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1.
Neutral trialanine (Ala3), which is geometrically constrained to have its peptide bond at Phi and Psi angles of alpha-helix and PPII-like conformers, are studied at the B3LYP/6-31+G(d,p) level of theory to examine vibrational interactions between adjacent peptide units. Delocalization of the amide I, amide II, and amide III3 vibrations are analyzed by calculating their potential energy distributions (PED). The vibrational coupling strengths are estimated from the frequency shifts between the amide vibrations of Ala3 and the local amide bond vibrations of isotopically substituted Ala3 derivatives. Our calculations show the absence of vibrational coupling of the amide I and amide II bands in the PPII conformations. In contrast, the alpha-helical conformation shows strong coupling between the amide I vibrations due to the favorable orientation of the C=O bonds and the strong transitional dipole coupling. The amide III3 vibration shows weak coupling in both the alpha-helix and PPII conformations; this band can be treated as a local independent vibration. Our calculated results in general agree with our previous experimental UV Raman studies of a 21-residue mainly alanine-based peptide (AP).  相似文献   

2.
We used UV resonance Raman (UVRR) spectroscopy exciting at approximately 200 nm within the peptide bond pi --> pi* transitions to selectively study the amide vibrations of peptide bonds during alpha-helix melting. The dependence of the amide frequencies on their Psi Ramachandran angles and hydrogen bonding enables us, for the first time, to experimentally determine the temperature dependence of the peptide bond Psi Ramachandran angle population distribution of a 21-residue mainly alanine peptide. These Psi distributions allow us to easily discriminate between alpha-helix, 3(10)-helix and pi-helix/bulge conformations, obtain their individual melting curves, and estimate the corresponding Zimm and Bragg parameters. A striking finding is that alpha-helix melting is more cooperative and shows a higher melting temperature than previously erroneously observed. These Psi distributions also enable the experimental determination of the Gibbs free energy landscape along the Psi reaction coordinate, which further allows us to estimate the free energy barriers along the AP melting pathway. These results will serve as a benchmark for the numerous untested theoretical studies of protein and peptide folding.  相似文献   

3.
Transient UV resonance Raman measurements excited within the amide pi --> pi transitions of a 21 unit alpha-helical peptide has for the first time determined a lower bound for the unfolding rate of the last alpha-helical turn to form a fully random coil peptide. A 3 ns T-jump is generated with 1.9 microm laser pulses, which are absorbed by water. Subsequent 3 ns 204 nm UV pulses excite the amide Raman spectra at delay times between 3 ns and 1 ms, to monitor the peptide conformational evolution. We find approximately 180 ns relaxation times which result in a rate constant of >5 x 10(6) s(-1) for unfolding of the last alpha-helical turn. Our data are inconsistent with slow alpha-helix nuclei melting.  相似文献   

4.
The performance of the Hartree-Fock method and the three density functionals B3LYP, PBE0, and CAM-B3LYP is compared to results based on the coupled cluster singles and doubles model in predictions of the solvatochromic effects on the vertical n-->pi* and pi-->pi* electronic excitation energies of acrolein. All electronic structure methods employed the same solvent model, which is based on the combined quantum mechanics/molecular mechanics approach together with a dynamical averaging scheme. In addition to the predicted solvatochromic effects, we have also performed spectroscopic UV measurements of acrolein in vapor phase and aqueous solution. The gas-to-aqueous solution shift of the n-->pi* excitation energy is well reproduced by using all density functional methods considered. However, the B3LYP and PBE0 functionals completely fail to describe the pi-->pi* electronic transition in solution, whereas the recent CAM-B3LYP functional performs well also in this case. The pi-->pi* excitation energy of acrolein in water solution is found to be very dependent on intermolecular induction and nonelectrostatic interactions. The computed excitation energies of acrolein in vacuum and solution compare well to experimental data.  相似文献   

