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Crabtree KN, Westerfield JH, Dim CA, Meyer KS, Johansen SL, Buchanan ZS, Stucky PA. Rotational spectroscopy of methyl tert-butyl ether with a new Ka band chirped-pulse Fourier transform microwave spectrometer. Phys Chem Chem Phys 2024; 26:13694-13709. [PMID: 38666410 DOI: 10.1039/d4cp00797b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2024]
Abstract
Chirped-pulse Fourier transform microwave (CP-FTMW) spectroscopy is a powerful tool for performing broadband gas-phase rotational spectroscopy, and its applications include discovery of new molecules, complex mixture analysis, and exploration of fundamental molecular physics. Here we report the development of a new Ka band (26.5-40 GHz) CP-FTMW spectrometer that is equipped with a pulsed supersonic expansion source and a heated reservoir for low-volatility samples. The spectrometer is built around a 150 W traveling wave tube amplifier and has an instantaneous bandwidth that covers the entire Ka band spectral range. To test the performance of the spectrometer, the rotational spectrum of methyl tert-butyl ether (MTBE), a former gasoline additive and environmental pollutant, has been measured for the first time in this spectral range. Over 1000 spectroscopic transitions have been measured and assigned to the vibrational ground state and a newly-identified torsionally excited state; all transitions were fit using the XIAM program to a root-mean-square deviation of 22 kHz. The spectrum displays internal rotation splitting, nominally forbidden transitions, and an intriguing axis-switching effect between the ground and torsionally excited state that is a consequence of MTBE's extreme near-prolate nature. Finally, the sensitivity of the spectrometer enabled detection of all singly-substituted 13C and 18O isotopologues in natural abundance. This set of isotopic spectra allowed for a partial r0 structure involving the heavy atoms to be derived, resolving a structural discrepancy in the literature between previous microwave and electron diffraction measurements.
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Affiliation(s)
- Kyle N Crabtree
- Department of Chemistry, University of California, Davis, Davis, CA, USA.
| | - J H Westerfield
- Department of Chemistry, University of California, Davis, Davis, CA, USA.
| | - Chisom A Dim
- Department of Chemistry, University of California, Davis, Davis, CA, USA.
| | - Kelly S Meyer
- Department of Chemistry, University of California, Davis, Davis, CA, USA.
| | - Sommer L Johansen
- Department of Chemistry, University of California, Davis, Davis, CA, USA.
| | - Zachary S Buchanan
- Department of Chemistry, University of California, Davis, Davis, CA, USA.
| | - Paul A Stucky
- Department of Chemistry, University of California, Davis, Davis, CA, USA.
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2
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Barone V. Quantum chemistry meets high-resolution spectroscopy for characterizing the molecular bricks of life in the gas-phase. Phys Chem Chem Phys 2024; 26:5802-5821. [PMID: 38099409 DOI: 10.1039/d3cp05169b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
Computation of accurate geometrical structures and spectroscopic properties of large flexible molecules in the gas-phase is tackled at an affordable cost using a general exploration/exploitation strategy. The most distinctive feature of the approach is the careful selection of different quantum chemical models for energies, geometries and vibrational frequencies with the aim of maximizing the accuracy of the overall description while retaining a reasonable cost for all the steps. In particular, a composite wave-function method is used for energies, whereas a double-hybrid functional (with the addition of core-valence correlation) is employed for geometries and harmonic frequencies and a cheaper hybrid functional for anharmonic contributions. A thorough benchmark based on a wide range of prototypical molecular bricks of life shows that the proposed strategy is close to the accuracy of state-of-the-art composite wave-function methods, and is applicable to much larger systems. A freely available web-utility post-processes the geometries optimized by standard electronic structure codes paving the way toward the accurate yet not prohibitively expensive study of medium- to large-sized molecules by experimentally-oriented researchers.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy.
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3
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Spaniol JT, Lee KLK, Pirali O, Puzzarini C, Martin-Drumel MA. A rotational investigation of the three isomeric forms of cyanoethynylbenzene (HCC-C 6H 4-CN): benchmarking experiments and calculations using the "Lego brick" approach. Phys Chem Chem Phys 2023; 25:6397-6405. [PMID: 36779600 DOI: 10.1039/d2cp04825f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We report the study of three structural isomers of phenylpropiolonitrile (3-phenyl-2-propynenitrile, C6H5-C3N) containing an alkyne function and a cyano group, namely ortho-, meta-, and para-cyanoethynylbenzene (HCC-C6H4-CN). The pure rotational spectra of these species have been recorded at room temperature in the millimeter-wave domain using a chirped-pulse spectrometer (75-110 GHz) and a source-frequency modulation spectrometer (140-220 GHz). Assignments of transitions in the vibrational ground state and several vibrationally excited states were supported by quantum chemical calculations using the so-called "Lego brick" approach [A. Melli, F. Tonolo, V. Barone and C. Puzzarini, J. Phys. Chem. A, 2021, 125, 9904-9916]. From these assignments, accurate spectroscopic (rotational and centrifugal distortion) constants have been derived: for all species and all observed vibrational states, predicted rotational constants show relative accuracy better than 0.1%, and often of the order of 0.01%, compared to the experimental values. The present work hence further validates the use of the "Lego brick" approach for predicting spectroscopic constants with high precision.
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Affiliation(s)
- Jean-Thibaut Spaniol
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405 Orsay, France.
| | - Kin Long Kelvin Lee
- Intel Accelerated Computing Systems and Graphics Group, Intel JF5 2111 NE 25th Ave, Hillsboro, OR 97124, USA
| | - Olivier Pirali
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405 Orsay, France.
| | - Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, via F. Selmi 2, 40126 Bologna, Italy.
