1
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Nguyen Thi Minh N, König C. The role of microenvironments on computed vibrationally-resolved emission spectra: The case of oxazines. J Comput Chem 2024; 45:2232-2241. [PMID: 38831461 DOI: 10.1002/jcc.27385] [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: 09/27/2023] [Revised: 04/05/2024] [Accepted: 04/12/2024] [Indexed: 06/05/2024]
Abstract
Oxazine dyes act as reporters of their near environment by the response of their fluorescence spectra. At the same time, their fluorescence spectra exhibit a pronounced vibrational progression. In this work, we computationally investigate the impact of near-environment models consisting of aggregated water as well as betaine molecules on the vibrational profile of fluorescence spectra of different oxazine derivatives. For aggregated betaine and a water molecule located above the plane of the dyes, we observe a distinct modification of the vibrational profile, which is more pronounced than the effect of a continuum description of a solvent environment. Our analysis shows that this effect cannot be explained by a pure change in the electronic structure, but that also vibrational degrees of freedom of the environment can be decisive for the vibrational profile and should, hence, not generally be neglected.
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Affiliation(s)
- Nghia Nguyen Thi Minh
- Institut für Physikalische Chemie und Elektrochemie, Leibniz Universität Hannover, Hannover, Germany
| | - Carolin König
- Institut für Physikalische Chemie und Elektrochemie, Leibniz Universität Hannover, Hannover, Germany
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2
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Mamedov K, Shrestha A, Whitcomb CA, Paolucci C, Davis RJ. Influence of Domain Size and Support Composition on the Reducibility of SiO 2 and TiO 2 Supported Tungsten Oxide Clusters. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2024; 128:13864-13878. [PMID: 39193254 PMCID: PMC11345822 DOI: 10.1021/acs.jpcc.4c03652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/20/2024] [Accepted: 07/26/2024] [Indexed: 08/29/2024]
Abstract
Supported tungsten oxides are widely used in a variety of catalytic reactions. Depending on the support, the cluster size, oxidation state, reducibility and speciation of the tungsten oxides can widely differ. When promoted with a platinum group metal, the resulting spillover of hydrogen may facilitate the reduction of supported tungsten oxide species, depending on the support. High resolution scanning transmission electron microscopy imaging showed nanometer scale WO x clusters were synthesized on SiO2 whereas highly dispersed species were formed on TiO2. Results from H2-temperature-programmed reduction showed the presence of Pd lowered the initial reduction temperature of SiO2-supported WO x species but interestingly did not affect that of TiO2-supported WO x . X-ray photoelectron and absorption spectroscopies showed the W atoms in SiO2-supported WO x species reduce from a +6 oxidation state to primarily +5 after thermal treatment in 5% H2, while the fraction of W in the +5 oxidation state was relatively unaffected by reduction treatment of TiO2-supported WO x . The unusual behavior of TiO2-supported WO x was explained by quantum chemical calculations that reveal the lack of change in the oxidation state of W is attributed to charge delocalization on the surface atoms of the titania support, which does not occur on silica. Moreover, modeling results at <600 K in the presence of H2 suggest the formation of Brønsted acid sites, and the absence of Lewis acid sites, on larger aggregates of WO x on silica and all cluster sizes on titania. These results provide experimental and theoretical insights into the nature of supported tungsten oxide clusters under conditions relevant to various catalytic reactions.
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Affiliation(s)
| | | | - Colby A. Whitcomb
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia 22903, United States
| | - Christopher Paolucci
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia 22903, United States
| | - Robert J. Davis
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia 22903, United States
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3
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Steeger P, Adnan M, Deilmann T, Li X, Müller S, Skrzyńska K, Hanfland M, Kolesnikov E, Kösters J, Block T, Schmidt R, Kupenko I, Sanchez-Valle C, Vijaya Prakash G, Michaelis de Vasconcellos S, Bratschitsch R. Hysteretic Piezochromism in a Lead Iodide-Based Two-Dimensional Inorganic-Organic Hybrid Perovskite. J Am Chem Soc 2024; 146:23205-23211. [PMID: 39120574 DOI: 10.1021/jacs.4c05557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
Two-dimensional inorganic-organic hybrid perovskites are in the limelight due to their potential applications in photonics and optoelectronics. They are environmentally stable, and their various chemical compositions offer a wide range of bandgap energies. Alternatively, crystal deformation enables in situ control over their optical properties. Here, we investigate (C6H9C2H4NH3)2PbI4, a hybrid perovskite whose organic linkers are 2-(1-cyclohexenyl)ethylammonium. Pressure-dependent optical absorption and emission spectroscopy reveal a hysteretic piezochromism that was not reported for other lead iodide-based 2D perovskites. We combine our optical studies with high-pressure X-ray diffraction experiments and first-principles calculations to demonstrate that the deformation of the inorganic lead iodide layers is the main reason for the observed changes in the optical bandgap.
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Affiliation(s)
- Paul Steeger
- Institute of Physics and Center for Nanotechnology, University of Münster, 48149 Münster, Germany
| | - Mohammad Adnan
- Institute of Physics and Center for Nanotechnology, University of Münster, 48149 Münster, Germany
| | - Thorsten Deilmann
- Institute of Solid State Theory, University of Münster, 48149 Münster, Germany
| | - Xiang Li
- Institute of Mineralogy, University of Münster, 48149 Münster, Germany
- European Synchrotron Radiation Facility, 38043 Grenoble, France
| | - Susanne Müller
- European Synchrotron Radiation Facility, 38043 Grenoble, France
| | - Katarzyna Skrzyńska
- Faculty of Natural Sciences, Institute of Earth Sciences, University of Silesia, Sosnowiec 41-200, Poland
| | | | - Efim Kolesnikov
- Institute of Mineralogy, University of Münster, 48149 Münster, Germany
| | - Jutta Kösters
- Insitut für Anorganische und Analytische Chemie, University of Münster, 48149 Münster, Germany
| | - Theresa Block
- Insitut für Anorganische und Analytische Chemie, University of Münster, 48149 Münster, Germany
| | - Robert Schmidt
- Institute of Physics and Center for Nanotechnology, University of Münster, 48149 Münster, Germany
| | - Ilya Kupenko
- Institute of Mineralogy, University of Münster, 48149 Münster, Germany
- European Synchrotron Radiation Facility, 38043 Grenoble, France
| | | | - G Vijaya Prakash
- Nanophotonics Lab, Department of Physics, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | | | - Rudolf Bratschitsch
- Institute of Physics and Center for Nanotechnology, University of Münster, 48149 Münster, Germany
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4
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Villavicencio N, Groves MN. Tuning Reinforcement Learning Parameters for Cluster Selection to Enhance Evolutionary Algorithms. ACS ENGINEERING AU 2024; 4:381-393. [PMID: 39185391 PMCID: PMC11342372 DOI: 10.1021/acsengineeringau.3c00068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 03/29/2024] [Accepted: 04/01/2024] [Indexed: 08/27/2024]
Abstract
The ability to find optimal molecular structures with desired properties is a popular challenge, with applications in areas such as drug discovery. Genetic algorithms are a common approach to global minima molecular searches due to their ability to search large regions of the energy landscape and decrease computational time via parallelization. In order to decrease the amount of unstable intermediate structures being produced and increase the overall efficiency of an evolutionary algorithm, clustering was introduced in multiple instances. However, there is little literature detailing the effects of differentiating the selection frequencies between clusters. In order to find a balance between exploration and exploitation in our genetic algorithm, we propose a system of clustering the starting population and choosing clusters for an evolutionary algorithm run via a dynamic probability that is dependent on the fitness of molecules generated by each cluster. We define four parameters, MFavOvrAll-A, MFavClus-B, NoNewFavClus-C, and Select-D, that correspond to a reward for producing the best structure overall, a reward for producing the best structure in its own cluster, a penalty for not producing the best structure, and a penalty based on the selection ratio of the cluster, respectively. A reward increases the probability of a cluster's future selection, while a penalty decreases it. In order to optimize these four parameters, we used a Gaussian distribution to approximate the evolutionary algorithm performance of each cluster and performed a grid search for different parameter combinations. Results show parameter MFavOvrAll-A (rewarding clusters for producing the best structure overall) and parameter Select-D (appearance penalty) have a significantly larger effect than parameters MFavClus-B and NoNewFavClus-C. In order to produce the most successful models, a balance between MFavOvrAll-A and Select-D must be made that reflects the exploitation vs exploration trade-off often seen in reinforcement learning algorithms. Results show that our reinforcement-learning-based method for selecting clusters outperforms an unclustered evolutionary algorithm for quinoline-like structure searches.
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Affiliation(s)
- Nathan Villavicencio
- Department
of Mathematics, California State University
Fullerton, Fullerton, California 92834, United States
| | - Michael N. Groves
- Department
of Chemistry and Biochemistry, California
State University Fullerton, Fullerton, California 92834, United States
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5
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Wang K. PGA: A new particle swarm optimization algorithm based on genetic operators for the global optimization of clusters. J Comput Chem 2024. [PMID: 39152778 DOI: 10.1002/jcc.27481] [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: 06/25/2024] [Revised: 07/31/2024] [Accepted: 08/02/2024] [Indexed: 08/19/2024]
Abstract
We have developed a global optimization program named PGA based on particle swarm optimization algorithm coupled with genetic operators for the structures of atomic clusters. The effectiveness and efficiency of the PGA program can be demonstrated by efficiently obtaining the tetrahedral Au20 and double-ring tubular B20, and identifying the ground stateZrSi 17 - 20 - $$ {\mathrm{ZrSi}}_{17\hbox{--} 20}^{-} $$ clusters through the comparison between the simulated and the experimental photoelectron spectra (PESs). Then, the PGA was applied to search for the global minimum structures ofMg n - $$ {\mathrm{Mg}}_n^{-} $$ (n = 3-30) clusters, new structures have been found for sizes n = 6, 7, 12, 14, and medium-sized 21-30 were first determined. The high consistency between the simulated spectra and the experimental ones once again demonstrates the efficiency of the PGA program. Based on the ground-state structures of theseMg n - $$ {\mathrm{Mg}}_n^{-} $$ (n = 3-30) clusters, their structural evolution and electronic properties were subsequently explored. The performance on Au20, B20,ZrSi 17 - 20 - $$ {\mathrm{ZrSi}}_{17\hbox{--} 20}^{-} $$ , andMg n - $$ {\mathrm{Mg}}_n^{-} $$ (n = 3-30) clusters indicates the promising potential of the PGA program for exploring the global minima of other clusters. The code is available for free upon request.
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Affiliation(s)
- Kai Wang
- Henan Engineering Research Centre of Building-Photovoltaics, School of Mathematics and Physics, Henan University of Urban Construction, Pingdingshan, China
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6
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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.
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Affiliation(s)
- Pulak Naskar
- Department of Chemistry, Mrinalini Datta Mahavidyapith, Kolkata, India
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7
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Cooper S, Robles-Navarro A, Smits OR, Schwerdtfeger P. From Hard to Soft Dense Sphere Packings: The Cohesive Energy of Barlow Structures Using Exact Lattice Summations for a General Lennard-Jones Potential. J Phys Chem Lett 2024; 15:8387-8392. [PMID: 39115313 DOI: 10.1021/acs.jpclett.4c01986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2024]
Abstract
There are infinitely many distinguishable dense sphere packings in dimension three (Barlow structures) with maximum packing density of ρ = π/√18. While Hales [Hales, T. C. Ann. Math. 2005, 162, 1065-1185.] proved that the packing density of the most dense cubic packing cannot be surpassed, it is currently not known how the infinite possibilities of densely packed Barlow structures with different sequences of hexagonal close packed layers are energetically related compared to the well-known face centered cubic (fcc) and hexagonal close packed (hcp) structures. We demonstrate that, for a general Lennard-Jones potential, which includes the hard-sphere model as a limiting case, Barlow packings lie energetically between fcc and hcp. Exceptions to this energy sequence only occur when fcc and hcp are energetically quasi-degenerate.
