1
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Cole TA, Davis SR, Flint AR, Fortenberry RC. Bridging the gap: viable reaction pathways from tetrahedrane to benzyne. Phys Chem Chem Phys 2024; 26:12510-12519. [PMID: 38619071 DOI: 10.1039/d3cp06199j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
The addition of sp-carbon-containing molecules to polycyclic sp3 tetrahedrane (c-C4H4) results in the formation of both o-benzyne (c-C6H4) and benzene (c-C6H6). Since both c-C6H4 and c-C6H6 have been detected in the interstellar medium (ISM), providing additional pathways for their possible astrochemical formation mechanisms can lead to the discovery of other molecules, such as c-C4H4, benzvalyne, and vinylidene (:CCH2). Addition of diatomic carbon (C2), the ethynyl radical (C2H), vinylidene, and acetylene (HCCH) to c-C4H4 is undertaken in individual pathways through high-level quantum chemical computations at the CCSD(T)-F12b/cc-pVTZ-F12 level of theory. The resulting C2 addition pathway proceeds barrierlessly through benzvalyne as an intermediate and reaches a true minimum at c-C6H4, but no leaving groups are produced which is required to dissipate excess energy within an interstellar chemical scheme. Similarly, the C2H addition to c-C4H4 produces benzvalyne as well as its related isomers. This pathway allows for the loss of a hydrogen leaving group to dissipate the resulting energy. Lastly, the HCCH and :CCH2 addition pathways follow through both benzvalene and benzvalyne in order to reach c-C6H6 (benzene) and c-C6H4 (o-benzyne) as well as H2 as the required leaving group. Although there is a barrier to the HCCH addition, the :CCH2 addition presents the contrary with only submerged barriers. These proposed mechanisms provide alternative possibilities for the formation of complex organic molecules in space.
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Affiliation(s)
- Taylor A Cole
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi, 38677, USA.
| | - Steven R Davis
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi, 38677, USA.
| | - Athena R Flint
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi, 38677, USA.
| | - Ryan C Fortenberry
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi, 38677, USA.
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2
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Esposito VJ, Ferrari P, Buma WJ, Fortenberry RC, Boersma C, Candian A, Tielens AGGM. The infrared absorption spectrum of phenylacetylene and its deuterated isotopologue in the mid- to far-IR. J Chem Phys 2024; 160:114312. [PMID: 38501470 DOI: 10.1063/5.0191404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/18/2024] [Indexed: 03/20/2024] Open
Abstract
Anharmonicity strongly influences the absorption and emission spectra of polycyclic aromatic hydrocarbon (PAH) molecules. Here, IR-UV ion-dip spectroscopy experiments together with detailed anharmonic computations reveal the presence of fundamental, overtone, as well as 2- and 3-quanta combination band transitions in the far- and mid-infrared absorption spectra of phenylacetylene and its singly deuterated isotopologue. Strong absorption features in the 400-900 cm-1 range originate from CH(D) in-plane and out-of-plane wags and bends, as well as bending motions including the C≡C and CH bonds of the acetylene substituent and the aromatic ring. For phenylacetylene, every absorption feature is assigned either directly or indirectly to a single or multiple vibrational mode(s). The measured spectrum is dense, broad, and structureless in many regions but well characterized by computations. Upon deuteration, large isotopic shifts are observed. At frequencies above 1500 cm-1 for d1-phenylacetylene, a one-to-one match is seen when comparing computations and experiments with all features assigned to combination bands and overtones. The C≡C stretch observed in phenylacetylene is not observed in d1-phenylacetylene due to a computed 40-fold drop in intensity. Overall, a careful treatment of anharmonicity that includes 2- and 3-quanta modes is found to be crucial to understand the rich details of the infrared spectrum of phenylacetylene. Based on these results, it can be expected that such an all-inclusive anharmonic treatment will also be key for unraveling the infrared spectra of PAHs in general.
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Affiliation(s)
- Vincent J Esposito
- NASA Ames Research Center, MS 245-6, Moffett Field, California 94035, USA
| | - Piero Ferrari
- Radboud University, Institute for Molecules and Materials, HFML-FELIX, 6525 ED Nijmegen, The Netherlands
| | - Wybren Jan Buma
- Radboud University, Institute for Molecules and Materials, HFML-FELIX, 6525 ED Nijmegen, The Netherlands
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Ryan C Fortenberry
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677-1848, USA
| | - Christiaan Boersma
- NASA Ames Research Center, MS 245-6, Moffett Field, California 94035, USA
| | - Alessandra Candian
- Anton Pannekoek Institute for Astronomy, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Alexander G G M Tielens
- Leiden Observatory, Leiden University, 2333 CA Leiden, The Netherlands
- Astronomy Department, University of Maryland, College Park, Maryland 20742-2421, USA
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3
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Watrous AG, Davis MC, Fortenberry RC. Performance of EOM-CCSD(T)(a)*-Based Quartic Force Fields in Computing Fundamental, Anharmonic Vibrational Frequencies of Molecular Electronically Excited States with Application to the Ã1A″ State of :CCH 2 (Vinylidene). J Phys Chem A 2024; 128:2150-2161. [PMID: 38466814 DOI: 10.1021/acs.jpca.3c08168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Highly accurate anharmonic vibrational frequencies of electronically excited states are not as easily computed as their ground electronic state counterparts, but recently developed approximate triple excited state methods may be changing that. One emerging excited state method is equation of motion coupled cluster theory at the singles and doubles level with perturbative triples computed via the (a)* formalism, EOMEE-CCSD(T)(a)*. One of the most employed means for the ready computation of vibrational anharmonic frequencies for ground electronic states is second-order vibrational perturbation theory (VPT2), a theory based on quartic force fields (QFFs),fourth-order Taylor series expansions of the potential portion of the internuclear Watson Hamiltonian. The combination of these two is herein benchmarked for its performance for use as a means of computing rovibrational spectra of electronically excited states. Specifically, the EOMEE-CCSD(T)(a)* approach employing a complete basis set extrapolation along with core electron inclusion and relativity (the so-called "CcCR" approach) defining the QFF produces anharmonic fundamental vibrational frequencies within 2.83%, on the average, of reported gas-phase experimentally assigned values for the test set including the A ~ 1 A ″ states of HCF, HCCl, HSiF, HNO, and HPO. However, some states have exceptional accuracy in the fundamentals, most notably for ν2 of A ~ 1 A ″ HCCl in which the CcCR QFF value is within 1.8 cm-1 at 927.9 cm-1 (or 0.2%) of the experiment. Additionally, this approach produces rotational constants to, on the absolute average, within 0.41% of available experimental data, showcasing notable accuracy in the computation of rovibronic spectral data. Furthermore, utilizing a hybrid approach composed of harmonic CcCR force constants along with a set of simple EOMEE-CCSD(T)(a)*/aug-cc-pVQZ QFF cubic and quartic force constants is faster than using pure CcCR and better represents those modes that suffer from numerical instability in the anharmonic portion of the QFF, implying that this so-called "CcCR + QZ" QFF approach may be the best for future applications. Finally, complete, rovibrational spectral data are provided for A ~ 1 A 2 :CCH2, a molecule of potential astrochemical interest, in order to aid in its potential future experimental rovibronic characterization.
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Affiliation(s)
- Alexandria G Watrous
- Department of Chemistry & Biochemistry, University of Mississippi, University, Mississippi 38677-1848, United States
| | - Megan C Davis
- Department of Chemistry & Biochemistry, University of Mississippi, University, Mississippi 38677-1848, United States
| | - Ryan C Fortenberry
- Department of Chemistry & Biochemistry, University of Mississippi, University, Mississippi 38677-1848, United States
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4
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Wang J, Marks JH, Fortenberry RC, Kaiser RI. Interstellar formation of glyceric acid [HOCH 2CH(OH)COOH]-The simplest sugar acid. Sci Adv 2024; 10:eadl3236. [PMID: 38478624 PMCID: PMC10936953 DOI: 10.1126/sciadv.adl3236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 02/08/2024] [Indexed: 03/17/2024]
Abstract
Glyceric acid [HOCH2CH(OH)COOH]-the simplest sugar acid-represents a key molecule in biochemical processes vital for metabolism in living organisms such as glycolysis. Although critically linked to the origins of life and identified in carbonaceous meteorites with abundances comparable to amino acids, the underlying mechanisms of its formation have remained elusive. Here, we report the very first abiotic synthesis of racemic glyceric acid via the barrierless radical-radical reaction of the hydroxycarbonyl radical (HOĊO) with 1,2-dihydroxyethyl (HOĊHCH2OH) radical in low-temperature carbon dioxide (CO2) and ethylene glycol (HOCH2CH2OH) ices. Using isomer-selective vacuum ultraviolet photoionization reflectron time-of-flight mass spectrometry, glyceric acid was identified in the gas phase based on the adiabatic ionization energies and isotopic substitution studies. This work reveals the key reaction pathways for glyceric acid synthesis through nonequilibrium reactions from ubiquitous precursor molecules, advancing our fundamental knowledge of the formation pathways of key biorelevant organics-sugar acids-in deep space.
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Affiliation(s)
- Jia Wang
- W. M. Keck Research Laboratory in Astrochemistry, University of Hawaii at Manoa, Honolulu, HI 96822, USA
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Joshua H. Marks
- W. M. Keck Research Laboratory in Astrochemistry, University of Hawaii at Manoa, Honolulu, HI 96822, USA
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Ryan C. Fortenberry
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, USA
| | - Ralf I. Kaiser
- W. M. Keck Research Laboratory in Astrochemistry, University of Hawaii at Manoa, Honolulu, HI 96822, USA
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, HI 96822, USA
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5
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Fortenberry RC. Quantum Chemistry and Astrochemistry: A Match Made in the Heavens. J Phys Chem A 2024; 128:1555-1565. [PMID: 38381079 DOI: 10.1021/acs.jpca.3c07601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Quantum chemistry can uniquely answer astrochemical questions that no other technique can provide. Computations can be parallelized, automated, and left to run continuously providing exceptional molecular throughput that cannot be done through experimentation. Additionally, the granularity of the individual computations that are required of potential energy surfaces, reaction mechanism pathways, or other quantum chemically derived observables produces a unique mosaic that make up the larger whole. These pieces can be dissected for their individual contributions or evaluated in an ad hoc fashion for each of their roles in generating the larger whole. No other scientific approach is capable of reporting such fine-grained insights. Quantum chemistry also works from a bottom-up approach in providing properties directly from the desired molecule instead of a top-down perspective as required of experiment where molecules have to be linked to observed phenomena. Furthermore, modern quantum chemistry is well within the range of "chemical accuracy" and is approaching "spectroscopic accuracy." As such, the seemingly difficult questions asked by astrochemistry that would not be asked initially for any other application require quantum chemical reference data. While the results of quantum chemical computations are needed to interpret astrochemical observation, modeling, or laboratory experimentation, such hard questions, regardless of the original need to answer them, produce unique solutions. While questions in astrochemistry often require novel developments in and implementations of quantum chemistry as outlined herein, the applications of these solutions will stretch beyond astrochemistry and may yet impact fields much closer to Earth.
