1
|
Naskar P, Talukder S. Energetics and spectroscopic studies of CNO (-) (H 2 O) n $$ {\mathbf{CNO}}^{\left(\hbox{-} \right)}{\left({\mathbf{H}}_{\mathbf{2}}\mathbf{O}\right)}_{\mathbf{n}} $$ clusters and the temperature dependencies of the isomers: An approach based on a combined recipe of parallel tempering and quantum chemical methods. J Comput Chem 2024. [PMID: 39151062 DOI: 10.1002/jcc.27480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 07/22/2024] [Accepted: 07/30/2024] [Indexed: 08/18/2024]
Abstract
A system associated with several number of weak interactions supports numerous number of stable structures within a narrow range of energy. Often, a deterministic search method fails to locate the global minimum geometry as well as important local minimum isomers for such systems. Therefore, in this work, the stochastic search technique, namely parallel tempering, has been executed on the quantum chemical surface of theCNO (-) (H 2 O) n $$ {\mathrm{CNO}}^{\left(\hbox{-} \right)}{\left({\mathrm{H}}_2\mathrm{O}\right)}_n $$ system forn = 1 $$ n=1 $$ -8 to generate global minimum as well as several number of local minimum isomers. IR spectrum can act as the fingerprint property for such system to be identified. Thus, IR spectroscopic features have also been included in this work. Vertical detachment energy has also been calculated to obtain clear information about number of water molecules in several spheres around the central anion. In addition, in a real experimental scenario, not only the global but also the local minimum isomers play an important role in determining the average value of a particular physically observable property. Therefore, the relative conformational populations have been determined for all the evaluated structures for the temperature range between 20K and 400K. Further to understand the phase change behavior, the configurational heat capacities have also been calculated for different sizes.
Collapse
Affiliation(s)
- Pulak Naskar
- Department of Chemistry, Mrinalini Datta Mahavidyapith, Kolkata, India
| | | |
Collapse
|
2
|
Hartke B. On the brink of self-hydration: the water heptadecamer. Phys Chem Chem Phys 2024; 26:15445-15451. [PMID: 38747364 DOI: 10.1039/d4cp00816b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
For pure, neutral, isolated molecular clusters, (H2O)17 marks the transition from structures with all water molecules on the cluster surface to water self-hydration, i.e., cluster structures around one central water molecule. Getting this right with water model potentials turns out to be challenging. Even the best water potentials currently available, which reproduce collective properties very well, still deliver contradicting results for (H2O)17, when different low-energy isomers from global structure optimizations are examined. Interestingly, ab initio quantum chemistry also struggles with the only seemingly simple question if (H2O)17 is all-surface or water-centered. Hence, although the long history of water potential development may be entering its final phase, it is not quite finished yet.
Collapse
Affiliation(s)
- Bernd Hartke
- Institute for Physical Chemistry, Kiel University, 24118 Kiel, Germany.
| |
Collapse
|
3
|
Roth M, Toker Y, Major DT. Monte Carlo-Simulated Annealing and Machine Learning-Based Funneled Approach for Finding the Global Minimum Structure of Molecular Clusters. ACS OMEGA 2024; 9:1298-1309. [PMID: 38222530 PMCID: PMC10785639 DOI: 10.1021/acsomega.3c07600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 01/16/2024]
Abstract
Understanding the physical underpinnings and geometry of molecular clusters is of great importance in many fields, ranging from studying the beginning of the universe to the formation of atmospheric particles. To this end, several approaches have been suggested, yet identifying the most stable cluster geometry (i.e., global potential energy minimum) remains a challenge, especially for highly symmetric clusters. Here, we suggest a new funneled Monte Carlo-based simulated annealing (SA) approach, which includes two key steps: generation of symmetrical clusters and classification of the clusters according to their geometry using machine learning (MCSA-ML). We demonstrate the merits of the MCSA-ML method in comparison to other approaches on several Lennard-Jones (LJ) clusters and four molecular clusters-Ser8(Cl-)2, H+(H2O)6, Ag+(CO2)8, and Bet4Cl-. For the latter of these clusters, the correct structure is unknown, and hence, we compare the experimental and simulated fragmentation patterns, and the fragmentation of the proposed global minimum matches experiments closely. Additionally, based on the fragmentation of the predicted betaine cluster, we were able to identify hitherto unknown neutral fragmentation channels. In comparison to results obtained with other methods, we demonstrated a superior ability of MCSA-ML to predict clusters with high symmetry and similar abilities to predict clusters with asymmetrical structures.
Collapse
Affiliation(s)
- Michal Roth
- Department
of Physics, Bar-Ilan University, Ramat-Gan 5290002, Israel
- Institute
of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Yoni Toker
- Department
of Physics, Bar-Ilan University, Ramat-Gan 5290002, Israel
- Institute
of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Dan T. Major
- Institute
of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
- Department
of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel
| |
Collapse
|
4
|
Freitas Gustavo M, Verstraelen T. GloMPO (Globally Managed Parallel Optimization): a tool for expensive, black-box optimizations, application to ReaxFF reparameterizations. J Cheminform 2022; 14:7. [PMID: 35172881 PMCID: PMC8848815 DOI: 10.1186/s13321-022-00581-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 12/31/2021] [Indexed: 11/10/2022] Open
Abstract
In this work we explore the properties which make many real-life global optimization problems extremely difficult to handle, and some of the common techniques used in literature to address them. We then introduce a general optimization management tool called GloMPO (Globally Managed Parallel Optimization) to help address some of the challenges faced by practitioners. GloMPO manages and shares information between traditional optimization algorithms run in parallel. We hope that GloMPO will be a flexible framework which allows for customization and hybridization of various optimization ideas, while also providing a substitute for human interventions and decisions which are a common feature of optimization processes of hard problems. GloMPO is shown to produce lower minima than traditional optimization approaches on global optimization test functions, the Lennard-Jones cluster problem, and ReaxFF reparameterizations. The novel feature of forced optimizer termination was shown to find better minima than normal optimization. GloMPO is also shown to provide qualitative benefits such a identifying degenerate minima, and providing a standardized interface and workflow manager.
