1
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Al-Hamdani YS, Zen A, Alfè D. Unraveling H2 chemisorption and physisorption on metal decorated graphene using quantum Monte Carlo. J Chem Phys 2023; 159:204708. [PMID: 38018756 DOI: 10.1063/5.0174232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/24/2023] [Indexed: 11/30/2023] Open
Abstract
Molecular hydrogen has the potential to significantly reduce the use of carbon dioxide emitting energy processes. However, hydrogen gas storage is a major bottleneck for its large-scale use as current storage methods are energy intensive. Among different storage methods, physisorbing molecular hydrogen at ambient pressure and temperatures is a promising alternative-particularly in light of the advancements in tunable lightweight nanomaterials and high throughput screening methods. Nonetheless, understanding hydrogen adsorption in well-defined nanomaterials remains experimentally challenging and reference information is scarce despite the proliferation of works predicting hydrogen adsorption. We focus on Li, Na, Ca, and K, decorated graphene sheets as substrates for molecular hydrogen adsorption, and compute the most accurate adsorption energies available to date using quantum diffusion Monte Carlo (DMC). Building on our previous insights at the density functional theory (DFT) level, we find that a weak covalent chemisorption of molecular hydrogen, known as Kubas interaction, is feasible on Ca decorated graphene according to DMC, in agreement with DFT. This finding is in contrast to previous DMC predictions of the 4H2/Ca+ gas cluster (without graphene) where chemisorption is not favored. However, we find that the adsorption energy of hydrogen on metal decorated graphene according to a widely used DFT method is not fully consistent with DMC. The reference adsorption energies reported herein can be used to find better work-horse methods for application in large-scale modeling of hydrogen adsorption. Furthermore, the implications of this work affect strategies for finding suitable hydrogen storage materials and high-throughput methods.
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Affiliation(s)
- Yasmine S Al-Hamdani
- Department of Earth Sciences, University College London, London WC1E 6BT, United Kingdom
- Thomas Young Centre, University College London, London WC1E 6BT, United Kingdom
- London Centre for Nanotechnology, University College London, London WC1E 6BT, United Kingdom
| | - Andrea Zen
- Department of Earth Sciences, University College London, London WC1E 6BT, United Kingdom
- Dipartimento di Fisica Ettore Pancini, Università di Napoli Federico II, Monte S. Angelo, I-80126 Napoli, Italy
| | - Dario Alfè
- Department of Earth Sciences, University College London, London WC1E 6BT, United Kingdom
- Thomas Young Centre, University College London, London WC1E 6BT, United Kingdom
- London Centre for Nanotechnology, University College London, London WC1E 6BT, United Kingdom
- Dipartimento di Fisica Ettore Pancini, Università di Napoli Federico II, Monte S. Angelo, I-80126 Napoli, Italy
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2
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Zen A, Grüneis A, Alfè D, Rossi M. Beyond GGA total energies for solids and surfaces. J Chem Phys 2022; 157:050401. [PMID: 35933211 DOI: 10.1063/5.0107716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Andrea Zen
- Dipartimento di Fisica Ettore Pancini, Università di Napoli Federico II, Monte S. Angelo, I-80126 Napoli, Italy
| | - Andreas Grüneis
- Institute for Theoretical Physics, Vienna University of Technology (TU Wien), Wiedner Hauptstraße 8-10/136, A-1040 Vienna, Austria
| | - Dario Alfè
- Dipartimento di Fisica Ettore Pancini, Università di Napoli Federico II, Monte S. Angelo, I-80126 Napoli, Italy
| | - Mariana Rossi
- MPI for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
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3
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Wan S, Bhati AP, Wade AD, Alfè D, Coveney PV. Thermodynamic and structural insights into the repurposing of drugs that bind to SARS-CoV-2 main protease. Mol Syst Des Eng 2022; 7:123-131. [PMID: 35223088 PMCID: PMC8820189 DOI: 10.1039/d1me00124h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 11/15/2021] [Indexed: 06/14/2023]
Abstract
Although researchers have been working tirelessly since the COVID-19 outbreak, so far only three drugs - remdesivir, ronapreve and molnupiravir - have been approved for use in some countries which directly target the SARS-CoV-2 virus. Given the slow pace and substantial costs of new drug discovery and development, together with the urgency of the matter, repurposing of existing drugs for the ongoing disease is an attractive proposition. In a recent study, a high-throughput X-ray crystallographic screen was performed for a selection of drugs which have been approved or are in clinical trials. Thirty-seven compounds have been identified from drug libraries all of which bind to the SARS-CoV-2 main protease (3CLpro). In the current study, we use molecular dynamics simulation and an ensemble-based free energy approach, namely, enhanced sampling of molecular dynamics with approximation of continuum solvent (ESMACS), to investigate a subset of the aforementioned compounds. The drugs studied here are highly diverse, interacting with different binding sites and/or subsites of 3CLpro. The predicted free energies are compared with experimental results wherever they are available and they are found to be in excellent agreement. Our study also provides detailed energetic insights into the nature of the associated drug-protein binding, in turn shedding light on the design and discovery of potential drugs.
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Affiliation(s)
- Shunzhou Wan
- Centre for Computational Science, Department of Chemistry, University College London UK
| | - Agastya P Bhati
- Centre for Computational Science, Department of Chemistry, University College London UK
| | - Alexander D Wade
- Centre for Computational Science, Department of Chemistry, University College London UK
| | - Dario Alfè
- Department of Earth Sciences, London Centre for Nanotechnology and Thomas Young Centre at University College London, University College London UK
- Dipartimento di Fisica Ettore Pancini, Università di Napoli Federico II Italy
| | - Peter V Coveney
- Centre for Computational Science, Department of Chemistry, University College London UK
- Institute for Informatics, Faculty of Science, University of Amsterdam The Netherlands
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4
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Barbosa N, Pagliai M, Sinha S, Barone V, Alfè D, Brancato G. Enhancing the Accuracy of Ab Initio Molecular Dynamics by Fine Tuning of Effective Two-Body Interactions: Acetonitrile as a Test Case. J Phys Chem A 2021; 125:10475-10484. [PMID: 34843249 DOI: 10.1021/acs.jpca.1c07576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Grimme's dispersion-corrected density functional theory (DFT-D) methods have emerged among the most practical approaches to perform accurate quantum mechanical calculations on molecular systems ranging from small clusters to microscopic and mesoscopic samples, i.e., including hundreds or thousands of molecules. Moreover, DFT-D functionals can be easily integrated into popular ab initio molecular dynamics (MD) software packages to carry out first-principles condensed-phase simulations at an affordable computational cost. Here, starting from the well-established D3 version of the dispersion-correction term, we present a simple protocol to improve the accurate description of the intermolecular interactions of molecular clusters of growing size, considering acetonitrile as a test case. Optimization of the interaction energy was performed with reference to diffusion quantum Monte Carlo calculations, successfully reaching the same inherent accuracy of the latter (statistical error of ∼0.1 kcal/mol per molecule). The refined DFT-D3 model was then used to perform ab initio MD simulations of liquid acetonitrile, again showing significant improvements toward available experimental data with respect to the default correction.
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Affiliation(s)
- Nuno Barbosa
- Scuola Normale Superiore and CSGI, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Marco Pagliai
- Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Sourab Sinha
- Scuola Normale Superiore and CSGI, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore and CSGI, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
| | - Dario Alfè
- Department of Earth Sciences, Thomas Young Center, University College London, 5 Gower Place, WC1E 6BS London, United Kingdom.,London Centre for Nanotechnology, Thomas Young Centre, University College London, 17-19 Gordon Street, WC1H 0AH London, United Kingdom.,Dipartimento di Fisica Ettore Pancini, Università di Napoli Federico II, Monte S. Angelo, 80126 Napoli, Italy
| | - Giuseppe Brancato
- Scuola Normale Superiore and CSGI, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
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5
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Bhati AP, Wan S, Alfè D, Clyde AR, Bode M, Tan L, Titov M, Merzky A, Turilli M, Jha S, Highfield RR, Rocchia W, Scafuri N, Succi S, Kranzlmüller D, Mathias G, Wifling D, Donon Y, Di Meglio A, Vallecorsa S, Ma H, Trifan A, Ramanathan A, Brettin T, Partin A, Xia F, Duan X, Stevens R, Coveney PV. Pandemic drugs at pandemic speed: infrastructure for accelerating COVID-19 drug discovery with hybrid machine learning- and physics-based simulations on high-performance computers. Interface Focus 2021; 11:20210018. [PMID: 34956592 PMCID: PMC8504892 DOI: 10.1098/rsfs.2021.0018] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2021] [Indexed: 12/13/2022] Open
Abstract
The race to meet the challenges of the global pandemic has served as a reminder that the existing drug discovery process is expensive, inefficient and slow. There is a major bottleneck screening the vast number of potential small molecules to shortlist lead compounds for antiviral drug development. New opportunities to accelerate drug discovery lie at the interface between machine learning methods, in this case, developed for linear accelerators, and physics-based methods. The two in silico methods, each have their own advantages and limitations which, interestingly, complement each other. Here, we present an innovative infrastructural development that combines both approaches to accelerate drug discovery. The scale of the potential resulting workflow is such that it is dependent on supercomputing to achieve extremely high throughput. We have demonstrated the viability of this workflow for the study of inhibitors for four COVID-19 target proteins and our ability to perform the required large-scale calculations to identify lead antiviral compounds through repurposing on a variety of supercomputers.
