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Uribe L, Lazzari F, Di Grande S, Crisci L, Mendolicchio M, Barone V. Accurate structures and rotational constants of bicyclic monoterpenes at DFT cost by means of the bond-corrected Pisa composite scheme (BPCS). J Chem Phys 2024; 161:014307. [PMID: 38958160 DOI: 10.1063/5.0216384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 06/17/2024] [Indexed: 07/04/2024] Open
Abstract
The structural, conformational, and spectroscopic properties in the gas phase of 20 bicyclic monoterpenes and monoterpenoids have been analyzed by a new accurate, reduced-cost computational strategy. In detail, the revDSD-PBEP86 double-hybrid functional in conjunction with the D3BJ empirical dispersion corrections and a suitable triple-zeta basis set provides accurate geometrical parameters, whence equilibrium rotational constants, which are further improved by proper account of core-valence correlation. Average deviations within 0.1% between computed and experimental rotational constants are reached when taking into account the vibrational corrections obtained by the B3LYP functional in conjunction with a double-zeta basis set in the framework of second-order vibrational perturbation theory. In addition to their intrinsic interest, the studied terpenes further extend the panel of systems for which the proposed strategy has provided accurate results at density functional theory cost. Therefore, a very accurate yet robust and user-friendly tool is now available for systematic investigations of the role of stereo-electronic effects on the properties of large systems of current technological and/or biological interest by experimentally oriented researchers.
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Affiliation(s)
- Lina Uribe
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Scuola Superiore Meridionale, Largo San Marcellino 10, 80138 Napoli, Italy
| | - Federico Lazzari
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Silvia Di Grande
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Scuola Superiore Meridionale, Largo San Marcellino 10, 80138 Napoli, Italy
| | - Luigi Crisci
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Marco Mendolicchio
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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2
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Fortenberry RC. Picking up Good Vibrations through Quartic Force Fields and Vibrational Perturbation Theory. J Phys Chem Lett 2024; 15:6528-6537. [PMID: 38875074 DOI: 10.1021/acs.jpclett.4c01089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2024]
Abstract
Quartic force fields (QFFs) define sparse potential energy surfaces (compared to semiglobal surfaces) that are the cheapest and easiest means of computing anharmonic vibrational frequencies, especially when utilized with second-order vibrational perturbation theory (VPT2). However, flat and shallow potential surfaces are exceedingly difficult for QFFs to treat through a combination of numerical noise in the often numerically computed derivatives and in competing energy factors in the composite energies often utilized to provide high-level spectroscopic predictions. While some of these issues can be alleviated with analytic derivatives, hybrid QFFs, and intelligent choices in coordinate systems, the best practice is for predicting good molecular vibrations via QFFs is to understand what they cannot do, and this manuscript documents such cases where QFFs may fail.
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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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3
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Di Grande S, Barone V. Toward Accurate Quantum Chemical Methods for Molecules of Increasing Dimension: The New Family of Pisa Composite Schemes. J Phys Chem A 2024; 128:4886-4900. [PMID: 38847454 DOI: 10.1021/acs.jpca.4c01673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
The new versions of the Pisa composite scheme introduced in the present paper are based on the careful selection of different quantum chemical models for energies, geometries, and vibrational frequencies, with the aim of maximizing the accuracy of the overall description while retaining a reasonable cost for all the steps. In particular, the computation of accurate electronic energies has been further improved introducing more reliable complete basis set extrapolations and estimation of core-valence correlation, together with improved basis sets for third-row atoms. Furthermore, the reduced-cost frozen natural orbital (FNO) model has been introduced and validated for large molecules. Accurate molecular structures can be obtained avoiding complete basis set extrapolation and evaluating core-valence correlation at the MP2 level. Unfortunately, analytical gradients are not available for the FNO version of the model. Therefore, for large molecules, an accurate reduced-cost alternative is offered by evaluation of valence contributions with a double-hybrid functional in conjunction with the same MP2 contribution for core-valence correlation or by means of a one-parameter approximation. The same double-hybrid functional and basis set are employed to evaluate zero-point energies and partition functions. After the validation of the new models for small systems, a panel of molecular bricks of life has been used to analyze their performances for problems of current fundamental or technological interest. The fully black-box implementation of the computational workflow paves the way toward the accurate yet not prohibitively expensive study of medium- to large-sized molecules also by experimentally oriented researchers.
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Affiliation(s)
- Silvia Di Grande
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Scuola Superiore Meridionale, Largo San Marcellino 10, 80138 Napoli, Italy
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4
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Firth RA, Palmer CZ, Francisco JS, Fortenberry RC. Rovibrational analysis of AlCO3, OAlO2, and HOAlO2 for possible atmospheric detection. J Chem Phys 2024; 160:214304. [PMID: 38832738 DOI: 10.1063/5.0212147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 05/19/2024] [Indexed: 06/05/2024] Open
Abstract
The lack of observational data for the AlO molecule in the mesosphere/lower thermosphere may be due to ablated aluminum reacting quickly to form other species. Previously proposed reaction pathways show that aluminum could be ablated in the atmosphere from meteoritic activity, but there currently exist very limited spectroscopic data on the intermediates in these reactions, limiting the possible detection of said molecules. As such, rovibrational spectroscopic data are computed herein using quartic force field methodology at four different levels of theory for the neutral intermediates AlCO3, OAlO2, and HOAlO2. Each molecule exhibits multiple vibrational modes with large vibrational transition intensities. For instance, the C-O stretch (ν1) in AlCO3 has a harmonic intensity of 536 km mol-1, the Al-O stretch (ν2) in OAlO2 has an intensity of 678 km mol-1, and the out-of-plane torsion (ν9) in HOAlO2 has an intensity of 158 km mol-1. All three molecules have exceptionally large dipole moments of 6.27, 4.21, and 5.04 D, respectively. These properties indicate that all three molecules are good candidates for potential atmospheric observation utilizing vibrational and/or rotational spectroscopic techniques.
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Affiliation(s)
- Rebecca A Firth
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, USA
| | - C Zachary Palmer
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, USA
| | - Joseph S Francisco
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6243, USA
| | - Ryan C Fortenberry
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, USA
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5
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Esposito VJ, Fortenberry RC, Boersma C, Allamandola LJ. Assigning the CH stretch overtone spectrum of benzene and naphthalene with extension to anthracene and tetracene using 2- and 3-quanta anharmonic quantum chemical computations. J Chem Phys 2024; 160:211101. [PMID: 38828805 DOI: 10.1063/5.0208597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 05/05/2024] [Indexed: 06/05/2024] Open
Abstract
The CH stretch overtone region (5750-6300 cm-1) of benzene and naphthalene is assigned herein using anharmonic quantum chemical computations, and the trend of how this extends to larger polycyclic aromatic hydrocarbons (PAHs) is established. The assignment of all experimental bands to specific vibrational states is performed for the first time. Resonance polyads and the inclusion of 3-quanta vibrational states are both needed to compute accurate vibrational frequencies with the proper density-of-states to match the experimental band shape. Hundreds of 3-quanta states produce the observed band structure in naphthalene, anthracene, and tetracene, and this number is expected to increase drastically for larger PAHs. The width and shape of the main peak are consistent from naphthalene to anthracene, necessitating further exploration of this trend to confirm whether it is representative of all PAHs in the CH stretch overtone region. Understanding observations of PAH sources in the 1-3 μm region from the NIRSpec instrument aboard JWST requires new computational data, and this study provides a benchmark and foundation for their computation.
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Affiliation(s)
- Vincent J Esposito
- Astrophysics Branch, NASA Ames Research Center, Moffett Field, California 94035, USA
| | - Ryan C Fortenberry
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677-1848, USA
| | - Christiaan Boersma
- Astrophysics Branch, NASA Ames Research Center, Moffett Field, California 94035, USA
| | - Louis J Allamandola
- Astrophysics Branch, NASA Ames Research Center, Moffett Field, California 94035, USA
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6
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Spencer RJ, Zhanserkeev AA, Yang EL, Steele RP. The Near-Sightedness of Many-Body Interactions in Anharmonic Vibrational Couplings. J Am Chem Soc 2024; 146:15376-15392. [PMID: 38771156 DOI: 10.1021/jacs.4c03198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Couplings between vibrational motions are driven by electronic interactions, and these couplings carry special significance in vibrational energy transfer, multidimensional spectroscopy experiments, and simulations of vibrational spectra. In this investigation, the many-body contributions to these couplings are analyzed computationally in the context of clathrate-like alkali metal cation hydrates, including Cs+(H2O)20, Rb+(H2O)20, and K+(H2O)20, using both analytic and quantum-chemistry potential energy surfaces. Although the harmonic spectra and one-dimensional anharmonic spectra depend strongly on these many-body interactions, the mode-pair couplings were, perhaps surprisingly, found to be dominated by one-body effects, even in cases of couplings to low-frequency modes that involved the motion of multiple water molecules. The origin of this effect was traced mainly to geometric distortion within water monomers and cancellation of many-body effects in differential couplings, and the effect was also shown to be agnostic to the identity of the ion. These outcomes provide new understanding of vibrational couplings and suggest the possibility of improved computational methods for the simulation of infrared and Raman spectra.
