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Biczysko M, Bloino J, Brancato G, Cacelli I, Cappelli C, Ferretti A, Lami A, Monti S, Pedone A, Prampolini G, Puzzarini C, Santoro F, Trani F, Villani G. Integrated computational approaches for spectroscopic studies of molecular systems in the gas phase and in solution: pyrimidine as a test case. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1201-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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202
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Botschwina P, Oswald R. Fulvenallenyl cation (C7H5(+)) and its complex with an argon atom: results of high-level quantum-chemical calculations. J Phys Chem A 2012; 116:3448-53. [PMID: 22380571 DOI: 10.1021/jp212376j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The fulvenallenyl cation (C(7)H(5)(+)) and its complex with an argon atom have been studied by explicitly correlated coupled cluster theory at the CCSD(T)-F12x(x = a, b) level and by the double-hybrid density functional B2PLYP-D. For the free cation, an accurate equilibrium structure has been established and ground-state rotational constants of A(0) = 8116.4 MHz, B(0) = 2004.3 MHz, and C(0) = 1606.9 MHz are predicted. The equilibrium dipole moment is calculated to be μ(e) = 1.305 D, with the positive end of the dipole at the acetylenic hydrogen site. Anharmonic wavenumbers of C(7)H(5)(+) were obtained by combination of harmonic CCSD(T*)-F12a values and B2PLYP-D anharmonic contributions. The most intense vibration is the pseudoantisymmetric CC stretching vibration at 2083 cm(-1). The potential energy surface of the complex C(7)H(5)(+)·Ar is characterized by two energy minima of C(s) symmetry which are separated by a very low energy barrier. The dissociation energy of the most stable structure is predicted to be D(0) = 530 ± 30 cm(-1).
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Affiliation(s)
- Peter Botschwina
- Institut für Physikalische Chemie, Universität Göttingen, Germany.
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203
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Cecchet F, Lis D, Caudano Y, Mani AA, Peremans A, Champagne B, Guthmuller J. Density functional theory-based simulations of sum frequency generation spectra involving methyl stretching vibrations: effect of the molecular model on the deduced molecular orientation and comparison with an analytical approach. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2012; 24:124110. [PMID: 22394554 DOI: 10.1088/0953-8984/24/12/124110] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The knowledge of the first hyperpolarizability tensor elements of molecular groups is crucial for a quantitative interpretation of the sum frequency generation (SFG) activity of thin organic films at interfaces. Here, the SFG response of the terminal methyl group of a dodecanethiol (DDT) monolayer has been interpreted on the basis of calculations performed at the density functional theory (DFT) level of approximation. In particular, DFT calculations have been carried out on three classes of models for the aliphatic chains. The first class of models consists of aliphatic chains, containing from 3 to 12 carbon atoms, in which only one methyl group can freely vibrate, while the rest of the chain is frozen by a strong overweight of its C and H atoms. This enables us to localize the probed vibrational modes on the methyl group. In the second class, only one methyl group is frozen, while the entire remaining chain is allowed to vibrate. This enables us to analyse the influence of the aliphatic chain on the methyl stretching vibrations. Finally, the dodecanethiol (DDT) molecule is considered, for which the effects of two dielectrics, i.e. n-hexane and n-dodecane, are investigated. Moreover, DDT calculations are also carried out by using different exchange-correlation (XC) functionals in order to assess the DFT approximations. Using the DFT IR vectors and Raman tensors, the SFG spectrum of DDT has been simulated and the orientation of the methyl group has then been deduced and compared with that obtained using an analytical approach based on a bond additivity model. This analysis shows that when using DFT molecular properties, the predicted orientation of the terminal methyl group tends to converge as a function of the alkyl chain length and that the effects of the chain as well as of the dielectric environment are small. Instead, a more significant difference is observed when comparing the DFT-based results with those obtained from the analytical approach, thus indicating the importance of a quantum chemical description of the hyperpolarizability tensor elements of the methyl group.
