J. Kong

Atomically precise single-crystal structures of electrically conducting 2D metal-organic frameworks

J.-H. Dou, M. Q. Arguilla, Y. Luo, J. Li, W. Zhang, L. Sun, J. L. Mancuso, L. Yang, T. Chen, L. R. Parent, G. Skorupskii, N. J. Libretto, C. Sun, M. C. Yang, P. V. Dip, E. J. Brignole, J. T. Miller, J. Kong, C. H. Hendon, J. Sun, M. Dincă
Nature Materials
Volume 20, Issue 2, Page 222-+
Published while none of the authors were employed at the CMM


Electrically conducting 2D metal-organic frameworks (MOFs) have attracted considerable interest, as their hexagonal 2D lattices mimic graphite and other 2D van der Waals stacked materials. However, understanding their intrinsic properties remains a challenge because their crystals are too small or of too poor quality for crystal structure determination. Here, we report atomically precise structures of a family of 2D pi-conjugated MOFs derived from large single crystals of sizes up to 200 mu m, allowing atomic-resolution analysis by a battery of high-resolution diffraction techniques. A designed ligand core rebalances the in-plane and out-of-plane interactions that define anisotropic crystal growth. We report two crystal structure types exhibiting analogous 2D honeycomb-like sheets but distinct packing modes and pore contents. Single-crystal electrical transport measurements distinctively demonstrate anisotropic transport normal and parallel to the pi-conjugated sheets, revealing a clear correlation between absolute conductivity and the nature of the metal cation and 2D sheet packing motif.

Two-dimensional MOFs can possess porosity and electrical conductivity but are difficult to grow as single crystals. Here, by balancing in-plane and out-of-plane interactions, single crystals of sizes up to 200 mu m are grown, allowing in-plane transport measurements and atomic-resolution analysis.

Vibrational subsystem analysis: A method for probing free energies and correlations in the harmonic limit

H. Lee Woodcock III, W. Zheng, A. Ghysels, Y. Shao, J. Kong, B.R. Brooks
Journal of Chemical Physics
129 (21), 214109


A new vibrational subsystem analysis (VSA) method is presented for coupling global motion to a local subsystem while including the inertial effects of the environment. The premise of the VSA method is a partitioning of a system into a smaller region of interest and a usually larger part referred to as environment. This method allows the investigation of local-global coupling, a more accurate estimation of vibrational free energy contribution for parts of a large system, and the elimination of the “tip effect” in elastic network model calculations. Additionally, the VSA method can be used as a probe of specific degrees of freedom that may contribute to free energy differences. The VSA approach can be employed in many ways, but it will likely be most useful for estimating activation free energies in QM/MM reaction path calculations. Four examples are presented to demonstrate the utility of this method.

Efficient Calculation of QM/MM Frequencies with the Mobile Block Hessian

A. Ghysels, H. Lee Woodcock III, J.D. Larkin, B.T. Miller, Y. Shao, J. Kong, D. Van Neck, V. Van Speybroeck, M. Waroquier, B.R. Brooks
Journal of Chemical Theory and Computation (JCTC)
7 (2), 496–514


The calculation of the analytical second derivative matrix (Hessian) is the bottleneck for vibrational analysis in QM/MM systems when an electrostatic embedding scheme is employed. Even with a small number of QM atoms in the system, the presence of MM atoms increases the computational cost dramatically: the long-range Coulomb interactions require that additional coupled perturbed self-consistent field (CPSCF) equations need to be solved for each MM atom displacement. This paper presents an extension to the Mobile Block Hessian (MBH) formalism for QM/MM calculations with blocks in the MM region and its implementation in a parallel version of the Q-Chem/CHARMM interface. MBH reduces both the CPU time and the memory requirements compared to the standard full Hessian QM/MM analysis, without the need to use a cutoff distance for the electrostatic interactions. Special attention is given to the treatment of link atoms which are usually present when the QM/MM border cuts through a covalent bond. Computational efficiency improvements are highlighted using a reduced chorismate mutase enzyme system, consisting of 24 QM atoms and 306 MM atoms, as a test example. In addition, the drug bortezomib, used for cancer treatment of myeloma, has been studied as a test case with multiple MBH block choices and both a QM and QM/MM description. The accuracy of the calculated Hessians is quantified by imposing Eckart constraints, which allows for the assessment of numerical errors in second derivative procedures. The results show that MBH within the QM/MM description not only is a computationally attractive method but also produces accurate results.

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