Center for Molecular Modeling - J. Kong

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

leen — Thu, 19 May 2022 12:37:45 +0000

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-+

2021

Published while none of the authors were employed at the CMM

Abstract

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.

DOI

http://dx.doi.org/10.1038/s41563-020-00847-7

Private attachment

s41563-020-00847-7.pdf

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

wim — Mon, 03 Oct 2011 09:58:51 +0000

H. Lee Woodcock III, W. Zheng, A. Ghysels, Y. Shao, J. Kong, B.R. Brooks

Journal of Chemical Physics

129 (21), 214109

2008

Abstract

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.

DOI

http://dx.doi.org/10.1063/1.3013558

Private attachment

08 j. chem. phys. 129(21)214109 woodcock.pdf

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

wim — Tue, 23 Aug 2011 07:07:28 +0000

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

2011

Abstract

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.

DOI

http://dx.doi.org/10.1021/ct100473f

Private attachment

11 j chem theory comp 7, 496 ghysels.pdf

The evaluation of the QM/MM full Hessian and some applications

wim — Mon, 17 Oct 2011 09:54:02 +0000

H. Lee Woodcock III, A. Ghysels, Y. Shao, J. Kong, B.R. Brooks

Talk

Conference / event / venue

238th ACS National Meeting

Washington DC

Sunday, 16 August, 2009 to Thursday, 20 August, 2009

Abstract

2009 abstract ACS_AnGhysels.pdf

Efficient calculation of QM/MM frequencies with the Mobile Block Hessian method

wim — Mon, 17 Oct 2011 08:30:55 +0000

A. Ghysels, H. Lee Woodcock III, Y. Shao, J. Kong, B.R. Brooks, D. Van Neck, V. Van Speybroeck, M. Waroquier

Talk

Conference / event / venue

North American Meeting on Industrial and Applied Mathematics (NAMIAM)

Huatulco, Mexico

Monday, 6 December, 2010 to Saturday, 11 December, 2010

Abstract

2010 efficient calculation NAMIAM.pdf