Integrated computational approaches for spectroscopic studies of molecular systems in the gas phase and in solution: pyrimidine as a test case

Biczysko, Małgorzata; Bloino, Julien; Brancato, Giuseppe; Cacelli, Ivo; Cappelli, Chiara; Ferretti, Alessandro; Lami, Alessandro; Monti, Susanna; Pedone, Alfonso; Prampolini, Giacomo; Puzzarini, Cristina; Santoro, Fabrizio; Trani, F.; Villani, Giovanni

doi:10.1007/978-3-642-34462-6_32

Cited by 29 publications

(66 citation statements)

References 106 publications

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“…However, more important effects, related to the changes in the normal modes, should other models a single, more intense band. These differences indicate clearly that the mode mixing can play an important role even for systems not undergoing significant structural changes on excitation, [204] and should not be readily discarded if accurate band-shape or high resolution spectra are required. Conversely, for low-resolution spectra, the VG model represents a cost-effective way to account realistically for the band envelopes.…”

Section: Small Structural Changes:mentioning

confidence: 99%

“…[210] In a similar way, a previous study based on a fulldimensional AHjFC model allowed us to correct an assignment of the low-intensity 0-0 transition for the phenyl radical. [204] Finally, we note that our simulation does not confirm the assignment of the vibronic structure in the 5.1-5.6 eV range from reference 89, where the most intense bands, displaced by about 0.119 eV (960 cm 21 ) have been attributed to the progressions of t 6 , starting from j 1 6 i. Instead, the most intense bands in the theoretical spectra are due to the progressions of modes 5 and 7 of the excited electronic state, which in turn can be described as the combination of the ground state modes t 20 ; t 17 , and t 8 (see Table 3).…”

Section: Marked Structural Changes: 1 a 1 X 1 A 1 Transition Of Thimentioning

confidence: 99%

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Aiming at an accurate prediction of vibrational and electronic spectra for medium‐to‐large molecules: An overview

Bloino

Baiardi

Biczysko

2016

Int J of Quantum Chemistry

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181

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In this tutorial review, we present some effective methodologies available for the simulation of vibrational and vibrationally resolved electronic spectra of medium-to-large molecules. They have been integrated into a unified platform and extended to support a wide range of spectroscopies.The resulting tool is particularly useful in assisting the extensive characterization of molecules, often achieved by combining multiple types of measurements. A correct assessment of the reliability of theoretical calculations is a necessary prelude to the interpretation of their results. For this reason, the key concepts of the underlying theories will be first presented and then illustrated through the study of thiophene and its smallest oligomer, bithiophene. While doing so, a complete computational protocol will be detailed, with emphasis on the strengths and potential shortcomings of the models employed here. Guidelines are also provided for performing similar studies on different molecular systems, with comments on the more common pitfalls and ways to overcome them. Finally, extensions to other cases, like chiral spectroscopies or mixtures, are also discussed. K E Y W O R D Sanharmonic vibrational spectroscopy, computational spectroscopy, large amplitude motion, medium-to-large molecules, vibronic spectroscopy | I N T R O D U C T I O NMolecular properties are commonly probed with a wide panel of spectroscopies, which can be combined to offer a unique picture, reflection of the property, its environment, and the experimental conditions. [1][2][3][4][5][6][7][8] The wealth of information contained in the recorded spectrum or spectra can become complex to analyze in a purely phenomenological way and theoretical models can provide a valuable aid in understanding the origin of the features observed in the band-shapes. [9][10][11] As a matter of fact, the predictive and interpretative power of computational spectroscopy has been clearly demonstrated already for small molecular systems in the gas phase, by comparison with the most sophisticated experimental techniques. [1,[12][13][14] However, depending on the target system and the required accuracy, the theoretical spectroscopic models can vary greatly in complexity. The situation is even more challenging when considering their actual implementation, often done in ad hoc, standalone programs, whose levels of completion, versatility and ease of use may be very different. As a result, getting an extensive picture of the experimental spectra can become a challenge as it may require multiple packages with their own usage and peculiarities.Hence, to facilitate the simulation and interpretation of multiple spectra, several conditions need to be met. A first challenge is to provide a simple interface, lowering the barrier to the broad adoption of state-of-the-art methods able to produce accurate data for the problems at hand. [11,[15][16][17] This can be achieved by automatizing most aspects of the calculations. Due to the inherent complexity of some theoretical models, such ...

