1
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Cheng Y, Ding C, Zhang T, Wang R, Mu R, Li Z, Li R, Shi J, Zhu C. Barrierless reactions of C2 Criegee intermediates with H 2SO 4 and their implication to oligomers and new particle formation. J Environ Sci (China) 2025; 149:574-584. [PMID: 39181669 DOI: 10.1016/j.jes.2023.12.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 08/27/2024]
Abstract
The formation of oligomeric hydrogen peroxide triggered by Criegee intermediate maybe contributes significantly to the formation and growth of secondary organic aerosol (SOA). However, to date, the reactivity of C2 Criegee intermediates (CH3CHOO) in areas contaminated with acidic gas remains poorly understood. Herein, high-level quantum chemical calculations and Born-Oppenheimer molecular dynamics (BOMD) simulations are used to explore the reaction of CH3CHOO and H2SO4 both in the gas phase and at the air-water interface. In the gas phase, the addition reaction of CH3CHOO with H2SO4 to generate CH3HC(OOH)OSO3H (HPES) is near-barrierless, regardless of the presence of water molecules. BOMD simulations show that the reaction at the air-water interface is even faster than that in the gas phase. Further calculations reveal that the HPES has a tendency to aggregate with sulfuric acids, ammonias, and water molecules to form stable clusters, meanwhile the oligomerization reaction of CH3CHOO with HPES in the gas phase is both thermochemically and kinetically favored. Also, it is noted that the interfacial HPES- ion can attract H2SO4, NH3, (COOH)2 and HNO3 for particle formation from the gas phase to the water surface. Thus, the results of this work not only elucidate the high atmospheric reactivity of C2 Criegee intermediates in polluted regions, but also deepen our understanding of the formation process of atmospheric SOA induced by Criegee intermediates.
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Affiliation(s)
- Yang Cheng
- Institute of Theoretical and Computational Chemistry, Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong, Shaanxi 723001, China
| | - Chao Ding
- Institute of Theoretical and Computational Chemistry, Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong, Shaanxi 723001, China
| | - Tianlei Zhang
- Institute of Theoretical and Computational Chemistry, Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong, Shaanxi 723001, China.
| | - Rui Wang
- Institute of Theoretical and Computational Chemistry, Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong, Shaanxi 723001, China
| | - Ruxue Mu
- Institute of Theoretical and Computational Chemistry, Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong, Shaanxi 723001, China
| | - Zeyao Li
- Institute of Theoretical and Computational Chemistry, Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong, Shaanxi 723001, China
| | - Rongrong Li
- Institute of Theoretical and Computational Chemistry, Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong, Shaanxi 723001, China
| | - Juan Shi
- Institute of Theoretical and Computational Chemistry, Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong, Shaanxi 723001, China
| | - Chongqin Zhu
- College of Chemistry, Key Laboratory of Theoretical & Computational Photochemistry of Ministry of Education, Beijing Normal University, Beijing 100190, China.
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2
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Kolek P, Andrzejak M, Uchacz T, Goclon J, Pogocki D, Kisała J, Bankiewicz B, Szlachcic P, Tulej M. LIF spectrum for the localised S 0 → S 1(ππ*) excitation in the H-bonded anthranilic acid dimer: Symmetry breaking or coupling of vibrations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 319:124491. [PMID: 38823243 DOI: 10.1016/j.saa.2024.124491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 03/07/2024] [Accepted: 05/19/2024] [Indexed: 06/03/2024]
Abstract
This study aims to investigate the impact of the π → π* excitation localised in one monomer on the equilibrium geometry and oscillations of the AA dimer. Several low-frequency vibrations appear in pairs in the LIF spectrum because oscillations involving intermolecular hydrogen bonds are coupled, generating approximately symmetric and antisymmetric combinations (especially the COOH rocking modes, LIF: 295 and 301 cm-1). Furthermore, quantitative evaluation based on the TDDFT(B3LYP) results indicates that a dozen among 90 intramolecular oscillations are strongly coupled. In contrast, most vibrations are decoupled or weakly coupled, since they involve remote parts of the monomers. This makes several single vibrations active in the LIF spectrum (including the bending mode of the NH···O intramolecular hydrogen bond associated the strongest vibronic band 442 cm-1), while the other in each pair remains inactive. The reason for decoupling of oscillations and symmetry breaking is that the π → π* electronic excitation is entirely localised within one of the monomers, which makes them no longer equivalent in terms of geometry and dynamics. Additionally, the excitation of one monomer induces strengthening and shortening by 6 pm of only one intermolecular hydrogen bond linking the carboxylic groups of both molecules. This causes the 1.7° in-plane distortion of the dimer and lowering of its symmetry to Cs group (from C2h for the S0 state). The distortion induces the activity of two low-frequency in-plane intermolecular vibrations, i.e. the geared oscillation (LIF: 58 cm-1) and the shearing motion (99 cm-1) of the monomers.
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Affiliation(s)
- Przemysław Kolek
- Institute of Physics, University of Rzeszów, 1 Pigonia Street, 35-310 Rzeszów, Poland.
| | - Marcin Andrzejak
- K. Gumiński Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | - Tomasz Uchacz
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | - Jakub Goclon
- Faculty of Chemistry, University of Bialystok, Ciolkowskiego 1K, 15-245 Bialystok, Poland
| | - Dariusz Pogocki
- Institute of Nuclear Chemistry and Technology, Dorodna 16, 03-195 Warsaw, Poland
| | - Joanna Kisała
- Institute of Biology University of Rzeszow, 1 Pigonia Street, 35-310 Rzeszow, Poland
| | - Barbara Bankiewicz
- Faculty of Chemistry, University of Bialystok, Ciolkowskiego 1K, 15-245 Bialystok, Poland
| | - Paweł Szlachcic
- Department of Chemistry, Faculty of Food Technology, University of Agriculture in Krakow, ul. Balicka 122, PL-31-149 Kraków, Poland
| | - Marek Tulej
- Physics Institute, Space Research and Planetary Sciences, University of Bern, Sidlerstrasse 5, CH-3012 Bern, Switzerland
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3
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Mifsud DV, Herczku P, Ramachandran R, Sundararajan P, Rahul KK, Kovács STS, Sulik B, Juhász Z, Rácz R, Biri S, Kaňuchová Z, Ioppolo S, Sivaraman B, McCullough RW, Mason NJ. A systematic mid-infrared spectroscopic study of thermally processed H 2S ices. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 319:124567. [PMID: 38843614 DOI: 10.1016/j.saa.2024.124567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/27/2024] [Accepted: 05/29/2024] [Indexed: 06/17/2024]
Abstract
The positive identification of the molecular components of interstellar icy grain mantles is critically reliant upon the availability of laboratory-generated mid-infrared absorption spectra which can be compared against data acquired by ground- and space-borne telescopes. However, one molecule which remains thus far undetected in interstellar ices is H2S, despite its important roles in astrochemical and geophysical processes. Such a lack of a detection is surprising, particularly in light of its relative abundance in cometary ices which are believed to be the most pristine remnants of pre-solar interstellar ices available for study. In this paper, we present the results of an extensive and quantitative mid-infrared spectroscopic characterisation of H2S ices deposited at 20, 40, and 70 K and thermally processed to sublimation in an ultrahigh-vacuum system. We anticipate our results to be useful in confirming the detection of interstellar H2S ice using high-resolution and high-sensitivity instruments such as the James Webb Space Telescope, as well as in the identification of solid H2S in icy environments in the outer Solar System, such as comets and moons.
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Affiliation(s)
- Duncan V Mifsud
- Centre for Astrophysics and Planetary Science, School of Physics and Astronomy, University of Kent, Canterbury CT2 7NH, United Kingdom; HUN-REN Institute for Nuclear Research (Atomki), Debrecen H-4026, Hungary
| | - Péter Herczku
- HUN-REN Institute for Nuclear Research (Atomki), Debrecen H-4026, Hungary
| | - Ragav Ramachandran
- Atomic, Molecular, and Optical Physics Division, Physical Research Laboratory, Ahmedabad 380009, India
| | - Pavithraa Sundararajan
- Atomic, Molecular, and Optical Physics Division, Physical Research Laboratory, Ahmedabad 380009, India
| | - K K Rahul
- HUN-REN Institute for Nuclear Research (Atomki), Debrecen H-4026, Hungary
| | - Sándor T S Kovács
- HUN-REN Institute for Nuclear Research (Atomki), Debrecen H-4026, Hungary
| | - Béla Sulik
- HUN-REN Institute for Nuclear Research (Atomki), Debrecen H-4026, Hungary
| | - Zoltán Juhász
- HUN-REN Institute for Nuclear Research (Atomki), Debrecen H-4026, Hungary
| | - Richárd Rácz
- HUN-REN Institute for Nuclear Research (Atomki), Debrecen H-4026, Hungary
| | - Sándor Biri
- HUN-REN Institute for Nuclear Research (Atomki), Debrecen H-4026, Hungary
| | - Zuzana Kaňuchová
- Astronomical Institute, Slovak Academy of Sciences, Tatranská Lomnica SK-059 60, Slovakia
| | - Sergio Ioppolo
- Centre for Interstellar Catalysis, Department of Physics and Astronomy, Aarhus University, Aarhus DK-8000, Denmark
| | - Bhalamurugan Sivaraman
- Atomic, Molecular, and Optical Physics Division, Physical Research Laboratory, Ahmedabad 380009, India
| | - Robert W McCullough
- Department of Physics and Astronomy, School of Mathematics and Physics, Queen's University Belfast, Belfast BT7 1NN, United Kingdom
| | - Nigel J Mason
- Centre for Astrophysics and Planetary Science, School of Physics and Astronomy, University of Kent, Canterbury CT2 7NH, United Kingdom; HUN-REN Institute for Nuclear Research (Atomki), Debrecen H-4026, Hungary.
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4
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Tognetti V, Joubert L. Exchange-correlation effects in interatomic energies for pure density functionals and their application to the molecular energy prediction. J Comput Chem 2024; 45:2270-2283. [PMID: 38847367 DOI: 10.1002/jcc.27431] [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: 11/28/2023] [Revised: 04/02/2024] [Accepted: 04/28/2024] [Indexed: 08/15/2024]
Abstract
In this proof-of-concept paper, we show how exchange-correlation effects can be simply recovered for interatomic energies within the interacting quantum atoms decomposition when local, gradient generalized, or meta-gradient generalized approximations are used in density functional theory (DFT) calculations. We also demonstrate how inhomogeneity and non-local effects can be introduced even from a pure local scheme, without resorting to any orbital information. Finally, we provide numerical evidence on a database of selected energetic molecules that this decomposition scheme can be efficiently used to build accurate models for the prediction of molecular energies from an initial "cheap" DFT calculation.
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Affiliation(s)
- Vincent Tognetti
- University of Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie University, Rouen, France
| | - Laurent Joubert
- University of Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie University, Rouen, France
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5
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Postnikov A, Majtyka-Piłat A, Chrobak D, Deniszczyk J. Calculated vibration spectrum of calcium hexahydroxodizincate dihydrate (qatranaite). SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 318:124414. [PMID: 38759573 DOI: 10.1016/j.saa.2024.124414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 05/01/2024] [Accepted: 05/05/2024] [Indexed: 05/19/2024]
Abstract
On the basis of first-principles electronic structure calculations, crystallographic parameters have been refined for calcium hydroxozincate (Qatranaite mineral), and the vibration properties (frequencies and eigenvectors) calculated. A detailed analysis of vibration modes is done, in the context of comparison with infrared and Raman spectra previously available. Special attention is paid to a posteriori symmetry analysis of vibration modes, discussing the latters' attribution to four irreducible representations of the P21/c space group, and to identifying stretchings and bendings of particular chemical bonds, pronounced in different vibrations. It turns out that high-frequency (>700 cm-1) vibrations of hydroxyl groups bridging the Ca or Zn cations differ quite considerably for crystallographically distinct hydroxyl positions. It is shown that the vibrations involving hydroxyl groups and crystalline water typically come about in quadruplets at very close frequencies, whereby different irreducible representations reflect different combinations of similar "molecular" vibrations of four identical entities (of each hydroxyl or water) present in the unit cell. However, some vibrations show exceptions from this rule. In addition to interpretation of earlier experimental investigations, our study indicates that the low-frequency (<700 cm-1) vibrations within the cation-hydroxyl connected skeleton are of more "solid-state-like" character and cannot be reasonably interpreted in terms of "molecular" vibrations within ZnO4 or CaO6 units.
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Affiliation(s)
- Andrei Postnikov
- LCP-A2MC, Université de Lorraine, Bd Arago 1, F-57078 Metz Cedex 3, France; Institute of Materials Engineering, University of Silesia in Katowice, 75 Pułku Piechoty 1A, 41-500, Chorzów, Poland.
| | - Anna Majtyka-Piłat
- Institute of Materials Engineering, University of Silesia in Katowice, 75 Pułku Piechoty 1A, 41-500, Chorzów, Poland
| | - Dariusz Chrobak
- Institute of Materials Engineering, University of Silesia in Katowice, 75 Pułku Piechoty 1A, 41-500, Chorzów, Poland
| | - Józef Deniszczyk
- Institute of Materials Engineering, University of Silesia in Katowice, 75 Pułku Piechoty 1A, 41-500, Chorzów, Poland.
