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Uribe L, Lazzari F, Di Grande S, Crisci L, Mendolicchio M, Barone V. Accurate structures and rotational constants of bicyclic monoterpenes at DFT cost by means of the bond-corrected Pisa composite scheme (BPCS). J Chem Phys 2024; 161:014307. [PMID: 38958160 DOI: 10.1063/5.0216384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 06/17/2024] [Indexed: 07/04/2024] Open
Abstract
The structural, conformational, and spectroscopic properties in the gas phase of 20 bicyclic monoterpenes and monoterpenoids have been analyzed by a new accurate, reduced-cost computational strategy. In detail, the revDSD-PBEP86 double-hybrid functional in conjunction with the D3BJ empirical dispersion corrections and a suitable triple-zeta basis set provides accurate geometrical parameters, whence equilibrium rotational constants, which are further improved by proper account of core-valence correlation. Average deviations within 0.1% between computed and experimental rotational constants are reached when taking into account the vibrational corrections obtained by the B3LYP functional in conjunction with a double-zeta basis set in the framework of second-order vibrational perturbation theory. In addition to their intrinsic interest, the studied terpenes further extend the panel of systems for which the proposed strategy has provided accurate results at density functional theory cost. Therefore, a very accurate yet robust and user-friendly tool is now available for systematic investigations of the role of stereo-electronic effects on the properties of large systems of current technological and/or biological interest by experimentally oriented researchers.
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Affiliation(s)
- Lina Uribe
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Scuola Superiore Meridionale, Largo San Marcellino 10, 80138 Napoli, Italy
| | - Federico Lazzari
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Silvia Di Grande
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Scuola Superiore Meridionale, Largo San Marcellino 10, 80138 Napoli, Italy
| | - Luigi Crisci
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Marco Mendolicchio
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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2
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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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Di Grande S, Barone V. Toward Accurate Quantum Chemical Methods for Molecules of Increasing Dimension: The New Family of Pisa Composite Schemes. J Phys Chem A 2024; 128:4886-4900. [PMID: 38847454 DOI: 10.1021/acs.jpca.4c01673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
The new versions of the Pisa composite scheme introduced in the present paper are based on the careful selection of different quantum chemical models for energies, geometries, and vibrational frequencies, with the aim of maximizing the accuracy of the overall description while retaining a reasonable cost for all the steps. In particular, the computation of accurate electronic energies has been further improved introducing more reliable complete basis set extrapolations and estimation of core-valence correlation, together with improved basis sets for third-row atoms. Furthermore, the reduced-cost frozen natural orbital (FNO) model has been introduced and validated for large molecules. Accurate molecular structures can be obtained avoiding complete basis set extrapolation and evaluating core-valence correlation at the MP2 level. Unfortunately, analytical gradients are not available for the FNO version of the model. Therefore, for large molecules, an accurate reduced-cost alternative is offered by evaluation of valence contributions with a double-hybrid functional in conjunction with the same MP2 contribution for core-valence correlation or by means of a one-parameter approximation. The same double-hybrid functional and basis set are employed to evaluate zero-point energies and partition functions. After the validation of the new models for small systems, a panel of molecular bricks of life has been used to analyze their performances for problems of current fundamental or technological interest. The fully black-box implementation of the computational workflow paves the way toward the accurate yet not prohibitively expensive study of medium- to large-sized molecules also by experimentally oriented researchers.
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Affiliation(s)
- Silvia Di Grande
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Scuola Superiore Meridionale, Largo San Marcellino 10, 80138 Napoli, Italy
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4
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Sahoo NP, Franke PR, Stanton JF. On the performance of composite schemes in determining equilibrium molecular structures. J Comput Chem 2024; 45:1419-1427. [PMID: 38450778 DOI: 10.1002/jcc.27312] [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: 10/15/2023] [Revised: 12/10/2023] [Accepted: 12/12/2023] [Indexed: 03/08/2024]
Abstract
Determination of equilibrium molecular structures is an essential ingredient in predicting spectroscopic parameters that help in identifying molecular carriers of microwave transitions. Here, the performance of two different ab initio composite approaches for obtaining equilibrium structures, "energy scheme" and "geometry scheme," is explored and compared to semi-experimental equilibrium structures. This study is performed for a set of 11 molecules which includes diatomics, linear triatomics, and a few non-linear molecules. The ab initio calculations were performed using three tiers of composite chemical recipes. The current results show that as the overall rigor of calculation is increased, the semi-experimental and the ab initio numbers agree to within 0.0003 Å for all molecules in the test set. The composite approach based on correcting the potential energy surface (energy scheme) and the one based on correcting the geometry directly (geometry scheme) show excellent agreement with each other. This work represents a step toward development of efficient and highly accurate procedures for computing ab initio equilibrium structures.
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Affiliation(s)
- Nitai P Sahoo
- Department of Chemistry, University of Florida, Gainesvillle, Florida, USA
| | - Peter R Franke
- Department of Chemistry, University of Florida, Gainesvillle, Florida, USA
| | - John F Stanton
- Department of Chemistry, University of Florida, Gainesvillle, Florida, USA
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5
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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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6
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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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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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8
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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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9
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Barone V. Quantum chemistry meets high-resolution spectroscopy for characterizing the molecular bricks of life in the gas-phase. Phys Chem Chem Phys 2024; 26:5802-5821. [PMID: 38099409 DOI: 10.1039/d3cp05169b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
Computation of accurate geometrical structures and spectroscopic properties of large flexible molecules in the gas-phase is tackled at an affordable cost using a general exploration/exploitation strategy. The most distinctive feature of the approach is the careful selection of different quantum chemical models for energies, geometries and vibrational frequencies with the aim of maximizing the accuracy of the overall description while retaining a reasonable cost for all the steps. In particular, a composite wave-function method is used for energies, whereas a double-hybrid functional (with the addition of core-valence correlation) is employed for geometries and harmonic frequencies and a cheaper hybrid functional for anharmonic contributions. A thorough benchmark based on a wide range of prototypical molecular bricks of life shows that the proposed strategy is close to the accuracy of state-of-the-art composite wave-function methods, and is applicable to much larger systems. A freely available web-utility post-processes the geometries optimized by standard electronic structure codes paving the way toward the accurate yet not prohibitively expensive study of medium- to large-sized molecules by experimentally-oriented researchers.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy.
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10
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Franke PR, Stanton JF. Influence of fourth-order vibrational corrections on semi-experimental (reSE) structures of linear molecules. J Chem Phys 2024; 160:014102. [PMID: 38174791 DOI: 10.1063/5.0177694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
Semi-experimental structures (reSE) are derived from experimental ground state rotational constants combined with theoretical vibrational corrections. They permit a meaningful comparison with equilibrium structures based on high-level ab initio calculations. Typically, the vibrational corrections are evaluated with second-order vibrational perturbation theory (VPT2). The amount of error introduced by this approximation is generally thought to be small; however, it has not been thoroughly quantified. Herein, we assess the accuracy of theoretical vibrational corrections by extending the treatment to fourth order (VPT4) for a series of small linear molecules. Typical corrections to bond distances are on the order of 10-5 Å. Larger corrections, nearly 0.0002 Å, are obtained to the bond lengths of NCCN and CNCN. A borderline case is CCCO, which will likely require variational computations for a satisfactory answer. Treatment of vibrational effects beyond VPT2 will thus be important when one wishes to know bond distances confidently to four decimal places (10-4 Å). Certain molecules with shallow bending potentials, e.g., HOC+, are not amenable to a VPT2 description and are not improved by VPT4.
