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Alessandrini S, Melosso M, Bizzocchi L, Barone V, Puzzarini C. The Semiexperimental Approach at Work: Equilibrium Structure of Radical Species. J Phys Chem A 2024. [PMID: 38991181 DOI: 10.1021/acs.jpca.4c01758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
The so-called semiexperimental (SE) approach is a powerful technique for obtaining highly accurate equilibrium structures for isolated systems. This Featured Article describes its extension to open-shell species, thus providing the first systematic investigation on radical equilibrium geometries to be used for benchmarking purposes. The small yet significant database obtained demonstrates that there is no reduction in accuracy when moving from closed-shell species to radicals. We also provide an extension of the applicability of the SE approach to medium-/large-sized radicals by exploiting the so-called "Lego-brick" approach, which is based on the assumption that a molecular system can be seen as formed by smaller fragments for which the SE equilibrium structure is available. In this Featured Article we show that this model can be successfully applied also to open-shell species.
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Affiliation(s)
- Silvia Alessandrini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, I-40126 Bologna, Italy
| | - Mattia Melosso
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, I-40126 Bologna, Italy
| | - Luca Bizzocchi
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, I-40126 Bologna, Italy
| | | | - Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, I-40126 Bologna, Italy
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2
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Puzzarini C, Alessandrini S. Carbamic acid and its dimer: A computational study. J Comput Chem 2024. [PMID: 38970400 DOI: 10.1002/jcc.27442] [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: 02/15/2024] [Revised: 05/15/2024] [Accepted: 05/17/2024] [Indexed: 07/08/2024]
Abstract
A recent work by Marks et al. on the formation of carbamic acid in NH3 $$ {}_3 $$ -CO2 $$ {}_2 $$ interstellar ices pointed out its stability in the gas phase and the concomitant production of its dimer. Prompted by these results and the lack of information on these species, we have performed an accurate structural, energetic and spectroscopic investigation of carbamic acid and its dimer. For the former, the structural and spectroscopic characterization employed composite schemes based on coupled cluster (CC) calculations that account for the extrapolation to the complete basis set limit and core correlation effects. A first important outcome is the definitive confirmation of the nonplanarity of carbamic acid, then followed by an accurate estimate of its rotational and vibrational spectroscopy parameters. As far as the carbamic acid dimer is concerned, the investigation started from the identification of its most stable forms. For them, structure and vibrational properties have been evaluated using density functional theory, while a composite scheme rooted in CC theory has been employed for the energetic characterization. Our results allowed us to provide a better interpretation of the feature observed in the recent experiment mentioned above.
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Affiliation(s)
- Cristina Puzzarini
- Department of Chemistry "Giacomo Ciamician", University of Bologna, Bologna, Italy
| | - Silvia Alessandrini
- Department of Chemistry "Giacomo Ciamician", University of Bologna, Bologna, Italy
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3
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Nonne M, Melosso M, Tonolo F, Bizzocchi L, Alessandrini S, Guillemin JC, Dore L, Puzzarini C. Tracing Prebiotic Molecules: Rotational Spectroscopy of Deuterated Glycolaldehyde and ( Z)-1,2-Ethenediol. J Phys Chem A 2024; 128:4850-4858. [PMID: 38842131 DOI: 10.1021/acs.jpca.4c02533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
Glycolaldehyde, an important prebiotic molecule, along with its monodeuterated species and its higher energy tautomer, (Z)-1,2-ethenediol, has been detected in the interstellar medium. Although the elemental D/H ratio in the universe is only ∼1.6 × 10-5, the deuterium relative abundance in interstellar molecules might be by far larger than this. As such, it provides a remarkable and almost unique diagnostic tool. In particular, it might help elucidate the reaction mechanisms that lead to the formation of the so-called complex organic molecules. It is therefore crucial to extend the census of the interstellar deuterated molecules. To this aim, in this work, we present for the first time a spectroscopic investigation of the rotational spectra of the CHDOD-CHO bideuterated variant of glycolaldehyde and of mono- and bideuterated species of (Z)-1,2-ethenediol (CHOD═CHOD, CHOD═CHOH, and CHOH═CHOD rotamers). For each species, more than a hundred transitions have been assigned. Their analysis led to the accurate determination of all rotational constants as well as quartic and sextic centrifugal distortion terms, thus providing spectroscopic line catalogs suitable for supporting astronomical searches. In addition, the rotational constants of the bideuterated glycolaldehyde isotopologue studied in this work allowed us to improve the semiexperimental equilibrium structure determination for this molecule.
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Affiliation(s)
- Michela Nonne
- Scuola Superiore Meridionale, Largo San Marcellino 10, 80138 Naples, Italy
| | - Mattia Melosso
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Francesca Tonolo
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Luca Bizzocchi
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Silvia Alessandrini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Jean-Claude Guillemin
- Univ Rennes, Ecole Nationale Supérieure de Chimie de Rennes, CNRS, ISCR-UMR6226, F-35000 Rennes, France
| | - Luca Dore
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
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Bonah L, Schlemmer S, Guillemin JC, Harding ME, Thorwirth S. On the Spectroscopy of Phosphaalkynes: Millimeter- and Submillimeter-Wave Study of C 2H 5CP. J Phys Chem A 2024; 128:4859-4866. [PMID: 38857201 DOI: 10.1021/acs.jpca.4c02566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
Ethyl phosphaethyne, C2H5CP, has been characterized spectroscopically in the gas phase for the first time, employing millimeter- and submillimeter-wave spectroscopy in the frequency regime from 75 to 760 GHz. Spectroscopic detection and analysis was guided by high-level quantum-chemical calculations of molecular structures and force fields performed at the coupled-cluster singles and doubles level extended by a perturbative correction for the contribution from triple excitations, CCSD(T), in combination with large basis sets. Besides the parent isotopologue, the three singly substituted 13C species were observed in natural abundance up to frequencies as high as 500 GHz. Despite the comparably low astronomical abundance of phosphorus, phosphaalkynes, R-CP, such as C2H5CP are promising candidates for future radio astronomical detection.
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Affiliation(s)
- Luis Bonah
- I. Physikalisches Institut, Universität zu Köln, Zülpicher Straße 77, Köln 50937, Germany
| | - Stephan Schlemmer
- I. Physikalisches Institut, Universität zu Köln, Zülpicher Straße 77, Köln 50937, Germany
| | - Jean-Claude Guillemin
- Université de Rennes, Ecole Nationale Supérieure de Chimie de Rennes, CNRS, ISCR─UMR6226, Rennes 35000, France
| | - Michael E Harding
- Institut für Nanotechnologie, Karlsruher Institut für Technologie (KIT), Kaiserstr. 12, Karlsruhe 76131, Germany
| | - Sven Thorwirth
- I. Physikalisches Institut, Universität zu Köln, Zülpicher Straße 77, Köln 50937, Germany
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5
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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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6
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Puzzarini C, Ye H, Alessandrini S. Isomerism of CH 2 SO : Accurate structural, energetic, and spectroscopic characterization. J Comput Chem 2024; 45:777-786. [PMID: 38116807 DOI: 10.1002/jcc.27283] [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: 10/17/2023] [Revised: 11/24/2023] [Accepted: 11/28/2023] [Indexed: 12/21/2023]
Abstract
A recent work [Ye et al. Mon. Not. R. Astron. Soc. 2023, 525, 1158] on the gas-phase formation of t-HC(O)SH, already detected in the interstellar medium, pointed out that the trans form of HC(S)OH is a potential candidate for astronomical observations. Prompted by these results, theCH 2 SO family of isomers has been investigated from an energetic point of view using a double-hybrid density functional in combination with a partially augmented triple-zeta basis set. This preliminary study showed that the most stable species of the family are the cis and trans forms of HC(O)SH and HC(S)OH. For their structural and spectroscopic characterization, a composite scheme based on coupled cluster (CC) calculations that incorporates up to the quadruple excitations and accounts for the extrapolation to the complete basis set limit and core correlation effects has been employed. This approach opens to the prediction of rotational constants with an accuracy of 0.1%. A hybrid scheme, based on harmonic frequencies computed using the CC singles, doubles and a perturbative treatment of triples method (CCSD(T)) in conjunction with a quadruple-zeta basis set, allowed us to obtain fundamental vibrational frequencies with a mean absolute error of about 1%.
