1
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Denjean AEF, Rio J, Ciofini I, Perrin MEL, Payard PA. Computed versus experimental energy barriers in solution: Influence of the type of the density functional approximation. J Comput Chem 2024; 45:2284-2293. [PMID: 38847601 DOI: 10.1002/jcc.27436] [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: 03/20/2024] [Revised: 04/18/2024] [Accepted: 04/24/2024] [Indexed: 08/15/2024]
Abstract
Mechanistic investigations at the density functional theory level of organic and organometallic reactions in solution are now broadly accessible and routinely implemented to complement experimental investigations. The selection of an appropriate functional among the plethora of developed ones is the first challenge on the way to reliable energy barrier calculations. To provide guidelines for the choice of an initial and reliable computational level, the performances of commonly used non-empirical (PBE, PBE0, PBE0-DH) and empirical density functionals (BLYP, B3LYP, B2PLYP) were evaluated relative to experimental activation enthalpies. Most reactivity databases to assess density functional performances are primarily based on high level calculations, here a set of experimental activation enthalpies of organic and organometallic reactions performed in solution were selected from the literature. As a general trend, the non-empirical functionals outperform the empirical ones. The most accurate energy barriers are obtained with hybrid PBE0 and double-hybrid PBE0-DH density functionals, both providing similar performance. Regardless of the functional under consideration, the addition of the GD3-BJ empirical dispersion correction does not enhance the accuracy of computed energy barriers.
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Affiliation(s)
- Aurore E F Denjean
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, Oslo, Norway
- Universite Claude Bernard Lyon I, CNRS, CPE-Lyon, INSA-Lyon, UMR 5246, ICBMS Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, Villeurbanne, France
| | - Jordan Rio
- Universite Claude Bernard Lyon I, CNRS, CPE-Lyon, INSA-Lyon, UMR 5246, ICBMS Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, Villeurbanne, France
| | - Ilaria Ciofini
- i-CLeHS (UMR 8060), CNRS Chimie Paris-Tech-PSL, Université Paris Sciences et Lettres, Paris, France
| | - Marie-Eve L Perrin
- Universite Claude Bernard Lyon I, CNRS, CPE-Lyon, INSA-Lyon, UMR 5246, ICBMS Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, Villeurbanne, France
| | - Pierre-Adrien Payard
- Universite Claude Bernard Lyon I, CNRS, CPE-Lyon, INSA-Lyon, UMR 5246, ICBMS Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, Villeurbanne, France
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2
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Doleschal ME, Kostenko A, Liu JY, Inoue S. Isolation of a NHC-stabilized heavier nitrile and its conversion into an isonitrile analogue. Nat Chem 2024:10.1038/s41557-024-01618-6. [PMID: 39256544 DOI: 10.1038/s41557-024-01618-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 07/30/2024] [Indexed: 09/12/2024]
Abstract
Nitriles (R-C≡N) have been investigated since the late eighteenth century and are ubiquitous encounters in organic and inorganic syntheses. In contrast, heavier nitriles, which contain the heavier analogues of carbon and nitrogen, are sparsely investigated species. Here we report the synthesis and isolation of a phosphino-silylene featuring an N-heterocyclic carbene-phosphinidene and a highly sterically demanding silyl group as substituents. Due to its unique structural motif, it can be regarded as a Lewis base-stabilized heavier nitrile. The Si-P bond displays multiple bond character and a bent R-Si-P geometry, the latter indicating fundamental differences between heavier and classical nitriles. In solution, a quantitative unusual rearrangement to a phosphasilenylidene occurs. This rearrangement is consistent with theoretical predictions of rearrangements from heavier nitriles to heavier isonitriles. Our preliminary reactivity studies revealed that both isomers exhibit highly nucleophilic silicon centres capable of oxidative addition and coordination to iron tetracarbonyl.
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Affiliation(s)
- Martin E Doleschal
- TUM School of Natural Sciences, Department of Chemistry, Catalysis Research Center and Wacker Institute of Silicon Chemistry, Technische Universität Müchen, Garching, Germany
| | - Arseni Kostenko
- TUM School of Natural Sciences, Department of Chemistry, Catalysis Research Center and Wacker Institute of Silicon Chemistry, Technische Universität Müchen, Garching, Germany
| | - Jin Yu Liu
- TUM School of Natural Sciences, Department of Chemistry, Catalysis Research Center and Wacker Institute of Silicon Chemistry, Technische Universität Müchen, Garching, Germany
| | - Shigeyoshi Inoue
- TUM School of Natural Sciences, Department of Chemistry, Catalysis Research Center and Wacker Institute of Silicon Chemistry, Technische Universität Müchen, Garching, Germany.
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3
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Pallikara I, Skelton JM, Hatcher LE, Pallipurath AR. Going beyond the Ordered Bulk: A Perspective on the Use of the Cambridge Structural Database for Predictive Materials Design. CRYSTAL GROWTH & DESIGN 2024; 24:6911-6930. [PMID: 39247224 PMCID: PMC11378158 DOI: 10.1021/acs.cgd.4c00694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 07/26/2024] [Accepted: 07/30/2024] [Indexed: 09/10/2024]
Abstract
When Olga Kennard founded the Cambridge Crystallographic Data Centre in 1965, the Cambridge Structural Database was a pioneering attempt to collect scientific data in a standard format. Since then, it has evolved into an indispensable resource in contemporary molecular materials science, with over 1.25 million structures and comprehensive software tools for searching, visualizing and analyzing the data. In this perspective, we discuss the use of the CSD and CCDC tools to address the multiscale challenge of predictive materials design. We provide an overview of the core capabilities of the CSD and CCDC software and demonstrate their application to a range of materials design problems with recent case studies drawn from topical research areas, focusing in particular on the use of data mining and machine learning techniques. We also identify several challenges that can be addressed with existing capabilities or through new capabilities with varying levels of development effort.
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Affiliation(s)
- Ioanna Pallikara
- School of Chemical and Process Engineering, University of Leeds, Leeds LS2 9JT, U.K
| | - Jonathan M Skelton
- Department of Chemistry, University of Manchester, Manchester M13 9PL, U.K
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4
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Hattori S, Zhu Q. Revisiting Aspirin Polymorphic Stability Using a Machine Learning Potential. ACS OMEGA 2024; 9:36589-36599. [PMID: 39220495 PMCID: PMC11360032 DOI: 10.1021/acsomega.4c04782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 07/26/2024] [Accepted: 07/30/2024] [Indexed: 09/04/2024]
Abstract
In this study, we present a systematic computational investigation to analyze the long-debated free energy stability of two well-known aspirin polymorphs, denoted as Form I and Form II. Specifically, we developed a strategy to collect training configurations covering diverse interatomic interactions between representative functional groups in aspirin crystals. Utilizing a state-of-the-art neural network interatomic potential (NNIP) model, we trained an accurate machine learning potential to simulate aspirin crystal dynamics under finite temperature conditions with ∼0.46 kJ/mol/molecule accuracy. Employing the trained NNIP model, we performed thermodynamic integration to assess the free energy difference between aspirins I and II, accounting for the anharmonic effects in a large supercell consisting of 512 molecules. For the first time, our results convincingly demonstrated that Form I is more stable than Form II at 300 K, ranging from 0.74 to 1.83 kJ/mol/molecule, aligning with experimental observations. Unlike the majority of previous simulations based on (quasi)harmonic approximations in a small super cell, which often found degenerate energies between aspirins I and II, our findings underscore the importance of anharmonic effects in determining polymorphic stability ranking. Furthermore, we proposed the use of the rotational degrees of freedom of methyl and ester/phenyl groups in aspirin crystals as characteristic motions to highlight rotational entropic contribution that favors the stability of Form I. From the structural perspective, we also found that the subtle free energy difference can be used to explain the distinct thermal expansion responses as observed in both experimental and simulation data. Beyond the aspirin polymorphism, we anticipate that such entropy-driven stabilization can be broadly applicable to many other organic systems, suggesting that our approach holds great promise for stability studies in small-molecule drug design.
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Affiliation(s)
- Shinnosuke Hattori
- Advanced
Research Laboratory, Research Platform, Sony Group Corporation, 4−14−1 Asahi-cho, Atsugi-shi 243−0014, Japan
| | - Qiang Zhu
- Department
of Mechanical Engineering and Engineering Science, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
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5
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Ripak A, Vega Salgado AK, Valverde D, Cristofaro S, de Gary A, Olivier Y, Elias B, Troian-Gautier L. Factors Controlling Cage Escape Yields of Closed- and Open-Shell Metal Complexes in Bimolecular Photoinduced Electron Transfer. J Am Chem Soc 2024; 146:22818-22828. [PMID: 39078742 DOI: 10.1021/jacs.4c08158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
The cage escape yield, i.e., the separation of the geminate radical pair formed immediately after bimolecular excited-state electron transfer, was studied in 11 solvents using six Fe(III), Ru(II), and Ir(III) photosensitizers and tri-p-tolylamine as the electron donor. Among all complexes, the largest cage escape yields (0.67-1) were recorded for the Ir(III) photosensitizer, showing the highest potential as a photocatalyst in photoredox catalysis. These yields dropped to values around 0.65 for both Ru(II) photosensitizers and to values around 0.38 for the Os(II) photosensitizer. Interestingly, for both open-shell Fe(III) complexes, the yields were small (<0.1) in solvents with dielectric constant greater than 20 but were shown to reach values up to 0.58 in solvents with low dielectric constants. The results presented herein on closed-shell photosensitizers suggest that the low rate of triplet-singlet intersystem crossing within the manifold of states of the geminate radical pair implies that charge recombination toward the ground state is a spin-forbidden process, favoring large cage escape yields that are not influenced by dielectric effects. Geminate charge recombination in open-shell metal complexes, such as the two Fe(III) photosensitizers studied herein, is no longer a spin-forbidden process and becomes highly sensitive to solvent effects. Altogether, this study provides general guidelines for factors influencing bimolecular excited-state reactivity using prototypical photosensitizers but also allows one to foresee a great development of Fe(III) photosensitizers with the 2LMCT excited state in photoredox catalysis, providing that solvents with low dielectric constants are used.
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Affiliation(s)
- Alexia Ripak
- Molecular Chemistry, Materials and Catalysis (MOST), UCLouvain, Institut de la Matière Condensée et des Nanosciences (IMCN), Place Louis Pasteur 1/L4.01.02, B-1348 Louvain-la-Neuve, Belgium
| | - Ana Karem Vega Salgado
- Molecular Chemistry, Materials and Catalysis (MOST), UCLouvain, Institut de la Matière Condensée et des Nanosciences (IMCN), Place Louis Pasteur 1/L4.01.02, B-1348 Louvain-la-Neuve, Belgium
| | - Danillo Valverde
- Laboratory for Computational Modeling of Functional Materials, Namur Institute of Structured Matter, University of Namur, Rue de Bruxelles 61, 5000 Namur, Belgium
| | - Silvia Cristofaro
- Laboratory for Computational Modeling of Functional Materials, Namur Institute of Structured Matter, University of Namur, Rue de Bruxelles 61, 5000 Namur, Belgium
| | - Alban de Gary
- Laboratory for Computational Modeling of Functional Materials, Namur Institute of Structured Matter, University of Namur, Rue de Bruxelles 61, 5000 Namur, Belgium
| | - Yoann Olivier
- Laboratory for Computational Modeling of Functional Materials, Namur Institute of Structured Matter, University of Namur, Rue de Bruxelles 61, 5000 Namur, Belgium
| | - Benjamin Elias
- Molecular Chemistry, Materials and Catalysis (MOST), UCLouvain, Institut de la Matière Condensée et des Nanosciences (IMCN), Place Louis Pasteur 1/L4.01.02, B-1348 Louvain-la-Neuve, Belgium
| | - Ludovic Troian-Gautier
- Molecular Chemistry, Materials and Catalysis (MOST), UCLouvain, Institut de la Matière Condensée et des Nanosciences (IMCN), Place Louis Pasteur 1/L4.01.02, B-1348 Louvain-la-Neuve, Belgium
- Wel Research Institute, Avenue Pasteur 6, 1300 Wavre, Belgium
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6
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Friede M, Hölzer C, Ehlert S, Grimme S. dxtb-An efficient and fully differentiable framework for extended tight-binding. J Chem Phys 2024; 161:062501. [PMID: 39120026 DOI: 10.1063/5.0216715] [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: 07/18/2024] [Indexed: 08/10/2024] Open
Abstract
Automatic differentiation (AD) emerged as an integral part of machine learning, accelerating model development by enabling gradient-based optimization without explicit analytical derivatives. Recently, the benefits of AD and computing arbitrary-order derivatives with respect to any variable were also recognized in the field of quantum chemistry. In this work, we present dxtb-an open-source, fully differentiable framework for semiempirical extended tight-binding (xTB) methods. Developed entirely in Python and leveraging PyTorch for array operations, dxtb facilitates extensibility and rapid prototyping while maintaining computational efficiency. Through comprehensive code vectorization and optimization, we essentially reach the speed of compiled xTB programs for high-throughput calculations of small molecules. The excellent performance also scales to large systems, and batch operability yields additional benefits for execution on parallel hardware. In particular, energy evaluations are on par with existing programs, whereas the speed of automatically differentiated nuclear derivatives is only 2 to 5 times slower compared to their analytical counterparts. We showcase the utility of AD in dxtb by calculating various molecular and spectroscopic properties, highlighting its capacity to enhance and simplify such evaluations. Furthermore, the framework streamlines optimization tasks and offers seamless integration of semiempirical quantum chemistry in machine learning, paving the way for physics-inspired end-to-end differentiable models. Ultimately, dxtb aims to further advance the capabilities of semiempirical methods, providing an extensible foundation for future developments and hybrid machine learning applications. The framework is accessible at https://github.com/grimme-lab/dxtb.
