1
|
Petrick TL, Grünwald A, Braun DE. Flavone Cocrystals: A Comprehensive Approach Integrating Experimental and Virtual Methods. CRYSTAL GROWTH & DESIGN 2024; 24:4195-4212. [PMID: 38766642 PMCID: PMC11099919 DOI: 10.1021/acs.cgd.4c00293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/22/2024]
Abstract
The dapsone/flavone cocrystal system served as a benchmark for both experimental and virtual screening methods. Expanding beyond this, two additional active pharmaceutical ingredients (APIs), sulfanilamide and sulfaguanidine, structurally related to dapsone were chosen to investigate the impact of substituents on cocrystal formation. The experimental screening involved mechanochemical methods, slurry experiments, hot-melt extrusion, and the contact preparation method. The virtual screening focused on crystal structure prediction (CSP), molecular complementarity, hydrogen-bond propensity, and molecular electrostatic potentials. The CSP studies not only indicated that each of the three APIs should form cocrystals with flavone but also reproduced the known single- and multicomponent phases. Experimentally, dapsone/flavone cocrystals ACC, BCC, CCC, and DCC were reproduced, CCC was identified as a nonstoichiometric hydrate, and a fifth cocrystal (ECC), a t-butanol solvate, was discovered. The cocrystal polymorphs ACC and BCC are enantiotripically related, and DCC, exhibiting a different stoichiometric ratio, is enthalpically stabilized over the other cocrystals. For the sulfaguanidine/flavone system, two novel, enantiotripically related cocrystals were identified. The crystal structures of two cocrystals and a flavone polymorph were solved from powder X-ray diffraction data, and the stability of all cocrystals was assessed through differential scanning calorimetry and lattice energy calculations. Despite computational indications, a diverse array of cocrystallization techniques did not result in a sulfanilamide/flavone cocrystal. The driving force behind dapsone's tendency to cocrystallize with flavone can be attributed to the overall strength of flavone interactions in the cocrystals. For sulfaguanidine, the potential to form strong API···API and API···coformer interactions in the cocrystal is a contributing factor. Furthermore, flavone was found to be trimorphic.
Collapse
Affiliation(s)
- Tom L. Petrick
- Institute of Pharmacy, University
of Innsbruck, Innrain 52c, 6020 Innsbruck, Austria
| | - Alexandra Grünwald
- Institute of Pharmacy, University
of Innsbruck, Innrain 52c, 6020 Innsbruck, Austria
| | - Doris E. Braun
- Institute of Pharmacy, University
of Innsbruck, Innrain 52c, 6020 Innsbruck, Austria
| |
Collapse
|
2
|
Menezes F, Popowicz GM. When catchers meet - a computational study on the dimerization of the Buckycatcher. Phys Chem Chem Phys 2023; 25:24031-24041. [PMID: 37646477 DOI: 10.1039/d3cp02903d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
We study the dimerization of the buckycatcher in gas phase and in toluene. We created an extensive library of 36 different complexes, which were characterized at semi-empirical and DFT levels. Semi-empirical geometries and dimerization energies compare well against reference data or Density Functional Theory calculations we performed. Born-Oppenheimer molecular dynamics was used to understand what happens when two molecules of the buckycatcher meet, allowing us to infer on the lack of kinetic barriers when dimers form. Thermodynamically, it is possible that room temperature solutions contain dimerized buckycatcher. Using a very simple exchange model, it is shown, however, that dimerization cannot compete thermodynamically against complexation with fullerenes, which accounts for experimental observations.
Collapse
Affiliation(s)
- Filipe Menezes
- Institute of Structural Biology, Helmholtz Munich, Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany.
| | - Grzegorz Maria Popowicz
- Institute of Structural Biology, Helmholtz Munich, Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany.
| |
Collapse
|
3
|
Racher F, Petrick TL, Braun DE. Exploring the Supramolecular Interactions and Thermal Stability of Dapsone:Bipyridine Cocrystals by Combining Computational Chemistry with Experimentation. CRYSTAL GROWTH & DESIGN 2023; 23:4638-4654. [PMID: 37304396 PMCID: PMC10251420 DOI: 10.1021/acs.cgd.3c00387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/21/2023] [Indexed: 06/13/2023]
Abstract
The application of computational screening methodologies based on H-bond propensity scores, molecular complementarity, molecular electrostatic potentials, and crystal structure prediction has guided the discovery of novel cocrystals of dapsone and bipyridine (DDS:BIPY). The experimental screen, which included mechanochemical and slurry experiments as well as the contact preparation, resulted in four cocrystals, including the previously known DDS:4,4'-BIPY (2:1, CC44-B) cocrystal. To understand the factors governing the formation of the DDS:2,2'-BIPY polymorphs (1:1, CC22-A and CC22-B) and the two DDS:4,4'-BIPY cocrystal stoichiometries (1:1 and 2:1), different experimental conditions (such as the influence of solvent, grinding/stirring time, etc.) were tested and compared with the virtual screening results. The computationally generated (1:1) crystal energy landscapes had the experimental cocrystals as the lowest energy structures, although distinct cocrystal packings were observed for the similar coformers. H-bonding scores and molecular electrostatic potential maps correctly indicated cocrystallization of DDS and the BIPY isomers, with a higher likelihood for 4,4'-BIPY. The molecular conformation influenced the molecular complementarity results, predicting no cocrystallization for 2,2'-BIPY with DDS. The crystal structures of CC22-A and CC44-A were solved from powder X-ray diffraction data. All four cocrystals were fully characterized by a range of analytical techniques, including powder X-ray diffraction, infrared spectroscopy, hot-stage microscopy, thermogravimetric analysis, and differential scanning calorimetry. The two DDS:2,2'-BIPY polymorphs are enantiotropically related, with form B being the stable polymorph at room temperature (RT) and form A being the higher temperature form. Form B is metastable but kinetically stable at RT. The two DDS:4,4'-BIPY cocrystals are stable at room conditions; however, at higher temperatures, CC44-A transforms to CC44-B. The cocrystal formation enthalpy order, derived from the lattice energies, was calculated as follows: CC44-B > CC44-A > CC22-A.
Collapse
|
4
|
Menezes F, Popowicz GM. A Buckycatcher in Solution-A Computational Perspective. Molecules 2023; 28:molecules28062841. [PMID: 36985812 PMCID: PMC10056437 DOI: 10.3390/molecules28062841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/17/2023] [Accepted: 03/19/2023] [Indexed: 03/30/2023] Open
Abstract
In this work, we study the buckycatcher (C60H28) in solution using quantum chemical models. We investigate the conformational equilibria in several media and the effects that molecules of solvent might have in interconversion barriers between the different conformers. These are studied in a hypothetical gas phase, in the dielectric of a solvent, as well as with hybrid solvation. In the latter case, due to a disruption of π-stacking interactions, the transition states are destabilized. We also evaluate the complexation of the buckycatcher with solvent-like molecules. In most cases studied, there should be no adducts formed because the enthalpy driving force cannot overcome entropic penalties.
Collapse
Affiliation(s)
- Filipe Menezes
- Institute of Structural Biology, Helmholtz Zentrum Muenchen, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Grzegorz M Popowicz
- Institute of Structural Biology, Helmholtz Zentrum Muenchen, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| |
Collapse
|
5
|
Sun R, Braun DE, Casali L, Braga D, Grepioni F. Searching for Suitable Kojic Acid Coformers: From Cocrystals and Salt to Eutectics. CRYSTAL GROWTH & DESIGN 2023; 23:1874-1887. [PMID: 36879772 PMCID: PMC9983005 DOI: 10.1021/acs.cgd.2c01364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/29/2023] [Indexed: 06/18/2023]
Abstract
The possibility of obtaining cocrystals of kojic acid with organic coformers has been investigated by both computational and experimental approaches. Cocrystallization attempts have been carried out with about 50 coformers, in different stoichiometric ratios, by solution, slurry, and mechanochemical methods. Cocrystals were obtained with 3-hydroxybenzoic acid, imidazole, 4-pyridone, DABCO, and urotropine, while piperazine yielded a salt with the kojiate anion; cocrystallization with theophylline and 4-aminopyridine resulted in stoichiometric crystalline complexes that could not be described with certainty as cocrystals or salts. In the cases of panthenol, nicotinamide, urea, and salicylic acid the eutectic systems with kojic acid were investigated via differential scanning calorimetry. In all other preparations the resulting materials were constituted of a mixture of the reactants. All compounds were investigated by powder X-ray diffraction; the five cocrystals and the salt were fully characterized via single crystal X-ray diffraction. The stability of the cocrystals and the intermolecular interactions in all characterized compounds have been investigated by computational methods based on the electronic structure and pairwise energy calculations, respectively.
