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Xu R, Jiang Z, Yang Q, Bloino J, Biczysko M. Harmonic and anharmonic vibrational computations for biomolecular building blocks: Benchmarking DFT and basis sets by theoretical and experimental IR spectrum of glycine conformers. J Comput Chem 2024; 45:1846-1869. [PMID: 38682874 DOI: 10.1002/jcc.27377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 05/01/2024]
Abstract
Advanced vibrational spectroscopic experiments have reached a level of sophistication that can only be matched by numerical simulations in order to provide an unequivocal analysis, a crucial step to understand the structure-function relationship of biomolecules. While density functional theory (DFT) has become the standard method when targeting medium-size or larger systems, the problem of its reliability and accuracy are well-known and have been abundantly documented. To establish a reliable computational protocol, especially when accuracy is critical, a tailored benchmark is usually required. This is generally done over a short list of known candidates, with the basis set often fixed a priori. In this work, we present a systematic study of the performance of DFT-based hybrid and double-hybrid functionals in the prediction of vibrational energies and infrared intensities at the harmonic level and beyond, considering anharmonic effects through vibrational perturbation theory at the second order. The study is performed for the six-lowest energy glycine conformers, utilizing available "state-of-the-art" accurate theoretical and experimental data as reference. Focusing on the most intense fundamental vibrations in the mid-infrared range of glycine conformers, the role of the basis sets is also investigated considering the balance between computational cost and accuracy. Targeting larger systems, a broad range of hybrid schemes with different computational costs is also tested.
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Affiliation(s)
- Ruiqin Xu
- Department of Physics, College of Sciences, Shanghai University, Shanghai, China
| | | | - Qin Yang
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czechia
| | - Julien Bloino
- Classe di Scienze, Scuola Normale Superiore, Pisa, Italy
| | - Malgorzata Biczysko
- Department of Physics, College of Sciences, Shanghai University, Shanghai, China
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2
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Avcı D, Cömert HE, Sönmez F, Dege N, Tamer Ö, Atalay Y. Comparative assessment of structure-property relationships of new Cu(II) complex in selected density functionals. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 305:123489. [PMID: 37844450 DOI: 10.1016/j.saa.2023.123489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 09/14/2023] [Accepted: 10/02/2023] [Indexed: 10/18/2023]
Abstract
In order to evaluate the structure-property relationships of Cu(II) complex by using DFT methods, the structure of the newly synthesized Cu(II) complex, [Cu(6-Brpic)2(bpy)], was investigated by XRD, FTIR, UV-Vis, and fluorescence spectroscopic methods. In addition, Hirshfeld surface and NBO analyses were fulfilled to identify possible interactions in the intermolecular and coordination environment. The five different DFT methods (HCTH, M06L, TPSSTPSS, B3LYP, and CAM-B3LYP levels), having four different functionalities (the GGA, meta-GGA, hybrid-GGA, and range-separated hybrid), were carried out so as to investigate the structure-property relationship, considering the geometric parameters (bond lengths and angles), vibrational frequencies, electronic absorption wavelengths, electronic transitions, and linear and nonlinear optical parameters. The R2 for structural and vibrational parameters, as well as MPD%, MAD, an optimal scaling factor (λ) and overall root mean square (RMS) deviation, were considered only at vibration frequencies. While it was determined that M06-L and TPSSTPSS levels gave the best results for the bond lengths and angles of the Cu(II) complex, the best results for vibrational frequencies were obtained in the HCTH method along with these methods. In NLO parameters, the static and dynamic first-order hyperpolarizability (<β(0;0,0)> and β(-ω;ω,0)/<β(-2ω;ω,ω)>) values, the largest values were obtained in the HCTH method (38.817 × 10-30 and 437.86 × 10-30/201.55 × 10-30 esu), whereas the smallest values were found to be in the CAM-B3LYP/TPSSTPSS levels (6.118 × 10-30 esu, 8.270 × 10-30/11.730 × 10-30 esu). By regarding the static γ (<γ(0;0,0,0)>) and dynamic (<γ(-ω;ω,0,0)> parameters, the largest values were calculated in the M06L (232.101 × 10-36) and HCTH (1711.52 × 10-36) methods and the smallest values were obtained in the CAM-B3LYP (43.281 × 10-36 and 60.844 × 10-36) method. In fact, it is obviously seen that the β and γ values obtained by the aforementioned DFT levels are many times higher than that of the standard molecule of urea. These results indicate that the Cu(II) complex may be used as a potential NLO material to evolve optoelectronic devices.
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Affiliation(s)
- Davut Avcı
- Sakarya University, Faculty of Science, Department of Physics, 54187 Sakarya, Turkey.
