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.

Two-Dimensional Correlation Spectroscopy: The Power of Power Spectra.

Power spectra are a powerful tool provided by two-dimensional correlation analysis. However, this tool is seldom used in practice. This work shows selected examples of using of the power spectra for the study of various kinds of samples with the aim to promote more common use of this tool. By examination of the power spectrum of specific sample, one can estimate the sensitivity of different molecular fragments on a given perturbation. Determination of the power spectra for smaller data subsets provides information on the dynamics of perturbation-induced spectral changes. If the experimental spectra of different samples in the same perturbation window are recorded, the comparison of the power spectra yields information on differences in the sensitivity of various samples on common perturbation. This possibility is particularly useful for studies of the spectra-structure correlations, interactions, and molecular dynamics. A comparison of the power spectra obtained by using different reference spectra provides information on the nature of spectral changes at different wavenumbers.

Author Correction: Simulated NIR spectra as sensitive markers of the structure and interactions in nucleobases.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Simulated NIR spectra as sensitive markers of the structure and interactions in nucleobases.

Near-infrared (near-IR; NIR) spectroscopy is continuously advancing in biophysical and biochemical fields of investigation. For instance, recent progresses in NIR hyperspectral imaging of biological systems may be noted. However, interpretation of NIR bands for biological samples is difficult and creates a considerable barrier in exploring the full potential of NIR spectroscopy in bioscience. For this reason, we carried out a systematic study of NIR spectra of adenine, cytosine, guanine, and thymine in polycrystalline state. Interpretation of NIR spectra of these nucleobases was supported by anharmonic vibrational analysis using Deperturbed Vibrational Second-Order Perturbation Theory (DVPT2). A number of molecular models of nucleobases was applied to study the effect of the inter-molecular interactions on the NIR spectra. The accuracy of simulated NIR spectra appears to depend on the intra-layer interactions; in contrast, the inter-layer interactions are less influential. The best results were achieved by combining the simulated spectra of monomers and dimers. It is of particular note that in-plane deformation bands are far more populated than out-of-plane ones and the importance of ring modes is relatively small. This trend is in contrast to that observed in mid-IR region. As shown, the local, short-range chemical neighborhood of nucleobase molecules influence their NIR spectra more considerably. This suggests that NIR spectra are more sensitive probe of the nucleobase pairing than mid-IR ones. The obtained results allow, for the first time, to construct a frequency correlation table for NIR spectra of purines and pyrimidines.

IR Spectra of Crystalline Nucleobases: Combination of Periodic Harmonic Calculations with Anharmonic Corrections Based on Finite Models.

This work reports a theoretical study of infrared (IR) spectra of four nucleobases (adenine, cytosine, guanine, and thymine) in the crystalline state. The effects responsible for the fine spectral features were revealed, and the nonfundamental bands significantly contributing to the IR fingerprint region were successfully reproduced. Additionally, we compared the fundamental bands simulated for periodic models in harmonic approximation with the results obtained for finite models in anharmonic approximation. On this basis, we concluded that accurate description of the chemical neighborhood is more essential for the IR fingerprint region than the anharmonicity. Comparison with previous results indicates that the vibrational properties and the nature of intermolecular interactions of nucleobases in the crystalline state remain similar to those in solution. Therefore, the conclusions obtained for well-defined crystalline structures of nucleobases are general and helpful in understanding the vibrational spectra and properties of nucleobases and their derivatives. Finally, this work evidences that anharmonic force field based on finite models may be applied as an inexpensive correction to the harmonic spectrum of an infinite periodic system.

Spectra-Structure Correlations in Isotopomers of Ethanol (CX3CX2OX; X = H, D): Combined Near-Infrared and Anharmonic Computational Study.

