Bulletin of the American Physical Society
APS March Meeting 2020
Volume 65, Number 1
Monday–Friday, March 2–6, 2020; Denver, Colorado
Session G44: Van Der Waals Interactions in Molecules, Materials, and Complex Environments IIFocus
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Sponsoring Units: DCOMP Chair: Robert Distasio, Cornell University Room: 704 |
Tuesday, March 3, 2020 11:15AM - 11:51AM |
G44.00001: The Role of Correlation Effects in Non-Valence Anions Invited Speaker: Kenneth Jordan Non-valence anions are especially challenging for traditional electronic structure methods due to the need to use very large basis sets and to include high-order electron correlation effects. The most widely studied class of non-valence anions are dipole-bound anions for which the excess electron binds in the Hartree-Fock approximation provided a sufficiently flexible basis set is used. Even more challenging are non-valence correlation bound (NVCB) anions for which the excess electron does not bind in the absence of dispersion-like correlation effects between the excess electron and the electrons of the molecule or cluster. In my talk, ab initio and model Hamiltonian approaches for characterizing correlation effects in dipole-bound and NVCB anions will be analyzed. Although those anions have very extended charge distributions, we find that the dominant correlation contributions to the electron binding energies are shorter-range in nature than is generally believed. |
Tuesday, March 3, 2020 11:51AM - 12:03PM |
G44.00002: Attracting Opposites: Promiscuous Ion-π Binding in the DNA Nucleobases Brian Ernst, Ka Un Lao, Andrew G. Sullivan, Robert Distasio Ion-π interactions between the face of a molecular π-system and a cation or anion are among the strongest non-covalent interactions known, with applications throughout biochemistry and structural biology, host-guest chemistry, as well as enzyme kinetics and organocatalysis. In this work, we perform a detailed theoretical case study of ion-π interactions in the DNA/RNA nucleobases by first demonstrating that these π-systems are promiscuous ion-π binders with the versatility to bind both cations (Li+/Na+) and anions (F-/Cl-). Using a novel SAPT-based energy decomposition analysis, we uncover the different physicochemical driving forces underlying the formation of cation- and anion-π complexes, as well as the crucial role played by charge penetration effects in anion-π systems. In doing so, a unified view of these rather distinct non-covalent binding motifs emerges with the finding that both cation- and anion-π complexes are strongly stabilized by an essentially ring-independent potential that can only be overcome by substantially unfavorable electrostatics. Interestingly, the analysis presented herein demonstrates that π-systems have an inherent propensity to bind both cations and anions, thereby implying that promiscuous ion-π binding should be quite common in nature. |
Tuesday, March 3, 2020 12:03PM - 12:15PM |
G44.00003: NENCI-2020: A Large Benchmark Non-Equilibrium Non-Covalent Interaction Database with Emphasis on the Repulsive Wall Zachary Sparrow, Brian Ernst, Paul Joo, Ka Un Lao, Robert Distasio In this work, we present NENCI-2020: a benchmark database of non-equilibrium non-covalent interaction energies for a large and diverse set of intermolecular complexes. NENCI-2020 contains ~8,000 interaction energies computed with CCSD(T)/CBS, and includes 7 non-equilibrium intermolecular distances (spanning 0.7-1.1x the equilibrium separation) and 8 non-equilibrium angles (per distance) for ~150 complexes. Using SAPT2+, we demonstrate that NENCI-2020 contains a diverse array of intermolecular binding motifs, making this database well suited for testing and developing next-generation force fields, density functional theory (DFT) approximations, quantum chemical (QC) methods, and machine-learning based approaches. This is followed by a critical assessment of ~75 dispersion/van der Waals-corrected DFT and QC methods, in which we find that most approaches can describe interaction energies for equilibrium and farther-than-equilibrium configurations with chemical accuracy (i.e., to within 1 kcal/mol). More importantly, we find that nearly all methods suffer from a rapid and systematic increase in error as the intermolecular distances become small, thereby suggesting that more work will be needed to describe intermolecular potential energy surfaces with uniform accuracy. |
Tuesday, March 3, 2020 12:15PM - 12:27PM |
G44.00004: Ab initio evaluation of complexation energies for cyclodextrin–drug inclusion complexes Kenji Oqmhula, Kenta Hongo, Ryo Maezono, Tom Ichibha Within the framework of density functional theory (DFT), an appropriate incorporation of van der Waals (vdW) into the exchange correlation (XC) functional is important to accurately predict complexation energies of noncovalent systems. This point has not been widely verified in large host-drug systems. Here we benchmarked various DFT to evaluate complexation energies of host-guest complexes, three types of β-cyclodextrins and plumbagin (known as anti-cancer drug). We modeled these systems as follows: (1) DFT geometry optimization of individual guest and hosts, (2) their docking conformation search based on genetic algorithm with semi-empirical simulations, and (3) DFT geometry optimization of the docking system. Then single-point energy calculations were performed to evaluate complexation energies. Furthermore, we applied DMC (diffuse Monte Carlo) to validate the DFT results. We found M06-2X-D3 and CAM-B3LYP-D3 give almost the same energies for all the cases and they are both consistent with DMC within the error bar. From these results, we concluded that a proper incorporation of vdW and long-range exchange corrections into XC functionals is essential for describing the cyclodextrin-plumbagin systems. |
Tuesday, March 3, 2020 12:27PM - 12:39PM |
