Ab initio potential energy surface and bound states of the Xe-CO complex

The first two-dimensional potential energy surface for the Xe-CO van der Waals interaction is calculated by the single and double excitation coupled-cluster theory with noniterative treatment of triple excitations. Mixed basis sets, aug-cc-pVQZ for the C and O atoms, and aug-cc-pVQZ-PP for the Xe atom, with an additional (3s3p2d2f1g) set of midbond functions, are used. Our potential energy surface has a single, nearly T-shaped minimum of -131.87 cm(-1) at R(e)=7.80a(0) and theta(e)=102.5 degrees. Based on the potential, the bound state energies are calculated for seven isotopomers of the Xe-(12)C(16)O complex, seven isotopomers of the Xe-(13)C(16)O complex, and three isotopomers of the Xe-(13)C(18)O complex. Compared with available experimental data, the predicted transition frequencies and spectroscopic constants are in good agreement with the experimental results.     

Sub-5-fs real-time spectroscopy of transition states in bacteriorhodopsin during retinal isomerization

By using a sub-5-fs visible laser pulse, we have made the first observation of the vibrational spectra of the transition state during trans-cis isomerization in the retinal chromophore of bacteriorhodopsin (bR(S68). No instant isomerization of the retinal occurs in spite of electron promotion from the bonding pi-orbital to the anti-bonding pi*-orbital. The difference between the in-plane and out-of-plane vibrational frequencies (about 1150-1250 and 900-1000 cm(-1), respectively) is reduced during the first time period. The vibrational spectra after this period became very broad and weak and are ascribed to a "silent state." The silent state lasts for 700-900 fs until the chromophore isomerizes to the cis-C13 = C14 conformation. The frequency of the C = C stretching mode was modulated by the torsion mode of the C13 = C14 double bond with a period of 200 fs. The modulation was clearly observed for four to five periods. Using the empirical equation for the relation between bond length and stretching frequency, we determined the transitional C = C bond length with about 0.01 angstroms accuracy during the torsion motion around the double bond with 1-fs time resolution.     

Ultrafast pump-probe study of the primary photoreaction process in pharaonis halorhodopsin: halide ion dependence and isomerization dynamics

Halorhodopsin is a retinal protein that acts as a light-driven chloride pump in the Haloarchaeal cell membrane. A chloride ion is bound near the retinal chromophore, and light-induced all- trans --> 13- cis isomerization triggers the unidirectional chloride ion pump. We investigated the primary ultrafast dynamics of Natronomonas pharaonis halorhodopsin that contains Cl (-), Br (-), or I (-) ( pHR-Cl (-), pHR-Br (-), or pHR-I (-)) using ultrafast pump-probe spectroscopy with approximately 30 fs time resolution. All of the temporal behaviors of the S n <-- S 1 absorption, ground-state bleaching, K intermediate (13- cis form) absorption, and stimulated emission were observed. In agreement with previous reports, the primary process exhibited three dynamics. The first dynamics corresponds to the population branching process from the Franck-Condon (FC) region to the reactive (S 1 (r)) and nonreactive (S 1 (nr)) S 1 states. With the improved time resolution, it was revealed that the time constant of this branching process (tau 1) is as short as 50 fs. The second dynamics was the isomerization process of the S 1 (r) state to generate the ground-state 13- cis form, and the time constant (tau 2) exhibited significant halide ion dependence (1.4, 1.6, and 2.2 ps for pHR-Cl (-), pHR-Br (-), and pHR-I (-), respectively). The relative quantum yield of the isomerization, which was evaluated from the pump-probe signal after 20 ps, also showed halide ion dependence (1.00, 1.14, and 1.35 for pHR-Cl (-), pHR-Br (-), and pHR-I (-), respectively). It was revealed that the halide ion that accelerates isomerization dynamics provides the lower isomerization yield. This finding suggests that there is an activation barrier along the isomerization coordinate on the S 1 potential energy surface, meaning that the three-state model, which is now accepted for bacteriorhodopsin, is more relevant than the two-state model for the isomerization process of halorhodopsin. We concluded that, with the three-state model, the isomerization rate is controlled by the height of the activation barrier on the S 1 potential energy surface while the overall isomerization yield is determined by the branching ratios at the FC region and the conical intersection. The third dynamics attributable to the internal conversion of the S 1 (nr) state also showed notable halide ion dependence (tau 3 = 4.5, 4.6, and 6.3 ps for pHR-Cl (-), pHR-Br (-), and pHR-I (-)). This suggests that some geometrical change may be involved in the relaxation process of the S 1 (nr) state.     

