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Sato H, Ueno N, Tanabe I. Electronic interaction between dimethyl carbonate and Li + studied by attenuated total reflectance far-ultraviolet spectroscopy. Chem Commun (Camb) 2024; 60:6375-6378. [PMID: 38808541 DOI: 10.1039/d4cc01775g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
Organic electrolytes with Li+ were analyzed by far-ultraviolet (≤200 nm) spectroscopy, achieved by an attenuated total reflectance setup. The spectra showed a redshift with Li+ addition, attributed to the charge transfer, as revealed by quantum chemical calculations. Multivariate analysis successfully decomposed the spectra into pure solvent and Li-coordinated solvent components.
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Affiliation(s)
- Hitomi Sato
- Department of Chemistry, College of Science, Rikkyo University, 3-34-1, Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan.
| | - Nami Ueno
- Department of Chemistry, College of Science, Rikkyo University, 3-34-1, Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan.
| | - Ichiro Tanabe
- Department of Chemistry, College of Science, Rikkyo University, 3-34-1, Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan.
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2
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Chen Y, Pios SV, Gelin MF, Chen L. Accelerating Molecular Vibrational Spectra Simulations with a Physically Informed Deep Learning Model. J Chem Theory Comput 2024; 20:4703-4710. [PMID: 38825857 DOI: 10.1021/acs.jctc.4c00173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
In recent years, machine learning (ML) surrogate models have emerged as an indispensable tool to accelerate simulations of physical and chemical processes. However, there is still a lack of ML models that can accurately predict molecular vibrational spectra. Here, we present a highly efficient multitask ML surrogate model termed Vibrational Spectra Neural Network (VSpecNN), to accurately calculate infrared (IR) and Raman spectra based on dipole moments and polarizabilities obtained on-the-fly via ML-enhanced molecular dynamics simulations. The methodology is applied to pyrazine, a prototypical polyatomic chromophore. The VSpecNN-predicted energies are well within the chemical accuracy (1 kcal/mol), and the errors for VSpecNN-predicted forces are only half of those obtained from a popular high-performance ML model. Compared to the ab initio reference, the VSpecNN-predicted frequencies of IR and Raman spectra differ only by less than 5.87 cm-1, and the intensities of IR spectra and the depolarization ratios of Raman spectra are well reproduced. The VSpecNN model developed in this work highlights the importance of constructing highly accurate neural network potentials for predicting molecular vibrational spectra.
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Affiliation(s)
| | | | - Maxim F Gelin
- School of Science, Hangzhou Dianzi University, Hangzhou 310018, China
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3
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Lu XY, Wu HP, Ma H, Li H, Li J, Liu YT, Pan ZY, Xie Y, Wang L, Ren B, Liu GK. Deep Learning-Assisted Spectrum-Structure Correlation: State-of-the-Art and Perspectives. Anal Chem 2024; 96:7959-7975. [PMID: 38662943 DOI: 10.1021/acs.analchem.4c01639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Spectrum-structure correlation is playing an increasingly crucial role in spectral analysis and has undergone significant development in recent decades. With the advancement of spectrometers, the high-throughput detection triggers the explosive growth of spectral data, and the research extension from small molecules to biomolecules accompanies massive chemical space. Facing the evolving landscape of spectrum-structure correlation, conventional chemometrics becomes ill-equipped, and deep learning assisted chemometrics rapidly emerges as a flourishing approach with superior ability of extracting latent features and making precise predictions. In this review, the molecular and spectral representations and fundamental knowledge of deep learning are first introduced. We then summarize the development of how deep learning assist to establish the correlation between spectrum and molecular structure in the recent 5 years, by empowering spectral prediction (i.e., forward structure-spectrum correlation) and further enabling library matching and de novo molecular generation (i.e., inverse spectrum-structure correlation). Finally, we highlight the most important open issues persisted with corresponding potential solutions. With the fast development of deep learning, it is expected to see ultimate solution of establishing spectrum-structure correlation soon, which would trigger substantial development of various disciplines.