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Affiliation(s)
- Shaun Cooper
- School of Mathematical and Computational Sciences, Massey University Auckland, Private Bag 102904, Auckland 0745, New Zealand
| | - Andres Robles-Navarro
- Centre for Theoretical Chemistry and Physics, The New Zealand Institute for Advanced Study, Massey University Auckland, Private Bag 102904, 0745 Auckland, New Zealand
| | - Odile R Smits
- The School of Mathematics and Physics, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Peter Schwerdtfeger
- Centre for Theoretical Chemistry and Physics, The New Zealand Institute for Advanced Study, Massey University Auckland, Private Bag 102904, 0745 Auckland, New Zealand
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8
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Klumpers B, Hensen EJM, Filot IAW. Transferable, Living Data Sets for Predicting Global Minimum Energy Nanocluster Geometries. J Chem Theory Comput 2024; 20:6801-6812. [PMID: 39044400 PMCID: PMC11325533 DOI: 10.1021/acs.jctc.4c00572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
Modeling of nanocluster geometries is essential for studying the dependence of catalytic activity on the available active sites. In heterogeneous catalysis, the interfacial interaction of the support with the metal can result in modification of the structural and electronic properties of the clusters. To tackle the study of a diverse array of cluster shapes, data-driven methodologies are essential to circumvent prohibitive computational costs. At their core, these methods require large data sets in order to achieve the necessary accuracy to drive structural exploration. Given the similarity in binding character of the transition metals, cluster shapes encountered for various systems show a large amount of overlap. This overlap has been utilized to construct a living data set which may be carried over across multiple studies. Iterative refinement of this data set provides a low-cost pathway for initialization of cluster studies. It is shown that utilization of transferable structural information can reduce model construction costs by more than 90%. The benefits of this approach are particularly notable for alloy systems, which possess significantly larger configurational spaces compared to the pure-phase counterparts.
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Affiliation(s)
- Bart Klumpers
- Laboratory of Inorganic Materials and Catalysis, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, Eindhoven 5600 MB, The Netherlands
| | - Emiel J M Hensen
- Laboratory of Inorganic Materials and Catalysis, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, Eindhoven 5600 MB, The Netherlands
| | - Ivo A W Filot
- Laboratory of Inorganic Materials and Catalysis, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, Eindhoven 5600 MB, The Netherlands
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9
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Gounaris G, Katifori E. Braess's Paradox Analog in Physical Networks of Optimal Exploration. PHYSICAL REVIEW LETTERS 2024; 133:067401. [PMID: 39178443 DOI: 10.1103/physrevlett.133.067401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 01/31/2024] [Accepted: 07/02/2024] [Indexed: 08/25/2024]
Abstract
In stochastic exploration of geometrically embedded graphs, intuition suggests that providing a shortcut between a pair of nodes reduces the mean first passage time of the entire graph. Counterintuitively, we find a Braess's paradox analog. For regular diffusion, shortcuts can worsen the overall search efficiency of the network, although they bridge topologically distant nodes. We propose an optimization scheme under which each edge adapts its conductivity to minimize the graph's search time. The optimization reveals a relationship between the structure and diffusion exponent and a crossover from dense to sparse graphs as the exponent increases.
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10
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Nicy, Morgan JWR, Wales DJ. Energy landscapes for clusters of hexapeptides. J Chem Phys 2024; 161:054112. [PMID: 39092941 DOI: 10.1063/5.0220652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 07/17/2024] [Indexed: 08/04/2024] Open
Abstract
We present the results for energy landscapes of hexapeptides obtained using interfaces to the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) program. We have used basin-hopping global optimization and discrete path sampling to explore the landscapes of hexapeptide monomers, dimers, and oligomers containing 10, 100, and 200 monomers modeled using a residue-level coarse-grained potential, Mpipi, implemented in LAMMPS. We find that the dimers of peptides containing amino acid residues that are better at promoting phase separation, such as tyrosine and arginine, have melting peaks at higher temperature in their heat capacity compared to phenylalanine and lysine, respectively. This observation correlates with previous work on the same uncapped hexapeptide monomers modeled using atomistic potential. For oligomers, we compare the variation in monomer conformations with radial distance and observe trends for selected angles calculated for each monomer. The LAMMPS interfaces to the GMIN and OPTIM programs for landscape exploration offer new opportunities to investigate larger systems and provide access to the coarse-grained potentials implemented within LAMMPS.
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Affiliation(s)
- Nicy
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - John W R Morgan
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - David J Wales
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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11
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Schön JC. Energy landscapes-Past, present, and future: A perspective. J Chem Phys 2024; 161:050901. [PMID: 39101536 DOI: 10.1063/5.0212867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 06/17/2024] [Indexed: 08/06/2024] Open
Abstract
Energy landscapes and the closely related cost function landscapes have been recognized in science, mathematics, and various other fields such as economics as being highly useful paradigms and tools for the description and analysis of the properties of many systems, ranging from glasses, proteins, and abstract global optimization problems to business models. A multitude of algorithms for the exploration and exploitation of such landscapes have been developed over the past five decades in the various fields of applications, where many re-inventions but also much cross-fertilization have occurred. Twenty-five years ago, trying to increase the fruitful interactions between workers in different fields led to the creation of workshops and small conferences dedicated to the study of energy landscapes in general instead of only focusing on specific applications. In this perspective, I will present some history of the development of energy landscape studies and try to provide an outlook on in what directions the field might evolve in the future and what larger challenges are going to lie ahead, both from a conceptual and a practical point of view, with the main focus on applications of energy landscapes in chemistry and physics.
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Affiliation(s)
- J C Schön
- Max-Planck-Institute for Solid State Research, Heisenbergstr. 1, D-70569 Stuttgart, Germany
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12
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Zhang Y, Li Z, Han ZK, Ouyang R. Global Optimization of Cation Ordering in Perovskites by Recommendation-Based Basin-Hopping. J Chem Theory Comput 2024. [PMID: 39088397 DOI: 10.1021/acs.jctc.4c00460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2024]
Abstract
Cation ordering in multication perovskites is related to many important material properties and performances, but computational determination of the cation ordering remains a major challenge. Here, we propose a new computational approach by introducing a machine learning recommender system into the basin-hopping framework (RBH) for optimizing cation ordering. Taking the electrocatalyst Ba0.5Sr0.5Co0.8Fe0.2O3 (BSCF5582) as a showcase example, we found that the efficiency of RBH in identifying low-energy configurations outperforms the methods of cluster expansion and conventional basin-hopping. The RBH results revealed that the BSCF5582 catalyst tended to have a layered ordering of A-site cations and disordered B-site cations both in bulk and on the surfaces. Further, on the A-site-terminated surface, we found the segregation of large Ba atoms. Similarly, on the A-site- terminated surface of the recently developed Cs0.2Sr0.8Co0.4Fe0.6O3 (CSCF2846) catalyst, layered ordering at the A-site and surface enrichment of large Cs atoms were also found. The layered ordering was robust against thermal effects, as found from molecular dynamics simulations at 800 K. This work provides a new approach for thermodynamic global optimization of chemical ordering in multicomponent materials.
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Affiliation(s)
- Yuxuan Zhang
- Materials Genome Institute, Shanghai University, Shanghai 200444, China
| | - Zhenjie Li
- Materials Genome Institute, Shanghai University, Shanghai 200444, China
| | - Zhong-Kang Han
- School of Materials Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Runhai Ouyang
- Materials Genome Institute, Shanghai University, Shanghai 200444, China
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13
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Zell L, Hofer TS, Schubert M, Popoff A, Höll A, Marschhofer M, Huber-Cantonati P, Temml V, Schuster D. Impact of 2-hydroxypropyl-β-cyclodextrin inclusion complex formation on dopamine receptor-ligand interaction - A case study. Biochem Pharmacol 2024; 226:116340. [PMID: 38848779 DOI: 10.1016/j.bcp.2024.116340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 05/10/2024] [Accepted: 06/04/2024] [Indexed: 06/09/2024]
Abstract
The octanol-water distribution coefficient (logP), used as a measure of lipophilicity, plays a major role in the drug design and discovery processes. While average logP values remain unchanged in approved oral drugs since 1983, current medicinal chemistry trends towards increasingly lipophilic compounds that require adapted analytical workflows and drug delivery systems. Solubility enhancers like cyclodextrins (CDs), especially 2-hydroxypropyl-β-CD (2-HP-β-CD), have been studied in vitro and in vivo investigating their ADMET (adsorption, distribution, metabolism, excretion and toxicity)-related properties. However, data is scarce regarding the applicability of CD inclusion complexes (ICs) in vitro compared to pure compounds. In this study, dopamine receptor (DR) ligands were used as a case study, utilizing a combined in silico/in vitro workflow. Media-dependent solubility and IC stoichiometry were investigated using HPLC. NMR was used to observe IC formation-caused chemical shift deviations while in silico approaches utilizing basin hopping global minimization were used to propose putative IC binding modes. A cell-based in vitro homogeneous time-resolved fluorescence (HTRF) assay was used to quantify ligand binding affinity at the DR subtype 2 (D2R). While all ligands showed increased solubility using 2-HP-β-CD, they differed regarding IC stoichiometry and receptor binding affinity. This case study shows that IC-formation was ligand-dependent and sometimes altering in vitro binding. Therefore, IC complex formation can't be recommended as a general means of improving compound solubility for in vitro studies as they may alter ligand binding.
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Affiliation(s)
- Lukas Zell
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Paracelsus Medical University, 5020 Salzburg, Austria; Research and Innovation Center for Novel Therapies and Regenerative Medicine, Austria
| | - Thomas S Hofer
- Institute of General, Inorganic and Theoretical Chemistry, Center for Biochemistry and Biomedicine, University of Innsbruck, 6020 Innsbruck, Austria
| | - Mario Schubert
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria; Department of Chemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Alexander Popoff
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Paracelsus Medical University, 5020 Salzburg, Austria; Research and Innovation Center for Novel Therapies and Regenerative Medicine, Austria
| | - Anna Höll
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Paracelsus Medical University, 5020 Salzburg, Austria; Research and Innovation Center for Novel Therapies and Regenerative Medicine, Austria
| | - Moritz Marschhofer
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Paracelsus Medical University, 5020 Salzburg, Austria; Research and Innovation Center for Novel Therapies and Regenerative Medicine, Austria
| | - Petra Huber-Cantonati
- Department of Pharmaceutical Biology, Institute of Pharmacy, Paracelsus Medical University, 5020 Salzburg, Austria; Research and Innovation Center for Novel Therapies and Regenerative Medicine, Austria
| | - Veronika Temml
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Paracelsus Medical University, 5020 Salzburg, Austria; Research and Innovation Center for Novel Therapies and Regenerative Medicine, Austria
| | - Daniela Schuster
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Paracelsus Medical University, 5020 Salzburg, Austria; Research and Innovation Center for Novel Therapies and Regenerative Medicine, Austria.