Alpha-gamma hybrid peptides that contain the conformationally constrained gabapentin residue: characterization of mimetics of chain reversals

The crystal structures of four dipeptides that contain the stereochemically constrained gamma-amino acid residue gabapentin (1-(aminomethyl)cyclohexaneacetic acid Gpn) are described. The molecular conformation of Piv-Pro-Gpn-OH (1), reveals a beta-turn mimetic conformation, stabilized by a ten atom C[bond]H...O hydrogen bond between the Piv CO group and the pro S hydrogen of the Gpn CH(2)[bond]CO group. The peptides Boc-Gly-Gpn-OH (2), Boc-Aib-Gpn-OH (3), and Boc-Aib-Gpn-OMe (4) form compact, folded structures, in which a distinct reversal of polypeptide chain direction is observed. In all cases, the Gpn residue adopts a gauche,gauche (g,g) conformation about the C(gamma)[bond]C(beta) (theta(1)) and C(beta)[bond]C(alpha) (theta(2)) bonds. Two distinct Gpn conformational families are observed. In peptides 1 and 3, the average backbone torsion angle values for the Gpn residue are phi=98 degrees, theta(1)=-62 degrees, theta(2)=-73 degrees, and psi=79 degrees, while in peptide 2 and 4 the average values are phi=-103 degrees, theta(1)=-46 degrees, theta(2)=-49 degrees, and psi=-92 degrees. In the case of 1 and 3, an intramolecular nine-membered O[bond]H...O hydrogen bond is formed between the C[double bond]O of the preceding residue and the terminal carboxylic acid OH group. All four alpha-gamma dipeptide sequences yield compact folded backbone conformations; this suggests that the Gpn residue may be employed successfully in the design of novel folded structures.     

用NMR法研究几种不对称双烃基硫桥六羰基二铁的异构化动力学

本文用常规核磁共振方法研究了(苄基硫)(烃基硫)六羰基二铁(烃基为甲基、乙基)和动态核磁共振方法研究了(苄基硫)(叔丁基硫)六羰基二铁的异构化反应动力学, 提出了可能的反应机理, 讨论了影响反应速率的因素.     

The ν2 bending vibrational structure of the X̃2Σ+ state of MgNC

We have generated MgNC in supersonic free jet expansions and observed the laser induced fluorescence (LIF) of the A?(2)Π-X?(2)Σ(+) transition. We measured the LIF dispersed spectra from the single vibronic levels of the A?(2)Π electronic state of MgNC, following excitation of each ν(2) bending vibronic band observed, i.e., the κ series of the (0,v(2)('),0)-(0,0,0), v(2)(') = 0, 1, 2, 4, and 6 vibronic bands. In the vibrational structure in the dispersed fluorescence spectra measured, the long progression of the ν(2) bending mode in the X?(2)Σ(+) state is identified, e.g., up to v(2)(')=14 in the (0,6,0)-(0,v(2)('),0) spectrum. This enables us to derive the potential curve of the ν(2) bending mode in the X?(2)Σ(+) state. We used two kinds of models to obtain the potential curve; (I) the customary formula expressed in the polynomial series of the (v(2)(')+(d(2)/2)) term and (II) the internal rotation model. The potential curve derived from model (I) indicates the convergence of the bending vibrational levels at about 800 cm(-1) from the vibrationless level of MgNC, which may correspond to the barrier height of the isomerization reaction, MgNC ? MgCN, in the X?(2)Σ(+) state. Model (II) gives a simple picture for the isomerization reaction pathway with a barrier height of about 630 cm(-1) from the vibrationless level of the more stable species, MgNC. This shows that the v(2)(')=8 bending vibrational level of MgNC is already contaminated by the v(2)(')=2 bending vibrational level of the isomer, MgCN, and implies that the isomerization reaction begins at the v(2) (')=8 level. The bending potential surface and the isomerization reaction pathway, MgNC ? MgCN, in the X?(2)Σ(+) state are discussed by comparing the potential derived in this study with the surface obtained by quantum chemical calculation.     