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Affiliation(s)
- Xin-Yu Lu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
- Tan Kah Kee Innovation Laboratory, Xiamen 361005, P. R. China
| | - Hao-Ping Wu
- State Key Laboratory of Marine Environmental Science, Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Center for Marine Environmental Chemistry & Toxicology, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, P. R. China
| | - Hao Ma
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
- Tan Kah Kee Innovation Laboratory, Xiamen 361005, P. R. China
| | - Hui Li
- Key Laboratory of Multimedia Trusted Perception and Efficient Computing, Ministry of Education of China, Xiamen University, Xiamen 361005, P. R. China
| | - Jia Li
- Institute of Artificial Intelligence, Xiamen University, Xiamen 361005, P. R. China
| | - Yan-Ti Liu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
- Tan Kah Kee Innovation Laboratory, Xiamen 361005, P. R. China
| | - Zheng-Yan Pan
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Yi Xie
- School of Informatics, Xiamen University, Xiamen 361005, P. R. China
| | - Lei Wang
- Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, P. R. China
| | - Bin Ren
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
- Tan Kah Kee Innovation Laboratory, Xiamen 361005, P. R. China
| | - Guo-Kun Liu
- State Key Laboratory of Marine Environmental Science, Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Center for Marine Environmental Chemistry & Toxicology, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, P. R. China
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4
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Gusarov S. Advances in Computational Methods for Modeling Photocatalytic Reactions: A Review of Recent Developments. MATERIALS (BASEL, SWITZERLAND) 2024; 17:2119. [PMID: 38730926 PMCID: PMC11085804 DOI: 10.3390/ma17092119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/19/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024]
Abstract
Photocatalysis is a fascinating process in which a photocatalyst plays a pivotal role in driving a chemical reaction when exposed to light. Its capacity to harness light energy triggers a cascade of reactions that lead to the formation of intermediate compounds, culminating in the desired final product(s). The essence of this process is the interaction between the photocatalyst's excited state and its specific interactions with reactants, resulting in the creation of intermediates. The process's appeal is further enhanced by its cyclic nature-the photocatalyst is rejuvenated after each cycle, ensuring ongoing and sustainable catalytic action. Nevertheless, comprehending the photocatalytic process through the modeling of photoactive materials and molecular devices demands advanced computational techniques founded on effective quantum chemistry methods, multiscale modeling, and machine learning. This review analyzes contemporary theoretical methods, spanning a range of lengths and accuracy scales, and assesses the strengths and limitations of these methods. It also explores the future challenges in modeling complex nano-photocatalysts, underscoring the necessity of integrating various methods hierarchically to optimize resource distribution across different scales. Additionally, the discussion includes the role of excited state chemistry, a crucial element in understanding photocatalysis.
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Affiliation(s)
- Sergey Gusarov
- Digital Technologies Research Centre, National Research Council Canada, Ottawa, ON K1A 0R6, Canada
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5
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Ozaki Y, Morisawa Y, Tanabe I. ATR-far-ultraviolet spectroscopy: a challenge to new σ chemistry. Chem Soc Rev 2024; 53:1730-1768. [PMID: 38287893 DOI: 10.1039/d3cs00437f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
This review reports the recent progress on ATR-far ultraviolet (FUV) spectroscopy in the condensed phase. ATR-FUV spectroscopy for liquids and solids enables one to explore various topics in physical chemistry, analytical chemistry, nanoscience and technology, materials science, electrochemistry, and organic chemistry. In this review, we put particular emphasis on the three major topics: (1) studies on electronic transitions and structures of various molecules, which one cannot investigate via ordinary UV spectroscopy. The combined use of ATR-FUV spectroscopy and quantum chemical calculations allows for the investigation of various electronic transitions, including σ, n-Rydberg transitions. ATR-FUV spectroscopy may open a new avenue for σ-chemistry. (2) ATR-FUV spectroscopy enables one to measure the first electronic transition of water at approximately 160 nm without peak saturation. Using this band, one can study the electronic structure of water, aqueous solutions, and adsorbed water. (3) ATR-FUV spectroscopy has its own advantages of the ATR method as a surface analysis method. ATR-FUV spectroscopy is a powerful technique for exploring a variety of top surface phenomena (∼50 nm) in adsorbed water, polymers, graphene, organic materials, ionic liquids, and so on. This review briefly describes the principles, characteristics, and instrumentation of ATR-FUV spectroscopy. Next, a detailed description about quantum chemical calculation methods for FUV and UV regions is given. The recent application of ATR-FUV-UV spectroscopy studies on electronic transitions from σ orbitals in various saturated molecules is introduced first, followed by a discussion on the applications of ATR-FUV spectroscopy to studies on water, aqueous solutions, and adsorbed water. Applications of ATR-FUV spectroscopy in the analysis of other materials such as polymers, ionic liquids, inorganic semiconductors, graphene, and carbon nanocomposites are elucidated. In addition, ATR-FUV-UV-vis spectroscopy focusing on electrochemical interfaces is outlined. Finally, FUV-UV-surface plasmon resonance studies are discussed.