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Affiliation(s)
- F Cecchet
- Research Centre in Physics of Matter and Radiation (PMR), FUNDP-University of Namur, 61 rue de Bruxelles, B-5000 Namur, Belgium.
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204
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Bloino J, Biczysko M, Barone V. General Perturbative Approach for Spectroscopy, Thermodynamics, and Kinetics: Methodological Background and Benchmark Studies. J Chem Theory Comput 2012; 8:1015-36. [DOI: 10.1021/ct200814m] [Citation(s) in RCA: 213] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Julien Bloino
- Scuola Normale Superiore, piazza
dei Cavalieri 7, I-56126 Pisa, Italy
- Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organometallici (CNR-ICCOM), UOS di Pisa, Via G. Moruzzi, 1 I-56124 Italy
| | - Malgorzata Biczysko
- Center for Nanotechnology Innovation
@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, I-56127
Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, piazza
dei Cavalieri 7, I-56126 Pisa, Italy
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205
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Biczysko M, Bloino J, Carnimeo I, Panek P, Barone V. Fully ab initio IR spectra for complex molecular systems from perturbative vibrational approaches: Glycine as a test case. J Mol Struct 2012. [DOI: 10.1016/j.molstruc.2011.10.012] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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206
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Cappelli C, Lipparini F, Bloino J, Barone V. Towards an accurate description of anharmonic infrared spectra in solution within the polarizable continuum model: reaction field, cavity field and nonequilibrium effects. J Chem Phys 2012; 135:104505. [PMID: 21932908 DOI: 10.1063/1.3630920] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
We present a newly developed and implemented methodology to perturbatively evaluate anharmonic vibrational frequencies and infrared (IR) intensities of solvated systems described by means of the polarizable continuum model (PCM). The essential aspects of the theoretical model and of the implementation are described and some numerical tests are shown, with special emphasis towards the evaluation of IR intensities, for which the quality of the present method is compared to other methodologies widely used in the literature. Proper account of an incomplete solvation regime in the treatment of the molecular vibration is also considered, as well as inclusion of the coupling between the solvent and the probing field (cavity field effects). In order to assess the quality of our approach, comparison with experimental findings is reported for selected cases.
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Affiliation(s)
- Chiara Cappelli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Risorgimento, 35 I-56126 Pisa, Italy.
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207
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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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208
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Choi TH, Han YK. Assessment of the Performance of B2PLYP-D for Describing Intramolecular π-π and σ-π Interactions. B KOREAN CHEM SOC 2011. [DOI: 10.5012/bkcs.2011.32.12.4195] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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209
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Puzzarini C, Biczysko M, Barone V. Accurate Anharmonic Vibrational Frequencies for Uracil: The Performance of Composite Schemes and Hybrid CC/DFT Model. J Chem Theory Comput 2011; 7:3702-10. [DOI: 10.1021/ct200552m] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Cristina Puzzarini
- Dipartimento di Chimica “G. Ciamician”, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Malgorzata Biczysko
- Center for Nanotechnology Innovation @NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro, 12 - 56127 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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210
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Fabiano E, Constantin LA, Della Sala F. Two-Dimensional Scan of the Performance of Generalized Gradient Approximations with Perdew–Burke–Ernzerhof-Like Enhancement Factor. J Chem Theory Comput 2011; 7:3548-59. [DOI: 10.1021/ct200510s] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- E. Fabiano
- National Nanotechnology Laboratory (NNL), Istituto Nanoscienze−CNR, Via per Arnesano 16, I-73100 Lecce, Italy
| | - Lucian A. Constantin
- Center for Biomolecular Nanotechnologies @UNILE, Istituto Italiano di Tecnologia (IIT), Via Barsanti, I-73010 Arnesano, Italy
| | - F. Della Sala
- National Nanotechnology Laboratory (NNL), Istituto Nanoscienze−CNR, Via per Arnesano 16, I-73100 Lecce, Italy
- Center for Biomolecular Nanotechnologies @UNILE, Istituto Italiano di Tecnologia (IIT), Via Barsanti, I-73010 Arnesano, Italy
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211
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Panek P, Biczysko M, Latajka Z. Reinvestigation of spectroscopic properties for ammonia–hydrogen halide complexes from Car–Parrinello Molecular Dynamics. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.08.060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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212
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Carnimeo I, Biczysko M, Bloino J, Barone V. Reliable structural, thermodynamic, and spectroscopic properties of organic molecules adsorbed on silicon surfaces from computational modeling: the case of glycine@Si(100). Phys Chem Chem Phys 2011; 13:16713-27. [PMID: 21858336 DOI: 10.1039/c1cp21636h] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chemisorption of glycine on Si(100) has been studied by an integrated computational strategy based on perturbative anharmonic computations employing geometries and harmonic force fields evaluated by hybrid density functionals coupled to purposely tailored basis sets. It is shown that such a strategy allows the prediction of spectroscopic properties of isolated and chemisorbed molecules with comparable accuracy, paving the route toward a detailed analysis of surface-induced changes of glycine vibrational spectra.