Bullvalene trisepoxide and its stereospecific rearrangement to 2,8,12-trioxahexacyclo[8.3.0.0(3,9)0(4,6)0(5,13)0(7,11)]tridecane: two new C3-symmetrical oligocycles with propeller chirality

Epoxidation of bullvalene (1) with a neutralized solution of Oxone gave racemic trisepoxide rac-6 in 93 % isolated yield. Its structure was examined by X-ray crystallography. The two enantiomers of 6 were separated by preparative HPLC and exhibited specific rotations of [alpha](25)(D)= +160, [alpha](25)(365)= +567 (c=0.946, CHCl(3)) for the firstly eluted and [alpha](25)(D)= -157, [alpha](25)(365)= -554 (c=0.986, CHCl3) for the secondly eluted enantiomer of 6. The geometry of (+)-6 and the absolute configuration of (-)-6 were determined by X-ray crystal structure analysis and anomalous diffraction, respectively. According to this, (-)-6 possesses (3R,5S,7S,9R,11R,13S)- and (+)-6 has (3S,5R,7R,9S,11S,13R)-configuration. Upon treatment with BF(3)Et(2)O at -78 degrees C, trisepoxide rac-6 rearranges with retention of the skeletal three-membered carbocycle to give the cage trisether rac-8, as proved by X-ray crystal structure analysis, in virtually quantitative yield. Enantiomers of rac-8 were separated by preparative HPLC and exhibited specific rotations of [alpha](25)(D)= +49, [alpha](25)(365)= +170 (c=1.01, CHCl3) (firstly eluting) and [alpha](25)(D)= -46, [alpha](25)(365)= -160 (c=1.02, CHCl(3)) (secondly eluting enantiomer). The absolute configuration of (-)-8 was determined by anomalous diffraction to be (1R,3R,7R,9R,11R,13R). DFT computations at the TD-B3 LYP/6-31+G(d,p)//B3 LYP/6-31+G(d) level of theory for (3R,5S,7S,9R,11R,13S)-6 and (1R,3R,7R,9R,11R,13R)-8 predicted specific rotations of -206.7 and -83.4, respectively. Acid-catalyzed isomerization of the enantiomerically pure (+)-6 proceeded without racemization to give exclusively (-)-8, and (-)-6 provided only (+)-8. Thus, this isomerization occurs with ring opening of the three C--O bonds in the epoxide moieties in the alpha-position relative to the three-membered carbocycle rather than in the beta-position.     

On the ultraviolet photodissociation of H(2)Te

The photodissociation of H(2)Te through excitation in the first absorption band is investigated by means of multireference spin-orbit configuration interaction (CI) calculations. Bending potentials for low-lying electronic states of H(2)Te are obtained in C(2v) symmetry for Te-H distances fixed at the ground state equilibrium value of 3.14a(0), as well as for the minimum energy path constrained to R(1)=R(2). Asymmetric cuts of potential energy surfaces for excited states (at R(1)=3.14a(0) and theta;=90.3 degrees ) are obtained for the first time. It is shown that vibrational structure in the 380-400 nm region of the long wavelength absorption tail is due to transitions to 3A('), which has a shallow minimum at large HTe-H separations. Transitions to this state are polarized in the molecular plane, and this state converges to the excited TeH((2)Pi(1/2))+H((2)S) limit. These theoretical data are in accord with the selectivity toward TeH((2)Pi(1/2)) relative to TeH((2)Pi(3/2)) that has been found experimentally for 355 nm H(2)Te photodissociation. The calculated 3A(')<--XA(') transition dipole moment increases rapidly with HTe-H distance; this explains the observation of 3A(') vibrational structure for low vibrational levels, despite unfavorable Franck-Condon factors. According to the calculated vertical energies and transition moment data, the maximum in the first absorption band at approximately 245 nm is caused by excitation to 4A("), which has predominantly 2(1)A(") ((1)B(1) in C(2v) symmetry) character.     

trans-cis Photoisomerization of the styrylpyridine Ligand in [Re(CO)3(2,2'-bipyridine)(t-4-styrylpyridine)]+: role of the metal-to-ligand charge-transfer excited states