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Affiliation(s)
- Peter R Franke
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA
| | - John F Stanton
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA
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11
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Esselman BJ, Zdanovskaia MA, Owen AN, Stanton JF, Woods RC, McMahon RJ. Precise Equilibrium Structure of Benzene. J Am Chem Soc 2023; 145:21785-21797. [PMID: 37774420 DOI: 10.1021/jacs.3c03109] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2023]
Abstract
Recent advances in gas-phase structure determination afford outstanding agreement between the CCSD(T)/cc-pCVTZ-corrected semi-experimental (reSE) equilibrium structures and their corresponding best theoretical estimates (BTEs) of the equilibrium structures (re) based upon corrections to the CCSD(T)/cc-pCV5Z geometries for the aromatic heterocycles pyrimidine and pyridazine. Herein, that same analysis is extended to the fundamental aromatic molecule benzene, using published experimental spectroscopic data for a total of 11 available isotopologues. The incorporation of rotational constants from all of these isotopologues and CCSD(T) corrections to address the impacts of both the vibration-rotation interaction and electron-mass distribution results in a highly precise and accurate reSE structure. The CCSD(T)/cc-pCV5Z optimized geometry has been further corrected to address a finite basis set, untreated electron correlation, relativistic effects, and a breakdown of the Born-Oppenheimer approximation. This analysis achieves outstanding agreement between the re (BTE) and reSE structural parameters of benzene to a highly satisfying level (0.0001 Å), an agreement that surpasses our recently published structures of the aforementioned nitrogen-substituted benzene analogues. The D6h geometry of benzene is now known to an unprecedented precision: RC-C = 1.3913 (1) Å and RC-H = 1.0809 (1) Å. The mutual agreement between theory and experiment presented in this work validates both, substantially resolving all discrepancies between the reSE and theoretical re structures available in the literature.
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Affiliation(s)
- Brian J Esselman
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706-1322, United States
| | - Maria A Zdanovskaia
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706-1322, United States
| | - Andrew N Owen
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706-1322, United States
| | - John F Stanton
- Quantum Theory Project, Departments of Physics and Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - R Claude Woods
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706-1322, United States
| | - Robert J McMahon
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706-1322, United States
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12
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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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13
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Franke PR, Stanton JF. Rotamers of Methanediol: Composite Ab Initio Predictions of Structures, Frequencies, and Rovibrational Constants. J Phys Chem A 2023; 127:924-937. [PMID: 36657011 DOI: 10.1021/acs.jpca.2c06686] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Geminal diols are known to be important intermediates in atmospheric ozonolysis and the aerosol cycle. Recently, the simplest member of this class, methanediol, was interrogated in the gas phase with infrared spectroscopy. To aid in future spectroscopic investigations of methanediol, including in the interstellar medium, we report fundamental frequencies and rovibrational constants for the two rotamers of this molecule using ab initio composite methods along with vibrational perturbation theory. Sensitivity of the predictions to the level of theory and the treatment of anharmonic resonances are carefully assessed. The OH stretching harmonic frequencies of both rotamers are particularly sensitive to the level of theory. The CH stretches of the Cs rotamer are sensitive to the treatment of anharmonic resonances with VPT2-based effective Hamiltonian models. Equilibrium bond distances and harmonic frequencies are converged conservatively to within 0.0005 Å and 3 cm-1, respectively. The effect of tunneling on the rotational constants is investigated with a 2D variational calculation, based on a relaxed hydroxyl torsional potential energy surface. Tunneling is found to be negligible in the lower energy C2 rotamer but should modify the rotational constants of the Cs rotamer on the order of MHz, giving rise to rotational line splittings of the same order. The rovibrational constants of the Cs rotamer are dominated by hydroxyl torsional effects, and here we see evidence for the breakdown of vibrational perturbation theory.
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Affiliation(s)
- Peter R Franke
- Department of Chemistry, University of Florida, Gainesville, Florida32611, United States
| | - John F Stanton
- Department of Chemistry, University of Florida, Gainesville, Florida32611, United States
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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: 17] [Impact Index Per Article: 17.0] [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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15
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Bunn HA, Esselman BJ, Franke PR, Kougias SM, McMahon RJ, Stanton JF, Widicus Weaver SL, Woods RC. Millimeter/Submillimeter-wave Spectroscopy and the Semi-experimental Equilibrium ( reSE) Structure of 1 H-1,2,4-Triazole ( c-C 2H 3N 3). J Phys Chem A 2022; 126:8196-8210. [DOI: 10.1021/acs.jpca.2c06038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Hayley A. Bunn
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin53706, United States
| | - Brian J. Esselman
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin53706, United States
| | - Peter R. Franke
- Department of Chemistry, University of Florida, Gainesville, Florida32611-7200, United States
| | - Samuel M. Kougias
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin53706, United States
| | - Robert J. McMahon
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin53706, United States
| | - John F. Stanton
- Quantum Theory Project, Departments of Physics and Chemistry, University of Florida, Gainesville, Florida32611-7200, United States
| | | | - R. Claude Woods
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin53706, United States
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16
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Buschmann P, Lengsfeld KG, Djahandideh J, Grabow JU. From rotational resolved spectra to an extended increment system of planar moments allowing ad-hoc conformational identification – Exemplification by the broadband microwave spectrum of α-hydroxyisobutyric acid. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131805] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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17
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Li X, Spada L, Alessandrini S, Zheng Y, Lengsfeld KG, Grabow J, Feng G, Puzzarini C, Barone V. Gestapelt, nicht geklebt: Enthüllung der π→π*‐Wechselwirkung mithilfe des Benzofuran‐Formaldehyd‐Komplexes. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202113737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Xiaolong Li
- School of Chemistry and Chemical Engineering Chongqing University Daxuecheng South Rd. 55 Chongqing 401331 China
| | - Lorenzo Spada
- Scuola Normale Superiore Piazza dei Cavalieri 7 56126 Pisa Italien
| | - Silvia Alessandrini
- Scuola Normale Superiore Piazza dei Cavalieri 7 56126 Pisa Italien
- Dipartimento di Chimica “Giacomo Ciamician” Università di Bologna Via F. Selmi 2 40126 Bologna Italien
| | - Yang Zheng
- School of Chemistry and Chemical Engineering Chongqing University Daxuecheng South Rd. 55 Chongqing 401331 China
| | - Kevin Gregor Lengsfeld
- Institut für Physikalische Chemie und Elektrochemie Gottfried Wilhelm Leibniz Universität Hannover Callinstraße 3A 30167 Hannover Deutschland
| | - Jens‐Uwe Grabow
- Institut für Physikalische Chemie und Elektrochemie Gottfried Wilhelm Leibniz Universität Hannover Callinstraße 3A 30167 Hannover Deutschland
| | - Gang Feng
- School of Chemistry and Chemical Engineering Chongqing University Daxuecheng South Rd. 55 Chongqing 401331 China
| | - Cristina Puzzarini
- Dipartimento di Chimica “Giacomo Ciamician” Università di Bologna Via F. Selmi 2 40126 Bologna Italien
| | - Vincenzo Barone
- Scuola Normale Superiore Piazza dei Cavalieri 7 56126 Pisa Italien
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18
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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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19
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Ceselin G, Barone V, Tasinato N. Accurate Biomolecular Structures by the Nano-LEGO Approach: Pick the Bricks and Build Your Geometry. J Chem Theory Comput 2021; 17:7290-7311. [PMID: 34666488 PMCID: PMC8582257 DOI: 10.1021/acs.jctc.1c00788] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The determination
of accurate equilibrium molecular structures
plays a fundamental role for understanding many physical–chemical
properties of molecules, ranging from the precise evaluation of the
electronic structure to the analysis of the role played by dynamical
and environmental effects in tuning their overall behavior. For small
semi-rigid systems in the gas phase, state-of-the-art quantum chemical
computations rival the most sophisticated experimental (from, for
example, high-resolution spectroscopy) results. For larger molecules,
more effective computational approaches must be devised. To this end,
we have further enlarged the compilation of available semi-experimental
(SE) equilibrium structures, now covering the most important fragments
containing H, B, C, N, O, F, P, S, and Cl atoms collected in the new
SE100 database. Next, comparison with geometries optimized by methods
rooted in the density functional theory showed that the already remarkable
results delivered by PW6B95 and, especially, rev-DSDPBEP86 functionals
can be further improved by a linear regression (LR) approach. Use
of template fragments (taken from the SE100 library) together with
LR estimates for the missing interfragment parameters paves the route
toward accurate structures of large molecules, as witnessed by the
very small deviations between computed and experimental rotational
constants. The whole approach has been implemented in a user-friendly
tool, termed nano-LEGO, and applied to a number of demanding case
studies.
