Two-dimensional infrared investigation of N-acetyl tryptophan methyl amide in solution

The linear infrared and two-dimensional infrared (2D IR) spectra in the amide-I region of N-acetyl tryptophan methyl amide (NATMA) in solvents of varying polarity are reported. The two amide-I transitions have been assigned unambiguously by using 13C isotopic substitution of the carbonyl group. The amide unit at the amino end shows a lower transition frequency in CH2Cl2 and methanol, while the acetyl end has a lower transition frequency in D2O. Multiple conformers exist in CH2Cl2 and methanol, but only one conformer is evident in D2O. The 2D IR cross peaks from the intermode coupling yield off-diagonal anharmonicities 2.5 +/- 0.5, 3.25 +/- 0.5, and 3.0 +/- 0.5 cm(-1) in CH2Cl2, methanol, and D2O, respectively, which by simple matrix diagonalization yield the coupling constants 8.0 +/- 0.5, 8.0 +/- 1.0, and 5.5 +/- 1.0 cm(-1). The major conformer in CH2Cl2 corresponds to a C7 structure, in agreement with that found in the gas phase [Dian, B. C.; Longarte, A.; Mercier, S.; Evans, D. A.; Wales, D. J.; Zwier, T. S. J. Chem. Phys. 2002, 117, 10688-10702] with intramolecular hydrogen bonding between the acetyl end C=O and the amino end N-H. The backbone dihedral angles (phi, psi) are determined to be in the ranges of (-55 +/- 5 degrees , 30 +/- 5 degrees ), (120 +/- 10 degrees , -20 +/- 10 degrees ), and (+/-160 +/- 10 degrees , +/-75 +/- 10 degrees ) in CH2Cl2, methanol, and D2O, respectively.     

Anharmonicity of amide modes

The principal contributions to the anharmonic coupling of amide vibrations are explored with the objective of comparing recent experiments with density functional theory and evaluating simple models of mode coupling. Experimental information obtained by means of two-dimensional infrared spectroscopy (2D IR) is reasonably well predicted by the computed one- and two-quantum anharmonic modes of amide-A, -I, and -II types in mono-, di- and tripeptides. The expansion of the vibrational energy up to the cubic and quartic coupling of harmonic modes suggested criteria to assess how localized are the forces determining the anharmonicity. The off-diagonal anharmonicity between an amide-A and one other amide mode was shown to be mainly determined by forces involving only these two modes, whereas the off-diagonal anharmonicity of two amide-I modes in peptides depended significantly on forces due to motions other than those of the amide-I type. Both the diagonal and off-diagonal anharmonicities exhibit sensitivity to peptide structures. These results should prove useful in linking 2D IR experimental results to secondary structure. Further, the results are used to evaluate the vibrational exciton model for the mixed-mode anharmonicities of the amide-I transitions.     

Two-dimensional infrared spectra of the 13C=18O isotopomers of alanine residues in an alpha-helix

The parameters needed to describe the two-dimensional infrared (2D IR) spectra of the isotopically labeled alpha-helix are presented. The 2D IR spectra in the amide-I' spectral region of a series of singly 13C=18O-labeled 25-residue alpha-helices were measured by three-pulse heterodyned spectral interferometry. The dependence of the spectra on the population time was measured. Individual isotopomer levels (residues 11-14) were clearly identified in 2D IR, downshifted by approximately 61 cm(-1) from the main helical band. By analyzing the line shapes of the 13C=18O diagonal peaks that appeared at approximately 1571.3 +/- 0.8 cm(-1) for all four labeled samples, we observed wider structural distributions for residues 14 and 11 than those for 12 and 13. A small fast component in the correlation function was used to estimate the dynamics of these distributions. In all cases, the v = 1 --> 2 transition showed a more Lorentzian-like line shape and also decayed faster than the v = 0 --> 1 transition, indicating that the population relaxation time of the v = 2 state was significantly faster than the v = 1 state. The amide transitions with naturally abundant 13C=16O appeared at approximately 1594 cm(-1), forming very weak and blurred cross-peaks with 13C=18O isotopomer modes. The effects of spectral interferences on the coherence time dependence of the detection frequency spectrum were also investigated. The methods of first moments and Wigner analysis were developed to circumvent the interference effects on the weak isotopomer transitions. The structural origin of the distributions for individual isotopomers was proposed to be an effect of nearby lysine residues on the intrahelical hydrogen-bond network.     

