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Yang P, Kumarasiri A, Hore D. Surface populations as a model for the distance-dependence of the interfacial refractive index. J Chem Phys 2024; 161:054703. [PMID: 39087546 DOI: 10.1063/5.0221234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Accepted: 07/16/2024] [Indexed: 08/02/2024] Open
Abstract
Vibrational sum frequency spectra provide information about interfaces that is sensitive to the orientation of molecules, their electronic environment, and the local electric fields. Here, we use molecular dynamics simulations in order to study a surfactant, para-cyanophenol, at the air-water interface. The volume fractions of water and the organic surfactant are considered at various points over the nanometer-scale region in a Lorentz-Lorenz model. We find that the calculated ratios of nonlinear susceptibility tensor elements are in agreement with experimental data only when this depth profile was considered. We also use these data to evaluate the ratio of the C-N hyperpolarizability tensor elements in the interfacial region.
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Affiliation(s)
- Peter Yang
- Department of Chemistry, University of Victoria, Victoria, British Columbia V8W 3V6, Canada
| | - Aruna Kumarasiri
- Department of Chemistry, University of Victoria, Victoria, British Columbia V8W 3V6, Canada
| | - Dennis Hore
- Department of Chemistry, University of Victoria, Victoria, British Columbia V8W 3V6, Canada
- Department of Computer Science, University of Victoria, Victoria, British Columbia V8W 3P6, Canada
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2
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Upshur MA, Bé AG, Luo J, Varelas JG, Geiger FM, Thomson RJ. Organic synthesis in the study of terpene-derived oxidation products in the atmosphere. Nat Prod Rep 2023; 40:890-921. [PMID: 36938683 DOI: 10.1039/d2np00064d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023]
Abstract
Covering: 1997 up to 2022Volatile biogenic terpenes involved in the formation of secondary organic aerosol (SOA) particles participate in rich atmospheric chemistry that impacts numerous aspects of the earth's complex climate system. Despite the importance of these species, understanding their fate in the atmosphere and determining their atmospherically-relevant properties has been limited by the availability of authentic standards and probe molecules. Advances in synthetic organic chemistry directly aimed at answering these questions have, however, led to exciting discoveries at the interface of chemistry and atmospheric science. Herein we provide a review of the literature regarding the synthesis of commercially unavailable authentic standards used to analyze the composition, properties, and mechanisms of SOA particles in the atmosphere.
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Affiliation(s)
- Mary Alice Upshur
- Department of Chemistry, Northwestern University, 2145 Sheridan Rd, Evanston, IL 60208, USA.
| | - Ariana Gray Bé
- Department of Chemistry, Northwestern University, 2145 Sheridan Rd, Evanston, IL 60208, USA.
| | - Jingyi Luo
- Department of Chemistry, Northwestern University, 2145 Sheridan Rd, Evanston, IL 60208, USA.
| | - Jonathan G Varelas
- Department of Chemistry, Northwestern University, 2145 Sheridan Rd, Evanston, IL 60208, USA.
| | - Franz M Geiger
- Department of Chemistry, Northwestern University, 2145 Sheridan Rd, Evanston, IL 60208, USA.
| | - Regan J Thomson
- Department of Chemistry, Northwestern University, 2145 Sheridan Rd, Evanston, IL 60208, USA.
