Improving the study of proton transfers between amino acid side chains in solution: choosing appropriate DFT functionals and avoiding hidden pitfalls

We have studied the influence of implicit solvent models, inclusion of explicit water molecules, inclusion of vibrational effects, and density functionals on the quality of the predicted pK a of small amino acid side chain models. We found that the inclusion of vibrational effects and explicit water molecules is crucial to improve the correlation between the computed and the experimental values. In these micro-solvated systems, the best agreement between DFT-computed electronic energies and benchmark values is afforded by BHHLYP and B97-2. However, approaching experimental results requires the addition of more than three explicit water molecules, which generates new problems related to the presence of multiple minima in the potential energy surface. It thus appears that a satisfactory ab initio prediction of amino acid side chain pK a will require methods that sample the configurational space in the presence of large solvation shells, while at the same time computing vibrational contributions to the enthalpy and entropy of the system under study in all points of that surface. Pending development of efficient algorithms for those computations, we strongly suggest that whenever counterintuitive protonation states are found in a computational study (e. g., the presence of a neutral aspartate/neutral histidine dyad instead of a deprotonated aspartate/protonated histidine pair), the reaction profile should be computed under each of the different protonation micro-states by constraining the relevant N-H or O-H bonds, in order to avoid artifacts inherent to the complex nature of the factors contributing to the pK a. © 2012 Springer-Verlag.

Beyond Static Structures: Putting Forth REMD as a Tool to Solve Problems in Computational Organic Chemistry

Michele Ceriotti, Adrien Georges Nicolai, Riccardo Petraglia, Matthew Wodrich

Computational studies of organic systems are frequently limited to static pictures that closely align with textbook style presentations of reaction mechanisms and isomerization processes. Of course, in reality chemical systems are dynamic entities where a multitude of molecular conformations exists on incredibly complex potential energy surfaces (PES). Here, we borrow a computational technique originally conceived to be used in the context of biological simulations, together with empirical force fields, and apply it to organic chemical problems. Replica-exchange molecular dynamics (REMD) permits thorough exploration of the potential energy surface. We combined REMD with density functional tight binding (DFTB), thereby establishing the level of accuracy necessary to analyze small molecular systems. Through the study of four prototypical problems: isomer identification, reaction mechanisms, temperature-dependent rotational processes, and catalysis, we reveal new insights and chemistry that likely would be missed using static electronic structure computations. The REMD-DFTB methodology at the heart of this study is powered by i-PI, which efficiently handles the interface between the DFTB and REMD codes.

Wiley-Blackwell2016

Capturing Non-local Effects in Kohn-Sham Density Functional Theory

Andrey Laktionov

Density Functional Theory (DFT) and its time-dependent extension (TDDFT) have become two of the most popular approaches for computer simulations of the electronic structure and response properties of quantum systems. A reasonable compromise between accuracy and computational cost allows to apply DFT to a wide range of systems from small molecules to biological complexes. Despite the in principle exact nature of DFT and TDDFT, practical calculations require the use of approximate DFT exchange-correlation (XC) functionals and TDDFT kernels and the accuracy of the obtained results is determined by the accuracy of the chosen XC description. These approximations inevitably introduce some limitations in the use of DFT-based methods.The inability of the local spin density approximation, generalized gradient approximations (GGA) and even some hybrid functionals to properly describe charge transfer (CT) excitations and predict intermolecular interaction energies of weakly bound complexes are two major drawbacks of current XC descriptions. This thesis is therefore devoted to the improvement of XC functionals for the special cases of weak interactions and charge-transfer excitations. Many original strategies have been suggested to cure DFT calculations from these failures. In particular, the Dispersion-Corrected Atom-Centered Potentials (DCACP) approach provides an accurate description of dispersion forces within generalized gradient approximations for the exchange-correlation functional. The DCACP method has been extensively used for the last seven years and has shown an excellent performance for a large class of applications. However, one of the drawbacks of the current implementation of DCACP is that the correct R-6 asymptotics of dispersion interaction is not reproduced. A first goal of this thesis was to enable DCACP to recover the R-6 asymptotic limit. To this end, we have designed a new 2-channel version of DCACP and carried out test calculations on both small molecules and large macromolecular complexes. The obtained results demonstrate the excellent performance and transferability of the DCACP approach. Moreover, for large macromolecular complexes, in which the binding energy is dominated by dispersion, [pi]-stacking, or hydrogen bonding, 2-channels DCACP were found to be the best method overall for correcting the popular BLYP functional. Our study clearly shows that account of R-6 asymptotics is crucial for the description of large complexes and that 2-channels DCACP are fully able to capture these effects. On the contrary, an account of R-6 asymptotics is of little importance for small molecules since the remaining errors of the underlying GGA functional are dominating. With the aim of deepening our understanding of the DCACP concept and the reasons for its excellent performance, we explored the properties of the two DCACP parameters and were able to establish some systematic trends. It turned out that variational tuning of the DCACP can be done in an analytical manner that enables the easy generation of DCACP potentials for the full periodic table. Furthermore, since DCACP have little but crucial impact on the electronic density, dispersion energies can be obtained from non-self-consistent electron densities. These empirical findings suggest that the high transferability of DCACP is due to their atom-centered form and the intrinsically weak nature of dispersion interactions. [...]

EPFL2014

Geometrical and energetical structural changes in organic dyes for dye-sensitized solar cells probed using photoelectron spectroscopy and DFT

Anna Eriksson, Ulf Anders Hagfeldt

The effects of alkoxy chain length in triarylamine based donor acceptor organic dyes are investigated with respect to the electronic and molecular surface structures on the performance of solar cells and the electron lifetime. The dyes were investigated when adsorbed on TiO2 in a configuration that can be used for dye sensitized solar cells (DSCs). Specifically, the two dyes D35 and D45 were compared using photoelectron spectroscopy (PES) and density functional theory (DFT) calculations. The differences in solar cell characteristics when longer alkoxy chains are introduced in the dye donor unit are attributed to geometrical changes in dye packing while only minor differences were observed in the electronic structure. A higher dye load was observed for D45 on TiO2. However, D35 based solar cells result in higher photocurrent although the dye load is lower. This is explained by different geometrical structures of the dyes on the surface.

Royal Soc Chemistry2016

Capturing Non-local Effects in Kohn-Sham Density Functional Theory

Andrey Laktionov

EPFL2014