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4
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Assignment-free chirality detection in unknown samples via microwave three-wave mixing. Commun Chem 2022; 5:31. [PMID: 36697786 PMCID: PMC9814651 DOI: 10.1038/s42004-022-00641-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 02/03/2022] [Indexed: 01/28/2023] Open
Abstract
Straightforward identification of chiral molecules in multi-component mixtures of unknown composition is extremely challenging. Current spectrometric and chromatographic methods cannot unambiguously identify components while the state of the art spectroscopic methods are limited by the difficult and time-consuming task of spectral assignment. Here, we introduce a highly sensitive generalized version of microwave three-wave mixing that uses broad-spectrum fields to detect chiral molecules in enantiomeric excess without any prior chemical knowledge of the sample. This method does not require spectral assignment as a necessary step to extract information out of a spectrum. We demonstrate our method by recording three-wave mixing spectra of multi-component samples that provide direct evidence of enantiomeric excess. Our method opens up new capabilities in ultrasensitive phase-coherent spectroscopic detection that can be applied for chiral detection in real-life mixtures, raw products of chemical reactions and difficult to assign novel exotic species.
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5
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Wahab MF, Aslani S, Mikhonin AV, Neill JL, Armstrong DW. Enhancing Sensitivity for High-Selectivity Gas Chromatography-Molecular Rotational Resonance Spectroscopy. Anal Chem 2021; 93:15525-15533. [PMID: 34748700 DOI: 10.1021/acs.analchem.1c03710] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A next-generation gas chromatograph-molecular rotational resonance (MRR) spectrometer (GC-MRR) with instrumental improvements and higher sensitivity is described. MRR serves as a structural information-rich detector for GC with extremely narrow linewidths and capabilities surpassing 1H nuclear magnetic resonance/Fourier transform infrared spectroscopy/mass spectrometry (MS) while offering unparalleled specificity in regard to a molecule's three-dimensional structure. With a Fabry-Pérot cavity and a supersonic jet incorporated into a GC-MRR, dramatic improvements in sensitivity for molecules up to 244 Da were achieved in the microwave region compared to the only prior work, which demonstrated the GC-MRR idea for the first time with millimeter waves. The supersonic jet cools the analytes to ∼2 K, resulting in a limited number of molecular rotational and vibrational levels and enabling us to obtain stronger GC-MRR signals. This has allowed the limits of detection of the GC-MRR to be comparable to a GC thermal conductivity detector with an optimized choice of gases. The performance of this GC-MRR system is reported for a range of molecules with permanent dipole moments, including alcohols, nitrogen heterocyclics, halogenated compounds, dioxins, and nitro compounds in the molecular mass range of 46-244 Da. The lowest amount of any substance yet detected by MRR in terms of mass is reported in this work. A theoretically unexpected finding is reported for the first time about the effect of the GC carrier gas (He, Ne, and N2) on the sensitivity of the analysis in the presence of the gas driving the supersonic jet (He, Ne, and N2) in the GC-MRR. Finally, the idea of total molecule monitoring in the GC-MRR analogous to selected ion monitoring in GC-MS is illustrated. Structural isomers and isotopologues of bromobutanes and bromonitrobenzenes are used to demonstrate this concept.
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Affiliation(s)
- M Farooq Wahab
- Department of Chemistry & Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, United States
| | - Saba Aslani
- Department of Chemistry & Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, United States
| | - Alexander V Mikhonin
- BrightSpec, Inc., 770 Harris St., Suite 104b, Charlottesville, Virginia 22903, United States
| | - Justin L Neill
- BrightSpec, Inc., 770 Harris St., Suite 104b, Charlottesville, Virginia 22903, United States
| | - Daniel W Armstrong
- Department of Chemistry & Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, United States.,AZYP, LLC, Arlington, Texas 76012, United States
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6
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Testing the Scalability of the HS-AUTOFIT Tool in a High-Performance Computing Environment. ELECTRONICS 2021. [DOI: 10.3390/electronics10182251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In the last years, the development of broadband chirped-pulse Fourier transform microwave spectrometers has revolutionized the field of rotational spectroscopy. Currently, it is possible to experimentally obtain a large quantity of spectra that would be difficult to analyze manually due to two main reasons. First, recent instruments allow obtaining a considerable amount of data in very short times, and second, it is possible to analyze complex mixtures of molecules that all contribute to the density of the spectra. AUTOFIT is a spectral assignment software application that was developed in 2013 to support and facilitate the analysis. Notwithstanding the benefits AUTOFIT brings in terms of automation of the analysis of the accumulated data, it still does not guarantee a good performance in terms of execution time because it leverages the computing power of a single computing machine. To cater to this requirement, we developed a parallel version of AUTOFIT, called HS-AUTOFIT, capable of running on high-performance computing (HPC) clusters to shorten the time to explore and analyze spectral big data. In this paper, we report some tests conducted on a real HPC cluster aimed at providing a quantitative assessment of HS-AUTOFIT’s scaling capabilities in a multi-node computing context. The collected results demonstrate the benefits of the proposed approach in terms of a significant reduction in computing time.
