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

Computational spectroscopy of complex systems

Numerous linear and non-linear spectroscopic techniques have been developed to elucidate structural and functional information of complex systems ranging from natural systems, such as proteins and light-harvesting systems, to synthetic systems, such as solar cell materials and light-emitting diodes. The obtained experimental data can be challenging to interpret due to the complexity and potential overlapping spectral signatures. Therefore, computational spectroscopy plays a crucial role in the interpretation and understanding of spectral observables of complex systems. Computational modeling of various spectroscopic techniques has seen significant developments in the past decade, when it comes to the systems that can be addressed, the size and complexity of the sample types, the accuracy of the methods, and the spectroscopic techniques that can be addressed. In this Perspective, I will review the computational spectroscopy methods that have been developed and applied for infrared and visible spectroscopies in the condensed phase. I will discuss some of the questions that this has allowed answering. Finally, I will discuss current and future challenges and how these may be addressed.

Optical spectra in the condensed phase: Capturing anharmonic and vibronic features using dynamic and static approaches

Simulating optical spectra in the condensed phase remains a challenge for theory due to the need to capture spectral signatures arising from anharmonicity and dynamical effects, such as vibronic progressions and asymmetry. As such, numerous simulation methods have been developed that invoke different approximations and vary in their ability to capture different physical regimes. Here, we use several models of chromophores in the condensed phase and ab initio molecular dynamics simulations to rigorously assess the applicability of methods to simulate optical absorption spectra. Specifically, we focus on the ensemble scheme, which can address anharmonic potential energy surfaces but relies on the applicability of extreme nuclear-electronic time scale separation; the Franck-Condon method, which includes dynamical effects but generally only at the harmonic level; and the recently introduced ensemble zero-temperature Franck-Condon approach, which straddles these limits. We also devote particular attention to the performance of methods derived from a cumulant expansion of the energy gap fluctuations and test the ability to approximate the requisite time correlation functions using classical dynamics with quantum correction factors. These results provide insights as to when these methods are applicable and able to capture the features of condensed phase spectra qualitatively and, in some cases, quantitatively across a range of regimes.

Development and single dose clinical pharmacokinetics investigation of novel zein assisted- alpha lipoic acid nanoencapsulation of vardenafil

The aim of this study was to utilize the biocompatibility of the natural ingredients zein and alpha lipoic acid (ALA) as a novel nanosphere matrix formulation that encapsulates vardenafil (VRD) for improved drug delivery and bioavailability. Three formulations were prepared using zein: ALA ratio of 1:1, 2:1 and 3:1 by liquid-liquid phase separation method. Physicochemical characterization and in vitro diffusion evaluation were carried out for the prepared formulations. A single dose clinical pharmacokinetic study was carried out for the selected formulation. Results revealed VRD formulations showed particle size of 836.7 ± 191.3, 179.8 ± 18.4 and 147.3 ± 18.1 nm and encapsulation efficiency of 55.72 ± 4.36, 65.33 ± 7.82 and 69.38 ± 6.83% for F1, F2 and F3, respectively. Single dose clinical pharmacokinetic results, in healthy human volunteers, showed improved VRD bioavailability by 2.5 folds from nanosphere formula (F3) compared with the marketed tablets. The formulation of novel zein-ALA nanospheres offers the possibility for application of a biocompatible nano-carrier system in drug delivery for improved drug delivery and efficacy.

Two-Dimensional Infrared Spectroscopy Reveals Cosolvent-Composition-Dependent Crossover in Intermolecular Hydrogen-Bond Dynamics

Cosolvents have versatile composition-dependent applications in chemistry and biology. The simultaneous presence of hydrophobic and hydrophilic groups in dimethyl sulfoxide (DMSO), an industrially important amphiphilic cosolvent, when combined with the unique properties of water, plays key roles in the diverse fields of pharmacology, cryoprotection, and cell biology. Moreover, molecules dissolved in aqueous DMSO exhibit an anomalous concentration-dependent nonmonotonic behavior in stability and activity near a critical DMSO mole fraction of 0.15. An experimental identification of the origin of this anomaly can lead to newer chemical and biological applications. We report a direct spectroscopic observation of the anomalous behavior using ultrafast two-dimensional infrared spectroscopy experiments. Our results demonstrate the cosolvent-concentration-dependent nonmonotonicity arises from nonidentical mechanisms in ultrafast hydrogen-bond-exchange dynamics of water above and below the critical cosolvent concentration. Comparison of experimental and theoretical results provides a molecular-level mechanistic understanding: a distinct difference in the stabilization of the solute through dynamic solute-solvent interactions is the key to the anomalous behavior.

