1
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Sinha S, Das S, Ray KK, Maity S, Roymahapatra G, Giri S. In silico investigation on the separation of disulfide bonds by N-heterocyclic carbene. Phys Chem Chem Phys 2024; 26:23073-23079. [PMID: 39176465 DOI: 10.1039/d4cp02672a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2024]
Abstract
Herein, the separation of a disulfide bond using different nucleophilic agents like tri-methyl phosphine (TMP), tris (2-carboxyethyl) phosphine (TCEP), and N-heterocyclic carbene (NHC) has been investigated. Both TMP and TCEP have demonstrated their ability to break disulfide bonds through the SN2 mechanism. However, it is worth noting that these reactions are endothermic. While searching for a suitable nucleophile, it was observed that the NHC-mediated reaction was exothermic. The natural bond orbital (NBO), principal interacting orbital (PIO) and extended transition state-natural orbitals for chemical valence (ETS-NOCV) studies help understand the electron transfer process between interacting orbitals during the chemical reactions.
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Affiliation(s)
- Swapan Sinha
- School of Applied Science and Humanities, Haldia Institute of Technology, Haldia, 721657, India.
- Maulana Abul Kalam Azad University of Technology, Haringhata, 741249, India
| | - Subhra Das
- School of Applied Science and Humanities, Haldia Institute of Technology, Haldia, 721657, India.
- Department of Chemistry, Cooch Behar Panchanan Barma University, Cooch Behar, West Bengal, 736101, India
| | - Kritish Kumar Ray
- Department of Chemistry, National Institute of Technology Rourkela, Odisha, 769008, India
| | - Sibaprasad Maity
- Sagardighi Kamada Kinkar Smriti Mahavidyalaya, Murshidabad, West Bengal, 742226, India
| | - Gourisankar Roymahapatra
- School of Applied Science and Humanities, Haldia Institute of Technology, Haldia, 721657, India.
| | - Santanab Giri
- School of Applied Science and Humanities, Haldia Institute of Technology, Haldia, 721657, India.
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2
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López R, Suárez D. Pyrolytic conversion of glucose into hydroxymethylfurfural and furfural: Benchmark quantum-chemical calculations. J Comput Chem 2024. [PMID: 39252435 DOI: 10.1002/jcc.27503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 08/26/2024] [Accepted: 08/27/2024] [Indexed: 09/11/2024]
Abstract
Quantum chemical methods have been intensively applied to study the pyrolytic conversion of glucose into hydroxymethylfurfural (HMF) and furfural (FF). Herein, we collect the most relevant mechanistic proposals from the recent literature and organize them into a single reaction network. All the transition structures (TSs) and intermediates are characterized using highly accurate ab initio methods and the possible reaction pathways are assessed in terms of the Gibbs energies of the TSs and intermediates with respect to β-glucopyranose, selecting a 2D ideal-gas standard state at 773 K to represent the pyrolysis conditions. Several pathways can lead to the formation of both HMF and FF passing through rate-determining TSs that have ΔG‡ values of ~49-50 kcal/mol. Both water-assisted mechanisms and nonspecific environmental effects have a minor impact on the Gibbs energy profiles. We find that the HMF → FF + CH2O fragmentation has a small ΔrxnG value and an accessible ΔG‡ barrier. Our computational results, which are in consonance with the kinetic parameters derived from lumped models, the results of isotopic labeling experiments and the reported HMF/FF molecular ratios, could be useful for modeling studies including on nonequilibrium kinetic effects that may render more information about product yields and the relevance of the various pathways.
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Affiliation(s)
- Roberto López
- Departamento de Química y Física Aplicadas, Universidad de León, León, Spain
| | - Dimas Suárez
- Departamento de Química Física y Analítica, Universidad de Oviedo, Oviedo, Spain
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3
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Branson JA, Smith PW, Sergentu DC, Russo DR, Gupta H, Booth CH, Arnold J, Schelter EJ, Autschbach J, Minasian SG. The Counterintuitive Relationship between Orbital Energy, Orbital Overlap, and Bond Covalency in CeF 62- and CeCl 62. J Am Chem Soc 2024. [PMID: 39241121 DOI: 10.1021/jacs.4c07459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2024]
Abstract
The 4f orbitals of Ce(IV) have shown appreciably enhanced covalent mixing with ligand orbitals relative to those of Ce(III). Here, X-ray spectroscopy, magnetic susceptibility measurements, and theoretical methods are used to investigate 4f covalency in CeF62- and CeCl62-. These techniques show covalent mixing between Ce 4f and F 2p orbitals to be about 25% less than mixing between Ce 4f and Cl 3p orbitals, placing CeF62- among the most ionic Ce(IV) compounds to-date. However, ligand field analysis using the experimental data shows significantly higher 4f orbital overlap with the F 2p orbitals compared to the Cl 3p. This result is counterintuitive since the Ce-F bonds display less 4f covalency despite their higher orbital overlap, and greater overlap is traditionally associated with enhanced bond covalency. The weaker covalency is attributed to the large energy gap between Ce 4f and F 2p orbitals strongly counteracting the higher orbital overlap. These results highlight that only a concerted consideration of both atomic orbital overlap and energy matching in f-element systems leads to an accurate picture of their bonding.
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Affiliation(s)
- Jacob A Branson
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Patrick W Smith
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Dumitru-Claudiu Sergentu
- RA-03 (RECENT AIR) Laboratory, Alexandru Ioan Cuza University of Iaşi, Iaşi 700506, Romania
- Faculty of Chemistry, Alexandru Ioan Cuza University of Iaşi, Iaşi 700506, Romania
| | - Dominic R Russo
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Himanshu Gupta
- P. Roy and Diana T. Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Corwin H Booth
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - John Arnold
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Eric J Schelter
- P. Roy and Diana T. Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Jochen Autschbach
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260, United States
| | - Stefan G Minasian
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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4
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Bucher G. Accessing the Cloke-Wilson Rearrangement via Conjugate Addition of Phosphoranes to Michael Acceptors: A Route to Cyclopropanes and 5-Membered Ring Heterocycles Investigated by Density Functional and Ab Initio Theory. J Org Chem 2024; 89:12020-12031. [PMID: 39136640 PMCID: PMC11382343 DOI: 10.1021/acs.joc.4c00757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2024]
Abstract
Conjugate addition of unstabilized Wittig-type phosphonium ylides to 1,1-diacceptor- and 1-acceptor-substituted alkenes is investigated by density functional theory and high-level ab initio (DLPNO-CCSD(T)) calculations. The results indicate that the initial conjugate addition step should be facile with barriers predicted to be between 0 and 21 kcal mol-1. Potential intramolecular follow-up reactions include the formation of acceptor-substituted cyclopropanes as well as the formation of dihydrofuran derivatives via intramolecular SN2-type transition state structures. The barriers calculated for these potentially valuable cyclization reactions are substantial with Gibbs free energies of activation between 19 and 40 kcal mol-1. Competing reaction channels include Wittig olefination (for ketones and aldehydes), as well as Claisen condensation reactions. The reaction offers an alternative entry point to the nucleophile-catalyzed Cloke-Wilson rearrangement.
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Affiliation(s)
- Götz Bucher
- School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, Glasgow G12 8QQ, U.K
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5
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Poirier N, Kottmann JS, Aspuru-Guzik A, Mongeau L, Najafi-Yazdi A. Range-separated density functional theory using multiresolution analysis and quantum computing. J Comput Chem 2024; 45:1987-2000. [PMID: 38709143 DOI: 10.1002/jcc.27384] [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: 01/19/2024] [Revised: 04/03/2024] [Accepted: 04/18/2024] [Indexed: 05/07/2024]
Abstract
Quantum computers are expected to outperform classical computers for specific problems in quantum chemistry. Such calculations remain expensive, but costs can be lowered through the partition of the molecular system. In the present study, partition was achieved with range-separated density functional theory (RS-DFT). The use of RS-DFT reduces both the basis set size and the active space size dependence of the ground state energy in comparison with the use of wave function theory (WFT) alone. The utilization of pair natural orbitals (PNOs) in place of canonical molecular orbitals (MOs) results in more compact qubit Hamiltonians. To test this strategy, a basis-set independent framework, known as multiresolution analysis (MRA), was employed to generate PNOs. Tests were conducted with the variational quantum eigensolver for a number of molecules. The results show that the proposed approach reduces the number of qubits needed to reach a target energy accuracy.
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Affiliation(s)
- Nicolas Poirier
- Department of Mechanical Engineering, McGill University, Montreal, Quebec, Canada
- Anyon Systems Inc., Dorval, Quebec, Canada
| | - Jakob S Kottmann
- Institute for Computer Science, University of Augsburg, Augsburg, Germany
| | - Alán Aspuru-Guzik
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
- Vector Institute for Artificial Intelligence, Toronto, Ontario, Canada
- Canadian Institute for Advanced Research (CIFAR), Toronto, Ontario, Canada
| | - Luc Mongeau
- Department of Mechanical Engineering, McGill University, Montreal, Quebec, Canada
| | - Alireza Najafi-Yazdi
- Department of Mechanical Engineering, McGill University, Montreal, Quebec, Canada
- Anyon Systems Inc., Dorval, Quebec, Canada
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6
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Loru D, Sun W, Nootebos H, Steber AL, Ferrari P, Schnell M. Probing the structure and dynamics of the heterocyclic PAH xanthene and its water complexes with infrared and microwave spectroscopy. Phys Chem Chem Phys 2024. [PMID: 39230416 DOI: 10.1039/d4cp03030c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
To assess the presence of oxygen-containing polycyclic aromatic hydrocarbons (OPAHs) in the interstellar medium and understand how water aggregates on an OPAH surface, we present a comprehensive gas-phase spectroscopy investigation of the OPAH xanthene (C13H10O) and its complexes with water using IR-UV ion dip spectroscopy and chirped-pulse Fourier transform microwave spectroscopy. The infrared spectrum of xanthene shows weak features at 3.42, 3.43, and 3.47 μm, which have been suggested to partly originate from vibrational modes of PAHs containing sp3 hybridized carbon atoms, in agreement with the molecular structure of xanthene. The high resolution of rotational spectroscopy reveals a tunneling splitting of the rotational transitions, which can be explained with an out-of-plane bending motion of the two lateral benzene rings of xanthene. The nature of the tunnelling motion is elucidated by observing a similar splitting pattern in the rotational transitions of the singly-substituted 13C isotopologues. The rotational spectroscopy investigation is extended to hydrates of xanthene with up to four water molecules. Different xanthene-water binding motifs are observed based on the degree of hydration, with O-H⋯π interactions becoming preferred over O-H⋯Oxanthene interactions as the degree of hydration increases. A structural comparison with water complexes of related molecular systems highlights the impact of the substrate's shape and chemical composition on the arrangement of the surrounding water molecules.
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Affiliation(s)
- Donatella Loru
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany.
| | - Wenhao Sun
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany.
| | - Hugo Nootebos
- Radboud University, Institute of Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Amanda L Steber
- Department of Physical and Inorganic Chemistry, Faculty of Science, University of Valladolid, 47011 Valladolid, Spain
| | - Piero Ferrari
- Radboud University, Institute of Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Melanie Schnell
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany.
- Institute of Physical Chemistry, Christian-Albrechts-Universität zu Kiel, Max-Eyth-Str. 1, 24118 Kiel, Germany
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7
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Pokhilko P, Yeh CN, Morales MA, Zgid D. Tensor hypercontraction for fully self-consistent imaginary-time GF2 and GWSOX methods: Theory, implementation, and role of the Green's function second-order exchange for intermolecular interactions. J Chem Phys 2024; 161:084108. [PMID: 39185845 DOI: 10.1063/5.0215954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 08/05/2024] [Indexed: 08/27/2024] Open
Abstract
We present an efficient MPI-parallel algorithm and its implementation for evaluating the self-consistent correlated second-order exchange term (SOX), which is employed as a correction to the fully self-consistent GW scheme called scGWSOX (GW plus the SOX term iterated to achieve full Green's function self-consistency). Due to the application of the tensor hypercontraction (THC) in our computational procedure, the scaling of the evaluation of scGWSOX is reduced from O(nτnAO5) to O(nτN2nAO2). This fully MPI-parallel and THC-adapted approach enabled us to conduct the largest fully self-consistent scGWSOX calculations with over 1100 atomic orbitals with only negligible errors attributed to THC fitting. Utilizing our THC implementation for scGW, scGF2, and scGWSOX, we evaluated energies of intermolecular interactions. This approach allowed us to circumvent issues related to reference dependence and ambiguity in energy evaluation, which are common challenges in non-self-consistent calculations. We demonstrate that scGW exhibits a slight overbinding tendency for large systems, contrary to the underbinding observed with non-self-consistent RPA. Conversely, scGWSOX exhibits a slight underbinding tendency for such systems. This behavior is both physical and systematic and is caused by exclusion-principle violating diagrams or corresponding corrections. Our analysis elucidates the role played by these different diagrams, which is crucial for the construction of rigorous, accurate, and systematic methods. Finally, we explicitly show that all perturbative fully self-consistent Green's function methods are size-extensive and size-consistent.