5.
Combined density functional and multireference configuration interaction methods have been used to calculate the electronic spectrum of 9H-adenine, the most stable tautomer of 6-aminopurine. In addition, constrained minimum energy paths on excited potential energy hypersurfaces have been determined along several relaxation coordinates. The minimum of the first (1)[n-->pi*] state has been located at an energy of 4.54 eV for a nuclear arrangement in which the amino group is pyramidal whereas the ring system remains planar. Close by, another minimum on the S(1) potential energy hypersurface has been detected in which the C(2) center is deflected out of the molecular plane and the electronic character of S(1) corresponds to a nearly equal mixture of (1)[pi-->pi*] and (1)[n-->pi*] configurations. The adiabatic excitation energy of this minimum amounts to 4.47 eV. Vertical and adiabatic excitation energies of the lowest n-->pi* and pi-->pi* transitions as well as transition moments and their directions are in very good agreement with experimental data and lend confidence to the present quantum chemical treatment. On the S(1) potential energy hypersurface, an energetically favorable path from the singlet n-->pi* minimum toward a conical intersection with the electronic ground state has been identified. Close to the conical intersection, the six-membered ring of adenine is strongly puckered and the electronic structure of the S(1) state corresponds to a pi-->pi* excitation. The energetic accessibility of this relaxation path at about 0.1 eV above the singlet n-->pi* minimum is presumably responsible for the ultrafast decay of 9H-adenine after photoexcitation and explains why sharp vibronic peaks can only be observed in a rather narrow wavelength range above the origin. The detected mechanism should be equally applicable to adenosine and 9-methyladenine because it involves primarily geometry changes in the six-membered ring whereas the nuclear arrangement of the five-membered ring (including the N(9) center) is largely preserved.  相似文献   

6.
We examined the 204-nm UV resonance Raman (UVR) spectra of the polyproline II (PPII) and alpha-helical states of a 21-residue mainly alanine peptide (AP) in different H2O/D2O mixtures. Our hypothesis is that if the amide backbone vibrations are coupled, then partial deuteration of the amide N will perturb the amide frequencies and Raman cross sections since the coupling will be interrupted; the spectra of the partially deuterated derivatives will not simply be the sum of the fully protonated and deuterated peptides. We find that the UVR spectra of the AmIII and AmII' bands of both the PPII conformation and the alpha-helical conformation (and also the PPII AmI, AmI', and AmII bands) can be exactly modeled as the linear sum of the fully N-H protonated and N-D deuterated peptides. Negligible coupling occurs for these vibrations between adjacent peptide bonds. Thus, we conclude that these peptide bond Raman bands can be considered as being independently Raman scattered by the individual peptide bonds. This dramatically simplifies the use of these vibrational bands in IR and Raman studies of peptide and protein structure. In contrast, the AmI and AmI' bands of the alpha-helical conformation cannot be well modeled as a linear sum of the fully N-H protonated and N-D deuterated derivatives. These bands show evidence of coupling between adjacent peptide bond vibrations. Care must be taken in utilizing the AmI and AmI' bands for monitoring alpha-helical conformations since these bands are likely to change as the alpha-helical length changes and the backbone conformation is perturbed.  相似文献   

7.
We examined the 204-nm UV Raman spectra of the peptide XAO, which was previously found by Shi et al.'s NMR study to occur in aqueous solution in a polyproline II (PPII) conformation. The UV Raman spectra of XAO are essentially identical to the spectra of small peptides such as ala(5) and to the large 21-residue predominantly Ala peptide, AP. We conclude that the non-alpha-helical conformations of these peptides are dominantly PPII. Thus, AP, which is highly alpha-helical at room temperature, melts to a PPII conformation. There is no indication of any population of intermediate disordered conformations. We continued our development of methods to relate the Ramachandran Psi-angle to the amide III band frequency. We describe a new method to estimate the Ramachandran Psi-angular distributions from amide III band line shapes measured in 204-nm UV Raman spectra. We used this method to compare the Psi-distributions in XAO, ala(5), the non-alpha-helical state of AP, and acid-denatured apomyoglobin. In addition, we estimated the Psi-angle distributions of peptide bonds which occur in non-alpha-helix and non-beta-sheet conformations in a small library of proteins.  相似文献   