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Affiliation(s)
- Marvin Friede
- Mulliken Center for Theoretical Chemistry, University of Bonn, Bonn 53115, Germany
| | - Christian Hölzer
- Mulliken Center for Theoretical Chemistry, University of Bonn, Bonn 53115, Germany
| | - Sebastian Ehlert
- AI4Science, Microsoft Research, Evert van de Beekstraat 354, 1118CZ Schiphol, Netherlands
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, University of Bonn, Bonn 53115, Germany
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7
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Wittmann L, Gordiy I, Friede M, Helmich-Paris B, Grimme S, Hansen A, Bursch M. Extension of the D3 and D4 London dispersion corrections to the full actinides series. Phys Chem Chem Phys 2024; 26:21379-21394. [PMID: 39092890 DOI: 10.1039/d4cp01514b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Efficient dispersion corrections are an indispensable component of modern density functional theory, semi-empirical quantum mechanical, and even force field methods. In this work, we extend the well established D3 and D4 London dispersion corrections to the full actinides series, francium, and radium. To keep consistency with the existing versions, the original parameterization strategy of the D4 model was only slightly modified. This includes improved reference Hirshfeld atomic partial charges at the ωB97M-V/ma-def-TZVP level to fit the required electronegativity equilibration charge (EEQ) model. In this context, we developed a new actinide data set called AcQM, which covers the most common molecular actinide compound space. Furthermore, the efficient calculation of dynamic polarizabilities that are needed to construct CAB6 dispersion coefficients was implemented into the ORCA program package. The extended models are assessed for the computation of dissociation curves of actinide atoms and ions, geometry optimizations of crystal structure cutouts, gas-phase structures of small uranium compounds, and an example extracted from a small actinide complex protein assembly. We found that the novel parameterizations perform on par with the computationally more demanding density-dependent VV10 dispersion correction. With the presented extension, the excellent cost-accuracy ratio of the D3 and D4 models can now be utilized in various fields of computational actinide chemistry and, e.g., in efficient composite DFT methods such as r2SCAN-3c. They are implemented in our freely available standalone codes (dftd4, s-dftd3) and the D4 version will be also available in the upcoming ORCA 6.0 program package.
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Affiliation(s)
- Lukas Wittmann
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstr. 4, 53115 Bonn, Germany.
| | - Igor Gordiy
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstr. 4, 53115 Bonn, Germany.
| | - Marvin Friede
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstr. 4, 53115 Bonn, Germany.
| | - Benjamin Helmich-Paris
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstr. 4, 53115 Bonn, Germany.
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstr. 4, 53115 Bonn, Germany.
| | - Markus Bursch
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.
- FACCTs GmbH, 50677, Köln, Germany
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8
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Schröder N, Bartalucci E, Wiegand T. Probing Noncovalent Interactions by Fast Magic-Angle Spinning NMR at 100 kHz and More. Chemphyschem 2024:e202400537. [PMID: 39129653 DOI: 10.1002/cphc.202400537] [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: 05/08/2024] [Revised: 06/19/2024] [Indexed: 08/13/2024]
Abstract
Noncovalent interactions are the basis for a large number of chemical and biological molecular-recognition processes, such as those occurring in supramolecular chemistry, catalysis, solid-state reactions in mechanochemistry, protein folding, protein-nucleic acid binding, and biomolecular phase separation processes. In this perspective article, some recent developments in probing noncovalent interactions by proton-detected solid-state Nuclear Magnetic Resonance (NMR) spectroscopy at Magic-Angle Spinning (MAS) frequencies of 100 kHz and more are reviewed. The development of MAS rotors with decreasing outer diameters, combined with the development of superconducting magnets operating at high static magnetic-field strengths up to 28.2 T (1200 MHz proton Larmor frequency) improves resolution and sensitivity in proton-detected solid-state NMR, which is the fundamental requirement for shedding light on noncovalent interactions in solids. The examples reported in this article range from protein-nucleic acid binding in large ATP-fueled motor proteins to a hydrogen-π interaction in a calixarene-lanthanide complex.
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Affiliation(s)
- Nina Schröder
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Ettore Bartalucci
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470, Mülheim/Ruhr, Germany
| | - Thomas Wiegand
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470, Mülheim/Ruhr, Germany
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9
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Silarski M, Dziedzic-Kocurek K, Drużbicki K, Reterski R, Grabowski P, Krzystyniak M. Non-invasive detection of hazardous materials with a thermal-to-epithermal neutron station: a feasibility study towards practical application. Sci Rep 2024; 14:18584. [PMID: 39127754 DOI: 10.1038/s41598-024-69290-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: 05/30/2024] [Accepted: 08/01/2024] [Indexed: 08/12/2024] Open
Abstract
The growing scale of the devastation that even a single terrorist attack can cause requires more effective methods for the detection of hazardous materials. In particular, there are no solutions for effectively monitoring threats at sea, both for the off-shore infrastructure and ports. Currently, state-of-the-art detection methods determine the density distribution and the shapes of tested subjects but only allow for a limited degree of substance identification. This work aims to present a feasibility study of the possible usage of several methods available on the thermal-to-epithermal neutron station, VESUVIO, at the ISIS neutron and muon spallation source, UK, for the detection of hazardous materials. To this end, we present the results of a series of experiments performed concurrently employing neutron transmission and Compton scattering using melamine, a commonly used explosive surrogate, in order to determine its signal characteristics and limits of detection and quantitation. The experiments are supported by first-principles modelling, providing detailed scrutiny of the material structure and the nuclear dynamics behind the neutron scattering observables.
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Affiliation(s)
- Michał Silarski
- M. Smoluchowski Institute of Physics of the Jagiellonian University, Łojasiewicza 11, 30-348, Cracow, Poland
| | - Katarzyna Dziedzic-Kocurek
- M. Smoluchowski Institute of Physics of the Jagiellonian University, Łojasiewicza 11, 30-348, Cracow, Poland
| | - Kacper Drużbicki
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Lodz, Poland
| | - Radosław Reterski
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Cracow, Poland
| | - Patryk Grabowski
- M. Smoluchowski Institute of Physics of the Jagiellonian University, Łojasiewicza 11, 30-348, Cracow, Poland
| | - Matthew Krzystyniak
- ISIS Neutron and Muon Source, STFC Rutherford Appleton Laboratory, Oxford, OX11 0QX, UK.
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10
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Cao Y, Balduf T, Beachy MD, Bennett MC, Bochevarov AD, Chien A, Dub PA, Dyall KG, Furness JW, Halls MD, Hughes TF, Jacobson LD, Kwak HS, Levine DS, Mainz DT, Moore KB, Svensson M, Videla PE, Watson MA, Friesner RA. Quantum chemical package Jaguar: A survey of recent developments and unique features. J Chem Phys 2024; 161:052502. [PMID: 39092934 DOI: 10.1063/5.0213317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 07/12/2024] [Indexed: 08/04/2024] Open
Abstract
This paper is dedicated to the quantum chemical package Jaguar, which is commercial software developed and distributed by Schrödinger, Inc. We discuss Jaguar's scientific features that are relevant to chemical research as well as describe those aspects of the program that are pertinent to the user interface, the organization of the computer code, and its maintenance and testing. Among the scientific topics that feature prominently in this paper are the quantum chemical methods grounded in the pseudospectral approach. A number of multistep workflows dependent on Jaguar are covered: prediction of protonation equilibria in aqueous solutions (particularly calculations of tautomeric stability and pKa), reactivity predictions based on automated transition state search, assembly of Boltzmann-averaged spectra such as vibrational and electronic circular dichroism, as well as nuclear magnetic resonance. Discussed also are quantum chemical calculations that are oriented toward materials science applications, in particular, prediction of properties of optoelectronic materials and organic semiconductors, and molecular catalyst design. The topic of treatment of conformations inevitably comes up in real world research projects and is considered as part of all the workflows mentioned above. In addition, we examine the role of machine learning methods in quantum chemical calculations performed by Jaguar, from auxiliary functions that return the approximate calculation runtime in a user interface, to prediction of actual molecular properties. The current work is second in a series of reviews of Jaguar, the first having been published more than ten years ago. Thus, this paper serves as a rare milestone on the path that is being traversed by Jaguar's development in more than thirty years of its existence.
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Affiliation(s)
- Yixiang Cao
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Ty Balduf
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Michael D Beachy
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - M Chandler Bennett
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Art D Bochevarov
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Alan Chien
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Pavel A Dub
- Schrödinger, Inc., 9868 Scranton Road, Suite 3200, San Diego, California 92121, USA
| | - Kenneth G Dyall
- Schrödinger, Inc., 101 SW Main St., Suite 1300, Portland, Oregon 97204, USA
| | - James W Furness
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Mathew D Halls
- Schrödinger, Inc., 9868 Scranton Road, Suite 3200, San Diego, California 92121, USA
| | - Thomas F Hughes
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Leif D Jacobson
- Schrödinger, Inc., 101 SW Main St., Suite 1300, Portland, Oregon 97204, USA
| | - H Shaun Kwak
- Schrödinger, Inc., 101 SW Main St., Suite 1300, Portland, Oregon 97204, USA
| | - Daniel S Levine
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Daniel T Mainz
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Kevin B Moore
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Mats Svensson
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Pablo E Videla
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Mark A Watson
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Richard A Friesner
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, USA
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11
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Jameel F, Stein M. Chemical accuracy for ligand-receptor binding Gibbs energies through multi-level SQM/QM calculations. Phys Chem Chem Phys 2024; 26:21197-21203. [PMID: 39073067 PMCID: PMC11305096 DOI: 10.1039/d4cp01529k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Accepted: 07/18/2024] [Indexed: 07/30/2024]
Abstract
Calculating the Gibbs energies of binding of ligand-receptor systems with a thermochemical accuracy of ± 1 kcal mol-1 is a challenge to computational approaches. After exploration of the conformational space of the host, ligand and their resulting complexes upon coordination by semi-empirical GFN2 MD and meta-MD simulations, the systematic refinement through a multi-level improvement of binding modes in terms of electronic energies and solvation is able to give Gibbs energies of binding of drug molecules to CB[8] and β-CD macrocyclic receptors with such an accuracy. The accurate treatment of a small number of structures outperforms system-specific force-matching and alchemical transfer model approaches without an extensive sampling and integration.
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Affiliation(s)
- Froze Jameel
- Molecular Simulations and Design Group, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany.
| | - Matthias Stein
- Molecular Simulations and Design Group, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany.
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12
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Li R. London Dispersion Effects on the Structure and Properties of Nonlinear Optical BiB 3O 6 Crystal. Chemphyschem 2024; 25:e202400142. [PMID: 38655698 DOI: 10.1002/cphc.202400142] [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: 02/07/2024] [Revised: 04/16/2024] [Accepted: 04/24/2024] [Indexed: 04/26/2024]
Abstract
α-BiB3O6 (BiBO) is an important nonlinear optical (NLO) material with high efficiency for applications in harmonic generations and quantum technology. Owing to its low symmetry and cooperative Bi3+ lone pair arrangement, it has also exceptional large piezoelectric and electro-optic coefficients and strong anisotropies on other material characteristics. Previous theoretical calculations on its physical (mainly optical) properties often gave confusing results. It is found here that London dispersion (LD) tends to stabilize structures with closer pack entities like lone pair heavy ion Bi3+ with large polarizabilities, which is ignored in most previous density functional theory (DFT) calculations. Present study shows that without considering the LD effect, the structure of α-BiB3O6 (BiBO) was predicted with an over-estimated (by over 10 %) unique b-axis while underestimates a and overestimates c in a less amount. Consequently it is not possible to use the calculated structure to obtain meaningful properties of this important material. By applying a modified post-DFT LD correction based on linear combination of atomic orbitals (LCAO) and B3LYP functional, the experimental structure is well reproduced with the theoretical optimized one. Many important material property tensors of BiBO crystal are calculated in unprecedented precisions, including: dielectric constants (static and in THz range), elastic and elasto-optic constants, piezoelectric constants, refractive indices, NLO and electro-optic (EO) coefficients. Among them, theoretical calculation of the refractive indices in the THz range by diagonalizing the clamped-ion dielectric constants was firstly achieved at least for BiBO crystal. The calculation also confirms that BiBO has an exceptional large piezoelectric constant d22=40 pC/N and largest free EO coefficientsγ 12 T ${{\gamma }_{12}^{T}}$ ,γ 22 T ${{\gamma }_{22}^{T}}$ ,γ 32 T ${{\gamma }_{32}^{T}}$ on the order of 10 pm/V among borate crystals. The calculation also reveals that the large free EO coefficients are largely originated from the piezoelectric induced photo-elastic effect and for practical high speed applications only the clamped-ion EO coefficients take effect. The clamped ion EO coefficient ofγ 53 S ${{\gamma }_{53}^{S}}$ =-4.17 pm/V,γ b 1 S ${{\gamma }_{{\rm b}1}^{S}}$ =-2.61 pm/V are obtained for the first time and may be consulted if one seeks to design BiBO crystal as a high-speed EO modulator. Furthermore, full tensor matrix of the elasto-optic constants was obtained on the first time. Together with the calculated elastic constants, it can help to design acoustic optic modulating devices with preferable figure of merits 10 times that of traditional quartz crystal.