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6
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Prell JS. Modeling collisional kinetic energy damping, heating, and cooling of ions in mass spectrometers: a tutorial perspective. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2024; 504:117290. [PMID: 39072228 PMCID: PMC11271708 DOI: 10.1016/j.ijms.2024.117290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Many powerful methods in mass spectrometry rely on activation of ions by high-energy collisions with gas particles. For example, multiple Collision Induced Dissociation (CID) has been used for many years to determine structural information for ions ranging from small organics to large, native-like protein complexes. More recently, Collision Induced Unfolding (CIU) has proved to be a very powerful method for understanding high-order protein structure and detecting differences between similar proteins. Quantifying the thermochemistry underlying dissociation/unfolding in these experiments can be quite challenging without reliable models of ion heating and cooling. Established physical models of CID are valuable in predicting ion heating but do not explicitly include mechanisms for cooling, which may play a large part in CID/CIU in modern instruments. Ab initio and Molecular Dynamics methods are extremely computationally expensive for modeling CID/CIU of large analytes such as biomolecular ions. In this tutorial perspective, limiting behaviors of ion kinetic energy damping, heating, and cooling set by "extreme" cases are explored, and an Improved Impulsive Collision Theory and associated software ("Ion Simulations of the Physics of Activation", IonSPA) are introduced that can model all of these for partially inelastic collisions. Finally, examples of modeled collisional activation of native-like protein ions under realistic experimental conditions are discussed, with an outlook toward the use of IonSPA in accessing the thermochemical information hidden in CID breakdown curves and CIU fingerprints.
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Affiliation(s)
- James S. Prell
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, OR, USA, 97403-1253
- Materials Science Institute, 1252 University of Oregon, OR, USA, 97403-1252
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7
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Malik U, Mazur M, Gudi RD, Mandaliya DD, Selvakannan PR, Bhargava SK. Colloidal carbon soot templated TiO 2/Ag surface functionalized 3D printed metal brushes as new generation surface enhanced Raman scattering substrates. J Colloid Interface Sci 2024; 671:325-335. [PMID: 38815369 DOI: 10.1016/j.jcis.2024.05.181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/14/2024] [Accepted: 05/23/2024] [Indexed: 06/01/2024]
Abstract
This present work demonstrated the functional transformation of 3D printed metal substrates into a new family of Surface-enhanced Raman Scattering substrates, a promising approach in developing SERS-based Point-of-care (PoC) analytical platforms. l-Powder Bed Fusion (l-PBF, Additive manufacturing or 3D printing technique) printed metal substrates have rough surfaces, and exhibit high thermal stability and intrinsic chemical inertness, necessitating a suitable surface functionalization approach. This present work demonstrated a unique multi-stage approach to transform l-PBF printed metal structures as recyclable SERS substrates by colloidal carbon templating, chemical vapor deposition, and electroless plating methods sequentially. The surface of the printed metal structures was functionalized using the colloidal carbon soot particles, that were formed by the eucalyptus oil flame deposition method. These carbon particles were shown to interact with the metals present in the printed structures by forming metal carbides and function as an adlayer on the surface. Subsequent deposition of TiO2 onto these templates led to strong grafting of TiO2 and retaining the fractal structure of the soot template onto the metal surface. Electroless deposition of silver nanoparticles resulted in the formation of fractally structured TiO2/Ag nanostructures and these functionalized printed metal structures were shown as excellent SERS substrates in enhancing the vibrational spectral features of Rhodamine B (RhB). The presence of TiO2 photocatalyst on the surface was shown to remove the RhB analyte from the surface under photochemical conditions, which enables the regeneration of SERS activity, and the substrate can be recycled. The migration of metals from the printed metal structures into the fractally ordered TiO2/Ag nanostructures was found to enhance the photocatalytic activity and increase the recyclability of these substrates. This study demonstrates the potential of 3D-printed Inconel metal substrates as next-generation recyclable SERS platforms, offering a substantial advancement over traditional colloidal, thin-film, flexible, and hard SERS substrates.
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Affiliation(s)
- Uzma Malik
- Centre for Advanced Materials and Industrial Chemistry (CAMIC), School of Science, RMIT University, Melbourne 3001, Victoria, Australia
| | - Maciej Mazur
- Centre for Additive Manufacturing, School of Engineering, RMIT University, 3001, Victoria, Australia
| | - Ravindra D Gudi
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Dharmendra D Mandaliya
- Department of Chemical Engineering, L.D. College of Engineering, Ahmedabad 380015, India
| | - P R Selvakannan
- Centre for Advanced Materials and Industrial Chemistry (CAMIC), School of Science, RMIT University, Melbourne 3001, Victoria, Australia.
| | - Suresh K Bhargava
- Centre for Advanced Materials and Industrial Chemistry (CAMIC), School of Science, RMIT University, Melbourne 3001, Victoria, Australia.
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8
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Iyer SS, Srivastava A. Membrane lateral organization from potential energy disconnectivity graph. Biophys Chem 2024; 313:107284. [PMID: 39002248 DOI: 10.1016/j.bpc.2024.107284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 06/17/2024] [Accepted: 06/19/2024] [Indexed: 07/15/2024]
Abstract
Understanding the thermodynamic and kinetic properties of biomolecules requires elucidation of their complex energy landscape. A disconnectivity graph analysis of the energy landscape provides a framework for mapping the multi-dimensional landscape onto a two-dimensional representation while preserving the key features of the energy landscape. Several studies show that the structure or shape of the disconnectity graph is directly associated with the function of protein and nucleic acid molecules. In this review, we discuss how disconnectivity analysis of the potential energy surface can be extended to lipid molecules to glean important information about membrane organization. The shape of the disconnectivity graphs can be used to predict the lateral organization of multi-component lipid bilayer. We hope that this review encourages the use of disconnectivity graphs routinely by membrane biophysicists to predict the lateral organization of lipids.
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Affiliation(s)
| | - Anand Srivastava
- Molecular Biophysics Unit, Indian Institute of Science Bangalore, C. V. Raman Road, Bangalore, Karnataka 560012, India.
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9
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Zeng D, Shen T, Hu Y, Liu F, Liu Z, Song J, Guan R, Zhou C. ZnIn 2S 4-based multi-interface coupled photocatalyst for efficient photothermal synergistic catalytic hydrogen evolution. J Colloid Interface Sci 2024; 670:395-408. [PMID: 38772256 DOI: 10.1016/j.jcis.2024.05.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 05/06/2024] [Accepted: 05/16/2024] [Indexed: 05/23/2024]
Abstract
Photothermal synergistic catalysis is a novel technology that converts energy. In this study, ZnIn2S4 with S-vacancy (ZIS-Vs) is combined with Nickel, Nickle Oxide and Carbon Nanofiber aggregates (Ni-NiO@CNFs) to create a multi-interface coupled photocatalyst with double Schottky barrier, double channel and mixed photothermal conversion effect. Theoretical calculation confirms that the Gibbs free energy (ΔG*H) of the S-scheme heterojunction in the composite material is -0.07 eV, which is close to 0. This promotes the adsorption of H* and accelerates the formation of H2. Internal photothermal catalysis is achieved by visible-near infrared (Vis-NIR, RT) irradiation. The internal photothermal catalytic hydrogen production rate of the best sample (0.9Ni-NiO@CNFs/ZIS-Vs) is as high as 17.24 mmol·g-1·h-1, and its photothermal conversion efficiency (η) is as high as 61.42 %. Its hydrogen production efficiency is 20.52 times that of ZIS-Vs (0.84 mmol·g-1·h-1) under visible light (Vis, RT) conditions. When the Vis-NIR light source is combined with external heating (75 ℃), the hydrogen production efficiency is further improved, and the hydrogen production efficiency (29.16 mmol·g-1·h-1) is 26.75 times that of ZIS-Vs (1.09 mmol·g-1·h-1, Vis-NIR, RT). Further analysis shows that the increase in hydrogen production resulted from the apparent activation energy (Ea) of the catalyst decreasing from 16.7 kJ·mol-1 to 9.28 kJ·mol-1. This study provides a valuable prototype for the design of an efficient photothermal synergistic catalytic system.
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Affiliation(s)
- Danni Zeng
- Key Laboratory for Advanced Technology in Environmental Protection of Jiangsu Province, Yancheng Institute of Technology, Jiangsu, China
| | - Tingzhe Shen
- Key Laboratory for Advanced Technology in Environmental Protection of Jiangsu Province, Yancheng Institute of Technology, Jiangsu, China
| | - Yadong Hu
- Key Laboratory for Advanced Technology in Environmental Protection of Jiangsu Province, Yancheng Institute of Technology, Jiangsu, China; School of Materials Science and Engineering, Henan Polytechnic University, Jiaozuo, China
| | - Fengjiao Liu
- Key Laboratory for Advanced Technology in Environmental Protection of Jiangsu Province, Yancheng Institute of Technology, Jiangsu, China
| | - Ze Liu
- Key Laboratory for Advanced Technology in Environmental Protection of Jiangsu Province, Yancheng Institute of Technology, Jiangsu, China
| | - Jun Song
- Key Laboratory for Advanced Technology in Environmental Protection of Jiangsu Province, Yancheng Institute of Technology, Jiangsu, China
| | - Rongfeng Guan
- Key Laboratory for Advanced Technology in Environmental Protection of Jiangsu Province, Yancheng Institute of Technology, Jiangsu, China.
| | - Changjian Zhou
- School of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Jiangsu, China.
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10
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Tian Y, Zeng W, Dong X, Huang L, Zhou Y, Zeng H, Lin Z, Zou G. Enhanced UV Nonlinear Optical Properties in Layered Germanous Phosphites through Functional Group Sequential Construction. Angew Chem Int Ed Engl 2024; 63:e202409093. [PMID: 38850113 DOI: 10.1002/anie.202409093] [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: 05/14/2024] [Revised: 06/07/2024] [Accepted: 06/07/2024] [Indexed: 06/09/2024]
Abstract
This study pioneers a novel strategy for synthesizing solar-blind ultraviolet (UV) nonlinear optical (NLO) crystals through functional groups sequential construction, effectively addressing the inherent trade-offs among broad transmittance, enhanced second-harmonic generation (SHG), and optimal birefringence. We have developed two innovative van der Waals layered germanous phosphites: GeHPO3, the first Ge(II)-based oxide NLO crystal which exhibits a black phosphorus-like structure, and K(GeHPO3)2Br, distinguished by its exceptional birefringence and graphene-like structure. Significantly, GeHPO3 exhibits a remarkable array of NLO properties, including the highest SHG coefficient recorded among all NLO crystals for phase-matching and generating 266 nm coherent light via quadruple frequency conversion. It delivers a potent SHG intensity, surpassing KH2PO4 (KDP) by 10.3 times at 1064 nm and β-BaB2O4 by 1.3 times at 532 nm, complemented by a distinct UV absorption edge at 211 nm and moderate birefringence of 0.062 at 546 nm. Comprehensive theoretical analysis links these exceptional characteristics to the unique NLO-active GeO3 4- units and the distinctive, highly ordered layered structures. Our findings deliver essential experimental insights into the development of Ge(II)-based optoelectronic materials and present a strategic blueprint for engineering structure-driven functional materials with customized properties.
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Affiliation(s)
- Yao Tian
- College of Chemistry, Sichuan University, Chengdu, 610065, P. R. China
| | - Wei Zeng
- College of Chemistry, Sichuan University, Chengdu, 610065, P. R. China
| | - Xuehua Dong
- College of Chemistry and Materials Science, Sichuan Normal University, Chengdu, 610066, P. R. China
| | - Ling Huang
- College of Chemistry and Materials Science, Sichuan Normal University, Chengdu, 610066, P. R. China
| | - Yuqiao Zhou
- College of Chemistry, Sichuan University, Chengdu, 610065, P. R. China
| | - Hongmei Zeng
- College of Chemistry, Sichuan University, Chengdu, 610065, P. R. China
| | - Zhien Lin
- College of Chemistry, Sichuan University, Chengdu, 610065, P. R. China
| | - Guohong Zou
- College of Chemistry, Sichuan University, Chengdu, 610065, P. R. China
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11
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Zhang W, Xu L, Zhang H. Recent advances in mass spectrometry techniques for atmospheric chemistry research on molecular-level. MASS SPECTROMETRY REVIEWS 2024; 43:1091-1134. [PMID: 37439762 DOI: 10.1002/mas.21857] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/06/2023] [Accepted: 06/21/2023] [Indexed: 07/14/2023]
Abstract
The Earth's atmosphere is composed of an enormous variety of chemical species associated with trace gases and aerosol particles whose composition and chemistry have critical impacts on the Earth's climate, air quality, and human health. Mass spectrometry analysis as a powerful and popular analytical technique has been widely developed and applied in atmospheric chemistry for decades. Mass spectrometry allows for effective detection, identification, and quantification of a broad range of organic and inorganic chemical species with high sensitivity and resolution. In this review, we summarize recently developed mass spectrometry techniques, methods, and applications in atmospheric chemistry research in the past several years on molecular-level. Specifically, new developments of ion-molecule reactors, various soft ionization methods, and unique coupling with separation techniques are highlighted. The new mass spectrometry applications in laboratory studies and field measurements focused on improving the detection limits for traditional and emerging volatile organic compounds, characterizing multiphase highly oxygenated molecules, and monitoring particle bulk and surface compositions.