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Affiliation(s)
- Ryan C Fortenberry
- Department of Chemistry & Biochemistry, University of Mississippi, Oxford, Mississippi 38677-1848, United States
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6
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Fortenberry RC. A Vision for the Future of Astrochemistry in the Interstellar Medium by 2050. ACS Phys Chem Au 2024; 4:31-39. [PMID: 38283789 PMCID: PMC10811777 DOI: 10.1021/acsphyschemau.3c00043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 11/14/2023] [Accepted: 11/16/2023] [Indexed: 01/30/2024]
Abstract
By 2050, many, but not nearly all, unattributed astronomical spectral features will be conclusively linked to molecular carriers (as opposed to nearly none today in the visible and IR); amino acids will have been observed remotely beyond our solar system; the largest observatories ever constructed on the surface of the Earth or launched beyond it will be operational; high-throughput computation either from brute force or machine learning will provide unprecedented amounts of reference spectral and chemical reaction data; and the chemical fingerprints of the universe delivered by those of us who call ourselves astrochemists will provide astrophysicists with unprecedented resolution for determining how the stars evolve, planets form, and molecules that lead to life originate. Astrochemistry is a relatively young field, but with the entire universe as its playground, the discipline promises to persist as long as telescopic observations are made that require reference data and complementary chemical modeling. While the recent commissionings of the James Webb Space Telescope and Atacama Large Millimeter Array are ushering in the second "golden age" of astrochemistry (with the first being the radio telescopic boom period of the 1970s), this current period of discovery should facilitate unprecedented advances within the next 25 years. Astrochemistry forces the asking of hard questions beyond the physical conditions of our "pale blue dot", and such questions require creative solutions that are influential beyond astrophysics. By 2050, more creative solutions will have been provided, but even more will be needed to answer the continuing question of our astrochemical ignorance.
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Affiliation(s)
- Ryan C. Fortenberry
- Department of Chemistry &
Biochemistry, University of Mississippi, University, Mississippi 38677-1848, United
States
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7
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Garrett NR, Davis MC, Fortenberry RC. DFT + F12 QFFs for Cost-Effective Rovibrational Spectral Data Predictions of Ground and Excited Electronic States. J Chem Theory Comput 2024. [PMID: 38230913 DOI: 10.1021/acs.jctc.3c01179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
The quest for faster computation of anharmonic vibrational frequencies of both ground and excited electronic states has led to combining coupled cluster theory harmonic force constants with density functional theory cubic and quartic force constants for defining a quartic force field (QFF) utilized in conjunction with vibrational perturbation theory at second order (VPT2). This work shows that explicitly correlated coupled cluster theory at the singles, doubles, and perturbative triples levels [CCSD(T)-F12] provides accurate anharmonic vibrational frequencies and rotational constants when conjoined with any of B3LYP, CAM-B3LYP, BHandHLYP, PBE0, and ωB97XD for roughly one-quarter of the computational time of the CCSD(T)-F12 QFF alone for our test set. As the number of atoms in the molecule increases, however, the anharmonic terms become a greater portion of the QFF, and the cost comparison improves with HOCO+ and formic acid, requiring less than 15 and 10% of the time, respectively. In electronically excited states, PBE0 produces more consistently accurate results. Additionally, as the size of the molecule and, in turn, QFF increase, the cost savings for utilizing such a hybrid approach for both ground- and excited-state computations grows. As such, these methods are promising for predicting accurate rovibrational spectral properties for electronically excited states. In cases where well-behaved potentials for a small selection of targeted excited states are needed, such an approach should reduce the computational cost compared to that of methods requiring semiglobal potential surfaces or variational treatments of the rovibronic Hamiltonian. Such applications include spectral characterization of comets, exoplanets, or any situation in which gas phase molecules are being excited by UV-vis radiation.
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Affiliation(s)
- Noah R Garrett
- Department of Chemistry & Biochemistry, University of Mississippi, University, Mississippi 38677-1848, United States
| | - Megan C Davis
- Theoretical Division, T-1, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Ryan C Fortenberry
- Department of Chemistry & Biochemistry, University of Mississippi, University, Mississippi 38677-1848, United States
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8
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Esposito VJ, Palmer CZ, Fortenberry RC, Francisco JS. Spectroscopy and Photochemistry of OAlNO and Implications for New Metal Chemistry in the Atmosphere. J Phys Chem A 2023; 127:7618-7629. [PMID: 37647609 DOI: 10.1021/acs.jpca.3c04437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
A new aluminum-bearing species, OAlNO, which has the potential to impact the chemistry of the Earth's upper atmosphere, is characterized via high-level, ab initio, spectroscopic methods. Meteor-ablated aluminum atoms are quickly oxidized to aluminum oxide (AlO) in the mesosphere and lower thermosphere (MLT), where a steady-state layer of AlO then builds up. Concurrent formation of nitric oxide (NO) in the same region of the atmosphere will lead to the bimolecular formation of the OAlNO molecule. Molecular orbital analysis provides fundamental insights into the chemical bonding and energetic arrangement of the triplet (1 3A″) ground state and singlet (1 1A') excited-state species of OAlNO. Additionally, unpaired electrons on the terminal oxygen atom of triplet (1 3A″) OAlNO cause it to be reactive to atmospheric species, potentially impacting climate science and high-altitude chemistry. The triplet (1 3A″) ground-state species exhibits a large permanent dipole moment useful for rotational spectroscopic detection; however, similar rotational constants to the singlet (1 1A') excited-state species will hamper differentiation in a spectrum. Strong infrared intensities will assist in detection and discrimination of the different spin states and isomers. Repulsive electronic excited states of OAlNO will lead to photolysis of the Al-N bond and formation of various electronic states of AlO + NO through nonadiabatic pathways. Reaction through the OAlNO intermediate represents a means for the production of electronically excited AlO, leading to new chemistry in the atmosphere. Excitation to higher-lying electronic states will lead to fluorescence with a minor Stokes shift, useful for laboratory investigation. Such physical properties of this molecule will allow for new, unexplored chemical pathways in the MLT to be considered.
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Affiliation(s)
- Vincent J Esposito
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6243, United States
| | - C Zachary Palmer
- Department of Chemistry and Biochemistry, University of Mississippi, University Park, Mississippi 38677-1848, United States
| | - Ryan C Fortenberry
- Department of Chemistry and Biochemistry, University of Mississippi, University Park, Mississippi 38677-1848, United States
| | - Joseph S Francisco
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6243, United States
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9
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Harwick OA, Fortenberry RC. Spectroscopic Constants and Anharmonic Vibrational Frequencies of C(O)OC, c-C 2O 2 and Their Silicon-Containing Analogues. Molecules 2023; 28:molecules28114563. [PMID: 37299037 DOI: 10.3390/molecules28114563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 06/12/2023] Open
Abstract
Comets are likely to contain various carbon oxide molecules potentially including C(O)OC and c-C2O2 on their surfaces and comae, as well as their silicon-substituted analogues possibly playing a role in the formation of interstellar dust grains. In this work, high-level quantum chemical data are provided to support such potential future astrophysical detection through the generation of predicted rovibrational data. Laboratory-based chemistry would also benefit from such aforementioned computational benchmarking considering these molecules' historic computational and experimental elusiveness. Coupled-cluster singles, doubles, and perturbative triples, the F12b formalism, and the cc-pCVTZ-F12 basis set garner the rapid, yet highly trusted F12-TcCR level of theory leveraged presently. This current work points to all four molecules' strong IR activity, coupled with large intensities, thus suggesting the potential for JWST detection. Although Si(O)OSi possesses a permanent dipole moment significantly larger than those of the other molecules of present interest, the significant abundance of the potential precursor carbon monoxide suggests that the dicarbon dioxide molecules may yet be observable in the microwave region of the electromagnetic spectrum. Thus, this present work details the likely existence and detectability of these four cyclic molecules, providing updated implications compared to previous work performed both experimentally and computationally.
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Affiliation(s)
- Olivia A Harwick
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, USA
| | - Ryan C Fortenberry
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, USA
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10
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Abstract
Quartic force fields (QFFs) constructed using a sum of ground-state CCSD(T)-F12b energies with EOM-CCSD excitation energies are proposed for computation of spectroscopic properties of electronically excited states. This is dubbed the F12+EOM approach and is shown to provide similar accuracy to previous methodologies at lower computational cost. Using explicitly correlated F12 approaches instead of canonical CCSD(T), as in the corresponding (T)+EOM approach, allows for 70-fold improvement in computational time. The mean percent difference between the two methods for anharmonic vibrational frequencies is only 0.10%. A similar approach is also developed herein which accounts for core correlation and scalar relativistic effects, named F12cCR+EOM. The F12+EOM and F12cCR+EOM approaches both match to within 2.5% mean absolute error of experimental fundamental frequencies. These new methods should help in clarifying astronomical spectra by assigning features to vibronic and vibrational transitions of small astromolecules when such data are not available experimentally.
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Affiliation(s)
- Megan C Davis
- Department of Chemistry & Biochemistry, University of Mississippi, University, Mississippi 38677-1848, United States
| | - Noah R Garrett
- Department of Chemistry & Biochemistry, University of Mississippi, University, Mississippi 38677-1848, United States
| | - Ryan C Fortenberry
- Department of Chemistry & Biochemistry, University of Mississippi, University, Mississippi 38677-1848, United States
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11
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Abstract
pbqff is an open-source program for fully automating the production of quartic force fields (QFFs) and their corresponding anharmonic spectroscopic data. Rather than being a monolithic piece of code, it consists of several key modules including a generic interface to quantum chemistry codes and, notably, queuing systems; a molecular point group symmetry library; an internal-to-Cartesian coordinate conversion module; a module for the ordinary least-squares fitting of potential energy surfaces; and an improved second-order rotational and vibrational perturbation theory package for asymmetric and symmetric tops that handles type-1 and -2 Fermi resonances, Fermi resonance polyads, and Coriolis resonances. All of these pieces are written in Rust, a modern, safe, and performant programming language that has much to offer for scientific programming. This work introduces pbqff and its surrounding ecosystem, in addition to reporting new anharmonic vibrational data for c-(C)C3H2 and describing how the components of pbqff can be leveraged in other projects.
