1
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Ajab H, Jafry AT, Sajid H, Addicoat MA, Ayub K, Haq MZU. An electrochemical sensing potential of cobalt oxide nanoparticles towards citric acid integrated with computational approach in food and biological media. Food Chem 2024; 455:139869. [PMID: 38850977 DOI: 10.1016/j.foodchem.2024.139869] [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: 03/13/2024] [Revised: 05/25/2024] [Accepted: 05/26/2024] [Indexed: 06/10/2024]
Abstract
Although citric acid (CA) has antioxidant, antibacterial, and acidulating properties, chronic ingestion of CA can cause urolithiasis, hypocalcemia, and duodenal cancer, emphasizing the need for early detection. There are very few documented electrochemical-based sensing methods for CA detection due to the challenging behavior of electrode fouling caused by reactive oxidation products. In this study, a novel, non-enzymatic, and economical electrochemical sensor based on cobalt oxide nanoparticles (CoOxNPs) is successfully reported for detection CA. The CoOxNPs were synthesized through a simple thermal decomposition method and characterized by SEM, FT-IR, EDX, and XRD techniques. The proposed sensing platform was optimized by various parameters, including pH (7.0), time (15 min), and concentration of nanoparticles (100 mM) etc. In a linear range of 0.05-2500 μM, a low detection limit (LOD) of 0.13 μM was achieved. Theoretical calculations (ΔRT), confirmed hydrogen bonding and electrostatic interactions between CoOxNPs and CA. The detection method exhibited high selectivity in real media like food and biological samples, with good recovery values when compared favorably to the HPLC method. To facilitate effective on-site investigation, such a sensing platform can be assembled into a portable device.
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Affiliation(s)
- Huma Ajab
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Pakistan.
| | - Ali Turab Jafry
- Faculty of Mechanical Engineering, GIK Institute of Engineering Sciences & Technology, Topi, District Swabi, KPK, 23640, Pakistan.
| | - Hasnain Sajid
- School of Science and Technology, Nottingham Trent University, Nottingham NG11 8NS, UK.
| | - Matthew A Addicoat
- School of Science and Technology, Nottingham Trent University, Nottingham NG11 8NS, UK.
| | - Khurshid Ayub
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Pakistan.
| | - Muhammad Zia Ul Haq
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Pakistan
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2
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Rojas C, Sarmiento N, Ayora E, Pis Diez R. Computational prediction of retention times of veterinary antibiotics obtained by liquid chromatography-mass spectrometry. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:6724-6732. [PMID: 38551410 DOI: 10.1002/jsfa.13499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 02/19/2024] [Accepted: 03/29/2024] [Indexed: 04/10/2024]
Abstract
BACKGROUND Veterinary antibiotics are chemical compounds used to kill or inhibit the growth of pathogenic bacteria associated with animal diseases. These molecules can be defined by their retention times (tR) in liquid chromatography-mass spectrometry (LC-MS). One strategy to predict the tR of new veterinary antibiotics is the development of predictive quantitative structure-property relationships (QSPRs), which were used in this study. RESULTS A database of 122 antibiotics was selected in which the tR was measured using a Hypersil GOLD column. An optimal three-feature model was developed by integrating the unsupervised variable reduction, replacement method variable subset selection, and multiple linear regression. The negligible differences among the coefficient of determination and the root-mean-square error for the training set (R2 = 0.902 and RMSEC = 0.871) and test set (Q2 = 0.854 and RMSEP = 1.064) indicate a stable and predictive model. In a further step, a more in-depth explanation of the mechanism of action of each descriptor in predicting the tR is provided, with the construction of the theoretical chemical space for accurate predictions of new antibiotics. CONCLUSION The in silico model developed in this work identified three molecular descriptors associated with aqueous solubility, octanol-water partition coefficient, and the presence of negative and lipophilic atom pairs. The QSPR developed here could be implemented by agricultural and food chemists to identify and monitor existing and new antibiotics within the framework of LC-MS. The computational model was developed in accordance with five principles outlined by the Organization for Economic Co-operation and Development. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Cristian Rojas
- Grupo de Investigación en Quimiometría y QSAR, Facultad de Ciencia y Tecnología, Universidad del Azuay, Cuenca, Ecuador
| | - Nicole Sarmiento
- Grupo de Investigación en Quimiometría y QSAR, Facultad de Ciencia y Tecnología, Universidad del Azuay, Cuenca, Ecuador
| | - Emilia Ayora
- Grupo de Investigación en Quimiometría y QSAR, Facultad de Ciencia y Tecnología, Universidad del Azuay, Cuenca, Ecuador
| | - Reinaldo Pis Diez
- CEQUINOR, Centro de Química Inorgánica (CONICET, UNLP), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata (UNLP), La Plata, Argentina
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3
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Ballweg T, Liu M, Grimm J, Sedghamiz E, Wenzel W, Franzreb M. All-atom modeling of methacrylate-based multi-modal chromatography resins for Langmuir constant prediction of peptides. J Chromatogr A 2024; 1730:465089. [PMID: 38879977 DOI: 10.1016/j.chroma.2024.465089] [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: 03/13/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 06/18/2024]
Abstract
In downstream processing, the intricate nature of the interactions between biomolecules and adsorbent materials presents a significant challenge in the prediction of their binding and elution behaviors. This complexity is further heightened in multi-modal chromatography (MMC), which employs two distinct binding mechanisms. To gain a deeper understanding of the involved interactions, simulating the adsorption of biomolecules on resin surfaces is a focal point of ongoing research. However, previous studies often simplified the adsorbent surface, modeling it as a flat or slightly curved plane without including a realistic backbone structure. Here, we introduce and validate two novel workflows aimed at predicting peptide binding behaviors in MMC, specifically targeting methacrylate-based resins. Our first achievement was the development of an all-atom model of a commercial MMC resin surface, incorporating its polymethacrylic backbone. Furthermore, we established and tested a workflow for rapid calculations of binding free energies (ΔG) with 10 linear peptides as target molecules. These ΔG calculations were effectively used to predict Langmuir constants, achieving a high coefficient of determination (R²) of 0.96. In subsequent benchmarking tests, our model outperformed established, simpler resin surface models in terms of predictive capabilities.
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Affiliation(s)
- Tim Ballweg
- Institute of Functional Interfaces, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen 76344, Germany
| | - Modan Liu
- Institute of Functional Interfaces, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen 76344, Germany
| | - Julian Grimm
- Institute of Functional Interfaces, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen 76344, Germany
| | - Elaheh Sedghamiz
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen 76344, Germany; Schrödinger, GmbH, Glücksteinallee 25, Mannheim 68163, Germany
| | - Wolfgang Wenzel
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen 76344, Germany
| | - Matthias Franzreb
- Institute of Functional Interfaces, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen 76344, Germany.
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4
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Souza TL, da Luz JZ, Barreto LDS, de Oliveira Ribeiro CA, Neto FF. Structure-based modeling to assess binding and endocrine disrupting potential of polycyclic aromatic hydrocarbons in Daniorerio. Chem Biol Interact 2024; 398:111109. [PMID: 38871163 DOI: 10.1016/j.cbi.2024.111109] [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: 01/19/2024] [Revised: 06/03/2024] [Accepted: 06/11/2024] [Indexed: 06/15/2024]
Abstract
Environmental contaminants, such as polycyclic aromatic hydrocarbons (PAHs), have raised concerns regarding their potential endocrine-disrupting effects on aquatic organisms, including fish. In this study, molecular docking and molecular dynamics techniques were employed to evaluate the endocrine-disrupting potential of PAHs in zebrafish, as a model organism. A virtual screening with 72 PAHs revealed a correlation between the number of PAH aromatic rings and their binding affinity to proteins involved in endocrine regulation. Furthermore, PAHs with the highest binding affinities for each protein were identified: cyclopenta[cd]pyrene for AR (-9.7 kcal/mol), benzo(g)chrysene for ERα (-11.5 kcal/mol), dibenzo(a,e)pyrene for SHBG (-8.7 kcal/mol), dibenz(a,h)anthracene for StAR (-11.2 kcal/mol), and 2,3-benzofluorene for TRα (-9.8 kcal/mol). Molecular dynamics simulations confirmed the stability of the protein-ligand complexes formed by the PAHs with the highest binding affinities throughout the simulations. Additionally, the effectiveness of the protocol used in this study was demonstrated by the receiver operating characteristic curve (ROC) analysis, which effectively distinguished decoys from true ligands. Therefore, this research provides valuable insights into the endocrine-disrupting potential of PAHs in fish, highlighting the importance of assessing their impact on aquatic ecosystems.
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Affiliation(s)
- Tugstênio L Souza
- Laboratório de Toxicologia Celular, Departamento de Biologia Celular, Universidade Federal do Paraná, CEP 81531-980, Curitiba, PR, Brazil.
| | - Jessica Zablocki da Luz
- Laboratório de Toxicologia Celular, Departamento de Biologia Celular, Universidade Federal do Paraná, CEP 81531-980, Curitiba, PR, Brazil
| | - Luiza Dos Santos Barreto
- Laboratório de Toxicologia Celular, Departamento de Biologia Celular, Universidade Federal do Paraná, CEP 81531-980, Curitiba, PR, Brazil
| | - Ciro Alberto de Oliveira Ribeiro
- Laboratório de Toxicologia Celular, Departamento de Biologia Celular, Universidade Federal do Paraná, CEP 81531-980, Curitiba, PR, Brazil
| | - Francisco Filipak Neto
- Laboratório de Toxicologia Celular, Departamento de Biologia Celular, Universidade Federal do Paraná, CEP 81531-980, Curitiba, PR, Brazil.
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5
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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 DOI: 10.1021/acs.inorgchem.4c01755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [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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6
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Zupanc A, Install J, Weckman T, Melander MM, Heikkilä MJ, Kemell M, Honkala K, Repo T. Sequential Selective Dissolution of Coinage Metals in Recyclable Ionic Media. Angew Chem Int Ed Engl 2024; 63:e202407147. [PMID: 38742485 DOI: 10.1002/anie.202407147] [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: 04/15/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 05/16/2024]
Abstract
Coinage metals Cu, Ag, and Au are essential for modern electronics and their recycling from waste materials is becoming increasingly important to guarantee the security of their supply. Designing new sustainable and selective procedures that would substitute currently used processes is crucial. Here, we describe an unprecedented approach for the sequential dissolution of single metals from Cu, Ag, and Au mixtures using biomass-derived ionic solvents and green oxidants. First, Cu can be selectively dissolved in the presence of Ag and Au with a choline chloride/urea/H2O2 mixture, followed by the dissolution of Ag in lactic acid/H2O2. Finally, the metallic Au, which is not soluble in either solution above, is dissolved in choline chloride/urea/Oxone. Subsequently, the metals were simply and quantitatively recovered from dissolutions, and the solvents were recycled and reused. The applicability of the developed approach was demonstrated by recovering metals from electronic waste substrates such as printed circuit boards, gold fingers, and solar panels. The dissolution reactions and selectivity were explored with different analytical techniques and DFT calculations. We anticipate our approach will pave a new way for the contemporary and sustainable recycling of multi-metal waste substrates.
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Affiliation(s)
- Anže Zupanc
- Department of Chemistry, Faculty of Science, University of Helsinki, A. I. Virtasen aukio 1, 00014, Helsinki, Finland
| | - Joseph Install
- Department of Chemistry, Faculty of Science, University of Helsinki, A. I. Virtasen aukio 1, 00014, Helsinki, Finland
| | - Timo Weckman
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, P.O. Box 35, FI-40014, Jyväskylä, Finland
| | - Marko M Melander
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, P.O. Box 35, FI-40014, Jyväskylä, Finland
| | - Mikko J Heikkilä
- Department of Chemistry, Faculty of Science, University of Helsinki, A. I. Virtasen aukio 1, 00014, Helsinki, Finland
| | - Marianna Kemell
- Department of Chemistry, Faculty of Science, University of Helsinki, A. I. Virtasen aukio 1, 00014, Helsinki, Finland
| | - Karoliina Honkala
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, P.O. Box 35, FI-40014, Jyväskylä, Finland
| | - Timo Repo
- Department of Chemistry, Faculty of Science, University of Helsinki, A. I. Virtasen aukio 1, 00014, Helsinki, Finland
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7
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Berquist E, Dumi A, Upadhyay S, Abarbanel OD, Cho M, Gaur S, Cano Gil VH, Hutchison GR, Lee OS, Rosen AS, Schamnad S, Schneider FSS, Steinmann C, Stolyarchuk M, Vandezande JE, Zak W, Langner KM. cclib 2.0: An updated architecture for interoperable computational chemistry. J Chem Phys 2024; 161:042501. [PMID: 39051837 DOI: 10.1063/5.0216778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 07/01/2024] [Indexed: 07/27/2024] Open
Abstract
Interoperability in computational chemistry is elusive, impeded by the independent development of software packages and idiosyncratic nature of their output files. The cclib library was introduced in 2006 as an attempt to improve this situation by providing a consistent interface to the results of various quantum chemistry programs. The shared API across programs enabled by cclib has allowed users to focus on results as opposed to output and to combine data from multiple programs or develop generic downstream tools. Initial development, however, did not anticipate the rapid progress of computational capabilities, novel methods, and new programs; nor did it foresee the growing need for customizability. Here, we recount this history and present cclib 2, focused on extensibility and modularity. We also introduce recent design pivots-the formalization of cclib's intermediate data representation as a tree-based structure, a new combinator-based parser organization, and parsed chemical properties as extensible objects.
