1
|
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%.
Collapse
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
| |
Collapse
|
2
|
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.
Collapse
|
3
|
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.
Collapse
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
| | | |
Collapse
|
4
|
Fortenberry RC. Quantum Chemistry and Astrochemistry: A Match Made in the Heavens. J Phys Chem A 2024; 128:1555-1565. [PMID: 38381079 DOI: 10.1021/acs.jpca.3c07601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Quantum chemistry can uniquely answer astrochemical questions that no other technique can provide. Computations can be parallelized, automated, and left to run continuously providing exceptional molecular throughput that cannot be done through experimentation. Additionally, the granularity of the individual computations that are required of potential energy surfaces, reaction mechanism pathways, or other quantum chemically derived observables produces a unique mosaic that make up the larger whole. These pieces can be dissected for their individual contributions or evaluated in an ad hoc fashion for each of their roles in generating the larger whole. No other scientific approach is capable of reporting such fine-grained insights. Quantum chemistry also works from a bottom-up approach in providing properties directly from the desired molecule instead of a top-down perspective as required of experiment where molecules have to be linked to observed phenomena. Furthermore, modern quantum chemistry is well within the range of "chemical accuracy" and is approaching "spectroscopic accuracy." As such, the seemingly difficult questions asked by astrochemistry that would not be asked initially for any other application require quantum chemical reference data. While the results of quantum chemical computations are needed to interpret astrochemical observation, modeling, or laboratory experimentation, such hard questions, regardless of the original need to answer them, produce unique solutions. While questions in astrochemistry often require novel developments in and implementations of quantum chemistry as outlined herein, the applications of these solutions will stretch beyond astrochemistry and may yet impact fields much closer to Earth.
Collapse
Affiliation(s)
- Ryan C Fortenberry
- Department of Chemistry & Biochemistry, University of Mississippi, Oxford, Mississippi 38677-1848, United States
| |
Collapse
|
5
|
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.
Collapse
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
| | | |
Collapse
|
6
|
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.
Collapse
Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy.
| |
Collapse
|
7
|
Garrett NR, Davis MC, Fortenberry RC. DFT + F12 QFFs for Cost-Effective Rovibrational Spectral Data Predictions of Ground and Excited Electronic States. J Chem Theory Comput 2024. [PMID: 38230913 DOI: 10.1021/acs.jctc.3c01179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
The quest for faster computation of anharmonic vibrational frequencies of both ground and excited electronic states has led to combining coupled cluster theory harmonic force constants with density functional theory cubic and quartic force constants for defining a quartic force field (QFF) utilized in conjunction with vibrational perturbation theory at second order (VPT2). This work shows that explicitly correlated coupled cluster theory at the singles, doubles, and perturbative triples levels [CCSD(T)-F12] provides accurate anharmonic vibrational frequencies and rotational constants when conjoined with any of B3LYP, CAM-B3LYP, BHandHLYP, PBE0, and ωB97XD for roughly one-quarter of the computational time of the CCSD(T)-F12 QFF alone for our test set. As the number of atoms in the molecule increases, however, the anharmonic terms become a greater portion of the QFF, and the cost comparison improves with HOCO+ and formic acid, requiring less than 15 and 10% of the time, respectively. In electronically excited states, PBE0 produces more consistently accurate results. Additionally, as the size of the molecule and, in turn, QFF increase, the cost savings for utilizing such a hybrid approach for both ground- and excited-state computations grows. As such, these methods are promising for predicting accurate rovibrational spectral properties for electronically excited states. In cases where well-behaved potentials for a small selection of targeted excited states are needed, such an approach should reduce the computational cost compared to that of methods requiring semiglobal potential surfaces or variational treatments of the rovibronic Hamiltonian. Such applications include spectral characterization of comets, exoplanets, or any situation in which gas phase molecules are being excited by UV-vis radiation.
Collapse
Affiliation(s)
- Noah R Garrett
- Department of Chemistry & Biochemistry, University of Mississippi, University, Mississippi 38677-1848, United States
| | - Megan C Davis
- Theoretical Division, T-1, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Ryan C Fortenberry
- Department of Chemistry & Biochemistry, University of Mississippi, University, Mississippi 38677-1848, United States
| |
Collapse
|
8
|
Melosso M, Alessandrini S, Spada L, Melli A, Wang X, Zheng Y, Duan C, Li J, Du W, Gou Q, Bizzocchi L, Dore L, Barone V, Puzzarini C. Rotational spectra and semi-experimental structures of furonitrile and its water cluster. Phys Chem Chem Phys 2023; 25:31281-31291. [PMID: 37955344 DOI: 10.1039/d3cp03984f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
Rotational spectroscopy represents an invaluable tool for several applications: from the identification of new molecules in interstellar objects to the characterization of van der Waals complexes, but also for the determination of very accurate molecular structures and for conformational analyses. In this work, we used high-resolution rotational spectroscopic techniques in combination with high-level quantum-chemical calculations to address all these aspects for two isomers of cyanofuran, namely 2-furonitrile and 3-furonitrile. In particular, we have recorded and analyzed the rotational spectra of both of them from 6 to 320 GHz; rotational transitions belonging to several singly-substituted isotopologues have been identified as well. The rotational constants derived in this way have been used in conjunction with computed rotation-vibration interaction constants in order to derive a semi-experimental equilibrium structure for both isomers. Moreover, we observed the rotational spectra of four different intermolecular adducts formed by furonitrile and water, whose identification has been supported by a conformational analysis and a theoretical spectroscopic characterization. A semi-experimental determination of the intermolecular parameters has been achieved for all of them and the results have been compared with those obtained for the analogous system formed by benzonitrile and water.
Collapse
Affiliation(s)
- Mattia Melosso
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
| | - Silvia Alessandrini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
| | - Lorenzo Spada
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Alessio Melli
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Xiujuan Wang
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331, Chongqing, China.
| | - Yang Zheng
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331, Chongqing, China.
| | - Chunguo Duan
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331, Chongqing, China.
| | - Jiayi Li
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331, Chongqing, China.
| | - Weiping Du
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331, Chongqing, China.
| | - Qian Gou
- Department of Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331, Chongqing, China.
| | - Luca Bizzocchi
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
| | - Luca Dore
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
| |
Collapse
|
9
|
Puzzarini C, Linguerri R, Hochlaf M. Insights into the Molecular Structure and Spectroscopic Properties of HONCO: An Accurate Ab Initio Study. J Phys Chem A 2023; 127:9502-9512. [PMID: 37922399 PMCID: PMC10658623 DOI: 10.1021/acs.jpca.3c05741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 11/05/2023]
Abstract
In an effort to provide the first accurate structural and spectroscopic characterization of the quasi-linear chain HONCO in its electronic ground state, state-of-the-art computational approaches mainly based on coupled-cluster (CC) theory have been employed. Equilibrium geometries have been calculated by means of a composite scheme based on CC calculations that incorporates up to the quadruple excitations and accounts for the extrapolation to the complete basis set limit and core correlation effects. This approach is proven to provide molecular structures with an accuracy better than 0.001 Å and 0.05° for bond lengths and angles, respectively. Incorporation of vibrational effects permits this level of theory to predict rotational constants with an estimated accuracy of 0.1% or better. Vibrational fundamental bands have been evaluated by means of a hybrid scheme based on harmonic frequencies computed using the CC singles, doubles, and a perturbative treatment of the triples method (CCSD(T)) in conjunction with a quadruple-ζ basis set, with all electrons being correlated, and anharmonic corrections from CCSD(T) calculations using a triple-ζ basis set, within the frozen-core approximation. Such a hybrid approach allowed us to obtain fundamental frequencies with a mean absolute error of about 1%. To complete the spectroscopic characterization, vertical electronic excitation energies have been calculated for the lowest singlet and triplet states using the internally contracted multireference configuration interaction (MRCI) method. Computations show that HONCO dissociates into OH + NCO upon the absorption of UV-vis light. In conclusion, we are confident that the highly accurate spectroscopic data provided herein can be useful for guiding future experimental investigations and supporting the characterization of this molecule in atmospheric and astrophysical media, as well as in combustion.