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7
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McCarthy MC, McGuire BA. Aromatics and Cyclic Molecules in Molecular Clouds: A New Dimension of Interstellar Organic Chemistry. J Phys Chem A 2021; 125:3231-3243. [DOI: 10.1021/acs.jpca.1c00129] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michael C. McCarthy
- Center for Astrophysics
- Harvard & Smithsonian, 60 Garden Street, Cambridge Massachusetts 02138, United States
| | - Brett A. McGuire
- Center for Astrophysics
- Harvard & Smithsonian, 60 Garden Street, Cambridge Massachusetts 02138, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- National Radio Astronomy Observatory, Charlottesville, Virginia 22903, United States
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8
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Zaleski DP, Sivaramakrishnan R, Weller HR, Seifert NA, Bross DH, Ruscic B, Moore KB, Elliott SN, Copan AV, Harding LB, Klippenstein SJ, Field RW, Prozument K. Substitution Reactions in the Pyrolysis of Acetone Revealed through a Modeling, Experiment, Theory Paradigm. J Am Chem Soc 2021; 143:3124-3142. [PMID: 33615780 DOI: 10.1021/jacs.0c11677] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The development of high-fidelity mechanisms for chemically reactive systems is a challenging process that requires the compilation of rate descriptions for a large and somewhat ill-defined set of reactions. The present unified combination of modeling, experiment, and theory provides a paradigm for improving such mechanism development efforts. Here we combine broadband rotational spectroscopy with detailed chemical modeling based on rate constants obtained from automated ab initio transition state theory-based master equation calculations and high-level thermochemical parametrizations. Broadband rotational spectroscopy offers quantitative and isomer-specific detection by which branching ratios of polar reaction products may be obtained. Using this technique, we observe and characterize products arising from H atom substitution reactions in the flash pyrolysis of acetone (CH3C(O)CH3) at a nominal temperature of 1800 K. The major product observed is ketene (CH2CO). Minor products identified include acetaldehyde (CH3CHO), propyne (CH3CCH), propene (CH2CHCH3), and water (HDO). Literature mechanisms for the pyrolysis of acetone do not adequately describe the minor products. The inclusion of a variety of substitution reactions, with rate constants and thermochemistry obtained from automated ab initio kinetics predictions and Active Thermochemical Tables analyses, demonstrates an important role for such processes. The pathway to acetaldehyde is shown to be a direct result of substitution of acetone's methyl group by a free H atom, while propene formation arises from OH substitution in the enol form of acetone by a free H atom.
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Affiliation(s)
- Daniel P Zaleski
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States.,Department of Chemistry, Colgate University, Hamilton, New York 13346, United States
| | - Raghu Sivaramakrishnan
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Hailey R Weller
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States.,Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Nathan A Seifert
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - David H Bross
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Branko Ruscic
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Kevin B Moore
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Sarah N Elliott
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Andreas V Copan
- Emmanuel College, Natural Sciences Department, Franklin Springs, Georgia 30639, United States
| | - Lawrence B Harding
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Stephen J Klippenstein
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Robert W Field
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Kirill Prozument
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
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9
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Förster A, Visscher L. Low-Order Scaling G0W0 by Pair Atomic Density Fitting. J Chem Theory Comput 2020; 16:7381-7399. [PMID: 33174743 PMCID: PMC7726916 DOI: 10.1021/acs.jctc.0c00693] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Indexed: 12/18/2022]
Abstract
We derive a low-scaling G0W0 algorithm for molecules using pair atomic density fitting (PADF) and an imaginary time representation of the Green's function and describe its implementation in the Slater type orbital (STO)-based Amsterdam density functional (ADF) electronic structure code. We demonstrate the scalability of our algorithm on a series of water clusters with up to 432 atoms and 7776 basis functions and observe asymptotic quadratic scaling with realistic threshold qualities controlling distance effects and basis sets of triple-ζ (TZ) plus double polarization quality. Also owing to a very small prefactor, a G0W0 calculation for the largest of these clusters takes only 240 CPU hours with these settings. We assess the accuracy of our algorithm for HOMO and LUMO energies in the GW100 database. With errors of 0.24 eV for HOMO energies on the quadruple-ζ level, our implementation is less accurate than canonical all-electron implementations using the larger def2-QZVP GTO-type basis set. Apart from basis set errors, this is related to the well-known shortcomings of the GW space-time method using analytical continuation techniques as well as to numerical issues of the PADF approach of accurately representing diffuse atomic orbital (AO) products. We speculate that these difficulties might be overcome by using optimized auxiliary fit sets with more diffuse functions of higher angular momenta. Despite these shortcomings, for subsets of medium and large molecules from the GW5000 database, the error of our approach using basis sets of TZ and augmented double-ζ (DZ) quality is decreasing with system size. On the augmented DZ level, we reproduce canonical, complete basis set limit extrapolated reference values with an accuracy of 80 meV on average for a set of 20 large organic molecules. We anticipate our algorithm, in its current form, to be very useful in the study of single-particle properties of large organic systems such as chromophores and acceptor molecules.
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Affiliation(s)
- Arno Förster
- Theoretical Chemistry, Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands
| | - Lucas Visscher
- Theoretical Chemistry, Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands
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10
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Rotational spectrum simulations of asymmetric tops in an astrochemical context. J Mol Model 2020; 26:278. [PMID: 32960366 DOI: 10.1007/s00894-020-04523-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 08/26/2020] [Indexed: 10/23/2022]
Abstract
Rotational spectroscopy plays a major role in the field of observational astrochemistry, enabling the detection of more than 200 species including a plethora of complex organic molecules in different space environments. Those line detections allow correctly determining the sources and physical properties, as well as exploring their morphology, evolutionary stage, and chemical evolution pathways. In this context, quantum chemistry is a powerful tool to the investigation of the molecular inventory of astrophysical environments, guiding laboratory experiments and assisting in both line assignments and extrapolation of the experimental data to unexplored frequency ranges. In the present work, we start by briefly reviewing the rotational model Hamiltonian for asymmetric tops beyond the rigid-rotor approximation, including rotational-vibrational, centrifugal, and anharmonic effects. Then, aiming at further contributing to the recording and analysis of laboratory microwave spectroscopy by means of accessible, less demanding quantum chemical methods, we performed density functional theory (DFT) calculations of the spectroscopic parameters of astrochemically relevant species, followed by their rotational spectrum simulations. Furthermore, dispersion-correction effects combined with different functionals were also investigated. Case studies are the asymmetric tops H2CO, H2CS, c-HCOOH, t-HCOOH, and HNCO. Spectroscopic parameter predictions were overall very close to experiment, with mean percentage errors smaller than 1% for zeroth order and [Formula: see text] for first-order constants. We discuss the implications and impacts of those constants on spectrum simulations, and compare line-frequency predictions at millimeter wavelengths. Moreover, theoretical spectroscopic parameters of c-HCOOH and HNCO are introduced for the first time in this work.
