IR-Spectroscopic Study of Complex Formation of Nitrogen Oxides (NO, N2O) with Cationic Forms of Zeolites and the Reactivity of Adsorbed Species in CO and CH4 Oxidation

The formation of complexes and disproportionation of nitrogen oxides (NO, N2O) on cationic forms of LTA, FAU, and MOR zeolites was investigated by diffuse-reflectance IR spectroscopy. N2O is adsorbed on the samples under study in the molecular form and the frequencies of the first overtone of the stretching vibrations ν10–2 and the combination bands of the stretching vibrations with other vibrational modes for N2O complexes with cationic sites in zeolites (ν30–1 + ν10–1, ν10–1 + δ0–2) are more significantly influenced by the nature of the zeolite. The presence of several IR bands in the region of 2400–2600 cm−1 (the ν10–1 + δ0–2 transitions) for different zeolite types was explained by the availability of different localization sites for cations in these zeolites. The frequencies in this region also depend on the nature of the cation (its charge and radius). The data can be explained by the specific geometry of the N2O complex formed, presumably two-point adsorption of N2O on a cation and a neighboring oxygen atom of the framework. Adsorption of CO or CH4 on the samples with preliminarily adsorbed N2O at 20–180 °C does not result in any oxidation of these molecules. NO+ and N2O3 species formed by disproportionation of NO are capable of oxidizing CO and CH4 molecules to CO2, whereas NOx is reduced simultaneously to N2 or N2O. The peculiarities in the behavior of cationic forms of different zeolites with respect to adsorbed nitrogen oxides determined by different density and localization of cations have been established.

Retinal Vibrations in Bacteriorhodopsin are Mechanically Harmonic but Electrically Anharmonic: Evidence From Overtone and Combination Bands

Fundamental vibrations of the chromophore in the membrane protein bacteriorhodopsin (BR), a protonated Schiff base retinal, have been studied for decades, both by resonance Raman and by infrared (IR) difference spectroscopy. Such studies started comparing vibrational changes between the initial BR state (all-trans retinal) and the K intermediate (13-cis retinal), being later extended to the rest of intermediates. They contributed to our understanding of the proton-pumping mechanism of BR by exploiting the sensitivity of fundamental vibrational transitions of the retinal to its conformation. Here, we report on new bands in the 2,500 to 1,800 cm−1 region of the K-BR difference FT-IR spectrum. We show that the bands between 2,500 and 2,300 cm−1 originate from overtone and combination transitions from C-C stretches of the retinal. We assigned bands below 2,300 cm−1 to the combination of retinal C-C stretches with methyl rocks and with hydrogen-out-of-plane vibrations. Remarkably, experimental C-C overtone bands appeared at roughly twice the wavenumber of their fundamentals, with anharmonic mechanical constants ≤3.5 cm−1, and in some cases of ∼1 cm−1. Comparison of combination and fundamental bands indicates that most of the mechanical coupling constants are also very small. Despite the mechanical quasi-harmonicity of the C-C stretches, the area of their overtone bands was only ∼50 to ∼100 times smaller than of their fundamental bands. We concluded that electrical anharmonicity, the second mechanism giving intensity to overtone bands, must be particularly high for the retinal C-C stretches. We corroborated the assignments of negative bands in the K-BR difference FT-IR spectrum by ab initio anharmonic vibrational calculations of all-trans retinal in BR using a quantum-mechanics/molecular mechanics approach, reproducing reasonably well the small experimental anharmonic and coupling mechanical constants. Yet, and in spite accounting for both mechanical and electrical anharmonicities, the intensity of overtone C-C transitions was underestimated by a factor of 4–20, indicating room for improvement in state-of-the-art anharmonic vibrational calculations. The relatively intense overtone and combination bands of the retinal might open the possibility to detect retinal conformational changes too subtle to significantly affect fundamental transitions but leaving a footprint in overtone and combination transitions.

A Simple guide to complex world of overtone and combination bands: Theoretical simulation and interpretation of NIR spectra – summary of the workshop at NIR-2021 Beijing Conference

Between 18 and 21 October 2021, the 20th International Conference on NIR spectroscopy in Beijing took place. Despite this time being held as a virtual event, it was a highly successful symposium met with high interest from the wide audience – as evidenced by many excellent presentations, around which numerous vivid discussions developed. During the conference, four workshops were offered, focused at discussing few areas essential for NIR spectroscopy and its applications. Excellent workshops were provided by Professors Heinz Siesler, Hui Yan, Dolores Pérez-Marín and Tom Fearn, in which invaluable knowledge was shared with the participants of the conference. Among these renowned experts, I had the honour to offer my contribution with the workshop aimed at the physicochemical foundations of NIR spectroscopy, an area that seldom is exhaustively presented in the textbooks. The workshop aimed at shedding light on the complex world of overtone and combination bands and was met with a considerable interest from the participants. As many questions have been asked both during the dedicated Q&A session, as well as through other channels and private correspondence, I would like to provide a short recapitulation of the workshop in the form of this brief article. Some of the most essential ‘take home messages’, such as the origin of the intensity variation of the overtone bands and the famous ‘selection rule’ of the harmonic oscillator, among others will be briefly outlined here.