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Affiliation(s)
- Cristina Puzzarini
- Department of Chemistry "Giacomo Ciamician", University of Bologna, Bologna, Italy
| | - Hexu Ye
- Department of Chemistry "Giacomo Ciamician", University of Bologna, Bologna, Italy
| | - Silvia Alessandrini
- Department of Chemistry "Giacomo Ciamician", University of Bologna, Bologna, Italy
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7
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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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8
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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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9
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Lazzari F, Mendolicchio M, Barone V. Accurate Geometries of Large Molecules by Integration of the Pisa Composite Scheme and the Templating Synthon Approach. J Phys Chem A 2024; 128:1385-1395. [PMID: 38347709 DOI: 10.1021/acs.jpca.3c08382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
An effective yet reliable computational workflow is proposed, which permits the computation of accurate geometrical structures for large flexible molecules at an affordable cost thanks to the integration of machine learning tools and DFT models together with reduced scaling computations of vibrational averaging effects. After validation of the different components of the overall strategy, a panel of molecules of biological interest have been analyzed. The results confirm that very accurate geometrical parameters can be obtained at reasonable cost for molecules including up to about 50 atoms, which are the largest ones for which comparison with high-resolution rotational spectra is possible. Since the whole computational workflow can be followed employing standard electronic structure codes, accurate results for large-sized molecules can be obtained at DFT cost also by nonspecialists.
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Affiliation(s)
- 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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10
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Moncada F, Quintero W, Posada E, Pettersson LGM, Reyes A. A nuclear configuration interaction approach to study nuclear spin effects: an application to ortho- and para- 3 He 2 @C 60. Chemphyschem 2024; 25:e202300498. [PMID: 38055206 DOI: 10.1002/cphc.202300498] [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: 07/13/2023] [Revised: 11/29/2023] [Accepted: 12/01/2023] [Indexed: 12/07/2023]
Abstract
We introduce a non-orthogonal configuration interaction approach to investigate nuclear quantum effects on energies and densities of confined fermionic nuclei. The Hamiltonian employed draws parallels between confined systems and many-electron atoms, where effective non-Coulombic potentials represent the interactions of the trapped particles. One advantage of this method is its generality, as it offers the potential to study the nuclear quantum effects of various confined species affected by effective isotropic or anisotropic potentials. As a first application, we analyze the quantum states of two 3 He atoms encapsulated in C60 . At the Hartree-Fock level, we observe the breaking of spin and spatial symmetries. To ensure wavefunctions with the correct symmetries, we mix the broken-symmetry Hartree-Fock states within the non-orthogonal configuration interaction expansion. Our proposed approach predicts singly and triply degenerate ground states for the singlet (para-3 He2 @C60 ) and triplet (ortho-3 He2 @C60 ) nuclear spin configurations, respectively. The ortho-3 He2 @C60 ground state is 5.69 cm-1 higher in energy than the para-3 He2 @C60 ground state. The nuclear densities obtained for these states exhibit the icosahedral symmetry of the C60 embedding potential. Importantly, our calculated energies for the lowest 85 states are in close agreement with perturbation theory results based on a harmonic oscillator plus rigid rotor model of 3 He2 @C60 .
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Affiliation(s)
- Félix Moncada
- Department of Physics, AlbaNova University Center, Stockholm University, 106 91, Stockholm, Sweden
- Department of Chemistry, Universidad Nacional de Colombia, Av. Cra 30 45-03, Bogotá, Colombia
| | - William Quintero
- Doctorado en Fisicoquímica Molecular, Universidad Andres Bello, Santiago de Chile, Chile
- Department of Chemistry, Universidad Nacional de Colombia, Av. Cra 30 45-03, Bogotá, Colombia
| | - Edwin Posada
- Institute for Computational Molecular Science, Temple University, Philadelphia, PA, USA
- Department of Chemistry, Universidad Nacional de Colombia, Av. Cra 30 45-03, Bogotá, Colombia
| | - Lars G M Pettersson
- Department of Physics, AlbaNova University Center, Stockholm University, 106 91, Stockholm, Sweden
| | - Andrés Reyes
- Department of Chemistry, Universidad Nacional de Colombia, Av. Cra 30 45-03, Bogotá, Colombia
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11
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Barone V, Lazzari F. Hunting for Complex Organic Molecules in the Interstellar Medium: The Role of Accurate Low-Cost Theoretical Geometries and Rotational Constants. J Phys Chem A 2023; 127:10517-10527. [PMID: 38033327 PMCID: PMC10726368 DOI: 10.1021/acs.jpca.3c06649] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 12/02/2023]
Abstract
A new approach to computation at affordable cost of accurate geometrical structures and rotational constants for medium-sized molecules in the gas phase is further improved and applied to a large panel of interstellar complex organic molecules. The most distinctive feature of the new model is the effective inclusion of core-valence correlation and vibrational averaging effects in the framework of density functional theory (DFT). In particular, a double-hybrid functional in conjunction with a quadruple-ζ valence/triple-ζ polarization basis set is employed for geometry optimizations, whereas a cheaper hybrid functional in conjunction with a split-valence basis set is used for the evaluation of vibrational corrections. A thorough benchmark based on a wide range of prototypical systems shows that the new scheme approaches the accuracy of state-of-the-art wave function methods with the computational cost of the standard methods (DFT or MP2) routinely employed in the interpretation of microwave spectra. Since the whole computational workflow involves the postprocessing of the output of standard electronic structure codes by a new freely available web utility, the way is paved for the accurate yet not prohibitively expensive study of medium- to large-sized molecules also by nonspecialists.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, di Pisa, Piazza dei Cavalieri 7, Pisa 56125, Italy
| | - Federico Lazzari
- Scuola Normale Superiore, di Pisa, Piazza dei Cavalieri 7, Pisa 56125, Italy
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12
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Melosso M, Alessandrini S, Spada L, Melli A, Wang X, Zheng Y, Duan C, Li J, Du W, Gou Q, Bizzocchi L, Dore L, Barone V, Puzzarini C. Rotational spectra and semi-experimental structures of furonitrile and its water cluster. Phys Chem Chem Phys 2023; 25:31281-31291. [PMID: 37955344 DOI: 10.1039/d3cp03984f] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
Rotational spectroscopy represents an invaluable tool for several applications: from the identification of new molecules in interstellar objects to the characterization of van der Waals complexes, but also for the determination of very accurate molecular structures and for conformational analyses. In this work, we used high-resolution rotational spectroscopic techniques in combination with high-level quantum-chemical calculations to address all these aspects for two isomers of cyanofuran, namely 2-furonitrile and 3-furonitrile. In particular, we have recorded and analyzed the rotational spectra of both of them from 6 to 320 GHz; rotational transitions belonging to several singly-substituted isotopologues have been identified as well. The rotational constants derived in this way have been used in conjunction with computed rotation-vibration interaction constants in order to derive a semi-experimental equilibrium structure for both isomers. Moreover, we observed the rotational spectra of four different intermolecular adducts formed by furonitrile and water, whose identification has been supported by a conformational analysis and a theoretical spectroscopic characterization. A semi-experimental determination of the intermolecular parameters has been achieved for all of them and the results have been compared with those obtained for the analogous system formed by benzonitrile and water.
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Affiliation(s)
- Mattia Melosso
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
| | - Silvia Alessandrini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
| | - Lorenzo Spada
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Alessio Melli
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Xiujuan Wang
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331, Chongqing, China.
| | - Yang Zheng
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331, Chongqing, China.
| | - Chunguo Duan
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331, Chongqing, China.
| | - Jiayi Li
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331, Chongqing, China.
| | - Weiping Du
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331, Chongqing, China.
| | - Qian Gou
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331, Chongqing, China.
| | - Luca Bizzocchi
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
| | - Luca Dore
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
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13
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Puzzarini C, Linguerri R, Hochlaf M. Insights into the Molecular Structure and Spectroscopic Properties of HONCO: An Accurate Ab Initio Study. J Phys Chem A 2023; 127:9502-9512. [PMID: 37922399 PMCID: PMC10658623 DOI: 10.1021/acs.jpca.3c05741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 11/05/2023]
Abstract
In an effort to provide the first accurate structural and spectroscopic characterization of the quasi-linear chain HONCO in its electronic ground state, state-of-the-art computational approaches mainly based on coupled-cluster (CC) theory have been employed. Equilibrium geometries have been calculated by means of a composite scheme based on CC calculations that incorporates up to the quadruple excitations and accounts for the extrapolation to the complete basis set limit and core correlation effects. This approach is proven to provide molecular structures with an accuracy better than 0.001 Å and 0.05° for bond lengths and angles, respectively. Incorporation of vibrational effects permits this level of theory to predict rotational constants with an estimated accuracy of 0.1% or better. Vibrational fundamental bands have been evaluated by means of a hybrid scheme based on harmonic frequencies computed using the CC singles, doubles, and a perturbative treatment of the triples method (CCSD(T)) in conjunction with a quadruple-ζ basis set, with all electrons being correlated, and anharmonic corrections from CCSD(T) calculations using a triple-ζ basis set, within the frozen-core approximation. Such a hybrid approach allowed us to obtain fundamental frequencies with a mean absolute error of about 1%. To complete the spectroscopic characterization, vertical electronic excitation energies have been calculated for the lowest singlet and triplet states using the internally contracted multireference configuration interaction (MRCI) method. Computations show that HONCO dissociates into OH + NCO upon the absorption of UV-vis light. In conclusion, we are confident that the highly accurate spectroscopic data provided herein can be useful for guiding future experimental investigations and supporting the characterization of this molecule in atmospheric and astrophysical media, as well as in combustion.