Broadband two dimensional infrared spectroscopy of cyclic amide 2-Pyrrolidinone

In the past one-and-a-half decade there has been a significant methodological and technological development of two dimensional infrared (2DIR) spectroscopy, which unfolds many underlying physical and chemical processes of complex molecules, especially for biological molecules.

Ester carbonyl vibration as a sensitive probe of protein local electric field

The ability to quantify the local electrostatic environment of proteins and protein/peptide assemblies is key to gaining a microscopic understanding of many biological interactions and processes. Herein, we show that the ester carbonyl stretching vibration of two non-natural amino acids, L-aspartic acid 4-methyl ester and L-glutamic acid 5-methyl ester, is a convenient and sensitive probe in this regard, since its frequency correlates linearly with the local electrostatic field for both hydrogen-bonding and non-hydrogen-bonding environments. We expect that the resultant frequency-electric-field map will find use in various applications. Furthermore, we show that, when situated in a non-hydrogen-bonding environment, this probe can also be used to measure the local dielectric constant (ε). For example, its application to amyloid fibrils formed by Aβ(16-22) revealed that the interior of such β-sheet assemblies has an ε value of approximately 5.6.

Discriminating trpzip2 and trpzip4 peptides' folding landscape using the two-dimensional infrared spectroscopy: a simulation study

We analyzed, based on the theoretical spectroscopic modeling, how the differences in the folding landscapes of two β-hairpin peptides trpzip2 and trpzip4 are reflected in their thermal unfolding infrared measurements. The isotope-edited equilibrium FTIR and two dimensional infrared spectra of the two peptides were calculated, using the nonlinear exciton propagation method, at a series of temperatures. The spectra calculations were based on the configuration distributions generated using the GB(OBC) implicit solvent MD simulation and the integrated tempering sampling technique. Conformational analysis revealed the different local thermal stabilities for these two peptides, which suggested the different folding landscapes. Our study further suggested that the ellipticities of the isotope peaks in the coherent IR signals are more sensitive to these local stability differences compared with other spectral features such as the peak intensities. Our technique can thus be combined with the relevant experimental measurements to achieve a better understanding of the peptide folding behaviors.

pH-Independence of trialanine and the effects of termini blocking in short peptides: a combined vibrational, NMR, UVCD, and molecular dynamics study

Several lines of evidence now well establish that unfolded peptides in general, and alanine in specific, have an intrinsic preference for the polyproline II (pPII) conformation. Investigation of local order in the unfolded state is, however, complicated by experimental limitations and the inherent dynamics of the system, which has in some cases yielded inconsistent results from different types of experiments. One method of studying these systems is the use of short model peptides, and specifically short alanine peptides, known for predominantly sampling pPII structure in aqueous solution. Recently, He et al. ( J. Am. Chem. Soc. 2012 , 134 , 1571 - 1576 ) proposed that unblocked tripeptides may not be suitable models for studying conformational propensities in unfolded peptides due to the presence of end effect, that is, electrostatic interactions between investigated amino acid residues and terminal charges. To determine whether changing the protonation states of the N- and C-termini influence the conformational manifold of the central amino acid residue in tripeptides, we have examined the pH-dependence of unblocked trialanine and the conformational preferences of alanine in the alanine dipeptide. To this end, we measured and globally analyzed amide I' band profiles and NMR J-coupling constants. We described conformational distributions as the superposition of two-dimensional Gaussian distributions assignable to specific subspaces of the Ramachandran plot. Results show that the conformational ensemble of trialanine as a whole, and the pPII content (χpPII = 0.84) in particular, remains practically unaffected by changing the protonation state. We found that compared to trialanine, the alanine dipeptide has slightly lower pPII content (χpPII = 0.74) and an ensemble more reminiscent of the unblocked Gly-Ala-Gly model peptide. In addition, a two-state thermodynamic analysis of the conformational sensitive Δε(T) and (3)J(H(N)H(α))(T) data obtained from electronic circular dichroism and H NMR spectra indicate that the free energy landscape of trialanine is similar in all protonation states. MD simulations for the investigated peptides corroborate this notion and show further that the hydration shell around unblocked trialanine is unaffected by the protonation/deprotonation of the C-terminal group. In contrast, the alanine dipeptide shows a reduced water density around the central residue as well as a less ordered hydration shell, which decreases the pPII propensity and reduces the lifetime of sampled conformations.