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14
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Roth E, Listyarini RV, Hofer TS, Cziferszky M. Host-Guest Interactions of Ruthenium(II) Arene Complexes with Cucurbit[7/8]uril. Inorg Chem 2024; 63:14021-14031. [PMID: 39016439 PMCID: PMC11289748 DOI: 10.1021/acs.inorgchem.4c01755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 07/10/2024] [Accepted: 07/11/2024] [Indexed: 07/18/2024]
Abstract
Cucurbit[n]urils (CB[n]s) have been recognized for their chemical and thermal stability, and their ability to bind many neutral and cationic guest molecules makes them excellent hosts in a range of supramolecular applications. In drug delivery, CB[n]s can enhance drug solubility, improve chemical and physical drug stability, and allow for triggered and controlled release. This study aimed to investigate the ability of CB[7] and CB[8] as molecular hosts to bind ruthenium(II) arene complexes that are current anticancer lead structures in the area of metallodrugs. Both, experimental and computational methods, led to insights into the binding preferences and geometries of [RuII(cym)Cl2]2 (1; cym = η6-p-cymene), [RuII(cym)(dmb)Cl2]) (2; cym = η6-p-cymene; dmb = 1,3-dimethylbenzimidazol-2-ylidene), and [RuII(cym)(pta)Cl2] (3, RAPTA-C; cym = η6-p-cymene; pta = 1,3,5-triaza-7-phospha-adamantane) with CB[7] and CB[8]. Competition experiments by mass spectrometry revealed clear preferences of 2 for CB[8] and 3 for CB[7]. Based on a comparison of the associated interaction energies from quantum chemical calculations as well as experimental data, 3@CB[7] clearly prefers a binding mode, where the pta ligand is located inside the cavity of the host, and the metal ion interacts with two of the carbonyl groups on the rim of CB[7]. In contrast, complex 2 binds in two different orientations with interaction energies similar to those of both CB[n]s, with the cym ligand being either inside or outside of the cavity. These findings suggest that ruthenium(II) arene complexes are able to form stable host-guest interactions with CB[n]s, which can be exploited as drug delivery vehicles in further metallodrug development to improve their chemical stability.
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Affiliation(s)
- Elisa Roth
- Institute
for Pharmacy, Pharmaceutical Chemistry, Department of Chemistry and
Pharmacy, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Risnita Vicky Listyarini
- Institute
of General, Inorganic and Theoretical Chemistry, Center for Chemistry
and Biomedicine, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
- Chemistry
Education Study Program, Sanata Dharma University, Yogyakarta 55282, Indonesia
| | - Thomas S. Hofer
- Institute
of General, Inorganic and Theoretical Chemistry, Center for Chemistry
and Biomedicine, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Monika Cziferszky
- Institute
for Pharmacy, Pharmaceutical Chemistry, Department of Chemistry and
Pharmacy, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
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15
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Cerasoli FT, Donadio D. Effective optimization of atomic decoration in giant and superstructurally ordered crystals with machine learning. J Chem Phys 2024; 161:044101. [PMID: 39037130 DOI: 10.1063/5.0213132] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 07/05/2024] [Indexed: 07/23/2024] Open
Abstract
Crystals with complicated geometry are often observed with mixed chemical occupancy among Wyckoff sites, presenting a unique challenge for accurate atomic modeling. Similar systems possessing exact occupancy on all the sites can exhibit superstructural ordering, dramatically inflating the unit cell size. In this work, a crystal graph convolutional neural network (CGCNN) is used to predict optimal atomic decorations on fixed crystalline geometries. This is achieved with a site permutation search (SPS) optimization algorithm based on Monte Carlo moves combined with simulated annealing and basin-hopping techniques. Our approach relies on the evidence that, for a given chemical composition, a CGCNN estimates the correct energetic ordering of different atomic decorations, as predicted by electronic structure calculations. This provides a suitable energy landscape that can be optimized according to site occupation, allowing the prediction of chemical decoration in crystals exhibiting mixed or disordered occupancy, or superstructural ordering. Verification of the procedure is carried out on several known compounds, including the superstructurally ordered clathrate compound Rb8Ga27Sb16 and vacancy-ordered perovskite Cs2SnI6, neither of which was previously seen during the neural network training. In addition, the critical temperature of an order-disorder phase transition in solid solution CuZn is probed with our SPS routines by sampling site configuration trajectories in the canonical ensemble. This strategy provides an accurate method for determining favorable decoration in complex crystals and analyzing site occupation at unprecedented speed and scale.
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Affiliation(s)
- Frank T Cerasoli
- Department of Chemistry, University of California, Davis, California 95616, USA
| | - Davide Donadio
- Department of Chemistry, University of California, Davis, California 95616, USA
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16
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Burton HGA. Tiled unitary product states for strongly correlated Hamiltonians. Faraday Discuss 2024. [PMID: 39049810 DOI: 10.1039/d4fd00064a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Approximating the electronic wave function for strongly correlated systems remains a major theoretical challenge. Emerging quantum computers can enable new types of wave-function ansatz to be considered, with the potential to overcome the exponential memory storage for strong correlation. I have recently introduced the tiled Unitary Product States (tUPS) ansatz, which successfully combines the preservation of particle-number and spin symmetry with shallow quantum circuits and local qubit connectivity [H. G. A. Burton, Phys. Rev. Res., 2024, 6, 023300]. In this contribution, I investigate the accuracy of this tUPS hierarchy for strongly-correlated Hamiltonians. I consider the picket-fence pairing Hamiltonian and the two-dimensional Hubbard lattice, which collectively describe a range of strong correlation mechanisms found in molecules. Numerical results demonstrate that highly accurate energies can be achieved with a compact approximation for both weak and strong correlation in the Hubbard model, and the repulsive pairing regime. These data provide valuable insights into the applicability of the tUPS hierarchy for strong electron correlation.
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Affiliation(s)
- Hugh G A Burton
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
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17
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Liu C, Aguirre NF, Cawkwell MJ, Batista ER, Yang P. Efficient Parameterization of Density Functional Tight-Binding for 5 f-Elements: A Th-O Case Study. J Chem Theory Comput 2024; 20:5923-5936. [PMID: 38990696 PMCID: PMC11270830 DOI: 10.1021/acs.jctc.4c00145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 06/23/2024] [Accepted: 06/26/2024] [Indexed: 07/13/2024]
Abstract
Density functional tight binding (DFTB) models for f-element species are challenging to parametrize owing to the large number of adjustable parameters. The explicit optimization of the terms entering the semiempirical DFTB Hamiltonian related to f orbitals is crucial to generating a reliable parametrization for f-block elements, because they play import roles in bonding interactions. However, since the number of parameters grows quadratically with the number of orbitals, the computational cost for parameter optimization is much more expensive for the f-elements than for the main group elements. In this work we present a set of efficient approaches for mitigating the hurdle imposed by the large size of the parameter space. A novel group-by-orbital correction functions for two-center bond integrals was developed. With this approach the number of parameters is reduced, and it grows linearly with the number of elements, maintaining the accuracy and the number of parameters, in the case of f elements, by more than 40%. The parameter optimization step was accelerated by means of the mini-batch BFGS method. This method allows parameter optimizations with much larger training sets than other single batch methods. A stochastic optimizer was employed that helped overcome shallow local minima in the objective function. The proposed algorithm was used to parametrize the DFTB Hamiltonian for the Th-O system, which was subsequently applied to the study of ThO2 nanoparticles. The training set consisted of 6322 unique structures, which is barely feasible with conventional optimization methods. The optimized parameter set, LANL-ThO, displays good agreement with DFT-calculated properties such as energies, forces, and structures for both clusters and bulk ThO2. Benefiting from the fewer number of parameters and lower computational costs for objective function evaluations, this new approach shows its potential applications in DFTB parametrization for elements with high angular momentum, which present a challenge to conventional methods.
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Affiliation(s)
- Chang Liu
- Theoretical Division, Los Alamos
National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Néstor F. Aguirre
- Theoretical Division, Los Alamos
National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Marc J. Cawkwell
- Theoretical Division, Los Alamos
National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Enrique R. Batista
- Theoretical Division, Los Alamos
National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Ping Yang
- Theoretical Division, Los Alamos
National Laboratory, Los Alamos, New Mexico 87545, United States
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18
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Rojas-González FE, Castillo-Quevedo C, Rodríguez-Kessler PL, Jimenez-Halla JOC, Vásquez-Espinal A, Eithiraj RD, Cortez-Valadez M, Cabellos JL. Exploration of Free Energy Surface of the Au 10 Nanocluster at Finite Temperature. Molecules 2024; 29:3374. [PMID: 39064952 PMCID: PMC11279810 DOI: 10.3390/molecules29143374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Revised: 07/08/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
The first step in comprehending the properties of Au10 clusters is understanding the lowest energy structure at low and high temperatures. Functional materials operate at finite temperatures; however, energy computations employing density functional theory (DFT) methodology are typically carried out at zero temperature, leaving many properties unexplored. This study explored the potential and free energy surface of the neutral Au10 nanocluster at a finite temperature, employing a genetic algorithm coupled with DFT and nanothermodynamics. Furthermore, we computed the thermal population and infrared Boltzmann spectrum at a finite temperature and compared it with the validated experimental data. Moreover, we performed the chemical bonding analysis using the quantum theory of atoms in molecules (QTAIM) approach and the adaptive natural density partitioning method (AdNDP) to shed light on the bonding of Au atoms in the low-energy structures. In the calculations, we take into consideration the relativistic effects through the zero-order regular approximation (ZORA), the dispersion through Grimme's dispersion with Becke-Johnson damping (D3BJ), and we employed nanothermodynamics to consider temperature contributions. Small Au clusters prefer the planar shape, and the transition from 2D to 3D could take place at atomic clusters consisting of ten atoms, which could be affected by temperature, relativistic effects, and dispersion. We analyzed the energetic ordering of structures calculated using DFT with ZORA and single-point energy calculation employing the DLPNO-CCSD(T) methodology. Our findings indicate that the planar lowest energy structure computed with DFT is not the lowest energy structure computed at the DLPN0-CCSD(T) level of theory. The computed thermal population indicates that the 2D elongated hexagon configuration strongly dominates at a temperature range of 50-800 K. Based on the thermal population, at a temperature of 100 K, the computed IR Boltzmann spectrum agrees with the experimental IR spectrum. The chemical bonding analysis on the lowest energy structure indicates that the cluster bond is due only to the electrons of the 6 s orbital, and the Au d orbitals do not participate in the bonding of this system.
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Affiliation(s)
| | - César Castillo-Quevedo
- Departamento de Fundamentos del Conocimiento, Centro Universitario del Norte, Universidad de Guadalajara, Carretera Federal No. 23, km. 191, Colotlán 46200, Jalisco, Mexico;
| | | | - José Oscar Carlos Jimenez-Halla
- Departamento de Química, División de Ciencias Exactas y Naturales, Universidad de Guanajuato, Noria Alta s/n, Guanajuato 36050, Guanajuato, Mexico;
| | - Alejandro Vásquez-Espinal
- Química y Farmacia, Facultad de Ciencias de la Salud, Universidad Arturo Prat. Casilla 121, Iquique 1100000, Chile;
| | | | - Manuel Cortez-Valadez
- CONAHCYT-Departamento de Investigación en Física, Universidad de Sonora, Apdo. Postal 5-88, Hermosillo 83190, Sonora, Mexico;
| | - José Luis Cabellos
- Coordinación de Investigación y Desarrollo Tecnológico, Universidad Politécnica de Tapachula, Carretera Tapachula a Puerto Madero km. 24, Tapachula 30830, Chiapas, Mexico
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19
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Barrios Herrera L, Lourenço MP, Hostaš J, Calaminici P, Köster AM, Tchagang A, Salahub DR. Active-learning for global optimization of Ni-Ceria nanoparticles: The case of Ce 4-xNi xO 8- x (x = 1, 2, 3). J Comput Chem 2024; 45:1643-1656. [PMID: 38551129 DOI: 10.1002/jcc.27346] [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: 10/19/2023] [Revised: 02/15/2024] [Accepted: 03/05/2024] [Indexed: 06/04/2024]
Abstract
Ni-CeO2 nanoparticles (NPs) are promising nanocatalysts for water splitting and water gas shift reactions due to the ability of ceria to temporarily donate oxygen to the catalytic reaction and accept oxygen after the reaction is completed. Therefore, elucidating how different properties of the Ni-Ceria NPs relate to the activity and selectivity of the catalytic reaction, is of crucial importance for the development of novel catalysts. In this work the active learning (AL) method based on machine learning regression and its uncertainty is used for the global optimization of Ce(4-x)NixO(8-x) (x = 1, 2, 3) nanoparticles, employing density functional theory calculations. Additionally, further investigation of the NPs by mass-scaled parallel-tempering Born-Oppenheimer molecular dynamics resulted in the same putative global minimum structures found by AL, demonstrating the robustness of our AL search to learn from small datasets and assist in the global optimization of complex electronic structure systems.
