Estimating the carbonyl anharmonic vibrational frequency from affordable harmonic frequency calculations (original) (raw)
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Vibrational Spectroscopy, 2012
The solvent dependence of harmonic and anharmonic vibrational wavenumbers of water, formaldehyde and formamide was studied using the B3LYP method. The results obtained with the hierarchy of Jensen's polarization-consistent basis sets were fitted with two-parameter formula toward the B3LYP Kohn-Sham complete basis set (CBS) limit. Anharmonic corrections have been obtained by a second order perturbation treatment (VPT2) and vibrational configuration interaction (VCI) method. The solvent environment was treated according to the self-consistent reaction field polarizable continuum model (SCRF PCM) approach.
Calculation of anharmonic vibrational spectroscopy of small biological molecules
PhysChemComm, 2002
The role of anharmonic effects in the vibrational spectroscopy of small biological molecules and their 1 : 1 complexes with water is discussed. The strengths and limitations of the vibrational self-consistent field (VSCF) method and its extensions as a computational tool for this purpose are examined. Anharmonic coupling between different vibrational modes is found to be very important for these systems, even for fundamental transitions, and incorporation of these effects seems essential for quantitative interpretation of experimental data. Both analytical, empirical force fields, and potential surfaces computed from electronic structure methods are used in VSCF calculations of several benchmark systems and compared with experimental spectroscopic data. Glycine in several conformers, the glycine-water complex, and N-methylacetamide are among the systems discussed. The main conclusions are: (1) Electronic structure methods such as MP2/DZP and density functional B97, give very good agreement with experimental data. Thus, MP2 and B97 clearly provide an accurate description of the anharmonic interactions. VSCF calculations, including all modes, with MP2, B97 and other successful methods are presently feasible for molecules with up to 15-20 atoms. (2) The electronic structure methods seem to give spectroscopic predictions in much better accord with experiment than standard empirical force fields such as AMBER or OPLS. The anharmonic couplings provided by these methods differ greatly, in the cases tested to date, from the ab initio ones. The implications of these results for future modeling of small biomolecules are discussed. Comments are provided on future directions in this subject, including extensions to large biomolecules.
Journal of Chemical Theory and Computation, 2010
We report some results on the calculation of vibrational spectra of molecules in condensed phase with accounting simultaneously for anharmonicity and solute-solvent interactions, the latter being described by means of the polarizable continuum model (PCM). Density functional theory force fields are employed as well as a new implementation of the PCM cavity and its derivatives. The results obtained for formaldehyde and simple peptide prototypes show that our approach is able to yield a quantitative agreement with experiments for vacuo-to-solvent harmonic and anharmonic frequency shifts.
International Journal of Quantum Chemistry, 2019
Anharmonic vibrational frequencies for closed-shell molecules computed with CCSD(T)-F12b/augcc-pVTZ differ from significantly more costly composite energy methods by a mean absolute error (MAE) of 7.5 cm −1 per fundamental frequency. Comparison to a few available gas phase experimental modes, however, actually lowers the MAE to 6.0 cm −1. Open-shell molecules have an MAE of nearly a factor of six greater. Hence, open-shell molecular anharmonic frequencies cannot be as well-described with only explicitly correlated coupled cluster theory as their closed-shell brethren. As a result, the use of quartic force fields and vibrational perturbation theory can be opened to molecules with six or more atoms, whereas previously such computations were limited to molecules of five or fewer atoms. This will certainly assist in studies of more chemically interesting species, especially for atmospheric and interstellar infrared spectroscopic characterization.