Collapse
Affiliation(s)
- Renren Sun
- Department
of Chemistry “G. Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, Italy
- School
of Chemical Engineering, Zhengzhou University, 450001 Zhengzou, Henan Province, The People’s
Republic of China
| | - Doris E. Braun
- Institute
of Pharmacy, University of Innsbruck, Innrain 52c, 6020 Innsbruck, Austria
| | - Lucia Casali
- Department
of Chemistry “G. Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Dario Braga
- Department
of Chemistry “G. Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Fabrizia Grepioni
- Department
of Chemistry “G. Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, Italy
| |
Collapse
|
6
|
Bloch WM, Horiuchi S, Holstein JJ, Drechsler C, Wuttke A, Hiller W, Mata RA, Clever GH. Maximized axial helicity in a Pd 2L 4 cage: inverse guest size-dependent compression and mesocate isomerism. Chem Sci 2023; 14:1524-1531. [PMID: 36794203 PMCID: PMC9906678 DOI: 10.1039/d2sc06629g] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/12/2023] [Indexed: 01/21/2023] Open
Abstract
Helicity is an archetypal structural motif of many biological systems and provides a basis for molecular recognition in DNA. Whilst artificial supramolecular hosts are often helical, the relationship between helicity and guest encapsulation is not well understood. We report a detailed study on a significantly coiled-up Pd2L4 metallohelicate with an unusually wide azimuthal angle (∼176°). Through a combination of NMR spectroscopy, single-crystal X-ray diffraction, trapped ion mobility mass spectrometry and isothermal titration calorimetry we show that the coiled-up cage exhibits extremely tight anion binding (K of up to 106 M-1) by virtue of a pronounced oblate/prolate cavity expansion, whereby the Pd-Pd separation decreases for mono-anionic guests of increasing size. Electronic structure calculations point toward strong dispersion forces contributing to these host-guest interactions. In the absence of a suitable guest, the helical cage exists in equilibrium with a well-defined mesocate isomer that possesses a distinct cavity environment afforded by a doubled Pd-Pd separation distance.
Collapse
Affiliation(s)
- Witold M. Bloch
- Department of Chemistry and Chemical Biology, TU Dortmund UniversityOtto-Hahn-Straße 644227 DortmundGermany,Institute for Nanoscale Science and Technology, College of Science and Engineering, Flinders UniversityAdelaideSouth Australia 5042Australia
| | - Shinnosuke Horiuchi
- Department of Chemistry and Chemical Biology, TU Dortmund University Otto-Hahn-Straße 6 44227 Dortmund Germany .,Division of Chemistry and Materials Science, Graduate School of Engineering, Nagasaki University Bunkyo-machi Nagasaki 852-8521 Japan
| | - Julian J. Holstein
- Department of Chemistry and Chemical Biology, TU Dortmund UniversityOtto-Hahn-Straße 644227 DortmundGermany
| | - Christoph Drechsler
- Department of Chemistry and Chemical Biology, TU Dortmund University Otto-Hahn-Straße 6 44227 Dortmund Germany
| | - Axel Wuttke
- Institute of Physical Chemistry, Georg-August University GöttingenTammannstraße 637077 GöttingenGermany
| | - Wolf Hiller
- Department of Chemistry and Chemical Biology, TU Dortmund University Otto-Hahn-Straße 6 44227 Dortmund Germany
| | - Ricardo A. Mata
- Institute of Physical Chemistry, Georg-August University GöttingenTammannstraße 637077 GöttingenGermany
| | - Guido H. Clever
- Department of Chemistry and Chemical Biology, TU Dortmund UniversityOtto-Hahn-Straße 644227 DortmundGermany
| |
Collapse
|
7
|
Menezes F, Popowicz GM. How to Catch the Ball: Fullerene Binding to the Corannulene Pincer. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123838. [PMID: 35744963 PMCID: PMC9228874 DOI: 10.3390/molecules27123838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/09/2022] [Accepted: 06/13/2022] [Indexed: 11/26/2022]
Abstract
The corannulene pincer (also known in the literature as the buckycatcher) is a fascinating system that may encapsulate, among other molecules, the C60 and C70 fullerenes. These complexes are held together by strong π-stacking interactions. Although these are quantum mechanical effects, their description by quantum chemical methods has proved very hard. We used three semi-empirical methods, PM6-D3H4X, PM6-D3H+ and GFN2-xTB, to model the interactions. Binding to fullerenes was extended to all open conformations of the buckycatcher, and with the proper choice of solvation model and partition functions, we obtained Gibbs free energies of binding that deviated by 1.0–1.5 kcal/mol from the experimental data. Adding three-body dispersion to PM6-D3H+ led to even better agreement. These results agree better with the experimental data than calculations using higher-level methods at a significantly lower fraction of the computational cost. Furthermore, the formation of adducts with C60 was studied using dynamical simulations, which helped to build a more complete picture of the behavior of the corannulene pincer with fullerenes. We also investigated the use of exchange-binding models to recover more information on this system in solution. Though the final Gibbs free energies in solution were worsened, gas-phase enthalpies and entropies better mirrored the experimental data.
Collapse
|
8
|
Badorrek J, Walter M. Computational study on noncovalent interactions between (n, n) single-walled carbon nanotubes and simple lignin model-compounds. J Comput Chem 2021; 43:340-348. [PMID: 34893979 DOI: 10.1002/jcc.26794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/18/2021] [Accepted: 11/23/2021] [Indexed: 11/10/2022]
Abstract
Composites of carbon nanotubes (CNTs) and lignin are promising and potentially cheap precursors of-to this day-expensive carbon fibers. Since the control of the CNT-lignin interface is crucial to maximize fiber performance, it is imperative to understand the fundamental noncovalent interactions between lignin and CNT. In the present study a density functional theory study is conducted to investigate the fundamental noncovalent interaction strength between metallic (n, n) single-walled CNT (SWCNT) and simple lignin model molecules. In particular, the respective adsorption energies are used to gauge the strength of interaction classes (ππ interaction, CHπ hydrogen bonding and OH-related hydrogen bonding. From the data, substituent-dependent interaction trends as well as class- and curvature-dependent interaction trends are derived. Overall, we find that most of the interaction strength trends appear to be strongly influenced by geometry: flat orientation of the test molecules relative to the (n, n) SWCNT surface and small (n, n) SWCNT curvature-that is, large diameter enhances the CHπ and ππ interactions.
Collapse
Affiliation(s)
- Jan Badorrek
- Freiburger Materialforschungszentrum, Freiburg im Breisgau, Germany
| | - Michael Walter
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), Universität Freiburg, Freiburg im Breisgau, Germany.,Cluster of Excellence livMatS @ FIT, Freiburg im Breisgau, Germany.,Fraunhofer IWM, Freiburg im Breisgau, Germany
| |
Collapse
|
9
|
Braun DE, Hald P, Kahlenberg V, Griesser UJ. Expanding the Solid Form Landscape of Bipyridines. CRYSTAL GROWTH & DESIGN 2021; 21:7201-7217. [PMID: 34867088 PMCID: PMC8640990 DOI: 10.1021/acs.cgd.1c01045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/19/2021] [Indexed: 06/13/2023]
Abstract
Two bipyridine isomers (2,2'- and 4,4'-), used as coformers and ligands in coordination chemistry, were subjected to solid form screening and crystal structure prediction. One anhydrate and a formic acid disolvate were crystallized for 2,2'-bipyridine, whereas multiple solid-state forms, anhydrate, dihydrate, and eight solvates with carboxylic acids, including a polymorphic acetic acid disolvate, were found for the 4,4'-isomer. Seven of the solvates are reported for the first time, and structural information is provided for six of the new solvates. All twelve solid-state forms were investigated comprehensively using experimental [thermal analysis, isothermal calorimetry, X-ray diffraction, gravimetric moisture (de)sorption, and IR spectroscopy] and computational approaches. Lattice and interaction energy calculations confirmed the thermodynamic driving force for disolvate formation, mediated by the absence of H-bond donor groups of the host molecules. The exposed location of the N atoms in 4,4'-bipyridine facilitates the accommodation of bigger carboxylic acids and leads to higher conformational flexibility compared to 2,2'-bipyridine. For the 4,4'-bipyridine anhydrate ↔ hydrate interconversion hardly any hysteresis and a fast transformation kinetics are observed, with the critical relative humidity being at 35% at room temperature. The computed anhydrate crystal energy landscapes have the 2,2'-bipyridine as the lowest energy structure and the 4,4'-bipyridine among the low-energy structures and suggest a different crystallization behavior of the two compounds.