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11
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McCarthy MC, Lee KLK, Carroll PB, Porterfield JP, Changala PB, Thorpe JH, Stanton JF. Exhaustive Product Analysis of Three Benzene Discharges by Microwave Spectroscopy. J Phys Chem A 2020; 124:5170-5181. [DOI: 10.1021/acs.jpca.0c02919] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michael C. McCarthy
- Center for Astrophysics, Harvard and Smithsonian, 60 Garden Street, Cambridge Massachusetts 02138, United States
| | - Kin Long Kelvin Lee
- Center for Astrophysics, Harvard and Smithsonian, 60 Garden Street, Cambridge Massachusetts 02138, United States
| | - P. Brandon Carroll
- Center for Astrophysics, Harvard and Smithsonian, 60 Garden Street, Cambridge Massachusetts 02138, United States
| | - Jessica P. Porterfield
- Center for Astrophysics, Harvard and Smithsonian, 60 Garden Street, Cambridge Massachusetts 02138, United States
| | - P. Bryan Changala
- JILA, University of Colorado, Boulder, Colorado 80309, United States
| | - James H. Thorpe
- Quantum Theory Project, Department of Chemistry and Physics, University of Florida, Gainesville, Florida 32611, United States
| | - John F. Stanton
- Quantum Theory Project, Department of Chemistry and Physics, University of Florida, Gainesville, Florida 32611, United States
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12
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McCarthy M, Lee KLK. Molecule Identification with Rotational Spectroscopy and Probabilistic Deep Learning. J Phys Chem A 2020; 124:3002-3017. [PMID: 32212702 DOI: 10.1021/acs.jpca.0c01376] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A proof-of-concept framework for identifying molecules of unknown elemental composition and structure using experimental rotational data and probabilistic deep learning is presented. Using a minimal set of input data determined experimentally, we describe four neural network architectures that yield information to assist in the identification of an unknown molecule. The first architecture translates spectroscopic parameters into Coulomb matrix eigenspectra as a method of recovering chemical and structural information encoded in the rotational spectrum. The eigenspectrum is subsequently used by three deep learning networks to constrain the range of stoichiometries, generate SMILES strings, and predict the most likely functional groups present in the molecule. In each model, we utilize dropout layers as an approximation to Bayesian sampling, which subsequently generates probabilistic predictions from otherwise deterministic models. These models are trained on a modestly sized theoretical dataset comprising ∼83 000 unique organic molecules (between 18 and 180 amu) optimized at the ωB97X-D/6-31+G(d) level of theory, where the theoretical uncertainties of the spectoscopic constants are well-understood and used to further augment training. Since chemical and structural properties depend strongly on molecular composition, we divided the dataset into four groups corresponding to pure hydrocarbons, oxygen-bearing species, nitrogen-bearing species, and both oxygen- and nitrogen-bearing species, training each type of network with one of these categories, thus creating "experts" within each domain of molecules. We demonstrate how these models can then be used for practical inference on four molecules and discuss both the strengths and shortcomings of our approach and the future directions these architectures can take.
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Affiliation(s)
- Michael McCarthy
- Center for Astrophysics
- Harvard & Smithsonian, 60 Garden Street, Cambridge, Massachusetts 02138, United States
| | - Kin Long Kelvin Lee
- Center for Astrophysics
- Harvard & Smithsonian, 60 Garden Street, Cambridge, Massachusetts 02138, United States
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13
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Lee KLK, McCarthy M. Bayesian Analysis of Theoretical Rotational Constants from Low-Cost Electronic Structure Methods. J Phys Chem A 2020; 124:898-910. [DOI: 10.1021/acs.jpca.9b09982] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kin Long Kelvin Lee
- Harvard & Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, Massachusetts 02138, United States
| | - Michael McCarthy
- Harvard & Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, Massachusetts 02138, United States
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14
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Hernandez-Castillo AO, Abeysekera C, Robicheaux F, Zwier TS. Propagating molecular rotational coherences through single-frequency pulses in the strong field regime. J Chem Phys 2019; 151:084312. [PMID: 31470710 DOI: 10.1063/1.5099049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In the weak-field limit in which microwave spectroscopy is typically carried out, an application of a single-frequency pulse that is resonant with a molecular transition will create a coherence between the pair of states involved in the rotational transition, producing a free-induction decay (FID) that, after Fourier transform, produces a molecular signal at that same resonance frequency. With the advent of chirped-pulse Fourier transform microwave methods, the high-powered amplifiers needed to produce broadband microwave spectra also open up other experiments that probe the molecular response in the high-field regime. This paper describes a series of experiments involving resonant frequency pulses interrogating jet-cooled molecules under conditions of sufficient power to Rabi oscillate the two-state system through many Rabi cycles. The Fourier-transformed FID shows coherent signal not only at the applied resonant frequency but also at a series of transitions initially connected to the original one by sharing an upper or lower level with it. As the duration of the single-frequency excitation is increased from 250 to 1500 ns, the number of observed off-resonant, but dipole-allowed, molecular coherences grow. The phenomenon is quite general, having been demonstrated in Z-phenylvinylnitrile, E-phenylvinylnitrile (E-PVN), benzonitrile, guaiacol, and 4-pentynenitrile. In E-PVN, the highest power/longest pulse duration, coherent signal is also present at energetically nearby but not directly connected transitions. Even in molecular samples containing more than one independent species, only transitions due to the single species responsible for the original resonant transition are present. We develop a time-dependent model of the molecular/photon system and use it in conjunction with the experiment to test possible sources of the phenomenon.
