2D Infrared Spectroscopy Research Articles

Force Fields for Deep Eutectic Mixtures: Application to Structure, Thermodynamics and 2D-Infrared Spectroscopy.

Parametrizing energy functions for ionic systems can be challenging. Here, the total energy function for an eutectic system consisting of water, SCN-, K+ and acetamide is improved vis-a-vis experimentally measured properties. Given the importance of electrostatic interactions, two different types of models are considered: the first (model M0) uses atom-centered multipole whereas the other two (models M1 and M2) are based on fluctuating minimal distributed charges (fMDCM) that respond to geometrical changes of SCN-. The Lennard-Jones parameters of the anion are adjusted to best reproduce experimentally known hydration free energies and densities, which are matched to within a few percent for the final models irrespective of the electrostatic model. Molecular dynamics simulations of the eutectic mixtures with varying water content (between 0 and 100%) yield radial distribution functions and frequency correlation functions for the CN-stretch vibration. Comparison with experiments indicates that models based on fMDCM are considerably more consistent than those using multipoles. Computed viscosities from models M1 and M2 are within 30% of measured values and their change with increasing water content is consistent with experiments. This is not the case for model M0.

Chemical and Biological Characterization of the Ethyl Acetate Fraction from the Red Sea Marine Sponge Hymedesmia sp.

Hymedesmiidae is one of the largest families of marine sponges and stands out as an exceptional source of variable metabolites with diverse biological activities. In this study, the ethyl acetate fraction (HE) of a Hymedesmia sp. marine sponge from the Red Sea, Egypt, was analyzed for the first time using Ultra-performance liquid chromatography electrospray ionization tandem mass spectrometry (UPLC-ESI-MS/MS) analysis. The analysis tentatively identified 29 compounds in this fraction, including the isolation and identification of six compounds (two pyrimidine nucleosides, one purine, and two pyrimidine bases in addition to one cerebroside) for the first time. The structures of the isolated compounds were established by 1D and 2D NMR (nuclear magnetic resonance), MS (mass spectrometry), and IR (infrared) spectroscopy. Furthermore, the cytotoxic, antioxidant, and antimicrobial activities of the ethyl acetate fraction were evaluated in vitro. The fraction exhibited strong DPPH scavenging activity with an IC50 of 78.7 µg/mL, compared to ascorbic acid as a positive control with an IC50 of 10.6 µg/mL. It also demonstrated significant cytotoxic activity with IC50 values of 13.5 µg/mL and 25.3 µg/mL against HCT-116 and HEP-2 cell lines, respectively, compared to vinblastine as a positive control with IC50 values of 2.34 µg/mL and 6.61 µg/mL against HCT-116 and HEP-2, respectively. Additionally, the ethyl acetate fraction displayed promising antibacterial activity against S. aureus with a MIC value of 62.5 µg/mL, compared to ciprofloxacin as a positive control with MIC values of 1.56 µg/mL for Gram-positive bacteria and 3.125 µg/mL for Gram-negative bacteria. It also exhibited activity against E. coli and P. aeruginosa with MIC values of 250 µg/mL and 500 µg/mL, respectively. Briefly, this is the first report on the biological activities and secondary metabolite content of the ethyl acetate fraction of Hymedesmia sp. marine sponge, emphasizing the potential for further research against resistant bacterial and fungal strains, as well as different cancer cell lines. The ethyl acetate fraction of Hymedesmia sp. is a promising source of safe and unique natural drugs with potential therapeutic and pharmaceutical benefits.

Strong H-bonding from Zeolite Bro̷nsted Acid Site to Water: Origin of the Broad IR Doublet.

