Justyna Grabska

Temperature Drift of Conformational Equilibria of Butyl Alcohols Studied by Near-Infrared Spectroscopy and Fully Anharmonic DFT

Conformational isomerism of aliphatic alcohols with respect to the internal rotation of C-O(H) group and its impact on near-infrared (NIR) spectra has been known in the literature. However, no attempt has ever been made to investigate systematically whether and how the conformational flexibility of the aliphatic chain determines the observed NIR data of aliphatic alcohols. In the present study NIR spectra of four kinds of butyl alcohols, 1-butanol, 2-butanol, isobutanol, and tert-butyl alcohol, were investigated in diluted (0.1 M) CCl4 solutions. The experimental NIR spectra of butyl alcohols were accurately reproduced and explained in a fully anharmonic DFT study by means of generalized second-order vibrational perturbation theory (GVPT2). Entire conformational populations were taken into account in each case. On the basis of the theoretical study, influences of conformational flexibility with respect to internal rotations not only about the C-O bond, but also about the C-C bonds have been well evidenced in the experimental spectra. The conformational isomerism affects significantly the shape of NIR spectra. The temperature-dependent NIR spectra of butyl alcohols show changes in the band shape and a blue-shift of the overtone band due to the stretching mode of free OH group, and its intensity decreases with increasing temperature. These effects can be closely monitored by two-dimensional correlation spectroscopy (2D-COS). In this work, the experimental 2D-COS patterns have been successfully reproduced, based on DFT calculated NIR spectra of conformational isomers of the studied molecules and their Boltzmann coefficients over the corresponding temperature range. Thus, the experimentally observed effects are fully reflected in the DFT study, which leads to the conclusion that the main factor in the temperature-dependent spectral changes of 2νOH band of aliphatic alcohols in the diluted phase, where no self-association occurs, is played by the changes in the relative population of their conformational isomers.

Correlations between Structure and Near-Infrared Spectra of Saturated and Unsaturated Carboxylic Acids. Insight from Anharmonic Density Functional Theory Calculations

By near-infrared (NIR) spectroscopy and anharmonic density functional theory (DFT) calculations, we investigate five kinds of saturated and unsaturated carboxylic acids belonging to the group of short-chain fatty acids: propionic acid, butyric acid, acrylic acid, crotonic acid, and vinylacetic acid. The experimental NIR spectra of these five kinds of carboxylic acids are reproduced by quantum chemical calculations in a broad spectral region of 7500-4000 cm-1 and for a wide range of concentrations. By employing anharmonic GVPT2 calculations on DFT level, a detailed interpretation of experimental spectra is achieved, elucidating structure-spectra correlations of these molecules in the NIR region. We emphasize the spectral features due to saturated and unsaturated alkyl chains, the location of a C═C bond within the alkyl chain, and the dimerization of carboxylic acids. In particular, the existence of a terminal C═C bond leads to the appearance of highly specific NIR bands. These pronounced bands are located at wavenumbers where no overlapping with other structure-specific bands occurs, thus making them good structural markers. Most of the spectral differences between these two groups of molecules remain subtle, and would be difficult to reliably ascribe without quantum chemically calculated NIR spectra. Moreover, anharmonic DFT calculations provide insights on the manifestation of hydrogen bonding through distinctive spectral features corresponding to cyclic dimers. The resulting spectral baseline elevation is common for all five investigated carboxylic acids, and remains consistent with previous results on acetic acid.

Influence of Non-fundamental Modes on Mid-infrared Spectra: Anharmonic DFT Study of Aliphatic Ethers

Fundamental and non-fundamental vibrational modes, first overtones, and binary combination modes of selected aliphatic ethers (di-n-propylether, di-iso-propylether, n-butylmethyl ether, n-butylethyl ether, di-n-butyl ether, tert-buytlmethyl ether, and tert-amylmethyl ether) were modeled in a fully anharmonic generalized second-order vibrational perturbation theory (GVPT2) approach on the DFT-B2PLYP/SNST level. The modeling procedure of theoretical line shapes took into account conformational isomers of studied molecules. The calculated spectra of the above ethers were compared to the corresponding experimental spectra in the infrared (IR) region (4000-560 cm-1) of the absorption index k(ν) derived from the neat liquid thin-film transmission data. It was found that IR spectra of aliphatic ethers are heavily influenced by the bands originating from non-fundamental modes, particularly from the combination modes in the C-H stretching region (3200-2800 cm-1). Because of the effects of vibrational resonances, the intensities of overtones and combination bands originating from methyl and methylene deformation modes increase sufficiently to influence the experimental line shape in this region. Less significant contributions from non-fundamental vibrational modes were noticed in the lower IR region (1600-560 cm-1), particularly in the vicinity of the C-O stretching band. The 2700-1600 cm-1 region, which is rich in weak bands due to non-fundamental vibrations, was reproduced accurately as well. It was concluded that a fully anharmonic approach allows significantly more accurate reproduction of the complex IR line shapes, particularly in the C-H stretching region of aliphatic ethers. On the basis of the achieved agreement between the experimental and calculated spectra, it may be concluded that the anharmonic GVPT2 method can adequately reproduce the anharmonic effects and vibrational resonances in particular, influencing the IR spectra of aliphatic ethers. The results obtained in this study show that the non-fundamental modes may play a significant role in shaping the IR spectra of aliphatic ethers and similar molecules in the neat liquid phase.