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Affiliation(s)
- Ryan J Spencer
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Asylbek A Zhanserkeev
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Emily L Yang
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Ryan P Steele
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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7
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Salzmann H, McCoy AB, Weber JM. Infrared Spectrum of the Pyrene Anion in the CH Stretching Region. J Phys Chem A 2024; 128:4225-4232. [PMID: 38753443 DOI: 10.1021/acs.jpca.4c00966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
In this work, we report the infrared spectrum of the pyrene anion, measured using messenger tagging with up to three Ar atoms. We assign the spectrum using density functional theory and vibrational perturbation theory. We discuss our results in the context of computed and experimental spectra from the literature as well as recent observations from astronomical sources, addressing the question of whether polycyclic aromatic hydrocarbon anions could contribute to the strong infrared emission bands at 3.29 μm from carbon-rich regions of space.
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Affiliation(s)
- Heinrich Salzmann
- JILA and Department of Chemistry, University of Colorado, Boulder, Colorado 80309-0440, United States
| | - Anne B McCoy
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - J Mathias Weber
- JILA and Department of Chemistry, University of Colorado, Boulder, Colorado 80309-0440, United States
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8
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Zou M, Hassan Y, Roy TK, McCoy AB, Lester MI. Infrared spectroscopy of the syn-methyl-substituted Criegee intermediate: A combined experimental and theoretical study. J Chem Phys 2024; 160:204309. [PMID: 38818894 DOI: 10.1063/5.0210122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 05/06/2024] [Indexed: 06/01/2024] Open
Abstract
An IR-vacuum ultraviolet (VUV) ion-dip spectroscopy method is utilized to examine the IR spectrum of acetaldehyde oxide (CH3CHOO) in the overtone CH stretch (2νCH) spectral region. IR activation creates a depletion of the ground state population that reduces the VUV photoionization signal on the parent mass channel. IR activation of the more stable and populated syn-CH3CHOO conformer results in rapid unimolecular decay to OH + vinoxy products and makes the most significant contribution to the observed spectrum. The resultant IR-VUV ion-dip spectrum of CH3CHOO is similar to that obtained previously for syn-CH3CHOO using IR action spectroscopy with UV laser-induced fluorescence detection of OH products. The prominent IR features at 5984 and 6081 cm-1 are also observed using UV + VUV photoionization of OH products. Complementary theoretical calculations utilizing a general implementation of second-order vibrational perturbation theory provide new insights on the vibrational transitions that give rise to the experimental spectrum in the overtone CH stretch region. The introduction of physically motivated small shifts of the harmonic frequencies yields remarkably improved agreement between experiment and theory in the overtone CH stretch region. The prominent features are assigned as highly mixed states with contributions from two quanta of CH stretch and/or a combination of CH stretch with an overtone in mode 4. The generality of this approach is demonstrated by applying it to three different levels of electronic structure theory/basis sets, all of which provide spectra that are virtually indistinguishable despite showing large deviations prior to introducing the shifts to the harmonic frequencies.
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Affiliation(s)
- Meijun Zou
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA
| | - Yarra Hassan
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA
| | - Tarun Kumar Roy
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA
| | - Anne B McCoy
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA
| | - Marsha I Lester
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA
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9
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Tang CL, Heide AG, Heide AD, Douberly GE, Turney JM, Schaefer HF. Exploring the Tl 2 H 2 potential energy surface: A comparative analysis with group 13 systems and experiment. J Comput Chem 2024; 45:985-994. [PMID: 38197269 DOI: 10.1002/jcc.27293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 12/04/2023] [Accepted: 12/10/2023] [Indexed: 01/11/2024]
Abstract
Thallium chemistry is experiencing unprecedented importance. Therefore, it is valuable to characterize some of the simplest thallium compounds. Stationary points along the singlet and triplet Tl 2 H 2 potential energy surface have been characterized. Stationary point geometries were optimized with the CCSD(T)/aug-cc-pwCVQZ-PP method. Harmonic vibrational frequencies were computed at the same level of theory while anharmonic vibrational frequencies were computed at the CCSD(T)/aug-cc-pwCVTZ-PP level of theory. Final energetics were obtained with the CCSDT(Q) method. Basis sets up to augmented quintuple-zeta cardinality (aug-cc-pwCV5Z-PP) were employed to obtain energetics in order to extrapolate to the complete basis set limits using the focal point approach. Zero-point vibrational energy corrections were appended to the extrapolated energies in order to determine relative energies at 0 K. It was found that the planar dibridged isomer lies lowest in energy while the linear structure lies highest in energy. The results were compared to other group 13 M 2 H 2 (M = B, Al, Ga, In, and Tl) theoretical studies and some interesting variations are found. With respect to experiment, incompatibilities exist.
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Affiliation(s)
- Carson L Tang
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia, USA
| | - Alexander G Heide
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia, USA
| | - Alexandra D Heide
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia, USA
| | - Gary E Douberly
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia, USA
| | - Justin M Turney
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia, USA
| | - Henry F Schaefer
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia, USA
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10
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Crabtree KN, Westerfield JH, Dim CA, Meyer KS, Johansen SL, Buchanan ZS, Stucky PA. Rotational spectroscopy of methyl tert-butyl ether with a new Ka band chirped-pulse Fourier transform microwave spectrometer. Phys Chem Chem Phys 2024; 26:13694-13709. [PMID: 38666410 DOI: 10.1039/d4cp00797b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2024]
Abstract
Chirped-pulse Fourier transform microwave (CP-FTMW) spectroscopy is a powerful tool for performing broadband gas-phase rotational spectroscopy, and its applications include discovery of new molecules, complex mixture analysis, and exploration of fundamental molecular physics. Here we report the development of a new Ka band (26.5-40 GHz) CP-FTMW spectrometer that is equipped with a pulsed supersonic expansion source and a heated reservoir for low-volatility samples. The spectrometer is built around a 150 W traveling wave tube amplifier and has an instantaneous bandwidth that covers the entire Ka band spectral range. To test the performance of the spectrometer, the rotational spectrum of methyl tert-butyl ether (MTBE), a former gasoline additive and environmental pollutant, has been measured for the first time in this spectral range. Over 1000 spectroscopic transitions have been measured and assigned to the vibrational ground state and a newly-identified torsionally excited state; all transitions were fit using the XIAM program to a root-mean-square deviation of 22 kHz. The spectrum displays internal rotation splitting, nominally forbidden transitions, and an intriguing axis-switching effect between the ground and torsionally excited state that is a consequence of MTBE's extreme near-prolate nature. Finally, the sensitivity of the spectrometer enabled detection of all singly-substituted 13C and 18O isotopologues in natural abundance. This set of isotopic spectra allowed for a partial r0 structure involving the heavy atoms to be derived, resolving a structural discrepancy in the literature between previous microwave and electron diffraction measurements.
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Affiliation(s)
- Kyle N Crabtree
- Department of Chemistry, University of California, Davis, Davis, CA, USA.
| | - J H Westerfield
- Department of Chemistry, University of California, Davis, Davis, CA, USA.
| | - Chisom A Dim
- Department of Chemistry, University of California, Davis, Davis, CA, USA.
| | - Kelly S Meyer
- Department of Chemistry, University of California, Davis, Davis, CA, USA.
| | - Sommer L Johansen
- Department of Chemistry, University of California, Davis, Davis, CA, USA.
| | - Zachary S Buchanan
- Department of Chemistry, University of California, Davis, Davis, CA, USA.
| | - Paul A Stucky
- Department of Chemistry, University of California, Davis, Davis, CA, USA.
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11
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Xu R, Jiang Z, Yang Q, Bloino J, Biczysko M. Harmonic and anharmonic vibrational computations for biomolecular building blocks: Benchmarking DFT and basis sets by theoretical and experimental IR spectrum of glycine conformers. J Comput Chem 2024. [PMID: 38682874 DOI: 10.1002/jcc.27377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 05/01/2024]
Abstract
Advanced vibrational spectroscopic experiments have reached a level of sophistication that can only be matched by numerical simulations in order to provide an unequivocal analysis, a crucial step to understand the structure-function relationship of biomolecules. While density functional theory (DFT) has become the standard method when targeting medium-size or larger systems, the problem of its reliability and accuracy are well-known and have been abundantly documented. To establish a reliable computational protocol, especially when accuracy is critical, a tailored benchmark is usually required. This is generally done over a short list of known candidates, with the basis set often fixed a priori. In this work, we present a systematic study of the performance of DFT-based hybrid and double-hybrid functionals in the prediction of vibrational energies and infrared intensities at the harmonic level and beyond, considering anharmonic effects through vibrational perturbation theory at the second order. The study is performed for the six-lowest energy glycine conformers, utilizing available "state-of-the-art" accurate theoretical and experimental data as reference. Focusing on the most intense fundamental vibrations in the mid-infrared range of glycine conformers, the role of the basis sets is also investigated considering the balance between computational cost and accuracy. Targeting larger systems, a broad range of hybrid schemes with different computational costs is also tested.