The trans-cis isomerization of the styrylpyridine carbon-carbon double bond induced by visible light irradiation in fac-[Re(CO)(3)(bpy)(stpy)](+) (bpy = 2,2'-bipyridine; stpy = t-4-styrylpyridine) has been investigated by means of quantum-chemical methods. The structures of the various cis and trans conformers of [Re(CO)(3)(bpy)(stpy)](+) have been optimized at the density functional theory (DFT) level. Three rotational conformers for the most stable trans isomer lie within 2.3 kJ mol(-1) each other. The energy difference between the cis and trans isomers is 27.0 kJ mol(-1). The electronic spectroscopy of the most stable conformers has been investigated by time-dependent DFT (TD-DFT) and complete active space self-consistent field/CAS second order perturbation theory (CASSCF/CASPT2) calculations. The lowest absorption bands are dominated by metal-to-ligand charge-transfer (MLCT, d(Re)-->pi*(bpy)) transitions calculated at about 25,000 cm(-1) and by a strong intraligand (1)IL (pi(stpy)-->pi*(stpy)) transition in the near UV region. On the basis of CASSCF potential energy curves (PECs) calculated as a function of the torsion angle of the C=C bond of the styrylpyridine ligand, it is shown that the role of the low-lying MLCT states is important in the photoisomerization mechanism. In contrast to the free organic ligand, in which the singlet mechanism is operational via the (1)IL (S(1)) and electronic ground (S(0)) states, coordination to the rhenium steers the isomerization to the triplet PEC corresponding to the (3)IL state. From the (3)IL(t) (t = trans) the system evolves to the perpendicular intermediate (3)IL(p) (p = perpendicular) following a 90 degrees rotation around the styrylpyridine C=C bond. The metal center acts as a photosensitizer because of the presence of photoactive MLCT states under visible irradiation. The position of the crossing between the (3)IL and electronic ground state PEC determines the quantum yield of the isomerization process.     

Heat-induced and light-induced isomerization of the xanthophyll pigment zeaxanthin

Zeaxanthin is a xanthophyll pigment that plays important physiological functions both in the plant and in the animal kingdom. All-trans is a stereochemical conformation of zeaxanthin reported as specific for the thylakoid membranes of the photosynthetic apparatus and the retina of an eye. On the other hand, the pigment is subjected, in natural environment, to the conditions that promote stereochemical isomerization, such as illumination and elevated temperature. In the present work, the light-induced and heat-induced (the temperature range 35-95 degrees C) isomerization of all-trans zeaxanthin in organic solvent environment has been analyzed by means of the HPLC technique. The 13-cis conformation has been identified as a major one among the isomerization products. The activation energy of the all-trans to 13-cis isomerization has been determined as 83 +/- 4 kJ/mol and the activation energy of the back reaction as 30 +/- 7 kJ/mol. The reaction of isomerization of the all-trans zeaxanthin at 25 degrees C was substantially more efficient upon illumination. Four different wavelengths of light have been selected for photo-isomerization experiments: 450, 540, 580 and 670 nm, corresponding to the electronic transitions of zeaxanthin from the ground state to the singlet excited states: 1(1)Bu+,3(1)Ag-,1(1)Bu- and 2(1)Ag-, respectively. The quantum efficiency of the all-trans zeaxanthin isomerization induced by light at different wavelengths: 450, 540, 580 and 670 nm was found to differ considerably and was in the ratio as 1:15:160:29. The sequence of the quantum efficiency values suggests that the carotenoid triplet state 1(3)Bu, populated via the internal conversion from the 1(3)Ag triplet state which is generated by the intersystem crossing from the 1(1)Bu- state may be involved in the light-induced isomerization. A physiological importance of the isomerization of zeaxanthin in the retina of an eye, photosynthetic apparatus and of the pigment active as a blue light photoreceptor in stomata is briefly discussed.     