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Affiliation(s)
- Lizandra Barrios Herrera
- Department of Chemistry, Department of Physics and Astronomy, CMS Centre for Molecular Simulation, IQST Institute for Quantum Science and Technology, Quantum Alberta, University of Calgary, Calgary, Canada
| | - Maicon Pierre Lourenço
- Departamento de Química e Física, Centro de Ciências Exatas, Naturais e da Saúde (CCENS), Universidade Federal do Espírito Santo, Espírito Santo, Brasil
| | - Jiří Hostaš
- Department of Chemistry, Department of Physics and Astronomy, CMS Centre for Molecular Simulation, IQST Institute for Quantum Science and Technology, Quantum Alberta, University of Calgary, Calgary, Canada
- Digital Technologies Research Centre, National Research Council of Canada, Ottawa, Canada
| | | | | | - Alain Tchagang
- Digital Technologies Research Centre, National Research Council of Canada, Ottawa, Canada
| | - Dennis R Salahub
- Department of Chemistry, Department of Physics and Astronomy, CMS Centre for Molecular Simulation, IQST Institute for Quantum Science and Technology, Quantum Alberta, University of Calgary, Calgary, Canada
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20
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Zhao X, Dong Z, Zhang C, Gupta H, Wu Z, Hua W, Zhang J, Huang P, Dong Y, Zhang Y. A step towards 6D WAXD tensor tomography. IUCRJ 2024; 11:502-509. [PMID: 38727172 PMCID: PMC11220869 DOI: 10.1107/s2052252524003750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/24/2024] [Indexed: 07/04/2024]
Abstract
X-ray scattering/diffraction tensor tomography techniques are promising methods to acquire the 3D texture information of heterogeneous biological tissues at micrometre resolution. However, the methods suffer from a long overall acquisition time due to multi-dimensional scanning across real and reciprocal space. Here, a new approach is introduced to obtain 3D reciprocal information of each illuminated scanning volume using mathematic modeling, which is equivalent to a physical scanning procedure for collecting the full reciprocal information required for voxel reconstruction. The virtual reciprocal scanning scheme was validated by a simulated 6D wide-angle X-ray diffraction tomography experiment. The theoretical validation of the method represents an important technological advancement for 6D diffraction tensor tomography and a crucial step towards pervasive applications in the characterization of heterogeneous materials.
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Affiliation(s)
- Xiaoyi Zhao
- Beijing Synchrotron Radiation Facility, Institute of High Energy PhysicsChinese Academy of Sciences (CAS)Beijing100049People’s Republic of China
- Spallation Neutron Source Science Center, Dongguan523803, People’s Republic of China
| | - Zheng Dong
- Beijing Synchrotron Radiation Facility, Institute of High Energy PhysicsChinese Academy of Sciences (CAS)Beijing100049People’s Republic of China
- Spallation Neutron Source Science Center, Dongguan523803, People’s Republic of China
| | - Chenglong Zhang
- Beijing Synchrotron Radiation Facility, Institute of High Energy PhysicsChinese Academy of Sciences (CAS)Beijing100049People’s Republic of China
| | - Himadri Gupta
- School of Engineering and Materials ScienceQueen Mary University of LondonLondonE1 4NSUnited Kingdom
| | - Zhonghua Wu
- Beijing Synchrotron Radiation Facility, Institute of High Energy PhysicsChinese Academy of Sciences (CAS)Beijing100049People’s Republic of China
- University of Chinese Academy of SciencesBeijing100049People’s Republic of China
| | - Wenqiang Hua
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research InstituteChinese Academy of SciencesShanghai201204People’s Republic of China
| | - Junrong Zhang
- Spallation Neutron Source Science Center, Dongguan523803, People’s Republic of China
- Institute of High Energy PhysicsChinese Academy of SciencesBeijing100049People’s Republic of China
| | - Pengyu Huang
- Institute of Biomedical Engineering, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin300192, People’s Republic of China
| | - Yuhui Dong
- Beijing Synchrotron Radiation Facility, Institute of High Energy PhysicsChinese Academy of Sciences (CAS)Beijing100049People’s Republic of China
- University of Chinese Academy of SciencesBeijing100049People’s Republic of China
| | - Yi Zhang
- Beijing Synchrotron Radiation Facility, Institute of High Energy PhysicsChinese Academy of Sciences (CAS)Beijing100049People’s Republic of China
- University of Chinese Academy of SciencesBeijing100049People’s Republic of China
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21
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Feuer-Forson P, Hartmann G, Mitzner R, Baumgärtel P, Weniger C, Agåker M, Meier D, Wernet P, Viefhaus J. Automated spectrometer alignment via machine learning. JOURNAL OF SYNCHROTRON RADIATION 2024; 31:698-705. [PMID: 38900459 PMCID: PMC11226169 DOI: 10.1107/s1600577524003850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 04/26/2024] [Indexed: 06/21/2024]
Abstract
During beam time at a research facility, alignment and optimization of instrumentation, such as spectrometers, is a time-intensive task and often needs to be performed multiple times throughout the operation of an experiment. Despite the motorization of individual components, automated alignment solutions are not always available. In this study, a novel approach that combines optimisers with neural network surrogate models to significantly reduce the alignment overhead for a mobile soft X-ray spectrometer is proposed. Neural networks were trained exclusively using simulated ray-tracing data, and the disparity between experiment and simulation was obtained through parameter optimization. Real-time validation of this process was performed using experimental data collected at the beamline. The results demonstrate the ability to reduce alignment time from one hour to approximately five minutes. This method can also be generalized beyond spectrometers, for example, towards the alignment of optical elements at beamlines, making it applicable to a broad spectrum of research facilities.
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Affiliation(s)
- Peter Feuer-Forson
- Helmholtz-Zentrum Berlin für Materialien und Energie GmbHAlbert-Einstein-Strasse 1512489BerlinGermany
| | - Gregor Hartmann
- Helmholtz-Zentrum Berlin für Materialien und Energie GmbHAlbert-Einstein-Strasse 1512489BerlinGermany
| | - Rolf Mitzner
- Helmholtz-Zentrum Berlin für Materialien und Energie GmbHAlbert-Einstein-Strasse 1512489BerlinGermany
| | - Peter Baumgärtel
- Helmholtz-Zentrum Berlin für Materialien und Energie GmbHAlbert-Einstein-Strasse 1512489BerlinGermany
| | - Christian Weniger
- Helmholtz-Zentrum Berlin für Materialien und Energie GmbHAlbert-Einstein-Strasse 1512489BerlinGermany
| | - Marcus Agåker
- Uppsala Universitet751 05UppsalaSweden
- MAX IV LaboratoryLund UniversityPO Box 118SE-22100LundSweden
| | - David Meier
- Helmholtz-Zentrum Berlin für Materialien und Energie GmbHAlbert-Einstein-Strasse 1512489BerlinGermany
| | | | - Jens Viefhaus
- Helmholtz-Zentrum Berlin für Materialien und Energie GmbHAlbert-Einstein-Strasse 1512489BerlinGermany
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22
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Mayrhofer L, Evans ME, Friesecke G. Robust self-assembly of nonconvex shapes in two dimensions. Phys Rev E 2024; 110:015309. [PMID: 39161005 DOI: 10.1103/physreve.110.015309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 06/20/2024] [Indexed: 08/21/2024]
Abstract
We present fast simulation methods for the self-assembly of complex shapes in two dimensions. The shapes are modeled via a general boundary curve and interact via a standard volume term promoting overlap and an interpenetration penalty. To efficiently realize the Gibbs measure on the space of possible configurations we employ the hybrid Monte Carlo algorithm together with a careful use of signed distance functions for energy evaluation. Motivated by the self-assembly of identical coat proteins of the tobacco mosaic virus which assemble into a helical shell, we design a nonconvex two-dimensional model shape and demonstrate its robust self-assembly into a unique final state. Our numerical experiments reveal certain essential prerequisites for this self-assembly process: blocking and matching (i.e., local repulsion and attraction) of different parts of the boundary, and nonconvexity and handedness of the shape.
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23
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Shi BX, Wales DJ, Michaelides A, Myung CW. Going for Gold(-Standard): Attaining Coupled Cluster Accuracy in Oxide-Supported Nanoclusters. J Chem Theory Comput 2024; 20:5306-5316. [PMID: 38856017 DOI: 10.1021/acs.jctc.4c00379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
The structure of oxide-supported metal nanoclusters plays an essential role in their sharply enhanced catalytic activity over that of bulk metals. Simulations provide the atomic-scale resolution needed to understand these systems. However, the sensitive mix of metal-metal and metal-support interactions, which govern their structure, puts stringent requirements on the method used, requiring calculations beyond standard density functional theory (DFT). The method of choice is coupled cluster theory [specifically CCSD(T)], but its computational cost has so far prevented its application to these systems. In this work, we showcase two approaches to make CCSD(T) accuracy readily achievable in oxide-supported nanoclusters. First, we leverage the SKZCAM protocol to provide the first benchmarks of oxide-supported nanoclusters, revealing that it is specifically metal-metal interactions that are challenging to capture with DFT. Second, we propose a CCSD(T) correction (ΔCC) to the metal-metal interaction errors in DFT, reaching accuracy comparable to that of the SKZCAM protocol at significantly lower cost. This approach forges a path toward studying larger systems at reliable accuracy, which we highlight by identifying a ground-state structure in agreement with experiments for Au20 on MgO, a challenging system where DFT models have yielded conflicting predictions.
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Affiliation(s)
- Benjamin X Shi
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - David J Wales
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Angelos Michaelides
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Chang Woo Myung
- Department of Energy Science, Sungkyunkwan University, Seobu-ro 2066, Suwon 16419, Korea
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24
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de Donato A, Ghejan BA, Bakker JM, Bernhardt TM, Bromley ST, Lang SM. Gas-Phase Production of Hydroxylated Silicon Oxide Cluster Cations: Structure, Infrared Spectroscopy, and Astronomical Relevance. ACS EARTH & SPACE CHEMISTRY 2024; 8:1154-1164. [PMID: 38919856 PMCID: PMC11194846 DOI: 10.1021/acsearthspacechem.3c00346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 06/27/2024]
Abstract
The interaction of free cationic silicon oxide clusters, Si x O y + (x = 2-5, y ≥ x), with dilute water vapor, was investigated in a flow tube reactor. Product mass distributions indicate cluster size-dependent dissociative water adsorption. To probe the structure and vibrational spectra of the resulting Si x O y H2 + (x = 2-4) clusters, we employed infrared multiple photon dissociation spectroscopy and density functional theory calculations. The planar rhombic cluster core of the disilicon oxides (x = 2) appears to be retained upon dissociative adsorption of one H2O unit, whereas a significant structural transformation of the tri- and tetra-silicon oxides (x = 3 and 4) is induced, resulting in an increased coordination of the Si atoms and more 3D cluster structures. In an astronomical context, we discuss the potential relevance of Si x O y H z + clusters as seeds for dust nucleation and catalysts for carbon-based chemistry in diffuse or translucent interstellar clouds, where all the necessary conditions for producing these species are found. In the produced clusters, the frequency of the isolated silanol Si-OH stretching vibrational mode is considerably blue-shifted compared to that in hydroxylated bulk silica and small inorganic compounds. This mode has a characteristic frequency range between 1200 cm-1 (8.3 μm) and 1090 cm-1 (9.2 μm) and is associated with the anomalously small Si-OH bond lengths in these ionised species. In infrared observations such high frequency Si-O stretching modes are usually associated with a pure bulk silica component of silicate cosmic dust. The presence of Si x O y H2 + clusters in low silica astrophysical environments could thus potentially be detected via their signature Si-O band using the James Webb space telescope.
