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Baerends EJ, Aguirre NF, Austin ND, Autschbach J, Bickelhaupt FM, Bulo R, Cappelli C, van Duin ACT, Egidi F, Fonseca Guerra C, Förster A, Franchini M, Goumans TPM, Heine T, Hellström M, Jacob CR, Jensen L, Krykunov M, van Lenthe E, Michalak A, Mitoraj MM, Neugebauer J, Nicu VP, Philipsen P, Ramanantoanina H, Rüger R, Schreckenbach G, Stener M, Swart M, Thijssen JM, Trnka T, Visscher L, Yakovlev A, van Gisbergen S. The Amsterdam Modeling Suite. J Chem Phys 2025; 162:162501. [PMID: 40260801 DOI: 10.1063/5.0258496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2025] [Accepted: 03/28/2025] [Indexed: 04/24/2025] Open
Abstract
In this paper, we present the Amsterdam Modeling Suite (AMS), a comprehensive software platform designed to support advanced molecular and materials simulations across a wide range of chemical and physical systems. AMS integrates cutting-edge quantum chemical methods, including Density Functional Theory (DFT) and time-dependent DFT, with molecular mechanics, fluid thermodynamics, machine learning techniques, and more, to enable multi-scale modeling of complex chemical systems. Its design philosophy allows for seamless coupling between components, facilitating simulations that range from small molecules to complex biomolecular and solid-state systems, making it a versatile tool for tackling interdisciplinary challenges, both in industry and in academia. The suite also emphasizes user accessibility, with an intuitive graphical interface, extensive scripting capabilities, and compatibility with high-performance computing environments.
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Affiliation(s)
- Evert Jan Baerends
- Vrije Universiteit Amsterdam, De Boelelaan 1105, 1081 HV Amsterdam, The Netherlands
| | - Nestor F Aguirre
- Software for Chemistry & Materials BV, De Boelelaan 1109, 1081HV Amsterdam, The Netherlands
| | - Nick D Austin
- Software for Chemistry & Materials BV, De Boelelaan 1109, 1081HV Amsterdam, The Netherlands
| | - Jochen Autschbach
- Department of Chemistry, University at Buffalo State University of New York, Buffalo, New York 14260-3000, USA
| | - F Matthias Bickelhaupt
- Vrije Universiteit Amsterdam, De Boelelaan 1105, 1081 HV Amsterdam, The Netherlands
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
- Department of Chemical Sciences, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa
| | - Rosa Bulo
- Software for Chemistry & Materials BV, De Boelelaan 1109, 1081HV Amsterdam, The Netherlands
| | - Chiara Cappelli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- IMT School for Advanced Studies Lucca, Piazza San Francesco 19, I-55100 Lucca, Italy
| | - Adri C T van Duin
- Department of Mechanical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Franco Egidi
- Software for Chemistry & Materials BV, De Boelelaan 1109, 1081HV Amsterdam, The Netherlands
| | - Célia Fonseca Guerra
- Vrije Universiteit Amsterdam, De Boelelaan 1105, 1081 HV Amsterdam, The Netherlands
| | - Arno Förster
- Vrije Universiteit Amsterdam, De Boelelaan 1105, 1081 HV Amsterdam, The Netherlands
| | - Mirko Franchini
- Software for Chemistry & Materials BV, De Boelelaan 1109, 1081HV Amsterdam, The Netherlands
| | - Theodorus P M Goumans
- Software for Chemistry & Materials BV, De Boelelaan 1109, 1081HV Amsterdam, The Netherlands
| | - Thomas Heine
- Faculty of Chemistry and Food Chemistry, TU Dresden, Bergstraße 66c, 01069 Dresden, Germany
| | - Matti Hellström
- Software for Chemistry & Materials BV, De Boelelaan 1109, 1081HV Amsterdam, The Netherlands
| | - Christoph R Jacob
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Lasse Jensen
- Department of Chemistry, The Pennsylvania State University, 104 Benkovic Building, University Park, Pennsylvania 16802, USA
| | - Mykhaylo Krykunov
- Insilico Medicine AI Limited, Level 6, Unit 08, Block A, IRENA HQ Building, Masdar City, P.O. Box 145748, Abu Dhabi, United Arab Emirates
| | - Erik van Lenthe
- Software for Chemistry & Materials BV, De Boelelaan 1109, 1081HV Amsterdam, The Netherlands
| | - Artur Michalak
- Jagiellonian University, Faculty of Chemistry, Gronostajowa 2, 30-387 Kraków, Poland
| | - Mariusz M Mitoraj
- Jagiellonian University, Faculty of Chemistry, Gronostajowa 2, 30-387 Kraków, Poland
| | - Johannes Neugebauer
- Universität Münster, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Corrensstraße 36, 48149 Münster, Germany
| | | | - Pier Philipsen
- Software for Chemistry & Materials BV, De Boelelaan 1109, 1081HV Amsterdam, The Netherlands
| | - Harry Ramanantoanina
- Department Chemie, Johannes Gutenberg-Universität, Fritz-Strassmann Weg 2, 55128 Mainz, Germany
| | - Robert Rüger
- Software for Chemistry & Materials BV, De Boelelaan 1109, 1081HV Amsterdam, The Netherlands
| | - Georg Schreckenbach
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Mauro Stener
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli studi di Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Marcel Swart
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
- IQCC and Department Química, Universitat de Girona, Campus Montilivi, 17003 Girona, Spain
| | - Jos M Thijssen
- Kavli Institute of Nanoscience, Delft University of Technology, 2628 CJ Delft, The Netherlands
| | - Tomáš Trnka
- Software for Chemistry & Materials BV, De Boelelaan 1109, 1081HV Amsterdam, The Netherlands
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Lucas Visscher
- Vrije Universiteit Amsterdam, De Boelelaan 1105, 1081 HV Amsterdam, The Netherlands
| | - Alexei Yakovlev
- Software for Chemistry & Materials BV, De Boelelaan 1109, 1081HV Amsterdam, The Netherlands
| | - Stan van Gisbergen
- Software for Chemistry & Materials BV, De Boelelaan 1109, 1081HV Amsterdam, The Netherlands
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Averyanov DV, Sokolov IS, Parfenov OE, Taldenkov AN, Karateev IA, Kondratev OA, Tokmachev AM, Storchak VG. Thickness-Dependent Superconductivity in a Layered Electride on Silicon. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2302065. [PMID: 37259278 DOI: 10.1002/smll.202302065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/04/2023] [Indexed: 06/02/2023]
Abstract
Layered materials exhibit a plethora of fascinating properties. The challenge is to make the materials into epitaxial films, preferably integrated with mature technological platforms to facilitate their potential applications. Progress in this direction can establish the film thickness as a valuable parameter to control various phenomena, superconductivity in particular. Here, a synthetic route to epitaxial films of SrAlSi, a layered superconducting electride, on silicon is designed. A set of films ranging in thickness is synthesized employing a silicene-based template. Their structure and superconductivity are explored by a combination of techniques. Two regimes of TC dependence on the film thickness are identified, the coherence length being the crossover parameter. The results can be extended to syntheses of other honeycomb-lattice ternary compounds on Si or Ge exhibiting superconducting, magnetic, and other properties.