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Affiliation(s)
- Agastya P. Bhati
- Centre for Computational Science, University College London, Gordon Street, London WC1H 0AJ, UK
| | - Shunzhou Wan
- Centre for Computational Science, University College London, Gordon Street, London WC1H 0AJ, UK
| | - Dario Alfè
- Department of Earth Sciences, London Centre for Nanotechnology and Thomas Young Centre at University College London, University College London, Gower Street, London WC1E 6BT, UK
- Dipartimento di Fisica Ettore Pancini, Università di Napoli Federico II, Monte Sant'Angelo, Napoli 80126, Italy
| | - Austin R. Clyde
- Department of Computer Science, University of Chicago, Chicago, IL, USA
| | - Mathis Bode
- Institute for Combustion Technology, RWTH Aachen University, Aachen 52056, Germany
| | - Li Tan
- Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Mikhail Titov
- Department of Electrical and Computer Engineering, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Andre Merzky
- Department of Electrical and Computer Engineering, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Matteo Turilli
- Department of Electrical and Computer Engineering, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Shantenu Jha
- Brookhaven National Laboratory, Upton, NY 11973, USA
- Department of Electrical and Computer Engineering, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | | | - Walter Rocchia
- Concept Lab, Italian Institute of Technology, Via Melen, Genova, Italy
| | - Nicola Scafuri
- Concept Lab, Italian Institute of Technology, Via Melen, Genova, Italy
| | - Sauro Succi
- Center for Life Nanosciences at La Sapienza, Italian Institute of Technology, viale Regina Elena, Roma, Italy
| | - Dieter Kranzlmüller
- Leibniz Supercomputing Centre (LRZ) of the Bavarian Academy of Sciences and Humanities, Boltzmannstrasse 1, Garching bei München 85748, Germany
| | - Gerald Mathias
- Leibniz Supercomputing Centre (LRZ) of the Bavarian Academy of Sciences and Humanities, Boltzmannstrasse 1, Garching bei München 85748, Germany
| | - David Wifling
- Leibniz Supercomputing Centre (LRZ) of the Bavarian Academy of Sciences and Humanities, Boltzmannstrasse 1, Garching bei München 85748, Germany
| | | | | | | | - Heng Ma
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Anda Trifan
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Arvind Ramanathan
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Tom Brettin
- Computing, Environment and Life Sciences Directorate, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Alexander Partin
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Fangfang Xia
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Xiaotan Duan
- Department of Computer Science, University of Chicago, Chicago, IL, USA
| | - Rick Stevens
- Computing, Environment and Life Sciences Directorate, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Peter V. Coveney
- Centre for Computational Science, University College London, Gordon Street, London WC1H 0AJ, UK
- Institute for Informatics, University of Amsterdam, Science Park 904, Amsterdam 1098 XH, The Netherlands
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6
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Curcio D, Sierda E, Pozzo M, Bignardi L, Sbuelz L, Lacovig P, Lizzit S, Alfè D, Baraldi A. Unusual reversibility in molecular break-up of PAHs: the case of pentacene dehydrogenation on Ir(111). Chem Sci 2021; 12:170-178. [PMID: 34168740 PMCID: PMC8179676 DOI: 10.1039/d0sc03734f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In this work, we characterise the adsorption of pentacene molecules on Ir(111) and their dissociation behaviour as a function of temperature.
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Affiliation(s)
- Davide Curcio
- Department of Physics, University of Trieste, Via Valerio 2, 34127 Trieste, Italy
| | - Emil Sierda
- Department of Physics, University of Hamburg, Jungiusstrasse 11, D-20355 Hamburg, Germany
- Institute of Physics, Poznan University of Technology, Piotrowo 3, 60-965 Poznan, Poland
| | - Monica Pozzo
- Department of Earth Sciences, Thomas Young Center, University College London, 5 Gower Place, London WC1E 6BS, UK
- London Centre for Nanotechnology, Thomas Young Centre, University College London, 17-19 Gordon Street, London WC1H 0AH, UK
| | - Luca Bignardi
- Department of Physics, University of Trieste, Via Valerio 2, 34127 Trieste, Italy
| | - Luca Sbuelz
- Department of Physics, University of Trieste, Via Valerio 2, 34127 Trieste, Italy
| | - Paolo Lacovig
- Elettra-Sincrotrone Trieste S.C.p.A., Strada Statale 14 - km 163.5 in AREA Science Park, 34149 Trieste, Italy
| | - Silvano Lizzit
- Elettra-Sincrotrone Trieste S.C.p.A., Strada Statale 14 - km 163.5 in AREA Science Park, 34149 Trieste, Italy
| | - Dario Alfè
- Department of Earth Sciences, Thomas Young Center, University College London, 5 Gower Place, London WC1E 6BS, UK
- London Centre for Nanotechnology, Thomas Young Centre, University College London, 17-19 Gordon Street, London WC1H 0AH, UK
- Dipartimento di Fisica “Ettore Pancini”, Università di Napoli “Federico II”, Monte S. Angelo, 80126 Napoli, Italy
| | - Alessandro Baraldi
- Department of Physics, University of Trieste, Via Valerio 2, 34127 Trieste, Italy
- Elettra-Sincrotrone Trieste S.C.p.A., Strada Statale 14 - km 163.5 in AREA Science Park, 34149 Trieste, Italy
- IOM-CNR, Laboratorio TASC, Strada Statale 14 - km 163.5 in AREA Science Park, 34149 Trieste, Italy
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7
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Curcio D, Sierda E, Pozzo M, Bignardi L, Sbuelz L, Lacovig P, Lizzit S, Alfè D, Baraldi A. Correction: Unusual reversibility in molecular break-up of PAHs: the case of pentacene dehydrogenation on Ir(111). Chem Sci 2021; 12:813. [PMID: 35381994 PMCID: PMC8905537 DOI: 10.1039/d0sc90287j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 12/21/2020] [Indexed: 11/28/2022] Open
Abstract
Correction for ‘Unusual reversibility in molecular break-up of PAHs: the case of pentacene dehydrogenation on Ir(111)’ by Davide Curcio et al., Chem. Sci., 2021, DOI: 10.1039/d0sc03734f.
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Affiliation(s)
- Davide Curcio
- Department of Physics, University of Trieste, Via Valerio 2, 34127 Trieste, Italy
| | - Emil Sierda
- Department of Physics, University of Hamburg, Jungiusstrasse 11, D-20355 Hamburg, Germany
- Institute of Physics, Poznan University of Technology, Piotrowo 3, 60-965 Poznan, Poland
| | - Monica Pozzo
- Department of Earth Sciences, Thomas Young Center, University College London, 5 Gower Place, London WC1E 6BS, UK
- London Centre for Nanotechnology, Thomas Young Centre, University College London, 17-19 Gordon Street, London WC1H 0AH, UK
| | - Luca Bignardi
- Department of Physics, University of Trieste, Via Valerio 2, 34127 Trieste, Italy
| | - Luca Sbuelz
- Department of Physics, University of Trieste, Via Valerio 2, 34127 Trieste, Italy
| | - Paolo Lacovig
- Elettra-Sincrotrone Trieste S.C.p.A., Strada Statale 14 – km 163.5 in AREA Science Park, 34149 Trieste, Italy
| | - Silvano Lizzit
- Elettra-Sincrotrone Trieste S.C.p.A., Strada Statale 14 – km 163.5 in AREA Science Park, 34149 Trieste, Italy
| | - Dario Alfè
- Department of Earth Sciences, Thomas Young Center, University College London, 5 Gower Place, London WC1E 6BS, UK
- London Centre for Nanotechnology, Thomas Young Centre, University College London, 17-19 Gordon Street, London WC1H 0AH, UK
- Dipartimento di Fisica “Ettore Pancini”, Università di Napoli “Federico II”, Monte S. Angelo, 80126 Napoli, Italy
| | - Alessandro Baraldi
- Department of Physics, University of Trieste, Via Valerio 2, 34127 Trieste, Italy
- Elettra-Sincrotrone Trieste S.C.p.A., Strada Statale 14 – km 163.5 in AREA Science Park, 34149 Trieste, Italy
- IOM-CNR, Laboratorio TASC, Strada Statale 14 – km 163.5 in AREA Science Park, 34149 Trieste, Italy
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8
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Pourovskii LV, Mravlje J, Pozzo M, Alfè D. Electronic correlations and transport in iron at Earth's core conditions. Nat Commun 2020; 11:4105. [PMID: 32796852 PMCID: PMC7429499 DOI: 10.1038/s41467-020-18003-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 07/21/2020] [Indexed: 11/20/2022] Open
Abstract
The transport properties of iron under Earth’s inner core conditions are essential input for the geophysical modelling but are poorly constrained experimentally. Here we show that the thermal and electrical conductivity of iron at those conditions remains high even if the electron-electron-scattering (EES) is properly taken into account. This result is obtained by ab initio simulations taking into account consistently both thermal disorder and electronic correlations. Thermal disorder suppresses the non-Fermi-liquid behavior of the body-centered cubic iron phase, hence, reducing the EES; the total calculated thermal conductivity of this phase is 220 Wm−1 K−1 with the EES reduction not exceeding 20%. The EES and electron-lattice scattering are intertwined resulting in breaking of the Matthiessen’s rule with increasing EES. In the hexagonal close-packed iron the EES is also not increased by thermal disorder and remains weak. Our main finding thus holds for the both likely iron phases in the inner core. The heat and electrical conductivity of Earth’s core matter represent key input quantities for geophysical models of the Earth’s core evolution and geodynamo. Here, the authors show how the scattering due to interactions between electrons has a relatively weak impact on the electrical and thermal conductivities of iron at core conditions.