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Affiliation(s)
- Giorgia Ceselin
- Scuola Normale Superiore, Piazza Dei Cavalieri 7, I-56126 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza Dei Cavalieri 7, I-56126 Pisa, Italy
| | - Nicola Tasinato
- Scuola Normale Superiore, Piazza Dei Cavalieri 7, I-56126 Pisa, Italy
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20
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Li X, Spada L, Alessandrini S, Zheng Y, Lengsfeld KG, Grabow JU, Feng G, Puzzarini C, Barone V. Stacked but not Stuck: Unveiling the Role of π→π* Interactions with the Help of the Benzofuran-Formaldehyde Complex. Angew Chem Int Ed Engl 2021; 61:e202113737. [PMID: 34697878 PMCID: PMC9298890 DOI: 10.1002/anie.202113737] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Indexed: 12/14/2022]
Abstract
The 1:1 benzofuran–formaldehyde complex has been chosen as model system for analyzing π→π* interactions in supramolecular organizations involving heteroaromatic rings and carbonyl groups. A joint “rotational spectroscopy–quantum chemistry” strategy unveiled the dominant role of π→π* interactions in tuning the intermolecular interactions of such adduct. The exploration of the intermolecular potential energy surface led to the identification of 14 low‐energy minima, with 4 stacked isomers being more stable than those linked by hydrogen bond or lone‐pair→π interactions. All energy minima are separated by loose transition states, thus suggesting an effective relaxation to the global minimum under the experimental conditions. This expectation has been confirmed by the experimental detection of only one species, which was unambiguously assigned owing to the computation of accurate spectroscopic parameters and the characterization of 11 isotopologues. The large number of isotopic species opened the way to the determination of the first semi‐experimental equilibrium structure for a molecular complex of such a dimension.
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Affiliation(s)
- Xiaolong Li
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, Chongqing, 401331, China
| | - Lorenzo Spada
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - Silvia Alessandrini
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy.,Dipartimento di Chimica "Giacomo Ciamician", University of Bologna, Via F. Selmi 2, 40126, Bologna, Italy
| | - Yang Zheng
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, Chongqing, 401331, China
| | - Kevin Gregor Lengsfeld
- Institut für Physikalische Chemie and Elektrochemie, Gottfried Wilhelm Leibniz Universität Hannover, Callinstrasse 3A, 30167, Hannover, Germany
| | - Jens-Uwe Grabow
- Institut für Physikalische Chemie and Elektrochemie, Gottfried Wilhelm Leibniz Universität Hannover, Callinstrasse 3A, 30167, Hannover, Germany
| | - Gang Feng
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, Chongqing, 401331, China
| | - Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician", University of Bologna, Via F. Selmi 2, 40126, Bologna, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy
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21
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Dindić C, Lüchow A, Vogt N, Demaison J, Nguyen HVL. Equilibrium Structure in the Presence of Methyl Internal Rotation: Microwave Spectroscopy and Quantum Chemistry Study of the Two Conformers of 2-Acetylfuran. J Phys Chem A 2021; 125:4986-4997. [PMID: 34080419 DOI: 10.1021/acs.jpca.1c01733] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
For 2-acetylfuran, quantum chemistry predicted and proton magnetic resonance study reported two conformers, anti and syn, differing in the position of the carbonyl group with respect to the O1-C2 bond of the furan ring. The microwave spectrum of the title molecule was recorded in the frequency range from 2 to 26.5 GHz using a molecular jet Fourier transform microwave spectrometer, confirming the presence of both conformers. Spectroscopic parameters such as the rotational and centrifugal distortion constants could be determined with high precision. The spectra of all 13C- and 18O-isotopologues of the energetically more favorable anti-conformer could be assigned, allowing the experimental determination of bond lengths and bond angles from the heavy atom substitution rs and the semi-experimental equilibrium reSE structures. Splittings arising from the internal rotation of the acetyl methyl group could be resolved for both conformers as well as for all assigned isotopologues, from which the barrier to methyl internal rotation was determined. The torsional barrier is largely invariant at around 319 cm-1 in the parent species of anti-2-acetylfuran and its isotopologues, showing that though isotopic substitution greatly influences the rotational properties of the molecule and causes a different microwave spectrum, its effect on the methyl torsion is negligible. On the other hand, conformational effects play a decisive role, as the torsional barrier of 239.780(13) cm-1 found for syn-2-acetylfuran differs significantly from the value for anti-2-acetylfuran. The results are compared and discussed with other methyl-substituted furan derivatives and acetyl group containing ketones for a better understanding of different effects influencing molecular geometry parameters and methyl internal rotations.
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Affiliation(s)
- Christina Dindić
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52074 Aachen, Germany
| | - Arne Lüchow
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52074 Aachen, Germany
| | - Natalja Vogt
- Section of Chemical Information Systems, University of Ulm, Albert-Einstein-Allee 47, 89069 Ulm, Germany.,Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russian Federation
| | - Jean Demaison
- Section of Chemical Information Systems, University of Ulm, Albert-Einstein-Allee 47, 89069 Ulm, Germany
| | - Ha Vinh Lam Nguyen
- Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA), CNRS UMR 7583, Université Paris-Est Créteil, Université de Paris, Institut Pierre Simon Laplace, 61 Avenue du Général de Gaulle, 94010 Créteil, France.,Institut Universitaire de France (IUF), 1 rue Descartes, 75231 Paris Cedex 05, France
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22
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Structural changes upon electronic excitation in 1,3-dimethoxybenzene from Franck-Condon/rotational constants fits of the fluorescence emission spectra †. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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23
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Saxena S, Panchagnula S, Sanz ME, Pérez C, Evangelisti L, Pate BH. Structural Changes Induced by Quinones: High-Resolution Microwave Study of 1,4-Naphthoquinone. Chemphyschem 2020; 21:2579-2584. [PMID: 32954594 PMCID: PMC7756206 DOI: 10.1002/cphc.202000665] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/26/2020] [Indexed: 12/20/2022]
Abstract
1,4-Naphthoquinone (1,4-NQ) is an important product of naphthalene oxidation, and it appears as a motif in many biologically active compounds. We have investigated the structure of 1,4-NQ using chirped-pulse Fourier transform microwave spectroscopy and quantum chemistry calculations. The rotational spectra of the parent species, and its 13 C and 18 O isotopologues were observed in natural abundance, and their spectroscopic parameters were obtained. This allowed the determination of the substitution rs , mass-weighted rm and semi-experimental reSE structures of 1,4-NQ. The obtained structural parameters show that the quinone moiety mainly changes the structure of the benzene ring where it is inserted, modifying the C-C bonds to having predominantly single or double bond character. Furthermore, the molecular electrostatic surface potential reveals that the quinone ring becomes electron deficient while the benzene ring remains a nucleophile. The most electrophilic areas are the hydrogens attached to the double bond in the quinone ring. Knowledge of the nucleophilic and electrophilic areas in 1,4-NQ will help understanding its behaviour interacting with other molecules and guide modifications to tune its properties.
