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.     

Bond connectivity measured via relaxation-assisted two-dimensional infrared spectroscopy

The relaxation-assisted two-dimensional infrared (RA 2DIR) method is a novel technique for probing structures of molecules, which relies on vibrational energy transport in molecules. In this article we demonstrate the ability of RA 2DIR to detect the bond connectivity patterns in molecules using two parameters, a characteristic intermode energy transport time (arrival time) and a cross-peak amplification coefficient. A correlation of the arrival time with the distance between the modes is demonstrated. An 18-fold amplification of the cross-peak amplitude for the modes separated by approximately 11 A is shown using RA 2DIR; larger cross-peak amplifications are expected for the modes separated by larger distances. The RA 2DIR method enhances the applicability of 2DIR spectroscopy by making practical the long-range measurements using a variety of structural reporters, including weak IR modes. The data presented demonstrate the analytical power of RA 2DIR which permits the speedy structural assessments of the bond connectivity patterns.     

Amide I two-dimensional infrared spectroscopy of beta-hairpin peptides

In this report, spectral simulations and isotope labeling are used to describe the two-dimensional IR spectroscopy of beta-hairpin peptides in the amide I spectral region. 2D IR spectra of Gramicidin S, PG12, Trpzip2 (TZ2), and TZ2-T3(*)T10(*), a dual (13)C(') isotope label, are qualitatively described by a model based on the widely used local mode amide I Hamiltonian. The authors' model includes methods for calculating site energies for individual amide oscillators on the basis of hydrogen bonding, nearest neighbor and long-range coupling between sites, and disorder in the site energy. The dependence of the spectral features on the peptide backbone structure is described using disorder-averaged eigenstates, which are visualized by mapping back onto the local amide I sites. beta-hairpin IR spectra are dominated by delocalized vibrations that vary by the phase of adjacent oscillators parallel and perpendicular to the strands. The dominant nu(perpendicular) band is sensitive to the length of the hairpin and the amount of twisting in the backbone structure, while the nu(parallel) band is composed of several low symmetry modes that delocalize along the strands. The spectra of TZ2-T3(*)T10(*) are used to compare coupling models, from which we conclude that transition charge coupling is superior to transition dipole coupling for amide groups directly hydrogen bound across the beta strands. The 2D IR spectra of TZ2-T3(*)T10(*) are used to resolve the redshifted amide I band and extract the site energy of the labeled groups. This allows the authors to compare several methods for calculating the site energies used in excitonic treatments of the amide I band. Gramicidin S is studied in dimethyl sulfoxide to test the role of solvent on the spectral simulations.     

Study on the molecular orientation of an anti-ferroelectric liquid crystal by two-dimensional correlation polarized infrared spectroscopy

Polarization-dependent infrared spectra of an antiferroelectric liquid crystal in the phase were measured at 60°C, for investigation of the relative orientation of the terminal alkyl chain and mesogen. The polarization angle-dependent infrared spectra obtained were analysed by two-dimensional (2D) correlation spectroscopy. The orientation of the mesogen segment and the alkyl chains in the phase is similar to that in the SmC* phase. Four new CH₃ and CH₂ stretching modes were observed from the 2D correlation spectra. From these we can clearly separate the vibrational mode for two hydrocarbon chains and conclude that the orientations of the two chains are different. The C=O group adjacent to the chiral segment is also separated by 2D correlation spectra into two bands, which may arise from either the C=O group hydrogen-bonded with the phenyl ring, or from another rotational conformation of the molecule.     

Transient two-dimensional infrared spectroscopy: exploring the polarization dependence

We present a general expression for the polarization dependence of transient two-dimensional IR spectroscopy (T2D-IR), a technique designed to measure 2D-IR spectra of transient species. T2D-IR is a UV pump narrowband-IR-pump broadband-IR-probe experiment of fifth order in the laser field which involves up to three different transition dipole moments. The UV pulse adds an additional degree of freedom in polarization as compared to 2D-IR spectroscopy and increases the versatility of signal manipulation and the potential structural information content of the signals. The polarization conditions leading to a maximum of structural information are discussed. Important special cases of polarization conditions are formulated. The application of polarization selectivity is demonstrated for different types of T2D-IR experiments on photo triggered metal-to-ligand charge transfer in the model system [Re(CO)(3)(dmbpy)Cl].     