G44.00005: Many-body dispersion effects and plasmonic correlations in the catalytic synchronization of a DNA-enzyme complex Matteo Gori, Martin Stoehr, Alexandre Tkatchenko, Philip Kurian Long-range van der Waals dispersion forces could play a significant role in explaining the action of certain restriction enzymes inducing DNA double-strand breaks [J. Theor. Biol. 2016, 391, 102-112]. In particular, dipolar interactions among spatially separated nucleotides and enzymatic molecular subunits may be responsible for long-range synchronization of quantum electronic density fluctuations. Zero-point modes of such plasmon-like oscillations may promote double-strand breakage, in lieu of external chemical energy from ATP. Our analysis of Many-Body Dispersion (MBD) effects in the catalytic behavior of EcoRI, a sequence-specific DNA-targeting enzyme used widely in genomic science, offers clues for more refined investigations of the collective electron fluctuations (plasmon) in complex (bio)molecular systems [Chem. Soc. Rev. 2019, 48, 4118]. We present analysis of these MBD eigenmodes applied to EcoRI at different steps along the catalytic trajectory, including entropic measures of the degree of collectivity of each mode (i.e., its vectorial distribution in the atomic site basis) and other quantum information metrics, to understand the delocalization properties in Hilbert space and their implications for distant “plasmonic allostery” in 3+1-dimensional physical space. |
Tuesday, March 3, 2020 12:39PM - 12:51PM |
G44.00006: Inversion Symmetry Breaking Probed by X-ray Absorption Spectroscopy in H-bonded Organic Ferroelectric Crystal Fujie Tang, Xuanyuan Jiang, Hsin-Yu Ko, Jianhang Xu, Mehmet Topsakal, Guanhua Hao, Alpha T. N'Diaye, Peter A Dowben, Deyu Lu, Xiaoshan Xu, Xifan Wu Molecular ferroelectrics (FE) based on ordering hydrogen bonds have potentially high electric polarization and ordering temperature compared with the conventional oxide FE materials. In particular, croconic acid (C5O5H2) with FE polarization of 30 μC/cm2, plays a prototype of ferroelectric organic molecular solid, whose electric polarization is generated by proton transfer. We carry out X-ray absorption spectroscopy experiment at oxygen K-edge in croconic acid crystal. The experimental spectrum is well reproduced by the electron-hole excitation theory simulations from configuration generated by ab initio molecular dynamics simulation. When inversion symmetry is broken in ferroelectric state, the hydrogen bonding environment on the two bonded molecules become inequivalent. Such a difference is sensitively probed by the bound excitation in the pre-edge, which are strongly localized on the excited molecules. Our analysis shows that a satellite peak in the pre-edge will emerge at higher excitation energy which serves as a clear signature of ferroelectricity in the material. |
Tuesday, March 3, 2020 12:51PM - 1:03PM |
G44.00007: van der Waals Phonons in Molecular Crystals Somayeh Khazaei, Alexandre Tkatchenko Low-frequency terahertz (THz) vibrations are ubiquitous in molecular materials throughout chemistry and biology [e.g. PRL 113, 055701; PRL 119, 097404]. Such delocalized vibrations play a key role in many phenomena, including entropic stabilization of molecular crystal polymorphs, protein folding, and signaling. However, our understanding of mechanisms behind THz vibrations in molecular materials is far from complete. Here we study a range of molecular crystals with DFT including many-body treatment of van der Waals (vdW) dispersion interactions (DFT+MBD). We find that THz vibrations are very sensitive to the correct treatment of electrostatic effects in DFT and explicit quantum-mechanical treatment of vdW interactions. We discuss a way to categorize vibrational modes in the THz range and show that these vibrations are crucial to achieve a better understanding of molecular materials. |
Tuesday, March 3, 2020 1:03PM - 1:15PM |
G44.00008: First-principles studies of small molecule absorption kinetics in diamine-appended metal-organic frameworks Alex Smith, Jeffrey B Neaton Recently, a family of diamine-appended metal-organic frameworks (MOFs) has demonstrated selective and tunable adsorption via novel reversible non-Langmuir stepped isotherms, making them promising for carbon capture applications. Here, we use first principles van der Waals-corrected density functional theory calculations, as well as molecular dynamics and computations of NMR chemical shifts, to understand the structure, kinetics, and selectivity associated with the stepped isotherms in environments relevant to flue gas conditions. We compare binding energies with experiments, and predict intermediate and final structures to understand the measured isotherms. We focus on the role that SO2, a component of flue gas, plays in degrading MOF CO2 adsorption through studying SO2 binding energies and how SO2 disrupts the kinetics of CO2 adsorption. This work is supported by DOE, and computational resources are provided by NERSC. |
Tuesday, March 3, 2020 1:15PM - 1:27PM |
G44.00009: Long-range Correlation Energy in the Interaction of Molecules with Surfaces Alina Umerbekova, Michele Pavanello
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Tuesday, March 3, 2020 1:27PM - 1:39PM |
G44.00010: Reproducibility of Molecular Adsorption Potential Energy Surfaces Lukas Hörmann, Andreas Jeindl, Oliver T. Hofmann The adsorption of molecules on surfaces depends on a variety of mechanisms: Covalent bonds, charge transfer and van-der-Waals (vdW) interactions shape the potential energy surface (PES), making it key to understanding molecule-substrate interfaces. To describe these interfaces with density functional theory, one can choose from many different exchange correlation functionals and vdW correction schemes. To explore how robust the PES is in relation to the choice of method, we present a benchmark of common local, semi-local and non-local functionals in combination with various vdW corrections for perylenetetracarboxylic dianhydride (PTCDA) on Ag(111), one of the most frequently studied system. |
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