Beyond Platonic Molecules

Bowman, Joel M.

doi:10.1126/science.290.5492.724

Cited by 31 publications

(18 citation statements)

References 10 publications

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“…On the contrary, consistent procedures can be derived from QM computations of vibrational properties beyond the harmonic approximation. Recently, exact solutions for the treatment of few active modes to the vibrational problem for a generic system has been proposed 55 and effective schemes to compute vibrational frequencies within the second order vibrational perturbative (VPT2) [56][57][58][59][60][61][62][63][64][65][66][67][68][69][70][71][72][73][74][75] or vibrational self-consistent field (VSCF) based [76][77][78][79][80][81][82][83][84][85] approaches have been developed and implemented. In particular, a general VPT2 framework to compute thermodynamic properties, vibrational energies and transition intensities from the vibrational ground state to fundamentals, overtones and combination bands 66,67,[86][87][88] has been developed in our group.…”

Section: Introductionmentioning

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.

100

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: Introductionmentioning

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.

100

113

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“…Starting from this point, perturbative or variational procedures can be used to solve the vibrational problem. A widely used approach is based on vibrational self‐consistent field (VSCF) using a potential truncated to two‐, three‐, and four‐mode couplings16–23, which is able to describe a large variety of systems, also involving large amplitude motions. Next, correlation is taken into account by vibrational Møller‐Plesset perturbation theory (VMP, also known as correlation‐corrected VSCF, cc‐VSCF)24, 25, vibrational configuration interaction (VCI)17, 26, or vibrational coupled clusters (VCC)27.…”

Section: Introductionmentioning

confidence: 99%

Toward anharmonic computations of vibrational spectra for large molecular systems

Barone

Biczysko

Bloino

et al. 2011

Int J of Quantum Chemistry

118

141

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The subtle interplay of several different effects makes the interpretation and analysis of experimental spectra in terms of structural and dynamic characteristics a very challenging task. In this context, theoretical studies can be very helpful, and this is the reason behind the rapid evolution of computational spectroscopy from a highly specialized research field toward a versatile and widespread tool. However, in the case of vibrational spectra of large molecular systems, the most popular approach still relies on a harmonic treatment, because of the difficulty to explore the multidimensional anharmonic potential energy surface. These can be overcome considering that, in many cases, the vibrational transitions are well localized and only some of them are observed experimentally. To this aim, the procedure for the simulation of vibrational spectra of large molecular systems beyond the harmonic approximation is discussed. The quality of system-specific reduced dimensional anharmonic approaches is first validated by comparison with computations taking into account all modes simultaneously for anisole and glycine. Next, the approach is applied to two larger systems, namely glycine adsorbed on a silicon surface and chlorophyll-a in solution, and the results are compared with experimental data showing significant improvement over the standard harmonic approximation. Our results show that properly tailored reduced dimension anharmonic approaches stand as feasible routes for state-of-the-art computational spectroscopy studies and allow to take into account both anharmonic and environmental effects on the spectra even for relatively large molecular systems.

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“…Regarding the isomerization reaction one of the key questions is how the isomerization manifests itself in the vibration-rotation eigenenergy spectrum of the HCN and HNC molecules. The spectroscopic signature describes how the wave functions of the two isomers H-CN and CN-H located in two different minima merge step by step to a single delocalized wave function 16 corresponding to a single "combined"H 0.5 -CN-H 0.5 molecule.…”

Section: Introductionmentioning

confidence: 99%

Complete experimental rovibrational eigenenergies of HCN up to 6880 cm−1 above the ground state

Mellau

2011

The Journal of Chemical Physics

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The [H,C,N] molecular system is a very important model system to many fields of chemical physics and the experimental characterization of highly excited vibrational states of this molecular system is of special interest. This paper reports the experimental characterization of all 3822 eigenenergies up to 6880 cm −1 relative to the ground state in the HCN part of the potential surface using high temperature hot gas emission spectroscopy. The spectroscopic constants for the first 71 vibrational states including highly excited bending vibrations up to v 2 = 10 are reported. The perturbed eigenenergies for all 20 rotational perturbations in the reported eigenenergy range have been determined. The 11 070 eigenenergies up to J = 90 for the first 123 vibrational substates are included as supplement to this paper. We show that a complete ab initio rovibrational analysis for a polyatomic molecule is possible. Using such an analysis we can understand the molecular physics behind the Schrödinger equation for problems for which perturbation theoretical calculations are no more valid. We show that the vibrational structure of the linear HCN molecule persists approximately up to the isomerization barrier and only above the barrier the accommodation of the vibrational states to the double well structure of the potential takes place.

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Beyond Platonic Molecules

Cited by 31 publications

References 10 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

Toward anharmonic computations of vibrational spectra for large molecular systems

Complete experimental rovibrational eigenenergies of HCN up to 6880 cm−1 above the ground state

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