Hydrogen bonding between water molecules and zeolite Bro̷nsted acid sites (BAS) has received much attention due to the significant influence of water on the adsorption and catalytic properties of these widely used porous materials. When a single water molecule is adsorbed at the BAS, the zeolite O-H stretch vibration decreases in frequency and splits into two extraordinarily broad bands peaked near 2500 and 2900 cm-1 in the infrared (IR) spectrum. This broad doublet feature is the predominant IR signature used to identify and interpret water-BAS H-bonding at low hydration levels, but the origin of the band splitting is not well understood. In this study, we used broadband two-dimensional infrared (2D IR) spectroscopy to investigate zeolite HZSM-5 prepared with a single water molecule per BAS. We find that the 2D IR spectrum is not explained by the most common interpretation of Fermi resonance coupling between the stretch and the bend of the BAS OH group, which predicts intense excited-state transitions that are absent from the experimental results. We present an alternative model of a double-well proton stretch potential, where the band splitting is caused by excited-state tunneling through the proton-transfer barrier. This one-dimensional model reproduces the basic experimental pattern of transition frequencies and amplitudes, suggesting that the doublet bands may originate from a highly anharmonic potential in which the excited state proton wave functions are delocalized over the H-bond between zeolite BAS and adsorbed H2O. Additional details about molecular orientation and coordination of the adsorbed water molecule are also resolved in the 2D IR spectroscopy.

Ground-state heterogeneity and vibrational energy redistribution in bacterial phytochrome observed with femtosecond 2D IR spectroscopy.

Phytochromes belong to a group of photoreceptor proteins containing a covalently bound biliverdin chromophore that inter-converts between two isomeric forms upon photoexcitation. The existence and stability of the photocycle products are largely determined by the protein sequence and the presence of conserved hydrogen-bonding interactions in the vicinity of the chromophore. The vibrational signatures of biliverdin, however, are often weak and obscured under more intense protein bands, limiting spectroscopic studies of its non-transient signals. In this study, we apply isotope-labeling techniques to isolate the vibrational bands from the protein-bound chromophore of the bacterial phytochrome from Deinococcus radiodurans. We elucidate the structure and ultrafast dynamics of the chromophore with 2D infra-red (IR) spectroscopy and molecular dynamics simulations. The carbonyl stretch vibrations of the pyrrole rings show the heterogeneous distribution of hydrogen-bonding structures, which exhibit distinct ultrafast relaxation dynamics. Moreover, we resolve a previously undetected 1678cm-1 band that is strongly coupled to the A- and D-ring of biliverdin and demonstrate the presence of complex vibrational redistribution pathways between the biliverdin modes with relaxation-assisted measurements of 2D IR cross peaks. In summary, we expect 2D IR spectroscopy to be useful in explaining how point mutations in the protein sequence affect the hydrogen-bonding structure around the chromophore and consequently its ability to photoisomerize to the light-activated states.

Metabolites Profiling and In Vitro Biological Characterization of Different Fractions of Cliona sp. Marine Sponge from the Red Sea Egypt.

Red Sea marine sponges are an important source of biologically active natural products. Therefore, the present study aimed to investigate, for the first time, the components of n-hexane, dichloromethane, and ethyl acetate fractions of Cliona sp. marine sponge collected from the Red Sea, Egypt using UPLC-ESI-MS/MS (Ultra-performance liquid chromatography electrospray ionization tandem mass spectrometry) analysis. The analysis revealed the tentative identification of 23, 16, and 24 compounds from the n-hexane, dichloromethane, and ethyl acetate fractions of Cliona sp., respectively. In addition, the examination of these fractions resulted in the isolation and identification of three sterols and one amino acid. The identification of the isolated compounds was confirmed by 1D and 2D NMR (Nuclear Magnetic Resonance), and MS (Mass spectrometry), and IR (Infrared) spectroscopy. The in vitro cytotoxic, antioxidant, and antimicrobial activities of the total ethanolic extract and its sub-fractions were also evaluated. Interestingly, the ethyl acetate fraction showed potent cytotoxic activity against colon (HCT-116) and human larynx carcinoma (HEP-2) cell lines with IC50 (Half-maximal Inhibitory Concentration) 6.11 ± 0.2 and 12.6 ± 0.9 µg/mL, respectively. However, the dichloromethane fraction showed strong antioxidant activity, with IC50 75.53 ± 3.41 µg/mL. Notably, the total ethanolic extract showed the strongest antibacterial activity against Staphylococcus aureus and Escherichia coli, with MIC (Minimum Inhibitory Concentration) 62.5 ± 0.82 and 125 ± 0.62 µg/mL, respectively, compared to other fractions. In conclusion, this is the first report on the secondary metabolites content and biological activities of Cliona sp. from the Red Sea, Egypt. It also highlights the need for further research on the most active fractions against various cancer cell lines and resistant bacterial and fungal strains. Cliona sp. extract and its fractions could be a potential source of novel and safe natural drugs with a wide range of medicinal and pharmaceutical applications.