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Affiliation(s)
- L V Pourovskii
- CPHT, CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, Route de Saclay, 91128, Palaiseau, France. .,Collège de France, 11 place Marcelin Berthelot, 75005, Paris, France.
| | - J Mravlje
- Jozef Stefan Institute, SI-1000, Ljubljana, Slovenia
| | - M Pozzo
- Department of Earth Sciences and London Centre for Nanotechnology, University College London, Gower Street, London, WC1E 6BT, UK
| | - D Alfè
- Department of Earth Sciences and London Centre for Nanotechnology, University College London, Gower Street, London, WC1E 6BT, UK.,Dipartimento di Fisica Ettore Pancini, Università di Napoli Federico II, Monte S. Angelo, I-80126, Napoli, Italy
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9
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Brandenburg JG, Zen A, Alfè D, Michaelides A. Interaction between water and carbon nanostructures: How good are current density functional approximations? J Chem Phys 2019; 151:164702. [DOI: 10.1063/1.5121370] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Jan Gerit Brandenburg
- Interdisciplinary Center for Scientific Computing, University of Heidelberg, Im Neuenheimer Feld 205A, 69120 Heidelberg, Germany
| | - Andrea Zen
- Department of Earth Sciences, University College London, Gower Street, London WC1E 6BT, United Kingdom
- Thomas Young Centre and London Centre for Nanotechnology, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
| | - Dario Alfè
- Department of Earth Sciences, University College London, Gower Street, London WC1E 6BT, United Kingdom
- Thomas Young Centre and London Centre for Nanotechnology, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
- Dipartimento di Fisica Ettore Pancini, Università di Napoli Federico II, Monte S. Angelo, I-80126 Napoli, Italy
| | - Angelos Michaelides
- Thomas Young Centre and London Centre for Nanotechnology, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
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10
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Presel F, Gijón A, Hernández ER, Lacovig P, Lizzit S, Alfè D, Baraldi A. Translucency of Graphene to van der Waals Forces Applies to Atoms/Molecules with Different Polar Character. ACS Nano 2019; 13:12230-12241. [PMID: 31589408 DOI: 10.1021/acsnano.9b07277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Graphene has been proposed to be either fully transparent to van der Waals interactions to the extent of allowing switching between hydrophobic and hydrophilic behavior, or partially transparent (translucent), yet there has been considerable debate on this topic, which is still ongoing. In a combined experimental and theoretical study we investigate the effects of different metal substrates on the adsorption energy of atomic (argon) and molecular (carbon monoxide) adsorbates on high-quality epitaxial graphene. We demonstrate that while the adsorption energy is certainly affected by the chemical composition of the supporting substrate and by the corrugation of the carbon lattice, the van der Waals interactions between adsorbates and the metal surfaces are partially screened by graphene. Our results indicate that the concept of graphene translucency, already introduced in the case of water droplets, is found to hold more generally also in the case of single polar molecules and atoms, which are apolar.
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Affiliation(s)
- Francesco Presel
- Physics Department , University of Trieste , Via Valerio 2 , 34127 Trieste , Italy
| | - Alfonso Gijón
- Instituto de Ciencia de Materiales de Madrid - ICMM-CSIC) , Campus de Cantoblanco , 28049 Madrid , Spain
| | - Eduardo R Hernández
- Instituto de Ciencia de Materiales de Madrid - ICMM-CSIC) , Campus de Cantoblanco , 28049 Madrid , Spain
| | - Paolo Lacovig
- Elettra-Sincrotrone Trieste S.C.p.A. , Strada Statale 14 Km 163.5 , 34149 Trieste , Italy
| | - Silvano Lizzit
- Elettra-Sincrotrone Trieste S.C.p.A. , Strada Statale 14 Km 163.5 , 34149 Trieste , Italy
| | - Dario Alfè
- Department of Earth Sciences, Department of Physics and Astronomy , TYC@UCL , London WC1E 6BT , United Kingdom
- London Centre for Nanotechnology , University College London , Gower Street , London WC1E 6BT , United Kingdom
- Dipartimento di Fisica Ettore Pancini , Università di Napoli Federico II , Monte S. Angelo, 80126 Napoli , Italy
| | - Alessandro Baraldi
- Physics Department , University of Trieste , Via Valerio 2 , 34127 Trieste , Italy
- Elettra-Sincrotrone Trieste S.C.p.A. , Strada Statale 14 Km 163.5 , 34149 Trieste , Italy
- IOM-CNR , Laboratorio TASC , AREA Science Park, S.S. 14 km 163.5 , 34149 Trieste , Italy
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11
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Zen A, Brandenburg JG, Michaelides A, Alfè D. A new scheme for fixed node diffusion quantum Monte Carlo with pseudopotentials: Improving reproducibility and reducing the trial-wave-function bias. J Chem Phys 2019; 151:134105. [DOI: 10.1063/1.5119729] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Andrea Zen
- Thomas Young Centre, University College London, London WC1H 0AH, United Kingdom
- London Centre for Nanotechnology, Gordon St., London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
- Department of Earth Sciences, University College London, London WC1E 6BT, United Kingdom
| | - Jan Gerit Brandenburg
- Thomas Young Centre, University College London, London WC1H 0AH, United Kingdom
- Interdisciplinary Center for Scientific Computing, University of Heidelberg, Im Neuenheimer Feld 205A, 69120 Heidelberg, Germany
| | - Angelos Michaelides
- Thomas Young Centre, University College London, London WC1H 0AH, United Kingdom
- London Centre for Nanotechnology, Gordon St., London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Dario Alfè
- Thomas Young Centre, University College London, London WC1H 0AH, United Kingdom
- London Centre for Nanotechnology, Gordon St., London WC1H 0AH, United Kingdom
- Department of Earth Sciences, University College London, London WC1E 6BT, United Kingdom
- Dipartimento di Fisica Ettore Pancini, Università di Napoli Federico II, Monte S. Angelo, I-80126 Napoli, Italy
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12
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Brandenburg JG, Zen A, Fitzner M, Ramberger B, Kresse G, Tsatsoulis T, Grüneis A, Michaelides A, Alfè D. Physisorption of Water on Graphene: Subchemical Accuracy from Many-Body Electronic Structure Methods. J Phys Chem Lett 2019; 10:358-368. [PMID: 30615460 DOI: 10.1021/acs.jpclett.8b03679] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Wet carbon interfaces are ubiquitous in the natural world and exhibit anomalous properties, which could be exploited by emerging technologies. However, progress is limited by lack of understanding at the molecular level. Remarkably, even for the most fundamental system (a single water molecule interacting with graphene), there is no consensus on the nature of the interaction. We tackle this by performing an extensive set of complementary state-of-the-art computer simulations on some of the world's largest supercomputers. From this effort a consensus on the water-graphene interaction strength has been obtained. Our results have significant impact for the physical understanding, as they indicate that the interaction is weaker than predicted previously. They also pave the way for more accurate and reliable studies of liquid water at carbon interfaces.
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Affiliation(s)
- Jan Gerit Brandenburg
- Department of Physics and Astronomy , University College London , Gower Street , London WC1E 6BT , United Kingdom
- Thomas Young Centre and London Centre for Nanotechnology , 17-19 Gordon Street , London WC1H 0AH , United Kingdom
| | - Andrea Zen
- Department of Physics and Astronomy , University College London , Gower Street , London WC1E 6BT , United Kingdom
- Thomas Young Centre and London Centre for Nanotechnology , 17-19 Gordon Street , London WC1H 0AH , United Kingdom
| | - Martin Fitzner
- Department of Physics and Astronomy , University College London , Gower Street , London WC1E 6BT , United Kingdom
- Thomas Young Centre and London Centre for Nanotechnology , 17-19 Gordon Street , London WC1H 0AH , United Kingdom
| | - Benjamin Ramberger
- University of Vienna , Faculty of Physics and Center for Computational Materials Sciences , Sensengasse 8/12 , 1090 Wien , Austria
| | - Georg Kresse
- University of Vienna , Faculty of Physics and Center for Computational Materials Sciences , Sensengasse 8/12 , 1090 Wien , Austria
| | - Theodoros Tsatsoulis
- Institute for Theoretical Physics , Vienna University of Technology , Wiedner Hauptstrasse 8-10 , 1040 Vienna , Austria
- Max Planck Institute for Solid State Research , Heisenbergstrasse 1 , 70569 Stuttgart , Germany
| | - Andreas Grüneis
- Institute for Theoretical Physics , Vienna University of Technology , Wiedner Hauptstrasse 8-10 , 1040 Vienna , Austria
- Max Planck Institute for Solid State Research , Heisenbergstrasse 1 , 70569 Stuttgart , Germany
| | - Angelos Michaelides
- Department of Physics and Astronomy , University College London , Gower Street , London WC1E 6BT , United Kingdom
- Thomas Young Centre and London Centre for Nanotechnology , 17-19 Gordon Street , London WC1H 0AH , United Kingdom
| | - Dario Alfè
- Thomas Young Centre and London Centre for Nanotechnology , 17-19 Gordon Street , London WC1H 0AH , United Kingdom
- Department of Earth Sciences , University College London , Gower Street , London WC1E 6BT , United Kingdom
- Dipartimento di Fisica Ettore Pancini , Università di Napoli Federico II , Monte S. Angelo, I-80126 Napoli , Italy
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13
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Al-Hamdani YS, Rossi M, Alfè D, Tsatsoulis T, Ramberger B, Brandenburg JG, Zen A, Kresse G, Grüneis A, Tkatchenko A, Michaelides A. Properties of the water to boron nitride interaction: From zero to two dimensions with benchmark accuracy. J Chem Phys 2017; 147:044710. [DOI: 10.1063/1.4985878] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yasmine S. Al-Hamdani
- Thomas Young Centre and London Centre for Nanotechnology, 17–19 Gordon Street, London WC1H 0AH, United Kingdom
- Physics and Materials Science Research Unit, University of Luxembourg, L-1511 Luxembourg, Luxembourg
| | - Mariana Rossi
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
| | - Dario Alfè
- Thomas Young Centre and London Centre for Nanotechnology, 17–19 Gordon Street, London WC1H 0AH, United Kingdom