8.
Replacement of the alpha-proton of an alanine residue to generate alpha-aminoisobutyric acid (Aib) in alanine-based oligopeptides favors the formation of a 3(10) helix when the length of the oligopeptide is about four to six residues. This research was aimed at experimentally identifying the structural impact of an individual Aib residue in an alanine context of short peptides in water and Aib's influence on the conformation of nearest-neighbor residues. The amide I band profile of the IR, isotropic and anisotropic Raman, and vibrational circular dichroism (VCD) spectra of Ac-Ala-Ala-Aib-OMe, Ac-Ala-Aib-Ala-OMe, and Ac-Aib-Ala-Ala-OMe were measured and analyzed in terms of different structural models by utilizing an algorithm that exploits the excitonic coupling between amide I' modes. The conformational search was guided by the respective 1H NMR and electronic circular dichroism spectra of the respective peptides, which were also recorded. From these analyses, all peptides adopted multiple conformations. Aib predominantly sampled the right-handed and left-handed 3(10)-helix region and to a minor extent the bridge region between the polyproline (PPII) and the helical regions of the Ramachandran plot. Generally, alanine showed the anticipated PPII propensity, but its conformational equilibrium was shifted towards helical conformations in Ac-Aib-Ala-Ala-OMe, indicating that Aib can induce helical conformations of neighboring residues positioned towards the C-terminal direction of the peptide. An energy landscape exploration by molecular dynamics simulations corroborated the results of the spectroscopic studies. They also revealed the dynamics and pathways of potential conformational transitions of the corresponding Aib residues.  相似文献   

9.
The calculations of the electronic structure and spectra of [Ru(NH3)5L]2+ (L = imidazole, histidine) and [Ru(NH3)5L]3+ (L = imidazole, N-imidazolate anion, 4-methylimidazole, 4-methyl-1N-imidazolate anion and 1N-bound histidine) complexes are performed in the framework of the CI method in the INDO/CNDO approximation. The MO diagram is obtained. The assignment of all transitions with energies of 4-5 eV is made and the nature of corresponding excited states is discussed. For the Ru(II) complexes, the lower energy observable transition is assigned to d-->pi* type, whereas the higher energy one is assigned to pi-->pi* type. In the spectra of the Ru(III) complexes with charged ligands both transitions are of pi-->d character, while in the case of uncharged ligands, the higher energy transition mostly incorporates pi-->pi* excitations.  相似文献   

10.
Ashton L  Barron LD  Hecht L  Hyde J  Blanch EW 《The Analyst》2007,132(5):468-479
Rich and complex Raman scattering and Raman optical activity (ROA) spectra have been measured monitoring the pH induced alpha-helix-to-disordered conformational transition in poly(L-glutamic acid). Two-dimensional (2D) correlation techniques have been applied to facilitate a comprehensive analysis of these two complementary spectral sets. Synchronous contour plots have identified band assignments of alpha-helical and disordered conformations, and have revealed bands characteristic of changes in the protonation state of the polypeptide. Asynchronous plots, on the other hand, have probed the relative sequential orders of intensity changes indicating a decrease in intensity of alpha-helical bands in the backbone skeletal stretch region, followed by a subsequent decrease in intensity in the extended amide III and amide I regions, underlying the appearance of disordered structure, including poly(L-proline) II (PPII) helix. The application of a 2D correlation 'moving' window has also disclosed two distinct phases during helix unfolding in the alpha-helix-to-disordered transition, occurring at approximately pH 4.9 and approximately pH 5.2, possibly a result of the difference in helical stability between the end and central regions of the alpha-helix. This paper demonstrates the potential value of combining 2D Raman, 2D ROA and moving window correlation techniques for the detailed investigation of complex and subtle changes of secondary structure during the unfolding mechanisms of polypeptides and proteins.  相似文献   

