for the C11-C13 ring-fused analog. The structural model of the C11-C13 ring-fused analog chromophore showed a characteristic flip of the cyclohexenyl moiety toward transmembrane segments 3 and 4. The structural models suggested that hula twist is a primary process for the photoisomerization of the analog chromophores.     

The role of the beta-ionone ring in the photochemical reaction of rhodopsin

Time-dependent density functional theory (TDDFT) calculations on the photoabsorption process of the 11-cis retinal protonated Schiff base (PSB) chromophore show that the Franck-Condon relaxation of the first excited state of the chromophore involves a torsional twist motion of the beta-ionone ring relative to the conjugated retinyl chain. For the ground state, the beta-ionone ring and the retinyl chain of the free retinal PSB chromophore form a -40 degrees dihedral angle as compared to -94 degrees for the first excited state. The double bonds of the retinal are shorter for the fully optimized structure of the excited state than for the ground state suggesting a higher cis-trans isomerization barrier for the excited state than for the ground state. According to the present TDDFT calculations, the excitation of the retinal PSB chromophore does not primarily lead to a reaction along the cis-trans torsional coordinate at the C11-C12 bond. The activation of the isomerization center seems to occur at a later stage of the photo reaction. The results obtained at the TDDFT level are supported by second-order M?ller-Plesset (MP2) and approximate singles and doubles-coupled cluster (CC2) calculations on retinal chromophore models; the MP2 and CC2 calculations yield for them qualitatively the same ground state and excited-state structures as obtained in the density functional theory and TDDFT calculations.     

Force field parameters for sulfates and sulfamates based on ab initio calculations: Extensions of AMBER and CHARMm fields

Ab initio self-consistent field (SCF) Hartree-Fock calculations of sulfates R? O? SO₃(?1) (R = Me, Et, i-Pr) and sulfamates R? NHSO₃(?1) (R = H, Me, Et, i-Pr) were performed at the 4-31G(*S*N) //3-21G(*S*N) basis set levels, where asterisks indicate d functions on sulfur and nitrogen atoms. These standard levels were determined by comparing calculation results with several basis sets up to MP2/6-31G*//6-31G*. Several conformations per compound were studied to obtain molecular geometries, rotational barriers, and potential derived point charges. In methyl sulfate, the rotational barrier around the C? O bond is 1.6 kcal/mol at the MP2 level and 1.4 kcal/mol at the standard level. Its ground state has one of three HCOS torsion angles trans and one of three COSO torsion angles trans. Rotation over 60° around the single O? S bond in the sulfate group costs 2.5 kcal/mol at the MP2 and 2.1 kcal/mol at the standard level. For ethyl sulfate, the calculated rotational barrier in going from the ground state, which has its CCOS torsion angle trans, to the syn-periplanar conformation (CCOS torsion angle cis) is 4.8 kcal/mol. However, a much lower barrier of 0.7 kcal/mol leads to a secondary gauchelike conformation about 0.4 kcal/mol above the ground state, with the CCOS torsion angle at 87.6°. Again, one of the COSO torsion angles is trans in the ground state, and the rotational barrier for a 60° rotation of the sulfate group amounts to 1.8 kcal/mol. For methyl sulfamate, the rotational barriers are 2.5 kcal/mol around the C? N bond and 3.3 kcal/mol around the N? S bond. This is noteworthy because sulfamate itself has a calculated rotational barrier around the N? S bond of only 1.7 kcal/mol. These and other data were used to parameterize the well-known empirical force fields AMBER and CHARMm. When the new fields were tested by means of vibrational frequency calculations at the 6-31G*//6-31G* level for methyl sulfate, sulfamate, and methyl sulfamate ground states, the frequencies compared favorably with the AMBER and CHARMm calculated frequencies. The transferability of the force parameters to β-D -glucose-6-sulfate and isopropyl sulfate appears to be better than to isopropyl sulfamate. © 1995 by John Wiley & Sons, Inc.     