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Affiliation(s)
- Cristina Puzzarini
- Dipartimento
di Chimica “Giacomo Ciamician″, Università di Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Roberto Linguerri
- Université
Gustave Eiffel, COSYS/IMSE, 5 Bd Descartes, 77454 Champs sur Marne, France
| | - Majdi Hochlaf
- Université
Gustave Eiffel, COSYS/IMSE, 5 Bd Descartes, 77454 Champs sur Marne, France
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14
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Mastin EM, Dutton SE, Blake GA. Supersonic jet chirped pulse microwave spectroscopy of ring-like methanol : water pentamers. Phys Chem Chem Phys 2023; 25:28595-28602. [PMID: 37850329 DOI: 10.1039/d3cp03005a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023]
Abstract
The potential energy surfaces of pure methanol and mixed methanol-water pentamers have been explored using chirped pulse Fourier-transform microwave spectroscopy aided by ab initio calculations. Rotational constants, anharmonic corrections, dipole moments, and relative energies were calculated for different conformers. Predicted rotational transitions were then fit to experimental spectra from 10-18 GHz and the assignments were confirmed using double resonance experiments where feasible. The results show all 23 of the lowest energy conformers are bound in a planar ring of hydrogen bonding that display a steady decrease in the RO-O distance along this ring as methanol content is increased. Interspersed methanol and water conformers have comparable relative abundances to those with micro-aggregation, but structures with micro-aggregated methanol and water have a higher rigid rotor fitting error. The computational methods' high degree of accuracy when compared to our experimental results suggests the strong donor-acceptor hydrogen bonding in these clusters leads to well-defined minima on the intermolecular potential energy surface.
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Affiliation(s)
- E M Mastin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E California Blvd., Pasadena, CA 91125, USA.
| | - S E Dutton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E California Blvd., Pasadena, CA 91125, USA.
| | - G A Blake
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E California Blvd., Pasadena, CA 91125, USA.
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15
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Puzzarini C, Alessandrini S, Bizzocchi L, Melosso M. Hunting for interstellar molecules: rotational spectra of reactive species. Faraday Discuss 2023; 245:309-326. [PMID: 37318358 DOI: 10.1039/d3fd00052d] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
Abstract
Interstellar molecules are often highly reactive species, which are unstable under terrestrial conditions, such as radicals, ions and unsaturated carbon chains. Their detection in space is usually based on the astronomical observation of their rotational fingerprints. However, laboratory investigations have to face the issue of efficiently producing these molecules and preserving them during rotational spectroscopy measurements. A general approach for producing and investigating unstable/reactive species is presented by means of selected case-study molecules. The overall strategy starts from quantum-chemical calculations that aim at obtaining accurate predictions of the missing spectroscopic information required to guide spectral analysis and assignment. Rotational spectra of these species are then recorded by exploiting the approach mentioned above, and their subsequent analysis leads to accurate spectroscopic parameters. These are then used for setting up accurate line catalogs for astronomical searches.
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Affiliation(s)
- Cristina Puzzarini
- ROT&Comp Lab, Department of Chemistry "Giacomo Ciamician", University of Bologna, Via F. Selmi 2, I-40126 Bologna, Italy.
| | - Silvia Alessandrini
- ROT&Comp Lab, Department of Chemistry "Giacomo Ciamician", University of Bologna, Via F. Selmi 2, I-40126 Bologna, Italy.
| | - Luca Bizzocchi
- ROT&Comp Lab, Department of Chemistry "Giacomo Ciamician", University of Bologna, Via F. Selmi 2, I-40126 Bologna, Italy.
| | - Mattia Melosso
- ROT&Comp Lab, Department of Chemistry "Giacomo Ciamician", University of Bologna, Via F. Selmi 2, I-40126 Bologna, Italy.
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16
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Barone V, Uribe Grajales LM, Di Grande S, Lazzari F, Mendolicchio M. DFT Meets Wave-Function Methods for Accurate Structures and Rotational Constants of Histidine, Tryptophan, and Proline. J Phys Chem A 2023; 127:7534-7543. [PMID: 37665117 PMCID: PMC10510395 DOI: 10.1021/acs.jpca.3c04227] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/12/2023] [Indexed: 09/05/2023]
Abstract
A new computational strategy has been applied to the conformational and spectroscopic properties in the gas phase of amino acids with very distinctive features, ranging from different tautomeric forms (histidine) to ring puckering (proline), and heteroaromatic structures with non-equivalent rings (tryptophan). The integration of modern double-hybrid functionals and wave-function composite methods has allowed us to obtain accurate results for a large panel of conformers with reasonable computer times. The remarkable agreement between computations and microwave experiments allows an unbiased interpretation of the latter in terms of stereoelectronic effects.
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Affiliation(s)
- Vincenzo Barone
- Scuola
Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Lina Marcela Uribe Grajales
- 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
| | - 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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17
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Thimmakondu VS, Karton A. CCSD(T) Rotational Constants for Highly Challenging C 5H 2 Isomers-A Comparison between Theory and Experiment. Molecules 2023; 28:6537. [PMID: 37764314 PMCID: PMC10537648 DOI: 10.3390/molecules28186537] [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: 07/30/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
We evaluate the accuracy of CCSD(T) and density functional theory (DFT) methods for the calculation of equilibrium rotational constants (Ae, Be, and Ce) for four experimentally detected low-lying C5H2 isomers (ethynylcyclopropenylidene (2), pentatetraenylidene (3), ethynylpropadienylidene (5), and 2-cyclopropen-1-ylidenethenylidene (8)). The calculated rotational constants are compared to semi-experimental rotational constants obtained by converting the vibrationally averaged experimental rotational constants (A0, B0, and C0) to equilibrium values by subtracting the vibrational contributions (calculated at the B3LYP/jun-cc-pVTZ level of the theory). The considered isomers are closed-shell carbenes, with cumulene, acetylene, or strained cyclopropene moieties, and are therefore highly challenging from an electronic structure point of view. We consider both frozen-core and all-electron CCSD(T) calculations, as well as a range of DFT methods. We find that calculating the equilibrium rotational constants of these C5H2 isomers is a difficult task, even at the CCSD(T) level. For example, at the all-electron CCSD(T)/cc-pwCVTZ level of the theory, we obtain percentage errors ≤0.4% (Ce of isomer 3, Be and Ce of isomer 5, and Be of isomer 8) and 0.9-1.5% (Be and Ce of isomer 2, Ae of isomer 5, and Ce of isomer 8), whereas for the Ae rotational constant of isomers 2 and 8 and Be rotational constant of isomer 3, high percentage errors above 3% are obtained. These results highlight the challenges associated with calculating accurate rotational constants for isomers with highly challenging electronic structures, which is further complicated by the need to convert vibrationally averaged experimental rotational constants to equilibrium values. We use our best CCSD(T) rotational constants (namely, ae-CCSD(T)/cc-pwCVTZ for isomers 2 and 5, and ae-CCSD(T)/cc-pCVQZ for isomers 3 and 8) to evaluate the performance of DFT methods across the rungs of Jacob's Ladder. We find that the considered pure functionals (BLYP-D3BJ, PBE-D3BJ, and TPSS-D3BJ) perform significantly better than the global and range-separated hybrid functionals. The double-hybrid DSD-PBEP86-D3BJ method shows the best overall performance, with percentage errors below 0.5% in nearly all cases.
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Affiliation(s)
- Venkatesan S Thimmakondu
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182-1030, USA
| | - Amir Karton
- School of Science and Technology, University of New England, Armidale, NSW 2351, Australia
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18
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Barone V. Accurate structures and spectroscopic parameters of α,α-dialkylated α-amino acids in the gas-phase: a joint venture of DFT and wave-function composite methods. Phys Chem Chem Phys 2023; 25:22768-22774. [PMID: 37591810 DOI: 10.1039/d3cp02503a] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
Accurate computations of structural, conformational and spectroscopic properties in the gas phase have been performed for two α,α-dialkylated α-amino acids, namely aminoisobutyric acid and cyclopropylglycine. Thanks to the integration of modern double hybrid functionals and wave-function methods, several low-energy structures of the title molecules could be analyzed employing standard computer resources. The computed features of all the most stable conformers of the target amino acids closely match the corresponding spectroscopic parameters issued from microwave spectroscopic studies in the gas-phase. Together with their intrinsic interest, the accuracy of the results obtained with reasonable computer times paves the way for accurate investigations of other flexible bricks of life.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy.