The effect of isotopic substitution on near-infrared (NIR) spectra has not been studied in detail. With an exception of few major bands, it is difficult to follow the spectral changes due to complexity of NIR spectra. Recent progress in anharmonic quantum mechanical calculations allows for accurate reconstruction of NIR spectra. Taking this opportunity, we carried out a systematic study of NIR spectra of six isotopomers of ethanol (CX3CX2OX; X = H, D). Besides, we calculated the theoretical spectra of two other isotopomers (CH3CD2OD and CD3CH2OD) for which the experimental spectra are not available. The anharmonic calculations were based on generalized vibrational second-order perturbation theory (GVPT2) at DFT and MP2 levels with several basis sets. We compared the accuracy and efficiency of various computational methods. It appears that the best results were obtained with B2PLYP-GD3BJ/def2-TZVP//CPCM approach. Our simulations included the first and second overtones, as well as binary and ternary combinations bands. This way, we reliably reproduced even minor bands in the spectra of diluted samples (0.1 M in CCl4). On this basis, the effect of isotopic substitution on NIR spectra of ethanol was accurately reproduced and comprehensively explained.

Spectra-structure correlations in NIR region: Spectroscopic and anharmonic DFT study of n-hexanol, cyclohexanol and phenol.

We investigated near-infrared (7500-4000 cm-1) spectra of n-hexanol, cyclohexanol and phenol in CCl4 (0.2 M) by using anharmonic quantum calculations. These molecules represent three major kinds of alcohols; linear and cyclic aliphatic, and aromatic ones. Vibrational second-order perturbation theory (VPT2) was employed to calculate the first overtones and binary combination modes and to reproduce the experimental NIR spectra. The level of conformational flexibility of these three alcohols varies from one stable conformer of phenol through four conformers of cyclohexanol to few hundreds conformers in the case of n-hexanol. To take into account the most relevant conformational population of n-hexanol, a systematic conformational search was performed. Accurate reproduction of the experimental NIR spectra was achieved and detailed spectra-structure correlations were obtained for these three alcohols. VPT2 approach provides less reliable description of highly anharmonic modes, i.e. OH stretching. In the present work this limitation was manifested in erroneous results yielded by VPT2 for 2νOH mode of cyclohexanol. To study the anharmonicity of this mode we solved the corresponding time-independent Schrödinger equation based on a dense-grid probing of the relevant vibrational potential. These results allowed for significant improvement of the agreement between the calculated and experimental 2νOH band of cyclohexanol. Various important biomolecules include similar structural units to the systems investigated here. A detailed knowledge on spectral properties of these three types of alcohols is therefore essential for advancing our understanding of NIR spectroscopy of biomolecules.

Microheterogeneity in CH3OH/CD3OH mixture.

Recently, we demonstrated the presence of microheterogeneity in binary mixtures of unlike alcohols. [RSC Adv. 2016, 6, 37195-37202] The aim of this work was examination if this phenomenon occurs also in the mixture of very similar alcohols like CH3OH and CD3OH. Theoretical calculations suggest that the isotopic substitution in methyl group influences properties of the OH group. Hence, one can expect that this effect may lead to partial separation of CH3OH and CD3OH at a molecular level and it contributes to deviation from the ideal mixture. This work evidences that CH3OH/CD3OH mixture also deviates from the ideal one, but the extent of this deviation is much smaller as compared with the mixtures of other alcohols. It is of particular note that this deviation results mainly from the difference between the CH3 and CD3 groups, while the contribution from the OH groups is small. The structure of CH3OH/CD3OH mixture at a molecular level is similar to the structure of binary mixtures of other alcohols. The mixture is composed of the homoclusters of both alcohols and the mixed clusters. The homoclusters existing in the mixture are similar to those present in bulk alcohols. The highest population of the heteroclusters and the largest deviation from the ideal mixture were observed at equimolar mixture. Both the experimental and theoretical results reveal that in CH3OH/CD3OH mixture dominate the cyclic tetramers and larger clusters, while the population of the linear clusters is negligible. Though the extent and strength of hydrogen bonding in both alcohols are the same, the position and intensity of the 2ν(OH) band for CH3OH and CD3OH are different. We propose possible explanation of this observation.

The Effect of Chain Length on Mid-Infrared and Near-Infrared Spectra of Aliphatic 1-Alcohols.