Limits in enhancement factor in near-brewster angle reflection pump-probe two-dimensional infrared spectroscopy

In this work, we simulated 2D infrared spectroscopy (IR) spectroscopy in both transmission geometry and Brewster-angle reflection geometry. Light dispersion and the leakage of s-polarized light are considered in simulating the enhancement factor of the reflection mode. Our simulation shows that the dispersion in reflection will only alter the 2D IR lineshape slightly and can be corrected. Leaking spolarized light due to imperfectness of IR polarizers in the reflection geometry may limit the enhancement factor, but such limit is above what a typical experiment can reach. In the current experiment, the enhancement factor is mainly limited by the precision of incident angle, for which ordinary rotation stages are probably not adequate enough. Moreover, traditional energy ratio of pump and probe pulses, which is 9:1, may not be ideal and could be changed to 2:1 in the reflection geometry. Considering all the above factors, the enhancement on the order of 1000 is possible in the current experiment. Nevertheless, near-Brewster angle reflection will enhance both the signal and the noise caused by the signal itself, therefore this method only works if the noise is unrelated to the signal, particularly if the noise is caused by the fluctuation in the probe. It cannot improve the signal to noise ratio when the dominate noise is from the signal itself. The theoretical results here agree reasonably well with published experiment results and pave way for realizing even higher enhancement at nearer-Brewster angle.

Characterization of Acetonitrile Isotopologues as Vibrational Probes of Electrolytes.

Acetonitrile has emerged as a solvent candidate for novel electrolyte formulations in metal-ion batteries and supercapacitors. It features a bright local C≡N stretch vibrational mode whose infrared (IR) signature is sensitive to battery-relevant cations (Li+, Mg2+, Zn2+, Ca2+) both in pure form and in the presence of water admixture across a full possible range of concentrations from the dilute to the superconcentrated regime. Stationary and time-resolved IR spectroscopy thus emerges as a natural tool to study site-specific intermolecular interactions from the solvent perspective without introducing an extrinsic probe that perturbs solution morphology and may not represent the intrinsic dynamics in these electrolytes. The metal-coordinated acetonitrile, water-separated metal–acetonitrile pair, and free solvent each have a distinct vibrational signature that allows their unambiguous differentiation. The IR band frequency of the metal-coordinated acetonitrile depends on the ion charge density. To study the ion transport dynamics, it is necessary to differentiate energy-transfer processes from structural interconversions in these electrolytes. Isotope labeling the solvent is a necessary prerequisite to separate these processes. We discuss the design principles and choice of the CD313CN label and characterize its vibrational spectroscopy in these electrolytes. The Fermi resonance between 13C≡N and C–D stretches complicates the spectral response but does not prevent its effective utilization. Time-resolved two-dimensional (2D) IR spectroscopy can be performed on a mixture of acetonitrile isotopologues and much can be learned about the structural dynamics of various species in these formulations.

Transparent window 2D IR spectroscopy of proteins.

Proteins are complex, heterogeneous macromolecules that exist as ensembles of interconverting states on a complex energy landscape. A complete, molecular-level understanding of their function requires experimental tools to characterize them with high spatial and temporal precision. Infrared (IR) spectroscopy has an inherently fast time scale that can capture all states and their dynamics with, in principle, bond-specific spatial resolution. Two-dimensional (2D) IR methods that provide richer information are becoming more routine but remain challenging to apply to proteins. Spectral congestion typically prevents selective investigation of native vibrations; however, the problem can be overcome by site-specific introduction of amino acid side chains that have vibrational groups with frequencies in the "transparent window" of protein spectra. This Perspective provides an overview of the history and recent progress in the development of transparent window 2D IR of proteins.