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Affiliation(s)
- Rukang Li
- Beijing Centre for Crystal Research and Development, Key Laboratory of Functional Crystals and Laser Technology, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190
- China and Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
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13
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Boronski JT, Crumpton AE, Roper AF, Aldridge S. A nucleophilic beryllyl complex via metathesis at [Be-Be] 2. Nat Chem 2024; 16:1295-1300. [PMID: 38760434 PMCID: PMC11321998 DOI: 10.1038/s41557-024-01534-9] [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: 01/12/2024] [Accepted: 04/10/2024] [Indexed: 05/19/2024]
Abstract
Owing to its high toxicity, the chemistry of element number four, beryllium, is poorly understood. However, as the lightest elements provide the basis for fundamental models of chemical bonding, there is a need for greater insight into the properties of beryllium. In this context, the chemistry of the homo-elemental Be-Be bond is of fundamental interest. Here the ligand metathesis chemistry of diberyllocene (1; CpBeBeCp)-a stable complex with a Be-Be bond-has been investigated. These studies yield two complexes with Be-Be bonds: Cp*BeBeCp (2) and [K{(HCDippN)2BO}2]BeBeCp (3; Dipp = 2,6-diisopropylphenyl). Quantum chemical calculations indicate that the Be-Be bond in 3 is polarized to such an extent that the complex could be formulated as a mixed-oxidation state Be0/BeII complex. Correspondingly, it is demonstrated that 3 can transfer the 'beryllyl' anion, [BeCp]-, to an organic substrate, by analogy with the reactivity of sp2-sp3 diboranes. Indeed, this work reveals striking similarities between the homo-elemental bonding linkages of beryllium and boron, despite the respective metallic and non-metallic natures of these elements.
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Affiliation(s)
- Josef T Boronski
- Chemistry Research Laboratory Department of Chemistry, University of Oxford, Oxford, UK.
| | - Agamemnon E Crumpton
- Chemistry Research Laboratory Department of Chemistry, University of Oxford, Oxford, UK
| | - Aisling F Roper
- Chemistry Research Laboratory Department of Chemistry, University of Oxford, Oxford, UK
| | - Simon Aldridge
- Chemistry Research Laboratory Department of Chemistry, University of Oxford, Oxford, UK.
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14
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Carder HM, Occhialini G, Bistoni G, Riplinger C, Kwan EE, Wendlandt AE. The sugar cube: Network control and emergence in stereoediting reactions. Science 2024; 385:456-463. [PMID: 39052778 DOI: 10.1126/science.adp2447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Accepted: 06/07/2024] [Indexed: 07/27/2024]
Abstract
Stereochemical editing strategies have recently enabled the transformation of readily accessible substrates into rare and valuable products. Typically, site selectivity is achieved by minimizing kinetic complexity by using protecting groups to suppress reactivity at undesired sites (substrate control) or by using catalysts with tailored shapes to drive reactivity at the desired site (catalyst control). We propose "network control," a contrasting paradigm that exploits hidden interactions between rate constants to greatly amplify modest intrinsic biases and enable precise multisite editing. When network control is applied to the photochemical isomerization of hexoses, six of the eight possible diastereomers can be selectively obtained. The amplification effect can be viewed as a mesoscale phenomenon between the limiting regimes of kinetic control in simple chemical systems and metabolic regulation in complex biological systems.
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Affiliation(s)
- Hayden M Carder
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Gino Occhialini
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Giovanni Bistoni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
| | | | | | - Alison E Wendlandt
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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15
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Grotjahn R, Purnomo J, Jin D, Lutfi N, Furche F. Chemically Accurate Singlet-Triplet Gaps of Arylcarbenes from Local Hybrid Density Functionals. J Phys Chem A 2024; 128:6046-6060. [PMID: 39012067 DOI: 10.1021/acs.jpca.4c02852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Singlet-triplet (ST) gaps are key descriptors of carbenes, because their properties and reactivity are strongly spin-dependent. However, the theoretical prediction of ST gaps is challenging and generally thought to require elaborate correlated wave function methods or double-hybrid density functionals. By evaluating two recent test sets of arylcarbenes (AC12 and AC18), we show that local hybrid functionals based on the "common t" local mixing function (LMF) model achieve mean absolute errors below 1 kcal/mol at a computational cost only slightly higher than that of global hybrid functionals. An analysis of correlation contributions to the ST gaps suggests that the accuracy of the common t-LMF model is mainly due to an improved description of nondynamical correlation which, unlike exchange, is not additive in each spin-channel. Although spin-nonadditivity can be achieved using the local spin polarization alone, using the "common", i.e., spin-unresolved, iso-orbital indicator t for constructing the LMF is found to be critical for consistent accuracy in ST gaps of arylcarbenes. The results support the view of LHs as vehicles to improve the description of nondynamical correlation rather than sophisticated exchange mixing approaches.
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Affiliation(s)
- Robin Grotjahn
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Justin Purnomo
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Dayun Jin
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Nicolas Lutfi
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Filipp Furche
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
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16
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Korb M, Ghazvini SMBH, Low PJ. Migration of Condensed Aromatic Hydrocarbons During Alkyne-Vinylidene Rearrangements. Chemistry 2024; 30:e202400930. [PMID: 38780030 DOI: 10.1002/chem.202400930] [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: 03/07/2024] [Revised: 05/20/2024] [Accepted: 05/22/2024] [Indexed: 05/25/2024]
Abstract
Diarylacetylenes ArC≡CAr featuring condensed aromatic hydrocarbon fragments (Ar) such as naphthalene, anthracene, phenanthrene and pyrene were converted into vinylidene ligands by 1,2-migration reactions within the coordination sphere of half-sandwich complexes [MII(dppe)Cp]+ (MII = RuII, FeII). Comparison of the extent of conversion of the alkyne substrates to the vinylidene complexes [Ru{=C=CAr2}(dppe)Cp]+ with those obtained from acetylenes functionalized by smaller groups (H, CH3, Ph) show that the molecular volume (VM) of the migrating group and relief of steric congestion plays a role during the rearrangement process. Conversely, the H-atoms from the larger condensed ring aryl groups that are in close proximity to the migrating sites also have a significant influence on the efficacy and extent of the reaction by restricting access of the alkyne to the metal center, resulting in a less effective migration reaction. This combination of competing steric factors (acceleration due to relief of steric congestion and restricted access of the alkyne moiety to the reaction site) is exemplified by the facile migration of 1-pyryl entities and the low yields of vinylidene products formed from 1,2-bis(9-anthryl)acetylene.
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Affiliation(s)
- Marcus Korb
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia
| | - Seyed M B H Ghazvini
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia
| | - Paul J Low
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia
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17
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Majumder R, Banerjee S, Paul S, Mondal S, Mandal M, Ghosh P, Maity D, Anoop A, Singh NDP, Mandal M. Riboflavin-Induced DNA Damage and Anticancer Activity in Breast Cancer Cells under Visible Light: A TD-DFT and In Vitro Study. J Chem Inf Model 2024; 64:5580-5589. [PMID: 38982947 DOI: 10.1021/acs.jcim.4c01104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
Targeted treatments for breast cancer that minimize harm to healthy cells are highly sought after. Our study explores the potentiality of riboflavin as a targeted anticancer compound that can be activated by light irradiation. Here, we integrated time-dependent density functional theory (TD-DFT) calculations and an in vitro study under visible light. The TD-DFT calculations revealed that the electronic charge transferred from the DNA base to riboflavin, with the most significant excitation peak occurring within the visible light range. Guided by these insights, an in vitro study was conducted on the breast cancer cell lines MCF-7 and MDA-MB-231. The results revealed substantial growth inhibition in these cell lines when exposed to riboflavin under visible light, with no such impact observed in the absence of light exposure. Interestingly, riboflavin exhibited no/minimal growth-inhibitory effects on the normal cell line L929, irrespective of light conditions. Moreover, through EtBr displacement (DNA-EtBr) and the TUNEL assay, it has been illustrated that, upon exposure to visible light, riboflavin can intercalate within DNA and induce DNA damage. In conclusion, under visible light conditions, riboflavin emerges as a promising candidate with a selective and effective potent anticancer agent against breast cancer while exerting a minimal influence on regular cellular activity.
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Affiliation(s)
- Ranabir Majumder
- Cancer Biology Lab, School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Shreya Banerjee
- Cancer Biology Lab, School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Sayan Paul
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Saugat Mondal
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Madhurima Mandal
- Cancer Biology Lab, School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Priya Ghosh
- Cancer Biology Lab, School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Debjit Maity
- Cancer Biology Lab, School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Anakuthil Anoop
- School of Digital Sciences, Kerala University of Digital Science, Innovation, and Technology, Technopark Phase IV, Pallipuram, Thiruvananthapuram, Kerala 695317, India
| | - N D Pradeep Singh
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Mahitosh Mandal
- Cancer Biology Lab, School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
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18
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Rivera P, Torres A, Romero J, Rodríguez F, Arrieta MP, Olea F, Silva T, Maldonado P, Quijada-Maldonado E, Tapia A. Experimental and theoretical characterization of the release kinetic of carvacrol as inclusion complexes with β-cyclodextrin in poly(lactic acid) and Mater-Bi® processed by supercritical impregnation. Int J Biol Macromol 2024; 278:133946. [PMID: 39029825 DOI: 10.1016/j.ijbiomac.2024.133946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 07/09/2024] [Accepted: 07/15/2024] [Indexed: 07/21/2024]
Abstract
The incorporation of active compounds into polymeric matrices using traditional methods has several drawbacks mainly due to the high volatility and thermal sensitivity of these substances. A solution to this problem could be the incorporation of bioactive compounds forming inclusion complexes as a strategy to improve the chemical stability, bioactivity and achieve controlled release. In this work, β-cyclodextrin/carvacrol inclusion complex was prepared by spray drying to be incorporated into poly(lactic acid) (PLA) and Mater-Bi® films by supercritical CO2 impregnation. The impregnation process was carried out at pressures of 10, 15 and 20 MPa and at 40 °C. Both polymers showed the highest amount of incorporated inclusion complex at 15 MPa, where the percentage of impregnation varied from 0.6 % to 7.1 % in Mater-Bi® and PLA, respectively. Release tests for PLA films impregnated with inclusion complex showed a slow release of the active compound, which did not reach equilibrium after 350 h under the experimental conditions. This prolonged release was not observed in Mater-Bi® due to the lower incorporation of the inclusion complex. The release rate was described herein by a comprehensive phenomenological model considering the decomplexation kinetics combined with the equilibrium and mass transfer expressions.
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Affiliation(s)
- Patricia Rivera
- Laboratory of Membrane Separation Processes (LabProSeM), Department of Chemical Engineering and Bioprocess, Engineering Faculty, University of Santiago de Chile, Santiago, Chile; Packaging Innovation Center (LABEN), Department of Food Science and Technology, Faculty of Technology, Center for the Development of Nanoscience and Nanotechnology (CEDENNA), University of Santiago de Chile (USACH), Santiago 9170201, Chile
| | - Alejandra Torres
- Packaging Innovation Center (LABEN), Department of Food Science and Technology, Faculty of Technology, Center for the Development of Nanoscience and Nanotechnology (CEDENNA), University of Santiago de Chile (USACH), Santiago 9170201, Chile
| | - Julio Romero
- Laboratory of Membrane Separation Processes (LabProSeM), Department of Chemical Engineering and Bioprocess, Engineering Faculty, University of Santiago de Chile, Santiago, Chile.
| | - Francisco Rodríguez
- Packaging Innovation Center (LABEN), Department of Food Science and Technology, Faculty of Technology, Center for the Development of Nanoscience and Nanotechnology (CEDENNA), University of Santiago de Chile (USACH), Santiago 9170201, Chile
| | - Marina P Arrieta
- Departamento de Ingeniería Química Industrial y del Medio Ambiente, Escuela Técnica Superior de Ingenieros Industriales, Universidad Politécnica de Madrid (ETSII-UPM), Calle José Gutiérrez Abascal 2, 28006 Madrid, Spain; Grupo de Investigación: Polímeros, Caracterización y Aplicaciones (POLCA), 28006 Madrid, Spain
| | - Felipe Olea
- Laboratory of Separation Process Intensification (SPI), Department of Chemical Engineering and Bioprocess, University of Santiago de Chile, Santiago, Chile
| | - Tannia Silva
- Packaging Innovation Center (LABEN), Department of Food Science and Technology, Faculty of Technology, Center for the Development of Nanoscience and Nanotechnology (CEDENNA), University of Santiago de Chile (USACH), Santiago 9170201, Chile
| | - Paola Maldonado
- Packaging Innovation Center (LABEN), Department of Food Science and Technology, Faculty of Technology, Center for the Development of Nanoscience and Nanotechnology (CEDENNA), University of Santiago de Chile (USACH), Santiago 9170201, Chile
| | - Esteban Quijada-Maldonado
- Laboratory of Separation Process Intensification (SPI), Department of Chemical Engineering and Bioprocess, University of Santiago de Chile, Santiago, Chile
| | - Andrea Tapia
- Packaging Innovation Center (LABEN), Department of Food Science and Technology, Faculty of Technology, Center for the Development of Nanoscience and Nanotechnology (CEDENNA), University of Santiago de Chile (USACH), Santiago 9170201, Chile
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19
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Sitek P, Lodowski P, Jaworska M. Mechanism of Methyl Transfer Reaction between CH 3Co(dmgBF 2) 2py and PPh 3Ni(Triphos). Molecules 2024; 29:3335. [PMID: 39064913 PMCID: PMC11280430 DOI: 10.3390/molecules29143335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/30/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
DFT calculations were performed for the methyl group transfer reaction between CH3Co (dmgBF2)py and PPh3Ni(Triphos). The reaction mechanism and its energetics were investigated. This reaction is relevant to the catalytic mechanism of the enzyme acetyl coenzyme A synthase. BP86 and PBE functionals and dispersion corrections were used. It was found that intermolecular interactions are very important for this reaction. The influence of the solvent on the reaction was studied.
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Affiliation(s)
| | | | - Maria Jaworska
- Institute of Chemistry, University of Silesia in Katowice, Szkolna 9, 40-006 Katowice, Poland (P.L.)
