scholarly journals Electronic excitations in molecular solids: bridging theory and experiment

2015 ◽  
Vol 177 ◽  
pp. 181-202 ◽  
Author(s):  
Jonathan M. Skelton ◽  
E. Lora da Silva ◽  
Rachel Crespo-Otero ◽  
Lauren E. Hatcher ◽  
Paul R. Raithby ◽  
...  
Keyword(s):  
Quantum Chemical ◽  
Molecular Crystals ◽  
Spectroscopic Properties ◽  
Implicit Solvent ◽  
Test Case ◽  
Electronic Excitations ◽  
Solvent Models ◽  
Chemical Techniques ◽  
High Level ◽  
Molecular Calculations

As the spatial and temporal resolution accessible to experiment and theory converge, computational chemistry is an increasingly powerful tool for modelling and interpreting spectroscopic data. However, the study of molecular processes, in particular those related to electronic excitations (e.g. photochemistry), frequently pushes quantum-chemical techniques to their limit. The disparity in the level of theory accessible to periodic and molecular calculations presents a significant challenge when modelling molecular crystals, since accurate calculations require a high level of theory to describe the molecular species, but must also take into account the influence of the crystalline environment on their properties. In this article, we briefly review the different classes of quantum-chemical techniques, and present an overview of methods that account for environmental influences with varying levels of approximation. Using a combination of solid-state and molecular calculations, we quantitatively evaluate the performance of implicit-solvent models for the [Ni(Et4dien)(η2-O,ON)(η1-NO2)] linkage-isomer system as a test case. We focus particularly on the accurate reproduction of the energetics of the isomerisation, and on predicting spectroscopic properties to compare with experimental results. This work illustrates how the synergy between periodic and molecular calculations can be exploited for the study of molecular crystals, and forms a basis for the investigation of more challenging phenomena, such as excited-state dynamics, and for further methodological developments.

scholarly journals The validation of quantum chemical lipophilicity prediction of alcohols

2016 ◽  
Vol 9 (2) ◽  
pp. 89-94 ◽  
Author(s):  
Martin Michalík ◽  
Vladimír Lukeš
Keyword(s):  
Linear Correlation ◽  
Quantum Chemical ◽  
Partition Coefficients ◽  
The Other ◽  
Basis Set ◽  
Implicit Solvent ◽  
Solvent Models ◽  
Lipophilicity Prediction ◽  
Triple Zeta ◽  
Implicit Solvent Models

AbstractThe validation of octanol-water partition coefficients (logP) quantum chemical calculations is presented for 27 alkane alcohols. The chemical accuracy of predicted logPvalues was estimated for six DFT functionals (B3LYP, PBE0, M06-2X, ωB97X-D, B97-D3, M11) and three implicit solvent models. Triple-zeta basis set 6-311++G(d,p) was employed. The best linear correlation with the experimental logPvalues was achieved for the B3LYP and B97-D3 functionals combined with the SMD model. On the other hand, no linearity was found when IEF-PCM or C-PCM implicit models were employed.

scholarly journals Evaluation of Docking Target Functions by the Comprehensive Investigation of Protein-Ligand Energy Minima

2015 ◽  
Vol 2015 ◽  
pp. 1-12 ◽  
Author(s):  
Igor V. Oferkin ◽  
Ekaterina V. Katkova ◽  
Alexey V. Sulimov ◽  
Danil C. Kutov ◽  
Sergey I. Sobolev ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Force Field ◽  
Quantum Chemical ◽  
Target Function ◽  
Binding Energies ◽  
Low Energy ◽  
Implicit Solvent ◽  
Energy Calculation ◽  
Solvent Models ◽  
Docking Program

The adequate choice of the docking target function impacts the accuracy of the ligand positioning as well as the accuracy of the protein-ligand binding energy calculation. To evaluate a docking target function we compared positions of its minima with the experimentally known pose of the ligand in the protein active site. We evaluated five docking target functions based on either the MMFF94 force field or the PM7 quantum-chemical method with or without implicit solvent models: PCM, COSMO, and SGB. Each function was tested on the same set of 16 protein-ligand complexes. For exhaustive low-energy minima search the novel MPI parallelized docking program FLM and large supercomputer resources were used. Protein-ligand binding energies calculated using low-energy minima were compared with experimental values. It was demonstrated that the docking target function on the base of the MMFF94 force field in vacuo can be used for discovery of native or near native ligand positions by finding the low-energy local minima spectrum of the target function. The importance of solute-solvent interaction for the correct ligand positioning is demonstrated. It is shown that docking accuracy can be improved by replacement of the MMFF94 force field by the new semiempirical quantum-chemical PM7 method.

scholarly journals Constant chemical potential approach for quantum chemical calculations in electrocatalysis

2014 ◽  
Vol 5 ◽  
pp. 668-676 ◽  
Author(s):  
Wolfgang B Schneider ◽  
Alexander A Auer
Keyword(s):  
Density Functional Theory ◽  
Quantum Chemical ◽  
Density Functional ◽  
Chemical Potential ◽  
Computational Effort ◽  
Electrochemical Potential ◽  
Implicit Solvent ◽  
Functional Theory ◽  
Solvent Models ◽  
Canonical Approach