Collapse
Affiliation(s)
- Doris E. Braun
- Institute
of Pharmacy, University of Innsbruck, Innrain 52c, 6020 Innsbruck, Austria
| | - Patricia Hald
- Institute
of Pharmacy, University of Innsbruck, Innrain 52c, 6020 Innsbruck, Austria
| | - Volker Kahlenberg
- Institute
of Mineralogy and Petrography, University
of Innsbruck, Innrain 52, 6020 Innsbruck, Austria
| | - Ulrich J. Griesser
- Institute
of Pharmacy, University of Innsbruck, Innrain 52c, 6020 Innsbruck, Austria
| |
Collapse
|
10
|
Abstract
A broad range of approaches to many-body dispersion are discussed, including empirical approaches with multiple fitted parameters, augmented density functional-based approaches, symmetry adapted perturbation theory, and a supermolecule approach based on coupled cluster theory. Differing definitions of "body" are considered, specifically atom-based vs molecule-based approaches.
Collapse
Affiliation(s)
- Peng Xu
- Department of Chemistry, Iowa State University, Ames, Iowa 50014, United States
| | - Melisa Alkan
- Department of Chemistry, Iowa State University, Ames, Iowa 50014, United States
| | - Mark S Gordon
- Department of Chemistry, Iowa State University, Ames, Iowa 50014, United States
| |
Collapse
|
11
|
Yamada M, Narita H, Maeda Y. A Fullerene‐Based Molecular Torsion Balance for Investigating Noncovalent Interactions at the C
60
Surface. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005888] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Michio Yamada
- Department of Chemistry Tokyo Gakugei University Nukuikitamachi 4-1-1 Koganei Tokyo 184-8501 Japan
| | - Haruna Narita
- Department of Chemistry Tokyo Gakugei University Nukuikitamachi 4-1-1 Koganei Tokyo 184-8501 Japan
| | - Yutaka Maeda
- Department of Chemistry Tokyo Gakugei University Nukuikitamachi 4-1-1 Koganei Tokyo 184-8501 Japan
| |
Collapse
|
12
|
Yamada M, Narita H, Maeda Y. A Fullerene-Based Molecular Torsion Balance for Investigating Noncovalent Interactions at the C 60 Surface. Angew Chem Int Ed Engl 2020; 59:16133-16140. [PMID: 32458522 DOI: 10.1002/anie.202005888] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Indexed: 12/12/2022]
Abstract
To investigate the nature and strength of noncovalent interactions at the fullerene surface, molecular torsion balances consisting of C60 and organic moieties connected through a biphenyl linkage were synthesized. NMR and computational studies show that the unimolecular system remains in equilibrium between well-defined folded and unfolded conformers owing to restricted rotation around the biphenyl C-C bond. The energy differences between the two conformers depend on the substituents and is ascribed to differences in the intramolecular noncovalent interactions between the organic moieties and the fullerene surface. Fullerenes favor interacting with the π-faces of benzenes bearing electron-donating substituents. The correlation between the folding free energies and corresponding Hammett constants of the substituents in the arene-containing torsion balances reflects the contributions of the electrostatic interactions and dispersion force to face-to-face arene-fullerene interactions.
Collapse
Affiliation(s)
- Michio Yamada
- Department of Chemistry, Tokyo Gakugei University, Nukuikitamachi 4-1-1, Koganei, Tokyo, 184-8501, Japan
| | - Haruna Narita
- Department of Chemistry, Tokyo Gakugei University, Nukuikitamachi 4-1-1, Koganei, Tokyo, 184-8501, Japan
| | - Yutaka Maeda
- Department of Chemistry, Tokyo Gakugei University, Nukuikitamachi 4-1-1, Koganei, Tokyo, 184-8501, Japan
| |
Collapse
|
13
|
Yang DC, Kim DY, Kim KS. Quantum Monte Carlo Study of the Water Dimer Binding Energy and Halogen-π Interactions. J Phys Chem A 2019; 123:7785-7791. [PMID: 31418568 DOI: 10.1021/acs.jpca.9b04072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Halogen-π systems are involved with competition between halogen bonding and π-interaction. Using the diffusion quantum Monte Carlo (DMC) method, we compare the interaction of benzene with diatomic halogens (X2: Cl2/Br2) with the typical hydrogen bonding in the water dimer, taking into account explicit correlations of up to three bodies. The benzene-Cl2/Br2 binding energies (13.07 ± 0.42/16.62 ± 0.02 kJ/mol) attributed to both halogen bonding and dispersion are smaller than but comparable to the typical hydrogen bonding in the water dimer binding energy (20.88 ± 0.27 kJ/mol). All of the above values are in good agreement with those from the coupled-cluster with single, double, and noniterative triple excitations (CCSD(T)) results at the complete basis set limit (benzene-Cl2/Br2: 12.78/16.17 kJ/mol; water dimer: 21.0 kJ/mol).
Collapse
Affiliation(s)
- D ChangMo Yang
- Center for Superfunctional Materials, Department of Chemistry , Ulsan National Institute of Science and Technology , Ulsan 44919 , Republic of Korea
| | - Dong Yeon Kim
- Center for Superfunctional Materials, Department of Chemistry , Ulsan National Institute of Science and Technology , Ulsan 44919 , Republic of Korea
| | - Kwang S Kim
- Center for Superfunctional Materials, Department of Chemistry , Ulsan National Institute of Science and Technology , Ulsan 44919 , Republic of Korea
| |
Collapse
|
14
|
Geatches D, Rosbottom I, Marchese Robinson RL, Byrne P, Hasnip P, Probert MIJ, Jochym D, Maloney A, Roberts KJ. Off-the-shelf DFT-DISPersion methods: Are they now “on-trend” for organic molecular crystals? J Chem Phys 2019; 151:044106. [PMID: 31370509 DOI: 10.1063/1.5108829] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Affiliation(s)
- Dawn Geatches
- Science and Technologies Facilities Council, Daresbury Laboratory, Sci-Tech Daresbury, Warrington WA4 4AD, United Kingdom
| | - Ian Rosbottom
- Centre for the Digital Design of Drug Products, School of Chemical and Process Engineering, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Richard L. Marchese Robinson
- Centre for the Digital Design of Drug Products, School of Chemical and Process Engineering, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Peter Byrne
- Department of Physics, University of York, Heslington YO10 5DD, United Kingdom
| | - Phil Hasnip
- Department of Physics, University of York, Heslington YO10 5DD, United Kingdom
| | - Matt I. J. Probert
- Department of Physics, University of York, Heslington YO10 5DD, United Kingdom
| | - Dominik Jochym
- Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 OQX, United Kingdom
| | - Andrew Maloney
- The Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, United Kingdom
| | - Kevin J. Roberts
- Centre for the Digital Design of Drug Products, School of Chemical and Process Engineering, University of Leeds, Leeds LS2 9JT, United Kingdom
| |
Collapse
|
15
|
Makuvaza JT, Kokkin DL, Loman JL, Reid SA. C-H/π and C-H-O Interactions in Concert: A Study of the Anisole-Methane Complex using Resonant Ionization and Velocity Mapped Ion Imaging. J Phys Chem A 2019; 123:2874-2880. [PMID: 30860841 DOI: 10.1021/acs.jpca.9b01020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Noncovalent forces such as hydrogen bonding, halogen bonding, π-π stacking, and C-H/π and C-H/O interactions hold the key to such chemical processes as protein folding, molecular self-assembly, and drug-substrate interactions. Invaluable insight into the nature and strength of these forces continues to come from the study of isolated molecular clusters. In this work, we report on a study of the isolated anisole-methane complex, where both C-H/π and C-H/O interactions are possible, using a combination of theory and experiments that include mass-selected two-color resonant two-photon ionization spectroscopy, two-color appearance potential (2CAP) measurements, and velocity mapped ion imaging (VMI). Using 2CAP and VMI, we derive the binding energies of the complex in ground, excited, and cation radical states. The experimental values from the two methods are in excellent agreement, and they are compared with selected theoretical values calculated using density functional theory and ab initio methods. The optimized ground-state cluster geometry, which is consistent with the experimental observations, shows methane sitting above the ring, interacting with anisole via both C-H/π and C-H/O interactions, and this dual mode of interaction is reflected in a larger ground-state binding energy as compared with the prototypical benzene-methane system.
