Linear and Two-Dimensional Infrared Spectroscopic Study of the Amide I and II Modes in Fully Extended Peptide Chains

Chasing weakly-bound biological water in aqueous environment near the peptide backbone by ultrafast 2D infrared spectroscopy

There has been a long-standing debate as to how many hydrogen bonds a peptide backbone amide can form in aqueous solution. Hydrogen-bonding structural dynamics of N-ethylpropionamide (a β-peptide model) in water was examined using infrared (IR) spectroscopy. Two amide-I sub bands arise mainly from amide C=O group that forms strong H-bonds with solvent water molecules (SHB state), and minorly from that involving one weak H-bond with water (WHB state). This picture is supported by molecular dynamics simulations and ab-initio calculations. Further, thermodynamics and kinetics of the SHB and WHB species were examined mainly by chemical-exchange two-dimensional IR spectroscopy, yielding an activation energy for the SHB-to-WHB exchange of 13.25 ± 0.52 kJ mol‒1, which occurs in half picosecond at room temperature. Our results provided experimental evidence of an unstable water molecule near peptide backbone, allowing us to gain more insights into the dynamics of the protein backbone hydration.

Two-Dimensional Infrared Spectroscopy of Isolated Molecular Ions

Two-dimensional infrared (2D IR) spectroscopy of mass-selected, cryogenically cooled molecular ions is presented. Nonlinear response pathways, encoded in the time-domain photodissociation action response of weakly bound N2 messenger tags, were isolated using pulse shaping techniques following excitation with four collinear ultrafast IR pulses. 2D IR spectra of Re(CO)3(CH3CN)3+ ions capture off-diagonal cross-peak bleach signals between the asymmetric and symmetric carbonyl stretching transitions. These cross peaks display intensity variations as a function of pump-probe delay time due to coherent coupling between the vibrational modes. Well-resolved 2D IR features in the congested fingerprint region of protonated caffeine (C8H10N4O2H+) are also reported. Importantly, intense cross-peak signals were observed at 3 ps waiting time, indicating that tag-loss dynamics are not competing with the measured nonlinear signals. These demonstrations pave the way for more precise studies of molecular interactions and dynamics that are not easily obtainable with current condensed-phase methodologies.

Structural Dependence of Extended Amide III Vibrations in Two-Dimensional Infrared Spectra

Two-dimensional infrared (2D-IR) spectroscopy is a powerful experimental method for probing the structure and dynamics of proteins in aqueous solution. So far, most experimental studies have focused on the amide I vibrations, for which empirical vibrational exciton models provide a means of interpreting such experiments. However, such models are largely lacking for other regions of the vibrational spectrum. To close this gap, we employ an efficient quantum-chemical methodology for the calculation of 2D-IR spectra, which is based on anharmonic theoretical vibrational spectroscopy with localized modes. We apply this approach to explore the potential of 2D-IR spectroscopy in the extended amide III region. Using calculations for a dipeptide model as well as alanine polypeptides, we show that distinct 2D-IR cross-peaks in the extended amide III region can potentially be used to distinguish α-helix and β-strand structures. We propose that the extended amide III region could be a promising target for future 2D-IR experiments.

Mechanism Insight into Rapid Photodriven Sterilization Based on Silver Bismuth Sulfide Quantum Dots

Microbial contamination and the prevalence of resistant bacteria is considered a worldwide public health problem. Therefore, recently, great efforts have been made to develop photoresponsive platforms for the simultaneous photodynamic antibacterial (PDA) and photothermal antibacterial (PTA) therapy processes as mediated by specific light. However, owing to the absorption mismatches of the photothermal agents and photodynamic photosensitizers, it has been discovered that many synergistic photoresponsive antibacterial platforms cannot be excited by a single-wavelength light. In this study, silver bismuth sulfide quantum dots (AgBiS₂ QDs) identified from the literature as a near-infrared light (NIR) that triggers bifunctional materials with simultaneous photodynamic and photothermal effects for photoresponsive bacterial killing were used. Specifically, AgBiS₂ QDs were successfully synthesized via a bottom-up approach, using polyethylenimine (PEI) as an assistant molecule. With PEI wrapping, the attachment between the negatively charged membrane surfaces of the bacterial cells and AgBiS₂ QDs was enhanced via the electrostatic interactions. The photodriven antibacterial activity of AgBiS₂ QDs was then investigated against both S. aureus and E. coli. The results revealed a significant reduction in bacterial survival. The killing effect was found to be independent of the AgBiS₂ QDs, and redox potentials controlled the photogenerated electrons that thermodynamically favored the formation of multiple reactive oxygen species (ROS). A possible phototriggered antibacterial mechanism was then proposed in which the AgBiS₂ QDs are anchored first to the bacterial surface and then induce breaking on its outer membrane by high local heat and ROS under single 808 nm NIR laser illumination to finally induce bacterial death.