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Affiliation(s)
- Shefali Saxena
- Department of ChemistryKing's College LondonLondonUnited Kingdom
| | | | - M. Eugenia Sanz
- Department of ChemistryKing's College LondonLondonUnited Kingdom
| | - Cristóbal Pérez
- Department of ChemistryUniversity of VirginiaCharlottesvilleVAUSA
| | - Luca Evangelisti
- Department of ChemistryUniversity of VirginiaCharlottesvilleVAUSA
- Department of Chemistry “G. Ciamician”University of BolognaVia Selmi 2Bologna40126Italy
| | - Brooks H. Pate
- Department of ChemistryUniversity of VirginiaCharlottesvilleVAUSA
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24
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Ye H, Mendolicchio M, Kruse H, Puzzarini C, Biczysko M, Barone V. The challenging equilibrium structure of HSSH: Another success of the rotational spectroscopy / quantum chemistry synergism. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.127933] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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25
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Uriarte I, Reviriego F, Calabrese C, Elguero J, Kisiel Z, Alkorta I, Cocinero EJ. Bond Length Alternation Observed Experimentally: The Case of 1H‐Indazole. Chemistry 2019; 25:10172-10178. [DOI: 10.1002/chem.201901666] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Iciar Uriarte
- Departamento de Química Física, Facultad de Ciencia y TecnologíaUniversidad del País Vasco (UPV/EHU) Apartado 644 48080 Bilbao Spain
- Biofisika InstituteCSICUPV/EHU Apartado 644 48080 Bilbao Spain
| | - Felipe Reviriego
- Instituto de Ciencia y Tecnología de Polímeros (ICTP)CSIC c/Juan de la Cierva, 3 28006 Madrid Spain
| | - Camilla Calabrese
- Departamento de Química Física, Facultad de Ciencia y TecnologíaUniversidad del País Vasco (UPV/EHU) Apartado 644 48080 Bilbao Spain
- Biofisika InstituteCSICUPV/EHU Apartado 644 48080 Bilbao Spain
| | - José Elguero
- Instituto de Química MédicaCSIC C/Juan de la Cierva, 3 28006 Madrid Spain
| | - Zbigniew Kisiel
- Institute of PhysicsPolish Academy of Sciences Al. Lotnikow 32/46 02-668 Warszawa Poland
| | - Ibon Alkorta
- Instituto de Química MédicaCSIC C/Juan de la Cierva, 3 28006 Madrid Spain
| | - Emilio J. Cocinero
- Departamento de Química Física, Facultad de Ciencia y TecnologíaUniversidad del País Vasco (UPV/EHU) Apartado 644 48080 Bilbao Spain
- Biofisika InstituteCSICUPV/EHU Apartado 644 48080 Bilbao Spain
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26
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Puzzarini C, Bloino J, Tasinato N, Barone V. Accuracy and Interpretability: The Devil and the Holy Grail. New Routes across Old Boundaries in Computational Spectroscopy. Chem Rev 2019; 119:8131-8191. [DOI: 10.1021/acs.chemrev.9b00007] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Cristina Puzzarini
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Via F. Selmi 2, I-40126 Bologna, Italy
| | - Julien Bloino
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Nicola Tasinato
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
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27
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Saragi RT, Juanes M, Abad JL, Lesarri A, Pinacho R, Rubio JE. Rotational spectroscopy of organophosphorous chemical agents: cresyl and phenyl saligenin phosphates. Phys Chem Chem Phys 2019; 21:16418-16422. [DOI: 10.1039/c9cp03093j] [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
Cresyl and phenyl saligenin phosphate have been probed in a jet expansion by broadband chirp-excitation microwave spectroscopy, revealing the most stable confirmations and their structural properties.
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Affiliation(s)
- Rizalina Tama Saragi
- Departamento de Química Física y Química Inorgánica – IU CINQUIMA
- Facultad de Ciencias
- Universidad de Valladolid
- 47011 Valladolid
- Spain
| | - Marcos Juanes
- Departamento de Química Física y Química Inorgánica – IU CINQUIMA
- Facultad de Ciencias
- Universidad de Valladolid
- 47011 Valladolid
- Spain
| | - José Luis Abad
- Departamento de Química Biológica
- Instituto de Química Avanzada de Cataluña (IQAC-CSIC)
- Consejo Superior de Investigaciones Científicas (CSIC)
- 08034 Barcelona
- Spain
| | - Alberto Lesarri
- Departamento de Química Física y Química Inorgánica – IU CINQUIMA
- Facultad de Ciencias
- Universidad de Valladolid
- 47011 Valladolid
- Spain
| | - Ruth Pinacho
- Departamento de Electrónica
- ETSIT
- Universidad de Valladolid
- 47011 Valladolid
- Spain
| | - José Emiliano Rubio
- Departamento de Electrónica
- ETSIT
- Universidad de Valladolid
- 47011 Valladolid
- Spain
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28
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Demaison J, Vogt N, Saragi RT, Juanes M, Rudolph HD, Lesarri A. The S−S Bridge: A Mixed Experimental‐Computational Estimation of the Equilibrium Structure of Diphenyl Disulfide. Chemphyschem 2018; 20:366-373. [DOI: 10.1002/cphc.201800973] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 11/26/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Jean Demaison
- Section of Chemical Information SystemsUniversity of Ulm 89069 Ulm Germany
| | - Natalja Vogt
- Section of Chemical Information SystemsUniversity of Ulm 89069 Ulm Germany
- Department of ChemistryLomonosov Moscow State University 119992 Moscow Russia
| | - Rizalina Tama Saragi
- Departamento de Química Física y Química Inorgánica - IU CINQUIMA, Facultad de CienciasUniversidad de Valladolid, Paseo de Belén, 7 47011 Valladolid Spain
| | - Marcos Juanes
- Departamento de Química Física y Química Inorgánica - IU CINQUIMA, Facultad de CienciasUniversidad de Valladolid, Paseo de Belén, 7 47011 Valladolid Spain
| | | | - Alberto Lesarri
- Departamento de Química Física y Química Inorgánica - IU CINQUIMA, Facultad de CienciasUniversidad de Valladolid, Paseo de Belén, 7 47011 Valladolid Spain
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29
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Belyakov AV, Kulishenko RY, Oskorbin AA. Semiexperimental equilibrium molecular structures of the maleimide and phthalimide. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1510139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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30
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Morgan WJ, Matthews DA, Ringholm M, Agarwal J, Gong JZ, Ruud K, Allen WD, Stanton JF, Schaefer HF. Geometric Energy Derivatives at the Complete Basis Set Limit: Application to the Equilibrium Structure and Molecular Force Field of Formaldehyde. J Chem Theory Comput 2018; 14:1333-1350. [DOI: 10.1021/acs.jctc.7b01138] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- W. James Morgan
- Center for Computational Quantum Chemistry (CCQC), University of Georgia, Athens, Georgia 30602, United States
| | - Devin A. Matthews