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19
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Barone V, Di Grande S, Lazzari F, Mendolicchio M. Accurate Structures and Spectroscopic Parameters of Guanine Tautomers in the Gas Phase by the Pisa Conventional and Explicitly Correlated Composite Schemes (PCS and PCS-F12). J Phys Chem A 2023; 127:6771-6778. [PMID: 37535450 PMCID: PMC10440789 DOI: 10.1021/acs.jpca.3c03999] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/21/2023] [Indexed: 08/05/2023]
Abstract
A general strategy for the accurate computation of structural and spectroscopic properties of biomolecule building blocks in the gas phase is proposed and validated for tautomeric equilibria. The main features of the new model are the inclusion of core-valence correlation in geometry optimizations by a double hybrid functional and the systematic use of wave-function composite methods in conjunction with cc-pVnZ-F12 basis sets with separate extrapolation of MP2 and post-MP2 contributions. The resulting Pisa composite scheme employing conventional (PCS) or explicitly correlated (PCS-F12) approaches is applied to the challenging problem of guanine tautomers in the gas phase. The results are in remarkable agreement with the experimental structures, relative stabilities, and spectroscopic signatures of different tautomers. The accuracy of the results obtained at reasonable cost by means of black-box parameter-free approaches paves the way toward systematic investigations of other molecular bricks of life also by non-specialists.
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Affiliation(s)
- Vincenzo Barone
- Scuola
Normale Superiore, Piazza dei Cavalieri 7, Pisa 56126, Italy
| | - Silvia Di Grande
- Scuola
Normale Superiore, Piazza dei Cavalieri 7, Pisa 56126, Italy
- Scuola
Superiore Meridionale, Largo San Marcellino 10, Napoli 80138, Italy
| | - Federico Lazzari
- Scuola
Normale Superiore, Piazza dei Cavalieri 7, Pisa 56126, Italy
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20
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Barone V. DFT Meets Wave-Function Composite Methods for Characterizing Cytosine Tautomers in the Gas Phase. J Chem Theory Comput 2023; 19:4970-4981. [PMID: 37479680 PMCID: PMC10413851 DOI: 10.1021/acs.jctc.3c00465] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Indexed: 07/23/2023]
Abstract
A general strategy for the accurate computation of structural and spectroscopic properties of biomolecule building blocks in the gas phase has been further improved and validated with a special reference to tautomeric equilibria. The main improvements concern the use of the cc-pVTZ-F12 basis set in both DFT and CCSD(T)-F12 computations, the inclusion of core-valence correlation in geometry optimizations by double hybrid functionals, and the use of the cc-pVQZ-F12 basis set for complete basis set extrapolation at the MP2-F12 level. The resulting model chemistry is applied to the challenging problem of cytosine tautomers in the gas phase. The results are in remarkable agreement with experiment concerning both rotational and vibrational spectroscopic parameters and permit their unbiased interpretation in terms of structural and thermochemical features. Together with the intrinsic interest of the studied molecule, the accuracy of the results obtained at reasonable cost without any empirical parameter suggests that the proposed composite method can be profitably employed for accurate investigations of other molecular bricks of life.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore
di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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21
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Schröder B. Ab Initio Rovibrational Spectroscopy of the Acetylide Anion. Molecules 2023; 28:5700. [PMID: 37570670 PMCID: PMC10420331 DOI: 10.3390/molecules28155700] [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: 07/03/2023] [Revised: 07/22/2023] [Accepted: 07/22/2023] [Indexed: 08/13/2023] Open
Abstract
In this work the rovibrational spectrum of the acetylide anion HCC- is investigated using high-level electronic structure methods and variational rovibrational calculations. Using a composite approach the potential energy surface and dipole surface is constructed from explicitly correlated coupled-cluster accounting for corrections due to core-valence correlation, scalar relativistic effects and higher-order excitation effects. Previous approaches for approximating the latter are critically evaluated. Employing the composite potential, accurate spectroscopic parameters determined from variational calculations are presented. In comparison to the few available reference data the present results show excellent agreement with ground state rotational constants within 0.005% of the experimental value. Intensities determined from the variational calculations suggest the bending fundamental transition ν2 around 510 cm-1 to be the best target for detection. The rather weak CD stretching fundamental ν1 in deuterated isotopologues show a second-order resonance with the (0,20,1) state and the consequences are discussed in some detail. The spectroscopic parameters and band intensities provided for a number of vibrational bands in isotopologues of the acetylide anion should facilitate future spectroscopic investigations.
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Affiliation(s)
- Benjamin Schröder
- Institute of Physical Chemistry, University of Goettingen, Tammannstr. 6, 37077 Göttingen, Germany
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22
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Changala PB, Genossar-Dan N, Brudner E, Gur T, Baraban JH, McCarthy MC. Structural and electronic trends of optical cycling centers in polyatomic molecules revealed by microwave spectroscopy of MgCCH, CaCCH, and SrCCH. Proc Natl Acad Sci U S A 2023; 120:e2303586120. [PMID: 37399375 PMCID: PMC10334755 DOI: 10.1073/pnas.2303586120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/23/2023] [Indexed: 07/05/2023] Open
Abstract
The unique optical cycling efficiency of alkaline earth metal-ligand molecules has enabled significant advances in polyatomic laser cooling and trapping. Rotational spectroscopy is an ideal tool for probing the molecular properties that underpin optical cycling, thereby elucidating the design principles for expanding the chemical diversity and scope of these platforms for quantum science. We present a comprehensive study of the structure and electronic properties in alkaline earth metal acetylides with high-resolution microwave spectra of 17 isotopologues of MgCCH, CaCCH, and SrCCH in their 2Σ+ ground electronic states. The precise semiexperimental equilibrium geometry of each species has been derived by correcting the measured rotational constants for electronic and zero-point vibrational contributions calculated with high-level quantum chemistry methods. The well-resolved hyperfine structure associated with the 1,2H, 13C, and metal nuclear spins provides further information on the distribution and hybridization of the metal-centered, optically active unpaired electron. Together, these measurements allow us to correlate trends in chemical bonding and structure with the electronic properties that promote efficient optical cycling essential to next-generation experiments in precision measurement and quantum control of complex polyatomic molecules.
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Affiliation(s)
- P. Bryan Changala
- Atomic and Molecular Physics Division, Center for Astrophysics | Harvard & Smithsonian, Cambridge, MA02138
| | - Nadav Genossar-Dan
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva8410501, Israel
| | - Ella Brudner
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva8410501, Israel
| | - Tomer Gur
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva8410501, Israel
| | - Joshua H. Baraban
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva8410501, Israel
| | - Michael C. McCarthy
- Atomic and Molecular Physics Division, Center for Astrophysics | Harvard & Smithsonian, Cambridge, MA02138
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23
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Melosso M, Jiang N, Gauss J, Puzzarini C. Hyperfine-resolved spectra of HDS together with a global ro-vibrational analysis. J Chem Phys 2023; 158:2888208. [PMID: 37139997 DOI: 10.1063/5.0148810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/17/2023] [Indexed: 05/05/2023] Open
Abstract
Despite their chemical simplicity, the spectroscopic investigation of light hydrides, such as hydrogen sulfide, is challenging due to strong hyperfine interactions and/or anomalous centrifugal-distortion effects. Several hydrides have already been detected in the interstellar medium, and the list includes H2S and some of its isotopologues. Astronomical observation of isotopic species and, in particular, those bearing deuterium is important to gain insights into the evolutionary stage of astronomical objects and to shed light on interstellar chemistry. These observations require a very accurate knowledge of the rotational spectrum, which is so far limited for mono-deuterated hydrogen sulfide, HDS. To fill this gap, high-level quantum-chemical calculations and sub-Doppler measurements have been combined for the investigation of the hyperfine structure of the rotational spectrum in the millimeter- and submillimeter-wave region. In addition to the determination of accurate hyperfine parameters, these new measurements together with the available literature data allowed us to extend the centrifugal analysis using a Watson-type Hamiltonian and a Hamiltonian-independent approach based on the Measured Active Ro-Vibrational Energy Levels (MARVEL) procedure. The present study thus permits to model the rotational spectrum of HDS from the microwave to far-infrared region with great accuracy, thereby accounting for the effect of the electric and magnetic interactions due to the deuterium and hydrogen nuclei.