Azide-water intermolecular coupling measured by two-color two-dimensional infrared spectroscopy

We utilize two-color two-dimensional infrared spectroscopy to measure the intermolecular coupling between azide ions and their surrounding water molecules in order to gain information about the nature of hydrogen bonding of water to ions. Our findings indicate that the main spectral contribution to the intermolecular cross-peak comes from population transfer between the asymmetric stretch vibration of azide and the OD-stretch vibration of D(2)O. The azide-bound D(2)O bleach/stimulated emission signal, which is spectrally much narrower than its linear absorption spectrum, shows that the experiment is selective to solvation shell water molecules for population times up to ~500 fs. The waters around the ion are present in an electrostatically better defined environment. Afterwards, ~1 ps, the sample thermalizes and selectivity is lost. On the other hand, the excited state absorption signal of the azide-bound D(2)O is much broader. The asymmetry in spectral width between bleach/stimulated emission versus excited absorption has been observed in very much the same way for isotope-diluted ice Ih, where it has been attributed to the anharmonicity of the OD potential.     

Probing intermolecular couplings in liquid water with two-dimensional infrared photon echo spectroscopy

Two-dimensional infrared photon echo and pump probe studies of the OH stretch vibration provide a sensitive probe of the correlations and couplings in the hydrogen bond network of liquid water. The nonlinear response is simulated using numerical integration of the Schrodinger equation with a Hamiltonian constructed to explicitly treat intermolecular coupling and nonadiabatic effects in the highly disordered singly and doubly excited vibrational exciton manifolds. The simulated two-dimensional spectra are in close agreement with our recent experimental results. The high sensitivity of the OH stretch vibration to the bath dynamics is found to arise from intramolecular mixing between states in the two-dimensional anharmonic OH stretch potential. Surprisingly small intermolecular couplings reproduce the experimentally observed intermolecular energy transfer times.     

Probing molecular conformations with electron momentum spectroscopy: the case of n-butane.

High-resolution (e,2e) measurements of the valence electronic structure and momentum-space electron density distributions of n-butane have been exhaustively reanalyzed in order to cope with the presence of two stable structures in the gas phase, namely the all-staggered and gauche conformers. The measurements are compared to a series of Boltzmann-weighted simulations based on the momentum-space form of Kohn-Sham (B3LYP) orbital densities, and to ionization spectra obtained from high-level [ADC(3)] one-particle Green's Function calculations. Indubitable improvements in the quality of the simulated (e,2e) ionization spectra and electron momentum profiles are seen when the contributions of the gauche form of n-butane are included. Both the one-electron binding energies and momentum distributions consistently image the distortions and topological changes that molecular orbitals undergo due to torsion of the carbon backbone, and thereby exhibit variations which can be traced experimentally. With regard to the intimate relation of (e,2e) cross sections with orbital densities, electron momentum spectroscopy can therefore be viewed as a very powerful, but up to now largely unexploited, conformational probe. The study also emphasizes the influence of thermal agitation in photoionization experiments of all kind.     

Domain formation in lipid bilayers probed by two-dimensional infrared spectroscopy

Two-dimensional infrared (2D-IR) spectroscopy has been used to probe structure and dynamics in binary sphingomyelin/phospholipid liposomes. The liposomes consist of 1-palmitoyl-2-linoleyl phosphatidylcholine (PLPC) and sphingomyelin (SPM) in the ratio 1:1. The diagonal part of the 2D-IR spectra shows two bands which are due to amide I of SPM and to the carbonyl moieties of PLPC. The diagonal components of the 2D-IR spectra reveal a difference in the molecular dynamics. The presence of off-diagonal cross-peaks indicates the occurrence of intermolecular structural correlation. The intensity of the cross-peaks is consistent with segregation of two lipid components into PLPC and SPM molecular domains.     

