Fully ab initio IR spectra for complex molecular systems from perturbative vibrational approaches: Glycine as a test case

Biczysko, Małgorzata; Bloino, Julien; Carnimeo, Ivan; Panek, Paweł T.; Barone, Vincenzo

doi:10.1016/j.molstruc.2011.10.012

Cited by 54 publications

(85 citation statements)

References 69 publications

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“…The B3LYP/N07D method has been employed to calculate anharmonic frequencies of several closed-and open-shell molecular systems 43,90,117,[125][126][127][128][129][130][131] , and a recent extension of N07D, the SNSD basis set, with the inclusion of diffuse s functions on all atoms and one set of diffuse polarized functions, d on heavy and p on hydrogen atoms, has improved its performance (Double and triple-ζ basis sets of SNS and N07 families, are available for download. 2012; visit http:// dreamslab.sns.it) 132,133 .…”

Section: Computational Detailsmentioning

confidence: 99%

Dispersion corrected DFT approaches for anharmonic vibrational frequency calculations: nucleobases and their dimers

Fornaro

Biczysko

Monti

et al. 2014

Phys. Chem. Chem. Phys.

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113

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Computational spectroscopy techniques have become in the last years effective means to analyze and assign infrared (IR) spectra for molecular systems of increasing dimensions and in different environments. However, transition from compilations of harmonic data to full anharmonic simulations of spectra is still under way. 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 to a quantitative reproduction of the spectra of nucleic acid bases 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 interaction, 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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Section: Computational Detailsmentioning

confidence: 99%

Dispersion corrected DFT approaches for anharmonic vibrational frequency calculations: nucleobases and their dimers

Fornaro

Biczysko

Monti

et al. 2014

Phys. Chem. Chem. Phys.

Self Cite

113

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“…Among other things, this choice allows direct comparison with the second order perturbative approach (VPT2) available in the same code [28][29][30][31] . In particular, we have made use of the double-hybrid B2PLYP functional [32][33][34] and the aug-cc-pVTZ basis set, in view of previous experience about the reliability of this computational model [34][35][36] .…”

Section: B Simple Moleculesmentioning

confidence: 99%

“…We have chosen this particular system because its study is a natural continuation of the VPT2 and reduced dimensionality VPT2 calculations previously performed by our group [28][29][30][31] . As mentioned previously, such an approach necessitates the use of low width Gaussian functions in order not to compromise the local harmonic approximation.…”

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confidence: 99%

A new Gaussian MCTDH program: Implementation and validation on the levels of the water and glycine molecules

Skouteris

Barone

2014

The Journal of Chemical Physics

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We report the main features of a new general implementation of the Gaussian Multi-Configuration Time-Dependent Hartree (G-MCTDH) model. The code allows effective computations of timedependent phenomena, including calculation of vibronic spectra (in one or more electronic states), relative state populations etc. Moreover, by expressing the Dirac-Frenkel variational principle in terms of an effective Hamiltonian we are able to provide a new reliable estimate of the representation error. After validating the code on simple one-dimensional systems, we analyze the harmonic and anharmonic vibrational spectra of water and glycine showing that reliable and converged energy levels can be obtained with reasonable computing resources. The data obtained on water and glycine are compared with results of previous calculations using the vibrational second-order perturbation theory (VPT2) method. Additional features and perspectives are also shortly discussed.

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“…[1][2][3][4][5] Alternatively, perturbative quantum methods have also been successfully applied to many systems, but they are intrinsically limited to a single reference geometry. [6][7][8][9][10][11] High dimensional systems, such as peptides, are instead usually simulated through ad-hoc scaled harmonic approaches or by means of classical mechanics, either using force fields [12][13][14] or employing ab initio molecular dynamics (AIMD) [15][16][17][18][19][20][21] approaches in which the nuclear forces are calculated using electronic structure codes. In classical simulations the curse of dimensionality is significantly tamed with respect to quantum mechanical counterparts.…”

Section: Introductionmentioning

confidence: 99%

“Divide and conquer” semiclassical molecular dynamics: A practical method for spectroscopic calculations of high dimensional molecular systems

Liberto

Conte

Ceotto

2018

The Journal of Chemical Physics

100

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We extensively describe our recently established "divide-and-conquer" semiclassical method [M. Ceotto, G. Di Liberto and R. Conte, Phys. Rev. Lett. 119, 010401 (2017)] and propose a new implementation of it to increase the accuracy of results. The technique permits to perform spectroscopic calculations of high dimensional systems by dividing the full-dimensional problem into a set of smaller dimensional ones. The partition procedure, originally based on a dynamical analysis of the Hessian matrix, is here more rigorously achieved through a hierarchical subspace-separation criterion based on Liouville's theorem. Comparisons of calculated vibrational frequencies to exact quantum ones for a set of molecules including benzene show that the new implementation performs better than the original one and that, on average, the loss in accuracy with respect to full-dimensional semiclassical calculations is reduced to only 10 wavenumbers. Furthermore, by investigating the challenging Zundel cation, we also demonstrate that the "divide-and-conquer" approach allows to deal with complex strongly anharmonic molecular systems. Overall the method very much helps the assignment and physical interpretation of experimental IR spectra by providing accurate vibrational fundamentals and overtones decomposed into reduced dimensionality spectra.

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Fully ab initio IR spectra for complex molecular systems from perturbative vibrational approaches: Glycine as a test case

Cited by 54 publications

References 69 publications

Dispersion corrected DFT approaches for anharmonic vibrational frequency calculations: nucleobases and their dimers

Dispersion corrected DFT approaches for anharmonic vibrational frequency calculations: nucleobases and their dimers

A new Gaussian MCTDH program: Implementation and validation on the levels of the water and glycine molecules

“Divide and conquer” semiclassical molecular dynamics: A practical method for spectroscopic calculations of high dimensional molecular systems

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