| | - Hatice Esra Cömert
- Sakarya University, Faculty of Science, Department of Physics, 54187 Sakarya, Turkey
| | - Fatih Sönmez
- Sakarya University of Applied Sciences, Pamukova Vocational High School, 54055 Sakarya, Turkey
| | - Necmi Dege
- Ondokuz Mayıs University, Faculty of Science, Department of Physics, 55139 Samsun, Turkey
| | - Ömer Tamer
- Sakarya University, Faculty of Science, Department of Physics, 54187 Sakarya, Turkey
| | - Yusuf Atalay
- Sakarya University, Faculty of Science, Department of Physics, 54187 Sakarya, Turkey
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3
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Study of copper removal by modified biomaterials using the response surface methodology, DFT Calculation, and molecular dynamic simulation. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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4
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Theoretical analysis of the influence of C–H$$\cdots $$O bonds on the NMR constants of uracil in DMSO. Theor Chem Acc 2020. [DOI: 10.1007/s00214-020-02670-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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5
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Beć KB, Grabska J, Ozaki Y, Czarnecki MA, Huck CW. Simulated NIR spectra as sensitive markers of the structure and interactions in nucleobases. Sci Rep 2019; 9:17398. [PMID: 31758033 PMCID: PMC6874539 DOI: 10.1038/s41598-019-53827-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 10/11/2019] [Indexed: 11/16/2022] Open
Abstract
Near-infrared (near-IR; NIR) spectroscopy is continuously advancing in biophysical and biochemical fields of investigation. For instance, recent progresses in NIR hyperspectral imaging of biological systems may be noted. However, interpretation of NIR bands for biological samples is difficult and creates a considerable barrier in exploring the full potential of NIR spectroscopy in bioscience. For this reason, we carried out a systematic study of NIR spectra of adenine, cytosine, guanine, and thymine in polycrystalline state. Interpretation of NIR spectra of these nucleobases was supported by anharmonic vibrational analysis using Deperturbed Vibrational Second-Order Perturbation Theory (DVPT2). A number of molecular models of nucleobases was applied to study the effect of the inter-molecular interactions on the NIR spectra. The accuracy of simulated NIR spectra appears to depend on the intra-layer interactions; in contrast, the inter-layer interactions are less influential. The best results were achieved by combining the simulated spectra of monomers and dimers. It is of particular note that in-plane deformation bands are far more populated than out-of-plane ones and the importance of ring modes is relatively small. This trend is in contrast to that observed in mid-IR region. As shown, the local, short-range chemical neighborhood of nucleobase molecules influence their NIR spectra more considerably. This suggests that NIR spectra are more sensitive probe of the nucleobase pairing than mid-IR ones. The obtained results allow, for the first time, to construct a frequency correlation table for NIR spectra of purines and pyrimidines.
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Affiliation(s)
- Krzysztof B Beć
- Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innrain 80/82, CCB-Center for Chemistry and Biomedicine, 6020, Innsbruck, Austria.
| | - Justyna Grabska
- Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innrain 80/82, CCB-Center for Chemistry and Biomedicine, 6020, Innsbruck, Austria
| | - Yukihiro Ozaki
- Department of Chemistry, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo, 669-1337, Japan
| | - Mirosław A Czarnecki
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383, Wrocław, Poland
| | - Christan W Huck
- Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innrain 80/82, CCB-Center for Chemistry and Biomedicine, 6020, Innsbruck, Austria
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6
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Beć KB, Grabska J, Czarnecki MA, Huck CW, Wójcik MJ, Nakajima T, Ozaki Y. IR Spectra of Crystalline Nucleobases: Combination of Periodic Harmonic Calculations with Anharmonic Corrections Based on Finite Models. J Phys Chem B 2019; 123:10001-10013. [DOI: 10.1021/acs.jpcb.9b06285] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Krzysztof B. Beć
- Institute of Analytical Chemistry, University of Innsbruck, A6020 Innsbruck, Austria
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Justyna Grabska
- Institute of Analytical Chemistry, University of Innsbruck, A6020 Innsbruck, Austria
| | - Mirosław A. Czarnecki
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Christian W. Huck
- Institute of Analytical Chemistry, University of Innsbruck, A6020 Innsbruck, Austria
| | - Marek J. Wójcik
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | - Takahito Nakajima
- RIKEN Center for Computational Science, 7-1-26, Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Yukihiro Ozaki
- Department of Chemistry, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo 669-1337, Japan
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Gabas F, Di Liberto G, Ceotto M. Vibrational investigation of nucleobases by means of divide and conquer semiclassical dynamics. J Chem Phys 2019; 150:224107. [PMID: 31202241 DOI: 10.1063/1.5100503] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this work, we report a computational study of the vibrational features of four different nucleobases employing the divide-and-conquer semiclassical initial value representation molecular dynamics method. Calculations are performed on uracil, cytosine, thymine, and adenine. Results show that the overall accuracy with respect to experiments is within 20 wavenumbers, regardless of the dimensionality of the nucleobase. Vibrational estimates are accurate even in the complex case of cytosine, where two relevant conformers are taken into account. These results are promising in the perspective of future studies on more complex systems, such as nucleotides or nucleobase pairs.
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Affiliation(s)
- Fabio Gabas
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy
| | - Giovanni Di Liberto
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy
| | - Michele Ceotto
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy
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8
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Zaleśny R, Medved' M, Sitkiewicz SP, Matito E, Luis JM. Can Density Functional Theory Be Trusted for High-Order Electric Properties? The Case of Hydrogen-Bonded Complexes. J Chem Theory Comput 2019; 15:3570-3579. [PMID: 31082215 DOI: 10.1021/acs.jctc.9b00139] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This work reports on an extensive assessment of the performance of a wide palette of density functional approximations in predicting the (high-order) electric properties of hydrogen-bonded complexes. To this end, we compute the electronic and vibrational contributions to the electric polarizability and the first and second hyperpolarizabilities, using the CCSD(T)/aug-cc-pVTZ level of theory as reference. For all the studied properties, the average absolute errors below 20% can only be obtained using the CAM-B3LYP functional, while LC-BLYP and MN15 are shown to be only slightly less accurate (average absolute errors not exceeding 30%). Among Minnesota density functionals, i.e., M06, M06-2X, and MN15, we only recommend the latter one, which quite accurately predicts the electronic and vibrational (hyper)polarizabilities. We also analyze the optimal tuning of the range-separation parameter μ for the LC-BLYP functional, finding that this approach does not bring any systematic improvement in the predictions of electronic and vibrational (hyper)polarizabilities and the accuracy of computed properties is largely system-dependent. Finally, we report huge errors in predicting the vibrational second hyperpolarizability by ωB97X, M06, and M06-2X functionals. Based on the explicit evaluation of anharmonic terms contributing to the second hyperpolarizability, this failure is traced down to a poor determination of third- and fourth-order energy derivatives with respect to normal modes. These results reveal serious flaws of some density functional approximations and suggest caution in selecting the appropriate functional to calculate not only electronic and vibrational (hyper)polarizabilities but also other molecular properties that contain vibrational anharmonic contributions.