Conformations of N-acetyl-L-prolinamide by two-dimensional infrared spectroscopy

Femtosecond two-dimensional infrared (2D IR) spectroscopy has been applied to study the conformations of a model dipeptide, N-acetyl-L-prolinamide (AcProNH2) in deuterated chloroform (CDCl3). Spectral features in the amide-I and -II regions are obtained by rephasing (R), nonrephasing (NR), and reverse photon echo (RPE) pulse sequences with two polarization conditions. The 2D spectra obtained by the RPE and NR sequences with (0, 0, 0, 0) polarization reveal new spectral features associated with the multiple conformers of AcProNH2 that are difficult to discern using R sequence and linear-IR spectroscopy. The high resolving power of the RPE sequence comes from destructive interference between the positive and negative peaks of nearby vibrators, similar to the NR sequence. The RPE response functions that are useful for 2D spectral simulations are evaluated, including the effects of vibrational frequency correlations. The 2D spectra obtained with (45, -45, 90, 0) polarization exhibit clear cross-peak patterns in the off-diagonal region for the R and RPE sequences but in the diagonal region for the NR sequence. These patterns, free from strong diagonal contributions, are crucial for structure determination. DFT calculations, normal-mode analysis, Hessian matrix reconstruction, and vibrational exciton Hamiltonian diagonalization yield molecular parameters needed for quantitative simulations of 2D spectra: angles between transition dipoles, coupling constants, and off-diagonal anharmonicities of the amide-I and -II modes are obtained for solvated trans-C7 and cis structures and for gas-phase trans conformers in the region of phi = -120 degrees to 0 degrees and psi = -100 degrees to 180 degrees in the Ramachandran space. Systematic simulations based on a 4:1 population ratio of the solvated trans-C7 and cis structures reproduce well the 2D spectral features obtained at both polarization conditions. However, better agreement between the experimental and simulated cross-peak patterns can be reached if the dihedral angles of the major trans conformer are close to (phi, psi) = (-80 degrees , 100 degrees ). Our results suggest that the major conformer of AcProNH2 in CDCl3 deviates from the gas-phase global minimum, the trans-C7 form, to an extended intermediate between the C7 and polyproline-II structure. These results are discussed in relationship with earlier findings obtained by NMR, transient IR studies, and MD simulations.     

Amide I infrared spectral features characteristic of some untypical conformations appearing in the structures suggested for amyloids

Amide I infrared (IR) spectral features are studied, by using the density functional theoretical method, for two untypical (but possibly rather prevalent) structures inspired from those recently suggested for amyloids: a structure consisting of loop regions in the (alpha L, alpha R) conformation stacked to form an alpha-sheet, and a structure involving some main-chain peptide groups (of any residues) and some side-chain amide groups of glutamine and asparagine residues closely located with each other. The amide I vibrational (off-diagonal) coupling constants are examined by extracting them from the calculated Cartesian-based force constants with the average partial vector method and by comparing them with those estimated on the basis of the transition dipole coupling mechanism. It is suggested that the amide I IR band characteristic of the alpha-sheet conformation in dry environment (without hydrogen bonding to solvent water molecules) is located in a high-frequency region (approximately >1670 cm(-1), somewhat higher than that of alpha-helix), because of the dependence of the diagonal (uncoupled) frequency and the off-diagonal coupling constant on the Phi and Psi dihedral angles. It is also shown that the amide I vibrations of the closely located peptide and amide groups are strongly coupled through-space with each other, and in the presence of this type of strong vibrational coupling, a noticeable change in the IR intensity upon (13)C=O substitution may occur even for a mode that arises mainly from an unsubstituted group and is not much shifted in frequency. The meaning of these results in the interpretation of observed amide I spectral profiles, especially the possible usefulness of IR spectroscopic measurements for detecting those untypical structures in the process of amyloid formation, is also discussed.     