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Affiliation(s)
- Brent R Westbrook
- Department of Chemistry & Biochemistry, University of Mississippi, University, Mississippi 38677-1848, United States
| | - Ryan C Fortenberry
- Department of Chemistry & Biochemistry, University of Mississippi, University, Mississippi 38677-1848, United States
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12
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Santaloci TJ, Fortenberry RC. Electronically Excited States of Closed-Shell Azabenzene and Purine Anion Structures: Is 2 Debye Enough for Dipole-Bound Excited States? J Chem Phys 2023; 158:124302. [PMID: 37003736 DOI: 10.1063/5.0141385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
Abstract
Deprotonated azabenzene anions require dipole moments in their corresponding neutral radicals of more than 3.5 D in order to exhibit dipole-bound excited states (DBXSs). This is notably larger than the typical 2.0 D to 2.5 D associated with such behavior. Similar computational analysis on deprotonated purine derivatives also conducted herein only requires the more traditional 2.5 D dipole moment implying that the single six-membered azabenezene rings have additional factors at play in binding diffuse electrons. The present study also shows that use of coupled cluster singles and doubles with a double-zeta correlation consistent basis set and additional diffuse functions originating from the center-of-charge for all aspects of the computations decreases the error in predicting DBXSs to less than 0.006 eV at worst and likely less than 0.003 eV for most cases. These results can influence the modeling of molecular spectra beyond fundamental chemical curiosity with application to astrochemistry, solar energy harvesting, and combustion chemistry among others.
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Affiliation(s)
| | - Ryan C. Fortenberry
- Department of Chemistry & Biochemistry, University of Mississippi, United States of America
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13
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Zhang C, Turner AM, Wang J, Marks JH, Fortenberry RC, Kaiser RI. Low-Temperature Thermal Formation of the Cyclic Methylphosphonic Acid Trimer [c-(CH 3 PO 2 ) 3 ]. Chemphyschem 2023; 24:e202200660. [PMID: 36283955 DOI: 10.1002/cphc.202200660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/22/2022] [Indexed: 11/11/2022]
Abstract
We report the formation of the cyclic methylphosphonic acid trimer [c-(CH3 PO2 )3 ] through condensation reactions during thermal processing of low-temperature methylphosphonic acid samples exploiting photoionization reflectron time-of-flight mass spectrometry (PI-ReTOF-MS) along with electronic structure calculations. Cyclic methylphosphonic acid trimers are formed in the solid state and detected together with its protonated species in the gas phase upon single photon ionization. Our studies provide an understanding of the preparation of phosphorus-bearing potentially prebiotic molecules and the fundamental knowledge of low-temperature phosphorus chemistry in extraterrestrial environments.
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Affiliation(s)
- Chaojiang Zhang
- Department of Chemistry, University of Hawaii at Manoa, 2545 McCarthy Mall, Honolulu, HI 96822, USA.,W. M. Keck Laboratory in Astrochemistry, University of Hawaii at Manoa, 2545 McCarthy Mall, Honolulu, HI, 96822, USA
| | - Andrew M Turner
- Department of Chemistry, University of Hawaii at Manoa, 2545 McCarthy Mall, Honolulu, HI 96822, USA.,W. M. Keck Laboratory in Astrochemistry, University of Hawaii at Manoa, 2545 McCarthy Mall, Honolulu, HI, 96822, USA
| | - Jia Wang
- Department of Chemistry, University of Hawaii at Manoa, 2545 McCarthy Mall, Honolulu, HI 96822, USA.,W. M. Keck Laboratory in Astrochemistry, University of Hawaii at Manoa, 2545 McCarthy Mall, Honolulu, HI, 96822, USA
| | - Joshua H Marks
- Department of Chemistry, University of Hawaii at Manoa, 2545 McCarthy Mall, Honolulu, HI 96822, USA.,W. M. Keck Laboratory in Astrochemistry, University of Hawaii at Manoa, 2545 McCarthy Mall, Honolulu, HI, 96822, USA
| | - Ryan C Fortenberry
- Department of Chemistry & Biochemistry, University of Mississippi, Oxford, Mississippi, MS, 38677, USA
| | - Ralf I Kaiser
- Department of Chemistry, University of Hawaii at Manoa, 2545 McCarthy Mall, Honolulu, HI 96822, USA.,W. M. Keck Laboratory in Astrochemistry, University of Hawaii at Manoa, 2545 McCarthy Mall, Honolulu, HI, 96822, USA
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14
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Haney OG, Westbrook BR, Santaloci TJ, Fortenberry RC. Red-Shifting the Excitation Energy of Carbonic Acid Clusters Via Nonminimum Structures. J Phys Chem A 2023; 127:489-494. [PMID: 36622286 DOI: 10.1021/acs.jpca.2c07589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Nonminimum carbonic acid clusters provide excitation energies and oscillator strengths in line with observed ice-phase UV absorptions better than traditional optimized minima. This equation-of-motion coupled cluster quantum chemical analysis on carbonic acid monomers and dimers shows that shifts to the dihedral angle for the internal heavy atoms in the monomer produce UV electronic excitations close to 200 nm with oscillator strengths that would produce observable features. This τ(OCOO) dihedral is actually a relatively floppy motion unlike what is often expected for sp2 carbons and can be distorted by 30° away from equilibrium for an energy cost of only 11 kcal/mol. As this dihedral decreases beyond 30°, the excitation energies decrease further. The oscillator strengths do, as well, but only to a point. Hence, the lower-energy distortions of τ(OCOO) are sufficient to produce structures that exhibit excitation energies and oscillator strengths that would red-shift observed spectra of carbonic acid ices away from the highest UV absorption feature at 139 nm. Such data imply that colder temperatures (20 K) in the experimental treatment of carbonic acid ices are freezing these structures out after annealing, whereas the warmer temperature experiments (80 K) are not.
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Affiliation(s)
- Olivia G Haney
- Department of Chemistry & Biochemistry, Belhaven University, Jackson, Mississippi 39212, United States
| | - Brent R Westbrook
- Department of Chemistry & Biochemistry, University of Mississippi, University, Mississippi 38677-1848, United States
| | - Taylor J Santaloci
- Department of Chemistry & Biochemistry, University of Mississippi, University, Mississippi 38677-1848, United States
| | - Ryan C Fortenberry
- Department of Chemistry & Biochemistry, University of Mississippi, University, Mississippi 38677-1848, United States
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15
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Fortenberry RC, McMahon RJ, Kaiser RI. 10 Years of the ACS PHYS Astrochemistry Subdivision. J Phys Chem A 2022; 126:6571-6574. [PMID: 36172712 DOI: 10.1021/acs.jpca.2c06091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ryan C Fortenberry
- Department of Chemistry and Biochemistry, University of Mississippi, 322 Coulter Hall, University, Mississippi 38677-1848, United States
| | - Robert J McMahon
- Department of Chemistry, University of Wisconsin─Madison, 1101 University Avenue, Madison, Wisconsin 53706-1322, United States
| | - Ralf I Kaiser
- Department of Chemistry, University of Hawaii, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
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16
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Davis MC, Garrett NR, Fortenberry RC. Confirmation of gaseous methanediol from state-of-the-art theoretical rovibrational characterization. Phys Chem Chem Phys 2022; 24:18552-18558. [PMID: 35904881 DOI: 10.1039/d2cp02076a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
High-level rovibrational characterization of methanediol, the simplest geminal diol, using state-of-the-art, purely ab initio techniques unequivocally confirms previously reported gas phase preparation of this simplest geminal diol in its C2 conformation. The F12-TZ-cCR and F12-DZ-cCR quartic force fields (QFFs) utilized in this work are among the largest coupled cluster-based anharmonic frequencies computed to date, and they match the experimental band origins of the spectral features in the 980-1100 cm-1 range to within 3 cm-1, representing a significant improvement over previous studies. The simulated spectrum also matches the experimental spectrum in the strong Q branch feature and qualitative shape of the 980-1100 cm-1 region. Additionally, the full set of rotational constants, anharmonic vibrational frequencies, and quartic and sextic distortion constants are provided for both the lowest energy C2 conformer as well as the slightly higher Cs conformer. Several vibrational modes have intensities of 60 km mol-1 or higher, facilitating potential astronomical or atmospheric detection of methanediol or further identification in laboratory work especially now that gas phase synthesis of this molecule has been established.
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Affiliation(s)
- Megan C Davis
- Department of Chemistry & Biochemistry, University of Mississippi, University, MS, 38677-1848, USA.
| | - Noah R Garrett
- Department of Chemistry & Biochemistry, University of Mississippi, University, MS, 38677-1848, USA.
| | - Ryan C Fortenberry
- Department of Chemistry & Biochemistry, University of Mississippi, University, MS, 38677-1848, USA.
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17
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Agbaglo DA, Cheng Q, Fortenberry RC, Stanton JF, DeYonker NJ. Theoretical Rovibrational Spectroscopy of Magnesium Tricarbide-Multireference Character Thwarts a Full Analysis of All Isomers. J Phys Chem A 2022; 126:4132-4146. [PMID: 35758849 DOI: 10.1021/acs.jpca.2c01340] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Magnesium tricarbide isomers are studied herein with coupled cluster theory and multireference configuration interaction to support their possible detection in astrochemical environments such as the circumstellar envelope surrounding the star IRC +10216 or in terrestrial laboratories. Magnesium-bearing species may abound in the interstellar medium (ISM), but only eight (MgNC, MgCN, HMgNC, MgC2H, MgC3N, MgC4H, MgC5N, and MgC6H) have been directly identified thus far. Several possible isomers for the related MgC3 system are explored in their singlet and triplet spin multiplicities. Overall, this work offers quantum chemical insight of rovibrational spectroscopic data for MgC3 using quartic force fields (QFFs) based on the CCSD(T) and CCSD(T)-F12 levels of theory at the complete basis set (CBS) limit. Additional corrections with small basis set CCSDT(Q) and scalar relativistic effects are also included in the analysis. Salient multireference character is found in the singlet diamond electronic state, which makes a definitive assignment of the ground state challenging. Nevertheless, coupled cluster-based composite energies and multireference configuration interaction both predict that the 1A1 diamond isomer is 1.6-2.2 kcal mol-1 lower in energy than the 3A1 diamond isomer. Furthermore, highly accurate binding energies of various isomers MgC3 are provided for comparison to photodetachment experiments. Dipole moments along with harmonic infrared intensities will guide efforts for astronomical and spectroscopic characterization.