Effect of the chain length on mid-infrared (MIR) and near-infrared (NIR) spectra of aliphatic 1-alcohols from methanol to 1-decanol was examined in detail. Of particular interest were the spectra-structure correlations in the NIR region and the correlation between MIR and NIR spectra of 1-alcohols. An application of two-dimensional correlation analysis (2D-COS) and chemometric methods provided comprehensive information on spectral changes in the data set. Principal component analysis (PCA) and cluster analysis evidenced that the spectra of methanol, ethanol, and 1-propanol are noticeably different from the spectra of higher 1-alcohols. The similarity between the spectra increases with an increase in the chain length. Hence, the most similar are the spectra of 1-nonanol and 1-decanol. Two-dimensional hetero-correlation analysis is very helpful for identification of the origin of bands and may guide selection of the best spectral ranges for the chemometric analysis. As shown, normalization of the spectra pronounces the intensity changes in various spectral regions and provides information not accessible from the raw data. The spectra of alcohols cannot be represented as a sum of the CH3, CH2, and OH group spectra since the OH group is involved in the hydrogen bonding. As a result, the spectral changes of this group are nonlinear and its spectral profile cannot be properly resolved. Finally, this work provides a lot of evidence that the degree of self-association of 1-alcohols decreases with the increase in chain length because of the growing meaning of the hydrophobic interactions. For butyl alcohol and higher 1-alcohols the hydrophobic interactions are more important than the OH OH interactions. Therefore, methanol, ethanol, and 1-propanol have unlimited miscibility with water, whereas 1-butanol and higher 1-alcohols have limited miscibility with water.

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.

MIR and NIR group spectra of n-alkanes and 1-chloroalkanes.

Numerous attempts were undertaken to resolve the absorption originating from different parts of alkanes. The separation of the contributions from the terminal and midchain methylene units was observed only in the spectra of solid alkanes at low temperatures. On the other hand, for liquid alkanes this effect was not reported as yet. In this study, ATR-IR, Raman and NIR spectra of eight n-alkanes and seven 1-chloroalkanes in the liquid phase were measured from 1000 to 12,000cm(-1). The spectra were analyzed by using two-dimensional (2D) correlation approach and chemometrics methods. It was shown that in 2D asynchronous contour plots, constructed from the spectra of n-alkanes and 1-chloroalkanes, the methylene band was resolved into two components. These two components were assigned to the terminal and midchain methylene groups. For the first time, the contributions from these two molecular fragments were resolved in the spectra of liquid n-alkanes and 1-chloroalkanes. MCR-ALS resolved these spectra into two components that were assigned to the ethyl and midchain methylene groups. These components represent the group spectra that can be used for assignment, spectral analysis and prediction of unknown spectra. The spectral prediction based on the group spectra provides very good results for n-alkanes, especially in the first and second overtone regions.

Resolution enhancement in second-derivative spectra.

Derivative spectroscopy is a powerful tool for the resolution enhancement in infrared, near-infrared, Raman, ultraviolet-visible, nuclear magnetic resonance, electron paramagnetic resonance, and fluorescence spectroscopy. Despite its great significance in analytical chemistry, not all aspects of the applications of this method have been explored as yet. This is the first systematic study of the parameters that influence the resolution enhancement in the second derivative spectra. The derivative spectra were calculated with the Savitzky-Golay method with different window size (5, 15, 25) and polynomial order (2, 4). The results obtained in this work show that the resolution enhancement in the second derivative spectra strongly depends on the data spacing in the original spectra, window size, polynomial order, and peak profile. As shown, the resolution enhancement is related to variations in the width of the peaks upon the differentiation. The present study reveals that in order to maximize the separation of the peaks in the second derivative spectra, the original spectra should be recorded at high resolution and differentiated using a small window size and high polynomial order. However, working with the real spectra one has to compromise between the noise reduction and optimization of the resolution enhancement in the second derivative spectra.

Combined IR/NIR and density functional theory calculations analysis of the solvent effects on frequencies and intensities of the fundamental and overtones of the C ═ O stretching vibrations of acetone and 2-hexanone.