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Affiliation(s)
- Eric Berquist
- Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - Amanda Dumi
- Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - Shiv Upadhyay
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Omri D Abarbanel
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, USA
| | - Minsik Cho
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139, USA
| | - Sagar Gaur
- MarkovML 23, Geary St. Suite 600, San Francisco, California 94108, USA
- International Institute of Information Technology, Prof. CR Rao Road Gachibowli, Hyderabad 500032, Telangana, India
| | | | - Geoffrey R Hutchison
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, USA
| | - Oliver S Lee
- Organic Semiconductor Centre, EaStCHEM School of Chemistry, University of St Andrews, St. Andrews KY16 9ST, United Kingdom
- Organic Semiconductor Centre, SUPA School of Physics and Astronomy, University of St Andrews, St. Andrews KY16 9SS, United Kingdom
| | - Andrew S Rosen
- Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
- Department of Materials Science and Engineering, University of California, Berkeley, California 94720, USA
| | | | | | - Casper Steinmann
- Department of Chemistry and Bioscience, Aalborg University, DK-9230 Aalborg, Denmark
| | | | | | - Weronika Zak
- Department of Computer Science, Loughborough University, Epinal Way, Loughborough, Leicestershire LE11 3TU, United Kingdom
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8
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Einsele R, Mitrić R. Nonadiabatic Exciton Dynamics and Energy Gradients in the Framework of FMO-LC-TDDFTB. J Chem Theory Comput 2024. [PMID: 39051619 DOI: 10.1021/acs.jctc.4c00539] [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
We introduce a novel methodology for simulating the excited-state dynamics of extensive molecular aggregates in the framework of the long-range corrected time-dependent density-functional tight-binding fragment molecular orbital method (FMO-LC-TDDFTB) combined with the mean-field Ehrenfest method. The electronic structure of the system is described in a quasi-diabatic basis composed of locally excited and charge-transfer states of all fragments. In order to carry out nonadiabatic molecular dynamics simulations, we derive and implement the excited-state gradients of the locally excited and charge-transfer states. Subsequently, the accuracy of the analytical excited-state gradients is evaluated. The applicability to the simulation of exciton transport in organic semiconductors is illustrated on a large cluster of anthracene molecules. Additionally, nonadiabatic molecular dynamics simulations of a model system of benzothieno-benzothiophene molecules highlight the method's utility in studying charge-transfer dynamics in organic materials. Our new methodology will facilitate the investigation of excitonic transfer in extensive biological systems, nanomaterials, and other complex molecular systems consisting of thousands of atoms.
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Affiliation(s)
- Richard Einsele
- Institut für Physikalische und Theoretische Chemie, Julius-Maximilians-Universität, Würzburg 97074, Germany
| | - Roland Mitrić
- Institut für Physikalische und Theoretische Chemie, Julius-Maximilians-Universität, Würzburg 97074, Germany
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9
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Wang L, Behara PK, Thompson MW, Gokey T, Wang Y, Wagner JR, Cole DJ, Gilson MK, Shirts MR, Mobley DL. The Open Force Field Initiative: Open Software and Open Science for Molecular Modeling. J Phys Chem B 2024; 128:7043-7067. [PMID: 38989715 DOI: 10.1021/acs.jpcb.4c01558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
Force fields are a key component of physics-based molecular modeling, describing the energies and forces in a molecular system as a function of the positions of the atoms and molecules involved. Here, we provide a review and scientific status report on the work of the Open Force Field (OpenFF) Initiative, which focuses on the science, infrastructure and data required to build the next generation of biomolecular force fields. We introduce the OpenFF Initiative and the related OpenFF Consortium, describe its approach to force field development and software, and discuss accomplishments to date as well as future plans. OpenFF releases both software and data under open and permissive licensing agreements to enable rapid application, validation, extension, and modification of its force fields and software tools. We discuss lessons learned to date in this new approach to force field development. We also highlight ways that other force field researchers can get involved, as well as some recent successes of outside researchers taking advantage of OpenFF tools and data.
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Affiliation(s)
- Lily Wang
- Open Force Field, Open Molecular Software Foundation, Davis, California 95616, United States
| | - Pavan Kumar Behara
- Center for Neurotherapeutics, University of California, Irvine, California 92697, United States
| | - Matthew W Thompson
- Open Force Field, Open Molecular Software Foundation, Davis, California 95616, United States
| | - Trevor Gokey
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Yuanqing Wang
- Simons Center for Computational Physical Chemistry and Center for Data Science, New York, New York 10004, United States
| | - Jeffrey R Wagner
- Open Force Field, Open Molecular Software Foundation, Davis, California 95616, United States
| | - Daniel J Cole
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California at San Diego, La Jolla, California 92093, United States
| | - Michael R Shirts
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80305, United States
| | - David L Mobley
- Department of Chemistry, University of California, Irvine, California 92697, United States
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
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10
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Pulgar A, Valentín M, Rauer C, Pla P, Alonso-Prados JL, Sandin-España P, Lamsabhi AM, Alcamí M. Theoretical Study of Structural and Electronic Trends of the Sulfonylurea Herbicides Family. J Phys Chem A 2024; 128:5941-5953. [PMID: 39013157 DOI: 10.1021/acs.jpca.4c03259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
The sulfonylurea herbicide family has been extensively studied using computational techniques. The most stable conformer structures of the 34 molecules analyzed in gaseous, aqueous, and octanol phases have been determined. The study employed CREST conformational search methods along with the CENSO script to explore all possible conformational structures. Additional evaluations conducted at the B3LYP-D3/6-311+G(d,p) level have enabled the identification of intramolecular stability patterns across the various compounds. It has been discovered that stability is primarily determined by two factors: intramolecular hydrogen bonding involving an NH group adjacent to the sulfonyl group with either N donors or the nearby carbonyl group and potential π-π interactions between the aromatic rings of the molecules. These have been characterized through QTAIM and NCI population analyses. Furthermore, with the goal of developing predictive models for the physicochemical properties of pesticides that include the sulfonylurea family, a statistical analysis among the different properties of the studied molecules has been conducted. Significant correlations have been found between various properties, predicting a promising future for the prediction of characteristics that could assist laboratories in selecting among different pesticides.
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Affiliation(s)
- Antonio Pulgar
- Departamento de Química, Facultad de Ciencias, Módulo 13, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Mónica Valentín
- Departamento de Química, Facultad de Ciencias, Módulo 13, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Clemens Rauer
- Departamento de Química, Facultad de Ciencias, Módulo 13, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Paula Pla
- Departamento de Química, Facultad de Ciencias, Módulo 13, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - José-Luis Alonso-Prados
- Plant Protection Products Unit/Plant Protection Department, National Institute for Agricultural and Food Research and Technology INIA-CSIC, Ctra. La Coruña, Km. 7.5, 28040 Madrid, Spain
| | - Pilar Sandin-España
- Plant Protection Products Unit/Plant Protection Department, National Institute for Agricultural and Food Research and Technology INIA-CSIC, Ctra. La Coruña, Km. 7.5, 28040 Madrid, Spain
| | - Al Mokhtar Lamsabhi
- Departamento de Química, Facultad de Ciencias, Módulo 13, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Manuel Alcamí
- Departamento de Química, Facultad de Ciencias, Módulo 13, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencias (IMDEA-Nanociencia), 28049 Madrid, Spain
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11
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Feng W, Hu Y, Wang M, Liu LY. Highly Defective Zirconium-Based Metal-Organic Frameworks for the Efficient Adsorption and Detection of Sugar Phosphates in the Biological Sample. ACS APPLIED MATERIALS & INTERFACES 2024; 16:37641-37655. [PMID: 38991175 DOI: 10.1021/acsami.4c06870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
Enrichment and quantification of sugar phosphates (SPx) in biological samples were of great significance in biological medicine. In this work, a series of zirconium-based metal-organic frameworks (MOFs) with different degrees of defects, namely, HP-UiO-66-NH2-X, were synthesized using acetic acid as a modulator and were utilized as high-capacity adsorbents for the adsorption of SPx in biological samples. The results indicated that the addition of acetic acid altered the morphology of HP-UiO-66-NH2-X, with corresponding changes in pore size (3.99-9.28 nm) and specific surface area (894.44-1142.50 m2·g-1). HP-UiO-66-NH2-10 showed the outstanding performance by achieving complete adsorption of all four SPx using only 80 μg of the adsorbent. The excellent adsorption efficiency of HP-UiO-66-NH2-10 was also obtained with a wide pH range and short adsorption time (10 min). Adsorption experiments demonstrated that the adsorption process involved chemical adsorption and multilayer adsorption. By utilizing X-ray photoelectron spectroscopy and density functional theory to explain the adsorption mechanism, it was found that various interactions (including coordination, hydrogen bonding, and electrostatic interactions) collectively contributed to the exceptional adsorption capability of HP-UiO-66-NH2-10. Those results indicated that the defect strategy not only increased the specific surface area and pore size, providing additional adsorption sites, but also reduced the adsorption energy between HP-UiO-66-NH2-10 and SPx. Moreover, HP-UiO-66-NH2-10 showed a low limit of detection (0.001-0.01 ng·mL-1), high precision (<13.77%), and accuracy (80.10-111.83%) in serum, liver, and cells, good stability, high selectivity (SPx/glucose, 1:100 molar ratio), and high adsorption capacity (292 mg·g-1 for SPx). The practical detection of SPx from human serum was also verified, prefiguring the great potentials of defective zirconium-based MOFs for the enrichment and detection of SPx in the biological medicine.
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Affiliation(s)
- Wanfang Feng
- Department of Sanitary Inspection, School of Public Health, Key Laboratory of Precision Nutrition and Health, Ministry of Education, Harbin Medical University, Harbin 150086, Heilongjiang, China
| | - Yuyan Hu
- Department of Sanitary Inspection, School of Public Health, Key Laboratory of Precision Nutrition and Health, Ministry of Education, Harbin Medical University, Harbin 150086, Heilongjiang, China
| | - Maoqing Wang
- Department of Sanitary Inspection, School of Public Health, Key Laboratory of Precision Nutrition and Health, Ministry of Education, Harbin Medical University, Harbin 150086, Heilongjiang, China
| | - Li-Yan Liu
- Department of Sanitary Inspection, School of Public Health, Key Laboratory of Precision Nutrition and Health, Ministry of Education, Harbin Medical University, Harbin 150086, Heilongjiang, China
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12
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Reinhardt CR, Manetsch MT, Li WL, Román-Leshkov Y, Head-Gordon T, Kulik HJ. Computational Screening of Putative Catalyst Transition Metal Complexes as Guests in a Ga 4L 612- Nanocage. Inorg Chem 2024. [PMID: 39049593 DOI: 10.1021/acs.inorgchem.4c02113] [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
Metal-organic cages form well-defined microenvironments that can enhance the catalytic proficiency of encapsulated transition metal complexes (TMCs). We introduce a screening protocol to efficiently identify TMCs that are promising candidates for encapsulation in the Ga4L612- nanocage. We obtain TMCs from the Cambridge Structural Database with geometric and electronic characteristics amenable to encapsulation and mine the text of associated manuscripts to curate TMCs with documented catalytic functionality. By docking candidate TMCs inside the nanocage cavity and carrying out electronic structure calculations, we identify a subset of successfully optimized candidates (TMC-34) and observe that encapsulated guests occupy an average of 60% of the cavity volume, in line with previous observations. Notably, some guests occupy as much as 72% of the cavity as a result of linker rotation. Encapsulation has a universal effect on the electrostatic potential (ESP), systematically decreasing the ESP at the metal center of each TMC in the TMC-34 data set, while minimally altering TMC metal partial charges. Collectively these observations support geometry-based screening of potential guests and suggest that encapsulation in Ga4L612- cages could electrostatically stabilize diverse cationic or electropositive intermediates. We highlight candidate guests with associated known reactivity and solubility most amenable for encapsulation in experimental follow-up studies.
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Affiliation(s)
- Clorice R Reinhardt
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Melissa T Manetsch
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Wan-Lu Li
- Kenneth S. Pitzer Center for Theoretical Chemistry, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Yuriy Román-Leshkov
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Teresa Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- Department of Bioengineering, University of California, Berkeley, California 94720, United States
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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13
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Piskorz T, Perez-Chirinos L, Qiao B, Sasselli IR. Tips and Tricks in the Modeling of Supramolecular Peptide Assemblies. ACS OMEGA 2024; 9:31254-31273. [PMID: 39072142 PMCID: PMC11270692 DOI: 10.1021/acsomega.4c02628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/17/2024] [Accepted: 06/19/2024] [Indexed: 07/30/2024]
Abstract
Supramolecular peptide assemblies (SPAs) hold promise as materials for nanotechnology and biomedicine. Although their investigation often entails adapting experimental techniques from their protein counterparts, SPAs are fundamentally distinct from proteins, posing unique challenges for their study. Computational methods have emerged as indispensable tools for gaining deeper insights into SPA structures at the molecular level, surpassing the limitations of experimental techniques, and as screening tools to reduce the experimental search space. However, computational studies have grappled with issues stemming from the absence of standardized procedures and relevant crystal structures. Fundamental disparities between SPAs and protein simulations, such as the absence of experimentally validated initial structures and the importance of the simulation size, number of molecules, and concentration, have compounded these challenges. Understanding the roles of various parameters and the capabilities of different models and simulation setups remains an ongoing endeavor. In this review, we aim to provide readers with guidance on the parameters to consider when conducting SPA simulations, elucidating their potential impact on outcomes and validity.