Near-infrared spectra and rovibrational dynamics on a four-dimensional ab initio potential energy surface of (HBr)2

Supersonic jet investigations of the (HBr)(2) dimer have been carried out using a tunable diode laser spectrometer to provide accurate data for comparison with results from a four-dimensional (4-D) ab initio potential energy surface (PES). The near-infrared nu(1) (+/-), nu(2) (+/-), and (nu(1)+nu(4))(-) bands of (H (79)Br)(2), (H (79)Br-H (81)Br), and (H (81)Br)(2) isotopomers have been recorded in the range 2500-2600 cm(-1) using a CW slit jet expansion with an upgraded near-infrared diode laser spectrometer. The 4-D PES has been calculated for (HBr)(2) using second-order M?ller-Plesset perturbation theory with an augmented and polarized 6-311G basis set. The potential is characterized by a global minimum occurring at the H bond structure with the distance between the center of masses (CM) of the monomer being R(CM)=4.10 A with angles theta(A)=10 degrees, theta(B)=100 degrees and a well depth of 692.2 cm(-1), theta(A) is the angle the HBr bond of monomer A makes with the vector from the CM of A to the CM of B, and theta(B) is the corresponding angle monomer B makes with the same CM-CM vector. The barrier for the H interchange occurs at the closed C(2h) structure for which R(CM)=4.07 A, theta(A)=45 degrees, theta(B)=135 degrees, and the barrier height is 73.9 cm(-1). The PES was fitted using a linear-least squares method and the rovibrational energy levels of the complex were calculated by a split pseudospectral method. The spectroscopic data provide accurate molecular parameters for the dimer that are then compared with the results predicted on the basis of the 4-D ab initio PES.     

N-甲硝胺异构化和分解反应机理和动力学的理论研究

The complex potential energy surface and reaction mechanisms for the unimolecular isomerization and decomposition of methyl-nitramine (CH3NHNO2) were theoretically probed at the QCISD(T)/6-311+G*//B3LYP/6-311+G* level of theory. The results demonstrated that there are four low-lying energy channels: (i) the NN bond fission pathway; (ii) a sequence of isomerization reactions via CH3NN(OH)O; (IS2a); (iii) the HONO elimination pathway; (iv) the isomerization and the dissociation reactions via CH3NHONO (IS3). The rate constants of each initial step (rate-determining step) for these channels were calculated using the canonical transition state theory. The Arrhenius expressions of the channels over the temperature range 298-2000 K are k6(T)=1014:8e-46:0=RT , k7(T)=1013:7e-42:1=RT , k8(T)=1013:6e-51:8=RT and k9(T)=1015:6e-54:3=RT s-1, respectively. The calculated overall rate constants is 6.9￡10-4 at 543 K, which is in good agreement with the experimental data. Based on the analysis of the rate constants, the dominant pathway is the isomerization reaction to form CH3NN(OH)O at low temperatures, while the NN bond fission and the isomerization reaction to produce CH3NHONO are expected to be competitive with the isomerization reaction to form CH3NN(OH)O at high temperatures.     

Effects of the residues on the excitation energies of protonated Schiff base of retinal (PSBR) in bR: a TD-DFT study

Effects of the residues on the excitation energies of protonated Schiff base of retinal (PSBR) in bacteriorhodopsin have been investigated by means of time-dependent density functional theory. The residues around PSBR are replaced by the point charges on atoms. The structures of PSBR and residues are referred from X-ray data. The atomic charges on the each residue were calculated the B3LYP/6-311G(d,p) level. The excitation energy of PSBR perturbed by the point charges on atoms of each residue was calculated at the B3LYP/6-31G(d,p) level. A total of 23 residues and five water molecules around PSBR were considered in the calculations. The large spectral shifts were caused by the Asp212 and Asp85. The origin of the spectral shifts was discussed on the basis of theoretical results.     

A CASSCF/MR-CI study toward the understanding of wavelength-dependent and geometrically memorized photodissociation of formic acid

