Backbone Modes Research Articles

Probing Backbone Coupling within Hydrated Proteins with Two-Color 2D Infrared Spectroscopy.

The vibrational coupling between protein backbone modes and the role of water interactions are important topics in biomolecular spectroscopy. Our work reports the first study of the coupling between amide I and amide A modes within peptides and proteins with secondary structure and water contacts. We use two-color two-dimensional infrared (2D IR) spectroscopy and observe cross peaks between amide I and amide A modes. In experiments with peptides with different secondary structures and side chains, we observe that the spectra are sensitive to secondary structure. Water interactions affect the cross peaks, which may be useful as probes for the accessibility of protein sites to hydration water. Moving to two-color 2D IR spectra of proteins, the data demonstrate that the cross peaks integrate the sensitivities of both amide I and amide A spectra and that a two-color detection scheme may be a promising tool for probing secondary structures in proteins.

Surface Structural Changes in Silicone Rubber Due to Electrical Tracking.

There is a growing interest in the use of silicone composite insulators for electrical power transmission and distribution applications. However, such materials are susceptible to degradation as they are exposed to electrical and environmental stresses during operating conditions. Therefore, it is crucial to gain a thorough understanding of the degradation mechanism through changes in the material structure that may provide insight into potential failures in the electrical grid. Attenuated total reflection Fourier transform infrared spectroscopy and two-dimensional correlation spectroscopy (2D-COS) were used along with contact angle measurements to characterize changes in silicone rubber samples from actual insulators subjected to tracking wheel testing. The results showed a decrease in absorbance of different infrared bands representing different functional groups, such as Si-O-Si, methyl functional groups, and both Al-O and hydroxyl groups of alumina trihydrate as a function of the number of tracking cycles. The sequence of changes in the functional groups was determined by 2D-COS as Al-O and OH followed by Si-O-Si polymer backbone modes, followed by polymer methyl side chains. An enhancement in the average contact angle with the number of tracking cycles revealed a concomitant increase in surface roughness with electrical tracking.

Crystal structure, vibrational and chemical properties and phase transitions in Glycyl-DL-Aspartic acid and Glycyl-DL-Aspartic acid monohydrated.

In this paper, the structural and vibrational analysis of the dipeptides glycyl-DL- aspartic acid hydrate (H-Gly-DL-Asp-OH.H2O) crystal, with P1¯ (C11) triclinic symmetry and glycyl-DL- aspartic acid (H-Gly-DL-Asp-OH) crystal, with Cc space group (Cs4) monoclinic structure, were studied. The crystallographic structures of these molecules were determined by single-crystal X-ray diffraction. Changes in the powder X-ray diffraction patterns of H-Gly-DL-Asp-OH.H2O as a function of the temperature were recorded. After 403 K, the water molecule detaches itself from H-Gly-DL-Asp-OH.H2O, causing its symmetry to change from triclinic to monoclinic. The normal modes of vibration were analyzed through calculations based on Density Functional Theory (DFT) using the B3LYP functional with the Gaussian bases 6–311++G (d,p) and potential energy distribution (PED) analysis. These results, together with literature data and Raman and infrared (IR) spectroscopy measurements, allowed the identification of the various vibrational normal modes. Furthermore, the effect of high pressure on H-Gly-DL-Asp-OH.H2O was studied by Raman spectroscopy experiments. The results obtained from the Raman spectra at high pressures indicate changes around 2.1 and 4.5 GPa, such as the disappearance, splitting and emergence of some modes, as well as discontinuities in the evolution of wavenumbers of several normal modes of vibration. Such changes involved modes localized in the region of external modes, while others involved molecular backbone modes and modes that participate in hydrogen bonding. The changes were related to small conformational changes associated with H bonds and small deformations in hydrated dipeptide molecules.

Stable Immobilization of DNA to Silica Surfaces by Sequential Michael Addition Reactions Developed with Insights from Confocal Raman Microscopy.