Collapse
Affiliation(s)
- Cristina Puzzarini
- Dipartimento
di Chimica “Giacomo Ciamician″, Università di Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Roberto Linguerri
- Université
Gustave Eiffel, COSYS/IMSE, 5 Bd Descartes, 77454 Champs sur Marne, France
| | - Majdi Hochlaf
- Université
Gustave Eiffel, COSYS/IMSE, 5 Bd Descartes, 77454 Champs sur Marne, France
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Charvati E, Sun H. Potential Energy Surfaces Sampled in Cremer-Pople Coordinates and Represented by Common Force Field Functionals for Small Cyclic Molecules. J Phys Chem A 2023; 127:2646-2663. [PMID: 36893434 DOI: 10.1021/acs.jpca.3c00095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
The complex conformations of the cyclic moieties impact the physical and chemical properties of molecules. In this work, we chose 22 molecules of four-, five-, and six-membered rings and performed a thorough conformational sampling using Cremer-Pople coordinates. With consideration of symmetries, we obtained a total of 1504 conformational structures for four-membered, 5576 for five-membered, and 13509 for six-membered rings. All well-known and many less well-known conformers for each molecule were identified. We represented the potential energy surfaces (PESs) by fitting the data to common analytical force field (FF) functional forms. We found that the general features of PESs can be described by the essential FF functional forms; however, the accuracy of representation can be improved remarkably by including the torsion-bond and torsion-angle coupling terms. The best fit yields R-squared (R2) values close to 1.0 and mean absolute errors in energy less than 0.3 kcal/mol.
Collapse
Affiliation(s)
- Evangelia Charvati
- School of Chemistry and Chemical Engineering, Materials Genome Initiative Center, and Key Laboratory of Scientific and Engineering Computing of Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huai Sun
- School of Chemistry and Chemical Engineering, Materials Genome Initiative Center, and Key Laboratory of Scientific and Engineering Computing of Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China
| |
Collapse
|
12
|
Ka S, Jang H, Peebles SA, Peebles RA, Oh JJ. Microwave spectrum, structure, and dipole moment of 2-fluorophenylacetylene. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
|
13
|
Barone V, Fusè M, Lazzari F, Mancini G. Benchmark Structures and Conformational Landscapes of Amino Acids in the Gas Phase: A Joint Venture of Machine Learning, Quantum Chemistry, and Rotational Spectroscopy. J Chem Theory Comput 2023; 19:1243-1260. [PMID: 36731119 PMCID: PMC9979611 DOI: 10.1021/acs.jctc.2c01143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The accurate characterization of prototypical bricks of life can strongly benefit from the integration of high resolution spectroscopy and quantum mechanical computations. We have selected a number of representative amino acids (glycine, alanine, serine, cysteine, threonine, aspartic acid and asparagine) to validate a new computational setup rooted in quantum-chemical computations of increasing accuracy guided by machine learning tools. Together with low-lying energy minima, the barriers ruling their interconversion are evaluated in order to unravel possible fast relaxation paths. Vibrational and thermal effects are also included in order to estimate relative free energies at the temperature of interest in the experiment. The spectroscopic parameters of all the most stable conformers predicted by this computational strategy, which do not have low-energy relaxation paths available, closely match those of the species detected in microwave experiments. Together with their intrinsic interest, these accurate results represent ideal benchmarks for more approximate methods.
Collapse
Affiliation(s)
- Vincenzo Barone
- Scuola
Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy,
| | - Marco Fusè
- DMMT-sede
Europa, Universitá di Brescia, viale Europa 11, 25121 Brescia, Italy
| | - Federico Lazzari
- Scuola
Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Giordano Mancini
- Scuola
Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
| |
Collapse
|
14
|
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.
Collapse
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.
| |
Collapse
|
15
|
Barone V, Di Grande S, Puzzarini C. Toward Accurate yet Effective Computations of Rotational Spectroscopy Parameters for Biomolecule Building Blocks. MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28020913. [PMID: 36677970 PMCID: PMC9863398 DOI: 10.3390/molecules28020913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 01/01/2023] [Accepted: 01/12/2023] [Indexed: 01/19/2023]
Abstract
The interplay of high-resolution rotational spectroscopy and quantum-chemical computations plays an invaluable role in the investigation of biomolecule building blocks in the gas phase. However, quantum-chemical methods suffer from unfavorable scaling with the dimension of the system under consideration. While a complete characterization of flexible systems requires an elaborate multi-step strategy, in this work, we demonstrate that the accuracy obtained by quantum-chemical composite approaches in the prediction of rotational spectroscopy parameters can be approached by a model based on density functional theory. Glycine and serine are employed to demonstrate that, despite its limited cost, such a model is able to predict rotational constants with an accuracy of 0.3% or better, thus paving the way toward the accurate characterization of larger flexible building blocks of biomolecules.
Collapse
Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-50126 Pisa, Italy
- Correspondence: (V.B.); (C.P.)
| | - Silvia Di Grande
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-50126 Pisa, Italy
- Scuola Superiore Meridionale, Largo San Marcellino 10, I-80138 Napoli, Italy
| | - Cristina Puzzarini
- Rotational and Computational Spectroscopy Lab, Department of Chemistry “Giacomo Ciamician”, University of Bologna, Via F. Selmi 2, I-40126 Bologna, Italy
- Correspondence: (V.B.); (C.P.)
| |
Collapse
|
16
|
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
| |
Collapse
|
17
|
Falbo E, Fusè M, Lazzari F, Mancini G, Barone V. Integration of Quantum Chemistry, Statistical Mechanics, and Artificial Intelligence for Computational Spectroscopy: The UV-Vis Spectrum of TEMPO Radical in Different Solvents. J Chem Theory Comput 2022; 18:6203-6216. [PMID: 36166322 PMCID: PMC9558374 DOI: 10.1021/acs.jctc.2c00654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The ongoing integration of quantum chemistry, statistical
mechanics,
and artificial intelligence is paving the route toward more effective
and accurate strategies for the investigation of the spectroscopic
properties of medium-to-large size chromophores in condensed phases.
In this context we are developing a novel workflow aimed at improving
the generality, reliability, and ease of use of the available computational
tools. In this paper we report our latest developments with specific
reference to unsupervised atomistic simulations employing non periodic
boundary conditions (NPBC) followed by clustering of the trajectories
employing optimized feature spaces. Next accurate variational computations
are performed for a representative point of each cluster, whereas
intracluster fluctuations are taken into account by a cheap yet reliable
perturbative approach. A number of methodological improvements have
been introduced including, e.g., more realistic reaction field effects
at the outer boundary of the simulation sphere, automatic definition
of the feature space by continuous perception of solute–solvent
interactions, full account of polarization and charge transfer in
the first solvation shell, and inclusion of vibronic contributions.
After its validation, this new approach has been applied to the challenging
case of solvatochromic effects on the UV–vis spectra of a prototypical
nitroxide radical (TEMPO) in different solvents. The reliability,
effectiveness, and robustness of the new platform is demonstrated
by the remarkable agreement with experiment of the results obtained
through an unsupervised approach characterized by a strongly reduced
computational cost as compared to that of conventional quantum mechanics
and molecular mechanics models without any accuracy reduction.
Collapse
Affiliation(s)
- Emanuele Falbo
- Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Marco Fusè
- Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy.,Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Federico Lazzari
- Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Giordano Mancini
- Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
| |
Collapse
|
18
|
Bizzocchi L, Alessandrini S, Melosso M, Puzzarini C. Dipolar spin-spin coupling as an auxiliary tool for the structure determination of small isolated molecules. Phys Chem Chem Phys 2022; 24:15173-15181. [PMID: 35703976 DOI: 10.1039/d2cp01124g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The "gold standard" for obtaining accurate equilibrium structures is the so-called semi-experimental (SE) approach, which exploits the structural information contained in rotational constants. Within the SE approach, ground-state rotational constants-accurately obtained from high-resolution spectroscopic studies-are computationally corrected in order to remove vibrational effects. The resulting SE equilibrium rotational constants for a significant set of isotopic species allow for retrieving a unique set of equilibrium bond lengths and angles for the molecule under consideration. However, in some cases, the lack of isotopic substitution hampers or even prevents a rigorous and complete structure determination. In this perspective, we introduce the use of dipolar spin-spin coupling constants as an additional source of structural information in support of the standard SE approach. As a proof-of-concept, we tested this new strategy on some prototypical species, such as water, ammonia, phosphine, and their fluorinated counterparts. Our results indicate that-even when the molecular structure can be obtained from a large set of isotopic rotational constants-the use of dipolar spin-spin coupling constants guarantees a better accuracy and reduces the correlations among the geometrical parameters. Moreover, we point out that our approach offers the possibility to fully derive the molecular structure of PF3, a species for which any isotopic substitution is not possible.