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Affiliation(s)
- Robert Zaleśny
- Department of Physical and Quantum Chemistry, Faculty of Chemistry , Wrocław University of Science and Technology , Wyb. Wyspiańskiego 27 , PL-50370 Wrocław , Poland
| | - Miroslav Medved'
- Department of Chemistry, Faculty of Natural Sciences , Matej Bel University , Tajovského 40 , 974 01 Banská Bystrica , Slovak Republic
| | - Sebastian P Sitkiewicz
- Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), 20080 Donostia , Euskadi , Spain.,Donostia International Physics Center (DIPC), Manuel Lardizabal Ibilbidea 4 , 20018 Donostia , Euskadi , Spain.,Institute of Computational Chemistry and Catalysis and Department of Chemistry , University of Girona , Campus de Montilivi , 17003 Girona , Catalonia , Spain
| | - Eduard Matito
- Donostia International Physics Center (DIPC), Manuel Lardizabal Ibilbidea 4 , 20018 Donostia , Euskadi , Spain.,Ikerbasque Foundation for Science , 48011 Bilbao , Euskadi , Spain
| | - Josep M Luis
- Institute of Computational Chemistry and Catalysis and Department of Chemistry , University of Girona , Campus de Montilivi , 17003 Girona , Catalonia , Spain
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9
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Pfaff P, Mouhib H, Kraft P. Challenging the Molecular Parameters of Vetiver: Can 4,5-Dimethyl-3-(3′-methylbut-1′-en-2′-yl)-4-phenylcyclopent-2-en-1-one Mimic Zizaenones in Structure and Odor? European J Org Chem 2019. [DOI: 10.1002/ejoc.201900163] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Patrick Pfaff
- Ingredients Research; Givaudan Fragrances S+T; Kemptpark 50 8310 Kemptthal Switzerland
| | - Halima Mouhib
- Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, 5 bd Descartes; Université Paris-Est; 77454 Marne-la-Vallée France
| | - Philip Kraft
- Ingredients Research; Givaudan Fragrances S+T; Kemptpark 50 8310 Kemptthal Switzerland
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10
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DFT modelling of the infrared spectra for the isolated and the micro-hydrated forms of uracil. Theor Chem Acc 2019. [DOI: 10.1007/s00214-019-2431-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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11
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Structural, spectroscopic and quantum chemical studies on copper(II) complex of 4-ethoxy-2-methyl-5-(4-morpholinyl)-3(2H)-pyridazinone. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.06.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Thicoipe S, Carbonniere P, Pouchan C. DFT modelling of the infrared spectra for isolated and aqueous forms of adenine. Theor Chem Acc 2017. [DOI: 10.1007/s00214-017-2076-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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Altürk S, Avcı D, Tamer Ö, Atalay Y. Comparison of different hybrid DFT methods on structural, spectroscopic, electronic and NLO parameters for a potential NLO material. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2016.12.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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14
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Fornaro T, Biczysko M, Bloino J, Barone V. Reliable vibrational wavenumbers for C=O and N-H stretchings of isolated and hydrogen-bonded nucleic acid bases. Phys Chem Chem Phys 2016; 18:8479-90. [PMID: 26940362 PMCID: PMC5612391 DOI: 10.1039/c5cp07386c] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The accurate prediction of vibrational wavenumbers for functional groups involved in hydrogen-bonded bridges remains an important challenge for computational spectroscopy. For the specific case of the C=O and N-H stretching modes of nucleobases and their oligomers, the paucity of experimental reference values needs to be compensated by reliable computational data, which require the use of approaches going beyond the standard harmonic oscillator model. Test computations performed for model systems (formamide, acetamide and their cyclic homodimers) in the framework of the second order vibrational perturbation theory (VPT2) confirmed that anharmonic corrections can be safely computed by global hybrid (GHF) or double hybrid (DHF) functionals, whereas the harmonic part is particularly challenging. As a matter of fact, GHFs perform quite poorly and even DHFs, while fully satisfactory for C=O stretchings, face unexpected difficulties when dealing with N-H stretchings. On these grounds, a linear regression for N-H stretchings has been obtained and validated for the heterodimers formed by 4-aminopyrimidine with 6-methyl-4-pyrimidinone (4APM-M4PMN) and by uracil with water. In view of the good performance of this computational model, we have built a training set of B2PLYP-D3/maug-cc-pVTZ harmonic wavenumbers (including linear regression scaling for N-H) for six-different uracil dimers and a validation set including 4APM-M4PMN, one of the most stable hydrogen-bonded adenine homodimers, as well as the adenine-uracil, adenine-thymine, guanine-cytosine and adenine-4-thiouracil heterodimers. Because of the unfavourable scaling of DHF harmonic wavenumbers with the dimensions of the investigated systems, we have optimized a linear regression of B3LYP-D3/N07D harmonic wavenumbers for the training set, which has been next checked against the validation set. This relatively cheap model, which shows very good agreement with experimental data (average errors of about 10 cm(-1)), paves the route toward a reliable analysis of spectroscopic signatures for larger polynucleotides.
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Affiliation(s)
- Teresa Fornaro
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.
| | - Malgorzata Biczysko
- International Centre for Quantum and Molecular Structures, College of Sciences, Shanghai University, 99 Shangda Road, Shanghai, 200444, China.
| | - Julien Bloino
- Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca CNR, Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.