The immobilization of DNA to surfaces is required for numerous biosensing applications related to the capture of target DNA sequences, proteins, or small-molecule analytes from solution. For these applications to be successful, the chemistry of DNA immobilization should be efficient, reproducible, and stable and should allow the immobilized DNA to adopt a secondary structure required for association with its respective target molecule. To develop and characterize surface immobilization chemistry to meet this challenge, it is invaluable to have a quantitative, surface-sensitive method that can report the interfacial chemistry at each step, while also being capable of determining the structure, stability, and activity of the tethered DNA product. In this work, we develop a method to immobilize DNA to silica, glass, or other oxide surfaces by carrying out the reactions in porous silica particles. Due to the high specific surface area of porous silica, the local concentrations of surface-immobilized molecules within the particle are sufficiently high that interfacial chemistry can be monitored at each step of the process with confocal Raman microscopy, providing a unique capability to assess the molecular composition, structure, yield, and surface coverage of these reactions. We employ this methodology to investigate the steps for immobilizing thiolated-DNA to thiol-modified silica surfaces through sequential Michael addition reactions with the cross-linker 1,4-phenylene-bismaleimide. A key advantage of employing a phenyl-bismaleimide over a comparable alkyl coupling reagent is the efficient conversion of the initial phenyl-thiosuccinimide to a more stable succinamic acid thioether linkage. This transformation was confirmed by in situ Raman spectroscopy measurements, and the resulting succinamic acid thioether product exhibited greater than 95% retention of surface-immobilized DNA after 12 days at room temperature in aqueous buffer. Confocal Raman microscopy was also used to assess the conformational freedom of surface-immobilized DNA by comparing the structure of a 23-mer DNA hairpin sequence under duplex-forming and unfolding conditions. We find that the immobilized DNA hairpin can undergo reversible intramolecular duplex formation based on the changes in frequencies and intensities of the phosphate backbone and base-specific vibrational modes that are informative of the hybridization state of DNA.

Extraction of road using soft computing techniques

One of the most challenging research topics is extraction of road network automatically from remotely sensed imagery. The roads are considered as backbone and important modes of transportation. For efficient automatic road network extraction, ground points and building points extracted were integrated and it was used with multistage road network extraction model. For road network extraction, a lane detection system is considered as a more important element. From the lane marking in the roads, the roads are easily detected from the remotely sensed images. In order to detect the lanes more effectively, B-snake with fuzzy C-means (FCM) clustering is proposed in this paper. The input image is divided into equal halves by using FCM clustering algorithm. Then, the lower part is binarized by analyzing RGB channel and it is analyzed by using B-snake model because it contains more information about road lane than upper part of the image. Then, the lane detection problem is formulated by finding the set of lane model control points. A good initial position to the B-snake lane model is provided by introducing Canny/Hough estimation of vanishing points. Moreover, the external force field for lane detection is constructed by using gradient vector flow. The correspondence between B-snake and the real edge image is determined by using minimum mean square error which is presented to find out the parameters of road model iteratively. The detected lane points are fused with the road and ground points by using constraint satisfaction neural network-complementary information integration. Moreover, the road and non-road regions are separated by using region part segmentation. Finally, the medial-axis-transform-based hypothesis verification is used to automatically complete the road network extraction framework. The performance of the existing road network extraction, ground point-based road extraction model, building and ground point-based road extraction model and proposed building, ground and lane point-based road extraction model is analyzed in terms of correctness and completeness.

Vibrational Dynamics and Couplings of the Hydrated RNA Backbone: A Two-Dimensional Infrared Study.