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Affiliation(s)
- Mattia Melosso
- Dipartimento di Chimica "Giacomo Ciamician," Università di Bologna, via F. Selmi 2, 40126 Bologna, Italy
| | - Ningjing Jiang
- Dipartimento di Chimica "Giacomo Ciamician," Università di Bologna, via F. Selmi 2, 40126 Bologna, Italy
| | - Jürgen Gauss
- Department Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician," Università di Bologna, via F. Selmi 2, 40126 Bologna, Italy
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24
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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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25
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Pandey A, Srivastav S, Vats A, Pathak A, Singh KAP. A comprehensive rotational study of astronomical iso-pentane within 84 to 111 GHz. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 290:122299. [PMID: 36608520 DOI: 10.1016/j.saa.2022.122299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 12/24/2022] [Accepted: 12/28/2022] [Indexed: 06/17/2023]
Abstract
The rotational line survey by ALMA (Atacama Large Millimeter/submillimeter Array) recently revealed the presence of i-C3H7CN (i-PrCN) and n-C3H7CN (n-PrCN) in 3-mm atmospheric window between 84 to 111 GHz towards the hot core region Sagittarius B2(N) (Sgr B2(N)). This was the first interstellar detection of a linear straight chain molecule. In this light, we report the rotational spectra of C5H12 isomeric group in the same frequency range. We performed quantum chemical calculations for spectroscopic parameters. The pure rotational spectrum of the species has been simulated using the PGOPHER program. The rotational spectrum of this molecule makes it a good candidate for future astronomical detections since the radio lines can be calculated to very high accuracy in mm/sub-mm wave region.
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Affiliation(s)
- Anshika Pandey
- Department of Physics, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
| | - Satyam Srivastav
- Department of Physics, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Akant Vats
- Department of Physics, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Amit Pathak
- Department of Physics, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
| | - K A P Singh
- Department of Physics, Institute of Science, Banaras Hindu University, Varanasi 221005, India
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26
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Alessandrini S, Melosso M, Rivilla VM, Bizzocchi L, Puzzarini C. Computational Protocol for the Identification of Candidates for Radioastronomical Detection and Its Application to the C3H3NO Family of Isomers. Molecules 2023; 28:molecules28073226. [PMID: 37049990 PMCID: PMC10096335 DOI: 10.3390/molecules28073226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 04/08/2023] Open
Abstract
The C3H3NO family of isomers is relevant in astrochemistry, even though its members are still elusive in the interstellar medium. To identify the best candidate for astronomical detection within this family, we developed a new computational protocol based on the minimum-energy principle. This approach aims to identify the most stable isomer of the family and consists of three steps. The first step is an extensive investigation that characterizes the vast number of compounds having the C3H3NO chemical formula, employing density functional theory for this purpose. The second step is an energy refinement, which is used to select isomers and relies on coupled cluster theory. The last step is a structural improvement with a final energy refinement that provides improved energies and a large set of accurate spectroscopic parameters for all isomers lying within 30 kJ mol−1 above the most stable one. According to this protocol, vinylisocyanate is the most stable isomer, followed by oxazole, which is about 5 kJ mol−1 higher in energy. The other stable species are pyruvonitrile, cyanoacetaldehyde, and cyanovinylalcohol. For all of these species, new computed rotational and vibrational spectroscopic data are reported, which complement those already available in the literature or fill current gaps.
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Affiliation(s)
- Silvia Alessandrini
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Mattia Melosso
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Víctor M. Rivilla
- Centro de Astrobiología (CSIC-INTA), Ctra. de Ajalvir km. 4, Torrejón de Ardoz, 28850 Madrid, Spain
| | - Luca Bizzocchi
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Cristina Puzzarini
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
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27
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Spaniol JT, Lee KLK, Pirali O, Puzzarini C, Martin-Drumel MA. A rotational investigation of the three isomeric forms of cyanoethynylbenzene (HCC-C 6H 4-CN): benchmarking experiments and calculations using the "Lego brick" approach. Phys Chem Chem Phys 2023; 25:6397-6405. [PMID: 36779600 DOI: 10.1039/d2cp04825f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We report the study of three structural isomers of phenylpropiolonitrile (3-phenyl-2-propynenitrile, C6H5-C3N) containing an alkyne function and a cyano group, namely ortho-, meta-, and para-cyanoethynylbenzene (HCC-C6H4-CN). The pure rotational spectra of these species have been recorded at room temperature in the millimeter-wave domain using a chirped-pulse spectrometer (75-110 GHz) and a source-frequency modulation spectrometer (140-220 GHz). Assignments of transitions in the vibrational ground state and several vibrationally excited states were supported by quantum chemical calculations using the so-called "Lego brick" approach [A. Melli, F. Tonolo, V. Barone and C. Puzzarini, J. Phys. Chem. A, 2021, 125, 9904-9916]. From these assignments, accurate spectroscopic (rotational and centrifugal distortion) constants have been derived: for all species and all observed vibrational states, predicted rotational constants show relative accuracy better than 0.1%, and often of the order of 0.01%, compared to the experimental values. The present work hence further validates the use of the "Lego brick" approach for predicting spectroscopic constants with high precision.
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Affiliation(s)
- Jean-Thibaut Spaniol
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405 Orsay, France.
| | - Kin Long Kelvin Lee
- Intel Accelerated Computing Systems and Graphics Group, Intel JF5 2111 NE 25th Ave, Hillsboro, OR 97124, USA
| | - Olivier Pirali
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405 Orsay, France.
| | - Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, via F. Selmi 2, 40126 Bologna, Italy.
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28
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Jiang N, Melosso M, Alessandrini S, Bizzocchi L, Martin-Drumel MA, Pirali O, Puzzarini C. Insights into the molecular structure and infrared spectrum of the prebiotic species aminoacetonitrile. Phys Chem Chem Phys 2023; 25:4754-4763. [PMID: 36691972 DOI: 10.1039/d2cp05179f] [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
Aminoacetonitrile is an interstellar molecule with a prominent prebiotic role, already detected in the chemically-rich molecular cloud Sagittarius B2(N) and postulated to be present in the atmosphere of the largest Saturn's moon, Titan. To further support its observation in such remote environments and laboratory experiments aimed at improving our understanding of interstellar chemistry, we report a thorough spectroscopic and structural characterization of aminoacetonitrile. Equilibrium geometry, fundamental bands as well as spectroscopic and molecular parameters have been accurately computed by exploiting a composite scheme rooted in the coupled-cluster theory that accounts for the extrapolation to the complete basis set limit and core-correlation effects. In addition, a semi-experimental approach that combines ground-state rotational constants for different isotopic species and calculated vibrational corrections has been employed for the structure determination. From the experimental side, we report the analysis of the three strongest fundamental bands of aminoacetonitrile observed between 500 and 1000 cm-1 in high-resolution infrared spectra. More generally, all computed band positions are in excellent agreement with the present and previous experiments. The only exception is the ν15 band, for which we provide a revision of the experimental assignment, now in good agreement with theory.
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Affiliation(s)
- Ningjing Jiang
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
| | - Mattia Melosso
- Scuola Superiore Meridionale, Largo San Marcellino 10, 80138 Naples, Italy.
| | - Silvia Alessandrini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy. .,Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Luca Bizzocchi
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
| | | | - Olivier Pirali
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405 Orsay, France.,SOLEIL Synchrotron, AILES beamline, l'Orme des Merisiers, 91190 Saint-Aubin, Gif-sur-Yvette, France
| | - Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
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29
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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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30
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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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31
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Puzzarini C, Stanton JF. Connections between the accuracy of rotational constants and equilibrium molecular structures. Phys Chem Chem Phys 2023; 25:1421-1429. [PMID: 36562443 DOI: 10.1039/d2cp04706c] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Rotational spectroscopy is the technique of choice for investigating molecular structures in the gas phase. Indeed, rotational constants are strongly connected to the geometry of the molecular system under consideration. Therefore, they are powerful tools for assessing the accuracy that quantum chemical approaches can reach in structural determinations. In this review article, it is shown how it is possible to measure the accuracy of a computed equilibrium geometry based on the comparison of rotational constants. But, it is also addressed what accuracy is required by computations for providing molecular structures and thus rotational constants that are useful to experiment. Quantum chemical methodologies for obtaining the "0.1% accuracy" for rotational constants are reviewed for systems ranging in size from small molecules to small polycyclic aromatic hydrocarbons. This accuracy for systems containing two dozen or so atoms opens the way towards future applications such as the accurate characterization of non-covalent interactions, which play a key role in several biological and technological processes.
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Affiliation(s)
- Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, via F. Selmi 2, 40126, Bologna, Italy.
| | - John F Stanton
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA.