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Affiliation(s)
- Ruiqin Xu
- Department of Physics, College of Sciences, Shanghai University, Shanghai, China
| | | | - Qin Yang
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czechia
| | - Julien Bloino
- Classe di Scienze, Scuola Normale Superiore, Pisa, Italy
| | - Malgorzata Biczysko
- Department of Physics, College of Sciences, Shanghai University, Shanghai, China
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12
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Fusè M, Mazzeo G, Longhi G, Abbate S, Yang Q, Bloino J. Scaling-up VPT2: A feasible route to include anharmonic correction on large molecules. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 311:123969. [PMID: 38330757 DOI: 10.1016/j.saa.2024.123969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 01/18/2024] [Accepted: 01/24/2024] [Indexed: 02/10/2024]
Abstract
Vibrational analysis plays a crucial role in the investigation of molecular systems. Though methodologies like second-order vibrational perturbation theory (VPT2) have paved the way to more accurate simulations, the computational cost remains a difficult barrier to overcome when the molecular size increases. Building upon recent advances in the identification of resonances, we propose an approach making anharmonic simulations possible for large-size systems, typically unreachable by standard means. This relies on the fact that, often, only portions of the whole spectra are of actual interest. Therefore, the anharmonic corrections can be included selectively on subsets of normal modes directly related to the regions of interest. Starting from the VPT2 equations, we evaluate rigorously and systematically the impact of the truncated anharmonic treatment onto simulations. The limit and feasibility of the reduced-dimensionality approach are detailed, starting on a smaller model system. The methodology is then challenged on the IR absorption and vibrational circular dichroism spectra of an organometallic complex in three different spectral ranges.
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Affiliation(s)
- Marco Fusè
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Viale Europa 11, 25123, Brescia, Italy.
| | - Giuseppe Mazzeo
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Viale Europa 11, 25123, Brescia, Italy
| | - Giovanna Longhi
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Viale Europa 11, 25123, Brescia, Italy; Istituto Nazionale di Ottica (INO), CNR, Research Unit of Brescia, c/o CSMT, VIA Branze 45, 25123, Brescia, Italy
| | - Sergio Abbate
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Viale Europa 11, 25123, Brescia, Italy; Istituto Nazionale di Ottica (INO), CNR, Research Unit of Brescia, c/o CSMT, VIA Branze 45, 25123, Brescia, Italy
| | - Qin Yang
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 542/2, 160 00, Prague, Czech Republic
| | - Julien Bloino
- Scuola Normale Superiore, Piazza dei Cavalieri, 56125, Pisa, Italy.
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13
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McDonnell RP, Oram K, Boyer MA, Kohler DD, Meyer KA, Sibert Iii EL, Wright JC. Direct Probe of Vibrational Fingerprint and Combination Band Coupling. J Phys Chem Lett 2024; 15:3975-3981. [PMID: 38569133 DOI: 10.1021/acs.jpclett.4c00297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Vibrational fingerprints and combination bands are a direct measure of couplings that control molecular properties. However, most combination bands possess small transition dipoles. Here we use multiple, ultrafast coherent infrared pulses to resolve vibrational coupling between CH3CN fingerprint modes at 918 and 1039 cm-1 and combination bands in the 2750-6100 cm-1 region via doubly vibrationally enhanced (DOVE) coherent multidimensional spectroscopy (CMDS). This approach provides a direct probe of vibrational coupling between fingerprint modes and near-infrared combination bands of large and small transition dipoles in a molecular system over a large frequency range.
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Affiliation(s)
- Ryan P McDonnell
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin - Madison, Madison, Wisconsin 53706, United States
| | - Kelson Oram
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin - Madison, Madison, Wisconsin 53706, United States
| | - Mark A Boyer
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin - Madison, Madison, Wisconsin 53706, United States
| | - Daniel D Kohler
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin - Madison, Madison, Wisconsin 53706, United States
| | - Kent A Meyer
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin - Madison, Madison, Wisconsin 53706, United States
| | - Edwin L Sibert Iii
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin - Madison, Madison, Wisconsin 53706, United States
| | - John C Wright
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin - Madison, Madison, Wisconsin 53706, United States
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14
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Mendolicchio M, Barone V. Unbiased Comparison between Theoretical and Experimental Molecular Structures and Properties: Toward an Accurate Reduced-Cost Evaluation of Vibrational Contributions. J Chem Theory Comput 2024; 20:2842-2857. [PMID: 38556752 DOI: 10.1021/acs.jctc.4c00023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
The tremendous development of hardware and software is constantly increasing the role of quantum chemical (QC) computations in the assignment and interpretation of experimental results. However, an unbiased comparison between theory and experiment requires the proper account of vibrational averaging effects. In particular, high-resolution spectra in the gas phase are now available for molecules containing up to about 50 atoms, which are too large for a brute-force approach with the available QC methods of sufficient accuracy. In the present paper, we introduce hybrid approaches, which allow the accurate evaluation of vibrational averaging effects for molecules of this size beyond the harmonic approximation, with special attention being devoted to rotational constants. After the validation of new tools for relatively small molecules, the β-estradiol hormone and a prototypical molecular motor have been considered to witness the feasibility of accurate computations for large molecules.
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15
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Uribe L, Di Grande S, Crisci L, Lazzari F, Mendolicchio M, Barone V. Accurate Structures and Rotational Constants of Steroid Hormones at DFT Cost: Androsterone, Testosterone, Estrone, β-Estradiol, and Estriol. J Phys Chem A 2024; 128:2629-2642. [PMID: 38530336 DOI: 10.1021/acs.jpca.4c00573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
A comprehensive analysis of the structural, conformational, and spectroscopic properties in the gas phase has been performed for five prototypical steroid hormones, namely, androsterone, testosterone, estrone, β-estradiol, and estriol. The revDSD-PBEP86 double-hybrid functional in conjunction with the D3BJ empirical dispersion and a suitable triple-ζ basis set provides accurate conformational energies and equilibrium molecular structures, with the latter being further improved by proper account of core-valence correlation. Average deviations within 0.1% between computed and experimental ground state rotational constants are reached when adding to those equilibrium values vibrational corrections obtained at the cost of standard harmonic frequencies thanks to the use of a new computational tool. Together with the intrinsic interest of the studied hormones, the accuracy of the results obtained at DFT cost for molecules containing about 50 atoms paves the way toward the accurate investigations of other flexible bricks of life.
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Affiliation(s)
- Lina Uribe
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Scuola Superiore Meridionale, Largo San Marcellino 10, 80138 Napoli, Italy
| | - Silvia Di Grande
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Scuola Superiore Meridionale, Largo San Marcellino 10, 80138 Napoli, Italy
| | - Luigi Crisci
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Federico Lazzari
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Marco Mendolicchio
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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16
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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] [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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17
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Schröder B, Rauhut G. From the Automated Calculation of Potential Energy Surfaces to Accurate Infrared Spectra. J Phys Chem Lett 2024; 15:3159-3169. [PMID: 38478898 PMCID: PMC10961845 DOI: 10.1021/acs.jpclett.4c00186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/20/2024] [Accepted: 02/28/2024] [Indexed: 03/22/2024]
Abstract
Advances in the development of quantum chemical methods and progress in multicore architectures in computer science made the simulation of infrared spectra of isolated molecules competitive with respect to established experimental methods. Although it is mainly the multidimensional potential energy surface that controls the accuracy of these calculations, the subsequent vibrational structure calculations need to be carefully converged in order to yield accurate results. As both aspects need to be considered in a balanced way, we focus on approaches for molecules of up to 12-15 atoms with respect to both parts, which have been automated to some extent so that they can be employed in routine applications. Alternatives to machine learning will be discussed, which appear to be attractive, as long as local regions of the potential energy surface are sufficient. The automatization of these methods is still in its infancy, and the generalization to molecules with large amplitude motions or molecular clusters is far from trivial, but many systems relevant for astrophysical studies are already in reach.
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Affiliation(s)
- Benjamin Schröder
- Institute
of Physical Chemistry, University of Goettingen, Tammannstrasse 6, Göttingen 37077, Germany
| | - Guntram Rauhut
- Institute
for Theoretical Chemistry, University of
Stuttgart, Pfaffenwaldring 55, Stuttgart 70569, Germany
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18
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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] [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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19
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Barone V. Quantum chemistry meets high-resolution spectroscopy for characterizing the molecular bricks of life in the gas-phase. Phys Chem Chem Phys 2024; 26:5802-5821. [PMID: 38099409 DOI: 10.1039/d3cp05169b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
Computation of accurate geometrical structures and spectroscopic properties of large flexible molecules in the gas-phase is tackled at an affordable cost using a general exploration/exploitation strategy. The most distinctive feature of the approach is the careful selection of different quantum chemical models for energies, geometries and vibrational frequencies with the aim of maximizing the accuracy of the overall description while retaining a reasonable cost for all the steps. In particular, a composite wave-function method is used for energies, whereas a double-hybrid functional (with the addition of core-valence correlation) is employed for geometries and harmonic frequencies and a cheaper hybrid functional for anharmonic contributions. A thorough benchmark based on a wide range of prototypical molecular bricks of life shows that the proposed strategy is close to the accuracy of state-of-the-art composite wave-function methods, and is applicable to much larger systems. A freely available web-utility post-processes the geometries optimized by standard electronic structure codes paving the way toward the accurate yet not prohibitively expensive study of medium- to large-sized molecules by experimentally-oriented researchers.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy.