The equilibrium structure of the RNA sugar-phosphate backbone and its hydration shell is distinctly different from hydrated DNA. Applying femtosecond two-dimensional infrared (2D-IR) spectroscopy in a range from 950 to 1300 cm-1, we elucidate the character, dynamics, and couplings of backbone modes of a double-stranded RNA A-helix geometry in its aqueous environment. The 2D-IR spectra display a greater number of backbone modes than for DNA, with distinctly different lineshapes of diagonal peaks. Phosphate-ribose interactions and local hydration structures are reflected in the complex coupling pattern of RNA modes. Interactions with the fluctuating water shell give rise to spectral diffusion on a 300 fs time scale, leading to a quasi-homogeneous line shape of the symmetric (PO2)- stretching mode of the strongly hydrated phosphate groups. The RNA results are benchmarked by 2D-IR spectra of DNA oligomers in water and analyzed by molecular dynamics and quantum mechanical molecular mechanics simulations.

Vibrational Relaxation of the Backbone and Base Modes in LacDNA Complexes by UV Resonance Raman Spectroscopy.

Vibrational band shape analysis through time correlation function concept is widely used to obtain experimental information on the molecular dynamics of medium-size molecules in different environments. Interesting details are revealed by extending this technique to biomolecules such as functional groups of the nucleic acids in media approaching the physiological conditions. In this work a study into the UV resonance Raman (UVRR) vibrational half bandwidths of functional groups in LacDNA, upon lowering the pH (pH 6.4, pH 3.45) and in the presence of Mn2+ and Ca2+ ions, respectively, was of interest. The corresponding global relaxation times have been derived. Also, the 793 cm-1 UVRR band, corresponding to ν (backbone O-P-O, dT) oscillator of LacDNA in aqueous solutions, was selected for band shape-analysis. Vibrational relaxation appears as the dominant relaxation process for this mode, with vibrational dephasing being the most efficient for this oscillator. Current theories developed for vibrational dephasing have been applied to this profile, and relevant relaxation parameters have been obtained and discussed. To our knowledge this is the first study on DNA oligomers vibrational band shape analysis through time correlation function concept.

Molecular couplings and energy exchange between DNA and water mapped by femtosecond infrared spectroscopy of backbone vibrations.

Molecular couplings between DNA and water together with the accompanying processes of energy exchange are mapped via the ultrafast response of DNA backbone vibrations after OH stretch excitation of the water shell. Native salmon testes DNA is studied in femtosecond pump-probe experiments under conditions of full hydration and at a reduced hydration level with two water layers around the double helix. Independent of their local hydration patterns, all backbone vibrations in the frequency range from 940 to 1120 cm–1 display a quasi-instantaneous reshaping of the spectral envelopes of their fundamental absorption bands upon excitation of the water shell. The subsequent reshaping kinetics encompass a one-picosecond component, reflecting the formation of a hot ground state of the water shell, and a slower contribution on a time scale of tens of picoseconds. Such results are benchmarked by measurements with resonant excitation of the backbone modes, resulting in distinctly different absorption changes. We assign the fast changes of DNA absorption after OH stretch excitation to structural changes in the water shell which couple to DNA through the local electric fields. The second slower process is attributed to a flow of excess energy from the water shell into DNA, establishing a common heated ground state in the molecular ensemble. This interpretation is supported by theoretical calculations of the electric fields exerted by the water shell at different temperatures.

Investigation of nonlinear rheological behavior of linear and 3-arm star 1,4-cis-polyisoprene (PI) under medium amplitude oscillatory shear (MAOS) flow via FT-rheology