Flat, Cα,β -Didehydroalanine Foldamers with Ferrocene Pendants: Assessing the Role of α-Peptide Dipolar Moments

The foldamer field is continuously expanding as it allows to produce molecules endowed with 3D-structures and functions never observed in nature. We synthesized flat foldamers based on the natural, but non-coded, Cα,β -didehydroalanine α-amino acid, and covalently linked to them two ferrocene (Fc) moieties, as redox probes. These conjugates retain the flat and extended conformation of the 2.05 -helix, both in solution and in the crystal state (X-ray diffraction). Cyclic voltammetry measurements agree with the adoption of the 2.05 -helix, characterized by a negligible dipole moment. Thus, elongated α-peptide stretches of this type are insulators rather than charge conductors, the latter being constituted by peptide α-helices. Also, our homo-tetrapeptide has a N-to-C length of about 18.2 Å, almost double than that (9.7 Å) of an α-helical α-tetrapeptide.

Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction

Vibrational spectroscopy is an essential tool in chemical analyses, biological assays, and studies of functional materials. Over the past decade, various coherent nonlinear vibrational spectroscopic techniques have been developed and enabled researchers to study time-correlations of the fluctuating frequencies that are directly related to solute-solvent dynamics, dynamical changes in molecular conformations and local electrostatic environments, chemical and biochemical reactions, protein structural dynamics and functions, characteristic processes of functional materials, and so on. In order to gain incisive and quantitative information on the local electrostatic environment, molecular conformation, protein structure and interprotein contacts, ligand binding kinetics, and electric and optical properties of functional materials, a variety of vibrational probes have been developed and site-specifically incorporated into molecular, biological, and material systems for time-resolved vibrational spectroscopic investigation. However, still, an all-encompassing theory that describes the vibrational solvatochromism, electrochromism, and dynamic fluctuation of vibrational frequencies has not been completely established mainly due to the intrinsic complexity of intermolecular interactions in condensed phases. In particular, the amount of data obtained from the linear and nonlinear vibrational spectroscopic experiments has been rapidly increasing, but the lack of a quantitative method to interpret these measurements has been one major obstacle in broadening the applications of these methods. Among various theoretical models, one of the most successful approaches is a semiempirical model generally referred to as the vibrational spectroscopic map that is based on a rigorous theory of intermolecular interactions. Recently, genetic algorithm, neural network, and machine learning approaches have been applied to the development of vibrational solvatochromism theory. In this review, we provide comprehensive descriptions of the theoretical foundation and various examples showing its extraordinary successes in the interpretations of experimental observations. In addition, a brief introduction to a newly created repository Web site (http://frequencymap.org) for vibrational spectroscopic maps is presented. We anticipate that a combination of the vibrational frequency map approach and state-of-the-art multidimensional vibrational spectroscopy will be one of the most fruitful ways to study the structure and dynamics of chemical, biological, and functional molecular systems in the future.

The Amide I Spectrum of Proteins-Optimization of Transition Dipole Coupling Parameters Using Density Functional Theory Calculations

The amide I region of the infrared spectrum is related to the protein backbone conformation and can provide important structural information. However, the interpretation of the experimental results is hampered because the theoretical description of the amide I spectrum is still under development. Quantum mechanical calculations, for example, using density functional theory (DFT), can be used to study the amide I spectrum of small systems, but the high computational cost makes them inapplicable to proteins. Other approaches that solve the eigenvalues of the coupled amide I oscillator system are used instead. An important interaction to be considered is transition dipole coupling (TDC). Its calculation depends on the parameters of the transition dipole moment. This work aims to find the optimal parameters for TDC in three major secondary structures: α-helices, antiparallel β-sheets, and parallel β-sheets. The parameters were suggested through a comparison between DFT and TDC calculations. The comparison showed a good agreement for the spectral shape and for the wavenumbers of the normal modes for all secondary structures. The matching between the two methods improved when hydrogen bonding to the amide oxygen was considered. Optimal parameters for individual secondary structures were also suggested.