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20
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Finney JM, McCoy AB. Correlations between the Structures and Spectra of Protonated Water Clusters. J Phys Chem A 2024; 128:868-879. [PMID: 38265889 DOI: 10.1021/acs.jpca.3c07338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
Badger's rule-like correlations between OH stretching frequencies and intensities and the OH bond length are used to develop a spectral mapping procedure for studies of pure and protonated water clusters. This approach utilizes the vibrationally averaged OH bond lengths, which were obtained from diffusion Monte Carlo simulations that were performed using the general potential developed by Yu and Bowman. Good agreement is achieved between the spectra obtained using this approach and previously reported spectra for H+(H2O)n clusters, with n = 3, 4, and 5, as well as their perdeuterated analogues. The analysis of the spectra obtained by this spectral mapping approach supports previous work that assigned the spectrum of H+(H2O)6 to a mixture of Eigen and Zundel-like structures. Analysis of the calculated spectra also suggests a reassignment of the frequency of one of the transitions that involves the OH stretching vibration of the OH bonds in the hydronium core in the Eigen-like structure of H+(H2O)6 from 1917 cm-1 to roughly 2100 cm-1. For D+(D2O)6, comparison of the measured spectrum to those obtained by using the spectral mapping approach suggests that the carrier of the measured spectrum is one or more of the isomers of D+(D2O)6 that contain a four-membered ring and two flanking water molecules. While there are several candidate structures, the two flanking water molecules most likely form a chain that is bound to the hydronium core.
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Affiliation(s)
- Jacob M Finney
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Anne B McCoy
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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21
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Mitoli D, Maul J, Erba A. First-Principles Anharmonic Infrared and Raman Vibrational Spectra of Materials: Fermi Resonance in Dry Ice. J Phys Chem Lett 2024; 15:888-894. [PMID: 38241167 DOI: 10.1021/acs.jpclett.3c03372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2024]
Abstract
We introduce a computational tool for the quantum-mechanical simulation of anharmonic infrared and Raman vibrational spectra of materials. The approach, implemented in the CRYSTAL software, stems from Taylor's expansion of the potential energy surface (PES) on the basis of normal modes up to cubic and quartic terms. The PES can be sampled with four different numerical schemes at the level of density functional theory (DFT), with local, generalized-gradient, and hybrid density functional approximations. Anharmonic states are obtained by solving Shrödinger's nuclear equation with either the vibrational self-consistent field (VSCF) or vibrational configuration interaction (VCI) methods. Nuclear quantum effects (NQEs) are thus fully accounted for. Infrared intensities are computed numerically through a Berry phase approach or analytically through a coupled-perturbed (CP) approach. Raman intensities are computed analytically via the CP approach. A variety of anharmonic features of vibrational spectra of materials can be simulated, including band shifts, combination bands, overtones, resonances (first-order Fermi, second-order Darling-Dennison), and hot bands. We showcase the effectiveness of the approach on the description of a first-order Fermi resonance (FR) in CO2 dry ice: a challenging test-case given that the FR occurs in the Raman spectrum, requires NQEs, and involves two- and three-mode couplings. Fundamental mechanistic differences with respect to the well-known FR in molecular CO2 are addressed. This application represents the first quantum-mechanical, periodic description of FR in dry ice.
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Affiliation(s)
- Davide Mitoli
- Dipartimento di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Jefferson Maul
- Dipartimento di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Alessandro Erba
- Dipartimento di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
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22
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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] [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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23
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Franke PR, Stanton JF. Influence of fourth-order vibrational corrections on semi-experimental (reSE) structures of linear molecules. J Chem Phys 2024; 160:014102. [PMID: 38174791 DOI: 10.1063/5.0177694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
Semi-experimental structures (reSE) are derived from experimental ground state rotational constants combined with theoretical vibrational corrections. They permit a meaningful comparison with equilibrium structures based on high-level ab initio calculations. Typically, the vibrational corrections are evaluated with second-order vibrational perturbation theory (VPT2). The amount of error introduced by this approximation is generally thought to be small; however, it has not been thoroughly quantified. Herein, we assess the accuracy of theoretical vibrational corrections by extending the treatment to fourth order (VPT4) for a series of small linear molecules. Typical corrections to bond distances are on the order of 10-5 Å. Larger corrections, nearly 0.0002 Å, are obtained to the bond lengths of NCCN and CNCN. A borderline case is CCCO, which will likely require variational computations for a satisfactory answer. Treatment of vibrational effects beyond VPT2 will thus be important when one wishes to know bond distances confidently to four decimal places (10-4 Å). Certain molecules with shallow bending potentials, e.g., HOC+, are not amenable to a VPT2 description and are not improved by VPT4.
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Affiliation(s)
- Peter R Franke
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA
| | - John F Stanton
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA
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24
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De Vos J, Schröder B, Rauhut G. Comprehensive quantum chemical analysis of the (ro)vibrational spectrum of thiirane and its deuterated isotopologue. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 302:123083. [PMID: 37423098 DOI: 10.1016/j.saa.2023.123083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/11/2023]
Abstract
The (ro)vibrational spectra of thiirane, c-C2H4S, and its fully deuterated isotopologue, c-C2D4S, have been studied by means of vibrational configuration interaction theory, VCI, its incremental variant, iVCI, and subsequent variational rovibrational calculations, RVCI, which rely on multidimensional potential energy surfaces of coupled-cluster quality including up to four-mode coupling terms. Accurate geometrical parameters, fundamental vibrational transitions and first overtones, rovibrational spectra and rotational spectroscopic constants have been determined from these calculations and were compared with experimental results whenever available. A number of tentative misassignments in the vibrational spectra could be resolved and most results for the deuterated thiirane are high-level predictions, which may guide experiments to come. Besides this, a new implementation of infrared intensities within the iVCI framework has been tested for the transitions of the title compounds and are compared with results obtained from standard VCI calculations.
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Affiliation(s)
- John De Vos
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany; Department of Chemistry, Ghent University, Krijgslaan 281, 9000, Ghent, Belgium.
| | - Benjamin Schröder
- Institute for Physical Chemistry, University of Göttingen, Tammannstr. 6, 37077, Göttingen, Germany.
| | - Guntram Rauhut
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany.
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25
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Yang EL, Talbot JJ, Spencer RJ, Steele RP. Pitfalls in the n-mode representation of vibrational potentials. J Chem Phys 2023; 159:204104. [PMID: 38010326 DOI: 10.1063/5.0176612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 10/19/2023] [Indexed: 11/29/2023] Open
Abstract
Simulations of anharmonic vibrational motion rely on computationally expedient representations of the governing potential energy surface. The n-mode representation (n-MR)-effectively a many-body expansion in the space of molecular vibrations-is a general and efficient approach that is often used for this purpose in vibrational self-consistent field (VSCF) calculations and correlated analogues thereof. In the present analysis, a lack of convergence in many VSCF calculations is shown to originate from negative and unbound potentials at truncated orders of the n-MR expansion. For cases of strong anharmonic coupling between modes, the n-MR can both dip below the true global minimum of the potential surface and lead to effective single-mode potentials in VSCF that do not correspond to bound vibrational problems, even for bound total potentials. The present analysis serves mainly as a pathology report of this issue. Furthermore, this insight into the origin of VSCF non-convergence provides a simple, albeit ad hoc, route to correct the problem by "painting in" the full representation of groups of modes that exhibit these negative potentials at little additional computational cost. Somewhat surprisingly, this approach also reasonably approximates the results of the next-higher n-MR order and identifies groups of modes with particularly strong coupling. The method is shown to identify and correct problematic triples of modes-and restore SCF convergence-in two-mode representations of challenging test systems, including the water dimer and trimer, as well as protonated tropine.
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Affiliation(s)
- Emily L Yang
- Department of Chemistry, The University of Utah, 315 S 1400 E, Salt Lake City, Utah 84112, USA
- Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, Utah 84112, USA
| | - Justin J Talbot
- Department of Chemistry, University of California-Berkeley, 420 Latimer Hall, Berkeley, California 94720, USA
| | - Ryan J Spencer
- Department of Chemistry, The University of Utah, 315 S 1400 E, Salt Lake City, Utah 84112, USA
- Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, Utah 84112, USA
| | - Ryan P Steele
- Department of Chemistry, The University of Utah, 315 S 1400 E, Salt Lake City, Utah 84112, USA
- Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, Utah 84112, USA
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26
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Schweer SM, Gawrilow M, Nejad A, Suhm MA. Formic acid-methanol complexation vs. esterification: elusive pre-reactive species identified by vibrational spectroscopy. Phys Chem Chem Phys 2023; 25:29982-29992. [PMID: 37904580 DOI: 10.1039/d3cp04705a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
Vibrational spectra of the mixed dimer and the two mixed trimers of methanol and formic acid as well as some of their isotopologues are presented. Out of the eight expected OH stretching fundamentals of these three pre-reactive hydrogen-bonded complexes, the three modes mainly involving an acid OH group bound to the alcohol appear to be missing in the jet-cooled spectra despite a combination of infrared and Raman probing. A possibility of spectral overlap is discussed in the mixed dimer case, but largely discarded. The missing modes correspond to (fractional) concerted elongation of all engaged OH bonds, promoting synchronous degenerate proton transfer between the molecules. One other trimer mode is very tentatively attributed to a broad spectral feature, whereas all OH bonds contacting carbonyl groups can be unambiguously identified by four relatively narrow infrared absorptions. The spectral features are confirmed by vibrational perturbation theory and deviate in a subtle but systematic way from scaled harmonic predictions which were previously validated for the formic acid complex with a more acidic alcohol. Despite being exothermic and exergonic, ester formation can only be detected in the rarefied gas expansions after extended pre-mixture of the gases, which somewhat contrasts the recent microwave spectroscopic evidence of in situ ester formation and in particular the lack of pre-reactive complex signals.