- Department of Earth Sciences, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Theodoros Tsatsoulis
- Max Planck Institute for Solid State Research, Heisenbergstraße 1, D-70569 Stuttgart, Germany
| | - Benjamin Ramberger
- University of Vienna, Faculty of Physics and Center for Computational Materials Sciences, Sensengasse 8/12, 1090 Wien, Austria
| | - Jan Gerit Brandenburg
- Thomas Young Centre and London Centre for Nanotechnology, 17–19 Gordon Street, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AH, United Kingdom
| | - Andrea Zen
- Thomas Young Centre and London Centre for Nanotechnology, 17–19 Gordon Street, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Georg Kresse
- University of Vienna, Faculty of Physics and Center for Computational Materials Sciences, Sensengasse 8/12, 1090 Wien, Austria
| | - Andreas Grüneis
- Max Planck Institute for Solid State Research, Heisenbergstraße 1, D-70569 Stuttgart, Germany
| | - Alexandre Tkatchenko
- Physics and Materials Science Research Unit, University of Luxembourg, L-1511 Luxembourg, Luxembourg
| | - Angelos Michaelides
- Thomas Young Centre and London Centre for Nanotechnology, 17–19 Gordon Street, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
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14
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Vlaisavljevich B, Huck J, Hulvey Z, Lee K, Mason JA, Neaton JB, Long JR, Brown CM, Alfè D, Michaelides A, Smit B. Performance of van der Waals Corrected Functionals for Guest Adsorption in the M 2(dobdc) Metal-Organic Frameworks. J Phys Chem A 2017; 121:4139-4151. [PMID: 28436661 PMCID: PMC5529028 DOI: 10.1021/acs.jpca.7b00076] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 04/21/2017] [Indexed: 11/29/2022]
Abstract
Small-molecule binding in metal-organic frameworks (MOFs) can be accurately studied both experimentally and computationally, provided the proper tools are employed. Herein, we compare and contrast properties associated with guest binding by means of density functional theory (DFT) calculations using nine different functionals for the M2(dobdc) (dobdc4- = 2,5-dioxido,1,4-benzenedicarboxylate) series, where M = Mg, Mn, Fe, Co, Ni, Cu, and Zn. Additionally, we perform Quantum Monte Carlo (QMC) calculations for one system to determine if this method can be used to assess the performance of DFT. We also make comparisons with previously published experimental results for carbon dioxide and water and present new methane neutron powder diffraction (NPD) data for further comparison. All of the functionals are able to predict the experimental variation in the binding energy from one metal to the next; however, the interpretation of the performance of the functionals depends on which value is taken as the reference. On the one hand, if we compare against experimental values, we would conclude that the optB86b-vdW and optB88-vdW functionals systematically overestimate the binding strength, while the second generation of van der Waals (vdW) nonlocal functionals (vdw-DF2 and rev-vdW-DF2) correct for this providing a good description of binding energies. On the other hand, if the QMC calculation is taken as the reference then all of the nonlocal functionals yield results that fall just outside the error of the higher-level calculation. The empirically corrected vdW functionals are in reasonable agreement with experimental heat of adsorptions but under bind when compared with QMC, while Perdew-Burke-Ernzerhof fails by more than 20 kJ/mol regardless of which reference is employed. All of the functionals, with the exception of vdW-DF2, predict reasonable framework and guest binding geometries when compared with NPD measurements. The newest of the functionals considered, rev-vdW-DF2, should be used in place of vdW-DF2, as it yields improved bond distances with similar quality binding energies.
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Affiliation(s)
| | | | - Zeric Hulvey
- Center for Neutron Research, National Institute of Standards and Technology , Gaithersburg, Maryland 20899, United States
- Department of Materials Science and Engineering, University of Maryland , College Park, Maryland 20742 United States
| | | | | | - Jeffrey B Neaton
- Kavli Energy Nanosciences Institute at Berkeley , Berkeley, California 94720, United States
| | | | - Craig M Brown
- Center for Neutron Research, National Institute of Standards and Technology , Gaithersburg, Maryland 20899, United States
- Department of Chemical and Biomolecular Engineering, University of Delaware , Newark, Delaware 19716, United States
| | - Dario Alfè
- Department of Earth Sciences, Thomas Young Centre and London Centre for Nanotechnology, University College London , Gower Street, London WC1E 6BT, United Kingdom
| | - Angelos Michaelides
- London Centre for Nanotechnology and Department of Physics and Astronomy, Thomas Young Centre, University College London , Gower Street, London WC1E 6BT, United Kingdom
| | - Berend Smit
- Institut des Sciences et Ingénierie Chimiques, Valais, Ecole Polytechnique Fédérale de Lausanne , Rue de l'Industrie 17, CH-1951 Sion, Switzerland
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15
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Tsatsoulis T, Hummel F, Usvyat D, Schütz M, Booth GH, Binnie SS, Gillan MJ, Alfè D, Michaelides A, Grüneis A. A comparison between quantum chemistry and quantum Monte Carlo techniques for the adsorption of water on the (001) LiH surface. J Chem Phys 2017; 146:204108. [PMID: 28571392 PMCID: PMC5446292 DOI: 10.1063/1.4984048] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 05/11/2017] [Indexed: 12/03/2022] Open
Abstract
We present a comprehensive benchmark study of the adsorption energy of a single water molecule on the (001) LiH surface using periodic coupled cluster and quantum Monte Carlo theories. We benchmark and compare different implementations of quantum chemical wave function based theories in order to verify the reliability of the predicted adsorption energies and the employed approximations. Furthermore we compare the predicted adsorption energies to those obtained employing widely used van der Waals density-functionals. Our findings show that quantum chemical approaches are becoming a robust and reliable tool for condensed phase electronic structure calculations, providing an additional tool that can also help in potentially improving currently available van der Waals density-functionals.
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Affiliation(s)
- Theodoros Tsatsoulis
- Max Planck Institute for Solid State Research, Heisenbergstraße 1, D-70569 Stuttgart, Germany
| | - Felix Hummel
- Max Planck Institute for Solid State Research, Heisenbergstraße 1, D-70569 Stuttgart, Germany
| | - Denis Usvyat
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-St. 2, D-12489 Berlin, Germany
| | - Martin Schütz
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-St. 2, D-12489 Berlin, Germany
| | - George H Booth
- Department of Physics, King's College London, Strand, London WC2R 2LS, United Kingdom
| | - Simon S Binnie
- London Centre for Nanotechnology, University College London, Gordon St., London WC1H 0AH, United Kingdom
| | - Michael J Gillan
- London Centre for Nanotechnology, University College London, Gordon St., London WC1H 0AH, United Kingdom
| | - Dario Alfè
- London Centre for Nanotechnology, University College London, Gordon St., London WC1H 0AH, United Kingdom
| | - Angelos Michaelides
- London Centre for Nanotechnology, University College London, Gordon St., London WC1H 0AH, United Kingdom
| | - Andreas Grüneis
- Max Planck Institute for Solid State Research, Heisenbergstraße 1, D-70569 Stuttgart, Germany
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16
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Affiliation(s)
- Yasmine S. Al-Hamdani
- Thomas Young Centre and London Centre for Nanotechnology, 17–19 Gordon Street, London WC1H 0AH, United Kingdom
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Dario Alfè
- Thomas Young Centre and London Centre for Nanotechnology, 17–19 Gordon Street, London WC1H 0AH, United Kingdom
- Department of Earth Sciences, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Angelos Michaelides
- Thomas Young Centre and London Centre for Nanotechnology, 17–19 Gordon Street, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
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17
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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18
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Zen A, Roch LM, Cox SJ, Hu XL, Sorella S, Alfè D, Michaelides A. Toward Accurate Adsorption Energetics on Clay Surfaces. J Phys Chem C Nanomater Interfaces 2016; 120:26402-26413. [PMID: 27917256 PMCID: PMC5126707 DOI: 10.1021/acs.jpcc.6b09559] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 10/31/2016] [Indexed: 05/31/2023]
Abstract
Clay minerals are ubiquitous in nature, and the manner in which they interact with their surroundings has important industrial and environmental implications. Consequently, a molecular-level understanding of the adsorption of molecules on clay surfaces is crucial. In this regard computer simulations play an important role, yet the accuracy of widely used empirical force fields (FF) and density functional theory (DFT) exchange-correlation functionals is often unclear in adsorption systems dominated by weak interactions. Herein we present results from quantum Monte Carlo (QMC) for water and methanol adsorption on the prototypical clay kaolinite. To the best of our knowledge, this is the first time QMC has been used to investigate adsorption at a complex, natural surface such as a clay. As well as being valuable in their own right, the QMC benchmarks obtained provide reference data against which the performance of cheaper DFT methods can be tested. Indeed using various DFT exchange-correlation functionals yields a very broad range of adsorption energies, and it is unclear a priori which evaluation is better. QMC reveals that in the systems considered here it is essential to account for van der Waals (vdW) dispersion forces since this alters both the absolute and relative adsorption energies of water and methanol. We show, via FF simulations, that incorrect relative energies can lead to significant changes in the interfacial densities of water and methanol solutions at the kaolinite interface. Despite the clear improvements offered by the vdW-corrected and the vdW-inclusive functionals, absolute adsorption energies are often overestimated, suggesting that the treatment of vdW forces in DFT is not yet a solved problem.