- Institute for Computational Engineering and Sciences (ICES), University of Texas at Austin, Austin, Texas 78712, United States
| | - Magnus Ringholm
- Hylleraas Centre for Quantum Molecular Science, Department of Chemistry, University of Tromsø − The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Jay Agarwal
- Center for Computational Quantum Chemistry (CCQC), University of Georgia, Athens, Georgia 30602, United States
| | - Justin Z. Gong
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Kenneth Ruud
- Hylleraas Centre for Quantum Molecular Science, Department of Chemistry, University of Tromsø − The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Wesley D. Allen
- Center for Computational Quantum Chemistry (CCQC), University of Georgia, Athens, Georgia 30602, United States
| | - John F. Stanton
- Quantum Theory Project, University of Florida, Gainesville, Florida 32611, United States
| | - Henry F. Schaefer
- Center for Computational Quantum Chemistry (CCQC), University of Georgia, Athens, Georgia 30602, United States
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31
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Puzzarini C, Barone V. Diving for Accurate Structures in the Ocean of Molecular Systems with the Help of Spectroscopy and Quantum Chemistry. Acc Chem Res 2018; 51:548-556. [PMID: 29400950 DOI: 10.1021/acs.accounts.7b00603] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The prediction and interpretation of structural properties are the starting points for a deep understanding of thermochemistry, kinetics, and spectroscopic signatures of molecular systems. To give an example, detailed knowledge of the conformational behavior of the main building blocks of biomolecules in the gas phase (i.e., without the perturbing effect of the environment) is a mandatory prerequisite toward the understanding of the role played by different interactions in determining the biological activity in terms of structure-activity relationships. The first step to take is an unambiguous definition of molecular structure. We address the so-called Born-Oppenheimer equilibrium structure, which is defined in a rigorous manner and isotopically independent, and the target accuracy. For the latter, we aim at so-called "spectroscopic" accuracy, which implies uncertainties of a few milliangstroms for bond lengths and smaller than a tenth of degree for angles. If on one side the continuous enhancements of the experimental techniques give access to new and unprecedented spectroscopic determinations, on the other side they require increasing efforts for an unbiased interpretation and analysis. Among the pieces of information, accurate molecular structures play a particularly important role. Indeed, there is a strong relationship between the experimental outcome and the electronic structure of the system. Spectroscopic techniques, in particular those exploited in the gas phase, are therefore accurate and reliable sources for structural information. However, it is seldom straightforward to derive molecular structures directly from the experimental information. Indeed, even in the favorable case of investigations in the gas phase, vibrational effects are always present, and disentangling their contributions requires collection of information for all vibrational modes, a nearly impossible task. To overcome these limitations, joint theory-spectroscopy strategies can be identified, which are referred to as "top-down" and "bottom-up". The first approach, denoted as the semiexperimental approach, relies on extracting from experimental outcomes the equilibrium structure by using quantum-chemical computations to recover vibrational effects. The bottom-up approach consists in verifying the computed equilibrium geometry by means of a comparison between calculated and experimental spectroscopic parameters that probe structural characteristics. In this contribution, we try to review the most important challenges in accurate molecular structure determinations, with particular emphasis on the "solution" provided by a joint theoretical-experimental approach and on the current state of the art. Starting from the illustration of different strategies, we proceed by addressing the increasing complexity in the derivation of equilibrium geometries: we start from the construction of a database of accurate structures, we then face the problem of extending the dimension of the systems amenable to accurate structural determinations, and finally we move to the challenge of understanding the nature of intermolecular interactions.
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Affiliation(s)
- Cristina Puzzarini
- Dipartimento di
Chimica “Giacomo Ciamician”, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei
Cavalieri 7, I-56126 Pisa, Italy
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32
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Den T, Menzi S, Frey HM, Leutwyler S. Accurate gas-phase structure of para-dioxane by fs Raman rotational coherence spectroscopy and ab initio calculations. J Chem Phys 2017; 147:074306. [PMID: 28830173 DOI: 10.1063/1.4997633] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
p-Dioxane is non-polar, hence its rotational constants cannot be determined by microwave rotational coherence spectroscopy (RCS). We perform high-resolution gas-phase rotational spectroscopy of para-dioxane-h8 and -d8 using femtosecond time-resolved Raman RCS in a gas cell at T = 293 K and in a pulsed supersonic jet at T∼130 K. The inertial tensor of p-dioxane-h8 is strongly asymmetric, leading to a large number of asymmetry transients in its RCS spectrum. In contrast, the d8-isotopomer is a near-oblate symmetric top that exhibits a much more regular RCS spectrum with few asymmetry transients. Fitting the fs Raman RCS transients of p-dioxane-h8 to an asymmetric-top model yields the ground-state rotational constants A0 = 5084.4(5) MHz, B0 = 4684(1) MHz, C0 = 2744.7(8) MHz, and (A0 + B0)/2 = 4884.5(7) MHz (±1σ). The analogous values for p-dioxane-d8 are A0 = 4083(2) MHz, B0 = 3925(4) MHz, C0 = 2347.1(6) MHz, and (A0 + B0)/2 = 4002.4(6) MHz. We determine the molecular structure with a semi-experimental approach involving the highly correlated coupled-cluster singles, doubles and iterated triples method and the cc-pCVXZ basis set series from double- to quadruple-zeta (X = D, T, Q). Combining the calculated vibrationally averaged rotational constants A0calc(X),B0calc(X),C0calc(X) for increasing basis-set size X with non-linear extrapolation to the experimental constants A0exp,B0exp,C0exp allows to determine the equilibrium ground state structure of p-dioxane. For instance, the equilibrium C-C and C-O bond lengths are re(CC) = 1.5135(3) Å and re(CO) = 1.4168(4) Å, and the four axial C-H bond lengths are 0.008 Å longer than the four equatorial ones. The latter is ascribed to the trans-effect (anomeric effect), i.e., the partial delocalization of the electron lone-pairs on the O atoms that are oriented trans, relative to the axial CH bonds.