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Arano-Martinez JA, Martínez-González CL, Salazar MI, Torres-Torres C. A Framework for Biosensors Assisted by Multiphoton Effects and Machine Learning. BIOSENSORS 2022; 12:710. [PMID: 36140093 PMCID: PMC9496380 DOI: 10.3390/bios12090710] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/22/2022] [Accepted: 08/25/2022] [Indexed: 11/25/2022]
Abstract
The ability to interpret information through automatic sensors is one of the most important pillars of modern technology. In particular, the potential of biosensors has been used to evaluate biological information of living organisms, and to detect danger or predict urgent situations in a battlefield, as in the invasion of SARS-CoV-2 in this era. This work is devoted to describing a panoramic overview of optical biosensors that can be improved by the assistance of nonlinear optics and machine learning methods. Optical biosensors have demonstrated their effectiveness in detecting a diverse range of viruses. Specifically, the SARS-CoV-2 virus has generated disturbance all over the world, and biosensors have emerged as a key for providing an analysis based on physical and chemical phenomena. In this perspective, we highlight how multiphoton interactions can be responsible for an enhancement in sensibility exhibited by biosensors. The nonlinear optical effects open up a series of options to expand the applications of optical biosensors. Nonlinearities together with computer tools are suitable for the identification of complex low-dimensional agents. Machine learning methods can approximate functions to reveal patterns in the detection of dynamic objects in the human body and determine viruses, harmful entities, or strange kinetics in cells.
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Affiliation(s)
- Jose Alberto Arano-Martinez
- Sección de Estudios de Posgrado e Investigación, Escuela Superior de Ingeniería Mecánica y Eléctrica, Unidad Zacatenco, Instituto Politécnico Nacional, Mexico City 07738, Mexico
| | - Claudia Lizbeth Martínez-González
- Sección de Estudios de Posgrado e Investigación, Escuela Superior de Ingeniería Mecánica y Eléctrica, Unidad Zacatenco, Instituto Politécnico Nacional, Mexico City 07738, Mexico
| | - Ma Isabel Salazar
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Carlos Torres-Torres
- Sección de Estudios de Posgrado e Investigación, Escuela Superior de Ingeniería Mecánica y Eléctrica, Unidad Zacatenco, Instituto Politécnico Nacional, Mexico City 07738, Mexico
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von Domaros M, Liu Y, Butman JL, Perlt E, Geiger FM, Tobias DJ. Molecular Orientation at the Squalene/Air Interface from Sum Frequency Generation Spectroscopy and Atomistic Modeling. J Phys Chem B 2021; 125:3932-3941. [DOI: 10.1021/acs.jpcb.0c11158] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michael von Domaros
- Department of Chemistry, University of California Irvine, Irvine, California 92697, United States
| | - Yangdongling Liu
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Jana L. Butman
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Eva Perlt
- Department of Chemistry, University of California Irvine, Irvine, California 92697, United States
| | - Franz M. Geiger
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Douglas J. Tobias
- Department of Chemistry, University of California Irvine, Irvine, California 92697, United States
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Upshur MA, Vega MM, Bé AG, Chase HM, Zhang Y, Tuladhar A, Chase ZA, Fu L, Ebben CJ, Wang Z, Martin ST, Geiger FM, Thomson RJ. Synthesis and surface spectroscopy of α-pinene isotopologues and their corresponding secondary organic material. Chem Sci 2019; 10:8390-8398. [PMID: 31803417 PMCID: PMC6844218 DOI: 10.1039/c9sc02399b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 07/21/2019] [Indexed: 12/02/2022] Open
Abstract
The synthesis and surface-specific spectroscopic analysis of α-pinene isotopologues and their corresponding secondary organic material is reported.
Atmospheric aerosol–cloud interactions remain among the least understood processes within the climate system, leaving large uncertainties in the prediction of future climates. In particular, the nature of the surfaces of aerosol particles formed from biogenic terpenes, such as α-pinene, is poorly understood despite the importance of surface phenomena in their formation, growth, radiative properties, and ultimate fate. Herein we report the coupling of a site-specific deuterium labeling strategy with vibrational sum frequency generation (SFG) spectroscopy to probe the surface C–H oscillators in α-pinene-derived secondary organic aerosol material (SOM) generated in an atmospheric flow tube reactor. Three α-pinene isotopologues with methylene bridge, bridgehead methine, allylic, and vinyl deuteration were synthesized and their vapor phase SFG spectra were compared to that of unlabeled α-pinene. Subsequent analysis of the SFG spectra of their corresponding SOM revealed that deuteration of the bridge methylene C–H oscillators present on the cyclobutane ring in α-pinene leads to a considerable signal intensity decrease (ca. 30–40%), meriting speculation that the cyclobutane moiety remains largely intact within the surface bound species present in the SOM formed upon α-pinene oxidation. These insights provide further clues as to the complexity of aerosol particle surfaces, and establish a framework for future investigations of the heterogeneous interactions between precursor terpenes and particle surfaces that lead to aerosol particle growth under dynamically changing conditions in the atmosphere.