Collapse
Affiliation(s)
- James T Makuvaza
- Department of Chemistry , Marquette University , Milwaukee , Wisconsin 53233 , United States
| | - Damian L Kokkin
- Department of Chemistry , Marquette University , Milwaukee , Wisconsin 53233 , United States
| | - John L Loman
- Department of Chemistry , Marquette University , Milwaukee , Wisconsin 53233 , United States
| | - Scott A Reid
- Department of Chemistry , Marquette University , Milwaukee , Wisconsin 53233 , United States
| |
Collapse
|
16
|
Al-Hamdani YS, Tkatchenko A. Understanding non-covalent interactions in larger molecular complexes from first principles. J Chem Phys 2019; 150:010901. [PMID: 30621423 PMCID: PMC6910608 DOI: 10.1063/1.5075487] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 12/05/2018] [Indexed: 01/02/2023] Open
Abstract
Non-covalent interactions pervade all matter and play a fundamental role in layered materials, biological systems, and large molecular complexes. Despite this, our accumulated understanding of non-covalent interactions to date has been mainly developed in the tens-of-atoms molecular regime. This falls considerably short of the scales at which we would like to understand energy trends, structural properties, and temperature dependencies in materials where non-covalent interactions have an appreciable role. However, as more reference information is obtained beyond moderately sized molecular systems, our understanding is improving and we stand to gain pertinent insights by tackling more complex systems, such as supramolecular complexes, molecular crystals, and other soft materials. In addition, accurate reference information is needed to provide the drive for extending the predictive power of more efficient workhorse methods, such as density functional approximations that also approximate van der Waals dispersion interactions. In this perspective, we discuss the first-principles approaches that have been used to obtain reference interaction energies for beyond modestly sized molecular complexes. The methods include quantum Monte Carlo, symmetry-adapted perturbation theory, non-canonical coupled cluster theory, and approaches based on the random-phase approximation. By considering the approximations that underpin each method, the most accurate theoretical references for supramolecular complexes and molecular crystals to date are ascertained. With these, we also assess a handful of widely used exchange-correlation functionals in density functional theory. The discussion culminates in a framework for putting into perspective the accuracy of high-level wavefunction-based methods and identifying future challenges.
Collapse
Affiliation(s)
- Yasmine S Al-Hamdani
- Physics and Materials Science Research Unit, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - Alexandre Tkatchenko
- Physics and Materials Science Research Unit, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
| |
Collapse
|
17
|
Jankiewicz W, Podeszwa R, Witek HA. Dispersion-Corrected DFT Struggles with Predicting Three-Body Interaction Energies. J Chem Theory Comput 2018; 14:5079-5089. [DOI: 10.1021/acs.jctc.8b00167] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Wojciech Jankiewicz
- Institute of Chemistry, University of Silesia, Szkolna 9, 41-006 Katowice, Poland
| | - Rafał Podeszwa
- Institute of Chemistry, University of Silesia, Szkolna 9, 41-006 Katowice, Poland
| | - Henryk A. Witek
- Department of Applied Chemistry, National Chiao Tung University, 1001 Ta-Hsueh Road, Hsinchu 30010, Taiwan
| |
Collapse
|
18
|
Heßelmann A. Geometry optimisations with a nonlocal density-functional theory method based on a double Hirshfeld partitioning. J Chem Phys 2018; 149:044103. [DOI: 10.1063/1.5032175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Andreas Heßelmann
- Lehrstuhl für Theoretische Chemie, Universität Erlangen-Nürnberg, Egerlandstr. 3, D-91058 Erlangen, Germany
| |
Collapse
|
19
|
Lao KU, Herbert JM. Atomic Orbital Implementation of Extended Symmetry-Adapted Perturbation Theory (XSAPT) and Benchmark Calculations for Large Supramolecular Complexes. J Chem Theory Comput 2018; 14:2955-2978. [DOI: 10.1021/acs.jctc.8b00058] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ka Un Lao
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - John M. Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| |
Collapse
|
20
|
Intermolecular dispersion energies from coupled exact-exchange Kohn-Sham excitation energies and vectors. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2018.02.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
21
|
Kowsalya PS, Bhuvanesh NSP, Neelakantan MA. Chemical Reactivity and Quantifying the Intra- and Intermolecular Interactions in Zwitterionic Compounds. ChemistrySelect 2018. [DOI: 10.1002/slct.201702730] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Perumal samy Kowsalya
- Chemistry Research Centre; National Engineering College, K.R. Nagar; Kovilpatti 628 503, Thoothukudi District, Tamil Nadu India
| | | | - Mallanpillai A. Neelakantan
- Chemistry Research Centre; National Engineering College, K.R. Nagar; Kovilpatti 628 503, Thoothukudi District, Tamil Nadu India
| |
Collapse
|
22
|
Denis PA. Theoretical characterization of supramolecular complexes formed by fullerenes and dimeric porphyrins. NEW J CHEM 2018. [DOI: 10.1039/c8nj01467a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Intramolecular stacking is very strong in dimeric porphyrins. However, in solution they are able to inhibit folding and can trap fullerenes with very high association constants. Diabatic interaction energies can be a useful approach to evaluate the strength of porphyrin/fullerene supramolecular complexes.
Collapse
Affiliation(s)
- Pablo A. Denis
- Computational Nanotechnology
- DETEMA
- Facultad de Química
- UDELAR
- CC 1157
| |
Collapse
|
23
|
Denis PA, Kramer M, Lee C, Yanney M. An effective tridental molecular clip for fullerenes. J PHYS ORG CHEM 2018. [DOI: 10.1002/poc.3727] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Pablo A. Denis
- Computational Nanotechnology, DETEMA, Facultad de Química; UDELAR; Montevideo Uruguay
| | | | - Catherine Lee
- Department of Chemistry; Hendrix College; Conway AR USA
| | | |
Collapse
|
24
|
Zhang Y, Wang W, Wang YB. The nature of the noncovalent interactions between fullerene C60 and aromatic hydrocarbons. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2017.11.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
25
|
Silva AF, Vincent MA, McDonagh JL, Popelier PLA. The Transferability of Topologically Partitioned Electron Correlation Energies in Water Clusters. Chemphyschem 2017; 18:3360-3368. [PMID: 29094804 DOI: 10.1002/cphc.201700890] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 09/21/2017] [Indexed: 11/06/2022]
Abstract
The electronic effects that govern the cohesion of water clusters are complex, demanding the inclusion of N-body, Coulomb, exchange and correlation effects. Here we present a much needed quantitative study of the effect of correlation (and hence dispersion) energy on the stabilization of water clusters. For this purpose we used a topological energy partitioning method called Interacting Quantum Atoms (IQA) to partition water clusters into topological atoms, based on a MP2/6-31G(d,p) wave function, and modified versions of GAUSSIAN09 and the Quantum Chemical Topology (QCT) program MORFI. Most of the cohesion in the water clusters provided by electron correlation comes from intramolecular energy stabilization. Hydrogen bond-related interactions tend to largely cancel each other. Electron correlation energies are transferable in almost all instances within 1 kcal mol-1 . This observed transferability is very important to the further development of the QCT force field FFLUX, especially to the future modelling of liquid water.