Stairway to the conical intersection: a computational study of the retinal isomerization

The potential-energy surface of the first excited state of the 11-cis-retinal protonated Schiff base (PSB11) chromophore has been studied at the density functional theory (DFT) level using the time-dependent perturbation theory approach (TDDFT) in combination with Becke's three-parameter hybrid functional (B3LYP). The potential-energy curves for torsion motions around single and double bonds of the first excited state have also been studied at the coupled-cluster approximate singles and doubles (CC2) level. The corresponding potential-energy curves for the ground state have been calculated at the B3LYP DFT and second-order M?ller-Plesset (MP2) levels. The TDDFT study suggests that the electronic excitation initiates a turn of the beta-ionone ring around the C6-C7 bond. The torsion is propagating along the retinyl chain toward the cis to trans isomerization center at the C11=C12 double bond. The torsion twist of the C10-C11 single bond leads to a significant reduction in the deexcitation energy indicating that a conical intersection is being reached by an almost barrierless rotation around the C10-C11 single bond. The energy released when passing the conical intersection can assist the subsequent cis to trans isomerization of the C11=C12 double bond. The CC2 calculations also show that the torsion barrier for the twist of the retinyl C10-C11 single bond adjacent to the isomerization center almost vanishes for the excited state. Because of the reduced torsion barriers of the single bonds, the retinyl chain can easily deform in the excited state. Thus, the CC2 and TDDFT calculations suggest similar reaction pathways on the potential-energy surface of the excited state leading toward the conical intersection and resulting in a cis to trans isomerization of the retinal chromophore. According to the CC2 calculations the cis to trans isomerization mechanism does not involve any significant torsion motion of the beta-ionone ring.     

A quatum-mechanical study of metheyl fluoroformate

It is found theoretically that the preferred conformation of methyl fluorofonnate is cis instead of trans as reported previously Semi-empirical(CNDO/2) and ab initio (STO-3G) methods were used and the geometry was partially optimized. The rotational barrier for the methyl group is calculated and its value, 1.07 kcal/mol (CNDO/2) and 1.08 kcal/mol (STO-3G), is in agreement with experiment. Dipole moments are also calculated but are smaller than the experimental values. Finally it is shown how the isomers can be identified using electronic spectra.     

Unexpected substituent effects in offset pi-pi stacked interactions in water

We have measured the rotational barriers of meta- and para-substituted N-benzyl-2-(2-fluorophenyl)pyridinium bromides in aqueous solution by dynamic NMR as a model system for offset-stacking interactions in proteins. Because the benzyl ring can stack with the 2-fluorophenyl ring in the offset conformation in the ground state, but not the transition state, the rotational barrier reflects the magnitude of the stacking interaction. Only a small (0.1 kcal/mol) change in rotational barrier was found for para substituents relative to hydrogen. A much larger energy difference was found for electronegative meta substituents (up to 0.66 kcal/mol for CF3). Evidence suggests that this is due at least in part to an electrostatic interaction between electron-poor hydrogens on one ring with the electronegative substituents on the other ring.     

密度泛函方法研究噻唑橙类菁染料的光谱性质

4-(二乙基氨基)丁基取代的三甲川噻唑橙(DEAB-TO3)具有极低的本底荧光可用于核酸检测。本文运用密度泛函理论研究了4-(二乙基氨基)丁基取代的一甲川噻唑橙(DEAB-TO1)和DEAB-TO3光谱性质。基态和激发态几何优化显示激发态构型高度扭曲;光谱计算和轨道分析得出第一激发态是暗态,出现了扭曲的分子内电荷转移;势能曲线计算可知,DEAB-TO1和DEAB-TO3有着极低的能隙和旋转能垒。以上结果解释了本底荧光极弱的实验现象。     

Density functional theory calculations of the internal rotations and vibrational spectra of 2-, 3- and 4-formyl pyridine

The torsional potentials, molecular conformations and vibrational spectra, of 2-, 3- and 4-formyl pyridine have been investigated using density functional theory (DFT) method with 6-31+G* basis set. From the calculations, 2-formyl pyridine and 3-formyl pyridine were predicted to exist predominantly in cis conformation with the cis-trans rotational barrier of 9.38 kcal/mol and 8.55 kcal/mol, respectively. The two equivalent planar structures of 4-formyl pyridine are separated by an energy barrier of 7.18 kcal/mol. The vibrational wavenumbers and the corresponding vibrational assignments of molecules in C(s) symmetry were examined theoretically and the calculated Infrared of the molecules in the cis conformation was plotted. Observed wavenumbers for normal modes were compared with those calculated from normal mode coordinate analysis carried out on the basis of DFT force fields using the standard 6-31+G* basis set of the theoretical optimized geometry.     