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32
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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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33
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Chitarra O, Pirali O, Spaniol JT, Hearne TS, Loison JC, Stanton JF, Martin-Drumel MA. Pure Rotational Spectroscopy of the CH 2CN Radical Extended to the Sub-Millimeter Wave Spectral Region. J Phys Chem A 2022; 126:7502-7513. [PMID: 36198131 DOI: 10.1021/acs.jpca.2c04399] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a thorough pure rotational investigation of the CH2CN radical in its ground vibrational state. Our measurements cover the millimeter and sub-millimeter wave spectral regions (79-860 GHz) using a W-band chirped-pulse instrument and a frequency multiplication chain-based spectrometer. The radical was produced in a flow cell at room temperature by H abstraction from acetonitrile using atomic fluorine. The newly recorded transitions of CH2CN (involving N″ and Ka″ up to 42 and 8, respectively) were combined with the literature data, leading to a refinement of the spectroscopic parameters of the species using a Watson S-reduced Hamiltonian. In particular, the A rotational constant and K-dependent parameters are significantly better determined than in previous studies. The present model, which reproduces all experimental transitions to their experimental accuracy, allows for confident searches for the radical in cold to warm environments of the interstellar medium.
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Affiliation(s)
- Olivia Chitarra
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405Orsay, France
| | - Olivier Pirali
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405Orsay, France
| | - Jean-Thibaut Spaniol
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405Orsay, France
| | - Thomas S Hearne
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405Orsay, France
| | | | - John F Stanton
- Quantum Theory Project, Department of Chemistry, University of Florida, Gainesville32611, Florida, United States
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34
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Bizzocchi L, Alessandrini S, Melosso M, Puzzarini C. Dipolar spin-spin coupling as an auxiliary tool for the structure determination of small isolated molecules. Phys Chem Chem Phys 2022; 24:15173-15181. [PMID: 35703976 DOI: 10.1039/d2cp01124g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The "gold standard" for obtaining accurate equilibrium structures is the so-called semi-experimental (SE) approach, which exploits the structural information contained in rotational constants. Within the SE approach, ground-state rotational constants-accurately obtained from high-resolution spectroscopic studies-are computationally corrected in order to remove vibrational effects. The resulting SE equilibrium rotational constants for a significant set of isotopic species allow for retrieving a unique set of equilibrium bond lengths and angles for the molecule under consideration. However, in some cases, the lack of isotopic substitution hampers or even prevents a rigorous and complete structure determination. In this perspective, we introduce the use of dipolar spin-spin coupling constants as an additional source of structural information in support of the standard SE approach. As a proof-of-concept, we tested this new strategy on some prototypical species, such as water, ammonia, phosphine, and their fluorinated counterparts. Our results indicate that-even when the molecular structure can be obtained from a large set of isotopic rotational constants-the use of dipolar spin-spin coupling constants guarantees a better accuracy and reduces the correlations among the geometrical parameters. Moreover, we point out that our approach offers the possibility to fully derive the molecular structure of PF3, a species for which any isotopic substitution is not possible.
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Affiliation(s)
- Luca Bizzocchi
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, via F. Selmi 2, 40126 Bologna, Italy.
| | - Silvia Alessandrini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, via F. Selmi 2, 40126 Bologna, Italy. .,Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy.
| | - Mattia Melosso
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, via F. Selmi 2, 40126 Bologna, Italy. .,Scuola Superiore Meridionale, Università di Napoli Federico II, Largo San Marcellino 10, 80138 Naples, Italy.
| | - Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, via F. Selmi 2, 40126 Bologna, Italy.
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35
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Dutton SE, Blake GA. High throughput chirped pulse Fourier-transform microwave spectroscopy of ethanol and water clusters. Phys Chem Chem Phys 2022; 24:13831-13838. [PMID: 35616604 DOI: 10.1039/d2cp01055k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here we discuss the design and performance of a novel high-throughput instrument for Chirped Pulse Fourier-transform Microwave (CP-FTMW) spectroscopy, and demonstrate its efficacy through the identification of the lowest energy conformers of the ethanol trimer and mixed water : ethanol trimers. Rotational constants for these trimers were calculated from observed lines in the spectra from 10 to 14 GHz, and compared to the results of anharmonic ab initio computations. As predicted, all trimers share a cyclic donor-acceptor hydrogen bonding structure, with the ethanol monomer favoring the gauche conformation in the lowest energy structures. The increased speed of data collection and resulting sensitivity opens a new avenue into rotational studies of higher order clusters.
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Affiliation(s)
- S E Dutton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E California Blvd., Pasadena, CA 91125, USA.
| | - G A Blake
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E California Blvd., Pasadena, CA 91125, USA.
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36
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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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37
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Melli A, Melosso M, Lengsfeld KG, Bizzocchi L, Rivilla VM, Dore L, Barone V, Grabow JU, Puzzarini C. Spectroscopic Characterization of 3-Aminoisoxazole, a Prebiotic Precursor of Ribonucleotides. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27103278. [PMID: 35630755 PMCID: PMC9147597 DOI: 10.3390/molecules27103278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/16/2022] [Accepted: 05/18/2022] [Indexed: 11/17/2022]
Abstract
The processes and reactions that led to the formation of the first biomolecules on Earth play a key role in the highly debated theme of the origin of life. Whether the first chemical building blocks were generated on Earth (endogenous synthesis) or brought from space (exogenous delivery) is still unanswered. The detection of complex organic molecules in the interstellar medium provides valuable support to the latter hypothesis. To gather more insight, here we provide the astronomers with accurate rotational frequencies to guide the interstellar search of 3-aminoisoxazole, which has been recently envisaged as a key reactive species in the scenario of the so-called RNA-world hypothesis. Relying on an accurate computational characterization, we were able to register and analyze the rotational spectrum of 3-aminoisoxazole in the 6–24 GHz and 80–320 GHz frequency ranges for the first time, exploiting a Fourier-transform microwave spectrometer and a frequency-modulated millimeter/sub-millimeter spectrometer, respectively. Due to the inversion motion of the −NH2 group, two states arise, and both of them were characterized, with more than 1300 lines being assigned. Although the fit statistics were affected by an evident Coriolis interaction, we were able to produce accurate line catalogs for astronomical observations of 3-aminoisoxazole.
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Affiliation(s)
- Alessio Melli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy; (A.M.); (V.B.)
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy; (L.B.); (L.D.)
| | - Mattia Melosso
- Scuola Superiore Meridionale, Università di Napoli Federico II, Largo San Marcellino 10, 80138 Naples, Italy
- Correspondence: (M.M.); (C.P.)
| | - Kevin G. Lengsfeld
- Institut für Physikalische Chemie und Elektrochemie, Gottfried Wilhelm Leibniz Universität Hannover, Callinstraße 3A, 30167 Hannover, Germany; (K.G.L.); (J.-U.G.)
| | - Luca Bizzocchi
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy; (L.B.); (L.D.)
| | - Víctor M. Rivilla
- Centro de Astrobiología (CSIC-INTA), Ctra. de Ajalvir Km. 4, Torrejón de Ardoz, 28850 Madrid, Spain;
| | - Luca Dore
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy; (L.B.); (L.D.)
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy; (A.M.); (V.B.)
| | - Jens-Uwe Grabow
- Institut für Physikalische Chemie und Elektrochemie, Gottfried Wilhelm Leibniz Universität Hannover, Callinstraße 3A, 30167 Hannover, Germany; (K.G.L.); (J.-U.G.)
| | - Cristina Puzzarini
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy; (L.B.); (L.D.)
- Correspondence: (M.M.); (C.P.)
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38
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Motta M, Rice JE. Emerging quantum computing algorithms for quantum chemistry. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1580] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Mario Motta
- IBM Quantum, IBM Research‐Almaden San Jose California USA
| | - Julia E. Rice
- IBM Quantum, IBM Research‐Almaden San Jose California USA
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39
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Zheng X, Zhang C, Liu J, Cheng L. Geometry Optimizations with Spinor-Based Relativistic Coupled-Cluster Theory. J Chem Phys 2022; 156:151101. [DOI: 10.1063/5.0086281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Development of analytic gradients for relativistic coupled-cluster singles and doubles augmented with a non-iterative triples [CCSD(T)] method using an all-electron exact two-component Hamiltonian with atomic mean-field spin-orbit integrals (X2CAMF) is reported. This enables efficient CC geometry optimizations with spin-orbit coupling included in orbitals. The applicability of the implementation is demonstrated using benchmark X2CAMF-CCSD(T) calculations of equilibrium structures and harmonic vibrational frequencies for methyl halides, CH3X, X=Br, I, At, as well as calculations of rotational constants and infrared spectrum for RaSH+, a radioactive molecular ion of interest to spectroscopic study.