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Affiliation(s)
- Ivan Carnimeo
- Scuola Normale Superiore and INSTM M3-Village, Pisa, Italy
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213
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Temelso B, Shields GC. The Role of Anharmonicity in Hydrogen-Bonded Systems: The Case of Water Clusters. J Chem Theory Comput 2011; 7:2804-17. [DOI: 10.1021/ct2003308] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Berhane Temelso
- Dean’s Office, College of Arts and Sciences, Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| | - George C. Shields
- Dean’s Office, College of Arts and Sciences, Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
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214
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Császár AG. Anharmonic molecular force fields. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.75] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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215
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Cirtog M, Alikhani ME, Madebène B, Soulard P, Asselin P, Tremblay B. Bonding Nature and Vibrational Signatures of Oxirane:(Water)n=1–3. Assessment of the Performance of the Dispersion-Corrected DFT Methods Compared to the ab initio Results and Fourier Transform Infrared Experimental Data. J Phys Chem A 2011; 115:6688-701. [DOI: 10.1021/jp202867t] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- M. Cirtog
- UPMC Université Paris 06, UMR 7075, Laboratoire de Dynamique, Interactions et Réactivité (LADIR), F-75005, Paris, France
- CNRS, UMR 7075, Laboratoire de Dynamique, Interactions et Réactivité (LADIR), F-75005, Paris, France
| | - M. E. Alikhani
- UPMC Université Paris 06, UMR 7075, Laboratoire de Dynamique, Interactions et Réactivité (LADIR), F-75005, Paris, France
- CNRS, UMR 7075, Laboratoire de Dynamique, Interactions et Réactivité (LADIR), F-75005, Paris, France
| | - B. Madebène
- UPMC Université Paris 06, UMR 7075, Laboratoire de Dynamique, Interactions et Réactivité (LADIR), F-75005, Paris, France
- CNRS, UMR 7075, Laboratoire de Dynamique, Interactions et Réactivité (LADIR), F-75005, Paris, France
| | - P. Soulard
- UPMC Université Paris 06, UMR 7075, Laboratoire de Dynamique, Interactions et Réactivité (LADIR), F-75005, Paris, France
- CNRS, UMR 7075, Laboratoire de Dynamique, Interactions et Réactivité (LADIR), F-75005, Paris, France
| | - P. Asselin
- UPMC Université Paris 06, UMR 7075, Laboratoire de Dynamique, Interactions et Réactivité (LADIR), F-75005, Paris, France
- CNRS, UMR 7075, Laboratoire de Dynamique, Interactions et Réactivité (LADIR), F-75005, Paris, France
| | - B. Tremblay
- UPMC Université Paris 06, UMR 7075, Laboratoire de Dynamique, Interactions et Réactivité (LADIR), F-75005, Paris, France
- CNRS, UMR 7075, Laboratoire de Dynamique, Interactions et Réactivité (LADIR), F-75005, Paris, France
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216
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Fábri C, Szidarovszky T, Magyarfalvi G, Tarczay G. Gas-phase and Ar-matrix SQM scaling factors for various DFT functionals with basis sets including polarization and diffuse functions. J Phys Chem A 2011; 115:4640-9. [PMID: 21495661 DOI: 10.1021/jp201907y] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Scaling factors for Pulay's scaled quantum mechanical (SQM) scheme have been determined for four different widely used DFT functionals (PBE, B3LYP, B3PW91, and M06-2X) and for two basis sets (6-31++G** and aug-cc-pVTZ) by fitting computed results to 347 fundamental experimental vibrational frequencies of 33 molecules. Measurements in the gas phase and in solid argon matrices were used independently in the fitting procedure in order to provide a simple method of estimating matrix shifts. The accuracy of the new scaling factors is demonstrated on test molecules including hydrogen-bonded systems and molecules containing chlorine and sulfur atoms.