Anharmonicity and Spectra–Structure Correlations in MIR and NIR Spectra of Crystalline Menadione (Vitamin K3)

Mid-infrared (MIR) and near-infrared (NIR) spectra of crystalline menadione (vitamin K3) were measured and analyzed with aid of quantum chemical calculations. The calculations were carried out using the harmonic approach for the periodic model of crystal lattice and the anharmonic DVPT2 calculations applied for the single molecule model. The theoretical spectra accurately reconstructed the experimental ones permitting for reliable assignment of the MIR and NIR bands. For the first time, a detailed analysis of the NIR spectrum of a molecular system based on a naphthoquinone moiety was performed to elucidate the relationship between the chemical structure of menadione and the origin of the overtones and combination bands. In addition, the importance of these bands during interpretation of the MIR spectrum was demonstrated. The overtones and combination bands contribute to 46.4% of the total intensity of menadione in the range of 3600–2600 cm−1. Evidently, these bands play a key role in shaping of the C-H stretching region of MIR spectrum. We have shown also that the spectral regions without fundamentals may provide valuable structural information. For example, the theoretical calculations reliably reconstructed numerous overtones and combination bands in the 4000–3600 and 2800–1800 cm−1 ranges. These results, provide a comprehensive origin of the fundamentals, overtones and combination bands in the NIR and MIR spectra of menadione, and the relationship of these spectral features with the molecular structure.

Identification of DNA Bases and Their Cations in Astrochemical Environments: Computational Spectroscopy of Thymine as a Test Case

Increased importance of vibrational fingerprints in the identification of molecular systems, can be highlighted by the upcoming interstellar medium (ISM) observations by the James Webb Space Telescope, or in a context of other astrochemical environments as meteorites or exoplanets, Mars robotic missions, such as instruments on board of Perseverance rover. These observations can be supported by combination of laboratory experiments and theoretical calculations, essential to verify and predict the spectral assignments. Astrochemical laboratory simulations have shown that complex organic molecules (COMs) can be formed from simple species by vacuum ultraviolet or X-ray irradiation expanding interest in searching for organic biological and prebiotic compounds. In this work an example of nucleobase, thymine, is selected as a test case for highlighting the utility of computational spectroscopic methods in astrochemical studies. We consider mid-infrared (MIR) and near-infrared (NIR) vibrational spectra of neutral (T) and cationic (T+) thymine ground states, and vibrationally-resolved photoelectron (PE) spectra in the far UV range from 8.7 to 9.4 eV. The theoretical framework is based on anharmonic calculations including overtones and combination bands. The same anharmonic wavenumbers are applied into the simulations of vibrationally-resolved photoelectron spectra based on Franck-Condon computations. The infrared and vibrationally-resolved photoelectron spectra are compared with the available experimental counterparts to verify their accuracy and provide assignment of the observed transitions. Finally, reliable predictions of spectra, going beyond currently available experimental data, either dealing with energy ranges, resolution or temperature, which can support astrochemistry studies are provided.

Anharmonic DFT Study of Near-Infrared Spectra of Caffeine: Vibrational Analysis of the Second Overtones and Ternary Combinations

Anharmonic quantum chemical calculations were employed to simulate and interpret a near-infrared (NIR) spectrum of caffeine. First and second overtones, as well as binary and ternary combination bands, were obtained, accurately reproducing the lineshape of the experimental spectrum in the region of 10,000–4000 cm−1 (1000–2500 nm). The calculations enabled performing a detailed analysis of NIR spectra of caffeine, including weak bands due to the second overtones and ternary combinations. A highly convoluted nature of NIR spectrum of caffeine was unveiled, with numerous overlapping bands found beneath the observed spectral lineshape. To properly reflect that intrinsic complexity, the band assignments were provided in the form of heat maps presenting the contributions to the NIR spectrum from various kinds of vibrational transitions. These contributions were also quantitatively assessed in terms of the integral intensities. It was found that the combination bands provide the decisively dominant contributions to the NIR spectrum of caffeine. The first overtones gain significant importance between 6500–5500 cm−1, while the second overtones are meaningful in the higher wavenumber regions, particularly in the 10,000–7000 cm−1 region. The obtained detailed band assignments enabled deep interpretation of the absorption regions of caffeine identified in the literature as meaningful for analytical applications of NIR spectroscopy focused on quantitative analysis of caffeine content in drugs and natural products.