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Affiliation(s)
- Pavel Pokhilko
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Chia-Nan Yeh
- Center for Computational Quantum Physics, Flatiron Institute, New York, New York 10010, USA
| | - Miguel A Morales
- Center for Computational Quantum Physics, Flatiron Institute, New York, New York 10010, USA
| | - Dominika Zgid
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Physics, University of Michigan, Ann Arbor, Michigan 48109, USA
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8
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Jiang A, Glick ZL, Poole D, Turney JM, Sherrill CD, Schaefer HF. Accurate and efficient open-source implementation of domain-based local pair natural orbital (DLPNO) coupled-cluster theory using a t1-transformed Hamiltonian. J Chem Phys 2024; 161:082502. [PMID: 39171707 DOI: 10.1063/5.0219963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 08/05/2024] [Indexed: 08/23/2024] Open
Abstract
We present an efficient, open-source formulation for coupled-cluster theory through perturbative triples with domain-based local pair natural orbitals [DLPNO-CCSD(T)]. Similar to the implementation of the DLPNO-CCSD(T) method found in the ORCA package, the most expensive integral generation and contraction steps associated with the CCSD(T) method are linear-scaling. In this work, we show that the t1-transformed Hamiltonian allows for a less complex algorithm when evaluating the local CCSD(T) energy without compromising efficiency or accuracy. Our algorithm yields sub-kJ mol-1 deviations for relative energies when compared with canonical CCSD(T), with typical errors being on the order of 0.1 kcal mol-1, using our TightPNO parameters. We extensively tested and optimized our algorithm and parameters for non-covalent interactions, which have been the most difficult interaction to model for orbital (PNO)-based methods historically. To highlight the capabilities of our code, we tested it on large water clusters, as well as insulin (787 atoms).
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Affiliation(s)
- Andy Jiang
- Center for Computational Quantum Chemistry, Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - Zachary L Glick
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
| | - David Poole
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
| | - Justin M Turney
- Center for Computational Quantum Chemistry, Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - C David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
| | - Henry F Schaefer
- Center for Computational Quantum Chemistry, Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
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9
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Nagy PR. State-of-the-art local correlation methods enable affordable gold standard quantum chemistry for up to hundreds of atoms. Chem Sci 2024:d4sc04755a. [PMID: 39246365 PMCID: PMC11376132 DOI: 10.1039/d4sc04755a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 07/30/2024] [Indexed: 09/10/2024] Open
Abstract
In this feature, we review the current capabilities of local electron correlation methods up to the coupled cluster model with single, double, and perturbative triple excitations [CCSD(T)], which is a gold standard in quantum chemistry. The main computational aspects of the local method types are assessed from the perspective of applications, but the focus is kept on how to achieve chemical accuracy (i.e., <1 kcal mol-1 uncertainty), as well as on the broad scope of chemical problems made accessible. The performance of state-of-the-art methods is also compared, including the most employed DLPNO and, in particular, our local natural orbital (LNO) CCSD(T) approach. The high accuracy and efficiency of the LNO method makes chemically accurate CCSD(T) computations accessible for molecules of hundreds of atoms with resources affordable to a broad computational community (days on a single CPU and 10-100 GB of memory). Recent developments in LNO-CCSD(T) enable systematic convergence and robust error estimates even for systems of complicated electronic structure or larger size (up to 1000 atoms). The predictive power of current local CCSD(T) methods, usually at about 1-2 order of magnitude higher cost than hybrid density functional theory (DFT), has become outstanding on the palette of computational chemistry applicable for molecules of practical interest. We also review more than 50 LNO-based and other advanced local-CCSD(T) applications for realistic, large systems across molecular interactions as well as main group, transition metal, bio-, and surface chemistry. The examples show that properly executed local-CCSD(T) can contribute to binding, reaction equilibrium, rate constants, etc. which are able to match measurements within the error estimates. These applications demonstrate that modern, open-access, and broadly affordable local methods, such as LNO-CCSD(T), already enable predictive computations and atomistic insight for complicated, real-life molecular processes in realistic environments.
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Affiliation(s)
- Péter R Nagy
- Department of Physical Chemistry and Materials Science, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics Műegyetem rkp. 3. H-1111 Budapest Hungary
- HUN-REN-BME Quantum Chemistry Research Group Műegyetem rkp. 3. H-1111 Budapest Hungary
- MTA-BME Lendület Quantum Chemistry Research Group Műegyetem rkp. 3. H-1111 Budapest Hungary
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10
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Korona K, Justyniak I, Pogrebetsky J, Lemieszka M, Bernatowicz P, Pietrzykowski A, Kubas A, Lewiński J. Controlled hydrolysis of AlMe 3 to tetramethylalumoxane and a new look at incipient adducts with water. Chem Commun (Camb) 2024; 60:9392-9395. [PMID: 39133042 DOI: 10.1039/d4cc03672g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
We present an efficient route to tetramethylalumoxane by the controlled hydrolysis of AlMe3 in the presence of pyridine. The AlMe3(pyr) hydrolysis by 0.5 and 1 equiv. of H2O has been followed with real-time 1H NMR. Based on high-level quantum-chemical calculations, we conclude that hypervalent, pentacoordinate aluminium species are critical in the first steps of hydrolysis.
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Affiliation(s)
- Krzesimir Korona
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland.
| | - Iwona Justyniak
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - James Pogrebetsky
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Marta Lemieszka
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland.
| | - Piotr Bernatowicz
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Antoni Pietrzykowski
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland.
| | - Adam Kubas
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Janusz Lewiński
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland.
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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11
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Kasprzyk W, Romańczyk PP, Kurek SS, Świergosz T. A switchable green emitting dye and its phenomenal properties: implications for the photoluminescence features of carbon dots. NANOSCALE 2024. [PMID: 39189364 DOI: 10.1039/d4nr02517b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/28/2024]
Abstract
New molecular fluorophores are constantly being discovered in post-synthetic mixtures of carbon dots (CDs), prompting researchers to elucidate their role in the optical properties of these nanomaterials. It has been reported that the green-emitting fluorophore that forms during the synthesis of popular citric acid/urea CDs is HPPT (4-hydroxy-1H-pyrrolo[3,4-c]pyridine-1,3,6(2H,5H)-trione). However, due to the low concentration of HPPT-like molecules within the structure of CDs, their actual binding and contribution to the optical properties of CDs has not so far been convincingly confirmed. In this joint experimental and quantum chemical study, we show that HPPT is a strong acid and only its anionic form, HPPT-, present in solutions of pH 0-10, is emissive. Next, its fluorescence can be switched off rapidly in strongly alkaline environments as a result of HPPT- hydrolysis, leading to the opening of its pyrrole ring and formation of CDPC (3-carbamoyl-2,6-dihydroxypyridine-4-carboxylic acid), existing as the CDPC2- dianion under these conditions. Eventually, we found that the ring opening hydrolysis is reversible and the green emission may be restored in acidic environments. The kinetics and mechanism of this hydrolysis were also revealed. The optical features of citric acid (CA)-urea CDs under various conditions were compared with a simpler CD system prepared by treating the CDs obtained from CA solely with HPPT- (HPPT@CDs). Our results indicate the feasibility of the post-synthetic modification of HPPT- present in the structures of CA-urea CDs and HPPT@CDs. Without HPPT- they emit blue fluorescence only. Thus, this makes the nanosystem switch the PL emission colour reversibly from green to blue owing to the opening and closing of the pyrrole ring in HPPT-like molecules. More importantly, the latter process may be considered a first step toward genuine fine tuning of the PL emission colour from CDs. These findings are of general importance to the further development of citric acid-based CDs with tailored properties.
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Affiliation(s)
- Wiktor Kasprzyk
- Biotechnology and Physical Chemistry, Faculty of Chemical Engineering and Technology, Cracow University of Technology, ul. Warszawska 24, 31-155 Kraków, Poland.
| | - Piotr P Romańczyk
- Biotechnology and Physical Chemistry, Faculty of Chemical Engineering and Technology, Cracow University of Technology, ul. Warszawska 24, 31-155 Kraków, Poland.
| | - Stefan S Kurek
- Biotechnology and Physical Chemistry, Faculty of Chemical Engineering and Technology, Cracow University of Technology, ul. Warszawska 24, 31-155 Kraków, Poland.
| | - Tomasz Świergosz
- Biotechnology and Physical Chemistry, Faculty of Chemical Engineering and Technology, Cracow University of Technology, ul. Warszawska 24, 31-155 Kraków, Poland.
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12
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Soriano-Agueda L, Guevara-García A. A refreshing approach to understanding the action on DNA of vanadium (IV) and (V) complexes derived from the anticancer VCp 2Cl 2. J Inorg Biochem 2024; 261:112705. [PMID: 39217821 DOI: 10.1016/j.jinorgbio.2024.112705] [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: 06/03/2024] [Revised: 08/21/2024] [Accepted: 08/21/2024] [Indexed: 09/04/2024]
Abstract
A computational study based on derivatives of the anticancer VCp2Cl2 compound and their interaction with representative models of deoxyribonucleic acid (DNA) is presented. The derivatives were obtained by substituting the cyclopentadienes of VCp2Cl2 with H2O, NH3, OH-, Cl-, O2- and C2O42- ligands. The oxidation states IV and V of vanadium were considered, so a total of 20 derivative complexes are included. The complexes interactions with DNA were studied using two different models, the first model considers the interactions of the complexes with the pair Guanine-Cytosine (G-C) and the second involves the interaction of the complexes with adjacent pairs, that is, d(GG). This study compares methodologies based on density functional theory with coupled cluster like calculations (DLPNO-CCSD(T)), the gold standard of electronic structure methods. Furthermore, the change in the electron density of the hydrogen bonds that keep bonded the G-C pair and d(GG) pairs, due to the presence of vanadium (IV) and (V) complexes is rationalize. To this aim, quantities obtained from the topology of the electron densities are inspected, particularly the value of the electron density at the hydrogen bond critical points. The approach allowed to identify vanadium complexes that lead to significant changes in the hydrogen bonds indicated above, a key aspect in the understanding, development, and proposal of mechanisms of action between metal complexes and DNA.
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Affiliation(s)
- Luis Soriano-Agueda
- Donostia International Physics Center (DIPC), 20018 Donostia, Euskadi, Spain.
| | - Alfredo Guevara-García
- Departamento de Química, CONAHCYT-Universidad Autónoma Metropolitana-Iztapalapa, Av. San Rafael Atlixco 186, Leyes de Reforma 1ra Secc, Iztapalapa, 09340 Ciudad de México, México
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13
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Zhang WW, Feng Z, You SL, Zheng C. Electrophile-Arene Affinity: An Energy Scale for Evaluating the Thermodynamics of Electrophilic Dearomatization Reactions. J Org Chem 2024; 89:11487-11501. [PMID: 39077910 DOI: 10.1021/acs.joc.4c01168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
Rational design and development of organic reactions are lofty goals in synthetic chemistry. Quantitative description of the properties of molecules and reactions by physical organic parameters plays an important role in this regard. In this Article, we report an energy scale, namely, electrophile-arene affinity (EAA), for evaluating the thermodynamics of electrophilic dearomatization reactions, a class of important transformations that can rapidly build up molecular complexity and structural diversity by converting planar aromatic compounds into three-dimensional cyclic molecules. The acquisition of EAA data can be readily achieved by theoretically calculating the enthalpy changes (ΔH) of the hypothetical reactions of various (cationic) electrophiles with aromatic systems (taking the 1-methylnaphthalen-2-olate ion as an example in this study). Linear correlations are found between the calculated ΔH values and established physical organic parameters such as the percentage of buried volume %VBur (steric effect), Hammett's σ or Brown's σ+ (electronic effect), and Mayr's E (reaction kinetics). Careful analysis of the ΔH values leads to the rational design of a dearomative alkynylation reaction using alkynyl hypervalent iodonium reagents as the electrophiles.