International Journal of Quantum Chemistry, 2005
The basis set superposition error (BSSE) influence in the geometry structure, interaction energies, and intermolecular harmonic and anharmonic vibrational frequencies of cyclic formamide–formamide and formamide–water dimers have been studied using different basis sets (6-31G, 6-31G**, 6-31++G**, D95V, D95V**, and D95V++**). The a posteriori “counterpoise” (CP) correction scheme has been compared with the a priori “chemical Hamiltonian approach” (CHA) both at the Hartree–Fock (HF) and second-order Møller–Plesset many-body perturbation (MP2) levels of theory. The effect of BSSE on geometrical parameters, interaction energies, and intermolecular harmonic vibrational frequencies are discussed and compared with the existing experimental data. As expected, the BSSE-free CP and CHA interaction energies usually show less deep minima than those obtained from the uncorrected methods at both the HF and MP2 levels. Focusing on the correlated level, the amount of BSSE in the intermolecular interaction energies is much larger than that at the HF level, and this effect is also conserved in the values of the force constants and harmonic vibrational frequencies. All these results clearly indicate the importance of the proper BSSE-free correlation treatment with the well-defined basis functions. At the same time, the results show a good agreement between the a priori CHA and a posteriori CP correction scheme; this agreement is remarkable in the case of large and well-balanced basis sets. The anharmonic frequency correction values also show an important BSSE dependence, especially for hydrogen bond stretching and for low frequencies belonging to the intermolecular normal modes. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
Journal of Physical Chemistry
The performance of some recently proposed DFT functionals by Truhlar's group (mPW1B95, mPWLYP1W, PBELYP1W, and PBE1W [Dahlke, E. E.; Truhlar, D. G. J. Phys. Chem. B 2005, 109, 317. Zhao, Y.; Truhlar, D. G. J. Phys. Chem. A 2004, 108, 6908.]) was tested primarily with respect to computation of anharmonic vibrational frequency shifts upon hydrogen bond formation in small molecular/ionic dimers. Five hydrogenbonded systems with varying hydrogen bond strengths were considered: methanol-fluorobenzene, phenol-carbon monoxide in ground neutral (S 0 ) and cationic (D 0 ) electronic states, phenol-acetylene, and phenol-benzene(+). Anharmonic OH stretching frequency shifts were calculated from the computed vibrational potentials for free and hydrogen-bonded proton-donor molecules. To test the basis set convergence properties, all calculations were performed with 6-31++G(d,p) and 6-311++G(2df,2pd) basis sets. The mPW1B95 functional was found to perform remarkably better in comparison to more standard functionals (such as B3LYP, mPW1PW91, PBE1PBE) in the case of neutral dimers. In the case of cationic dimers, however, this is not always the case. With respect to prediction of anharmonic OH stretching frequency shifts upon ionization of free phenol, all DFT levels of theory outperform MP2. Some other aspects of the functional performances with respect to computation of interaction and dissociation energies were considered as well.
Toward anharmonic computations of vibrational spectra for large molecular systems
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.
Acta Crystallographica Section A Foundations of Crystallography, 2011
Molecular-dynamics-derived numerical probability density functions (PDFs) have been used to illustrate the effect of different models for thermal motion on the parameters refined in a crystal structure determination. Specifically, anharmonic curved or asymmetric PDFs have been modelled using the traditional harmonic approximation and the anharmonic Gram-Charlier series treatment. The results show that in cases of extreme anharmonicity the mean and covariance matrix of the harmonic treatment can deviate significantly from physically meaningful values. The use of a Gram-Charlier anharmonic PDF gives means and covariance matrices closer to the true (numerically determined) anharmonic values. The physical significance of the maxima of the anharmonic distributions (the most probable or mode positions) is also discussed. As the data sets used for the modelling process are theoretical in origin, these most probable positions can be compared to equilibrium positions that represent the system at the bottom of its potential-energy surface. The two types of position differ significantly in some cases but the most probable position is still worthy of report in crystal structure determinations.
Physical Chemistry Chemical Physics, 2014
Computational spectroscopy techniques have become in the last few years an effective means to analyze and assign infrared (IR) spectra of molecular systems of increasing dimensions and in different environments. However, transition from compilation of harmonic data to fully anharmonic simulations of spectra is still underway. 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 at quantitative reproduction of the spectra of nucleic acid base 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 interactions, 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. † Electronic supplementary information (ESI) available: (i) Harmonic and anharmonic vibrational frequencies and IR intensities for adenine, cytosine, uracil, hypoxanthine and thymine molecules; (ii) statistical analysis of the vibrational frequency discrepancies for monomers; (iii) binding energies and structural parameters for dimers; and (iv) anharmonic vibrational frequencies of uracil and adenine complexes. See