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Kitzmann WR, Hunger D, Reponen APM, Förster C, Schoch R, Bauer M, Feldmann S, van Slageren J, Heinze K. Electronic Structure and Excited-State Dynamics of the NIR-II Emissive Molybdenum(III) Analogue to the Molecular Ruby. Inorg Chem 2023; 62:15797-15808. [PMID: 37718553 DOI: 10.1021/acs.inorgchem.3c02186] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
Photoactive chromium(III) complexes saw a conceptual breakthrough with the discovery of the prototypical molecular ruby mer-[Cr(ddpd)2]3+ (ddpd = N,N'-dimethyl-N,N'-dipyridin-2-ylpyridine-2,6-diamine), which shows intense long-lived near-infrared (NIR) phosphorescence from metal-centered spin-flip states. In contrast to the numerous studies on chromium(III) photophysics, only 10 luminescent molybdenum(III) complexes have been reported so far. Here, we present the synthesis and characterization of mer-MoX3(ddpd) (1, X = Cl; 2, X = Br) and cisfac-[Mo(ddpd)2]3+ (cisfac-[3]3+), an isomeric heavy homologue of the prototypical molecular ruby. For cisfac-[3]3+, we found strong zero-field splitting using magnetic susceptibility measurements and electron paramagnetic resonance spectroscopy. Electronic spectra covering the spin-forbidden transitions show that the spin-flip states in mer-1, mer-2, and cisfac-[3]3+ are much lower in energy than those in comparable chromium(III) compounds. While all three complexes show weak spin-flip phosphorescence in NIR-II, the emission of cisfac-[3]3+ peaking at 1550 nm is particularly low in energy. Femtosecond transient absorption spectroscopy reveals a short excited-state lifetime of 1.4 ns, 6 orders of magnitude shorter than that of mer-[Cr(ddpd)2]3+. Using density functional theory and ab initio multireference calculations, we break down the reasons for this disparity and derive principles for the design of future stable photoactive molybdenum(III) complexes.
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Affiliation(s)
- Winald R Kitzmann
- Department of Chemistry, Johannes Gutenberg University of Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
- Rowland Institute, Harvard University, 100 Edwin H. Land Boulevard, Cambridge, Massachusetts 02142, United States
| | - David Hunger
- Institute of Physical Chemistry and Center for Integrated Quantum Science and Technology, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Antti-Pekka M Reponen
- Rowland Institute, Harvard University, 100 Edwin H. Land Boulevard, Cambridge, Massachusetts 02142, United States
| | - Christoph Förster
- Department of Chemistry, Johannes Gutenberg University of Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Roland Schoch
- Faculty of Science, Chemistry Department and Centre for Sustainable Systems Design, Paderborn University, 33098 Paderborn, Germany
| | - Matthias Bauer
- Faculty of Science, Chemistry Department and Centre for Sustainable Systems Design, Paderborn University, 33098 Paderborn, Germany
| | - Sascha Feldmann
- Rowland Institute, Harvard University, 100 Edwin H. Land Boulevard, Cambridge, Massachusetts 02142, United States
| | - Joris van Slageren
- Institute of Physical Chemistry and Center for Integrated Quantum Science and Technology, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Katja Heinze
- Department of Chemistry, Johannes Gutenberg University of Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
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Litvynchuk S, Galenko O, Cavicchi A, Ceccanti C, Mignani C, Guidi L, Shevchenko A. Conformational Changes in the Structure of Dough and Bread Enriched with Pumpkin Seed Flour. PLANTS (BASEL, SWITZERLAND) 2022; 11:2762. [PMID: 36297786 PMCID: PMC9607130 DOI: 10.3390/plants11202762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/07/2022] [Accepted: 10/16/2022] [Indexed: 06/16/2023]
Abstract
Pumpkin seed flour is a promising raw material for use in the technology of various bakery products. It has a high biological value and valuable amino acid profile. During the technological process of making bread, there are conformational changes in the protein structure. The purpose of the study was to determine the effect of pumpkin seed flour on conformational changes in the structure of protein substances of dough and bread from wheat flour by near-infrared reflection spectroscopy. The protein profile changed to complete when replacing 10% or more of wheat flour because the score for all amino acids was higher than 100%. The utilitarian coefficient indicates the same balance of amino acids in proteins of all samples. As the percentage of substitution increases, the number of amino acids used for anabolic purposes decreases, and these are more fully utilized by the body.