Quantum chemical calculation of NIR spectra of practical materials

In the third issue of the series on modern quantum chemical methods in the support role of NIR spectroscopy we continue to introduce the researchers from the field of experimental spectroscopy to practical aspects and applications of modern anharmonic theoretical approaches. The first two issues focused on explaining the necessary theoretical and practical background, allowing readers to get more familiar with the topic. An overview of recent literature reports highlighted the advantages stemming from using quantum chemical calculation in the support role to NIR spectroscopy. These deliberations were based on several cases of small- to medium-sized molecules. This part overviews the topic of applications of quantum theoretical methods to complex molecules with practical significance, which typically prove to be challenging objects for theoretical studies. An exemplary application of presented methodology to the case of Rosmarini folium biological samples is also examined here. The rosemary specific active compound, rosmarinic acid, is a relatively complex polyphenol with growing phytopharmaceutical importance, and therefore provides an excellent object of applied studies. The possibilities of combining the information stemming from quantum chemical calculation with the methods of advanced spectral data analysis, which are commonly used in experimental NIR spectroscopy (chemometrics, two-dimensional (2D) correlation spectra) are also overviewed. Again, these deliberations are based directly on the most recent reports published in the field.

Spectroscopic and Quantum Mechanical Calculation Study of the Effect of Isotopic Substitution on NIR Spectra of Methanol

In this work, we studied methanol and its deuterated derivatives (CH3OH, CH3OD, CD3OH, CD3OD) by NIR spectroscopy and anharmonic quantum chemical calculations. Vibrational bands corresponding to up to three quanta transitions (first and second overtones, binary and ternary combination modes) were predicted by the use of the VPT2 route. The accuracy of prediction of NIR modes was evaluated through density functional theory (DFT) with selected density functionals and basis sets. On the basis of the theoretical NIR spectra, detailed band assignments for all studied molecules were proposed. It was found that the pattern of bands in NIR spectra of deuterated methanols can be used for identification of isotopically equalized forms. Calculations of NIR spectra of all possible forms of CXXXOX (X = H, D) molecules demonstrated that the isotopic contamination can be identified due to a coexistence of bands specific to OH and OD groups. Also, bands from partially deuterated methyl groups can be distinguished in NIR spectra. Since the VPT2 framework is known to be sensitive to inaccuracy in the case of highly anharmonic modes, we obtained an independent insight by numerical solving of the time-independent Schrödinger equation corresponding to the O-X stretching mode scanned within -0.4 to 2.0 Å over a dense grid of 0.005 Å. This way the energies of vibrational levels of the CX1X2X3OX4 (X = H, D) isotopomers and the corresponding transition frequencies were obtained with high accuracy (<0.1 cm-1). The change in normal coordinate influences the reduced mass of the oscillator and thus its frequency. Our results lead to a conclusion that the effect of deuterization of the methyl group introduces a very specific and consistent frequency shift of the first overtone of the O-X stretching mode depending on the substitution of X1, X2, or X3 positions (<2 cm-1). However, the pattern of this shift is not reproduced accurately and is also largely overestimated by VPT2 calculations.

Quantum mechanically calculated NIR spectra of fatty acids

The advances in theory as well as steady development of the computing power have made quantum mechanical simulation of NIR spectra feasible. Recently, we have demonstrated the ability to accurately reproduce in theory the NIR spectra of several complex biomolecules, including fatty acids. In the present technical article, some of these achievements are overviewed. Examples of theoretical modelling of NIR spectra of short- (aliphatic chain up to four carbon atoms) and medium-chain (aliphatic chain counting six carbon atoms) fatty acids are presented and discussed. The calculated data are used directly for explaining the experimental NIR spectra of these systems. Spectral features distinctive to saturated vs. unsaturated fatty acids are essential in various types of samples typically treated by NIR spectroscopy; i.e. food, tissue, biomaterial, etc. Therefore, the theoretical study offers considerable support for basic and applied NIRS. An example of possible practical application of the results of theoretical study for biochemical studies is provided. The topic discussed here has been presented during the 18th International Conference on Near Infrared Spectroscopy (ICNIRS-2017) in Copenhagen, June 2017.

Quantum mechanical simulations of near-infrared spectra of biomolecules – Long-chain fatty acids

Exact and in-depth interpretation of near-infrared spectra has often appeared problematic in any case stepping beyond the simplest molecules. The inherent complexity of near-infrared spectra due to the abundance of combination modes and the resulting extensive band overlay frequently limits our comprehension of the spectral bands to vague wavenumber regions in which certain modes likely appear. Coincidently, quantum mechanical simulation of spectra which could offer momentous support in solving such problems has rather been rare in the case of near-infrared region due to practical limitations. Recent years have seen a trending development of accurate and affordable methods of near-infrared spectra simulation. A trend in modelling increasingly complex molecules can be noticed reaching even fairly large biomolecules. In this technical article we overview the most recent accomplishments in the field on the example of long-chain fatty acids and their cyclic dimers, which extend beyond 100 atoms.

Computer simulations of NIR spectra of thymol – Towards linking basic and analytical NIRS

Analytical near-infrared spectroscopy has been evolving rapidly over the last decades reaching a remarkable value for both industrial and institutional laboratories nowadays. Its growth has been strongly connected to focussed development of the instrumentation and multi-variate analytical methods. Multi-variate analysis gives near-infrared spectroscopy the desired analytical performance level but lacks the ability to provide physical insights into the analysed molecular system. Large amount of information carried in an NIR spectrum is omitted in analytical routines. In the present article, we review the latest accomplishments in cross-field research aimed at connecting the basic and analytical near-infrared spectroscopy. An example of thymol molecule, an important constituent of a traditional herbal medicine Thymi herba, is discussed. The key novelty in this case is computer simulation of NIR spectra which allows gaining better understanding of how spectra forming factors correspond to the partial least squares regression coefficients with special attention paid to the role of intermolecular interactions.