Formation Of Intramolecular Hydrogen Bond Research Articles

Antioxidant and spectral properties of chalcones and analogous aurones: Theoretical insights

AbstractDensity functional theory (DFT) and time‐dependent DFT (TD‐DFT) have been employed to elucidate the radical scavenging capacity and the UV–Vis spectral property of several chalcones and analogous aurones. Three main antioxidant mechanisms, hydrogen atom transfer (HAT), electron transfer followed by proton transfer (SET‐PT) and sequential proton loss electron transfer (SPLET) were investigated. The results indicate that all the studied compounds adopt a fully planar conformation in their neutral, radical, cationic as well as anionic forms. 2′‐OH plays important role in the stabilization of phenolic radicals due to the formation of intramolecular hydrogen bonds (IHBs). Introduction of electron‐donating substituent on B‐ring is helpful for improving the activity. For the considered compounds, HAT is proposed as the thermodynamically favored mechanism in gas phase and nonpolar environment, while SPLET is preferred in polar media. The results confirmed the crucial role of hydroxyl group on A‐ring, especially on position 5′/5, in terms of the radical scavenging ability. The absorption spectra of title compounds were successfully simulated and the lowest energy transitions predominantly correspond to the π‐π* transitions from HOMO to LUMO with charge transfer (CT) character.

Conformational Effects in the Transport of Glucose through a Cyclic Peptide Nanotube: A Molecular Dynamics Simulation Study.

The transport behavior of glucose through a cyclic peptide nanotube (CPN), composed of 8 × cyclo[-(Trp-d-Leu)4-Gln-d-Leu-] rings embedded in DMPC lipid bilayers was examined using all-atom molecular dynamics (AAMD) simulations. Two conformational isomers of β-d-glucose, equatorial (4C1) and axial (1C4) chair conformers, were used to examine conformational effects on the hydrogen bond network, energetics, and diffusivity of glucose transport through the CPN. Calculations of the number of hydrogen bonds of the two glucose conformers with water molecules and with the CPN illustrate that the total number of hydrogen bonds of the conformers decreases inside the channel compared to bulk water due to the confinement characteristics of the interior of the CPNs although new hydrogen bonds between the hydroxyl and hydroxymethyl hydrogens of glucose and the carbonyl oxygens in the CPN backbone are formed. Despite the decrease of the number of hydrogen bonds inside the CPN, intramolecular hydrogen bonds of 1C4 are maintained during permeation of 1C4 through the CPN. The retention of intramolecular hydrogen bonds and the spherical shape of 1C4 give rise to considerably weaker orientational preferences and higher diffusion coefficients for 1C4 than those of 4C1 inside and outside the CPN. Due to larger dipole moments induced by the alignment of hydroxyl and hydroxymethyl groups, 1C4 has more favorable interactions with the CPN backbone at the channel entrances and inside the channel than 4C1. In the middle of the CPN channel, entropic gains originating from higher orientational and translational degrees of freedom of 1C4 than those of 4C1 also contribute to lower free energy wells for 1C4 inside the CPN. This work reveals that the conformational variation and intramolecular hydrogen bond formation of β-d-glucose can have important effects on the energetics and dynamics of glucose transport through CPNs, providing insight into the translocation mechanism of d-glucose into the cell through glucose transporters (GLUTs) and the dynamics of glucose confined in silica nanochannels. It is also demonstrated that CPNs can indeed facilitate the permeation of small hydrophilic molecules such as glucose and can be utilized as a novel carrier system for hydrophilic drug compounds into the cell.

Exploring and elaborating the excited state mechanism of a novel AIE material 2-(5-(4-carboxyphenyl)-2-hydroxyphenyl)benzothiazole

