1. ABOUT THE DATASET -------------------- Title: First Principles Modelling of Organic-Inorganic Interfaces in Renal Calculi Creator(s): Rhiannon Morris [1] Organisation(s): 1. University of Leeds. Rights-holder(s):Unless otherwise stated, Copyright 2023 University of Leeds Publication Year: 2023 Description: This dataset holds video files which show the trajectories of AIMD simulations. Or alternatively, 3D representations in a rotating image of geometry optimisations. Cite as: Rhiannon Morris (2023): PhD Thesis Video Files. [Dataset]. https://doi.org/10.5518/1385 Related publication: Contact: fsrwm@leeds.ac.uk 2. TERMS OF USE --------------- [A standard copyright notice and licence statement with URL can be used, e.g. Copyright [publication year] [University of Leeds, name of other rights-holder(s)]. Unless otherwise stated, this dataset is licensed under a Creative Commons Attribution 4.0 International Licence: https://creativecommons.org/licenses/by/4.0/.] 3. PROJECT AND FUNDING INFORMATION ---------------------------------- Title: First Principles Modelling of Organic-Inorganic Interfaces in Renal Calculi Dates: Oct 2019- March 2023 Funding organisation: EPSRC and School of Food Science and Nutrition Grant no.: [Include in this section acknowledgements of all relevant funding sources, including e.g. public and charitable funders, industrial sponsors, and the University. If the dataset was not generated as part of a specific project or with dedicated project funding, you can say e.g. 'This dataset was not created in the course of a funded project.'] 4. CONTENTS ----------- File listing Video trajectories for Chapter 7 and 8 are in directory Chapter 7 and Chapter 8. Fig 7.20 PC adsorbing onto COD (110) Surface-AIMD Fig 7.21- Lowest energy binding configuration of PC head group to COD (110) surface - 12.483ps Fig 7.22 Bonding of i. Adsorbate free surface. ii. PC on COD (110) surface at 6 ps Fig 7.23- GO of PC on COD (110) surface at 6 ps showing RMSD values over 0.6 Å in green.mov Fig 7.26 AIMD of CaOx adsorbed on PC bound COD (110) surface Fig 7.27- Geometry optimisation of CaOx on PC bound COD (110) surface at 10.9365ps Fig 7.28- GO of CaOx on PC bound COD (110) surface at 10.9365 ps showing RMSD values over 0.6 Å Fig 7.29- PC sandwiched between layers of COD (110) surface at 12 ps showing RMSD values over 0.6 Å Fig 7.30- AIMD of PC in between two COD (110) surfaces Fig 7.31- COD 110 surface with PC sandwiched between layers at 10 ps Fig 8.2- Kcitrate adsorbing onto COD (110) surface AIMD trajectory to 14 ps Fig 8.3- GO of Kcitrate on COD (110) surface at 13.662 ps Fig 8.4- RMSD of Kcitrate adsorbed onto COD (110) Fig 8.6- Caox adsorbing onto Kcitrate bound COD (110) surface AIMD to 15ps Fig 8.8 CaOx on Kcitrate bound COD (110) surface at 12 ps Fig 8.11- AIMD timeline of KCitrate between two COD (110) surfaces -8 ps.zip Fig 8.13 Kcitrate agglomerating COD (110) surfaces - 6ps Fig 8.14- A close-up of the lowest potential energy structure from the AIMD - 7.4425 ps Fig 8.16- AIMD of lysine and CaOx cluster with 12 waters Fig 8.18 i. Clusters of 1 CaOx and lysine Fig 8.18 ii. Cluster of 2 CaOx and lysine Fig 8.18 iii. Cluster of 4 CaOx and lysine Fig 8.19 Clusters of 6 CaOx and lysine Fig 8.19 ii. Cluster of 6 CaOx and 12 H2O and lysine 5. METHODS ---------- AIMD simulations were carried out using the DFT plane-wave code CASTEP[1], using the on-the-fly pseudopotentials and a plane wave basis set with a cut off energy of 390 eV. The Perdew-Burke-Ernzerhof functional with the generalised gradient approximation (PBE-GGA) [2] was used to describe the exchange-correlation. The TS dispersion correction [3] was employed to maintain consistency and allow for comparison between geometry optimisations and dynamics results. Simulations were carried out by minimising the total energy using a conjugated gradient algorithm within 10−2 eV. Visualisation of the trajectories were carried out in OVITO [4]. 6. REFERENCES -------------- [1] S. J. Clark, M. D. Segall, C. J. Pickard, P. J. Hasnip, M. I. Probert, K. Refson and M. C. Payne, Zeitschrift für Kristallographie, 2005, 220, 567–570. [2] J. P. Perdew, K. Burke and M. Ernzerhof, Physical Review Letters, 1996, 77, 3865. [3] A. Tkatchenko and M. Scheffler, Physical Review Letters, 2009, 102, 073005. [4] A.StukowskiandK.Albe,ModellingandSimulationinMaterialsScienceandEngineering, 2010, 18, 085001.