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15
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16
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Fornaro T, Burini D, Biczysko M, Barone V. Hydrogen-Bonding Effects on Infrared Spectra from Anharmonic Computations: Uracil–Water Complexes and Uracil Dimers. J Phys Chem A 2015; 119:4224-36. [DOI: 10.1021/acs.jpca.5b01561] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Teresa Fornaro
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, I-56126 Pisa, Italy
| | - Diletta Burini
- Dipartimento
di Matematica e Informatica, Università di Perugia, INFN Sezione
Perugia Via Vanvitelli, I-106123 Perugia, Italy
| | - Malgorzata Biczysko
- Physics
Department, and International Centre for Quantum and Molecular Structures, Shanghai University, 99 Shangda Road, Shanghai, 200444 China
- Consiglio
Nazionale delle Ricerche, Istituto di Chimica dei Composti OrganoMetallici
(ICCOM-CNR), UOS di Pisa, Area della Ricerca CNR, Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, I-56126 Pisa, Italy
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17
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Fornaro T, Carnimeo I, Biczysko M. Toward Feasible and Comprehensive Computational Protocol for Simulation of the Spectroscopic Properties of Large Molecular Systems: The Anharmonic Infrared Spectrum of Uracil in the Solid State by the Reduced Dimensionality/Hybrid VPT2 Approach. J Phys Chem A 2014; 119:5313-26. [DOI: 10.1021/jp510101y] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Teresa Fornaro
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, I-56126 Pisa, Italy
| | - Ivan Carnimeo
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, I-56126 Pisa, Italy
- Compunet, Istituto Italiano di Tecnologia (IIT), Via Morego 30, I-16163 Genova, Italy
| | - Malgorzata Biczysko
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, I-56126 Pisa, Italy
- Istituto di Chimica
dei Composti OrganoMetallici (ICCOM-CNR), UOS di Pisa, Area della
Ricerca CNR, Consiglio Nazionale delle Ricerche, Via G. Moruzzi 1, I-56124 Pisa, Italy
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18
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Gautam P, Prakash O, Dani RK, Singh NK, Singh RK. Vibrational and quantum chemical investigation of cyclization of thiosemicarbazide group in 1-benzoyl-4-phenyl-3-thiosemicarbazide. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 132:278-287. [PMID: 24873893 DOI: 10.1016/j.saa.2014.03.095] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 02/28/2014] [Accepted: 03/18/2014] [Indexed: 06/03/2023]
Abstract
1-Benzoyl-4-phenyl-3-thiosemicarbazide (H3bpt) was treated with acid - base in one sequence and base - acid in other sequence, both of which lead to ring formation of thiosemicarbazide group, giving N-phenyl-5-phenyl-1,3,4-thiadiazol-2-amine (Hppta) in the first case and 4,5-diphenyl-2,4-dihydro-1,2,4-triazole-3-thione (Hdptt) in the second case. The primary (H3bpt) as well as the resulting compounds (Hppta & Hdptt) has been characterized by elemental analyses, NMR, FTIR and Raman spectroscopic techniques. The quantum chemical calculations of the compounds are performed using DFT/B3LYP/6311G(d,p) method for geometry optimizations and also for prediction of the molecular properties. The cyclization is confirmed by disappearance of many bands belonging to the open chain subgroups of H3bpt such as; NH stretching, NH bending, CN stretching, NH puckering, CO stretching etc. The ring formation of 1-benzoyl-4-phenyl-3-thiosemicarbazide (H3bpt) has been further confirmed by the appearance of many bands belonging to the closed ring of thiosemicarbazide in the resulting compounds Hppta and Hdptt.
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Affiliation(s)
- Priyanka Gautam
- Department of Physics, Banaras Hindu University, Varanasi 221005, India
| | - Om Prakash
- Department of Physics, Banaras Hindu University, Varanasi 221005, India
| | - R K Dani
- Department of Chemistry, Banaras Hindu University, Varanasi 221005, India
| | - N K Singh
- Department of Chemistry, Banaras Hindu University, Varanasi 221005, India
| | - Ranjan K Singh
- Department of Physics, Banaras Hindu University, Varanasi 221005, India.
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19
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Alam MJ, Ahmad S. Quantum chemical and spectroscopic investigations of 3-methyladenine. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 128:653-664. [PMID: 24704482 DOI: 10.1016/j.saa.2014.02.170] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 02/17/2014] [Accepted: 02/21/2014] [Indexed: 06/03/2023]
Abstract
FTIR, FT-Raman and UV-Vis spectra of 3-methyladenine have been recorded and investigated using quantum chemical calculations. The molecular geometry and vibrational spectra of 3-methyladenine in the ground state are computed by using HF and DFT methods with 6-311G(d,p) basis set. VSCF, CC-VSCF methods based on 2MR-QFF and PT2 (Barone method) have been utilized for computing anharmonic vibrational frequencies. These methods yield results that are in remarkable agreement with the experimental data. The magnitudes of coupling between pair of modes have been also computed. Vibrational modes are assigned with the help of visual inspection of atomic displacements. The electronic spectra, simulated at TD-B3LYP/6-311++G(d,p) level of theory, are compared to the experiment. The global quantities: electronic chemical potential, electrophilicity index, chemical hardness and softness based on HOMO and LUMO energy eigenvalues are also computed at B3LYP/6-311++G(d,p) level of theory.
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Affiliation(s)
| | - Shabbir Ahmad
- Department of Physics, Aligarh Muslim University, Aligarh 202002, India.
