Ensemble Calculations of Structural Trajectories: Coupling Molecular Dynamics Simulation in Data Analysis

Solar energy conversion functions often depend on dynamic structures in so­lution or on a supporting matrix where a transiently appearing dynamic structure could evolve into a precursor for catalytic intermediates. Such dy­namic structures are implicitly depicted by the Debye-Weller factor in the conventional XAS data analysis in Equation (12.1), without specific description of the structural origin. In many homogeneous photochemical reactions, metal complexes interact with solvent molecules to form transient dynamic solvated structures, such as dynamic bonding between the catalyst molecule and the solvent or substrate molecules. These dynamic structures may well be the precursor or transition states in catalytic reactions, but were unfortunately obscured in the conventional data analysis.

Molecular dynamics (MD) simulation for many years has been used as a ‘‘partner’’ in analyzing XAFS data for studying the atomic radial distribution function of materials without long range order.166,167 Unfortunately XAFS is not sensitive enough to the bond angles and thus the MD-XAFS combination is not capable of extracting the full three-dimensional (3D) molecular structure, even though bond angles are very important for gaining deep insight into the ‘‘structure-function’’ relationship of catalytic systems. XANES analysis using a MIA or MXAN scheme has proven to be sensitive enough to extract full 3D local structural parameters around active metal centers in complex sys – tems.44,168 Recently, MD simulations were applied in advanced XANES an­alysis of the 3D local atomic structure of a metal ion in water169,170 using the XANES analysis program MXAN.45,46 However, the full molecular potential XANES simulation (i. e. simulations beyond muffin-tin approximation171) used were computationally very expensive, limiting the calculations to a small number of atoms surrounding the metal ion. Hence, a more effective approach is needed to deal with the relatively large number of atoms in multi-metallic catalytic metal complexes for solar energy conversion.

12.2 Summary

Advances in third generation synchrotron sources for XTA over the past decade have significantly enhanced our understanding of photon-matter interactions and the structural origins of photochemical properties of excited state molecules relevant to photoinduced homogeneous and heterogeneous electron and energy transfer processes. As the technique develops, higher quality data and better theoretical modeling are crucial in advancing XTA to become a common method for solving transient structures along excited state trajectories during photochemical processes involving multiple temporal and spatial scales. Emerging ultrafast X-ray sources with pulse durations compar­able to ultrafast lasers open new opportunities to study molecular structural dynamics in real time with atomic resolution during fundamental chemical events, such as bond breaking. Making molecular movies is no longer a fantasy, but a reality. Therefore, we expect many future breakthroughs in solving mo­lecular and electronic reorganization during solar energy conversion, which will provide guidance for the design of efficient catalysts for solar fuel generation and materials for efficient photovoltaic generation of electricity.


The experimental work was funded by the Division of Chemical Sciences, Geosciences and Biosciences, Office of Basic Energy Sciences of the US Department of Energy through Grant DE-AC02-06CH11357. The authors would like to thank Drs. Klaus Attenkofer, Guy Jennings and Xiaoyi Zhang from the Advanced Photon Source for their long term collaboration and postdoctoral research associates and students who have contributed to the development of XTA method and samples, and Drs. Wighard Jager, Tao Liu, George B. Shaw, Erik C. Wasinger, Jenny V. Lockard, Andrew B. Stickrath, Michael R. Harpham, Jier Huang, Mr. Michael W. Mara, Ms. Nosheen Gothard and Megan Shelby. The author is thankful for collaboration with colleagues at Argonne, Drs. David J. Gosztola, Jan Hessler, Di-Jia Liu, David M. Tiede and the Solar Energy Conversion (Photosynthesis) Group. Dr. Grigory Smolentsev and Prof. Alexander Soldatov have collaborated in implementing MIA into XTA data analyses. LXC is grateful for collaboration with Profs. Gerald J. Meyer, Jonathan S. Lindsey, Michael D. Hopkins, Michael R. Wasielewski, F. Castellano, Jean-Pierre Sauvage, Fraser Stoddart, M. Benfatto, S. Della Longa and Daniel G. Nocera and their groups in various institutions. The long term support from the Sector 11 & 12 staff at the Advanced Photon Source has been invaluable to the work presented here. Use of the Advanced Photon Source was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. DE-AC02-06CH11357. The author would like to acknowledge the assistance received from Brian Roczynski, Michael Mara and Michael Harpham in proof reading the manuscript.

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Updated: August 18, 2015 — 3:33 pm