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Affiliation(s)
- Svitlana Litvynchuk
- Department of Physics, National University of Food Technologies, 01601 Kyiv, Ukraine
| | - Oleg Galenko
- Department of Technology of Meat and Meat Products, National University of Food Technologies, 01601 Kyiv, Ukraine
| | - Alessio Cavicchi
- Department of Agriculture, Food and Environment, University of Pisa, 56124 Pisa, Italy
- Interdepartmental Research Center Nutrafood “Nutraceuticals and Food for Health”, University of Pisa, 56124 Pisa, Italy
| | - Costanza Ceccanti
- Department of Agriculture, Food and Environment, University of Pisa, 56124 Pisa, Italy
- Interdepartmental Research Center Nutrafood “Nutraceuticals and Food for Health”, University of Pisa, 56124 Pisa, Italy
| | - Chiara Mignani
- Department of Political Sciences, Communication and International Relations, University of Macerata, 62100 Macerata, Italy
| | - Lucia Guidi
- Department of Agriculture, Food and Environment, University of Pisa, 56124 Pisa, Italy
- Interdepartmental Research Center Nutrafood “Nutraceuticals and Food for Health”, University of Pisa, 56124 Pisa, Italy
| | - Anastasiia Shevchenko
- Department of Bakery and Confectionery Goods Technologies, National University of Food Technologies, 01601 Kyiv, Ukraine
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Beć KB, Grabska J, Huck CW. In silico NIR spectroscopy - A review. Molecular fingerprint, interpretation of calibration models, understanding of matrix effects and instrumental difference. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 279:121438. [PMID: 35667136 DOI: 10.1016/j.saa.2022.121438] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/20/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
Quantum mechanical calculations are routinely used as a major support in mid-infrared (MIR) and Raman spectroscopy. In contrast, practical limitations for long time formed a barrier to developing a similar synergy between near-infrared (NIR) spectroscopy and computational chemistry. Recent advances in theoretical methods suitable for calculation of NIR spectra opened the pathway to modeling NIR spectra of various molecules. Accurate theoretical reproduction of NIR spectra of molecules reaching the size of long-chain fatty acids was accomplished so far. In silico NIR spectroscopy, where the spectra are calculated ab initio, provides substantial improvement in our understanding of the overtones and combination bands that overlap in staggering numbers and create complex lineshape typical for NIR spectra. This improves the comprehension of the spectral information enabling access to rich and detail molecular footprint, essential for fundamental research and useful in routine analysis by NIR spectroscopy and chemometrics. This review article summarizes the most recent accomplishments in the emerging field with examples of simulated NIR spectra of molecules reaching long-chain fatty acids and polymers. In addition to detailed NIR band assignments and new physical insights, simulated spectra enable innovative support in applications. Understanding of the difference in the performance observed between miniaturized NIR spectrometers and chemical interpretation of the chemometric models are noteworthy here. These new elements integrated into NIR spectroscopy framework enable a knowledge-based design of the analysis with comprehension of the processed chemical information.
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Affiliation(s)
- Krzysztof B Beć
- University of Innsbruck, Institute of Analytical Chemistry and Radiochemistry, Innrain 80-82, 6020 Innsbruck, Austria.
| | - Justyna Grabska
- University of Innsbruck, Institute of Analytical Chemistry and Radiochemistry, Innrain 80-82, 6020 Innsbruck, Austria.
| | - Christian W Huck
- University of Innsbruck, Institute of Analytical Chemistry and Radiochemistry, Innrain 80-82, 6020 Innsbruck, Austria.