Collapse
Affiliation(s)
- Luca Bizzocchi
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, via F. Selmi 2, 40126 Bologna, Italy.
| | - Silvia Alessandrini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, via F. Selmi 2, 40126 Bologna, Italy. .,Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy.
| | - Mattia Melosso
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, via F. Selmi 2, 40126 Bologna, Italy. .,Scuola Superiore Meridionale, Università di Napoli Federico II, Largo San Marcellino 10, 80138 Naples, Italy.
| | - Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, via F. Selmi 2, 40126 Bologna, Italy.
| |
Collapse
|
19
|
Spectroscopic constants and anharmonic force field of dithioformic acid and its isomers: a theoretical study. J Mol Model 2022; 28:173. [DOI: 10.1007/s00894-022-05166-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 05/19/2022] [Indexed: 11/26/2022]
|
20
|
Brémond É, Li H, Pérez-Jiménez ÁJ, Sancho-García JC, Adamo C. Tackling an accurate description of molecular reactivity with double-hybrid density functionals. J Chem Phys 2022; 156:161101. [DOI: 10.1063/5.0087586] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this Communication, we assess a panel of 18 double-hybrid density functionals for the modeling of the thermochemical and kinetic properties of an extended dataset of 449 organic chemistry reactions belonging to the BH9 database. We show that most of DHs provide a statistically robust performance to model barrier height and reaction energies in reaching the “chemical accuracy.” In particular, we show that nonempirical DHs, such as PBE0-DH and PBE-QIDH, or minimally parameterized alternatives, such as ωB2PLYP and B2K-PLYP, succeed to accurately model both properties in a balanced fashion. We demonstrate, however, that parameterized approaches, such as ωB97X-2 or DSD-like DHs, are more biased to only one of both properties.
Collapse
Affiliation(s)
- Éric Brémond
- ITODYS, CNRS, Université de Paris, F-75006 Paris, France
| | - Hanwei Li
- Chimie ParisTech, PSL Research University, CNRS, Institute of Chemistry for Life and Health Sciences (i-CLeHS), F-75005 Paris, France
| | | | | | - Carlo Adamo
- Chimie ParisTech, PSL Research University, CNRS, Institute of Chemistry for Life and Health Sciences (i-CLeHS), F-75005 Paris, France
- Institut Universitaire de France, 103 Boulevard Saint Michel, F-75005 Paris, France
| |
Collapse
|
21
|
Vuckovic S. Quantification of Geometric Errors Made Simple: Application to Main-Group Molecular Structures. J Phys Chem A 2022; 126:1300-1311. [PMID: 35144382 DOI: 10.1021/acs.jpca.1c10688] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nearly all electronic structure simulations begin with obtaining approximate geometries, making a systematic quantification of errors in approximate molecular structures of key importance. Recently, the geometric energy offset (GEO) framework based on a single and natural measure for quantifying and analyzing these errors has been proposed ( J. Phys. Chem. Lett. 2020, 11, 99579964). An accurate and far less costly approximation to GEO is utilized here to readily quantify errors in main-group structures and analyze them in a chemically intuitive way. The use of semiexperimental geometries as a reference further simplifies the analysis. The analysis reveals new insights into the geometric performance of methods, their rankings, as well as patterns across different classes of methods and basis sets that arise from the analysis.
Collapse
Affiliation(s)
- Stefan Vuckovic
- Institute for Microelectronics and Microsystems (CNR-IMM), Via Monteroni, Campus Unisalento, 73100 Lecce, Italy.,Department of Chemistry & Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Faculty of Science, Vrije Universiteit, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands
| |
Collapse
|
22
|
Bizzocchi L, Alessandrini S, Melosso M, Rivilla VM, Puzzarini C. Ab Initio Study of Fine and Hyperfine Interactions in Triplet POH. Molecules 2022; 27:302. [PMID: 35011533 PMCID: PMC8746536 DOI: 10.3390/molecules27010302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/28/2021] [Accepted: 12/30/2021] [Indexed: 11/16/2022] Open
Abstract
Phosphorous-containing molecules have a great relevance in prebiotic chemistry in view of the fact that phosphorous is a fundamental constituent of biomolecules, such as RNA, DNA, and ATP. Its biogenic importance has led astrochemists to investigate the possibility that P-bearing species could have formed in the interstellar medium (ISM) and subsequently been delivered to early Earth by rocky bodies. However, only two P-bearing molecules have been detected so far in the ISM, with the chemistry of interstellar phosphorous remaining poorly understood. Here, in order to shed further light on P-carriers in space, we report a theoretical spectroscopic characterisation of the rotational spectrum of POH in its 3A″ ground electronic state. State-of-the-art coupled-cluster schemes have been employed to derive rotational constants, centrifugal distortion terms, and most of the fine and hyperfine interaction parameters, while the electron spin-spin dipolar coupling has been investigated using the multi-configuration self-consistent-field method. The computed spectroscopic parameters have been used to simulate the appearance of triplet POH rotational and ro-vibrational spectra in different conditions, from cold to warm environments, either in gas-phase experiments or in molecular clouds. Finally, we point out that the predicted hyperfine structures represent a key pattern for the recognition of POH in laboratory and interstellar spectra.
Collapse
Affiliation(s)
- Luca Bizzocchi
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy; (L.B.); (S.A.)
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy;
| | - Silvia Alessandrini
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy; (L.B.); (S.A.)
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy;
| | - Mattia Melosso
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy;
- Scuola Superiore Meridionale, Università di Napoli Federico II, Largo San Marcellino 10, 80138 Naples, Italy
| | - Víctor M. Rivilla
- Centro de Astrobiología (CSIC-INTA), Ctra. de Ajalvir Km. 4, Torrejón de Ardoz, 28850 Madrid, Spain;
- INAF—Osservatorio Astrofisico di Arcetri, Largo E. Fermi 5, 50125 Florence, Italy
| | - Cristina Puzzarini
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy;
| |
Collapse
|
23
|
Ye H, Alessandrini S, Melosso M, Puzzarini C. Exploiting the “Lego brick” approach to predict accurate molecular structures of PAHs and PANHs. Phys Chem Chem Phys 2022; 24:23254-23264. [DOI: 10.1039/d2cp03294e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) and polycyclic aromatic nitrogen heterocycles (PANHs) are important and ubiquitous species in space. However, their accurate structural and spectroscopic characterization is often missing. To fill this...
Collapse
|
24
|
Brémond É, Tognetti V, Chermette H, Sancho-García JC, Joubert L, Adamo C. Electronic Energy and Local Property Errors at QTAIM Critical Points while Climbing Perdew's Ladder of Density-Functional Approximations. J Chem Theory Comput 2021; 18:293-308. [PMID: 34958205 DOI: 10.1021/acs.jctc.1c00981] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We investigate the relationships between electron-density and electronic-energy errors produced by modern exchange-correlation density-functional approximations belonging to all of the rungs of Perdew's ladder. To this aim, a panel of relevant (semi)local properties evaluated at critical points of the electron-density field (as defined within the framework of Bader's atoms-in-molecules theory) are computed on a large selection of molecular systems involved in thermodynamic, kinetic, and noncovalent interaction chemical databases using density functionals developed in a nonempirical and minimally and highly parametrized fashion. The comparison of their density- and energy-based performance, also discussed in terms of density-driven errors, casts light on the strengths and weaknesses of the most recent and efficient density-functional approximations.