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20
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Zhang Y, Hong Z, Ye Z, Pan X. Theoretical Understanding of Electromigration-Related Surface Diffusion and Current-Induced Force in Ag-Pd Systems. ACS OMEGA 2024; 9:29576-29584. [PMID: 39005816 PMCID: PMC11238235 DOI: 10.1021/acsomega.4c02663] [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: 03/19/2024] [Revised: 06/14/2024] [Accepted: 06/18/2024] [Indexed: 07/16/2024]
Abstract
Electromigration, as a common reason for interconnect failure, is becoming increasingly important in the ongoing decrease in the integrated circuit manufacturing process. A study is being carried out utilizing the ab initio calculational method to gain a deeper understanding of electromigration, with a focus on the atom diffusion process in the Ag-Pd alloy system, a commonly used interconnect material. We begin by establishing that the primary mechanism of diffusion is step-edge diffusion on the (111) surface. Following this, we examine the current-induced force exerted on the migrating Ag atom. The Pd substitutional defect reveals an effect that increases the energy barrier of diffusion and decreases the current-induced force that powers the directional migration.
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Affiliation(s)
- Yumin Zhang
- School
of Materials Science and Engineering, Zhejiang
University, Hangzhou 310027, P. R. China
| | - Zijian Hong
- School
of Materials Science and Engineering, Zhejiang
University, Hangzhou 310027, P. R. China
| | - Zhizhen Ye
- School
of Materials Science and Engineering, Zhejiang
University, Hangzhou 310027, P. R. China
- Wenzhou
Key Laboratory of Novel Optoelectronic and Nano Materials, Institute
of Wenzhou, Zhejiang University, Wenzhou 325006, P. R. China
| | - Xinhua Pan
- School
of Materials Science and Engineering, Zhejiang
University, Hangzhou 310027, P. R. China
- Wenzhou
Key Laboratory of Novel Optoelectronic and Nano Materials, Institute
of Wenzhou, Zhejiang University, Wenzhou 325006, P. R. China
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Antipas GSE, Reul R, Voges K, Kyeremateng SO, Ntallis NA, Karalis KT, Miroslaw L. System-agnostic prediction of pharmaceutical excipient miscibility via computing-as-a-service and experimental validation. Sci Rep 2024; 14:15106. [PMID: 38956156 PMCID: PMC11219749 DOI: 10.1038/s41598-024-65978-2] [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: 01/29/2024] [Accepted: 06/26/2024] [Indexed: 07/04/2024] Open
Abstract
We applied computing-as-a-service to the unattended system-agnostic miscibility prediction of the pharmaceutical surfactants, Vitamin E TPGS and Tween 80, with Copovidone VA64 polymer at temperature relevant for the pharmaceutical hot melt extrusion process. The computations were performed in lieu of running exhaustive hot melt extrusion experiments to identify surfactant-polymer miscibility limits. The computing scheme involved a massively parallelized architecture for molecular dynamics and free energy perturbation from which binodal, spinodal, and mechanical mixture critical points were detected on molar Gibbs free energy profiles at 180 °C. We established tight agreement between the computed stability (miscibility) limits of 9.0 and 10.0 wt% vs. the experimental 7 and 9 wt% for the Vitamin E TPGS and Tween 80 systems, respectively, and identified different destabilizing mechanisms applicable to each system. This paradigm supports that computational stability prediction may serve as a physically meaningful, resource-efficient, and operationally sensible digital twin to experimental screening tests of pharmaceutical systems. This approach is also relevant to amorphous solid dispersion drug delivery systems, as it can identify critical stability points of active pharmaceutical ingredient/excipient mixtures.
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Affiliation(s)
| | - Regina Reul
- AbbVie Deutschland GmbH & Co. KG, Development Sciences, 67061, Ludwigshafen, Germany
| | - Kristin Voges
- AbbVie Deutschland GmbH & Co. KG, Development Sciences, 67061, Ludwigshafen, Germany
| | - Samuel O Kyeremateng
- AbbVie Deutschland GmbH & Co. KG, Development Sciences, 67061, Ludwigshafen, Germany.
| | | | | | - Lukasz Miroslaw
- Azure High Performance Computing and Artificial Intelligence, Microsoft Switzerland, The Circle 02, 8058, Zurich, Switzerland
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22
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Kuzderová G, Sovová S, Rendošová M, Gyepes R, Sabolová D, Kožárová I, Balážová Ľ, Vilková M, Kello M, Liška A, Vargová Z. Influence of proline and hydroxyproline as antimicrobial and anticancer peptide components on the silver(I) ion activity: structural and biological evaluation with a new theoretical and experimental SAR approach. Dalton Trans 2024; 53:10834-10850. [PMID: 38661536 DOI: 10.1039/d4dt00389f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Silver(I) complexes with proline and hydroxyproline were synthesized and structurally characterized and crystal structure analysis shows that the formulas of the compounds are {[Ag2(Pro)2(NO3)]NO3}n (AgPro) (Pro = L-proline) and {[Ag2(Hyp)2(NO3)]NO3}n (AgHyp) (Hyp = trans-4-hydroxy-L-proline). Both complexes crystallize in the monoclinic lattice with space group P21 with a carboxylate bidentate-bridging coordination mode of the organic ligands Pro and Hyp (with NH2+ and COO- groups in zwitterionic form). Both complexes have a distorted seesaw (C2v) geometry around one silver(I) ion with τ4 values of 58% (AgPro) and 51% (AgHyp). Moreover, the results of spectral and thermal analyses correlate with the structural ones. 1H and 13C NMR spectra confirm the complexes species' presence in the DMSO biological testing medium and their stability in the time range of the bioassays. In addition, molar conductivity measurements indicate complexes' behaviour like 1 : 1 electrolytes. Both complexes showed higher or the same antibacterial activity against Bacillus cereus, Pseudomonas aeruginosa and Staphylococcus aureus as AgNO3 (MIC = 0.063 mM) and higher than silver(I) sulfadiazine (AgSD) (MIC > 0.5 mM) against Pseudomonas aeruginosa. In addition, complex AgPro exerted a strong cytotoxic effect against the tested MDA-MB-231 and Jurkat cancer cell lines (IC50 values equal to 3.7 and 3.0 μM, respectively) compared with AgNO3 (IC50 = 6.1 (5.7) μM) and even significantly higher selectivity than cisplatin (cisPt) against MDA-MB-231 cancer cell lines (SI = 3.05 (AgPro); 1.16 (cisPt), SI - selectivity index). The binding constants and the number of binding sites (n) of AgPro and AgHyp complexes with bovine serum albumin (BSA) were determined at four different temperatures, and the zeta potential of BSA in the presence of silver(I) complexes was also measured. The in ovo method shows the safety of the topical and intravenous application of AgPro and AgHyp. Moreover, the complexes' bioavailability was verified by lipophilicity evaluation from the experimental and theoretical points of view.
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Affiliation(s)
- Gabriela Kuzderová
- Department of Inorganic Chemistry, Faculty of Science, P.J.Šafárik University, Moyzesova 11, 041 54 Košice, Slovak Republic.
| | - Simona Sovová
- Department of Biochemistry, Faculty of Science, P.J.Šafárik University, Moyzesova 11, 041 54 Košice, Slovak Republic
- Department of Food Hygiene, Technology and Safety, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovak Republic
| | - Michaela Rendošová
- Department of Inorganic Chemistry, Faculty of Science, P.J.Šafárik University, Moyzesova 11, 041 54 Košice, Slovak Republic.
| | - Róbert Gyepes
- Department of Inorganic Chemistry, Faculty of Science, Charles University, Hlavova 2030, 128 00 Prague, Czech Republic
| | - Danica Sabolová
- Department of Biochemistry, Faculty of Science, P.J.Šafárik University, Moyzesova 11, 041 54 Košice, Slovak Republic
| | - Ivona Kožárová
- Department of Food Hygiene, Technology and Safety, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovak Republic
| | - Ľudmila Balážová
- Department of Pharmaceutical Technology, Pharmacognosy and Botany, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovak Republic
| | - Mária Vilková
- NMR laboratory, Faculty of Science, P.J.Šafárik University, Moyzesova 11, 041 54 Košice, Slovak Republic
| | - Martin Kello
- Department of Pharmacology, Faculty of Medicine, P.J.Šafárik University, Trieda SNP 1, 040 11 Košice, Slovak Republic
| | - Alan Liška
- Department of Molecular Electrochemistry and Catalysis, J. Heyrovský Institute of Physical Chemistry of the CAS, Dolejškova 3/2155, 182 23 Praha 8, Czech Republic
| | - Zuzana Vargová
- Department of Inorganic Chemistry, Faculty of Science, P.J.Šafárik University, Moyzesova 11, 041 54 Košice, Slovak Republic.
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Fischer M, Brauer J. Studying the adsorption of emerging organic contaminants in zeolites with dispersion-corrected density functional theory calculations: From numbers to recommendations. ChemistryOpen 2024; 13:e202300273. [PMID: 38385822 PMCID: PMC11230941 DOI: 10.1002/open.202300273] [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: 11/21/2023] [Revised: 01/10/2024] [Indexed: 02/23/2024] Open
Abstract
Adsorption energies obtained from dispersion-corrected density functional theory (DFT) calculations show a considerable dependence on the choice of exchange-correlation functional and dispersion correction. A number of investigations have employed different approaches to compute adsorption energies of small molecules in zeolites, using reference values from high-level calculations and/or experiments. Such comparative studies are lacking for larger functional organic molecules such as pharmaceuticals or personal care products, despite their potential relevance for applications, e. g., in contaminant removal or drug delivery. The present study aims to fill this gap by comparing adsorption energies and, for selected cases, equilibrium structures of emerging organic contaminants adsorbed in MOR- and FAU-type all-silica zeolites. A total of 13 dispersion-corrected DFT approaches are compared, including methods using a pairwise dispersion correction as well as non-local van der Waals density functionals. While absolute values of adsorption energies vary widely, qualitative trends across the set of zeolite-guest combinations are not strongly dependent on the choice of functional. For selected cluster models, DFT adsorption energies are compared to reference values from coupled cluster (DLPNO-CCSD(T)) calculations. Although all DFT approaches deliver systematically more negative adsorption energies than the coupled cluster reference, this tendency is least pronounced for the rev-vdW-DF2 functional.
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Affiliation(s)
- Michael Fischer
- Crystallography and GeomaterialsFaculty of GeosciencesUniversity of BremenKlagenfurter Straße 2–428359BremenGermany
- Bremen Center for Computational Materials Science and MAPEX Center for Materials and ProcessesUniversity of Bremen28359BremenGermany
| | - Jakob Brauer
- Crystallography and GeomaterialsFaculty of GeosciencesUniversity of BremenKlagenfurter Straße 2–428359BremenGermany
- Bremen Center for Computational Materials Science and MAPEX Center for Materials and ProcessesUniversity of Bremen28359BremenGermany
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24
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Leyser da Costa Gouveia T, Maganas D, Neese F. Restricted Open-Shell Hartree-Fock Method for a General Configuration State Function Featuring Arbitrarily Complex Spin-Couplings. J Phys Chem A 2024; 128:5041-5053. [PMID: 38886177 PMCID: PMC11215774 DOI: 10.1021/acs.jpca.4c00688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/30/2024] [Accepted: 05/30/2024] [Indexed: 06/20/2024]
Abstract
In this work, we present a general spin restricted open-shell Hartree-Fock (ROHF) implementation that is able to generate self-consistent field (SCF) wave functions for an arbitrary configuration state function (CSF). These CSFs can contain an arbitrary number of unpaired electrons in arbitrary spin-couplings. The resulting method is named CSF-ROHF. We demonstrate that starting from the ROHF energy expression, for example, the one given by Edwards and Zerner, it is possible to obtain the values of the ROHF vector-coupling coefficients by setting up an open-shell for each group of consecutive parallel-coupled spins dictated by the unique spin-coupling pattern of any given CSF. To achieve this important and nontrivial goal, we employ the machinery of the iterative configuration expansion configuration interaction (ICE-CI) method, which is able to tackle general CI problems on the basis of spin-adapted CSFs. This development allows for the efficient generation of SCF spin-eigenfunctions for systems with complex spin-coupling patterns, such as polymetallic chains and metal clusters, while maintaining SCF scaling with system size (quadratic or less, depending on the specific algorithm and approximations chosen).
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Affiliation(s)
| | - Dimitrios Maganas
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr 45470, Germany
| | - Frank Neese
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr 45470, Germany
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25
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Santos AS, Pereira PH, Abrantes PP, Farina C, Maia Neto PA, de Melo e Souza R. Time-Dependent Effective Hamiltonians for Light-Matter Interactions. ENTROPY (BASEL, SWITZERLAND) 2024; 26:527. [PMID: 38920535 PMCID: PMC11203030 DOI: 10.3390/e26060527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 06/27/2024]
Abstract
In this paper, we present a systematic approach to building useful time-dependent effective Hamiltonians in molecular quantum electrodynamics. The method is based on considering part of the system as an open quantum system and choosing a convenient unitary transformation based on the evolution operator. We illustrate our formalism by obtaining four Hamiltonians, each suitable to a different class of applications. We show that we may treat several effects of molecular quantum electrodynamics with a direct first-order perturbation theory. In addition, our effective Hamiltonians shed light on interesting physical aspects that are not explicit when employing more standard approaches. As applications, we discuss three examples: two-photon spontaneous emission, resonance energy transfer, and dispersion interactions.
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Affiliation(s)
- Aroaldo S. Santos
- Instituto de Física, Universidade Federal Fluminense, Niterói 24210-346, Rio de Janeiro, Brazil; (A.S.S.); (P.H.P.); (R.d.M.e.S.)