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Affiliation(s)
- Andreu
A. de Donato
- Departament
de Ciència de Materials i Química Física &
Institut de Química Teòrica i Computacio-nal (IQTCUB), Universitat de Barcelona, c/Martí i Franquès 1-11, Barcelona 08028, Spain
| | | | - Joost M. Bakker
- Radboud
University, Institute of Molecules and Materials, FELIX Laboratory, Nijmegen 6525 ED, The Netherlands
| | | | - Stefan T. Bromley
- Departament
de Ciència de Materials i Química Física &
Institut de Química Teòrica i Computacio-nal (IQTCUB), Universitat de Barcelona, c/Martí i Franquès 1-11, Barcelona 08028, Spain
- Institució
Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, Bar-celona E-08010, Spain
| | - Sandra M. Lang
- Institute
of Surface Chemistry and Catalysis, University
of Ulm, Ulm 89069, Germany
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25
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Knattrup Y, Kubečka J, Wu H, Jensen F, Elm J. Reparameterization of GFN1-xTB for atmospheric molecular clusters: applications to multi-acid-multi-base systems. RSC Adv 2024; 14:20048-20055. [PMID: 38911834 PMCID: PMC11191700 DOI: 10.1039/d4ra03021d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 06/16/2024] [Indexed: 06/25/2024] Open
Abstract
Atmospheric molecular clusters, the onset of secondary aerosol formation, are a major part of the current uncertainty in modern climate models. Quantum chemical (QC) methods are usually employed in a funneling approach to identify the lowest free energy cluster structures. However, the funneling approach highly depends on the accuracy of low-cost methods to ensure that important low-lying minima are not missed. Here we present a reparameterized GFN1-xTB model based on the clusteromics I-V datasets for studying atmospheric molecular clusters (AMC), denoted AMC-xTB. The AMC-xTB model reduces the mean of electronic binding energy errors from 7-11.8 kcal mol-1 to roughly 0 kcal mol-1 and the root mean square deviation from 7.6-12.3 kcal mol-1 to 0.81-1.45 kcal mol-1. In addition, the minimum structures obtained with AMC-xTB are closer to the ωB97X-D/6-31++G(d,p) level of theory compared to GFN1-xTB. We employ the new parameterization in two new configurational sampling workflows that include an additional meta-dynamics sampling step using CREST with the AMC-xTB model. The first workflow, denoted the "independent workflow", is a commonly used funneling approach with an additional CREST step, and the second, the "improvement workflow", is where the best configuration currently known in the literature is improved with a CREST + AMC-xTB step. Testing the new workflow we find configurations lower in free energy for all the literature clusters with the largest improvement being up to 21 kcal mol-1. Lastly, by employing the improvement workflow we massively screened 288 new multi-acid-multi-base clusters containing up to 8 different species. For these new multi-acid-multi-base cluster systems we observe that the improvement workflow finds configurations lower in free energy for 245 out of 288 (85.1%) cluster structures. Most of the improvements are within 2 kcal mol-1, but we see improvements up to 8.3 kcal mol-1. Hence, we can recommend this new workflow based on the AMC-xTB model for future studies on atmospheric molecular clusters.
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Affiliation(s)
- Yosef Knattrup
- Department of Chemistry, Aarhus University Langelandsgade 140, Aarhus C 8000 Denmark +45 28938085
| | - Jakub Kubečka
- Department of Chemistry, Aarhus University Langelandsgade 140, Aarhus C 8000 Denmark +45 28938085
| | - Haide Wu
- Department of Chemistry, Aarhus University Langelandsgade 140, Aarhus C 8000 Denmark +45 28938085
| | - Frank Jensen
- Department of Chemistry, Aarhus University Langelandsgade 140, Aarhus C 8000 Denmark +45 28938085
| | - Jonas Elm
- Department of Chemistry, Aarhus University Langelandsgade 140, Aarhus C 8000 Denmark +45 28938085
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26
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Keith A, Brichtová EP, Barber JG, Wales DJ, Jackson SE, Röder K. Energy Landscapes and Structural Ensembles of Glucagon-like Peptide-1 Monomers. J Phys Chem B 2024; 128:5601-5611. [PMID: 38831581 PMCID: PMC11182347 DOI: 10.1021/acs.jpcb.4c01794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/16/2024] [Accepted: 05/20/2024] [Indexed: 06/05/2024]
Abstract
While GLP-1 and its analogues are important pharmaceutical agents in the treatment of type 2 diabetes and obesity, their susceptibility to aggregate into amyloid fibrils poses a significant safety issue. Many factors may contribute to the aggregation propensity, including pH. While it is known that the monomeric structure of GLP-1 has a strong impact on primary nucleation, probing its diverse structural ensemble is challenging. Here, we investigated the monomer structural ensembles at pH 3, 4, and 7.5 using state-of-the-art computational methods in combination with experimental data. We found significant stabilization of β-strand structures and destabilization of helical structures at lower pH, correlating with observed aggregation lag times, which are lower under these conditions. We further identified helical defects at pH 4, which led to the fastest observed aggregation, in agreement with our far-UV circular dichroism data. The detailed atomistic structures that result from the computational studies help to rationalize the experimental results on the aggregation propensity of GLP-1. This work provides a new insight into the pH-dependence of monomeric structural ensembles of GLP-1 and connects them to experimental observations.
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Affiliation(s)
- Alasdair
D. Keith
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
- Now:
Department of Biochemistry, School of Medicine, Emory University, 1510 Clifton Rd NE, Atlanta, Georgia 30322, United States
| | - Eva Přáda Brichtová
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
- Now:
Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Gumpendorferstr. 1A, Vienna 1060, Austria
| | - Jack G. Barber
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - David J. Wales
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Sophie E. Jackson
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Konstantin Röder
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
- Now:
Randall Centre for Cell & Molecular Biophysics, King’s College London, Great Maze Pond, London SE1 1UL, U.K.
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27
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Zhu B, Huang W, Lin H, Feng H, Palotás K, Lv J, Ren Y, Ouyang R, Yang F. Vacancy Ordering in Ultrathin Copper Oxide Films on Cu(111). J Am Chem Soc 2024; 146:15887-15896. [PMID: 38825776 DOI: 10.1021/jacs.4c02424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Oxide thin films grown on metal surfaces have wide applications in catalysis and beyond owing to their unique surface structures compared to their bulk counterparts. Despite extensive studies, the atomic structures of copper surface oxides on Cu(111), commonly referred to as "44" and "29", have remained elusive. In this work, we demonstrated an approach for the structural determination of oxide surfaces using element-specific scanning tunneling microscopy (STM) imaging enhanced by functionalized tips. This approach enabled us to resolve the atomic structures of "44" and "29" surface oxides, which were further corroborated by noncontact atomic force microscopy (nc-AFM) measurements and Monte Carlo (MC) simulations. The stoichiometry of the "44" and "29" frameworks was identified as Cu23O16 and Cu16O11, respectively. Contrary to the conventional hypothesis, we observed ordered Cu vacancies within the "44" structure manifesting as peanut-shaped cavities in the hexagonal lattice. Similarly, a combination of Cu and O vacancies within the "29" structure leads to bean-shaped cavities within the pentagonal lattice. Our study has thus resolved the decades-long controversy on the atomic structures of "44" and "29" surface oxides, advancing our understanding of copper oxidation processes and introducing a robust framework for the analysis of complex oxide surfaces.
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Affiliation(s)
- Bowen Zhu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Wugen Huang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Haiping Lin
- School of Physics and Information Technology, Shaanxi Normal University, Xi'an 710119, China
| | - Hao Feng
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | | | - Jiayu Lv
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yihui Ren
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Runhai Ouyang
- Materials Genome Institute, Shanghai University, Shanghai 200444, China
| | - Fan Yang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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28
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López-Castro C, Ortiz-Chi F, Merino G. An Efficient Growth Pattern Algorithm (GrowPAL) for Cluster Structure Prediction. J Chem Theory Comput 2024; 20:4939-4948. [PMID: 38820048 PMCID: PMC11171261 DOI: 10.1021/acs.jctc.4c00365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/17/2024] [Accepted: 05/19/2024] [Indexed: 06/02/2024]
Abstract
Identifying the lowest energy isomers in large clusters is a major challenge. Here, we introduce the Growth Pattern Algorithm (GrowPAL), a new approach that generates initial seeds composed of n+1 atoms from the system with n atoms through an interstitial-type addition (I-type) mechanism. We evaluated the effectiveness of GrowPAL on Lennard-Jones (LJ) clusters with up to n = 80 atoms, verifying the algorithm's ability to find challenging minima such as LJ38 and the partially icosahedral LJ69 with fewer optimizations than existing methods. In addition, we discuss the advantages and limitations of GrowPAL using our deconstruction scheme, which identifies "forebears" structures to study growth pathways. Having evaluated the strengths and weaknesses of GrowPAL, we employed it to explore Sutton-Chen clusters containing 5 to 80 atoms, uncovering three new lowest energy forms. We then applied GrowPAL to boron clusters containing 8 to 15 atoms, successfully identifying all reported minima. Overall, GrowPAL offers a practical solution for efficiently identifying global minima in hierarchical systems, thereby reducing computational costs.
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Affiliation(s)
- Carlos López-Castro
- Departamento
de Física Aplicada, Centro de Investigación
y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida 97310, Yucatán, México
| | - Filiberto Ortiz-Chi
- Conahcyt-Departamento
de Física Aplicada, Centro de Investigación
y de Estudios Avanzados del Instituto Politécnico Nacional, Antigua Carretera a Progreso km
6, Mérida, Yucatán 97310, México
| | - Gabriel Merino
- Departamento
de Física Aplicada, Centro de Investigación
y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida 97310, Yucatán, México
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29
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Röder K, Pasquali S. Assessing RNA atomistic force fields via energy landscape explorations in implicit solvent. Biophys Rev 2024; 16:285-295. [PMID: 39099837 PMCID: PMC11297004 DOI: 10.1007/s12551-024-01202-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 05/29/2024] [Indexed: 08/06/2024] Open
Abstract
Predicting the structure and dynamics of RNA molecules still proves challenging because of the relative scarcity of experimental RNA structures on which to train models and the very sensitive nature of RNA towards its environment. In the last decade, several atomistic force fields specifically designed for RNA have been proposed and are commonly used for simulations. However, it is not necessarily clear which force field is the most suitable for a given RNA molecule. In this contribution, we propose the use of the computational energy landscape framework to explore the energy landscape of RNA systems as it can bring complementary information to the more standard approaches of enhanced sampling simulations based on molecular dynamics. We apply the EL framework to the study of a small RNA pseudoknot, the Aquifex aeolicus tmRNA pseudoknot PK1, and we compare the results of five different RNA force fields currently available in the AMBER simulation software, in implicit solvent. With this computational approach, we can not only compare the predicted 'native' states for the different force fields, but the method enables us to study metastable states as well. As a result, our comparison not only looks at structural features of low energy folded structures, but provides insight into folding pathways and higher energy excited states, opening to the possibility of assessing the validity of force fields also based on kinetics and experiments providing information on metastable and unfolded states. Supplementary Information The online version contains supplementary material available at 10.1007/s12551-024-01202-9.