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Fornaro T, Biczysko M, Monti S, Barone V. Dispersion corrected DFT approaches for anharmonic vibrational frequency calculations: nucleobases and their dimers. Phys Chem Chem Phys 2014; 16:10112-28. [PMID: 24531740 PMCID: PMC4612423 DOI: 10.1039/c3cp54724h] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Computational spectroscopy techniques have become in the last few years an effective means to analyze and assign infrared (IR) spectra of molecular systems of increasing dimensions and in different environments. However, transition from compilation of harmonic data to fully anharmonic simulations of spectra is still underway. The most promising results for large systems have been obtained, in our opinion, by perturbative vibrational approaches based on potential energy surfaces computed by hybrid (especially B3LYP) density functionals and medium size (e.g. SNSD) basis sets. In this framework, we are actively developing a comprehensive and robust computational protocol aimed at quantitative reproduction of the spectra of nucleic acid base complexes and their adsorption on solid supports (organic/inorganic). In this contribution we report the essential results of the first step devoted to isolated monomers and dimers. It is well known that in order to model the vibrational spectra of weakly bound molecular complexes dispersion interactions should be taken into proper account. In this work we have chosen two popular and inexpensive approaches to model dispersion interactions, namely the semi-empirical dispersion correction (D3) and pseudopotential based (DCP) methodologies both in conjunction with the B3LYP functional. These have been used for simulating fully anharmonic IR spectra of nucleobases and their dimers through generalized second order vibrational perturbation theory (GVPT2). We have studied, in particular, isolated adenine, hypoxanthine, uracil, thymine and cytosine, the hydrogen-bonded and stacked adenine and uracil dimers, and the stacked adenine-naphthalene heterodimer. Anharmonic frequencies are compared with standard B3LYP results and experimental findings, while the computed interaction energies and structures of complexes are compared to the best available theoretical estimates.
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Affiliation(s)
- Teresa Fornaro
- Scuola Normale Superiore, piazza dei Cavalieri 7, I-56126 Pisa, Italy.
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Prakash O, Gautam P, Dani R, Nandi A, Singh N, Singh RK. Structural analysis of complexes formed by ethyl 4-phenylthiocarbamoyl piperazine-1-carboxylate with Ni(II), Zn(II) and Cd(II) through spectroscopic and DFT techniques. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.01.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Barone V, Biczysko M, Bloino J. Fully anharmonic IR and Raman spectra of medium-size molecular systems: accuracy and interpretation. Phys Chem Chem Phys 2014; 16:1759-87. [PMID: 24346191 PMCID: PMC4604664 DOI: 10.1039/c3cp53413h] [Citation(s) in RCA: 304] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Computation of full infrared (IR) and Raman spectra (including absolute intensities and transition energies) for medium- and large-sized molecular systems beyond the harmonic approximation is one of the most interesting challenges of contemporary computational chemistry. Contrary to common beliefs, low-order perturbation theory is able to deliver results of high accuracy (actually often better than those issuing from current direct dynamics approaches) provided that anharmonic resonances are properly managed. This perspective sketches the recent developments in our research group toward the development of a robust and user-friendly virtual spectrometer rooted in second-order vibrational perturbation theory (VPT2) and usable also by non-specialists essentially as a black-box procedure. Several examples are explicitly worked out in order to illustrate the features of our computational tool together with the most important ongoing developments.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, piazza dei Cavalieri 7, I-56126 Pisa, Italy.
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Carnimeo I, Puzzarini C, Tasinato N, Stoppa P, Charmet AP, Biczysko M, Cappelli C, Barone V. Anharmonic theoretical simulations of infrared spectra of halogenated organic compounds. J Chem Phys 2013; 139:074310. [PMID: 23968095 PMCID: PMC4604659 DOI: 10.1063/1.4817401] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The recent implementation of the computation of infrared (IR) intensities beyond the double-harmonic approximation [J. Bloino and V. Barone, J. Chem. Phys. 136, 124108 (2012)] paved the route to routine calculations of infrared spectra for a wide set of molecular systems. Halogenated organic compounds represent an interesting class of molecules, from both an atmospheric and computational point of view, due to the peculiar chemical features related to the halogen atoms. In this work, we simulate the IR spectra of eight halogenated molecules (CH2F2, CHBrF2, CH2DBr, CF3Br, CH2CHF, CF2CFCl, cis-CHFCHBr, cis-CHFCHI), using two common hybrid and double-hybrid density functionals in conjunction with both double- and triple-ζ quality basis sets (SNSD and cc-pVTZ) as well as employing the coupled-cluster theory with basis sets of at least triple-ζ quality. Finally, we compare our results with available experimental spectra, with the aim of checking the accuracy and the performances of the computational approaches.
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Affiliation(s)
- Ivan Carnimeo
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento 35, I-56126 Pisa, Italy.
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Prakash O, Singh SK, Singh B, Singh RK. Investigation of coordination properties of isolated adenine to copper metal: a systematic spectroscopic and DFT study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 112:410-416. [PMID: 23694899 DOI: 10.1016/j.saa.2013.04.040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 04/08/2013] [Accepted: 04/10/2013] [Indexed: 06/02/2023]
Abstract
The coordination properties of copper with adenine have been studied by the analyzing the changes in Fourier Transform Infra-red (FTIR) and Raman spectra of adenine and adenine-copper complex. The geometry of adenine and adenine copper complex were optimized and theoretical Infra-red and Raman spectra of the optimized structures were calculated using Density Functional Theory (DFT). During synthesis of adenine-copper complex specific procedure was adopted to attach the Cu atom with particular N-atom of adenine (N9). The results of Raman and DFT confirmed the attachment. The Raman bands at 625, 330 and 230 cm(-1) of adenine-copper complex contain significant contribution of the vibrational motions of Cu metal coordinated to N9 and Cl atoms. The DFT calculations give additional vibrational modes containing the Cu, N9 and N9* atoms, which are not observed in FTIR and Raman spectra. The Raman, IR and DFT study confirm that Cu metal has good binding affinity to the isolated adenine base.