MOLECULAR MECHANISMS IN VISUAL PIGMENT REGENERATION

The photochemical bleaching of vertebrate rhodopsin results in the cis to trans isomerization of the 11-cis-retinal protonated Schiff base. Hydrolysis of the Schiff base leads to the formation of opsin and all-trans-retinal. In order for vision to proceed, the enzymatic trans to cis isomerization of a retinoid must occur. Since retinoids exist as alcohols, aldehydes, or esters in the eye, there are potentially nine different routes for isomerization. Moreover, 11-cis-retinoids are approximately 4 kcal/mol higher in energy than their all-trans isomers. Thus, not only must the isomerization route be defined, but an energy source must be identified to power this process. It was discovered that the energy is provided for in a minimally two-step process involving membrane phospholipids as the energy source. First, all-trans-retinol (vitamin A) is esterified in the retinal pigment epithelium by lecithin retinol acyl transferase to produce an all-trans-retinyl ester. Second, this ester is directly transformed into 11-cis-retinol by an isomerohydrolase enzyme, in a process that couples the negative free energy of hydrolysis of the acyl ester to the formation of the strained 11-cis-retinoid.     

Visual pigments. V. Ground and excited-state acid dissociation constants of protonated all-trans retinal schiff base and correlation with theory.

Abstract— The acid dissociation constants of protonated all-trans retinal Schiff base (SB-H⁺) in a 50% water-methanol solution at 0°C is 6–95 for the ground state and nominally 16–65 for the first excited singlet state, with a potential range of ? 12–21. These values are in qualitative agreement with the results of semiempirical MO calculations, which indicate that the total charge density on nitrogen is greater in the first excited singlet than in the ground state (Q_N* > Q_N). However, pertinent to vision, CNDO/2 calculations on all-trans and 11-cis Schiff base and SB-H⁺ indicate that, for torsional angles of approximately 80–100° around the 11–12 double bond, Q_N* < Q_N. This result suggests that it may be possible for the proton to come off the imine nitrogen during isomerization from 11 -cis SB-H⁺ to all-trans SB-H⁺. The potential consequence of this during isomerization of rhodopsin is the initiation of unfolding of the protein opsin.     

Direct evidence for nonadiabatic dynamics in atom+polyatom reactions: crossed-jet laser studies of F+D2O-->DF+OD

Quantum-state-resolved reactive-scattering dynamics of F+D(2)O-->DF+OD have been studied at E(c.m.)=5(1) kcal/mol in low-density crossed supersonic jets, exploiting pulsed discharge sources of F atom and laser-induced fluorescence to detect the nascent OD product under single-collision conditions. The product OD is formed exclusively in the v(OD)=0 state with only modest rotational excitation ( =0.50(1) kcal/mol), consistent with the relatively weak coupling of the 18.1(1) kcal/mol reaction exothermicity into "spectator" bond degrees of freedom. The majority of OD products [68(1)%] are found in the ground ((2)Pi(32) (+/-)) spin-orbit state, which adiabatically correlates with reaction over the lowest and only energetically accessible barrier (DeltaE( not equal) approximately 4 kcal/mol). However, 32(1)% of molecules are produced in the excited spin-orbit state ((2)Pi(12) (+/-)), although from a purely adiabatic perspective, this requires passage over a DeltaE( not equal) approximately 25 kcal/mol barrier energetically inaccessible at these collision energies. This provides unambiguous evidence for nonadiabatic surface hopping in F+D(2)O atom abstraction reactions, indicating that reactive-scattering dynamics even in simple atom+polyatom systems is not always isolated on the ground electronic surface. Additionally, the nascent OD rotational states are well fitted by a two-temperature Boltzmann distribution, suggesting correlated branching of the reaction products into the DF(v=2,3) vibrational manifold.     

Synthesis, characterization, and spectroscopic investigation of benzoxazole conjugated Schiff bases

Two Schiff bases were synthesized by reaction of 2-(4'-aminophenyl)benzoxazole derivatives with 4-N,N-diethylaminobenzaldehyde. UV-visible (UV-vis) and steady-state fluorescence in solution were applied in order to characterize its photophysical behavior. The Schiff bases present absorption in the UV region with fluorescence emission in the blue-green region, with a large Stokes' shift. The UV-vis data indicates that each dye behaves as two different chromophores in solution in the ground state. The fluorescence emission spectra of the dye 5a show that an intramolecular proton transfer (ESIPT) mechanism takes place in the excited state, whereas a twisted internal charge transfer (TICT) state is observed for the dye 5b. Theoretical calculations were performed in order to study the conformation and polarity of the molecules at their ground and excited electronic states. Using density functional theory (DFT) methods at theoretical levels BLYP/Aug-SV(P) for geometry optimizations and B3LYP/6-311++G(2d,p) for single-point energy evaluations, the calculations indicate that the lowest energy conformations are in all cases nonplanar and that the dipole moments of the excited state relaxed structures are much larger than those of the ground state structures, which corroborates the experimental UV-vis absorption results.     