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Affiliation(s)
- Konstantin Röder
- Randall Centre for Cell & Molecular Biophysics, King’s College London, London, SE1 1UL UK
| | - Samuela Pasquali
- Laboratoire Biologie Functionnelle Et Adaptative, CNRS UMR 8251, Inserm ERL U1133, Université Paris Cité , 35 Rue Hélène Brion, Paris, France
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30
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Halonen R. Assessment of Anharmonicities in Clusters: Developing and Validating a Minimum-Information Partition Function. J Chem Theory Comput 2024; 20:4099-4114. [PMID: 38747413 DOI: 10.1021/acs.jctc.4c00121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Precise thermodynamic calculations are essential for understanding the dynamics of cluster systems and new particle formation. However, the widely employed harmonic statistical mechanical approach often falls short in terms of accuracy. In this study, we present an improved statistical model that incorporates vibrational anharmonicity via a novel partition function that requires only one additional system-specific input parameter. In addition to considering vibrational aspects, we also account for anharmonicity related to the configurational space. The role of anharmonicities is thoroughly examined in the case of general clusters, where the complete sets of conformers, mechanically stable spatial arrangements, are known up to clusters composed of 14 monomers. By performing consistent Monte Carlo simulations on these systems, we benchmark the statistical model's efficacy in reproducing key thermodynamic properties (formation free energy and potential energy) in the classical limit. The model exhibits exceptional alignment with simulations, accurately reproducing free energies within a precision of 2kBT and reliably capturing cluster melting temperatures. Furthermore, we demonstrate the significance and applicability of the model by reproducing thermodynamic barriers in homogeneous gas-phase nucleation of larger clusters. The transferability of our developed approach extends to more complex molecular systems and bears relevance for atmospheric multicomponent clusters, in particular.
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Affiliation(s)
- Roope Halonen
- Center for Joint Quantum Studies and Department of Physics, School of Science, Tianjin University, 92 Weijin Road, Tianjin 300072, China
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31
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Undurraga JA, Luke R, Van Yper L, Monaghan JJM, McAlpine D. The neural representation of an auditory spatial cue in the primate cortex. Curr Biol 2024; 34:2162-2174.e5. [PMID: 38718798 DOI: 10.1016/j.cub.2024.04.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/14/2024] [Accepted: 04/12/2024] [Indexed: 05/23/2024]
Abstract
Humans make use of small differences in the timing of sounds at the two ears-interaural time differences (ITDs)-to locate their sources. Despite extensive investigation, however, the neural representation of ITDs in the human brain is contentious, particularly the range of ITDs explicitly represented by dedicated neural detectors. Here, using magneto- and electro-encephalography (MEG and EEG), we demonstrate evidence of a sparse neural representation of ITDs in the human cortex. The magnitude of cortical activity to sounds presented via insert earphones oscillated as a function of increasing ITD-within and beyond auditory cortical regions-and listeners rated the perceptual quality of these sounds according to the same oscillating pattern. This pattern was accurately described by a population of model neurons with preferred ITDs constrained to the narrow, sound-frequency-dependent range evident in other mammalian species. When scaled for head size, the distribution of ITD detectors in the human cortex is remarkably like that recorded in vivo from the cortex of rhesus monkeys, another large primate that uses ITDs for source localization. The data solve a long-standing issue concerning the neural representation of ITDs in humans and suggest a representation that scales for head size and sound frequency in an optimal manner.
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Affiliation(s)
- Jaime A Undurraga
- Department of Linguistics, Macquarie University, 16 University Avenue, Sydney, NSW 2109, Australia; Interacoustics Research Unit, Technical University of Denmark, Ørsteds Plads, Building 352, 2800 Kgs. Lyngby, Denmark.
| | - Robert Luke
- Department of Linguistics, Macquarie University, 16 University Avenue, Sydney, NSW 2109, Australia; The Bionics Institute, 384-388 Albert St., East Melbourne, VIC 3002, Australia
| | - Lindsey Van Yper
- Department of Linguistics, Macquarie University, 16 University Avenue, Sydney, NSW 2109, Australia; Institute of Clinical Research, University of Southern Denmark, 5230 Odense, Denmark; Research Unit for ORL, Head & Neck Surgery and Audiology, Odense University Hospital & University of Southern Denmark, 5230 Odense, Denmark
| | - Jessica J M Monaghan
- Department of Linguistics, Macquarie University, 16 University Avenue, Sydney, NSW 2109, Australia; National Acoustic Laboratories, Australian Hearing Hub, 16 University Avenue, Sydney, NSW 2109, Australia
| | - David McAlpine
- Department of Linguistics, Macquarie University, 16 University Avenue, Sydney, NSW 2109, Australia; Macquarie University Hearing and the Australian Hearing Hub, Macquarie University, 16 University Avenue, Sydney, NSW 2109, Australia.
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32
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Schwerdtfeger P, Wales DJ. 100 Years of the Lennard-Jones Potential. J Chem Theory Comput 2024; 20:3379-3405. [PMID: 38669689 DOI: 10.1021/acs.jctc.4c00135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
It is now 100 years since Lennard-Jones published his first paper introducing the now famous potential that bears his name. It is therefore timely to reflect on the many achievements, as well as the limitations, of this potential in the theory of atomic and molecular interactions, where applications range from descriptions of intermolecular forces to molecules, clusters, and condensed matter.
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Affiliation(s)
- Peter Schwerdtfeger
- Centre for Theoretical Chemistry and Physics, The New Zealand Institute for Advanced Study, Massey University Auckland, Private Bag 102904, Auckland 0745, New Zealand
| | - David J Wales
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
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33
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Chakraborty B, Pal R, Pratihar DK, Chattaraj PK. Bonobo Optimizer: A New Tool Toward the Global Optimization of Small Atomic Clusters. J Phys Chem A 2024. [PMID: 38696762 DOI: 10.1021/acs.jpca.4c02024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2024]
Abstract
In the realm of structural and bonding investigations within chemical systems, elucidating global minimum energy configurations stands as a paramount goal. As the systems increase in size and complexity, this pursuit becomes progressively challenging. Herein, we introduce Bonobo optimizer (BO), a metaheuristic algorithm inspired by the social and reproductive behaviors of bonobos, to the domain of chemical problem solving. Focusing on small carbon clusters, this study systematically evaluates BO's performance, showcasing its robustness and efficiency. Parametric studies highlight the algorithm's adaptability, consistently converging to global minimum structures. Rigorous statistical validation supports the results, and a comparative analysis against established global optimization algorithms underlines BO's superior efficiency. This exploration extends the applicability of BO to the optimization of atomic clusters, providing a promising avenue for future advancements in computational chemistry.
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Affiliation(s)
- Bhrigu Chakraborty
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Ranita Pal
- Advanced Technology Development Centre, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Dilip Kumar Pratihar
- Department of Mechanical Engineering, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Pratim Kumar Chattaraj
- Department of Chemistry, Birla Institute of Technology, Mesra, Ranchi, Jharkhand 835215, India
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34
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Van Brandt S, Kapusuz KY, Sennesael J, Lemey S, Van Torre P, Verhaevert J, Van Hecke T, Rogier H. Reliability Analysis and Optimization of a Reconfigurable Matching Network for Communication and Sensing Antennas in Dynamic Environments through Gaussian Process Regression. SENSORS (BASEL, SWITZERLAND) 2024; 24:2689. [PMID: 38732793 PMCID: PMC11085883 DOI: 10.3390/s24092689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/13/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024]
Abstract
During the implementation of the Internet of Things (IoT), the performance of communication and sensing antennas that are embedded in smart surfaces or smart devices can be affected by objects in their reactive near field due to detuning and antenna mismatch. Matching networks have been proposed to re-establish impedance matching when antennas become detuned due to environmental factors. In this work, the change in the reflection coefficient at the antenna, due to the presence of objects, is first characterized as a function of the frequency and object distance by applying Gaussian process regression on experimental data. Based on this characterization, for random object positions, it is shown through simulation that a dynamic environment can lower the reliability of a matching network by up to 90%, depending on the type of object, the probability distribution of the object distance, and the required bandwidth. As an alternative to complex and power-consuming real-time adaptive matching, a new, resilient network tuning strategy is proposed that takes into account these random variations. This new approach increases the reliability of the system by 10% to 40% in these dynamic environment scenarios.
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Affiliation(s)
- Seppe Van Brandt
- Internet Technology and Data Science Lab, Department of Information Technology, Faculty of Engineering and Architecture, Ghent University and Imec, 9052 Gent, Belgium (J.V.); (H.R.)
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35
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Milia V, Tarrat N, Zanon C, Cortés J, Rapacioli M. Exploring Molecular Energy Landscapes by Coupling the DFTB Potential with a Tree-Based Stochastic Algorithm: Investigation of the Conformational Diversity of Phthalates. J Chem Inf Model 2024; 64:3290-3301. [PMID: 38497727 DOI: 10.1021/acs.jcim.3c01981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Exploring the global energy landscape of relatively large molecules at the quantum level is a challenging problem. In this work, we report the coupling of a nonredundant conformational space exploration method, namely, the robotics-inspired iterative global exploration and local optimization (IGLOO) algorithm, with the quantum-chemical density functional tight binding (DFTB) potential. The application of this fast and efficient computational approach to three close-sized molecules of the phthalate family (DBP, BBP, and DEHP) showed that they present different conformational landscapes. These differences have been rationalized by making use of descriptors based on distances and dihedral angles. Coulomb interactions, steric hindrance, and dispersive interactions have been found to drive the geometric properties. A strong correlation has been evidenced between the two dihedral angles describing the side-chain orientation of the phthalate molecules. Our approach identifies low-energy minima without prior knowledge of the potential energy surface, paving the way for future investigations into transition paths and states.
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Affiliation(s)
- Valentin Milia
- LAAS-CNRS, Université de Toulouse, CNRS, 31031 Toulouse, France
- Laboratoire de Chimie et Physique Quantiques LCPQ/FERMI, UMR 5626, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Nathalie Tarrat
- CEMES, Université de Toulouse, CNRS, 29 Rue Jeanne Marvig, F-31055 Toulouse, France
| | | | - Juan Cortés
- LAAS-CNRS, Université de Toulouse, CNRS, 31031 Toulouse, France
| | - Mathias Rapacioli
- Laboratoire de Chimie et Physique Quantiques LCPQ/FERMI, UMR 5626, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
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36
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Tao S, Shao X, Zhu L. Accelerating Structural Optimization through Fingerprinting Space Integration on the Potential Energy Surface. J Phys Chem Lett 2024; 15:3185-3190. [PMID: 38478975 DOI: 10.1021/acs.jpclett.4c00275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Structural optimization has been a crucial component in computational materials research, and structure predictions have relied heavily on this technique, in particular. In this study, we introduce a novel method that enhances the efficiency of local optimization by integrating extra fingerprint space into the optimization process. Our approach utilizes a mixed energy concept in the hyper potential energy surface (PES), combining real energy and a newly introduced fingerprint energy derived from the symmetry of the local atomic environment. This method strategically guides the optimization process toward high-symmetry, low-energy structures by leveraging the intrinsic symmetry of the atomic configurations. The effectiveness of our approach was demonstrated through structural optimizations of silicon, silicon carbide, and Lennard-Jones cluster systems. Our results show that the fingerprint space biasing technique significantly enhances the performance and probability of discovering energetically favorable, high-symmetry structures as compared to conventional optimizations. The proposed method is anticipated to streamline the search for new materials and facilitate the discovery of novel energetically favorable configurations.
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Affiliation(s)
- Shuo Tao
- Department of Physics, Rutgers University, Newark, New Jersey 07102, United States
| | - Xuecheng Shao
- Department of Physics, Rutgers University, Newark, New Jersey 07102, United States
| | - Li Zhu
- Department of Physics, Rutgers University, Newark, New Jersey 07102, United States
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37
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Pracht P, Grimme S, Bannwarth C, Bohle F, Ehlert S, Feldmann G, Gorges J, Müller M, Neudecker T, Plett C, Spicher S, Steinbach P, Wesołowski PA, Zeller F. CREST-A program for the exploration of low-energy molecular chemical space. J Chem Phys 2024; 160:114110. [PMID: 38511658 DOI: 10.1063/5.0197592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 02/29/2024] [Indexed: 03/22/2024] Open
Abstract
Conformer-rotamer sampling tool (CREST) is an open-source program for the efficient and automated exploration of molecular chemical space. Originally developed in Pracht et al. [Phys. Chem. Chem. Phys. 22, 7169 (2020)] as an automated driver for calculations at the extended tight-binding level (xTB), it offers a variety of molecular- and metadynamics simulations, geometry optimization, and molecular structure analysis capabilities. Implemented algorithms include automated procedures for conformational sampling, explicit solvation studies, the calculation of absolute molecular entropy, and the identification of molecular protonation and deprotonation sites. Calculations are set up to run concurrently, providing efficient single-node parallelization. CREST is designed to require minimal user input and comes with an implementation of the GFNn-xTB Hamiltonians and the GFN-FF force-field. Furthermore, interfaces to any quantum chemistry and force-field software can easily be created. In this article, we present recent developments in the CREST code and show a selection of applications for the most important features of the program. An important novelty is the refactored calculation backend, which provides significant speed-up for sampling of small or medium-sized drug molecules and allows for more sophisticated setups, for example, quantum mechanics/molecular mechanics and minimum energy crossing point calculations.