2D IR correlation spectroscopy and chemometric methods in gastric cancer diagnosis

The aim of this paper was to find a methodology to identify the specific biochemical characteristics of gastric malignant tissues in different stages using 2DIR correlation spectroscopy and chemometric methods. For this, a group of 15 patients in stage 3 and 4a of gastric cancer evolution were used as subjects. From every patient, 5 pairs of normal and malignant tissues were collected and investigated just after surgical rejection, by infrared spectroscopy (IR), principal component analysis (PCA) and two dimensional IR correlation spectroscopy (2D-COS). The spectral differences could be correlated with the modified molecular structure of proteins and lipids from the two tissue types, and with the variation in their glycogen content. A discrimination between the stage of the cancer evolution was not possible through simple IR spectroscopy, therefore PCA analysis was used. However, PCA alone did not give a clear discrimination between normal and malignant tissue, because the scores of the normal and cancer samples were partial overlapped. By 2D-COS we were able to obtain additional information about the structural changes. Although, synchronous spectra look similar for different stages of cancer evolution, the asynchronous spectra allowed a clear distinction between them. Moreover, using the Noda’s rules, the sequential order of bands evolution was obtained. Following the results we can conclude that this technique may be suitable as a screening method to discriminate the stage of the cancer evolution and also for establishing the sequences of the variation of different structural entities.

2D-IR studies of cyanamides (NCN) as spectroscopic reporters of dynamics in biomolecules: Uncovering the origin of mysterious peaks.

Cyanamides (NCN) have been shown to have a larger transition dipole strength than cyano-probes. In addition, they have similar structural characteristics and vibrational lifetimes to the azido-group, suggesting their utility as infrared (IR) spectroscopic reporters for structural dynamics in biomolecules. To access the efficacy of NCN as an IR probe to capture the changes in the local environment, several model systems were evaluated via 2D IR spectroscopy. Previous work by Cho [G. Lee, D. Kossowska, J. Lim, S. Kim, H. Han, K. Kwak, and M. Cho, J. Phys. Chem. B 122(14), 4035-4044 (2018)] showed that phenylalanine analogues containing NCN show strong anharmonic coupling that can complicate the interpretation of structural dynamics. However, when NCN is embedded in 5-membered ring scaffolds, as in N-cyanomaleimide and N-cyanosuccinimide, a unique band structure is observed in the 2D IR spectrum that is not predicted by simple anharmonic frequency calculations. Further investigation indicated that electron delocalization plays a role in the origins of the band structure. In particular, the origin of the lower frequency transitions is likely a result of direct interaction with the solvent.

Ultrafast Intermolecular Vibrational Energy Transfer in Hexahydro-1,3,5-trinitro-1,3,5-triazine in Molecular Crystal by 2D IR Spectroscopy

Cyclic nitramine hexahydro-1,3,5-trinitro-s-triazine (HHTT) is an important energetic molecule with a variety of applications. In this work, structural dynamics and vibrational-energy transfer dynamics of HHTT were investigated using steady-state infrared (IR), femtosecond time-resolved IR, and two-dimensional (2D) IR spectroscopic methods. Two different structural forms of HHTT (isolated molecules dissolved in DMSO and microcrystal dispersed in paraffin oil) were examined using the NO2 asymmetric stretching mode as a structural marker. Both intra- and intermolecular vibrational energy transfers were observed in HHTT microcrystal, where the well-known α-conformation was retained. However, less perfect α-HHTT species was found in DMSO. An intermolecular energy dissipation pathway was found to be related to Davydov splitting in the microcrystal form of HHTT, which originates from intermolecular interactions (e.g., electrostatic and hydrogen bonds). Experimental results were supported by quantum-chemistry computations. In addition, both vibrational excited-state relaxation and vibrational energy-transfer processes were found to be more efficient in HHTT microcrystal than in the solvated form. Our work provides a chemical-bond level of insight into the nitro group-containing energetic materials.

Rational Design of an Acetylenic Infrared Probe with Enhanced Dipole Strength and Increased Vibrational Lifetime.