Collapse
Affiliation(s)
- Éric Brémond
- Université de Paris, ITODYS, CNRS, F-75006 Paris, France
| | - Vincent Tognetti
- Normandy University, COBRA UMR 6014 and FR 3038, Université de Rouen INSA Rouen, CNRS, F-76821 Mont St Aignan, France
| | - Henry Chermette
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1, 5 rue de la Doua, F-69100 Villeurbanne, France
| | | | - Laurent Joubert
- Normandy University, COBRA UMR 6014 and FR 3038, Université de Rouen INSA Rouen, CNRS, F-76821 Mont St Aignan, France
| | - Carlo Adamo
- Chimie ParisTech, PSL Research University, CNRS, Institute of Chemistry for Life and Health Sciences (i-CLeHS), UMR 8060, F-75005 Paris, France.,Institut Universitaire de France, 103 Boulevard Saint Michel, F-75005 Paris, France
| |
Collapse
|
25
|
Watrous AG, Westbrook BR, Fortenberry RC. F12-TZ-cCR: A Methodology for Faster and Still Highly Accurate Quartic Force Fields. J Phys Chem A 2021; 125:10532-10540. [PMID: 34846883 DOI: 10.1021/acs.jpca.1c08355] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The F12-TZ-cCR quartic force field (QFF) methodology, defined here as CCSD(T)-F12b/cc-pCVTZ-F12 with further corrections for relativity, is introduced as a cheaper and even more accurate alternative to more costly composite QFF methods like those containing complete basis set extrapolations within canonical coupled cluster theory. F12-TZ-cCR QFFs produce B0 and C0 vibrationally averaged principal rotational constants within 7.5 MHz of gas-phase experimental values for tetraatomic and larger molecules, offering higher accuracy in these constants than the previous composite methods. In addition, F12-TZ-cCR offers an order of magnitude decrease in the computational cost of highly accurate QFF methodologies accompanying this increase in accuracy. An additional order of magnitude in cost reduction is achieved in the F12-DZ-cCR method, while also matching the accuracy of the traditional composite method's B0 and C0 constants. Finally, F12-DZ and F12-TZ are benchmarked on the same test set, revealing that both methods can provide anharmonic vibrational frequencies that are comparable in accuracy to all three of the more expensive methodologies, although their rotational constants lag behind. Hence, the present work demonstrates that highly accurate theoretical rovibrational spectral data can be obtained for a fraction of the cost of conventional QFF methodologies, extending the applicability of QFFs to larger molecules.
Collapse
Affiliation(s)
- Alexandria G Watrous
- Department of Chemistry & Biochemistry, University of Mississippi, University, Mississippi 38677-1848, United States
| | - Brent R Westbrook
- Department of Chemistry & Biochemistry, University of Mississippi, University, Mississippi 38677-1848, United States
| | - Ryan C Fortenberry
- Department of Chemistry & Biochemistry, University of Mississippi, University, Mississippi 38677-1848, United States
| |
Collapse
|
26
|
Wang P, Shu C, Ye H, Biczysko M. Structural and Energetic Properties of Amino Acids and Peptides Benchmarked by Accurate Theoretical and Experimental Data. J Phys Chem A 2021; 125:9826-9837. [PMID: 34752094 DOI: 10.1021/acs.jpca.1c06504] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Structural, energetic, and spectroscopic data derived in this work aim at the setup of an "experimentally validated" database for amino acids and polypeptides conformers. First, the "cheap" composite scheme (ChS, CCSD(T)/(CBS+CV)MP2) is tested for evaluation of conformational energies of all eight stable conformers of glycine, by comparing to the more accurate CCSD(T)/CBS+CV computations (Phys. Chem. Chem. Phys. 2013, 15, 10094-10111 and J Mol. Model. 2020, 26, 129). The recently proposed jun-ChS (J. Chem. Theory and Comput. 2020, 16, 988-1006), employing the jun-cc-pVnZ basis set family for CCSD(T) computations and CBS extrapolation, yields conformational energies accurate to 0.2 kJ·mol-1, at reduced computational cost with respect to aug-ChS employing aug-cc-pVnZ basis sets. The jun-ChS composite scheme is further applied to derive conformational energies for three dipeptide analogues Ac-Gly-NH2, Ac-Ala-NH2, and Gly-Gly. Finally, dipeptide conformational energies and semiexperimental equilibrium rotational constants along with the CCSD(T)/(CBS+CV)MP2 structural parameters (J. Phys. Chem. Lett. 2014, 5, 534-540) stand as the reference for benchmarking of selected density functional methodologies. The double-hybrid functionals B2-PLYP-D3(BJ) and DSD-PBEP86, perform best for structural and energetic characterization of all dipeptide analogues. From hybrid functionals CAM-B3LYP-D3(BJ) and ωB97X-D3(BJ) represent promising methods applicable for larger peptide-based systems for which computations with double-hybrid functionals are not feasible.
Collapse
Affiliation(s)
- Ping Wang
- International Centre for Quantum and Molecular Structures, Physics Department, College of Science, Shanghai University, 99 Shangda Road, Shanghai 200444, China
| | - Chong Shu
- International Centre for Quantum and Molecular Structures, Physics Department, College of Science, Shanghai University, 99 Shangda Road, Shanghai 200444, China
| | - Hexu Ye
- International Centre for Quantum and Molecular Structures, Physics Department, College of Science, Shanghai University, 99 Shangda Road, Shanghai 200444, China
| | - Malgorzata Biczysko
- International Centre for Quantum and Molecular Structures, Physics Department, College of Science, Shanghai University, 99 Shangda Road, Shanghai 200444, China
| |
Collapse
|
27
|
Melli A, Tonolo F, Barone V, Puzzarini C. Extending the Applicability of the Semi-experimental Approach by Means of "Template Molecule" and "Linear Regression" Models on Top of DFT Computations. J Phys Chem A 2021; 125:9904-9916. [PMID: 34752702 PMCID: PMC8607424 DOI: 10.1021/acs.jpca.1c07828] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/20/2021] [Indexed: 11/28/2022]
Abstract
The accurate determination of equilibrium structures for isolated molecules plays a central role in the evaluation and interpretation of stereoelectronic, thermodynamic, and spectroscopic properties. For small semi-rigid systems, state-of-the-art quantum-chemical computations can rival the most sophisticated experimental results. For larger molecules, cheaper yet accurate approaches need to be defined. The double-hybrid rev-DSD-PBEP86 functional already delivers remarkable results that can be further improved by means of a "Lego brick" model. This is based on the idea that a molecular system can be seen as formed by different fragments (the "Lego bricks"), whose accurate semi-experimental (SE) equilibrium geometries are available. The template molecule (TM) approach can be used to account for the modifications occurring when going from the isolated fragment to the molecular system under investigation, with the linear regression (LR) model employed to correct the linkage between the different fragments. The resulting TM-SE_LR approach has been tested with respect to available SE equilibrium structures and rotational constants. Indeed, the latter parameters straightforwardly depend on the equilibrium geometry of the system under consideration. The main outcome of our study is the reliability, robustness, and accuracy of this novel approach. The molecular systems considered for benchmarking the TM-SE_LR scheme are those formally issued from addition/elimination reactions of nucleophilic unsaturated radicals (e.g., CN, C2H, and phenyl) to alkenes, imines, and aldehydes, whose rotational spectra have been investigated, but accurate structural determinations are not yet available.
Collapse
Affiliation(s)
- Alessio Melli
- Scuola
Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Dipartimento
di Chimica “Giacomo Ciamician”, Università di Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Francesca Tonolo
- Scuola
Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Dipartimento
di Chimica “Giacomo Ciamician”, Università di Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Vincenzo Barone
- Scuola
Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Cristina Puzzarini
- Dipartimento
di Chimica “Giacomo Ciamician”, Università di Bologna, Via Selmi 2, 40126 Bologna, Italy
| |
Collapse
|
28
|
Lupi J, Alessandrini S, Puzzarini C, Barone V. junChS and junChS-F12 Models: Parameter-free Efficient yet Accurate Composite Schemes for Energies and Structures of Noncovalent Complexes. J Chem Theory Comput 2021; 17:6974-6992. [PMID: 34677974 DOI: 10.1021/acs.jctc.1c00869] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A recently developed model chemistry (denoted as junChS [Alessandrini, S.; et al. J. Chem. Theory Comput. 2020, 16, 988-1006]) has been extended to the employment of explicitly correlated (F12) methods. This led us to propose a family of effective, reliable, and parameter-free schemes for the computation of accurate interaction energies of molecular complexes ruled by noncovalent interactions. A thorough benchmark based on a wide range of interactions showed that the so-called junChS-F12 model, which employs cost-effective revDSD-PBEP86-D3(BJ) reference geometries, has an improved performance with respect to its conventional counterpart and outperforms well-known model chemistries. Without employing any empirical parameter and at an affordable computational cost, junChS-F12 reaches subchemical accuracy. Accurate characterizations of molecular complexes are usually limited to energetics. To take a step forward, the conventional and F12 composite schemes developed for interaction energies have been extended to structural determinations. A benchmark study demonstrated that the most effective option is to add MP2-F12 core-valence correlation corrections to fc-CCSD(T)-F12/jun-cc-pVTZ geometries without the need of recovering the basis set superposition error and the extrapolation to the complete basis set.