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Affiliation(s)
- Yukihiro Ozaki
- School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Hyogo 669-1330, Japan.
- Toyota Physical and Chemical Research Institute, Nagakute, Aichi 480-1192, Japan
| | - Yusuke Morisawa
- School of Science and Engineering, Kindai University, Higashi-Osaka, Osaka 577-8502, Japan.
| | - Ichiro Tanabe
- Department of Chemistry, School of Science, Rikkyo University, Toshima, Tokyo 171-8501, Japan.
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6
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Khanh Nguyen D, Ponce-Pérez R, Guerrero-Sanchez J, Hoat DM. Surface functionalization of graphene-like boron arsenide monolayer: a first-principles study. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2023; 36:055001. [PMID: 37871594 DOI: 10.1088/1361-648x/ad05fa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 10/23/2023] [Indexed: 10/25/2023]
Abstract
In this work, the effects of hydrogen (H) and oxygen (O) adsorption on the electronic and magnetic properties of graphene-like boron arsenide (BAs) monolayer are investigated using first-principles calculations. Pristine monolayer is a non-magnetic two-dimensional (2D) material, exhibiting direct gap semiconductor character with band gap of 0.75 (1.18) eV as calculated by generalized gradient approximation with Perdew-Burke-Ernzerhof (HSE06) functional. Four high-symmetry adsorption sites are considered, including on-top of B atom (TB), on-top of As atom (TAs), on-top of hollow site (TH), and on-top of bridge site (Tbridge). Using the criterion of adsorption energy, it is found thatTBandTbridgesites are favorable adsorption sites for H and O adatom, respectively. The analysis of electronic interactions indicate the charge transfer from host BAs monolayer to both adatoms. H adsorption conducts to the emergence of magnetic semiconductor nature in BAs monolayer with a total magnetic moment of 1.00 μB. Herein, the magnetism is originated mainly from H adatom and its neighbor As atoms. In contrast, the non-magnetic nature of BAs monolayer is preserved upon absorbing O atoms. In this case, the energy gap exhibits a slight reduction of 4%. Further, the effects of adatom coverage are also analyzed. The presented results suggest an effective modification of ground state electronic properties, as well as induction of new feature-rich properties to make new multifunctional 2D materials from non-magnetic BAs monolayer.
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Affiliation(s)
- Duy Khanh Nguyen
- Laboratory for Computational Physics, Institute for Computational Science and Artificial Intelligence, Van Lang University, Ho Chi Minh City, Vietnam
- Faculty of Mechanical-Electrical and Computer Engineering, School of Technology, Van Lang University, Ho Chi Minh City, Vietnam
| | - R Ponce-Pérez
- Universidad Nacional Autónoma de México, Centro de Nanociencias y Nanotecnología, Apartado Postal 14, Ensenada, Baja California Código Postal 22800, Mexico
| | - J Guerrero-Sanchez
- Universidad Nacional Autónoma de México, Centro de Nanociencias y Nanotecnología, Apartado Postal 14, Ensenada, Baja California Código Postal 22800, Mexico
| | - D M Hoat
- Institute of Theoretical and Applied Research, Duy Tan University, Ha Noi 100000, Vietnam
- Faculty of Natural Sciences, Duy Tan University, Da Nang 550000, Vietnam
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7
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Liu L, Wu X, Wang F, Zhang L, Wang X, Song S, Zhang H. Dual-Site Metal Catalysts for Electrocatalytic CO 2 Reduction Reaction. Chemistry 2023; 29:e202300583. [PMID: 37367498 DOI: 10.1002/chem.202300583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 06/25/2023] [Accepted: 06/25/2023] [Indexed: 06/28/2023]
Abstract
Electrocatalytic CO2 reduction reaction (CO2 RR) is a promising and green approach for reducing atmospheric CO2 concentration and achieving high-valued conversion of CO2 under the carbon-neutral policy. In CO2 RR, the dual-site metal catalysts (DSMCs) have received wide attention for their ingenious design strategies, abundant active sites, and excellent catalytic performance attributed to the synergistic effect between dual-site in terms of activity, selectivity and stability, which plays a key role in catalytic reactions. This review provides a systematic summary and detailed classification of DSMCs for CO2 RR, describes the mechanism of synergistic effects in catalytic reactions, and also introduces in situ characterization techniques commonly used in CO2 RR. Finally, the main challenges and prospects of dual-site metal catalysts and even multi-site catalysts for CO2 recycling are analyzed. It is believed that based on the understanding of bimetallic site catalysts and synergistic effects in CO2 RR, well-designed high-performance, low-cost electrocatalysts are promising for achieving CO2 conversion, electrochemical energy conversion and storage in the future.