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Affiliation(s)
- Wen Zhang
- Department of Chemistry, University of California, Riverside, California, USA
| | - Lu Xu
- NOAA Chemical Sciences Laboratory, Boulder, Colorado, USA
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, Colorado, USA
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Missouri, USA
| | - Haofei Zhang
- Department of Chemistry, University of California, Riverside, California, USA
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12
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Mancini L, Vanuzzo G, Recio P, Caracciolo A, Faginas-Lago N, Rosi M, Casavecchia P, Balucani N. Unveiling the Reaction Mechanism of the N( 2D) + Pyridine Reaction: Ring-Contraction versus 7-Membered-Ring Formation Channels. J Phys Chem A 2024; 128:7177-7194. [PMID: 39141013 DOI: 10.1021/acs.jpca.4c02924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
Despite the relevance of the reactions of the prototypical nitrogen-containing six-membered aromatic molecule (N-heterocyclic) of pyridine (C6H5N) in environmental science, astrochemistry, planetary science, prebiotic chemistry, and materials science, few experimental/theoretical studies exist on the bimolecular reactions involving pyridine and neutral atomic/molecular radicals. We report a combined experimental and theoretical study on the elementary reaction of pyridine with excited nitrogen atoms, N(2D), aimed at providing information about the primary reaction products and their branching fractions (BFs). From previous crossed molecular beam (CMB) experiments with mass-spectrometric detection and present synergistic calculations of the reactive potential energy surface (PES) and product BFs we have unveiled the reaction mechanism. It is found that the reaction proceeds via N(2D) barrierless addition to pyridine that, via bridged intermediates followed by N atom "sliding" into the ring, leads to 7-membered-ring structures. They further evolve, mainly via ring-contraction mechanisms toward 5-membered-ring radical products and, to a smaller extent, via H-displacement mechanisms toward 7-membered-ring isomeric products and their isomers. Using the theoretical statistical estimates, an improved fit of the experimental data previously reported has been obtained, leading to the following results for the dominant product channels: C4H4N (pyrrolyl) + HCN (BF = 0.61 ± 0.20), C3H3N2 (1H-imidazolyl/1H-pyrazolyl) + C2H2 (BF = 0.11 ± 0.06), and C5H4N2 (7-membered-ring molecules or pyrrole carbonitriles) + H (BF = 0.28 ± 0.10). The ring-contraction product channels C4H4N (pyrrolyl) + HCN, C3H3N2 (1H-imidazolyl) + C2H2, C3H3N2 (1H-pyrazolyl) + C2H2, and C5H5 (cyclopentadienyl) + N2 have statistical BFs of 0.54, 0.09, 0.11, and 0.07, respectively. Among the H-displacement channels, the cyclic-CHCHCHCHNCN + H channel and cyclic-CHCHCHCHCN2 + H are theoretically predicted to have a comparable BF (0.07 and 0.06, respectively), while the other isomeric 7-membered-ring molecule + H channel has a BF of 0.03. Pyrrole-carbonitriles and 1H-ethynyl-1H-imidazole (+ H) isomeric channels have an overall BF of 0.03. Implications for the chemistry of Saturn's moon Titan and prebiotic chemistry, as well as for understanding the N-doping of graphene or carbon nanotubes, are noted.
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Affiliation(s)
- Luca Mancini
- Dipartimento di Chimica Biologia e Biotecnologie, Università degli Studi di Perugia, 06123 Perugia, Italy
| | - Gianmarco Vanuzzo
- Dipartimento di Chimica Biologia e Biotecnologie, Università degli Studi di Perugia, 06123 Perugia, Italy
| | - Pedro Recio
- Dipartimento di Chimica Biologia e Biotecnologie, Università degli Studi di Perugia, 06123 Perugia, Italy
| | - Adriana Caracciolo
- Dipartimento di Chimica Biologia e Biotecnologie, Università degli Studi di Perugia, 06123 Perugia, Italy
| | - Noelia Faginas-Lago
- Dipartimento di Chimica Biologia e Biotecnologie, Università degli Studi di Perugia, 06123 Perugia, Italy
- Master-Tec Srl, 06128 Perugia, Italy
| | - Marzio Rosi
- Dipartimento di Ingegneria Civile e Ambientale, Università degli Studi di Perugia, 06125 Perugia, Italy
- Computational Laboratory for Hybrid/Organic Photovoltaics (CLHYO), Istituto CNR di Scienze e Tecnologie Chimiche "Giulio Natta" (CNR-SCITEC), 06123 Perugia, Italy
| | - Piergiorgio Casavecchia
- Dipartimento di Chimica Biologia e Biotecnologie, Università degli Studi di Perugia, 06123 Perugia, Italy
- Computational Laboratory for Hybrid/Organic Photovoltaics (CLHYO), Istituto CNR di Scienze e Tecnologie Chimiche "Giulio Natta" (CNR-SCITEC), 06123 Perugia, Italy
| | - Nadia Balucani
- Dipartimento di Chimica Biologia e Biotecnologie, Università degli Studi di Perugia, 06123 Perugia, Italy
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13
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Bödecker M, Mihrin D, Suhm MA, Wugt Larsen R. Regularities and Anomalies in Neon Matrix Shifts of Hydrogen-Bonded O-H Stretching Fundamentals. J Phys Chem A 2024; 128:7124-7136. [PMID: 39155731 DOI: 10.1021/acs.jpca.4c03468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2024]
Abstract
O-H bond stretching vibrations in hydrogen-bonded complexes embedded into cryogenic neon matrices are subtly downshifted from cold gas phase reference wavenumbers. To the extent that this shift is systematic, it enables neon matrices as more universally applicable spectroscopic benchmark environments for quantum chemical predictions. Outliers are indicative of either an assignment problem in one of the two cryogenic experiments or they reveal interesting dynamics or structural effects on the complexes as a function of the environment. We compile 6 literature-known pairs of experimental data in jet and neon matrix expansions and realize a 6-fold expansion of that number through targeted matrix isolation and/or slit jet expansion spectroscopy presented in this work. In many cases, the neon matrix shift is less than the uncertainty of the currently best-performing blind quantum chemical predictions for the gas phase, but in specific cases, it may exceed the currently achievable theoretical accuracy. Some evidence for a positive correlation of the matrix shift with the hydrogen bond shift is found, similar to observations for helium nanodroplets. Outliers in particular for water acting as a donor are discussed, and in a few cases they call for a future reinvestigation. Substantial improvement in the correlation of the matrix shift with the hydrogen bond shift is achieved for ketone monohydrates by removing a vibrational resonance. New insights into nitrile hydration isomerism are obtained, and the linear OH stretching spectrum of the jet-cooled ammonia-water complex is presented for the first time. Vibrational spectroscopy in weakly perturbing solid rare gas quantum matrices for the benchmarking of gas phase theory and future explicit theoretical treatments of the quantum matrix environment to better understand the outliers are both encouraged.
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Affiliation(s)
- Margarethe Bödecker
- Institute of Physical Chemistry, University of Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany
| | - Dmytro Mihrin
- Department of Chemistry, Technical University of Denmark, Kemitorvet 206, 2800 Kgs. Lyngby, Denmark
| | - Martin A Suhm
- Institute of Physical Chemistry, University of Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany
| | - René Wugt Larsen
- Department of Chemistry, Technical University of Denmark, Kemitorvet 206, 2800 Kgs. Lyngby, Denmark
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14
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Terry LM, Klumb MK, Nemchick DJ, Hodyss R, Maiwald F, Weber JM. Cryogenic Ion Vibrational Spectroscopy of Protonated Valine: Messenger Tag Effects. J Phys Chem A 2024; 128:7137-7144. [PMID: 39150465 DOI: 10.1021/acs.jpca.4c03552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
We report the infrared photodissociation spectrum of tagged protonated valine in the range 1000-1900 cm-1, prepared in a cryogenic ion trap. Comparison of experimental results with calculated infrared spectra based on density functional theory shows that the hydroxyl group of the carboxylic acid functionality and the protonated amine group adopt a trans configuration. Nitrogen and methane molecules were used as messenger tags with optimal tagging temperatures of 30 K for N2 and 60 K for CH4. While the calculated infrared spectra of the tagged ion suggest only a weak influence of the messenger tag on the frequency positions of ValH+, the measured intensities for N2-tagged ValH+ appear strongly suppressed for all but the highest frequency feature at 1773 cm-1. We trace this behavior to the binding energy of the N2 tag, which is significantly higher than that of CH4, based on density functional and coupled cluster calculations and rate estimates for photoinduced unimolecular dissociation from statistical theory.
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Affiliation(s)
- Lane M Terry
- JILA and Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309-0440, United States
| | - Maddie K Klumb
- JILA and Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309-0440, United States
| | - Deacon J Nemchick
- California Institute of Technology, NASA Jet Propulsion Laboratory, Pasadena, California 91109, United States
| | - Robert Hodyss
- California Institute of Technology, NASA Jet Propulsion Laboratory, Pasadena, California 91109, United States
| | - Frank Maiwald
- JILA and Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309-0440, United States
| | - J Mathias Weber
- JILA and Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309-0440, United States
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15
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Xu A, Ma Y, Yan D, Li F, Song F, Zhou T, Yuan Z, Liu X, Liu J, Wang F. Imaging Spin-Orbit Excitation of Yttrium through High-Energy Collisions with Rare Gas Atoms. J Phys Chem Lett 2024; 15:8721-8727. [PMID: 39162198 DOI: 10.1021/acs.jpclett.4c01924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/21/2024]
Abstract
The energy required for spin-orbit excitation plays a critical role in understanding translational-to-electronic energy conversion, particularly in chemical reactions involving changes in spin states. This is particularly important for transition metal atoms possessing d-orbitals, which result in multiple spin-orbit split energy levels at low energies. The accurate identification and characterization of spin-orbit transitions in such species require advanced experimental techniques and theoretical support. In this study, the spin-orbit excited collisions of Y(2D3/2) with rare gas atoms Ne, Ar, and Kr leading to Y(2D5/2) were observed using laser-ablated crossed-beam and time-sliced ion velocity mapping imaging techniques. Through a comparison of the forward angular distributions of Y(2D3/2) to the backward and sideway scattering distributions of Y(2D5/2) from elastic and inelastic collisions of Y(2D) with rare gas atoms, this study reveals that the spin-orbit electronic excitation occurs with high collision energy and low impact parameters from backward and sideway collisions. The effectiveness of the spin-orbit excitation process is strongly dependent on the collision energy or temperature, suggesting that energy requirements of the process have to be considered in chemical reactions involving changes in spin states.
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Affiliation(s)
- Ang Xu
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Collaborative Innovation Centre of Chemistry for Energy Materials (iChEM), Fudan University, Shanghai 200438, China
| | - Yujie Ma
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Collaborative Innovation Centre of Chemistry for Energy Materials (iChEM), Fudan University, Shanghai 200438, China
| | - Dong Yan
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Collaborative Innovation Centre of Chemistry for Energy Materials (iChEM), Fudan University, Shanghai 200438, China
| | - Fangfang Li
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Collaborative Innovation Centre of Chemistry for Energy Materials (iChEM), Fudan University, Shanghai 200438, China
| | - Fei Song
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Collaborative Innovation Centre of Chemistry for Energy Materials (iChEM), Fudan University, Shanghai 200438, China
| | - Ti Zhou
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Collaborative Innovation Centre of Chemistry for Energy Materials (iChEM), Fudan University, Shanghai 200438, China
| | - Zihan Yuan
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Collaborative Innovation Centre of Chemistry for Energy Materials (iChEM), Fudan University, Shanghai 200438, China
| | - Xiyu Liu
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Collaborative Innovation Centre of Chemistry for Energy Materials (iChEM), Fudan University, Shanghai 200438, China
| | - Jiaxing Liu
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Collaborative Innovation Centre of Chemistry for Energy Materials (iChEM), Fudan University, Shanghai 200438, China
| | - Fengyan Wang
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Collaborative Innovation Centre of Chemistry for Energy Materials (iChEM), Fudan University, Shanghai 200438, China
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16
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Cigrang LLE, Worth GA. Modeling Photodissociation: Quantum Dynamics Simulations of Methanol. J Phys Chem A 2024. [PMID: 39194169 DOI: 10.1021/acs.jpca.4c03612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
Abstract
A comprehensive computational study of the gas-phase photodissociation dynamics of methanol is presented. Using a multiconfigurational active space based method (RASSCF) to obtain multidimensional potential energy surfaces (PESs) on-the-fly, direct quantum dynamics simulations were run using the variational multi-configurational Gaussian method (DD-vMCG). Different initial excitation energies were simulated to investigate the dependence of the branching ratios on the electronic state being populated. A detailed mechanistic explanation is provided for the observed differences with respect to the excitation energy. Population of the lowest lying excited state of methanol leads to rapid hydroxyl hydrogen loss as the main dissociation channel. This is rationalized by the strongly dissociative nature of the PES cut along the O-H stretching coordinate, confirmed by the broad feature in the absorption spectrum. In contrast, more energetic excitations lead mainly to C-O bond breaking. Again, analysis of the diabatic surfaces offers a clear explanation in terms of the nature of the electronic states involved and the coupling between them. The type of calculations presented, as well as the subsequent analysis of the results, should be seen as a general workflow for the modeling of photochemical reactions.