Collapse
Affiliation(s)
- Michael Freitas Gustavo
- Center for Molecular Modeling, Ghent University, Ghent, Belgium
- Software for Chemistry and Materials, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | | |
Collapse
|
5
|
Dittner M, Hartke B. Globally optimal catalytic fields for a Diels-Alder reaction. J Chem Phys 2020; 152:114106. [PMID: 32199410 DOI: 10.1063/1.5142839] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
In a previous paper [M. Dittner and B. Hartke, J. Chem. Theory Comput. 14, 3547 (2018)], we introduced a preliminary version of our GOCAT (globally optimal catalyst) concept in which electrostatic catalysts are designed for arbitrary reactions by global optimization of distributed point charges that surround the reaction. In this first version, a pre-defined reaction path was kept fixed. This unrealistic assumption allowed for only small catalytic effects. In the present work, we extend our GOCAT framework by a sophisticated and robust on-the-fly reaction path optimization, plus further concomitant algorithm adaptions. This allows smaller and larger excursions from a pre-defined reaction path under the influence of the GOCAT point-charge surrounding, all the way to drastic mechanistic changes. In contrast to the restricted first GOCAT version, this new version is able to address real-life catalysis. We demonstrate this by applying it to the electrostatic catalysis of a prototypical Diels-Alder reaction. Without using any prior information, this procedure re-discovers theoretically and experimentally established features of electrostatic catalysis of this very reaction, including a field-dependent transition from the synchronous, concerted textbook mechanism to a zwitterionic two-step mechanism, and diastereomeric discrimination by suitable electric field components.
Collapse
Affiliation(s)
- Mark Dittner
- Institute for Physical Chemistry, Christian-Albrechts-University Kiel, 24098 Kiel, Germany
| | - Bernd Hartke
- Institute for Physical Chemistry, Christian-Albrechts-University Kiel, 24098 Kiel, Germany
| |
Collapse
|
6
|
Freibert A, Dieterich JM, Hartke B. Exploring self-organization of molecular tether molecules on a gold surface by global structure optimization. J Comput Chem 2019; 40:1978-1989. [PMID: 31069834 DOI: 10.1002/jcc.25853] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 04/16/2019] [Accepted: 04/22/2019] [Indexed: 11/11/2022]
Abstract
We employ nondeterministic global cluster structure optimization, based on the evolutionary algorithms paradigm, to model the self-assembly of complex molecules on a surface. As a real-life application example directly related to many recent experiments, we use this approach for the assembly of triazatriangulene "platform" molecules on the Au(111) surface. Without additional restrictions like spatial discretizations, coarse-graining or precalculated adsorption poses, and despite the proof-of-principle character of this study, we achieve satisfactory qualitative agreement with several experimental observations and can provide answers to questions that experiments on these species had left open so far. © 2019 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Antonia Freibert
- Institute for Physical Chemistry, Christian-Albrechts-University, Olshausenstr. 40, 24098, Kiel, Germany.,Department of Chemistry, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - Johannnes M Dieterich
- Institute for Physical Chemistry, Christian-Albrechts-University, Olshausenstr. 40, 24098, Kiel, Germany
| | - Bernd Hartke
- Institute for Physical Chemistry, Christian-Albrechts-University, Olshausenstr. 40, 24098, Kiel, Germany
| |
Collapse
|
7
|
Dittner M, Hartke B. Globally Optimal Catalytic Fields - Inverse Design of Abstract Embeddings for Maximum Reaction Rate Acceleration. J Chem Theory Comput 2018; 14:3547-3564. [PMID: 29883539 DOI: 10.1021/acs.jctc.8b00151] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The search for, and understanding of, good catalysts for chemical reactions is a central issue for chemists. Here, we present first steps toward developing a general computational framework to better support this task. This framework combines efficient, unbiased global optimization techniques with an abstract representation of the catalytic environment, to shrink the search space. To analyze the resulting catalytic embeddings, we employ dimensionality reduction and clustering techniques. This not only provides an inverse design approach to new catalytic embeddings but also illuminates the actual interactions behind catalytic effects. All this is illustrated here with a strictly electrostatic model for the environment and with two versions of a selected example reaction. We close with detailed discussions of future improvements of our framework.
Collapse
Affiliation(s)
- Mark Dittner
- Institute for Physical Chemistry , Christian-Albrechts-University Kiel , 24098 Kiel , Germany
| | - Bernd Hartke
- Institute for Physical Chemistry , Christian-Albrechts-University Kiel , 24098 Kiel , Germany
| |
Collapse
|
8
|
Witt C, Dieterich JM, Hartke B. Cluster structures influenced by interaction with a surface. Phys Chem Chem Phys 2018; 20:15661-15670. [DOI: 10.1039/c8cp02694g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Systematic investigation of how cluster structures change upon interaction with a surface, using global structure optimization by evolutionary algorithms.
Collapse
Affiliation(s)
- Christopher Witt
- Institut für Physikalische Chemie
- Christian-Albrechts-Universität
- D-24098 Kiel
- Germany
| | | | - Bernd Hartke
- Institut für Physikalische Chemie
- Christian-Albrechts-Universität
- D-24098 Kiel
- Germany
| |
Collapse
|