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Affiliation(s)
- Li Liu
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5265, Renmin Street, Chaoyang District, Changchun, Jilin, 130022, P.R. China
- University of Science and Technology of China, 96, Jinzhai Road, Baohe District, Hefei, Anhui, 230026, P. R. China
| | - Xueting Wu
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5265, Renmin Street, Chaoyang District, Changchun, Jilin, 130022, P.R. China
- University of Science and Technology of China, 96, Jinzhai Road, Baohe District, Hefei, Anhui, 230026, P. R. China
| | - Fei Wang
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5265, Renmin Street, Chaoyang District, Changchun, Jilin, 130022, P.R. China
| | - Lingling Zhang
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5265, Renmin Street, Chaoyang District, Changchun, Jilin, 130022, P.R. China
| | - Xiao Wang
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5265, Renmin Street, Chaoyang District, Changchun, Jilin, 130022, P.R. China
- University of Science and Technology of China, 96, Jinzhai Road, Baohe District, Hefei, Anhui, 230026, P. R. China
| | - Shuyan Song
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5265, Renmin Street, Chaoyang District, Changchun, Jilin, 130022, P.R. China
- University of Science and Technology of China, 96, Jinzhai Road, Baohe District, Hefei, Anhui, 230026, P. R. China
| | - Hongjie Zhang
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5265, Renmin Street, Chaoyang District, Changchun, Jilin, 130022, P.R. China
- University of Science and Technology of China, 96, Jinzhai Road, Baohe District, Hefei, Anhui, 230026, P. R. China
- Department of Chemistry, Tsinghua University, 30, Shuangqing Road, Haidian District, Beijing, 100084, P. R. China
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8
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Thi Dieu Truong H, Reddy P, Reis MM, Archer R. Internal reflectance cell fluorescence measurement combined with multi-way analysis to detect fluorescence signatures of undiluted honeys and a fusion of fluorescence and NIR to enhance predictability. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 290:122274. [PMID: 36580751 DOI: 10.1016/j.saa.2022.122274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/30/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Honey is a complex food matrix that contains diverse polyphenolic compounds. Some phenolics exhibit fluorescence signatures which can be used to evaluate honey quality, and authenticity and to determine botanical origin. Mānuka honey contains two unique fluorescence markers: Leptosperin (MM1) and LepteridineTM (MM2) that are derived from Leptospermum scoparium nectar. Fluorescence measurement of supersaturated solutions such as undiluted honeys can be challenged by complex inner filter effects. The current study shows the ability of internal reflectance cell fluorescence measurement and multi-way analysis to detect fluorophores in undiluted honeys. This study scanned honeys from different geographic districts generating excitation emission matrices (250-400/300-600 nm), and by near infrared (NIR) hyperspectral camera (547-1701 nm). PARAFAC and tri-PLS could track two fluorescence markers: MM1 (R2 = 0.82 & RMSEP = 138.65) and MM2 (R2 = 0.82 & RMSEP = 2.75) from undiluted honey fluorescence data with > 80 % accuracy. Classification of mono-floral, multi-floral and non-mānuka honeys achieved 90 % overall accuracy. Fusion of fluorescence data at ƛex 270 & 330 nm and NIR hyperspectral data combined with multi-block PLS analysis enhances predictability of fluorescence markers further. The study revealed the potential of internal reflectance cell fluorescence measurement combined with chemometrics and data fusion for rapid evaluation of honey quality and botanical origin.