Monodisperse linear and 3-arm star polyisoprene (PI) melts were investigated under dynamic oscillatory shear flow. Master curves of linear rheological properties, G′ (ω) and G″ (ω), obtained by small amplitude oscillatory shear (SAOS) testing and nonlinear rheological properties, Q0 (ω), obtained by medium amplitude oscillatory shear (MAOS) testing, were created using the same shift factors by applying the time–temperature superposition (TTS) principle. Linear master curves of 3-arm star PIs were broader than those of linear PIs because of the contribution made by an additional relaxation mode due to arm retraction. This difference was clearer in nonlinear master curves. In nonlinear master curves (Q0 (ω)), linear PIs showed only one peak corresponding to relaxation of the backbone chain, whereas two weak local peaks were observed for 3-arm star PIs. One peak at lower frequency reflected backbone relaxation and the other at higher frequency reflected branch relaxation. These findings confirm that Q0 is a highly sensitive parameter for characterizing the effect of one branch by detecting backbone and branch relaxation modes. Based on the hierarchical relaxation concept of branched polymers, three characteristic relaxation times of 3-arm star PIs were determined from a nonlinear master curve: backbone relaxation time (τb) from local maximum Q0 at lower frequency, backbone Rouse time (τR,b) from local minimum Q0, and arm relaxation time (τa) from local maximum Q0 at higher frequency. Backbone relaxation times (τb) from nonlinear master curves almost coincided with linear viscoelastic terminal relaxation times (τw) from linear master curves within the limits imposed by experimental error. These relaxation times, especially τR,b, were used for molecular stress function (MSF) model predictions of 3-arm star PIs as a criterion parameter to determine the terminal relaxation mode of the backbone chain, and τR,b was found to be a reasonable fitting parameter for the MSF model. Fitting results showed that the weak peak arising from the one branch could be quantified using the MSF model. However, both linear and 3-arm star PIs had the same β value of 1, meaning a linear topology without a branch. It was concluded that the effect of only one branch could not be detected using β values. Our results suggest the possibility of using the nonlinear parameter Q0 for determining model parameters for constitutive model equations.

Large α‐helical movements observed in ternary crystals of RB69 DNA polymerase following nucleotide incorporation

Raman difference spectroscopy is used to monitor the conformational changes associated with dNMP incorporation in single crystals of a RB69 DNA polymerase (RB69pol) ternary complex. An inactive crystal of L415G RB69pol exo‐ with a primer/template duplex and a cognate dATP was produced in the presence of Ca2+. The Raman spectrum of the crystallized complex was obtained using a Raman microscope. Phosphodiester bond formation is triggered by soaking in Mg2+. The Raman difference spectra [ie, (ternary complex + Mg2+)–(ternary complex with no Mg2+)] show that conformational changes are complete prior to the acquisition of the first Raman spectrum following magnesium incorporation into the crystal. Polyacrylamide gel electrophoresis experiments carried in parallel show that dNMP incorporation occurs rapidly in the crystal. The Raman data indicate that significant changes in protein amide features, tyrosine ring modes, and nucleic acid base backbone modes have occurred. Overall, they are dominated by the dichroic effect with the molecular groups changing orientation with respect to the laser beam following nucleotide incorporation. The amide I and amide III α‐helix features are unusually narrow and are assigned to movement of the P and N helices. These results demonstrate the ability of Raman spectroscopy to monitor conformational changes in proteins via dichroism. The Raman spectra and the gel electrophoresis support the hypothesis that the major spectroscopic changes are because of structural changes in the ternary complex crystal following correct dNMP incorporation. Copyright © 2015 John Wiley & Sons, Ltd.

Ultrafast vibrational dynamics of the DNA backbone at different hydration levels mapped by two-dimensional infrared spectroscopy.

DNA oligomers are studied at 0% and 92% relative humidity, corresponding to N < 2 and N > 20 water molecules per base pair. Two-dimensional (2D) infrared spectroscopy of DNA backbone modes between 920 and 1120 cm−1 maps fluctuating interactions at the DNA surface. At both hydration levels, a frequency fluctuation correlation function with a 300 fs decay and a slow decay beyond 10 ps is derived from the 2D lineshapes. The fast component reflects motions of DNA helix, counterions, and water shell. Its higher amplitude at high hydration level reveals a significant contribution of water to the fluctuating forces. The slow component reflects disorder-induced inhomogeneous broadening.

