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Benchmark studies of non-covalent interactions

EMSL Project ID


Non-covalent interactions have manifested their importance as the dominant types of interactions that control supramolecular chemistry with applications in molecular self-assembly, folding, molecular recognition and guest-host selectivity. They are critical in maintaining the 3-dimensional structure of many biological molecules such as proteins and nucleic acids and controlling the selectivity of various guests (such as metals and energy-related compounds) when binding to molecular host scaffolds (such as MOFs, hydrate lattices and chelating agents).
A special category of non-covalent interactions is the one resulting from the stacking between aromatic rings (pi-pi stacking). These types of interactions control the structure of DNA and RNA fragments and play a role in protein folding and are the basis for template-directed synthesis, to name a few important applications. Despite numerous experimental and theoretical studies and continuing interest in the field, a unified description of the nature of those interactions and the factors that control them is still lacking.

Project Details

Start Date
End Date


Principal Investigator

Edoardo Apra
Environmental Molecular Sciences Laboratory

Team Members

Jonas Warneke
Universitat Bremen

Patrick El-Khoury
Pacific Northwest National Laboratory

Jeffrey Daily
Pacific Northwest National Laboratory

Sotiris Xantheas
Pacific Northwest National Laboratory

Alessandro Fortunelli
CNR - Consiglio Nazionale delle Ricerche

Related Publications

Agrachev M, S Antonello, T Dainese, M Ruzzi, A Zoleo, E Apra, N Govind, A Fortunelli, L Sementa, and F Maran. 2017. "Magnetic Ordering in Gold Nanoclusters." ACS Omega 2(6):2607–2617. doi:10.1021/acsomega.7b00472
Apra E., J. Warneke, S.S. Xantheas, and X. Wang. 2019. "A benchmark photoelectron spectroscopic and theoretical study of the electronic stability of [B12H12]2-." Journal of Chemical Physics 105, no. 16:164306. PNNL-SA-140650. doi:10.1063/1.5089510
Chang L., O. Baseggio, L. Sementa, D. Cheng, G. Fronzoni, D. Toffoli, and E. Apra, et al. 2018. "Individual Component Map of Rotatory Strength and Rotatory Strength Density Plots As Analysis Tools of Circular Dichroism Spectra of Complex Systems." Journal of Chemical Theory and Computation 14, no. 7:3703-3714. PNNL-SA-132925. doi:10.1021/acs.jctc.8b00250
Dass A, TC Jones, M Rambukwella, D Crasto, KJ Gagnon, M De Vetta, O Baseggio, E Apra, M Stener, and A Fortunelli. 2016. "Crystal Structure and Theoretical Analysis of Green Gold Au30(S-tBu)18 Nanomolecules and its Relation to Au30S(S-tBu)18." PNNL-SA-116252, Pacific Northwest National Laboratory, Richland, WA. [Unpublished]
Dass A, TC Jones, S Theivendran, L Sementa, and A Fortunelli. 2017. "Core Size Interconversions of Au30(S-tBu)18 and Au36(SPhX)24." Journal of Physical Chemistry C 121(27):14914–14919. doi:10.1021/acs.jpcc.7b03860
Doudin N, D Kuhness, M Blatnik, G Barcaro, FR Negreiros, L Sementa, A Fortunelli, S Surnev, and F Netzer. 2016. "Nanoscale Domain Structure and Defects in a 2-D WO3 Layer on Pd(100)." Journal of Physical Chemistry C 120(50):28682–28693. doi:10.1021/acs.jpcc.6b10504
Fortunelli A, L Sementa, V Dhanushka Thanthirige, TC Jones, M Stener, KJ Gagnon, A Dass, and G Ramakrishna. 2017. "Au21S(SAdm)15: An Anisotropic Gold Nanomolecule. Optical and Photoluminescence Spectroscopy and First-Principles Theoretical Analysis." Journal of Physical Chemistry Letters 8(2):457–462. doi:10.1021/acs.jpclett.6b02810