Efficiencies and mechanisms of the chemical cleaning of fouled polytetrafluoroethylene (PTFE) membranes during the microfiltration of alkali/surfactant/polymer flooding oilfield wastewater

The chemical cleaning of fouled polytetrafluoroethylene (PTFE) membranes with different reagents after the microfiltration of alkali/surfactant/polymer (ASP) flooding oilfield wastewater was examined in this study.

Chlorine migration mechanisms during torrefaction of fermentation residue from food waste

Fermentation residue from food waster (FRFW) has a large amount of residual chlorine (Cl), and the high-salt of FRFW is either landfilled or treated as a fertilizer. The transfer of chlorine to the atmosphere and soil can cause pollution and soil salinization. This work primarily investigated the combined forms and migration mechanisms of Cl during the torrefaction of FRFW from 250 to 400 °C. The results showed that the form and amount of Cl released during the torrefaction of FRFW depended on temperature. The absolute content of soluble Cl and total Cl in torrefied solid products decreased, and the absolute content of insoluble Cl reached a maximum at 350 °C, which indicated that some soluble Cl was transferred to the insoluble Cl (CCl forms). The Cl-containing products in non-condensable gas was too little to be detected, so the majority of the reduced Cl was in liquids with different organic compounds.

How Molecular Crowding Differs from Macromolecular Crowding: A Femtosecond Mid-Infrared Pump-Probe Study

Crowding is an inherent property of living systems in which biochemical processes occur in highly concentrated solutions of various finite-sized species of both low (molecular crowding) and high (macromolecular crowding) molecular weights. Is molecular crowding fundamentally different from macromolecular crowding? To answer this question, we use a femtosecond mid-infrared pump-probe technique with three vibrational probes in molecular (diethylene glycol) and macromolecular (polyethylene glycol) solutions. In less crowded media, both molecular and macromolecular crowders fail to affect the dynamics of interstitial bulk-like water molecules and those at the crowder/water interface. In highly crowded media, interstitial water dynamics strongly depends on molecular crowding, but macromolecular crowding does not alter the bulk-like hydration dynamics and has a modest crowding effect on water at the crowder/water interface. The results of this study provide a molecular level understanding of the structural and dynamic changes to water and the water-mediated cross-linking of crowders.

Solvent-dependent structural dynamics of an azido-platinum complex revealed by linear and nonlinear infrared spectroscopy

The vibrational and anisotropic relaxation dynamics and structural dynamics of a potential anticancer prodrug, trans,trans,trans-[Pt(N3)2(OH)2(py)2], were investigated using time-resolved infrared pump-probe spectroscopy and ultrafast two-dimensional infrared (2D IR) spectroscopy. Herein, two representative bio-friendly solvents, H2O and DMSO, were used, in which the local structural and dynamical variations were monitored using the antisymmetric linear combination of the two N3 stretching vibrational modes as an infrared probe. It was found that the vibrational relaxation process of the N3 antisymmetric stretching (as) mode in H2O is two to three times faster than that in DMSO. The anisotropic relaxation process of the anticancer prodrug was observed to be hindered in DMSO; this indicated a tighter solvent environment around the sample molecule in this solvent. The vibrational frequency time correlation of the N3 antisymmetric stretching mode in H2O decays with a time constant of 1.94 ps, in agreement with the hydrogen bond formation and breaking times of water. In DMSO, the frequency time correlation of the N3 as mode decays on a much longer time scale; this further indicates its sensitivity to the out-layer DMSO structural dynamics, which are relatively static in the experimental time window.