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Affiliation(s)
- Donatus A Agbaglo
- Department of Chemistry, University of Memphis, Memphis, Tennessee 38151, United States
| | - Qianyi Cheng
- Department of Chemistry, University of Memphis, Memphis, Tennessee 38151, United States
| | - Ryan C Fortenberry
- Department of Chemistry & Biochemistry, University of Mississippi, University, Mississippi 38677-1848, United States
| | - John F Stanton
- Department of Chemistry and Physics, University of Florida, Gainesville, Florida 32611, United States
| | - Nathan J DeYonker
- Department of Chemistry, University of Memphis, Memphis, Tennessee 38151, United States
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18
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Abstract
Two theoretical structural motifs are proposed to match two experimental solid carbonic acid UV spectra from previous literature ( Astron. Astrophys. 2021, 646, A172): a linear ribbon structure as a single octamer and nonplanar orientations of carbonic acid clusters. The latter have some contribution from approximated amorphous solid carbonic acid in the form of 40 different clusters of 8 carbonic acid molecules ensemble-averaged together, but unoptimized pairs of optimized dimers oriented perpendicular to one another give the strongest intensities of lower energy UV transitions. The linear ribbon structure's predicted spectrum computed with CAM-B3LYP/6-311G(d,p) agrees well with Experimental Solid B─the β-carbonic acid experimental data in the UV region. Meanwhile, the 40 amorphous clusters are built with a randomization script, and the electronically excited states are calculated with both CAM-B3LYP/6-311G(d,p) and ωB97XD/6-311G(d,p). The resulting theoretical spectrum is constructed by employing a Boltzmann distribution of the intensities and artificially broadening the simulated spectra. The nonplanar dimer pairs are computed with CAM-B3LYP and B3LYP with the 6-311G(d,p) basis set. The results of the amorphous simulation weakly correspond with the Experimental Solid A spectrum, but the fully nonplanar motif matches the experiment much more convincingly. As a result, the previous work appears to have observed the traditional crystalline phase of solid carbonic acid in Experimental Solid B, whereas the nonplanar orientations of the carbonic acids in the clusters appear to correlate with Experimental Solid A. This spectral classification will aid in future laboratory work exploring the role that carbonic acid can play in low temperature, low pressure desorbed environments with potential application to astrochemistry.
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Affiliation(s)
- Austin M Wallace
- Department of Chemistry & Biochemistry, University of Mississippi, University, Mississippi 38677-1848, United States
| | - Ryan C Fortenberry
- Department of Chemistry & Biochemistry, University of Mississippi, University, Mississippi 38677-1848, United States
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19
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Poland KN, Yang W, Fortenberry RC, Davis SR. The thermal isomerization of benzvalyne to benzyne. Phys Chem Chem Phys 2022; 24:14573-14578. [PMID: 35666233 DOI: 10.1039/d2cp00794k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The isomerization of the highly strained benzvalyne structure to o-benzyne has been investigated using MCSCF and CCSD(T) levels of theory. Two reaction channels were modeled: the disrotatory one which leads directly to the benzyne product, and the conrotatory one which leads to an intermediate which can subsequently lead to the benzyne product. Energies at the MRMP2 level give 22.9 kcal mol-1 for the disrotatory channel and 21.7 and 1.4 kcal mol-1 for the two steps in the conrotatory one. However, the CCSD(T) energies give 19.3 and 14.2 kcal mol-1 for the two conrotatory steps. The first step of the conrotatory channel is significantly higher than the second so is rate determining for this channel. Comparison of the two separate channels shows that the conrotatory has just a slight energetic edge of 1.2 kcal mol-1 at the MRMP2 level. We did not compute the disrotatory channel at the CCSD(T) level due to the significant biradical nature of the wavefunction with natural orbital occupation numbers of 1.2 and 0.8 in the active space.
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Affiliation(s)
- Kimberley N Poland
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi, USA.
| | - Weiwei Yang
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi, USA.
| | - Ryan C Fortenberry
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi, USA.
| | - Steven R Davis
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi, USA.
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20
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Lambert EC, Williams AE, Fortenberry RC, Hammer NI. Probing halogen bonding interactions between heptafluoro-2-iodopropane and three azabenzenes with Raman spectroscopy and density functional theory. Phys Chem Chem Phys 2022; 24:11713-11720. [PMID: 35506511 DOI: 10.1039/d2cp00463a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The potential formation of halogen bonded complexes between a donor, heptafluoro-2-iodopropane (HFP), and the three acceptor heterocyclic azines (azabenzenes: pyridine, pyrimidine, and pyridazine) is investigated herein through normal mode analysis via Raman spectroscopy, density functional theory, and natural electron configuration analysis. Theoretical Raman spectra of the halogen bonded complexes are in good agreement with experimental data providing insight into the Raman spectra of these complexes. The exhibited shifts in vibrational frequency of as high as 8 cm-1 for each complex demonstrate, in conjunction with NEC analysis, significant evidence of charge transfer from the halogen bond acceptor to donor. Here, an interesting charge flow mechanism is proposed involving the donated nitrogen lone pair electrons pushing the dissociated fluorine atoms back to their respective atoms. This mechanism provides further insight into the formation and fundamental nature of halogen bonding and its effects on neighboring atoms. The present findings provide novel and deeper characterization of halogen bonding with applications in supramolecular and organometallic chemistry.
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Affiliation(s)
- Ethan C Lambert
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38655, USA.
| | - Ashley E Williams
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38655, USA. .,University of Mississippi Medical Center, School of Medicine, Office of Student Affairs, 2500 N. State Street, Jackson, MS, 39216, USA
| | - Ryan C Fortenberry
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38655, USA.
| | - Nathan I Hammer
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38655, USA.
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21
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Williams AE, Hammer N, Fortenberry RC, Reinemann DN. Elucidating tubulin E-hook peptide structure using spectroscopic approaches. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.1819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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22
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Abstract
Benzvalyne (C6H4) is a bicyclic structural isomer of o-benzyne that some typically trusted levels of theory do not report as a minimum on the potential energy surface (PES). The structure was found to be a C2v minimum at the MCSCF, MP2, coupled-cluster single double, coupled-cluster single double triple (CCSDT)-1b, and CCSDT-2 levels of theory. Density functionals at the B3LYP-D3, B2PLYP-D3, and M06-D3 levels also produced a minimum structure. On the other hand, the CCSD(T), CCSD(T)-F12, and CCSDT-1a methods produced a single imaginary frequency for benzvalyne. However, the increase in the correlation for the CCSDT-1b and CCSDT-2 methods implies that benzvalyne is, in fact, a true, if highly strained, minimum on the PES. The C-C≡C bond angle was found to be only 108°; this angle is 180° for an unstrained C-C≡C triple bond moiety. As a result, the strain energy is notably high at 159 kcal mol-1. Comparing the strain energy of the rest of the molecule gives a strain energy of 92 kcal mol-1 for this triple bond region alone. The computed harmonic frequencies contain normal modes consisting of two hindered rotations of the C≡C diatomic part of the molecule, suggesting that the dissociation of this diatomic from the bicylobutane moiety may be important in the chemistry of this molecule. Because the putative C2v minimum is predicted to have a significant dipole moment (2.6 D), benzvalyne may be detectable in TMC-1, where the related o-benzyne molecule has recently been observed by radio astronomy.
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Affiliation(s)
- Kimberley N Poland
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38655, USA
| | - Brent R Westbrook
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38655, USA
| | - David H Magers
- Department of Chemistry and Biochemistry, Mississippi College, Clinton, Mississippi 39056, USA
| | - Ryan C Fortenberry
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38655, USA
| | - Steven R Davis
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38655, USA
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23
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Westbrook B, Beasley G, Fortenberry RC. Polycyclic Aliphatic Hydrocarbons: Is Tetrahedrane Present in UIR Spectra? Phys Chem Chem Phys 2022; 24:14348-14353. [DOI: 10.1039/d2cp01103d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The smallest Platonic hydrocarbon, tetrahedrane, has been subject to frequent theoretical and experimental study for 50 years, but its infrared spectrum and synthetic pathway remain a mystery. The recent partial...
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24
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Lu B, Trabelsi T, Esposito VJ, Fortenberry RC, Francisco JS, Zeng X. Spectroscopic Characterization of HSO 2• and HOSO • Intermediates Involved in SO 2 Geoengineering. J Phys Chem A 2021; 125:10615-10621. [PMID: 34890193 DOI: 10.1021/acs.jpca.1c09311] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Sulfur-containing radicals HSO2• and HOSO• are key intermediates involved in stratospheric sulfur geoengineering by SO2 injection. The spectroscopic characterization and photochemistry of both radicals are crucial to understanding the chemical impact of SO2 chemistry in the stratosphere. On the basis of the efficient generation of HOSO• by flash pyrolysis of gaseous sulfinic acid, CHF2S(O)OH, a strong absorption is observed at 270 nm along with a shoulder up to 350 nm for HOSO• isolated in low-temperature noble gas matrixes (Ar and Ne). These mainly arise from the excitations from the ground state (X2A) to the C2A/D2A and A2A/B2A states, respectively. Upon a 266 nm laser irradiation, the broad absorption band in the range 320-500 nm for HSO2• appears, and it corresponds to the combination of three excitations from the X2A state to the first (A2A), second (B2A), and third (C2A) excited states. Assignment of the UV-vis spectra is consistent with the photochemistry of HOSO• and HSO2• as observed by matrix-isolation IR spectroscopy and also by the agreement with high-level ab initio calculations.