Jones TC, L Sementa, M Stener, KJ Gagnon, V Dhanushka Thanthirige, G Ramakrishna, A Fortunelli, and A Dass. 2017. "Au21S(SAdm)15: Crystal Structure, Mass Spectrometry, Optical Spectroscopy, and First-Principles Theoretical Analysis." Journal of Physical Chemistry C 121(20):10865–10869. doi:10.1021/acs.jpcc.6b12075
Luque-Ceballos J.C., L. Sementa, E. Apra, A. Fortunelli, and A. Posada-Amarillas. 2018. "TDDFT Study of the Optical Spectra of Free and Supported Binary Coinage Metal Hexamers: Effect of Doping and Support." The Journal of Physical Chemistry 122, no. 40:23143–23152. PNNL-SA-137797. doi:10.1021/acs.jpcc.8b06397
Mayer M., M. Rohdenburg, V. Van Lessen, M. Nierstenhfer, E. Apra, S. Grabowsky, and K.R. Asmis, et al. 2020. "First steps towards a stable neon compound: Observation and Bonding Analysis of [B12(CN)11Ne]-." Chemical Communications 56, no. 33:4591-4594. PNNL-SA-151724. doi:10.1039/D0CC01423K
Mayer M., V. Van Lessen, M. Rohdenburg, G. Hou, Z. Yang, R.M. Exner, and E. Apra, et al. 2019. "Rational design of an argon-binding superelectrophilic anion." Proceedings of the National Academy of Sciences of the United States of America 116, no. 17:8167–8172. PNNL-SA-140803. doi:10.1073/pnas.1820812116
Milan Rambukwella, Luca Sementa, Alessandro Fortunelli, and Amala Dass. 2017. "Core-Size Conversion of Au38(SCH2CH2Ph)24 to Au30(S−tBu)18 Nanomolecules" J. Phys. Chem. C 2017, 121, 14929−14935, DOI: 10.1021/acs.jpcc.7b04201Rambukwella M, L Sementa, A Fortunelli, and A Dass. 2017. "Core-Size Conversion of Au38(SCH2CH2Ph)24 to Au30(S?tBu)18 Nanomolecules." Journal of Physical Chemistry C 121(27):14929–14935. doi:10.1021/acs.jpcc.7b04201
Rambukwella M, S Burrage, M Neubrander, O Baseggio, E Apra, M Stener, A Fortunelli, and A Dass. 2017. "Au38(SPh)24: Au38 Protected with Aromatic Thiolate Ligands." The Journal of Physical Chemistry Letters 8(7):1530–1537. doi:10.1021/acs.jpclett.7b00193
Sementa L, G Barcaro, O Baseggio, M De Vetta, A Dass, E Apra, M Stener, and A Fortunelli. 2017. "Ligand-Enhanced Optical Response of Gold Nanomolecules and Its Fragment Projection Analysis: The Case of Au30(SR)18." Journal of Physical Chemistry C 121(20):10832–10842. doi:10.1021/acs.jpcc.6b12029
Theivendran S., L. Chang, A. Mukherjee, L. Sementa, M. Stener, A. Fortunelli, and A. Dass. 2018. "Principles of Optical Spectroscopy of Aromatic Alloy Nanomolecules: Au36-xAgx(SPh-tBu)24." Journal of Physical Chemistry C 122, no. 8:4524-4531. doi:10.1021/acs.jpcc.8b00556
Toffoli D., O. Baseggio, G. Fronzoni, M. Stener, A. Fortunelli, and L. Sementa. 2018. "Pd Doping, Conformational, and Charge Effects on the Dichroic Response of a Monolayer Protected Au38(SR)24 Nanocluster." Physical Chemistry Chemical Physics. PCCP 21, no. 7:3585. doi:10.1039/c8cp04107e
Warneke J, GL Hou, E Apra, C Jenne, Z Yang, Z Qin, K Kowalski, XB Wang, and SS Xantheas. 2017. "Electronic Structure and Stability of [B12X12]2- (X=F?At): A Combined Photoelectron Spectroscopic and Theoretical Study." Journal of the American Chemical Society 139:14749-14756. doi:10.1021/jacs.7b08598
Warneke J., M. Rohdenburg, J.K. Liu, E. Johnson, X. Ma, R. Kumar, and P. Su, et al. 2019. "Gas Phase Fragmentation of Adducts Between Dioxygen and closo-Borate Radical Anions." International Journal of Mass Spectrometry 436. PNNL-SA-136763. doi:10.1016/j.ijms.2018.11.005
Warneke J., S.Z. Konieczka, G. Hou, E. Apra, C. Kerpen, F. Keppner, and T.C. Schaefer, et al. 2019. "Properties of perhalogenated {closo-B10} and {closo-B11} multiply charged anions and a critical comparison with {closo-B12} in the gas and the condensed phase." Physical Chemistry Chemical Physics 21, no. 11:5903-5915. PNNL-SA-135487. doi:10.1039/C8CP05313H
Yu C, W Harbich, L Sementa, L Ghiringhelli, E Apra, M Stener, A Fortunelli, and H Brune. 2017. "Intense Fluorescence of Au20." Journal of Chemical Physics 147(7):074301. doi:10.1063/1.4996687