Photoisomerization mechanism of 11-cis-locked artificial retinal chromophores: acceleration and primary photoproduct assignment

CASPT2//CASSCF/6-31G photochemical reaction path computations for two 4-cis-nona-2,4,6,8-tetraeniminium cation derivatives, with the 4-cis double bond embedded in a seven- and eight-member ring, are carried out to model the reactivity of the corresponding ring-locked retinal chromophores. The comparison of the excited state branches of the two reaction paths with that of the native chromophore, is used to unveil the factors responsible for the remarkably short (60 fs) excited state (S(1)) lifetime observed when an artificial rhodopsin containing an eight member ring-locked retinal is photoexcited. Indeed, it is shown that the strain imposed by the eight-member ring on the chromophore backbone leads to a dramatic change in the shape of the S(1) energy surface. Our models are also used to investigate the nature of the primary photoproducts observed in different artificial rhodopsins. It is seen that only the eight member ring-locked retinal model can access a shallow energy minimum on the ground state. This result implies that the primary, photorhodopsin-like, transient observed in artificial rhodopsins could correspond to a shallow excited state minimum. Similarly, the second, bathorhodopsin-like, transient species could be assigned to a ground state structure displaying a nearly all-trans conformation.     

Tuning of retinal twisting in bacteriorhodopsin controls the directionality of the early photocycle steps

Productive proton pumping by bacteriorhodopsin requires that, after the all-trans to 13-cis photoisomerization of the retinal chromophore, the photocycle proceeds with proton transfer and not with thermal back-isomerization. The question of how the protein controls these events in the active site is addressed here using quantum mechanical/molecular mechanical reaction-path calculations. The results indicate that, while retinal twisting significantly contributes to lowering the barrier for the thermal cis-trans back-isomerization, the rate-limiting barrier for this isomerization is still 5-6 kcal/mol larger than that for the first proton-transfer step. In this way, the retinal twisting is finely tuned so as to store energy to drive the subsequent photocycle while preventing wasteful back-isomerization.     

Activity switches of rhodopsin

Rhodopsin, the visual pigment of the rod photoreceptor cell contains as its light-sensitive cofactor 11-cis retinal, which is bound by a protonated Schiff base between its aldehyde group and the Lys296 side chain of the apoprotein. Light activation is achieved by 11-cis to all-trans isomerization and subsequent thermal relaxation into the active, G protein-binding metarhodopsin II state. Metarhodopsin II decays via two parallel pathways, which both involve hydrolysis of the Schiff base eventually to opsin and released all-trans retinal. Subsequently, rhodopsin's dark state is regenerated by a complicated retinal metabolism, termed the retinoid cycle. Unlike other retinal proteins, such as bacteriorhodopsin, this regeneration cycle cannot be short cut by light, because blue illumination of active metarhodopsin II does not lead back to the ground state but to the formation of largely inactive metarhodopsin III. In this review, mechanistic details of activating and deactivating pathways of rhodopsin, particularly concerning the roles of the retinal, are compared. Based on static and time-resolved UV/Vis and FTIR spectroscopic data, we discuss a model of the light-induced deactivation. We describe properties and photoreactions of metarhodopsin III and suggest potential roles of this intermediate for vision.     