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Affiliation(s)
- Bo Lu
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysts and Innovative Materials, Fudan University, Shanghai, 200433, China
| | - Tarek Trabelsi
- Department of Earth and Environmental Science and Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Vincent J Esposito
- Department of Earth and Environmental Science and Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Ryan C Fortenberry
- Department of Chemistry & Biochemistry, University of Mississippi, University, Mississippi 38677-1848, United States
| | - Joseph S Francisco
- Department of Earth and Environmental Science and Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Xiaoqing Zeng
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysts and Innovative Materials, Fudan University, Shanghai, 200433, China
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25
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Abstract
The F12-TZ-cCR quartic force field (QFF) methodology, defined here as CCSD(T)-F12b/cc-pCVTZ-F12 with further corrections for relativity, is introduced as a cheaper and even more accurate alternative to more costly composite QFF methods like those containing complete basis set extrapolations within canonical coupled cluster theory. F12-TZ-cCR QFFs produce B0 and C0 vibrationally averaged principal rotational constants within 7.5 MHz of gas-phase experimental values for tetraatomic and larger molecules, offering higher accuracy in these constants than the previous composite methods. In addition, F12-TZ-cCR offers an order of magnitude decrease in the computational cost of highly accurate QFF methodologies accompanying this increase in accuracy. An additional order of magnitude in cost reduction is achieved in the F12-DZ-cCR method, while also matching the accuracy of the traditional composite method's B0 and C0 constants. Finally, F12-DZ and F12-TZ are benchmarked on the same test set, revealing that both methods can provide anharmonic vibrational frequencies that are comparable in accuracy to all three of the more expensive methodologies, although their rotational constants lag behind. Hence, the present work demonstrates that highly accurate theoretical rovibrational spectral data can be obtained for a fraction of the cost of conventional QFF methodologies, extending the applicability of QFFs to larger molecules.
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Affiliation(s)
- Alexandria G Watrous
- Department of Chemistry & Biochemistry, University of Mississippi, University, Mississippi 38677-1848, United States
| | - Brent R Westbrook
- Department of Chemistry & Biochemistry, University of Mississippi, University, Mississippi 38677-1848, United States
| | - Ryan C Fortenberry
- Department of Chemistry & Biochemistry, University of Mississippi, University, Mississippi 38677-1848, United States
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26
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Westbrook BR, Fortenberry RC. Anharmonic Vibrational Frequencies of Water Borane and Associated Molecules. Molecules 2021; 26:molecules26237348. [PMID: 34885929 PMCID: PMC8658819 DOI: 10.3390/molecules26237348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 12/03/2022] Open
Abstract
Water borane (BH3OH2) and borinic acid (BH2OH) have been proposed as intermediates along the pathway of hydrogen generation from simple reactants: water and borane. However, the vibrational spectra for neither water borane nor borinic acid has been investigaged experimentally due to the difficulty of isolating them in the gas phase, making accurate quantum chemical predictions for such properties the most viable means of their determination. This work presents theoretical predictions of the full rotational and fundamental vibrational spectra of these two potentially application-rich molecules using quartic force fields at the CCSD(T)-F12b/cc-pCVTZ-F12 level with additional corrections included for the effects of scalar relativity. This computational scheme is further benchmarked against the available gas-phase experimental data for the related borane and HBO molecules. The differences are found to be within 3 cm−1 for the fundamental vibrational frequencies and as close as 15 MHz in the B0 and C0 principal rotational constants. Both BH2OH and BH3OH2 have multiple vibrational modes with intensities greater than 100 km mol−1, namely ν2 and ν4 in BH2OH, and ν1, ν3, ν4, ν9, and ν13 in BH3OH2. Finally, BH3OH2 has a large dipole moment of 4.24 D, which should enable it to be observable by rotational spectroscopy, as well.
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27
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Abstract
Ices in the interstellar medium largely exist as amorphous solids composed of small molecules including ammonia, water, and carbon dioxide. Describing gas-phase molecules can be readily accomplished with current high-level quantum chemical calculations with the description of crystalline solids becoming more readily accomplished. Differently, amorphous solids require more novel approaches. The present work describes a method for generating amorphous structures and constructing electronic spectra through a combination of quantum chemical calculations and statistical mechanics. The structures are generated through a random positioning program and DFT methods, such as ωB97-XD and CAM-B3LYP. A Boltzmann distribution weights the excitations to compile a final spectrum from a sampling of molecular clusters. Three ice analogs are presented herein consisting of ammonia, carbon dioxide, and water. Ammonia and carbon dioxide provide semi-quantitative agreement with experiment for CAM-B3LYP/6-311++G(2d,2p) from 30 clusters of 8 molecules. Meanwhile, the amorphous water description improves when the sample size is increased in cluster size and count to as many as 105 clusters of 32 water molecules. The described methodology can produce highly comparative descriptions of electronic spectra for ice analogs and can be used to predict electronic spectra for other ice analogs.
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Affiliation(s)
- Austin M Wallace
- Department of Chemistry & Biochemistry, University of Mississippi, University, Mississippi 38677-1848, USA.
| | - Ryan C Fortenberry
- Department of Chemistry & Biochemistry, University of Mississippi, University, Mississippi 38677-1848, USA.
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28
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Westbrook BR, Patel DJ, Dallas JD, Swartzfager GC, Lee TJ, Fortenberry RC. Fundamental Vibrational Frequencies and Spectroscopic Constants of Substituted Cyclopropenylidene (c-C 3HX, X = F, Cl, CN). J Phys Chem A 2021; 125:8860-8868. [PMID: 34609881 DOI: 10.1021/acs.jpca.1c06576] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The recent detection of ethynyl-functionalized cyclopropenylidene (c-C3HC2H) has initiated the search for other functional forms of cyclopropenylidene (c-C3H2) in space. There is existing gas-phase rotational spectroscopic data for cyano-cyclopropenylidene (c-C3HCN), but the present work provides the first anharmonic vibrational spectral data for that molecule, as well as the first full set of both rotational and vibrational spectroscopic data for fluoro- and chloro-cyclopropenylidenes (c-C3HF and c-C3HCl). All three molecules have fundamental vibrational frequencies with substantial infrared intensities. Namely, c-C3HCN has a moderately intense fundamental frequency at 1244.4 cm-1, while c-C3HF has two large intensity modes at 1765.4 and 1125.3 cm-1 and c-C3HCl again has two large intensity modes at 1692.0 and 1062.5 cm-1. All of these frequencies are well within the spectral range covered by the high-resolution EXES instrument on NASA's Stratospheric Observatory for Infrared Astronomy (SOFIA). Further, all three molecules have dipole moments of around 3.0 D in line with c-C3H2, enabling them to be observed by pure rotational spectroscopy, as well. Thus, the rovibrational spectral data presented herein should assist with future laboratory studies of functionalized cyclopropenylidenes and may lead to their interstellar or circumstellar detection.
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Affiliation(s)
- Brent R Westbrook
- Department of Chemistry & Biochemistry, University of Mississippi, University, Mississippi 38677-1848, United States
| | - Dev J Patel
- Department of Chemistry & Biochemistry, University of Mississippi, University, Mississippi 38677-1848, United States
| | - Jax D Dallas
- Department of Chemistry & Biochemistry, University of Mississippi, University, Mississippi 38677-1848, United States.,Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - G Clark Swartzfager
- Department of Chemistry & Biochemistry, University of Mississippi, University, Mississippi 38677-1848, United States.,Cleveland Central High School, 300 West Sunflower Road, Cleveland, Mississippi 38732, United States
| | - Timothy J Lee
- MS 245-3, NASA Ames Research Center, Moffett Field, California 94035, United States
| | - Ryan C Fortenberry
- Department of Chemistry & Biochemistry, University of Mississippi, University, Mississippi 38677-1848, United States
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29
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Fortenberry RC, Francisco JS. Anharmonic fundamental vibrational frequencies and spectroscopic constants of the potential HSO 2 radical astromolecule. J Chem Phys 2021; 155:114301. [PMID: 34551550 DOI: 10.1063/5.0062560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The recent report that HSO2 is likely kinetically favored over the HOSO thermodynamic product in hydrogen addition to sulfur dioxide in simulated Venusian atmospheric conditions has led to the need for reference rotational, vibrational, and rovibrational spectral data for this molecule. While matrix-isolation spectroscopy has been able to produce vibrational frequencies for some of the vibrational modes, the full infrared to microwave spectrum of 1 2A' HSO2 is yet to be generated. High-level quantum chemical computations show in this work that the >2.5 D dipole moment of this radical makes it a notable target for possible radioastronomical observation. Additionally, the high intensity antisymmetric S-O stretch is computed here to be 1298.3 cm-1, a 13.9 cm-1 blueshift up from H2 matrix analysis. In any case, the full set of rotational and spectroscopic constants and anharmonic fundamental vibrational frequencies is provided in this work in order to help characterize HSO2 and probe its kinetic favorability.
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Affiliation(s)
- Ryan C Fortenberry
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677-1848, USA
| | - Joseph S Francisco
- Department of Earth and Environmental Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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30
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Curiac C, Rodrigues RR, Watson J, Hunt LA, Devdass A, Jurss JW, Hammer NI, Fortenberry RC, Delcamp JH. Iron Redox Shuttles with Wide Optical Gap Dyes for High-Voltage Dye-Sensitized Solar Cells. ChemSusChem 2021; 14:3084-3096. [PMID: 34019740 DOI: 10.1002/cssc.202100884] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/19/2021] [Indexed: 06/12/2023]
Abstract
A series of iron polypyridyl redox shuttles were synthesized in the 2+ and 3+ oxidation states and paired with a series of wide optical gap organic dyes with weak aryl ether electron-donating groups. High voltage dye-sensitized solar cell (HV-DSC) devices were obtained through controlling the redox shuttle energetics and dye donor structure. The use of aryl ether donor groups, in place of commonly used aryl amines, allowed for the lowering of the dye ground-state oxidation potential which enabled challenging to oxidize redox shuttles based on Fe2+ polypyridyl structures to be used in functional devices. By carefully designing a dye series that varies the number of alkyl chains for TiO2 surface protection, the recombination of electrons in TiO2 to the oxidized redox shuttle could be controlled, leading to HV-DSC devices of up to 1.4 V.