Analysis of G-quadruplex conformations using Raman and polarized Raman spectroscopy

G-quadruplexes (G4s) are four-stranded DNA structures formed within nucleic acid sequences that are rich in guanines. G4 formation within DNA strands is believed to have significant biological relevance for the control of cell replication and gene expression. Therefore, the development and validation of experimental techniques that can easily and reliably characterize G4 structures under biologically relevant measurement conditions, like Raman spectroscopy, are desirable for G4-targeted structure based drug design. Here we report Raman and polarized Raman studies of solutions of three oligonucleotides, thrombin binding aptamer (TBA) 5′-GGTTGGTGTGGTTGG-3′, human telomeric (HT) 5′-(TTAGGG)4-3′, and a modified c-Myc NHE-III1 sequence (MycL1) 5′-TGAGGGTGGGTAGGGTGGGTAA-3′, which were previously reported to form four distinct intramolecular G4 structures in the presence of Na+ or K+, as determined by NMR. Our results support the previously proposed antiparallel (TBA), antiparallel and hybrid (HT), and parallel with double-chain reversal (DCR) loop (MycL1) structures. Large sample-dependent variations in the intensity of bands associated with deoxyribose backbone modes in the 840–930 cm−1 and 1420–1460 cm−1 spectral regions were observed. Most notably, a highly polarized deoxyribose ring symmetric stretch (~930 cm−1) appeared strongly in the solution spectra for HT and TBA, but was very weak or absent in the solution spectrum for MycL1 and the drop deposition (dried sample) spectra for all three oligonucleotides. It is hypothesized that the intensity of this band is likely controlled by furanose ring structure uniformity and/or solvent accessibility to certain nucleotide binding sites. Raman depolarization ratios measured for the G4s in solution were generally very similar to those previously reported for canonical B DNA, with the possible exception of base ring modes that consistently yielded slightly lower depolarization ratios for G4s compared to B DNA. The results further underscore the utility of Raman and polarized Raman spectroscopy for G4 structure elucidation under biologically relevant solution conditions. Copyright © 2015 John Wiley & Sons, Ltd.

Anharmonic Backbone Vibrations in Ultrafast Processes at the DNA-Water Interface.

The vibrational modes of the deoxyribose-phosphodiester backbone moiety of DNA and their interactions with the interfacial aqueous environment are addressed with two-dimensional (2D) infrared spectroscopy on a femto- to picosecond time scale. Beyond the current understanding in the harmonic approximation, the anharmonic character and delocalization of the backbone modes in the frequency range from 900 to 1300 cm(-1) are determined with both diagonal anharmonicities and intermode couplings on the order of 10 cm(-1). Mediated by the intermode couplings, energy transfer between the backbone modes takes place on a picosecond time scale, parallel to vibrational relaxation and energy dissipation into the environment. Probing structural dynamics noninvasively via the time evolution of the 2D lineshapes, limited structural fluctuations are observed on a 300 fs time scale of low-frequency motions of the helix, counterions, and water shell. Structural disorder of the DNA-water interface and DNA-water hydrogen bonds are, however, preserved for times beyond 10 ps. The different interactions of limited strength ensure ultrafast vibrational relaxation and dissipation of excess energy in the backbone structure, processes that are important for the structural integrity of hydrated DNA.

Encapsulation of Poly(3-hexylthiophene) J-Aggregate Nanofibers with an Amphiphilic Block Copolymer

Poly(3-hexylthiophene) (P3HT) nanofibers (NF) displaying J-aggregate exciton coupling behavior are encapsulated with the amphiphilic block copolymer (BCP), poly(3-hexyl-thiophene)-block-poly(ethylene-glycol), (PHT(20)-b-PEG(108)). Encapsulation results in the formation of hierarchical superstructures, and the BCP coating is expected to exert a mild chemical pressure on the periphery of the NFs. Photoluminescence from encapsulated NF superstructures show line shape distortions due to self-absorption of the 0-0 transition which is consistent with preservation of J-aggregate character (intrachain order). Detailed resonance Raman spectra of encapsulated BCP-NF structures show no discernible changes in the P3HT aggregation state, and overtone and combination bands involving the symmetric stretching C═C (~1450 cm(-1)) and C-C (~1380 cm(-1)) backbone modes are observed. These features permit quantitative estimates of vibrational mode-specific excited state structural displacements using a time-dependent Raman intensity analysis which is not possible from conventional vibronic analysis of optical lineshapes.