In order to simulate electrochemical reactions in the framework of quantum chemical methods, density functional theory, methods can be devised that explicitly include the electrochemical potential. In this work we discuss a Grand Canonical approach in the framework of density functional theory in which fractional numbers of electrons are used to represent an open system in contact with an electrode at a given electrochemical potential. The computational shortcomings and the additional effort in such calculations are discussed. An ansatz for a SCF procedure is presented, which can be applied routinely and only marginally increases the computational effort of standard constant electron number approaches. In combination with the common implicit solvent models this scheme can become a powerful tool, especially for the investigation of omnipresent non-faradaic effects in electrochemistry.

scholarly journals Thermodynamic Cyclic Voltammograms: Peak Positions and Shapes

2021 ◽  
Author(s):  
Nicolas G Hörmann ◽  
Karsten Reuter
Keyword(s):  
Background Electrolyte ◽  
Mean Field ◽  
Potential Drop ◽  
Implicit Solvent ◽  
Test Case ◽  
Cyclic Voltammograms ◽  
Experimental Conditions ◽  
Full Generality ◽  
Coverage Dependence ◽  
Solvent Models

Based on a mean-field description of thermodynamic cyclic voltammograms (CVs), we analyse here in full generality, how CV peak positions and shapes are related to the underlying interface energetics, in particular when also including electrostatic double layer (DL) effects. We show in particular, how non-Nernstian behaviour is related to capacitive DL charging, and how this relates to common adsorbate-centered interpretations such as a changed adsorption energetics due to dipole-field interactions and the electrosorption valency -- the number of exchanged electrons upon electrosorption per adsorbate. Using Ag(111) in halide-containing solutions as test case, we demonstrate that DL effects can introduce peak shifts that are already explained by rationalizing the interaction of isolated adsorbates with the interfacial fields, while alterations of the peak shape are mainly driven by the coverage-dependence of the adsorbate dipoles. In addition, we analyse in detail how changing the experimental conditions such as the ion concentrations in the solvent but also of the background electrolyte can affect the CV peaks via their impact on the potential drop in the DL and the DL capacitance, respectively. These results suggest new routes to analyse experimental CVs and use of those for a detailed assessment of the accuracy of atomistic models of electrified interfaces e.g. with and without explicitly treated interfacial solvent and/or approximate implicit solvent models.

Crossover from hydrogen to chemical bonding

Science ◽  
2021 ◽  
Vol 371 (6525) ◽  
pp. 160-164 ◽  
Author(s):  
Bogdan Dereka ◽  
Qi Yu ◽  
Nicholas H. C. Lewis ◽  
William B. Carpenter ◽  
Joel M. Bowman ◽  
...  
Keyword(s):  
Chemical Bonding ◽  
Quantum Chemical ◽  
Spectroscopic Properties ◽  
Experimental Methods ◽  
Strongly Coupled ◽  
Donor Acceptor ◽  
Bond Bending ◽  
High Level ◽  
Two Dimensional Infrared Spectroscopy ◽  
Covalent Chemical Bond

Hydrogen bonds (H-bonds) can be interpreted as a classical electrostatic interaction or as a covalent chemical bond if the interaction is strong enough. As a result, short strong H-bonds exist at an intersection between qualitatively different bonding descriptions, with few experimental methods to understand this dichotomy. The [F-H-F]− ion represents a bare short H-bond, whose distinctive vibrational potential in water is revealed with femtosecond two-dimensional infrared spectroscopy. It shows the superharmonic behavior of the proton motion, which is strongly coupled to the donor-acceptor stretching and disappears on H-bond bending. In combination with high-level quantum-chemical calculations, we demonstrate a distinct crossover in spectroscopic properties from conventional to short strong H-bonds, which identify where hydrogen bonding ends and chemical bonding begins.

scholarly journals Thermodynamic Cyclic Voltammograms: Peak Positions and Shapes

2021 ◽  
Author(s):  
Nicolas G Hörmann ◽  
Karsten Reuter
Keyword(s):  
Background Electrolyte ◽  
Mean Field ◽  
Potential Drop ◽  
Implicit Solvent ◽  
Test Case ◽  
Cyclic Voltammograms ◽  
Experimental Conditions ◽  
Full Generality ◽  
Coverage Dependence ◽  
Solvent Models

Based on a mean-field description of thermodynamic cyclic voltammograms (CVs), we analyse here in full generality, how CV peak positions and shapes are related to the underlying interface energetics, in particular when also including electrostatic double layer (DL) effects. We show in particular, how non-Nernstian behaviour is related to capacitive DL charging, and how this relates to common adsorbate-centered interpretations such as a changed adsorption energetics due to dipole-field interactions and the electrosorption valency -- the number of exchanged electrons upon electrosorption per adsorbate. Using Ag(111) in halide-containing solutions as test case, we demonstrate that DL effects can introduce peak shifts that are already explained by rationalizing the interaction of isolated adsorbates with the interfacial fields, while alterations of the peak shape are mainly driven by the coverage-dependence of the adsorbate dipoles. In addition, we analyse in detail how changing the experimental conditions such as the ion concentrations in the solvent but also of the background electrolyte can affect the CV peaks via their impact on the potential drop in the DL and the DL capacitance, respectively. These results suggest new routes to analyse experimental CVs and use of those for a detailed assessment of the accuracy of atomistic models of electrified interfaces e.g. with and without explicitly treated interfacial solvent and/or approximate implicit solvent models.

Sign in / Sign up

Export Citation Format

Share Document