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Affiliation(s)
- Andrea Zen
- Thomas
Young Centre and London Centre for Nanotechnology, 17−19 Gordon Street, London WC1H 0AH, United
Kingdom
- Department
of Physics and Astronomy, University College
London, Gower Street, London WC1E 6BT, United Kingdom
| | - Loïc M. Roch
- Thomas
Young Centre and London Centre for Nanotechnology, 17−19 Gordon Street, London WC1H 0AH, United
Kingdom
- Department
of Physics and Astronomy, University College
London, Gower Street, London WC1E 6BT, United Kingdom
| | - Stephen J. Cox
- Thomas
Young Centre and London Centre for Nanotechnology, 17−19 Gordon Street, London WC1H 0AH, United
Kingdom
- Department
of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Xiao Liang Hu
- Thomas
Young Centre and London Centre for Nanotechnology, 17−19 Gordon Street, London WC1H 0AH, United
Kingdom
- Department
of Physics and Astronomy, University College
London, Gower Street, London WC1E 6BT, United Kingdom
| | - Sandro Sorella
- SISSA−International
School for Advanced Studies, Via Bonomea 26, 34136 Trieste, Italy
- INFM
Democritos National Simulation Center, 34151 Trieste, Italy
| | - Dario Alfè
- Thomas
Young Centre and London Centre for Nanotechnology, 17−19 Gordon Street, London WC1H 0AH, United
Kingdom
- Department
of Earth Sciences, University College London, Gower Street, London WC1E 6BT, United
Kingdom
| | - Angelos Michaelides
- Thomas
Young Centre and London Centre for Nanotechnology, 17−19 Gordon Street, London WC1H 0AH, United
Kingdom
- Department
of Physics and Astronomy, University College
London, Gower Street, London WC1E 6BT, United Kingdom
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19
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Al-Hamdani YS, Alfè D, von Lilienfeld OA, Michaelides A. Tuning dissociation using isoelectronically doped graphene and hexagonal boron nitride: Water and other small molecules. J Chem Phys 2016; 144:154706. [DOI: 10.1063/1.4945783] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yasmine S. Al-Hamdani
- Thomas Young Centre and London Centre for Nanotechnology, 17–19 Gordon Street, London WC1H 0AH, United Kingdom
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Dario Alfè
- Thomas Young Centre and London Centre for Nanotechnology, 17–19 Gordon Street, London WC1H 0AH, United Kingdom
- Department of Earth Sciences, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - O. Anatole von Lilienfeld
- Institute of Physical Chemistry and National Center for Computational Design and Discovery of Novel Materials (MARVEL), Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Angelos Michaelides
- Thomas Young Centre and London Centre for Nanotechnology, 17–19 Gordon Street, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
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20
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Affiliation(s)
- Michael J. Gillan
- London Centre for Nanotechnology, Gordon St., London WC1H 0AH, United Kingdom
- Thomas Young Centre, University College London, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Dario Alfè
- London Centre for Nanotechnology, Gordon St., London WC1H 0AH, United Kingdom
- Thomas Young Centre, University College London, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
- Department of Earth Sciences, University College London, London WC1E 6BT, United Kingdom
| | - Angelos Michaelides
- London Centre for Nanotechnology, Gordon St., London WC1H 0AH, United Kingdom
- Thomas Young Centre, University College London, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
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21
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Abstract
We report on the temperature dependence of the electrical resistivity of solid iron at high pressure, up to and including conditions likely to be found at the centre of the Earth. We have extended some of the calculations of the resistivities of pure solid iron we recently performed at Earth's core conditions (Pozzo et al. in Earth Planet Sci Lett 393:159-164, 2014) to lower temperature. We show that at low temperature the resistivity increases linearly with temperature, and saturates at high temperature. This saturation effect is well known as the Mott-Ioffe-Regel limit in metals, but has been largely ignored to estimate the resistivity of iron at Earth's core conditions. Recent experiments (Gomi et al. in Phys Earth Planet Int 224:88-103, 2013) coupled new high pressure data and saturation to predict the resitivity of iron and iron alloys at Earth's core conditions, and reported values up to three times lower than previous estimates, confirming recent first principles calculations (de Koker et al. in Proc Natl Acad Sci 109:4070-4073, 2012; Pozzo et al. in Nature 485:355-358, 2012, Phys Rev B 87:014110-10, 2013, Earth Planet Sci Lett 393:159-164, 2014; Davies et al. in Nat Geosci 8:678-685, 2015). The present results support the saturation effect idea.
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Affiliation(s)
- Monica Pozzo
- />Department of Earth Sciences, and Thomas Young Centre@UCL, University College London, Gower Street, London, WC1E 6BT United Kingdom
| | - Dario Alfè
- />Department of Earth Sciences, and Thomas Young Centre@UCL, University College London, Gower Street, London, WC1E 6BT United Kingdom
- />Department of Physics and Astronomy, and London Centre for Nanotechnology, University College London, Gower Street, London, WC1E 6BT United Kingdom
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22
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Curcio D, Omiciuolo L, Pozzo M, Lacovig P, Lizzit S, Jabeen N, Petaccia L, Alfè D, Baraldi A. Molecular Lifting, Twisting, and Curling during Metal-Assisted Polycyclic Hydrocarbon Dehydrogenation. J Am Chem Soc 2016; 138:3395-402. [PMID: 26829531 DOI: 10.1021/jacs.5b12504] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The atomistic understanding of the dissociation mechanisms for large molecules adsorbed on surfaces is still a challenge in heterogeneous catalysis. This is especially true for polycyclic aromatic hydrocarbons, which represent an important class of organic compounds used to produce novel graphene-based architectures. Here, we show that coronene molecules adsorbed on Ir(111) undergo major conformational changes during dissociation. They first tilt upward with respect to the surface, still keeping their planar configuration, and subsequently experience a rotation, which changes the molecular axis orientation. Upon lifting, the internal C-C strain is initially relieved; as the dehydrogenation proceeds, the molecules experience a progressive increase in the average interatomic distance and gradually settle to form dome-shaped nanographene flakes. Our results provide important insight into the complex mechanism of molecular breakup, which could have implications in the synthesis of new carbon-based nanostructured materials.
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Affiliation(s)
- Davide Curcio
- Physics Department, University of Trieste , Via Valerio 2, 34127 Trieste, Italy
| | - Luca Omiciuolo
- Physics Department, University of Trieste , Via Valerio 2, 34127 Trieste, Italy
| | - Monica Pozzo
- Department of Earth Sciences, Department of Physics and Astronomy, Thomas Young Centre@UCL, London Centre for Nanotechnology, University College London , Gower Street, London WC1E 6BT, United Kingdom
| | - Paolo Lacovig
- Elettra-Sincrotrone Trieste S.C.p.A. , Strada Statale 14 km 163.5, 34149 Trieste, Italy
| | - Silvano Lizzit
- Elettra-Sincrotrone Trieste S.C.p.A. , Strada Statale 14 km 163.5, 34149 Trieste, Italy
| | - Naila Jabeen
- Physics Department, University of Trieste , Via Valerio 2, 34127 Trieste, Italy.,International Centre for Theoretical Physics , Strada Costiera 11, 34151 Trieste, Italy.,Nanosciences & Catalysis Division, National Centre for Physics , Islamabad 44000, Pakistan
| | - Luca Petaccia
- Elettra-Sincrotrone Trieste S.C.p.A. , Strada Statale 14 km 163.5, 34149 Trieste, Italy
| | - Dario Alfè
- Department of Earth Sciences, Department of Physics and Astronomy, Thomas Young Centre@UCL, London Centre for Nanotechnology, University College London , Gower Street, London WC1E 6BT, United Kingdom
| | - Alessandro Baraldi
- Physics Department, University of Trieste , Via Valerio 2, 34127 Trieste, Italy.,Elettra-Sincrotrone Trieste S.C.p.A. , Strada Statale 14 km 163.5, 34149 Trieste, Italy.,Laboratorio TASC, IOM-CNR , AREA Science Park, Strada Statale 14 km 163.5, 34149 Trieste, Italy
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23
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Gillan MJ, Alfè D, Manby FR. Energy benchmarks for methane-water systems from quantum Monte Carlo and second-order Møller-Plesset calculations. J Chem Phys 2015; 143:102812. [PMID: 26374005 DOI: 10.1063/1.4926444] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The quantum Monte Carlo (QMC) technique is used to generate accurate energy benchmarks for methane-water clusters containing a single methane monomer and up to 20 water monomers. The benchmarks for each type of cluster are computed for a set of geometries drawn from molecular dynamics simulations. The accuracy of QMC is expected to be comparable with that of coupled-cluster calculations, and this is confirmed by comparisons for the CH4-H2O dimer. The benchmarks are used to assess the accuracy of the second-order Møller-Plesset (MP2) approximation close to the complete basis-set limit. A recently developed embedded many-body technique is shown to give an efficient procedure for computing basis-set converged MP2 energies for the large clusters. It is found that MP2 values for the methane binding energies and the cohesive energies of the water clusters without methane are in close agreement with the QMC benchmarks, but the agreement is aided by partial cancelation between 2-body and beyond-2-body errors of MP2. The embedding approach allows MP2 to be applied without loss of accuracy to the methane hydrate crystal, and it is shown that the resulting methane binding energy and the cohesive energy of the water lattice agree almost exactly with recently reported QMC values.
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Affiliation(s)
- M J Gillan
- London Centre for Nanotechnology, University College London, Gordon St., London WC1H 0AH, United Kingdom
| | - D Alfè
- London Centre for Nanotechnology, University College London, Gordon St., London WC1H 0AH, United Kingdom
| | - F R Manby
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
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24
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Al-Hamdani YS, Alfè D, von Lilienfeld OA, Michaelides A. Water on BN doped benzene: a hard test for exchange-correlation functionals and the impact of exact exchange on weak binding. J Chem Phys 2015; 141:18C530. [PMID: 25399195 DOI: 10.1063/1.4898356] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Density functional theory (DFT) studies of weakly interacting complexes have recently focused on the importance of van der Waals dispersion forces, whereas the role of exchange has received far less attention. Here, by exploiting the subtle binding between water and a boron and nitrogen doped benzene derivative (1,2-azaborine) we show how exact exchange can alter the binding conformation within a complex. Benchmark values have been calculated for three orientations of the water monomer on 1,2-azaborine from explicitly correlated quantum chemical methods, and we have also used diffusion quantum Monte Carlo. For a host of popular DFT exchange-correlation functionals we show that the lack of exact exchange leads to the wrong lowest energy orientation of water on 1,2-azaborine. As such, we suggest that a high proportion of exact exchange and the associated improvement in the electronic structure could be needed for the accurate prediction of physisorption sites on doped surfaces and in complex organic molecules. Meanwhile to predict correct absolute interaction energies an accurate description of exchange needs to be augmented by dispersion inclusive functionals, and certain non-local van der Waals functionals (optB88- and optB86b-vdW) perform very well for absolute interaction energies. Through a comparison with water on benzene and borazine (B3N3H6) we show that these results could have implications for the interaction of water with doped graphene surfaces, and suggest a possible way of tuning the interaction energy.