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Affiliation(s)
| | - Laura Perez-Chirinos
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 182, 20014 Donostia-San Sebastián, Spain
| | - Baofu Qiao
- Department
of Natural Sciences, Baruch College, City
University of New York, New York, New York 10010, United States
| | - Ivan R. Sasselli
- Centro
de Física de Materiales (CFM), CSIC-UPV/EHU, Paseo Manuel de Lardizabal 5, 20018 San Sebastián, Spain
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14
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Engsvang M, Wu H, Elm J. Iodine Clusters in the Atmosphere I: Computational Benchmark and Dimer Formation of Oxyacids and Oxides. ACS OMEGA 2024; 9:31521-31532. [PMID: 39072118 PMCID: PMC11270685 DOI: 10.1021/acsomega.4c01235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 06/19/2024] [Accepted: 06/21/2024] [Indexed: 07/30/2024]
Abstract
The contribution of iodine-containing compounds to atmospheric new particle formation is still not fully understood, but iodic acid and iodous acid are thought to be significant contributors. While several quantum chemical studies have been carried out on clusters containing iodine, there is no comprehensive benchmark study quantifying the accuracy of the applied methods. Here, we present the first study in a series that investigate the role of iodine species in atmospheric cluster formation. In this work, we have studied the iodic acid, iodous acid, iodine tetroxide, and iodine pentoxide monomers and their dimers formed with common atmospheric precursors. We have tested the accuracy of commonly applied methods for calculating the geometry of the monomers, thermal corrections of monomers and dimers, the contribution of spin-orbit coupling to monomers and dimers, and finally, the accuracy of the electronic energy correction calculated at different levels of theory. We find that optimizing the structures either at the ωB97X-D3BJ/aug-cc-pVTZ-PP or the M06-2X/aug-cc-pVTZ-PP level achieves the best thermal contribution to the binding free energy. The electronic energy correction can then be calculated at the ZORA-DLPNO-CCSD(T0) level with the SARC-ZORA-TZVPP basis for iodine and ma-ZORA-def2-TZVPP for non-iodine atoms. We applied this methodology to calculate the binding free energies of iodine-containing dimer clusters, where we confirm the qualitative trends observed in previous studies. However, we identify that previous studies overestimate the stability of the clusters by several kcal/mol due to the neglect of relativistic effects. This means that their contributions to the currently studied nucleation pathways of new particle formation are likely overestimated.
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Affiliation(s)
- Morten Engsvang
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Haide Wu
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Jonas Elm
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
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15
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Qi K, Qi H, Wang M, Ma X, Wang Y, Yao Q, Liu W, Zhao Y, Wang J, Wang Y, Qi W, Zhang J, Lu JR, Xu H. Chiral inversion induced by aromatic interactions in short peptide assembly. Nat Commun 2024; 15:6186. [PMID: 39043665 PMCID: PMC11266598 DOI: 10.1038/s41467-024-50448-0] [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: 02/08/2024] [Accepted: 07/09/2024] [Indexed: 07/25/2024] Open
Abstract
Although hydrophobic interactions provide the main driving force for initial peptide aggregation, their role in regulating suprastructure handedness of higher-order architectures remains largely unknown. We here interrogate the effects of hydrophobic amino acids on handedness at various assembly stages of peptide amphiphiles. Our studies reveal that relative to aliphatic side chains, aromatic side chains set the twisting directions of single β-strands due to their strong steric repulsion to the backbone, and upon packing into multi-stranded β-sheets, the side-chain aromatic interactions between strands form the aromatic ladders with a directional preference. This ordering not only leads to parallel β-sheet arrangements but also induces the chiral flipping over of single β-strands within a β-sheet. In contrast, the lack of orientational hydrophobic interactions in the assembly of aliphatic peptides implies no chiral inversion upon packing into β-sheets. This study opens an avenue to harness peptide aggregates with targeted handedness via aromatic side-chain interactions.
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Affiliation(s)
- Kai Qi
- State Key Laboratory of Heavy Oil Processing and Department of Biological and Energy Chemical Engineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao, 266580, China
| | - Hao Qi
- State Key Laboratory of Heavy Oil Processing and Department of Biological and Energy Chemical Engineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao, 266580, China
| | - Muhan Wang
- Department of Civil Engineering, Qingdao University of Technology, Qingdao, 266033, China
| | - Xiaoyue Ma
- State Key Laboratory of Heavy Oil Processing and Department of Biological and Energy Chemical Engineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao, 266580, China
| | - Yan Wang
- State Key Laboratory of Heavy Oil Processing and Department of Biological and Energy Chemical Engineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao, 266580, China
| | - Qiang Yao
- State Key Laboratory of Heavy Oil Processing and Department of Biological and Energy Chemical Engineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao, 266580, China
| | - Wenliang Liu
- State Key Laboratory of Heavy Oil Processing and Department of Biological and Energy Chemical Engineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao, 266580, China
| | - Yurong Zhao
- State Key Laboratory of Heavy Oil Processing and Department of Biological and Energy Chemical Engineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao, 266580, China
| | - Jiqian Wang
- State Key Laboratory of Heavy Oil Processing and Department of Biological and Energy Chemical Engineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao, 266580, China
| | - Yuefei Wang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Wei Qi
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Jun Zhang
- School of Materials Science and Engineering, China University of Petroleum (East China), Qingdao, 266580, China.
| | - Jian R Lu
- Biological Physics Group, Department of Physics and Astronomy, The University of Manchester, Manchester, M13 9PL, United Kingdom.
| | - Hai Xu
- State Key Laboratory of Heavy Oil Processing and Department of Biological and Energy Chemical Engineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao, 266580, China.
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16
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Haji Dehabadi M, Saidi H, Zafari F, Irani M. Assessing the accuracy and efficacy of multiscale computational methods in predicting reaction mechanisms and kinetics of S N2 reactions and Claisen rearrangement. Sci Rep 2024; 14:16791. [PMID: 39039180 PMCID: PMC11263649 DOI: 10.1038/s41598-024-67468-x] [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: 04/29/2024] [Accepted: 07/11/2024] [Indexed: 07/24/2024] Open
Abstract
This study investigates the application of quantum mechanical (QM) and multiscale computational methods in understanding the reaction mechanisms and kinetics of SN2 reactions involving methyl iodide with NH2OH and NH2O-, as well as the Claisen rearrangement of 8-(vinyloxy)dec-9-enoate. Our aim is to evaluate the accuracy and effectiveness of these methods in predicting experimental outcomes for these organic reactions. We achieve this by employing QM-only calculations and several hybrids of QM and molecular mechanics (MM) methods, namely QM/MM, QM1/QM2, and QM1/QM2/MM methodologies. For the SN2 reactions, our results demonstrate the importance of explicitly including solvent effects in the calculations to accurately reproduce the transition state geometry and energetics. The multiscale methods, particularly QM/MM and QM1/QM2, show promising performance in predicting activation energies. Moreover, we observe that the size of the MM active region significantly affects the accuracy of calculated activation energies, highlighting the need for careful consideration during the setup of multiscale calculations. In the case of the Claisen rearrangement, both QM-only and multiscale methods successfully reproduce the proposed reaction mechanism. However, the activation free energies calculated using a continuum solvation model, based on single-point calculations of QM-only structures, fail to account for solvent effects. On the other hand, multiscale methods more accurately capture the impact of solvents on activation free energies, with systematic error correction enhancing the accuracy of the results. Furthermore, we introduce a Python code for setting up multiscale calculations with ORCA, which is available on GitHub at https://github.com/iranimehdi/pdbtoORCA .
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Affiliation(s)
| | - Hamid Saidi
- Department of Chemistry, University of Kurdistan, Sanandaj, 66177-15175, Iran
| | - Faezeh Zafari
- Department of Chemistry, University of Kurdistan, Sanandaj, 66177-15175, Iran
| | - Mehdi Irani
- Department of Chemistry, University of Kurdistan, Sanandaj, 66177-15175, Iran.
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17
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Ho TH, Tong HD, Trinh TT. Molecular insights into the interactions between PEG carriers and drug molecules from Celastrus hindsii: a multi-scale simulation study. Sci Rep 2024; 14:16777. [PMID: 39039128 PMCID: PMC11263547 DOI: 10.1038/s41598-024-67720-4] [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: 06/10/2024] [Accepted: 07/15/2024] [Indexed: 07/24/2024] Open
Abstract
Efficient drug delivery is crucial for the creation of effective pharmaceutical treatments, and polyethylene glycol (PEG) carriers have been emerged as promising candidates for this purpose due to their bio-compatibility, enhancement of drug solubility, and stability. In this study, we utilized molecular simulations to examine the interactions between PEG carriers and selected drug molecules extracted from Celastrus hindsii: Hindsiilactone A, Hindsiiquinoflavan B, Maytenfolone A, and Celasdin B. The simulations provided detailed insights into the binding affinity, stability, and structural properties of these drug molecules when complexed with PEG carriers. A multi-scale approach combining density functional theory (DFT), extended tight-binding (xTB), and molecular dynamics (MD) simulations was conducted to investigate both unbound and bound states of PEG/drug systems. The results from DFT and xTB calculations revealed that the unbound complex has an unfavorable binding free energy, primarily due to negative contributions of delta solvation free energy and entropy. The MD simulations provided more detailed insights into the interactions between PEG and drug molecules in water solutions. By integrating the findings from the multi-scale simulations, a comprehensive picture of the unbound and bound states of PEG and drug systems were obtained. This information is valuable for understanding the molecular mechanisms governing the binding of drugs in PEG-based delivery platforms, and it contributes to the rational design and optimization of these systems.
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Affiliation(s)
- Thi H Ho
- Laboratory for Computational Physics, Institute for Computational Science and Artificial Intelligence, Van Lang University, Ho Chi Minh City, 70000, Vietnam
- Faculty of Mechanical - Electrical and Computer Engineering, School of Technology, Van Lang University, Ho Chi Minh City, 70000, Vietnam
| | - Hien Duy Tong
- Faculty of Engineering, Vietnamese-German University (VGU), Thu Dau Mot City, Binh Duong Province, 75000, Vietnam
| | - Thuat T Trinh
- Porelab, Department of Chemistry, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway.
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18
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Overstreet R, King E, Clopton G, Nguyen J, Ciesielski D. QC-GN 2oMS 2: a Graph Neural Net for High Resolution Mass Spectra Prediction. J Chem Inf Model 2024. [PMID: 39013165 DOI: 10.1021/acs.jcim.4c00446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
Predicting the mass spectrum of a molecular ion is often accomplished via three generalized approaches: rules-based methods for bond breaking, deep learning, or quantum chemical (QC) modeling. Rules-based approaches are often limited by the conditions for different chemical subspaces and perform poorly under chemical regimes with few defined rules. QC modeling is theoretically robust but requires significant amounts of computational time to produce a spectrum for a given target. Among deep learning techniques, graph neural networks (GNNs) have performed better than previous work with fingerprint-based neural networks in mass spectra prediction. To explore this technique further, we investigate the effects of including quantum chemically derived information as edge features in the GNN to increase predictive accuracy. The models we investigated include categorical bond order, bond force constants derived from extended tight-binding (xTB) quantum chemistry, and acyclic bond dissociation energies. We evaluated these models against a control GNN with no edge features in the input graphs. Bond dissociation enthalpies yielded the best improvement with a cosine similarity score of 0.462 relative to the baseline model (0.437). In this work we also apply dynamic graph attention which improves performance on benchmark problems and supports the inclusion of edge features. Between implementations, we investigate the nature of the molecular embedding for spectra prediction and discuss the recognition of fragment topographies in distinct chemistries for further development in tandem mass spectrometry prediction.
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Affiliation(s)
- Richard Overstreet
- Signature Science and Technology Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Ethan King
- Computing and Analytics Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Grady Clopton
- Department of Chemistry, Tennessee State University, Nashville, Tennessee 37209, United States
| | - Julia Nguyen
- Computing and Analytics Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Danielle Ciesielski
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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19
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Tarek Ibrahim M, Wait E, Ren P. Quantum Mechanics Characterization of Non-Covalent Interaction in Nucleotide Fragments. Molecules 2024; 29:3258. [PMID: 39064837 PMCID: PMC11279843 DOI: 10.3390/molecules29143258] [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: 05/31/2024] [Revised: 07/03/2024] [Accepted: 07/06/2024] [Indexed: 07/28/2024] Open
Abstract
Accurate calculation of non-covalent interaction energies in nucleotides is crucial for understanding the driving forces governing nucleic acid structure and function, as well as developing advanced molecular mechanics forcefields or machine learning potentials tailored to nucleic acids. Here, we dissect the nucleotides' structure into three main constituents: nucleobases (A, G, C, T, and U), sugar moieties (ribose and deoxyribose), and phosphate group. The interactions among these fragments and between fragments and water were analyzed. Different quantum mechanical methods were compared for their accuracy in capturing the interaction energy. The non-covalent interaction energy was decomposed into electrostatics, exchange-repulsion, dispersion, and induction using two ab initio methods: Symmetry-Adapted Perturbation Theory (SAPT) and Absolutely Localized Molecular Orbitals (ALMO). These calculations provide a benchmark for different QM methods, in addition to providing a valuable understanding of the roles of various intermolecular forces in hydrogen bonding and aromatic stacking. With SAPT, a higher theory level and/or larger basis set did not necessarily give more accuracy. It is hard to know which combination would be best for a given system. In contrast, ALMO EDA2 did not show dependence on theory level or basis set; additionally, it is faster.