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Affiliation(s)
| | - Chamara Abeysekera
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA
| | - F Robicheaux
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana 47907-2084, USA
| | - Timothy S Zwier
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA
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15
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Western CM, Billinghurst BE. Automatic and semi-automatic assignment and fitting of spectra with PGOPHER. Phys Chem Chem Phys 2019; 21:13986-13999. [PMID: 30534688 DOI: 10.1039/c8cp06493h] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two new tools for computer assisted assignment of rotational spectra with the PGOPHER program are presented, aimed particularly at spectra where many individual lines are resolved. The first tool tries many different assignments, presenting a small number for possible refinement and a preliminary version of this has already been presented. The second tool, the nearest lines plot (a new style of residual plot) provides a clear indication as to whether a trial calculation is plausible, and allows rapid assignment of sets of related lines. It gives good results even for dense spectra with no obvious structure and in the presence of multiple interfering absorptions. The effectiveness of these tools is demonstrated by the analysis of high resolution IR spectra of 8 bands of cis- and trans-1,2-dichloroethene where, including hot bands and isotopologues, 31 vibrational transitions and 158 316 individual lines have been analysed, including perturbations for the higher energy states. Walkthroughs are presented to show this process is rapid.
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16
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Puzzarini C, Bloino J, Tasinato N, Barone V. Accuracy and Interpretability: The Devil and the Holy Grail. New Routes across Old Boundaries in Computational Spectroscopy. Chem Rev 2019; 119:8131-8191. [DOI: 10.1021/acs.chemrev.9b00007] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Cristina Puzzarini
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Via F. Selmi 2, I-40126 Bologna, Italy
| | - Julien Bloino
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Nicola Tasinato
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
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17
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Yeh L, Satterthwaite L, Patterson D. Automated, context-free assignment of asymmetric rotor microwave spectra. J Chem Phys 2019; 150:204122. [PMID: 31153211 DOI: 10.1063/1.5085794] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
We present a new algorithm, Robust Automated Assignment of Rigid Rotors (RAARR), for assigning rotational spectra of asymmetric tops. The RAARR algorithm can automatically assign experimental spectra under a broad range of conditions, including spectra comprised of multiple mixture components, in ≲100 s. The RAARR algorithm exploits constraints placed by the conservation of energy to find sets of connected lines in an unassigned spectrum. The highly constrained structure of these sets eliminates all but a handful of plausible assignments for a given set, greatly reducing the number of potential assignments that must be evaluated. We successfully apply our algorithm to automatically assign 15 experimental spectra, including 5 previously unassigned species, without prior estimation of molecular rotational constants. In 9 of the 15 cases, the RAARR algorithm successfully assigns two or more mixture components.
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Affiliation(s)
- Lia Yeh
- Department of Physics, University of California, Santa Barbara, California 93106, USA
| | - Lincoln Satterthwaite
- Department of Physics, University of California, Santa Barbara, California 93106, USA
| | - David Patterson
- Department of Physics, University of California, Santa Barbara, California 93106, USA
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18
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Lee KLK, McCarthy M. Study of Benzene Fragmentation, Isomerization, and Growth Using Microwave Spectroscopy. J Phys Chem Lett 2019; 10:2408-2413. [PMID: 31021635 DOI: 10.1021/acs.jpclett.9b00586] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Using a combination of broadband and cavity Fourier transform microwave spectroscopies, and newly developed analysis and assignment tools, the discharge products of benzene have been extensively studied in the 2-18 GHz frequency range. More than 450 spectral features with intensities greater than 6σ of the noise RMS were identified, of which of roughly four-fifths (82%) constituting 90% of the total spectral intensity were assigned to 38 species previously detected in the radio band, and nine entirely new hydrocarbon molecules were identified. The new species include both branched and chain fragments of benzene, high energy C6H6 isomers, and larger molecules such as phenyldiacetylene and isomers of fulvenallene; taken together they account for roughly half of the number of observed transitions and 51% of the spectral line intensity. Transitions from vibrationally excited states of several molecules were also identified in the course of this investigation. A key aspect of the present analysis was implementation of a rapid and efficient workflow to assign spectral features from known molecules and to identify line progressions by pattern recognition techniques.
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Affiliation(s)
- Kin Long Kelvin Lee
- Harvard-Smithsonian Center for Astrophysics , 60 Garden Street , Cambridge , Massachusetts 02138 , United States
| | - Michael McCarthy
- Harvard-Smithsonian Center for Astrophysics , 60 Garden Street , Cambridge , Massachusetts 02138 , United States
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19
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Martin-Drumel MA, Baraban JH, Changala PB, Stanton JF, McCarthy MC. The Hunt for Elusive Molecules: Insights from Joint Theoretical and Experimental Investigations. Chemistry 2019; 25:7243-7258. [PMID: 30673130 DOI: 10.1002/chem.201805986] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Indexed: 11/10/2022]
Abstract
Rotational spectroscopy is an invaluable tool to unambiguously determine the molecular structure of a species, and sometimes even to establish its very existence. This article illustrates how experimental and theoretical state-of-the-art tools can be used in tandem to investigate the rotational structure of molecules, with particular emphasis on those that have long remained elusive. The examples of three emblematic species-gauche-butadiene, disilicon carbide, and germanium dicarbide-highlight the close, mutually beneficial interaction between high-level theoretical calculations and sensitive microwave measurements. Prospects to detect other elusive molecules of chemical and astronomical interest are discussed.
