Anharmonic vibrational frequency calculations for solvated molecules in the B3LYP Kohn–Sham basis set limit (original) (raw)
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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.
Journal of molecular modeling, 2012
A linear correlation between harmonic and anharmonic frequencies of water calculated at B3LYP level of theory was observed with a number of basis sets. Similar relationships were found in both the gas phase and solution for several small molecules. The best correlation was found for C = O stretch mode in formaldehyde, formamide and N-methylacetamide. The average difference between B3LYP harmonic and anharmonic ν(C = O) frequencies calculated with several basis sets in these molecules was 30 cm−1. The ad hoc correction of −30 cm−1, added to harmonic frequencies of two different carbonyl groups present in a structure of a larger molecule was tested as a fast way of predicting anharmonic frequencies without elaborated calculations. The proposed approach was tested successfully on a larger molecule of E and Z isomers of N-acetyl-α,β-dehydrophenylalanine N′,N′-dimethylamide [Ac-(E/Z)-ΔPhe-NMe2] and the estimated anharmonic ν(C = O) frequencies were close to directly calculated results. Figure Correlation between calculated harmonic and anharmonic ν(C = O) frequencies of formamide in the gas phase and several solvents calculated with the B3LYP hybrid exchange-correlation functional using 21 basis sets in vacuum and 11 in solution
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
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.
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.
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.
2001
The reliability of density functional theory and other electronic structure methods is examined for anharmonicities and spectroscopic constants of the ground electronic states of several diatomic molecules. The equilibrium bond length r e , harmonic vibrational frequency e , vibrational anharmonicity e x e , rotational constant B e , centrifugal distortion constant D e , and vibration-rotation interaction constant ␣ e have been obtained theoretically for BF, CO, N 2 , CH ϩ , and H 2 . Predictions using Hartree-Fock, coupled-cluster singles and doubles ͑CCSD͒, coupled cluster singles and doubles with perturbative triples ͓CCSD͑T͔͒, and various density functional methods ͑S-VWN, BLYP, and B3LYP͒ have been made using the 6-31G*, aug-cc-pVDZ, and aug-cc-pVTZ basis sets and compared to experimental values. Density functional theory predictions of the spectroscopic constants are reliable ͑particularly for B3LYP͒ and often perform as well as the more expensive CCSD and CCSD͑T͒ estimates.
The Journal of Physical Chemistry A, 2014
Anharmonic vibrational spectroscopy calculations using MP2 and B3LYP computed potential surfaces are carried out for a series of molecules, and frequencies and intensities are compared with those from experiment. The vibrational self-consistent field with second-order perturbation correction (VSCF-PT2) is used in computing the spectra. The test calculations have been performed for the molecules HNO 3 , C 2 H 4 , C 2 H 4 O, H 2 SO 4 , CH 3 COOH, glycine, and alanine. Both MP2 and B3LYP give results in good accord with experimental frequencies, though, on the whole, MP2 gives very slightly better agreement. A statistical analysis of deviations in frequencies from experiment is carried out that gives interesting insights. The most probable percentage deviation from experimental frequencies is about −2% (to the red of the experiment) for B3LYP and +2% (to the blue of the experiment) for MP2. There is a higher probability for relatively large percentage deviations when B3LYP is used. The calculated intensities are also found to be in good accord with experiment, but the percentage deviations are much larger than those for frequencies. The results show that both MP2 and B3LYP potentials, used in VSCF-PT2 calculations, account well for anharmonic effects in the spectroscopy of molecules of the types considered.
Journal of Chemical Theory and Computation, 2010
This work aims to provide reliable benchmark data on the accuracy of harmonic and anharmonic vibrational frequencies computed with the B2PLYP double-hybrid density functional method. The exchange-correlation contributions required for the B2PLYP analytical second derivatives are presented here, which allow for the effective calculation of harmonic frequency as well as cubic and semidiagonal quartic force fields. The latter, in turn, are necessary to compute the anharmonic vibrational frequencies with the perturbative approach (VPT2). The quality of harmonic vibrational frequencies computed in conjunction with basis sets of double-to quadruple-quality has been checked against reference data from the F38 benchmark set. Then, for an additional set of small closed-and open-shell systems, both harmonic frequencies and anharmonic contributions computed at the B2PLYP/N07D and the B2PLYP/aug-cc-pVTZ levels have been compared to their CCSD(T) counterparts. Moreover, for selected medium-size molecules (furan, pyrrole, thiophene, uracil, anisole, phenol, and pyridine), anharmonic frequencies have been compared to well established experimental results. Such benchmark studies have shown that the B2PLYP/N07D model provides good quality harmonic frequencies and describes correctly anharmonic contributions, the latter being of similar accuracy to their B3LYP/N07D counterparts, but obtained at significantly larger computational cost. Additionally, increased accuracy can be obtained by adopting hybrid models where the B2PLYP/N07D anharmonic contributions are combined with harmonic frequencies computed with more accurate quantum mechanical (QM) approaches or by B2PLYP with larger basis sets. This work confirmed also that most of the recently developed density functionals are significantly less suited for vibrational computations, while the B2PLYP method can be recommended for spectroscopic studies where a good accuracy of vibrational properties is required.
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.