11.
The electronic absorption spectra of: 2-, 3-, and 4-azidopyridines have been investigated in a wide variety of polar and non-polar solvents. According to Onsager model, the studied spectra indicate that the orientation polarization of solvent dipoles affects the electronic spectrum much stronger than the induction polarization of solvent dipoles. The effect of solvent dipole moment predominates that of solvent refractive index in determining the values of band maxima of an electronic spectrum. The spectra of azidopyridines differ basically from these of pyridine or mono-substituted pyridine. Results at hand indicate that the azide group perturbs the pyridine ring in the case of 3-azidopyridine much more than it does in the case of 2-azidopyridine. This result agrees with the predictions of the resonance theory. Although the equilibrium <==> azide tetrazole is well known, yet the observed spectra prove that such an equilibrium does not exist at the studied conditions. The spectra of the studied azidopyridines are characterized by the existence of overlapping transitions. Gaussian analysis is used to obtain nice, resolved spectra. All the observed bands correspond to pi-->pi* transitions, n-->pi* may be overlapped with the stronger pi-->pi* ones.  相似文献   

12.
The electronic states of different conformations of platinum acetylides Pt(PH3)2(C[triple bond]C-Ph)2 and Pt(PH3)2(C[triple bond]C-PhC[triple bond]C-Ph)2 (PE1 and PE2) were calculated with density functional theory (DFT) using effective core potential basis sets. Time dependent DFT calculations of UV absorption spectra showed strong dependence of the intense absorption band maxima on mutual orientation of the phenyl rings with respect to the P-Pt-P axis. Geometry optimization of the first excited triplet state (T1) indicates broken symmetry structure with the excitation being localized in one ligand. This splits the two substitution ligands into a nondistorted aromatic ring with the C[triple bond]C-Ph bonds for one side and into a quinoid structure with a cumulenic C=C=C link on the other side. Quadratic response (QR) calculations of spin-orbit coupling and phosphorescence radiative lifetime (tauR) indicated a good agreement with experimental tauR values reported for solid PE1 and PE2 and PE2 capped with dendrimers in tetrahydrofuran solutions. The QR calculations reproduced an increase of tauR upon prolongation of pi chain of ligands and concommittant redshift of the phosphorescence. Moreover, it is shown how the phosphorescence borrows intensity from sigma-->pi* transitions localized at the C[triple bond]C-Pt-P fragments and that there is no intensity borrowing from delocalized pi-->pi* transitions.  相似文献   

13.
A truncated version of the GCN4 coiled-coil peptide has been studied by ultraviolet resonance Raman (UVRR) spectroscopy with 197 nm excitation, where amide modes are optimally enhanced. Although the CD melting curve could be satisfactorily described with a two-state transition having Tm = 30 degrees C, singular value decomposition of the UVRR data yielded three principal components, whose temperature dependence implicates an intermediate form between the folded and unfolded forms, with formation and melting temperatures of 10 and 40 degrees C. Two alpha-helical amide III bands, at 1340 and 1300 cm(-1), melted out selectively at 10 and 40 degrees C, respectively, and are assigned to hydrated and unhydrated helical regions. The hydrated regions are proposed to be melted in the intermediate form, while the unhydrated regions are intact. Time-resolved UVRR spectra following laser-induced temperature jumps revealed two relaxations, with time constants of 0.2 and 15 mus. These are suggested to reflect the melting times of hydrated and unhydrated helices. The unhydrated helical region may be associated with a 14-residue "trigger" sequence that has been identified in the C-terminal half of GCN4. Dehydration of helices may be a key step in the folding of coiled-coils.  相似文献   

14.
Transient absorption spectroscopy has been used to elucidate the nature of the S1 intermediate state populated following excitation of cob(III)alamin (Cbl(III)) compounds. This state is sensitive both to axial ligation and to solvent polarity. The excited-state lifetime as a function of temperature and solvent environment is used to separate the dynamic and electrostatic influence of the solvent. Two distinct types of excited states are identified, both assigned to pi3d configurations. The spectra of both types of excited states are characterized by a red absorption band (ca. 600 nm) assigned to Co 3d --> 3d or Co 3d --> corrin pi* transitions and by visible absorption bands similar to the corrin pi-->pi* transitions observed for ground state Cbl(III) compounds. The excited state observed following excitation of nonalkyl Cbl(III) compounds has an excited-state spectrum characteristic of Cbl(III) molecules with a weakened bond to the axial ligand (Type I). A similar excited-state spectrum is observed for adenosylcobalamin (AdoCbl) in water and ethylene glycol. The excited-state spectrum of methyl, ethyl, and n-propylcobalamin is characteristic of a Cbl(III) species with a sigma-donating alkyl anion ligand (Type II). This Type II excited-state spectrum is also observed for AdoCbl bound to glutamate mutase. The results are discussed in the context of theoretical calculations of Cbl(III) species reported in the literature and highlight the need for additional calculations exploring the influence of the alkyl ligand on the electronic structure of cobalamins.  相似文献   