Amide-Functionalized Chalcogen-Bridged Flexible Tetranuclear Rhenacycles: Synthesis, Characterization, Solvent Effect on the Structure, and Guest Binding

The synthesis of flexible rhenium(I)-based amide-functionalized chalcogen-bridged tetranuclear metallacycles of general formula [{(CO)₃Re(μ-ER)₂Re(CO)₃}₂(μ-L)₂] (1-8) was achieved by treating rhenium carbonyl with dialkyl/diaryl chalcogenide (RE-ER; E = S and Se) in the presence of ditopic flexible or semiflexible pyridyl ligand with amide functionality (L = N,N'-bis(4-pyridylcarboxamide)-1,2-ethane (bpce) and N,N'-bis(4-(4-pyridylcarboxamide)phenyl)methane (bpcpm)). Compounds 1-8 were formed by multicomponent self-assembly under one-pot reaction conditions via oxidative addition of dialkyl/diaryl chalcogenide to rhenium carbonyl with pyridyl ligands. The resultant metallacyclophanes were characterized using elemental analyses, infrared, ultraviolet-visible, and NMR spectroscopic techniques. Metallacyclophanes 1-3 and 7 were structurally characterized by single-crystal X-ray diffraction methods. The solvent-induced structural change of flexible tetranuclear metallacyclophane 2 was demonstrated by crystallizing 2 in dichloroethane and dimethylformamide. Molecular recognition capabilities of 2 and 7 were studied with few aromatic compounds containing ethereal linkages.

Innovative chemical gels meet enzymes: A smart combination for cleaning paper artworks

HYPOTHESIS

Due to their highly retentive properties, innovative recently developed, semi-interpenetrated hydrogels made up of poly(vinyl pyrrolidone) (PVP) chains embedded in a poly(2-hydroxyethyl methacrylate) (p(HEMA)) network should be efficiently used as cleaning material for fragile and degraded paper artworks. In restoration practice, indeed the wet cleaning of these artworks is usually performed by immersion of paper in water, a procedure which may lead to several drawbacks, including paper fibers swelling and dissolution of water-soluble original components.

EXPERIMENTS

This class of gels were yet presented in literature, but their interactions with paper materials and ability to be spiked with active enzymes (as cleaning agents), have not been analyzed. To establish the suitability of these hydrogels as paper cleaning materials, first, a rheological and microstructural characterization of the gels was performed. Moreover, diffusion of macromolecules inside gels was studied using fluorescence microscopy, to check if these innovative hydrogels can be used as carriers for hydrolytic enzymes. Indeed, pastes and glues are usually found in old paper artworks, and their removal is a very delicate operation that requires a selective action, which is granted by specific hydrolytic enzymes. At the same time, spectroscopic analyses on paper samples under investigation before and after cleaning treatment has been performed, thus assessing the capabilty of these gels as cleaning materials.

FINDINGS

With the aim of demonstrating the versatility of these hydrogels, several case studies, i.e., the removal of grime and water-soluble cellulose degradation byproducts, the removal of animal glue and the removal of starch paste from real samples, are presented. Results obtained with these gels have been compared to those obtained by using another gel used for paper artworks cleaning, i.e., Gellan gel.

Structure of Penta-Alanine Investigated by Two-Dimensional Infrared Spectroscopy and Molecular Dynamics Simulation

We have studied the structure of (Ala)5, a model unfolded peptide, using a combination of 2D IR spectroscopy and molecular dynamics (MD) simulation. Two different isotopomers, each bis-labeled with (13)C═O and (13)C═(18)O, were strategically designed to shift individual site frequencies and uncouple neighboring amide-I' modes. 2D IR spectra taken under the double-crossed ⟨π/4, -π/4, Y, Z⟩ polarization show that the labeled four-oscillator systems can be approximated by three two-oscillator systems. By utilizing the different polarization dependence of diagonal and cross peaks, we extracted the coupling constants and angles between three pairs of amide-I' transition dipoles through spectral fitting. These parameters were related to the peptide backbone dihedral angles through DFT calculated maps. The derived dihedral angles are all located in the polyproline-II (ppII) region of the Ramachandran plot. These results were compared to the conformations sampled by Hamiltonian replica-exchange MD simulations with three different CHARMM force fields. The C36 force field predicted that ppII is the dominant conformation, consistent with the experimental findings, whereas C22/CMAP predicted similar population for α+, β, and ppII, and the polarizable Drude-2013 predicted dominating β structure. Spectral simulation based on MD representative conformations and structure ensembles demonstrated the need to include multiple 2D spectral features, especially the cross-peak intensity ratio and shape, in structure determination. Using 2D reference spectra defined by the C36 structure ensemble, the best spectral simulation is achieved with nearly 100% ppII population, although the agreement with the experimental cross-peak intensity ratio is still insufficient. The dependence of population determination on the choice of reference structures/spectra and the current limitations on theoretical modeling relating peptide structures to spectral parameters are discussed. Compared with the previous results on alanine based oligopeptides, the dihedral angles of our fitted structure, and the most populated ppII structure from the C36 simulation are in good agreement with those suggesting a major ppII population. Our results provide further support for the importance of ppII conformation in the ensemble of unfolded peptides.