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Beć KB, Grabska J, Huck CW. Miniaturized NIR Spectroscopy in Food Analysis and Quality Control: Promises, Challenges, and Perspectives. Foods 2022; 11:foods11101465. [PMID: 35627034 PMCID: PMC9140213 DOI: 10.3390/foods11101465] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/05/2022] [Accepted: 05/13/2022] [Indexed: 01/27/2023] Open
Abstract
The ongoing miniaturization of spectrometers creates a perfect synergy with the common advantages of near-infrared (NIR) spectroscopy, which together provide particularly significant benefits in the field of food analysis. The combination of portability and direct onsite application with high throughput and a noninvasive way of analysis is a decisive advantage in the food industry, which features a diverse production and supply chain. A miniaturized NIR analytical framework is readily applicable to combat various food safety risks, where compromised quality may result from an accidental or intentional (i.e., food fraud) origin. In this review, the characteristics of miniaturized NIR sensors are discussed in comparison to benchtop laboratory spectrometers regarding their performance, applicability, and optimization of methodology. Miniaturized NIR spectrometers remarkably increase the flexibility of analysis; however, various factors affect the performance of these devices in different analytical scenarios. Currently, it is a focused research direction to perform systematic evaluation studies of the accuracy and reliability of various miniaturized spectrometers that are based on different technologies; e.g., Fourier transform (FT)-NIR, micro-optoelectro-mechanical system (MOEMS)-based Hadamard mask, or linear variable filter (LVF) coupled with an array detector, among others. Progressing technology has been accompanied by innovative data-analysis methods integrated into the package of a micro-NIR analytical framework to improve its accuracy, reliability, and applicability. Advanced calibration methods (e.g., artificial neural networks (ANN) and nonlinear regression) directly improve the performance of miniaturized instruments in challenging analyses, and balance the accuracy of these instruments toward laboratory spectrometers. The quantum-mechanical simulation of NIR spectra reveals the wavenumber regions where the best-correlated spectral information resides and unveils the interactions of the target analyte with the surrounding matrix, ultimately enhancing the information gathered from the NIR spectra. A data-fusion framework offers a combination of spectral information from sensors that operate in different wavelength regions and enables parallelization of spectral pretreatments. This set of methods enables the intelligent design of future NIR analyses using miniaturized instruments, which is critically important for samples with a complex matrix typical of food raw material and shelf products.
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Beć KB, Grabska J, Badzoka J, Huck CW. Spectra-structure correlations in NIR region of polymers from quantum chemical calculations. The cases of aromatic ring, C=O, C≡N and C-Cl functionalities. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 262:120085. [PMID: 34174679 DOI: 10.1016/j.saa.2021.120085] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/08/2021] [Accepted: 06/12/2021] [Indexed: 06/13/2023]
Abstract
Near-infrared (NIR) spectroscopy is a valued analytical tool in various applications involving polymers. However, complex nature of NIR spectra imposes difficulties in their direct interpretation. Here, anharmonic quantum chemical calculations are used to simulate NIR spectra of nine polymers; acrylonitrile butadiene styrene (ABS), ethylene-vinyl acetate (EVAC), polycarbonate (PC), polyethylene terephthalate (PET), polylactide or polylactic acid (PLA), polymethylmethacrylate (PMMA), polyoxymethylene (POM), polystyrene (PS) and polyvinylchloride (PVC). The generalized spectra-structure correlations are derived for these systems with focus given to the manifestation in NIR spectra of aromatic ring, C=O, C≡N and C-Cl functionalities. It is concluded that the nature of NIR polymer bands is only moderately sensitive to the remote chemical neighborhood. The majority of NIR absorption of polymers originates from binary combination bands, while the first overtones are meaningful only in ca. 6200-5500 cm-1 region. The contribution of the overtone bands is relatively higher for the polymers bearing aromatic rings because of higher intensity of C-H stretching overtones. Highly characteristic combination bands of the modes localized in aromatic ring (ring deformation and CH stretching) are relatively independent on the remaining structure of the polymer. The combination bands originating from C=O group are more sensitive to the chemical neighborhood in near proximity, forming a useful fingerprint for a specific polymer. In contrast, the vibrational bands of C≡N functionality are far less useful in NIR region than in infrared (IR) region. With aid of the calculated absorption bands, structural specificity of NIR spectroscopy of polymers can be markedly improved.
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Affiliation(s)
- Krzysztof B Beć
- Institute of Analytical Chemistry and Radiochemistry, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria.
| | - Justyna Grabska
- Institute of Analytical Chemistry and Radiochemistry, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Jovan Badzoka
- Institute of Analytical Chemistry and Radiochemistry, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Christian W Huck
- Institute of Analytical Chemistry and Radiochemistry, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
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Grabska J, Beć KB, Ozaki Y, Huck CW. Anharmonic DFT Study of Near-Infrared Spectra of Caffeine: Vibrational Analysis of the Second Overtones and Ternary Combinations. Molecules 2021; 26:molecules26175212. [PMID: 34500645 PMCID: PMC8433751 DOI: 10.3390/molecules26175212] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 11/16/2022] Open
Abstract
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.