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Affiliation(s)
- Marie-Aline Martin-Drumel
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405, Orsay, France
| | - Joshua H Baraban
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel
| | - P Bryan Changala
- JILA, National Institute of Standards and Technology and Department of, Physics, University of Colorado, Boulder, CO, 80309, USA
| | - John F Stanton
- Quantum Theory Project, Departments of Chemistry and Physics, Univ. of Florida, Gainesville, FL, 32611, USA
| | - Michael C McCarthy
- Harvard-Smithsonian Center for Astrophysics, Cambridge, Massachusetts, 02138, USA
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20
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Riffe EJ, Shipman ST, Gaster SA, Funderburk CM, Brown GG. Rotational Spectrum of Eugenol As Analyzed with Double Resonance and Grid-Based Autofit. J Phys Chem A 2019; 123:1091-1099. [DOI: 10.1021/acs.jpca.8b09169] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Erika J. Riffe
- Division of Natural Sciences, New College of Florida, Sarasota, Florida 34243, United States
| | - Steven T. Shipman
- Division of Natural Sciences, New College of Florida, Sarasota, Florida 34243, United States
| | - Sydney A. Gaster
- Department of Science and Mathematics, Coker College, Hartsville, South Carolina 29550, United States
| | - Cameron M. Funderburk
- Department of Science and Mathematics, Coker College, Hartsville, South Carolina 29550, United States
| | - Gordon G. Brown
- Department of Science and Mathematics, Coker College, Hartsville, South Carolina 29550, United States
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21
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Porterfield JP, Lee KLK, Dell'Isola V, Carroll PB, McCarthy MC. Characterization of the simplest hydroperoxide ester, hydroperoxymethyl formate, a precursor of atmospheric aerosols. Phys Chem Chem Phys 2019; 21:18065-18070. [DOI: 10.1039/c9cp03466h] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Atmospheric aerosols are large clusters of molecules and particulate matter that profoundly affect the Earth's radiation budget and climate.
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Affiliation(s)
| | | | - Valentina Dell'Isola
- Dipartimento di Chimica “Giacomo Ciamician”
- Universita' di Bologna
- 40126 Bologna
- Italy
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22
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Zaleski DP, Prozument K. Automated assignment of rotational spectra using artificial neural networks. J Chem Phys 2018; 149:104106. [DOI: 10.1063/1.5037715] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Daniel P. Zaleski
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439,
USA
| | - Kirill Prozument
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439,
USA
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23
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Roenitz KM, Hays BM, Powers CR, McCabe MN, Smith H, Widicus Weaver SL, Shipman ST. AC Stark Effect Observed in a Microwave-Millimeter/Submillimeter Wave Double-Resonance Experiment. J Phys Chem A 2018; 122:6321-6327. [PMID: 29993251 DOI: 10.1021/acs.jpca.8b02116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Microwave-millimeter/submillimeter wave double-resonance spectroscopy has been developed with the use of technology typically employed in chirped pulse Fourier transform microwave spectroscopy and fast-sweep direct absorption (sub)millimeter-wave spectroscopy. This technique offers the high sensitivity provided by millimeter/submillimeter fast-sweep techniques with the rapid data acquisition offered by chirped pulse Fourier transform microwave spectrometers. Rather than detecting the movement of population as is observed in a traditional double-resonance experiment, instead we detected the splitting of spectral lines arising from the AC Stark effect. This new technique will prove invaluable when assigning complicated rotational spectra of complex molecules. The experimental design is presented along with the results from the double-resonance spectra of methanol as a proof-of-concept for this technique.
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Affiliation(s)
- Kevin M Roenitz
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Brian M Hays
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Carson R Powers
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Morgan N McCabe
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Houston Smith
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | | | - Steven T Shipman
- Division of Natural Sciences , New College of Florida , Sarasota , Florida 34243 , United States
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24
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McCarthy MC, Zou L, Martin-Drumel MA. To kink or not: A search for long-chain cumulenones using microwave spectral taxonomy. J Chem Phys 2018; 146:154301. [PMID: 28433021 DOI: 10.1063/1.4981125] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A systematic search for carbon-chain cumulenones beyond H2C4O has been undertaken using microwave spectral taxonomy in combination with a pulsed jet discharge source. No evidence was found for the C2υ isomer of H2C5O or its longer derivatives, but HC(O)C4H, the longer variant of propynal, HC(O)CCH, was identified instead. Its rotational and leading centrifugal distortion constants have been derived to high accuracy from detection of both a- and b-type lines; those below 40 GHz were measured using a Fabry-Perot cavity, while lines between 40 and 72 GHz were recorded by double resonance techniques. Overwhelming evidence for the identification is provided by detection of HC(O)C4D, DC(O)C4H, and HC(18O)C4H at the expected frequencies using isotopically enriched samples. Because HC(18O)C4H is produced with comparable abundance when using either 18O2 or C18O as the source of oxygen, and because H13C(O)C4H is not preferentially formed when starting from 13CO, atomic oxygen appears to be a key reactant in formation, plausibly via O insertion, e.g., H2CC2n+2H + O → HC(O)C2n+2H + H. Under the same experimental conditions, HC(O)CCH is more than 10 times more abundant than H2C3O, regardless of the source of oxygen, and no evidence is found for cyclopropenone, c-C3H2O. Taken together, these observations indicate that propynal and longer chains with an odd number of carbon atoms are either energetically more stable than cumulenones of the same size, are kinetically favored products, or both. On the basis of the HC(O)C4H discovery, searches for the isovalent sulfur species, HC(S)C4H, and HC(O)C6H have been conducted. Guided by new quantum chemical calculations, the rotational spectra of both were observed in the centimeter-wave band with the same spectrometer.