The 2.0₅-helix in hetero-oligopeptides entirely composed of C(α,α)-disubstituted glycines with both side chains longer than methyls

The existence of the very uncommon, but potentially quite interesting, multiple, consecutive fully-extended conformation (2.0₅-helix) has been already clearly demonstrated in homo-oligopeptides based on quaternary α-amino acids with both side chains longer than methyls, but not cyclized on the α-carbon atom. To extend the scope of this research, in this work we investigated the occurrence of this flat 3D-structure in hetero-oligopeptides, each composed of two or three different residues of that class. The synthesis of a terminally protected peptide series to the tetrapeptide level was carried out by solution methods. The resulting oligomers were chemically and conformationally characterized. The data obtained point to an overwhelming population of the fully-extended conformation in CDCl3. However, a solvent-driven switch to a predominant 3₁₀-helical structure was seen in CD3CN. A delicate, local balance between these two conformations is confirmed to occur in the crystalline state. Molecular dynamics simulations in CHCl3 on a hetero-tetrapeptide converged to the fully-extended conformation even starting from the 3₁₀-helical structure.

Multiple, consecutive, fully-extended 2.0₅-helix peptide conformation

The peptide 2.0(5)-helix does exist. It has been experimentally authenticated both in the crystalline state (by X-ray diffraction) and in solution (by several spectroscopic techniques). It is the most common conformation for C(α)-tetrasubstituted α-amino acids with at least two atoms in each side chain, provided that cyclization on the C(α)-atom is absent. X-Ray diffraction has allowed a detailed description of its geometrical and three-dimensional (3D)-structural features. The infrared absorption and the nuclear magnetic resonance parameters characteristics of this multiple, consecutive, fully-extended structure have been described. Conformational energy calculations are in agreement with the experimental findings. As the contribution per amino acid residue to the length of this helix is the longest possible, its exploitation as a molecular spacer is quite promising. However, it is a rather fragile 3D-structure and particularly sensitive to solvent polarity. Interestingly, in such a case, it may reversibly convert to the much shorter 3(10)-helix, thus generating an attractive molecular spring.

Amide I Vibrational Properties Affected by Hydrogen Bonding Out-of-Plane of the Peptide Group

The amide I vibrational properties of a peptide-water complex in various intermolecular configurations are analyzed theoretically to see whether a water molecule with a weak out-of-plane hydrogen bond really induces a large low-frequency shift. It is shown that the frequency shift strongly depends on the C═O···H angle, with a larger low-frequency shift as the C═O···H becomes more bent, suggesting that the so-called hydrated helix with a rather low amide I frequency has an additional water molecule located out-of-plane of the peptide group as compared with a typical α-helix. The infrared intensity also depends on the angular position of water. A new model parameter set (that can be combined with molecular dynamics) is developed for a more correct representation of the hydration-induced frequency shift. The question regarding the scalar and vectorial nature of the molecular properties related to the frequency shift is also discussed.

Site-specific infrared probes of proteins

Infrared spectroscopy has played an instrumental role in the study of a wide variety of biological questions. However, in many cases, it is impossible or difficult to rely on the intrinsic vibrational modes of biological molecules of interest, such as proteins, to reveal structural and environmental information in a site-specific manner. To overcome this limitation, investigators have dedicated many recent efforts to the development and application of various extrinsic vibrational probes that can be incorporated into biological molecules and used to site-specifically interrogate their structural or environmental properties. In this review, we highlight recent advancements in this rapidly growing research area.