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Affiliation(s)
- Takuya Den
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3000 Bern 9, Switzerland
| | - Samuel Menzi
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3000 Bern 9, Switzerland
| | - Hans-Martin Frey
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3000 Bern 9, Switzerland
| | - Samuel Leutwyler
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3000 Bern 9, Switzerland
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33
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Mendolicchio M, Penocchio E, Licari D, Tasinato N, Barone V. Development and Implementation of Advanced Fitting Methods for the Calculation of Accurate Molecular Structures. J Chem Theory Comput 2017; 13:3060-3075. [PMID: 28437115 DOI: 10.1021/acs.jctc.7b00279] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The determination of accurate equilibrium molecular structures plays a fundamental role for understanding many physical-chemical properties of molecules, ranging from the precise evaluation of the electronic structure to the analysis of dynamical and environmental effects in tuning their overall behavior. For this purpose the so-called semiexperimental approach, based on a nonlinear least-squares fit of the moments of inertia associated with a set of available isotopologues, allows one to obtain very accurate results, without the unfavorable computational cost characterizing high-level quantum chemical methods. In the present work the MSR (Molecular Structure Refinement) software for the determination of equilibrium structures by means of the semiexperimental approach is presented, and its implementation is discussed in some detail. The software, which is interfaced with a powerful graphical user interface, includes different optimization algorithms, an extended error analysis, and a number of advanced features, the most remarkable ones concerning the choice of internal coordinates and the method of predicate observations. In particular, a new black-box scheme for defining automatically a suitable set of nonredundant internal coordinates of A1 symmetry in place of the customary Z-matrix has been designed and tested. Finally, the implementation of the method of the predicate observations is discussed and validated for a set of test molecules. As an original application, the method is employed for the determination of the semiexperimental structure for the most stable conformer of glycine.
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Affiliation(s)
| | | | - Daniele Licari
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Nicola Tasinato
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
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Penocchio E, Mendolicchio M, Tasinato N, Barone V. Structural features of the carbon-sulfur chemical bond: a semi-experimental perspective. CAN J CHEM 2016; 94:1065-1076. [PMID: 28912608 PMCID: PMC5595238 DOI: 10.1139/cjc-2016-0282] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this work semi-experimental and theoretical equilibrium geometries of 10 sulfur-containing organic molecules, as well as 4 oxygenated ones, are determined by means of a computational protocol based on density functional theory. The results collected in the present paper further enhance our online database of accurate semi-experimental equilibrium molecular geometries, adding 13 new molecules containing up to 8 atoms, for 12 of which the first semi-experimental equilibrium structure is reported, to the best of our knowledge. We focus in particular on sulfur-containing compounds, aiming both to provide new accurate data on some rather important chemical moieties, only marginally represented in the literature of the field, and to examine the structural features of carbon-sulfur bonds in the light of the previously presented linear regression approach. The structural changes issuing from substitution of oxygen by sulfur are discussed to get deeper insights on how modifications in electronic structure and nuclear potential can affect equilibrium geometries. With respect to our previous works, we perform non-linear constrained optimizations of equilibrium SE structures with a new general and user-friendly software under development in our group with updated definition of useful statistical indicators.
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35
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Den T, Frey HM, Felker PM, Leutwyler S. Rotational constants and structure of para-difluorobenzene determined by femtosecond Raman coherence spectroscopy: A new transient type. J Chem Phys 2016; 143:144306. [PMID: 26472378 DOI: 10.1063/1.4932602] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Femtosecond Raman rotational coherence spectroscopy (RCS) detected by degenerate four-wave mixing is a background-free method that allows to determine accurate gas-phase rotational constants of non-polar molecules. Raman RCS has so far mostly been applied to the regular coherence patterns of symmetric-top molecules, while its application to nonpolar asymmetric tops has been hampered by the large number of RCS transient types, the resulting variability of the RCS patterns, and the 10(3)-10(4) times larger computational effort to simulate and fit rotational Raman RCS transients. We present the rotational Raman RCS spectra of the nonpolar asymmetric top 1,4-difluorobenzene (para-difluorobenzene, p-DFB) measured in a pulsed Ar supersonic jet and in a gas cell over delay times up to ∼2.5 ns. p-DFB exhibits rotational Raman transitions with ΔJ = 0, 1, 2 and ΔK = 0, 2, leading to the observation of J -, K -, A -, and C-type transients, as well as a novel transient (S-type) that has not been characterized so far. The jet and gas cell RCS measurements were fully analyzed and yield the ground-state (v = 0) rotational constants A0 = 5637.68(20) MHz, B0 = 1428.23(37) MHz, and C0 = 1138.90(48) MHz (1σ uncertainties). Combining the A0, B0, and C0 constants with coupled-cluster with single-, double- and perturbatively corrected triple-excitation calculations using large basis sets allows to determine the semi-experimental equilibrium bond lengths re(C1-C2) = 1.3849(4) Å, re(C2-C3) = 1.3917(4) Å, re(C-F) = 1.3422(3) Å, and re(C2-H2) = 1.0791(5) Å.
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Affiliation(s)
- Takuya Den
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3000 Bern 9, Switzerland
| | - Hans-Martin Frey
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3000 Bern 9, Switzerland
| | - Peter M Felker
- Department of Chemistry and Biochemistry, University of California at Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, USA
| | - Samuel Leutwyler
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3000 Bern 9, Switzerland
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36
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Feller D. Application of a convergent, composite coupled cluster approach to bound state, adiabatic electron affinities in atoms and small molecules. J Chem Phys 2016; 144:014105. [DOI: 10.1063/1.4939184] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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37
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The Impact of Larger Basis Sets and Explicitly Correlated Coupled Cluster Theory on the Feller–Peterson–Dixon Composite Method. ANNUAL REPORTS IN COMPUTATIONAL CHEMISTRY 2016. [DOI: 10.1016/bs.arcc.2016.02.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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38
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Bellili A, Linguerri R, Hochlaf M, Puzzarini C. Accurate structural and spectroscopic characterization of prebiotic molecules: The neutral and cationic acetyl cyanide and their related species. J Chem Phys 2015; 143:184314. [DOI: 10.1063/1.4935493] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- A. Bellili
- Laboratoire de Modélisation et Simulation Multi Echelle, Université Paris-Est, MSME UMR 8208 CNRS, 5 boulevard Descartes, 77454 Marne-la-Vallée, France
| | - R. Linguerri
- Laboratoire de Modélisation et Simulation Multi Echelle, Université Paris-Est, MSME UMR 8208 CNRS, 5 boulevard Descartes, 77454 Marne-la-Vallée, France
| | - M. Hochlaf
- Laboratoire de Modélisation et Simulation Multi Echelle, Université Paris-Est, MSME UMR 8208 CNRS, 5 boulevard Descartes, 77454 Marne-la-Vallée, France
| | - C. Puzzarini
- Dipartimento di Chimica “Giacomo Ciamician,” Università di Bologna, Via F. Selmi 2, I-40126 Bologna, Italy
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39