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Section: Small Structural Changes:mentioning

confidence: 99%

Section: Marked Structural Changes: 1 a 1 X 1 A 1 Transition Of Thimentioning

confidence: 99%

Aiming at an accurate prediction of vibrational and electronic spectra for medium‐to‐large molecules: An overview

Bloino

Baiardi

Biczysko

2016

Int J of Quantum Chemistry

Self Cite

181

196

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“…Alternatively, the percentages of different species can be estimated by the analysis of some relevant features of experimental spectra and then used to simulate overall band shapes. [29] It is also possible to estimate relative amounts of subcomponents by fitting theoretical spectra (varying the contributions of singlecomponents) to the observed experimental data. In all cases such an analysis is facilitated by a graphical tool included into VMS-Draw, which allows both inclusion of accurate data for relative populations (as an example the IR spectrum of glycine [28] is shown Fig.…”

Section: Generic Spectra and Common Featuresmentioning

confidence: 99%

Implementation of a graphical user interface for the virtual multifrequency spectrometer: The VMS‐Draw tool

et al. 2014

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This article presents the setup and implementation of a graphical user interface (VMS-Draw) for a virtual multifrequency spectrometer. Special attention is paid to ease of use, generality and robustness for a panel of spectroscopic techniques and quantum mechanical approaches. Depending on the kind of data to be analyzed, VMS-Draw produces different types of graphical representations, including two-dimensional or three-dimesional (3D) plots, bar charts, or heat maps. Among other integrated features, one may quote the convolution of stick spectra to obtain realistic line-shapes. It is also possible to analyze and visualize, together with the structure, the molecular orbitals and/or the vibrational motions of molecular systems thanks to 3D interactive tools. On these grounds, VMS-Draw could represent a useful additional tool for spectroscopic studies integrating measurements and computer simulations.

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“…The n ← π character of theÃ 2 B 1 ←X 2 A 1 transition from the ground to the first excited state is in agreement with both experimental and theoretical studies. 40,41 The high-resolution cavity ring-down spectroscopic study of the phenyl radical predicted a planar geometry of the excited electronic state, involving an expansion of the carbon ring, and excited-state lifetime of 96 ps. 41 The vibronic band corresponding to this transition, first characterized by Porter and Ward 42 and later by Radziszewski, 43 exhibits a rich structure arising from the considerable differences between the potential energy surfaces of the ground and excited electronic states.…”

Section: Introductionmentioning

confidence: 99%

“…41 The vibronic band corresponding to this transition, first characterized by Porter and Ward 42 and later by Radziszewski, 43 exhibits a rich structure arising from the considerable differences between the potential energy surfaces of the ground and excited electronic states. Ab initio calculations 12,40 found strong coupling between the modes, also known as the Duschinsky rotation or mixing, and a large displacement of multiple normal modes 44,45 -the two most displaced modes correspond to the in-plane carbon ring vibrations (shown in Fig. 1 of the Supporting Information).…”

Section: Introductionmentioning

confidence: 99%

On-the-fly ab initio semiclassical evaluation of time-resolved electronic spectra

Begušić

Roulet

Vaníček

2018

The Journal of Chemical Physics

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We present a methodology for computing vibrationally and time-resolved pump-probe spectra, which takes into account all vibrational degrees of freedom and is based on the combination of the thawed Gaussian approximation with on-the-fly ab initio evaluation of the electronic structure. The method is applied to the phenyl radical and compared with two more approximate approaches based on the global harmonic approximation-the global harmonic method expands both the ground-and excitedstate potential energy surfaces to the second order about the corresponding minima, while the combined global harmonic/on-the-fly method retains the on-the-fly scheme for the excited-state wavepacket propagation. We also compare the spectra by considering their means and widths, and show analytically how these measures are related to the properties of the semiclassical wavepacket. We find that the combined approach is better than the global harmonic one in describing the vibrational structure, while the global harmonic approximation estimates better the overall means and widths of the spectra due to a partial cancellation of errors.Although the full-dimensional onthe-fly ab initio result seems to reflect the dynamics of only one mode, we show, by performing exact quantum calculations, that this simple structure cannot be recovered using a one-dimensional model. Yet, the agreement between the quantum and semiclassical spectra in this simple, but anharmonic model lends additional support for the full-dimensional ab initio thawed Gaussian calculation of the phenyl radical spectra. We conclude that the thawed Gaussian approximation provides a viable alternative to the expensive or unfeasible exact quantum calculations in cases, where low-dimensional models are not sufficiently accurate to represent the full system.

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Integrated computational approaches for spectroscopic studies of molecular systems in the gas phase and in solution: pyrimidine as a test case

Cited by 29 publications

References 106 publications

Aiming at an accurate prediction of vibrational and electronic spectra for medium‐to‐large molecules: An overview

Aiming at an accurate prediction of vibrational and electronic spectra for medium‐to‐large molecules: An overview

Implementation of a graphical user interface for the virtual multifrequency spectrometer: The VMS‐Draw tool

On-the-fly ab initio semiclassical evaluation of time-resolved electronic spectra

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