Two-dimensional infrared spectral signatures of 3(10)- and alpha-helical peptides

Two-dimensional infrared (2D IR) spectra of Calpha-alkylated model octapeptides Z-(Aib)8-OtBu, Z-(Aib)5-L-Leu-(Aib)2-OMe, and Z-[L-(alphaMeVal)]8-OtBu have been measured in the amide I region to acquire 2D spectral signatures characteristic of 3(10)- and alpha-helical conformations. Phase-adjusted 2D absorptive spectra recorded with parallel polarizations are dominated by intense diagonal peaks, whereas 2D rephasing spectra obtained at the double-crossed polarization configuration reveal cross-peak patterns that are essential for structure determination. In CDCl3, all three peptides are of the 3(10)-helix conformation and exhibit a doublet cross-peak pattern. In 1,1,1,3,3,3-hexafluoroisopropanol, Z-[L-(alphaMeVal)]8-OtBu undergoes slow acidolysis and 3(10)-to-alpha-helix transition. In the course of this conformational change, its 2D rephasing spectrum evolves from an elongated doublet, characteristic of a distorted 3(10)-helix, to a multiple-peak pattern, after becoming an alpha-helix. The linear IR and 2D absorptive spectra are much less informative in discerning the structural changes. The experimental spectra are compared to simulations based on a vibrational exciton Hamiltonian model. The through-bond and through-space vibrational couplings are modeled by ab initio coupling maps and transition dipole interactions. The local amide I frequency is evaluated by a new approach that takes into account the effects of hydrogen-bond geometry and sites. The static diagonal and off-diagonal disorders are introduced into the Hamiltonian through statistical models to account for conformational fluctuations and inhomogeneous broadening. The sensitivity of cross-peak patterns to different helical conformations and the chain length dependence of the spectral features for short 3(10)- and alpha-helices are discussed.     

Accidental vibrational degeneracy in vibrational excited states observed with ultrafast two-dimensional IR vibrational echo spectroscopy

The coupling between the OD stretch v=2 level and benzene-ring modes in 2-methoxyphenol-OD (hydroxyl H replaced by D) is observed with ultrafast two-dimensional (2D) IR vibrational echo spectroscopy. Because of this coupling, the 1-2 transition peak in the 2D spectrum is split into a doublet with peaks of approximately equal amplitudes. Several molecules and solvents were used to study this phenomenon. Near-IR (NIR) spectroscopy measurements and density-functional theory calculations (B3LYP6-31+G(d,p) level) were also applied. Experimental results and calculations show that the OD stretch 1-2 transition is coupled to a combination band related to the benzene-ring motions. A simple quantum-mechanical model indicates that the combination band has a frequency of 5172 and 5176.5 cm(-1) in CCl4 and hexane, respectively. The transition between this combination band and the ground state is too weak to detect by NIR. The transition between this band and the OD stretch first excited state is also so weak that most of the intensity of the doublet comes from the oscillator strength produced by coupling to the OD stretch. The model gives the coupling strengths as 6.5 and 7 cm(-1) in CCl4 and hexane, respectively.     

Conformational dependence of anharmonic vibrations in peptides: amide-I modes in model dipeptide

The conformational dependence of a set of anharmonic vibrational parameters for the amide-I modes in peptides has been examined at the level of Hartree-Fock theory. By using glycine dipeptide as a model molecule, the phi-psi maps of diagonal and off-diagonal anharmonicities, local mode mixing angle, zero-order local mode frequencies, as well as intermode coupling, were calculated, and all were found to exhibit certain conformational sensitivities. The characteristics of the phi-psi maps of the diagonal and off-diagonal anharmonicities were found to be complementary to each other, and the latter was found to correlate well with that of the mixing angle, reflecting the fact that these anharmonic parameters are interconnected and all determined by the same set of underlying anharmonic force field. The mean values of the diagonal and off-diagonal anharmonicities were found to be 15.7 cm(-1) and 9.9 cm(-1) respectively. The mean value for the two local mode frequency differences was estimated to be 9.7 cm(-1), showing a nondegenerate local mode picture. For significant peptide conformations, the calculated anharmonic parameters were found to be in reasonable agreement with values obtained at the level of density functional theory as well as values obtained with recent two-dimensional infrared experiments.     