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Affiliation(s)
- Csaba Fábri
- Laboratory of Molecular Spectroscopy, Institute of Chemistry, Eötvös University, Budapest, Hungary
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217
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Guthmuller J. Assessment of TD-DFT and CC2 Methods for the Calculation of Resonance Raman Intensities: Application to o-Nitrophenol. J Chem Theory Comput 2011; 7:1082-9. [DOI: 10.1021/ct200010p] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Julien Guthmuller
- Institut für Physikalische Chemie, Friedrich Schiller Universität Jena, Helmholtzweg 4, 07743, Jena, Germany
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218
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de Wergifosse M, Champagne B. Electron correlation effects on the first hyperpolarizability of push–pull π-conjugated systems. J Chem Phys 2011; 134:074113. [DOI: 10.1063/1.3549814] [Citation(s) in RCA: 156] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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219
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Gancheff JS, Denis PA. Time-dependent density functional theory investigation of the electronic spectra of hexanuclear chalcohalide rhenium(III) clusters. J Phys Chem A 2011; 115:211-8. [PMID: 21158477 DOI: 10.1021/jp110100w] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The UV-vis spectra of the hexanuclear chalcohalide rhenium(III) clusters of formula [Re(6)S(8)X(6)](4-) (X(-) = Cl(-), Br(-), I(-)) were investigated at the time-dependent density functional theory (TD-DFT) level employing B3LYP, PBE1PBE, and the double-hybrid B2PLYP functional in combination with the LANL2DZ basis set. We were able to reproduce the red shift experimentally observed when the halide changes from chloride to iodide. However, some discrepancies between experimental results and theory were found. First, we did not observe a remarkable dependence of the experimental ill-resolved bands on the solvent. Indeed, similar spectra were obtained taken CH(2)Cl(2) or CH(3)CN as solvents into account. Second, all calculations explained the origin of the band peaked at the low-energy region in contraposition with the one experimentally assumed by R. Long et al. (J. Am. Chem. Soc. 1996, 118, 4603), and theoretically made available by Arratia-Pérez et al. (J. Chem. Phys. 1999, 110, 2529). These authors have proposed a ligand-to-cluster charge transfer (LCCT) for all title complexes. Our findings undoubtedly allow such origin to be discarded. While the HGGA functionals lead to a cluster-to-halide ligand charge transfer (CLCT), an intracluster charge transfer (ICCT) has been considered by employing B2PLYP. This contribution showed B2PLYP in the presence of the solvent to be the best performer in studying the UV-vis spectra of large complexes of rhenium(III) containing the Re-S bond. We strongly recommended the use of the double-hybrid B2PLYP in studying UV-vis spectrum of rhenium complexes of size making the computational cost affordable. We expect that our work stimulates new experimental and theoretical investigations of the title complexes to confirm our assignment.
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Affiliation(s)
- Jorge S Gancheff
- Departamento Estrella Campos, Facultad de Química, Universidad de la República, CC 1157, 11800, Montevideo, Uruguay.
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220
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Puzzarini C, Barone V. Extending the molecular size in accurate quantum-chemical calculations: the equilibrium structure and spectroscopic properties of uracil. Phys Chem Chem Phys 2011; 13:7189-97. [DOI: 10.1039/c0cp02636k] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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221
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