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Affiliation(s)
- Mary Alice Upshur
- Department of Chemistry , Northwestern University , Evanston , IL 60208 , USA . ;
| | - Marvin M Vega
- Department of Chemistry , Northwestern University , Evanston , IL 60208 , USA . ;
| | - Ariana Gray Bé
- Department of Chemistry , Northwestern University , Evanston , IL 60208 , USA . ;
| | - Hilary M Chase
- Department of Chemistry , Northwestern University , Evanston , IL 60208 , USA . ;
| | - Yue Zhang
- John A. Paulson School of Engineering and Applied Sciences , Harvard University , Cambridge , MA 02138 , USA
| | - Aashish Tuladhar
- William R. Wiley Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , WA 99352 , USA
| | - Zizwe A Chase
- William R. Wiley Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , WA 99352 , USA
| | - Li Fu
- William R. Wiley Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , WA 99352 , USA
| | - Carlena J Ebben
- Department of Chemistry , Northwestern University , Evanston , IL 60208 , USA . ;
| | - Zheming Wang
- William R. Wiley Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , WA 99352 , USA
| | - Scot T Martin
- John A. Paulson School of Engineering and Applied Sciences , Harvard University , Cambridge , MA 02138 , USA.,Department of Earth and Planetary Sciences , Harvard University , Cambridge , MA 02138 , USA
| | - Franz M Geiger
- Department of Chemistry , Northwestern University , Evanston , IL 60208 , USA . ;
| | - Regan J Thomson
- Department of Chemistry , Northwestern University , Evanston , IL 60208 , USA . ;
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Ivanova B, Spiteller M. Noncentrosymmetric organic crystals of barbiturates as potential nonlinear optical phores: experimental and theoretical analyses. CHEMICAL PAPERS 2019. [DOI: 10.1007/s11696-019-00835-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Abdeldjebar H, Belmiloud Y, Djitli W, Achour S, Brahimi M, Tangour B. Proton transfer in the benzimidazolone and benzimidazolthione tautomerism process catalyzed by polar protic solvents. PROGRESS IN REACTION KINETICS AND MECHANISM 2019. [DOI: 10.1177/1468678319825740] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The tautomeric equilibrium of benzimidazolone and benzimidazolthione have been studied by the density functional theory method using the CAM-B3LYP functional together with the 6-311G(d,p) basis set. Two separate mechanisms have been investigated: a direct intramolecular transfer using the polarizable continuum model and an indirect proton transfer assisted by a molecule of solvent (C6H12, H2O, CH3OH, and H2O2). In both cases, the results obtained indicate that ketone and thione are the most stable forms. However, the enhanced height of the activation barrier for the four-center mechanisms describing the tautomerism reaction as a direct intramolecular transfer implicates a relatively disadvantaged process. The participation of a polar protic solvent molecule allows the lowering of the activation energy barrier. Potential energy profiles of keto-enol and thio-enol tautomerism assisted by methanol and water are very different. The former one describes a concerted mechanism but the latter does not because it is associated with asynchronous processes that take place during the thio-enol tautomerism.