- Instituto Federal do Paraná, Telêmaco Borba 84269-090, Paraná, Brazil
| | - Pedro H. Pereira
- Instituto de Física, Universidade Federal Fluminense, Niterói 24210-346, Rio de Janeiro, Brazil; (A.S.S.); (P.H.P.); (R.d.M.e.S.)
| | - Patrícia P. Abrantes
- Instituto de Física, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-972, Rio de Janeiro, Brazil; (P.P.A.); (C.F.)
| | - Carlos Farina
- Instituto de Física, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-972, Rio de Janeiro, Brazil; (P.P.A.); (C.F.)
| | - Paulo A. Maia Neto
- Instituto de Física, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-972, Rio de Janeiro, Brazil; (P.P.A.); (C.F.)
| | - Reinaldo de Melo e Souza
- Instituto de Física, Universidade Federal Fluminense, Niterói 24210-346, Rio de Janeiro, Brazil; (A.S.S.); (P.H.P.); (R.d.M.e.S.)
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26
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O’Neill N, Shi BX, Fong K, Michaelides A, Schran C. To Pair or not to Pair? Machine-Learned Explicitly-Correlated Electronic Structure for NaCl in Water. J Phys Chem Lett 2024; 15:6081-6091. [PMID: 38820256 PMCID: PMC11181334 DOI: 10.1021/acs.jpclett.4c01030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/02/2024]
Abstract
The extent of ion pairing in solution is an important phenomenon to rationalize transport and thermodynamic properties of electrolytes. A fundamental measure of this pairing is the potential of mean force (PMF) between solvated ions. The relative stabilities of the paired and solvent shared states in the PMF and the barrier between them are highly sensitive to the underlying potential energy surface. However, direct application of accurate electronic structure methods is challenging, since long simulations are required. We develop wave function based machine learning potentials with the random phase approximation (RPA) and second order Møller-Plesset (MP2) perturbation theory for the prototypical system of Na and Cl ions in water. We show both methods in agreement, predicting the paired and solvent shared states to have similar energies (within 0.2 kcal/mol). We also provide the same benchmarks for different DFT functionals as well as insight into the PMF based on simple analyses of the interactions in the system.
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Affiliation(s)
- Niamh O’Neill
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- Cavendish
Laboratory, Department of Physics, University
of Cambridge, Cambridge CB3 0HE, United
Kingdom
- Lennard-Jones
Centre, University of Cambridge, Trinity Ln, Cambridge CB2 1TN, United Kingdom
| | - Benjamin X. Shi
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- Lennard-Jones
Centre, University of Cambridge, Trinity Ln, Cambridge CB2 1TN, United Kingdom
| | - Kara Fong
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- Lennard-Jones
Centre, University of Cambridge, Trinity Ln, Cambridge CB2 1TN, United Kingdom
| | - Angelos Michaelides
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- Lennard-Jones
Centre, University of Cambridge, Trinity Ln, Cambridge CB2 1TN, United Kingdom
| | - Christoph Schran
- Cavendish
Laboratory, Department of Physics, University
of Cambridge, Cambridge CB3 0HE, United
Kingdom
- Lennard-Jones
Centre, University of Cambridge, Trinity Ln, Cambridge CB2 1TN, United Kingdom
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27
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Burguera S, Bauzá A, Frontera A. A novel approach for estimating the strength of argentophilic and aurophilic interactions using QTAIM parameters. Phys Chem Chem Phys 2024; 26:16550-16560. [PMID: 38829286 DOI: 10.1039/d4cp00410h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Metallophilic interactions, specifically argentophilic (Ag⋯Ag) and aurophilic (Au⋯Au) interactions, play a crucial role in stabilizing various molecular and solid-state structures. In this manuscript, we present a convenient method to estimate the strength of argentophilic and aurophilic interactions based on quantum theory of atoms in molecules (QTAIM) parameters evaluated at the bond critical points connecting the metal centres. We employ density functional theory (DFT) calculations and the QTAIM parameters to develop this energy predictor. To validate the reliability and applicability of our method, we test it using a selection of X-ray crystal structures extracted from the cambridge structural database (CSD), where argentophilic and aurophilic interactions are known to be significant in their solid-state arrangements. This method offers a distinct advantage in systems where multiple interactions, beyond metallophilic interactions, contribute to the overall stability of the structure. By employing our approach, researchers can distinctly quantify the strength of argentophilic and aurophilic interactions, facilitating a deeper understanding of their impact on molecular and solid-state properties. This method fills a critical gap in the existing literature, offering a valuable tool to researchers seeking to unravel the intricate interactions in metal-containing compounds.
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Affiliation(s)
- Sergi Burguera
- Department of Chemistry, Universitat de les Illes Balears, Crta de Valldemossa km 7.5, 07122 Palma de Mallorca (Baleares), Spain.
| | - Antonio Bauzá
- Department of Chemistry, Universitat de les Illes Balears, Crta de Valldemossa km 7.5, 07122 Palma de Mallorca (Baleares), Spain.
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Crta de Valldemossa km 7.5, 07122 Palma de Mallorca (Baleares), Spain.
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28
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Shukla A, Biswal AS, Chowdhury A, Halder R, Chatterjee S. Aggregation-Induced Modulation of Ground and Excited State Photophysics of 5-( tert-Butyl)-2-Hydroxy-1,3-Isophthalaldehyde (5- tBHI). J Phys Chem B 2024; 128:5437-5453. [PMID: 38662934 DOI: 10.1021/acs.jpcb.4c00258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
5-(tert-Butyl)-2-hydroxy-1,3-isophthalaldehyde (5-tBHI) is a photochromic material susceptible to either excited state proton transfer or excited state intramolecular proton transfer, depending upon the solvent. However, it has also been found to aggregate in the presence of sodium dodecyl sulfate. In this current study, based on the steady-state and time-resolved spectroscopy, supported by crystallography, quantum chemical density functional theory calculation, and molecular dynamics (MD) simulation, we report on the aggregation of this potential single benzene-based emitter (SBBE) in neat solvents as well as solid phase to modulate its photophysics. It has been found that 5-tBHI forms mixed aggregates of different orders, owing to the presence of both enolic and tautomeric forms, to yield tunable emission, although the emission intensity is quenched. These findings suggest that the intramolecular hydrogen bonding of 5-tBHI not only limits intermolecular interactions but also promotes nonradiative deactivation pathways. Hence, designing and structural engineering, with a focus to suppressing intramolecular hydrogen bonding as well as increasing through space conjugation by replacing the aldehydic moieties with bulky aliphatic or aromatic ketonic groups, can be a plausible approach to yielding improved probes with tunable emission and higher fluorescence quantum yields.
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Affiliation(s)
- Aparna Shukla
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (Indian School of Mines) Dhanbad, Dhanbad 826004 Jharkhand, India
| | - Abhipsa Sekhar Biswal
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (Indian School of Mines) Dhanbad, Dhanbad 826004 Jharkhand, India
| | - Arkaprava Chowdhury
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076, India
| | - Ritaban Halder
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, United States
| | - Soumit Chatterjee
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (Indian School of Mines) Dhanbad, Dhanbad 826004 Jharkhand, India
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29
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Chen X, Cifuentes-Lopez A, Shao X, Lin L, Prokopchuk D, Pavanello M. Unraveling the Hydration Shell Structure and Dynamics of Group 10 Aqua Ions. J Phys Chem Lett 2024; 15:5517-5528. [PMID: 38749061 DOI: 10.1021/acs.jpclett.4c00464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2024]
Abstract
We present ab initio simulations based on subsystem DFT of group 10 aqua ions accurately compared against experimental data on hydration structure. Our simulations provide insights into the molecular structures and dynamics of hydration shells, offering recalibrated interpretations of experimental results. We observe a soft, but distinct second hydration shell in Palladium (Pd) due to a balance between thermal fluctuations, metal-water interactions, and hydrogen bonding. Nickel (Ni) and platinum (Pt) exhibit more rigid hydration shells. Notably, our simulations align with experimental findings for Pd, showing axial hydration marked by a broad peak at about 3 Å in the Pd-O radial distribution function, revising the previously sharp "mesoshell" prediction. We introduce the "hydrogen bond dome" concept to describe a resilient network of hydrogen-bonded water molecules around the metal, which plays a critical role in the axial hydration dynamics.
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Affiliation(s)
- Xin Chen
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
- Department of Physics, Rutgers University, Newark, New Jersey 07102, United States
| | | | - Xuecheng Shao
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
| | - Lirong Lin
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
| | - Demyan Prokopchuk
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
| | - Michele Pavanello
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
- Department of Physics, Rutgers University, Newark, New Jersey 07102, United States
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30
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Beletsan OB, Gordiy I, Lunkov SS, Kalinin MA, Alkhimova LE, Nosach EA, Ilin EA, Bespalov AV, Dallakyan OL, Chamkin AA, Prolomov IV, Zaripov RA, Pershin AA, Protsenko BO, Rusalev YV, Oganov RA, Kovaleva DK, Mironov VA, Dotsenko VV, Genaev AM, Sharapa DI, Tikhonov DS. From a humorous post to a detailed quantum-chemical study: isocyanate synthesis revisited. Phys Chem Chem Phys 2024; 26:13850-13861. [PMID: 38656824 DOI: 10.1039/d3cp04654k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Isocyanates play an essential role in modern manufacturing processes, especially in polyurethane production. There are numerous synthesis strategies for isocyanates both under industrial and laboratory conditions, which do not prevent searching for alternative highly efficient synthetic protocols. Here, we report a detailed theoretical investigation of the mechanism of sulfur dioxide-catalyzed rearrangement of phenylnitrile oxide into phenyl isocyanate, which was first reported in 1977. The DLPNO-CCSD(T) method and up-to-date DFT protocols were used to perform a highly accurate quantum-chemical study of the rearrangement mechanism. An overview of various organic and inorganic catalysts has revealed other potential catalysts, such as sulfur trioxide and selenium dioxide. Furthermore, the present study elucidated how substituents in phenylnitrile oxide influence reaction kinetics. This study was performed by a self-organized collaboration of scientists initiated by a humorous post on the VK social network.
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Affiliation(s)
- Oleg B Beletsan
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Igor Gordiy
- ChemU Corporation Ltd, 17 17 Gr. Xenopoulou St., 3106 Limassol, Cyprus
| | - Sergey S Lunkov
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
- N. D. Zelinsky Institute of Organic Chemistry, Leninsky prosp. 47, 119991 Moscow, Russia
| | - Mikhail A Kalinin
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Larisa E Alkhimova
- Center for Nature-Inspired Engineering, University of Tyumen, 625003 Tyumen, Russia
- School of Natural Sciences, University of Tyumen, 625003 Tyumen, Russia
| | - Egor A Nosach
- Department of Fundamental Physical and Chemical Engineering, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Egor A Ilin
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
- N. D. Zelinsky Institute of Organic Chemistry, Leninsky prosp. 47, 119991 Moscow, Russia
| | - Alexandr V Bespalov
- Department of Chemistry and High Technologies, Kuban State University, 149 Stavropolskaya St., 350040 Krasnodar, Russia
| | - Olgert L Dallakyan
- Computational Material Science Laboratory, Department of Physics, Yerevan State University, 0025 Yerevan, Armenia
| | - Aleksandr A Chamkin
- A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, 119334 Moscow, Russia
| | - Ilya V Prolomov
- D. Mendeleev University of Chemical Technology of Russia, 125047 Moscow, Russia
- N. D. Zelinsky Institute of Organic Chemistry, Leninsky prosp. 47, 119991 Moscow, Russia
| | - Radion A Zaripov
- Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Andrey A Pershin
- Samara Branch of Lebedev Physical Institute, 443011 Samara, Russia
- Department of Physics, Samara University, 443086 Samara, Russia
| | - Bogdan O Protsenko
- The Smart Materials Research Institute, Southern Federal University, 344090 Rostov-on-Don, Russia
| | - Yury V Rusalev
- The Smart Materials Research Institute, Southern Federal University, 344090 Rostov-on-Don, Russia
| | - Ruslan A Oganov
- Department of Biochemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Diana K Kovaleva
- Department of Biochemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Vladimir A Mironov
- A. M. Butlerov Chemistry Institute, Kazan Federal University, 420008 Kazan, Russia
| | - Victor V Dotsenko
- Department of Chemistry and High Technologies, Kuban State University, 149 Stavropolskaya St., 350040 Krasnodar, Russia
- Faculty of Chemistry and Pharmacy, North-Caucasus Federal University, 355017 Stavropol, Russia
| | - Alexandr M Genaev
- N.N. Vorozhtsov Institute of Organic Chemistry, 630090 Novosibirsk, Russia.
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31
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Xu F, Sheng J, Stindt CN, Crespi S, Danowski W, Hilbers MF, Buma WJ, Feringa BL. All-visible-light-driven stiff-stilbene photoswitches. Chem Sci 2024; 15:6763-6769. [PMID: 38725493 PMCID: PMC11077541 DOI: 10.1039/d4sc00983e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 03/27/2024] [Indexed: 05/12/2024] Open
Abstract
Molecular photoswitches are potent tools to construct dynamic functional systems and responsive materials that can be controlled in a non-invasive manner. As P-type photoswitches, stiff-stilbenes attract increasing interest, owing to their superiority in quantum yield, significant geometric differences between isomers, excellent thermostability and robust switching behavior. Nevertheless, the UV-light-triggered photoisomerization of stiff-stilbenes has been a main drawback for decades as UV light is potentially harmful and has low penetration depth. Here, we provided a series of para-formylated stiff-stilbenes by Rieche ortho-formylation to achieve all-visible-light-responsiveness. Additional phenolic groups provide access to late-stage chemical modification facilitating design of molecules responsive to visible light. Remarkably, the photoisomerization of aldehyde-appended stiff-stilbenes could be fully manipulated using visible light, accompanied by a high photostationary state (PSS) distribution. These features render them excellent candidates for future visible-light-controllable smart materials and dynamic systems.