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Affiliation(s)
- Mayar Tarek Ibrahim
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA;
| | - Elizabeth Wait
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, TX 78712, USA;
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA;
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, TX 78712, USA;
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20
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Stishenko P, McSloy A, Onat B, Hourahine B, Maurer RJ, Kermode JR, Logsdail A. Integrated workflows and interfaces for data-driven semi-empirical electronic structure calculations. J Chem Phys 2024; 161:012502. [PMID: 38958157 DOI: 10.1063/5.0209742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 06/07/2024] [Indexed: 07/04/2024] Open
Abstract
Modern software engineering of electronic structure codes has seen a paradigm shift from monolithic workflows toward object-based modularity. Software objectivity allows for greater flexibility in the application of electronic structure calculations, with particular benefits when integrated with approaches for data-driven analysis. Here, we discuss different approaches to create deep modular interfaces that connect big-data workflows and electronic structure codes and explore the diversity of use cases that they can enable. We present two such interface approaches for the semi-empirical electronic structure package, DFTB+. In one case, DFTB+ is applied as a library and provides data to an external workflow; in another, DFTB+receives data via external bindings and processes the information subsequently within an internal workflow. We provide a general framework to enable data exchange workflows for embedding new machine-learning-based Hamiltonians within DFTB+ or enabling deep integration of DFTB+ in multiscale embedding workflows. These modular interfaces demonstrate opportunities in emergent software and workflows to accelerate scientific discovery by harnessing existing software capabilities.
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Affiliation(s)
- Pavel Stishenko
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, United Kingdom
| | - Adam McSloy
- Warwick Centre for Predictive Modelling, School of Engineering, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Berk Onat
- Warwick Centre for Predictive Modelling, School of Engineering, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Ben Hourahine
- SUPA, Department of Physics, John Anderson Building, University of Strathclyde, 107 Rottenrow, Glasgow G4 0NG, United Kingdom
| | - Reinhard J Maurer
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom and Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - James R Kermode
- Warwick Centre for Predictive Modelling, School of Engineering, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Andrew Logsdail
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, United Kingdom
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21
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Medrano Sandonas L, Van Rompaey D, Fallani A, Hilfiker M, Hahn D, Perez-Benito L, Verhoeven J, Tresadern G, Kurt Wegner J, Ceulemans H, Tkatchenko A. Dataset for quantum-mechanical exploration of conformers and solvent effects in large drug-like molecules. Sci Data 2024; 11:742. [PMID: 38972891 PMCID: PMC11228031 DOI: 10.1038/s41597-024-03521-8] [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: 03/18/2024] [Accepted: 06/13/2024] [Indexed: 07/09/2024] Open
Abstract
We here introduce the Aquamarine (AQM) dataset, an extensive quantum-mechanical (QM) dataset that contains the structural and electronic information of 59,783 low-and high-energy conformers of 1,653 molecules with a total number of atoms ranging from 2 to 92 (mean: 50.9), and containing up to 54 (mean: 28.2) non-hydrogen atoms. To gain insights into the solvent effects as well as collective dispersion interactions for drug-like molecules, we have performed QM calculations supplemented with a treatment of many-body dispersion (MBD) interactions of structures and properties in the gas phase and implicit water. Thus, AQM contains over 40 global and local physicochemical properties (including ground-state and response properties) per conformer computed at the tightly converged PBE0+MBD level of theory for gas-phase molecules, whereas PBE0+MBD with the modified Poisson-Boltzmann (MPB) model of water was used for solvated molecules. By addressing both molecule-solvent and dispersion interactions, AQM dataset can serve as a challenging benchmark for state-of-the-art machine learning methods for property modeling and de novo generation of large (solvated) molecules with pharmaceutical and biological relevance.
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Affiliation(s)
- Leonardo Medrano Sandonas
- Department of Physics and Materials Science, University of Luxembourg, L-1511, Luxembourg City, Luxembourg.
- Institute for Materials Science and Max Bergmann Center of Biomaterials, TU Dresden, 01062, Dresden, Germany.
| | - Dries Van Rompaey
- Drug Discovery Data Sciences (D3S), Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Alessio Fallani
- Department of Physics and Materials Science, University of Luxembourg, L-1511, Luxembourg City, Luxembourg
- Drug Discovery Data Sciences (D3S), Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Mathias Hilfiker
- Department of Physics and Materials Science, University of Luxembourg, L-1511, Luxembourg City, Luxembourg
| | - David Hahn
- Computational Chemistry, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Laura Perez-Benito
- Computational Chemistry, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Jonas Verhoeven
- Drug Discovery Data Sciences (D3S), Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Gary Tresadern
- Computational Chemistry, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Joerg Kurt Wegner
- Drug Discovery Data Sciences (D3S), Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
- Drug Discovery Data Sciences (D3S), Johnson & Johnson Innovative Medicine, 301 Binney Street, MA 02142, Cambridge, USA
| | - Hugo Ceulemans
- Drug Discovery Data Sciences (D3S), Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Alexandre Tkatchenko
- Department of Physics and Materials Science, University of Luxembourg, L-1511, Luxembourg City, Luxembourg.
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22
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Giese TJ, Zeng J, Lerew L, McCarthy E, Tao Y, Ekesan Ş, York DM. Software Infrastructure for Next-Generation QM/MM-ΔMLP Force Fields. J Phys Chem B 2024; 128:6257-6271. [PMID: 38905451 DOI: 10.1021/acs.jpcb.4c01466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/23/2024]
Abstract
We present software infrastructure for the design and testing of new quantum mechanical/molecular mechanical and machine-learning potential (QM/MM-ΔMLP) force fields for a wide range of applications. The software integrates Amber's molecular dynamics simulation capabilities with fast, approximate quantum models in the xtb package and machine-learning potential corrections in DeePMD-kit. The xtb package implements the recently developed density-functional tight-binding QM models with multipolar electrostatics and density-dependent dispersion (GFN2-xTB), and the interface with Amber enables their use in periodic boundary QM/MM simulations with linear-scaling QM/MM particle-mesh Ewald electrostatics. The accuracy of the semiempirical models is enhanced by including machine-learning correction potentials (ΔMLPs) enabled through an interface with the DeePMD-kit software. The goal of this paper is to present and validate the implementation of this software infrastructure in molecular dynamics and free energy simulations. The utility of the new infrastructure is demonstrated in proof-of-concept example applications. The software elements presented here are open source and freely available. Their interface provides a powerful enabling technology for the design of new QM/MM-ΔMLP models for studying a wide range of problems, including biomolecular reactivity and protein-ligand binding.
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Affiliation(s)
- Timothy J Giese
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Jinzhe Zeng
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Lauren Lerew
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Erika McCarthy
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Yujun Tao
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Şölen Ekesan
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Darrin M York
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
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23
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Polynski MV, Vlasova YS, Solovev YV, Kozlov SM, Ananikov VP. Computational analysis of R-X oxidative addition to Pd nanoparticles. Chem Sci 2024; 15:9977-9986. [PMID: 38966374 PMCID: PMC11220582 DOI: 10.1039/d4sc00628c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 05/11/2024] [Indexed: 07/06/2024] Open
Abstract
Oxidative addition (OA) is a necessary step in mechanisms of widely used synthetic methodologies such as the Heck reaction, cross-coupling reactions, and the Buchwald-Hartwig amination. This study pioneers the exploration of OA of aryl halide to palladium nanoparticles (NPs), a process previously unaddressed in contrast to the activity of well-studied Pd(0) complexes. Employing DFT modeling and semi-empirical metadynamics simulations, the oxidative addition of phenyl bromide to Pd nanoparticles was investigated in detail. Energy profiles of oxidative addition to Pd NPs were analyzed and compared to those involving Pd(0) complexes forming under both ligand-stabilized (phosphines) and ligandless (amine base) conditions. Metadynamics simulations highlighted the edges of the (1 1 1) facets of Pd NPs as the key element of oxidative addition activity. We demonstrate that OA to Pd NPs is not only kinetically facile at ambient temperatures but also thermodynamically favorable. This finding accentuates the necessity of incorporating OA to Pd NPs in future investigations, thus providing a more realistic view of the involved catalytic mechanisms. These results enhance the understanding of aryl halide (cross-)coupling reactions, reinforcing the concept of a catalytic "cocktail". This concept posits dynamic interconversions between diverse active and inactive centers, collectively affecting the outcome of the reaction. High activity of Pd NPs in direct C-X activation paves the way for novel approaches in catalysis, potentially enhancing the field and offering new catalytic pathways to consider.
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Affiliation(s)
- Mikhail V Polynski
- Department of Chemical and Biomolecular Engineering, National University of Singapore 4 Engineering Drive 4 Singapore 117585 Singapore
| | - Yulia S Vlasova
- Faculty of Chemistry, Moscow State University Leninskiye Gory 1-3 Moscow 119991 Russia
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences Leninsky Prospect 47 Moscow 119991 Russia
| | - Yaroslav V Solovev
- M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences Miklukho-Maklaya 16/10 Moscow 117997 Russia
| | - Sergey M Kozlov
- Department of Chemical and Biomolecular Engineering, National University of Singapore 4 Engineering Drive 4 Singapore 117585 Singapore
| | - Valentine P Ananikov
- Faculty of Chemistry, Moscow State University Leninskiye Gory 1-3 Moscow 119991 Russia
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences Leninsky Prospect 47 Moscow 119991 Russia
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24
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Ofodum NM, Qi Q, Chandradat R, Warfle T, Lu X. Advancing Dynamic Polymer Mechanochemistry through Synergetic Conformational Gearing. J Am Chem Soc 2024; 146:17700-17711. [PMID: 38888499 DOI: 10.1021/jacs.4c02066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Harnessing mechanical force to modulate material properties and enhance biomechanical functions is essential for advancing smart materials and bioengineering. Polymer mechanochemistry provides an emerging toolkit for exploring unconventional chemical transformations and modulating molecular structures through mechanical force. One of the key challenges is developing innovative force-sensing mechanisms for precise and in situ force detection. This study introduces mDPAC, a dynamic and sensitive mechanophore, demonstrating its mechanochromic properties through synergetic conformational gearing. Its unique mechanoresponsive mechanism is based on the simultaneous conformational synergy between its phenazine and phenyl moieties, facilitated by a worm-gear-like structure. We confirm mDPAC's complex mechanochemical response and elucidate its mechanotransduction mechanism through our experimental data and comprehensive simulations. The compatibility of mDPAC with hydrogels is particularly notable, highlighting its potential for applications in aqueous biological environments as a dynamic force sensor. Moreover, mDPAC's multicolored mechanochromic responses facilitate direct force sensing and visual detection, paving the way for precise and real-time mechanical force sensing in bulk materials.
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Affiliation(s)
- Nnamdi M Ofodum
- Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Ave, Potsdam, New York 13699, United States
| | - Qingkai Qi
- Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Ave, Potsdam, New York 13699, United States
| | - Richard Chandradat
- Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Ave, Potsdam, New York 13699, United States
| | - Theodore Warfle
- Department of Chemical and Biomolecular Engineering, Clarkson University, 8 Clarkson Ave, Potsdam, New York 13699, United States
| | - Xiaocun Lu
- Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Ave, Potsdam, New York 13699, United States
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25
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Garg D, Chopra P, Lee JWL, Tikhonov DS, Kumar S, Akcaalan O, Allum F, Boll R, Butler AA, Erk B, Gougoula E, Gruet SP, He L, Heathcote D, Jones E, Kazemi MM, Lahl J, Lemmens AK, Liu Z, Loru D, Maclot S, Mason R, Merrick J, Müller E, Mullins T, Papadopoulou CC, Passow C, Peschel J, Plach M, Ramm D, Robertson P, Rompotis D, Simao A, Steber AL, Tajalli A, Tul-Noor A, Vadassery N, Vinklárek IS, Techert S, Küpper J, Rijs AM, Rolles D, Brouard M, Bari S, Eng-Johnsson P, Vallance C, Burt M, Manschwetus B, Schnell M. Ultrafast dynamics of fluorene initiated by highly intense laser fields. Phys Chem Chem Phys 2024. [PMID: 38958416 DOI: 10.1039/d3cp05063g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
We present an investigation of the ultrafast dynamics of the polycyclic aromatic hydrocarbon fluorene initiated by an intense femtosecond near-infrared laser pulse (810 nm) and probed by a weak visible pulse (405 nm). Using a multichannel detection scheme (mass spectra, electron and ion velocity-map imaging), we provide a full disentanglement of the complex dynamics of the vibronically excited parent molecule, its excited ionic states, and fragments. We observed various channels resulting from the strong-field ionization regime. In particular, we observed the formation of the unstable tetracation of fluorene, above-threshold ionization features in the photoelectron spectra, and evidence of ubiquitous secondary fragmentation. We produced a global fit of all observed time-dependent photoelectron and photoion channels. This global fit includes four parent ions extracted from the mass spectra, 15 kinetic-energy-resolved ionic fragments extracted from ion velocity map imaging, and five photoelectron channels obtained from electron velocity map imaging. The fit allowed for the extraction of 60 lifetimes of various metastable photoinduced intermediates.
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Affiliation(s)
- Diksha Garg
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.
- Department of Physics, Universität Hamburg, Hamburg, Germany
| | - Pragya Chopra
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.
- Institute of Physical Chemistry, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Jason W L Lee
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | | | - Sonu Kumar
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.