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Affiliation(s)
- Om Prakash
- Department of Physics, Banaras Hindu University, Varanasi 221 005, India
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Thicoipe S, Carbonniere P, Pouchan C. The Use of the GSAM Approach for the Structural Investigation of Low-Lying Isomers of Molecular Clusters from Density-Functional-Theory-Based Potential Energy Surfaces: The Structures of Microhydrated Nucleic Acid Bases. J Phys Chem A 2013; 117:7236-45. [DOI: 10.1021/jp401130a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sandrine Thicoipe
- Groupe de Chimie Théorique et Réactivité,
IPREM/ECP UMR CNRS 5254, Université de Pau et des Pays de l’Adour, F-64000 Pau, France
| | - Philippe Carbonniere
- Groupe de Chimie Théorique et Réactivité,
IPREM/ECP UMR CNRS 5254, Université de Pau et des Pays de l’Adour, F-64000 Pau, France
| | - Claude Pouchan
- Groupe de Chimie Théorique et Réactivité,
IPREM/ECP UMR CNRS 5254, Université de Pau et des Pays de l’Adour, F-64000 Pau, France
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Barone V, Biczysko M, Bloino J, Puzzarini C. Characterization of the Elusive Conformers of Glycine from State-of-the-Art Structural, Thermodynamic, and Spectroscopic Computations: Theory Complements Experiment. J Chem Theory Comput 2013; 9:1533-47. [DOI: 10.1021/ct3010672] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, I-56126 Pisa, Italy
| | - Malgorzata Biczysko
- Center for Nanotechnology Innovation
@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, I-56127
Pisa, Italy
| | - Julien Bloino
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, I-56126 Pisa, Italy
- Consiglio Nazionale
delle Ricerche,
Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), UOS
di Pisa, Area della Ricerca CNR, Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Cristina Puzzarini
- Dipartimento di Chimica “G.
Ciamician,” Università di Bologna, Via F. Selmi 2, 40126
Bologna, Italy
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Thicoipe S, Carbonnière P, Pouchan C. Structural investigation of microhydrated thymine clusters and vibrational study of isolated and aqueous forms of thymine using DFT level of theory. Phys Chem Chem Phys 2013; 15:11646-52. [DOI: 10.1039/c3cp50424g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Dargiewicz M, Biczysko M, Improta R, Barone V. Solvent effects on electron-driven proton-transfer processes: adenine–thymine base pairs. Phys Chem Chem Phys 2012; 14:8981-9. [DOI: 10.1039/c2cp23890j] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Barone V, Baiardi A, Biczysko M, Bloino J, Cappelli C, Lipparini F. Implementation and validation of a multi-purpose virtual spectrometer for large systems in complex environments. Phys Chem Chem Phys 2012; 14:12404-22. [DOI: 10.1039/c2cp41006k] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Punyain K, Kelterer AM, Grampp G. Theoretical studies on the dimerization of substituted paraphenylenediamine radical cations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2011; 83:368-378. [PMID: 21925928 DOI: 10.1016/j.saa.2011.08.048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Revised: 06/01/2011] [Accepted: 08/24/2011] [Indexed: 05/31/2023]
Abstract
Organic radical cations form dicationic dimers in solution, observed experimentally as diamagnetic species in temperature-dependent EPR and low temperature UV/Vis spectroscopy. Dimerization of paraphenylenediamine, N,N-dimethyl-paraphenylenediamine and 2,3,5,6-tetramethyl-paraphenylenediamine radical cation in ethanol/diethylether mixture was investigated theoretically according to geometry, energetics and UV/Vis spectroscopy. Density Functional Theory including dispersion correction describes stable dimers after geometry optimization with conductor-like screening model of solvation and inclusion of the counter-ion. Energy corrections were done on double-hybrid Density Functional Theory with perturbative second-order correlation (B2PLYP-D) including basis set superposition error (BSSE), and multireference Møller-Plesset second-order perturbation theory method (MRMP2) based on complete active space method (CASSCF(2,2)) single point calculation, respectively. All three dication π-dimers exhibit long multicenter π-bonds around 2.9±0.1Å with strongly interacting orbitals. Substitution with methyl groups does not influence the dimerization process substantially. Dispersion interaction and electrostatic attraction from counter-ion play an important role to stabilize the dication dimers in solution. Dispersion-corrected double hybrid functional B2PLYP-D and CASSCF(2,2) can describe the interaction energetics properly. Vertical excitations were computed with Tamm-Dancoff approximation for time-dependent Density Functional Theory (TDA-DFT) at the B3LYP level with the cc-pVTZ basis set including ethanol solvent molecules explicitly. A strong interaction of the counter-ion and the solvent ethanol with the monomeric species is observed, whereas in the dimers the strong interaction of both radical cation species is the dominating factor for the additional peak in UV/Vis spectra.