A peptide's perspective of water dynamics

This Perspective is focused on amide groups of peptides interacting with water. The 2D IR spectroscopy has already enabled structural aspects of the peptide backbone to be determined through its ability to measure the coupling between different amide-I modes. Here we describe why nonlinear IR is emerging as the method of choice to examine the fast components of the water dynamics near peptides and how isotopically edited peptide links can be used to probe the local water at a residue level in proteins. This type of research necessarily involves an intimate mix of theory and experiment. The description of the results is underpinned by relatively well established quantum-statistical theories that describe the important manifestations of peptide vibrational frequency fluctuations.

Solvent-dependent spectral diffusion in a hydrogen bonded "vibrational aggregate"

Two-dimensional infrared spectroscopy (2DIR) is used to measure the viscosity-dependent spectral diffusion of a model vibrational probe, Mn(2)(CO)(10) (dimanganese decacarbonyl, DMDC), in a series of alcohols with time scales ranging from 2.67 ps in methanol to 5.33 ps in 1-hexanol. Alcohol-alkane solvent mixtures were found to produce indistinguishable linear IR spectra, while still demonstrating viscosity-dependent spectral diffusion. Using a vibrational exciton model to characterize the inhomogeneous energy landscape, several analogies emerge with multichromophoric electronic systems, such as J-aggregates and light-harvesting protein complexes. An excitonic, local vibrational mode Hamiltonian parametrized to reproduce the vibrational structure of DMDC serves as a starting point from which site energies (i.e., local carbonyl frequencies) are given Gaussian distributed disorder. The model gives excellent agreement with both the linear IR spectrum and the inhomogeneous widths extracted from 2DIR, indicating the system can be considered to be a "vibrational aggregate." This model naturally leads to exchange narrowing due to disorder-induced exciton localization, producing line widths consistent with our 1D and 2D measurements. Further, the diagonal disorder alone effectively reduces the molecular symmetry, leading to the appearance of Raman bands in the IR spectrum in accord with the measurements. Here, we show that the static inhomogeneity of the excitonic model with disorder successfully captures the essential details of the 1D spectrum while predicting the degree of IR activity of forbidden modes as well as the inhomogeneous widths and relative magnitudes of the transition moments.

Melting of a beta-hairpin peptide using isotope-edited 2D IR spectroscopy and simulations

Isotope-edited two-dimensional infrared spectroscopy has been used to characterize the conformational heterogeneity of the beta-hairpin peptide TrpZip2 (TZ2) across its thermal unfolding transition. Four isotopologues were synthesized to probe hydrogen bonding and solvent exposure of the beta-turn (K8), the N-terminus (S1), and the midstrand region (T10 and T3T10). Isotope-shifts, 2D lineshapes, and other spectral changes to the amide I 2D IR spectra of labeled TZ2 isotopologues were observed as a function of temperature. Data were interpreted on the basis of structure-based spectroscopic modeling of conformers obtained from extensive molecular dynamics simulations. The K8 spectra reveal two unique turn geometries, the type I' beta-turn observed in the NMR structure, and a less populated disordered or bulged loop. The data indicate that structures at low temperature resemble the folded NMR structure with typical cross-strand hydrogen bonds, although with a subpopulation of misformed turns. As the temperature is raised from 25 to 85 degrees C, the fraction of population with a type I' turn increases, but the termini also fray. Hydrogen bonding contacts in the midstrand region remain at all temperatures although with increasing thermal disorder. Our data show no evidence of an extended chain or random coil state for the TZ2 peptide at any temperature. The methods demonstrated here offer an approach to characterizing conformational variation within the folded or unfolded states of proteins and peptides.