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Affiliation(s)
- Hien Thi Dieu Truong
- School of Food and Advanced Technology, Massey University, Riddet Road, Fitzherbert, Palmerston North 4410, New Zealand.
| | - Pullanagari Reddy
- School of Food and Advanced Technology, Massey University, Riddet Road, Fitzherbert, Palmerston North 4410, New Zealand
| | - Marlon M Reis
- Food Informatics, AgResearch, Riddet Road, Massey University Manawatu Tennent Drive, Turitea 4474, New Zealand
| | - Richard Archer
- School of Food and Advanced Technology, Massey University, Riddet Road, Fitzherbert, Palmerston North 4410, New Zealand; Riddet Institute, University Avenue, Fitzherbert, Palmerston North 4474, New Zealand
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9
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Ziegler R, Purtscher FRS, Schwartz HA, Hofer TS, Heymann G. First ternary tungsten tellurate(IV) WTe 2O 7 with unique crystal structure type. Dalton Trans 2023; 52:2243-2254. [PMID: 36525293 DOI: 10.1039/d2dt03419k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
At multianvil high-pressure/high-temperature conditions of 10 GPa and 1273 K, the first ternary tungsten tellurate WTe2O7 is formed, starting from a stoichiometric mixture of WO3 and TeO2. The compound crystallizes triclinic in a hitherto unknown crystal structure type with the space group P1̄; (no. 2), and was refined from single-crystal X-ray diffractometer data: a = 538.3(1), b = 687.5(1), c = 802.3(1) pm, α = 72.4(1)°, β = 85.7(1)°, γ = 68.1(1)°, wR2 = 0.0323, GooF = 1.048, 3157 F2 values, and 106 variables. The main motifs of the crystal structure are pairs of edge-linked [WO6]6- octahedra and fourfold oxygen-coordinated Te4+ atoms. The oxidation state of W6+ and Te4+ was further verified by measuring the characteristic binding energy values for the W 4f and the Te 3d core levels via X-ray photoelectron spectroscopy (XPS). In addition, DFT calculations of the structure, the associated electron localisation functions (ELF) and vibrational spectra have been carried out. The theoretical data clearly demonstrates the impact of the residual electron density located at the Te4+ ions, which can be directly interpreted as the presence of lone electron pairs within the solid structure.
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Affiliation(s)
- Raimund Ziegler
- University of Innsbruck, Department for General, Inorganic and Theoretical Chemistry, Innrain 80-82, 6020 Innsbruck, Austria.
| | - Felix R S Purtscher
- University of Innsbruck, Department for General, Inorganic and Theoretical Chemistry, Innrain 80-82, 6020 Innsbruck, Austria.
| | - Heidi A Schwartz
- University of Innsbruck, Department for General, Inorganic and Theoretical Chemistry, Innrain 80-82, 6020 Innsbruck, Austria.
| | - Thomas S Hofer
- University of Innsbruck, Department for General, Inorganic and Theoretical Chemistry, Innrain 80-82, 6020 Innsbruck, Austria.
| | - Gunter Heymann
- University of Innsbruck, Department for General, Inorganic and Theoretical Chemistry, Innrain 80-82, 6020 Innsbruck, Austria.