Ab initio-based all-mode two-dimensional infrared spectroscopy of a sugar molecule

To construct two-dimensional infrared (2D IR) spectra having all vibrational modes of a molecule included is still quite challenging, both experimentally and theoretically. Here we report an ab initio-based all-mode 2D IR spectra simulation approach. Using deuterated glycolaldehyde (CH2OHCDO), the smallest sugar as a model molecule, we have calculated correlation 2D IR spectrum of its entire 3N-6 (N=8) normal modes in the mid-to-far-IR region (4000-0 cm(-1)), using quantum chemical anharmonic frequency and anharmonicity computations in conjunction with time-domain third-order nonlinear response functions. The calculated 2D IR spectra were found to contain a network of structural and dynamical parameters of the molecule. It is found that certain spectral regions, once enlarged, show features that are in reasonable agreement with limited but already available single- and dual-frequency 2D IR experimental results. The extension of narrow-band 2D IR spectroscopy into the full mid-to-far-IR regime would allow us to characterize the structural distributions and dynamics of molecular complexes in condensed phases with sufficient number of parameters.     

Dimers of dipyrrometheneboron difluoride (BODIPY) with light spectroscopic applications in chemistry and biology.

A ground-state dimer (denoted D(I)) exhibiting a strong absorption maximum at 477 nm (epsilon = 97 000 M(-1)cm(-1)) can form between adjacent BODIPY groups attached to mutant forms of the protein, plasminogen activator inhibitor type 1 (PAI-1). No fluorescence from excited D(I) was detected. A locally high concentration of BODIPY groups was also achieved by doping lipid phases (micelles, vesicles) with BODIPY-labeled lipids. In addition to an absorption band located at about 480 nm, a new weak absorption band is also observed at ca. 570 nm. Both bands are ascribed to the formation of BODIPY dimers of different conformation (D(I) and D(II)). Contrary to D(I) in PAI-1, the D(II) aggregates absorbing at 570 nm are emitting light observed as a broad band centered at about 630 nm. The integrated absorption band of D(I) is about twice that of the monomer, which is compatible with exciton coupling within a dimer. The F?rster radius of electronic energy transfer between a BODIPY excited monomer and the ground-state dimer (D(I)()) is 57 +/- 2 A. A simple model of exciton coupling suggests that in D(I) two BODIPY groups are stacked on top of each other in a sandwich-like configuration with parallel electronic transition dipoles. For D(II) the model suggests that the S(0) --> S(1) transition dipoles are colinear. An explanation for the previously reported (J. Am. Chem. Soc. 1994, 116, 7801) exceptional light spectroscopic properties of BODIPY is also presented. These are ascribed to the extraordinary electric properties of the BODIPY chromophore. First, changes of the permanent electric dipole moment (Delta(mu) approximately -0.05 D) and polarizability (-26 x 10(-40) C m(2) V(-1)) between the ground and the first excited states are small. Second, the S(0) <--> S(1) electronic transition dipole moments are perpendicular to Delta(mu).     

Time-dependent fifth-order bands in nominally third-order 2D IR vibrational echo spectra

Progress in the field of 2D IR vibrational spectroscopy has been bolstered by the production of intense mid-IR laser pulses. As higher-energy pulses are employed, a concomitant increase occurs in the likelihood of fifth-order contributions to the 2D IR spectra. We report the appearance of fifth-order signals in 2D IR spectra of CO bound to the active site of the enzyme cytochrome P450(cam) with the substrate norcamphor. Two bands with novel time dependences, one on the diagonal and one off-diagonal, are not accounted for by normal third-order interactions. These bands are associated with a ν = 1-2 vibrational transition frequency. Both bands decay to 0 and then grow back in with opposite sign. The diagonal band is positive at short time, decays to 0, reappears with negative sign, before eventually decaying to 0. The off-diagonal band is negative at short time, decays to 0, reappears positive, and then decays to 0. The appearance and time dependence of these bands are characterized. Understanding these fifth-order bands is useful because they may be misidentified with time-dependent bands that arise from other processes, such as chemical exchange, vibrational coupling, or energy transfer. The presence and unusual time dependences of the fifth-order bands are reproduced with model calculations that account for the fact that vibrational relaxation from the ν = 2 to 1 level is approximately a factor of 2 faster than that from the ν = 1 to 0 level.     