Vibrational overtone studies primarily focus on X-H stretching overtone transitions, where X is an atom like C, O, N, or S. In contrast, the studies on the C ═ O stretching overtones are very scattered. To advance the research in this field, we measured the fundamental, first, and second overtones of the C ═ O stretching vibration of acetone and 2-hexanone in n-hexane, CCl4, and CHCl3, as well as in the vapor phase using FT-IR/FT-NIR spectroscopy. Density functional theory (DFT) calculations have also been performed to help the assignment of the C ═ O stretching bands and to guide interpretation of the experimental results. It was found that the wavenumbers, absorption intensities, and oscillator strengths of the C ═ O stretching bands show marked solvent dependence. In the fundamental and the first overtone regions, the intensities of the C ═ O stretching vibration were found to be pronouncedly more intense than those of the C-H stretching vibration. In the second overtone region, the intensities of the C-H stretching vibration are comparable to those of the C ═ O stretching vibration. The theoretical and observed decrease in integrated intensity upon going from the fundamental to the first overtone of the C ═ O stretching vibration is around 50, which is significantly larger than those of the O-H, C-H, and S-H stretching vibration. Both the calculated and experimental results suggest that excessive weakness in the C ═ O stretching overtone was shown to be a result of both a low anharmonicity and a substantial reduction in the oscillator strength. These results provide new insight into our understanding of the C ═ O stretching vibration.

Molecular structure and hydrogen bonding in pure liquid ethylene glycol and ethylene glycol-water mixtures studied using NIR spectroscopy.

The molecular structure and hydrogen bonding of ethylene glycol (EG) and EG-water mixtures in the liquid phase were studied by using near-infrared (NIR) spectroscopy. The spectra were evaluated using a two-dimensional (2D) correlation approach, moving-window 2D correlation analysis and chemometric methods. The minor changes for the CH stretching bands indicate that the structures of pure liquid EG and EG-water mixtures are determined by the intermolecular hydrogen bonding through the OH groups. The analysis of the ν2 + ν3 combination band of water reveals that in EG-rich solutions the molecules of water are predominantly bonded with two molecules of EG and this cooperative hydrogen bonding is stronger than that in bulk water. Further increase in the water content leads to formation of small water clusters around OH groups of EG. Comparing results for the binary mixtures of water with different organic solvents one can conclude that the total amount and distribution of the polar groups are the most important factors determining the solubility of water in the organic phase. The distribution of these groups depends on the length and structure of the hydrocarbon chain. Due to high population and relatively uniform distribution of the OH groups of EG water has unlimited solubility in liquid EG.

FT-IR and two-dimensional correlation analysis of the liquid crystalline phase transitions in the 4-Bromobenzylidene-4'-alkyloxyanilines.

The FT-IR spectra of the 4-bromobenzylidene-4'-alkyloxyanilines (nBBAA, for n = 4-12) were studied as a function of temperature. The molten state of the alkyloxy chain in smectic B (SmB), smectic A (SmA), and isotropic phases was analyzed. Generalized two-dimensional (2D) correlation spectroscopy has been applied to study changes in the conformational structure and specific interactions of molecules at phase transition in homologous series of nBBAA. A windowed autocorrelation analysis enabled us to locate transition points basing on the spectroscopic data.

Determination of relative rate of spectral events by novel modification of two-dimensional correlation spectroscopy.

Sign of two-dimensional (2D) correlation peaks provides information on sequence of spectral events. This information is related to molecular mechanism of changes in a given system. Recently, few papers addressing the problems with interpretation of the sign of 2D correlation peaks have been published. To overcome these problems, a modification of the generalized 2D correlation method has been proposed. This method compares variations in the dynamic spectrum with a linear change at a reference point. The rates of spectral responses at individual wavenumbers are proportional to magnitudes of the peaks in the slice of asynchronous spectrum at the reference point. This way, analysis of complex 2D contour plots is replaced by a simple examination of one-dimensional (1D) slice spectrum. In spite of reduced ability of the resolution enhancement, in special cases the proposed method provides information not accessible from the classical 2D correlation analysis. At first, the principles of this method are shown with the synthetic data. Next, the influence of spectral separation, band width and position changes on the slice spectrum is evaluated. Finally, the proposed approach is applied to the experimental spectra of two hydrogen-bonded systems.

Two-dimensional attenuated total reflection infrared and near-infrared correlation study of the structure of butyl alcohol/water mixtures.

The effect of temperature on attenuated total reflection infrared (ATR-IR) and near-infrared (NIR) transmission spectra of pure butan-1-ol, butan-2-ol, 2-methyl-propan-1-ol, 2-methyl-propan-2-ol, and mixtures with a small water content (X(H2O)

Effect of temperature and concentration on the structure of sec-butyl alcohol and isobutyl alcohol/water mixtures: near-infrared spectroscopic study.