The S(0), T(1), and S(1) potential energy surfaces for the HCOOH dissociation and isomerization processes have been mapped with different ab initio methods. The wavelength-dependent mechanism for the HCOOH dissociation was elucidated through the computed potential energy surfaces and the surface crossing points. The HCOOH molecules in S(1) by excitation at 248 nm mainly decay to the ground state via the S(0) and S(1) vibronic interaction, followed by molecular eliminations in the ground state. The S(1) direct dissociation to HCO((2)A') + OH((2)Pi) is the dominant pathway upon photoexcitation at 240-210 nm. Meanwhile, there is a slight probability that the system relaxes to the ground state via the S(0) and S(1) vibronic interaction at these wavelengths. After irradiation of HCOOH at 193 nm, the S(1) direct dissociation into HCO((2)A') + OH((2)Pi) is energetically the most favorable pathway. In view of high IC efficiency at the S(0)/S(1) conical crossing, the S(1) --> S(0) internal conversion via the S(0)/S(1) point can occur with considerable efficiency. In addition, the S(1) isomerization probably plays a dominant role in the partially conformational memory of the HCOOH photodissociation, which has been discussed in detail.     

Predicting Potential Stable Isomers on the Singlet Surface of the [H,P,C,S] System by the MP2 and QCISD(T) Methods

A detailed singlet potential energy surface of [H,P, C,S] system is investigated by means of the MP2 and QCISD(T) methods. Eight isomers are located on the potential energy surface, and at the final QCISD(T)/6-311++G (3df,2p)//MP2/6-311++G(d,p) level with zero-point energy correction, the chainlike isomer HPCS is found to be kinetically and thermodynamically the most stable species followed by the chainlike HSCP, planar three-membered ring HC(S)P, chainlike HCPS, and stereo three-membered ring HP(C)S, which are predicted to be also kinetically stable isomers and should be experimentally observable provided that accurate experimental conditions are available. The dissociation processes from the kinetically and thermodynamically most stable species HPCS to the low-lying molecular dissociation fragments are not more favorable in energy than the isomerization process from HPCS to HSCP. Therefore, the experimental observation for potential isomer HSCP with C ≡ P triple bond is possible by means of photoisomerization technology using HPCS as precursor.     

On equilibrium structures of the water molecule

Equilibrium structures are fundamental entities in molecular sciences. They can be inferred from experimental data by complicated inverse procedures which often rely on several assumptions, including the Born-Oppenheimer approximation. Theory provides a direct route to equilibrium geometries. A recent high-quality ab initio semiglobal adiabatic potential-energy surface (PES) of the electronic ground state of water, reported by Polyansky et al. [ ibid. 299, 539 (2003)] and called CVRQD here, is analyzed in this respect. The equilibrium geometries resulting from this direct route are deemed to be of higher accuracy than those that can be determined by analyzing experimental data. Detailed investigation of the effect of the breakdown of the Born-Oppenheimer approximation suggests that the concept of an isotope-independent equilibrium structure holds to about 3 x 10(-5) A and 0.02 degrees for water. The mass-independent [Born-Oppenheimer (BO)] equilibrium bond length and bond angle on the ground electronic state PES of water is r(e) (BO)=0.957 82 A and theta e (BO)=104.48(5) degrees , respectively. The related mass-dependent (adiabatic) equilibrium bond length and bond angle of H2 (16)O is r(e) (ad)=0.957 85 A and theta e (ad)=104.50(0) degrees , respectively, while those of D2 (16)O are r(e) (ad)=0.957 83 A and theta e (ad)=104.49(0) degrees . Pure ab initio prediction of J=1 and 2 rotational levels on the vibrational ground state by the CVRQD PESs is accurate to better than 0.002 cm(-1) for all isotopologs of water considered. Elaborate adjustment of the CVRQD PESs to reproduce all observed rovibrational transitions to better than 0.05 cm(-1) (or the lower ones to better than 0.0035 cm(-1)) does not result in noticeable changes in the adiabatic equilibrium structure parameters. The expectation values of the ground vibrational state rotational constants of the water isotopologs, computed in the Eckart frame using the CVRQD PESs and atomic masses, deviate from the experimentally measured ones only marginally, especially for A0 and B0. The small residual deviations in the effective rotational constants are due to centrifugal distortion, electronic, and non-Born-Oppenheimer effects. The spectroscopic (nonadiabatic) equilibrium structural parameters of H2 16O, obtained from experimentally determined A'0 and B'0 rotational constants corrected empirically to obtain equilibrium rotational constants, are r(e) (sp)=0.957 77 A and theta e (sp)=104.48 degrees .     