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Affiliation(s)
- Léon L E Cigrang
- Department of Chemistry, University College London, London WC1H 0AJ, United Kingdom
| | - Graham A Worth
- Department of Chemistry, University College London, London WC1H 0AJ, United Kingdom
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17
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Konings M, González-Lezana T, Camps S, Loreau J. Quantum and statistical state-to-state studies of cold Ar + H 2+ collisions. Phys Chem Chem Phys 2024; 26:22463-22471. [PMID: 39141100 DOI: 10.1039/d4cp02179g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
In this work we present new state-to-state integral scattering cross sections and initial-state selected rate coefficients for the 36Ar (1S) + H2+ (X2Σg+,v = 0,j) reactive system for collision energies up to 0.1 eV (with respect to the 36Ar (1S) + H2+ (X2Σg+,v = 0,j = 0) channel). To the best of our knowledge, these cross sections are the first fully state resolved ones that were obtained by performing time-independent quantum mechanical and quantum statistical calculations. For this purpose a new full-dimensional ground state 2A' adiabatic electronic potential energy surface was calculated at the MRCI+Q/aug-cc-pVQZ level of theory, which was fitted by means of machine learning methods. We find that a statistical quantum method and a statistical adiabatic channel model reproduce quantum mechanical initial-state selected cross sections fairly well, thus suggesting that complex-forming mechanisms seem to be playing an important role in the reaction dynamics of the reaction that was studied.
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Affiliation(s)
- Maarten Konings
- KU Leuven, Department of Chemistry, Celestijnenlaan 200F, B-3001 Leuven, Belgium.
| | | | - Simen Camps
- KU Leuven, Department of Chemistry, Celestijnenlaan 200F, B-3001 Leuven, Belgium.
| | - Jérôme Loreau
- KU Leuven, Department of Chemistry, Celestijnenlaan 200F, B-3001 Leuven, Belgium.
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18
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Zhao H, Sun Z. An improved method for reactive scatterings in ultra-cold conditions using the time-dependent approach. Phys Chem Chem Phys 2024; 26:22790-22797. [PMID: 39163005 DOI: 10.1039/d4cp02340d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/21/2024]
Abstract
A new efficient method for considering the long-range effect of reactive scattering processes in ultra-cold conditions has been developed using the time-dependent quantum wave packet theory, where the initial wave packet could be placed at a position near the interaction region. This is in contrast to previous methods, where the initial wave packet has to be placed far from the interaction region. The new method reduces the numerical effort significantly. Typical reactions, such as S(1D) + H2, D+ + H2, and 7Li + 7Li2 (v0 = 1, j0 = 0), under cold or ultra-cold conditions, are used to demonstrate the numerical efficiency of the new method.
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Affiliation(s)
- Hailin Zhao
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China.
| | - Zhigang Sun
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China.
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19
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Barclay AJ, McKellar ARW, Moazzen-Ahmadi N. New Infrared Spectra of Acetylene-Water Dimers: First Determination of the A Rotational Constant and Another K-Dependent Anomaly. J Phys Chem A 2024. [PMID: 39197045 DOI: 10.1021/acs.jpca.4c04599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2024]
Abstract
Infrared spectra of acetylene-water complexes are studied in the regions of the H2O ν2 bend (1600 cm-1) and the D2O ν1/ν3 stretches (2670-2808 cm-1), using tunable infrared sources to probe a pulsed supersonic slit jet expansion. In the H2O bend region, there is a puzzling absence of Ka = 0 transitions for C2H2-H2O, while both Ka = 0 and 1 are observed for C2D2-H2O. This continues a pattern of "missing" Ka states noted in previous infrared studies of acetylene-water. Noticeable line broadening gives estimates of upper state predissociation lifetimes of about 1.6 ns for C2D2-H2O with Ka' = 1, 0.8 ns for C2H2-H2O with Ka' = 1, and 0.8 ns for C2D2-H2O with Ka' = 0. The lifetime for C2H2-H2O Ka' = 0 must be much shorter (<0.05 ns) since rapid predissociation seems to be the only explanation for its absence in the spectrum. In the D2O ν3 region, clear sub-bands with Ka = 0 ← 1, 1 ← 0, and 2 ← 1 are observed which enable a good determination of the A rotational constant of C2H2-D2O (7.313 ± 0.007 cm-1), a first for acetylene-water dimer and larger than previously expected.
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Affiliation(s)
- A J Barclay
- Department of Physics and Astronomy, University of Calgary, 2500 University Drive North West, Calgary, Alberta T2N 1N4, Canada
| | - A R W McKellar
- National Research Council of Canada, Ottawa, Ontario K1A 0R6, Canada
| | - N Moazzen-Ahmadi
- Department of Physics and Astronomy, University of Calgary, 2500 University Drive North West, Calgary, Alberta T2N 1N4, Canada
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20
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DeCecco AC, Conrad AR, Floyd AM, Jasper AW, Hansen N, Dagaut P, Moody NE, Popolan-Vaida DM. Tracking the reaction networks of acetaldehyde oxide and glyoxal oxide Criegee intermediates in the ozone-assisted oxidation reaction of crotonaldehyde. Phys Chem Chem Phys 2024; 26:22319-22336. [PMID: 38980126 DOI: 10.1039/d4cp01942c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
The reaction of unsaturated compounds with ozone (O3) is recognized to lead to the formation of Criegee intermediates (CIs), which play a key role in controlling the atmospheric budget of hydroxyl radicals and secondary organic aerosols. The reaction network of two CIs with different functionality, i.e. acetaldehyde oxide (CH3CHOO) and glyoxal oxide (CHOCHOO) formed in the ozone-assisted oxidation reaction of crotanaldehyde (CA), is investigated over a temperature range between 390 K and 840 K in an atmospheric pressure jet-stirred reactor (JSR) at a residence time of 1.3 s, stoichiometry of 0.5 with a mixture of 1% crotonaldehyde, 10% O2, at an fixed ozone concentration of 1000 ppm and 89% Ar dilution. Molecular-beam mass spectrometry in conjunction with single photon tunable synchrotron vacuum-ultraviolet (VUV) radiation is used to identify elusive intermediates by means of experimental photoionization energy scans and ab initio threshold energy calculations for isomer identification. Addition of ozone (1000 ppm) is observed to trigger the oxidation of CA already at 390 K, which is below the temperature where the oxidation reaction of CA was observed in the absence of ozone. The observed CA + O3 product, C4H6O4, is found to be linked to a ketohydroperoxide (2-hydroperoxy-3-oxobutanal) resulting from the isomerization of the primary ozonide. Products corresponding to the CIs uni- and bi-molecular reactions were observed and identified. A network of CI reactions is identified in the temperature region below 600 K, characterized by CIs bimolecular reactions with species like aldehydes, i.e., formaldehyde, acetaldehyde, and crotonaldehyde and alkenes, i.e., ethene and propene. The region below 600 K is also characterized by the formation of important amounts of typical low-temperature oxidation products, such as hydrogen peroxide (H2O2), methyl hydroperoxide (CH3OOH), and ethyl hydroperoxide (C2H5OOH). Detection of additional oxygenated species such as alcohols, ketene, and aldehydes are indicative of multiple active oxidation routes. This study provides important information about the initial step involved in the CIs assisted oligomerization reactions in complex reactive environments where CIs with different functionalities are reacting simultaneously. It provides new mechanistic insights into ozone-assisted oxidation reactions of unsaturated aldehydes, which is critical for the development of improved atmospheric and combustion kinetics models.
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Affiliation(s)
- Alec C DeCecco
- Department of Chemistry, University of Central Florida, Orlando, FL 32816, USA.
| | - Alan R Conrad
- Department of Chemistry, University of Central Florida, Orlando, FL 32816, USA.
| | - Arden M Floyd
- Department of Chemistry, University of Central Florida, Orlando, FL 32816, USA.
| | - Ahren W Jasper
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Nils Hansen
- Combustion Research Facility, Sandia National Laboratories, Livermore, CA 94551, USA
| | - Philippe Dagaut
- Centre National de la Recherche Scientifique (CNRS), ICARE, 1C Avenue de la Recherche Scientifique, 45071 Orléans Cedex 2, France
| | - Nath-Eddy Moody
- Department of Chemistry, University of Central Florida, Orlando, FL 32816, USA.
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21
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Harville PA, Moss OC, Rana A, Snowden EA, Johnson MA. Demonstration of Capture, Cooling, Tagging, and Spectroscopic Characterization of UV Photoproduct Ions in a Cryogenic Ion Trap: Application to 266 nm Photofragment Ions from Rhodamine 6G. J Phys Chem A 2024. [PMID: 39194345 DOI: 10.1021/acs.jpca.4c04283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
Abstract
We demonstrate a method to determine the structures of the primary photodissociation products from a cryogenically cooled parent ion. In this approach, a target ion is cooled by a pulse of buffer gas and tagged in a 20 K Paul trap. The cold ion is then photodissociated by pulsed (∼5 ns) UV laser excitation, and the ionic products are trapped, cooled, and tagged by introduction of a second buffer gas pulse in the same trap. The tagged fragments are then ejected into a triple focusing, UV/vis/IR time-of-flight photofragmentation mass spectrometer which yields vibrational and electronic spectra of the mass-selected photofragments. These methods are demonstrated by application to the 266 nm photodissociation of the Rhodamine 6G cation to yield the R575 fragment ion based on loss of ethene as well as to a weaker secondary fragment arising from loss of m/z 43.
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Affiliation(s)
- Payten A Harville
- Sterling Chemistry Laboratory, Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Olivia C Moss
- Sterling Chemistry Laboratory, Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Abhijit Rana
- Sterling Chemistry Laboratory, Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Elizabeth A Snowden
- Sterling Chemistry Laboratory, Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Mark A Johnson
- Sterling Chemistry Laboratory, Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
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22
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Jambrina PG, Croft JFE, Balakrishnan N, Guo H, Aoiz FJ. Determination of collision mechanisms at low energies using four-vector correlations. Faraday Discuss 2024; 251:104-124. [PMID: 38836438 DOI: 10.1039/d3fd00173c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
In molecular dynamics, a fundamental question is how the outcome of a collision depends on the relative orientation of the collision partners before their interaction begins (the stereodynamics of the process). The preference for a particular orientation of the reactant complex is intimately related to the idea of a collision mechanism and the possibility of control, as revealed in recent experiments. Indeed, this preference holds not only for chemical reactions involving complex polyatomic molecules, but also for the simplest inelastic atom-diatom collisions at cold collision energies. In this work, we report how the outcome of rotationally inelastic collisions between two D2 molecules can be controlled by changing the alignment of their internuclear axes under the same or different polarization vectors. Our results demonstrate that a higher degree of control can be achieved when two internuclear axes are aligned, especially when both molecules are relaxed in the collision. The possibility of control extends to very low energies, even to the ultracold regime, when no control could be achieved just by the alignment of the internuclear axis of one of the colliding partners.
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Affiliation(s)
- P G Jambrina
- Departamento de Química Física, Universidad de Salamanca, Salamanca 37008, Spain.
| | - J F E Croft
- Department of Chemistry, Durham University, Durham, DH1 3LE, UK.
| | - N Balakrishnan
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Nevada 89154, USA.
| | - Hua Guo
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA.
| | - F J Aoiz
- Departamento de Química Física, Universidad Complutense, Madrid 28040, Spain.
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23
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Xiong L, Zhang L, Zhao B, Jiang B. Six-dimensional quantum dynamics of an Eley-Rideal reaction between gaseous and adsorbed hydrogen atoms on Cu(111). Faraday Discuss 2024; 251:457-470. [PMID: 38757528 DOI: 10.1039/d3fd00163f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
In the form of direct abstraction of a surface adsorbate by a gaseous projectile, the Eley-Rideal (ER) reaction at the gas-surface interface manifests interesting dynamics. Unfortunately, high-dimensional quantum dynamical (QD) studies for ER reactions remain very challenging, which demands a large configuration space and the coordinate transformation of wavefunctions. Here, we report the first six-dimensional (6D) fully coupled quantum scattering method for studying the ER reaction between gas phase H(D) atoms and adsorbed D(H) atoms on a rigid Cu(111) surface. Reaction probabilities and product rovibrational state distributions obtained by this 6D model are found to be quite different from those obtained by reduced-dimensional QD models, demonstrating the high-dimensional nature of the ER reaction. Using two distinct potential energy surfaces (PESs), we further discuss the influence of the PES on the calculated product vibrational and rotational state distributions, in comparison with experimental results. The lateral corrugation and the exothermicity of the PES are found to play a critical role in controlling the energy disposal in the ER reaction.
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Affiliation(s)
- Longlong Xiong
- Department of Chemical Physics, Key Laboratory of Precision and Intelligent Chemistry, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes, University of Science and Technology of China, Hefei, Anhui 230026, China.
| | - Liang Zhang
- Department of Chemical Physics, Key Laboratory of Precision and Intelligent Chemistry, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes, University of Science and Technology of China, Hefei, Anhui 230026, China.
| | - Bin Zhao
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, P. R. China.
| | - Bin Jiang
- Department of Chemical Physics, Key Laboratory of Precision and Intelligent Chemistry, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes, University of Science and Technology of China, Hefei, Anhui 230026, China.