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10
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Böselt L, Aerts R, Herrebout W, Riniker S. Improving the IR spectra alignment algorithm with spectra deconvolution and combination with Raman or VCD spectroscopy. Phys Chem Chem Phys 2023; 25:2063-2074. [PMID: 36546852 PMCID: PMC9847344 DOI: 10.1039/d2cp04907d] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022]
Abstract
The relative stereochemistry of organic molecules can be determined by comparing theoretical and experimental infrared (IR) spectra of all isomers and assessing the best match. For this purpose, we have recently developed the IR spectra alignment (IRSA) algorithm for automated optimal alignment. IRSA provides a set of quantitative metrics to identify the candidate structure that agrees best with the experimental spectrum. While the correct diastereomer could be determined for the tested sets of rigid and flexible molecules, two issues were identified with more complex compounds that triggered further development. First, strongly overlapping peaks in the IR spectrum are not treated adequately in the current IRSA implementation. Second, the alignment of multiple spectra from different sources (e.g. IR and VCD or Raman) can be improved. In this study, we present an in-depth discussion of these points, followed by the description of modifications to the IRSA algorithm to address them. In particular, we introduce the concept of deconvolution of the experimental and theoretical spectra with a set of pseudo-Voigt bands. The pseudo-Voigt bands have a set of parameters, which can be employed in the alignment algorithm, leading to improved scoring functions. We test the modified algorithm on two data sets. The first set contains compounds with IR and Raman spectra measured in this study, and the second set contains compounds with IR and VCD spectra available in the literature. We show that the algorithm is able to determine the correct diastereomer in all cases. The results highlight that vibrational spectroscopy can be a valuable alternative or complementary method to inform about the stereochemistry of compounds, and the performance of the updated IRSA algorithm suggests that it is a powerful tool for quantitative-based spectral assignments in academia and industry.
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Affiliation(s)
- Lennard Böselt
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland.
| | - Roy Aerts
- Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
| | - Wouter Herrebout
- Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
| | - Sereina Riniker
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland.
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11
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W. Huck C. Present and Future of Miniaturized NIR Spectrometers Combined with Challenging Data Management Strategies. MAKEDONSKO FARMACEVTSKI BILTEN 2022. [DOI: 10.33320/maced.pharm.bull.2022.68.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Affiliation(s)
- Christian W. Huck
- 1 Institute of Analytical Chemistry and Radiochemistry, CCB – Center for Chemistry and Radiochemistry, Leopold-Franzens University, Innsbruck, Austria
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12
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Moura RT, Quintano M, Antonio JJ, Freindorf M, Kraka E. Automatic Generation of Local Vibrational Mode Parameters: From Small to Large Molecules and QM/MM Systems. J Phys Chem A 2022; 126:9313-9331. [DOI: 10.1021/acs.jpca.2c07871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Renaldo T. Moura
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas75275-0314, United States
- Department of Chemistry and Physics Center of Agrarian Sciences, Federal University of Paraiba, Areia, PB58397-000, Brazil
| | - Mateus Quintano
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas75275-0314, United States
| | - Juliana J. Antonio
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas75275-0314, United States
| | - Marek Freindorf
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas75275-0314, United States
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas75275-0314, United States
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13
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Kraka E, Quintano M, La Force HW, Antonio JJ, Freindorf M. The Local Vibrational Mode Theory and Its Place in the Vibrational Spectroscopy Arena. J Phys Chem A 2022; 126:8781-8798. [DOI: 10.1021/acs.jpca.2c05962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, Texas75275-0314, United States
| | - Mateus Quintano
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, Texas75275-0314, United States
| | - Hunter W. La Force
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, Texas75275-0314, United States
| | - Juliana J. Antonio
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, Texas75275-0314, United States
| | - Marek Freindorf
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, Texas75275-0314, United States
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Zhang Y, Shen T, Zuo Z, Wang Y. ResNet and MaxEnt modeling for quality assessment of Wolfiporia cocos based on FT-NIR fingerprints. FRONTIERS IN PLANT SCIENCE 2022; 13:996069. [PMID: 36407623 PMCID: PMC9666765 DOI: 10.3389/fpls.2022.996069] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
As a fungus with both medicinal and edible value, Wolfiporia cocos (F. A. Wolf) Ryvarden & Gilb. has drawn more public attention. Chemical components' content fluctuates in wild and cultivated W. cocos, whereas the accumulation ability of chemical components in different parts is different. In order to perform a quality assessment of W. cocos, we proposed a comprehensive method which was mainly realized by Fourier transform near-infrared (FT-NIR) spectroscopy and ultra-fast liquid chromatography (UFLC). A qualitative analysis means was built a residual convolutional neural network (ResNet) to recognize synchronous two-dimensional correlation spectroscopy (2DCOS) images. It can rapidly identify samples from wild and cultivated W. cocos in different parts. As a quantitative analysis method, UFLC was used to determine the contents of three triterpene acids in 547 samples. The results showed that a simultaneous qualitative and quantitative strategy could accurately evaluate the quality of W. cocos. The accuracy of ResNet models combined synchronous FT-NIR 2DCOS in identifying wild and cultivated W. cocos in different parts was as high as 100%. The contents of three triterpene acids in Poriae Cutis were higher than that in Poria, and the one with wild Poriae Cutis was the highest. In addition, the suitable habitat plays a crucial role in the quality of W. cocos. The maximum entropy (MaxEnt) model is a common method to predict the suitable habitat area for W. cocos under the current climate. Through the results, we found that suitable habitats were mostly situated in Yunnan Province of China, which accounted for approximately 49% of the total suitable habitat area of China. The research results not only pave the way for the rational planting in Yunnan Province of China and resource utilization of W. cocos, but also provide a basis for quality assessment of medicinal fungi.