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Affiliation(s)
- Philipp Pracht
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Christoph Bannwarth
- Institute for Physical Chemistry, RWTH Aachen University, Melatener Str. 20, 52056 Aachen, Germany
| | - Fabian Bohle
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Sebastian Ehlert
- AI4Science, Microsoft Research, Evert van de Beekstraat 354, 1118 CZ Schiphol, The Netherlands
| | - Gereon Feldmann
- Institute for Physical Chemistry, RWTH Aachen University, Melatener Str. 20, 52056 Aachen, Germany
| | - Johannes Gorges
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Marcel Müller
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Tim Neudecker
- Institute for Physical and Theoretical Chemistry, University of Bremen, 28359 Bremen, Germany
| | - Christoph Plett
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | | | - Pit Steinbach
- Institute for Physical Chemistry, RWTH Aachen University, Melatener Str. 20, 52056 Aachen, Germany
| | - Patryk A Wesołowski
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Felix Zeller
- Institute for Physical and Theoretical Chemistry, University of Bremen, 28359 Bremen, Germany
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38
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Jestilä JS, Wu N, Priante F, Foster AS. Accelerated Lignocellulosic Molecule Adsorption Structure Determination. J Chem Theory Comput 2024; 20:2297-2312. [PMID: 38408381 PMCID: PMC10939001 DOI: 10.1021/acs.jctc.3c01292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/28/2024]
Abstract
Here, we present a study combining Bayesian optimization structural inference with the machine learning interatomic potential Neural Equivariant Interatomic Potential (NequIP) to accelerate and enable the study of the adsorption of the conformationally flexible lignocellulosic molecules β-d-xylose and 1,4-β-d-xylotetraose on a copper surface. The number of structure evaluations needed to map out the relevant potential energy surfaces are reduced by Bayesian optimization, while NequIP minimizes the time spent on each evaluation, ultimately resulting in cost-efficient and reliable sampling of large systems and configurational spaces. Although the applicability of Bayesian optimization for the conformational analysis of the more flexible xylotetraose molecule is restricted by the sample complexity bottleneck, the latter can be effectively bypassed with external conformer search tools, such as the Conformer-Rotamer Ensemble Sampling Tool, facilitating the subsequent lower-dimensional global minimum adsorption structure determination. Finally, we demonstrate the applicability of the described approach to find adsorption structures practically equivalent to the density functional theory counterparts at a fraction of the computational cost.
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Affiliation(s)
- Joakim S. Jestilä
- Department
of Applied Physics, Aalto University, 00076 Aalto, Espoo, Finland
| | - Nian Wu
- Department
of Applied Physics, Aalto University, 00076 Aalto, Espoo, Finland
| | - Fabio Priante
- Department
of Applied Physics, Aalto University, 00076 Aalto, Espoo, Finland
| | - Adam S. Foster
- Department
of Applied Physics, Aalto University, 00076 Aalto, Espoo, Finland
- Nano
Life Science Institute (WPI-NanoLSI), Kanazawa
University, 920-1192 Kanazawa, Japan
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39
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Garcia-Escobar F, Taniike T, Takahashi K. MonteCat: A Basin-Hopping-Inspired Catalyst Descriptor Search Algorithm for Machine Learning Models. J Chem Inf Model 2024; 64:1512-1521. [PMID: 38385190 DOI: 10.1021/acs.jcim.3c01952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Proposing relevant catalyst descriptors that can relate the information on a catalyst's composition to its actual performance is an ongoing area in catalyst informatics, as it is a necessary step to improve our understanding on the target reactions. Herein, a small descriptor-engineered data set containing 3289 descriptor variables and the performance of 200 catalysts for the oxidative coupling of methane (OCM) is analyzed, and a descriptor search algorithm based on the workflow of the Basin-hopping optimization methodology is proposed to select the descriptors that better fit a predictive model. The algorithm, which can be considered wrapper in nature, consists of the successive generation of random-based modifications to the descriptor subset used in a regression model and adopting them depending on their effect on the model's score. The results are presented after being tested on linear and Support Vector Regression models with average cross-validation r2 scores of 0.8268 and 0.6875, respectively.
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Affiliation(s)
| | - Toshiaki Taniike
- Graduate School of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Keisuke Takahashi
- Department of Chemistry, Hokkaido University, North 10, West 8, Sapporo 060-8510, Japan
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40
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Hu X, Amin KS, Schneider M, Lim C, Salahub D, Baldauf C. System-Specific Parameter Optimization for Nonpolarizable and Polarizable Force Fields. J Chem Theory Comput 2024; 20:1448-1464. [PMID: 38279917 PMCID: PMC10867808 DOI: 10.1021/acs.jctc.3c01141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 01/29/2024]
Abstract
The accuracy of classical force fields (FFs) has been shown to be limited for the simulation of cation-protein systems despite their importance in understanding the processes of life. Improvements can result from optimizing the parameters of classical FFs or by extending the FF formulation by terms describing charge transfer (CT) and polarization (POL) effects. In this work, we introduce our implementation of the CTPOL model in OpenMM, which extends the classical additive FF formula by adding CT and POL. Furthermore, we present an open-source parametrization tool, called FFAFFURR, that enables the (system-specific) parametrization of OPLS-AA and CTPOL models. The performance of our workflow was evaluated by its ability to reproduce quantum chemistry energies and by molecular dynamics simulations of a zinc-finger protein.
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Affiliation(s)
- Xiaojuan Hu
- Fritz-Haber-Institut
der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Kazi S. Amin
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Markus Schneider
- Fritz-Haber-Institut
der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Carmay Lim
- Institute
of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
- Department
of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Dennis Salahub
- Centre
for Molecular Simulation and Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Carsten Baldauf
- Fritz-Haber-Institut
der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
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41
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Kim HJ, Lee G, Oh SHV, Stampfl C, Soon A. Recalibrating the Experimentally Derived Structure of the Metastable Surface Oxide on Copper via Machine Learning-Accelerated In Silico Global Optimization. ACS NANO 2024; 18:4559-4569. [PMID: 38264984 DOI: 10.1021/acsnano.3c12249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
The oxidation of copper and its surface oxides are gaining increasing attention due to the enhanced CO2 reduction reaction (CO2RR) activity exhibited by partially oxidized copper among the copper-based catalysts. The "8" surface oxide on Cu(111) is seen as a promising structure for further study due to its resemblance to the highly active Cu2O(110) surface in the C-C coupling of the CO2RR, setting it apart from other O/Cu(111) surface oxides resembling Cu2O(111). However, recent X-ray photoelectron spectroscopy analysis challenges the currently accepted atomic structure of the "8" surface oxide, prompting a need for reevaluation. This study highlights the limitations of conventional methods when addressing such challenges, leading us to adopt global optimization search techniques. After a rigorous process to ensure robustness, the unbiased global minimum of the "8" surface oxide is identified. Interestingly, this configuration differs significantly from other surface oxides and also from previous "8" models while retaining similarities to the Cu2O(110) surface.
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Affiliation(s)
- Hyun Jun Kim
- Department of Materials Science & Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Giyeok Lee
- Department of Materials Science & Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Seung-Hyun Victor Oh
- Department of Materials Science & Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Catherine Stampfl
- School of Physics, The University of Sydney, Sydney, New South Wales 2006, Australia
- The University of Sydney Nano Institute, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Aloysius Soon
- Department of Materials Science & Engineering, Yonsei University, Seoul 03722, Republic of Korea
- School of Physics, The University of Sydney, Sydney, New South Wales 2006, Australia
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42
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Luna-Valenzuela A, Pedroza-Montero JN, Köster AM, Calaminici P, Gálvez-González LE, Posada-Amarillas A. Pd 8 Cluster: Too Small to Melt? A BOMD Study. J Phys Chem A 2024; 128:572-580. [PMID: 38207112 DOI: 10.1021/acs.jpca.3c06173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
The question of whether a solid-liquid phase transition occurs in small clusters poses a fundamental challenge. In this study, we attempt to elucidate this phenomenon through a thorough examination of the thermal behavior and structural stability of Pd8 clusters employing ab initio simulations. Initially, a systematic global search is carried out to identify the various isomers of the Pd8 cluster. This is accomplished by employing an ab initio basin-hopping algorithm and using the PBE/SDD scheme integrated in the Gaussian code. The resulting isomers are further refined through reoptimization using the deMon2k package. To ensure the structural firmness of the lowest-energy isomer, we calculated normal modes. The structural stability as a function of temperature is analyzed through the Born-Oppenheimer molecular dynamics (BOMD) approach. Multiple BOMD trajectories at distinct simulated temperatures are examined with data clustering analysis to determine cluster isomers. This analysis establishes a connection between the potential energy landscape and the simulated temperature. To address the question of cluster melting, canonical parallel-tempering BOMD runs are performed and analyzed with the multiple-histogram method. A broad maximum in the heat capacity curve indicates a melting transition between 500 and 600 K. To further examine this transition, the mean-squared displacement and the pair-distance distribution function are calculated. The results of these calculations confirm the existence of a solid-liquid phase transition, as indicated by the heat capacity curve.
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Affiliation(s)
- Analila Luna-Valenzuela
- Departamento de Ciencias de la Salud, Unidad Regional Los Mochis, Universidad Autónoma de Occidente, Blvd. Macario Gaxiola S/N, 81217 Los Mochis, Sinaloa, México
| | - Jesús N Pedroza-Montero
- Departamento de Química, CINVESTAV, Av. Instituto Politécnico Nacional, 2508 Ciudad de Mexico, México
| | - Andreas M Köster
- Departamento de Química, CINVESTAV, Av. Instituto Politécnico Nacional, 2508 Ciudad de Mexico, México
| | - Patrizia Calaminici
- Departamento de Química, CINVESTAV, Av. Instituto Politécnico Nacional, 2508 Ciudad de Mexico, México
| | - Luis E Gálvez-González
- Departamento de Investigación en Física, Universidad de Sonora, Blvd. Luis Encinas & Rosales, 83000 Hermosillo, Sonora, México
| | - Alvaro Posada-Amarillas
- Departamento de Investigación en Física, Universidad de Sonora, Blvd. Luis Encinas & Rosales, 83000 Hermosillo, Sonora, México
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43
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Wijerathne A, Sawyer A, Daya R, Paolucci C. Competition between Mononuclear and Binuclear Copper Sites across Different Zeolite Topologies. JACS AU 2024; 4:197-215. [PMID: 38274255 PMCID: PMC10806779 DOI: 10.1021/jacsau.3c00632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/12/2023] [Accepted: 12/20/2023] [Indexed: 01/27/2024]
Abstract
A key challenge for metal-exchanged zeolites is the determination of metal cation speciation and nuclearity under synthesis and reaction conditions. Copper-exchanged zeolites, which are widely used in automotive emissions control and potential catalysts for partial methane oxidation, have in particular evidenced a wide variety of Cu structures that are observed to change with exposure conditions, zeolite composition, and topology. Here, we develop predictive models for Cu cation speciation and nuclearity in CHA, MOR, BEA, AFX, and FER zeolite topologies using interatomic potentials, quantum chemical calculations, and Monte Carlo simulations to interrogate this vast configurational and compositional space. Model predictions are used to rationalize experimentally observed differences between Cu-zeolites in a wide-body of literature, including nuclearity populations, structural variations, and methanol per Cu yields. Our results show that both topological features and commonly observed Al-siting biases in MOR zeolites increase the population of binuclear Cu sites, explaining the small population of mononuclear Cu sites observed in these materials relative to other zeolites such as CHA and BEA. Finally, we used a machine learning classification model to determine the preference to form mononuclear or binuclear Cu sites at different Al configurations in 200 zeolites in the international zeolite database. Model results reveal several zeolite topologies at extreme ends of the mononuclear vs binuclear spectrum, highlighting synthetic options for realization of zeolites with strong Cu nuclearity preferences.