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Affiliation(s)
- Fan Xu
- Center for System Chemistry, Stratingh Institute for Chemistry, University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Jinyu Sheng
- Center for System Chemistry, Stratingh Institute for Chemistry, University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Charlotte N Stindt
- Center for System Chemistry, Stratingh Institute for Chemistry, University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Stefano Crespi
- Department of Chemistry-Ångström Laboratory, Uppsala University Box 523 Uppsala Sweden
| | - Wojciech Danowski
- University of Strasbourg CNRS ISIS UMR 7006, 8 Allée Gaspard Monge Strasbourg F-67000 France
- Faculty of Chemistry, University of Warsaw Pasteura 1 02-093 Warsaw Poland
| | - Michiel F Hilbers
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam Science Park 904, 1098 XH Amsterdam The Netherlands
| | - Wybren Jan Buma
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam Science Park 904, 1098 XH Amsterdam The Netherlands
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University Toernooiveld 7c, 6525 ED Nijmegen The Netherlands
| | - Ben L Feringa
- Center for System Chemistry, Stratingh Institute for Chemistry, University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
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32
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Gasevic T, Bursch M, Ma Q, Grimme S, Werner HJ, Hansen A. The p-block challenge: assessing quantum chemistry methods for inorganic heterocycle dimerizations. Phys Chem Chem Phys 2024; 26:13884-13908. [PMID: 38661329 DOI: 10.1039/d3cp06217a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The elements of the p-block of the periodic table are of high interest in various chemical and technical applications like frustrated Lewis-pairs (FLP) or opto-electronics. However, high-quality benchmark data to assess approximate density functional theory (DFT) for their theoretical description are sparse. In this work, we present a benchmark set of 604 dimerization energies of 302 "inorganic benzenes" composed of all non-carbon p-block elements of main groups III to VI up to polonium. This so-called IHD302 test set comprises two classes of structures formed by covalent bonding and by weaker donor-acceptor (WDA) interactions, respectively. Generating reliable reference data with ab initio methods is challenging due to large electron correlation contributions, core-valence correlation effects, and especially the slow basis set convergence. To compute reference values for these dimerization reactions, after thorough testing, we applied a computational protocol using state-of-the-art explicitly correlated local coupled cluster theory termed PNO-LCCSD(T)-F12/cc-VTZ-PP-F12(corr.). It includes a basis set correction at the PNO-LMP2-F12/aug-cc-pwCVTZ level. Based on these reference data, we assess 26 DFT methods in combination with three different dispersion corrections and the def2-QZVPP basis set, five composite DFT approaches, and five semi-empirical quantum mechanical methods. For the covalent dimerizations, the r2SCAN-D4 meta-GGA, the r2SCAN0-D4 and ωB97M-V hybrids, and the revDSD-PBEP86-D4 double-hybrid functional are found to be the best-performing methods among the evaluated functionals of the respective class. However, since def2 basis sets for the 4th period are not associated to relativistic pseudo-potentials, we obtained significant errors in the covalent dimerization energies (up to 6 kcal mol-1) for molecules containing p-block elements of the 4th period. Significant improvements were achieved for systems containing 4th row elements by using ECP10MDF pseudopotentials along with re-contracted aug-cc-pVQZ-PP-KS basis sets introduced in this work with the contraction coefficients taken from atomic DFT (PBE0) calculations. Overall, the IHD302 set represents a challenge to contemporary quantum chemical methods. This is due to a large number of spatially close p-element bonds which are underrepresented in other benchmark sets, and the partial covalent bonding character for the WDA interactions. The IHD302 set may be helpful to develop more robust and transferable approximate quantum chemical methods in the future.
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Affiliation(s)
- Thomas Gasevic
- Mulliken Center for Theoretical Chemistry, Rheinische Friedrich-Wilhelms-Universität Bonn, Beringstr. 4, 53115 Bonn, Germany.
| | - Markus Bursch
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.
- FACCTs GmbH, 50677, Koeln, Germany
| | - Qianli Ma
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany.
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Rheinische Friedrich-Wilhelms-Universität Bonn, Beringstr. 4, 53115 Bonn, Germany.
| | - Hans-Joachim Werner
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany.
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Rheinische Friedrich-Wilhelms-Universität Bonn, Beringstr. 4, 53115 Bonn, Germany.
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33
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Žugec I, Geilhufe RM, Lončarić I. Global machine learning potentials for molecular crystals. J Chem Phys 2024; 160:154106. [PMID: 38624120 DOI: 10.1063/5.0196232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 03/29/2024] [Indexed: 04/17/2024] Open
Abstract
Molecular crystals are difficult to model with accurate first-principles methods due to large unit cells. On the other hand, accurate modeling is required as polymorphs often differ by only 1 kJ/mol. Machine learning interatomic potentials promise to provide accuracy of the baseline first-principles methods with a cost lower by orders of magnitude. Using the existing databases of the density functional theory calculations for molecular crystals and molecules, we train global machine learning interatomic potentials, usable for any molecular crystal. We test the performance of the potentials on experimental benchmarks and show that they perform better than classical force fields and, in some cases, are comparable to the density functional theory calculations.
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Affiliation(s)
- Ivan Žugec
- Centro de Física de Materiales CFM/MPC (CSIC-UPV/EHU), Donostia-San Sebastián, Spain
| | - R Matthias Geilhufe
- Department of Physics, Chalmers University of Technology, Gothenburg, Sweden
| | - Ivor Lončarić
- Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia
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Ansari M, Bhattacharjee S, Pantazis DA. Correlating Structure with Spectroscopy in Ascorbate Peroxidase Compound II. J Am Chem Soc 2024; 146:9640-9656. [PMID: 38530124 PMCID: PMC11009960 DOI: 10.1021/jacs.3c13169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 03/15/2024] [Accepted: 03/15/2024] [Indexed: 03/27/2024]
Abstract
Structural and spectroscopic investigations of compound II in ascorbate peroxidase (APX) have yielded conflicting conclusions regarding the protonation state of the crucial Fe(IV) intermediate. Neutron diffraction and crystallographic data support an iron(IV)-hydroxo formulation, whereas Mössbauer, X-ray absorption (XAS), and nuclear resonance vibrational spectroscopy (NRVS) studies appear consistent with an iron(IV)-oxo species. Here we examine APX with spectroscopy-oriented QM/MM calculations and extensive exploration of the conformational space for both possible formulations of compound II. We establish that irrespective of variations in the orientation of a vicinal arginine residue and potential reorganization of proximal water molecules and hydrogen bonding, the Fe-O distances for the oxo and hydroxo forms consistently fall within distinct, narrow, and nonoverlapping ranges. The accuracy of geometric parameters is validated by coupled-cluster calculations with the domain-based local pair natural orbital approach, DLPNO-CCSD(T). QM/MM calculations of spectroscopic properties are conducted for all structural variants, encompassing Mössbauer, optical, X-ray absorption, and X-ray emission spectroscopies and NRVS. All spectroscopic observations can be assigned uniquely to an Fe(IV)═O form. A terminal hydroxy group cannot be reconciled with the spectroscopic data. Under no conditions can the Fe(IV)═O distance be sufficiently elongated to approach the crystallographically reported Fe-O distance. The latter is consistent only with a hydroxo species, either Fe(IV) or Fe(III). Our findings strongly support the Fe(IV)═O formulation of APX-II and highlight unresolved discrepancies in the nature of samples used across different experimental studies.
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Affiliation(s)
- Mursaleem Ansari
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz
1, Mülheim an der Ruhr 45470, Germany
| | - Sinjini Bhattacharjee
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz
1, Mülheim an der Ruhr 45470, Germany
| | - Dimitrios A. Pantazis
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz
1, Mülheim an der Ruhr 45470, Germany
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35
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Silva RC, Canisares FSM, Saraiva LF, Pires AM, Lima SAM. Featuring long-lifetime deep-red emitting iridium III complexes with high colour purity: insights into the excited state dynamics from spectroscopic and theoretical perspectives. Dalton Trans 2024; 53:5466-5477. [PMID: 38414337 DOI: 10.1039/d3dt02531d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
The significant attention drawn to IrIII-complexes in recent years has boosted the development of new compounds with advantageous photophysical features. However, obtaining IrIII deep-red-emitting complexes with long lived excited state, high colour purity and high quantum yield (Φ) remains a challenging task. To address this issue, this study reports the synthesis and photophysical investigation of three novel zwitterionic complexes, [Ir(C^N)2bqdc] (C^N = ppy, phq, and bzq), with ppy = 2-phenylpyridine (Ir-pb), phq = 2-phenylquinoline (Ir-qb), bzq = benzo[h]quinoline (Ir-bb), and bqdc = potassium 2,2'-biquinoline-4,4'-dicarboxylate. These complexes exhibit high quantum yields and long emission lifetimes with high colour purity in the deep-red region. The structural characterisation carried out by usual spectroscopic measurements supports the proposed structures, while the photophysical study unveiled the high contribution of the 3MLCT state to the hybrid emitter state, as endorsed by theoretical investigations. The desired correspondence between the calculations and the experimental data set affirmed the accuracy of the theoretical analysis, which enabled us to establish a relationship between the ground-to-excited-state geometry distortion and the lifetime through the nonradiative decay (knr). Furthermore, these newly synthesized complexes exhibit quenching in the presence of molecular oxygen. In deoxygenated DMSO solution the knr values halve, increasing the quantum yields (34.0, 10.6, and 26.6%) and the lifetimes (1.13, 1.11, and 1.72 μs), while leading to quite pure deep-red emission - CIE coordinates: (0.67, 0.33), (0.60, 0.40;), (0.65, 0.35) for Ir-pb, Ir-qb, and Ir-bb, respectively. These complexes display considerable potential for a wide range of applications, such as photodynamic therapy, due to their attractive photophysical properties, and are among the deep-red-emitting complexes reported in the literature with longer lifetimes and higher Φ.
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Affiliation(s)
- Renan C Silva
- São Paulo State University (Unesp), School of Technology and Sciences, Presidente Prudente, SP, Brazil.
- São Paulo State University (Unesp), Institute of Biosciences, Humanities and Exact Sciences, São José do Rio Preto, SP, Brazil
| | - Felipe S M Canisares
- São Paulo State University (Unesp), School of Technology and Sciences, Presidente Prudente, SP, Brazil.
- São Paulo State University (Unesp), Institute of Chemistry, Araraquara, SP, Brazil
| | - Leonardo F Saraiva
- São Paulo State University (Unesp), School of Technology and Sciences, Presidente Prudente, SP, Brazil.
- São Paulo State University (Unesp), Institute of Biosciences, Humanities and Exact Sciences, São José do Rio Preto, SP, Brazil
| | - Ana M Pires
- São Paulo State University (Unesp), School of Technology and Sciences, Presidente Prudente, SP, Brazil.
- São Paulo State University (Unesp), Institute of Biosciences, Humanities and Exact Sciences, São José do Rio Preto, SP, Brazil
- São Paulo State University (Unesp), Institute of Chemistry, Araraquara, SP, Brazil
| | - Sergio A M Lima
- São Paulo State University (Unesp), School of Technology and Sciences, Presidente Prudente, SP, Brazil.
- São Paulo State University (Unesp), Institute of Biosciences, Humanities and Exact Sciences, São José do Rio Preto, SP, Brazil
- São Paulo State University (Unesp), Institute of Chemistry, Araraquara, SP, Brazil
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36
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Rummel L, Schreiner PR. Advances and Prospects in Understanding London Dispersion Interactions in Molecular Chemistry. Angew Chem Int Ed Engl 2024; 63:e202316364. [PMID: 38051426 DOI: 10.1002/anie.202316364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 12/03/2023] [Accepted: 12/05/2023] [Indexed: 12/07/2023]
Abstract
London dispersion (LD) interactions are the main contribution of the attractive part of the van der Waals potential. Even though LD effects are the driving force for molecular aggregation and recognition, the role of these omnipresent interactions in structure and reactivity had been largely underappreciated over decades. However, in the recent years considerable efforts have been made to thoroughly study LD interactions and their potential as a chemical design element for structures and catalysis. This was made possible through a fruitful interplay of theory and experiment. This review highlights recent results and advances in utilizing LD interactions as a structural motif to understand and utilize intra- and intermolecularly LD-stabilized systems. Additionally, we focus on the quantification of LD interactions and their fundamental role in chemical reactions.
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Affiliation(s)
- Lars Rummel
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
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37
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Wu J, Kreimendahl L, Tao S, Anhalt O, Greenfield JL. Photoswitchable imines: aryliminopyrazoles quantitatively convert to long-lived Z-isomers with visible light. Chem Sci 2024; 15:3872-3878. [PMID: 38487238 PMCID: PMC10935669 DOI: 10.1039/d3sc05841g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 02/14/2024] [Indexed: 03/17/2024] Open
Abstract
Arylimines offer promise in dynamic-covalent materials due to their recyclability and ease of synthesis. However, their light-triggered E/Z isomerism has received little attention. This is attributed to challenges that include low thermal stability of their metastable state (<60 s at 20 °C), incomplete photoswitching (<50% to the metastable state), and the need for UV light (≤365 nm). We overcome these limitations with a novel class of imine photoswitch, the aryliminopyrazoles (AIPs). These AIPs can be switched using visible light (470 nm), attain photostationary states with over 95% of the Z-isomer, exhibit great resistance to fatigue, and have thermal half-lives up to 19.2 hours at room temperature. Additionally, they display T-type and negative photochromism under visible light irradiation-a useful property. The photochromic properties, quantitative assembly and accessibility of precursors set these photoswitches apart from their azo-based analogues. These findings open avenues for next-generation photoresponsive dynamic-covalent materials driven solely by these new photochromic linkages and further exploration of photocontrolled dynamic combinatorial chemistry.