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Affiliation(s)
- YanYing Zhang
- Medicinal Plants Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, China
| | - Tao Shen
- College of Chemistry, Biology and Environment, Yuxi Normal University, Yuxi, China
| | - ZhiTian Zuo
- Medicinal Plants Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - YuanZhong Wang
- Medicinal Plants Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, China
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15
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Reagent-less and sub-minute quantification of sulfite in food samples using substrate-integrated hollow waveguide gas sensors coupled to deep-UV LED. Anal Chim Acta 2022; 1236:340596. [DOI: 10.1016/j.aca.2022.340596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/27/2022] [Accepted: 11/05/2022] [Indexed: 11/09/2022]
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16
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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: 7] [Impact Index Per Article: 3.5] [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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17
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Xenides D, Karamanis P. How do the available density functionals perform on the calculation of eigenvalues of frontier to deeper orbitals? A metric space evaluation of experimental and quantum chemical findings. Chem Phys 2022. [DOI: 10.1016/j.chemphys.2022.111600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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18
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Li L, Zuo Z, Wang Y. Practical Qualitative Evaluation and Screening of Potential Biomarkers for Different Parts of Wolfiporia cocos Using Machine Learning and Network Pharmacology. Front Microbiol 2022; 13:931967. [PMID: 35875572 PMCID: PMC9304917 DOI: 10.3389/fmicb.2022.931967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/09/2022] [Indexed: 11/26/2022] Open
Abstract
Wolfiporia cocos is a widely used traditional Chinese medicine and dietary supplement. Artificial intelligence algorithms use different types of data based on the different strategies to complete multiple tasks such as search and discrimination, which has become a trend to be suitable for solving massive data analysis problems faced in network pharmacology research. In this study, we attempted to screen the potential biomarkers in different parts of W. cocos from the perspective of measurability and effectiveness based on fingerprint, machine learning, and network pharmacology. Based on the conclusions drawn from the results, we noted the following: (1) exploratory analysis results showed that differences between different parts were greater than those between different regions, and the partial least squares discriminant analysis and residual network models were excellent to identify Poria and Poriae cutis based on Fourier transform near-infrared spectroscopy spectra; (2) from the perspective of effectiveness, the results of network pharmacology showed that 11 components such as dehydropachymic acid and 16α-hydroxydehydrotrametenolic acid, and so on had high connectivity in the “component-target-pathway” network and were the main active components. (3) From a measurability perspective, through orthogonal partial least squares discriminant analysis and the variable importance projection > 1, it was confirmed that three components, namely, dehydrotrametenolic acid, poricoic acid A, and pachymic acid, were the main potential biomarkers based on high-performance liquid chromatography. (4) The content of the three components in Poria was significantly higher than that in Poriae cutis. (5) The integrated analysis showed that dehydrotrametenolic acid, poricoic acid A, and pachymic acid were the potential biomarkers for Poria and Poriae cutis. Overall, this approach provided a novel strategy to explore potential biomarkers with an explanation for the clinical application and reasonable development and utilization in Poria and Poriae cutis.