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Affiliation(s)
- Hasnia Abdeldjebar
- Laboratoire de Physico-Chimie Théorique et de Chimie Informatique, Faculté de Chimie, Université des Sciences et de la Technologie Houari Boumediene, Alger, Algeria
| | - Yamina Belmiloud
- Laboratoire de Physico-Chimie Théorique et de Chimie Informatique, Faculté de Chimie, Université des Sciences et de la Technologie Houari Boumediene, Alger, Algeria
| | - Wassila Djitli
- Laboratoire de Physico-Chimie Théorique et de Chimie Informatique, Faculté de Chimie, Université des Sciences et de la Technologie Houari Boumediene, Alger, Algeria
| | - Sofien Achour
- Research Unit of Modelisation on Fundamental Sciences and Didactics, IPEIEM, Université de Tunis El Manar, Tunis, Tunisia
| | - Meziane Brahimi
- Laboratoire de Physico-Chimie Théorique et de Chimie Informatique, Faculté de Chimie, Université des Sciences et de la Technologie Houari Boumediene, Alger, Algeria
| | - Bahoueddine Tangour
- Laboratoire de Physico-Chimie Théorique et de Chimie Informatique, Faculté de Chimie, Université des Sciences et de la Technologie Houari Boumediene, Alger, Algeria
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Shen Z, Lin CK, Zhu C, Lin SH. First-principles study on sum-frequency generation spectroscopy of methanol adsorbed on TiO 2(110) surface: Effects of substrate and molecular coverages. J Chem Phys 2019; 150:184112. [PMID: 31091896 DOI: 10.1063/1.5088885] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this work, starting from the general theory of sum-frequency generation (SFG), we proposed a computational strategy utilizing density functional theory with periodic boundary conditions to simulate the vibrational SFG of molecules/solid surface adsorption system. The method has been applied to the CH3OH/TiO2(110) system successfully. Compared with the isolated molecule model, our theoretical calculations showed that the TiO2 substrate can significantly alter the second-order susceptibilities of a methanol molecule which is directly related to the SFG intensity. In addition, the SFG spectra have obvious changes while the methanol coverage increases, especially for the OH vibration peaks. Our theoretical spectra agree reasonably well with experimental measurements at 1 ML coverage, and an interesting peak which is absent in the theoretical spectra is tentatively assigned to some CH3 stretch vibration of methanol adsorbed on the oxygen vacancy of TiO2.
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Affiliation(s)
- Zhitao Shen
- Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, Hsinchu 30010, Taiwan
| | - Chih-Kai Lin
- Center for Condensed Matter Sciences, National Taiwan University, Taipei 106, Taiwan
| | - Chaoyuan Zhu
- Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, Hsinchu 30010, Taiwan
| | - Sheng Hsien Lin
- Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, Hsinchu 30010, Taiwan
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Chase HM, Chen S, Fu L, Upshur MA, Rudshteyn B, Thomson RJ, Wang HF, Batista VS, Geiger FM. Orientations of nonlocal vibrational modes from combined experimental and theoretical sum frequency spectroscopy. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.01.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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10
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Ohto T, Hunger J, Backus EHG, Mizukami W, Bonn M, Nagata Y. Trimethylamine-N-oxide: its hydration structure, surface activity, and biological function, viewed by vibrational spectroscopy and molecular dynamics simulations. Phys Chem Chem Phys 2017; 19:6909-6920. [DOI: 10.1039/c6cp07284d] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Vibrational spectroscopy and molecular simulations revealed the hydrophilicity and hydrophobicity of TMAO in aqueous solution.
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Affiliation(s)
- Tatsuhiko Ohto
- Graduate School of Engineering Science
- Osaka University
- Toyonaka
- Japan
| | | | | | - Wataru Mizukami
- Department of Energy and Material Sciences
- Faculty of Engineering Sciences
- Kyushu University
- Fukuoka
- Japan
| | - Mischa Bonn
- Max Planck Institute for Polymer Research
- 55128 Mainz
- Germany
| | - Yuki Nagata
- Max Planck Institute for Polymer Research
- 55128 Mainz
- Germany
- Department of Theoretical and Computational Molecular Science
- Institute for Molecular Science
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Lin Y, Akimov AV. Dependence of Nonadiabatic Couplings with Kohn–Sham Orbitals on the Choice of Density Functional: Pure vs Hybrid. J Phys Chem A 2016; 120:9028-9041. [DOI: 10.1021/acs.jpca.6b09660] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Yuhan Lin
- Department
of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000, United States
| | - Alexey V. Akimov
- Department
of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000, United States
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