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Affiliation(s)
- Christine Curiac
- Department of Chemistry and Biochemistry, University of Mississippi, 322 Coulter Hall, University, MS 38655, USA
| | - Roberta R Rodrigues
- Department of Chemistry and Biochemistry, University of Mississippi, 322 Coulter Hall, University, MS 38655, USA
| | - Jonathon Watson
- Department of Chemistry and Biochemistry, University of Mississippi, 322 Coulter Hall, University, MS 38655, USA
| | - Leigh Anna Hunt
- Department of Chemistry and Biochemistry, University of Mississippi, 322 Coulter Hall, University, MS 38655, USA
| | - Anthony Devdass
- Department of Chemistry and Biochemistry, University of Mississippi, 322 Coulter Hall, University, MS 38655, USA
| | - Jonah W Jurss
- Department of Chemistry and Biochemistry, University of Mississippi, 322 Coulter Hall, University, MS 38655, USA
| | - Nathan I Hammer
- Department of Chemistry and Biochemistry, University of Mississippi, 322 Coulter Hall, University, MS 38655, USA
| | - Ryan C Fortenberry
- Department of Chemistry and Biochemistry, University of Mississippi, 322 Coulter Hall, University, MS 38655, USA
| | - Jared H Delcamp
- Department of Chemistry and Biochemistry, University of Mississippi, 322 Coulter Hall, University, MS 38655, USA
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31
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Williams AE, Hammer NI, Fortenberry RC, Reinemann DN. Tracking the Amide I and αCOO- Terminal ν(C=O) Raman Bands in a Family of l-Glutamic Acid-Containing Peptide Fragments: A Raman and DFT Study. Molecules 2021; 26:4790. [PMID: 34443382 PMCID: PMC8399447 DOI: 10.3390/molecules26164790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/02/2021] [Accepted: 08/04/2021] [Indexed: 11/16/2022] Open
Abstract
The E-hook of β-tubulin plays instrumental roles in cytoskeletal regulation and function. The last six C-terminal residues of the βII isotype, a peptide of amino acid sequence EGEDEA, extend from the microtubule surface and have eluded characterization with classic X-ray crystallographic techniques. The band position of the characteristic amide I vibration of small peptide fragments is heavily dependent on the length of the peptide chain, the extent of intramolecular hydrogen bonding, and the overall polarity of the fragment. The dependence of the E residue's amide I ν(C=O) and the αCOO- terminal ν(C=O) bands on the neighboring side chain, the length of the peptide fragment, and the extent of intramolecular hydrogen bonding in the structure are investigated here via the EGEDEA peptide. The hexapeptide is broken down into fragments increasing in size from dipeptides to hexapeptides, including EG, ED, EA, EGE, EDE, DEA, EGED, EDEA, EGEDE, GEDEA, and, finally, EGEDEA, which are investigated with experimental Raman spectroscopy and density functional theory (DFT) computations to model the zwitterionic crystalline solids (in vacuo). The molecular geometries and Boltzmann sum of the simulated Raman spectra for a set of energetic minima corresponding to each peptide fragment are computed with full geometry optimizations and corresponding harmonic vibrational frequency computations at the B3LYP/6-311++G(2df,2pd) level of theory. In absence of the crystal structure, geometry sampling is performed to approximate solid phase behavior. Natural bond order (NBO) analyses are performed on each energetic minimum to quantify the magnitude of the intramolecular hydrogen bonds. The extent of the intramolecular charge transfer is dependent on the overall polarity of the fragment considered, with larger and more polar fragments exhibiting the greatest extent of intramolecular charge transfer. A steady blue shift arises when considering the amide I band position moving linearly from ED to EDE to EDEA to GEDEA and, finally, to EGEDEA. However, little variation is observed in the αCOO- ν(C=O) band position in this family of fragments.
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Affiliation(s)
- Ashley E. Williams
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, USA; (A.E.W.); (N.I.H.)
| | - Nathan I. Hammer
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, USA; (A.E.W.); (N.I.H.)
| | - Ryan C. Fortenberry
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, USA; (A.E.W.); (N.I.H.)
| | - Dana N. Reinemann
- Department of Biomedical Engineering, University of Mississippi, University, MS 38677, USA
- Department of Chemical Engineering, University of Mississippi, University, MS 38677, USA
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32
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Davis MC, Fortenberry RC. (T)+EOM Quartic Force Fields for Theoretical Vibrational Spectroscopy of Electronically Excited States. J Chem Theory Comput 2021; 17:4374-4382. [PMID: 34165980 DOI: 10.1021/acs.jctc.1c00307] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
(T)+EOM quartic force fields (QFFs) are proposed for ab initio rovibrational properties of electronically excited states of small molecules. The (T)+EOM method is a simple treatment of the potential surface of the excited state using a composite energy from the CCSD(T) energy for the ground-state configuration and the EOM-CCSD excitation energy for the target state. The method is benchmarked with two open-shell species, HOO and HNF, and two closed-shell species, HNO and HCF. A (T)+EOM QFF with a complete basis set extrapolation (C) and corrections for core correlation (cC) and scalar relativity (R), dubbed (T)+EOM/CcCR, achieves a mean absolute error (MAE) as low as 1.6 cm-1 for the à 2A' state of HOO versus an established benchmark QFF with CCSD(T)-F12b/cc-pVTZ-F12 (F12-TZ) for this variationally accessible electronically excited state. The MAE for anharmonic frequencies for (T)+EOM/CcCR versus F12-TZ for HNF is 7.5 cm-1. The closed-shell species are compared directly with the experiment, where a simpler (T)+EOM QFF using the aug-cc-pVTZ basis set compares more favorably than the more costly (T)+EOM/CcCR, suggesting a possible influence of decreasing accuracy with basis set size. Scans along internal coordinates are also provided which show reasonable modeling of the potential surface by (T)+EOM compared to benchmark QFFs computed for variationally accessible electronic states. The agreement between (T)+EOM/CcCR with F12-TZ and CcCR benchmarks is also shown to be quite accurate for rotational constants and geometries, with an MAE of 0.008 MHz for the rotational constants of (T)+EOM/CcCR versus CcCR for à 2A' HOO and agreement within 0.003 Šfor bond lengths.
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Affiliation(s)
- Megan C Davis
- Department of Chemistry & Biochemistry, University of Mississippi, University, Mississippi 38677-1848, United States
| | - Ryan C Fortenberry
- Department of Chemistry & Biochemistry, University of Mississippi, University, Mississippi 38677-1848, United States
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Abstract
Crystallization of carbonic acid likely begins with a linear or ribbon-esque oligomerization, but a helical spiral is shown here to be a new, competing motif for this process. The present combined density functional theory and coupled-cluster theory work examines both the ribbon and the new helical spiral motifs in terms of relative energies, sequential binding energies, and electronic spectra which could potentially aid in distinguishing between the two forms. The helix diverges in energy from the ribbon by roughly 0.2 eV (∼4 kcal/mol) per dimer addition, but the largest intensity absorption features at 9.16 eV (135 nm) and 7.11 eV (175 nm), respective of the ribbon and spiral, will allow these to be separately observed and classified via electronic spectroscopy to determine more conclusively which motif holds in the earliest formation stages of solid carbonic acid.
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Affiliation(s)
- Austin M Wallace
- Department of Chemistry & Biochemistry, University of Mississippi, University, Mississippi 38677-1848, United States
| | - Ryan C Fortenberry
- Department of Chemistry & Biochemistry, University of Mississippi, University, Mississippi 38677-1848, United States
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34
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Turner AM, Chandra S, Fortenberry RC, Kaiser RI. A Photoionization Reflectron Time-of-Flight Mass Spectrometric Study on the Detection of Ethynamine (HCCNH 2 ) and 2H-Azirine (c-H 2 CCHN). Chemphyschem 2021; 22:985-994. [PMID: 33797172 DOI: 10.1002/cphc.202100064] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/23/2021] [Indexed: 11/07/2022]
Abstract
Ices of acetylene (C2 H2 ) and ammonia (NH3 ) were irradiated with energetic electrons to simulate interstellar ices processed by galactic cosmic rays in order to investigate the formation of C2 H3 N isomers. Supported by quantum chemical calculations, experiments detected product molecules as they sublime from the ices using photoionization reflectron time-of-flight mass spectrometry (PI-ReTOF-MS). Isotopically-labeled ices confirmed the C2 H3 N assignments while photon energies of 8.81 eV, 9.80 eV, and 10.49 eV were utilized to discriminate isomers based on their known ionization energies. Results indicate the formation of ethynamine (HCCNH2 ) and 2H-azirine (c-H2 CCHN) in the irradiated C2 H2 :NH3 ices, and the energetics of their formation mechanisms are discussed. These findings suggest that these two isomers can form in interstellar ices and, upon sublimation during the hot core phase, could be detected using radio astronomy.
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Affiliation(s)
- Andrew M Turner
- Department of Chemistry, University of Hawaii at Manoa, 2545 McCarthy Mall, Honolulu, HI 96822, USA.,W. M. Keck Laboratory in Astrochemistry, University of Hawaii at Manoa, 2545 McCarthy Mall, Honolulu, HI 96822, USA
| | - Sankhabrata Chandra
- Department of Chemistry, University of Hawaii at Manoa, 2545 McCarthy Mall, Honolulu, HI 96822, USA.,W. M. Keck Laboratory in Astrochemistry, University of Hawaii at Manoa, 2545 McCarthy Mall, Honolulu, HI 96822, USA
| | - Ryan C Fortenberry
- Department of Chemistry & Biochemistry, University of Mississippi, Mississippi, 38677-1848, USA
| | - Ralf I Kaiser
- Department of Chemistry, University of Hawaii at Manoa, 2545 McCarthy Mall, Honolulu, HI 96822, USA.,W. M. Keck Laboratory in Astrochemistry, University of Hawaii at Manoa, 2545 McCarthy Mall, Honolulu, HI 96822, USA
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35
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Widicus Weaver SL, Fortenberry RC. Space is the Future: Interdisciplinary Research in Astrochemistry and Planetary Science Leads to Innovations That Impact All of Chemistry. Acc Chem Res 2021; 54:1309-1310. [PMID: 33722001 DOI: 10.1021/acs.accounts.1c00105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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36
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Lee TJ, Fortenberry RC. The unsolved issue with out-of-plane bending frequencies for CC multiply bonded systems. Spectrochim Acta A Mol Biomol Spectrosc 2021; 248:119148. [PMID: 33293227 DOI: 10.1016/j.saa.2020.119148] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 10/26/2020] [Indexed: 06/12/2023]
Abstract
More than 30 years ago two groups independently identified a problem in the calculation of the out-of-plane bending (OPB) vibrational frequencies for the ethylene molecule using correlated electronic structure methods. Several studies have been done in the meantime to try and understand and resolve this issue. In so doing this problem has been found to be far more insidious than previously realized for acetylene-like and benzene-like molecules, which can become non-linear and non-planar, respectively. The one common feature that all molecules with this problem have is that they contain CC multiple bonds, and so this has been called the "CC multiple bond OPB frequency issue" or "the CC OPB problem." Various explanations for this problem have been advanced such as basis set superposition error, basis set incompleteness error, linear dependences in the basis set, proper balancing of the basis set between saturation and inclusion of higher angular momentum functions, etc. and possible solutions have arisen from these suggestions. All of these proposed solutions, however, amount to one main point connecting them all: modifying the one-particle basis set in some way. None of the explanations that have been advanced, however, really fit all of the data for all of the molecules where this problem has been identified, and importantly, none of these diagnostic tests have been applied to similar molecules where this issue does not appear. In this review, the studies over the last 30 plus years are discussed and relevant data from each of these is compared and contrasted. It is hoped that by collecting and analyzing the data from these studies a path forward to understanding and resolving this issue will become evident.