Developing infrared (IR) probes is of great interest in biomolecular imaging and spectroscopy. We report our attempt to improve the IR properties of alkyne-derivatized compounds. The vibrational properties of the alkyne (C≡C) stretch mode of aromatic silylacetylene 1 and aliphatic silylacetylene 2 were studied using Fourier transform infrared and femtosecond IR pump-probe spectroscopies. We find that the insertion of silicon at the position adjacent to the alkyne group, separating it from the compound's main body, causes an approximately 10-fold increase in the dipole strength of the C≡C stretch mode and a lengthening of its vibrational lifetime from 5.6 ps for the acetylenic compound without a silicon atom acting like a thermal insulator to 50.6 and 50.4 ps for 1 and 2, respectively. The enhanced dipole strength and the increased lifetime of 1 allowed us to measure the 2D IR spectra for long waiting times up to 450 ps, which suggests that the dynamic observation range of 2D IR spectroscopy with these IR probes can be extended into the subnanosecond range where protein skeletal movements occur.

Site-Specific 1D and 2D IR Spectroscopy to Characterize the Conformations and Dynamics of Protein Molecular Recognition.

Proteins exist as ensembles of interconverting states on a complex energy landscape. A complete, molecular-level understanding of their function requires knowledge of the populated states and thus the experimental tools to characterize them. Infrared (IR) spectroscopy has an inherently fast time scale that can capture all states and their dynamics with, in principle, bond-specific spatial resolution, and 2D IR methods that provide richer information are becoming more routine. Although application of IR spectroscopy for investigation of proteins is challenged by spectral congestion, the issue can be overcome by site-specific introduction of amino acid side chains that have IR probe groups with frequency-resolved absorptions, which furthermore enables selective characterization of different locations in proteins. Here, we briefly introduce the biophysical methods and summarize the current progress toward the study of proteins. We then describe our efforts to apply site-specific 1D and 2D IR spectroscopy toward elucidation of protein conformations and dynamics to investigate their involvement in protein molecular recognition, in particular mediated by dynamic complexes: plastocyanin and its binding partner cytochrome f, cytochrome P450s and substrates or redox partners, and Src homology 3 domains and proline-rich peptide motifs. We highlight the advantages of frequency-resolved probes to characterize specific, local sites in proteins and uncover variation among different locations, as well as the advantage of the fast time scale of IR spectroscopy to detect rapidly interconverting states. In addition, we illustrate the greater insight provided by 2D methods and discuss potential routes for further advancement of the field of biomolecular 2D IR spectroscopy.

Ultrafast structural molecular dynamics investigated with 2D infrared spectroscopy methods.

Ultrafast, multi-dimensional infrared (IR) spectroscopy has been advanced in recent years to a versatile analytical tool with a broad range of applications to elucidate molecular structure on ultrafast timescales, and it can be used for samples in a many different environments. Following a short and general introduction on the benefits of 2D IR spectroscopy, the first part of this chapter contains a brief discussion on basic descriptions and conceptual considerations of 2D IR spectroscopy. Outstanding classical applications of 2D IR are used afterwards to highlight the strengths and basic applicability of the method. This includes the identification of vibrational coupling in molecules, characterization of spectral diffusion dynamics, chemical exchange of chemical bond formation and breaking, as well as dynamics of intra- and intermolecular energy transfer for molecules in bulk solution and thin films. In the second part, several important, recently developed variants and new applications of 2D IR spectroscopy are introduced. These methods focus on (i) applications to molecules under two- and three-dimensional confinement, (ii) the combination of 2D IR with electrochemistry, (iii) ultrafast 2D IR in conjunction with diffraction-limited microscopy, (iv) several variants of non-equilibrium 2D IR spectroscopy such as transient 2D IR and 3D IR, and (v) extensions of the pump and probe spectral regions for multi-dimensional vibrational spectroscopy towards mixed vibrational-electronic spectroscopies. In light of these examples, the important open scientific and conceptual questions with regard to intra- and intermolecular dynamics are highlighted. Such questions can be tackled with the existing arsenal of experimental variants of 2D IR spectroscopy to promote the understanding of fundamentally new aspects in chemistry, biology and materials science. The final part of the chapter introduces several concepts of currently performed technical developments, which aim at exploiting 2D IR spectroscopy as an analytical tool. Such developments embrace the combination of 2D IR spectroscopy and plasmonic spectroscopy for ultrasensitive analytics, merging 2D IR spectroscopy with ultra-high-resolution microscopy (nanoscopy), future variants of transient 2D IR methods, or 2D IR in conjunction with microfluidics. It is expected that these techniques will allow for groundbreaking research in many new areas of natural sciences.