Theoretical study on the excited-state intramolecular proton transfer in the aromatic schiff base salicylidene methylamine: an electronic structure and quantum dynamical approach

The proton-transfer dynamics in the aromatic Schiff base salicylidene methylamine has been theoretically analyzed in the ground and first singlet (pi,pi) excited electronic states by density functional theory calculations and quantum wave-packet dynamics. The potential energies obtained through electronic calculations that use the time-dependent density functional theory formalism, which predict a barrierless excited-state intramolecular proton transfer, are fitted to a reduced three-dimensional potential energy surface. The time evolution in this surface is solved by means of the multiconfiguration time-dependent Hartree algorithm applied to solve the time-dependent Schr?dinger equation. It is shown that the excited-state proton transfer occurs within 11 fs for hydrogen and 25 fs for deuterium, so that a large kinetic isotope effect is predicted. These results are compared to those of the only previous theoretical work published on this system [Zgierski, M. Z.; Grabowska, A. J. Chem. Phys. 2000, 113, 7845], reporting a configuration interaction singles barrier of 1.6 kcal mol(-1) and time reactions of 30 and 115 fs for the hydrogen and deuterium transfers, respectively, evaluated with the semiclassical instanton approach.     

Dissociation dynamics of thiolactic acid at 193 nm: detection of the nascent OH product by laser-induced fluorescence

Electronically excited thiolactic acid (2-mercaptopropionic acid), H(3)C-CH(SH)-COOH, undergoes the C-OH bond cleavage on excitation to the S(2) state at 193 nm, generating the primary product OH (v,J), which is detected by laser-induced fluorescence technique in a collisionless condition of flow system. The partitioning of the available energy between vibrational, rotational, and translational degrees of freedom of nascent photofragments is obtained from relative intensities of ro-vibronic lines in laser-induced fluorescence spectrum of OH, and their Doppler profiles. The rotational population of OH (v(")=0) is characterized by rotational temperature of 408+/-25 K. OH is produced in a vibrationally cold state, i.e., mostly in v(")=0. The average translational energy of OH (v(")=0,J(")) is found to be 21.5+/-2.0 kcal/mol, which implies 25.6 kcal/mol of energy in relative translation of photoproducts corresponding to the f(t) value of approximately 0.6. The observed high translational energy is due to the presence of a barrier in the exit channel, implying that the C-OH bond scission takes place on an electronically excited potential energy surface. The observed partitioning of the available energy between various degrees of the photofragments is theoretically modeled, and the hybrid model, with 26.0 kcal/mol of barrier in the exit channel, is found to explain the measured data quite well. The experimental results are also supported with ab initio molecular orbital calculations for both the ground and the excited electronic states. Time-dependent density functional theory is used to understand the nature of various electronic transitions connecting the lower excited states. Potential energy curves as a function of the C-OH bond length of thiolactic acid suggest distinct exit barriers in the S(1), T(1), and T(2) states. But, we could locate the transition state structure for OH formation in the S(1) state alone. Thus, although thiolactic acid is excited to the S(2) state at 193 nm, it undergoes internal conversion to S(1) where it dissociates to yield OH. In addition to the OH channel from excited electronic states, we studied theoretically all probable dissociation channels occurring on the ground electronic state of thiolactic acid.     

Conformational Study of 8—C—glucosyl—prunetin by Dynamic NMR Spectroscopy

By means of variable temperature NMR spectra,conformation of 8-C-glucosyl prunetin, isolated from the leaves of Dalbergia hainanensis (Leguminosae), was studied. The restricted rotation around the C(sp^3)-C(sp^2) bond in the C-glucosides isoflavonoid results in two main conformers (syn and anti). With the help of MM calculation, the preferred conformation A has H-1″ gauche to the 7-OCH3. The barrier to rotation was 18.1 kcal/mol. This result agrees with the calculated value 16.2 kcal/mol of free energy of activation for the interconversion between the conformers.     

MINDO-SCF-MO-berechnung der cis-trans-isomerisierung von N-methyl- und N-phenylazomethin

MINDO/2-SCF-MO calculations for the ground state properties of N-methyl- and N-phenyl-azomethin have been carried out. The calculated rotation barrier for the methyl group in N-methyl-azomethin was 0·8 kcal/mol, the eclipsed conformation being most stable. The calculated rotation barrier about the CN bond in the protonated methylazomethin was 27·9 kcal/mol. MINDO/1-SCF-MO treatment for the N-inversion barrier of the unprotonated species yielded 13·00 kcal/mol. Similar MINDO/2 calculations for N-phenylazomethin yielded 4·0 kcal/mol for the rotation barrier of the phenyl ring around the CN= bond, the perpendicular conformation of the ring to the CNC plane being most stable. For the corresponding N protonated derivative the value 27·3 kcal/mol was calculated for the rotation barrier around the CN bond. MINDO/1 treatment yielded an inversion barrier of 14·0 kcal/mol for N-phenylazomethin.