Electron transfer through a prenucleated bimetalated alanine-based peptide helix

We have synthesized a 22 residue alanine-based peptide with a tris(bipyridyl)ruthenium(II) amino acid near the middle of the peptide which can act as a photoinducible electron donor. Two histidines spaced i, i + 4 near the C-terminus of the peptide were then cross-linked with a tetraammineruthenium(III) moiety to prenucleate the helix and provide an electron acceptor site. Introduction of the cross-link enhances the average helix content from 67% to 84% at 0 degrees C, as judged by circular dichroism spectroscopy. The temperature dependence of the mean molar residue ellipticity at 222 nm, [THETAV;](222), for the bimetalated peptide was fit to a modified Lifson-Roig helix-coil model to permit extraction of the population of helical conformation at each residue separating the electron donor and acceptor. On average, the residues between the donor and acceptor are 92% helical. Photoinduced electron transfer with a driving force of -1.0 eV and an estimated reorganization energy of 0.82 eV was measured by fluorescence quenching methods in H(2)O and D(2)O, yielding rate constants, k(ET), of 7 +/- 3 x 10(6) s(-)(1) and 5 +/- 1 x 10(6) s(-)(1) at 0 degrees C. Calculation of the electronic coupling matrix element, H(ab), with the Marcus equation yields a value of 0.19 +/- 0.4 cm(-)(1). Analysis in terms of the pathway model for electronic coupling indicates that this magnitude of H(ab) is consistent with the participation of hydrogen bonds in electronic coupling for an isolated alpha-helix.     

Electronic transition dipole moment directions of reduced anionic flavin in stretched poly(vinyl alcohol) films

The IR and UV/vis linear dichroic spectra of reduced anionic flavin mononucleotide (FMNH-) partially oriented in poly(vinyl alcohol) (PVA) films have been measured to determine the direction of the major electronic transition dipole moments. The IR linear dichroism (LD) was measured in the 1750-1350 cm(-1) region to provide the overall molecular orientation of the FMNH- in the stretched films. Time-dependent density functional theory using the B3LYP functional was used to calculate the normal modes and the transition dipole moments of reduced lumiflavin. The calculated normal modes assisted in IR band assignments and in the determination of the IR transition dipole moment directions which were required for the determination of the orientation parameters for FMNH- in PVA films. The UV/vis LD spectrum was measured over the 200-700 nm region and was resolved into contributions from three pi-->pi* transitions. The directions of the transitions are 90 degrees+/-4 degrees at 440 nm, 79 degrees+/-4 degrees at 350 nm, and 93 degrees+/-4 degrees at 290 nm with counterclockwise rotations with respect to the N5-N10 axis. Comparison of the calculated and experimentally determined transition dipole moments allowed for refined assignment of the transition dipole moment directions. To our knowledge, this is the first experimental evidence that the 350-450 nm absorption arises from two unique transitions. Remarkably, the two lowest energy transition dipole moments for FMNH- are nearly parallel to those obtained in prior studies for both oxidized and semiquinone flavin.     

Dispersion of the Raman depolarization ratio of HDO in water and heavy water from 295 to 368 K, and from concentrated NaClO4D2OH2O