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Affiliation(s)
- Sophie M Schweer
- Institute of Physical Chemistry, University of Goettingen, Tammannstr. 6, 37077 Goettingen, Germany.
| | - Maxim Gawrilow
- Institute of Physical Chemistry, University of Goettingen, Tammannstr. 6, 37077 Goettingen, Germany.
| | - Arman Nejad
- Institute of Physical Chemistry, University of Goettingen, Tammannstr. 6, 37077 Goettingen, Germany.
| | - Martin A Suhm
- Institute of Physical Chemistry, University of Goettingen, Tammannstr. 6, 37077 Goettingen, Germany.
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27
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Tsybizova A, Fritsche L, Miloglyadova L, Kräutler B, Chen P. Cryogenic Ion Vibrational Predissociation (CIVP) Spectroscopy of Aryl Cobinamides in the Gas Phase: How Good Are the Calculations for Vitamin B 12 Derivatives? J Am Chem Soc 2023; 145:19561-19570. [PMID: 37656981 PMCID: PMC10510309 DOI: 10.1021/jacs.3c03001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Indexed: 09/03/2023]
Abstract
Aryl corrins represent a novel class of designed B12 derivatives with biological properties of "antivitamins B12". In our previous study, we experimentally determined bond strength in a series of aryl-corrins by the threshold collision-induced dissociation experiments (T-CID) and compared the measured bond dissociation energies (BDEs) with those calculated with density functional theory (DFT). We found that the BDEs are modulated by the side chains around the periphery of the corrin unit. Given that aryl cobinamides have many side chains that increase their conformational space and that the question of a specific structure, measured in the gas phase, was important for further evaluation of our T-CID experiment, we proceeded to analyze structural properties of aryl cobinamides using cryogenic ion vibrational predissociation (CIVP) spectroscopy, static DFT, and Born-Oppenheimer molecular dynamic (BOMD) simulations. We found that none of the examined DFT models could reproduce the CIVP spectra convincingly; both "static" DFT calculations and "dynamic" BOMD simulations provide a surprisingly poor representation of the vibrational spectra, specifically of the number, position, and intensity of bands assigned to hydrogen-bonded versus non-hydrogen-bonded NH and OH moieties. We conclude that, for a flexible molecule with ca. 150 atoms, more accurate approaches are needed before definitive conclusions about computed properties, specifically the structure of the ground-state conformer, may be made.
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Affiliation(s)
- Alexandra Tsybizova
- Laboratorium
für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Lukas Fritsche
- Laboratorium
für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Larisa Miloglyadova
- Laboratorium
für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Bernhard Kräutler
- Institute
of Organic Chemistry, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Peter Chen
- Laboratorium
für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
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28
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Nelson PM, Glick ZL, Sherrill CD. Approximating large-basis coupled-cluster theory vibrational frequencies using focal-point approximations. J Chem Phys 2023; 159:094104. [PMID: 37655773 DOI: 10.1063/5.0168608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 08/09/2023] [Indexed: 09/02/2023] Open
Abstract
The focal-point approximation can be used to estimate a high-accuracy, slow quantum chemistry computation by combining several lower-accuracy, faster computations. We examine the performance of focal-point methods by combining second-order Møller-Plesset perturbation theory (MP2) with coupled-cluster singles, doubles, and perturbative triples [CCSD(T)] for the calculation of harmonic frequencies and that of fundamental frequencies using second-order vibrational perturbation theory (VPT2). In contrast to standard CCSD(T), the focal-point CCSD(T) method approaches the complete basis set (CBS) limit with only triple-ζ basis sets for the coupled-cluster portion of the computation. The predicted harmonic and fundamental frequencies were compared with the experimental values for a set of 20 molecules containing up to six atoms. The focal-point method combining CCSD(T)/aug-cc-pV(T + d)Z with CBS-extrapolated MP2 has mean absolute errors vs experiment of only 7.3 cm-1 for the fundamental frequencies, which are essentially the same as the mean absolute error for CCSD(T) extrapolated to the CBS limit using the aug-cc-pV(Q + d)Z and aug-cc-pV(5 + d)Z basis sets. However, for H2O, the focal-point procedure requires only 3% of the computation time as the extrapolated CCSD(T) result, and the cost savings will grow for larger molecules.
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Affiliation(s)
- Philip M Nelson
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
| | - Zachary L Glick
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
| | - C David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
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29
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Nejad A, Li X, Zhu T, Liu Y, Duan C. Mid-infrared Laser Spectroscopy of Jet-Cooled Formic Acid Trimer: Mode-Dependent Line Broadening in the C-O Stretching Region. J Phys Chem Lett 2023; 14:7795-7801. [PMID: 37616473 PMCID: PMC10786437 DOI: 10.1021/acs.jpclett.3c01860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 08/17/2023] [Indexed: 08/26/2023]
Abstract
Building on recent progress in the vibrational spectroscopy of the formic acid trimer, we present the first high-resolution measurements of the jet-cooled laser absorption spectrum of (HCOOH)3. The spectra of the lowest- and highest-frequency C-O stretching fundamentals are analyzed whereas the third band is not observed, complicated by monomer and dimer absorptions at 1219 cm-1 (8.2 μm). Vibration-rotation parameters are obtained for the band at 1172.31512(68) cm-1 whereas the C-O stretch at 1246.33(5) cm-1 exhibits a significantly larger breadth, allowing only resolution of the coarse PQR structure. Vibrational predissociation can be ruled out, and intramolecular vibrational redistribution mechanisms are discussed, particularly coupling to the concerted proton exchange within the cyclic dimer subunit. Ultimately, the question remains open. The prospects of high-resolution measurements of other trimer bands or isotope substitution experiments, which might assist in revealing the mode-specificity of the underlying broadening mechanisms, are discussed.
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Affiliation(s)
- Arman Nejad
- Institute
of Physical Chemistry, Georg-August University
of Göttingen, Tammannstraße 6, Göttingen 37077, Germany
| | - Xiang Li
- College
of Physical Science and Technology, Central
China Normal University, Wuhan 430079, China
| | - Tianxin Zhu
- College
of Physical Science and Technology, Central
China Normal University, Wuhan 430079, China
| | - Yun Liu
- College
of Physical Science and Technology, Central
China Normal University, Wuhan 430079, China
| | - Chuanxi Duan
- College
of Physical Science and Technology, Central
China Normal University, Wuhan 430079, China
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30
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Sharma D, Roy TK. Accuracy of Different Electronic Basis Set Families for Anharmonic Molecular Vibrations: A Comprehensive Benchmark Study. J Phys Chem A 2023; 127:7132-7147. [PMID: 37603414 DOI: 10.1021/acs.jpca.3c02874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
In this work, the accuracy and convergence of different electronic basis set families for the computation of anharmonic molecular vibrational spectroscopic calculations are benchmarked. A series of 39 different basis sets from different families following their hierarchy are assessed on VSCF and VSCF-PT2 algorithms with commonly used MP2 and DFT based B3LYP-D potentials for a set of molecular systems. Such an effort has been validated in a previous work ( J. Phys. Chem. A 2020, 124, 9203-9221) with split-valence basis sets for fundamentals and intensities. Here, fundamental transitions, vibrationally excited states, and intensities are compared with the experimental data to estimate the accuracy for a series of Jensen, Dunning, Calendar, Karlsruhe, and Sapporo basis set families. The convergence of basis sets are also compared with the large ANO basis set. Comprehensive statistical error analysis in terms of accuracy and precision was carried out to assess the performance of each basis set. It is observed that the improvement for the calculated harmonic and anharmonic values from the smaller basis sets to the medium (i.e., triple-ξ) is considerable. Beyond this, from medium to large basis sets, the convergence is slow and mostly posits nearly converged values. Basis sets with and without diffuse functions offer characteristically different accuracies and convergence patterns. Finally, recommendations are given on the choice of basis set chosen as black-box which can balance between accuracy and computational time, estimation of the errors, and their selections especially for large molecules.
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Affiliation(s)
- Dhiksha Sharma
- Department of Chemistry and Chemical Sciences, Central University of Jammu, Rahya-Suchani (Bagla), Jammu, J&K 181143 India
| | - Tapta Kanchan Roy
- Department of Chemistry and Chemical Sciences, Central University of Jammu, Rahya-Suchani (Bagla), Jammu, J&K 181143 India
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31
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Zhanserkeev AA, Yang EL, Steele RP. Accelerating Anharmonic Spectroscopy Simulations via Local-Mode, Multilevel Methods. J Chem Theory Comput 2023; 19:5572-5585. [PMID: 37555634 DOI: 10.1021/acs.jctc.3c00589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
Ab initio computer simulations of anharmonic vibrational spectra provide nuanced insight into the vibrational behavior of molecules and complexes. The computational bottleneck in such simulations, particularly for ab initio potentials, is often the generation of mode-coupling potentials. Focusing specifically on two-mode couplings in this analysis, the combination of a local-mode representation and multilevel methods is demonstrated to be particularly symbiotic. In this approach, a low-level quantum chemistry method is employed to predict the pairwise couplings that should be included at the target level of theory in vibrational self-consistent field (and similar) calculations. Pairs that are excluded by this approach are "recycled" at the low level of theory. Furthermore, because this low-level pre-screening will eventually become the computational bottleneck for sufficiently large chemical systems, distance-based truncation is applied to these low-level predictions without substantive loss of accuracy. This combination is demonstrated to yield sub-wavenumber fidelity with reference vibrational transitions when including only a small fraction of target-level couplings; the overhead of predicting these couplings, particularly when employing distance-based, local-mode cutoffs, is a trivial added cost. This combined approach is assessed on a series of test cases, including ethylene, hexatriene, and the alanine dipeptide. Vibrational self-consistent field (VSCF) spectra were obtained with an RI-MP2/cc-pVTZ potential for the dipeptide, at approximately a 5-fold reduction in computational cost. Considerable optimism for increased accelerations for larger systems and higher-order couplings is also justified, based on this investigation.