15.
UV resonance Raman spectroscopy has been used to determine the conformational energy landscape of poly-L-lysine (PLL) in the presence of NaClO4 as a function of temperature. At 1 degree C, in the presence of 0.83 M NaClO4, PLL shows an approximately 86% alpha-helix-like content, which contains alpha-helix and pi-bulge/helix conformations. The high alpha-helix-like content of PLL occurs because of charge screening due to strong ion-pair formation between ClO4- and the lysine side chain -NH3+. As the temperature increases from 1 to 60 degrees C, the alpha-helix and pi-bulge/helix conformations melt into extended conformations (PPII and 2.51-helix). We calculate the Psi Ramachandran angle distribution of the PLL peptide bonds from the UV Raman spectra which allows us to calculate the PLL (un)folding energy landscapes along the Psi reaction coordinate. We observe a basin in the Psi angle conformational space associated with alpha-helix and pi-bulge/helix conformations and another basin for the extended PPII and 2.51-helical conformations.  相似文献   

16.
Excitation profiles of SERS (surface-enhanced Raman scattering) and/or SERRS (surface-enhanced resonance Raman scattering) spectral bands of two forms of a Ag-bpy (bpy = 2,2'-bipyridine) surface complex and of [Ru(bpy)3]2+ on Ag nanoparticle (hydrosol) surfaces were determined from the spectra excited in the 458-600 nm region and are reported together with the FT-SERS spectra of the Ag-bpy surface complex and FT Raman spectra of [Ru(bpy)3] Cl2. Seven of the observed 11 fundamentals as well as their first overtones and combination bands are selectively enhanced in SERS of the Ag-bpy surface complex formed in the Ag colloid/HCl/bpy system. The profiles of these bands show a common maximum at approximately 540 nm. The selectively enhanced bands of the Ag-bpy surface complex have nearly the same wavenumbers as those enhanced in the SERRS and resonance Raman spectra of [Ru(bpy)3]2+ upon excitation close to the 453 nm maximum of its MLCT absorption band. Moreover, the intensity patterns of the bpy vibrations of the two species match both in resonance (541 nm excitation for Ag-bpy, 458 nm for [Ru(bpy)3]2+) and in off-resonance (458 and 1064 nm for Ag-bpy, 1064 nm for [Ru(bpy)3]2+). The distinct band shapes of the excitation profiles of the selectively enhanced vibrational modes of the Ag-bpy surface complex, as well as the observation of overtones and combination bands in the SERS spectra upon excitation into this "band", are interpreted in terms of a charge-transfer resonance contribution to the overall SERS enhancement. In view of the near-coincidence of the vibrational modes coupled to the resonant electronic transition of Ag-bpy with those coupled to the MLCT transition of [Ru(bpy)3]2+, the resonant electronic transition is tentatively assigned to a Ag metal to bpy (pi*) CT transition.  相似文献   

17.
《Chemical physics》1987,114(1):137-147
Excitation profiles for the intensities of electronic Raman transitions between crystal field components of the 7F6 and 7F5 manifolds of terbium aluminum garnet are recorded for excitation in the spectral region where absorption bands due to levels of the 5D4 manifold occur. The intensities of the electronic transitions are not enhanced which is thought to be caused by the small values of electric dipole matrix elements of the resonating electronic states in comparison to the values of such elements to other intermediate states which occur in the expression for the scattering tensor. Fluorescence from the 5D4 levels is induced and resonance fluorescence are time resolved with respect to the Raman transitions. We report electronic Raman transitions excited with the 308.0 nm line of an XeCl excimer laser. As opposed to excitation with visible laser sources, transitions are recorded which terminate on all the crystal field levels of the 7F5…0 levels. In addition, fluorescence from 5D3 to the ground state of terbium aluminum garnet is also observed.  相似文献   