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Affiliation(s)
- Kraiwan Punyain
- Institute of Physical and Theoretical Chemistry, Graz University of Technology, Graz, Austria
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31
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Anharmonic vibrations of nucleobases: Structural basis of one- and two-dimensional infrared spectra for canonical and mismatched base pairs. Sci China Chem 2011. [DOI: 10.1007/s11426-011-4309-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Asami H, Urashima SH, Saigusa H. Structural identification of uric acid and its monohydrates by IR-UV double resonance spectroscopy. Phys Chem Chem Phys 2011; 13:20476-80. [DOI: 10.1039/c1cp22540e] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Pedone A, Biczysko M, Barone V. Environmental effects in computational spectroscopy: accuracy and interpretation. Chemphyschem 2010; 11:1812-32. [PMID: 20358575 DOI: 10.1002/cphc.200900976] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Spectroscopic techniques are valuable tools for understanding the structure and dynamics of complex systems, such as biomolecules or nanomaterials. Most of the current research is devoted to the development of new experimental techniques for improving the intrinsic resolution of different spectra. However, the subtle interplay of several different effects acting at different length and time scales still makes the interpretation and analysis of such spectra a very difficult task. In this respect, computational spectroscopy is becoming a needful and versatile tool for the assignment and interpretation of experimental spectra. It is in fact possible nowadays to model with relatively high accuracy the physical-chemical properties of complex molecules in different environments, and to link spectroscopic evidence directly to the structural and dynamical properties of optically or magnetically active solvated probes. In this Review, significant steps toward the simulation of entire spectra in condensed phases are presented together with some basic aspects of computational spectroscopy, which highlight how intramolecular and intermolecular degrees of freedom influence several spectroscopic parameters.
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Affiliation(s)
- Alfonso Pedone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, Pisa, Italy
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Biczysko M, Panek P, Scalmani G, Bloino J, Barone V. Harmonic and Anharmonic Vibrational Frequency Calculations with the Double-Hybrid B2PLYP Method: Analytic Second Derivatives and Benchmark Studies. J Chem Theory Comput 2010; 6:2115-25. [PMID: 26615939 DOI: 10.1021/ct100212p] [Citation(s) in RCA: 221] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This work aims to provide reliable benchmark data on the accuracy of harmonic and anharmonic vibrational frequencies computed with the B2PLYP double-hybrid density functional method. The exchange-correlation contributions required for the B2PLYP analytical second derivatives are presented here, which allow for the effective calculation of harmonic frequency as well as cubic and semidiagonal quartic force fields. The latter, in turn, are necessary to compute the anharmonic vibrational frequencies with the perturbative approach (VPT2). The quality of harmonic vibrational frequencies computed in conjunction with basis sets of double- to quadruple-ζ quality has been checked against reference data from the F38 benchmark set. Then, for an additional set of small closed- and open-shell systems, both harmonic frequencies and anharmonic contributions computed at the B2PLYP/N07D and the B2PLYP/aug-cc-pVTZ levels have been compared to their CCSD(T) counterparts. Moreover, for selected medium-size molecules (furan, pyrrole, thiophene, uracil, anisole, phenol, and pyridine), anharmonic frequencies have been compared to well established experimental results. Such benchmark studies have shown that the B2PLYP/N07D model provides good quality harmonic frequencies and describes correctly anharmonic contributions, the latter being of similar accuracy to their B3LYP/N07D counterparts, but obtained at significantly larger computational cost. Additionally, increased accuracy can be obtained by adopting hybrid models where the B2PLYP/N07D anharmonic contributions are combined with harmonic frequencies computed with more accurate quantum mechanical (QM) approaches or by B2PLYP with larger basis sets. This work confirmed also that most of the recently developed density functionals are significantly less suited for vibrational computations, while the B2PLYP method can be recommended for spectroscopic studies where a good accuracy of vibrational properties is required.
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Affiliation(s)
- Malgorzata Biczysko
- Scuola Normale Superiore, piazza dei Cavalieri 7, 56126 Pisa, Italy, Dipartimento di Chimica "Paolo Corradini" and CR-INSTM Village Università di Napoli Federico II, Complesso Univ. Monte S. Angelo, via Cintia, 80126 Napoli, Italy, Faculty of Chemistry, University of Wroclaw, ul. Joliot-Curie 14, 50-383 Wroclaw, Poland, Gaussian, Inc., 340 Quinnipiac St., Bldg 40, Wallingford, Connecticut 06492, and Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Pisa, Pisa, Italy
| | - Pawel Panek
- Scuola Normale Superiore, piazza dei Cavalieri 7, 56126 Pisa, Italy, Dipartimento di Chimica "Paolo Corradini" and CR-INSTM Village Università di Napoli Federico II, Complesso Univ. Monte S. Angelo, via Cintia, 80126 Napoli, Italy, Faculty of Chemistry, University of Wroclaw, ul. Joliot-Curie 14, 50-383 Wroclaw, Poland, Gaussian, Inc., 340 Quinnipiac St., Bldg 40, Wallingford, Connecticut 06492, and Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Pisa, Pisa, Italy
| | - Giovanni Scalmani
- Scuola Normale Superiore, piazza dei Cavalieri 7, 56126 Pisa, Italy, Dipartimento di Chimica "Paolo Corradini" and CR-INSTM Village Università di Napoli Federico II, Complesso Univ. Monte S. Angelo, via Cintia, 80126 Napoli, Italy, Faculty of Chemistry, University of Wroclaw, ul. Joliot-Curie 14, 50-383 Wroclaw, Poland, Gaussian, Inc., 340 Quinnipiac St., Bldg 40, Wallingford, Connecticut 06492, and Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Pisa, Pisa, Italy
| | - Julien Bloino