- Hefei National Laboratory, University of Science and Technology of China, Hefei, 230088, China
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24
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Gray M, Bowling PE, Herbert JM. Comment on "Benchmarking Basis Sets for Density Functional Theory Thermochemistry Calculations: Why Unpolarized Basis Sets and the Polarized 6-311G Family Should Be Avoided". J Phys Chem A 2024. [PMID: 39190891 DOI: 10.1021/acs.jpca.4c00283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
Affiliation(s)
- Montgomery Gray
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Paige E Bowling
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
| | - John M Herbert
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
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25
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Schatz GC, Wodtke AM, Yang X. Spiers Memorial Lecture: New directions in molecular scattering. Faraday Discuss 2024; 251:9-62. [PMID: 38764350 DOI: 10.1039/d4fd00015c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2024]
Abstract
The field of molecular scattering is reviewed as it pertains to gas-gas as well as gas-surface chemical reaction dynamics. We emphasize the importance of collaboration of experiment and theory, from which new directions of research are being pursued on increasingly complex problems. We review both experimental and theoretical advances that provide the modern toolbox available to molecular-scattering studies. We distinguish between two classes of work. The first involves simple systems and uses experiment to validate theory so that from the validated theory, one may learn far more than could ever be measured in the laboratory. The second class involves problems of great complexity that would be difficult or impossible to understand without a partnership of experiment and theory. Key topics covered in this review include crossed-beams reactive scattering and scattering at extremely low energies, where quantum effects dominate. They also include scattering from surfaces, reactive scattering and kinetics at surfaces, and scattering work done at liquid surfaces. The review closes with thoughts on future promising directions of research.
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Affiliation(s)
- George C Schatz
- Dept of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
| | - Alec M Wodtke
- Institute for Physical Chemistry, Georg August University, Goettingen, Germany
- Max Planck Institute for Multidisciplinary Natural Sciences, Goettingen, Germany.
- International Center for the Advanced Studies of Energy Conversion, Georg August University, Goettingen, Germany
| | - Xueming Yang
- Dalian Institute for Chemical Physics, Chinese Academy of Sciences, Dalian, China
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen, China
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26
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Zagorec-Marks C, Kocheril GS, Krohn OA, Kieft T, Karpinska A, Softley TP, Lewandowski HJ. To form or not to form a reaction complex: exploring ion-molecule reactions between C 3H 4 isomers and Xe + and O 2. Faraday Discuss 2024; 251:125-139. [PMID: 38764353 DOI: 10.1039/d4fd00005f] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2024]
Abstract
Ion-molecule reactions are an essential contributor to the chemistry of a diverse range of environments. While a great deal of work has been done to understand the fundamental mechanisms driving these reactions, there is still much more to discover. Here, we expand upon prior studies on ion-molecule reactions involving two isomers of C3H4, allene (H2C3H2) and propyne (H3C3H). Specifically, we probe the previously observed isomeric dependent reactivity of these molecules by reacting them with two ions with nearly identical ionization potentials, Xe+ and O2+. Our goal is to determine if the isomer-dependent reaction mechanisms previously observed are universal for C3H4 or if they depend on the ion character as well. Through the combination of experimental measurements and theoretical calculations, we found that both isomeric structure and identity of the ion contribute to the propensity of a reaction complex forming or for only long-range charge transfer to occur.
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Affiliation(s)
- C Zagorec-Marks
- Department of Physics, University of Colorado, Boulder, CO 80309, USA.
- JILA, National Institute of Standards and Technology and the University of Colorado, Boulder, CO 80309, USA
| | - G S Kocheril
- Department of Physics, University of Colorado, Boulder, CO 80309, USA.
- JILA, National Institute of Standards and Technology and the University of Colorado, Boulder, CO 80309, USA
| | - O A Krohn
- Department of Physics, University of Colorado, Boulder, CO 80309, USA.
- JILA, National Institute of Standards and Technology and the University of Colorado, Boulder, CO 80309, USA
| | - T Kieft
- Department of Physics, University of Colorado, Boulder, CO 80309, USA.
- JILA, National Institute of Standards and Technology and the University of Colorado, Boulder, CO 80309, USA
| | - A Karpinska
- Department of Physics, University of Colorado, Boulder, CO 80309, USA.
- JILA, National Institute of Standards and Technology and the University of Colorado, Boulder, CO 80309, USA
- Department of Chemistry and Applied Life Sciences, ETH Zürich, 8093 Zürich, Switzerland
| | - T P Softley
- School of Chemistry, University of Birmingham, Edgbaston, B15 2TT, UK
| | - H J Lewandowski
- Department of Physics, University of Colorado, Boulder, CO 80309, USA.
- JILA, National Institute of Standards and Technology and the University of Colorado, Boulder, CO 80309, USA
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27
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Ritter ME, DeSouza SA, Ogden HM, Michael TJ, Mullin AS. Transient IR spectroscopy of optically centrifuged CO 2 (R186-R282) and collision dynamics for the J = 244-282 states. Faraday Discuss 2024; 251:140-159. [PMID: 38766993 DOI: 10.1039/d3fd00179b] [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
Collisions of optically centrifuged CO2 molecules with J = 244-282 (Erot = 22 800-30 300 cm-1) are investigated with high-resolution transient IR absorption spectroscopy to reveal collisional and orientational phenomena of molecules with hyper-thermal rotational energies. The optical centrifuge is a non-resonant optical excitation technique that uses ultrafast, 800 nm chirped pulses to drive molecules to extreme rotational states through sequential Raman transitions. The extent of rotational excitation is controlled by tuning the optical bandwidth of the excitation pulses. Frequencies of 30 R-branch ν3 fundamental IR probe transitions are measured for the J = 186-282 states of CO2, expanding beyond previously reported IR transitions up to J = 128. The optically centrifuged molecules have oriented angular momentum and unidirectional rotation. Polarization-sensitive transient IR absorption of individual rotational states of optically centrifuged molecules and their collision products reveals information about collisional energy transfer, relaxation kinetics, and dynamics of rotation-to-translation energy transfer. The transient IR probe also measures the extent of polarization anisotropy. Rotational energy transfer for lower energy molecules is discussed in terms of statistical models and a comparison highlights the role of increasing energy gap with J and angular momentum of the optically centrifuged molecules.
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Affiliation(s)
- Michael E Ritter
- Department of Chemistry and Biochemistry, University of Maryland College Park, College Park, Maryland 20742, USA.
| | - Simone A DeSouza
- Department of Chemistry and Biochemistry, University of Maryland College Park, College Park, Maryland 20742, USA.
| | - Hannah M Ogden
- Department of Chemistry and Biochemistry, University of Maryland College Park, College Park, Maryland 20742, USA.
| | - Tara J Michael
- Department of Chemistry and Biochemistry, University of Maryland College Park, College Park, Maryland 20742, USA.
| | - Amy S Mullin
- Department of Chemistry and Biochemistry, University of Maryland College Park, College Park, Maryland 20742, USA.
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28
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Lang J, Foley CD, Thawoos S, Behzadfar A, Liu Y, Zádor J, Suits AG. Reaction dynamics of S( 3P) with 1,3-butadiene and isoprene: crossed-beam scattering, low-temperature flow experiments, and high-level electronic structure calculations. Faraday Discuss 2024; 251:550-572. [PMID: 38807494 DOI: 10.1039/d4fd00009a] [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
Sulfur atoms serve as key players in diverse chemical processes, from astrochemistry at very low temperature to combustion at high temperature. Building upon our prior findings, showing cyclization to thiophenes following the reaction of ground-state sulfur atoms with dienes, we here extend this investigation to include many additional reaction products, guided by detailed theoretical predictions. The outcomes highlight the complex formation of products during intersystem crossing (ISC) to the singlet surfaces. Here, we employed crossed-beam velocity map imaging and high-level ab initio methods to explore the reaction of S(3P) with 1,3-butadiene and isoprene under single-collision conditions and in low-temperature flows. For the butadiene reaction, our experimental results show the formation of thiophene via H2 loss, a 2H-thiophenyl radical through H loss, and thioketene through ethene loss at a slightly higher collision energy compared to previous observations. Complementary Chirped-Pulse Fourier-Transform mmWave spectroscopy (CP-FTmmW) measurements in a uniform flow confirmed the formation of thioketene in the reaction at 20 K. For the isoprene reaction, we observed analogous products along with the 2H-thiophenyl radical arising from methyl loss and C3H4S (loss of ethene or H2 + acetylene). CP-FTmmW detected the formation of thioformaldehyde via loss of 1,3-butadiene, again in the 20 K flow. Coupled-cluster calculations on the pathways found by the automated kinetic workflow code KinBot support these findings and indicate ISC to the singlet surface, leading to the generation of various long-lived intermediates, including 5-membered heterocycles.
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Affiliation(s)
- Jinxin Lang
- Department of Chemistry, University of Missouri, Columbia, MO 65211, USA.
| | - Casey D Foley
- Department of Chemistry, University of Missouri, Columbia, MO 65211, USA.
| | - Shameemah Thawoos
- Department of Chemistry, University of Missouri, Columbia, MO 65211, USA.
| | - Abbas Behzadfar
- Department of Chemistry, University of Missouri, Columbia, MO 65211, USA.
| | - Yanan Liu
- Department of Chemistry, University of Missouri, Columbia, MO 65211, USA.
| | - Judit Zádor
- Combustion Research Facility, Sandia National Laboratories, Livermore, California 94551, USA.
| | - Arthur G Suits
- Department of Chemistry, University of Missouri, Columbia, MO 65211, USA.
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29
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Balucani N, Vanuzzo G, Recio P, Caracciolo A, Rosi M, Cavallotti C, Baggioli A, Della Libera A, Casavecchia P. Crossed molecular beam experiments and theoretical simulations on the multichannel reaction of toluene with atomic oxygen. Faraday Discuss 2024; 251:523-549. [PMID: 38868901 DOI: 10.1039/d3fd00181d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
Despite extensive experimental and theoretical studies on the kinetics of the O(3P) + C7H8 (toluene) reaction and a pioneering crossed molecular beam (CMB) investigation, the branching fractions (BFs) of the CH3C6H4O(methylphenoxy) + H, C6H5O(phenoxy) + CH3, and spin-forbidden C5H5CH3 (methylcyclopentadiene) + CO product channels remain an open question, which has hampered the proper inclusion of this important reaction in the chemical modelling of various chemical environments. We report a CMB study with universal soft electron-ionization mass-spectrometric detection of the reactions O(3P,1D) + toluene at the collision energy of 34.7 kJ mol-1. From CMB data we have inferred the reaction dynamics and quantified the BFs of the primary products and the role of intersystem crossing (ISC). The CH3-elimination channel dominates (BF = 0.69 ± 0.22) in the O(3P) reaction, while the H-displacement and CO-formation channels are minor (BF = 0.22 ± 0.07 and 0.09 ± 0.05, respectively), with ISC accounting for more than 50% of the reactive flux. Synergistic transition-state theory (TST)-based master equation simulations including nonadiabatic TST on ab initio coupled triplet/singlet potential energy surfaces were employed to compute the product BFs and assist in the interpretation of the CMB results. In the light of the good agreement between the theoretical predictions for the O(3P) + toluene reaction and the CMB results as well as the absolute rate constant as a function of temperature (T) (from literature), the so-validated computational methodology was used to predict channel-specific rate constants as a function of T at 1 atm.
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Affiliation(s)
- Nadia Balucani
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Perugia 06123, Italy.
| | - Gianmarco Vanuzzo
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Perugia 06123, Italy.
| | - Pedro Recio
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Perugia 06123, Italy.
| | - Adriana Caracciolo
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Perugia 06123, Italy.
| | - Marzio Rosi
- Dipartimento di Ingegneria Civile e Ambientale, Università degli Studi di Perugia, Perugia 06125, Italy
| | - Carlo Cavallotti
- Politecnico di Milano, Dipartimento di Chimica, Materiali e Ingegneria Chimica, Milano 20131, Italy
| | - Alberto Baggioli
- Politecnico di Milano, Dipartimento di Chimica, Materiali e Ingegneria Chimica, Milano 20131, Italy
| | - Andrea Della Libera
- Politecnico di Milano, Dipartimento di Chimica, Materiali e Ingegneria Chimica, Milano 20131, Italy
| | - Piergiorgio Casavecchia
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Perugia 06123, Italy.
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30
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Mishra A, Kim J, Kim SK, Willitsch S. Isomeric and rotational effects in the chemi-ionisation of 1,2-dibromoethene with metastable neon atoms. Faraday Discuss 2024; 251:92-103. [PMID: 38805255 PMCID: PMC11349061 DOI: 10.1039/d3fd00172e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 01/31/2024] [Indexed: 05/29/2024]
Abstract
The specific geometry of a molecule can have a pronounced influence on its chemical reactivity. However, experimental data on reactions of individual molecular isomers are still sparse because they are often difficult to separate and frequently interconvert into one another under ambient conditions. Here, we employ a novel crossed-beam experiment featuring an electrostatically controlled molecular beam combined with a source for radicals and metastables to spatially separate the cis and trans stereoisomers as well as individual rotational states of 1,2-dibromoethene and study their specific reactivities in the chemi-ionisation reaction with excited neon atoms. The experiments reveal pronounced isomeric and rotational specificities in the rates and product branching ratios of the reaction. The present study underlines the importance and combined role of molecular geometry and of rotational motion in the dynamics of chemi-ionisation reactions.
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Affiliation(s)
- Amit Mishra
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056, Basel, Switzerland.
| | - Junggil Kim
- Department of Chemistry, KAIST, Daejeon 34141, Republic of Korea.
| | - Sang Kyu Kim
- Department of Chemistry, KAIST, Daejeon 34141, Republic of Korea.
| | - Stefan Willitsch
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056, Basel, Switzerland.