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.     

The molecular structure and orientation of antiferroelectric liquid crystal using the density-functional theory and two-dimensional correlation-polarized infrared spectroscopy

The structure and vibrational frequencies of the chiral antiferroelectric liquid-crystal molecule, 4-(1-methyheptyloxycarbonyl) phenyl-4-(4'-octyloxy) benzoate (MHOCPOOB), have been calculated using the density-functional theory (DFT) with the Becke-3 Lee-Yang-Parr/6-31G(d,p) level. The observed vibrational spectra have been resolved and assigned in detail by comparison to the computed values. The results indicate that the computed and observed spectra are in good agreement with each other. The stable molecular structure obtained with the DFT theory shows that the two hydrocarbon chains are all-trans zigzag conformer and nearly perpendicular to each other. The orientation of the mesogen part and the hydrocarbon chains for MHOCPOOB in the Sm-C*A phase are investigated by employing the polarization-angle-dependent infrared spectra in the electric-field induced and the two-dimensional correlation spectroscopy. After combining the experimental and theoretical results, it can be concluded that the azimuth of the achiral and chiral chains is opposite to each other, the orientation of the achiral chain is almost the same direction as the mesogen core, and the orientation of the chiral chain is nearly perpendicular to the mesogen part. The achiral and chiral CH2 chains are both a probable all-trans zigzag conformer.     

High-resolution infrared absorption spectroscopy of jet-cooled molecular ions

Rovibrational spectra of H₃⁺, HN₂⁺, and H₃O⁺ generated in discharge jet-expansion have been studied using a difference-frequency infrared source. The rotational temperatures were determined to be 120 ± 20, 273 ± 20 and 150 ± 20 K for H₃⁺, HN₂⁺, and H₃O⁺, respectively. Some dynamic phenomena of the jet-discharges are also discussed.     

Tryptophol cation conformations studied with ZEKE spectroscopy

The relative energies of several conformations of the tryptophol cation are determined by zero kinetic energy (ZEKE) photoelectron spectroscopy and photoionization efficiency measurements. Recently published high-resolution electronic spectroscopy on the neutral species determined the absolute configuration of the different conformers in the S1 spectrum. These assignments are utilized in the photoelectron experiments by pumping through conformer specific S1 resonances yielding ZEKE spectra of the specific, assigned conformations. The adiabatic ionization of one specific conformation is definitively determined, and two others are estimated. The photoelectron spectra, coupled with calculations, reveal that structural changes upon ionization are dominated by interactions of the hydroxyl group with the changes of electronic structure in the aromatic system.     

Computational insights of two-dimensional infrared spectroscopy under electric fields in phosphorylcholine

Influence of static electric field in biological cells causes electroporation, which results in the increase of permeability of the cells and phospholipid bilayer. However, the precise mode of action of electric fields on phospholipid bilayer and their quantum mechanics are still unclear. Therefore, to understand the quantum-based biological effect, we aimed to study two-dimensional infrared (2D-IR) spectra-adopted quantum mechanics/molecular mechanics (QM/MM) simulations under the influence of static electric fields on Phosphorylcholine, an important component in phospholipid membrane. Initially, QM/MM studies were performed under the influence of electric field, ranging from −1.543 to 1.028 V/nm. A multilayer ONIOM model (in combination with DFT/B3LYP/6-31G [d, p] and DREIDING force fields) was used to obtain 2D-IR simulated spectra to calculate electrostatic interaction in the biological system. The results demonstrated that the phosphate group played an important role on α-rotation in LUMO and the chlorine atom had a major contribution in HOMO. In addition, decreased number of hydrogen bonds demonstrated that uncoupling reaction of the P-O stretching vibrations while the electric field was −1.542 V/nm. Moreover, we observed that the electric field is −1.028 V/nm, there is no rotational isomerization in phosphorylcholine. We concluded that the static electric fields significantly affect the anharmonic frequencies, vibration coupling and the structure of the phosphorylcholine.     