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Affiliation(s)
- Wen-Wen Zhang
- Chang-Kung Chuang Institute, East China Normal University, 3663 N. Zhongshan Road, Shanghai 200062, China
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Lu, Shanghai 200032, China
| | - Zuolijun Feng
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Lu, Shanghai 200032, China
| | - Shu-Li You
- Chang-Kung Chuang Institute, East China Normal University, 3663 N. Zhongshan Road, Shanghai 200062, China
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Lu, Shanghai 200032, China
| | - Chao Zheng
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Lu, Shanghai 200032, China
- Shanghai-Hong Kong Joint Laboratory of Chemical Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Lu, Shanghai 200032, China
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14
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Křížková A, Bastien G, Rončević I, Císařová I, Rybáček J, Kašička V, Kaleta J. Chlorinated Cubane-1,4-dicarboxylic Acids. J Org Chem 2024; 89:11100-11108. [PMID: 36724049 PMCID: PMC11334191 DOI: 10.1021/acs.joc.2c02872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Indexed: 02/02/2023]
Abstract
Herein, we report radical chlorination of cubane-1,4-dicarboxylic acid leading preferentially to one monochlorinated cubane dicarboxylate (ca. 70%) that is accompanied by four dichlorinated derivatives (ca. 20% in total). The exact positions of the chlorine atoms have been confirmed by X-ray diffraction of the corresponding single crystals. The acidity constants of all dicarboxylic acids in water were determined by capillary electrophoresis (3.17 ± 0.04 and 4.09 ± 0.05 for monochlorinated and ca. 2.71 ± 0.05 and 3.75 ± 0.05 for dichlorinated cubanes). All chlorinated derivatives as well as the parent diacid showed high thermal stability (decomposition above 250 °C) as documented by differential scanning calorimetry. The probable reaction pathways leading to individual isomers were proposed, and the energies of individual transition states and intermediates were obtained using density functional theory calculations (B3LYP-D3BJ/6-311+G(d,p)). The relative strain energies for all newly prepared derivatives as well as for hypothetical hexahalogenated (fluorinated, chlorinated, brominated, and iodinated) derivatives of cubane-1,4-dicarboxylic acids were predicted using wavefunction theory methods. The hexafluorinated derivative was identified as the most strained compound (57.5 kcal/mol), and the relative strain decreased as the size of halogen atoms increased (23.7 for hexachloro, 16.7 for hexabromo, and 4.0 kcal/mol for the hexaiodo derivative).
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Affiliation(s)
- Adéla Křížková
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague 6, Czech Republic
| | - Guillaume Bastien
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague 6, Czech Republic
| | - Igor Rončević
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague 6, Czech Republic
| | - Ivana Císařová
- Department
of Inorganic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030, 128
40 Prague 2, Czech Republic
| | - Jiří Rybáček
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague 6, Czech Republic
| | - Václav Kašička
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague 6, Czech Republic
| | - Jiří Kaleta
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague 6, Czech Republic
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15
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Armbruster C, Sellin M, Seiler M, Würz T, Oesten F, Schmucker M, Sterbak T, Fischer J, Radtke V, Hunger J, Krossing I. Pushing redox potentials to highly positive values using inert fluorobenzenes and weakly coordinating anions. Nat Commun 2024; 15:6721. [PMID: 39112470 PMCID: PMC11306567 DOI: 10.1038/s41467-024-50669-3] [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: 02/10/2024] [Accepted: 07/16/2024] [Indexed: 08/10/2024] Open
Abstract
While the development of weakly coordinating anions (WCAs) received much attention, the progress on weakly coordinating and inert solvents almost stagnated. Here we study the effect of strategic F-substitution on the solvent properties of fluorobenzenes C6FxH6-x (xFB, x = 1-5). Asymmetric fluorination leads to dielectric constants as high as 22.1 for 3FB that exceeds acetone (20.7). Combined with the WCAs [Al(ORF)4]- or [(FRO)3Al-F-Al(ORF)3]- (RF = C(CF3)3), the xFB solvents push the potentials of Ag+ and NO+ ions to +1.50/+1.52 V vs. Fc+/Fc. The xFB/WCA-system has electrochemical xFB stability windows that exceed 5 V for all xFBs with positive upper limits between +1.82 V (1FB) and +2.67 V (5FB) vs. Fc+/Fc. High-level ab initio calculations with inclusion of solvation energies show that these high potentials result from weak interactions of the ions with solvent and counterion. To access the available positive xFB potential range with stable reagents, the innocent deelectronator salts [anthraceneF]+∙[WCA]- and [phenanthreneF]+∙[WCA]- with potentials of +1.47 and +1.89 V vs. Fc+/Fc are introduced.
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Affiliation(s)
- Christian Armbruster
- Institut für Anorganische und Analytische Chemie and Freiburger Materialforschungszentrum (FMF), Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Malte Sellin
- Institut für Anorganische und Analytische Chemie and Freiburger Materialforschungszentrum (FMF), Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Matthis Seiler
- Institut für Anorganische und Analytische Chemie and Freiburger Materialforschungszentrum (FMF), Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Tanja Würz
- Institut für Anorganische und Analytische Chemie and Freiburger Materialforschungszentrum (FMF), Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Friederike Oesten
- Institut für Anorganische und Analytische Chemie and Freiburger Materialforschungszentrum (FMF), Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Maximilian Schmucker
- Institut für Anorganische und Analytische Chemie and Freiburger Materialforschungszentrum (FMF), Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Tabea Sterbak
- Institut für Anorganische und Analytische Chemie and Freiburger Materialforschungszentrum (FMF), Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Julia Fischer
- Institut für Anorganische und Analytische Chemie and Freiburger Materialforschungszentrum (FMF), Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Valentin Radtke
- Institut für Anorganische und Analytische Chemie and Freiburger Materialforschungszentrum (FMF), Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Johannes Hunger
- Molecular Spectroscopy Department, Max-Planck-Institut for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany.
| | - Ingo Krossing
- Institut für Anorganische und Analytische Chemie and Freiburger Materialforschungszentrum (FMF), Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany.
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16
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Shahidi N, Laub JA, Vogiatzis KD, Doxastakis M. Multiscale Modeling of Vinyl-Addition Polynorbornenes: The Effect of Stereochemistry. Polymers (Basel) 2024; 16:2243. [PMID: 39204463 PMCID: PMC11358979 DOI: 10.3390/polym16162243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Revised: 08/01/2024] [Accepted: 08/03/2024] [Indexed: 09/04/2024] Open
Abstract
Vinyl-addition polynorbornenes are candidates for designing high-performance polymers due to unique characteristics, which include a high glass transition temperature associated with a rigid backbone. Recent studies have established that the processability and properties of these polymers can be fine-tuned by using targeted substitutions. However, synthesis with different catalysts results in materials with distinct properties, potentially due to the presence of various stereoisomers that are difficult to quantify experimentally. Herein, we develop all-atom models of polynorbornene oligomers based on classical force fields and density functional theory. To establish the relationship between chemical architecture, chain conformations, and melt structure, we perform detailed molecular dynamics simulations with the fine-tuned atomistic force field and propose simpler coarse-grained descriptions to address the high molecular weight limit. All-atom simulations of oligomers suggest high glass transition temperatures in the range of 550-600 K. In the melt state (800 K), meso chains form highly rigid extended coils (C∞≈11) with amorphous structural characteristics similar to the X-ray diffraction data observed in the literature. In contrast, simulations with racemo chains predict highly helical tubular chain conformations that could promote assembly into crystalline structures.
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Affiliation(s)
- Nobahar Shahidi
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, USA
| | - Jeffrey A. Laub
- Department of Chemistry, University of Tennessee, Knoxville, TN 37996, USA
| | | | - Manolis Doxastakis
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, USA
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17
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Gray M, Herbert JM. Assessing the domain-based local pair natural orbital (DLPNO) approximation for non-covalent interactions in sizable supramolecular complexes. J Chem Phys 2024; 161:054114. [PMID: 39105555 PMCID: PMC11305816 DOI: 10.1063/5.0206533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 07/18/2024] [Indexed: 08/07/2024] Open
Abstract
The titular domain-based local pair natural orbital (DLPNO) approximation is the most widely used method for extending correlated wave function models to large molecular systems, yet its fidelity for intermolecular interaction energies in large supramolecular complexes has not been thoroughly vetted. Non-covalent interactions are sensitive to tails of the electron density and involve nonlocal dispersion that is discarded or approximated if the screening of pair natural orbitals (PNOs) is too aggressive. Meanwhile, the accuracy of the DLPNO approximation is known to deteriorate as molecular size increases. Here, we test the DLPNO approximation at the level of second-order Møller-Plesset perturbation theory (MP2) and coupled-cluster theory with singles, doubles, and perturbative triples [CCSD(T)] for a variety of large supramolecular complexes. DLPNO-MP2 interaction energies are within 3% of canonical values for small dimers with ≲10 heavy atoms, but for larger systems, the DLPNO approximation is often quite poor unless the results are extrapolated to the canonical limit where the threshold for discarding PNOs is taken to zero. Counterpoise correction proves to be essential in reducing errors with respect to canonical results. For a sequence of nanoscale graphene dimers up to (C96H24)2, extrapolated DLPNO-MP2 interaction energies agree with canonical values to within 1%, independent of system size, provided that the basis set does not contain diffuse functions; these cause the DLPNO approximation to behave erratically, such that results cannot be extrapolated in a meaningful way. DLPNO-CCSD(T) calculations are typically performed using looser PNO thresholds as compared to DLPNO-MP2, but this significantly impacts accuracy for large supramolecular complexes. Standard DLPNO-CCSD(T) settings afford errors of 2-6 kcal/mol for dimers involving coronene (C24H12) and circumcoronene (C54H18), even at the DLPNO-CCSD(T1) level.
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Affiliation(s)
- Montgomery Gray
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - John M. Herbert
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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18
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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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19
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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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20
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Okoročenkova J, Filgas J, Khan NM, Slavíček P, Klán P. Thermal Truncation of Heptamethine Cyanine Dyes. J Am Chem Soc 2024; 146:19768-19781. [PMID: 38995720 PMCID: PMC11273355 DOI: 10.1021/jacs.4c02116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 06/24/2024] [Accepted: 06/25/2024] [Indexed: 07/14/2024]
Abstract
Cyanine dyes are a class of organic, usually cationic molecules containing two nitrogen centers linked through conjugated polymethine chains. The synthesis and reactivity of cyanine derivatives have been extensively investigated for decades. Unlike the recently described phototruncation process, the thermal truncation (chain shortening) reaction is a phenomenon that has rarely been reported for these important fluorophores. Here, we present a systematic investigation of the truncation of heptamethine cyanines (Cy7) to pentamethine (Cy5) and trimethine (Cy3) cyanines via homogeneous, acid-base-catalyzed nucleophilic exchange reactions. We demonstrate how different substituents at the C3' and C4' positions of the chain and different heterocyclic end groups, the presence of bases, nucleophiles, and oxygen, solvent properties, and temperature affect the truncation process. The mechanism of chain shortening, studied by various analytical and spectroscopic techniques, was verified by extensive ab initio calculation, implying the necessity to model catalytic reactions by highly correlated wave function-based methods. In this study, we provide critical insight into the reactivity of cyanine polyene chains and elucidate the truncation mechanism and methods to mitigate side processes that can occur during the synthesis of cyanine derivatives. In addition, we offer alternative routes to the preparation of symmetrical and unsymmetrical meso-substituted Cy5 derivatives.