Exciton Conformational Dynamics of Poly(3-hexylthiophene) (P3HT) in Solution from Time-Resolved Resonant-Raman Spectroscopy.

We have used time-resolved resonant-Raman spectroscopy to investigate the picosecond conformational relaxation of regioregular poly(3-hexylthiophene) (RR-P3HT) in chlorobenzene after 510 nm photoexcitation. Vibrational signatures from modes along and peripheral to the exciton's backbone have been identified according to the time dependence of excited-state Raman features and from comparisons to Raman spectra of other polymer states. Measured spectral dynamics reflect initial changes in the resonance enhancement of backbone modes on a time scale of 9 ± 1 ps. In contrast, contributions from peripheral modes exhibit time-dependent decay determined only by exciton intersystem-crossing kinetics. Spectral dynamics are interpreted in terms of evolution in bond lengths along the exciton's backbone resulting from increased conjugation allowed by torsional reordering. Possible origins of peripheral features are discussed, including distorted inter-ring modes at exciton termini. Findings provide a glimpse of the underlying molecular dynamics responsible for the red shift in the exciton's near-IR transient absorption occurring on the same time scale.

Analysis of resonance Raman data on the blue copper site in pseudoazurin: Excited state π and σ charge transfer distortions and their relation to ground state reorganization energy

The short Cu2+–S(Met) bond in pseudoazurin (PAz) results in the presence of two relatively intense Sp(π) and Sp(σ) charge transfer (CT) transitions. This has enabled resonance Raman (rR) data to be obtained for each excited state. The rR data show very different intensity distribution patterns for the vibrations in the 300–500cm−1 region. Time-dependent density functional theory (TDDFT) calculations have been used to determine that the change in intensity distribution between the Sp(π) and Sp(σ) excited states reflects the differential enhancement of S(Cys) backbone modes with Cu–S(Cys)–Cβ out-of-plane (oop) and in-plane (ip) bend character in their respective potential energy distributions (PEDs). The rR excited state distortions have been related to ground state reorganization energies (λs) and predict that, in addition to M–L stretches, the Cu–S(Cys)–Cβ oop bend needs to be considered. DFT calculations predict a large distortion in the Cu–S(Cys)–Cβ oop bending coordinate upon reduction of a blue copper (BC) site; however, this distortion is not present in the X-ray crystal structures of reduced BC sites. The lack of Cu–S(Cys)–Cβ oop distortion upon reduction corresponds to a previously unconsidered constraint on the thiolate ligand orientation in the reduced state of BC proteins and can be considered as a contribution to the entatic/rack nature of BC sites.

Far-infrared spectroscopy analysis of linear and cyclic peptides, and lysozyme

The far-infrared spectra of lysozyme, alanine-rich peptides and small cyclic helical peptides were studied. Both lysozyme and the alanine-rich peptides had a dome in the spectral background centred on 180–220cm−1 consistent with either structural collective modes or an ensemble of hydrogen bond vibrational modes associated with the peptide backbone. Molecular dynamics simulation of the alanine-rich peptide's infrared spectrum produced bands with similar positions to the experimental data and vibrational density of states simulation was able to attribute several of these bands to backbone and side chain vibrational modes. Evidence is presented that peaks at 333 and 375cm−1 are associated with alpha-helices in lysozyme and the alanine-rich peptides, and the peak at 445cm−1 is associated with beta-pleated sheet. Also, results suggest that peaks at 385, 402 and 470cm−1 are associated with the secondary structure of the cyclic helical peptide KARAD. This supports the hypothesis the low energy vibrational modes between 300 and 500cm−1 are diagnostic of the presence of secondary structures in (poly)peptides.