Collapse
Affiliation(s)
- Jacopo Lupi
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Silvia Alessandrini
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, I-40126 Bologna, Italy
| | - Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, I-40126 Bologna, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| |
Collapse
|
29
|
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.
Collapse
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
| |
Collapse
|
30
|
Assis LC, de Castro AA, de Jesus JPA, da Cunha EFF, Nepovimova E, Krejcar O, Kuca K, Ramalho TC, La Porta FDA. Theoretical insights into the effect of halogenated substituent on the electronic structure and spectroscopic properties of the favipiravir tautomeric forms and its implications for the treatment of COVID-19. RSC Adv 2021; 11:35228-35244. [PMID: 35493173 PMCID: PMC9042810 DOI: 10.1039/d1ra06309j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/16/2021] [Indexed: 02/02/2023] Open
Abstract
In this study, we systematically investigated the electronic structure, spectroscopic (nuclear magnetic resonance, infrared, Raman, electron ionization mass spectrometry, UV-Vis, circular dichroism, and emission) properties, and tautomerism of halogenated favipiravir compounds (fluorine, chlorine, and bromine) from a computational perspective. Additionally, the effects of hydration on the proton transfer mechanism of the tautomeric forms of the halogenated favipiravir compounds are discussed. Our results suggest that spectroscopic properties allow for the elucidation of such tautomeric forms. As is well-known, the favipiravir compound has excellent antiviral properties and hence was recently tested for the treatment of new coronavirus (SARS-CoV-2). Through in silico modeling, in the current study, we evaluate the role of such tautomeric forms in order to consider the effect of drug-metabolism in the inhibition process of the main protease (Mpro) and RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 virus. According to the molecular docking, all halogenated compounds presented a better interaction energy than the co-crystallized active ligand (−3.5 kcal mol−1) in the viral RdRp, in both wild-type (−6.3 to −6.5 kcal mol−1) and variant (−5.4 to −5.6 kcal mol−1) models. The variant analyzed for RdRp (Y176C) decreases the affinity of the keto form of the compounds in the active site, and prevented the ligands from interacting with RNA. These findings clearly indicated that all these compounds are promising as drug candidates for this molecular target. In this study, we systematically investigated the electronic structure, spectroscopic properties, and tautomerism of halogenated favipiravir compounds (fluorine, chlorine, and bromine) from a computational perspective.![]()
Collapse
Affiliation(s)
- Letícia Cristina Assis
- Department of Chemistry, Federal University of Lavras CEP 37200-000 Lavras Minas Gerais Brazil
| | | | - João Paulo Almirão de Jesus
- Post-graduation Program in Materials Science and Engineering and Laboratory of Nanotechnology and Computational Chemistry, Federal Technological University of Paraná Avenida dos Pioneiros 3131 86036-370 Londrina Paraná Brazil
| | | | - Eugenie Nepovimova
- Department of Chemistry, Faculty of Science, University of Hradec Kralove Hradec Kralove Czech Republic
| | - Ondrej Krejcar
- Center for Basic and Applied Research, Faculty of Informatics and Management, University of Hradec Kralove Hradec Kralove Czech Republic
| | - Kamil Kuca
- Department of Chemistry, Faculty of Science, University of Hradec Kralove Hradec Kralove Czech Republic
| | - Teodorico Castro Ramalho
- Department of Chemistry, Federal University of Lavras CEP 37200-000 Lavras Minas Gerais Brazil .,Department of Chemistry, Faculty of Science, University of Hradec Kralove Hradec Kralove Czech Republic
| | - Felipe de Almeida La Porta
- Post-graduation Program in Materials Science and Engineering and Laboratory of Nanotechnology and Computational Chemistry, Federal Technological University of Paraná Avenida dos Pioneiros 3131 86036-370 Londrina Paraná Brazil
| |
Collapse
|
31
|
Sheng M, Silvestrini F, Biczysko M, Puzzarini C. Structural and Vibrational Properties of Amino Acids from Composite Schemes and Double-Hybrid DFT: Hydrogen Bonding in Serine as a Test Case. J Phys Chem A 2021; 125:9099-9114. [PMID: 34623165 DOI: 10.1021/acs.jpca.1c06993] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The structures, relative stabilities, and vibrational wavenumbers of the two most stable conformers of serine, stabilized by the O-H···N, O-H···O═C and N-H···O-H intramolecular hydrogen bonds, have been evaluated by means of state-of-the-art composite schemes based on coupled-cluster (CC) theory. The so-called "cheap" composite approach (CCSD(T)/(CBS+CV)MP2) allowed determination of accurate equilibrium structures and harmonic vibrational wavenumbers, also pointing out significant corrections beyond the CCSD(T)/cc-pVTZ level. These accurate results stand as a reference for benchmarking selected hybrid and double-hybrid, dispersion-corrected DFT functionals. B2PLYP-D3 and DSDPBEP86 in conjunction with a triple-ζ basis set have been confirmed as effective methodologies for structural and spectroscopic studies of medium-sized flexible biomolecules, also showing intramolecular hydrogen bonding. These best performing double-hybrid functionals have been employed to simulate IR spectra by means of vibrational perturbation theory, also considering hybrid CC/DFT schemes. The best overall agreement with experiment, with mean absolute error of 8 cm-1, has been obtained by combining CCSD(T)/(CBS+CV)MP2 harmonic wavenumbers with B2PLYP-D3/maug-cc-pVTZ anharmonic corrections. Finally, a composite scheme entirely based on CCSD(T) calculations (CCSD(T)/CBS+CV) has been employed for energetics, further confirming that serine II is the most stable conformer, also when zero-point vibrational energy corrections are included.
Collapse
Affiliation(s)
- Mingzhu Sheng
- International Centre for Quantum and Molecular Structures, Physics Department, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Filippo Silvestrini
- Department of Chemistry "Giacomo Ciamician", University of Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Malgorzata Biczysko
- International Centre for Quantum and Molecular Structures, Physics Department, Shanghai University, 99 Shangda Road, Shanghai, 200444, China
| | - Cristina Puzzarini
- Department of Chemistry "Giacomo Ciamician", University of Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| |
Collapse
|
32
|
Owen AN, Zdanovskaia MA, Esselman BJ, Stanton JF, Woods RC, McMahon RJ. Semi-Experimental Equilibrium ( reSE) and Theoretical Structures of Pyridazine ( o-C 4H 4N 2). J Phys Chem A 2021; 125:7976-7987. [PMID: 34478298 DOI: 10.1021/acs.jpca.1c06187] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A semi-experimental equilibrium structure (reSE) of pyridazine (o-C4H4N2) has been determined using the rotational spectra of 18 isotopologues. Spectroscopic constants of four isotopologues are reported for the first time (measured from 235 to 360 GHz), while spectroscopic constants for previously reported isotopologues are improved by extending the frequency coverage (measured from 130 to 375 GHz). The experimental values of the ground-state rotational constants (A0, B0, and C0) from each isotopologue were converted to determinable constants (A0″, B0″, and C0″), which were then corrected for the effects of vibration-rotation interactions and electron-mass distributions using CCSD(T)/cc-pCVTZ calculations. The resultant reSE for pyridazine determines bond distances to within 0.001 Å and bond angles within 0.04°, a reduction in the statistical uncertainties by at least a factor of two relative to the previously reported reSE. The improvement in precision appears to be largely due to the use of higher-level theoretical calculations of the vibration-rotation and electron-mass effects, though the incorporation of the newly measured isotopologues ([4-2H, 4-13C]-, [4-2H, 5-13C]-, [4-2H, 6-13C]-, and [4,5-2H, 4-13C]-pyridazine) is partially responsible for the improved determination of the hydrogen-containing bond angles. The computed equilibrium structure (re) (CCSD(T)/cc-pCV5Z) and a "best theoretical estimate" of the equilibrium structure (re) both agree with the updated reSE structure within the statistical experimental uncertainty (2σ) of each structural parameter.