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Affiliation(s)
- Jana Okoročenkova
- Department
of Chemistry, Faculty of Science, Masaryk
University, Kamenice 5, 625 00 Brno, Czech Republic
- RECETOX,
Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech
Republic
| | - Josef Filgas
- Department
of Physical Chemistry, University of Chemistry
and Technology, Technická 5, 16628 Prague 6, Czech Republic
| | - Nasrulla Majid Khan
- Department
of Chemistry, Faculty of Science, Masaryk
University, Kamenice 5, 625 00 Brno, Czech Republic
- RECETOX,
Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech
Republic
| | - Petr Slavíček
- Department
of Physical Chemistry, University of Chemistry
and Technology, Technická 5, 16628 Prague 6, Czech Republic
| | - Petr Klán
- Department
of Chemistry, Faculty of Science, Masaryk
University, Kamenice 5, 625 00 Brno, Czech Republic
- RECETOX,
Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech
Republic
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21
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Sterling AJ, Smith RC, Anderson EA, Duarte F. Beyond Strain Release: Delocalization-Enabled Organic Reactivity. J Org Chem 2024; 89:9979-9989. [PMID: 38970491 PMCID: PMC11267611 DOI: 10.1021/acs.joc.4c00857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 06/03/2024] [Accepted: 06/21/2024] [Indexed: 07/08/2024]
Abstract
The release of strain energy is a fundamental driving force for organic reactions. However, absolute strain energy alone is an insufficient predictor of reactivity, evidenced by the similar ring strain but disparate reactivity of cyclopropanes and cyclobutanes. In this work, we demonstrate that electronic delocalization is a key factor that operates alongside strain release to boost, or even dominate, reactivity. This delocalization principle extends across a wide range of molecules containing three-membered rings such as epoxides, aziridines, and propellanes and also applies to strain-driven cycloaddition reactions. Our findings lead to a "rule of thumb" for the accurate prediction of activation barriers in such systems, which can be easily applied to reactions involving many of the strained building blocks commonly encountered in organic synthesis, medicinal chemistry, polymer science, and bioconjugation. Given the significance of electronic delocalization in organic chemistry, for example in aromatic π-systems and hyperconjugation, we anticipate that this concept will serve as a versatile tool to understand and predict organic reactivity.
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Affiliation(s)
- Alistair J. Sterling
- Chemistry
Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
- Department
of Chemistry & Biochemistry, The University
of Texas at Dallas, 800
W. Campbell Rad, Richardson, Texas 75080, United States
| | - Russell C. Smith
- Abbvie
Drug Discovery Science & Technology (DDST), 1 North Waukegan Road, North
Chicago, Illinois 60064, United States
| | - Edward A. Anderson
- Chemistry
Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Fernanda Duarte
- Chemistry
Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
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22
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Wei Y, Debnath S, Weber JL, Mahajan A, Reichman DR, Friesner RA. Scalable Ab Initio Electronic Structure Methods with Near Chemical Accuracy for Main Group Chemistry. J Phys Chem A 2024; 128:5796-5807. [PMID: 38970826 DOI: 10.1021/acs.jpca.4c02853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2024]
Abstract
This study evaluates the precision of widely recognized quantum chemical methodologies, CCSD(T), DLPNO-CCSD(T), and localized ph-AFQMC, for determining the thermochemistry of main group elements. DLPNO-CCSD(T) and localized ph-AFQMC, which offer greater scalability compared to canonical CCSD(T), have emerged over the past decade as pivotal in producing precise benchmark chemical data. Our investigation includes closed-shell, neutral molecules, focusing on their heat of formation and atomization energy sourced from four specific small molecule data sets. First, we selected molecules from the G2 and G3 data sets, noted for their reliable experimental heat of formation data. Additionally, we incorporate molecules from the W4-11 and W4-17 sets, which provide high-level theoretical reference values for atomization energy at 0 K. Our findings reveal that both DLPNO-CCSD(T) and ph-AFQMC methods are capable of achieving a root-mean-square deviation of less than 1 kcal/mol across the combined data set, aligning with the threshold for chemical accuracy. Moreover, we make efforts to confine the maximum deviations within 2 kcal/mol, a degree of precision that significantly broadens the applicability of these methods in fields such as biology and materials science.
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Affiliation(s)
- Yujing Wei
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Sibali Debnath
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - John L Weber
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Ankit Mahajan
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - David R Reichman
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Richard A Friesner
- Department of Chemistry, Columbia University, New York, New York 10027, United States
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23
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McGinnis KR, McGee CJ, Sommerfeld T, Jarrold CC. Anion Photoelectron Imaging Spectroscopy of C 6F 5X - (X = F, Cl, Br, I). J Phys Chem A 2024; 128:5646-5658. [PMID: 38980699 DOI: 10.1021/acs.jpca.4c03434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
The photoelectron (PE) spectra of C6F5X- (X = Cl, Br, I) and computational results on the anions and neutrals are presented and compared to previously reported results on C6F6- [McGee, C. J. J. Phys. Chem. A 2023, 127, 8556-8565.]. The spectra all exhibit broad, vibrationally unresolved detachment transitions, indicating that the equilibrium structures of the anions are significantly different from the neutrals. The PE spectrum of C6F5Cl- exhibits a parallel photoelectron angular distribution (PAD), similar to that of the previously reported C6F6- spectrum, while the PE spectra of C6F5Br- and C6F5I- have isotropic PADs, and also exhibit a prominent X- PE feature due to photodissociation of C6F5X- resulting in X- formation. Identification of the C6F5X- detachment transition origins, which is equivalent to the neutral electron affinity (EA), in all three cases is difficult, since the broadness of the detachment feature is accompanied by vanishingly small detachment cross section near the origin. Upper limits on the EAs were determined to be 1.70 eV for C6F5Cl, 2.10 eV for C6F5Br, and 2.00 eV for C6F5I, all significantly higher than the 0.76 eV upper limit determined for C6F6 with the same experiment. The broad detachment transitions are consistent with computational results, which predict very large differences between the neutral and anionic C-X (X = Cl, Br, I) bond lengths. Based on differences between the MBIS atom charges in the anions and neutrals, the excess charge in the anion is on the unique C atom and X, in contrast to the nonplanar C2v structured C6F6- anion, for which the charge is delocalized over the molecule. In C6F5Cl-, the C-Cl bond is predicted to be bent out of the plane, while both C6F5Br- and C6F5I- are predicted to be planar on average. The impact of the interruption of the symmetry in the hexafluorobenzene neutral and anion on the molecular and electronic structure of C6F5X/C6F5X- is considered, as well as the possible dissociative state leading to X- (X = Br, I) formation, and the nature of the C-X bond.
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Affiliation(s)
- Kristen Rose McGinnis
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Conor J McGee
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Thomas Sommerfeld
- Department of Chemistry and Physics, Southeast Louisiana University, SLU 10878, Hammond, Louisiana 70402, United States
| | - Caroline Chick Jarrold
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
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24
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Haack A, Schaefer C, Zimmermann S. On the Arrival Time Distribution of Reacting Systems in Ion Mobility Spectrometry. Anal Chem 2024; 96. [PMID: 39009503 PMCID: PMC11295131 DOI: 10.1021/acs.analchem.4c02010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 06/13/2024] [Accepted: 07/09/2024] [Indexed: 07/17/2024]
Abstract
Ion mobility spectrometry (IMS) is a widely used gas-phase separation technique, particularly when coupled with mass spectrometry (MS). Modern IMS instruments often apply elevated reduced field strengths for improved ion separation and ion focusing. These alter the collision dynamics and further drive ion reaction processes that can change the analyte's structure. As a result, the measured arrival time distribution (ATD) can change with the applied reduced field strengths. In this work, we systematically study how the ion collision dynamics and the ion reaction dynamics, as a function of the reduced field strength, can alter the ATD. To this end, we investigate 2,6-di-tert-butylpyridine, methanol, and ethyl acetate using a home-built drift tube IMS coupled to a home-built MS and extensive first-principles Monte Carlo modeling. We show how elevated reduced field strengths can actually lower resolving power through increased ion diffusion and how the field dependency of the ion mobility can introduce uncertainties to collision cross sections (CCS) calculated from the measured mobilities. On top of the collision dynamics, we show how chemical transformation processes that alter the analyte's CCS, e.g., dynamic clustering or fragmentation, can lead to broadened, shifted, or non-Gaussian ATDs and how sensitive these processes are to the applied field strengths. We highlight how first-principles ion dynamics simulations can help to understand and even harness the mentioned effects.
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Affiliation(s)
- Alexander Haack
- Department of Sensors and
Measurement Technology, Institute of Electrical Engineering and Measurement
Technology, Leibniz University Hannover, 30167 Hannover, Germany
| | - Christoph Schaefer
- Department of Sensors and
Measurement Technology, Institute of Electrical Engineering and Measurement
Technology, Leibniz University Hannover, 30167 Hannover, Germany
| | - Stefan Zimmermann
- Department of Sensors and
Measurement Technology, Institute of Electrical Engineering and Measurement
Technology, Leibniz University Hannover, 30167 Hannover, Germany
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25
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Cao Y, Wang Z, Liu J, Ma Q, Li S, Liu J, Li H, Zhang P, Chen T, Wang Y, Chu B, Zhang X, Saiz-Lopez A, Francisco JS, He H. Spontaneous Molecular Bromine Production in Sea-Salt Aerosols. Angew Chem Int Ed Engl 2024:e202409779. [PMID: 38989722 DOI: 10.1002/anie.202409779] [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: 05/23/2024] [Revised: 06/28/2024] [Accepted: 07/09/2024] [Indexed: 07/12/2024]
Abstract
Bromine chemistry is responsible for the catalytic ozone destruction in the atmosphere. The heterogeneous reactions of sea-salt aerosols are the main abiotic sources of reactive bromine in the atmosphere. Here, we present a novel mechanism for the activation of bromide ions (Br-) by O2 and H2O in the absence of additional oxidants. The laboratory and theoretical calculation results demonstrated that under dark conditions, Br-, O2 and H3O+ could spontaneously generate Br and HO2 radicals through a proton-electron transfer process at the air-water interface and in the liquid phase. Our results also showed that light and acidity could significantly promote the activation of Br- and the production of Br2. The estimated gaseous Br2 production rate was up to 1.55×1010 molecules cm-2 ⋅ s-1 under light and acidic conditions; these results showed a significant contribution to the atmospheric reactive bromine budget. The reactive oxygen species (ROS) generated during Br- activation could promote the multiphase oxidation of SO2 to produce sulfuric acid, while the increase in acidity had a positive feedback effect on Br- activation. Our findings highlight the crucial role of the proton-electron transfer process in Br2 production; here, H3O+ facilitates the activation of Br- by O2, serves as a significant source of atmospheric reactive bromine and exerts a profound impact on the atmospheric oxidation capacity.
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Affiliation(s)
- Yiqun Cao
- State Key Joint Laboratory of Environment Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhuo Wang
- Key Laboratory of Cluster Science, Ministry of Education of China, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, China
| | - Jiarong Liu
- Key Laboratory of Cluster Science, Ministry of Education of China, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, China
| | - Qingxin Ma
- State Key Joint Laboratory of Environment Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuying Li
- State Key Joint Laboratory of Environment Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun Liu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Hao Li
- State Key Joint Laboratory of Environment Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Peng Zhang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Tianzeng Chen
- State Key Joint Laboratory of Environment Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yonghong Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Biwu Chu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiuhui Zhang
- Key Laboratory of Cluster Science, Ministry of Education of China, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, China
| | - Alfonso Saiz-Lopez
- Department of Atmospheric Chemistry and Climate, Institute of Physical Chemistry Blas Cabrera, CSIC, Madrid, 28006, Spain
| | - Joseph S Francisco
- Department of Earth and Environmental Science and Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, United States
| | - Hong He
- State Key Joint Laboratory of Environment Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
- Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
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26
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Fernandes AJ, Valsamidou V, Katayev D. Overcoming Challenges in O-Nitration: Selective Alcohol Nitration Deploying N,6-Dinitrosaccharin and Lewis Acid Catalysis. Angew Chem Int Ed Engl 2024:e202411073. [PMID: 38984498 DOI: 10.1002/anie.202411073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 07/05/2024] [Accepted: 07/09/2024] [Indexed: 07/11/2024]
Abstract
Nitrate esters hold pivotal roles in pharmaceuticals, energetic materials, and atmospheric processes, motivating the development of efficient synthesis routes. Here, we present a novel catalytic method for the synthesis of nitrates via the direct O-nitration of alcohols, addressing limitations of current traditional methods. Leveraging bench-stable and recoverable N,6-dinitrosaccharin reagent, our catalytic strategy employs magnesium triflate to achieve mild and selective O-nitration of alcohols, offering broad substrate scope and unprecedentedly large functional group tolerance (e.g. alkenes, alkynes, carbonyls). DFT mechanistic studies reveal a dual role of the magnesium catalyst in the activation of both the nitrating reagent and the alcohol substrate. They also unveil a barrierless proton transfer upon formation of a widely-accepted - yet elusive in solution - nitrooxonium ion intermediate. Overall, our work contributes to the development of mild, selective, and sustainable approaches to nitrates synthesis, with potential applications in drug discovery, materials science, and environmental chemistry.