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31
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Gorelov S, Titov A, Tolicheva O, Konevega A, Shvetsov A. Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome Memory Limitation. J Chem Inf Model 2024; 64:6241-6246. [PMID: 39119674 DOI: 10.1021/acs.jcim.3c02087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
This work introduces a new faster implementation of the hydrogen bond network (complex arrangement of hydrogen bonds between or within molecules) search algorithm in biomacromolecules and their environment. Existing implementation of such an algorithm in GROMACS [Abraham et al. GROMACS 2024.2 Manual. 2024.] has limitations in the analysis of large structures and trajectories. The new implementation, in the form of a native GROMACS trajectory analysis module, allows for quick analysis of molecular dynamics trajectories without restrictions, thus overcoming the limitations of the original algorithm. The application of the developed method enabled the acquisition and analysis of hydrogen bond networks in the studied defensin-like protein Pentadiplandra brazzeana, as well as the study of hydrogen bond occupancies between the protein's residues and water molecules. The data obtained using the new implementation coincided with the experimental data.
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Affiliation(s)
- Sergey Gorelov
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre "Kurchatov Institute", Gatchina 188300, Russia
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
| | - Anatoly Titov
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre "Kurchatov Institute", Gatchina 188300, Russia
| | - Olga Tolicheva
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre "Kurchatov Institute", Gatchina 188300, Russia
| | - Andrey Konevega
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre "Kurchatov Institute", Gatchina 188300, Russia
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
- National Research Centre "Kurchatov Institute", Moscow 123098, Russia
| | - Alexey Shvetsov
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre "Kurchatov Institute", Gatchina 188300, Russia
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
- National Research Centre "Kurchatov Institute", Moscow 123098, Russia
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32
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Boidachenko K, Liberka M, Wang J, Tokoro H, Ohkoshi SI, Chorazy S. Chiral cadmium-amine complexes for stimulating non-linear optical activity and photoluminescence in solids based on aurophilic stacks. JOURNAL OF MATERIALS CHEMISTRY. C 2024:d4tc01042f. [PMID: 39184233 PMCID: PMC11343038 DOI: 10.1039/d4tc01042f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 08/15/2024] [Indexed: 08/27/2024]
Abstract
The design of high-performance optical materials can be realized using coordination polymers (CPs) often supported by non-covalent interactions, such as metallophilicity. The challenge is to control two or more optical effects, e.g., non-linear optics (NLO) and photoluminescence (PL). We present a new strategy for the combination of the NLO effect of second-harmonic generation (SHG) and the visible PL achieved by linking dicyanidoaurate(i) ions, which form luminescent metallophilic stacks, with cadmium(ii) complexes bearing chiral amine ligands, used to break the crystal's symmetry. We report a family of NLO- and PL-active materials based on heterometallic Cd(ii)-Au(i) coordination systems incorporating enantiopure propane-1,2-diamine (pda) ligands (1-S, 1-R), their racemate (2), and enantiopure trans-cyclopentane-1,2-diamine (cpda) ligands (3-S, 3-R). Due to acentric space groups, they exhibit the SHG signal, tunable within the range of 11-24% of the KDP reference, which was correlated with the dipole moments of Cd(ii) units. They show efficient blue PL whose energy and quantum yield, the latter ranging from 0.40 to 0.83, are controlled by Cd(ii) complexes affecting the Au-Au distances and vibrational modes. We prove that chiral Cd(ii)-amine complexes play the role of molecular agents for the stimulation of both the NLO and PL of the materials based on aurophilic stacks.
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Affiliation(s)
- Kseniia Boidachenko
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2 30-387 Krakow Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Łojasiewicza 11 30-348 Kraków Poland
| | - Michal Liberka
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2 30-387 Krakow Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Łojasiewicza 11 30-348 Kraków Poland
| | - Junhao Wang
- Department of Materials Science, Institute of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba Ibaraki 305-8573 Japan
| | - Hiroko Tokoro
- Department of Materials Science, Institute of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba Ibaraki 305-8573 Japan
| | - Shin-Ichi Ohkoshi
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Szymon Chorazy
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2 30-387 Krakow Poland
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33
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Zhu X, Gu B. Making Peace with Random Phases: Ab Initio Conical Intersection Quantum Dynamics in Random Gauges. J Phys Chem Lett 2024; 15:8487-8493. [PMID: 39133253 DOI: 10.1021/acs.jpclett.4c01688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Ab initio modeling of conical intersection wave packet dynamics is crucial for various photochemical, photophysical, and biological processes. However, adiabatic electronic states obtained from electronic structure computations involve random phases, or more generally, random gauge fixings, which cannot be directly used in the modeling of nonadiabatic wave packet simulations. Here we develop a random-gauge local diabatic representation that allows an exact modeling of conical intersection dynamics directly using the adiabatic electronic states with phases randomly assigned during the electronic structure computations. Its utility is demonstrated by an exact ab initio modeling of the two-dimensional Shin-Metiu model with and without an external magnetic field. Our results provide a simple approach to integrating the electronic structure computations into nonadiabatic quantum dynamics, thus paving the way for ab initio modeling of conical intersection dynamics.
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Affiliation(s)
- Xiaotong Zhu
- Department of Chemistry and Department of Physics, Westlake University, Hangzhou, Zhejiang 310030, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Bing Gu
- Department of Chemistry and Department of Physics, Westlake University, Hangzhou, Zhejiang 310030, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China
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34
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George MAR, Dopfer O. IR spectrum of SiH 3OH 2+SiH 4: cationic OH⋯HSi dihydrogen bond versus charge-inverted SiH⋯Si hydrogen bond. Phys Chem Chem Phys 2024. [PMID: 39171378 DOI: 10.1039/d4cp02428a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
The low electronegativity of Si gives rise to a variety of nonconventional intermolecular interactions in clusters of silanes and their derivatives, which have not been well characterized yet. Herein, we characterize the structures of various isomers of bare and Ar-tagged SiH3OH2+SiH4 dimers composed of protonated silanol and silane by infrared photodissociation (IRPD) of mass-selected ions and dispersion-corrected density functional calculations (B3LYP-D3/aug-cc-pVTZ). The analysis of the IRPD spectra recorded in the OH stretch range reveals the competition between two types of nonconventional hydrogen bonds (H-bonds). The first one represents a OH⋯HSi ionic dihydrogen bond (DHB), in which SiH4 interacts with the H2O moiety of SiH3OH2+. The second one represents a charge-inverted SiH⋯Si ionic H-bond (CIHB), in which the SiH4 ligand interacts with the SiH3 moiety of SiH3OH2+. The latter may also be considered as a weak three-centre two-electron (3c-2e) bond. Although both types of H-bonds are computed to have comparable interaction strengths for SiH3OH2+SiH4 (D0 ≈ 35-40 kJ mol-1), DHB isomers dominate the population in the supersonic plasma expansion, while the abundance of CIHB isomers is roughly one order of magnitude lower, probably as a result of entropic factors.
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Affiliation(s)
| | - Otto Dopfer
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Berlin 10623, Germany.
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35
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Barclay AJ, McKellar ARW, Pietropolli Charmet A, Moazzen-Ahmadi N. Water-carbon disulfide dimers: observation of a new isomer and ab initio structure theory. Phys Chem Chem Phys 2024. [PMID: 39172124 DOI: 10.1039/d4cp02281e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
The weakly bound dimer water-carbon disulfide is studied by ab initio structure theory and high-resolution infrared spectroscopy. The calculations yield three stable minima in the potential energy surface, all planar. The most stable, isomer 1, was observed previously by microwave spectroscopy. It has C2v symmetry, an S-O bond, and a linear O-S-C-S backbone. Isomer 2, the next most stable, has not been considered previously by theory or experiment. It also has C2v symmetry, but with a side-by-side structure. Isomer 3, which is slightly less stable, is side-by-side with one O-H bond pointing toward an S atom. The first gas phase water-CS2 infrared spectra are reported. For isomer 1, H2O-, HDO-, and D2O-CS2 are observed in the CS2ν1 + ν3 region, H2O-CS2 in the H2O ν2 bend region, and D2O-CS2 in the D2O ν1 and ν3 stretch regions. The latter ν3 spectrum enables an experimental determination of the A rotational parameter, which turns out to be larger than expected. The new isomer 2 is observed by means of a band in the H2O ν2 region, confirming its C2v symmetry and calculated structure.
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Affiliation(s)
- A J Barclay
- Department of Physics and Astronomy, University of Calgary, 2500 University Drive North West, Calgary, Alberta T2N 1N4, Canada.
| | - A R W McKellar
- National Research Council of Canada, Ottawa, Ontario K1A 0R6, Canada
| | - A Pietropolli Charmet
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari Venezia, Via Torino 155, I-30172, Mestre, Venezia, Italy
| | - N Moazzen-Ahmadi
- Department of Physics and Astronomy, University of Calgary, 2500 University Drive North West, Calgary, Alberta T2N 1N4, Canada.
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36
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Beckmann R, Schran C, Brieuc F, Marx D. Theoretical infrared spectroscopy of protonated methane isotopologues. Phys Chem Chem Phys 2024. [PMID: 39171731 DOI: 10.1039/d4cp02295e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
The vibrational spectroscopy of protonated methane and its mixed hydrogen/deuterium isotopologues remains a challenge to both experimental and computational spectroscopy due to the iconic floppiness of CH5+. Here, we compute the finite-temperature broadband infrared spectra of CH5+ and all its isotopologues, i.e. CHnD5-n+ up to CD5+, from path integral molecular dynamics in conjunction with interactions and dipoles computed consistently at CCSD(T) coupled cluster accuracy. The potential energy and dipole moment surfaces have been accurately represented in full dimensionality in terms of high-dimensional neural networks. The resulting computational efficiency allows us to establish CCSD(T) accuracy at the level of converged path integral simulations. For all six isotopologues, the computed broadband spectra compare very favorably to the available experimental broadband spectra obtained from laser induced reactions action vibrational spectroscopy. The current approach is found to consistently and significantly improve on previous calculations of these broadband vibrational spectra and defines the new cutting-edge for what has been dubbed the "enfant terrible" of molecular spectroscopy in view of its pronounced large-amplitude motion that involves all intramolecular degrees of freedom.
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Affiliation(s)
- Richard Beckmann
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany.
| | - Christoph Schran
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany.
| | - Fabien Brieuc
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany.
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany.
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37
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Cao W, Hu Z, Sun H, Wang XB. Photoelectron Spectroscopy and Computational Study on Microsolvated [B 10H 10] 2- Clusters and Comparisons to Their [B 12H 12] 2- Analogues. J Phys Chem A 2024; 128:6981-6988. [PMID: 39112434 DOI: 10.1021/acs.jpca.4c04772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
Microhydrated closo-boranes have attracted great interest due to their superchaotropic activity related to the well-known Hofmeister effect and important applications in biomedical and battery fields. In this work, we report a combined negative ion photoelectron spectroscopy and quantum chemical investigation on hydrated closo-decaborate clusters [B10H10]2-·nH2O (n = 1-7) with a direct comparison to their analogues [B12H12]2-·nH2O and free water clusters. A single H2O molecule is found to be sufficient to stabilize the intrinsically unstable [B10H10]2- dianion. The first two water molecules strongly interact with the solute forming B-H···H-O dihydrogen bonds while additional water molecules show substantially reduced binding energies. Unlike [B12H12]2-·nH2O possessing a highly structured water network with the attached H2O molecules arranged in a unified pattern by maximizing B-H···H-O dihydrogen bonding, distinct structural arrangements of the water clusters within [B10H10]2-·nH2O are achieved with the water cluster networks from trimer to heptamer resembling free water clusters. Such a distinct difference arises from the variations in size, symmetry, and charge distributions between these two dianions. The present finding again confirms the structural diversity of hydrogen-bonding networks in microhydrated closo-boranes and enriches our understanding of aqueous borate chemistry.
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Affiliation(s)
- Wenjin Cao
- Physical Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, Richland, Washington 99352, United States
| | - Zhubin Hu
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200241, China
| | - Haitao Sun
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200241, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Xue-Bin Wang
- Physical Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, Richland, Washington 99352, United States
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38
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Raymond JJ, Chowdhury MSI, Crawley MR, Morrow JR. Co(II) Macrocyclic Complexes with Amide-Glycinate Pendants as ParaCEST and Liposomal CEST Agents. Chemistry 2024; 30:e202401638. [PMID: 38861702 DOI: 10.1002/chem.202401638] [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: 04/26/2024] [Revised: 05/28/2024] [Accepted: 06/11/2024] [Indexed: 06/13/2024]
Abstract
Macrocyclic Co(II) complexes with appended amide-glycinate groups were prepared to develop paramagnetic Co(II) chemical exchange saturation transfer (CEST) agents of reduced overall charge. Complexes with reduced charge and lowered osmolarity are important for their loading into liposomes and to provide complexes that are highly water soluble and well tolerated in animals. Co(L1) has two non-coordinating benzyl groups and two amide-glycinate pendants, whereas Co(L2) has two unsubstituted amide pendants and two amide-glycinate pendants on cyclam (1,4,8,11-tetraazacyclododecane). The 1H NMR spectrum of Co(L1) is consistent with a single cis-pendant isomer with both amide protons in the trans-configuration, as supported by an X-ray crystal structure. Co(L2) has a mixture of different isomers in solution, including the trans-1,4 and 1,8 pendant isomers. The Z-spectrum of Co(L1) shows one highly-shifted CEST peak, whereas Co(L2) exhibits six CEST peaks. Encapsulation of 40 mM Co(L1) in a liposome with osmotically-induced shrinking at 300 mOsm/L produces a liposomal CEST agent with saturation frequency offset of 3 ppm. Addition of the amphiphilic 1,4,7-triazacyclononane-based complex Co(L5) to the liposomal bilayer at 18 mM with Co(L1) encapsulated in the liposome at 50 mM changes the sign and increases the magnitude of the saturation frequency offset to -7.5 ppm at 300 mOsm/L.