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Affiliation(s)
- Asanka Wijerathne
- Department
of Chemical Engineering, University of Virginia, Charlottesville, Virginia 22903, United States
| | - Allison Sawyer
- Department
of Chemical Engineering, University of Virginia, Charlottesville, Virginia 22903, United States
| | - Rohil Daya
- Cummins
Inc, Columbus, Indiana 47201, United States
| | - Christopher Paolucci
- Department
of Chemical Engineering, University of Virginia, Charlottesville, Virginia 22903, United States
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44
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Woods EJ, Wales DJ. Analysis and interpretation of first passage time distributions featuring rare events. Phys Chem Chem Phys 2024; 26:1640-1657. [PMID: 38059562 DOI: 10.1039/d3cp04199a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
In this contribution we consider theory and associated computational tools to treat the kinetics associated with competing pathways on multifunnel energy landscapes. Multifunnel landscapes are associated with molecular switches and multifunctional materials, and are expected to exhibit multiple relaxation time scales and associated thermodynamic signatures in the heat capacity. Our focus here is on the first passage time distribution, which is encoded in a kinetic transition network containing all the locally stable states and the pathways between them. This network can be renormalised to reduce the dimensionality, while exactly conserving the mean first passage time and approximately conserving the full distribution. The structure of the reduced network can be visualised using disconnectivity graphs. We show how features in the first passage time distribution can be associated with specific kinetic traps, and how the appearance of competing relaxation time scales depends on the starting conditions. The theory is tested for two model landscapes and applied to an atomic cluster and a disordered peptide. Our most important contribution is probably the reconstruction of the full distribution for long time scales, where numerical problems prevent direct calculations. Here we combine accurate treatment of the mean first passage time with the reliable part of the distribution corresponding to faster time scales. Hence we now have a fundamental understanding of both thermodynamic and kinetic signatures of multifunnel landscapes.
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Affiliation(s)
- Esmae J Woods
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge CB3 0HE, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - David J Wales
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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45
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Peng YH, He CC, Zhao YJ, Yang XB. High-throughput computational materials screening of transition metal peroxides. Phys Chem Chem Phys 2024; 26:2093-2100. [PMID: 38131363 DOI: 10.1039/d3cp03968d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Semiconductor materials of abnormal stoichiometric ratio often exhibit unique properties, yet it is still a challenge to determine the structures of such materials in an efficient way. Herein, we propose a method for structurally biased screening according to the coordination numbers and the numbers of Wyckoff positions, balancing the atom local environment and the global symmetry of structures. Based on first-principles calculations, we have predicted two metastable peroxides P21/c-ScO2 and Pmmn-TiO3 with more than six coordination points. For these two structures, the most stable intrinsic defect is the oxygen vacancy (VO) at the peroxide anion (O2-2), which induces the absence of antibonding orbital formed by O2-2 near the valence band maximum. With the introduction of VO, the decrease of coordination numbers leads to charge recombination, and results in the appearance of an ordered phase TiO2.5 with stronger Ti-O orbital hybridization. The proposed method presents a promising and feasible approach for the screening of novel compounds.
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Affiliation(s)
- Yin-Hui Peng
- School of Physics and Optoelectronics, South China University of Technology, Guangzhou 510640, China.
| | - Chang-Chun He
- School of Physics and Optoelectronics, South China University of Technology, Guangzhou 510640, China.
| | - Yu-Jun Zhao
- School of Physics and Optoelectronics, South China University of Technology, Guangzhou 510640, China.
| | - Xiao-Bao Yang
- School of Physics and Optoelectronics, South China University of Technology, Guangzhou 510640, China.
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46
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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.
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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
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47
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Liu YR, Jiang Y. Growth mechanism prediction for nanoparticles via structure matching polymerization. Phys Chem Chem Phys 2024; 26:1267-1273. [PMID: 38105690 DOI: 10.1039/d3cp04702d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Exploring structural and component evolution remains a challenging scientific problem for nanoscience. We propose a novel approach called principle of minimization of structure matching polymerization (SMP) change to rapidly explore the global minimum structure on the potential energy surface (PES). The new method can map low-dimensional stable structures to high-dimensional local minima, and this will make it possible for us to study the growth mechanisms of nanoparticles. Some new lowest-energy structures were found by SMP methods for sulfuric acid (SA)-dimethylamine (DMA) systems relative to previous studies. Additionally, we found that the growth process of boron clusters is mainly that the small-size boron clusters are continuously added to large-size boron clusters by structure matching for Bn (n = 2-36) systems, Bm + Bk → Bn, where m + k = n and 1 ≤ k ≤ 3. The SMP approach can greatly improve the search efficiency of other unbiased global optimization algorithms, such as basin-hopping (BH) and genetic algorithm (GA), with an enhancement of up to 19- and 7-fold relative to traditional BH and GA algorithms for searching the global minima of Bn (n = 14-22) systems. The SMP approach is general and flexible and can be applied to different kinds of problems, such as material structure design, crystal structure prediction, and new drug generation.
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Affiliation(s)
- Yi-Rong Liu
- Public Experimental Teaching Center, Panzhihua University, Panzhihua, Sichuan 61700, China.
| | - Yan Jiang
- School of Vanadium and Titanium, Panzhihua University, Panzhihua, Sichuan 61700, China
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48
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Keith AD, Sawyer EB, Choy DCY, Xie Y, Biggs GS, Klein OJ, Brear PD, Wales DJ, Barker PD. Combining experiment and energy landscapes to explore anaerobic heme breakdown in multifunctional hemoproteins. Phys Chem Chem Phys 2024; 26:695-712. [PMID: 38053511 DOI: 10.1039/d3cp03897a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
To survive, many pathogens extract heme from their host organism and break down the porphyrin scaffold to sequester the Fe2+ ion via a heme oxygenase. Recent studies have revealed that certain pathogens can anaerobically degrade heme. Our own research has shown that one such pathway proceeds via NADH-dependent heme degradation, which has been identified in a family of hemoproteins from a range of bacteria. HemS, from Yersinia enterocolitica, is the main focus of this work, along with HmuS (Yersinia pestis), ChuS (Escherichia coli) and ShuS (Shigella dysenteriae). We combine experiments, Energy Landscape Theory, and a bioinformatic investigation to place these homologues within a wider phylogenetic context. A subset of these hemoproteins are known to bind certain DNA promoter regions, suggesting not only that they can catalytically degrade heme, but that they are also involved in transcriptional modulation responding to heme flux. Many of the bacterial species responsible for these hemoproteins (including those that produce HemS, ChuS and ShuS) are known to specifically target oxygen-depleted regions of the gastrointestinal tract. A deeper understanding of anaerobic heme breakdown processes exploited by these pathogens could therefore prove useful in the development of future strategies for disease prevention.
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Affiliation(s)
- Alasdair D Keith
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
| | - Elizabeth B Sawyer
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
| | - Desmond C Y Choy
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
| | - Yuhang Xie
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
| | - George S Biggs
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
| | - Oskar James Klein
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
| | - Paul D Brear
- Department of Biochemistry, University of Cambridge, Sanger Building, Cambridge CB2 1GA, UK
| | - David J Wales
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
| | - Paul D Barker
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
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49
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Dearg M, Roncaglia C, Nelli D, El Koraychy EY, Ferrando R, Slater TJA, Palmer RE. Frame-by-frame observations of structure fluctuations in single mass-selected Au clusters using aberration-corrected electron microscopy. NANOSCALE HORIZONS 2023; 9:143-147. [PMID: 37877366 DOI: 10.1039/d3nh00291h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
The multi-dimensional potential energy surface (PES) of a nanoparticle, such as a bare cluster of metal atoms, controls both the structure and dynamic behaviour of the particle. These properties are the subject of numerous theoretical simulations. However, quantitative experimental measurements of critical PES parameters are needed to regulate the models employed in the theoretical work. Experimental measurements of parameters are currently few in number, while model parameters taken from bulk systems may not be suitable for nanosystems. Here we describe a new measurement methodology, in which the isomer structures of a single deposited nanocluster are obtained frame-by-frame in an aberration-corrected scanning transmission electron microscope (ac-STEM) in high angle annular dark field (HAADF) mode. Several gold clusters containing 309 ± 15 atoms were analysed individually after deposition from a mass-selected cluster source onto an amorphous carbon film. The main isomers identified are icosahedral (Ih), decahedral (Dh) and face-centred-cubic (fcc) (the bulk structure), alongside many amorphous (glassy) structures. The results, which are broadly consistent with static ac-STEM measurements of an ensemble of such clusters, open the way to dynamic measurements of many different nanoparticles of diverse sizes, shapes and compositions.
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Affiliation(s)
- Malcolm Dearg
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF24 4HF, UK.
- School of Physics, Engineering and Technology, University of York, York YO10 5DD, UK
| | - Cesare Roncaglia
- Dipartimento di Fisica, Universita di Genova, Via Dodecaneso 33, 16146 Genova, Italy
| | - Diana Nelli
- Dipartimento di Fisica, Universita di Genova, Via Dodecaneso 33, 16146 Genova, Italy
| | - El Yakout El Koraychy
- Dipartimento di Fisica, Universita di Genova, Via Dodecaneso 33, 16146 Genova, Italy
| | - Riccardo Ferrando
- Dipartimento di Fisica, Universita di Genova, Via Dodecaneso 33, 16146 Genova, Italy
| | - Thomas J A Slater
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF24 4HF, UK.
| | - Richard E Palmer
- Nanomaterials Lab, Swansea University, Bay Campus, Fabian Way, Swansea SA1 8EN, UK.
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50
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Meadows J, Röder K. The Effect of Pulling and Twisting Forces on Chameleon Sequence Peptides. Chemphyschem 2023; 24:e202300351. [PMID: 37818741 DOI: 10.1002/cphc.202300351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 10/06/2023] [Accepted: 10/06/2023] [Indexed: 10/13/2023]
Abstract
Chameleon sequences are amino acid sequences found in several distinct configurations in experiment. They challenge our understanding of the link between sequence and structure, and provide insight into structural competition in proteins. Here, we study the energy landscapes for three such sequences, and interrogate how pulling and twisting forces impact the available structural ensembles. Chameleon sequences do not necessarily exhibit multiple structural ensembles on a multifunnel energy landscape when we consider them in isolation. The application of even small forces leads to drastic changes in the energy landscapes. For pulling forces, we observe transitions from helical to extended structures in a very small span of forces. For twisting forces, the picture is much more complex, and highly dependent on the magnitude and handedness of the applied force as well as the reference angle for the twist. Depending on these parameters, more complex and more simplistic energy landscapes are observed alongside more and less diverse structural ensembles. The impact of even small forces is significant, confirming their likely role in folding events. In addition, small forces exerted by the remaining scaffold of a protein may be sufficient to lead to the adoption of a specific structural ensemble by a chameleon sequence.
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Affiliation(s)
- James Meadows
- Department of Chemistry, Durham University, Stockton Road, Durham, DH1 3LE, UK
- Previous affiliation: Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Konstantin Röder
- Randall Centre for Cell & Molecular Biophysics, King's College London, Guy's Campus, Great Maze Pond, London, SE1 1UL, UK
- Previous affiliation: Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
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