Collapse
Affiliation(s)
- Andrew N Owen
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Maria A Zdanovskaia
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Brian J Esselman
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, 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, Madison, Wisconsin 53706, United States
| | - Robert J McMahon
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| |
Collapse
|
33
|
Barone V, Puzzarini C, Mancini G. Integration of theory, simulation, artificial intelligence and virtual reality: a four-pillar approach for reconciling accuracy and interpretability in computational spectroscopy. Phys Chem Chem Phys 2021; 23:17079-17096. [PMID: 34346437 DOI: 10.1039/d1cp02507d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The established pillars of computational spectroscopy are theory and computer based simulations. Recently, artificial intelligence and virtual reality are becoming the third and fourth pillars of an integrated strategy for the investigation of complex phenomena. The main goal of the present contribution is the description of some new perspectives for computational spectroscopy, in the framework of a strategy in which computational methodologies at the state of the art, high-performance computing, artificial intelligence and virtual reality tools are integrated with the aim of improving research throughput and achieving goals otherwise not possible. Some of the key tools (e.g., continuous molecular perception model and virtual multifrequency spectrometer) and theoretical developments (e.g., non-periodic boundaries, joint variational-perturbative models) are shortly sketched and their application illustrated by means of representative case studies taken from recent work by the authors. Some of the results presented are already well beyond the state of the art in the field of computational spectroscopy, thereby also providing a proof of concept for other research fields.
Collapse
Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.
| | | | | |
Collapse
|
34
|
Melli A, Barone V, Puzzarini C. Unveiling Bifunctional Hydrogen Bonding with the Help of Quantum Chemistry: The Imidazole-Water Adduct as Test Case. J Phys Chem A 2021; 125:2989-2998. [PMID: 33818109 PMCID: PMC8154618 DOI: 10.1021/acs.jpca.1c01679] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/22/2021] [Indexed: 11/30/2022]
Abstract
The ubiquitous role of water and its amphiprotic nature call for a deeper insight into the physical-chemical properties of hydrogen-bonded complexes formed with building blocks of biomolecules. In this work, the semiexperimental (SE) approach combined with the template model (TM) protocol allowed the accurate determination of the equilibrium structure of two isomeric forms of the imidazole-water complex. In this procedure, the integration of experiment (thanks to a recent rotational spectroscopy investigation) and theory is exploited, also providing the means of assessing the reliability and accuracy of different quantum-chemical approaches. Overall, this study demonstrated the robustness of the combined SE-TM approach, which can provide accurate results using affordable quantum-chemical methods. Finally, the structural and energetic characteristics of these complexes have been examined in detail and compared with those of analogous heterocycle-water adducts, also exploiting energy decomposition analyses.
Collapse
Affiliation(s)
- Alessio Melli
- Scuola
Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Dipartimento
di Chimica “Giacomo Ciamician”, Università di Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Vincenzo Barone
- Scuola
Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Cristina Puzzarini
- Dipartimento
di Chimica “Giacomo Ciamician”, Università di Bologna, Via Selmi 2, 40126 Bologna, Italy
| |
Collapse
|
35
|
Gardner MB, Westbrook BR, Fortenberry RC, Lee TJ. Highly-accurate quartic force fields for the prediction of anharmonic rotational constants and fundamental vibrational frequencies. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 248:119184. [PMID: 33293226 DOI: 10.1016/j.saa.2020.119184] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/29/2020] [Accepted: 11/01/2020] [Indexed: 06/12/2023]
Abstract
The CcCR quartic force field (QFF) methodology is capable of computing B0 and C0 rotational constants to within 35 MHz (0.14%) of experiment for triatomic and larger molecules with at least two heavy atoms. Additionally, the same constants for molecules with four or more atoms agree to within 20 MHz (0.12%) of experiment for the current test set. This work also supports previous claims that the same QFF methodology can produce fundamental vibrational frequencies with a deviation less than 5.7 cm-1 from experiment. Consequently, this approach of augmenting complete basis set extrapolated energies with treatments of core electron correlation and scalar relativity produces some of the most accurate rovibrational spectroscopic data available.
Collapse
Affiliation(s)
- Mason B Gardner
- Department of Chemistry & Biochemistry, University of Mississippi, University, MS 38677-1848, United States
| | - Brent R Westbrook
- Department of Chemistry & Biochemistry, University of Mississippi, University, MS 38677-1848, United States
| | - Ryan C Fortenberry
- Department of Chemistry & Biochemistry, University of Mississippi, University, MS 38677-1848, United States.
| | - Timothy J Lee
- MS 245-3, NASA Ames Research Center, Moffett Field, CA 94035, United States
| |
Collapse
|
36
|
Alonso ER, Fusè M, León I, Puzzarini C, Alonso JL, Barone V. Exploring the Maze of Cycloserine Conformers in the Gas Phase Guided by Microwave Spectroscopy and Quantum Chemistry. J Phys Chem A 2021; 125:2121-2129. [DOI: 10.1021/acs.jpca.1c00455] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Elena R. Alonso
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB), Barrio Sarriena s/n, Leioa, Spain
| | - Marco Fusè
- SMART Laboratory, Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Iker León
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia Parque Cientifico UVa, Universidad de Valladolid, 47005 Valladolid, Spain
| | - Cristina Puzzarini
- Dipartimento di “Chimica Giacomo Ciamician”, University of Bologna, via F. Selmi 2, 40126, Bologna, Italy
| | - José L. Alonso
- Grupo de Espectroscopia Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia Parque Cientifico UVa, Universidad de Valladolid, 47005 Valladolid, Spain
| | - Vincenzo Barone
- SMART Laboratory, Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
| |
Collapse
|
37
|
Barone V, Puzzarini C. Looking for the bricks of the life in the interstellar medium: The fascinating world of astrochemistry. EPJ WEB OF CONFERENCES 2020. [DOI: 10.1051/epjconf/202024600021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The discovery in the interstellar medium of molecules showing a certain degree of complexity, and in particular those with a prebiotic character, has attracted great interest. A complex chemistry takes place in space, but the processes that lead to the production of molecular species are a matter of intense discussion, the knowledge still being at a rather primitive stage. Debate on the origins of interstellar molecules has been further stimulated by the identification of biomolecular building blocks, such as nucleobases and amino acids, in meteorites and comets. Since many of the molecules found in space play a role in the chemistry of life, the issue of their molecular genesis and evolution might be related to the profound question of the origin of life itself. Understanding the underlying chemical processes, including the production, reactions and destruction of compounds, requires the concomitant study of spectroscopy, gas-phase reactivity, and heterogeneous processes on dust-grains. The aim of this contribution is to provide a general view of a complex and multifaceted challenge, while focusing on the role played by molecular spectroscopy and quantum-chemical computations. In particular, the derivation of the molecular spectroscopic features and the investigation of gas-phase formation routes of prebiotic species in the interstellar medium are addressed from a computational point of view.
Collapse
|
38
|
Förster A, Visscher L. Low-Order Scaling G0W0 by Pair Atomic Density Fitting. J Chem Theory Comput 2020; 16:7381-7399. [PMID: 33174743 PMCID: PMC7726916 DOI: 10.1021/acs.jctc.0c00693] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Indexed: 12/18/2022]
Abstract
We derive a low-scaling G0W0 algorithm for molecules using pair atomic density fitting (PADF) and an imaginary time representation of the Green's function and describe its implementation in the Slater type orbital (STO)-based Amsterdam density functional (ADF) electronic structure code. We demonstrate the scalability of our algorithm on a series of water clusters with up to 432 atoms and 7776 basis functions and observe asymptotic quadratic scaling with realistic threshold qualities controlling distance effects and basis sets of triple-ζ (TZ) plus double polarization quality. Also owing to a very small prefactor, a G0W0 calculation for the largest of these clusters takes only 240 CPU hours with these settings. We assess the accuracy of our algorithm for HOMO and LUMO energies in the GW100 database. With errors of 0.24 eV for HOMO energies on the quadruple-ζ level, our implementation is less accurate than canonical all-electron implementations using the larger def2-QZVP GTO-type basis set. Apart from basis set errors, this is related to the well-known shortcomings of the GW space-time method using analytical continuation techniques as well as to numerical issues of the PADF approach of accurately representing diffuse atomic orbital (AO) products. We speculate that these difficulties might be overcome by using optimized auxiliary fit sets with more diffuse functions of higher angular momenta. Despite these shortcomings, for subsets of medium and large molecules from the GW5000 database, the error of our approach using basis sets of TZ and augmented double-ζ (DZ) quality is decreasing with system size. On the augmented DZ level, we reproduce canonical, complete basis set limit extrapolated reference values with an accuracy of 80 meV on average for a set of 20 large organic molecules. We anticipate our algorithm, in its current form, to be very useful in the study of single-particle properties of large organic systems such as chromophores and acceptor molecules.