- Department of Physics, Universität Hamburg, Hamburg, Germany
| | | | - Felix Allum
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | | | - Alexander A Butler
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Benjamin Erk
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.
| | - Eva Gougoula
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.
| | | | - Lanhai He
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Germany
| | - David Heathcote
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Ellen Jones
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Mehdi M Kazemi
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.
| | - Jan Lahl
- Department of Physics, Lund University, Lund, Sweden
| | - Alexander K Lemmens
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
- FELIX Laboratory, Radboud University, Nijmegen, The Netherlands
| | - Zhihao Liu
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Donatella Loru
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.
| | | | - Robert Mason
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - James Merrick
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Erland Müller
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.
| | - Terry Mullins
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Germany
- European XFEL, Schenefeld, Germany
| | | | | | | | - Marius Plach
- Department of Physics, Lund University, Lund, Sweden
| | - Daniel Ramm
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.
| | - Patrick Robertson
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Dimitrios Rompotis
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.
- European XFEL, Schenefeld, Germany
| | - Alcides Simao
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.
| | | | - Ayhan Tajalli
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.
| | - Atia Tul-Noor
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.
| | - Nidin Vadassery
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Germany
- Department of Chemistry, Universität Hamburg, Hamburg, Germany
| | - Ivo S Vinklárek
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Germany
| | - Simone Techert
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.
| | - Jochen Küpper
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Germany
- Department of Physics, Universität Hamburg, Hamburg, Germany
- Center for Ultrafast Imaging, Universität Hamburg, Hamburg, Germany
- Department of Chemistry, Universität Hamburg, Hamburg, Germany
| | - Anouk M Rijs
- Division of BioAnalytical Chemistry, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Daniel Rolles
- J. R. Macdonald Laboratory, Department of Physics, Kansas State University, Manhattan, KS, USA
| | - Mark Brouard
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Sadia Bari
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | | | - Claire Vallance
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Michael Burt
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | | | - Melanie Schnell
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.
- Institute of Physical Chemistry, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
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26
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Laranjeira JS, Martins N, Denis PA, Sambrano J. Unveiling a New 2D Semiconductor: Biphenylene-Based InN. ACS OMEGA 2024; 9:28879-28887. [PMID: 38973873 PMCID: PMC11223256 DOI: 10.1021/acsomega.4c03511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 06/10/2024] [Accepted: 06/12/2024] [Indexed: 07/09/2024]
Abstract
The two-dimensional (2D) materials class earned a boost in 2021 with biphenylene synthesis, which is structurally formed by the fusion of four-, six-, and eight-membered carbon rings, usually named 4-6-8-biphenylene network (BPN). This research proposes a detailed study of electronic, structural, dynamic, and mechanical properties to demonstrate the potential of the novel biphenylene-like indium nitride (BPN-InN) via density functional theory and molecular dynamics simulations. The BPN-InN has a direct band gap energy transition of 2.02 eV, making it promising for optoelectronic applications. This structure exhibits maximum and minimum Young modulus of 22.716 and 22.063 N/m, Poisson ratio of 0.018 and -0.008, and Shear modulus of 11.448 and 10.860 N/m, respectively. To understand the BPN-InN behavior when subjected to mechanical deformations, biaxial and uniaxial strains in armchair and zigzag directions from -8 to 8% were applied, achieving a band gap energy modulation of 1.36 eV over tensile deformations. Our findings are expected to motivate both theorists and experimentalists to study and obtain these new 2D inorganic materials that exhibit promising semiconductor properties.
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Affiliation(s)
- José
A. S. Laranjeira
- Modeling
and Molecular Simulation Group, School of Sciences, São Paulo State University (UNESP), Bauru 17033-360, Brazil
| | - Nicolas Martins
- Modeling
and Molecular Simulation Group, School of Sciences, São Paulo State University (UNESP), Bauru 17033-360, Brazil
| | - Pablo A. Denis
- Computational
Nanotechnology, DETEMA, Facultad de Química, UDELAR, CC 1157, 11800 Montevideo, Uruguay
| | - Julio Sambrano
- Modeling
and Molecular Simulation Group, School of Sciences, São Paulo State University (UNESP), Bauru 17033-360, Brazil
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27
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Kaupp M, Wodyński A, Arbuznikov AV, Fürst S, Schattenberg CJ. Toward the Next Generation of Density Functionals: Escaping the Zero-Sum Game by Using the Exact-Exchange Energy Density. Acc Chem Res 2024; 57:1815-1826. [PMID: 38905497 PMCID: PMC11223257 DOI: 10.1021/acs.accounts.4c00209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Revised: 05/29/2024] [Accepted: 06/03/2024] [Indexed: 06/23/2024]
Abstract
ConspectusKohn-Sham density functional theory (KS DFT) is arguably the most widely applied electronic-structure method with tens of thousands of publications each year in a wide variety of fields. Its importance and usefulness can thus hardly be overstated. The central quantity that determines the accuracy of KS DFT calculations is the exchange-correlation functional. Its exact form is unknown, or better "unknowable", and therefore the derivation of ever more accurate yet efficiently applicable approximate functionals is the "holy grail" in the field. In this context, the simultaneous minimization of so-called delocalization errors and static correlation errors is the greatest challenge that needs to be overcome as we move toward more accurate yet computationally efficient methods. In many cases, an improvement on one of these two aspects (also often termed fractional-charge and fractional-spin errors, respectively) generates a deterioration in the other one. Here we report on recent notable progress in escaping this so-called "zero-sum-game" by constructing new functionals based on the exact-exchange energy density. In particular, local hybrid and range-separated local hybrid functionals are discussed that incorporate additional terms that deal with static correlation as well as with delocalization errors. Taking hints from other coordinate-space models of nondynamical and strong electron correlations (the B13 and KP16/B13 models), position-dependent functions that cover these aspects in real space have been devised and incorporated into the local-mixing functions determining the position-dependence of exact-exchange admixture of local hybrids as well as into the treatment of range separation in range-separated local hybrids. While initial functionals followed closely the B13 and KP16/B13 frameworks, meanwhile simpler real-space functions based on ratios of semilocal and exact-exchange energy densities have been found, providing a basis for relatively simple and numerically convenient functionals. Notably, the correction terms can either increase or decrease exact-exchange admixture locally in real space (and in interelectronic-distance space), leading even to regions with negative admixture in cases of particularly strong static correlations. Efficient implementations into a fast computer code (Turbomole) using seminumerical integration techniques make such local hybrid and range-separated local hybrid functionals promising new tools for complicated composite systems in many research areas, where simultaneously small delocalization errors and static correlation errors are crucial. First real-world application examples of the new functionals are provided, including stretched bonds, symmetry-breaking and hyperfine coupling in open-shell transition-metal complexes, as well as a reduction of static correlation errors in the computation of nuclear shieldings and magnetizabilities. The newest versions of range-separated local hybrids (e.g., ωLH23tdE) retain the excellent frontier-orbital energies and correct asymptotic exchange-correlation potential of the underlying ωLH22t functional while improving substantially on strong-correlation cases. The form of these functionals can be further linked to the performance of the recent impactful deep-neural-network "black-box" functional DM21, which itself may be viewed as a range-separated local hybrid.
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Affiliation(s)
- Martin Kaupp
- Institut für Chemie,
Theoretische Chemie/Quantenchemie, Technische
Universität Berlin, Sekr. C7, Strasse des 17. Juni 115, 10623 Berlin, Germany
| | - Artur Wodyński
- Institut für Chemie,
Theoretische Chemie/Quantenchemie, Technische
Universität Berlin, Sekr. C7, Strasse des 17. Juni 115, 10623 Berlin, Germany
| | - Alexei V. Arbuznikov
- Institut für Chemie,
Theoretische Chemie/Quantenchemie, Technische
Universität Berlin, Sekr. C7, Strasse des 17. Juni 115, 10623 Berlin, Germany
| | - Susanne Fürst
- Institut für Chemie,
Theoretische Chemie/Quantenchemie, Technische
Universität Berlin, Sekr. C7, Strasse des 17. Juni 115, 10623 Berlin, Germany
| | - Caspar J. Schattenberg
- Institut für Chemie,
Theoretische Chemie/Quantenchemie, Technische
Universität Berlin, Sekr. C7, Strasse des 17. Juni 115, 10623 Berlin, Germany
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28
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Yang N, Wang ST, Li CS, Zhang J, Zhang MY, Fang WH. Designing External Pores of Aluminum Oxo Polyhedrons for Efficient Iodine Capture. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2311083. [PMID: 38268236 DOI: 10.1002/smll.202311083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/10/2024] [Indexed: 01/26/2024]
Abstract
Although metal-organic polyhedra (MOPs) expansion has been studied to date, it is still a rare occurrence for their porous intermolecular assembly for iodine capture. The major limitation is the lack of programmable and controllable methods for effectively constructing and utilizing the exterior cavities. Herein, the goal of programmable porous intermolecular assembly is realized in the first family of aluminum oxo polyhedrons (AlOPs) using ligands with directional H-bonding donor/acceptor pairs and auxiliary alcohols as structural regulation sites. The approach has the advantage of avoiding the use of expensive edge-directed ditopic and face-directed tritopic ligands in the general synthesis strategy of MOPs. Combining theoretical calculations and experiments, the intrinsic relationship is revealed between alcohol ligands and the growth mechanism of AlOPs. The maximum I2 uptake based on the mass gain during sorption corresponds to 2.35 g g-1, representing the highest reported I2 sorption by an MOP. In addition, it can be easily regenerated and maintained the iodine sorption capacity, revealing its further potential application. This method of constructing stable and programmable porous materials will provide a new way to solve problems such as radionuclide capture.
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Affiliation(s)
- Ning Yang
- State Key Laboratory of Structural Chemistry, Chinese Academy of Sciences, Fujian Institute of Research on the Structure of Matter, Fuzhou, Fujian, 350002, P. R. China
- Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - San-Tai Wang
- State Key Laboratory of Structural Chemistry, Chinese Academy of Sciences, Fujian Institute of Research on the Structure of Matter, Fuzhou, Fujian, 350002, P. R. China
| | - Chun-Sen Li
- State Key Laboratory of Structural Chemistry, Chinese Academy of Sciences, Fujian Institute of Research on the Structure of Matter, Fuzhou, Fujian, 350002, P. R. China
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, Fujian, 361005, P. R. China
| | - Jian Zhang
- State Key Laboratory of Structural Chemistry, Chinese Academy of Sciences, Fujian Institute of Research on the Structure of Matter, Fuzhou, Fujian, 350002, P. R. China
| | - Min-Yi Zhang
- State Key Laboratory of Structural Chemistry, Chinese Academy of Sciences, Fujian Institute of Research on the Structure of Matter, Fuzhou, Fujian, 350002, P. R. China
| | - Wei-Hui Fang
- State Key Laboratory of Structural Chemistry, Chinese Academy of Sciences, Fujian Institute of Research on the Structure of Matter, Fuzhou, Fujian, 350002, P. R. China
- Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
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29
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Tikhonov DS, Lee JWL, Schnell M. On the thermodynamic stability of polycations. J Chem Phys 2024; 160:244110. [PMID: 38934634 DOI: 10.1063/5.0207526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
We present a simple approximation to estimate the largest charge that a given molecule can hold until fragmentation into smaller charged species becomes more energetically favorable. This approximation solely relies on the ionization potentials, electron affinities of the parent and fragment species, and also on the neutral parent's dissociation energy. By parameterizing these quantities, it is possible to obtain analytical phase diagrams of polycationic stability. We demonstrate the applicability of this approach by discussing the maximal charge dependence on the size of the molecular system. A numerical demonstration for linear polyenes, monocyclic annulenes, and helium clusters is provided.
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Affiliation(s)
- Denis S Tikhonov
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Jason W L Lee
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Melanie Schnell
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- Institute of Physical Chemistry, Christian-Albrechts-Universität zu Kiel, Max-Eyth-Str. 1, 24118 Kiel, Germany
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30
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He D, Ji H, Liu T, Yang M, Clowes R, Little MA, Liu M, Cooper AI. Self-Assembly of Chiral Porous Metal-Organic Polyhedra from Trianglsalen Macrocycles. J Am Chem Soc 2024; 146:17438-17445. [PMID: 38860872 PMCID: PMC11212058 DOI: 10.1021/jacs.4c04928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/24/2024] [Accepted: 05/28/2024] [Indexed: 06/12/2024]
Abstract
Metal-organic polyhedra (MOPs) can exhibit tunable porosity and functionality, suggesting potential for applications such as molecular separations. MOPs are typically constructed by the bottom-up multicomponent self-assembly of organic ligands and metal ions, and the final functionality can be hard to program. Here, we used trianglsalen macrocycles as preorganized building blocks to assemble octahedral-shaped MOPs. The resultant MOPs inherit most of the preorganized properties of the macrocyclic ligands, including their well-defined cavities and chirality. As a result, the porosity in the MOPs could be tuned by modifying the structure of the macrocycle building blocks. Using this strategy, we could systematically enlarge the size of the MOPs from 26.3 to 32.1 Å by increasing the macrocycle size. The family of MOPs shows experimental surface areas of up to 820 m2/g, and they are stable in water. One of these MOPs can efficiently separate the rare gases Xe from Kr because the prefabricated macrocyclic windows of MOPs can be modified to sit at the Xe/Kr size cutoff range.