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Affiliation(s)
- Timothy J Lee
- MS245-3, Planetary Systems Branch, Space Science and Astrobiology Division, NASA Ames Research Center, Moffett Field, CA 94035, USA.
| | - Ryan C Fortenberry
- Department of Chemistry & Biochemistry, University of Mississippi, University, MS 38677-1848, USA
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Gardner MB, Westbrook BR, Fortenberry RC, Lee TJ. Highly-accurate quartic force fields for the prediction of anharmonic rotational constants and fundamental vibrational frequencies. Spectrochim Acta A Mol Biomol Spectrosc 2021; 248:119184. [PMID: 33293226 DOI: 10.1016/j.saa.2020.119184] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/29/2020] [Accepted: 11/01/2020] [Indexed: 06/12/2023]
Abstract
The CcCR quartic force field (QFF) methodology is capable of computing B0 and C0 rotational constants to within 35 MHz (0.14%) of experiment for triatomic and larger molecules with at least two heavy atoms. Additionally, the same constants for molecules with four or more atoms agree to within 20 MHz (0.12%) of experiment for the current test set. This work also supports previous claims that the same QFF methodology can produce fundamental vibrational frequencies with a deviation less than 5.7 cm-1 from experiment. Consequently, this approach of augmenting complete basis set extrapolated energies with treatments of core electron correlation and scalar relativity produces some of the most accurate rovibrational spectroscopic data available.
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Affiliation(s)
- Mason B Gardner
- Department of Chemistry & Biochemistry, University of Mississippi, University, MS 38677-1848, United States
| | - Brent R Westbrook
- Department of Chemistry & Biochemistry, University of Mississippi, University, MS 38677-1848, United States
| | - Ryan C Fortenberry
- Department of Chemistry & Biochemistry, University of Mississippi, University, MS 38677-1848, United States.
| | - Timothy J Lee
- MS 245-3, NASA Ames Research Center, Moffett Field, CA 94035, United States
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Abbott-Lyon H, Baiz CR, Bera PP, Crabtree K, Cui Q, Fortenberry RC, Landes CF, McCoy AB, Noriega R, Woon DE. Viewpoint on ACS PHYS Division Sponsored Virtual Seminars. J Phys Chem A 2021; 125:1680. [PMID: 33508194 DOI: 10.1021/acs.jpca.1c00302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Carlos R Baiz
- University of Texas at Austin, Chair-Elect, Biophysical subdivision
| | - Partha P Bera
- NASA-Ames Research Center, Chair, Astrochemistry subdivision
| | - Kyle Crabtree
- University of California, Davis, Vice-Chair, Astrochemistry subdivision
| | - Qiang Cui
- Boston University, Secretary/Treasurer, PHYS
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39
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Abbott-Lyon H, Baiz CR, Bera PP, Crabtree K, Cui Q, Fortenberry RC, Landes CF, McCoy AB, Noriega R, Woon DE. Viewpoint on ACS PHYS Division Sponsored Virtual Seminars. J Phys Chem B 2021; 125:1973. [PMID: 33508191 DOI: 10.1021/acs.jpcb.1c00531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Carlos R Baiz
- University of Texas at Austin, Chair-Elect, Biophysical subdivision
| | - Partha P Bera
- NASA-Ames Research Center, Chair, Astrochemistry subdivision
| | - Kyle Crabtree
- University of California, Davis, Vice-Chair, Astrochemistry subdivision
| | - Qiang Cui
- Boston University, Secretary/Treasurer, PHYS
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40
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Westbrook BR, Valencia EM, Rushing SC, Tschumper GS, Fortenberry RC. Anharmonic vibrational frequencies of ammonia borane (BH 3NH 3). J Chem Phys 2021; 154:041104. [PMID: 33514082 DOI: 10.1063/5.0040050] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The fundamental vibrational frequency of the B-N stretch in BH3NH3 has eluded gas-phase experimental observation for decades. This work offers a theoretical anharmonic prediction of this mode to be 644 cm-1, using a Cartesian quartic force field at the CCSD(T)-F12/cc-pVTZ-F12 level of theory. The other fundamental frequencies reported herein have a mean absolute error of only 5 cm-1 from the seven available gas-phase experimental frequencies, making the anharmonic vibrational frequencies and rotational constants the most accurate computational data available for BH3NH3 to date. The inclusion of Fermi, Coriolis, and Darling-Dennison resonances is a major source of this accuracy, with the non-resonance-corrected frequencies having a mean absolute error of 10 cm-1. In particular, the inclusion of the 2ν6 = ν5 type 1 Fermi resonance increases the B-N stretching frequency by 14 cm-1 compared to previous work. Ammonia borane also represents one of the largest molecules ever studied by quartic force fields, making this work an important step in extending the breadth of application for these theoretical rovibrational techniques.
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Affiliation(s)
- Brent R Westbrook
- The University of Mississippi, University, Mississippi 38677-1848, USA
| | | | - Spencer C Rushing
- The University of Mississippi, University, Mississippi 38677-1848, USA
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Abstract
ConspectusOur two groups have both independently and collaboratively been pushing quantum-chemical techniques to produce highly accurate predictions of anharmonic vibrational frequencies and spectroscopic constants for molecules containing atoms outside of the typical upper p block. Methodologies employ composite approaches, relying on various levels of coupled cluster theory-most often at the singles, doubles, and perturbative triples level-and quartic force field constructions of the potential portion of the intramolecular Watson Hamiltonian. Such methods are known to perform well for organic species, and we have extended this to molecules containing atoms outside of this realm.One notable atom that has received much attention in this application is magnesium. Mg is the second-most-abundant element in the Earth's mantle, and while molecules containing this element are among the confirmed astrochemicals, its further atomic abundance in the galaxy implies that many more molecules (both purely inorganic and organometallic) containing element 12 exist in astrophysical regions in chemical sizes between those of atoms and dust-sized nanocrystals. Our approach discussed herein is producing quality benchmarks and predicting novel data for magnesium-bearing molecules.The story is similar for Al and Si, which are also notably abundant in both rocky bodies and the universe at large. While Na, Sc, and Cu may not be as abundant as Mg, Al, and Si, molecules containing Na and transition metals have also previously been reported to be detected beyond the Earth. Consequently, the need to produce spectral reference data for molecules containing such atoms is growing. While several experimental groups (including, notably, the groups in Arizona, Boston, and France/Spain) have clearly led the way in detection of inorganic/organometallic molecules in space, computational support and even rational design can provide novel avenues for the detection of molecules containing atoms not typically studied in most laboratories. The application of quantum chemistry to other elements beyond carbon and its cronies at the top right of the periodic table promises a better understanding of the observable universe. It will also provide novel and fundamental chemical insights pushing the "central science" into new molecular territory.
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Affiliation(s)
- Ryan C. Fortenberry
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677-1848, United States
| | - Nathan J. DeYonker
- Department of Chemistry, University of Memphis, Memphis, Tennessee 38152, United States
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Williams AE, Davis JE, Reynolds JE, Fortenberry RC, Hammer NI, Reinemann DN. Determination of vibrational band positions in the E-hook of β-tubulin. Spectrochim Acta A Mol Biomol Spectrosc 2021; 244:118895. [PMID: 32919160 DOI: 10.1016/j.saa.2020.118895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 05/22/2020] [Accepted: 08/25/2020] [Indexed: 06/11/2023]
Abstract
Raman spectral characterization of the β-TUBB2A E-hook hexapeptide, EGEDEA, is determined through experimental analysis combined with full geometry optimizations and corresponding harmonic vibrational frequency computations employing DFT methods. The hexapeptide is first broken down into di- and tetrapeptide fragments which are analyzed both quantum chemically and experimentally, and then combined to achieve an energetic minimum of the large EGEDEA hexapeptide. The Raman spectral characterization of EGEDEA band positions are then verified via the literature and comparison to the small fragment's similarly located band positions. The approach employed provides further evidence for the use of fragments as a helpful tool in characterization of the vibrational band positions of large peptides. STATEMENT OF SIGNIFICANCE: To investigate β-TUBB2A E-hook hexapeptide, a unique approach is employed whereby the hexapeptide is broken into fragments, EG, ED, EA, EGED, and EDEA and analyzed via experimental Raman spectroscopy of the crystalline solids. The experimentally observed vibrational band positions are compared to those computed using and scaled from DFT methods and Pople's 6-311+G(2df,2pd) basis set. The reported vibrational band positions are also confirmed by previously reported bands of similar peptides in the literature. This methodology facilitates differentiation between the behaviors of various side chains and their influence on the structure of the hexapeptide, providing insight into not only the nature of the peptide but also defining regions for potential protein and cytoplasmic interactions, without requiring excessive computing resources or overly-sensitive experimental methods.
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Affiliation(s)
- Ashley E Williams
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, United States of America
| | - Juliana E Davis
- Department of Biomedical Engineering, University of Mississippi, University, MS 38677, United States of America
| | - Justin E Reynolds
- Department of Biomedical Engineering, University of Mississippi, University, MS 38677, United States of America
| | - Ryan C Fortenberry
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, United States of America
| | - Nathan I Hammer
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, United States of America
| | - Dana N Reinemann
- Department of Biomedical Engineering, University of Mississippi, University, MS 38677, United States of America; Department of Chemical Engineering, University of Mississippi, University, MS 38677, United States of America.
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Fortenberry RC, Trabelsi T, Francisco JS. Anharmonic Frequencies and Spectroscopic Constants of OAlOH and AlOH: Strong Bonding but Unhindered Motion. J Phys Chem A 2020; 124:8834-8841. [PMID: 33044814 DOI: 10.1021/acs.jpca.0c07945] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The astrophysical buildup of premineral nanocrystals from atoms to the smallest network-covalent solids will require observations of various small molecules containing the most common elements in minerals including aluminum and oxygen. The present work utilizes high-level quantum chemical quartic force field (QFF) approaches to produce anharmonic vibrational frequencies and spectroscopic constants for such species. The computed Beff for the astrochemically known AlOH molecule at 15780.5 MHz is a mere 40 MHz above the experimental value implying that the Beff for OAlOH at 5580.9 MHz is similarly accurate. The additional 7.31 D dipole moment in OAlOH implies that this molecule is a viable target for interstellar observation. Unlike the other anharmonic vibrational frequencies reported in this work, the Al-O-H bending frequencies in both AlOH and OAlOH are poorly described in the present QFF results. However, this failing actually highlights the fact that these bends are exceptionally floppy yet with counterintuitive exceedingly strong bonding. The Al-O bond energies are 128.2 and 107.2 kcal/mol, respective of AlOH and OAlOH, while the barriers to linearity are meager 16.6 and 380.7 cm-1 (0.1 and 1.1 kcal/mol).