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Affiliation(s)
- Asylbek A Zhanserkeev
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Emily L Yang
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Ryan P Steele
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
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32
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Boychuk BTA, Wetmore SD. Assessment of Density Functional Theory Methods for the Structural Prediction of Transition and Post-Transition Metal-Nucleic Acid Complexes. J Chem Theory Comput 2023. [PMID: 37399186 DOI: 10.1021/acs.jctc.3c00127] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2023]
Abstract
Understanding the structure of metal-nucleic acid systems is important for many applications such as the design of new pharmaceuticals, metal detection platforms, and nanomaterials. Herein, we explore the ability of 20 density functional theory (DFT) functionals to reproduce the crystal structure geometry of transition and post-transition metal-nucleic acid complexes identified in the Protein Data Bank and Cambridge Structural Database. The environmental extremes of the gas phase and implicit water were considered, and analysis focused on the global and inner coordination geometry, including the coordination distances. Although gas-phase calculations were unable to describe the structure of 12 out of the 53 complexes in our test set regardless of the DFT functional considered, accounting for the broader environment through implicit solvation or constraining the model truncation points to crystallographic coordinates generally afforded agreement with the experimental structure, suggesting that functional performance for these systems is likely due to the models rather than the methods. For the remaining 41 complexes, our results show that the reliability of functionals depends on the metal identity, with the magnitude of error varying across the periodic table. Furthermore, minimal changes in the geometries of these metal-nucleic acid complexes occur upon use of the Stuttgart-Dresden effective core potential and/or inclusion of an implicit water environment. The overall top three performing functionals are ωB97X-V, ωB97X-D3(BJ), and MN15, which reliably describe the structure of a broad range of metal-nucleic acid systems. Other suitable functionals include MN15-L, which is a cheaper alternative to MN15, and PBEh-3c, which is commonly used in QM/MM calculations of biomolecules. In fact, these five methods were the only functionals tested to reproduce the coordination sphere of Cu2+-containing complexes. For metal-nucleic acid systems that do not contain Cu2+, ωB97X and ωB97X-D are also suitable choices. These top-performing methods can be utilized in future investigations of diverse metal-nucleic acid complexes of relevance to biology and material science.
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Affiliation(s)
- Briana T A Boychuk
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB T1K 3M4, Canada
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33
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Finney JM, Choi TH, Huchmala RM, Heindel JP, Xantheas SS, Jordan KD, McCoy AB. Isotope Effects in the Zundel-Eigen Isomerization of H +(H 2O) 6. J Phys Chem Lett 2023; 14:4666-4672. [PMID: 37167485 DOI: 10.1021/acs.jpclett.3c00952] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The isomerization pathway between the energetically low-lying Zundel and Eigen isomers of the protonated water hexamer was investigated using high-level ab initio calculations including a treatment of zero-point corrections. On the basis of these calculations, the Zundel-Eigen isomerization was found to proceed through a stable intermediate isomer, which consists of a four-membered ring with two single acceptor water molecules. The inclusion of vibrational zero-point energy is shown to be important for accurately establishing the relative energies of the three relevant isomers involved in the Zundel-Eigen isomerization. Diffusion Monte Carlo calculations including anharmonic vibrational effects show that all three isomers of H+(H2O)6 and D+(D2O)6 have well-defined structures. The energetic ordering of the three isomers changes upon deuteration. The implications of these results for the vibrational spectra of H+(H2O)6 and D+(D2O)6 are also discussed.
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Affiliation(s)
- Jacob M Finney
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Tae Hoon Choi
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Rachel M Huchmala
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Joseph P Heindel
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Sotiris S Xantheas
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
- Advanced Computing, Mathematics and Data Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MS J7-10, Richland, Washington 99352, United States
| | - Kenneth D Jordan
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Anne B McCoy
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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34
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Neumark DM. Spectroscopy of Radicals, Clusters, and Transition States Using Slow Electron Velocity-Map Imaging of Cryogenically Cooled Anions. J Phys Chem A 2023; 127:4207-4223. [PMID: 37094039 DOI: 10.1021/acs.jpca.3c01537] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Slow electron velocity-map imaging of cryogenically cooled anions (cryo-SEVI) is a high-resolution variant of anion photoelectron spectroscopy that has been applied with considerable success over the years to the study of radicals, size-selected clusters, and transition states for unimolecular and bimolecular reactions. Cryo-SEVI retains the versatility of conventional anion photoelectron spectroscopy while offering sub-meV resolution, thereby enabling the resolution of vibrational structure in the photoelectron spectra of complex anions. This Feature Article describes recent experiments in our laboratory using cryo-SEVI, including a new research direction in which anions are vibrationally pre-excited with an infrared laser pulse prior to photodetachment.
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Affiliation(s)
- Daniel M Neumark
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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35
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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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36
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Barone V, Fusè M. Accurate Structures and Spectroscopic Parameters of Phenylalanine and Tyrosine in the Gas Phase: A Joint Venture of DFT and Composite Wave-Function Methods. J Phys Chem A 2023; 127:3648-3657. [PMID: 37052318 PMCID: PMC10150396 DOI: 10.1021/acs.jpca.3c01174] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
A general strategy for the accurate computation of conformational and spectroscopic properties of flexible molecules in the gas phase is applied to two representative proteinogenic amino acids with aromatic side chains, namely, phenylalanine and tyrosine. The main features of all the most stable conformers predicted by this computational strategy closely match those of the species detected in microwave and infrared experiments. Together with their intrinsic interest, the accuracy of the results obtained with reasonable computer times paves the route for accurate investigations of other flexible bricks of life.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Marco Fusè
- DMMT-sede Europa, Università di Brescia, Viale Europa 11, 25121 Brescia, Italy
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37
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Barone V, Fusè M, Aguado R, Potenti S, León I, Alonso ER, Mata S, Lazzari F, Mancini G, Spada L, Gualandi A, Cozzi PG, Puzzarini C, Alonso JL. Bringing Machine-Learning Enhanced Quantum Chemistry and Microwave Spectroscopy to Conformational Landscape Exploration: the Paradigmatic Case of 4-Fluoro-Threonine. Chemistry 2023; 29:e202203990. [PMID: 36734519 DOI: 10.1002/chem.202203990] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/02/2023] [Accepted: 02/02/2023] [Indexed: 02/04/2023]
Abstract
A combined experimental and theoretical study has been carried out on 4-fluoro-threonine, the only naturally occurring fluorinated amino acid. Fluorination of the methyl group significantly increases the conformational complexity with respect to the parent amino acid threonine. The conformational landscape has been characterized in great detail, with special attention given to the inter-conversion pathways between different conformers. This led to the identification of 13 stable low-energy minima. The equilibrium population of so many conformers produces a very complicated and congested rotational spectrum that could be assigned through a strategy that combines several levels of quantum chemical calculations with the principles of machine learning. Twelve conformers out of 13 could be experimentally characterized. The results obtained from the analysis of the intra-molecular interactions can be exploited to accurately model fluorine-substitution effects in biomolecules.
