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

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.

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

Marta Andreia Da Silva Perez

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.

2012

Bridging Static and Dynamical Descriptions of Chemical Reactions: An ab Initio Study of CO2 Interacting with Water Molecules

Wanda Andreoni, Fabio Pietrucci

Extracting reliable thermochemical parameters from molecular dynamics simulations of chemical reactions, although based on ab initio methods, is generally hampered by difficulties in reproducing the results and controlling the statistical errors. This is a serious drawback with respect to the quantum chemical description based on potential energy surfaces. This work is an attempt to fill this gap. We apply molecular dynamics, based on density functional theory (DFT) and empowered by path metadynamics (MTD), to simulate the reaction of CO2 with (one, two, and three) water molecules in the gas phase. This study relies on a strategy that ensures a precise control of the accuracy of the reaction coordinates and of the reconstructed free-energy surface on this space, namely, on (i) fully reversible MTD simulations, (ii) a committor probability analysis for the diagnosis of the collective variables, and (iii) a cluster analysis for the characterization of the reconstructed free energy surfaces. This robust procedure permits a meaningful comparison with more traditional calculations of the potential energy surfaces that we also perform within the same DFT computational scheme. This comparison shows in particular that the reactants and products of systems with only three water molecules can no longer be understood in terms of one structure but must be described as statistical configuration ensembles. Calculations carried out with different prescriptions for the exchange-correlation functionals also allow us to establish their quantitative effect on the activation barriers for the formation and the dissociation of carbonic acid. Their decrease induced by the addition of one water molecule (catalytic effect) is found to be largely independent of the specific functional.

Amer Chemical Soc2012

Computational studies of the structural and optical properties of organic-inorganic lead halide perovskites.

Ariadni Boziki

The rapid rise of organic-inorganic lead halide perovskites has amazed the photovoltaic community. As the efficiency race continues for this revolutionary class of light-harvesting materials, many questions on the structural, electronic and optical properties of perovskite solar cells have still to be addressed. Computational chemistry as well as computational materials' science and engineering have developed into interdisciplinary and powerful scientific fields. They enclose a portfolio of theories and methods developed in mathematics, physics and chemistry, to help scrutinize and tackle problems that can often not be solved in real experiments. In this dissertation, a compendium of available computational methods that treat matter in the quantum mechanical sense and appropriately link its microscopic behavior with its macroscopic properties are employed. Density Functional Theory (DFT) both in the form of static calculations at zero temperature and in the form of first-principles Molecular Dynamics (MD) simulations have been performed in order to study the structural characteristics, the relative stability and the electronic and optical properties of a variety of lead halide perovskites. Many of the computational studies presented here have been performed in close collaboration with experimental groups. More specifically, in order to tackle the challenge of limited phase stability, the atomistic origins of the preferential stabilization or destabilization of the perovskite phase at room temperature is addressed in the case of mixed cations/mixed halide lead perovskites. Their electronic properties, in turn are investigated in order to examine how mixing affects the properties of the pure compounds. Through these studies, it was possible to formulate new design principles for the synthesis of stable mixed cation/mixed halide perovskites with enhanced optical properties. Furthermore, some fundamental open issues related to the nature of the excited states of lead halide perovskites are addressed by simulating the transient absorption spectra and by studying the possible formation of polarons at room temperature for cesium lead bromide. An understanding of the correlations between the nature of the excited states and the atomistic characteristics of these materials is paving the way for the design of lead halide perovskites with enhanced optical properties. Finally, the anomalous low-temperature behavior of the photoluminescence spectra of cesium lead bromide is rationalized in terms of the structural characteristics of the material at low temperatures. The exploration of such phenomena allowed to gain more insights about the properties of organic-inorganic lead halide perovskites that may make them more suitable for applications within and beyond photovoltaics.

EPFL2019

Computational studies of the structural and optical properties of organic-inorganic lead halide perovskites.

Ariadni Boziki

EPFL2019