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Affiliation(s)
- Donglin He
- Materials
Innovation Factory and Department of Chemistry, University of Liverpool, 51 Oxford Street, Liverpool L7 3NY, U.K.
| | - Heng Ji
- ZJU-Hangzhou
Global Scientific and Technological Innovation Center, Hangzhou 311215, China
- Department
of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Tao Liu
- Materials
Innovation Factory and Department of Chemistry, University of Liverpool, 51 Oxford Street, Liverpool L7 3NY, U.K.
- Leverhulme
Research Centre for Functional Materials Design, University of Liverpool, 51 Oxford Street, Liverpool L7 3NY, U.K.
| | - Miao Yang
- ZJU-Hangzhou
Global Scientific and Technological Innovation Center, Hangzhou 311215, China
- Department
of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Rob Clowes
- Materials
Innovation Factory and Department of Chemistry, University of Liverpool, 51 Oxford Street, Liverpool L7 3NY, U.K.
| | - Marc A. Little
- Institute
of Chemical Sciences, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, U.K.
| | - Ming Liu
- ZJU-Hangzhou
Global Scientific and Technological Innovation Center, Hangzhou 311215, China
- Department
of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Andrew I. Cooper
- Materials
Innovation Factory and Department of Chemistry, University of Liverpool, 51 Oxford Street, Liverpool L7 3NY, U.K.
- Leverhulme
Research Centre for Functional Materials Design, University of Liverpool, 51 Oxford Street, Liverpool L7 3NY, U.K.
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31
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Csizi KS, Steiner M, Reiher M. Nanoscale chemical reaction exploration with a quantum magnifying glass. Nat Commun 2024; 15:5320. [PMID: 38909029 PMCID: PMC11193806 DOI: 10.1038/s41467-024-49594-2] [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: 09/29/2023] [Accepted: 06/04/2024] [Indexed: 06/24/2024] Open
Abstract
Nanoscopic systems exhibit diverse molecular substructures by which they facilitate specific functions. Theoretical models of them, which aim at describing, understanding, and predicting these capabilities, are difficult to build. Viable quantum-classical hybrid models come with specific challenges regarding atomistic structure construction and quantum region selection. Moreover, if their dynamics are mapped onto a state-to-state mechanism such as a chemical reaction network, its exhaustive exploration will be impossible due to the combinatorial explosion of the reaction space. Here, we introduce a "quantum magnifying glass" that allows one to interactively manipulate nanoscale structures at the quantum level. The quantum magnifying glass seamlessly combines autonomous model parametrization, ultra-fast quantum mechanical calculations, and automated reaction exploration. It represents an approach to investigate complex reaction sequences in a physically consistent manner with unprecedented effortlessness in real time. We demonstrate these features for reactions in bio-macromolecules and metal-organic frameworks, diverse systems that highlight general applicability.
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Affiliation(s)
- Katja-Sophia Csizi
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Miguel Steiner
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
- ETH Zurich, NCCR Catalysis, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Markus Reiher
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
- ETH Zurich, NCCR Catalysis, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
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32
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Müller DS, Charki P, Cordier M, Gellrich U. Utilization of 13C NMR Carbon Shifts for the Attribution of Diastereomers in Methyl-Substituted Cyclohexanes. J Org Chem 2024; 89:8668-8675. [PMID: 38856090 DOI: 10.1021/acs.joc.4c00602] [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
In this report, we address the challenge of assigning diastereomers for methyl cyclohexanes, particularly those with quaternary centers, which remains nontrivial despite modern NMR techniques. By utilizing a HSQC NMR experiment to identify methyl-carbons coupled with a simple conformational analysis, we identified an effective and quite general method for assigning stereochemistry, even in cases where diastereomeric mixtures are inseparable.
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Affiliation(s)
- Daniel S Müller
- Univ Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes)-UMR 6226, F-35000 Rennes, France
| | - Paul Charki
- Univ Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes)-UMR 6226, F-35000 Rennes, France
| | - Marie Cordier
- Univ Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes)-UMR 6226, F-35000 Rennes, France
| | - Urs Gellrich
- Department of Organic Chemistry, University of Hohenheim, Garbenstrasse 30, 70599 Stuttgart, Germany
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33
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Liang RR, Yang Y, Han Z, Bakhmutov VI, Rushlow J, Fu Y, Wang KY, Zhou HC. Zirconium-Based Metal-Organic Frameworks with Free Hydroxy Groups for Enhanced Perfluorooctanoic Acid Uptake in Water. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024:e2407194. [PMID: 38896032 DOI: 10.1002/adma.202407194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 06/10/2024] [Indexed: 06/21/2024]
Abstract
Perfluorooctanoic acid (PFOA) is a highly recalcitrant organic pollutant, and its bioaccumulation severely endangers human health. While various methods are developed for PFOA removal, the targeted design of adsorbents with high efficiency and reusability remains largely unexplored. Here the rational design and synthesis of two novel zirconium-based metal‒organic frameworks (MOFs) bearing free ortho-hydroxy sites, namely noninterpenetrated PCN-1001 and twofold interpenetrated PCN-1002, are presented. Single crystal analysis of the pure ligand reveals that intramolecular hydrogen bonding plays a pivotal role in directing the formation of MOFs with free hydroxy groups. Furthermore, the transformation from PCN-1001 to PCN-1002 is realized. Compared to PCN-1001, PCN-1002 displays higher chemical stability due to interpenetration, thereby demonstrating an exceptional PFOA adsorption capacity of up to 632 mg g-1 (1.53 mmol g-1), which is comparable to the reported record values. Moreover, PCN-1002 shows rapid kinetics, high selectivity, and long-life cycles in PFOA removal tests. Solid-state nuclear magnetic resonance results and density functional theory calculations reveal that multiple hydrogen bonds between the free ortho-hydroxy sites and PFOA, along with Lewis acid-base interaction, work collaboratively to enhance PFOA adsorption.
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Affiliation(s)
- Rong-Ran Liang
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Yihao Yang
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Zongsu Han
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | | | - Joshua Rushlow
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Yubin Fu
- Center for Advancing Electronics Dresden (cfaed) & Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Mommsenstrasse 4, 01062, Dresden, Germany
- Max Planck Institute of Microstructure Physics, Weinberg 2, 06120, Halle, Germany
| | - Kun-Yu Wang
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Hong-Cai Zhou
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
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34
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Johnson N, Pattinson C, Burgoyne K, Hijazi K, Houssen WE, Milne BF. SARS-CoV-2 Spike Protein-Derived Cyclic Peptides as Modulators of Spike Interaction with GRP78. Chembiochem 2024; 25:e202300789. [PMID: 38613462 DOI: 10.1002/cbic.202300789] [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: 11/22/2023] [Revised: 04/12/2024] [Accepted: 04/12/2024] [Indexed: 04/15/2024]
Abstract
The human glucose-regulated protein GRP78 is a human chaperone that translocactes to the cell surface when cells are under stress. Theoretical studies suggested it could be involved in SARS-CoV-2 virus entry to cells. In this work, we used in vitro surface plasmon resonance-based assays to show that human GRP78 indeed binds to SARS-CoV-2 spike protein. We have designed and synthesised cyclic peptides based on the loop structure of amino acids 480-488 of the SARS-CoV-2 spike protein S1 domain from the Wuhan and Omicron variants and showed that both peptides bind to GRP78. Consistent with the greater infectiousness of the Omicron variant, the Omicron-derived peptide displays slower dissociation from the target protein. Both peptides significantly inhibit the binding of wild-type S1 protein to the human protein GRP78 suggesting that further development of these cyclic peptide motifs may provide a viable route to novel anti-SARS-CoV-2 agents.
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Affiliation(s)
- Nicholas Johnson
- Institute of Medical Sciences, University of Aberdeen, Ashgrove Road West, Aberdeen, AB25 2ZD, UK
| | - Craig Pattinson
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, AB25 2ZD, UK
| | - Kate Burgoyne
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, AB25 2ZD, UK
| | - Karolin Hijazi
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, AB25 2ZD, UK
| | - Wael E Houssen
- Institute of Medical Sciences, University of Aberdeen, Ashgrove Road West, Aberdeen, AB25 2ZD, UK
- Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen, AB24 3UE, UK
| | - Bruce F Milne
- Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen, AB24 3UE, UK
- CFisUC, Department of Physics, University of Coimbra, Rua Larga, 3004-516, Coimbra, Portugal
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35
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Tao Y, Giese TJ, Ekesan Ş, Zeng J, Aradi B, Hourahine B, Aktulga HM, Götz AW, Merz KM, York DM. Amber free energy tools: Interoperable software for free energy simulations using generalized quantum mechanical/molecular mechanical and machine learning potentials. J Chem Phys 2024; 160:224104. [PMID: 38856060 DOI: 10.1063/5.0211276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 05/15/2024] [Indexed: 06/11/2024] Open
Abstract
We report the development and testing of new integrated cyberinfrastructure for performing free energy simulations with generalized hybrid quantum mechanical/molecular mechanical (QM/MM) and machine learning potentials (MLPs) in Amber. The Sander molecular dynamics program has been extended to leverage fast, density-functional tight-binding models implemented in the DFTB+ and xTB packages, and an interface to the DeePMD-kit software enables the use of MLPs. The software is integrated through application program interfaces that circumvent the need to perform "system calls" and enable the incorporation of long-range Ewald electrostatics into the external software's self-consistent field procedure. The infrastructure provides access to QM/MM models that may serve as the foundation for QM/MM-ΔMLP potentials, which supplement the semiempirical QM/MM model with a MLP correction trained to reproduce ab initio QM/MM energies and forces. Efficient optimization of minimum free energy pathways is enabled through a new surface-accelerated finite-temperature string method implemented in the FE-ToolKit package. Furthermore, we interfaced Sander with the i-PI software by implementing the socket communication protocol used in the i-PI client-server model. The new interface with i-PI allows for the treatment of nuclear quantum effects with semiempirical QM/MM-ΔMLP models. The modular interoperable software is demonstrated on proton transfer reactions in guanine-thymine mispairs in a B-form deoxyribonucleic acid helix. The current work represents a considerable advance in the development of modular software for performing free energy simulations of chemical reactions that are important in a wide range of applications.
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Affiliation(s)
- Yujun Tao
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Timothy J Giese
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Şölen Ekesan
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Jinzhe Zeng
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Bálint Aradi
- Bremen Center for Computational Materials Science, University of Bremen, D-28334 Bremen, Germany
| | - Ben Hourahine
- SUPA, Department of Physics, University of Strathclyde, Glasgow G4 0NG, United Kingdom
| | - Hasan Metin Aktulga
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - Andreas W Götz
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, USA
| | - Kenneth M Merz
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - Darrin M York
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
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36
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Weymuth T, Unsleber JP, Türtscher PL, Steiner M, Sobez JG, Müller CH, Mörchen M, Klasovita V, Grimmel SA, Eckhoff M, Csizi KS, Bosia F, Bensberg M, Reiher M. SCINE-Software for chemical interaction networks. J Chem Phys 2024; 160:222501. [PMID: 38857173 DOI: 10.1063/5.0206974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 05/09/2024] [Indexed: 06/12/2024] Open
Abstract
The software for chemical interaction networks (SCINE) project aims at pushing the frontier of quantum chemical calculations on molecular structures to a new level. While calculations on individual structures as well as on simple relations between them have become routine in chemistry, new developments have pushed the frontier in the field to high-throughput calculations. Chemical relations may be created by a search for specific molecular properties in a molecular design attempt, or they can be defined by a set of elementary reaction steps that form a chemical reaction network. The software modules of SCINE have been designed to facilitate such studies. The features of the modules are (i) general applicability of the applied methodologies ranging from electronic structure (no restriction to specific elements of the periodic table) to microkinetic modeling (with little restrictions on molecularity), full modularity so that SCINE modules can also be applied as stand-alone programs or be exchanged for external software packages that fulfill a similar purpose (to increase options for computational campaigns and to provide alternatives in case of tasks that are hard or impossible to accomplish with certain programs), (ii) high stability and autonomous operations so that control and steering by an operator are as easy as possible, and (iii) easy embedding into complex heterogeneous environments for molecular structures taken individually or in the context of a reaction network. A graphical user interface unites all modules and ensures interoperability. All components of the software have been made available as open source and free of charge.
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Affiliation(s)
- Thomas Weymuth
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Jan P Unsleber
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Paul L Türtscher
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Miguel Steiner
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Jan-Grimo Sobez
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Charlotte H Müller
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Maximilian Mörchen
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Veronika Klasovita
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Stephanie A Grimmel
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Marco Eckhoff
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Katja-Sophia Csizi
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Francesco Bosia
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Moritz Bensberg
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Markus Reiher
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
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37
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Keto A, Guo T, Underdue M, Stuyver T, Coley CW, Zhang X, Krenske EH, Wiest O. Data-Efficient, Chemistry-Aware Machine Learning Predictions of Diels-Alder Reaction Outcomes. J Am Chem Soc 2024; 146:16052-16061. [PMID: 38822795 DOI: 10.1021/jacs.4c03131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2024]
Abstract
The application of machine learning models to the prediction of reaction outcomes currently needs large and/or highly featurized data sets. We show that a chemistry-aware model, NERF, which mimics the bonding changes that occur during reactions, allows for highly accurate predictions of the outcomes of Diels-Alder reactions using a relatively small training set, with no pretraining and no additional features. We establish a diverse data set of 9537 intramolecular, hetero-, aromatic, and inverse electron demand Diels-Alder reactions. This data set is used to train a NERF model, and the performance is compared against state-of-the-art classification and generative machine learning models across low- and high-data regimes, with and without pretraining. The predictive accuracy (regio- and site selectivity in the major product) achieved by NERF exceeds 90% when as little as 40% of the data set is used for training. Another high-performing model, Chemformer, requires a larger training data set (>45%) and pretraining to reach 90% Top-1 accuracy. Accurate predictions of less-represented reaction subclasses, such as those involving heteroatomic or aromatic substrates, require higher percentages of training data. We also show how NERF can use small amounts of additional training data to quickly learn new systems and improve its overall understanding of reactivity. Synthetic chemists stand to benefit as this model can be rapidly expanded and tailored to areas of chemistry corresponding to the low-data regime.