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Affiliation(s)
- V Barone
- SMART Laboratory, Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - M Fusè
- SMART Laboratory, Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - R Aguado
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia Parque Cientifico UVa, Universidad de Valladolid, 47005, Valladolid, Spain
| | - S Potenti
- SMART Laboratory, Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126, Pisa, Italy
- Dipartimento di "Chimica Giacomo Ciamician", University of Bologna, via F. Selmi 2, 40126, Bologna, Italy
| | - I León
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia Parque Cientifico UVa, Universidad de Valladolid, 47005, Valladolid, Spain
| | - E R Alonso
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia Parque Cientifico UVa, Universidad de Valladolid, 47005, Valladolid, Spain
| | - S Mata
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia Parque Cientifico UVa, Universidad de Valladolid, 47005, Valladolid, Spain
| | - F Lazzari
- SMART Laboratory, Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - G Mancini
- SMART Laboratory, Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - L Spada
- SMART Laboratory, Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - A Gualandi
- Dipartimento di "Chimica Giacomo Ciamician", University of Bologna, via F. Selmi 2, 40126, Bologna, Italy
| | - P G Cozzi
- Dipartimento di "Chimica Giacomo Ciamician", University of Bologna, via F. Selmi 2, 40126, Bologna, Italy
| | - C Puzzarini
- Dipartimento di "Chimica Giacomo Ciamician", University of Bologna, via F. Selmi 2, 40126, Bologna, Italy
| | - J L Alonso
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia Parque Cientifico UVa, Universidad de Valladolid, 47005, Valladolid, Spain
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Franke PR, Stanton JF. Rotamers of Methanediol: Composite Ab Initio Predictions of Structures, Frequencies, and Rovibrational Constants. J Phys Chem A 2023; 127:924-937. [PMID: 36657011 DOI: 10.1021/acs.jpca.2c06686] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Geminal diols are known to be important intermediates in atmospheric ozonolysis and the aerosol cycle. Recently, the simplest member of this class, methanediol, was interrogated in the gas phase with infrared spectroscopy. To aid in future spectroscopic investigations of methanediol, including in the interstellar medium, we report fundamental frequencies and rovibrational constants for the two rotamers of this molecule using ab initio composite methods along with vibrational perturbation theory. Sensitivity of the predictions to the level of theory and the treatment of anharmonic resonances are carefully assessed. The OH stretching harmonic frequencies of both rotamers are particularly sensitive to the level of theory. The CH stretches of the Cs rotamer are sensitive to the treatment of anharmonic resonances with VPT2-based effective Hamiltonian models. Equilibrium bond distances and harmonic frequencies are converged conservatively to within 0.0005 Å and 3 cm-1, respectively. The effect of tunneling on the rotational constants is investigated with a 2D variational calculation, based on a relaxed hydroxyl torsional potential energy surface. Tunneling is found to be negligible in the lower energy C2 rotamer but should modify the rotational constants of the Cs rotamer on the order of MHz, giving rise to rotational line splittings of the same order. The rovibrational constants of the Cs rotamer are dominated by hydroxyl torsional effects, and here we see evidence for the breakdown of vibrational perturbation theory.
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Affiliation(s)
- Peter R Franke
- Department of Chemistry, University of Florida, Gainesville, Florida32611, United States
| | - John F Stanton
- Department of Chemistry, University of Florida, Gainesville, Florida32611, United States
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39
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Barone V, Fusè M, Lazzari F, Mancini G. Benchmark Structures and Conformational Landscapes of Amino Acids in the Gas Phase: A Joint Venture of Machine Learning, Quantum Chemistry, and Rotational Spectroscopy. J Chem Theory Comput 2023; 19:1243-1260. [PMID: 36731119 PMCID: PMC9979611 DOI: 10.1021/acs.jctc.2c01143] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The accurate characterization of prototypical bricks of life can strongly benefit from the integration of high resolution spectroscopy and quantum mechanical computations. We have selected a number of representative amino acids (glycine, alanine, serine, cysteine, threonine, aspartic acid and asparagine) to validate a new computational setup rooted in quantum-chemical computations of increasing accuracy guided by machine learning tools. Together with low-lying energy minima, the barriers ruling their interconversion are evaluated in order to unravel possible fast relaxation paths. Vibrational and thermal effects are also included in order to estimate relative free energies at the temperature of interest in the experiment. The spectroscopic parameters of all the most stable conformers predicted by this computational strategy, which do not have low-energy relaxation paths available, closely match those of the species detected in microwave experiments. Together with their intrinsic interest, these accurate results represent ideal benchmarks for more approximate methods.
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Affiliation(s)
- Vincenzo Barone
- Scuola
Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy,
| | - Marco Fusè
- DMMT-sede
Europa, Universitá di Brescia, viale Europa 11, 25121 Brescia, Italy
| | - Federico Lazzari
- Scuola
Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Giordano Mancini
- Scuola
Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
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40
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Baptista L, de Almeida AA. Phosphine Reactivity and Its Implications for Pyrolysis Experiments and Astrochemistry. J Phys Chem A 2023; 127:1000-1012. [PMID: 36661302 DOI: 10.1021/acs.jpca.2c07782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Despite the importance of phosphorus-bearing molecules for life and their abundance outside Earth, the chemistry of those compounds still is poorly described. The present study investigates phosphine (PH3) decomposition and formation pathways. The reactions studied include phosphine thermal dissociation, conversion into PO(2Π), PN(1Σ+), and reactions in the presence of H2O+. The thermodynamic and rate coefficients of all reactions are calculated in the range of 50-2000 K considering the CCSD(T)/6-311G(3df,3pd)//ωB97xD/6-311G(3df,3pd) electronic structure data. The rate coefficients were calculated by RRKM and semiclassical transition-state theory (SCTST). According to our results, PH3 is stable to thermal decomposition at T < 100 K and can be formed promptly by a reaction network involving PH(3Σ-), PO(2Π), and PN(1Σ+). In the presence of radiation or ions, PH3 is readily decomposed. For this reason, it should be mainly associated with dust grains or icy mantles to be observed under the physical conditions prevailing in the interstellar medium (ISM). The intersystem crossing associated with the dissociation of the isomers PON, NPO, and PNO is accessed by multireference methods, and its importance for the gas-phase PH3 formation/destruction is discussed. Also, the implications of the present outcomes on phosphorus astrochemistry are highlighted.
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Affiliation(s)
- Leonardo Baptista
- Departamento de Química e Ambiental, Campus Regional de Resende, Universidade do Estado do Rio de Janeiro, Faculdade de Tecnologia, Rodovia Presidente Dutra km 298, Rio de Janeiro, RJCEP 27537-000, Brazil
| | - Amaury A de Almeida
- Departamento de Astronomia, Cidade Universitária, Universidade de São Paulo, Instituto de Astronomia, Geofísica e Ciências Atmosféricas, Rua do Matão 1226, São Paulo, SPCEP 05508-090, Brazil
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41
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Fayaz A, Banik S, Kanchan Roy T. The importance of electron correlations on vibrational anharmonicities and potential energy surfaces. COMPUT THEOR CHEM 2023. [DOI: 10.1016/j.comptc.2023.114059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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42
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Zdanovskaia MA, Franke PR, Esselman BJ, Billinghurst BE, Zhao J, Stanton JF, Woods RC, McMahon RJ. Vibrationally excited states of 1H- and 2H-1,2,3-triazole isotopologues analyzed by millimeter-wave and high-resolution infrared spectroscopy with approximate state-specific quartic distortion constants. J Chem Phys 2023; 158:044301. [PMID: 36725515 DOI: 10.1063/5.0137340] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
In this work, we present the spectral analysis of 1H- and 2H-1,2,3-triazole vibrationally excited states alongside provisional and practical computational predictions of the excited-state quartic centrifugal distortion constants. The low-energy fundamental vibrational states of 1H-1,2,3-triazole and five of its deuteriated isotopologues ([1-2H]-, [4-2H]-, [5-2H]-, [4,5-2H]-, and [1,4,5-2H]-1H-1,2,3-triazole), as well as those of 2H-1,2,3-triazole and five of its deuteriated isotopologues ([2-2H]-, [4-2H]-, [2,4-2H]-, [4,5-2H]-, and [2,4,5-2H]-2H-1,2,3-triazole), are studied using millimeter-wave spectroscopy in the 130-375 GHz frequency region. The normal and [2-2H]-isotopologues of 2H-1,2,3-triazole are also analyzed using high-resolution infrared spectroscopy, determining the precise energies of three of their low-energy fundamental states. The resulting spectroscopic constants for each of the vibrationally excited states are reported for the first time. Coupled-cluster vibration-rotation interaction constants are compared with each of their experimentally determined values, often showing agreement within 500 kHz. Newly available coupled-cluster predictions of the excited-state quartic centrifugal distortion constants based on fourth-order vibrational perturbation theory are benchmarked using a large number of the 1,2,3-triazole tautomer isotopologues and vibrationally excited states studied.
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Affiliation(s)
- Maria A Zdanovskaia
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Peter R Franke
- Quantum Theory Project, Departments of Physics and Chemistry, University of Florida, Gainesville, Florida 32611, USA
| | - Brian J Esselman
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Brant E Billinghurst
- Canadian Light Source, Inc., University of Saskatchewan, Saskatoon, Saskatchewan S7N 2V3, Canada
| | - Jianbao Zhao
- Canadian Light Source, Inc., University of Saskatchewan, Saskatoon, Saskatchewan S7N 2V3, Canada
| | - John F Stanton
- Quantum Theory Project, Departments of Physics and Chemistry, University of Florida, Gainesville, Florida 32611, USA
| | - R Claude Woods
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Robert J McMahon
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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43
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Barone V, Di Grande S, Puzzarini C. Toward Accurate yet Effective Computations of Rotational Spectroscopy Parameters for Biomolecule Building Blocks. MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28020913. [PMID: 36677970 PMCID: PMC9863398 DOI: 10.3390/molecules28020913] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 01/01/2023] [Accepted: 01/12/2023] [Indexed: 01/19/2023]
Abstract
The interplay of high-resolution rotational spectroscopy and quantum-chemical computations plays an invaluable role in the investigation of biomolecule building blocks in the gas phase. However, quantum-chemical methods suffer from unfavorable scaling with the dimension of the system under consideration. While a complete characterization of flexible systems requires an elaborate multi-step strategy, in this work, we demonstrate that the accuracy obtained by quantum-chemical composite approaches in the prediction of rotational spectroscopy parameters can be approached by a model based on density functional theory. Glycine and serine are employed to demonstrate that, despite its limited cost, such a model is able to predict rotational constants with an accuracy of 0.3% or better, thus paving the way toward the accurate characterization of larger flexible building blocks of biomolecules.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-50126 Pisa, Italy
- Correspondence: (V.B.); (C.P.)
| | - Silvia Di Grande
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-50126 Pisa, Italy
- Scuola Superiore Meridionale, Largo San Marcellino 10, I-80138 Napoli, Italy
| | - Cristina Puzzarini
- Rotational and Computational Spectroscopy Lab, Department of Chemistry “Giacomo Ciamician”, University of Bologna, Via F. Selmi 2, I-40126 Bologna, Italy
- Correspondence: (V.B.); (C.P.)