The dispersion of the Raman depolarization ratio rho(L) was measured for HDO in H(2)O and in D(2)O. rho(L) for the decoupled OD stretch displays a maximum at 2575 +/- 15 cm(-1) at 296 K and a minimum at 2675 +/- 15 cm(-1), in agreement with the isosbestic point 2570 +/- 10 cm(-1), and the enthalpy dispersion maximum, 2650-2675 cm(-1), respectively. However, three extrema were uncovered in rho(L) for the OH stretch of HDO in D(2)O, and their positions agree with the frequencies of a minimum and a maximum in the enthalpy dispersion and with the isosbestic frequency. The frequency of the rho(L) maximum (OH stretch) lies just above the frequency corresponding to the joint angle-frequency probability maximum. [Lawrence and Skinner, J. Chem. Phys. 118, 264 (2003)]. The low- and high-frequency minima in rho(L) (OH stretch), correspond, respectively, to very strong H-bonds, and extremely weak, long, bent H bonds. The frequencies of the maxima and minima in rho(L) for the decoupled OH and OD stretches are independent of temperature within experimental error between 295 and 368 K. rho(L) was also measured for the OD stretch from saturated NaClO(4) in D(2)OH(2)O; it displays a maximum at 2560 +/- 20 cm(-1) and a sharp minimum at 2650 +/- 5 cm(-1). The shape of the dispersion of (betaalpha)(2) approximately rho(L) for HDO in D(2)O was calculated with the aid of the molecular dynamics results of Lawrence and Skinner. beta(2) is the anisotropic polarizability and alpha is the isotropic polarizability. A maximum resulted in the calculated dispersion at 3400 +/- 10 cm(-1), in excellent agreement with the measured maximum of 3395 +/- 15 cm(-1). The H-bond angles decrease far below 180 degrees as the OH-stretching frequency increases to 3700 cm(-1) and above. Such small H-bond angles, and very large O-O distances, are tantamount to broken H-bonds and are thought to produce the minimum in rho(L) near 2650 cm(-1).     

Poly-L-proline type II peptide mimics based on the 3-azabicyclo[3.1.0]hexane system.

This paper describes conformational studies of proline-templated amino acids (PTAAs) based on the 3-azabicyclo[3.1.0]hexane system as well as conformational studies on short peptides composed of these PTAAs. NOE data, coupling constants, and molecular modeling are consistent with a flattened boat conformation for monomeric and oligomeric residues based on this bicyclic system. NMR studies on dimeric and trimeric oligomers are consistent with a populated poly-L-proline type II conformation in CDCl3 and D2O. Solution studies and molecular modeling predicts phi approximately -70 degrees, psi approximately 131 degrees, chi 1 approximately -57 degrees, and chi 2 approximately -158 degrees for oligomeric residues.     

The 2D IR responses of amide and carbonyl modes in water cannot be described by Gaussian frequency fluctuations

The two-dimensional (2D) IR spectral shapes seen for aqueous amide-I' or carbonyls having apparently single bands are not those predicted by Gaussian frequency fluctuations. Their population evolution exposes discrete distributions undergoing picosecond time scale exchange. The energy transfer to other modes provides a clear view of this underlying structure, which is largely attributed to exchanging water configurations. The results suggest new approaches to examine protein-bound water at the residue level.     

Detection and measurement of noncoincidence between the principal axes of the g-matrix and zero-field splitting tensor using multifrequency powder EPR spectroscopy: application to cis-[(NH(3))(2)Pt(1-MeU)(2)Cu(H(2)O)(2)](SO(4)) x 4.5H(2)O (1-MeU = monoanion of 1-methyluracil)

Multifrequency continuous wave EPR spectra (4-34 GHz) on a powder of the title compound are consistent with a spin-triplet state. This arises from interaction between centrosymmetrically related pairs of copper(II) ions in the solid. The spectra at all frequencies have been simulated with a single set of spin-Hamiltonian parameters. The results show that there is noncoincidence between the principal axes of the g-matrices on each copper center and those of the zero-field splitting (D) tensor. This noncoincidence is a single rotation of 33 degrees +/- 2 degrees. The parameters from the powder spectra have been verified by a subsequent single-crystal EPR study which yielded the spin-Hamiltonian parameters g(XX) = 2.074, g(YY) = 2.093, g(ZZ) = 2.385, D(XX) = +/-0.0228 cm(-1), D(YY) = +/-0.0211 cm(-1), D(ZZ) = -/+0.0439 cm(-1) with Euler angles of alpha = 179 degrees, chi = 33.4 degrees, and gamma = 328 degrees. Analysis of the zero-field splitting tensor in terms of exchange indicates that the interaction between the pairs of copper(II) ions is almost entirely dipolar in origin. This study shows that multifrequency EPR spectroscopy on powders, coupled with spectrum simulation, can detect and measure noncoincidence between the principal axes of the g-matrix and zero-field splitting tensor, and does not necessarily require the presence of metal hyperfine interactions.     