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Affiliation(s)
- Angus Keto
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Taicheng Guo
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Morgan Underdue
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Thijs Stuyver
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Connor W Coley
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Xiangliang Zhang
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Elizabeth H Krenske
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Olaf Wiest
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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38
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Domingos SR, Tikhonov DS, Steber AL, Eschenbach P, Gruet S, Hrodmarsson HR, Martin K, Garcia GA, Nahon L, Neugebauer J, Avarvari N, Schnell M. Evolution of the ionisation energy with the stepwise growth of chiral clusters of [4]helicene. Nat Commun 2024; 15:4928. [PMID: 38858352 PMCID: PMC11164862 DOI: 10.1038/s41467-024-48778-0] [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: 09/19/2023] [Accepted: 05/13/2024] [Indexed: 06/12/2024] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are widely established as ubiquitous in the interstellar medium (ISM), but considering their prevalence in harsh vacuum environments, the role of ionisation in the formation of PAH clusters is poorly understood, particularly if a chirality-dependent aggregation route is considered. Here we report on photoelectron spectroscopy experiments on [4]helicene clusters performed with a vacuum ultraviolet synchrotron beamline. Aggregates (up to the heptamer) of [4]helicene, the smallest PAH with helical chirality, were produced and investigated with a combined experimental and theoretical approach using several state-of-the-art quantum-chemical methodologies. The ionisation onsets are extracted for each cluster size from the mass-selected photoelectron spectra and compared with calculations of vertical ionisation energies. We explore the complex aggregation topologies emerging from the multitude of isomers formed through clustering of P and M, the two enantiomers of [4]helicene. The very satisfactory benchmarking between experimental ionisation onsets vs. predicted ionisation energies allows the identification of theoretically predicted potential aggregation motifs and corresponding energetic ordering of chiral clusters. Our structural models suggest that a homochiral aggregation route is energetically favoured over heterochiral arrangements with increasing cluster size, hinting at potential symmetry breaking in PAH cluster formation at the scale of small grains.
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Affiliation(s)
- Sérgio R Domingos
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.
- CFisUC, Department of Physics, University of Coimbra, 3004-516, Coimbra, Portugal.
| | - Denis S Tikhonov
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.
| | - Amanda L Steber
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.
- Department of Physical Chemistry, Faculty of Science, University of Valladolid, 47011, Valladolid, Spain.
| | - Patrick Eschenbach
- Organisch-Chemisches Institut, University of Münster, 48149, Münster, Germany
- Center for Multiscale Theory and Computation (CMTC), University of Münster, 48149, Münster, Germany
| | - Sebastien Gruet
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Helgi R Hrodmarsson
- Synchrotron SOLEIL, L'Orme des Merisiers, 91192, Gif sur Yvette, Cedex, France
- LISA UMR 7583 Université Paris-Est Créteil and Université de Paris, Institut Pierre et Simon Laplace, 61 Avenue du Général de Gaulle, 94010, Créteil, France
| | - Kévin Martin
- Univ Angers, CNRS, MOLTECH-Anjou, SFR MATRIX, 49000, Angers, France
| | - Gustavo A Garcia
- Synchrotron SOLEIL, L'Orme des Merisiers, 91192, Gif sur Yvette, Cedex, France
| | - Laurent Nahon
- Synchrotron SOLEIL, L'Orme des Merisiers, 91192, Gif sur Yvette, Cedex, France
| | - Johannes Neugebauer
- Organisch-Chemisches Institut, University of Münster, 48149, Münster, Germany
- Center for Multiscale Theory and Computation (CMTC), University of Münster, 48149, Münster, Germany
| | - Narcis Avarvari
- Univ Angers, CNRS, MOLTECH-Anjou, SFR MATRIX, 49000, Angers, France
| | - Melanie Schnell
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.
- Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Max-Eyth-Str. 1, 24118, Kiel, Germany.
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39
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Bensberg M, Reiher M. Uncertainty-Aware First-Principles Exploration of Chemical Reaction Networks. J Phys Chem A 2024; 128:4532-4547. [PMID: 38787736 PMCID: PMC11163430 DOI: 10.1021/acs.jpca.3c08386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 05/13/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024]
Abstract
Exploring large chemical reaction networks with automated exploration approaches and accurate quantum chemical methods can require prohibitively large computational resources. Here, we present an automated exploration approach that focuses on the kinetically relevant part of the reaction network by interweaving (i) large-scale exploration of chemical reactions, (ii) identification of kinetically relevant parts of the reaction network through microkinetic modeling, (iii) quantification and propagation of uncertainties, and (iv) reaction network refinement. Such an uncertainty-aware exploration of kinetically relevant parts of a reaction network with automated accuracy improvement has not been demonstrated before in a fully quantum mechanical approach. Uncertainties are identified by local or global sensitivity analysis. The network is refined in a rolling fashion during the exploration. Moreover, the uncertainties are considered during kinetically steering of a rolling reaction network exploration. We demonstrate our approach for Eschenmoser-Claisen rearrangement reactions. The sensitivity analysis identifies that only a small number of reactions and compounds are essential for describing the kinetics reliably, resulting in efficient explorations without sacrificing accuracy and without requiring prior knowledge about the chemistry unfolding.
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Affiliation(s)
- Moritz Bensberg
- Department of Chemistry and Applied
Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Markus Reiher
- Department of Chemistry and Applied
Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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40
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Cheng G, Komatsu N. Diameter-selective extraction of single-walled carbon nanotubes by interlocking with Cu-tethered square nanobrackets. Beilstein J Org Chem 2024; 20:1298-1307. [PMID: 38887570 PMCID: PMC11181202 DOI: 10.3762/bjoc.20.113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 05/14/2024] [Indexed: 06/20/2024] Open
Abstract
We have been working with carbon nanotube separation through host-guest chemistry. Herein, a new macrocyclic host molecule, Cu-tethered square nanobrackets, is designed, synthesized and applied to single-walled carbon nanotubes (SWNTs) for their diameter-based separation. The complexation between copper ions and dipyrrin moieties of the nanobracket gives Cu-tethered square nanobrackets, which is confirmed by absorption, Raman and MALDI-TOF mass spectra. Upon extraction of SWNTs with the nanobracket and copper(II), in situ-formed square Cu-nanobrackets are found to interlock SWNTs to disperse them in 2-propanol. The interlocking is confirmed by Raman spectroscopy after thorough washing of the extracted SWNTs. Pristine SWNTs were recovered through demetalation of the interlocked ones along with the nanobracket. Raman and absorption spectroscopies of the extracted SWNTs reveals the diameter enrichment of only several kinds of SWNTs in the diameter range from 0.94 to 1.10 nm among ≈20 kinds of SWNTs from 0.76 to 1.20 nm in their diameter range. The diameter selectivity is supported by the theoretical calculations with the GFN2-xTB method, indicating that the most preferred SWNT diameter for the square Cu-nanobrackets is 1.04 nm.
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Affiliation(s)
- Guoqing Cheng
- Graduate School of Human and Environmental Studies, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Naoki Komatsu
- Graduate School of Human and Environmental Studies, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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41
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Hosoya S, Shoji S, Nakanishi T, Kobayashi M, Wang M, Fushimi K, Taketsugu T, Kitagawa Y, Hasegawa Y. Guest-Responsive Near-Infrared-Luminescent Metal-Organic Cage Organized by Porphyrin Dyes and Yb(III) Complexes. Inorg Chem 2024; 63:10108-10113. [PMID: 38771149 DOI: 10.1021/acs.inorgchem.4c01348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Metal-organic cages (MOCs) with luminophores have significant advantages for the facile detection of specific molecules based on turn-on or turn-off luminescence changes induced by host-guest complexation. One important challenge is the development of turn-on-type near-infrared (NIR)-luminescent MOCs. In this study, we synthesized a novel MOC consisting of two porphyrin dyes linked by four Yb(III) complexes, which exhibit bimodal red and NIR fluorescence signals upon photoexcitation of the porphyrin π system. Single-crystal X-ray structural analysis and computational molecular modeling revealed that planar aromatic perfluorocarbons were intercalated into the MOC. The tight packing between the MOC and guests enhanced the NIR fluorescence of Yb(III) by suppressing energy transfer from the photoexcited porphyrin to oxygen molecules. Guest-responsive turn-on NIR fluorescence changes in an MOC were successfully demonstrated.
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Affiliation(s)
- Shota Hosoya
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Kita 13, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Sunao Shoji
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21, Nishi 10, Kita-ku, Sapporo, Hokkaido 001-0021, Japan
- Faculty of Engineering, Hokkaido University, Kita 13, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Takayuki Nakanishi
- Research Center for Electronic and Optical Materials, National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
| | - Masato Kobayashi
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21, Nishi 10, Kita-ku, Sapporo, Hokkaido 001-0021, Japan
- Department of Chemistry, Faculty of Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Mengfei Wang
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21, Nishi 10, Kita-ku, Sapporo, Hokkaido 001-0021, Japan
- Faculty of Engineering, Hokkaido University, Kita 13, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Koji Fushimi
- Faculty of Engineering, Hokkaido University, Kita 13, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Tetsuya Taketsugu
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21, Nishi 10, Kita-ku, Sapporo, Hokkaido 001-0021, Japan
- Department of Chemistry, Faculty of Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Yuichi Kitagawa
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21, Nishi 10, Kita-ku, Sapporo, Hokkaido 001-0021, Japan
- Faculty of Engineering, Hokkaido University, Kita 13, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Yasuchika Hasegawa
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21, Nishi 10, Kita-ku, Sapporo, Hokkaido 001-0021, Japan
- Faculty of Engineering, Hokkaido University, Kita 13, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
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42
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Kairys V, Baranauskiene L, Kazlauskiene M, Zubrienė A, Petrauskas V, Matulis D, Kazlauskas E. Recent advances in computational and experimental protein-ligand affinity determination techniques. Expert Opin Drug Discov 2024; 19:649-670. [PMID: 38715415 DOI: 10.1080/17460441.2024.2349169] [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: 03/18/2024] [Accepted: 04/25/2024] [Indexed: 05/22/2024]
Abstract
INTRODUCTION Modern drug discovery revolves around designing ligands that target the chosen biomolecule, typically proteins. For this, the evaluation of affinities of putative ligands is crucial. This has given rise to a multitude of dedicated computational and experimental methods that are constantly being developed and improved. AREAS COVERED In this review, the authors reassess both the industry mainstays and the newest trends among the methods for protein - small-molecule affinity determination. They discuss both computational affinity predictions and experimental techniques, describing their basic principles, main limitations, and advantages. Together, this serves as initial guide to the currently most popular and cutting-edge ligand-binding assays employed in rational drug design. EXPERT OPINION The affinity determination methods continue to develop toward miniaturization, high-throughput, and in-cell application. Moreover, the availability of data analysis tools has been constantly increasing. Nevertheless, cross-verification of data using at least two different techniques and careful result interpretation remain of utmost importance.
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Affiliation(s)
- Visvaldas Kairys
- Department of Bioinformatics, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Lina Baranauskiene
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | | | - Asta Zubrienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Vytautas Petrauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Egidijus Kazlauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
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43
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Nielsen RV, Salimi M, Andersen JEV, Elm J, Dantan A, Pedersen HB. A new setup for measurements of absolute saturation vapor pressures using a dynamical method: Experimental concept and validation. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2024; 95:065007. [PMID: 38912913 DOI: 10.1063/5.0215176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 06/10/2024] [Indexed: 06/25/2024]
Abstract
We describe a new experimental system for direct measurements of the absolute saturation vapor pressures of liquid or solid samples. The setup allows the isolation of the sample under steady conditions in an ultra-high vacuum chamber, where the measurement of the sample's vapor pressure as a function of its temperature can be performed in a range around room temperature and in a pressure range defined only by the applied absolute pressure sensor. We characterize the setup and illustrate its capability to measure saturation vapor pressures as well as enthalpies of evaporation around room temperature with explicit measurements on four liquid compounds (diethyl phthalate, 1-decanol, 1-heptanol, and 1-hexanol) for which accurate vapor pressures have previously been reported.
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Affiliation(s)
- Robin V Nielsen
- Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Mohsen Salimi
- Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus C, Denmark
| | - John E V Andersen
- Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Jonas Elm
- Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Aurélien Dantan
- Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Henrik B Pedersen
- Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus C, Denmark
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44
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Keller BG, Bolhuis PG. Dynamical Reweighting for Biased Rare Event Simulations. Annu Rev Phys Chem 2024; 75:137-162. [PMID: 38941527 DOI: 10.1146/annurev-physchem-083122-124538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Dynamical reweighting techniques aim to recover the correct molecular dynamics from a simulation at a modified potential energy surface. They are important for unbiasing enhanced sampling simulations of molecular rare events. Here, we review the theoretical frameworks of dynamical reweighting for modified potentials. Based on an overview of kinetic models with increasing level of detail, we discuss techniques to reweight two-state dynamics, multistate dynamics, and path integrals. We explore the natural link to transition path sampling and how the effect of nonequilibrium forces can be reweighted. We end by providing an outlook on how dynamical reweighting integrates with techniques for optimizing collective variables and with modern potential energy surfaces.