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44
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Kelemen AK, Luber S. On the vibrations of formic acid predicted from first principles. Phys Chem Chem Phys 2022; 24:28109-28120. [PMID: 36385362 PMCID: PMC9710498 DOI: 10.1039/d2cp04417j] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/09/2022] [Indexed: 08/26/2023]
Abstract
In this article, we review recent first principles, anharmonic studies on the molecular vibrations of gaseous formic acid in its monomer form. Transitions identified as fundamentals for both cis- and trans form reported in these studies are collected and supported by results from high-resolution experiments. Attention is given to the effect of coordinate coupling on the convergence of the computed vibrational states.
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Affiliation(s)
- Anna Klára Kelemen
- Department of Chemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Sandra Luber
- Department of Chemistry, University of Zurich, CH-8057 Zurich, Switzerland.
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45
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Yang Q, Bloino J. An Effective and Automated Processing of Resonances in Vibrational Perturbation Theory Applied to Spectroscopy. J Phys Chem A 2022; 126:9276-9302. [DOI: 10.1021/acs.jpca.2c06460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Affiliation(s)
- Qin Yang
- Faculty of Science, Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126Pisa, Italy
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610Prague, Czech Republic
| | - Julien Bloino
- Faculty of Science, Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126Pisa, Italy
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46
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Kitzmiller NL, Wolf ME, Turney JM, Schaefer HF. Toward the Observation of the Tin and Lead Analogs of Formaldehyde. J Phys Chem A 2022; 126:7930-7937. [PMID: 36264195 DOI: 10.1021/acs.jpca.2c05964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Heavy aldehyde and ketone analogues, R2X═O (X = Si, Ge, Sn, or Pb), differ from their R2C═O counterparts due to their greater tendency to oligeramize as the X═O bond polarity increases as one goes down the periodic table. To date, H2Sn═O and H2Pb═O have eluded experimental detection. Herein we present the most rigorous theoretical study to date on these structures, providing CCSD(T)/pwCVTZ fundamental frequencies computed on CCSD(T)/CBS optimized structures for the H2X═O (X = Sn, Pb) potential energy surface. The focal point approach is employed to produce the CCSDTQ/CBS relative energies. For the Sn and Pb structures, the carbene-like cis-HXOH was the global minima, with the trans species being less than 0.6 and 1.1 kcal mol-1 above the cis structures, respectively. The formaldehyde-like H2X═O structure is in an energy well of at least 34.8 and 25.4 kcal mol-1 for Sn and Pb, respectively. Our results provide guidance for future work that may detect H2Sn═O or H2Pb═O for the first time.
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Affiliation(s)
- Nathaniel L Kitzmiller
- The Center for Computational Quantum Chemistry, Department of Chemistry, University of Georgia, Athens, Georgia30602, United States
| | - Mark E Wolf
- The Center for Computational Quantum Chemistry, Department of Chemistry, University of Georgia, Athens, Georgia30602, United States
| | - Justin M Turney
- The Center for Computational Quantum Chemistry, Department of Chemistry, University of Georgia, Athens, Georgia30602, United States
| | - Henry F Schaefer
- The Center for Computational Quantum Chemistry, Department of Chemistry, University of Georgia, Athens, Georgia30602, United States
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47
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McCoy AB, Boyer MA. Exploring Expansions of the Potential and Dipole Surfaces Used for Vibrational Perturbation Theory. J Phys Chem A 2022; 126:7242-7249. [PMID: 36194755 DOI: 10.1021/acs.jpca.2c05792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A scheme for evaluating expansions of the potential and dipole moment surfaces for vibrational perturbation theory is described. The approach is based on numerical differentiation of the Hessian in the coordinates of interest. It is shown that performing these calculations in internal coordinates generates expansions that are transferable among isotopologues of the molecule of interest. Additionally, re-expressing the expansion of the potential in terms of functions of the internal coordinates, for example, cosines of angles or exponential functions of the bond length displacements, provides expansions that can be used for higher-order perturbation theory calculations. The approach is explored and the results are discussed for water, HOD, ammonia, isomers of HNO3, and halogenated methane.
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Affiliation(s)
- Anne B McCoy
- Department of Chemistry, University of Washington, Seattle, Washington98195, United States
| | - Mark A Boyer
- Department of Chemistry, University of Washington, Seattle, Washington98195, United States
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48
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King KE, Franke PR, Pullen GT, Schaefer HF, Douberly GE. Helium Droplet Infrared Spectroscopy of the Butyl Radicals. J Chem Phys 2022; 157:084311. [DOI: 10.1063/5.0102287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Butyl radicals ( n-, s-, i-,} and tert-butyl) are formed from the pyrolysis of stable precursors (1-pentyl nitrite, 2-methyl-1-butyl nitrite, isopentyl nitrite, and azo- tert-butane, respectively). The radicals are doped into a beam of liquid helium droplets and probed with infrared action spectroscopy from 2700-3125 cm-1, allowing for a low temperature measurement of the CH stretching region. The presence of anharmonic resonance polyads in the 2800-3000 cm-1 region complicates its interpretation. To facilitate spectral assignment, the anharmonic resonances are modeled with two model Hamiltonian approaches that explicitly couple CH stretch fundamentals to HCH bend overtones and combinations: a VPT2+K normal mode model based on CCSD(T) quartic force fields and a semi-empirical local mode model. Both of these computational methods provide generally good agreement with the experimental spectra.
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Affiliation(s)
- Kale E King
- University of Georgia, United States of America
| | | | | | - Henry F. Schaefer
- Center for Computational Quantum Chemistry, University of Georgia, United States of America
| | - Gary E. Douberly
- Department of Chemistry, University of Georgia, United States of America
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49
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Tyuterev V, Tashkun S, Rey M, Nikitin A. High-order contact transformations of molecular Hamiltonians: general approach, fast computational algorithm and convergence of ro-vibrational polyad models. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2096140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Vladimir Tyuterev
- Groupe de Spectrométrie Moléculaire et Atmosphérique, Université de Reims, Reims, France
- Laboratory of Molecular Quantum Mechanics and Radiative Transfer, Tomsk State University, Tomsk, Russia
| | - Sergey Tashkun
- Laboratory of Theoretical Spectroscopy, V.E. Zuev Institute of Atmospheric Optics, Siberian Branch, Russian Academy of Sciences, Tomsk, Russia
| | - Michael Rey
- Groupe de Spectrométrie Moléculaire et Atmosphérique, Université de Reims, Reims, France
| | - Andrei Nikitin
- Laboratory of Theoretical Spectroscopy, V.E. Zuev Institute of Atmospheric Optics, Siberian Branch, Russian Academy of Sciences, Tomsk, Russia
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50
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Meyer KS, Westerfield JH, Johansen SL, Keane J, Wannenmacher AC, Crabtree KN. Rotational and Vibrational Spectra of the Pyridyl Radicals: A Coupled-Cluster Study. J Phys Chem A 2022; 126:3185-3197. [PMID: 35549287 DOI: 10.1021/acs.jpca.2c01761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pyridyl is a prototypical nitrogen-containing aromatic radical that may be a key intermediate in the formation of nitrogen-containing aromatic molecules under astrophysical conditions. On meteorites, a variety of complex molecules with nitrogen-containing rings have been detected with nonterrestrial isotopic abundances, and larger nitrogen-containing polycyclic aromatic hydrocarbons (PANHs) have been proposed to be responsible for certain unidentified infrared emission bands in the interstellar medium. In this work, the three isomers of pyridyl (2-, 3-, and 4-pyridyl) have been investigated with coupled cluster methods. For each species, structures were optimized at the CCSD(T)/cc-pwCVTZ level of theory and force fields were calculated at the CCSD(T)/ANO0 level of theory. Second-order vibrational perturbation theory (VPT2) was used to derive anharmonic vibrational frequencies and vibrationally corrected rotational constants, and resonances among vibrational states below 3500 cm-1 were treated variationally with the VPT2+K method. The results yield a complete set of spectroscopic parameters needed to simulate the pure rotational spectrum of each isomer, including electron-spin, spin-spin, and nuclear hyperfine interactions, and the calculated hyperfine parameters agree well with the limited available data from electron paramagnetic resonance spectroscopy. For the handful of experimentally measured vibrational frequencies determined from photoelectron spectroscopy and matrix isolation spectroscopy, the typical agreement is comparable to experimental uncertainty. The predicted parameters for rotational spectroscopy reported here can guide new experimental investigations into the yet-unobserved rotational spectra of these radicals.
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Affiliation(s)
- Kelly S Meyer
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - John H Westerfield
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Sommer L Johansen
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Jasmine Keane
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Anna C Wannenmacher
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Kyle N Crabtree
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
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