Signatures of beta-sheet secondary structures in linear and two-dimensional infrared spectroscopy

Using idealized models for parallel and antiparallel beta sheets, we calculate the linear and two-dimensional infrared spectra of the amide I vibration as a function of size and secondary structure. The model assumes transition-dipole coupling between the amide I oscillators in the sheet and accounts for the anharmonic nature of these oscillators. Using analytical and numerical methods, we show that the nature of the one-quantum vibrational eigenstates, which govern the linear spectrum, is, to a large extent, determined by the symmetry of the system and the relative magnitude of interstrand interactions. We also find that the eigenstates, in particular their trends with system size, depend sensitively on the secondary structure of the sheet. While in practice these differences may be difficult to distinguish in congested linear spectra, we demonstrate that they give rise to promising markers for secondary structure in the two-dimensional spectra. In particular, distinct differences occur between the spectra of parallel and antiparallel beta sheets and between beta hairpins and extended beta sheets.     

DNA vibrational coupling revealed with two-dimensional infrared spectroscopy: insight into why vibrational spectroscopy is sensitive to DNA structure

Two-dimensional infrared (2D IR) spectroscopy was used to study the carbonyl vibrational modes of guanine and cytosine bases in A- and B-form DNA. Located between 1600 and 1700 cm(-1), these modes are often used to monitor DNA secondary structure with traditional infrared spectroscopies such as FTIR, but traditional spectroscopies lack the necessary observables to unravel the coupling mechanisms that make these modes sensitive to secondary structure. By using 2D IR spectroscopy and electronic structure calculations on d(G(5)C(5)) and d(GC)(8) model nucleic acids, we find that hydrogen-bonded guanine/cytosine base pairs are primarily electrostatically coupled and that the coupling between these modes can be modeled with a transition dipole density approach. In comparison, electrostatics is insufficient to model stacked bases because of cooperative charge-sharing effects, but the coupling can be accurately calculated using a finite difference method. We find that the coupling is very strong for both hydrogen-bonded and stacked base geometries, creating vibrational modes that extend both across the base pairs and along the lengths of the helices. Our results provide a physical basis for understanding how strong coupling gives rise to the empirically established relationship between infrared spectroscopy and DNA/RNA secondary structure.     

Annealing behavior of ultrahigh molecular weight polyethylene investigated by confocal micro-Raman spectroscopy combined with two-dimensional correlation spectroscopy

Annealing was performed for ultrahigh molecular weight polyethylene (UHMWPE), including an isothermal process at 110.0°C and cooling process from 110.0 to 30.0°C. The processes were in situ investigated by confocal micro-Raman spectroscopy combined with two-dimensional correlation spectroscopy. Two phase transitions were directly observed in the annealing processes, i.e., from the amorphous phase to the intermediate phase and from the intermediate phase to the crystalline phase. The phase transitions derive from molecular chain segments sliding between different phases of UHMWPE and occur in different orders during the isothermal and cooling processes.     

Proton transport in biological systems can be probed by two-dimensional infrared spectroscopy

We propose a new method to determine the proton transfer (PT) rate in channel proteins by two-dimensional infrared (2DIR) spectroscopy. Proton transport processes in biological systems, such as proton channels, trigger numerous fundamental biochemical reactions. Due to the limitation in both spatial and time resolution of the traditional experimental approaches, describing the whole proton transport process and identifying the rate limiting steps at the molecular level is challenging. In the present paper, we focus on proton transport through the Gramicidin A channel. Using a kinetic PT model derived from all-atom molecular dynamics simulations, we model the amide I region of the 2DIR spectrum of the channel protein to examine its sensitivity to the proton transport process. We demonstrate that the 2DIR spectrum of the isotope-labeled channel contain information on the PT rate, which may be extracted by analyzing the antidiagonal linewidth of the spectral feature related to the labeled site. Such experiments in combination with detailed numerical simulations should allow the extraction of site dependent PT rates, providing a method for identifying possible rate limiting steps for proton channel transfer.