Collapse
Affiliation(s)
- Arno Förster
- Theoretical Chemistry, Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands
| | - Lucas Visscher
- Theoretical Chemistry, Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands
| |
Collapse
|
39
|
Barone V, Ceselin G, Fusè M, Tasinato N. Accuracy Meets Interpretability for Computational Spectroscopy by Means of Hybrid and Double-Hybrid Functionals. Front Chem 2020; 8:584203. [PMID: 33195078 PMCID: PMC7645164 DOI: 10.3389/fchem.2020.584203] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 08/17/2020] [Indexed: 11/13/2022] Open
Abstract
Accuracy and interpretability are often seen as the devil and holy grail in computational spectroscopy and their reconciliation remains a primary research goal. In the last few decades, density functional theory has revolutionized the situation, paving the way to reliable yet effective models for medium size molecules, which could also be profitably used by non-specialists. In this contribution we will compare the results of some widely used hybrid and double hybrid functionals with the aim of defining the most suitable recipe for all the spectroscopic parameters of interest in rotational and vibrational spectroscopy, going beyond the rigid rotor/harmonic oscillator model. We will show that last-generation hybrid and double hybrid functionals in conjunction with partially augmented double- and triple-zeta basis sets can offer, in the framework of second order vibrational perturbation theory, a general, robust, and user-friendly tool with unprecedented accuracy for medium-size semi-rigid molecules.
Collapse
Affiliation(s)
- Vincenzo Barone
- SMART Laboratory, Scuola Normale Superiore di Pisa, Pisa, Italy
| | - Giorgia Ceselin
- SMART Laboratory, Scuola Normale Superiore di Pisa, Pisa, Italy
| | - Marco Fusè
- SMART Laboratory, Scuola Normale Superiore di Pisa, Pisa, Italy
| | - Nicola Tasinato
- SMART Laboratory, Scuola Normale Superiore di Pisa, Pisa, Italy
| |
Collapse
|
40
|
Alessandrini S, Dell'Isola V, Spada L, Barone V, Puzzarini C. A computational journey in the CH 2O 2S land: an accurate rotational and ro-vibrational analysis of the sulfene molecule and the O,S- and O,O-monothiocarbonic acids. Mol Phys 2020. [DOI: 10.1080/00268976.2020.1766707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- S. Alessandrini
- Scuola Normale Superiore, Pisa, Italy
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Bologna, Italy
| | - V. Dell'Isola
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Bologna, Italy
| | - L. Spada
- Scuola Normale Superiore, Pisa, Italy
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Bologna, Italy
| | - V. Barone
- Scuola Normale Superiore, Pisa, Italy
| | - C. Puzzarini
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Bologna, Italy
| |
Collapse
|
41
|
Kruse H, Szabla R, Šponer J. Surprisingly broad applicability of the cc-pVnZ-F12 basis set for ground and excited states. J Chem Phys 2020; 152:214104. [PMID: 32505162 DOI: 10.1063/5.0006871] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Excellent convergence properties for the (aug-)cc-pVnZ-F12 basis set family, purpose-made for explicitly correlated calculations, are demonstrated with conventional wave function methods and Kohn-Sham density functional theory for various ground and excited-state calculations. Among the ground-state properties studied are dipole moments, covalent bond lengths, and interaction and reaction energies. For excited states, we looked at vertical excitation energies, UV absorption, and excited-state absorption spectra. Convergence is compared against the basis sets cc-pVnZ, def2-nVD, aug-pcseg-n, and nZaPa-NR. It is established that the cc-pVnZ-F12 family consistently yields results of n + 1 quality and better. Especially, the cc-pVDZ-F12 basis set is found to be a basis set of good cost vs performance trade-off.
Collapse
Affiliation(s)
- Holger Kruse
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61265 Brno, Czech Republic
| | - Rafał Szabla
- EaStCHEM, School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, United Kingdom
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61265 Brno, Czech Republic
| |
Collapse
|
42
|
Puzzarini C, Spada L, Alessandrini S, Barone V. The challenge of non-covalent interactions: theory meets experiment for reconciling accuracy and interpretation. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2020; 32:343002. [PMID: 32203942 DOI: 10.1088/1361-648x/ab8253] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 03/23/2020] [Indexed: 06/10/2023]
Abstract
In the past decade, many gas-phase spectroscopic investigations have focused on the understanding of the nature of weak interactions in model systems. Despite the fact that non-covalent interactions play a key role in several biological and technological processes, their characterization and interpretation are still far from being satisfactory. In this connection, integrated experimental and computational investigations can play an invaluable role. Indeed, a number of different issues relevant to unraveling the properties of bulk or solvated systems can be addressed from experimental investigations on molecular complexes. Focusing on the interaction of biological model systems with solvent molecules (e.g., water), since the hydration of the biomolecules controls their structure and mechanism of action, the study of the molecular properties of hydrated systems containing a limited number of water molecules (microsolvation) is the basis for understanding the solvation process and how structure and reactivity vary from gas phase to solution. Although hydrogen bonding is probably the most widespread interaction in nature, other emerging classes, such as halogen, chalcogen and pnicogen interactions, have attracted much attention because of the role they play in different fields. Their understanding requires, first of all, the characterization of the directionality, strength, and nature of such interactions as well as a comprehensive analysis of their competition with other non-covalent bonds. In this review, it is shown how state-of-the-art quantum-chemical computations combined with rotational spectroscopy allow for fully characterizing intermolecular interactions taking place in molecular complexes from both structural and energetic points of view. The transition from bi-molecular complex to microsolvation and then to condensed phase is shortly addressed.
Collapse
Affiliation(s)
- Cristina Puzzarini
- Dipartimento di Chimica 'Giacomo Ciamician', Via F. Selmi 2, I-40126 Bologna, Italy
| | - Lorenzo Spada
- Dipartimento di Chimica 'Giacomo Ciamician', Via F. Selmi 2, I-40126 Bologna, Italy
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Silvia Alessandrini
- Dipartimento di Chimica 'Giacomo Ciamician', Via F. Selmi 2, I-40126 Bologna, Italy
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| |
Collapse
|
43
|
DFT meets the segmented polarization consistent basis sets: Performances in the computation of molecular structures, rotational and vibrational spectroscopic properties. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.127886] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
44
|
Boussessi R, Tasinato N, Pietropolli Charmet A, Stoppa P, Barone V. Sextic centrifugal distortion constants: interplay of density functional and basis set for accurate yet feasible computations. Mol Phys 2020. [DOI: 10.1080/00268976.2020.1734678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
| | | | | | - Paolo Stoppa
- Università Ca’ Foscari Venezia, Dipartimento di Scienze Molecolari e Nanosistemi, Mestre Venezia, Italy
| | | |
Collapse
|
45
|
A never-ending story in the sky: The secrets of chemical evolution. Phys Life Rev 2020; 32:59-94. [DOI: 10.1016/j.plrev.2019.07.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/26/2019] [Accepted: 07/02/2019] [Indexed: 01/13/2023]
|
46
|
Chen J, Zheng Y, Melli A, Spada L, Lu T, Feng G, Gou Q, Barone V, Puzzarini C. Theory meets experiment for elucidating the structure and stability of non-covalent complexes: water–amine interaction as a proof of concept. Phys Chem Chem Phys 2020; 22:5024-5032. [DOI: 10.1039/c9cp06768j] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A joint experimental-theoretical spectroscopic investigation has focused on a better understanding of the nature of weak, non-covalent interactions in amine-water model systems.