A novel aggregation-induced emission material 2-(5-(4-carboxyphenyl)-2-hydroxyphenyl)benzothiazole (2-CHBT) has been investigated based on density functional theory (DFT) and time-dependent density functional theory (TDDFT) methods. Via reduced density gradient (RDG) versus sign(λ2)ρ analyses, we firstly verify the formation of intramolecular hydrogen bond in 2-CHBT system. Analyzing the primary geometrical parameters in 2-CHBT and comparing the changes about infrared (IR) vibrational spectra, we confirm that the hydrogen bond O-H···N is strengthened in the S1 state upon excitation. Exploring photo-excitation process, the frontier molecular orbitals (MOs) and charge density difference (CDD) analyses have been performed using TDDFT/B3LYP/TZVP theoretical level, based on which we verify the charge transfer phenomenon referring to the S0 → S1 transition. And the CDD around the hydrogen bond moiety provides the tendency of ESIPT for 2-CHBT molecule. Comparing the energy gap between HOMO and LUMO orbitals in cyclohexane, toluene, chloroform, and DMSO solvents, we predict the ESIPT reaction might be more active in non-polar solvents. In addition, constructing potential energy curves and searching transition state (TS) structures, we further clarify the ESIPT mechanism and verify that non-polar solvents might facilitate the ESIPT process. Our simulated results reappear experimental spectral results and successfully explain experimental phenomenon.

Theoretical insights into the excited state intramolecular proton transfer mechanism for a novel 4‐methoxy‐3‐hydroxyflavone system

A novel 3‐hydroxyflavone derivative, 4‐methoxy‐3‐hydroxyflavone (4M3HF), is theoretically investigated regarding its excited state intramolecular proton transfer (ESIPT) mechanism based on density functional theory (DFT) and time‐dependent DFT (TDDFT) methods. By comparing the solvent polarity, we selected acetonitrile and toluene in this work. First, based on atoms in molecules (AIM) analyses, we verified the formation of intramolecular hydrogen bond of the 4M3HF structure. On investigating the geometrical parameters (i.e., bond lengths and bond angles), we found that the hydrogen bond strength should be enhanced in the S1 state. By calculating the infrared vibrational spectra, we confirmed the strengthening of the intramolecular hydrogen bond in the S1 state. We further studied the excitation process using the frontier molecular orbitals method, based on which we concluded that the charge redistribution in solvents facilitates the ESIPT tendency. For exploring the ESIPT behavior, we constructed the potential energy curves along with ESIPT paths in both solvents (acetonitrile and toluene). We found that low potential energy barriers facilitate the ESIPT process in the 4M3HF system, which was also verified by searching the transition state (TS) structure. Comparing these two solvents, we concluded that solvent effects play little role in the ESIPT reaction in the 4M3HF system. And we could successfully explain the previous experimental result.

Electrochemical recognition of nitrophenol isomers by assembly of pillar[5]arenes mutifilms

The rational design of electrochemical methods for isomer recognition is a focus of research in the molecular recognition and separation fields. In this work, a novel, rapid, and convenient electrochemical approach for recognition of nitrophenol isomers was constructed based on the alternating layer-by-layer (LbL) assembly of water-soluble cationic and anionic pillar [5]arene on a carboxylic graphene (C-Gra) modified glass carbon electrode. The electrochemical recognition of nitrophenol isomers was investigated by differential pulse voltammetry (DPV). The electrochemical results reveal that both the peak currents of m-nitrophenol (m-NP) and p-nitrophenol (p-NP) increased with the increasing of the layer number of the assembled pillar [5]arene, whereas the peak current of o-nitrophenol (o-NP) decreased with the increased layers, which demonstrated an efficient route for discriminating the nitrophenol isomers. The molecular recognition mechanism was studied by 1H NMR spectra, which indicated that the m-NP and p-NP can be included in the cavity of the pillar [5]arene host. However, the o-NP could not enter into the host of pillar [5]arene, which was ascribed to the formation of intramolecular hydrogen bond of o-NP. The LbL assembly modified GCE was used for detecting p-NP and m-NP. A low detection limit of 0.33 μM (S/N = 3) and a linear response range of 1–90 μM for p-NP were obtained by using this method. And the detection limit of 0.16 μM (S/N = 3) and a linear response range of 0.5–70 μM for m-NP were obtained. This method of LbL assembly modified GCE has potential application in molecular recognition and separation.