Molecular Dynamics Simulation of the Excited-State Dynamics of Bacteriorhodopsin

Abstract— The excited-state dynamics of bacteriorhodopsin was studied by molecular dynamics simulation. For the purpose of suppressing large displacement of amino acid residues on the surface of bacteriorhodopsin, positional restraints were imposed on these residues. A new method was developed to investigate the movement of amino acid residues upon photoexcitation and their role on the ultrafast photoisomerization of the chromophore. The structural change of bacteriorhodopsin was then traced up to 200 fs, i.e. until the formation of the intermediate I. We found that when all the conjugated bonds of the chromophore were allowed to twist freely in the excited state, many bonds including the C13=C14 bond twist in large scale within 100 fs. When only the C13=C14 bond and the single bonds were allowed to twist freely, the twisting took place at most 20° within 200 fs. From these results, it is claimed that a special potential surface is provided for the C13=C14 bond twisting by the protein environment in the course of the isomerization reaction, giving rise to the specific, ultrafast photoisomerization of bacteriorhodopsin. As a trace of such a mechanism, we observed that several functionally important residues incuding Asp85, Asp212 and Tyr185 responded quickly to the photoexcitation of the chromophore.     

Photoisomerization dynamics of N-1-methyl-2-(tolylazo) imidazole and the effect of complexation with Cu(ii)

Azo-compounds containing an imidazole moiety have the potential to photoregulate biofunctions, such as gene-expression and enzymatic action. Photoinduced isomerization of the azo-backbone is the vital process for such applications, but the photoisomerization dynamics of azo-imidazole compounds has not been well explored. We investigated the photoisomerization dynamics of trans-N-1-methyl-2-(tolylazo) imidazole (trans-MTAI) using femtosecond transient absorption spectroscopy following photoexcitation to the S(2) state. Time evolution of the transient electronic spectra and the global analysis of the temporal profiles reveal a three state relaxation (S(2) → S(1) → S(0)) process in different kinds of solvents. The lifetime of the S(2) state is independent of the viscosity of solvent, whereas that of the S(1) state becomes longer with increasing solvent viscosity. This observation clearly indicates that the large amplitude motion that leads to the trans → cis isomerization occurs only in the S(1) state and relaxation of the S(2) state is not associated with the isomerization process. We have also investigated the excited state dynamics of [Cu(trans-MTAI)(2)]Cl(2) to examine the effect of complexation with the metal ion on the isomerization dynamics of trans-MTAI. It is observed that the photoinduced isomerization of the azo-backbone in trans-MTAI is completely inhibited upon complexation with Cu(ii).     

Sub-picosecond mid-infrared spectroscopy of phytochrome Agp1 from Agrobacterium tumefaciens.

The photoinduced primary reaction of the biliverdin binding phytochrome Agp1 (Agp1-BV) from Agrobacterium tumefaciens was investigated by sub-picosecond time-resolved Vis pump-IR probe spectroscopy. Three time constants of tau(1)=0.7+/-0.05 ps, tau(2)=3.3+/-0.2 ps and tau(3)=33.3+/-1.5 ps could be isolated from the dynamics of structurally specific marker bands of the BV chromophore. These results together with those of accompanying sub-picosecond Vis pump-Vis probe spectroscopy allow the extension of the reaction scheme for the primary process by a vibrationally excited electronic ground state. The isomerization at the C15=C16 bond occurs within the lifetime of the excited electronic state. A quantum yield of 0.094 for the primary reaction is determined, suggesting that the quantum yield of formation of the P(fr) far-red-absorbing form is already established in the primary photoreaction of the P(r) (red-absorbing) form.     

Time-resolved IR spectroscopy of N-methylthioacetamide: trans-->cis isomerization upon n-pi and pi-pi excitation and cis-->trans photoreaction

Time-resolved infrared spectroscopy was used to study the photoisomerization of N-Methylthioacetamide (NMTAA) in D2O in both the cis-->trans and the trans-->cis direction upon selective excitation of the n-pi (S1) and pi-pi (S2) electronic transitions. While isomerization and the return to the ground state takes place on two distinct time scales (cis isomerization is 30-40%, independent of the electronic state excited, while the cis-->trans isomerization proceeds with a 60-70% quantum efficiency. These results support a mechanism by which isomerization takes place via one common intermediate state independent of electronic excitation energy and initial conformation.