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Affiliation(s)
- Anthony J Fernandes
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Vasiliki Valsamidou
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Dmitry Katayev
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
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27
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Gałyńska M, de Moraes MMF, Tecmer P, Boguslawski K. Delving into the catalytic mechanism of molybdenum cofactors: a novel coupled cluster study. Phys Chem Chem Phys 2024; 26:18918-18929. [PMID: 38952220 DOI: 10.1039/d4cp01500b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
In this work, we use modern electronic structure methods to model the catalytic mechanism of different variants of the molybdenum cofactor (Moco). We investigate the dependence of various Moco model systems on structural relaxation and the importance of environmental effects for five critical points along the reaction coordinate with the DMSO and NO3- substrates. Furthermore, we scrutinize the performance of various coupled-cluster approaches for modeling the relative energies along the investigated reaction paths, focusing on several pair coupled cluster doubles (pCCD) flavors and conventional coupled cluster approximations. Moreover, we elucidate the Mo-O bond formation using orbital-based quantum information measures, which highlight the flow of σM-O bond formation and σN/S-O bond breaking. Our study shows that pCCD-based models are a viable alternative to conventional methods and offer us unique insights into the bonding situation along a reaction coordinate. Finally, this work highlights the importance of environmental effects or changes in the core and, consequently, in the model itself to elucidate the change in activity of different Moco variants.
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Affiliation(s)
- Marta Gałyńska
- Institute of Physics, Faculty of Physics, Astronomy, and Informatics, Nicolaus Copernicus University in Toruń, Grudziądzka 5, 87-100 Toruń, Poland.
| | - Matheus Morato F de Moraes
- Institute of Physics, Faculty of Physics, Astronomy, and Informatics, Nicolaus Copernicus University in Toruń, Grudziądzka 5, 87-100 Toruń, Poland.
| | - Paweł Tecmer
- Institute of Physics, Faculty of Physics, Astronomy, and Informatics, Nicolaus Copernicus University in Toruń, Grudziądzka 5, 87-100 Toruń, Poland.
| | - Katharina Boguslawski
- Institute of Physics, Faculty of Physics, Astronomy, and Informatics, Nicolaus Copernicus University in Toruń, Grudziądzka 5, 87-100 Toruń, Poland.
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28
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Zhang X, Li C, Ye HZ, Berkelbach TC, Chan GKL. Performant automatic differentiation of local coupled cluster theories: Response properties and ab initio molecular dynamics. J Chem Phys 2024; 161:014109. [PMID: 38949583 DOI: 10.1063/5.0212274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 06/12/2024] [Indexed: 07/02/2024] Open
Abstract
In this work, we introduce a differentiable implementation of the local natural orbital coupled cluster (LNO-CC) method within the automatic differentiation framework of the PySCFAD package. The implementation is comprehensively tuned for enhanced performance, which enables the calculation of first-order static response properties on medium-sized molecular systems using coupled cluster theory with single, double, and perturbative triple excitations [CCSD(T)]. We evaluate the accuracy of our method by benchmarking it against the canonical CCSD(T) reference for nuclear gradients, dipole moments, and geometry optimizations. In addition, we demonstrate the possibility of property calculations for chemically interesting systems through the computation of bond orders and Mössbauer spectroscopy parameters for a [NiFe]-hydrogenase active site model, along with the simulation of infrared spectra via ab initio LNO-CC molecular dynamics for a protonated water hexamer.
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Affiliation(s)
- Xing Zhang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Chenghan Li
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Hong-Zhou Ye
- Department of Chemistry, Columbia University, New York, New York 10027, USA
| | | | - Garnet Kin-Lic Chan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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29
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Hashimoto Y, Kong WY, Tantillo DJ. Discovery of a Formal Dyotropic Rearrangement during Acid-Mediated Dioxabicyclo[4.2.1]nonanone Formation. Org Lett 2024; 26:5441-5446. [PMID: 38900922 DOI: 10.1021/acs.orglett.4c01616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
A new reaction mechanism for the construction of dioxabicyclo[4.2.1]nonanone skeletons via a cation cascade has been proposed and examined by DFT and ab initio computations. This mechanism features the following steps: (1) intramolecular Friedel-Crafts-type cyclization with a methyl oxocarbenium cation formed by carboxylate disconnection, (2) electron-rich aromatic ring assisted methoxide loss followed by lactone formation, and (3) stepwise dyotropic rearrangement resulting in skeletal isomerization from a dioxabicyclo[3.2.2]nonanone to the dioxabicyclo[4.2.1]nonanone product observed experimentally. The high regioselectivity and driving force for the overall rearrangement were rationalized, and Lewis and Brønsted acid mediated reactivities were compared.
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Affiliation(s)
- Yoshimitsu Hashimoto
- Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States
| | - Wang-Yeuk Kong
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States
| | - Dean J Tantillo
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States
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30
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Sinha S, Giri S. Ab initio investigation on the mechanism of SO 2 activation by P/B intermolecular frustrated Lewis pairs. J Mol Model 2024; 30:241. [PMID: 38954102 DOI: 10.1007/s00894-024-06038-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 06/20/2024] [Indexed: 07/04/2024]
Abstract
CONTEXT In silico study investigates the activation of sulfur dioxide by newly designed frustrated Lewis pairs, i.e., [P(tBu)3…B(C2NBSHF2)3], where the Lewis acid part is a super Lewis acid. The activation process involves the making of P-S and B-O bonds, leading to the formation of an FLP-SO2 adduct. The calculated results demonstrate that the activation of SO2 by the FLP is almost barrierless and exothermic. Exploration of the impact of the solvent environment on the feasibility and energetics of the reaction has been investigated. The exothermicity is increasing in nonpolar solvents. METHODS This study focuses on understanding the electronic activity of SO2 activation by FLP with the help of the Minnesota 06 functional, M06-2X (global hybrid functional with 54% HF exchange) along with Pople's basis set, 6-311G (d, p). Principal interacting orbital and extended transition state-natural orbitals for chemical valence studies, giving impactful insight into the favorable orbital interaction and electron transfer in this reaction. Furthermore, useful CDFT descriptors such as reaction force constant and reaction electronic flux profiles along the intrinsic reaction coordinate give insights into the synchronicity and total electronic activity of the reaction.
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Affiliation(s)
- Swapan Sinha
- School of Applied Science and Humanities, Haldia Institute of Technology, Haldia, 721657, India
- Maulana Abul Kalam Azad University of Technology, Haringhata, 741249, India
| | - Santanab Giri
- School of Applied Science and Humanities, Haldia Institute of Technology, Haldia, 721657, India.
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31
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Zubova E, Pokluda A, Dvořáková H, Krupička M, Cibulka R. Exploring the Reactivity of Flavins with Nucleophiles Using a Theoretical and Experimental Approach. Chempluschem 2024; 89:e202300547. [PMID: 38064649 DOI: 10.1002/cplu.202300547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/30/2023] [Indexed: 01/13/2024]
Abstract
Covalent adducts of flavin cofactors with nucleophiles play an important role in non-canonical function of flavoenzymes as well as in flavin-based catalysis. Herein, the interaction of flavin derivatives including substituted flavins (isoalloxazines), 1,10-ethylene-bridged flavinium salts, and non-substituted alloxazine and deazaflavin with selected nucleophiles was investigated using an experimental and computational approach. Triphenylphosphine or trimethylphosphine, 1-nitroethan-1-ide, and methoxide were selected as representatives of neutral soft, anionic soft, and hard nucleophiles, respectively. The interactions were investigated using UV/Vis and 1H NMR spectroscopy as well as by DFT calculations. The position of nucleophilic attack estimated using the calculated Gibbs free energy values was found to correspond with the experimental data, favouring the addition of phosphine and 1-nitroethan-1-ide into position N(5) and methoxide into position C(10a) of 1,10-ethylene-bridged flavinium salts. The calculated Gibbs free energy values were found to correlate with the experimental redox potentials of the flavin derivatives tested. These findings can be utilized as valuable tools for the design of artificial flavin-based catalytic systems or investigating the mechanism of flavoenzymes.
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Affiliation(s)
- Ekaterina Zubova
- Department of Organic Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28, Prague, Czech Republic
| | - Adam Pokluda
- Department of Organic Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28, Prague, Czech Republic
| | - Hana Dvořáková
- Central Laboratories, University of Chemistry and Technology, Prague, Technická 5, 166 28, Prague, Czech Republic
| | - Martin Krupička
- Department of Organic Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28, Prague, Czech Republic
| | - Radek Cibulka
- Department of Organic Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28, Prague, Czech Republic
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32
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Masoumifeshani E, Korona T. Intermolecular interaction energies with AROFRAG-A systematic approach for fragmentation of aromatic molecules. J Comput Chem 2024. [PMID: 38946399 DOI: 10.1002/jcc.27429] [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: 12/30/2023] [Revised: 04/02/2024] [Accepted: 04/25/2024] [Indexed: 07/02/2024]
Abstract
Intermolecular interactions with polycyclic aromatic hydrocarbons (PAHs) represent an important area of physisorption studies. These investigations are often hampered by a size of interacting PAHs, which makes the calculation prohibitively expensive. Therefore, methods designed to deal with large molecules could be helpful to reduce the computational costs of such studies. Recently we have introduced a new systematic approach for the molecular fragmentation of PAHs, denoted as AROFRAG, which decomposes a large PAH molecule into a set of predefined small PAHs with a benzene ring being the smallest unbreakable unit, and which in conjunction with the Molecules-in-Molecules (MIM) approach provides an accurate description of total molecular energies. In this contribution we propose an extension of the AROFRAG, which provides a description of intermolecular interactions for complexes composed of PAH molecules. The examination of interaction energy partitioning for various test cases shows that the AROFRAG3 model connected with the MIM approach accurately reproduces all important components of the interaction energy. An additional important finding in our study is that the computationally expensive long-range electron-correlation part of the interaction energy, that is, the dispersion component, is well described at lower AROFRAG levels even without MIM, which makes the latter models interesting alternatives to existing methods for an accurate description of the electron-correlated part of the interaction energy.
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Affiliation(s)
| | - Tatiana Korona
- Faculty of Chemistry, University of Warsaw, Warsaw, Poland
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33
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Beer H, Siewert JE, Schröder M, Fischer M, Corzilius B, Hering-Junghans C. Phosphaarsenes - Combining Phospha- and Arsa-Wittig-Reagents. Chempluschem 2024; 89:e202400120. [PMID: 38488262 DOI: 10.1002/cplu.202400120] [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: 02/27/2024] [Revised: 03/12/2024] [Indexed: 04/14/2024]
Abstract
Dipnictenes of the type RPn=PnR (Pn=P, As, Sb, Bi) can be viewed as dimers of the corresponding pnictinidenes R-Pn. Phosphanylidene- and arsanylidenephosphoranes (R-Pn(PMe3); Pn=P, As) have been shown to be versatile synthetic surrogates for the delivery of pnictinidene fragments. We now report that thermal treatment of 1 : 1 mixtures of R-P(PMe3) and R'-As(PMe3) gives access to arsaphosphenes of the type RP=AsR'. Three examples are presented and the properties and reactivity of Mes*P=AsDipTer (1) (Mes*=2,4,6-tBu3-C6H2; DipTer=2,6-(2,6-iPr2C6H3)2-C6H3) were studied in detail. Solid state 31P NMR spectroscopy revealed a large 31P NMR chemical shift anisotropy with a span of ca. 920 ppm for 1 while computational methods were employed to investigate this pronounced magnetic deshielding of the P atom in 1. In the presence of the carbene IMe4 (IMe4=:C(MeNCMe)2) 1 is shown to be split into the corresponding NHC adducts Mes*P(IMe4) and DipTerAs(IMe4), which is additionally shown for diarsenes.