Theoretical insights into the ESIPT process for π‐conjugated benzimidazole compounds

AbstractTwo active benzimidazole derivatives (1 and 2 compounds) [J. Org. Chem. 2017, 82, 12173.] have been selected to explore their excited state dynamical properties. Spectroscopic studies about excited state intramolecular proton transfer (ESIPT) of 1 and 2 compounds have been investigated in details. Combing the density functional theory and time‐dependent density functional theory methods, we theoretically analyze the hydrogen bond properties for 1 and 2 compounds. Using atoms in molecules methodology, we confirm the formation of intramolecular hydrogen bond in the S0 state. Further, the primary bond lengths, bond angles, and the infrared vibrational spectra involved in hydrogen bond moieties have been analyzed revealing that the intramolecular hydrogen bonds are strengthened in the S1 state. Analyses about frontier molecular orbitals theory prove that the ESIPT process could be facilitated by charge transfer upon the photoexcitation. Based on constructing potential energy curves of both S0 and S1 states, we provide the excited state dynamical overall perspective about ESIPT mechanism for both 1 and 2 compounds. This work not only clarifies the ESIPT mechanism for 2 novel active benzimidazole derivatives 1 and 2 compounds but also makes contributions for the applications of such kinds of systems.

Construction compositions based on integrated binding of thermoplastic waste

The paper suggests a solution of the actual problem of processing polymeric municipal waste in building materials with a high complex of decorative and operational properties. The work is aimed at studying the processes of structure formation and hardening in the system “multicomponent thermoplastic binder - mineral filler” in the manufacture of polymer concrete products for construction purposes. During the research methods of infrared spectroscopy, differential thermal analysis, standard methods for determining the structure and properties of building products were used. As a result of the research, compositions of a complex thermoplastic binder including polymeric consumption waste (PET, PP) are proposed taking into account the volumes of their sampling at the waste sorting stations. An additive - a compatibilizer based on an ethylene-vinyl acetate copolymer with grafted reactive polar acrylate and epoxy groups, is also included. It was found that the introduction of a compatibilizer promotes the activation of the physicochemical interaction between the components of the polymer binder and between the polymer matrix and the mineral surface of the fillers. There was also an increase in the density and strength of the resulting artificial stone. The optimal content of the additive in an amount of 5% of the total mass of the complex binder was experimentally determined. With the introduction of a compatibilizer in smaller amounts, the effect of strengthening the flexural strength decreases, and when more compatibilizers are introduced, the strength of the products remains the same at bending, and the compressive strength decreases. Mechanisms of interphase interactions are proposed, taking into account the chemical-mineralogical composition of mineral fillers (based on carbonates and aluminosilicates). The possibility of participation of epoxide and acrylate functional groups in the formation of intramolecular and intermolecular hydrogen bonds with the formation of polyassociates was established. The revealed patterns of interaction make it possible to ensure the compatibility of weakly polar PET with other multitonnage thermoplastics, as well as compatibility of the complex polymer binder with mineral fillers. The management of the processes of structure formation in the studied systems makes it possible to obtain high decorative and operational parameters of the construction products.

Microscopic Insight into the Protein Denaturation Action of Urea and Its Methyl Derivatives.

We employ site-specific, linear and nonlinear infrared spectroscopic techniques as well as fluorescence spectroscopy and molecular dynamics simulations to investigate the binding interactions of urea and three of its derivatives, methylurea, 1,3-dimethylurea, and tetramethylurea, with protein aromatic and polar side chains. We find that (1) urea methylation leads to preferential interactions between the cosolvent molecules and aromatic side chains with an affinity that increases with the number of methyl groups; (2) interactions with tetramethylurea cause significant dehydration of aromatic side chains and the effect is most pronounced for tryptophan; and (3) while neither urea nor tetramethylurea shows preferential accumulation around a polar side chain, the number of hydrogen-bond donors around this side chain is significantly decreased in the presence of tetramethylurea. Taken together, our findings suggest that these urea derivatives, especially tetramethylurea, can effectively disrupt hydrophobic interactions in proteins. Additionally, tetramethylurea can promote intramolecular hydrogen-bond formation and hence induce α-helix folding in peptides, as observed.

N-propyl nitrate vibrational spectrum analysis using DFT B3LYP quantum-chemical method

Calculation of a molecular structure, conformation and related vibrational spectra of the n- propyl nitrate C3H7NO3 was carried out by means of density functional theory (DFT) by employing the Gaussian 03 package. The molecular geometries were fully optimized by using the Becker's three-parameter hybrid exchange functional combined with the Lee–Yang–Parr correlation functional (B3LYP) and using the 6-31G(d) basis set. By scanning the dihedral angles around C-O and C-C bonds, five energetically most favorable conformers of n-propyl nitrate - TG, TT, GT, GG and G´G forms were found. Vibrational spectra of the most energetically favorable conformers were calculated. The comparative analysis of calculated and experimental spectra is carried out, the spectral features of the conformational state of n-propyl nitrate and the spectral effects of formation of intramolecular hydrogen bonds are established.