Collapse
Affiliation(s)
- Arnaldo F Silva
- Manchester Institute of Biotechnology (MIB), the University of Manchester, 131 Princess Street, Manchester, M1 7DN, Great Britain), Fax: (+44) 161 3064511.,School of Chemistry, the University of Manchester, Oxford Road, Manchester, M13 9PL, Great Britain
| | - Mark A Vincent
- Manchester Institute of Biotechnology (MIB), the University of Manchester, 131 Princess Street, Manchester, M1 7DN, Great Britain), Fax: (+44) 161 3064511.,School of Chemistry, the University of Manchester, Oxford Road, Manchester, M13 9PL, Great Britain
| | - James L McDonagh
- Manchester Institute of Biotechnology (MIB), the University of Manchester, 131 Princess Street, Manchester, M1 7DN, Great Britain), Fax: (+44) 161 3064511.,School of Chemistry, the University of Manchester, Oxford Road, Manchester, M13 9PL, Great Britain
| | - Paul L A Popelier
- Manchester Institute of Biotechnology (MIB), the University of Manchester, 131 Princess Street, Manchester, M1 7DN, Great Britain), Fax: (+44) 161 3064511.,School of Chemistry, the University of Manchester, Oxford Road, Manchester, M13 9PL, Great Britain
| |
Collapse
|
26
|
Dubecký M. Noncovalent Interactions by Fixed-Node Diffusion Monte Carlo: Convergence of Nodes and Energy Differences vs Gaussian Basis-Set Size. J Chem Theory Comput 2017; 13:3626-3635. [DOI: 10.1021/acs.jctc.7b00537] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matúš Dubecký
- Department of Physics, Faculty of Science, University of Ostrava, 30. dubna 22, 701
03 Ostrava, Czech Republic
- ATRI, Faculty of Materials
Science and Technology, Slovak University of Technology, Paulínska
16, 917 24 Trnava, Slovakia
| |
Collapse
|
27
|
Zhang M, Levaray N, Daniel JR, Waldron KC, Zhu X. Cholic acid dimers as invertible amphiphilic pockets: synthesis, molecular modeling, and inclusion studies. CAN J CHEM 2017. [DOI: 10.1139/cjc-2016-0621] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Two dimers of cholic acid were synthesized through simple covalent linkers. The dimers form invertible molecular pockets in media of different polarity; hydrophobic pockets are formed in water and hydrophilic pockets are formed in organic media. Fluorescence studies show that pockets formed by these dimers can serve as invertible hosts for the hydrophobic guest pyrene and the hydrophilic guest coumarin 343. The molecular pocket also enhances dissolution of the weakly soluble cresol red sodium salt in organic media. Molecular modeling was performed to better understand the host–guest complexation process of the invertible amphiphilic pockets. The calculated free energy changes indicate that the two dimers form the most stable complexes with coumarin 343 at a host to guest ratio of 2:2, whereas the host to guest ratio differs in the formation of complexes with pyrene for the two dimers. The dimer with the shorter, less flexible linker seems to form host–guest complexes that are more stable in both water and organic solvents.
Collapse
Affiliation(s)
- Meng Zhang
- Department of Chemistry, Université de Montréal, C.P. 6128, Succursale Centre-ville, Montréal, QC H3C 3J7, Canada
- Department of Chemistry, Université de Montréal, C.P. 6128, Succursale Centre-ville, Montréal, QC H3C 3J7, Canada
| | - Nicolas Levaray
- Department of Chemistry, Université de Montréal, C.P. 6128, Succursale Centre-ville, Montréal, QC H3C 3J7, Canada
- Department of Chemistry, Université de Montréal, C.P. 6128, Succursale Centre-ville, Montréal, QC H3C 3J7, Canada
| | - Josée R. Daniel
- Department of Chemistry, Université de Montréal, C.P. 6128, Succursale Centre-ville, Montréal, QC H3C 3J7, Canada
- Department of Chemistry, Université de Montréal, C.P. 6128, Succursale Centre-ville, Montréal, QC H3C 3J7, Canada
| | - Karen C. Waldron
- Department of Chemistry, Université de Montréal, C.P. 6128, Succursale Centre-ville, Montréal, QC H3C 3J7, Canada
- Department of Chemistry, Université de Montréal, C.P. 6128, Succursale Centre-ville, Montréal, QC H3C 3J7, Canada
| | - X.X. Zhu
- Department of Chemistry, Université de Montréal, C.P. 6128, Succursale Centre-ville, Montréal, QC H3C 3J7, Canada
- Department of Chemistry, Université de Montréal, C.P. 6128, Succursale Centre-ville, Montréal, QC H3C 3J7, Canada
| |
Collapse
|
28
|
Pnicogen bond interaction between PF2Y (Y = –C☰N, –N☰C) with NH3, CH3OH, H2O, and HF molecules. Struct Chem 2017. [DOI: 10.1007/s11224-017-0968-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
29
|
Dubecký M. Bias cancellation in one-determinant fixed-node diffusion Monte Carlo: Insights from fermionic occupation numbers. Phys Rev E 2017; 95:033308. [PMID: 28415179 DOI: 10.1103/physreve.95.033308] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Indexed: 06/07/2023]
Abstract
The accuracy of the fixed-node diffusion Monte Carlo (FNDMC) depends on the node location of the supplied trial state Ψ_{T}. The practical FNDMC approaches available for large systems rely on compact yet effective Ψ_{T}, most often containing an explicitly correlated single Slater determinant (SD). However, SD nodes may be better suited to one system than to another, which may possibly lead to inaccurate FNDMC energy differences. It remains a challenge how to estimate nonequivalence or appropriateness of SDs. Here we use the differences of a measure based on the Euclidean distance between the natural orbital occupation number (NOON) vector of the SD and the exact solution in the NOON vector space, which can be viewed as a measure of SD nonequivalence and as a qualitative measure of the expected degree of nondynamic-correlation-related bias in FNDMC energy differences. This is explored on a set of small noncovalent complexes and covalent bond breaking of Si_{2} vs N_{2}. It turns out that NOON-based measures well reflect the magnitude and sign of the bias present in the data available, thus providing insights into the nature of bias cancellation in SD FNDMC energy differences.
Collapse
Affiliation(s)
- Matúš Dubecký
- Department of Physics, Faculty of Science, University of Ostrava, 30. dubna 22, 701 03 Ostrava, Czech Republic and ATRI, Faculty of Materials Science and Technology, Slovak University of Technology, Paulínska 16, 917 24 Trnava, Slovakia
| |
Collapse
|
30
|
Hermann J, Alfè D, Tkatchenko A. Nanoscale π-π stacked molecules are bound by collective charge fluctuations. Nat Commun 2017; 8:14052. [PMID: 28169280 PMCID: PMC5309697 DOI: 10.1038/ncomms14052] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 11/15/2016] [Indexed: 11/24/2022] Open
Abstract
Non-covalent π−π interactions are central to chemical and biological processes, yet the full understanding of their origin that would unite the simplicity of empirical approaches with the accuracy of quantum calculations is still missing. Here we employ a quantum-mechanical Hamiltonian model for van der Waals interactions, to demonstrate that intermolecular electron correlation in large supramolecular complexes at equilibrium distances is appropriately described by collective charge fluctuations. We visualize these fluctuations and provide connections both to orbital-based approaches to electron correlation, as well as to the simple London pairwise picture. The reported binding energies of ten supramolecular complexes obtained from the quantum-mechanical fluctuation model joined with density functional calculations are within 5% of the reference energies calculated with the diffusion quantum Monte-Carlo method. Our analysis suggests that π−π stacking in supramolecular complexes can be characterized by strong contributions to the binding energy from delocalized, collective charge fluctuations—in contrast to complexes with other types of bonding. Attractive, non-covalent interactions between aromatic rings—termed π−π stacking—is common in chemistry but difficult to model. Here the authors report a quantum-mechanical model to show the importance of collective charge fluctuations for understanding pi-stacked supramolecular systems.