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Affiliation(s)
- Justyna Grabska
- CCB—Center for Chemistry and Biomedicine, Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innrain 80/82, 6020 Innsbruck, Austria; (K.B.B.); (C.W.H.)
- Correspondence:
| | - Krzysztof B. Beć
- CCB—Center for Chemistry and Biomedicine, Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innrain 80/82, 6020 Innsbruck, Austria; (K.B.B.); (C.W.H.)
| | - Yukihiro Ozaki
- School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda 669-1337, Hyogo, Japan;
- Toyota Physical and Chemical Research Institute, Yokomichi, Nagakute 480-1192, Aichi, Japan
| | - Christian W. Huck
- CCB—Center for Chemistry and Biomedicine, Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innrain 80/82, 6020 Innsbruck, Austria; (K.B.B.); (C.W.H.)
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Ozaki Y, Beć KB, Morisawa Y, Yamamoto S, Tanabe I, Huck CW, Hofer TS. Advances, challenges and perspectives of quantum chemical approaches in molecular spectroscopy of the condensed phase. Chem Soc Rev 2021; 50:10917-10954. [PMID: 34382961 DOI: 10.1039/d0cs01602k] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The purpose of this review is to demonstrate advances, challenges and perspectives of quantum chemical approaches in molecular spectroscopy of the condensed phase. Molecular spectroscopy, particularly vibrational spectroscopy and electronic spectroscopy, has been used extensively for a wide range of areas of chemical sciences and materials science as well as nano- and biosciences because it provides valuable information about structure, functions, and reactions of molecules. In the meantime, quantum chemical approaches play crucial roles in the spectral analysis. They also yield important knowledge about molecular and electronic structures as well as electronic transitions. The combination of spectroscopic approaches and quantum chemical calculations is a powerful tool for science, in general. Thus, our article, which treats various spectroscopy and quantum chemical approaches, should have strong implications in the wider scientific community. This review covers a wide area of molecular spectroscopy from far-ultraviolet (FUV, 120-200 nm) to far-infrared (FIR, 400-10 cm-1)/terahertz and Raman spectroscopy. As quantum chemical approaches, we introduce several anharmonic approaches such as vibrational self-consistent field (VSCF) and the combination of periodic harmonic calculations with anharmonic corrections based on finite models, grid-based techniques like the Numerov approach, the Cartesian coordinate tensor transfer (CCT) method, Symmetry-Adapted Cluster Configuration-Interaction (SAC-CI), and the ZINDO (Semi-empirical calculations at Zerner's Intermediate Neglect of Differential Overlap). One can use anharmonic approaches and grid-based approaches for both infrared (IR) and near-infrared (NIR) spectroscopy, while CCT methods are employed for Raman, Raman optical activity (ROA), FIR/terahertz and low-frequency Raman spectroscopy. Therefore, this review overviews cross relations between molecular spectroscopy and quantum chemical approaches, and provides various kinds of close-reality advanced spectral simulation for condensed phases.