Onset of 3(10)-helical secondary structure in aib oligopeptides probed by coherent 2D IR spectroscopy

We have investigated the onset of the secondary structure and the evolution of two-dimensional infrared (2D IR) spectral patterns as a function of chain length with a study of 3(10)-helical peptides. The results show that 2D IR is highly sensitive to peptide conformation, disorder, and size. An extensive set of 2D IR spectra of C (alpha)-methylated homopeptides, Z-(Aib) n -O tBu ( n = 3, 5, 8, and 10), in CDCl 3 was measured in the amide-I region. The 2D spectral patterns of the tripeptide are quite different from those of the longer peptides. The spectral signatures begin to converge at the pentapeptide and become almost the same for the octa- and decapeptide. Simulations employing a vibrational exciton model were performed, with the local mode frequency shifts estimated from the intramolecular hydrogen bond electrostatic energies. The 2D spectra are well simulated using dihedral angle distributions around the average values (phi, psi) approximately (-57 degrees , -31 degrees) with a width of approximately 21 degrees. The simulated site-dependent amide-I local mode frequencies are in agreement with those from scaled semiempirical AM1 calculations. The tripeptide exhibits a more noticeable discrepancy between the experimental and simulated cross-peak patterns. This behavior suggests the presence of a peptide population outside the single beta-turn conformation. The onset of the 3(10)-helical secondary structure appears to already occur at the pentapeptide level.     

Nonperturbative vibrational energy relaxation effects on vibrational line shapes

A general formulation of nonperturbative quantum dynamics of solutes in a condensed phase is proposed to calculate linear and nonlinear vibrational line shapes. In the weak solute-solvent interaction limit, the temporal absorption profile can be approximately factorized into the population relaxation profile from the off-diagonal coupling and the pure-dephasing profile from the diagonal coupling. The strength of dissipation and the anharmonicity-induced dephasing rate are derived in Appendix A. The vibrational energy relaxation (VER) rate is negligible for slow solvent fluctuations, yet it does not justify the Markovian treatment of off-diagonal contributions to vibrational line shapes. Non-Markovian VER effects are manifested as asymmetric envelops in the temporal absorption profile, or equivalently as side bands in the frequency domain absorption spectrum. The side bands are solvent-induced multiple-photon effects which are absent in the Markovian VER treatment. Exact path integral calculations yield non-Lorentzian central peaks in absorption spectrum resulting from couplings between population relaxations of different vibrational states. These predictions cannot be reproduced by the perturbative or the Markovian approximations. For anharmonic potentials, the absorption spectrum shows asymmetric central peaks and the asymmetry increases with anharmonicity. At large anharmonicities, all the approximation schemes break down and a full nonperturbative path integral calculation that explicitly accounts for the exact VER effects is needed. A numerical analysis of the O-H stretch of HOD in D(2)O solvent reveals that the non-Markovian VER effects generate a small recurrence of the echo peak shift around 200 fs, which cannot be reproduced with a Markovian VER rate. In general, the nonperturbative and non-Markovian VER contributions have a stronger effect on nonlinear vibrational line shapes than on linear absorption.     

A scanning tunneling microscopy study of self-assembled nickel(II) octaethylporphyrin deposited from solutions on HOPG

The adsorption of nickel(II) octaethylporphyrin (NiOEP) from benzene and chloroform solutions on highly ordered pyrolytic graphite (HOPG) was investigated with a scanning tunneling microscope (STM) operated in ambient conditions. STM images show that NiOEP self-assembles on the graphite surface and that the molecules lie flat and form 2D lattices with spacings of 1.58 +/- 0.03 nm by 1.46 +/- 0.06 nm with a lattice angle of 69 degrees +/- 4 degrees averaged over both solvents. We were unable to eliminate the possibility that one unit cell distance is twice the above-reported distance. The corresponding molecular packing density, 4.5 +/- 0.3 x 10(13) molecules/cm(2), was essentially the same for benzene and chloroform solution deposition. These results differ somewhat from the structure revealed by high-resolution STM images of NiOEP on Au (111). The lack of apparent height (image intensity) in the constant current STM image of the alkane region of alkane-substituted metal porphyrins is attributed to a combination of changes in alkane configuration relative to the ring and associated changes in electronic coupling with HOMO and LUMO.