Collapse
Affiliation(s)
- Jan Hermann
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Dario Alfè
- Department of Earth Sciences, University College London, London WC1E 6BT, UK.,Department of Physics and Astronomy, University College London, London WC1E 6BT, UK.,London Centre for Nanotechnology and Thomas Young Centre@UCL, University College London, London WC1E 6BT, UK
| | - Alexandre Tkatchenko
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany.,Physics and Materials Science Research Unit, University of Luxembourg, 162a Avenue de la Faiencerie, Luxembourg L-1511, Luxembourg
| |
Collapse
|
31
|
Lozano A, Escribano B, Akhmatskaya E, Carrasco J. Assessment of van der Waals inclusive density functional theory methods for layered electroactive materials. Phys Chem Chem Phys 2017; 19:10133-10139. [DOI: 10.1039/c7cp00284j] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This work provides solid guidance for the selection of accurate and robust vdW-inclusive methods for high-throughput computational screening of layered electroactive materials.
Collapse
Affiliation(s)
- Ariel Lozano
- Basque Center for Applied Mathematics
- (48009) Bilbao
- Spain
- CIC Energigune
- Álava
| | | | - Elena Akhmatskaya
- Basque Center for Applied Mathematics
- (48009) Bilbao
- Spain
- IKERBASQUE
- Basque Foundation for Science
| | | |
Collapse
|
32
|
Shukla R, Saeed A, Simpson J, Chopra D. Quantitative investigation of C–H⋯π and other intermolecular interactions in a series of crystalline N-(substituted phenyl)-2-naphthamide derivatives. CrystEngComm 2017. [DOI: 10.1039/c7ce01310h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study, we have investigated the nature and characteristics of different intermolecular interactions present in a series of sevenN-(substituted phenyl)-2-naphthamides.
Collapse
Affiliation(s)
- Rahul Shukla
- Crystallography and Crystal Chemistry Laboratory
- Department of Chemistry
- IISER Bhopal
- Bhopal 462066
- India
| | - Aamer Saeed
- Department of Chemistry
- Quaid-i-Azam University-45320
- Islamabad
- Pakistan
| | - Jim Simpson
- Department of Chemistry
- University of Otago
- Dunedin 9054
- New Zealand
| | - Deepak Chopra
- Crystallography and Crystal Chemistry Laboratory
- Department of Chemistry
- IISER Bhopal
- Bhopal 462066
- India
| |
Collapse
|
33
|
Shukla R, Khan I, Ibrar A, Simpson J, Chopra D. Complex electronic interplay of σ-hole and π-hole interactions in crystals of halogen substituted 1,3,4-oxadiazol-2(3H)-thiones. CrystEngComm 2017. [DOI: 10.1039/c7ce00678k] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
|
34
|
Sure R, Grimme S. Comprehensive Benchmark of Association (Free) Energies of Realistic Host-Guest Complexes. J Chem Theory Comput 2016; 11:3785-801. [PMID: 26574460 DOI: 10.1021/acs.jctc.5b00296] [Citation(s) in RCA: 153] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The S12L test set for supramolecular Gibbs free energies of association ΔGa (Grimme, S. Chem. Eur. J. 2012, 18, 9955-9964) is extended to 30 complexes (S30L), featuring more diverse interaction motifs, anions, and higher charges (-1 up to +4) as well as larger systems with up to 200 atoms. Various typical noncovalent interactions like hydrogen and halogen bonding, π-π stacking, nonpolar dispersion, and CH-π and cation-dipolar interactions are represented by "real" complexes. The experimental Gibbs free energies of association (ΔGa exp) cover a wide range from -0.7 to -24.7 kcal mol-1. In order to obtain a theoretical best estimate for ΔGa, we test various dispersion corrected density functionals in combination with quadruple-ζ basis sets for calculating the association energies in the gas phase. Further, modern semiempirical methods are employed to obtain the thermostatistical corrections from energy to Gibbs free energy, and the COSMO-RS model with several parametrizations as well as the SMD model are used to include solvation contributions. We investigate the effect of including counterions for the charged systems (S30L-CI), which is found to overall improve the results. Our best method combination consists of PW6B95-D3 (for neutral and charged systems) or ωB97X-D3 (for systems with counterions) energies, HF-3c thermostatistical corrections, and Gibbs free energies of solvation obtained with the COSMO-RS 2012 parameters for nonpolar solvents and 2013-fine for water. This combination gives a mean absolute deviation for ΔGa of only 2.4 kcal mol-1 (S30L) and 2.1 kcal mol-1 (S30L-CI), with a mean deviation of almost zero compared to experiment. Regarding the relative Gibbs free energies of association for the 13 pairs of complexes which share the same host, the correct trend in binding affinities could be reproduced except for two cases. The MAD compared to experiment amounts to 1.2 kcal mol-1, and the MD is almost zero. The best-estimate theoretical corrections are used to back-correct the experimental ΔGa values in order to get an empirical estimate for the "experimental", zero-point vibrational energy exclusive, gas phase binding energies. These are then utilized to benchmark the performance of various "lowcost" quantum chemical methods for noncovalent interactions in large systems. The performance of other common DFT methods as well as the use of semiempirical methods for structure optimizations is discussed.
Collapse
Affiliation(s)
- Rebecca Sure
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Universität Bonn Beringstr. 4, D-53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Universität Bonn Beringstr. 4, D-53115 Bonn, Germany
| |
Collapse
|
35
|
Desgranges C, Delhommelle J. Evaluation of the grand-canonical partition function using expanded Wang-Landau simulations. IV. Performance of many-body force fields and tight-binding schemes for the fluid phases of silicon. J Chem Phys 2016; 144:124510. [PMID: 27036464 DOI: 10.1063/1.4944619] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We extend Expanded Wang-Landau (EWL) simulations beyond classical systems and develop the EWL method for systems modeled with a tight-binding Hamiltonian. We then apply the method to determine the partition function and thus all thermodynamic properties, including the Gibbs free energy and entropy, of the fluid phases of Si. We compare the results from quantum many-body (QMB) tight binding models, which explicitly calculate the overlap between the atomic orbitals of neighboring atoms, to those obtained with classical many-body (CMB) force fields, which allow to recover the tetrahedral organization in condensed phases of Si through, e.g., a repulsive 3-body term that favors the ideal tetrahedral angle. Along the vapor-liquid coexistence, between 3000 K and 6000 K, the densities for the two coexisting phases are found to vary significantly (by 5 orders of magnitude for the vapor and by up to 25% for the liquid) and to provide a stringent test of the models. Transitions from vapor to liquid are predicted to occur for chemical potentials that are 10%-15% higher for CMB models than for QMB models, and a ranking of the force fields is provided by comparing the predictions for the vapor pressure to the experimental data. QMB models also reveal the formation of a gap in the electronic density of states of the coexisting liquid at high temperatures. Subjecting Si to a nanoscopic confinement has a dramatic effect on the phase diagram with, e.g. at 6000 K, a decrease in liquid densities by about 50% for both CMB and QMB models and an increase in vapor densities between 90% (CMB) and 170% (QMB). The results presented here provide a full picture of the impact of the strategy (CMB or QMB) chosen to model many-body effects on the thermodynamic properties of the fluid phases of Si.
Collapse
Affiliation(s)
- Caroline Desgranges
- Department of Chemistry, University of North Dakota, 151 Cornell Street Stop 9024, Grand Forks, North Dakota 58202, USA
| | - Jerome Delhommelle
- Department of Chemistry, University of North Dakota, 151 Cornell Street Stop 9024, Grand Forks, North Dakota 58202, USA
| |
Collapse
|
36
|
Li MM, Wang YB, Zhang Y, Wang W. The Nature of the Noncovalent Interactions between Benzene and C60 Fullerene. J Phys Chem A 2016; 120:5766-72. [DOI: 10.1021/acs.jpca.6b06492] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ming-Ming Li
- Department
of Chemistry and Key Laboratory of Guizhou High Performance Computational
Chemistry, Guizhou University, Guiyang 550025, P.R. China
| | - Yi-Bo Wang
- Department
of Chemistry and Key Laboratory of Guizhou High Performance Computational
Chemistry, Guizhou University, Guiyang 550025, P.R. China
| | - Yu Zhang
- College
of Chemistry and Chemical Engineering and Henan Key Laboratory of
Function-Oriented Porous Materials, Luoyang Normal University, Luoyang 471934, P.R. China
| | - Weizhou Wang
- College
of Chemistry and Chemical Engineering and Henan Key Laboratory of
Function-Oriented Porous Materials, Luoyang Normal University, Luoyang 471934, P.R. China
| |
Collapse
|
37
|
Flores-Huerta AG, Tkatchenko A, Galván M. Nature of Hydrogen Bonds and S···S Interactions in the l-Cystine Crystal. J Phys Chem A 2016; 120:4223-30. [DOI: 10.1021/acs.jpca.6b03167] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anaid G. Flores-Huerta
- Departamento
de Química, Área de Fisicoquímica
Teórica, Universidad Autónoma Metropolitana-Iztapalapa, Av. San Rafael Atlixco 186, Col. Vicentina CP 09340, México, D.F., Mexico
| | - Alexandre Tkatchenko
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Marcelo Galván
- Departamento
de Química, Área de Fisicoquímica
Teórica, Universidad Autónoma Metropolitana-Iztapalapa, Av. San Rafael Atlixco 186, Col. Vicentina CP 09340, México, D.F., Mexico
| |
Collapse
|
38
|
Affiliation(s)
- Matúš Dubecký
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký University Olomouc, tř.