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Affiliation(s)
- Jaclyn J Raymond
- Department of Chemistry, University at Buffalo, the State University of New York, Amherst, NY 14260
| | - Md Saiful I Chowdhury
- Department of Chemistry, University at Buffalo, the State University of New York, Amherst, NY 14260
| | - Matthew R Crawley
- Department of Chemistry, University at Buffalo, the State University of New York, Amherst, NY 14260
| | - Janet R Morrow
- Department of Chemistry, University at Buffalo, the State University of New York, Amherst, NY 14260
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39
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Mashhadimoslem H, Abdol MA, Karimi P, Zanganeh K, Shafeen A, Elkamel A, Kamkar M. Computational and Machine Learning Methods for CO 2 Capture Using Metal-Organic Frameworks. ACS NANO 2024. [PMID: 39173133 DOI: 10.1021/acsnano.3c13001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2024]
Abstract
Machine learning (ML) using data sets of atomic and molecular force fields (FFs) has made significant progress and provided benefits in the fields of chemistry and material science. This work examines the interactions between chemistry and materials computational science at the atomic and molecular scales for metal-organic framework (MOF) adsorbent development toward carbon dioxide (CO2) capture. Herein, a connection will be drawn between atomic forces predicted by ML algorithms and the structures of MOFs for CO2 adsorption. Our study also takes into account the successes of atomic computational screening in the field of materials science, especially quantum ML, and its relationship to ML algorithms that clarify advancements in the area of CO2 adsorption by MOFs. Additionally, we reviewed the processes for supplying data to ML algorithms for algorithm training, including text mining from scientific articles, and MOF's formula processing linked to the chemical properties of MOFs. To create ML algorithms for future research, we recommend that the digitization of scientific records can help efficiently synthesize advanced MOFs. Finally, a future vision for developing pioneer MOF synthesis routes for CO2 capture is presented in this review article.
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Affiliation(s)
- Hossein Mashhadimoslem
- Chemical Engineering Department, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Mohammad Ali Abdol
- Chemical Engineering Department, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Peyman Karimi
- Chemical Engineering Department, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Kourosh Zanganeh
- Natural Resources Canada (NRCan), Canmet ENERGY-Ottawa (CE-O), 1 Haanel Dr., Ottawa, ON K1A 1M1 Canada
| | - Ahmed Shafeen
- Natural Resources Canada (NRCan), Canmet ENERGY-Ottawa (CE-O), 1 Haanel Dr., Ottawa, ON K1A 1M1 Canada
| | - Ali Elkamel
- Chemical Engineering Department, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
- Department of Chemical Engineering, Khalifa University, P.O. Box 127788, Abu Dhabi, United Arab Emirates
| | - Milad Kamkar
- Chemical Engineering Department, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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40
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Mukherjee S, Saha S, Ghosh S, Adhikari S, Sathyamurthy N, Baer M. Quasi-Classical Trajectory Calculations on a Two-State Potential Energy Surface Including Nonadiabatic Coupling Terms as Friction for D + + H 2 Collisions. J Phys Chem A 2024. [PMID: 39172694 DOI: 10.1021/acs.jpca.4c03237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2024]
Abstract
Akin to the traditional quasi-classical trajectory method for investigating the dynamics on a single adiabatic potential energy surface for an elementary chemical reaction, we carry out the dynamics on a 2-state ab initio potential energy surface including nonadiabatic coupling terms as friction terms for D+ + H2 collisions. It is shown that the resulting dynamics correctly accounts for nonreactive charge transfer, reactive non-charge transfer and reactive charge transfer processes. In addition, it leads to the formation of triatomic DH2+ species as well.
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Affiliation(s)
- Soumya Mukherjee
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
- Department of Chemistry, Maulana Azad National Institute of Technology, Bhopal 462003, India
| | - Swagato Saha
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Sandip Ghosh
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia 741246, India
| | - Satrajit Adhikari
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Narayanasami Sathyamurthy
- Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, SAS Nagar, Manauli 140306, India
| | - Michael Baer
- The Fritz Haber Center for Molecular Dynamics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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41
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Lei D, Wang L, Lv Y, Luo N, Wang Z. A Comprehensive Review of Solar Photocatalysis & Photothermal Catalysis for Hydrogen Production from Biomass: from Material Characteristics to Engineering Application. Chemistry 2024; 30:e202401486. [PMID: 38865111 DOI: 10.1002/chem.202401486] [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: 04/18/2024] [Revised: 06/08/2024] [Accepted: 06/10/2024] [Indexed: 06/13/2024]
Abstract
Biomass photoreforming is a promising way of producing sustainable hydrogen thanks to the abundant sources of biomass feedstocks. Solar energy provides the heat and driven force to initial biomass oxidation coupled with H2 evolution. Currently, biomass photoreforming is still far from plant-scale applications due to the lower solar energy utilization efficiencies, the low H2 yield, and the lack of appropriate photoreactors. The production of H2 from photoreforming of native biomass and platform molecules was summarized and discussed with particular attention to the prospects of scaling up the catalysis technology for mass hydrogen production. The types of photoreforming, including photocatalysis and photothermal catalysis, were discussed, consequently considering the different requirements for photoreactors. We also reviewed the photoreactors that support biomass photoreforming. Numerical simulation methods were implemented for the solid-liquid two-phase flow and inter-particle radiative transfer involved in the reaction process. Developing concentrated photothermal catalytic flowed reactors is beneficial to scale-up catalytic hydrogen production from biomass.
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Affiliation(s)
- Dongqiang Lei
- Institute of Electrical Engineering, Chinese Academy of Sciences, No.6 Beiertiao, Zhongguancun, Beijing, 100190, China
- University of Chinese Academy of Sciences, No.19 (A) Yuquan Rd, Shijingshan District, Beijing, 100049, China
- Laboratory of Long-Duration and Large-Scale Energy Storage, Chinese Academy of Sciences, Beijing, China
| | - Linhao Wang
- Institute of Electrical Engineering, Chinese Academy of Sciences, No.6 Beiertiao, Zhongguancun, Beijing, 100190, China
- University of Chinese Academy of Sciences, No.19 (A) Yuquan Rd, Shijingshan District, Beijing, 100049, China
- Laboratory of Long-Duration and Large-Scale Energy Storage, Chinese Academy of Sciences, Beijing, China
| | - Yue Lv
- School of Energy & Power Engineering, Changsha University of Science & Technology, Changsha, 410114, China
| | - Nengchao Luo
- University of Chinese Academy of Sciences, No.19 (A) Yuquan Rd, Shijingshan District, Beijing, 100049, China
- State Key Laboratory of Catalysis, Dalian National Laboratory for Clean Energy, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023, Dalian, China
| | - Zhifeng Wang
- Institute of Electrical Engineering, Chinese Academy of Sciences, No.6 Beiertiao, Zhongguancun, Beijing, 100190, China
- University of Chinese Academy of Sciences, No.19 (A) Yuquan Rd, Shijingshan District, Beijing, 100049, China
- Laboratory of Long-Duration and Large-Scale Energy Storage, Chinese Academy of Sciences, Beijing, China
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42
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Fellows AP, Duque ÁD, Balos V, Lehmann L, Netz RR, Wolf M, Thämer M. How Thick is the Air-Water Interface?─A Direct Experimental Measurement of the Decay Length of the Interfacial Structural Anisotropy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024. [PMID: 39171356 DOI: 10.1021/acs.langmuir.4c02571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
The air-water interface is a highly prevalent phase boundary impacting many natural and artificial processes. The significance of this interface arises from the unique properties of water molecules within the interfacial region, with a crucial parameter being the thickness of its structural anisotropy, or "healing depth". This quantity has been extensively assessed by various simulations which have converged to a prediction of a remarkably short length of ∼6 Å. Despite the absence of any direct experimental measurement of this quantity, this predicted value has surprisingly become widely accepted as fact. Using an advancement in nonlinear vibrational spectroscopy, we provide the first measurement of this thickness and, indeed, find it to be ∼6-8 Å, finally confirming the prior predictions. Lastly, by combining the experimental results with depth-dependent second-order spectra calculated from ab initio parametrized molecular dynamics simulations, which are also in excellent agreement with this experimental result, we shed light on this surprisingly short correlation length of molecular orientations at the interface.
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Affiliation(s)
- Alexander P Fellows
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Álvaro Díaz Duque
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Vasileios Balos
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia), 28049 Madrid, Spain
| | - Louis Lehmann
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Roland R Netz
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Martin Wolf
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Martin Thämer
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
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43
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Iyer GR, Whelpley N, Tiihonen J, Kent PRC, Krogel JT, Rubenstein BM. Force-Free Identification of Minimum-Energy Pathways and Transition States for Stochastic Electronic Structure Theories. J Chem Theory Comput 2024. [PMID: 39172163 DOI: 10.1021/acs.jctc.4c00214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
The accurate mapping of potential energy surfaces (PESs) is crucial to our understanding of the numerous physical and chemical processes mediated by atomic rearrangements, such as conformational changes and chemical reactions, and the thermodynamic and kinetic feasibility of these processes. Stochastic electronic structure theories, e.g., Quantum Monte Carlo (QMC) methods, enable highly accurate total energy calculations that in principle can be used to construct the PES. However, their stochastic nature poses a challenge to the computation and use of forces and Hessians, which are typically required in algorithms for minimum-energy pathway (MEP) and transition state (TS) identification, such as the nudged elastic band (NEB) algorithm and its climbing image formulation. Here, we present strategies that utilize the surrogate Hessian line-search method, previously developed for QMC structural optimization, to efficiently identify MEP and TS structures without requiring force calculations at the level of the stochastic electronic structure theory. By modifying the surrogate Hessian algorithm to operate in path-orthogonal subspaces and at saddle points, we show that it is possible to identify MEPs and TSs by using a force-free QMC approach. We demonstrate these strategies via two examples, the inversion of the ammonia (NH3) molecule and the nucleophilic substitution (SN2) reaction F- + CH3F → FCH3 + F-. We validate our results using Density Functional Theory (DFT)- and Coupled Cluster (CCSD, CCSD(T))-based NEB calculations. We then introduce a hybrid DFT-QMC approach to compute thermodynamic and kinetic quantities, free energy differences, rate constants, and equilibrium constants that incorporates stochastically optimized structures and their energies, and show that this scheme improves upon DFT accuracy. Our methods generalize straightforwardly to other systems and other high-accuracy theories that similarly face challenges computing energy gradients, paving the way for highly accurate PES mapping, transition state determination, and thermodynamic and kinetic calculations at significantly reduced computational expense.
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Affiliation(s)
- Gopal R Iyer
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Noah Whelpley
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Juha Tiihonen
- Department of Physics, Nanoscience Center, University of Jyväskylä, Jyväskylä 40014, Finland
| | - Paul R C Kent
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Jaron T Krogel
- Materials Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Brenda M Rubenstein
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
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44
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Murakami T, Hayashi D, Kikuma Y, Yamaki K, Takayanagi T. Temperature effects on the branching dynamics in the model ambimodal (6 + 4)/(4 + 2) intramolecular cycloaddition reaction. J Comput Chem 2024. [PMID: 39166899 DOI: 10.1002/jcc.27484] [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: 04/16/2024] [Revised: 07/23/2024] [Accepted: 07/31/2024] [Indexed: 08/23/2024]
Abstract
C14H20 (tetradecapentaene) is a simple model system exhibiting post transition-state behavior, wherein both the (6 + 4) and (4 + 2) cycloaddition products are formed from one ambimocal transition state structure. We studied the bifurcation dynamics starting from the two ambimodal transition state structures, the chair-form and boat-form, using the quasi-classical trajectory, classical molecular dynamics, and ring-polymer molecular dynamics methods on the parameter-optimized semiempirical GFN2-xTB potential energy surface. It was found that the calculated branching fractions differ between the chair-form and boat-form due to the different nature in the IRC pathways. We also investigated the effects of temperature on bifurcation dynamics and found that, at higher temperatures, trajectories stay longer in the intermediate region of the potential energy surface.