Colorimetric chemosensors based on diketopyrrolopyrrole for selective and reversible recognition of fluoride ions

A series of colorimetric and reversible receptors for fluoride anions based on diketopyrrolopyrrole (DPP) were designed and synthesized successfully. The position of nitro substituent on the phenylhydrazide affected the alteration of photophysical properties to varying degrees. While the photoluminescence intensity of receptor 1 was weaker than that of receptor 2 and receptor 3 on account of the formation of intramolecular hydrogen bond deriving from oxygen atom of nitro substituent and hydrogen atom of hydrazide. The receptor 2 was a preferable chemosensor for responding fluoride anions. The fluorescence was quenched in the presence of fluoride anion resulted from the photo-induced electron transfer (PET) effect from the amide. The formation of deprotonation species, which produced by hydrazide NH moiety and F− was answerable for the spectral changes. Especially, the spectral and color responses of receptors could be switched back and forth successively by adding F− and HSO4− anions in DMSO solution. These receptors could response fluoride anion sensitively, visually and selectively in a manner of reversible with a low determination.

Anharmonic calculations of frequencies and intensities of O[sbnd]H stretching vibrations of (R)-1,3-butanediol conformers in the fundamentals and first overtones by density functional theory

The frequencies and absorption intensities of the five kinds of conformers of 1,3-butanediol with the same carbon skeleton (GG′) were calculated by anharmonic calculation for the fundamentals and first overtones of OH stretching vibrations. The four kinds of conformers form intramolecular hydrogen bonds and one conformer did not. Intramolecular hydrogen bond formation shifted the frequency of fundamental and first overtone of H-bonding OH stretching vibration to the lower frequency. The absorption intensities of the fundamentals as well as the vibrational anharmonicities increased upon hydrogen bond formation, while the intensities of first overtones decreased. The differences of conformers were clearly seen in the frequencies of the first overtones of free OH.

Seeded Polymerization through the Interplay of Folding and Aggregation of an Amino‐Acid‐based Diamide

AbstractAmino acid based diamides are widely used as a substructure in supramolecular polymers and are also key components of polypeptides that help to understand protein folding. The interplay of folding and aggregation of a diamide was used to achieve seed‐initiated supramolecular polymerization. For that purpose, a pyrene‐substituted diamide was synthesized in which pyrene is used as a tracer to monitor the supramolecular polymerization. Thermodynamics and time‐dependent studies revealed that the folding of the diamide moiety, via the formation of intramolecular hydrogen bonds, effectively prevents a spontaneous nucleation that leads to supramolecular polymerization. Under such out‐of‐equilibrium conditions, the addition of seeds successfully initiates the supramolecular polymerization. These results demonstrate the utility of such amino acid based diamides in programmable supramolecular polymerizations.

Nature of Intramolecular Resonance Assisted Hydrogen Bonding in Malonaldehyde and Its Saturated Analogue

The nature of resonance-assisted hydrogen bonds (RAHB) is still subject of an ongoing debate. We therefore analyzed the σ and π charge redistributions associated with the formation of intramolecular hydrogen bonds in malonaldehyde (MA) and its saturated analogue 3-hydroxypropanal (3-OH) and addressed the question whether there is a resonance assistance phenomenon in the sense of a synergistic interplay between the σ and π electron systems. Our quantum chemical calculations at the BP86/TZ2P level of theory show that the π charge flow is indeed in line with the Lewis structure as proposed by the RAHB model. This typical rearrangement of charge is only present in the unsaturated system, and not in its saturated analogue. Resonance in the π electron system assists the intramolecular hydrogen bond by reducing the hydrogen bond distance, and by providing an additional stabilizing component to the net bonding energy. The σ orbital interaction plays an important role in the enhanced hydrogen bond strength in MA as well. However, there is no resonance assistance in the sense of an interplay between σ charge transfer and π polarization; σ and π contribute independently from each other.

Seeded Polymerization through the Interplay of Folding and Aggregation of an Amino-Acid-based Diamide.

