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.     

Transition state infrared spectra for the trans-->cis isomerization of a simple peptide model

Trans-->cis isomerization of N-methylacetylamide (MeCO-NHMe) has been studied at the G3MP2B3 level of theory and the vibration spectrum has been calculated as a function of the torsional mode of motion along the peptide bond. Noticeable spectral differences have been observed for the transition state interconnecting the cis and trans isomers.     

Unexpectedly fast cis/trans isomerization of Xaa-Pro peptide bonds in disulfide-constrained cyclic peptides

Acyclic dithiol and cyclic disulfide forms of the peptides Ac-Cys-Pro-Xaa-Cys-NH2 (Xaa = Phe, His, Tyr, Gly, and Thr) and Ac-Cys-Gly-Pro-Cys-NH2 and the peptide Ac-Ala-Gly-Pro-Ala-NH2 were synthesized and characterized by mass spectrometry and NMR spectroscopy. Rate constants kct and ktc for cis-to-trans and trans-to-cis isomerization, respectively, across the Cys-Pro or Gly-Pro peptide bonds were determined by magnetization transfer NMR techniques over a range of temperatures, and activation parameters were derived from the temperature dependence of the rate constants. It was found that constraints imposed by the disulfide bond confer an unexpected rate enhancement for cis/trans isomerization, ranging from a factor of 2 to 13. It is proposed that the rate enhancements are a result of an intramolecular catalysis mechanism in which the NH proton of the Pro-Xaa peptide bond hydrogen bonds to the proline nitrogen in the transition state. The peptides Ac-Cys-Pro-Xaa-Cys-NH2 and Ac-Cys-Gly-Pro-Cys-NH2 are model compounds for proline-containing active sites of the thioredoxin superfamily of oxidoreductase enzymes; the results suggest that the backbones of the active sites of the oxidized form of these enzymes may have unusual conformational flexibility.     

Femtosecond fluorescence dynamics of rotation-restricted azobenzenophanes: new evidence on the mechanism of trans --> cis photoisomerization of azobenzene

The ultrafast relaxation dynamics of two rotation-restricted (azobenzeno-2S-phane and azobenzeno-4S-phane) and one rotation-free (4,4'-dimethylazobenzene) azobenzene derivatives were investigated using femtosecond fluorescence up-conversion on both S(1)(n,pi) and S(2)(pi,pi) excitations. On S(2) excitation, pulse-limited kinetics with a decay coefficient of approximately 100 fs corresponding to ultrafast S(2) --> S(1) relaxation is found to be common for all molecules under investigation regardless of the molecular structure. This indicates that a direct rotational relaxation on the S(2) surface is unfavorable. On S(1) excitation, we observed biphasic fluorescence decay with a femtosecond component attributed to the decay of the Franck-Condon state prepared by excitation and a picosecond component attributed to the deactivation of the relaxed molecule on the S(1) surface. This picosecond component is slowed by at least a factor of 2 for the rotation-restricted 2S-bridged molecule compared to that of the rotation-free molecule; for the even stronger rotation-restricted azobenzeno-4S-phane, the decrease is by a factor of 10. These differences in deactivation suggest that the relaxed states and probably the trajectories for rotation-free and rotation-restricted molecules are different on the S(1) surface, which should be important for the quantum yield of photoisomerization.     

Transient Raman studies of the cis—trans photoisomerization processes in stilbene and retinal

This article reviews the present status of the application of transient or time-resolved Raman spectroscopy to the mechanistic studies of the cis—trans photoisomerization in conjugated molecules. Attention is focused on the vibrational information about the molecular structure of the electronically excited intermediates which are involved in the process of photoisomerization. Two examples, the trans to cis photoisomerization of stilbene through the lower excited singlet state and the cist to trans isomerization of retinal through the lowest excited triplet state, are included.     

