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A Multifrequency Virtual Spectrometer for Complex Bio-Organic Systems: Vibronic and Environmental Effects on the UV/Vis Spectrum of Chlorophyll a
No full textThe subtle interplay of several different effects means that the interpretation and analysis of experimental spectra in terms of structural and dynamic characteristics is a challenging task. In this context, theoretical studies can be helpful, and as such, computational spectroscopy is rapidly evolving from a highly specialized research field toward a versatile and widespread tool. However, in the case of electronic spectra (e.g. UV/Vis, circular dichroism, photoelectron, and X-ray spectra), the most commonly used methods still rely on the computation of vertical excitation energies, which are further convoluted to simulate line shapes. Such treatment completely neglects the influence of nuclear motions, despite the well-recognized notion that a proper account of vibronic effects is often mandatory to correctly interpret experimental findings. Development and validation of improved models rooted into density functional theory (DFT) and its time-dependent extension (TD-DFT) is of course instrumental for the optimal balance between reliability and favorable scaling with the number of electrons. However, the implementation of easy-to-use and effective procedures to simulate vibrationally resolved electronic spectra, and their availability to a wide community of users, is at least equally important for reliable simulations of spectral line shapes for compounds of biological and technological interest. Here, such an approach has been applied to the study of the UV/Vis spectra of chlorophyll a. The results show that properly tailored approaches are feasible for state-of-the-art computational spectroscopy studies, and allow, with affordable computational resources, vibrational and environmental effects on the spectral line shapes to be taken into account for large systems
Simulation of theoretical IR spectra for complex molecular systems from vibrational perturbative approaches: glycine as a test case
No full textStructural and Vibrational Properties of Amino Acids from Composite Schemes and Double-Hybrid DFT: Hydrogen Bonding in Serine as a Test Case
Full text linkThe structures, relative stabilities, and vibrational wavenumbers of the two most stable conformers of serine, stabilized by the O-H···N, O-H···O═C and N-H···O-H intramolecular hydrogen bonds, have been evaluated by means of state-of-the-art composite schemes based on coupled-cluster (CC) theory. The so-called "cheap"composite approach (CCSD(T)/(CBS+CV)MP2) allowed determination of accurate equilibrium structures and harmonic vibrational wavenumbers, also pointing out significant corrections beyond the CCSD(T)/cc-pVTZ level. These accurate results stand as a reference for benchmarking selected hybrid and double-hybrid, dispersion-corrected DFT functionals. B2PLYP-D3 and DSDPBEP86 in conjunction with a triple-ζ basis set have been confirmed as effective methodologies for structural and spectroscopic studies of medium-sized flexible biomolecules, also showing intramolecular hydrogen bonding. These best performing double-hybrid functionals have been employed to simulate IR spectra by means of vibrational perturbation theory, also considering hybrid CC/DFT schemes. The best overall agreement with experiment, with mean absolute error of 8 cm-1, has been obtained by combining CCSD(T)/(CBS+CV)MP2 harmonic wavenumbers with B2PLYP-D3/maug-cc-pVTZ anharmonic corrections. Finally, a composite scheme entirely based on CCSD(T) calculations (CCSD(T)/CBS+CV) has been employed for energetics, further confirming that serine II is the most stable conformer, also when zero-point vibrational energy corrections are included
Reprint of "Environmental and dynamical effects on the optical properties of molecular systems by time-independent and time-dependent approaches: Coumarin derivatives as test cases"
No full textThe main building blocks of a virtual spectrometer aimed at the vis-à-vis comparison between computed and experimental electronic spectra of large-size molecules in condensed phases are shortly analyzed with special attention to stereo-electronic, dynamic and environmental effects. The combined use of time-dependent and time-independent models allows to deal effectively with both high- and low-resolution spectra involving several electronic states at finite temperatures and in different environments ranging from isotropic solutions to surfaces and interiors of nanoparticles. The most salient features of virtual spectrometer are next illustrated by studying absorption and emission spectra of several coumarin derivatives in different environments. © 2014
Computational Tools for Structure, Spectroscopy and Thermochemistry
No full textIn this chapter we will review the main methodological aspects providing the background for the computational study of thermochemical and spectroscopic properties of molecular systems. A variety of spectroscopies covering a large interval of the electromagnetic spectrum, from the radiofrequencies to the UV-Vis zones, have been applied to a selected set of molecular systems of interest in organometallic chemistry. Both isolated molecules in the gas and condensed phases and nanosystems have been studied, giving particular emphasis to the interplay between experiment and theory: stereoelectronic, vibrational, vibronic, and environmental effects are discussed for few illustrative examples. © 2015 Wiley-VCH Verlag GmbH & Co. KGaA. All rights reserved
Anharmonic Effects on Vibrational Spectra Intensities: Infrared, Raman, Vibrational Circular Dichroism, and Raman Optical Activity
Full text linkThe aim of this paper is 2-fold. First, we want to report the extension of our virtual multifrequency spectrometer (VMS) to anharmonic intensities for Raman optical activity (ROA) with the full inclusion of first- and second-order resonances for both frequencies and intensities in the framework of the generalized second-order vibrational perturbation theory (GVPT2) for all kinds of vibrational spectroscopies. Then, from a more general point of view, we want to present and validate the performance of VMS for the parallel analysis of different vibrational spectra for medium-sized molecules (IR, Raman, VCD, ROA) including both mechanical and electric/magnetic anharmonicity. For the well-known methyloxirane benchmark, careful selection of density functional, basis set, and resonance thresholds permitted us to reach qualitative and quantitative agreement between experimental and computed band positions and shapes. Next, the whole series of halogenated azetidinones is analyzed, showing that it is now possible to interpret different spectra in terms of mass, electronegativity, polarizability, and hindrance variation between closely related substituents, chiral spectroscopies being particular effective in this connection
Reliable structural, thermodynamic, and spectroscopic properties of organic molecules adsorbed on silicon surfaces from computational modeling: the case of glycine@Si(100)
No full textChemisorption 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
Fully ab initio IR spectra for complex molecular systems from perturbative vibrational approaches: Glycine as a test case
No full textPerturbative anharmonic computations have been used to simulate the IR spectrum of glycine, taking into account its three most stable conformers. The theoretical results have been directly compared with their experimental counterparts, showing good agreement between the latter and the spectra obtained after proper averaging of the contributions from the three most stable glycine conformers. The results show that direct simulation of the overall vibrational spectrum within a second-order perturbative treatment is feasible and leads to a better understanding of experimental data. Additionally, it has been shown that accurate results can be obtained even when several molecular species need to be considered simultaneously. The computations performed at the B3LYP/aug-N07D level have shown their reliability in the prediction of both vibrational energy levels and IR intensities beyond the harmonic approximation. This kind of computations represents an important tool for the analysis of vibrational spectra for complex medium-to-large molecular systems. (C) 2011 Elsevier B.V. All rights reserved
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