The effects of alpha-helical structure and cyanylated cysteine on each other

β-Thiocyanatoalanine, or cyanylated cysteine, is an artificial amino acid that can be introduced at solvent-exposed cysteine residues in proteins via chemical modification. Its facile post-translational synthesis means that it may find broad use in large protein systems as a probe of site-specific structure and dynamics. The C≡N stretching vibration of this artificial side chain provides an isolated infrared chromophore. To test both the perturbative effect of this side chain on local secondary structure and its sensitivity to structural changes, three variants of a model water-soluble alanine-repeat helix were synthesized containing cyanylated cysteine at different sites. The cyanylated cysteine side chain is shown to destabilize, but not completely disrupt, the helical structure of the folded peptide when substituted for alanine. In addition, the C≡N stretching bandwidth of the artificial side chain is sensitive to the helix−coil structural transition. These model system results indicate that cyanylated cysteine can be placed into protein sequences with a native helical propensity without destroying the helix, and further that the CN probe may be able to report local helix formation events even when it is water-exposed in both the ordered and disordered conformational states. These results indicate that cyanylated cysteine could be a widely useful probe of structure-forming events in proteins with large in vitro structural distributions.

2D IR provides evidence for mobile water molecules in beta-amyloid fibrils

The motion of water molecules close to amide groups causes their vibrational frequencies to vary rapidly in time. These variations are uniquely sensed by 2-dimensional infrared spectroscopy (2D IR). Here, it is proposed from 2-dimensional experiments on fibrils of amyloid beta (Abeta)40 that there are water molecules in the fibrils. The spatial locations of the water (D(2)O) were inferred from the responses of 18 amide modes of Abeta40 labeled with (13)C = (18)O. Fast frequency variations were found for residues L17 and V18 and for the apposed residues L34 and V36, suggesting cavities or channels containing mobile water molecules can form between the 2 sheets. Spectroscopic analysis showed that there are 1.2 water molecules per strand in the fibrils. The (13)C = (18)O substitution of 1 residue per strand creates a linear array of isotopologs along the fibril axis that manifests clearly identifiable vibrational transitions. Here, it is shown from the distributions of amide-I' vibrational frequencies that the regularity of these chains is strongly residue dependent and in most cases the distorted regions are also those associated with the putative mobile water molecules. It is proposed that Abeta40 fibrils contain structurally significant mobile water molecules within the intersheet region.

Applications of 2D IR spectroscopy to peptides, proteins, and hydrogen-bond dynamics

Following a survey of 2D IR principles, this article describes recent experiments on the hydrogen-bond dynamics of small ions, amide-I modes, nitrile probes, peptides, reverse transcriptase inhibitors, and amyloid fibrils.

2D IR photon echo spectroscopy reveals hydrogen bond dynamics of aromatic nitriles

The CN vibrations of two aromatic nitriles, cinnamonitrile, PhCH=CH-CN and benzonitrile, PhCN, representative of components of common enzyme inhibitors, are examined by two dimensional infrared spectroscopy. In methanol, these spectra display cross peaks between the two CN components whose evolution exposes the few picosecond (4.5 ps for CIN and 5.3 ps for BN) equilibrium dynamics of hydrogen bond making and breaking. The main features of the 2D IR spectra are reproduced by simulations only with exchange incorporated. The lowest free energy state is the non-hydrogen bonded form. Both alkyl and aryl nitriles have now shown this picosecond exchange process.

Determining transition-state geometries in liquids using 2D-IR

Many properties of chemical reactions are determined by the transition state connecting reactant and product, yet it is difficult to directly obtain any information about these short-lived structures in liquids. We show that two-dimensional infrared (2D-IR) spectroscopy can provide direct information about transition states by tracking the transformation of vibrational modes as a molecule crossed a transition state. We successfully monitored a simple chemical reaction, the fluxional rearrangement of Fe(CO)5, in which the exchange of axial and equatorial CO ligands causes an exchange of vibrational energy between the normal modes of the molecule. This energy transfer provides direct evidence regarding the time scale, transition state, and mechanism of the reaction.