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Affiliation(s)
- Xuechen Zheng
- Johns Hopkins University Department of Chemistry, United States of America
| | - Chaoqun Zhang
- Johns Hopkins University Department of Chemistry, United States of America
| | - Junzi Liu
- Chemistry, Johns Hopkins University Department of Chemistry, United States of America
| | - Lan Cheng
- Chemistry, Johns Hopkins University Department of Chemistry, United States of America
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40
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Jiang N, Melosso M, Bizzocchi L, Alessandrini S, Guillemin JC, Dore L, Puzzarini C. Spectroscopic and Computational Characterization of 2-Aza-1,3-butadiene, a Molecule of Astrochemical Significance. J Phys Chem A 2022; 126:1881-1888. [PMID: 35275628 PMCID: PMC8958585 DOI: 10.1021/acs.jpca.2c00831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Being N-substituted
unsaturated species, azabutadienes are molecules
of potential relevance in astrochemistry, ranging from the interstellar
medium to Titan’s atmosphere. 2-Azabutadiene and butadiene
share a similar conjugated π system, thus allowing investigation
of the effects of heteroatom substitution. More interestingly, 2-azabutadiene
can be used to proxy the abundance of interstellar butadiene. To enable
future astronomical searches, the rotational spectrum of 2-azabutadiene
has been investigated up to 330 GHz. The experimental work has been
supported and guided by accurate computational characterization of
the molecular structure, energetics, and spectroscopic properties
of the two possible forms, trans and gauche. The trans species, more stable by about 7 kJ/mol
than gauche-2-azabutadiene, has been experimentally
observed, and its rotational and centrifugal distortion constants
have been obtained with remarkable accuracy, while theoretical estimates
of the spectroscopic parameters are reported for gauche-2-azabutadiene.
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Affiliation(s)
- Ningjing Jiang
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Mattia Melosso
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.,Scuola Superiore Meridionale, Università di Napoli Federico II, Largo San Marcellino 10, 80138 Naples, Italy
| | - Luca Bizzocchi
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | | | - Jean-Claude Guillemin
- University of Rennes, Ecole Nationale Supérieure de Chimie de Rennes, CNRS, ISCR-UMR6226, F-35000 Rennes, France
| | - Luca Dore
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
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41
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Simmie JM. C 2H 5NO Isomers: From Acetamide to 1,2-Oxazetidine and Beyond. J Phys Chem A 2022; 126:924-939. [PMID: 35113546 PMCID: PMC8859852 DOI: 10.1021/acs.jpca.1c09984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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This work documents
the properties of a number of isomers of molecular
formula C2H5NO from the most stable, acetamide,
through 1,2-oxazetidine and including even higher energy species largely
of a dipolar nature. Only two of the isomers have been detected in
emissions from the interstellar medium (ISM); possible further candidates
are identified, and the likelihood of their being detectable is considered.
In general, hardly any of these compounds have been discussed in the
existing chemical literature, so this work represents an important
contribution extending the canon of chemical bonding which can contribute
to machine learning, providing a more exacting test of AI applications.
The presence in the ISM of acetamide, CH3C(O)NH2, is the subject of current debate with no clear and obvious paths
to its formation; it is shown that a 1,3-[H]-transfer from (E,Z)-ethanimidic acid, CH3C(OH)=NH, is
feasible in spite of an energy barrier of 130 kJ mol–1. It is speculated that imidic acid can itself be formed from abundant
precursors, H2O and CH3C≡N, in an acid-induced,
water addition, autocatalytic reaction on water–ice grains.
H3CC≡NH3CC≡NH+ +
H2OH3CC(O+H2)=NHH3CC(OH)=NH
+ H3O+
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Affiliation(s)
- John M Simmie
- School of Chemistry, National University of Ireland, Galway H91 TK33, Ireland
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42
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Bizzocchi L, Alessandrini S, Melosso M, Rivilla VM, Puzzarini C. Ab Initio Study of Fine and Hyperfine Interactions in Triplet POH. Molecules 2022; 27:302. [PMID: 35011533 PMCID: PMC8746536 DOI: 10.3390/molecules27010302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/28/2021] [Accepted: 12/30/2021] [Indexed: 11/16/2022] Open
Abstract
Phosphorous-containing molecules have a great relevance in prebiotic chemistry in view of the fact that phosphorous is a fundamental constituent of biomolecules, such as RNA, DNA, and ATP. Its biogenic importance has led astrochemists to investigate the possibility that P-bearing species could have formed in the interstellar medium (ISM) and subsequently been delivered to early Earth by rocky bodies. However, only two P-bearing molecules have been detected so far in the ISM, with the chemistry of interstellar phosphorous remaining poorly understood. Here, in order to shed further light on P-carriers in space, we report a theoretical spectroscopic characterisation of the rotational spectrum of POH in its 3A″ ground electronic state. State-of-the-art coupled-cluster schemes have been employed to derive rotational constants, centrifugal distortion terms, and most of the fine and hyperfine interaction parameters, while the electron spin-spin dipolar coupling has been investigated using the multi-configuration self-consistent-field method. The computed spectroscopic parameters have been used to simulate the appearance of triplet POH rotational and ro-vibrational spectra in different conditions, from cold to warm environments, either in gas-phase experiments or in molecular clouds. Finally, we point out that the predicted hyperfine structures represent a key pattern for the recognition of POH in laboratory and interstellar spectra.
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Affiliation(s)
- Luca Bizzocchi
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy; (L.B.); (S.A.)
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy;
| | - Silvia Alessandrini
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy; (L.B.); (S.A.)
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy;
| | - Mattia Melosso
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy;
- Scuola Superiore Meridionale, Università di Napoli Federico II, Largo San Marcellino 10, 80138 Naples, Italy
| | - Víctor M. Rivilla
- Centro de Astrobiología (CSIC-INTA), Ctra. de Ajalvir Km. 4, Torrejón de Ardoz, 28850 Madrid, Spain;
- INAF—Osservatorio Astrofisico di Arcetri, Largo E. Fermi 5, 50125 Florence, Italy
| | - Cristina Puzzarini
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy;
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43
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Ye H, Alessandrini S, Melosso M, Puzzarini C. Exploiting the “Lego brick” approach to predict accurate molecular structures of PAHs and PANHs. Phys Chem Chem Phys 2022; 24:23254-23264. [DOI: 10.1039/d2cp03294e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) and polycyclic aromatic nitrogen heterocycles (PANHs) are important and ubiquitous species in space. However, their accurate structural and spectroscopic characterization is often missing. To fill this...
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44
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Rocha CMR, Linnartz H. High-level ab initio quartic force fields and spectroscopic characterization of C 2N . Phys Chem Chem Phys 2021; 23:26227-26240. [PMID: 34787132 DOI: 10.1039/d1cp03505c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
While it is now well established that large carbon chain species and radiative electron attachment (REA) are key ingredients triggering interstellar anion chemistry, the role played by smaller molecular anions, for which REA appears to be an unlikely formation pathway, is as yet elusive. Advancing this research undoubtedly requires the knowledge (and modeling) of their astronomical abundances which, for the case of C2N-, is largely hindered by a lack of accurate spectroscopic signatures. In this work, we provide such data for both ground -CCN-(3Σ-) and low-lying c-CNC-(1A1) isomers and their singly-substituted isotopologues by means of state-of-the-art rovibrational quantum chemical techniques. Their quartic force fields are herein calibrated using a high-level composite energy scheme that accounts for extrapolations to both one-particle and (approximate) -particle basis set limits, in addition to relativistic effects, with the final forms being subsequently subject to nuclear motion calculations. Besides standard spectroscopic attributes, the full set of computed properties includes fine and hyperfine interaction constants and can be readily introduced as guesses in conventional experimental data reduction analyses through effective Hamiltonians. On the basis of benchmark calculations performed anew for a minimal test set of prototypical triatomics and limited (low-resolution) experimental data for -CCN-(3Σ-), the target accuracies are determined to be better than 0.1% of experiment for rotational constants and 0.3% for vibrational fundamentals. Apart from laboratory investigations, the results here presented are expected to also prompt future astronomical surveys on C2N-. To this end and using the theoretically-predicted spectroscopic constants, the rotational spectra of both -CCN-(3Σ-) and c-CNC-(1A1) are derived and their likely detectability in the interstellar medium is further explored in connection with working frequency ranges of powerful astronomical facilities. Our best theoretical estimate places c-CNC-(1A1) at about 15.3 kcal mol-1 above the ground-state -CCN-(3Σ-) species.