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Affiliation(s)
- Yasmine S Al-Hamdani
- Thomas Young Centre and London Centre for Nanotechnology, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
| | - Dario Alfè
- Thomas Young Centre and London Centre for Nanotechnology, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
| | - O Anatole von Lilienfeld
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Angelos Michaelides
- Thomas Young Centre and London Centre for Nanotechnology, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
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Al-Hamdani YS, Ma M, Alfè D, von Lilienfeld OA, Michaelides A. Communication: Water on hexagonal boron nitride from diffusion Monte Carlo. J Chem Phys 2015; 142:181101. [PMID: 25978876 DOI: 10.1063/1.4921106] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Despite a recent flurry of experimental and simulation studies, an accurate estimate of the interaction strength of water molecules with hexagonal boron nitride is lacking. Here, we report quantum Monte Carlo results for the adsorption of a water monomer on a periodic hexagonal boron nitride sheet, which yield a water monomer interaction energy of -84 ± 5 meV. We use the results to evaluate the performance of several widely used density functional theory (DFT) exchange correlation functionals and find that they all deviate substantially. Differences in interaction energies between different adsorption sites are however better reproduced by DFT.
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Affiliation(s)
- Yasmine S Al-Hamdani
- Thomas Young Centre and London Centre for Nanotechnology, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
| | - Ming Ma
- Thomas Young Centre and London Centre for Nanotechnology, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
| | - Dario Alfè
- Thomas Young Centre and London Centre for Nanotechnology, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
| | - O Anatole von Lilienfeld
- Institute of Physical Chemistry and National Center for Computational Design and Discovery of Novel Materials, Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Angelos Michaelides
- Thomas Young Centre and London Centre for Nanotechnology, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
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26
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Abstract
Using ab initio methods, we examine the stability of ice 0, a recently proposed tetragonal form of ice implicated in the homogeneous freezing of water [J. Russo, F. Romano, and H. Tanaka, Nat. Mater. 13, 670 (2014)]. Vibrational frequencies are computed across the complete Brillouin Zone using Density Functional Theory (DFT), to confirm mechanical stability and quantify the free energy of ice 0 relative to ice I(h). The robustness of this result is tested via dispersion corrected semi-local and hybrid DFT, and Quantum Monte-Carlo calculation of lattice energies. Results indicate that popular molecular models only slightly overestimate the stability of ice zero. In addition, we study all possible realisations of proton disorder within the ice zero unit cell, and identify the ground state as ferroelectric. Comparisons are made to other low density metastable forms of ice, suggesting that the ice i structure [C. J. Fennel and J. D. Gezelter, J. Chem. Theory Comput. 1, 662 (2005)] may be equally relevant to ice formation.
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Affiliation(s)
- D Quigley
- Department of Physics and Centre for Scientific Computing, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - D Alfè
- Department of Earth Sciences and Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - B Slater
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
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27
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Fortes AD, Alfè D, Hernández ER, Gutmann MJ. Structure of magnesium selenate enneahydrate, MgSeO4·9H2O, from 5 to 250 K using neutron time-of-flight Laue diffraction. Acta Crystallogr B Struct Sci Cryst Eng Mater 2015; 71:313-327. [PMID: 26027007 PMCID: PMC4450603 DOI: 10.1107/s2052520615006824] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 04/05/2015] [Indexed: 06/04/2023]
Abstract
The complete structure of MgSeO4·9H2O has been refined from neutron single-crystal diffraction data obtained at 5, 100, 175 and 250 K. It is monoclinic, space group P2₁/c, Z = 4, with unit-cell parameters a = 7.222 (2), b = 10.484 (3), c = 17.327 (4) Å, β = 109.57 (2)°, and V = 1236.1 (6) Å(3) [ρ(calc) = 1770 (1) kg m(-3)] at 5 K. The structure consists of isolated [Mg(H2O)6](2+) octahedra, [SeO4](2-) tetrahedra and three interstitial lattice water molecules, all on sites of symmetry 1. The positions of the H atoms agree well with those inferred on the basis of geometrical considerations in the prior X-ray powder diffraction structure determination: no evidence of orientational disorder of the water molecules is apparent in the temperature range studied. Six of the nine water molecules are hydrogen bonded to one another to form a unique centrosymmetric dodecamer, (H2O)12. Raman spectra have been acquired in the range 170-4000 cm(-1) at 259 and 78 K; ab initio calculations, using density functional theory, have been carried out in order to aid in the analysis of the Raman spectrum as well as providing additional insights into the geometry and thermodynamics of the hydrogen bonds. Complementary information concerning the thermal expansion, crystal morphology and the solubility are also presented.
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Affiliation(s)
- A. Dominic Fortes
- Department of Earth Sciences, University College London, Gower Street, London WC1E 6BT, England
- Department of Earth and Planetary Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, England
- ISIS Facility, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0QX, England
| | - Dario Alfè
- Department of Earth and Planetary Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, England
| | - Eduardo R. Hernández
- Instituto de Ciencia de Materiales de Madrid (ICMM-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Matthias J. Gutmann
- ISIS Facility, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0QX, England
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28
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Chen J, Ren X, Li XZ, Alfè D, Wang E. On the room-temperature phase diagram of high pressure hydrogen: an ab initio molecular dynamics perspective and a diffusion Monte Carlo study. J Chem Phys 2015; 141:024501. [PMID: 25028021 DOI: 10.1063/1.4886075] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The finite-temperature phase diagram of hydrogen in the region of phase IV and its neighborhood was studied using the ab initio molecular dynamics (MD) and the ab initio path-integral molecular dynamics (PIMD). The electronic structures were analyzed using the density-functional theory (DFT), the random-phase approximation, and the diffusion Monte Carlo (DMC) methods. Taking the state-of-the-art DMC results as benchmark, comparisons of the energy differences between structures generated from the MD and PIMD simulations, with molecular and dissociated hydrogens, respectively, in the weak molecular layers of phase IV, indicate that standard functionals in DFT tend to underestimate the dissociation barrier of the weak molecular layers in this mixed phase. Because of this underestimation, inclusion of the quantum nuclear effects (QNEs) in PIMD using electronic structures generated with these functionals leads to artificially dissociated hydrogen layers in phase IV and an error compensation between the neglect of QNEs and the deficiencies of these functionals in standard ab initio MD simulations exists. This analysis partly rationalizes why earlier ab initio MD simulations complement so well the experimental observations. The temperature and pressure dependencies for the stability of phase IV were also studied in the end and compared with earlier results.
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Affiliation(s)
- Ji Chen
- International Center for Quantum Materials, Peking University, Beijing 100871, People's Republic of China
| | - Xinguo Ren
- Key Laboratory of Quantum Information, University of Science and Technology of China, Hefei 230026, Anhui, People's Republic of China
| | - Xin-Zheng Li
- School of Physics, Peking University, Beijing 100871, People's Republic of China
| | - Dario Alfè
- London Centre for Nanotechnology, University College London, London WC1H 0AH, United Kingdom
| | - Enge Wang
- International Center for Quantum Materials, Peking University, Beijing 100871, People's Republic of China
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29
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Cox SJ, Towler MD, Alfè D, Michaelides A. Benchmarking the performance of density functional theory and point charge force fields in their description of sI methane hydrate against diffusion Monte Carlo. J Chem Phys 2015; 140:174703. [PMID: 24811651 DOI: 10.1063/1.4871873] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
High quality reference data from diffusion Monte Carlo calculations are presented for bulk sI methane hydrate, a complex crystal exhibiting both hydrogen-bond and dispersion dominated interactions. The performance of some commonly used exchange-correlation functionals and all-atom point charge force fields is evaluated. Our results show that none of the exchange-correlation functionals tested are sufficient to describe both the energetics and the structure of methane hydrate accurately, while the point charge force fields perform badly in their description of the cohesive energy but fair well for the dissociation energetics. By comparing to ice Ih, we show that a good prediction of the volume and cohesive energies for the hydrate relies primarily on an accurate description of the hydrogen bonded water framework, but that to correctly predict stability of the hydrate with respect to dissociation to ice Ih and methane gas, accuracy in the water-methane interaction is also required. Our results highlight the difficulty that density functional theory faces in describing both the hydrogen bonded water framework and the dispersion bound methane.