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Affiliation(s)
- Lian Li
- Medicinal Plants Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, China
| | - ZhiTian Zuo
- Medicinal Plants Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
- *Correspondence: ZhiTian Zuo
| | - YuanZhong Wang
- Medicinal Plants Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
- YuanZhong Wang
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Yanes-Rodríguez R, Cabrera-Ramírez A, Prosmiti R. Delving into guest-free and He-filled sI and sII clathrate hydrates: a first-principles computational study. Phys Chem Chem Phys 2022; 24:13119-13129. [PMID: 35587105 DOI: 10.1039/d2cp00701k] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The dynamics of the formation of a specific clathrate hydrate as well as its thermodynamic transitions depend on the interactions between the trapped molecules and the host water lattice. The molecular-level understanding of the different underlying processes benefits not only the description of the properties of the system, but also allows the development of multiple technological applications such as gas storage, gas separation, energy transport, etc. In this work we investigate the stability of periodic crystalline structures, such as He@sI and He@sII clathrate hydrates by first-principles computations. We consider such host water networks interacting with a guest He atom using selected density functional theory approaches, in order to explore the effects on the encapsulation of a light atom in the sI/sII crystals, by deriving all energy components (guest-water, water-water, guest-guest). Structural properties and energies were first computed by structural relaxations of the He-filled and empty sI/sII unit cells, yielding lattice and compressibility parameters comparable to experimental and theoretical values available for those hydrates. According to the results obtained, the He enclathration in the sI/sII unit cells is a stabilizing process, and both He@sI and He@sII clathrates, considering single cage occupancy, are predicted to be stable whatever the XDM or D4 dispersion correction applied. Our results further reveal that despite the weak underlying interactions the He encapsulation has a rather notable effect on both lattice parameters and energetics, with the He@sII being the most energetically favorable in accord with recent experimental observations.
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Affiliation(s)
- Raquel Yanes-Rodríguez
- Institute of Fundamental Physics (IFF-CSIC), CSIC, Serrano 123, 28006 Madrid, Spain. .,Doctoral Programme in Theoretical Chemistry and Computational Modelling, Doctoral School, Universidad Autónoma de Madrid, Spain
| | - Adriana Cabrera-Ramírez
- Institute of Fundamental Physics (IFF-CSIC), CSIC, Serrano 123, 28006 Madrid, Spain. .,Doctoral Programme in Theoretical Chemistry and Computational Modelling, Doctoral School, Universidad Autónoma de Madrid, Spain
| | - Rita Prosmiti
- Institute of Fundamental Physics (IFF-CSIC), CSIC, Serrano 123, 28006 Madrid, Spain.
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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: 33] [Impact Index Per Article: 16.5] [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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21
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Biliškov N. Infrared spectroscopic monitoring of solid-state processes. Phys Chem Chem Phys 2022; 24:19073-19120. [DOI: 10.1039/d2cp01458k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We put a spotlight on IR spectroscopic investigations in materials science by providing a critical insight into the state of the art, covering both fundamental aspects, examples of its utilisation, and current challenges and perspectives focusing on the solid state.
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Affiliation(s)
- Nikola Biliškov
- Rudjer Bošković Institute, Bijenička c. 54, 10000 Zagreb, Croatia
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC, H3A 0B8, Canada
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22
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Beć KB, Grabska J, Huck CW, Mazurek S, Czarnecki MA. Anharmonicity and Spectra-Structure Correlations in MIR and NIR Spectra of Crystalline Menadione (Vitamin K 3). Molecules 2021; 26:6779. [PMID: 34833871 PMCID: PMC8620535 DOI: 10.3390/molecules26226779] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/03/2021] [Accepted: 11/08/2021] [Indexed: 12/03/2022] Open
Abstract
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.
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Affiliation(s)
- Krzysztof B. Beć
- CCB-Center for Chemistry and Biomedicine, Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, 6020 Innsbruck, Austria; (J.G.); (C.W.H.)
| | - Justyna Grabska
- CCB-Center for Chemistry and Biomedicine, Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, 6020 Innsbruck, Austria; (J.G.); (C.W.H.)
| | - Christian W. Huck
- CCB-Center for Chemistry and Biomedicine, Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, 6020 Innsbruck, Austria; (J.G.); (C.W.H.)
| | - Sylwester Mazurek
- Faculty of Chemistry, University of Wrocław, 50-383 Wrocław, Poland;
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