Structural investigation of "cis" and "trans" vinylogous peptides: cis-vinylog turn in folded cis-vinylogous peptides, an excellent mimic of the natural beta-turn

[structure: see text] Various sequences of modified peptides including those containing a cis- or trans-vinylogous residue have been studied using X-ray diffraction in the solid state and 1H NMR and IR spectroscopy in solution. A cis-vinylogous residue promotes an NH to CO intramolecular H-bond, closing a nine-membered pseudocycle that stabilizes a folded moiety that we proposed to name the cis-vinylogous turn. A trans-vinylogous residue involves an extended conformation. Two consecutive vinylogous residues retain their own structural propensity: "Xaa(tr)"-"Xaa(cis)" or "Xaa(cis)"-"Xaa(tr)" sequence is singly folded, whereas "Xaa(cis)"-"Xaa(cis)" sequence is doubly folded. Oligo vinylogs with all-trans or all-cis or alternating cis-trans motifs could constitute new classes of foldamers.     

Counterion controlled photoisomerization of retinal chromophore models: a computational investigation

CASPT2//CASSCF photoisomerization path computations have been used to unveil the effects of an acetate counterion on the photochemistry of two retinal protonated Schiff base (PSB) models: the 2-cis-penta-2,4-dieniminium and the all-trans-epta-2,4,6-trieniminium cations. Different positions/orientations of the counterion have been investigated and related to (i) the spectral tuning and relative stability of the S0, S1, and S2 singlet states; (ii) the selection of the photochemically relevant excited state; (iii) the control of the radiationless decay and photoisomerization rates; and, finally, (iv) the control of the photoisomerization stereospecificity. A rationale for the results is given on the basis of a simple (electrostatic) qualitative model. We show that the model readily explains the computational results providing a qualitative explanation for different aspects of the experimentally observed "environment" dependent PSB photochemistry. Electrostatic effects likely involved in controlling retinal photoisomerization stereoselectivity in the protein are also discussed under the light of these results, and clues for a stereocontrolled electrostatically driven photochemical process are presented. These computations provide a rational basis for the formulation of a mechanistic model for photoisomerization electrostatic catalysis.     

The cis—trans isomerization of nitrostilbenes XV: mixed singlet and triplet mechanism for trans → cis photoisomerization of 4-nitro-4′-dialkylaminostilbenes in non-polar solvents

The quantum yields of direct cis trans photoisomerization (φ_c → _t and φ_{t → c}) and of fluorescence of the trans isomers (φ_f) of three 4-nitro-4′-R-stilbenes (R amino (1), dimethylamino (2) and diethylamino (3)) were measured in several saturated hydrocarbons. Formation and decay of the lowest triplet state was observed by nanosecond laser flash photolysis. The triplet yield (φ_T), the triplet lifetime (τ_T), φ_{t → c} and φ_f were measured as a function of temperature and of the concentration of the quenchers ferrocene, azulene (Q) and oxygen. Twisting in the triplet, involving a ³t* ³p* equilibrium, analogous to that in other 4-nitrostilbenes, is suggested on the basis of the effects of temperature and quenchers on φ_T and τ_T. The trans → cis photoisomerization of 1 follows the triplet route almost completely. The existence of a singlet pathway (20% – 30% contribution) for 2 and 3 in non-polar solvents at room temperature is concluded from the non-linear dependence of the φ⁰_{t → c}/φ_{t → c} ratio on the concentration of Q. For these two nitrostilbenes a mixed singlet—triplet mechanism for the trans → cis photoisomerization is suggested.     

A theoretical study on the photoisomerization of thiophene

The photoisomerization of thiophene (3–5 and 2–4 transpositions of carbon atoms) has been studied with ab initio SCF and CI calculations. A possible reaction mechanism from the lowest excited singlet state ¹B₂ of thiophene can be proposed from potential surface via Dewar thiophene. The ¹B₂ state of thiophene would easily convert to the biradical intermediate by almost one step. The internal conversion of this species to the S₀ state would cause to the transposition of carbon atoms. The effect of phenyl substituent is also discussed.     

Mass spectrometry in the investigation of β-lysine-containing peptides

Mass spectrometry can be used for amino acid sequence determination in β-lysine-containing peptides and for the identification of α- and β-lysine residues in peptides, as well as for amide bond type determination in β-lysine peptides. The peptide bond in streptothricin D is shown to be formed through the participation of an ε-amino group of the L-β-lysine residue.     