17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Lubos Mitas
- Department
of Physics and CHiPS, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Petr Jurečka
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký University Olomouc, tř.
17 listopadu 12, 771 46 Olomouc, Czech Republic
| |
Collapse
|
39
|
Cabaleiro-Lago EM, Rodríguez-Otero J, Gil A. Comment on "Theoretical studies on a carbonaceous molecular bearing: association thermodynamics and dual-mode rolling dynamics" by H. Isobe, K. Nakamura, S. Hitosugi, S. Sato, H. Tokoyama, H. Yamakado, K. Ohno and H. Kono, Chem. Sci., 2015, 6, 2746. Chem Sci 2016; 7:2924-2928. [PMID: 30090286 PMCID: PMC6054031 DOI: 10.1039/c5sc04676a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 02/05/2016] [Indexed: 12/03/2022] Open
Abstract
The LC-BLYP functional accompanied with proper calculations leads to unreliable results for systems governed by π···π interactions. It seems quite clear that a good representation of dispersion interactions is required, so DFT must be supplemented (through the DFT-D formalism or the many-body dispersion method) in order to afford good results.
Collapse
Affiliation(s)
- Enrique M Cabaleiro-Lago
- Departamento de Química Física , Facultad de Ciencias , Universidade de Santiago de Compostela , Campus de Lugo , Av. Alfonso X El Sabio, s/n , 27002 Lugo , Galicia , Spain .
| | - Jesús Rodríguez-Otero
- CIQUS and Facultade de Química (Departamento de Química Física) , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Galicia , Spain .
| | - Adrià Gil
- Centro de Química e Bioquímica , DQB , Faculdade de Ciências , Universidade de Lisboa , Campo Grande , 1749-016 Lisboa , Portugal
| |
Collapse
|
40
|
Abstract
Interest in molecular crystals has grown thanks to their relevance to pharmaceuticals, organic semiconductor materials, foods, and many other applications. Electronic structure methods have become an increasingly important tool for modeling molecular crystals and polymorphism. This article reviews electronic structure techniques used to model molecular crystals, including periodic density functional theory, periodic second-order Møller-Plesset perturbation theory, fragment-based electronic structure methods, and diffusion Monte Carlo. It also discusses the use of these models for predicting a variety of crystal properties that are relevant to the study of polymorphism, including lattice energies, structures, crystal structure prediction, polymorphism, phase diagrams, vibrational spectroscopies, and nuclear magnetic resonance spectroscopy. Finally, tools for analyzing crystal structures and intermolecular interactions are briefly discussed.
Collapse
Affiliation(s)
- Gregory J O Beran
- Department of Chemistry, University of California , Riverside, California 92521, United States
| |
Collapse
|
41
|
Blood-Forsythe MA, Markovich T, DiStasio RA, Car R, Aspuru-Guzik A. Analytical nuclear gradients for the range-separated many-body dispersion model of noncovalent interactions. Chem Sci 2016; 7:1712-1728. [PMID: 29899903 PMCID: PMC5964951 DOI: 10.1039/c5sc03234b] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 10/27/2015] [Indexed: 11/26/2022] Open
Abstract
An accurate treatment of the long-range electron correlation energy, including van der Waals (vdW) or dispersion interactions, is essential for describing the structure, dynamics, and function of a wide variety of systems. Among the most accurate models for including dispersion into density functional theory (DFT) is the range-separated many-body dispersion (MBD) method [A. Ambrosetti et al., J. Chem. Phys., 2014, 140, 18A508], in which the correlation energy is modeled at short-range by a semi-local density functional and at long-range by a model system of coupled quantum harmonic oscillators. In this work, we develop analytical gradients of the MBD energy with respect to nuclear coordinates, including all implicit coordinate dependencies arising from the partitioning of the charge density into Hirshfeld effective volumes. To demonstrate the efficiency and accuracy of these MBD gradients for geometry optimizations of systems with intermolecular and intramolecular interactions, we optimized conformers of the benzene dimer and isolated small peptides with aromatic side-chains. We find excellent agreement with the wavefunction theory reference geometries of these systems (at a fraction of the computational cost) and find that MBD consistently outperforms the popular TS and D3(BJ) dispersion corrections. To demonstrate the performance of the MBD model on a larger system with supramolecular interactions, we optimized the C60@C60H28 buckyball catcher host-guest complex. In our analysis, we also find that neglecting the implicit nuclear coordinate dependence arising from the charge density partitioning, as has been done in prior numerical treatments, leads to an unacceptable error in the MBD forces, with relative errors of ∼20% (on average) that can extend well beyond 100%.
Collapse
Affiliation(s)
| | - Thomas Markovich
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , MA , USA .
| | - Robert A DiStasio
- Department of Chemistry , Princeton University , Princeton , NJ , USA
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , NY , USA
| | - Roberto Car
- Department of Chemistry , Princeton University , Princeton , NJ , USA
- Princeton Institute for the Science and Technology of Materials , Princeton University , Princeton , NJ , USA
- Department of Physics , Princeton University , Princeton , NJ , USA
- Program in Applied and Computational Mathematics , Princeton University , Princeton , NJ , USA
| | - Alán Aspuru-Guzik
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , MA , USA .
| |
Collapse
|
42
|
Shukla R, Chopra D. Characterization of N⋯O non-covalent interactions involving σ-holes: “electrostatics” or “dispersion”. Phys Chem Chem Phys 2016; 18:29946-29954. [DOI: 10.1039/c6cp05899j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Exploring the possibility of formation of pnicogen bonds or chalcogen bonds by utilizing the σ-holes present on nitrogen and oxygen atoms in per-halo substituted complexes.
Collapse
Affiliation(s)
- Rahul Shukla
- Crystallography and Crystal Chemistry Laboratory
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- Bhopal-462066
- India
| | - Deepak Chopra
- Crystallography and Crystal Chemistry Laboratory
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- Bhopal-462066
- India
| |
Collapse
|
43
|
Denis PA, Yanney M. Porphyrins bearing corannulene pincers: outstanding fullerene receptors. RSC Adv 2016. [DOI: 10.1039/c6ra11482b] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Porphyrins and corannulenes join forces to trap fullerenes with unprecedented strength!
Collapse
Affiliation(s)
- Pablo A. Denis
- Computational Nanotechnology
- DETEMA
- Facultad de Química
- UDELAR
- 11800 Montevideo
| | | |
Collapse
|
44
|
Shukla R, Chopra D. “Pnicogen bonds” or “chalcogen bonds”: exploiting the effect of substitution on the formation of P⋯Se noncovalent bonds. Phys Chem Chem Phys 2016; 18:13820-9. [DOI: 10.1039/c6cp01703g] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A direct comparison of pnicogen bonds and chalcogen bonds in P⋯Se non-covalent interactions.