Exploring the consequences of a representative "disallowed" conformation of Aib on a 3₁₀-helical fold

The structural effects of a representative "disallowed" conformation of Aib on the 3(10)-helical fold of an octapeptidomimetic are explored. The 1D ((1)H, (13)C) & 2D NMR, FT-IR and CD data reveal that the octapeptide 1, adopts a 3(10)-helical conformation in solution, as it does in its crystal structure. The C-terminal methyl carboxylate (CO2Me) of 1 was modified into an 1,3-oxazine (Oxa) functional group in the peptidomimetic 2. This modification results in the stabilization of the backbone of the C-terminal Aib (Aib*-Oxa) of 2, in a conformation (ϕ, ψ = 180, 0) that is natively disallowed to Aib. Consequent to the presence of this natively disallowed conformation, the 3(10)-helical fold is not disrupted in the body of the peptidomimetic 2. But the structural distortions that do occur in 2 are primarily in residues in the immediate vicinity of the natively disallowed conformation, rather than in the whole peptide body. Non-native electronic effects resulting from modifications in backbone functional groups can be at the origin of stabilizing residues in natively disallowed conformations.

Capping amyloid β-sheets of the tau-amyloid structure VQIVYK with hexapeptides designed to arrest growth. An ONIOM and density functional theory study

We present ONIOM calculations using density functional theory (DFT) as the high and AM1 as the medium level that explore the abilities of different hexapeptide sequences to terminate the growth of a model for the tau-amyloid implicated in Alzheimer’s disease. We delineate and explore several design principles (H-bonding in the side chains, using antiparallel interactions on the growing edge of a parallel sheet, using all-d residues to form rippled interactions at the edge of the sheet, and replacing the H-bond donor N–H’s that inhibit further growth) that can be used individually and in combination to design such peptides that will have a greater affinity for binding to the parallel β-sheet of acetyl-VQIVYK-NHCH₃ than the natural sequence and will prevent another strand from binding to the sheet, thus providing a cap to the growing sheet that arrests further growth. We found peptides in which the Q is replaced by an acetyllysine (aK) residue to be particularly promising candidates, particularly if the reverse sequence (KYVIaKV) is used to form an antiparallel interaction with the sheet.

Structure dependent energy transport: relaxation-assisted 2DIR measurements and theoretical studies

Vibrational energy relaxation and transport in a molecule that is far from thermal equilibrium can affect its chemical reactivity. Understanding the energy transport dynamics in such molecules is also important for measuring molecular structural constraints via relaxation-assisted two-dimensional infrared (RA 2DIR) spectroscopy. In this paper we investigated vibrational relaxation and energy transport in the ortho, meta, and para isomers of acetylbenzonitrile (AcPhCN) originated from excitation of the CN stretching mode. The amplitude of the cross-peak among the CN and CO stretching modes served as an indicator for the energy transport from the CN group toward the CO group. A surprisingly large difference is observed in both the lifetimes of the CN mode and in the energy transport rates for the three isomers. The anharmonic DFT calculations and energy transport modeling performed to understand the origin of the differences and to identify the main cross-peak contributors in these isomers described well the majority of the experimental results including mode excited-state lifetimes and the energy transport dynamics. The strong dependence of the energy transport on molecular structure found in this work could be useful for recognizing different isomers of various compounds via RA 2DIR spectroscopy.

Comparison of β-sheets of capped polyalanine with those of the tau-amyloid structures VQIVYK and VQIINK. A density functional theory study

We present ONIOM calculations using B3LYP/d95(d,p) as the high and AM1 as the low level on parallel β-sheets containing from two to ten strands of Ac-VQIVYK-NHMe and Ac-VQIINK-NHMe, as well as both parallel and antiparallel Ac-AAAAAA-NHMe. We find that the first two sequences form more stable sheets due to the additional H-bonding between the Q's in the side chains of both and the N's in the side chain of Ac-VQIINK-NHMe. However, the H-bonds in the amyloid chains are significantly weakened by attractive strain, which prevents all the interstrand H-bonds from achieving their optimal geometries simultaneously and requires high distortion energies for the individual strands in the sheets. The antiparallel Ac-AAAAAA-NHMe's are generally more stable and more cooperative than the parallel sheets, principally due to the higher distortion energies of the latter.