The effect of temperature and concentration on the structure of sec-butyl alcohol and isobutyl alcohol/water binary mixtures in the alcohol-rich region (mole fraction of water X(H2O) < 0.3) has been studied using Fourier transform (FT) near-infrared (NIR) spectroscopy. The experimental data were analyzed by a two-dimensional (2D) correlation approach and chemometric methods. It was found that molecules of both alcohols in the mixture with water are in the same environment as those in the pure alcohols. Even at very low water content (X(H2O) = 0.001) we did not observe water free from any specific interactions. The molecules of water are attached to the end free OH groups in the open chain associates of alcohol. In this way the structure of neat alcohol remains intact by addition of water. The water-alcohol interactions in sec-butyl alcohol and isobutyl alcohol/water mixtures are stronger than those in bulk water. The results obtained at higher water content or elevated temperatures indicate the possibility of water-water interaction. In the alcohol-rich region the hydrophobic effects are of minor importance and the structure and properties of these systems are determined by hydrogen bonding through the hydroxyl groups. Both alcohols behave similarly on the temperature or water content variation; the minor difference results from a different degree of self-association for sec-butyl alcohol and isobutyl alcohol.

Effect of temperature and concentration on the structure of N-methylacetamide-water complexes: Near-infrared spectroscopic study.

Generalized two-dimensional (2D) FT-NIR correlation spectroscopy and chemometric methods have been used to study temperature-dependent spectral changes in pure N-methylacetamide (NMA) and NMA-water mixtures. We also examined the effect of varying water content on the structure of the mixture. It has been found that the extent of self-association of NMA in CCl4 is very high; the association occurs even at concentration of 0.001 M. In the pure liquid NMA, the population of the monomers is negligible and the structure is dominated by the linear associates. An increase in temperature reduces the number of hydrogen bonds, but in contrast to alcohols their strength remains nearly the same. This reflects a difference in the mechanism of thermal breaking of the associates of NMA and alcohols. The present results reveal that the interaction between NMA and water in the NMA-rich region (X(H2O) < 0.1) does not have a significant effect on the intrinsic structure of NMA. The structure of NMA is dominant, and the molecules of water do not form separate clusters but are dispersed and incorporated into the structure of NMA. We did not observe the presence of the free OH groups in the mixture. This led to the suggestion that each molecule of water forms two hydrogen bonds to two different molecules of NMA. An analysis of the asynchronous spectra reveals that most of the peaks observed in the asynchronous spectra, constructed from the temperature-dependent data, simply result from the frequency shift. This assumption is supported by the simulation studies.

Effect of temperature and concentration on the structure of tert-butyl alcohol/water mixtures: near-infrared spectroscopic study.

The effect of temperature and concentration on the structure of tert-butyl alcohol/water binary mixtures in the alcohol-rich region (X(H2O) < 0.3) has been studied by using Fourier transform near-infrared (FT-NIR) spectroscopy. The obtained results demonstrate that the addition of a small amount of water to tert-butyl alcohol (2-methyl-2-propanol, abbreviated as TBA) leads to minor changes in the structure of neat TBA and suggest that molecules of TBA in the mixture are in the same environment as those in pure TBA. The bands of water are red-shifted in the mixture relative to bulk water, implying that the molecules of water in TBA are involved in stronger hydrogen bonding. The present experimental data give no evidence for the existence of nonbonded water in the mixture. Even at a very low content of water, the main NIR bands of water (nu(2) + nu(3) and nu(1) + nu(3)) have two components showing markedly different behavior upon an increase in temperature. From the power spectra, it is seen that the extent of intensity changes due to the free OH groups of TBA is smaller in the mixture relative to pure TBA. All of these results support the model of chain-end bonding of water molecules to TBA associates. An increase in X(H2O) reduces the population of nonbonded OH groups of TBA, yet both processes do not appear at the same rate. The amount of bonded OH groups of water increases faster than that of the nonbonded ones. It seems that the water-water interaction becomes more important as X(H2O) increases. At high alcohol content, the position of the CH alkyl stretching bands is constant, evidencing a negligible role of the hydrophobic hydration in the mixture.