18.
The title compound, 1-acetyl-3-(2,4-dichloro-5-fluoro-phenyl)-5-phenyl-pyrazoline, has been synthesized and characterized by elemental analysis, IR, UV-vis and X-ray single crystal diffraction. Density functional (DFT) calculations have been carried out for the title compound by using B3LYP method at 6-31G* basis set. The calculated results show that the predicted geometry can well reproduce the structural parameters. Predicted vibrational frequencies have been assigned and compared with experimental IR spectra and they are supported each other. The theoretical electronic absorption spectra have been calculated by using TD-DFT method. Molecular orbital coefficients analyses suggest that the above electronic transitions are mainly assigned to n-->pi* and pi-->pi* electronic transitions. On the basis of vibrational analyses, the thermodynamic properties of the title compound at different temperatures have been calculated, revealing the correlations between C(p,m)(0),S(m)(0),H(m)(0) and temperatures.  相似文献   

19.
Two-photon-resonant hyper-Raman spectra are reported for three "push-pull" conjugated organic chromophores bearing -NO(2) acceptor groups, two dipolar and one octupolar. The excitation source is an unamplified picosecond mode-locked Ti:sapphire laser tunable from 720 to 950 nm. The linear resonance Raman spectra of the same molecules are measured using excitation from the laser second harmonic. Excitation on resonance with the lowest-lying band in the linear absorption spectrum yields nearly identical resonance Raman and resonance hyper-Raman spectra. However, excitation into a region that appears to contain more than one electronic transition gives rise to different intensity patterns in the linear and nonlinear spectra, indicating that different transitions contribute differently to the one-photon and two-photon oscillator strength. The promise of the hyper-Raman technique for examining electronic transitions that are both one- and two-photon allowed is discussed.  相似文献   

20.
The novel charge-transfer ground state found in alpha,alpha'-diimine adducts of ytterbocene (C(5)Me(5))(2)Yb(L) [L = 2,2'-bipyridine (bpy) and 1,10-phenanthroline (phen)] in which an electron is spontaneously transferred from the f(14) metal center into the lowest unoccupied (pi*) molecular orbital (LUMO) of the diimine ligand to give an f(13)-L(*)(-) ground-state electronic configuration has been characterized by cyclic voltammetry, UV-vis-near-IR electronic absorption, and resonance Raman spectroscopies. The voltammetric data demonstrate that the diimine ligand LUMO is stabilized and the metal f orbital is destabilized by approximately 1.0 V each upon complexation for both bpy and phen adducts. The separation between the ligand-based oxidation wave (L(0/-)) and the metal-based reduction wave (Yb(3+/2+)) in the ytterbocene adducts is 0.79 V for both bpy and phen complexes. The UV-vis-near-IR absorption spectroscopic data for both the neutral adducts and the one-electron-oxidized complexes are consistent with those reported recently, but previously unreported bands in the near-IR have been recorded and assigned to ligand (pi*)-to-metal (f orbital) charge-transfer (LMCT) transitions. These optical electronic excited states are the converse of the ground-state charge-transfer process (e.g., f(13)-L(*-) <--> f(14)-L(0)). These new bands occur at approximately 5000 cm(-1) in both adducts, consistent with predictions from electrochemical data, and the spacings of the resolved vibronic bands in these transitions are consistent with the removal of an electron from the ligand pi* orbital. The unusually large intensity observed in the f --> f intraconfiguration transitions for the neutral phenanthroline adduct is discussed in terms of an intensity-borrowing mechanism involving the low-energy LMCT states. Raman vibrational data clearly reveal resonance enhancement for excitation into the low-lying pi* --> pi* ligand-localized excited states, and comparison of the vibrational energies with those reported for alkali-metal-reduced diimine ligands confirms that the ligands in the adducts are reduced radical anions. Differences in the resonance enhancement pattern for the modes in the bipyridine adduct with excitation into different pi* --> pi* levels illustrate the different nodal structures that exist in the various low-lying pi* orbitals.  相似文献   

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