Structural and Dynamic Response to Core Repacking Substitutions in T4 Lysozyme Detected by Site-Directed Spin Labeling

Proteins can evolve to gain new functionality via mutations that decrease stability, and presumably, increase flexibility. Particularly interesting examples are mutations that modify the hydrophobic core packing and create new functions, e.g. novel ligand binding sites created by cavity-forming mutants. Many core repacking mutants of T4 Lysozyme (T4L) have been characterized, some of which bind non-polar ligands. Overall, the crystal structures of these mutants are very similar to the WT and offer little insight into the mechanism whereby the ligand reaches the cavity. Site-Directed Spin Labeling (SDSL) has been applied to investigate the structural and dynamical response of T4L in solution to 28 core repacking mutations, many of which have known crystal structures. Remarkably, the most common response in the cavity-creating susbtitutions is the appearance of a second conformational substate, with populations as high as 70 %, showing that the cavities allows for an alternative protein fold, at least locally. Osmotic perturbation shows that the conformations are in slow exchange on the EPR time scale. Thus, the cavity mutations excite molecular flexibility, with a characteristic time scale > 100 ns, probably in the μs-ms range. Interspin distance measurements carried out for two of the cavity mutants to study the magnitude and nature of the conformational rearrangement suggest the interesting possibility that the alternative states are also present in the WT protein, but at a different ratio.In some cases, ns backbone modes were also excited by the core mutation, but the effects were subtle. Remarkably, the type and magnitude of the changes in the protein flexibility were not necessarily correlated with the extent of destabilization by the substitution. The relationship of the cavity-excited states to the mechanism of ligand entry is under study.

Far infrared spectra of solid state aliphatic amino acids in different protonation states

Far infrared spectra of zwitterionic, cationic, and anionic forms of aliphatic amino acids in solid state have been studied experimentally. Measurements were done on glycine, L-alanine, L-valine, L-leucine, and L-isoleucine powder samples and film samples obtained from dried solutions prepared at pH ranging from 1 to 13. Solid state density functional theory calculations were also performed, and detailed potential energy distributions were obtained from normal mode results. A good correspondence between experimental and simulated spectra was achieved and this allowed us to propose an almost complete band assignment for the far infrared spectra of zwitterionic forms. In the 700-50 cm(-1) range, three regions were identified, each corresponding to a characteristic set of normal modes. A first region between 700 and 450 cm(-1) mainly contained the carboxylate bending, rocking, and wagging modes as well as the ammonium torsional mode. The 450-250 cm(-1) region was representative of backbone and sidechain skeletal bending modes. At last, the low wavenumber zone, below 250 cm(-1), was characteristic of carboxylate and skeletal torsional modes and of lattice modes. Assignments are also proposed for glycine cationic and anionic forms, but could not be obtained for all aliphatic amino acids due to the lack of structural data. This work is intended to provide fundamental information for the understanding of peptides vibrational properties.

Vibrational dynamics of poly(L -histidine)

Normal mode analysis and their dispersion for poly(L-histidine) (PLH) are reported by using Urey Bradley force field and Fourier Transform IR PLH exists in the α helical form. There are 17 atoms in one residue, which gives rise to 51 dispersion curves. To simplify, it is convenient to discuss the normal frequencies under three separate heads namely amide modes, side chain modes, and mixed mode. The calculated frequencies are found to be in reasonably good agreement with the Fourier Transform IR spectra. There exists exchange of character, attraction, and repulsion for selective dispersion curves with change in the phase value. Contributions to the heat capacity were calculated separately for the side chain, backbone, and mixed modes. The major contribution comes from the side chain and mixed modes. The sum of these three contributions gives the total heat capacity, which is in agreement with the reported experimental value. © 2009 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 48: 128–137, 2010