Direct quantum mechanical/molecular mechanical simulations of two-dimensional vibrational responses: N-methylacetamide in water

Multidimensional infrared (IR) spectroscopy has emerged as a viable tool to study molecular structure and dynamics in condensed phases, and the third-order vibrational response function is the central quantity underlying various nonlinear IR spectroscopic techniques, such as pump–probe, photon echo and two-dimensional (2D) IR spectroscopy. In this paper, a new computational method is presented that calculates this nonlinear response function in the classical limit from a series of classical molecular dynamics (MD) simulations, employing a quantum mechanical/molecular mechanical (QM/MM) force field. The method relies on the stability matrix formalism where the dipole–dipole quantum mechanical commutators appearing in the exact quantum response function are replaced by the corresponding Poisson brackets. We present the formulation and computational algorithm of the method for both the classical and the QM/MM force fields and apply it to the 2D IR spectroscopy of carbon monoxide (CO) and N-methylacetamide (NMA), each solvated in a water cluster. The conventional classical force field with harmonic bond potentials is shown to be incapable of producing a reliable 2D IR signal because intramolecular vibrational anharmonicity, essential to the production of the nonlinear signal, is absent in such a model. The QM/MM force field, on the other hand, produces distinct 2D spectra for the NMA and CO systems with clear vertical splitting and cross peaks, reflecting the vibrational anharmonicities and the vibrational couplings between the underlying vibrational modes, respectively. In the NMA spectrum, the coupling between the amide I and II modes is also well reproduced. While attaining the converged spectrum is found to be challenging with this method, with an adequate amount of computing it can be straightforwardly applied to new systems containing multiple chromophores with little modeling effort, and therefore it would be useful in understanding the multimode 2D IR spectrum of complex molecular systems.

Generation of narrowband subpicosecond mid-infrared pulses via difference frequency mixing of chirped near-infrared pulses

The widely used setup for the generation of femtosecond infrared (IR) pulses based on parametric amplifiers (OPAs) and difference frequency mixing (DFM) is extended to produce tunable narrowband mid-IR pulses. The insertion of pairs of silicon prisms after the OPA induces adjustable chirp, which leads to the generation of narrowband pulses in the DFM stage. Rapid tunability of the mid-IR wavelength via a computer-controllable actuator can be achieved in a range of approximately 200 cm(-1) at a bandwidth of the IR-pulses between approximately 15 and approximately 50 cm(-1) and pulse energies up to 0.4 microJ. The narrowband mid-IR pulses are well suited for 2D IR spectroscopy.

Two-dimensional infrared correlation spectroscopy studies on secondary structures and hydrogen bondings of side chains of proteins

This review paper reports usefulness of two-dimensional (2D) correlation spectroscopy in analyzing infrared (IR) spectra of proteins in aqueous solutions. In the 2D approach, spectral peaks are spread over the second dimension, thereby simplifying the visualization of complex spectra consisting of many overlapped bands, and enhancing spectral resolution. 2D correlation spectroscopy has a powerful deconvolution ability for highly overlapped amide I, amide II, and amide III bands of proteins, enabling these bands to be assigned to various secondary structures. It also provides the specific order of the spectral intensity changes taking place during the measurement on the value of controlling variable affecting the spectra. Therefore, one can monitor the order of secondary structure variations in proteins by using 2D IR correlation spectroscopy. 2D correlation spectroscopy also provides new insight into the hydrogen bondings of side chains of proteins. In this review the principles and advantages of 2D correlation spectroscopy are outlined first and then three examples of the applications of 2D IR spectroscopy to protein research are presented.