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Kowalewski P, Frey HM, Infanger D, Leutwyler S. Probing the Structure, Pseudorotation, and Radial Vibrations of Cyclopentane by Femtosecond Rotational Raman Coherence Spectroscopy. J Phys Chem A 2015; 119:11215-25. [DOI: 10.1021/acs.jpca.5b07930] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Philipp Kowalewski
- Department
of Chemistry and Biochemistry, University of Bern, Freiestrasse
3, CH-3012 Bern, Switzerland
| | - Hans-Martin Frey
- Department
of Chemistry and Biochemistry, University of Bern, Freiestrasse
3, CH-3012 Bern, Switzerland
| | - Daniel Infanger
- Department
of Chemistry and Biochemistry, University of Bern, Freiestrasse
3, CH-3012 Bern, Switzerland
| | - Samuel Leutwyler
- Department
of Chemistry and Biochemistry, University of Bern, Freiestrasse
3, CH-3012 Bern, Switzerland
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40
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Barone V, Biczysko M, Bloino J, Cimino P, Penocchio E, Puzzarini C. CC/DFT Route toward Accurate Structures and Spectroscopic Features for Observed and Elusive Conformers of Flexible Molecules: Pyruvic Acid as a Case Study. J Chem Theory Comput 2015; 11:4342-63. [PMID: 26575928 PMCID: PMC5905675 DOI: 10.1021/acs.jctc.5b00580] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The structures and relative stabilities as well as the rotational and vibrational spectra of the three low-energy conformers of pyruvic acid (PA) have been characterized using a state-of-the-art quantum-mechanical approach designed for flexible molecules. By making use of the available experimental rotational constants for several isotopologues of the most stable PA conformer, Tc-PA, the semiexperimental equilibrium structure has been derived. The latter provides a reference for the pure theoretical determination of the equilibrium geometries for all conformers, thus confirming for these structures an accuracy of 0.001 Å and 0.1 deg for bond lengths and angles, respectively. Highly accurate relative energies of all conformers (Tc-, Tt-, and Ct-PA) and of the transition states connecting them are provided along with the thermodynamic properties at low and high temperatures, thus leading to conformational enthalpies accurate to 1 kJ mol(-1). Concerning microwave spectroscopy, rotational constants accurate to about 20 MHz are provided for the Tt- and Ct-PA conformers, together with the computed centrifugal-distortion constants and dipole moments required to simulate their rotational spectra. For Ct-PA, vibrational frequencies in the mid-infrared region accurate to 10 cm(-1) are reported along with theoretical estimates for the transitions in the near-infrared range, and the corresponding infrared spectrum including fundamental transitions, overtones, and combination bands has been simulated. In addition to the new data described above, theoretical results for the Tc- and Tt-PA conformers are compared with all available experimental data to further confirm the accuracy of the hybrid coupled-cluster/density functional theory (CC/DFT) protocol applied in the present study. Finally, we discuss in detail the accuracy of computational models fully based on double-hybrid DFT functionals (mainly at the B2PLYP/aug-cc-pVTZ level) that avoid the use of very expensive CC calculations.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore,
Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Malgorzata Biczysko
- Consiglio Nazionale delle
Ricerche, Istituto di Chimica dei Composti
OrganoMetallici (ICCOM-CNR), UOS di Pisa, Area
della Ricerca CNR, Via G. Moruzzi 1, I-56124 Pisa,
Italy
| | - Julien Bloino
- Consiglio Nazionale delle
Ricerche, Istituto di Chimica dei Composti
OrganoMetallici (ICCOM-CNR), UOS di Pisa, Area
della Ricerca CNR, Via G. Moruzzi 1, I-56124 Pisa,
Italy
| | - Paola Cimino
- Dipartimento di Scienze
Farmaceutiche, Università degli Studi di
Salerno, via Ponte don Melillo, I-84084 Fisciano
(SA), Italy
| | | | - Cristina Puzzarini
- Dipartimento di Chimica
“Giacomo Ciamician”,
Università di Bologna, Via Selmi 2, I-40126
Bologna, Italy
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41
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Penocchio E, Piccardo M, Barone V. Semiexperimental equilibrium structures for building blocks of organic and biological molecules: the B2PLYP route. J Chem Theory Comput 2015; 11:4689-707. [PMID: 26574259 DOI: 10.1021/acs.jctc.5b00622] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The B2PLYP double hybrid functional, coupled with the correlation-consistent triple-ζ cc-pVTZ (VTZ) basis set, has been validated in the framework of the semiexperimental (SE) approach for deriving accurate equilibrium structures of molecules containing up to 15 atoms. A systematic comparison between new B2PLYP/VTZ results and several equilibrium SE structures previously determined at other levels, in particular B3LYP/SNSD and CCSD(T) with various basis sets, has put in evidence the accuracy and the remarkable stability of such model chemistry for both equilibrium structures and vibrational corrections. New SE equilibrium structures for phenylacetylene, pyruvic acid, peroxyformic acid, and phenyl radical are discussed and compared with literature data. Particular attention has been devoted to the discussion of systems for which lack of sufficient experimental data prevents a complete SE determination. In order to obtain an accurate equilibrium SE structure for these situations, the so-called templating molecule approach is discussed and generalized with respect to our previous work. Important applications are those involving biological building blocks, like uracil and thiouracil. In addition, for more general situations the linear regression approach has been proposed and validated.
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42
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Piccardo M, Penocchio E, Puzzarini C, Biczysko M, Barone V. Semi-Experimental Equilibrium Structure Determinations by Employing B3LYP/SNSD Anharmonic Force Fields: Validation and Application to Semirigid Organic Molecules. J Phys Chem A 2015; 119:2058-82. [DOI: 10.1021/jp511432m] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Matteo Piccardo
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, I-56126 Pisa, Italy
| | - Emanuele Penocchio
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, I-56126 Pisa, Italy
- Dipartimento
di Chimica “Giacomo Ciamician”, Universitá di Bologna, Via Selmi 2, I-40126 Bologna, Italy
| | - Cristina Puzzarini
- Dipartimento
di Chimica “Giacomo Ciamician”, Universitá di Bologna, Via Selmi 2, I-40126 Bologna, Italy
| | - Malgorzata Biczysko
- Consiglio Nazionale delle Ricerche, Istituto di Chimica
dei Composti OrganoMetallici (ICCOM-CNR), Area della Ricerca CNR,
UOS di Pisa, Via G. Moruzzi
1, I-56124 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, I-56126 Pisa, Italy
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43
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Craig NC, Demaison J, Groner P, Rudolph HD, Vogt N. Electron delocalization in polyenes: a semiexperimental equilibrium structure for (3E)-1,3,5-hexatriene and theoretical structures for (3Z,5Z)-, (3E,5E)-, and (3E,5Z)-1,3,5,7-octatetraene. J Phys Chem A 2015; 119:195-204. [PMID: 25465856 DOI: 10.1021/jp510237h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Electronic structure theory reveals that π-electron delocalization increases with the chain length in polyenes. To analyze quantitatively this effect a semiexperimental equilibrium structure has been determined for trans-hexatriene by the mixed estimation method. For this fit rotational constants for a number of carbon and hydrogen isotopologues as well as a high-level ab initio structure have been used. The accuracy is 0.001 Å for bond lengths and 0.1° for bond angles. For the three isomers of octatetraene, high-level ab initio calculations have given a comparably accurate structure. These structures have been used in comparison with the structure of s-trans-butadiene to show that "C═C" bonds increase in length and "C-C" bonds decrease in length as the polyene chain lengthens. These structural effects of π-electron delocalization increase toward the center of polyenes. Most likely, π-π conjugation in the molecules studied plays a large part in their planarity that, in turn, forces the hydrogen atoms of cis fragments in bay regions to be in a close contact. Their distance is indeed shorter than the sum of their van der Waals radii, and they seem to participate in a six-membered ring.