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Affiliation(s)
- Stephen J Cox
- Thomas Young Centre and London Centre for Nanotechnology, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
| | - Michael D Towler
- Department of Earth Sciences, University College London Gower Street, London WC1E 6BT, United Kingdom
| | - Dario Alfè
- Thomas Young Centre and London Centre for Nanotechnology, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
| | - Angelos Michaelides
- Thomas Young Centre and London Centre for Nanotechnology, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
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30
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Affiliation(s)
- Yexin Feng
- International Center for Quantum Materials and School of Physics, Peking University, Beijing 100871, People’s Republic of China
| | - Ji Chen
- International Center for Quantum Materials and School of Physics, Peking University, Beijing 100871, People’s Republic of China
| | - Dario Alfè
- London Centre for Nanotechnology, UCL, London WC1H 0AH, United Kingdom; Department of Physics and Astronomy, University College London, London WC1E6BT, United Kingdom; and Department of Earth Sciences, University College London, London WC1E6BT, United Kingdom
| | - Xin-Zheng Li
- International Center for Quantum Materials and School of Physics, Peking University, Beijing 100871, People’s Republic of China
- Collaborative Innovation Center of Quantum Matter, Beijing 100871, People’s Republic of China
| | - Enge Wang
- International Center for Quantum Materials and School of Physics, Peking University, Beijing 100871, People’s Republic of China
- Collaborative Innovation Center of Quantum Matter, Beijing 100871, People’s Republic of China
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31
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Fortes AD, Wood IG, Alfè D, Hernández ER, Gutmann MJ, Sparkes HA. Structure, hydrogen bonding and thermal expansion of ammonium carbonate monohydrate. Acta Crystallogr B Struct Sci Cryst Eng Mater 2014; 70:948-62. [PMID: 25449618 PMCID: PMC4468514 DOI: 10.1107/s205252061402126x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 09/24/2014] [Indexed: 06/04/2023]
Abstract
We have determined the crystal structure of ammonium carbonate monohydrate, (NH4)2CO3·H2O, using Laue single-crystal diffraction methods with pulsed neutron radiation. The crystal is orthorhombic, space group Pnma (Z = 4), with unit-cell dimensions a = 12.047 (3), b = 4.453 (1), c = 11.023 (3) Å and V = 591.3 (3) Å(3) [ρcalc = 1281.8 (7) kg m(-3)] at 10 K. The single-crystal data collected at 10 and 100 K are complemented by X-ray powder diffraction data measured from 245 to 273 K, Raman spectra measured from 80 to 263 K and an athermal zero-pressure calculation of the electronic structure and phonon spectrum carried out using density functional theory (DFT). We find no evidence of a phase transition between 10 and 273 K; above 273 K, however, the title compound transforms first to ammonium sesquicarbonate monohydrate and subsequently to ammonium bicarbonate. The crystallographic and spectroscopic data and the calculations reveal a quite strongly hydrogen-bonded structure (EHB ≃ 30-40 kJ mol(-1)), on the basis of H...O bond lengths and the topology of the electron density at the bond critical points, in which there is no free rotation of the ammonium cation at any temperature. The barrier to free rotation of the ammonium ions is estimated from the observed librational frequency to be ∼ 36 kJ mol(-1). The c-axis exhibits negative thermal expansion, but the thermal expansion behaviour of the a and b axes is ormal.
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Affiliation(s)
- A. Dominic Fortes
- Department of Earth and Planetary Sciences, Birbeck, University of London, Malet Street, London WC1E 7HX, England
- Department of Earth Sciences, University College London, Gower Street, London WC1E 6BT, England
| | - Ian G. Wood
- Department of Earth Sciences, University College London, Gower Street, London WC1E 6BT, England
| | - Dario Alfè
- Department of Earth Sciences, University College London, Gower Street, London WC1E 6BT, England
| | - Eduardo R. Hernández
- Instituto de Ciencia de Materiales de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain
| | - Matthias J. Gutmann
- ISIS Facility, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0QX, England
| | - Hazel A. Sparkes
- School of Chemisty, University of Bristol, Bristol BS8 1TS, England
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32
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Davidson ERM, Klimeš J, Alfè D, Michaelides A. Cooperative interplay of van der Waals forces and quantum nuclear effects on adsorption: H at graphene and at coronene. ACS Nano 2014; 8:9905-9913. [PMID: 25300825 DOI: 10.1021/nn505578x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The energetic barriers that atoms and molecules often experience when binding to surfaces are incredibly important to a myriad of chemical and physical processes. However, these barriers are difficult to describe accurately with current computer simulation approaches. Two prominent contemporary challenges faced by simulation are the role of van der Waals forces and nuclear quantum effects. Here we examine the widely studied model systems of hydrogen on graphene and coronene using a van der Waals inclusive density functional theory approach together with path integral molecular dynamics at 50 K. We find that both van der Waals and quantum nuclear effects work together in a cooperative manner to dramatically reduce the barriers for hydrogen atoms to adsorb. This suggests that the low temperature hydrogenation of graphene is easier than previously thought and in more general terms that the combined roles of van der Waals and quantum tunnelling can lead to qualitative changes in adsorption.
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Affiliation(s)
- Erlend R M Davidson
- London Centre for Nanotechnology, University College London , London WC1E 6BT, U.K
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33
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Omiciuolo L, Hernández ER, Miniussi E, Orlando F, Lacovig P, Lizzit S, Menteş TO, Locatelli A, Larciprete R, Bianchi M, Ulstrup S, Hofmann P, Alfè D, Baraldi A. Bottom-up approach for the low-cost synthesis of graphene-alumina nanosheet interfaces using bimetallic alloys. Nat Commun 2014; 5:5062. [DOI: 10.1038/ncomms6062] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 08/26/2014] [Indexed: 01/20/2023] Open
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34
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Affiliation(s)
- D. Alfè
- Department of Earth Sciences, UCL, London WC1E 6BT, United Kingdom
- London Centre for Nanotechnology, UCL, London WC1H 0AH, United Kingdom
- Thomas Young Centre, UCL, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, UCL, London WC1E 6BT, United Kingdom
| | - A. P. Bartók
- Department of Engineering, University of Cambridge, Cambridge CB2 1PZ, United Kingdom
| | - G. Csányi
- Department of Engineering, University of Cambridge, Cambridge CB2 1PZ, United Kingdom
| | - M. J. Gillan
- London Centre for Nanotechnology, UCL, London WC1H 0AH, United Kingdom
- Thomas Young Centre, UCL, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, UCL, London WC1E 6BT, United Kingdom
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35
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Palumbo M, Fries SG, Pasturel A, Alfè D. Anharmonicity, mechanical instability, and thermodynamic properties of the Cr-Re σ-phase. J Chem Phys 2014; 140:144502. [PMID: 24735300 DOI: 10.1063/1.4869800] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Using density-functional theory in combination with the direct force method and molecular dynamics we investigate the vibrational properties of a binary Cr-Re σ-phase. In the harmonic approximation, we have computed phonon dispersion curves and density of states, evidencing structural and chemical effects. We found that the σ-phase is mechanically unstable in some configurations, for example, when all crystallographic sites are occupied by Re atoms. By using a molecular-dynamics-based method, we have analysed the anharmonicity in the system and found negligible effects (~0.5 kJ/mol) on the Helmholtz energy of the binary Cr-Re σ-phase up to 2000 K (~0.8T(m)). Finally, we show that the vibrational contribution has significant consequences on the disordering of the σ-phase at high temperature.
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Affiliation(s)
- Mauro Palumbo
- ICAMS, Ruhr University Bochum, Universität Str. 150, D-44801 Bochum, Germany
| | - Suzana G Fries
- ICAMS, Ruhr University Bochum, Universität Str. 150, D-44801 Bochum, Germany
| | - Alain Pasturel
- SIMAP, UMR CNRS-INPG-UJF 5266, BP 75, F-38402 Saint Martin d'Hères, France
| | - Dario Alfè
- Department of Earth Sciences, Department of Physics and Astronomy, London Centre for Nanotechnology and Thomas Young Centre@UCL, University College London, Gower Street, London WC1E 6BT, United Kingdom
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36
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Abstract
Noncovalent interactions are ubiquitous in molecular and condensed-phase environments, and hence a reliable theoretical description of these fundamental interactions could pave the way toward a more complete understanding of the microscopic underpinnings for a diverse set of systems in chemistry and biology. In this work, we demonstrate that recent algorithmic advances coupled to the availability of large-scale computational resources make the stochastic quantum Monte Carlo approach to solving the Schrödinger equation an optimal contender for attaining "chemical accuracy" (1 kcal/mol) in the binding energies of supramolecular complexes of chemical relevance. To illustrate this point, we considered a select set of seven host-guest complexes, representing the spectrum of noncovalent interactions, including dispersion or van der Waals forces, π-π stacking, hydrogen bonding, hydrophobic interactions, and electrostatic (ion-dipole) attraction. A detailed analysis of the interaction energies reveals that a complete theoretical description necessitates treatment of terms well beyond the standard London and Axilrod-Teller contributions to the van der Waals dispersion energy.
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Affiliation(s)
- Alberto Ambrosetti
- †Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Dario Alfè
- ‡Department of Earth Sciences and Department of Physics and Astronomy and London Centre for Nanotechnology and Thomas Young Centre@UCL, University College, London WC1E6BT, United Kingdom
| | - Robert A DiStasio
- §Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Alexandre Tkatchenko
- †Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
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Gillan MJ, Alfè D, Bartók AP, Csányi G. First-principles energetics of water clusters and ice: A many-body analysis. J Chem Phys 2013; 139:244504. [DOI: 10.1063/1.4852182] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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38
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Santra B, Klimeš J, Tkatchenko A, Alfè D, Slater B, Michaelides A, Car R, Scheffler M. On the accuracy of van der Waals inclusive density-functional theory exchange-correlation functionals for ice at ambient and high pressures. J Chem Phys 2013; 139:154702. [DOI: 10.1063/1.4824481] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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39
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Gillan MJ, Alfè D, Bygrave PJ, Taylor CR, Manby FR. Energy benchmarks for water clusters and ice structures from an embedded many-body expansion. J Chem Phys 2013; 139:114101. [DOI: 10.1063/1.4820906] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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40
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Alfè D, Bartók AP, Csányi G, Gillan MJ. Communication: Energy benchmarking with quantum Monte Carlo for water nano-droplets and bulk liquid water. J Chem Phys 2013; 138:221102. [DOI: 10.1063/1.4810882] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
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41
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Taioli S, Garberoglio G, Simonucci S, Beccara SA, Aversa L, Nardi M, Verucchi R, Iannotta S, Dapor M, Alfè D. Non-adiabatic ab initio molecular dynamics of supersonic beam epitaxy of silicon carbide at room temperature. J Chem Phys 2013; 138:044701. [DOI: 10.1063/1.4774376] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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42
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Alfè D, Pozzo M, Miniussi E, Günther S, Lacovig P, Lizzit S, Larciprete R, Burgos BS, Menteş TO, Locatelli A, Baraldi A. Fine tuning of graphene-metal adhesion by surface alloying. Sci Rep 2013; 3:2430. [PMID: 23938361 PMCID: PMC3741623 DOI: 10.1038/srep02430] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 07/29/2013] [Indexed: 11/11/2022] Open
Abstract
We show that bimetallic surface alloying provides a viable route for governing the interaction between graphene and metal through the selective choice of the elemental composition of the surface alloy. This concept is illustrated by an experimental and theoretical characterization of the properties of graphene on a model PtRu surface alloy on Ru(0001), with a concentration of Pt atoms in the first layer between 0 and 50%. The progressive increase of the Pt content determines the gradual detachment of graphene from the substrate, which results from the modification of the carbon orbital hybridization promoted by Pt. Alloying is also found to affect the morphology of graphene, which is strongly corrugated on bare Ru, but becomes flat at a Pt coverage of 50%. The method here proposed can be readily extended to several supports, thus opening the way to the conformal growth of graphene on metals and to a full tunability of the graphene-substrate interaction.