Cis-->trans, trans-->cis isomerizations and N-O bond dissociation of nitrous acid (HONO) on an ab initio potential surface obtained by novelty sampling and feed-forward neural network fitting

The isomerization and dissociation dynamics of HONO are investigated on an ab initio potential surface obtained by fitting the results of electronic structure calculations at 21 584 configurations by using previously described novelty sampling and feed-forward neural network (NN) methods. The electronic structure calculations are executed by using GAUSSIAN 98 with a 6-311G(d) basis set at the MP4(SDQ) level of accuracy. The average absolute error of the NN fits varies from 0.012 eV (1.22 kJ mol(-1)) to 0.017 eV (1.64 kJ mol(-1)). The average computation time for a HONO trajectory using a single NN surface is approximately 4.8 s. These computation times compare very favorably with those required by other methods primarily because the NN fitting needs to be executed only one time rather than at every integration point. If the average result obtained from a committee of NNs is employed at each point rather than a single NN, increased fitting accuracy can be achieved at the expense of increased computational requirements. In the present investigation, we find that a committee comprising five NN potentials reduces the average absolute interpolation error to 0.0111 eV (1.07 kJ mol(-1)). Cis-trans isomerization rates with total energy of 1.70 eV (including zero point energy) have been computed for a variety of different initial distributions of the internal energy. In contrast to results previously reported by using an empirical potential, where cis-->trans to trans-->cis rate coefficient ratios at 1.70 eV total energy were found to lie in the range of 2.0-12.9 depending on the vibration mode excited, these ratios on the ab initio NN potential lie in the range of 0.63-1.94. It is suggested that this result is a reflection of much larger intramode coupling terms present in the ab initio potential surface. A direct consequence of this increased coupling is a significant decrease in the mode specific rate enhancement when compared to results obtained by using empirical surfaces. All isomerizations are found to be first order in accordance with the results reported by using empirical potentials. The dissociation rate to NO+OH has been investigated at internal HONO energies of 3.10 and 3.30 eV for different distributions of this energy among the six vibrational modes of HONO. These dissociations are also found to be first order. The computed dissociation rate coefficients exhibit only modest mode specific rate enhancement that is significantly smaller than that obtained on an empirical surface because of the much larger mode couplings present on the ab initio surface.     

Trans→cis photoisomerization of the quaternary iodides of 4-cyano- and 4-nitro-4′-azastilbene in ethanol solution: Singlet versus triplet mechanism

Quantum yield measurements have been made for the trans→cis photoisomerizations of the quaternary iodides of 4-cyano- and 4-nitro-4′-azastilbene (CP and NP, respectively) in ethanol solution at room temperature in the presence and absence of ferrocene and azulene. A triplet mechanism is suggested for the photoisomerization of NP and a singlet mechanism for that of CP. These mechanisms are supported by laser flash-photolysis studies of the trans triplet state of CP and NP as a function of temperature and quencher concentration.     

Experimental evidence for the photoisomerization of higher fullerenes

The initial relaxation dynamics of the photoexcited fullerenes C60, C70, C76, C84, C86, and C90 were investigated by dispersion-free femtosecond pump-probe spectroscopy. Under identical excitation conditions, the formation of the lowest excited state slows down for the larger fullerenes. This trend in dynamics, monitored throughout the visible and NIR range, is found to correlate with the number of isomers in accordance with the isomerization mechanism suggested by Stone and Wales. The Stone-Wales isomerization was calculated as thermally inaccessible but photoinduced barrierless. The energy difference of the isomers is in the 1 meV range, and back-isomerization is observed on the picosecond time scale. The characteristic spectrally broad transient absorption of the investigated fullerenes is promising for fast optical gating applications.     

A fast method for the measurement of diffusion coefficients: one‐dimensional DOSY

A new experiment for the single‐scan measurement of diffusion coefficients is presented. The principle is to introduce a spatial variation in the parameters of a conventional pulse sequence, so that all of the scans required to determine some physical parameter can be recorded simultaneously from different parts of the sample. The spectrum is acquired in the presence of a weak read gradient so that the resulting lineshapes contain the information required. The pulse sequence is described in detail and demonstrated on a sample containing three components; its advantages and limitations are discussed in relation to those of existing techniques. For uncrowded spectra with high signal‐to‐noise ratio, this experiment provides an order of magnitude reduction in experiment time compared with conventional methods and is likely to be of most benefit where samples are changing rapidly with time or where a long period of polarization, which may be difficult to reproduce accurately, prohibits the use of multiple‐scan techniques. Copyright © 2003 John Wiley & Sons, Ltd.     