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Affiliation(s)
- Henrik Beer
- Leibniz-Institut für Katalyse (LIKAT), Albert-Einstein-Straße 29a, 18059, Rostock, Germany
| | - Jan-Erik Siewert
- Leibniz-Institut für Katalyse (LIKAT), Albert-Einstein-Straße 29a, 18059, Rostock, Germany
| | - Mirjam Schröder
- Leibniz-Institut für Katalyse (LIKAT), Albert-Einstein-Straße 29a, 18059, Rostock, Germany
- Institut für Chemie und Department Life, Light & Matter, Universität Rostock, Albert-Einstein-Str. 27, 18059, Rostock, Germany
| | - Malte Fischer
- Leibniz-Institut für Katalyse (LIKAT), Albert-Einstein-Straße 29a, 18059, Rostock, Germany
- Georg-August-Universität Göttingen, Institut für Anorganische Chemie, Tammannstraße 4, 37077, Göttingen, Germany
| | - Björn Corzilius
- Leibniz-Institut für Katalyse (LIKAT), Albert-Einstein-Straße 29a, 18059, Rostock, Germany
- Institut für Chemie und Department Life, Light & Matter, Universität Rostock, Albert-Einstein-Str. 27, 18059, Rostock, Germany
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34
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Gosch MA, Wilson DJD. Prediction of Covalent Metal-Metal Bonding in Cp-M-M'-Nacnac Complexes of Group 2 and 12 Metals (Be, Mg, Ca, Zn, Cd, Hg). Chemistry 2024:e202402118. [PMID: 38935331 DOI: 10.1002/chem.202402118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/27/2024] [Accepted: 06/27/2024] [Indexed: 06/28/2024]
Abstract
Bimetallic CpMM'Nacnac molecules with group 2 and 12 metals (M=Be, Mg, Ca, Zn, Cd, Hg) that contain novel metal-metal bonding have been investigated in a theoretical study of their molecular and electronic structure, thermodynamic stability, and metal-metal bonding. In all cases the metal-metal bonds are characterized as electron-sharing covalent single bonds from natural bond orbital (NBO) and energy-decomposition analysis with natural orbitals of chemical valence (EDA-NOCV) analysis. The sum of [MM'] charges is relatively constant, with all complexes exhibiting a [MM']2+ core. Quantum theory of atoms in molecules (QTAIM) analysis indicates the presence of non-nuclear attractors (NNA) in the metal-metal bonds of the BeBe, MgMg, and CaCa complexes. There is substantial electron density (0.75-1.33 e) associated with the NNAs, which indicates that these metal-metal bonds, while classified as covalent electron-sharing bonds, retain significant metallic character that can be associated with reducing reactivity of the complex. The predicted stability of these complexes, combined with their novel covalent metal-metal bonding and potential as reducing agents, make them appealing targets for the synthesis of new metal-metal bonds.
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Affiliation(s)
- Matthew A Gosch
- Department of Chemistry, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne, Victoria, 3086, Australia
| | - David J D Wilson
- Department of Chemistry, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne, Victoria, 3086, Australia
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35
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Sodré PT, Aguilar AM, Alves WA, Coutinho-Neto MD. Intrinsic and environmental modulation of stereoselective aldol organocatalyzed reactions by proline-containing lipopeptides. RSC Adv 2024; 14:21035-21046. [PMID: 38962095 PMCID: PMC11220607 DOI: 10.1039/d4ra03222e] [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: 04/30/2024] [Accepted: 06/14/2024] [Indexed: 07/05/2024] Open
Abstract
Proline, along with its derivatives, has been employed as an efficient organocatalyst for aldol reactions, with the ability to promote the creation of stereoselective C-C bonds. Even though the Houk-List transition state model is able to explain the stereoselectivity observed when proline is used as a catalyst, few studies investigate the role of microheterogeneous media in modulating the reaction outcome. In this work, molecular dynamics and electronic structure calculations were used to investigate the aldol reaction in the condensed phase. Our research focused on a lipopeptide compound incorporating the proline residue within the sequence PRWG-(C18H37), where P represents l-proline, R stands for l-arginine, W for l-tryptophan, and G for l-glycine. This sequence is covalently bonded to a hydrophobic segment formed by a long aliphatic chain, acting as an organocatalyst in an aqueous solution. This catalytic phase utilizes the complex chemical environment of the solution to achieve high selectivity. Our findings indicate a Houk-List-like mechanism, in which the amide acts as an H-bond donor, complemented by a mechanism in which the counter ion, trifluoracetic acid (TFA), acts as a proton shuttle. Both mechanisms demonstrated low energy barriers-12.23 and 1.42 kcal mol-1 for the (S,R) stereoisomer formation, computed using DLPNO-CCSD with def2-TZVPP basis set. Further, to explore the catalytic effect of the PRWG-(C18H37) lipopeptide in water, molecular dynamics simulations were conducted. It was observed that the micellar phase significantly enhances stereospecific encounters, favouring the experimentally observed ratio of (SR/SS) isomers, in contrast to reactions in a pure cyclohexanone medium. By quantifying the effects enabled by the supramolecular assembly, we were able to shed light on the factors that modify and enhance the stereoslectivity of the reaction.
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Affiliation(s)
- Pedro Tendrih Sodré
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC 09210-580 Santo André Brazil
| | - Andrea Maria Aguilar
- Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo 09972-270 Diadema Brazil
| | - Wendel Andrade Alves
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC 09210-580 Santo André Brazil
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36
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Tang Z, Zhu H, Pan Z, Gao J, Zhang J. A many-body energy decomposition analysis (MB-EDA) scheme based on a target state optimization self-consistent field (TSO-SCF) method. Phys Chem Chem Phys 2024; 26:17549-17560. [PMID: 38884195 DOI: 10.1039/d4cp01259c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
In this paper, we combine an energy decomposition analysis (EDA) scheme with many-body expansion (MBE) to develop a MB-EDA method to study the cooperative and anti-cooperative effects in molecular cluster systems. Based on the target state optimization self-consistent field (TSO-SCF) method, the intermolecular interaction energy can be decomposed into five chemically meaningful terms, i.e., electrostatic, exchange, polarization, charge transfer and dispersion interaction energies. MB-EDA can decompose each of these terms in MBE. This MB-EDA has been applied to 3 different cluster systems: water clusters, ionic liquid clusters, and acetonitrile-methane clusters. This reveals that electrostatic, exchange, and dispersion interactions are highly pairwise additive in all systems. In water and ionic liquid clusters, the many-body effects are significant in both polarization and charge transfer interactions, but are cooperative and anti-cooperative, respectively. For acetonitrile-methane clusters, which do not involve hydrogen bonds or charge-charge Coulombic interactions, the many-body effects are quite small. The chemical origins of different many-body effects are deeply analyzed. The MB-EDA method has been implemented in Qbics (https://qbics.info) and can be a useful tool for understanding the many-body behavior in molecular aggregates at the quantum chemical level of theory.
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Affiliation(s)
- Zhen Tang
- Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, People's Republic of China.
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518055, People's Republic of China.
| | - Hong Zhu
- Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, People's Republic of China.
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518055, People's Republic of China.
| | - Zhijun Pan
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518055, People's Republic of China.
| | - Jiali Gao
- Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, People's Republic of China.
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518055, People's Republic of China.
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jun Zhang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518055, People's Republic of China.
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37
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Shi BX, Wales DJ, Michaelides A, Myung CW. Going for Gold(-Standard): Attaining Coupled Cluster Accuracy in Oxide-Supported Nanoclusters. J Chem Theory Comput 2024; 20:5306-5316. [PMID: 38856017 DOI: 10.1021/acs.jctc.4c00379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
The structure of oxide-supported metal nanoclusters plays an essential role in their sharply enhanced catalytic activity over that of bulk metals. Simulations provide the atomic-scale resolution needed to understand these systems. However, the sensitive mix of metal-metal and metal-support interactions, which govern their structure, puts stringent requirements on the method used, requiring calculations beyond standard density functional theory (DFT). The method of choice is coupled cluster theory [specifically CCSD(T)], but its computational cost has so far prevented its application to these systems. In this work, we showcase two approaches to make CCSD(T) accuracy readily achievable in oxide-supported nanoclusters. First, we leverage the SKZCAM protocol to provide the first benchmarks of oxide-supported nanoclusters, revealing that it is specifically metal-metal interactions that are challenging to capture with DFT. Second, we propose a CCSD(T) correction (ΔCC) to the metal-metal interaction errors in DFT, reaching accuracy comparable to that of the SKZCAM protocol at significantly lower cost. This approach forges a path toward studying larger systems at reliable accuracy, which we highlight by identifying a ground-state structure in agreement with experiments for Au20 on MgO, a challenging system where DFT models have yielded conflicting predictions.
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Affiliation(s)
- Benjamin X Shi
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - David J Wales
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Angelos Michaelides
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Chang Woo Myung
- Department of Energy Science, Sungkyunkwan University, Seobu-ro 2066, Suwon 16419, Korea
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38
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Obeng A, Autschbach J. How Much Electron Donation Is There In Transition Metal Complexes? A Computational Study. J Chem Theory Comput 2024; 20:4965-4976. [PMID: 38857528 DOI: 10.1021/acs.jctc.4c00404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
The "dative" covalent interactions between metals and ligands in coordination compounds, i.e., metal-to-ligand and ligand-to-metal donation, are manifestations of electron delocalization and subject to errors in approximate calculations. This work addresses the extent of dative bonding/donation in a series of closed-shell transition metal complexes. Several Kohn-Sham density functionals, representing different "rungs" of approximations, along with post-Hartree-Fock methods are assessed in comparison to CCSD(T). Two widely used nonhybrid and global hybrid density functionals (B3LYP, PBE0) tend to produce notably too strong donation. Global hybrids with elevated fractions of exact exchange (40 to 50%) and the range-separated exchange functional CAM-B3LYP tend to perform better for the description of the donation. The performance of a double-hybrid functional is found to be quite satisfactory, correcting errors seen in MP2 calculations. A fast approximate coupled-cluster model (DLPNO-CCSD) also gives a reasonable description of the donation, with a tendency to underestimate its extent.
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Affiliation(s)
- Augustine Obeng
- Department of Chemistry, University at Buffalo State University of New York Buffalo, New York 14260-3000, United States
| | - Jochen Autschbach
- Department of Chemistry, University at Buffalo State University of New York Buffalo, New York 14260-3000, United States
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39
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Costain TS, Ogden V, Neville SP, Schuurman MS. A DFT/MRCI Hamiltonian parameterized using only ab initio data: I. valence excited states. J Chem Phys 2024; 160:224106. [PMID: 38856682 DOI: 10.1063/5.0210897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 05/22/2024] [Indexed: 06/11/2024] Open
Abstract
A new combined density functional theory and multi-reference configuration interaction (DFT/MRCI) Hamiltonian parameterized solely using the benchmark ab initio vertical excitation energies obtained from the QUEST databases is presented. This new formulation differs from all previous versions of the method in that the choice of the underlying exchange-correlation (XC) functional employed to construct the one-particle (orbital) basis is considered, and a new XC functional, QTP17, is chosen for its ability to generate a balanced description of core and valence vertical excitation energies. The ability of the new DFT/MRCI Hamiltonian, termed QE8, to furnish accurate excitation energies is confirmed using benchmark quantum chemistry computations, and a mean absolute error of 0.16 eV is determined for the wide range of electronic excitations included in the validation dataset. In particular, the QE8 Hamiltonian dramatically improves the performance of DFT/MRCI for doubly excited states. The performance of fast approximate DFT/MRCI methods, p-DFT/MRCI and DFT/MRCI(2), is also evaluated using the QE8 Hamiltonian, and they are found to yield excitation energies in quantitative agreement with the parent DFT/MRCI method, with the two methods exhibiting a mean difference of 0.01 eV with respect to DFT/MRCI over the entire benchmark set.
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Affiliation(s)
- Teagan Shane Costain
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Victoria Ogden
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Simon P Neville
- National Research Council Canada, 100 Sussex Dr., Ottawa, Ontario K1A 0R6, Canada
| | - Michael S Schuurman
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
- National Research Council Canada, 100 Sussex Dr., Ottawa, Ontario K1A 0R6, Canada
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40
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Rahrt R, Hein-Janke B, Amarasinghe KN, Shafique M, Feldt M, Guo L, Harvey JN, Pollice R, Koszinowski K, Mata RA. The Fe-MAN Challenge: Ferrates-Microkinetic Assessment of Numerical Quantum Chemistry. J Phys Chem A 2024; 128:4663-4673. [PMID: 38832568 PMCID: PMC11182345 DOI: 10.1021/acs.jpca.4c01361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Organometallic species, such as organoferrate ions, are prototypical nucleophiles prone to reacting with a wide range of electrophiles, including proton donors. In solution, the operation of dynamic equilibria and the simultaneous presence of several organometallic species severely complicate the analysis of these fundamentally important reactions. This can be overcome by gas-phase experiments on mass-selected ions, which allow for the determination of the microscopic reactivity of the target species. In this contribution, we focus on the reactivity of a series of trisarylferrate complexes toward 2,2,2-trifluoroethanol and 2,2-difluoroethanol. By means of mass-spectrometric measurements, we determined the experimental bimolecular rate constants kexp of the gas-phase protolysis reactions of the trisarylferrate anions FePh3- and FeMes3- with the aforementioned acids. Based on these experiments, we carried out a dual blind challenge, inviting theoretical groups to submit their best predictions for the activation barriers and/or theoretical rate constants ktheo. This provides a unique opportunity to evaluate different computational protocols under minimal bias and sets the stage for further benchmarking of quantum chemical methods and data-driven approaches in the future.