- Scuola Normale Superiore, piazza dei Cavalieri 7, 56126 Pisa, Italy, Dipartimento di Chimica "Paolo Corradini" and CR-INSTM Village Università di Napoli Federico II, Complesso Univ. Monte S. Angelo, via Cintia, 80126 Napoli, Italy, Faculty of Chemistry, University of Wroclaw, ul. Joliot-Curie 14, 50-383 Wroclaw, Poland, Gaussian, Inc., 340 Quinnipiac St., Bldg 40, Wallingford, Connecticut 06492, and Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Pisa, Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, piazza dei Cavalieri 7, 56126 Pisa, Italy, Dipartimento di Chimica "Paolo Corradini" and CR-INSTM Village Università di Napoli Federico II, Complesso Univ. Monte S. Angelo, via Cintia, 80126 Napoli, Italy, Faculty of Chemistry, University of Wroclaw, ul. Joliot-Curie 14, 50-383 Wroclaw, Poland, Gaussian, Inc., 340 Quinnipiac St., Bldg 40, Wallingford, Connecticut 06492, and Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Pisa, Pisa, Italy
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Jacquemin D, Perpète EA, Ciofini I, Adamo C, Valero R, Zhao Y, Truhlar DG. On the Performances of the M06 Family of Density Functionals for Electronic Excitation Energies. J Chem Theory Comput 2010; 6:2071-85. [DOI: 10.1021/ct100119e] [Citation(s) in RCA: 339] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Denis Jacquemin
- Unité de Chimie Physique Théorique et Structurale (UCPTS), Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium, Ecole Nationale Supérieure de Chimie de Paris, Laboratoire Electrochimie et Chimie Analytique, UMR CNRS-ENSCP no. 7575, 11, rue Pierre et Marie Curie, F-75321 Paris Cedex 05, France, Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Commercial Print Engine Lab, HP Laboratories, Hewlett
| | - Eric A. Perpète
- Unité de Chimie Physique Théorique et Structurale (UCPTS), Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium, Ecole Nationale Supérieure de Chimie de Paris, Laboratoire Electrochimie et Chimie Analytique, UMR CNRS-ENSCP no. 7575, 11, rue Pierre et Marie Curie, F-75321 Paris Cedex 05, France, Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Commercial Print Engine Lab, HP Laboratories, Hewlett
| | - Ilaria Ciofini
- Unité de Chimie Physique Théorique et Structurale (UCPTS), Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium, Ecole Nationale Supérieure de Chimie de Paris, Laboratoire Electrochimie et Chimie Analytique, UMR CNRS-ENSCP no. 7575, 11, rue Pierre et Marie Curie, F-75321 Paris Cedex 05, France, Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Commercial Print Engine Lab, HP Laboratories, Hewlett
| | - Carlo Adamo
- Unité de Chimie Physique Théorique et Structurale (UCPTS), Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium, Ecole Nationale Supérieure de Chimie de Paris, Laboratoire Electrochimie et Chimie Analytique, UMR CNRS-ENSCP no. 7575, 11, rue Pierre et Marie Curie, F-75321 Paris Cedex 05, France, Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Commercial Print Engine Lab, HP Laboratories, Hewlett
| | - Rosendo Valero
- Unité de Chimie Physique Théorique et Structurale (UCPTS), Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium, Ecole Nationale Supérieure de Chimie de Paris, Laboratoire Electrochimie et Chimie Analytique, UMR CNRS-ENSCP no. 7575, 11, rue Pierre et Marie Curie, F-75321 Paris Cedex 05, France, Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Commercial Print Engine Lab, HP Laboratories, Hewlett
| | - Yan Zhao
- Unité de Chimie Physique Théorique et Structurale (UCPTS), Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium, Ecole Nationale Supérieure de Chimie de Paris, Laboratoire Electrochimie et Chimie Analytique, UMR CNRS-ENSCP no. 7575, 11, rue Pierre et Marie Curie, F-75321 Paris Cedex 05, France, Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Commercial Print Engine Lab, HP Laboratories, Hewlett
| | - Donald G. Truhlar
- Unité de Chimie Physique Théorique et Structurale (UCPTS), Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium, Ecole Nationale Supérieure de Chimie de Paris, Laboratoire Electrochimie et Chimie Analytique, UMR CNRS-ENSCP no. 7575, 11, rue Pierre et Marie Curie, F-75321 Paris Cedex 05, France, Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, and Commercial Print Engine Lab, HP Laboratories, Hewlett
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Puzzarini C, Biczysko M, Barone V. Accurate Harmonic/Anharmonic Vibrational Frequencies for Open-Shell Systems: Performances of the B3LYP/N07D Model for Semirigid Free Radicals Benchmarked by CCSD(T) Computations. J Chem Theory Comput 2010; 6:828-38. [DOI: 10.1021/ct900594h] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Cristina Puzzarini
- Dipartimento di Chimica “G. Ciamician”, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy, Dipartimento di Chimica “Paolo Corradini” and CR-INSTM Village, Università di Napoli Federico II, Complesso Univ. Monte S. Angelo, via Cintia, 80126 Napoli, Italy, and Scuola Normale Superiore, piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Malgorzata Biczysko
- Dipartimento di Chimica “G. Ciamician”, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy, Dipartimento di Chimica “Paolo Corradini” and CR-INSTM Village, Università di Napoli Federico II, Complesso Univ. Monte S. Angelo, via Cintia, 80126 Napoli, Italy, and Scuola Normale Superiore, piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Vincenzo Barone
- Dipartimento di Chimica “G. Ciamician”, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy, Dipartimento di Chimica “Paolo Corradini” and CR-INSTM Village, Università di Napoli Federico II, Complesso Univ. Monte S. Angelo, via Cintia, 80126 Napoli, Italy, and Scuola Normale Superiore, piazza dei Cavalieri 7, 56126 Pisa, Italy
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37
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Toroz D, van Mourik T. Structure of the gas-phase glycine tripeptide. Phys Chem Chem Phys 2010; 12:3463-73. [DOI: 10.1039/b921897a] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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38
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Barone V, Biczysko M, Brancato G. Extending the Range of Computational Spectroscopy by QM/MM Approaches: Time-Dependent and Time-Independent Routes. ADVANCES IN QUANTUM CHEMISTRY 2010. [DOI: 10.1016/s0065-3276(10)59002-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
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