Retrieving Water Turbidity in Araucanian Lakes (South-Central Chile) Based on Multispectral Landsat Imagery

Remote sensing was used as an early alert tool for water clarity changes in five Araucanian Lakes in South-Central Chile. Turbidity records are scarce or unavailable over large and remote areas needed to fully understand the factors associated with turbidity, and their spatial-temporal representation remains a limitation. This work aimed to develop and validate empirical models to estimate values of turbidity from Landsat images and determine the spatial distribution of estimated turbidity in the selected Araucanian Lakes. Secchi disk depth measurements were linked with turbidity measurements to obtain a turbidity dataset. This in turn was used to develop and validate a set of empirical models to predict turbidity based on four single bands and 16 combination bands from 15 multispectral Landsat images. The best empirical models predicted turbidity over the range of 0.3–12.3 NTUs with RMSE values around 0.31–1.03 NTU, R2 (Index of Agreement IA) around 0.93–0.99 (0.85–0.97) and mean bias error (MBE) around (−0.36–0.44 NTU). Estimation maps to analyze the temporal-spatial turbidity variation in the lakes were constructed. Finally, it was found that the meteorological conditions may affect the variation of turbidity, mainly precipitation and wind speed. The data indicate that the turbidity has slightly increased in winter–spring. These models will be used in the future to reconstruct large datasets that allow analyzing transparency trends in those lakes.

Retinal vibrations in bacteriorhodopsin are mechanically harmonic but electronically anharmonic: evidence from overtone and combination bands

Vibrations of the chromophore in the membrane protein bacteriorhodopsin (BR), a protonated Schiff base retinal, have been studied for decades, both by resonance Raman and by infrared (IR) difference spectroscopy. In spite the light-induced IR difference spectrum between the K intermediate (13-cis retinal) and the initial BR state (all-trans retinal) being first published almost 40 years ago, we present here unreported bands in the 2500 to 1800 cm-1 region. We show that the bands between 2500 and 2300 cm-1 originate from overtone and combination transitions of retinal C-C stretches. We assigned some of the newly reported bands below 2300 cm-1 to the combination of retinal C-C stretches with methyl rocks and with hydrogen-out-of-plane vibrations. Remarkably, experimental C-C overtone bands appeared at roughly twice the wavenumber of their fundamentals, with anharmonic mechanical constants ≤ 3.5 cm-1, and in some cases of ≈ 1 cm-1. Comparison of combination and fundamental bands indicates that most of the mechanical coupling constants are also very small. Despite the mechanical quasi-harmonicity of the C-C stretches, the area of their overtone bands was only ≈50 to ≈100 times smaller than of their fundamental bands. We concluded that electronic anharmonicity, the second mechanism giving intensity to overtone bands, must be particularly high for the retinal C-C stretches. We corroborated the assignments of negative bands in the K-BR difference spectrum by ab initio anharmonic spectral calculations of all-trans retinal in BR, which also reproduced reasonably well the small experimental anharmonic and coupling mechanical constants. Yet, and in spite accounting for both mechanical and electronic anharmonicities, the intensity of overtone C-C transitions was underestimated by a factor of 4 to 20, indicating room for improvement in state-of-the-art anharmonic vibrational calculations.

Coherent vibrational dynamics reveals lattice anharmonicity in organic–inorganic halide perovskite nanocrystals

The halide ions of organic-inorganic hybrid perovskites can strongly influence the interaction between the central organic moiety and the inorganic metal halide octahedral units and thus their lattice vibrations. Here, we report the halide-ion-dependent vibrational coherences in formamidinium lead halide (FAPbX3, X = Br, I) perovskite nanocrystals (PNCs) via the combination of femtosecond pump–probe spectroscopy and density functional theory calculations. We find that the FAPbX3 PNCs generate halide-dependent coherent vibronic wave packets upon above-bandgap non-resonant excitation. More importantly, we observe several higher harmonics of the fundamental modes for FAPbI3 PNCs as compared to FAPbBr3 PNCs. This is likely due to the weaker interaction between the central FA moiety and the inorganic cage for FAPbI3 PNCs, and thus the PbI64− unit can vibrate more freely. This weakening reveals the intrinsic anharmonicity in the Pb-I framework, and thus facilitating the energy transfer into overtone and combination bands. These findings not only unveil the superior stability of Br–based PNCs over I–based PNCs but are also important for a better understanding of their electronic and polaronic properties.