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Affiliation(s)
- D. Alfè
- Department of Earth Sciences, Department of Physics and Astronomy, TYC@UCL, and London Centre for Nanotechnology, University College London, Gower Street, London WC1E 6BT, United Kingdom
- IOM-CNR, DEMOCRITOS National Simulation Centre, I-34100 Trieste, Italy
| | - M. Pozzo
- Department of Earth Sciences, Department of Physics and Astronomy, TYC@UCL, and London Centre for Nanotechnology, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - E. Miniussi
- Physics Department and CENMAT, University of Trieste, Via Valerio 2, I-34127 Trieste, ITALY
- IOM-CNR, Laboratorio TASC, S.S. 14 Km 163.5, I-34149 Trieste, ITALY
| | - S. Günther
- Technische Universität München, Chemie Department, Physikalische Chemie mit Schwerpunkt Katalyse, Lichtenbergstr. 4, D-85748 Garching, Germany
| | - P. Lacovig
- Elettra - Sincrotrone Trieste S.C.p.A., S.S. 14 Km 163.5, 34149 Trieste, ITALY
| | - S. Lizzit
- Elettra - Sincrotrone Trieste S.C.p.A., S.S. 14 Km 163.5, 34149 Trieste, ITALY
| | - R. Larciprete
- CNR-Institute for Complex Systems, via Fosso del Cavaliere 100, I-00133 Roma, Italy
| | - B. Santos Burgos
- Elettra - Sincrotrone Trieste S.C.p.A., S.S. 14 Km 163.5, 34149 Trieste, ITALY
| | - T. O. Menteş
- Elettra - Sincrotrone Trieste S.C.p.A., S.S. 14 Km 163.5, 34149 Trieste, ITALY
| | - A. Locatelli
- Elettra - Sincrotrone Trieste S.C.p.A., S.S. 14 Km 163.5, 34149 Trieste, ITALY
| | - A. Baraldi
- Physics Department and CENMAT, University of Trieste, Via Valerio 2, I-34127 Trieste, ITALY
- IOM-CNR, Laboratorio TASC, S.S. 14 Km 163.5, I-34149 Trieste, ITALY
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Tkatchenko A, Alfè D, Kim KS. First-Principles Modeling of Non-Covalent Interactions in Supramolecular Systems: The Role of Many-Body Effects. J Chem Theory Comput 2012; 8:4317-22. [DOI: 10.1021/ct300711r] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alexandre Tkatchenko
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195,
Berlin, Germany
- Department
of Chemistry, Pohang University of Science and Technology, Pohang
790−784, South Korea
| | - Dario Alfè
- London Centre for Nanotechnology, University College London, London WC1E 6BT, United
Kingdom
| | - Kwang S. Kim
- Department
of Chemistry, Pohang University of Science and Technology, Pohang
790−784, South Korea
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44
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Verucchi R, Aversa L, Nardi MV, Taioli S, a Beccara S, Alfè D, Nasi L, Rossi F, Salviati G, Iannotta S. Epitaxy of Nanocrystalline Silicon Carbide on Si(111) at Room Temperature. J Am Chem Soc 2012; 134:17400-3. [DOI: 10.1021/ja307804v] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Roberto Verucchi
- Istituto dei Materiali per l’Elettronica ed il Magnetismo, IMEM-CNR,
Sezione FBK di Trento, 38123 Trento, Italy
| | - Lucrezia Aversa
- Istituto dei Materiali per l’Elettronica ed il Magnetismo, IMEM-CNR,
Sezione FBK di Trento, 38123 Trento, Italy
| | - Marco V. Nardi
- Istituto dei Materiali per l’Elettronica ed il Magnetismo, IMEM-CNR,
Sezione FBK di Trento, 38123 Trento, Italy
| | - Simone Taioli
- Interdisciplinary Laboratory
for Computational Science, FBK-CMM and University of Trento, 38123 Trento, Italy
- Department of Physics, University of Trento, 38123 Trento, Italy, and Istituto Nazionale di Fisica Nucleare, Sezione di Perugia,
06123 Perugia, Italy
- Dipartimento
di Chimica, Università di Bologna, 40126 Bologna, Italy
| | - Silvio a Beccara
- Interdisciplinary Laboratory
for Computational Science, FBK-CMM and University of Trento, 38123 Trento, Italy
- Department of Physics, University of Trento, 38123 Trento, Italy, and Istituto Nazionale di Fisica Nucleare, Sezione di Perugia,
06123 Perugia, Italy
| | | | - Lucia Nasi
- Istituto dei Materiali per l’Elettronica ed il Magnetismo, IMEM-CNR,
Parco Area delle Scienze 37/A, 43124 Parma, Italy
| | - Francesca Rossi
- Istituto dei Materiali per l’Elettronica ed il Magnetismo, IMEM-CNR,
Parco Area delle Scienze 37/A, 43124 Parma, Italy
| | - Giancarlo Salviati
- Istituto dei Materiali per l’Elettronica ed il Magnetismo, IMEM-CNR,
Parco Area delle Scienze 37/A, 43124 Parma, Italy
| | - Salvatore Iannotta
- Istituto dei Materiali per l’Elettronica ed il Magnetismo, IMEM-CNR,
Parco Area delle Scienze 37/A, 43124 Parma, Italy
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45
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Droghetti A, Alfè D, Sanvito S. Assessment of density functional theory for iron(II) molecules across the spin-crossover transition. J Chem Phys 2012; 137:124303. [DOI: 10.1063/1.4752411] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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46
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Gillan MJ, Manby FR, Towler MD, Alfè D. Assessing the accuracy of quantum Monte Carlo and density functional theory for energetics of small water clusters. J Chem Phys 2012; 136:244105. [DOI: 10.1063/1.4730035] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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47
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Cavallin A, Pozzo M, Africh C, Baraldi A, Vesselli E, Dri C, Comelli G, Larciprete R, Lacovig P, Lizzit S, Alfè D. Local electronic structure and density of edge and facet atoms at Rh nanoclusters self-assembled on a graphene template. ACS Nano 2012; 6:3034-3043. [PMID: 22404459 DOI: 10.1021/nn300651s] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The chemical and physical properties of nanoclusters largely depend on their sizes and shapes. This is partly due to finite size effects influencing the local electronic structure of the nanocluster atoms which are located on the nanofacets and on their edges. Here we present a thorough study on graphene-supported Rh nanocluster assemblies and their geometry-dependent electronic structure obtained by combining high-energy resolution core level photoelectron spectroscopy, scanning tunneling microscopy, and density functional theory. We demonstrate the possibility to finely control the morphology and the degree of structural order of Rh clusters grown in register with the template surface of graphene/Ir(111). By comparing measured and calculated core electron binding energies, we identify edge, facet, and bulk atoms of the nanoclusters. We describe how small interatomic distance changes occur while varying the nanocluster size, substantially modifying the properties of surface atoms. The properties of under-coordinated Rh atoms are discussed in view of their importance in heterogeneous catalysis and magnetism.
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Affiliation(s)
- Alberto Cavallin
- Physics Department and CENMAT, University of Trieste, Via Valerio 2, I-34127 Trieste, Italy
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48
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Pozzo M, Davies C, Gubbins D, Alfè D. Thermal and electrical conductivity of iron at Earth’s core conditions. Nature 2012; 485:355-8. [DOI: 10.1038/nature11031] [Citation(s) in RCA: 458] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 03/07/2012] [Indexed: 11/09/2022]
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49
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Karalti O, Alfè D, Gillan MJ, Jordan KD. Adsorption of a water molecule on the MgO(100) surface as described by cluster and slab models. Phys Chem Chem Phys 2012; 14:7846-53. [DOI: 10.1039/c2cp00015f] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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50
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Abstract
Molecular dynamics simulation is used to study the time-scales involved in the homogeneous melting of a superheated crystal. The interaction model used is an embedded-atom model for Fe developed in previous work, and the melting process is simulated in the microcanonical (N, V, E) ensemble. We study periodically repeated systems containing from 96 to 7776 atoms, and the initial system is always the perfect crystal without free surfaces or other defects. For each chosen total energy E and number of atoms N, we perform several hundred statistically independent simulations, with each simulation lasting for between 500 ps and 10 ns, in order to gather statistics for the waiting time τ(w) before melting occurs. We find that the probability distribution of τ(w) is roughly exponential, and that the mean value <τ(w)> depends strongly on the excess of the initial steady temperature of the crystal above the superheating limit identified by other researchers. The mean <τ(w)> also depends strongly on system size in a way that we have quantified. For very small systems of ~100 atoms, we observe a persistent alternation between the solid and liquid states, and we explain why this happens. Our results allow us to draw conclusions about the reliability of the recently proposed Z method for determining the melting properties of simulated materials and to suggest ways of correcting for the errors of the method.
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Affiliation(s)
- D Alfè
- Thomas Young Centre at UCL, London WC1E 6BT, United Kingdom.
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