Amino acid based diamides are widely used as a substructure in supramolecular polymers and are also key components of polypeptides that help to understand protein folding. The interplay of folding and aggregation of a diamide was used to achieve seed-initiated supramolecular polymerization. For that purpose, a pyrene-substituted diamide was synthesized in which pyrene is used as a tracer to monitor the supramolecular polymerization. Thermodynamics and time-dependent studies revealed that the folding of the diamide moiety, via the formation of intramolecular hydrogen bonds, effectively prevents a spontaneous nucleation that leads to supramolecular polymerization. Under such out-of-equilibrium conditions, the addition of seeds successfully initiates the supramolecular polymerization. These results demonstrate the utility of such amino acid based diamides in programmable supramolecular polymerizations.

DFT investigation on the selective complexation of Fe3+ and Al3+ with hydroxypyridinones used for treatment of the aluminium and iron overload diseases

The chelating agents for Al3+ and Fe3+ metal cations with therapeutic applications have been considered in the recent years. In designing of the hydroxypyridinones (HPOs) as the therapeutic chelating agents for iron and aluminium overload pathologies, quantum mechanical (QM) calculations are necessary for predicting the binding energies and thermodynamic parameters of the metal−HPO complexes. Three derivatives of the HPOs called 3-hydroxy-1,2-dimethylpyridin-4(1H)-one (DFP), 3-hydroxy-4(1H)-pyridinone (HOPO) and 5-hydroxy-2-(hydroxymethyl)pyridin-4(1H)-one (P1) were investigated for complexation with Fe3+ and Al3+ metal ions. Because of the maximum interaction between Fe3+ and HPOs, all HPOs form stable complexes with Fe3+ metal ion. Moreover, it was found that [Fe−P1]2+ is a more stable complex than [Fe−DFP]2+ and [Fe−3,4-HOPO]2+ in the gas phase and water, confirming that P1 is the strongest selective iron chelator. The more stability of [Fe−P1]2+ was attributed to an intramolecular hydrogen bond formation between the hydrogen atom of NH group and the oxygen atom of CH2OH chain. All complexes of the HPOs with Fe3+ and Al3+ were formed through the oxygen atoms of the CO and OH groups of the HPO. Natural bond orbital analysis showed that the interaction of the lone pair electrons of the oxygen atom of the chelator and antibonding orbitals of the Al3+ and Fe3+ are important in the complex formation. Topological parameters at the bond critical points confirmed the effective interaction between the Al3+ and Fe3+ metal ions and HPO as well as the nature of the metal−oxygen bonds.

Supramolecular packing and polymorph screening of N-isonicotinoyl arylketone hydrazones with phenol and amino modifications

Thirteen structural variants based on the (E)-N′-(1-arylethylidene)pyridohydrazide template were prepared, investigated and screened for possible polymorphic behaviour. Four variants showed from Differential Scanning Calorimetry Scans thermal events indicative of new solid-state phases. The thirteen variants included substituents R = OH or NH2 placed at ortho, meta and para positions on the phenyl ring; and shifting the pyridyl nitrogen between positions 4-, 3- and 2-. The crystal structures of twelve of the compounds were determined to explore their supramolecular structures. The outcomes of these modifications demonstrated that the pyridyl nitrogen at the 2- position is ‘locked’ by forming a hydrogen bond with the amide hydrogen; while placing the pyridyl nitrogen at positions 3- and 4- offers a greater opportunity for hydrogen bonding with neighbouring molecules. Such interactions include OH⋯N, NH⋯N, OH⋯O, NH⋯O, NH⋯π, π⋯π stacking, as well as other weaker interactions such as CH⋯N, CH⋯O, CH⋯N(pyridyl). When OH or NH2 donors are placed in the ortho position, an intramolecular hydrogen bond is formed between the acceptor hydrazone nitrogen and the respective donor. The meta- and para-positioned donors form an unpredictable array of supramolecular structures by forming hydrogen-bonded chains with the pyridyl nitrogen and carbonyl acceptors respectively. In addition to the intramolecular and chain hydrogen bond formation demonstrated throughout the crystal structures under investigation, larger order hydrogen-bonded rings were also observed in some of the supramolecular aggregations. The extent of the hydrogen-bonded ring formations range from two to six molecular participants depending on the specific crystal structure.