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Affiliation(s)
- Ryan C Fortenberry
- Department of Chemistry & Biochemistry, University of Mississippi, University, Mississippi 38677-1848, United States
| | - Tarek Trabelsi
- Department of Earth and Environmental Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Joseph S Francisco
- Department of Earth and Environmental Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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McDonald DC, Rittgers BM, Theis RA, Fortenberry RC, Marks JH, Leicht D, Duncan MA. Infrared spectroscopy and anharmonic theory of H 3 +Ar 2,3 complexes: The role of symmetry in solvation. J Chem Phys 2020; 153:134305. [PMID: 33032436 DOI: 10.1063/5.0023205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The vibrational spectra of H3 +Ar2,3 and D3 +Ar2,3 are investigated in the 2000 cm-1 to 4500 cm-1 region through a combination of mass-selected infrared laser photodissociation spectroscopy and computational work including the effects of anharmonicity. In the reduced symmetry of the di-argon complex, vibrational activity is detected in the regions of both the symmetric and antisymmetric hydrogen stretching modes of H3 +. The tri-argon complex restores the D3h symmetry of the H3 + ion, with a concomitant reduction in the vibrational activity that is limited to the region of the antisymmetric stretch. Throughout these spectra, additional bands are detected beyond those predicted with harmonic vibrational theory. Anharmonic theory is able to reproduce some of the additional bands, with varying degrees of success.
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Affiliation(s)
- D C McDonald
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - B M Rittgers
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - R A Theis
- Department of Chemistry and Biochemistry, Georgia Southern University, Statesboro, Georgia 30460, USA
| | - R C Fortenberry
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, USA
| | - J H Marks
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - D Leicht
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - M A Duncan
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
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Kleimeier NF, Turner AM, Fortenberry RC, Kaiser RI. Cover Feature: On the Formation of the Popcorn Flavorant 2,3‐Butanedione (CH
3
COCOCH
3
) in Acetaldehyde‐Containing Interstellar Ices (ChemPhysChem 14/2020). Chemphyschem 2020. [DOI: 10.1002/cphc.202000552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- N. Fabian Kleimeier
- Department of Chemistry and W. M. Keck Research Laboratory in AstrochemistryUniversity of Hawai'i at Manoa 2545 McCarthy Mall Honolulu HI 96822 USA
| | - Andrew M. Turner
- Department of Chemistry and W. M. Keck Research Laboratory in AstrochemistryUniversity of Hawai'i at Manoa 2545 McCarthy Mall Honolulu HI 96822 USA
| | - Ryan C. Fortenberry
- Department of Chemistry & BiochemistryUniversity of Mississippi 322 Coulter Hall, University MS 38677-1848 USA
| | - Ralf I. Kaiser
- Department of Chemistry and W. M. Keck Research Laboratory in AstrochemistryUniversity of Hawai'i at Manoa 2545 McCarthy Mall Honolulu HI 96822 USA
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Kleimeier NF, Turner AM, Fortenberry RC, Kaiser RI. On the Formation of the Popcorn Flavorant 2,3-Butanedione (CH 3 COCOCH 3 ) in Acetaldehyde-Containing Interstellar Ices. Chemphyschem 2020; 21:1531-1540. [PMID: 32458552 DOI: 10.1002/cphc.202000116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/25/2020] [Indexed: 11/06/2022]
Abstract
Acetaldehyde (CH3 CHO) is ubiquitous throughout the interstellar medium and has been observed in cold molecular clouds, star forming regions, and in meteorites such as Murchison. As the simplest methyl-bearing aldehyde, acetaldehyde constitutes a critical precursor to prebiotic molecules such as the sugar deoxyribose and amino acids via the Strecker synthesis. In this study, we reveal the first laboratory detection of 2,3-butanedione (diacetyl, CH3 COCOCH3 ) - a butter and popcorn flavorant - synthesized within acetaldehyde-based interstellar analog ices exposed to ionizing radiation at 5 K. Detailed isotopic substitution experiments combined with tunable vacuum ultraviolet (VUV) photoionization of the subliming molecules demonstrate that 2,3-butanedione is formed predominantly via the barrier-less radical-radical reaction of two acetyl radicals (CH3 ĊO). These processes are of fundamental importance for a detailed understanding of how complex organic molecules (COMs) are synthesized in deep space thus constraining the molecular structures and complexity of molecules forming in extraterrestrial ices containing acetaldehyde through a vigorous galactic cosmic ray driven non-equilibrium chemistry.
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Affiliation(s)
- N Fabian Kleimeier
- Department of Chemistry and W. M. Keck Research Laboratory in Astrochemistry, University of Hawai'i at Manoa 2545 McCarthy Mall, Honolulu, HI, 96822, USA
| | - Andrew M Turner
- Department of Chemistry and W. M. Keck Research Laboratory in Astrochemistry, University of Hawai'i at Manoa 2545 McCarthy Mall, Honolulu, HI, 96822, USA
| | - Ryan C Fortenberry
- Department of Chemistry & Biochemistry, University of Mississippi, 322 Coulter Hall, University, MS, 38677-1848, USA
| | - Ralf I Kaiser
- Department of Chemistry and W. M. Keck Research Laboratory in Astrochemistry, University of Hawai'i at Manoa 2545 McCarthy Mall, Honolulu, HI, 96822, USA
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Nguyen QLD, Peters WK, Fortenberry RC. Highly-excited state properties of cumulenone chlorides in the vacuum-ultraviolet. Phys Chem Chem Phys 2020; 22:11838-11849. [PMID: 32426777 DOI: 10.1039/d0cp01835j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recent observations of chloromethane in interstellar environments suggest that other organohalogens, which are known to be critically important in Earth's atmosphere, may also be of significance beyond our own terrestrial veil. This raises the question of how such molecules behave under extreme conditions such as when exposed to vacuum ultraviolet (VUV) radiation. VUV photons promote molecules to highly excited states that fragment in non-statistical patterns controlled by the initial femtosecond dynamics. A detailed understanding of VUV-driven photochemistry in complex organic molecules that consist of more than one functional group is a particularly challenging task. This quantum chemical analysis reports the electronic states and ionization potentials up to the VUV range (6-11 eV) of the chlorine-substituted cumulenone series molecules. The valence and Rydberg properties of lone-pair terminated, π-conjugated systems are explored for their potential resonance with lone pairs from elsewhere in the system. The carbon chain elongation within the family ClHCnO, where n = 1-4, influences the electronic excitations, associated wavefunctions, and ionization potentials of the molecules. The predicted geometries and ionization potentials are in good agreement with the available experimental photoelectron spectra for formyl chloride and chloroketene, n = 1-2. Furthermore, comparison between the regular cumulenone species and the corresponding chlorinated derivatives exhibit similar behaviors especially for n = 3, where the allene backbone in propadienone chloride is severely bent. Most notably for the excited states is that the Rydberg character becomes more dominant as the energy increases, with some retaining valence characters.
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Affiliation(s)
- Quynh L D Nguyen
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado, USA.
| | - William K Peters
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado, USA.
| | - Ryan C Fortenberry
- Department of Chemistry & Biochemistry, University of Mississippi, University, MS 38677-1848, USA
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Westbrook BR, Del Rio WA, Lee TJ, Fortenberry RC. Overcoming the out-of-plane bending issue in an aromatic hydrocarbon: the anharmonic vibrational frequencies of c-(CH)C 3H 2. Phys Chem Chem Phys 2020; 22:12951-12958. [PMID: 32478782 DOI: 10.1039/d0cp01889a] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The challenges associated with the out-of-plane bending problem in multiply-bonded hydrocarbon molecules can be mitigated in quartic force field analyses by varying the step size in the out-of-plane coordinates. Carbon is a highly prevalent element in astronomical and terrestrial environments, but this major piece of its spectra has eluded theoretical examinations for decades. Earlier explanations for this problem focused on method and basis set issues, while this work seeks to corroborate the recent diagnosis as a numerical instability problem related to the generation of the potential energy surface. Explicit anharmonic frequencies for c-(CH)C3H2+ are computed using a quartic force field and the CCSD(T)-F12b method with cc-pVDZ-F12, cc-pVTZ-F12, and aug-cc-pVTZ basis sets. The first of these is shown to offer accuracy comparable to that of the latter two with a substantial reduction in computational time. Additionally, c-(CH)C3H2+ is shown to have two fundamental frequencies at the onset of the interstellar unidentified infrared bands, at 5.134 and 6.088 μm or 1947.9 and 1642.6 cm-1, respectively. This suggests that the results in the present study should assist in the attribution of parts of these aromatic bands, as well as provide data in support of the laboratory or astronomical detection of c-(CH)C3H2+.
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Affiliation(s)
- Brent R Westbrook
- Department of Chemistry & Biochemistry, University of Mississippi, MS 38677-1848, USA.
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Abstract
HeHHe+ is the only potential molecule comprised of atoms present in the early universe that is also easily observable in the infrared. This molecule has been known to exist in mass spectrometry experiments for nearly half-a-century and is likely present, but as-of-yet unconfirmed, in cold plasmas. There can exist only a handful of plausible primordial molecules in the epochs before metals (elements with nuclei heavier than 4He as astronomers call them) were synthesized in the universe, and most of these are both rotationally and vibrationally dark. The current work brings HeHHe+ into the discussion as a possible (and potentially only) molecular candle for probing high-z and any metal-deprived regions due to its exceptionally bright infrared feature previously predicted to lie at 7.43 μm. Furthermore, the present study provides new insights into its possible formation mechanisms as well as marked stability, along with the decisive role of anharmonic zero-point energies. A new entrance pathway is proposed through the triplet state (3B1) of the He2H+ molecule complexed with a hydrogen atom and a subsequent 10.90 eV charge transfer/photon emission into the linear and vibrationally-bright 1Σg+ HeHHe+ form.
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Affiliation(s)
- Ryan C. Fortenberry
- Department of Chemistry & Biochemistry, University of Mississippi, University, MS 38677-1848, USA
- Correspondence: ; Tel.: +1-662-915-1687
| | - Laurent Wiesenfeld
- Laboratoire Aimé-Cotton, CNRS & Université Paris-Saclay, 91405 Orsay, France;
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