Collapse
Affiliation(s)
- Rahul Shukla
- Crystallography and Crystal Chemistry Laboratory Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- Bhopal 462066
- India
| | - Deepak Chopra
- Crystallography and Crystal Chemistry Laboratory Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- Bhopal 462066
- India
| |
Collapse
|
45
|
Bhimanapati GR, Lin Z, Meunier V, Jung Y, Cha J, Das S, Xiao D, Son Y, Strano MS, Cooper VR, Liang L, Louie SG, Ringe E, Zhou W, Kim SS, Naik RR, Sumpter BG, Terrones H, Xia F, Wang Y, Zhu J, Akinwande D, Alem N, Schuller JA, Schaak RE, Terrones M, Robinson JA. Recent Advances in Two-Dimensional Materials beyond Graphene. ACS NANO 2015; 9:11509-39. [PMID: 26544756 DOI: 10.1021/acsnano.5b05556] [Citation(s) in RCA: 875] [Impact Index Per Article: 97.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The isolation of graphene in 2004 from graphite was a defining moment for the "birth" of a field: two-dimensional (2D) materials. In recent years, there has been a rapidly increasing number of papers focusing on non-graphene layered materials, including transition-metal dichalcogenides (TMDs), because of the new properties and applications that emerge upon 2D confinement. Here, we review significant recent advances and important new developments in 2D materials "beyond graphene". We provide insight into the theoretical modeling and understanding of the van der Waals (vdW) forces that hold together the 2D layers in bulk solids, as well as their excitonic properties and growth morphologies. Additionally, we highlight recent breakthroughs in TMD synthesis and characterization and discuss the newest families of 2D materials, including monoelement 2D materials (i.e., silicene, phosphorene, etc.) and transition metal carbide- and carbon nitride-based MXenes. We then discuss the doping and functionalization of 2D materials beyond graphene that enable device applications, followed by advances in electronic, optoelectronic, and magnetic devices and theory. Finally, we provide perspectives on the future of 2D materials beyond graphene.
Collapse
Affiliation(s)
- Ganesh R Bhimanapati
- Department of Materials Science and Engineering, Center for Two-Dimensional and Layered Materials, Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Zhong Lin
- Department of Physics, Center for Two-Dimensional and Layered Materials, Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Vincent Meunier
- Department of Physics, Applied Physics, and Astronomy, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - Yeonwoong Jung
- Nanoscience Technology Center, Department of Materials Science and Engineering, University of Central Florida , Orlando, Florida 32826, United States
| | - Judy Cha
- Department of Mechanical Engineering and Material Science, Yale School of Engineering and Applied Sciences , New Haven, Connecticut 06520, United States
| | - Saptarshi Das
- Birck Nanotechnology Center & Department of ECE, Purdue University , West Lafayette, Indiana 47907, United States
| | - Di Xiao
- Department of Physics, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Youngwoo Son
- Department of Chemical Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Michael S Strano
- Department of Chemical Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Valentino R Cooper
- Center for Nanophase Materials Sciences and Computer Science & Mathematics Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - Liangbo Liang
- Department of Physics, Applied Physics, and Astronomy, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - Steven G Louie
- Department of Physics, University of California at Berkeley , Berkeley, California 94720, United States
- Lawrence Berkeley National Lab , Berkeley, California 94720, United States
| | - Emilie Ringe
- Department of Materials Science & Nano Engineering, Rice University , Houston, Texas 77005, United States
| | - Wu Zhou
- Center for Nanophase Materials Sciences and Computer Science & Mathematics Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - Steve S Kim
- Air Force Laboratory, Materials & Manufacturing directorate, Wright-Patterson AFB , Dayton, Ohio 45433, United States
- UES Inc. , Beavercreek, Ohio 45432, United States
| | - Rajesh R Naik
- Air Force Laboratory, Materials & Manufacturing directorate, Wright-Patterson AFB , Dayton, Ohio 45433, United States
| | - Bobby G Sumpter
- Center for Nanophase Materials Sciences and Computer Science & Mathematics Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - Humberto Terrones
- Department of Physics, Applied Physics, and Astronomy, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - Fengnian Xia
- Department of Electrical Engineering, Yale University , New Haven, Connecticut 06511, United States
| | - Yeliang Wang
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences , Beijing 100190, China
| | - Jun Zhu
- Department of Physics, Center for Two-Dimensional and Layered Materials, Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Deji Akinwande
- Microelectronics Research Centre, The University of Texas at Austin , Austin, Texas 78758, United States
| | - Nasim Alem
- Department of Materials Science and Engineering, Center for Two-Dimensional and Layered Materials, Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Jon A Schuller
- Electrical and Computer Engineering Department, University of California at Santa Barbara , Santa Barbara, California 93106, United States
| | - Raymond E Schaak
- Department of Chemistry and Materials Research Institute, Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Mauricio Terrones
- Department of Materials Science and Engineering, Center for Two-Dimensional and Layered Materials, Pennsylvania State University , University Park, Pennsylvania 16802, United States
- Department of Physics, Center for Two-Dimensional and Layered Materials, Pennsylvania State University , University Park, Pennsylvania 16802, United States
- Department of Chemistry and Materials Research Institute, Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Joshua A Robinson
- Department of Materials Science and Engineering, Center for Two-Dimensional and Layered Materials, Pennsylvania State University , University Park, Pennsylvania 16802, United States
| |
Collapse
|
46
|
Maurer RJ, Ruiz VG, Tkatchenko A. Many-body dispersion effects in the binding of adsorbates on metal surfaces. J Chem Phys 2015; 143:102808. [PMID: 26374001 DOI: 10.1063/1.4922688] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
A correct description of electronic exchange and correlation effects for molecules in contact with extended (metal) surfaces is a challenging task for first-principles modeling. In this work, we demonstrate the importance of collective van der Waals dispersion effects beyond the pairwise approximation for organic-inorganic systems on the example of atoms, molecules, and nanostructures adsorbed on metals. We use the recently developed many-body dispersion (MBD) approach in the context of density-functional theory [Tkatchenko et al., Phys. Rev. Lett. 108, 236402 (2012) and Ambrosetti et al., J. Chem. Phys. 140, 18A508 (2014)] and assess its ability to correctly describe the binding of adsorbates on metal surfaces. We briefly review the MBD method and highlight its similarities to quantum-chemical approaches to electron correlation in a quasiparticle picture. In particular, we study the binding properties of xenon, 3,4,9,10-perylene-tetracarboxylic acid, and a graphene sheet adsorbed on the Ag(111) surface. Accounting for MBD effects, we are able to describe changes in the anisotropic polarizability tensor, improve the description of adsorbate vibrations, and correctly capture the adsorbate-surface interaction screening. Comparison to other methods and experiment reveals that inclusion of MBD effects improves adsorption energies and geometries, by reducing the overbinding typically found in pairwise additive dispersion-correction approaches.
Collapse
Affiliation(s)
- Reinhard J Maurer
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Victor G Ruiz
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
| | - Alexandre Tkatchenko
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
| |
Collapse
|
47
|
Denis PA, Yanney M. Subphthalocyanines hydrogen bonded capsules featuring norbornadiene tethers: Promising fullerene receptors. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.10.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
48
|
Desgranges C, Delhommelle J. Many-Body Effects on the Thermodynamics of Fluids, Mixtures, and Nanoconfined Fluids. J Chem Theory Comput 2015; 11:5401-14. [DOI: 10.1021/acs.jctc.5b00693] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Caroline Desgranges
- Department of Chemistry, University of North Dakota, Grand Forks, North Dakota 58202, United States
| | - Jerome Delhommelle
- Department of Chemistry, University of North Dakota, Grand Forks, North Dakota 58202, United States
| |
Collapse
|
49
|
Cazorla C. The role of density functional theory methods in the prediction of nanostructured gas-adsorbent materials. Coord Chem Rev 2015. [DOI: 10.1016/j.ccr.2015.05.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
50
|
Otero-de-la-Roza A, Johnson ER. Predicting Energetics of Supramolecular Systems Using the XDM Dispersion Model. J Chem Theory Comput 2015; 11:4033-40. [DOI: 10.1021/acs.jctc.5b00044] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- A. Otero-de-la-Roza
- National
Institute for Nanotechnology, National Research Council of Canada, 11421
Saskatchewan Drive, Edmonton, Alberta, Canada T6G 2M9
| | - Erin R. Johnson
- Department
of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, Nova Scotia, Canada B3H 4R2
| |
Collapse
|