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Affiliation(s)
- Dmitry V Averyanov
- National Research Center "Kurchatov Institute", Kurchatov Sq. 1, Moscow, 123182, Russia
| | - Ivan S Sokolov
- National Research Center "Kurchatov Institute", Kurchatov Sq. 1, Moscow, 123182, Russia
| | - Oleg E Parfenov
- National Research Center "Kurchatov Institute", Kurchatov Sq. 1, Moscow, 123182, Russia
| | - Alexander N Taldenkov
- National Research Center "Kurchatov Institute", Kurchatov Sq. 1, Moscow, 123182, Russia
| | - Igor A Karateev
- National Research Center "Kurchatov Institute", Kurchatov Sq. 1, Moscow, 123182, Russia
| | - Oleg A Kondratev
- National Research Center "Kurchatov Institute", Kurchatov Sq. 1, Moscow, 123182, Russia
| | - Andrey M Tokmachev
- National Research Center "Kurchatov Institute", Kurchatov Sq. 1, Moscow, 123182, Russia
| | - Vyacheslav G Storchak
- National Research Center "Kurchatov Institute", Kurchatov Sq. 1, Moscow, 123182, Russia
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Li X, Liu H, Lu S. Versatile transition metal monolayers with catalytic and superconducting properties: a computational study. Phys Chem Chem Phys 2023. [PMID: 37378891 DOI: 10.1039/d3cp01205k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Due to their abundant valence electrons and unique electronic properties, transition metals have garnered great interest in the search for novel materials displaying various properties, including superconductivity, catalysis and so on. XRu2 (X: V, Mn, Fe, etc.) compounds, which are isostructural to AlB2, were used as examples for which we performed extensive simulations to screen for superconductivity and possible potential catalytic activity. On this basis, we found that VRu2 could achieve a superconducting critical temperature (Tc) of about 13 K. Meanwhile, our simulations showed the lowest adsorption free energy of atomic hydrogen (ΔGH) on the (0 0 1) surface of VRu2 to be about 2 meV, indicating its almost zero free energy of hydrogen adsorption with excellent catalytic performance. In addition, the results suggested potential superconducting and catalytic properties of VXRu (X = Os, Fe). Our current results have shed light on possible applications of Ru-based AlB2-type intermetallic compounds and have presented a new strategy for further designing superconductors and catalysts based on transition metals.
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Affiliation(s)
- Xue Li
- Henan Institute of Advanced Technology, Green Catalysis Center, and College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Hanyu Liu
- International Center for Computational Method & Software, State Key Laboratory of Superhard Materials, Laboratory of Physics and Technology for Advanced Batteries (Ministry of Education), College of Physics, Jilin University, Changchun 130012, China
| | - Siyu Lu
- Henan Institute of Advanced Technology, Green Catalysis Center, and College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
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Wang L, Pan S, Wang G, Zeng X, Zhou M, Frenking G. Triple bonding between beryllium and nitrogen in HNBeCO. Chem Commun (Camb) 2022; 58:8532-8535. [PMID: 35802125 DOI: 10.1039/d2cc02969c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The HNBeCO complex is generated via the reaction of a beryllium atom with a HNCO molecule in a solid neon matrix, which is identified via infrared absorption spectroscopy with isotopic substitutions. The complex is characterized to have a linear structure with a very short Be-N bond distance. Bonding analyses indicate that the complex involves an unprecedented HNBeCO triple bond consisting of two degenerate electron-sharing π bonds and a dative σ bond with the π bonds being much stronger than the σ bond.
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Affiliation(s)
- Lina Wang
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysts and Innovative Materials, Fudan University, Shanghai, 200438, China.
| | - Sudip Pan
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, D-35043, Marburg, Germany.
| | - Guanjun Wang
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysts and Innovative Materials, Fudan University, Shanghai, 200438, China.
| | - Xiaoqing Zeng
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysts and Innovative Materials, Fudan University, Shanghai, 200438, China.
| | - Mingfei Zhou
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysts and Innovative Materials, Fudan University, Shanghai, 200438, China.
| | - Gernot Frenking
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, D-35043, Marburg, Germany. .,Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, China.,Donostia International Physics Center (DIPC), P.K. 1072, 20080 Donostia, Euskadi, Spain
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