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Affiliation(s)
- Michael C McCarthy
- Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, Massachusetts 02138, USA and School of Engineering and Applied Sciences, Harvard University, 29 Oxford Street, Cambridge, Massachusetts 02138, USA
| | - Luyao Zou
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA
| | - Marie-Aline Martin-Drumel
- Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, Massachusetts 02138, USA and School of Engineering and Applied Sciences, Harvard University, 29 Oxford Street, Cambridge, Massachusetts 02138, USA
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25
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Sulfur monoxide thermal release from an anthracene-based precursor, spectroscopic identification, and transfer reactivity. Proc Natl Acad Sci U S A 2018; 115:5866-5871. [PMID: 29773708 DOI: 10.1073/pnas.1804035115] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sulfur monoxide (SO) is a highly reactive molecule and thus, eludes bulk isolation. We report here on synthesis and reactivity of a molecular precursor for SO generation, namely 7-sulfinylamino-7-azadibenzonorbornadiene (1). This compound has been shown to fragment readily driven by dinitrogen expulsion and anthracene formation on heating in the solid state and in solution, releasing SO at mild temperatures (<100 °C). The generated SO was detected in the gas phase by MS and rotational spectroscopy. In solution, 1 allows for SO transfer to organic molecules as well as transition metal complexes.
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26
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Abstract
Chiroptical spectroscopy techniques for the differentiation of enantiomers in the condensed phase are based on an established paradigm that relies on symmetry breaking using circularly polarized light. We review a novel approach for the study of chiral molecules in the gas phase using broadband rotational spectroscopy, namely microwave three-wave mixing, which is a coherent, nonlinear, and resonant process. This technique can be used to generate a coherent molecular rotational signal that can be detected in a manner similar to that in conventional Fourier transform microwave spectroscopy. The structure (and thermal distribution of conformations), handedness, and enantiomeric excess of gas-phase samples can be determined unambiguously by employing tailored microwave fields. We discuss the theoretical and experimental aspects of the method, the significance of the first demonstrations of the technique for enantiomer differentiation, and the method's rapid advance into a robust choice to study molecular chirality in the gas phase. Very recently, the microwave three-wave mixing approach was extended to enantiomer-selective population transfer, an important step toward spatial enantiomer separation on the fly.
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Affiliation(s)
- Sérgio R. Domingos
- Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany
- Christian-Albrechts-Universität zu Kiel, Institut für Physikalische Chemie, 24118 Kiel, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, 22761 Hamburg, Germany
| | - Cristóbal Pérez
- Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany
- Christian-Albrechts-Universität zu Kiel, Institut für Physikalische Chemie, 24118 Kiel, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, 22761 Hamburg, Germany
| | - Melanie Schnell
- Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany
- Christian-Albrechts-Universität zu Kiel, Institut für Physikalische Chemie, 24118 Kiel, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, 22761 Hamburg, Germany
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27
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Uriarte I, Melandri S, Maris A, Calabrese C, Cocinero EJ. Shapes, Dynamics, and Stability of β-Ionone and Its Two Mutants Evidenced by High-Resolution Spectroscopy in the Gas Phase. J Phys Chem Lett 2018; 9:1497-1502. [PMID: 29510049 DOI: 10.1021/acs.jpclett.8b00256] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The conformational landscapes of β-ionone and two mutants (α-ionone and β-damascone) have been analyzed by means of state-of-the-art rotational spectroscopy and quantum-chemical calculations. The experiments performed at high resolution and sensitivity have provided a deep insight into their conformational spaces, assigning more than 8000 transitions corresponding to the rotational structures of 54 different species (3 isomers, 14 conformers, and 40 isotopologues). Methyl internal rotation dynamics were also observed and analyzed. The work proved the great flexibility of β-ionone due to its flatter potential energy surface. This feature confers on β-ionone a wider ability to interconvert between conformers with rather similar energies with respect to its mutants, allowing the retinal ligand to better adapt inside the binding pocket.
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Affiliation(s)
- Iciar Uriarte
- Dpto. Química Física, Facultad de Ciencia y Tecnología , Universidad del País Vasco (UPV/EHU) , Apartado 644 , E-48080 Bilbao , Spain
| | - Sonia Melandri
- Dipartimento di Chimica "G. Ciamician" , Università degli Studi di Bologna , via Selmi 2 , I-40126 Bologna , Italy
| | - Assimo Maris
- Dipartimento di Chimica "G. Ciamician" , Università degli Studi di Bologna , via Selmi 2 , I-40126 Bologna , Italy
| | - Camilla Calabrese
- Dipartimento di Chimica "G. Ciamician" , Università degli Studi di Bologna , via Selmi 2 , I-40126 Bologna , Italy
- Dpto. Química Física, Facultad de Ciencia y Tecnología , Universidad del País Vasco (UPV/EHU) , Apartado 644 , E-48080 Bilbao , Spain
| | - Emilio J Cocinero
- Dpto. Química Física, Facultad de Ciencia y Tecnología , Universidad del País Vasco (UPV/EHU) , Apartado 644 , E-48080 Bilbao , Spain
- Biofisika Institute (CSIC, UPV/EHU) , Universidad del Paı́s Vasco (UPV/EHU) , E-48940 Leioa , Spain
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28
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Western CM, Billinghurst BE. Automatic assignment and fitting of spectra with pgopher. Phys Chem Chem Phys 2018; 19:10222-10226. [PMID: 28393944 DOI: 10.1039/c7cp00266a] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An initial implementation of a tool for automatic assignment of spectra within the pgopher program is presented, together with its application to rotational analysis of the ν11 band of cis-1,2-dichloroethene. It is based on the autofit algorithm presented by N. A. Seifert et al. (J. Mol. Spectrosc., 2015, 312, 13) but implemented in a more efficient and general way, allowing it to be applied to a much wider variety of spectra.