Signature of the conformational preferences of small peptides: a theoretical investigation

An extensive computational study of the conformational preferences of N-acetylphenylalaninylamide (NAPA) is reported, including conformational and anharmonic frequency analyses, as well as calculations of excitation energies of the four NAPA conformers lowest in energy. Particular attention is paid to the influence of hydrogen-bonding interactions on the relative stability of the conformers, which was found to be very sensitive to both the level of quantum chemical computations and the anharmonic treatment of molecular vibrations. The assignments of the UV spectral peaks are well supported by the multireference CASSCF/MS-CASPT2 calculations. Upon consideration of the second-order M?ller-Plesset (MP2) and density functional theory (DFT) structures, overall energetics, and harmonic and anharmonic corrections, we found no conclusive theoretical evidence for the assumed conformational propensity of small model peptides toward extended beta-strand structures.     

Preparation of phenyl‐functionalized magnetic mesoporous silica microspheres for the fast separation and selective enrichment of phenyl‐containing peptides

Peptide enrichment before mass spectrometry analysis is essential for large‐scale peptidomic studies, but challenges still remain. Herein, magnetic mesoporous silica microspheres with phenyl group modified interior pore walls were prepared by a facile sol–gel coating strategy, and were successfully applied for selective enrichment of phenyl‐containing peptides in complex biological samples. The newly prepared nanomaterials possessed abundant silanol groups in the exterior surface and numerous phenyl groups in the interior pore walls, as well as a large surface area (592.6 m²/g), large pore volume (0.33 cm³/g), uniform mesopores (3.8 nm), strong magnetic response (29.3 emu/g), and good dispersibility in aqueous solution. As a result of the unique structural properties and size‐exclusion effect, the core–shell phenyl‐functionalized magnetic mesoporous silica microspheres exhibited excellent performance in fast separation and selective enrichment of phenyl‐containing peptides, and the adsorption capacity for bradykinin reached 22.55 mg/g. In addition, selective enrichment of phenyl‐containing peptides from complex samples that are consist of peptides, large proteins, and human serum were achieved by using the as‐prepared microspheres, followed by high‐performance liquid chromatography with ultraviolet detection and electrospray ionization quadrupole time‐of‐flight mass spectrometry analysis. These results demonstrated the as‐prepared microspheres would be a potential candidate for endogenous phenyl‐containing peptides enrichment and biomarkers discovery in peptidome analysis.     

A simple approach for improving the hybrid MMVB force field: application to the photoisomerization of s-cis butadiene

MMVB is a QM/MM hybrid method, consisting of a molecular mechanics force field coupled to a valence bond Heisenberg Hamiltonian parametrized from ab initio CASSCF calculations on several prototype molecules. The Heisenberg Hamiltonian matrix elements Q(ij) and K(ij), whose expressions are partitioned here into a primary contribution and second-order correction terms, are calculated analytically in MMVB. When the original MMVB force field fails to produce potential energy surfaces accurate enough for dynamics calculations, we show that significant improvements can be made by refitting the second-order correction terms for the particular molecule(s) being studied. This "local" reparametrization is based on values of K(ij) extracted (using effective Hamiltonian techniques) from CASSCF calculations on the same molecule(s). The method is demonstrated for the photoisomerization of s-cis butadiene, and we explain how the correction terms that enabled a successful MMVB dynamics study [Garavelli, M.; Bernardi, F.; Olivucci, M.; Bearpark, M. J.; Klein, S.; Robb, M. A. J Phys Chem A 2001, 105, 11496] were refitted.     

Technology for the identification of unusual cis, cis octadecadienoic fatty acids.

In this article methods are presented for the separation and identification of unusual cis, cis dienoic and polygnoic long chain fatty acids. Special emphasis has been laid on the identification of cis, cis octadecadienoic acids. The steps followed are: after transesterification the fatty acid methyl esters are separated by preparative gas chromatography according to chain length followed by argentation chromatography on thin-layer plates. After hydroxylation of the double bonds with osmium tetroxide the polyhydroxy compounds are derivatized to the per-O-trimethylsilyl-ethers. Separation and identification of individual compounds are achieved by combined gas chromatography-mass spectrometry using SCOT columns and low ionization energy.