Tracing potential energy surfaces of electronic excitations via their transition origins: application to Oxirane

We show that the transition origins of electronic excitations identified by quantified natural transition orbital (QNTO) analysis can be employed to connect potential energy surfaces (PESs) according to their character across a widerange of molecular geometries. This is achieved by locating the switching of transition origins of adiabatic potential surfaces as the geometry changes. The transition vectors for analysing transition origins are provided by linear response time-dependent density functional theory (TDDFT) calculations under the Tamm-Dancoff approximation. We study the photochemical CO ring opening of oxirane as an example and show that the results corroborate the traditional Gomer-Noyes mechanism derived experimentally. The knowledge of specific states for the reaction also agrees well with that given by previous theoretical work using TDDFT surface-hopping dynamics that was validated by high-quality quantum Monte Carlo calculations. We also show that QNTO can be useful for considerably larger and more complex systems: by projecting the excitations to those of a reference oxirane molecule, the approach is able to identify and analyse specific excitations of a trans-2,3-diphenyloxirane molecule.Comment: 14 pages, 12 figure

Photophysics and photochemistry of DNA molecules : electronic excited states leading to thymine dimerization

We combine quantified natural transition orbital (QNTO) analysis with large-scale linear response time-dependent DFT (TDDFT) to investigate the concerted [2 + 2] thymine dimerisation reaction. This reaction is a main cause of UV-light induced damage to DNA, but its mechanism has remained poorly understood. QNTO analysis enables the electronic excitations of a molecule to be identified on the basis of their transition origins across a wide range of molecular geometries, allowing the participating excited states to be identified relatively straightforwardly. We identify a barrierless funnel that is responsible for the ultrafast reaction previously indicated in experiments. The reactive state is found to have crossings with several bright excited states, revealing how the initially populated bright states can decay rapidly to the reactive state. We also examine the contribution of environmental factors such as inclusion of the DNA backbone, which can affect the conformation of the potential energy surfaces of the relevant states

Input files and raw data for publication publication "First-principles treatment of solvent effects on electronic excitations in alizarin"

This file was created by Tim J. Zuehlsdorff on the 15th of October 2015. It contains all input files necessary to reproduce the results of the publication "First-principles treatment of solvent effects on electronic excitations in alizarin". The data in this file is organised as follows. The folders alizarin_frame1 to alizarin_frame5 contain the input files associated with the MD snapshots that are referred to as frame 1 to frame 5 in the publication. The subfolders labelled NWChem contain the NWChem input files for the vacuum, the implicit solvent and the 4 angstrom calculation. All ONETEP input files are labelled with a .dat file label. Note that the ONETEP calculations making use of implicit solvation were all performed in several stages. First a calculation in vacuum and open BC was performed. Then the resulting density was used to define a cavitiy for the dielectric medium felt by the system and a ground state, conduction optimisation and LR_TDDFT calculation was perfomed sequentially. Please refer to the user manuals on the ONETEP website (www.onetep.org) for further details regarding how to perform these calculations. For frame 1, frame 3 and frame 5, the atoms in the 8ang, 10ang and 12ang .dat files are labelled in such a way that waters to within 7 ang are denoted with a H1 and O1 label, while in the 6 ang .dat file, waters within the 4 ang region are denoted in the same way. This labelling enables the performance of TDDFT calculaions using a truncated density matrix in order to reproduce Fig. 5 (please again refer to the manuals on the ONETEP website for further details). The frame5 folder contains 2 additional files where atoms beyond the 7ang and 4ang region are replaced by cassical charges. These files can be used to obtain the black data points in the lower part of figure 5. The folder raw_data/ contains all the raw data used to generate the plots in this work. The NWChem calculations performed in this work were carried out unsing version 6.3, while all ONETEP calculations were performed using version 4.1.12.7This work was supported by the EPSRC [grant numbers EP/J017639/1 and EP/J015059/1] and the ARCHER eCSE programme

Input data for ONETEP calculations in "Linear-scaling time-dependent density-functional theory beyond the Tamm-Dancoff approximation: obtaining efficiency and accuracy with in situ optimised local orbitals"

The file contains all input files used to generate the data in the publication "Linear-scaling time-dependent density-functional theory beyond the Tamm-Dancoff approximation: obtaining efficiency and accuracy with in situ optimised local orbitals" submitted to the Journal of Chemical Physics (JCP). The folder azobenzene/ contains input data necessary to reproduce Fig. 1 and Table 1. The folder bacteriochlorophyll/ contains data necessary to reproduce Fig. 2, Fig. 3, Fig 4 and Fig. 5. The folder linear_scaling_test contains data necessary to reproduce Fig. 6 and Fig 7. Furthermore, the folder bacteriochlorophyll/ also contains the raw excitation energy and oscillator strength data necessary to generate Fig. 4 and Fig 5. All calculations were performed using ONETEP Version 4.1.12.7This work was supported by the EPSRC [grant numbers EP/J017639/1, EP/J015059/1 ] and the ARCHER eCSE programme

Taming the 3rd order cumulant

Produced data set, and Python code used to produce the GBOM scan outlined within the text

Opening the Density-Functional Theory Black Box: a Collection of Pedagogic Jupyter Notebooks

Density-Functional Theory (DFT) is indubitably the most popular and among the most successful approaches for approximately solving the many-electron Schrödinger equation. The level of understanding on the part of both researchers and students using DFT, however, is lacking given the availability of black box software. The present work addresses this knowledge gap by providing three Jupyter notebooks, easily accessible through the Google Colaboratory (GitHub repository: https://github.com/tjz21/DFT_PIB_Code), that provide a short skirmish with the fundamentals of DFT through a particle in a box-type model system. These notebooks were tested in conjunction with a problem worksheet in a graduate-level quantum chemistry course; pre- and post-activity survey results reveal largely positive reactions to this implementation and sustained enthusiasm for the subject

The Effect of Ions on the Optical Absorption Spectra of Aqueously Solvated Chromophores

In the condensed phase, ions often create heterogeneous local environments around a solute, which may impart chemical reactivity or perturbations to physico-chemical properties. Although the former has been the subject of some study, the latter - particularly as is pertains to optical absorption spectroscopy - is much less understood. In this work, the computed UV-Vis absorption spectrum is examined for the aqueously solvated chromophore anion of green fluorescent protein for different local ion configurations. The strong ability of water to screen the ions from the chromophore results in little change in excitation energy compared to a purely aqueous environment. However, upon forming a contact ion pair with a sodium ion at either of the two electronegative oxygen sites of the chromophore, there is a spectral shift to either higher or lower energies. Surprisingly, our analysis suggests that the cause of the spectral shift is dominated not by the electrostatic presence of the ion, but instead by ion disruption of the hydrogen bond network at the oxygen contact ion pair site