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29
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McGuire BA, Martin-Drumel MA, Lee KLK, Stanton JF, Gottlieb CA, McCarthy MC. Vibrational satellites of C2S, C3S, and C4S: microwave spectral taxonomy as a stepping stone to the millimeter-wave band. Phys Chem Chem Phys 2018; 20:13870-13889. [DOI: 10.1039/c8cp01102h] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present a microwave spectral taxonomy study of several hydrocarbon/CS2 discharge mixtures, in which more than 60 distinct species/vibrational states were detected and analyzed.
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Affiliation(s)
- Brett A. McGuire
- National Radio Astronomy Observatory
- Charlottesville
- USA
- Harvard-Smithsonian Center for Astrophysics
- Cambridge
| | | | | | | | | | - Michael C. McCarthy
- Harvard-Smithsonian Center for Astrophysics
- Cambridge
- USA
- School of Engineering and Applied Sciences
- Harvard University
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30
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Licari D, Tasinato N, Spada L, Puzzarini C, Barone V. VMS-ROT: A New Module of the Virtual Multifrequency Spectrometer for Simulation, Interpretation, and Fitting of Rotational Spectra. J Chem Theory Comput 2017; 13:4382-4396. [PMID: 28742339 PMCID: PMC5636176 DOI: 10.1021/acs.jctc.7b00533] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Virtual Multifrequency Spectrometer (VMS) is a tool that aims at integrating a wide range of computational and experimental spectroscopic techniques with the final goal of disclosing the static and dynamic physical-chemical properties "hidden" in molecular spectra. VMS is composed of two parts, namely, VMS-Comp, which provides access to the latest developments in the field of computational spectroscopy, and VMS-Draw, which provides a powerful graphical user interface (GUI) for an intuitive interpretation of theoretical outcomes and a direct comparison to experiment. In the present work, we introduce VMS-ROT, a new module of VMS that has been specifically designed to deal with rotational spectroscopy. This module offers an integrated environment for the analysis of rotational spectra: from the assignment of spectral transitions to the refinement of spectroscopic parameters and the simulation of the spectrum. While bridging theoretical and experimental rotational spectroscopy, VMS-ROT is strongly integrated with quantum-chemical calculations, and it is composed of four independent, yet interacting units: (1) the computational engine for the calculation of the spectroscopic parameters that are employed as a starting point for guiding experiments and for the spectral interpretation, (2) the fitting-prediction engine for the refinement of the molecular parameters on the basis of the assigned transitions and the prediction of the rotational spectrum of the target molecule, (3) the GUI module that offers a powerful set of tools for a vis-à-vis comparison between experimental and simulated spectra, and (4) the new assignment tool for the assignment of experimental transitions in terms of quantum numbers upon comparison with the simulated ones. The implementation and the main features of VMS-ROT are presented, and the software is validated by means of selected test cases ranging from isolated molecules of different sizes to molecular complexes. VMS-ROT therefore offers an integrated environment for the analysis of the rotational spectra, with the innovative perspective of an intimate connection to quantum-chemical calculations that can be exploited at different levels of refinement, as an invaluable support and complement for experimental studies.
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Affiliation(s)
- Daniele Licari
- Scuola Normale Superiore , Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Nicola Tasinato
- Scuola Normale Superiore , Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Lorenzo Spada
- Scuola Normale Superiore , Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna , Via Selmi 2, I-40126 Bologna, Italy
| | - Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna , Via Selmi 2, I-40126 Bologna, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore , Piazza dei Cavalieri 7, I-56126 Pisa, Italy
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32
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Wist J. Complex mixtures by NMR and complex NMR for mixtures: experimental and publication challenges. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:22-28. [PMID: 27668407 DOI: 10.1002/mrc.4533] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 09/14/2016] [Accepted: 09/22/2016] [Indexed: 06/06/2023]
Abstract
Untargeted strategies have changed the rules of the game in complex mixture analysis, introducing an amazing potential for medical and biological applications that is just starting to be tapped. But with great power come great challenges; although untargeted mixture analysis opens the road for many exciting possibilities, the road is still full of perils. On the one hand, this article highlights some of the difficulties that need to be sorted for mixture analysis by NMR to fulfill its potential, along with insight on how they may be managed. Highlighted key points include the need for 'computer friendly' solutions for sharing data, experimental design and algorithm to facilitate the steady growth of knowledge and modeling ability in the field, and the need for large-scale studies to improve confidence in newly identified biomarkers. On the other hand, the second part of this article presents some breakthroughs in NMR experiments that, when combined, may modify the landscape of mixture analysis. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Julien Wist
- Chemistry Department, Universidad del Valle, Cali, Colombia
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33
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Nonlinear two-dimensional terahertz photon echo and rotational spectroscopy in the gas phase. Proc Natl Acad Sci U S A 2016; 113:11800-11805. [PMID: 27702903 DOI: 10.1073/pnas.1609558113] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ultrafast 2D spectroscopy uses correlated multiple light-matter interactions for retrieving dynamic features that may otherwise be hidden under the linear spectrum; its extension to the terahertz regime of the electromagnetic spectrum, where a rich variety of material degrees of freedom reside, remains an experimental challenge. We report a demonstration of ultrafast 2D terahertz spectroscopy of gas-phase molecular rotors at room temperature. Using time-delayed terahertz pulse pairs, we observe photon echoes and other nonlinear signals resulting from molecular dipole orientation induced by multiple terahertz field-dipole interactions. The nonlinear time domain orientation signals are mapped into the frequency domain in 2D rotational spectra that reveal J-state-resolved nonlinear rotational dynamics. The approach enables direct observation of correlated rotational transitions and may reveal rotational coupling and relaxation pathways in the ground electronic and vibrational state.
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