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Affiliation(s)
- Norman C Craig
- Department of Chemistry and Biochemistry, Oberlin College , Oberlin, Ohio 44074, United States
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44
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Puzzarini C, Biczysko M. Microsolvation of 2-thiouracil: molecular structure and spectroscopic parameters of the thiouracil-water complex. J Phys Chem A 2014; 119:5386-95. [PMID: 25474644 DOI: 10.1021/jp510511d] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
State-of-the-art quantum-chemical computations have been employed to accurately determine the equilibrium structure and interaction energy of the 2-thiouracil-water complex, thus extending available reference data for biomolecule solvation patterns. The coupled-cluster level of theory in conjunction with a triple-ζ basis set has been considered together with extrapolation to the basis set limit, performed by employing second-order Møller-Plesset perturbation theory, and inclusion of core-correlation and diffuse-function corrections. On the basis of the comparison of experiment and theory for 2-thiouracil [ Puzzarini et al. Phys. Chem. Chem. Phys. 2013 , 15 , 16965 - 16975 ], structural changes due to water complexation have been pointed out. Molecular and spectroscopic properties of the 2-thiouracil-water complex have then been studied by means of the composite computational approach introduced for the molecular structure evaluation. Among the results achieved, we mention the accurate determination of the molecular dipole moment and of the spectroscopic parameters required for predicting the rotational spectrum.
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Affiliation(s)
- Cristina Puzzarini
- †Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via Selmi 2, I-40126 Bologna, Italy
| | - Malgorzata Biczysko
- ‡Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,§Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca CNR, Consiglio Nazionale delle Ricerche, Via G. Moruzzi 1, I-56124 Pisa, Italy
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45
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Den TS, Frey HM, Leutwyler S. Accurate rotational constant and bond lengths of hexafluorobenzene by femtosecond rotational Raman coherence spectroscopy and ab initio calculations. J Chem Phys 2014; 141:194303. [DOI: 10.1063/1.4901284] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Takuya S. Den
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3000 Bern 9, Switzerland
| | - Hans-Martin Frey
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3000 Bern 9, Switzerland
| | - Samuel Leutwyler
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3000 Bern 9, Switzerland
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46
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Barone V, Biczysko M, Bloino J, Puzzarini C. Accurate molecular structures and infrared spectra of trans-2,3-dideuterooxirane, methyloxirane, and trans-2,3-dimethyloxirane. J Chem Phys 2014; 141:034107. [PMID: 25053301 PMCID: PMC4612369 DOI: 10.1063/1.4887357] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Oxirane derivatives are the most used benchmarks for chiroptical spectroscopies in view of their small size and relative rigidity. The molecular structure, vibrational harmonic and anharmonic frequencies, and infrared intensities of the ground electronic states are analyzed in this paper. Equilibrium structure and harmonic force fields have been evaluated by means of high-level quantum-chemical calculations at the coupled-cluster level including single and double excitations together with a perturbative treatment of triples (CCSD(T)). Extrapolation to the complete basis-set limit as well as core-correlation effects have also been taken into account. Anharmonic contributions have been computed at the CCSD(T)/cc-pVTZ level for trans-2,3-dideuterooxirane. These data can serve as references to evaluate the accuracy of less expensive computational approaches rooted in the density functional theory (DFT). The latter have been used within hybrid CC/DFT approaches, which have been applied to simulate fully anharmonic infrared (IR) spectra. Finally, the best theoretical estimates of the equilibrium structures and vibrational wavenumbers are compared to the most accurate experimental data and show in all cases very good agreement, i.e., within 0.001 Å, 0.1 deg, 10 cm(-1), and 0.5 km mol(-1), for bond lengths, angles, wavenumbers, and IR intensities, respectively.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | | | - Julien Bloino
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician," Università di Bologna, Via F. Selmi 2, I-40126 Bologna, Italy
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47
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Demaison J, Craig NC, Groner P, Écija P, Cocinero EJ, Lesarri A, Rudolph HD. Accurate Equilibrium Structures for Piperidine and Cyclohexane. J Phys Chem A 2014; 119:1486-93. [DOI: 10.1021/jp505765t] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jean Demaison
- Laboratoire
de Physique des Lasers, Atomes et Molécules, Université de Lille 1, 59655 Villeneuve d’Ascq Cedex, France
| | - Norman C. Craig
- Department
of Chemistry and Biochemistry, Oberlin College, Oberlin, Ohio 44074, United States
| | - Peter Groner
- Department
of Chemistry, University of Missouri—Kansas City, Kansas City, Missouri 64110-2499, United States
| | - Patricia Écija
- Departamento
de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV-EHU), Ap. 644, E-48080 Bilbao, Spain
| | - Emilio J. Cocinero
- Departamento
de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV-EHU), Ap. 644, E-48080 Bilbao, Spain
| | - Alberto Lesarri
- Departamento
de Química Física y Química Inorgánica,
Facultad de Ciencias, Universidad de Valladolid, E-47011 Valladolid, Spain
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48
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Perrin A, Flores Antognini A, Zeng X, Beckers H, Willner H, Rauhut G. Vibrational Spectrum and Gas-Phase Structure of Disulfur Dinitride (S2N2). Chemistry 2014; 20:10323-31. [DOI: 10.1002/chem.201402404] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Indexed: 11/08/2022]
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49
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Puzzarini C, Penocchio E, Biczysko M, Barone V. Molecular structure and spectroscopic signatures of acrolein: theory meets experiment. J Phys Chem A 2014; 118:6648-56. [PMID: 24842714 DOI: 10.1021/jp503672g] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A comprehensive study of the molecular structure and IR spectrum of cis and trans acrolein has been performed by an integrated computational approach coupling methods rooted in the coupled-cluster ansatz and the density functional theory. From the one side, DFT anharmonic force fields allow us to determine very reliable semiexperimental structures for both isomers, which are in remarkable agreement with the geometries issuing from CCSD(T) computations accounting for the extrapolation to the complete basis set and core correlation. The same kind of coupled-cluster computations provide dipole moment, relative energies, and interconversion barrier in remarkable agreement with experiments. Finally, harmonic CCSD(T) results coupled to DFT evaluation of mechanical and electrical anharmonicity allow us, in the framework of second-order perturbative vibrational theory, to confirm most of the experimental assignments of IR spectra, and to suggest some additional interpretations for congested regions including fundamental bands together with overtones and combination bands.
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Affiliation(s)
- Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna , Via Selmi 2, I-40126 Bologna, Italy
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50
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Goubet M, Asselin P, Soulard P, Madebène B. Structural and Dynamic Properties of a Hydrogen Bond from the Study of the CH3Cl–HCl Complex and Isotopic Species. J Phys Chem A 2013; 117:12569-80. [DOI: 10.1021/jp407309a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Manuel Goubet
- Laboratoire
de Physique des Lasers, Atomes et Molécules, UMR 8523, CNRS Université Lille 1, F-59655 Villeneuve d’Ascq Cedex, France
| | - Pierre Asselin
- Laboratoire
de Dynamique, Interactions et Réactivité (LADIR), UPMC Université Paris 06, UMR 7075, F-75005 Paris, France
- Laboratoire
de Dynamique, Interactions et Réactivité (LADIR), CNRS, UMR 7075, F-75005 Paris, France
| | - Pascale Soulard
- Laboratoire
de Dynamique, Interactions et Réactivité (LADIR), UPMC Université Paris 06, UMR 7075, F-75005 Paris, France
- Laboratoire
de Dynamique, Interactions et Réactivité (LADIR), CNRS, UMR 7075, F-75005 Paris, France
| | - Bruno Madebène
- Laboratoire
de Dynamique, Interactions et Réactivité (LADIR), UPMC Université Paris 06, UMR 7075, F-75005 Paris, France
- Laboratoire
de Dynamique, Interactions et Réactivité (LADIR), CNRS, UMR 7075, F-75005 Paris, France
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