Molecular insights into inclusion complexes of mansonone E and H enantiomers with various β-cyclodextrins

The structural dynamics and stability of inclusion complexes of mansonone E (ME) and H (MH) including their stereoisomers with various βCDs (methylated- and hydroxypropylated-βCDs) were investigated by classical molecular dynamics (MD) simulations and binding free energy calculations. The simulation results revealed that mansonones are able to form inclusion complexes with βCDs. The guest molecules are not completely inserted into the host cavity, their preferably positions are nearby the secondary rim with the oxane ring dipping into the hydrophobic inner cavity. The encapsulation process leads to a higher rigidity of the βCDs enhancing the intramolecular hydrogen bond formation ability and decreasing the chance of glucopyranose rotation. According to the MM-PBSA binding free energy calculation, all considered inclusion complexes are stable and the binding energies are mainly caused by van der Waals interactions. Moreover, the free energy calculations showed significant differences in the complexation energies for the stereoisomers, which could enable the separation of the isomers by analytical techniques for further pharmaceutical applications.

Intra- and intermolecular hydrogen bonding in solutions of N-(2-hydroxy-3,8-diiodocyclooctyl)trifluoroacetamide and N-(4-iodo-2,2,5,5-tetramethyltetrahydrofuran-3-yl)trifluoroacetamide

The methods of IR spectroscopy and quantum chemistry (B3LYP/DGDZVP) were applied to investigation of the types of self-associates formed in solutions of N-(2-hydroxy-3,8-diiodocyclooctyl)trifluoroacetamide and N-(4-iodo-2,2,5,5-tetramethyltetrahydrofuran-3-yl)trifluoroacetamide in CCl4 by means of hydrogen bonding. The ОН group of N-(2-hydroxy-3,8-diiodocyclooctyl)trifluoroacetamide participates in the formation of intramolecular hydrogen bond ОH···О=С, while chain dimers are formed due to interactions between the NH and С=О groups of the neighboring molecules. Due to the formation of the intramolecular bond, the dimers of N-(2-hydroxy-3,8-diiodocyclooctyl)trifluoroacetamide are energetically less stable than the chain dimer of N-(4-iodo-2,2,5,5-tetramethyltetrahydrofuran-3-yl)trifluoroacetamide.

Comprehension of the Effect of a Hydroxyl Group in Ancillary Ligand on Phosphorescent Property for Heteroleptic Ir(III) Complexes: A Computational Study Using Quantitative Prediction.

A new Ir(III) complex (dfpypya)2Ir(pic-OH) (2) is theoretically designed by introduction of a simple hydroxyl group into the ancillary ligand on the basis of (dfpypya)2Ir(pic) (1) with the aim to get the high-efficiency and stable blue-emitting phosphors, where dfpypya is 3-methyl-6-(2',4'-difluoro-pyridinato)pyridazine, pic is picolinate, and pic-OH is 3-hydroxypicolinic acid. The other configuration (dfpypya)2Ir(pic-OH)' (3) is also investigated to compare with 2. The difference between 2 and 3 is whether the intramolecular hydrogen bond is formed in the (dfpypya)2Ir(pic-OH). The quantum yield is determined by three different methods including the semiquantitative and quantitative methods. To quantitatively determine the quantum yield is still not an easy task to be completed. This work would provide some useful advices to select the suitable method to reliably evaluate the quantum yield. Complex 2 has larger quantum yield and more stability as compared with 1 and 3. The formation of intramolecular hydrogen bond would become a new method to design new phosphor with the desired properties.

Amyloid Beta Peptide Folding in Reverse Micelles.

Previously published experimental studies have suggested that when the 40-residue amyloid beta peptide is encapsulated in a reverse micelle, it folds into a structure that may nucleate amyloid fibril formation (Yeung, P. S.-W.; Axelsen, P. H. J. Am. Chem. Soc. 2012, 134, 6061 ). The factors that induce the formation of this structure have now been identified in a multi-microsecond simulation of the same reverse micelle system that was studied experimentally. Key features of the polypeptide-micelle interaction include the anchoring of a hydrophobic residue cluster into gaps in the reverse micelle surface, the formation of a beta turn at the anchor point that brings N- and C-terminal segments of the polypeptide into proximity, high ionic strength that promotes intramolecular hydrogen bond formation, and deformation of the reverse micelle surface to facilitate interactions with the surface along the entire length of the polypeptide. Together, these features cause the simulation-derived vibrational spectrum to red shift in a manner that reproduces the red-shift previously reported experimentally. On the basis of these findings, a new mechanism is proposed whereby membranes nucleate fibril formation and facilitate the in-register alignment of polypeptide strands that is characteristic of amyloid fibrils.