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Affiliation(s)
- Jiarong Wu
- Institut für Organische Chemie, Universität Würzburg 97074 Würzburg Germany
- Center for Nanosystems Chemistry (CNC), Universität Würzburg 97074 Würzburg Germany
| | - Lasse Kreimendahl
- Institut für Organische Chemie, Universität Würzburg 97074 Würzburg Germany
| | - Suyuan Tao
- Institut für Organische Chemie, Universität Würzburg 97074 Würzburg Germany
- Center for Nanosystems Chemistry (CNC), Universität Würzburg 97074 Würzburg Germany
| | - Olga Anhalt
- Center for Nanosystems Chemistry (CNC), Universität Würzburg 97074 Würzburg Germany
| | - Jake L Greenfield
- Institut für Organische Chemie, Universität Würzburg 97074 Würzburg Germany
- Center for Nanosystems Chemistry (CNC), Universität Würzburg 97074 Würzburg Germany
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38
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Butera V. Density functional theory methods applied to homogeneous and heterogeneous catalysis: a short review and a practical user guide. Phys Chem Chem Phys 2024; 26:7950-7970. [PMID: 38385534 DOI: 10.1039/d4cp00266k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
The application of density functional theory (DFT) methods in catalysis has been growing fast in the last few decades thanks to both the availability of more powerful high computing resources and the development of new efficient approximations and approaches. DFT calculations allow for the understanding of crucial catalytic aspects that are difficult or even impossible to access by experiments, thus contributing to faster development of more efficient and selective catalysts. Depending on the catalytic system and properties under investigation, different approaches should be used. Moreover, the reliability of the obtained results deeply depends on the approximations involved in both the selected method and model. This review addresses chemists, physicists and materials scientists whose interest deals with the application of DFT-based computational tools in both homogeneous catalysis and heterogeneous catalysis. First, a brief introduction to DFT is presented. Then, the main approaches based on atomic centered basis sets and plane waves are discussed, underlining the main differences, advantages and limitations. Eventually, guidance towards the selection of the catalytic model is given, with a final focus on the evaluation of the energy barriers, which represents a crucial step in all catalytic processes. Overall, the review represents a rational and practical guide for both beginners and more experienced users involved in the wide field of catalysis.
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Affiliation(s)
- Valeria Butera
- CEITEC - Central European Institute of Technology Central European Institute of Technology, Brno University of Technology, Purkyňova 123, Brno 612 00, Czech Republic
- Department of Science and Biological Chemical and Pharmaceutical Technologies, University of Palermo, Palermo 90128, Italy.
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39
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Chen KH, Fathi F, Maxson T, Hossain M, Khisamutdinov E, Szilvási T, Zeng X, Li Z. Probe the Dynamic Adsorption and Phase Transition of Underpotential Deposition Processes at Electrode-Electrolyte Interfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:4914-4926. [PMID: 38385347 DOI: 10.1021/acs.langmuir.3c03899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Electrochemical scanning tunneling microscopy (EC-STM) and electrochemical quartz crystal microbalance (E-QCM) techniques in combination with DFT calculations have been applied to reveal the static phase and the phase transition of copper underpotential deposition (UPD) on a gold electrode surface. EC-STM demonstrated, for the first time, the direct visualization of the disintegration of (√3 × √3)R30° copper UPD adlayer with coadsorbed SO42- while changing sample potential (ES) toward the redox Pa2/Pc2 peaks, which are associated with the phase transition between the Cu UPD (√3 × √3)R30° phase II and disordered randomly adsorbed phase III. DFT calculations show that SO42- binds via three oxygens to the bridge sites of the copper with sulfate being located directly above the copper vacancy in the (√3 × √3)R30° adlayer, whereas the remaining oxygen of the sulfate points away from the surface. E-QCM measurement of the change of the electric charge due to Cu UPD Faradaic processes, the change of the interfacial mass due to the adsorption and desorption of Cu(II) and SO42-, and the formation and stripping of UPD copper on the gold surface provide complementary information that validates the EC-STM and DFT results. This work demonstrated the advantage of using complementary in situ experimental techniques (E-QCM and EC-STM) combined with simulations to obtain an accurate and complete picture of the dynamic interfacial adsorption and UPD processes at the electrode/electrolyte interface.
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Affiliation(s)
- Kuo-Hao Chen
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Fatemeh Fathi
- Department of Chemistry, Oakland University, Rochester, Michigan 48309, United States
- Department of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Tristan Maxson
- Department of Chemical and Biological Engineering, University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Mezbah Hossain
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Emil Khisamutdinov
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
| | - Tibor Szilvási
- Department of Chemical and Biological Engineering, University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Xiangqun Zeng
- Department of Chemistry, Oakland University, Rochester, Michigan 48309, United States
- Department of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Zhihai Li
- Department of Chemistry, Ball State University, Muncie, Indiana 47306, United States
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40
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Strasser N, Wieser S, Zojer E. Predicting Spin-Dependent Phonon Band Structures of HKUST-1 Using Density Functional Theory and Machine-Learned Interatomic Potentials. Int J Mol Sci 2024; 25:3023. [PMID: 38474269 DOI: 10.3390/ijms25053023] [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: 01/23/2024] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 03/14/2024] Open
Abstract
The present study focuses on the spin-dependent vibrational properties of HKUST-1, a metal-organic framework with potential applications in gas storage and separation. Employing density functional theory (DFT), we explore the consequences of spin couplings in the copper paddle wheels (as the secondary building units of HKUST-1) on the material's vibrational properties. By systematically screening the impact of the spin state on the phonon bands and densities of states in the various frequency regions, we identify asymmetric -COO- stretching vibrations as being most affected by different types of magnetic couplings. Notably, we also show that the DFT-derived insights can be quantitatively reproduced employing suitably parametrized, state-of-the-art machine-learned classical potentials with root-mean-square deviations from the DFT results between 3 cm-1 and 7 cm-1. This demonstrates the potential of machine-learned classical force fields for predicting the spin-dependent properties of complex materials, even when explicitly considering spins only for the generation of the reference data used in the force-field parametrization process.
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Affiliation(s)
- Nina Strasser
- Institute of Solid State Physics, NAWI Graz, Graz University of Technology, 8010 Graz, Austria
| | - Sandro Wieser
- Institute of Solid State Physics, NAWI Graz, Graz University of Technology, 8010 Graz, Austria
| | - Egbert Zojer
- Institute of Solid State Physics, NAWI Graz, Graz University of Technology, 8010 Graz, Austria
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41
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Vysotskiy VP, Filippi C, Ryde U. Scalar Relativistic All-Electron and Pseudopotential Ab Initio Study of a Minimal Nitrogenase [Fe(SH) 4H] - Model Employing Coupled-Cluster and Auxiliary-Field Quantum Monte Carlo Many-Body Methods. J Phys Chem A 2024; 128:1358-1374. [PMID: 38324717 PMCID: PMC10895656 DOI: 10.1021/acs.jpca.3c05808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 01/03/2024] [Accepted: 01/03/2024] [Indexed: 02/09/2024]
Abstract
Nitrogenase is the only enzyme that can cleave the triple bond in N2, making nitrogen available to organisms. The detailed mechanism of this enzyme is currently not known, and computational studies are complicated by the fact that different density functional theory (DFT) methods give very different energetic results for calculations involving nitrogenase models. Recently, we designed a [Fe(SH)4H]- model with the fifth proton binding either to Fe or S to mimic different possible protonation states of the nitrogenase active site. We showed that the energy difference between these two isomers (ΔE) is hard to estimate with quantum-mechanical methods. Based on nonrelativistic single-reference coupled-cluster (CC) calculations, we estimated that the ΔE is 101 kJ/mol. In this study, we demonstrate that scalar relativistic effects play an important role and significantly affect ΔE. Our best revised single-reference CC estimates for ΔE are 85-91 kJ/mol, including energy corrections to account for contributions beyond triples, core-valence correlation, and basis-set incompleteness error. Among coupled-cluster approaches with approximate triples, the canonical CCSD(T) exhibits the largest error for this problem. Complementary to CC, we also used phaseless auxiliary-field quantum Monte Carlo calculations (ph-AFQMC). We show that with a Hartree-Fock (HF) trial wave function, ph-AFQMC reproduces the CC results within 5 ± 1 kJ/mol. With multi-Slater-determinant (MSD) trials, the results are 82-84 ± 2 kJ/mol, indicating that multireference effects may be rather modest. Among the DFT methods tested, τ-HCTH, r2SCAN with 10-13% HF exchange with and without dispersion, and O3LYP/O3LYP-D4, and B3LYP*/B3LYP*-D4 generally perform the best. The r2SCAN12 (with 12% HF exchange) functional mimics both the best reference MSD ph-AFQMC and CC ΔE results within 2 kJ/mol.
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Affiliation(s)
- Victor P. Vysotskiy
- Department
of Computational Chemistry, Lund University,
Chemical Centre, SE-221 00 Lund, Sweden
| | - Claudia Filippi
- MESA+
Institute for Nanotechnology, University
of Twente, P.O. Box 217, Enschede 7500 AE, Netherlands
| | - Ulf Ryde
- Department
of Computational Chemistry, Lund University,
Chemical Centre, SE-221 00 Lund, Sweden
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42
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Ning J, Lane C, Barbiellini B, Markiewicz RS, Bansil A, Ruzsinszky A, Perdew JP, Sun J. Comparing first-principles density functionals plus corrections for the lattice dynamics of YBa2Cu3O6. J Chem Phys 2024; 160:064106. [PMID: 38341785 DOI: 10.1063/5.0181349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 01/15/2024] [Indexed: 02/13/2024] Open
Abstract
The enigmatic mechanism underlying unconventional high-temperature superconductivity, especially the role of lattice dynamics, has remained a subject of debate. Theoretical insights have long been hindered due to the lack of an accurate first-principles description of the lattice dynamics of cuprates. Recently, using the r2SCAN meta-generalized gradient approximation (meta-GGA) functional, we have been able to achieve accurate phonon spectra of an insulating cuprate YBa2Cu3O6 and discover significant magnetoelastic coupling in experimentally interesting Cu-O bond stretching optical modes [Ning et al., Phys. Rev. B 107, 045126 (2023)]. We extend this work by comparing Perdew-Burke-Ernzerhof and r2SCAN performances with corrections from the on-site Hubbard U and the D4 van der Waals (vdW) methods, aiming at further understanding on both the materials science side and the density functional side. We demonstrate the importance of vdW and self-interaction corrections for accurate first-principles YBa2Cu3O6 lattice dynamics. Since r2SCAN by itself partially accounts for these effects, the good performance of r2SCAN is now more fully explained. In addition, the performances of the Tao-Mo series of meta-GGAs, which are constructed in a different way from the strongly constrained and appropriately normed (SCAN) meta-GGA and its revised version r2SCAN, are also compared and discussed.
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Affiliation(s)
- Jinliang Ning
- Department of Physics and Engineering Physics, Tulane University, New Orleans, Louisiana 70118, USA
| | - Christopher Lane
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Bernardo Barbiellini
- Department of Physics, School of Engineering Science, LUT University, FI-53851 Lappeenranta, Finland
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, USA
| | - Robert S Markiewicz
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, USA
| | - Arun Bansil
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, USA
| | - Adrienn Ruzsinszky
- Department of Physics and Engineering Physics, Tulane University, New Orleans, Louisiana 70118, USA
| | - John P Perdew
- Department of Physics and Engineering Physics, Tulane University, New Orleans, Louisiana 70118, USA
| | - Jianwei Sun
- Department of Physics and Engineering Physics, Tulane University, New Orleans, Louisiana 70118, USA
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43
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Melinao F, Vidal M, Aliaga C, Domínguez M. Inverting the Solvatochromism of Pyridinium- N-phenolate Dyes by the Addition of a Second Pyridinium Unit. J Org Chem 2024; 89:1534-1542. [PMID: 38224496 DOI: 10.1021/acs.joc.3c02158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
Three bipyridinium phenolates were synthesized, and their spectral behavior was recorded at various solvent polarities and compared to a classic pyridinium phenolate dye possessing only one pyridinium acceptor ring in its structure. The addition of a second pyridinium unit to the classic solvatochromic core results in an unexpected change in the spectral behavior from negative solvatochromism (displacement of the absorption band to shorter wavelengths) to inverted solvatochromism, characterized by the transition from negative to positive solvatochromism (displacement of the absorption band to longer wavelengths) at moderate solvent polarities.
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Affiliation(s)
- Fabián Melinao
- Facultad de Química y Biología, Universidad de Santiago de Chile, Av. Bernardo O'Higgins 3363, Santiago 9170022, Chile
| | - Matías Vidal
- Facultad de Química y Biología, Universidad de Santiago de Chile, Av. Bernardo O'Higgins 3363, Santiago 9170022, Chile
| | - Carolina Aliaga
- Facultad de Química y Biología, Universidad de Santiago de Chile, Av. Bernardo O'Higgins 3363, Santiago 9170022, Chile
- Centro para el Desarrollo de la Nanociencia y la Nanotecnología (CEDENNA), Av. Bernardo O'Higgins 3363, Santiago 9170022, Chile
| | - Moisés Domínguez
- Facultad de Química y Biología, Universidad de Santiago de Chile, Av. Bernardo O'Higgins 3363, Santiago 9170022, Chile
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44
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Yanes-Rodríguez R, Prosmiti R. Analysing the stability of He-filled hydrates: how many He atoms fit in the sII crystal? Phys Chem Chem Phys 2024; 26:2519-2528. [PMID: 38170811 DOI: 10.1039/d3cp05410a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Clathrate hydrates have the ability to encapsulate atoms and molecules within their cavities, and thus they could be potentially large storage capacity materials. The present work studies the multiple cage occupancy effects in the recently discovered He@sII crystal. On the basis of previous theoretical and experimental findings, the stability of He(1/1)@sII, He(1/4)@sII and He(2/4)@sII crystals was analysed in terms of structural, mechanical and energetic properties. For this purpose, first-principles DFT/DFT-D computations were performed by using both semi-local and non-local functionals, not only to elucidate which configuration is the most energetically favoured, but also to scrutinize the relevance of the long-range dispersion interactions in these kinds of compounds. We have encountered that dispersion interactions play a fundamental role in describing the underlying interactions, and different tendencies were observed depending on the choice of the functional. We found that PW86PBE-XDM shows the best performance, while the non-local functionals tested here were not able to correctly account for them. The present results reveal that the most stable configuration is the one presenting singly occupied D cages and tetrahedrally occupied H cages (He(1/4)@sII) in line with the experimental observation.