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Affiliation(s)
- Bettina G Keller
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany;
| | - Peter G Bolhuis
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
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45
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Chan B. Limiting factors in the accuracy of DFT calculation for redox potentials. J Comput Chem 2024; 45:1177-1186. [PMID: 38311976 DOI: 10.1002/jcc.27320] [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: 11/13/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 02/06/2024]
Abstract
In the present study, we have investigated factors affecting the accuracy of computational chemistry calculation of redox potentials, namely the gas-phase ionization energy (IE) and electron affinity (EA), and the continuum solvation effect. In general, double-hybrid density functional theory methods yield IEs and EAs that are on average within ~0.1 eV of our high-level W3X-L benchmark, with the best performing method being DSD-BLYP/ma-def2-QZVPP. For lower-cost methods, the average errors are ~0.2-0.3 eV, with ωB97X-3c being the most accurate (~0.15 eV). For the solvation component, essentially all methods have an average error of ~0.3 eV, which shows the limitation of the continuum solvation model. Curiously, the directly calculated redox potentials show errors of ~0.3 eV for all methods. These errors are notably smaller than what can be expected from error propagation with the two components (IE and EA, and solvation effect). Such a discrepancy can be attributed to the cancellation of errors, with the lowest-cost GFN2-xTB method benefiting the most, and the most accurate ωB97X-3c method benefiting the least. For organometallic species, the redox potentials show large deviations exceeding ~0.5 eV even for DSD-BLYP. The large errors are attributed to those for the gas-phase IEs and EAs, which represents a major barrier to the accurate calculation of redox potentials for such systems.
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Affiliation(s)
- Bun Chan
- Graduate School of Engineering, Nagasaki University, Nagasaki, Japan
- RIKEN Center for Computational Science, Kobe, Japan
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46
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Mun H, Lorpaiboon W, Ho J. In Search of the Best Low-Cost Methods for Efficient Screening of Conformers. J Phys Chem A 2024; 128:4391-4400. [PMID: 38754085 DOI: 10.1021/acs.jpca.4c01407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Locating the lowest energy conformer is crucial for the accurate computation of equilibrium properties of molecular systems. This paper examines the performance of efficient low-cost methods in terms of the alignment and relative energies of their energy minima against the benchmark revDSD-PBEP86-D4/def2-TZVPP//MP2/cc-pVTZ potential energy surface. The low-cost methods considered include GFN-FF, GFN2-xTB, DFTB3, HF-3c, B97-3c, PBEh-3c, and r2SCAN-3c composite methods against a diverse test set of 20 compounds including alkanes, perfluoroalkyl molecules, peptides, open-shell radicals, and Zn(II) complexes of varying sizes. The "3c" composite methods are generally more accurate, but are at least 2-3 orders of magnitude more expensive than tight-binding methods which have energy minima that align well with the benchmark potential energy surface. The findings of this paper were further exploited to introduce a simple strategy involving Grimme's CENSO energy-sorting algorithm that resulted in up to an order of magnitude reduction in computational time for locating the lowest energy conformer on the revDSD-PBEP86-D4/def2-TZVPP//MP2/cc-pVTZ surface.
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Affiliation(s)
- Haedam Mun
- School of Chemistry, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Wanutcha Lorpaiboon
- School of Chemistry, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Junming Ho
- School of Chemistry, The University of New South Wales, Sydney, NSW 2052, Australia
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47
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Wilhelmer R, Diez M, Krondorfer JK, Hauser AW. Molecular Pseudorotation in Phthalocyanines as a Tool for Magnetic Field Control at the Nanoscale. J Am Chem Soc 2024; 146:14620-14632. [PMID: 38743819 PMCID: PMC11140746 DOI: 10.1021/jacs.4c01915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/29/2024] [Accepted: 04/30/2024] [Indexed: 05/16/2024]
Abstract
Metal phthalocyanines, a highly versatile class of aromatic, planar, macrocyclic molecules with a chelated central metal ion, are topical objects of ongoing research and particularly interesting due to their magnetic properties. However, while the current focus lies almost exclusively on spin-Zeeman-related effects, the high symmetry of the molecule and its circular shape suggests the exploitation of light-induced excitation of 2-fold degenerate vibrational states in order to generate, switch, and manipulate magnetic fields at the nanoscale. The underlying mechanism is a molecular pseudorotation that can be triggered by infrared pulses and gives rise to a quantized, small, but controllable magnetic dipole moment. We investigate the optical stimulation of vibrationally induced molecular magnetism and estimate changes in the magnetic shielding constants for confirmation by future experiments.
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Affiliation(s)
- Raphael Wilhelmer
- Institute of Experimental Physics, Graz University of Technology, Petersgasse 16, A-8010 Graz, Austria
| | - Matthias Diez
- Institute of Experimental Physics, Graz University of Technology, Petersgasse 16, A-8010 Graz, Austria
| | - Johannes K Krondorfer
- Institute of Experimental Physics, Graz University of Technology, Petersgasse 16, A-8010 Graz, Austria
| | - Andreas W Hauser
- Institute of Experimental Physics, Graz University of Technology, Petersgasse 16, A-8010 Graz, Austria
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48
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Wahab A, Gershoni-Poranne R. COMPAS-3: a dataset of peri-condensed polybenzenoid hydrocarbons. Phys Chem Chem Phys 2024; 26:15344-15357. [PMID: 38758092 DOI: 10.1039/d4cp01027b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
We introduce the third installment of the COMPAS Project - a COMputational database of Polycyclic Aromatic Systems, focused on peri-condensed polybenzenoid hydrocarbons. In this installment, we develop two datasets containing the optimized ground-state structures and a selection of molecular properties of ∼39k and ∼9k peri-condensed polybenzenoid hydrocarbons (at the GFN2-xTB and CAM-B3LYP-D3BJ/cc-pvdz//CAM-B3LYP-D3BJ/def2-SVP levels, respectively). The manuscript details the enumeration and data generation processes and describes the information available within the datasets. An in-depth comparison between the two types of computation is performed, and it is found that the geometrical disagreement is maximal for slightly-distorted molecules. In addition, a data-driven analysis of the structure-property trends of peri-condensed PBHs is performed, highlighting the effect of the size of peri-condensed islands and linearly annulated rings on the HOMO-LUMO gap. The insights described herein are important for rational design of novel functional aromatic molecules for use in, e.g., organic electronics. The generated datasets provide a basis for additional data-driven machine- and deep-learning studies in chemistry.
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Affiliation(s)
- Alexandra Wahab
- The Laboratory for Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Renana Gershoni-Poranne
- The Schulich Faculty of Chemistry and the Resnick Sustainability Center for Catalysis, Technion - Israel Institute of Technology, Haifa 32000, Israel.
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49
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Mailhiot S, Peuravaara P, Egleston BD, Kearsey RJ, Mareš J, Komulainen S, Selent A, Kantola AM, Cooper AI, Vaara J, Greenaway RL, Lantto P, Telkki VV. Gas Uptake and Thermodynamics in Porous Liquids Elucidated by 129Xe NMR. J Phys Chem Lett 2024; 15:5323-5330. [PMID: 38724016 PMCID: PMC11129303 DOI: 10.1021/acs.jpclett.4c00223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/22/2024] [Accepted: 04/11/2024] [Indexed: 05/24/2024]
Abstract
We exploited 129Xe NMR to investigate xenon gas uptake and dynamics in a porous liquid formed by dissolving porous organic cages in a cavity-excluded solvent. Quantitative 129Xe NMR shows that when the amount of xenon added to the sample is lower than the amount of cages present (subsaturation), the porous liquid absorbs almost all xenon atoms from the gas phase, with 30% of the cages occupied with a Xe atom. A simple two-site exchange model enables an estimate of the chemical shift of 129Xe in the cages, which is in good agreement with the value provided by first-principles modeling. T2 relaxation times allow the determination of the exchange rate of Xe between the solvent and cage sites as well as the activation energies of the exchange. The 129Xe NMR analysis also enables determination of the free energy of confinement, and it shows that Xe binding is predominantly enthalpy-driven.
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Affiliation(s)
- Sarah
E. Mailhiot
- NMR
Research Unit, Faculty of Science, University
of Oulu, P.O.Box 3000, FI-90014 Oulu, Finland
| | - Petri Peuravaara
- NMR
Research Unit, Faculty of Science, University
of Oulu, P.O.Box 3000, FI-90014 Oulu, Finland
| | - Benjamin D. Egleston
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, W12 0BZ, U.K.
| | - Rachel J. Kearsey
- Department
of Chemistry and Materials Innovation Factory, University of Liverpool, Crown Street, Liverpool L69 7ZD, U.K.
| | - Jiří Mareš
- NMR
Research Unit, Faculty of Science, University
of Oulu, P.O.Box 3000, FI-90014 Oulu, Finland
| | - Sanna Komulainen
- NMR
Research Unit, Faculty of Science, University
of Oulu, P.O.Box 3000, FI-90014 Oulu, Finland
| | - Anne Selent
- NMR
Research Unit, Faculty of Science, University
of Oulu, P.O.Box 3000, FI-90014 Oulu, Finland
| | - Anu M. Kantola
- NMR
Research Unit, Faculty of Science, University
of Oulu, P.O.Box 3000, FI-90014 Oulu, Finland
| | - Andrew I. Cooper
- Department
of Chemistry and Materials Innovation Factory, University of Liverpool, Crown Street, Liverpool L69 7ZD, U.K.
| | - Juha Vaara
- NMR
Research Unit, Faculty of Science, University
of Oulu, P.O.Box 3000, FI-90014 Oulu, Finland
| | - Rebecca L. Greenaway
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, W12 0BZ, U.K.
| | - Perttu Lantto
- NMR
Research Unit, Faculty of Science, University
of Oulu, P.O.Box 3000, FI-90014 Oulu, Finland
| | - Ville-Veikko Telkki
- NMR
Research Unit, Faculty of Science, University
of Oulu, P.O.Box 3000, FI-90014 Oulu, Finland
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50
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Jirasek M, Sharma A, Bame JR, Mehr SHM, Bell N, Marshall SM, Mathis C, MacLeod A, Cooper GJT, Swart M, Mollfulleda R, Cronin L. Investigating and Quantifying Molecular Complexity Using Assembly Theory and Spectroscopy. ACS CENTRAL SCIENCE 2024; 10:1054-1064. [PMID: 38799656 PMCID: PMC11117308 DOI: 10.1021/acscentsci.4c00120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/16/2024] [Accepted: 04/09/2024] [Indexed: 05/29/2024]
Abstract
Current approaches to evaluate molecular complexity use algorithmic complexity, rooted in computer science, and thus are not experimentally measurable. Directly evaluating molecular complexity could be used to study directed vs undirected processes in the creation of molecules, with potential applications in drug discovery, the origin of life, and artificial life. Assembly theory has been developed to quantify the complexity of a molecule by finding the shortest path to construct the molecule from building blocks, revealing its molecular assembly index (MA). In this study, we present an approach to rapidly infer the MA of molecules from spectroscopic measurements. We demonstrate that the MA can be experimentally measured by using three independent techniques: nuclear magnetic resonance (NMR), tandem mass spectrometry (MS/MS), and infrared spectroscopy (IR). By identifying and analyzing the number of absorbances in IR spectra, carbon resonances in NMR, or molecular fragments in tandem MS, the MA of an unknown molecule can be reliably estimated. This represents the first experimentally quantifiable approach to determining molecular assembly. This paves the way to use experimental techniques to explore the evolution of complex molecules as well as a unique marker of where an evolutionary process has been operating.
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Affiliation(s)
- Michael Jirasek
- School
of Chemistry, The University of Glasgow, University Avenue, Glasgow G12 8QQ, U.K.
| | - Abhishek Sharma
- School
of Chemistry, The University of Glasgow, University Avenue, Glasgow G12 8QQ, U.K.
| | - Jessica R. Bame
- School
of Chemistry, The University of Glasgow, University Avenue, Glasgow G12 8QQ, U.K.
| | - S. Hessam M. Mehr
- School
of Chemistry, The University of Glasgow, University Avenue, Glasgow G12 8QQ, U.K.
| | - Nicola Bell
- School
of Chemistry, The University of Glasgow, University Avenue, Glasgow G12 8QQ, U.K.
| | - Stuart M. Marshall
- School
of Chemistry, The University of Glasgow, University Avenue, Glasgow G12 8QQ, U.K.
| | - Cole Mathis
- School
of Chemistry, The University of Glasgow, University Avenue, Glasgow G12 8QQ, U.K.
| | - Alasdair MacLeod
- School
of Chemistry, The University of Glasgow, University Avenue, Glasgow G12 8QQ, U.K.
| | - Geoffrey J. T. Cooper
- School
of Chemistry, The University of Glasgow, University Avenue, Glasgow G12 8QQ, U.K.
| | - Marcel Swart
- University
of Girona, Campus Montilivi (Ciencies), c/M.A. Capmany 69, 17003 Girona, Spain
- ICREA, Pg. Lluis Companys
23, 08010 Barcelona, Spain
| | - Rosa Mollfulleda
- University
of Girona, Campus Montilivi (Ciencies), c/M.A. Capmany 69, 17003 Girona, Spain
| | - Leroy Cronin
- School
of Chemistry, The University of Glasgow, University Avenue, Glasgow G12 8QQ, U.K.
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