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Affiliation(s)
- Rene Rahrt
- Institut
für Organische und Biomolekulare Chemie, Universität Göttingen, Tammannstr. 2, Göttingen 37077, Germany
| | - Björn Hein-Janke
- Institut
für Physikalische Chemie, Universität
Göttingen, Tammannstr.
6, Göttingen 37077, Germany
| | - Kosala N. Amarasinghe
- Leibniz
Institute for Catalysis (LIKAT), Albert-Einstein-Str. 29A, Rostock 18059, Germany
| | - Muhammad Shafique
- Leibniz
Institute for Catalysis (LIKAT), Albert-Einstein-Str. 29A, Rostock 18059, Germany
| | - Milica Feldt
- Leibniz
Institute for Catalysis (LIKAT), Albert-Einstein-Str. 29A, Rostock 18059, Germany
| | - Luxuan Guo
- Department
of Chemistry, KU Leuven, Celestijnenlaan 200F, Leuven B-3001, Belgium
| | - Jeremy N. Harvey
- Department
of Chemistry, KU Leuven, Celestijnenlaan 200F, Leuven B-3001, Belgium
| | - Robert Pollice
- Stratingh
Institute for Chemistry, University of Groningen, Nijenborgh 4, Groningen 9747 AG, The
Netherlands
| | - Konrad Koszinowski
- Institut
für Organische und Biomolekulare Chemie, Universität Göttingen, Tammannstr. 2, Göttingen 37077, Germany
| | - Ricardo A. Mata
- Institut
für Physikalische Chemie, Universität
Göttingen, Tammannstr.
6, Göttingen 37077, Germany
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41
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Coates MR, Banerjee A, Jay RM, Wernet P, Odelius M. Theoretical Investigation of Transient Species Following Photodissociation of Ironpentacarbonyl in Ethanol Solution. Inorg Chem 2024; 63:10634-10647. [PMID: 38804078 PMCID: PMC11167646 DOI: 10.1021/acs.inorgchem.4c01100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 05/08/2024] [Accepted: 05/10/2024] [Indexed: 05/29/2024]
Abstract
Photodissociation of ironpentacarbonyl [1Fe(CO)5] in solution generates transient species in different electronic states, which we studied theoretically. From ab initio molecular dynamics simulations in ethanol solution, the closed-shell parent compound 1Fe(CO)5 is found to interact weakly with the solvent, whereas the irontetracarbonyl [Fe(CO)4] species, formed after photodissociation, has a strongly spin-dependent behavior. It coordinates a solvent molecule tightly in the singlet state [1Fe(CO)4] and weakly in the triplet state [3Fe(CO)4]. From the simulations, we have gained insights into intersystem crossing in solvated irontetracarbonyl based on the distinct structural differences induced by the change in multiplicity. Alternative forms of coordination between 1Fe(CO)4 and functional groups of the ethanol molecule are simulated, and a quantum chemical investigation of the energy landscape for the coordinated irontetracarbonyl gives information about the interconversion of different transient species in solution. Furthermore, insights from the simulations, in which we find evidence of a solvent exchange mechanism, challenge the previously proposed mechanism of chain walking for under-coordinated metal carbonyls in solution.
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Affiliation(s)
- Michael R. Coates
- Department
of Physics, Stockholm University, AlbaNova University Center, SE-106 91 Stockholm, Sweden
| | - Ambar Banerjee
- Department
of Physics, Stockholm University, AlbaNova University Center, SE-106 91 Stockholm, Sweden
- Department
of Physics and Astronomy, Uppsala University, P.O. Box 516, SE-751 20 Uppsala, Sweden
| | - Raphael M. Jay
- Department
of Physics and Astronomy, Uppsala University, P.O. Box 516, SE-751 20 Uppsala, Sweden
| | - Philippe Wernet
- Department
of Physics and Astronomy, Uppsala University, P.O. Box 516, SE-751 20 Uppsala, Sweden
| | - Michael Odelius
- Department
of Physics, Stockholm University, AlbaNova University Center, SE-106 91 Stockholm, Sweden
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42
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Domingos SR, Tikhonov DS, Steber AL, Eschenbach P, Gruet S, Hrodmarsson HR, Martin K, Garcia GA, Nahon L, Neugebauer J, Avarvari N, Schnell M. Evolution of the ionisation energy with the stepwise growth of chiral clusters of [4]helicene. Nat Commun 2024; 15:4928. [PMID: 38858352 PMCID: PMC11164862 DOI: 10.1038/s41467-024-48778-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 05/13/2024] [Indexed: 06/12/2024] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are widely established as ubiquitous in the interstellar medium (ISM), but considering their prevalence in harsh vacuum environments, the role of ionisation in the formation of PAH clusters is poorly understood, particularly if a chirality-dependent aggregation route is considered. Here we report on photoelectron spectroscopy experiments on [4]helicene clusters performed with a vacuum ultraviolet synchrotron beamline. Aggregates (up to the heptamer) of [4]helicene, the smallest PAH with helical chirality, were produced and investigated with a combined experimental and theoretical approach using several state-of-the-art quantum-chemical methodologies. The ionisation onsets are extracted for each cluster size from the mass-selected photoelectron spectra and compared with calculations of vertical ionisation energies. We explore the complex aggregation topologies emerging from the multitude of isomers formed through clustering of P and M, the two enantiomers of [4]helicene. The very satisfactory benchmarking between experimental ionisation onsets vs. predicted ionisation energies allows the identification of theoretically predicted potential aggregation motifs and corresponding energetic ordering of chiral clusters. Our structural models suggest that a homochiral aggregation route is energetically favoured over heterochiral arrangements with increasing cluster size, hinting at potential symmetry breaking in PAH cluster formation at the scale of small grains.
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Affiliation(s)
- Sérgio R Domingos
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.
- CFisUC, Department of Physics, University of Coimbra, 3004-516, Coimbra, Portugal.
| | - Denis S Tikhonov
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.
| | - Amanda L Steber
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.
- Department of Physical Chemistry, Faculty of Science, University of Valladolid, 47011, Valladolid, Spain.
| | - Patrick Eschenbach
- Organisch-Chemisches Institut, University of Münster, 48149, Münster, Germany
- Center for Multiscale Theory and Computation (CMTC), University of Münster, 48149, Münster, Germany
| | - Sebastien Gruet
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Helgi R Hrodmarsson
- Synchrotron SOLEIL, L'Orme des Merisiers, 91192, Gif sur Yvette, Cedex, France
- LISA UMR 7583 Université Paris-Est Créteil and Université de Paris, Institut Pierre et Simon Laplace, 61 Avenue du Général de Gaulle, 94010, Créteil, France
| | - Kévin Martin
- Univ Angers, CNRS, MOLTECH-Anjou, SFR MATRIX, 49000, Angers, France
| | - Gustavo A Garcia
- Synchrotron SOLEIL, L'Orme des Merisiers, 91192, Gif sur Yvette, Cedex, France
| | - Laurent Nahon
- Synchrotron SOLEIL, L'Orme des Merisiers, 91192, Gif sur Yvette, Cedex, France
| | - Johannes Neugebauer
- Organisch-Chemisches Institut, University of Münster, 48149, Münster, Germany
- Center for Multiscale Theory and Computation (CMTC), University of Münster, 48149, Münster, Germany
| | - Narcis Avarvari
- Univ Angers, CNRS, MOLTECH-Anjou, SFR MATRIX, 49000, Angers, France
| | - Melanie Schnell
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.
- Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Max-Eyth-Str. 1, 24118, Kiel, Germany.
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43
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Cusumano AQ, Chaffin BC, Doyle AG. Mechanism of Ni-Catalyzed Photochemical Halogen Atom-Mediated C(sp 3)-H Arylation. J Am Chem Soc 2024; 146:15331-15344. [PMID: 38778454 PMCID: PMC11246173 DOI: 10.1021/jacs.4c03099] [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] [Indexed: 05/25/2024]
Abstract
Within the context of Ni photoredox catalysis, halogen atom photoelimination from Ni has emerged as a fruitful strategy for enabling hydrogen atom transfer (HAT)-mediated C(sp3)-H functionalization. Despite the numerous synthetic transformations invoking this paradigm, a unified mechanistic hypothesis that is consistent with experimental findings on the catalytic systems and accounts for halogen radical formation and facile C(sp2)-C(sp3) bond formation remains elusive. We employ kinetic analysis, organometallic synthesis, and computational investigations to decipher the mechanism of a prototypical Ni-catalyzed photochemical C(sp3)-H arylation reaction. Our findings revise the previous mechanistic proposals, first by examining the relevance of SET and EnT processes from Ni intermediates relevant to the HAT-based arylation reaction. Our investigation highlights the ability for blue light to promote efficient Ni-C(sp2) bond homolysis from cationic NiIII and C(sp2)-C(sp3) reductive elimination from bipyridine NiII complexes. However interesting, the rates and selectivities of these processes do not account for the productive catalytic pathway. Instead, our studies support a mechanism that involves halogen atom evolution from in situ generated NiII dihalide intermediates, radical capture by a NiII(aryl)(halide) resting state, and key C-C bond formation from NiIII. Oxidative addition to NiI, as opposed to Ni0, and rapid NiIII/NiI comproportionation play key roles in this process. The findings presented herein offer fundamental insight into the reactivity of Ni in the broader context of catalysis.
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Affiliation(s)
- Alexander Q Cusumano
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Braden C Chaffin
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Abigail G Doyle
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
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44
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Otlyotov AA, Moshchenkov AD, Minenkov Y. Ni, Cu, Zn, Pd, Ag and Cd Tetraphenylporphyrin Ab Initio Thermochemistry: Enthalpy of Formation of ZnTPP Revisited. Inorg Chem 2024; 63:10230-10239. [PMID: 38780084 DOI: 10.1021/acs.inorgchem.4c00662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Groups 10-12 metalloporphyrins have been recognized for their numerous properties essential for the development of new sensing materials. In this work, accurate gas-phase enthalpies of formation, ΔfHm0(g,298.15), are predicted for the series of Ni, Cu, Zn, Pd, Ag, and Cd tetraphenylporphyrins (MTPPs) on the basis of the reaction-based Feller-Peterson-Dixon approach and high-level ab initio DLPNO-CCSD(T) calculations. Our recently developed automatic generator of the balanced chemical reactions was employed to reduce the bias of the theoretical ΔfHm0(g,298.15) toward a particular reaction. Theoretical ΔfHm0(g,298.15) for ZnTPP (227.0 ± 3.4 kcal mol-1) does not support the previously reported experimental value of 132 ± 2 kcal mol-1. The origin of the discrepancy probably lies in the experimental solid-state ΔfHm0(ZnTPP, cr,298.15) as it stems from our theoretical evaluations of the ΔfHm0(cr,298.15) values for the entire set of transition metal TPP complexes. The large discrepancy between experiment and theory also holds when different DFT functionals (ωB97M-V, PBE0-D4, and B3LYP-D4) paired with quadruple-ζ quality basis sets are used for the theoretical calculations. Experimental revisiting of the solid-state enthalpy of formation of ZnTPP and analogue measurements for other transition metal TPPs are needed to resolve the observed discrepancy. Based on the predicted enthalpies of formation of MTPPs, the relative energies of the metal-ligand bonding are evaluated and the trends are compared to those for the complexes of the unsubstituted porphyrin with the same set of metals derived in [Can. J. Chem., 2009, 87, 1063]. According to both studies, Pd complexes exhibit the strongest bonding, while the Cd species are the least stable metallocomplexes within the considered series.
