“Multi-Scale” QM/MM Methods with Self-Consistent-Charge Density-Functional-Tight-Binding (SCC-DFTB). In: York DM, Lee T, editors. Multi-scale Quantum Models for Biocatalysis. Dordrecht: Springer Netherlands; 2009. pp. 173-96. [DOI: 10.1007/978-1-4020-9956-4_7]

Benchmarking density functional tight binding models for barrier heights and reaction energetics of organic molecules

Density Functional Tight Binding (DFTB) models are two to three orders of magnitude faster than ab initio and Density Functional Theory (DFT) methods and therefore are particularly attractive in applications to large molecules and condensed phase systems. To establish the applicability of DFTB models to general chemical reactions, we conduct benchmark calculations for barrier heights and reaction energetics of organic molecules using existing databases and several new ones compiled in this study. Structures for the transition states and stable species have been fully optimized at the DFTB level, making it possible to characterize the reliability of DFTB models in a more thorough fashion compared to conducting single point energy calculations as done in previous benchmark studies. The encouraging results for the diverse sets of reactions studied here suggest that DFTB models, especially the most recent third-order version (DFTB3/3OB augmented with dispersion correction), in most cases provide satisfactory description of organic chemical reactions with accuracy almost comparable to popular DFT methods with large basis sets, although larger errors are also seen for certain cases. Therefore, DFTB models can be effective for mechanistic analysis (e.g., transition state search) of large (bio)molecules, especially when coupled with single point energy calculations at higher levels of theory. © 2017 Wiley Periodicals, Inc.

SCC-DFTB calculation of the static first hyperpolarizability: from gas phase molecules to functionalized surfaces

The performance of the self-consistent charge density functional tight binding (SCC-DFTB) method for calculating the first hyperpolarizability of π-conjugated compounds has been assessed with respect to results obtained with high-level ab initio methods and density functional theory (DFT). The SCC-DFTB method performs similarly or better than DFT with the PBE XC functional. Thus, if for small π-conjugated linkers SCC-DFTB can reproduce trends, for longer chains the first hyperpolarizabilities are overestimated. In the case of push-pull thiophenes, the β values are strongly overestimated, as it is also the case with the B3LYP and PBE XC functionals. On the other hand, the SCC-DFTB method closely reproduces the evolution of β in p-disubstituted benzenes as a function of the donor and acceptor groups, as estimated at the MP2 level. The reliability of SCC-DFTB to determine the bond length alternation and the dihedral angles between the aromatic rings has also been tackled, demonstrating that both are underestimated. Overall, the SCC-DFTB calculations are of the same quality as those performed with the conventional PBE XC functional on which the method was parameterized but the SCC-DFTB calculations are computationally very little demanding, and it can therefore be adopted for very large systems for screening nonlinear optical materials as well as for assessing structure-property relationships. This is illustrated with an application on the first hyperpolarizability of an indolino-oxazolidine molecular switch grafted on a SiO2 surface. This has enabled to pinpoint (i) the effect of the surface on the donor/acceptor character of the linking substituent, (ii) the impact of molecular orientation, (iii) the role of a spacer between the π-conjugated switch and the surface, (iv) the global effect of the surface on the β contrast, and also (v) the fact that the molecular switches can maintain this contrast when adsorbed.

Origin of the Surface-Induced First Hyperpolarizability in the C60/SiO2 System: SCC-DFTB Insight

Using the self-consistent charge density functional tight binding (SCC-DFTB) method, C60 molecules physisorbed on an α-quartz slab are shown to display a first hyperpolarizability, whereas, owing to their symmetry, both the α-quartz slab and C60 molecule have no first hyperpolarizabilities. A larger first hyperpolarizability is achieved when the lowest-lying (five- or six-membered) ring is situated in between two hydroxyl rows, rather than on top, because this situation favors orbital overlaps and charge transfer. Further analysis has demonstrated that (i) the first hyperpolarizability originates from the MO overlap and field-induced charge transfers from the neighboring substrate/adsorbate moieties but not to geometric relaxation of the C60 molecules at the interface and that (ii) larger first hyperpolarizabilities are associated with low surface coverage and with small distances between C60 and the surface. This contribution is a clear illustration of the emergence of second-order nonlinear optical responses (first hyperpolarizability) as a result of breaking the centrosymmetry.

Color tuning in binding pocket models of the chlamydomonas-type channelrhodopsins

We examined the shift of absorption maxima between the chlamydomonas-type channelrhodopsins (ChRs) and bacteriorhodopsin (BR). Starting from the BR X-ray structure, we modeled the color tuning in the binding pockets of the ChRs by mutating up to 28 amino acids in the vicinity of the chromophore. By applying the efficient self-consistent charge density functional tight binding (SCC-DFTB) method in a quantum mechanical/molecular mechanical (QM/MM) framework, including explicit polarization and calculating excitation energies with the semiempirical OM2/MRCI method and the ab initio SORCI method, we have shown that multiple mutations in the binding pocket of BR causes large hypsochromic shifts that are of the same order as the experimentally observed shifts of the absorption maxima between BR and the ChRs. This study further demonstrates that mutations in the proximity of the Schiff base and complex counterion lead to a stronger but more flexible interaction with the retinal, which could serve as a possible explanation for the spectral patterns found in the ChRs.

Application of the SCC-DFTB method to neutral and protonated water clusters and bulk water

The self-consistent charge density functional tight-binding (SCC-DFTB) method has been actively employed to study proton-transfer processes in biological systems. Recent studies in the literature employing SCC-DFTB reported that the method favors the Zundel form of the hydrated proton over the Eigen form, both in gas-phase water clusters and in bulk water, in disagreement with both higher-level calculations and experimental data. In this work, we explore the performance of SCC-DFTB for protonated gas-phase water clusters and bulk water (the latter both with and without an excess proton) with a modified O-H repulsive potential reported in our earlier work and with on-site third-order expansion of the DFT energy. Our results show that, with the proper set of published parameters, SCC-DFTB does correctly favor the Eigen form of the hydrated proton as compared to the Zundel form, both in gas-phase clusters and in the bulk; the amphiphilic character of the hydrated proton discussed in the literature has also been observed. The analyses do, however, bring forth remaining limitations in terms of the solvation structure around the hydrated proton as well as the structure of bulk water, which can guide future improvements of the method.