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Affiliation(s)
- C M R Rocha
- Laboratory for Astrophysics, Leiden Observatory, Leiden University, P.O. Box 9513, NL-2300 RA Leiden, The Netherlands.
| | - H Linnartz
- Laboratory for Astrophysics, Leiden Observatory, Leiden University, P.O. Box 9513, NL-2300 RA Leiden, The Netherlands.
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45
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Wang P, Shu C, Ye H, Biczysko M. Structural and Energetic Properties of Amino Acids and Peptides Benchmarked by Accurate Theoretical and Experimental Data. J Phys Chem A 2021; 125:9826-9837. [PMID: 34752094 DOI: 10.1021/acs.jpca.1c06504] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Structural, energetic, and spectroscopic data derived in this work aim at the setup of an "experimentally validated" database for amino acids and polypeptides conformers. First, the "cheap" composite scheme (ChS, CCSD(T)/(CBS+CV)MP2) is tested for evaluation of conformational energies of all eight stable conformers of glycine, by comparing to the more accurate CCSD(T)/CBS+CV computations (Phys. Chem. Chem. Phys. 2013, 15, 10094-10111 and J Mol. Model. 2020, 26, 129). The recently proposed jun-ChS (J. Chem. Theory and Comput. 2020, 16, 988-1006), employing the jun-cc-pVnZ basis set family for CCSD(T) computations and CBS extrapolation, yields conformational energies accurate to 0.2 kJ·mol-1, at reduced computational cost with respect to aug-ChS employing aug-cc-pVnZ basis sets. The jun-ChS composite scheme is further applied to derive conformational energies for three dipeptide analogues Ac-Gly-NH2, Ac-Ala-NH2, and Gly-Gly. Finally, dipeptide conformational energies and semiexperimental equilibrium rotational constants along with the CCSD(T)/(CBS+CV)MP2 structural parameters (J. Phys. Chem. Lett. 2014, 5, 534-540) stand as the reference for benchmarking of selected density functional methodologies. The double-hybrid functionals B2-PLYP-D3(BJ) and DSD-PBEP86, perform best for structural and energetic characterization of all dipeptide analogues. From hybrid functionals CAM-B3LYP-D3(BJ) and ωB97X-D3(BJ) represent promising methods applicable for larger peptide-based systems for which computations with double-hybrid functionals are not feasible.
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Affiliation(s)
- Ping Wang
- International Centre for Quantum and Molecular Structures, Physics Department, College of Science, Shanghai University, 99 Shangda Road, Shanghai 200444, China
| | - Chong Shu
- International Centre for Quantum and Molecular Structures, Physics Department, College of Science, Shanghai University, 99 Shangda Road, Shanghai 200444, China
| | - Hexu Ye
- International Centre for Quantum and Molecular Structures, Physics Department, College of Science, Shanghai University, 99 Shangda Road, Shanghai 200444, China
| | - Malgorzata Biczysko
- International Centre for Quantum and Molecular Structures, Physics Department, College of Science, Shanghai University, 99 Shangda Road, Shanghai 200444, China
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46
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Melli A, Tonolo F, Barone V, Puzzarini C. Extending the Applicability of the Semi-experimental Approach by Means of "Template Molecule" and "Linear Regression" Models on Top of DFT Computations. J Phys Chem A 2021; 125:9904-9916. [PMID: 34752702 PMCID: PMC8607424 DOI: 10.1021/acs.jpca.1c07828] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/20/2021] [Indexed: 11/28/2022]
Abstract
The accurate determination of equilibrium structures for isolated molecules plays a central role in the evaluation and interpretation of stereoelectronic, thermodynamic, and spectroscopic properties. For small semi-rigid systems, state-of-the-art quantum-chemical computations can rival the most sophisticated experimental results. For larger molecules, cheaper yet accurate approaches need to be defined. The double-hybrid rev-DSD-PBEP86 functional already delivers remarkable results that can be further improved by means of a "Lego brick" model. This is based on the idea that a molecular system can be seen as formed by different fragments (the "Lego bricks"), whose accurate semi-experimental (SE) equilibrium geometries are available. The template molecule (TM) approach can be used to account for the modifications occurring when going from the isolated fragment to the molecular system under investigation, with the linear regression (LR) model employed to correct the linkage between the different fragments. The resulting TM-SE_LR approach has been tested with respect to available SE equilibrium structures and rotational constants. Indeed, the latter parameters straightforwardly depend on the equilibrium geometry of the system under consideration. The main outcome of our study is the reliability, robustness, and accuracy of this novel approach. The molecular systems considered for benchmarking the TM-SE_LR scheme are those formally issued from addition/elimination reactions of nucleophilic unsaturated radicals (e.g., CN, C2H, and phenyl) to alkenes, imines, and aldehydes, whose rotational spectra have been investigated, but accurate structural determinations are not yet available.
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Affiliation(s)
- Alessio Melli
- Scuola
Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Dipartimento
di Chimica “Giacomo Ciamician”, Università di Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Francesca Tonolo
- Scuola
Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Dipartimento
di Chimica “Giacomo Ciamician”, Università di Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Vincenzo Barone
- Scuola
Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Cristina Puzzarini
- Dipartimento
di Chimica “Giacomo Ciamician”, Università di Bologna, Via Selmi 2, 40126 Bologna, Italy
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47
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Alessandrini S, Melosso M, Jiang N, Bizzocchi L, Dore L, Puzzarini C. Conformational stability of cyclopropanecarboxaldehyde is ruled by vibrational effects. Mol Phys 2021. [DOI: 10.1080/00268976.2021.1955988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Silvia Alessandrini
- Scuola Normale Superiore, Pisa, Italy
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Bologna, Italy
| | - Mattia Melosso
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Bologna, Italy
| | - Ningjing Jiang
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Bologna, Italy
| | - Luca Bizzocchi
- Scuola Normale Superiore, Pisa, Italy
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Bologna, Italy
| | - Luca Dore
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Bologna, Italy
| | - Cristina Puzzarini
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Bologna, Italy
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48
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Changala PB. Vibronic mean-field and perturbation theory for Jahn-Teller and pseudo-Jahn-Teller molecules. Mol Phys 2021. [DOI: 10.1080/00268976.2021.1962556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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49
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From Molecular to Cluster Properties: Rotational Spectroscopy of 2-Aminopyridine and of Its Biomimetic Cluster with Water. Molecules 2021; 26:molecules26226870. [PMID: 34833962 PMCID: PMC8623352 DOI: 10.3390/molecules26226870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 11/16/2022] Open
Abstract
We report the observation and analysis of the rotational spectrum of a 1:1 cluster between 2-aminopyridine and water (AMW) carried out with supersonic expansion Fourier transform microwave spectroscopy at 4.7–16.5 GHz. Measurements of the 2-aminopyridine monomer (AMP) were also extended up to 333 GHz for the room-temperature rotational spectrum and to resolved hyperfine splitting resulting from the presence of two 14N quadrupolar nuclei. Supersonic expansion measurements for both AMP and AMW were also carried out for two synthesized isotopic species with single deuteration on the phenyl ring. Nuclear quadrupole hyperfine structure has also been resolved for AMW and the derived splitting constants were used as an aid in structural analysis. The structure of the AMW cluster was determined from the three sets of available rotational constants and the hydrogen bonding configuration is compared with those for clusters with water of similarly sized single-ring molecules. Experimental results aided by quantum chemistry computations allow the conclusion that the water molecule is unusually strongly bound by two hydrogen bonds, OH...N and O...HN, to the NCNH atomic chain of AMP with the potential to replace hydrogen bonds to the identical structural segment in cytosine and adenine in CT and AT nucleic acid base pairs.
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50
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Barone V, Puzzarini C, Mancini G. Integration of theory, simulation, artificial intelligence and virtual reality: a four-pillar approach for reconciling accuracy and interpretability in computational spectroscopy. Phys Chem Chem Phys 2021; 23:17079-17096. [PMID: 34346437 DOI: 10.1039/d1cp02507d] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The established pillars of computational spectroscopy are theory and computer based simulations. Recently, artificial intelligence and virtual reality are becoming the third and fourth pillars of an integrated strategy for the investigation of complex phenomena. The main goal of the present contribution is the description of some new perspectives for computational spectroscopy, in the framework of a strategy in which computational methodologies at the state of the art, high-performance computing, artificial intelligence and virtual reality tools are integrated with the aim of improving research throughput and achieving goals otherwise not possible. Some of the key tools (e.g., continuous molecular perception model and virtual multifrequency spectrometer) and theoretical developments (e.g., non-periodic boundaries, joint variational-perturbative models) are shortly sketched and their application illustrated by means of representative case studies taken from recent work by the authors. Some of the results presented are already well beyond the state of the art in the field of computational spectroscopy, thereby also providing a proof of concept for other research fields.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.
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