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Affiliation(s)
- Arseniy A Otlyotov
- N. N. Semenov Federal Research Center for Chemical Physics RAS, Kosygina Street 4, 119991 Moscow, Russian Federation
| | - Andrey D Moshchenkov
- N. N. Semenov Federal Research Center for Chemical Physics RAS, Kosygina Street 4, 119991 Moscow, Russian Federation
| | - Yury Minenkov
- N. N. Semenov Federal Research Center for Chemical Physics RAS, Kosygina Street 4, 119991 Moscow, Russian Federation
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45
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Wu H, Payne AM, Pang HW, Menon A, Grambow CA, Ranasinghe DS, Dong X, Grinberg Dana A, Green WH. Toward Accurate Quantum Mechanical Thermochemistry: (1) Extensible Implementation and Comparison of Bond Additivity Corrections and Isodesmic Reactions. J Phys Chem A 2024; 128:4335-4352. [PMID: 38752854 DOI: 10.1021/acs.jpca.4c00949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
Obtaining accurate enthalpies of formation of chemical species, ΔHf, often requires empirical corrections that connect the results of quantum mechanical (QM) calculations with the experimental enthalpies of elements in their standard state. One approach is to use atomization energy corrections followed by bond additivity corrections (BACs), such as those defined by Petersson et al. or Anantharaman and Melius. Another approach is to utilize isodesmic reactions (IDRs) as shown by Buerger et al. We implement both approaches in Arkane, an open-source software that can calculate species thermochemistry using results from various QM software packages. In this work, we collect 421 reference species from the literature to derive ΔHf corrections and fit atomization energy corrections and BACs for 15 commonly used model chemistries. We find that both types of BACs yield similar accuracy, although Anantharaman- and Melius-type BACs appear to generalize better. Furthermore, BACs tend to achieve better accuracy than IDRs for commonly used model chemistries, and IDRs can be less robust because of the sensitivity to the chosen reference species and reactions. Overall, Anantharaman- and Melius-type BACs are our recommended approach for achieving accurate QM corrections for enthalpies.
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Affiliation(s)
- Haoyang Wu
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - A Mark Payne
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Hao-Wei Pang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Angiras Menon
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Colin A Grambow
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Duminda S Ranasinghe
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Xiaorui Dong
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Alon Grinberg Dana
- Wolfson Department of Chemical Engineering and Grand Technion Energy Program, Technion─Israel Institute of Technology, Haifa 3200003, Israel
| | - William H Green
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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46
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Lechner MH, Papadopoulos A, Sivalingam K, Auer AA, Koslowski A, Becker U, Wennmohs F, Neese F. Code generation in ORCA: progress, efficiency and tight integration. Phys Chem Chem Phys 2024; 26:15205-15220. [PMID: 38767596 DOI: 10.1039/d4cp00444b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
An improved version of ORCA's automated generator environment (ORCA-AGE II) is presented. The algorithmic improvements and the move to C++ as the programming language lead to a performance gain of up to two orders of magnitude compared to the previously developed PYTHON toolchain. Additionally, the restructured modular design allows for far more complex code engines to be implemented readily. Importantly, we have realised an extremely tight integration with the ORCA host program. This allows for a workflow in which only the wavefunction Ansatz is part of the source code repository while all actual high-level code is generated automatically, inserted at the appropriate place in the host program before it is compiled and linked together with the hand written code parts. This construction ensures longevity and uniform code quality. Furthermore the new developments allow ORCA-AGE II to generate parallelised production-level code for highly complex theories, such as fully internally contracted multireference coupled-cluster theory (fic-MRCC) with an enormous number of contributing tensor contractions. We also discuss the automated implementation of nuclear gradients for arbitrary theories. All these improvements enable the implementation of theories that are too complex for the human mind and also reduce development times by orders of magnitude. We hope that this work enables researchers to concentrate on the intellectual content of the theories they develop rather than be concerned with technical details of the implementation.
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Affiliation(s)
- Marvin H Lechner
- Department of Molecular Theory and Spectroscopy, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.
| | - Anastasios Papadopoulos
- Department of Molecular Theory and Spectroscopy, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.
| | - Kantharuban Sivalingam
- Department of Molecular Theory and Spectroscopy, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.
| | - Alexander A Auer
- Department of Molecular Theory and Spectroscopy, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.
| | - Axel Koslowski
- Department of Molecular Theory and Spectroscopy, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.
| | - Ute Becker
- Department of Molecular Theory and Spectroscopy, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.
| | - Frank Wennmohs
- Department of Molecular Theory and Spectroscopy, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.
| | - Frank Neese
- Department of Molecular Theory and Spectroscopy, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.
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Zhang Q, Liu T, Guo Y, Zhang Y, Lv C, Zhang Y, Cao Z. Narrowband emission from fully-bridged triphenylamine derivatives: insights into effects of structure modification and pressure. Phys Chem Chem Phys 2024; 26:15559-15568. [PMID: 38757566 DOI: 10.1039/d4cp00906a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Triphenylamine derivatives with narrowband emission have attracted growing attention in purely organic thermally-activated fluorescence (TADF) materials owing to their enhanced color purity and flexible molecular design strategy. Combined time-dependent density functional theory (TD-DFT) and ONIOM (QM/MM) calculations indicate that the excellent planarity of the experimentally developed DQAO could result in gradually decreased intermolecular interactions in the aggregated state at ambient pressure and upon compression, which is unfavorable for suppressing structural relaxation and achieving narrowband emission in its non-doped practical application. Therefore, three structure-modified derivatives, DQAO-Cb, DQAO-Ph, and DQAO-PhCb, were theoretically designed by introducing the spherical o-carborane and dangling phenyl units positioned para to the N atom of the DQAO to provide additional geometrical distortion and steric hindrance. The explorations on the reported DQAO, OQAO, and SQAO found that small structural relaxations, suppressed low-frequency vibrations, and noticeable short-range charge-transfer (SR-CT) natures of DQAO and OQAO are responsible for their much narrower emission spectral full-width at half-maxima (FWHMs) compared to that of SQAO. Introducing the o-carborane unit directly at the para position of the N atom could result in additional scissoring and stretching vibrations of the corresponding DQAO-Cb while the presence of the phenyl unit in DQAO-Ph is beneficial for suppressing the high-frequency vibrations of the pristine DQAO. More importantly, the bridged phenyl unit incorporated in DQAO-PhCb is of particular importance to inhibit the undesired low-frequency scissoring and high-frequency stretching vibrations of the o-carborane unit, which is crucial to reduce the reorganization energy of DQAO-PhCb and achieve narrowband emission. Also, the phenyl unit in DQAO-Ph and DQAO-PhCb helps to shorten charge transfer distances and improve ISC and RISC processes. Since the o-carborane unit is an adopted building block to achieve piezochromic behaviors, the theoretically structure-modified DQAO-PhCb is expected to exhibit narrowband emission, TADF, and piezochromic features all together. Our findings will hopefully provide ideas for designing triphenylamine-based TADF emitters with narrowband emission and piezochromic behaviors.
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Affiliation(s)
- Qing Zhang
- Department of Materials Chemistry, Huzhou University, Huzhou, 313000, People's Republic of China.
| | - Tao Liu
- Department of Materials Chemistry, Huzhou University, Huzhou, 313000, People's Republic of China.
| | - Yuhua Guo
- Department of Materials Chemistry, Huzhou University, Huzhou, 313000, People's Republic of China.
| | - Yujian Zhang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, Jinhua 321004, People's Republic of China
| | - Chunyan Lv
- Department of Materials Chemistry, Huzhou University, Huzhou, 313000, People's Republic of China.
| | - Yue Zhang
- School of Intelligent Manufacturing, Huzhou College, Huzhou, 313000, People's Republic of China.
| | - Zexing Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, People's Republic of China.
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48
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Gómez S, Flórez E, Acelas N, Cappelli C, Hadad C, Restrepo A. Encapsulation of charged halogens by the 5 12 water cage. Phys Chem Chem Phys 2024; 26:15426-15436. [PMID: 38747303 DOI: 10.1039/d4cp01340a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
This study focuses on the encapsulation of the entire series of halides by the 512 cage of twenty water molecules and on the characterization of water to water and water to anion interactions. State-of-the-art computations are used to determine equilibrium geometries, energy related quantities, and thermal stability towards dissociation and to dissect the nature and strength of intermolecular interactions holding the clusters as stable units. Two types of structures are revealed: heavily deformed cages for F- indicating a preference for microsolvation, and slightly deformed cages for the remaining anions indicating a preference for encapsulation. The primary variable dictating the properties of the clusters is the charge density of the central halide, with the most severe effects observed for the F- case. For the remaining halides, the anion may be safely viewed as a sort of "big electron" with little local disruptive power, enough to affect the network of non-covalent hydrogen bonds in the cage, but not enough to break it. Gibbs energies for dissociation either into cavity and halide or into water molecules and halide suggest that, in a similar way as to methane clathrate, a more weakly bonded complex that has been detected in the gas phase, all halide containing clathrate-like structures should be amenable to experimental detection in the gas phase at moderate temperature and pressure conditions.
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Affiliation(s)
- Sara Gómez
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy.
| | - Elizabeth Flórez
- Grupo de Materiales con Impacto, Mat&mpac. Facultad de Ciencias Básicas, Universidad de Medellín, Carrera 87 No. 30-65, 050026 Medellín, Colombia
| | - Nancy Acelas
- Grupo de Materiales con Impacto, Mat&mpac. Facultad de Ciencias Básicas, Universidad de Medellín, Carrera 87 No. 30-65, 050026 Medellín, Colombia
| | - Chiara Cappelli
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy.
| | - Cacier Hadad
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia.
| | - Albeiro Restrepo
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia.
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Duignan TT. The Potential of Neural Network Potentials. ACS PHYSICAL CHEMISTRY AU 2024; 4:232-241. [PMID: 38800721 PMCID: PMC11117678 DOI: 10.1021/acsphyschemau.4c00004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/04/2024] [Accepted: 03/05/2024] [Indexed: 05/29/2024]
Abstract
In the next half-century, physical chemistry will likely undergo a profound transformation, driven predominantly by the combination of recent advances in quantum chemistry and machine learning (ML). Specifically, equivariant neural network potentials (NNPs) are a breakthrough new tool that are already enabling us to simulate systems at the molecular scale with unprecedented accuracy and speed, relying on nothing but fundamental physical laws. The continued development of this approach will realize Paul Dirac's 80-year-old vision of using quantum mechanics to unify physics with chemistry and providing invaluable tools for understanding materials science, biology, earth sciences, and beyond. The era of highly accurate and efficient first-principles molecular simulations will provide a wealth of training data that can be used to build automated computational methodologies, using tools such as diffusion models, for the design and optimization of systems at the molecular scale. Large language models (LLMs) will also evolve into increasingly indispensable tools for literature review, coding, idea generation, and scientific writing.
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50
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Pesara P, Szafran K, Nguyen HC, Sirohiwal A, Pantazis DA, Gabruk M. Elucidating substrate binding in the light-dependent protochlorophyllide oxidoreductase. Chem Sci 2024; 15:7767-7780. [PMID: 38784751 PMCID: PMC11110527 DOI: 10.1039/d4sc00923a] [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: 02/06/2024] [Accepted: 04/23/2024] [Indexed: 05/25/2024] Open
Abstract
The Light-Dependent Protochlorophyllide Oxidoreductase (LPOR) catalyzes a crucial step in chlorophyll biosynthesis: the rare biological photocatalytic reduction of the double C[double bond, length as m-dash]C bond in the precursor, protochlorophyllide (Pchlide). Despite its fundamental significance, limited structural insights into the active complex have hindered understanding of its reaction mechanism. Recently, a high-resolution cryo-EM structure of LPOR in its active conformation challenged our view of pigment binding, residue interactions, and the catalytic process. Surprisingly, this structure contrasts markedly with previous assumptions, particularly regarding the orientation of the bound Pchlide. To gain insights into the substrate binding puzzle, we conducted molecular dynamics simulations, quantum-mechanics/molecular-mechanics (QM/MM) calculations, and site-directed mutagenesis. Two Pchlide binding modes were considered, one aligning with historical proposals (mode A) and another consistent with the recent experimental data (mode B). Binding energy calculations revealed that in contrast to the non-specific interactions found for mode A, mode B exhibits distinct stabilizing interactions that support more thermodynamically favorable binding. A comprehensive analysis incorporating QM/MM-based local energy decomposition unraveled a complex interaction network involving Y177, H319, and the C131 carboxy group, influencing the pigment's excited state energy and potentially contributing to substrate specificity. Importantly, our results uniformly favor mode B, challenging established interpretations and emphasizing the need for a comprehensive re-evaluation of the LPOR reaction mechanism in a way that incorporates accurate structural information on pigment interactions and substrate-cofactor positioning in the binding pocket. The results shed light on the intricacies of LPOR's catalytic mechanism and provide a solid foundation for further elucidating the secrets of chlorophyll biosynthesis.
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Affiliation(s)
- Penelope Pesara
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
| | - Katarzyna Szafran
- Department of Plant Physiology and Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Gronostajowa 7 30-387 Cracow Poland
| | - Henry C Nguyen
- Department of Biochemistry & Biophysics, Quantitative Biosciences Institute, University of California San Francisco CA USA
| | - Abhishek Sirohiwal
- Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University 10691 Stockholm Sweden
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
| | - Michal Gabruk
- Department of Plant Physiology and Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Gronostajowa 7 30-387 Cracow Poland
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