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Affiliation(s)
- Tatsuhiro Murakami
- Department of Chemistry, Saitama University, Saitama, Japan
- Department of Materials & Life Sciences, Faculty of Science & Technology, Sophia University, Tokyo, Japan
| | - Daiki Hayashi
- Department of Chemistry, Saitama University, Saitama, Japan
| | - Yuya Kikuma
- Department of Chemistry, Saitama University, Saitama, Japan
| | - Keita Yamaki
- Department of Chemistry, Saitama University, Saitama, Japan
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45
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Rap D, Schrauwen JGM, Redlich B, Brünken S. Noncovalent Interactions Steer the Formation of Polycyclic Aromatic Hydrocarbons. J Am Chem Soc 2024; 146:23022-23033. [PMID: 39110663 PMCID: PMC11345775 DOI: 10.1021/jacs.4c03395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 07/04/2024] [Accepted: 07/29/2024] [Indexed: 08/22/2024]
Abstract
Aromatic molecules play an important role in the chemistry of astronomical environments such as the cold interstellar medium (ISM) and (exo)planetary atmospheres. The observed abundances of (polycyclic) aromatic hydrocarbons such as benzonitrile and cyanonaphthalenes are, however, highly underestimated by astrochemical models. This demonstrates the need for more experimentally verified reaction pathways. The low-temperature ion-molecule reaction of benzonitrile•+ with acetylene is studied here using a multifaceted approach involving kinetics and spectroscopic probing of the reaction products. A fast radiative association reaction via an in situ experimentally observed prereactive complex shows the importance of noncovalent interactions in steering the pathway during cold ion-molecule reactions. Product structures of subsequent reactions are unambiguously identified using infrared action spectroscopy and reveal the formation of nitrogen-containing, linked bicyclic structures such as phenylpyridine•+ and benzo-N-pentalene+ structures. The results, contradicting earlier assumptions on the product structure, demonstrate the importance of spectroscopic probing of reaction products and emphasize the possible formation of linked bicyclic molecules and benzo-N-pentalene+ structures in astronomical environments.
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Affiliation(s)
- Daniël
B. Rap
- FELIX Laboratory, Institute
for Molecules and Materials, Radboud University, Nijmegen 6525 ED, The Netherlands
| | - Johanna G. M. Schrauwen
- FELIX Laboratory, Institute
for Molecules and Materials, Radboud University, Nijmegen 6525 ED, The Netherlands
| | - Britta Redlich
- FELIX Laboratory, Institute
for Molecules and Materials, Radboud University, Nijmegen 6525 ED, The Netherlands
| | - Sandra Brünken
- FELIX Laboratory, Institute
for Molecules and Materials, Radboud University, Nijmegen 6525 ED, The Netherlands
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46
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Yang L, Zhang J. Effect of Carbon Chain Length on Nascent Yields of Stabilized Criegee Intermediates in Ozonolysis of a Series of Terminal Alkenes. J Am Chem Soc 2024. [PMID: 39169747 DOI: 10.1021/jacs.4c08051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
The yields of stabilized Criegee intermediates (sCIs), CH2OO and RCHOO (C2H5CHOO, C3H7CHOO, C4H9CHOO, and C5H11CHOO), produced from ozonolysis of asymmetrical 1-alkenes (1-butene, 1-pentene, 1-hexene, and 1-heptene) were investigated at low pressures (5-16 Torr) using cavity ring-down spectroscopy and chemical titration with sulfur dioxide (SO2). By extrapolating the low-pressure measurements to zero-pressure limit, nascent sCI yields were obtained. Combined with our previous studies on ethene and propene ozonolysis, the nascent sCI yields demonstrated an intriguing trend of increasing with the addition of CH2 groups and eventually reached a plateau at around 31% for longer chain 1-alkenes. In particular, the fraction of nascent stabilized CH2OO reached the plateau from 1-butene, indicating that CH2OO was produced with nearly the same internal energy distribution from 1-butene to 1-heptene. The comparison between the experiments and RRKM calculations suggests that the dissociation of primary ozonide (POZ) of O3 + ethene and propene can be treated by statistical theory, while that of O3 + 1-butene to 1-heptene is nonstatistical and intramolecular vibrational redistribution of the initial energy on the 1,2,3-trioxolane of POZ throughout the entire molecule was incomplete on the dissociation time scale.
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Affiliation(s)
- Lei Yang
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Jingsong Zhang
- Department of Chemistry, University of California, Riverside, California 92521, United States
- Air Pollution Research Center, University of California, Riverside, California 92521, United States
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47
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Joshi PR, Lee YP. Identification of HOC •HC(O)H, HOCH 2C •O, and HOCH 2CH 2O • Intermediates in the Reaction of H + Glycolaldehyde in Solid Para-Hydrogen and Its Implication to the Interstellar Formation of Complex Sugars. J Am Chem Soc 2024; 146:23306-23320. [PMID: 39121440 PMCID: PMC11345754 DOI: 10.1021/jacs.4c05896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 07/23/2024] [Accepted: 07/23/2024] [Indexed: 08/11/2024]
Abstract
Glycolaldehyde [HOCH2C(O)H, GA], the primitive sugar-like molecule detected in the interstellar medium (ISM), is a potential precursor for the synthesis of complex sugars. Despite its importance, the mechanism governing the formation of these higher-order sugars from GA under interstellar circumstances remains elusive. Radical intermediates HOCH2CH2O• (1), HOCH2C•HOH (2), HOCH2C•O (3), HOC•HC(O)H (4), and O•CH2C(O)H (5) derived from GA could be potential precursors for the formation of glyceraldehyde (aldose sugar), dihydroxyacetone (ketose sugar), and ethylene glycol (sugar alcohol) in dark regions of ISM. However, the spectral identification of these intermediates and their roles were little investigated. We conducted reactions involving H atoms and the Cis-cis conformer of GA (Cc-GA) in solid p-H2 at 3.2 K and identified IR spectra of radicals Cc-HOCH2C•O (3) and Cc-HOC•HC(O)H (4) produced from H abstraction as well as closed-shell HOCHCO (6) produced via consecutive H abstraction of GA. In addition, Cc-HOCH2CH2O• (1) and C•H2OH + H2CO (7) were produced through the H addition and the H-induced fragmentation channels, respectively. In darkness, when only H-tunneling reactions occurred, the formation of (3) was major and that of (1) was minor. In contrast, during IR irradiation to produce H atoms with higher energy, the formation of (4) and C•H2OH + H2CO (7) became important. We also successfully converted most Cc-GA to the second-lowest-energy conformer Trans-trans-GA (Tt-GA) by prolonged IR irradiation at 2827 nm to investigate H + Tt-GA; Tt-HOCH2C•O (3'), Tt-HOC•HC(O)H (4'), HOCHCO (6), Tt-HOCH2CH2O• (1'), and C•H2OH + H2CO (7) were observed. We discuss possible routes for the formation of higher-order sugars or related compounds involving (7), (1), (3), and (4), but neither (2), which was proposed previously, nor (5) plays a significant role in H + GA. Such previously unreported rich chemistry in the reaction of H + GA, with four channels of three distinct types, indicates the multiple roles that GA might play in astronomical chemistry.
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Affiliation(s)
- Prasad Ramesh Joshi
- Department
of Applied Chemistry and Institute of Molecular Science, National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
| | - Yuan-Pern Lee
- Department
of Applied Chemistry and Institute of Molecular Science, National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
- Center
for Emergent Functional Matter Science, National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
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Wang LS. Borozenes: Benzene-Like Planar Aromatic Boron Clusters. Acc Chem Res 2024; 57:2428-2436. [PMID: 39096510 DOI: 10.1021/acs.accounts.4c00380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2024]
Abstract
ConspectusWith three valence electrons and four valence orbitals, boron (2s22p1) is an electron-deficient element, resulting in interesting chemical bonding and structures in both borane molecules and bulk boron materials. The electron deficiency leads to electron sharing and delocalization in borane compounds and bulk boron allotropes, characterized by polyhedral cages, in particular, the ubiquitous B12 icosahedral cage. During the past two decades, the structures and bonding of size-selected boron clusters have been elucidated via combined photoelectron spectroscopy and theoretical investigations. Unlike bulk boron materials, finite boron clusters have been found to possess 2D structures consisting of B3 triangles, dotted with tetragonal, pentagonal, or hexagonal holes. The discovery of the planar B36 cluster with a central hexagonal hole provided the first experimental evidence for the viability of 2D boron nanostructures (borophene), which have been synthesized on inert substrates. The B7-, B8-, and B9- clusters were among the first few boron clusters to be investigated by joint photoelectron spectroscopy and theoretical calculations, and they were all found to possess 2D structures with a central B atom inside a Bn ring. Recently, the B73- (C6v), B82- (D7h), and B9- (D8h) series of closed-shell species were shown to possess similar π bonding akin to that in the C5H5-, C6H6, and C7H7+ series, respectively, and the name "borozene" was coined to highlight their analogy to the classical aromatic hydrocarbon molecules.Among the borozenes, the D7h B82- species is unique for its high stability originating from both its double aromaticity and the fact that the B7 ring has the perfect size to host a central B atom. The B82- borozene has been realized experimentally in a variety of MB8 and M2B8 complexes. In particular, the B82- borozene has been observed to stabilize the rare valence-I oxidation state of lanthanides in LnB8- complexes, as well as a Cu2+ species in Cu2B8-. The B6 ring in B73- is too small to host a B atom, resulting in a slight out-of-plane distortion. Interestingly, the bowl-shaped B7 borozene is perfect for coordination to a metal atom, leading to the observation of a series of highly stable MB7 borozene complexes. On the other hand, the B8 ring is slightly too large to host the central B atom, such that a low-lying and low-symmetry isomer also exists for B9-. Even though most 2D boron clusters are aromatic, the B73-, B82-, and B9- borozenes are special because of their high symmetries and their analogy to the series of C5H5-, C6H6, and C7H7+ prototypical aromatic compounds. This Account discusses recent experimental and theoretical advances on the investigations of various borozene complexes. It is expected that many new borozene compounds can be designed and may be eventually synthesized.
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Affiliation(s)
- Lai-Sheng Wang
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
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Fleck M, Kopp WA, Viswanathan N, Hansen N, Gross J, Leonhard K. Efficient Generation of Torsional Energy Profiles by Multifidelity Gaussian Processes for Hindered Rotor Corrections. J Chem Theory Comput 2024. [PMID: 39163246 DOI: 10.1021/acs.jctc.4c00475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2024]
Abstract
Accurate thermochemistry computations often require proper treatment of torsional modes. The one-dimensional hindered rotor model has proven to be a computationally efficient solution, given a sufficiently accurate potential energy surface. Methods that provide potential energies at various compromises of uncertainty and computational time demand can be optimally combined within a multifidelity treatment. In this study, we demonstrate how multifidelity modeling leads to (1) smooth interpolation along low-fidelity scan points with uncertainty estimates, (2) inclusion of high-fidelity data that change the energetic order of conformations, and (3) predicting best next-point calculations to extend an initial coarse grid. Our diverse application set comprises molecules, clusters, and transition states of alcohols, ethers, and rings. We discuss limitations for cases in which the low-fidelity computation is highly unreliable. Different features of the potential energy curve affect different quantities. To obtain "optimal" fits, we apply strategies ranging from simple minimization of deviations to developing an acquisition function tailored for statistical thermodynamics. Bayesian prediction of best next calculations can save a substantial amount of computation time for one- and multidimensional hindered rotors.
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Affiliation(s)
- Maximilian Fleck
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Pfaffenwaldring 9, 70569 Stuttgart, Germany
| | - Wassja A Kopp
- Institute of Technical Thermodynamics, RWTH Aachen University, Schinkelstr. 8, 52062 Aachen, Germany
| | - Narasimhan Viswanathan
- Institute of Technical Thermodynamics, RWTH Aachen University, Schinkelstr. 8, 52062 Aachen, Germany
| | - Niels Hansen
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Pfaffenwaldring 9, 70569 Stuttgart, Germany
| | - Joachim Gross
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Pfaffenwaldring 9, 70569 Stuttgart, Germany
| | - Kai Leonhard
- Institute of Technical Thermodynamics, RWTH Aachen University, Schinkelstr. 8, 52062 Aachen, Germany
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Gomez A, Thompson WH, Laage D. Neural-network-based molecular dynamics simulations reveal that proton transport in water is doubly gated by sequential hydrogen-bond exchange. Nat Chem 2024:10.1038/s41557-024-01593-y. [PMID: 39164581 DOI: 10.1038/s41557-024-01593-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 07/03/2024] [Indexed: 08/22/2024]
Abstract
The transport of excess protons in water is central to acid-base chemistry, biochemistry and energy production. However, elucidating its mechanism has been challenging. Recent nonlinear vibrational spectroscopy experiments could not be explained by existing models. Here we use both vibrational spectroscopy calculations and neural-network-based molecular dynamics simulations that account for nuclear quantum effects for all atoms to determine the proton transport mechanism. Our simulations reveal an equilibrium between two stable proton-localized structures with distinct Eigen-like and Zundel-like hydrogen-bond motifs. Proton transport follows a three-step mechanism gated by two successive hydrogen-bond exchanges: the first reduces the proton-acceptor water coordination, leading to proton transfer, and the second, the rate-limiting step, prevents rapid back-transfer by increasing the proton-donor coordination. This sequential mechanism is consistent with experimental characterizations of proton diffusion, explaining the low activation energy and the prolonged intermediate lifetimes in vibrational spectroscopy. These results are crucial for understanding proton dynamics in biochemical and technological systems.
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Affiliation(s)
- Axel Gomez
- PASTEUR, Department of Chemistry, École normale supérieure, PSL University, Sorbonne Université, CNRS, Paris, France
| | - Ward H Thompson
- Department of Chemistry, University of Kansas, Lawrence, KS, USA
| | - Damien Laage
- PASTEUR, Department of Chemistry, École normale supérieure, PSL University, Sorbonne Université, CNRS, Paris, France.
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