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Affiliation(s)
| | - Rita Prosmiti
- Institute of Fundamental Physics (IFF-CSIC), CSIC, Serrano 123, 28006 Madrid, Spain.
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45
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Jaykhedkar N, Bystrický R, Sýkora M, Bučko T. Investigating the role of dispersion corrections and anharmonic effects on the phase transition in SrZrS3: A systematic analysis from AIMD free energy calculations. J Chem Phys 2024; 160:014710. [PMID: 38180257 DOI: 10.1063/5.0185319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 12/13/2023] [Indexed: 01/06/2024] Open
Abstract
A thermally driven needle-like (NL) to distorted perovskite (DP) phase transition in SrZrS3 was investigated by means of ab initio free energy calculations accelerated by machine learning. As a first step, a systematic screening of the methods to include long-range interactions in semilocal density functional theory Perdew-Burke-Ernzerhof calculations was performed. Out of the ten correction schemes tested, the Tkatchenko-Scheffler method with iterative Hirshfeld partitioning method was found to yield the best match between calculated and experimental lattice geometries, while predicting the correct order of stability of NL and DP phases at zero temperature. This method was then used in free energy calculations, performed using several approaches, so as to determine the effect of various anharmonicity contributions, such as the anisotropic thermal lattice expansion or the thermally induced internal structure changes, on the phase transition temperature (TNP→DP). Accounting for the full anharmonicity by combining the NPT molecular dynamics data with thermodynamic integration with harmonic reference provided our best estimate of TNL→DP = 867 K. Although this result is ∼150 K lower than the experimental value, it still provides an improvement by nearly 300 K compared to the previous theoretical report by Koocher et al. [Inorg. Chem. 62, 11134-11141 (2023)].
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Affiliation(s)
- Namrata Jaykhedkar
- Laboratory of Advanced Materials, Comenius University, Ilkovičova 6, 84104 Bratislava, Slovakia
| | - Roman Bystrický
- Laboratory of Advanced Materials, Comenius University, Ilkovičova 6, 84104 Bratislava, Slovakia
- Institute of Inorganic Chemistry, Slovak Academy of Sciences, Dúbravská Cesta 9, 84236 Bratislava, Slovakia
| | - Milan Sýkora
- Laboratory of Advanced Materials, Comenius University, Ilkovičova 6, 84104 Bratislava, Slovakia
| | - Tomáš Bučko
- Institute of Inorganic Chemistry, Slovak Academy of Sciences, Dúbravská Cesta 9, 84236 Bratislava, Slovakia
- Department of Physical and Theoretical Chemistry, Comenius University, Ilkovičova 6, 84104 Bratislava, Slovakia
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Malenfant J, Kuster L, Gagné Y, Signo K, Denis M, Canesi S, Frenette M. Towards routine organic structure determination using Raman microscopy. Chem Sci 2024; 15:701-709. [PMID: 38179529 PMCID: PMC10763559 DOI: 10.1039/d3sc02954a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 11/08/2023] [Indexed: 01/06/2024] Open
Abstract
Raman microscopy can reveal a compound-specific vibrational "fingerprint" from micrograms of material with no sample preparation. We expect this increasingly available instrumentation to routinely assist synthetic chemists in structure determination; however, interpreting the information-dense spectra can be challenging for unreported compounds. Appropriate theoretical calculations using the highly efficient r2SCAN-3c method can accurately predict peak positions but are less precise in matching peak heights. To limit incorrect biases while comparing experimental and theoretical spectra, we introduce a user-friendly software that gives a match score to assist with structure determination. The capabilities and limitations of this approach are demonstrated for several proof-of-concept examples including the characterization of intermediates in the total synthesis of deoxyaspidodispermine.
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Affiliation(s)
- Jason Malenfant
- Department of Chemistry, NanoQAM, Centre Québécois des Matériaux Fonctionnels (CQMF), Université du Québec à Montréal Montreal Quebec H3C 3P8 Canada
| | - Lucille Kuster
- Department of Chemistry, NanoQAM, Centre Québécois des Matériaux Fonctionnels (CQMF), Université du Québec à Montréal Montreal Quebec H3C 3P8 Canada
| | - Yohann Gagné
- Department of Chemistry, NanoQAM, Centre Québécois des Matériaux Fonctionnels (CQMF), Université du Québec à Montréal Montreal Quebec H3C 3P8 Canada
| | - Kouassi Signo
- Department of Chemistry, NanoQAM, Centre Québécois des Matériaux Fonctionnels (CQMF), Université du Québec à Montréal Montreal Quebec H3C 3P8 Canada
| | - Maxime Denis
- Department of Chemistry, NanoQAM, Centre Québécois des Matériaux Fonctionnels (CQMF), Université du Québec à Montréal Montreal Quebec H3C 3P8 Canada
| | - Sylvain Canesi
- Department of Chemistry, NanoQAM, Centre Québécois des Matériaux Fonctionnels (CQMF), Université du Québec à Montréal Montreal Quebec H3C 3P8 Canada
| | - Mathieu Frenette
- Department of Chemistry, NanoQAM, Centre Québécois des Matériaux Fonctionnels (CQMF), Université du Québec à Montréal Montreal Quebec H3C 3P8 Canada
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Robles-Navarro A, Jerabek P, Schwerdtfeger P. Tipping the Balance Between the bcc and fcc Phase Within the Alkali and Coinage Metal Groups. Angew Chem Int Ed Engl 2024; 63:e202313679. [PMID: 37877444 DOI: 10.1002/anie.202313679] [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: 09/14/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 10/26/2023]
Abstract
Why the Group 1 elements crystallize in the body-centered cubic (bcc) structure, and the iso-electronic Group 11 elements in the face-centered cubic (fcc) structure, remains a mystery. Here we show that a delicate interplay between many-body effects, vibrational contributions and dispersion interactions obtained from relativistic density functional theory offers an answer to this long-standing controversy. It also sheds light on the Periodic Table of Crystal Structures. A smooth diffusionless transition through cuboidal lattices gives a detailed insight into the bcc→fcc phase transition for the Groups 1 and 11 elements.
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Affiliation(s)
- Andrés Robles-Navarro
- Centre for Theoretical Chemistry and Physics, The New Zealand Institute for Advanced Study (NZIAS), Massey University Albany, Private Bag 102904, Auckland, 0745, New Zealand
| | - Paul Jerabek
- Institute of Hydrogen Technology, Helmholtz-Zentrum Hereon, Max-Planck-Str. 1, 21502, Geesthacht, Germany
| | - Peter Schwerdtfeger
- Centre for Theoretical Chemistry and Physics, The New Zealand Institute for Advanced Study (NZIAS), Massey University Albany, Private Bag 102904, Auckland, 0745, New Zealand
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48
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Bursch M, Grimme S, Hansen A. Influence of Steric and Dispersion Interactions on the Thermochemistry of Crowded (Fluoro)alkyl Compounds. Acc Chem Res 2024; 57:153-163. [PMID: 38102118 DOI: 10.1021/acs.accounts.3c00634] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
ConspectusAlkanes play a pivotal role in industrial, environmental, and biological processes. They are characterized by their carbon-carbon single-bond structure, remarkable stability, and conformational diversity. Fluorination of such compounds imparts unique physicochemical properties that often enhance pharmacokinetic profiles, metabolic stability, and receptor interactions while keeping beneficial properties. However, such per- and polyfluoroalkyl substances (PFAS) show a persistent presence in the environment and potential adverse health effects, which propelled them to the forefront of global environmental and health discussions. Alkyl compounds are also prototypical for stereoelectronic (SE) effects that are widely applied in chemistry. Substituents are typically described as electron-density-donating/withdrawing and/or responsible for sterically interacting with reagents or strategic groups in the molecule. That alkane branching can result in higher stability compared to less-branched isomers has been investigated in detail also by testing quantum chemical methods, in particular density functional theory (DFT). Alkane branching results in spatially compact structures with close intramolecular contacts so that at a specific size the detailed balance of attractive London dispersion and covalent versus repulsive Pauli exchange interactions shifts to new, chemically unfragile situations. This may lead to dissociation at room temperature and opens the central question: what is the smallest crowed alkane that cannot be made synthetically? In this Account, we try to shed light on the interplay among the various (free) energy components for crowded (fluoro)alkane dissociation. In this context, homolytic cleavage of the central C-C bond in a series of model alkanes of increasing size with tert-butyl (tBu), adamantyl (Ad), and [1.1.1]propellanyl (Prop) substituents is investigated. Reference energies are calculated at the PNO-LCCSD(T)-F12b level and used to benchmark the performance of contemporary DFT functionals. In line with previous conclusions, the application of dispersion corrections to density functionals is mandatory. For crowed structures, the accurate description of the midrange correlation effects, specifically repulsive van der Waals interactions, is crucial, and we observed that the density-dependent VV10 correction is superior to D4 in this context, although the asymptotic region is better described by the latter. The best available dispersion-inclusive functionals show systematic and reasonably small residual errors and can be safely applied to large systems (>100 atoms), for which coupled cluster methods with large basis sets are not computationally feasible anymore. For qualitatively correct predictions of synthetic accessibility under equilibrium conditions (free energy), the inclusion of thermostatistical (entropy) contributions is also essential. According to our results, tetra-tert-butylmethane (C17tBu) is the largest and most crowded system with a positive dissociation free energy and should be synthesizable. The difference between hydrogenated and perfluorinated systems originates from the increase in the steric repulsion of spatially close substituents, which is not compensated to the same extent by attractive orbital and dispersion interactions. A sometimes-assumed similar steric demand for fluorine and hydrogen atoms is not corroborated by our investigations on crowded systems. Perfluorination is found to substantially decrease thermal stability, rendering perfluorinated hexamethylethane (C8tBuF) the last potentially stable representative.
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Affiliation(s)
- Markus Bursch
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Beringstraße 4, D-53115 Bonn, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Beringstraße 4, D-53115 Bonn, Germany
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49
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Haasler M, Maier TM, Kaupp M. Toward a correct treatment of core properties with local hybrid functionals. J Comput Chem 2023; 44:2461-2477. [PMID: 37635647 DOI: 10.1002/jcc.27211] [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: 07/04/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 08/29/2023]
Abstract
In local hybrid functionals (LHs), a local mixing function (LMF) determines the position-dependent exact-exchange admixture. We report new LHs that focus on an improvement of the LMF in the core region while retaining or partly improving upon the high accuracy in the valence region exhibited by the LH20t functional. The suggested new pt-LMFs are based on a Padé form and modify the previously used ratio between von Weizsäcker and Kohn-Sham local kinetic energies by different powers of the density to enable flexibly improved approximations to the correct high-density and iso-orbital limits relevant for the innermost core region. Using TDDFT calculations for a set of K-shell core excitations of second- and third-period systems including accurate state-of-the-art relativistic orbital corrections, the core part of the LMF is optimized, while the valence part is optimized as previously reported for test sets of atomization energies and reaction barriers (Haasler et al., J Chem Theory Comput 2020, 16, 5645). The LHs are completed by a calibration function that minimizes spurious nondynamical correlation effects caused by the gauge ambiguities of exchange-energy densities, as well as by B95c meta-GGA correlation. The resulting LH23pt functional relates to the previous LH20t functional but specifically improves upon the core region.
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Affiliation(s)
- Matthias Haasler
- Technische Universität Berlin, Institute of Chemistry Theoretical Chemistry/Quantum Chemistry, Berlin, Germany
| | - Toni M Maier
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry, Braunschweig, Germany
| | - Martin Kaupp
- Technische Universität Berlin, Institute of Chemistry Theoretical Chemistry/Quantum Chemistry, Berlin, Germany
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50
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Friede M, Ehlert S, Grimme S, Mewes JM. Do Optimally Tuned Range-Separated Hybrid Functionals Require a Reparametrization of the Dispersion Correction? It Depends. J Chem Theory Comput 2023; 19:8097-8107. [PMID: 37955590 DOI: 10.1021/acs.jctc.3c00717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
For ground- and excited-state studies of large molecules, it is the state of the art to combine (time-dependent) DFT with dispersion-corrected range-separated hybrid functionals (RSHs), which ensures an asymptotically correct description of exchange effects and London dispersion. Specifically for studying excited states, it is common practice to tune the range-separation parameter ω (optimal tuning), which can further improve the accuracy. However, since optimal tuning essentially changes the functional, it is unclear if and how much the parameters used for the dispersion correction depend on the chosen ω value. To answer this question, we explore this interdependency by refitting the DFT-D4 dispersion model for six established RSHs over a wide range of ω values (0.05-0.45 a0-1) using a set of noncovalently bound molecular complexes. The results reveal some surprising differences among the investigated functionals: While PBE-based RSHs and ωB97M-D4 generally exhibit a weak interdependency and robust performance over a wide range of ω values, B88-based RSHs, specifically LC-BLYP, are strongly affected. For these, even a minor reduction of ω from the default value manifests in strong systematic overbinding and poor performance in the typical range of optimally tuned ω values. Finally, we discuss strategies to mitigate these issues and reflect the results in the context of the employed D4 parameter optimization algorithm and fit set, outlining strategies for future improvements.
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Affiliation(s)
- Marvin Friede
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Sebastian Ehlert
- AI4Science, Microsoft Research, Evert van de Beekstraat 354, 1118 CZ Schiphol, The Netherlands
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Jan-Michael Mewes
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
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