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Affiliation(s)
- Yukihiro Ozaki
- School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Hyogo 669-1337, Japan. and Toyota Physical and Chemical Research Institute, Yokomichi, Nagakute, Aichi 480-1192, Japan
| | - Krzysztof B Beć
- Institute of Analytical Chemistry and Radiochemistry, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Yusuke Morisawa
- Department of Chemistry, School of Science and Engineering, Kindai University, Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Shigeki Yamamoto
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Ichiro Tanabe
- Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Christian W Huck
- Institute of Analytical Chemistry and Radiochemistry, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Thomas S Hofer
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80-82, A6020 Innsbruck, Austria
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Singh S, Czarnecki MA. How much anharmonicity is in vibrational spectra of CH 3I and CD 3I? SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 248:119176. [PMID: 33257247 DOI: 10.1016/j.saa.2020.119176] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 10/29/2020] [Accepted: 11/01/2020] [Indexed: 06/12/2023]
Abstract
This work presents new experimental and theoretical insights on vibrational spectra of CH3I and CD3I in the liquid phase. For the first time, we provided the contributions from different vibrational modes to mid-infrared (MIR) and near-infrared (NIR) spectra and estimated the extent of anharmonicity in the MIR region. Direct comparison of the intensities from ATR-IR and NIR transmission spectra was possible due to normalization of ATR-IR spectra. As a reference for normalization, we applied the area of the νs(CH3)/νs(CD3) band recorded in transmission mode. Our results show that the corresponding vibrational modes of CH3I and CD3I have similar contributions to the total intensity (MIR + NIR), however, these contributions are distributed in a different way between MIR and NIR regions. As expected, most of intensity in MIR spectra originates from the fundamental transitions (>90%). The fundamental bands together with the first overtones and the binary combinations contribute to more than 99% of MIR intensity for both compounds. Therefore, reliable reconstruction of MIR spectra can be achieved by considering only these vibrational modes. On the other hand, accurate simulation of NIR spectra requires including the higher-order transitions. In the case of CD3I, the fourth-order transitions contribute to 12.7% of NIR intensity. The contributions from NIR region are significantly smaller than those from MIR range and were estimated to be 6.7% for CH3I and 2.3% for CD3I. The theoretical calculations provide a reasonable estimation of the total contribution from the fundamental bands. Yet, the calculated contributions from the anharmonic transitions are different from those obtained from the experimental data. MIR spectra of CH3I and CD3I reveal an unexpected increase in the intensity of some overtones and combination bands indicating the presence of Fermi resonances. These resonances are responsible for differences in contributions from the first overtones and binary combinations between CH3I and CD3I.
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Affiliation(s)
- Swapnil Singh
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
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Roy D, Kovalenko A. Application of the Approximate 3D-Reference Interaction Site Model (RISM) Molecular Solvation Theory to Acetonitrile as Solvent. J Phys Chem B 2020; 124:4590-4597. [PMID: 32392049 DOI: 10.1021/acs.jpcb.0c03230] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The integral equation formalism based reference interaction site model (RISM) molecular solvation theory is applied to pure liquid acetonitrile and water-acetonitrile binary mixtures of different compositions. Solvate formation of d- and f-block ions by ACN is also calculated to check applicability of the RISM theory. The generalized Amber force field (GAFF) and the universal force field (UFF) parameters were found to be suitable for applications with the RISM theory for acetonitrile solvent. The presence of local microsolvated clusters for water-acetonitrile mixtures is validated in the RISM calculations.
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Affiliation(s)
- Dipankar Roy
- Department of Mechanical Engineering, University of Alberta, 10-203 Donadeo Innovation Centre for Engineering, 9211-116 Street NW, Edmonton, Alberta T6G 1H9, Canada
| | - Andriy Kovalenko
- Department of Mechanical Engineering, University of Alberta, 10-203 Donadeo Innovation Centre for Engineering, 9211-116 Street NW, Edmonton, Alberta T6G 1H9, Canada.,Nanotechnology Research Centre, 11421 Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
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Beć KB, Grabska J, Ozaki Y, Czarnecki MA, Huck CW. Simulated NIR spectra as sensitive markers of the structure and interactions in nucleobases. Sci Rep 2019; 9:17398. [PMID: 31758033 PMCID: PMC6874539 DOI: 10.1038/s41598-019-53827-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 10/11/2019] [Indexed: 11/16/2022] Open
Abstract
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.
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Affiliation(s)
- Krzysztof B Beć
- Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innrain 80/82, CCB-Center for Chemistry and Biomedicine, 6020, Innsbruck, Austria.
| | - Justyna Grabska
- Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innrain 80/82, CCB-Center for Chemistry and Biomedicine, 6020, Innsbruck, Austria
| | - Yukihiro Ozaki
- Department of Chemistry, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo, 669-1337, Japan
| | - Mirosław A Czarnecki
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383, Wrocław, Poland
| | - Christan W Huck
- Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innrain 80/82, CCB-Center for Chemistry and Biomedicine, 6020, Innsbruck, Austria
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Spectra-Structure Correlations in Isotopomers of Ethanol (CX 3CX 2OX; X = H, D): Combined Near-Infrared and Anharmonic Computational Study. Molecules 2019; 24:molecules24112189. [PMID: 31212669 PMCID: PMC6600318 DOI: 10.3390/molecules24112189] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/03/2019] [Accepted: 06/08/2019] [Indexed: 11/21/2022] Open
Abstract
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.
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