Collapse
Affiliation(s)
- Junhua Chen
- Department of Chemistry
- School of Chemistry and Chemical Engineering
- Chongqing University
- 401331 Chongqing
- China
| | - Yang Zheng
- Department of Chemistry
- School of Chemistry and Chemical Engineering
- Chongqing University
- 401331 Chongqing
- China
| | - Alessio Melli
- Department of Chemistry “Giacomo Ciamician”
- University of Bologna
- 40126 Bologna
- Italy
| | - Lorenzo Spada
- Department of Chemistry “Giacomo Ciamician”
- University of Bologna
- 40126 Bologna
- Italy
- Scuola Normale Superiore
| | - Tao Lu
- Department of Chemistry
- School of Chemistry and Chemical Engineering
- Chongqing University
- 401331 Chongqing
- China
| | - Gang Feng
- Department of Chemistry
- School of Chemistry and Chemical Engineering
- Chongqing University
- 401331 Chongqing
- China
| | - Qian Gou
- Department of Chemistry
- School of Chemistry and Chemical Engineering
- Chongqing University
- 401331 Chongqing
- China
| | | | - Cristina Puzzarini
- Department of Chemistry “Giacomo Ciamician”
- University of Bologna
- 40126 Bologna
- Italy
| |
Collapse
|
47
|
Puzzarini C, Barone V. The challenging playground of astrochemistry: an integrated rotational spectroscopy - quantum chemistry strategy. Phys Chem Chem Phys 2020; 22:6507-6523. [PMID: 32163090 DOI: 10.1039/d0cp00561d] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
While it is now well demonstrated that the interstellar medium (ISM) is characterized by a diverse and complex chemistry, a significant number of features in radioastronomical spectra are still unassigned and call for new laboratory efforts, which are increasingly based on integrated experimental and computational strategies. In parallel, the identification of an increasing number of molecules containing more than five atoms and at least one carbon atom (the so-called "interstellar" complex organic molecules), which can play a relevant role in the chemistry of life, raises the additional issue of how these species can be produced in the typical harsh conditions of the ISM. On these grounds, this perspective aims to present an integrated rotational spectroscopy - quantum chemistry approach for supporting radioastronomical observations and a computational strategy for contributing to the elucidation of chemical reactivity in the interstellar space.
Collapse
Affiliation(s)
- Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician", University of Bologna, via F. Selmi 2, I-40126 Bologna, Italy.
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, Pisa, I-56126, Italy
| |
Collapse
|
48
|
Zhang J, Ye H, Jin Y, Gou Q, Biczysko M, Feng G. Conformational Equilibria and Molecular Structures of Model Sulfur-Sulfur Bridge Systems: Diisopropyl Disulfide. J Phys Chem A 2019; 123:10714-10720. [PMID: 31765568 DOI: 10.1021/acs.jpca.9b07198] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The conformations and molecular structures of diisopropyl disulfide have been studied by high-resolution microwave spectroscopy and quantum chemical calculations. Three conformers, G'GG', G'GT, and GGG', have been observed in the jet expansion. The global minimum, G'GG', adopts a configuration with the G' orientation of H-C-S-S and S-S-C-H and the G orientation of C-S-S-C showing the C2 symmetry. The rotational spectra of monosubstituted 13C and 34S isotopologues have also been recorded for G'GG', leading to an accurate structural determination of this conformer. Two additional 34S isotopologues have also been measured for G'GT. The relative energies of three observed conformers calculated at the MP2/6-311++(d,p) level of theory are within 2 kJ mol-1, while the relative intensity measurements suggested their population ratio to be NG'GG'/NG'GT/NGGG' ≈ 5:3:2.
Collapse
Affiliation(s)
- Jiaqi Zhang
- School of Chemistry and Chemical Engineering , Chongqing University , Daxuecheng South Road 55 , 401331 Chongqing , China
| | - Hexu Ye
- International Centre for Quantum and Molecular Structures , Shanghai University , Shangda Road 99 , 200444 Shanghai , China
| | - Yan Jin
- School of Chemistry and Chemical Engineering , Chongqing University , Daxuecheng South Road 55 , 401331 Chongqing , China
| | - Qian Gou
- School of Chemistry and Chemical Engineering , Chongqing University , Daxuecheng South Road 55 , 401331 Chongqing , China
| | - Malgorzata Biczysko
- International Centre for Quantum and Molecular Structures , Shanghai University , Shangda Road 99 , 200444 Shanghai , China
| | - Gang Feng
- School of Chemistry and Chemical Engineering , Chongqing University , Daxuecheng South Road 55 , 401331 Chongqing , China
| |
Collapse
|
49
|
d'Ischia M, Manini P, Moracci M, Saladino R, Ball V, Thissen H, Evans RA, Puzzarini C, Barone V. Astrochemistry and Astrobiology: Materials Sciencein Wonderland? Int J Mol Sci 2019; 20:E4079. [PMID: 31438518 PMCID: PMC6747172 DOI: 10.3390/ijms20174079] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/14/2019] [Accepted: 08/19/2019] [Indexed: 02/04/2023] Open
Abstract
Astrochemistry and astrobiology, the fascinating disciplines that strive to unravel the origin of life, have opened unprecedented and unpredicted vistas into exotic compounds as well as extreme or complex reaction conditions of potential relevance for a broad variety of applications. Representative, and so far little explored sources of inspiration include complex organic systems, such as polycyclic aromatic hydrocarbons (PAHs) and their derivatives; hydrogen cyanide (HCN) and formamide (HCONH2) oligomers and polymers, like aminomalononitrile (AMN)-derived species; and exotic processes, such as solid-state photoreactions on mineral surfaces, phosphorylation by minerals, cold ice irradiation and proton bombardment, and thermal transformations in fumaroles. In addition, meteorites and minerals like forsterite, which dominate dust chemistry in the interstellar medium, may open new avenues for the discovery of innovative catalytic processes and unconventional methodologies. The aim of this review was to offer concise and inspiring, rather than comprehensive, examples of astrochemistry-related materials and systems that may be of relevance in areas such as surface functionalization, nanostructures, and hybrid material design, and for innovative technological solutions. The potential of computational methods to predict new properties from spectroscopic data and to assess plausible reaction pathways on both kinetic and thermodynamic grounds has also been highlighted.
Collapse
Affiliation(s)
- Marco d'Ischia
- Department of Chemical Sciences, University of Naples "Federico II", Complesso Universitario di Monte S. Angelo, Via Cupa Nuova Cinthia 21, 80126 Naples, Italy.
| | - Paola Manini
- Department of Chemical Sciences, University of Naples "Federico II", Complesso Universitario di Monte S. Angelo, Via Cupa Nuova Cinthia 21, 80126 Naples, Italy
| | - Marco Moracci
- Department of Biology, University of Naples "Federico II", Complesso Universitario di Monte S. Angelo, Via Cupa Nuova Cinthia 21, 80126 Naples, Italy
- Institute of Biosciences and BioResources, National Research Council of Italy, Via P. Castellino 111, 80131 Naples, Italy
| | - Raffaele Saladino
- Department of Ecological and Biological Sciences, Via S. Camillo de Lellis, University of Tuscia, 01100 Viterbo, Italy
| | - Vincent Ball
- Institut National de la Santé et de la RechercheMédicale, 11 rue Humann, 67085 Strasbourg Cedex, France
- Faculté de Chirurgie Dentaire, Université de Strasbourg, 1 Place de l'Hôpital, 67000 Strasbourg, France
| | - Helmut Thissen
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Manufacturing, Clayton, VIC 3168, Australia
| | - Richard A Evans
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Manufacturing, Clayton, VIC 3168, Australia
| | - Cristina Puzzarini
- Department of Chemistry "Giacomo Ciamician", University of Bologna, Via F. Selmi 2, I-40126 Bologna, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| |
Collapse
|
50
|
Paoloni L, Rampino S, Barone V. Potential-Energy Surfaces for Ring-Puckering Motions of Flexible Cyclic Molecules through Cremer-Pople Coordinates: Computation, Analysis, and Fitting. J Chem Theory Comput 2019; 15:4280-4294. [PMID: 31244128 DOI: 10.1021/acs.jctc.9b00363] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Ring-puckering motion in 12 flexible cyclic molecules is investigated by calculation and analysis of two-dimensional potential-energy surfaces (PESs) using the so-called ring-puckering coordinates proposed by Cremer and Pople. The PESs are calculated by means of density-functional theory using a B2PLYP-D3BJ exchange-correlation functional with a maug-cc-pVTZ basis set, and results are compared to the available experimental and theoretical data. Special care is devoted to the aspect of symmetry in such two-dimensional PESs, which are here reported for the first time also for molecules whose planar form has symmetry lower than D5 h or C2 v. The issue of PES fitting and that of solving the nuclear dynamics using ring-puckering coordinates are also addressed. Analytical formulations of the computed PESs using suitable functional forms with a limited set of parameters are provided.
Collapse
Affiliation(s)
- Lorenzo Paoloni
- SMART Laboratory , Scuola Normale Superiore , Piazza dei Cavalieri 7 , 56126 Pisa , Italia
| | - Sergio Rampino
- SMART Laboratory , Scuola Normale Superiore , Piazza dei Cavalieri 7 , 56126 Pisa , Italia
| | - Vincenzo Barone
- SMART Laboratory , Scuola Normale Superiore , Piazza dei Cavalieri 7 , 56126 Pisa , Italia
| |
Collapse
|