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Fleck M, Kopp WA, Viswanathan N, Hansen N, Gross J, Leonhard K. Efficient Generation of Torsional Energy Profiles by Multifidelity Gaussian Processes for Hindered Rotor Corrections. J Chem Theory Comput 2024; 20:7574-7585. [PMID: 39163246 DOI: 10.1021/acs.jctc.4c00475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2024]
Abstract
Accurate thermochemistry computations often require proper treatment of torsional modes. The one-dimensional hindered rotor model has proven to be a computationally efficient solution, given a sufficiently accurate potential energy surface. Methods that provide potential energies at various compromises of uncertainty and computational time demand can be optimally combined within a multifidelity treatment. In this study, we demonstrate how multifidelity modeling leads to (1) smooth interpolation along low-fidelity scan points with uncertainty estimates, (2) inclusion of high-fidelity data that change the energetic order of conformations, and (3) predicting best next-point calculations to extend an initial coarse grid. Our diverse application set comprises molecules, clusters, and transition states of alcohols, ethers, and rings. We discuss limitations for cases in which the low-fidelity computation is highly unreliable. Different features of the potential energy curve affect different quantities. To obtain "optimal" fits, we apply strategies ranging from simple minimization of deviations to developing an acquisition function tailored for statistical thermodynamics. Bayesian prediction of best next calculations can save a substantial amount of computation time for one- and multidimensional hindered rotors.
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Affiliation(s)
- Maximilian Fleck
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Pfaffenwaldring 9, 70569 Stuttgart, Germany
| | - Wassja A Kopp
- Institute of Technical Thermodynamics, RWTH Aachen University, Schinkelstr. 8, 52062 Aachen, Germany
| | - Narasimhan Viswanathan
- Institute of Technical Thermodynamics, RWTH Aachen University, Schinkelstr. 8, 52062 Aachen, Germany
| | - Niels Hansen
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Pfaffenwaldring 9, 70569 Stuttgart, Germany
| | - Joachim Gross
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Pfaffenwaldring 9, 70569 Stuttgart, Germany
| | - Kai Leonhard
- Institute of Technical Thermodynamics, RWTH Aachen University, Schinkelstr. 8, 52062 Aachen, Germany
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2
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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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3
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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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4
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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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Kulsha AV, Ivashkevich OA, Lyakhov DA, Michels D. Strong Bases Design: Key Techniques and Stability Issues. Int J Mol Sci 2024; 25:8716. [PMID: 39201404 PMCID: PMC11354936 DOI: 10.3390/ijms25168716] [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: 07/24/2024] [Revised: 08/06/2024] [Accepted: 08/08/2024] [Indexed: 09/02/2024] Open
Abstract
Theoretical design of molecular superbases has been attracting researchers for more than twenty years. General approaches were developed to make the bases potentially stronger, but less attention was paid to the stability of the predicted structures. Hence, only a small fraction of the theoretical research has led to positive experimental results. Possible stability issues of extremely strong bases are extensively studied in this work using quantum chemical calculations on a high level of theory. Several step-by-step design examples are discussed in detail, and general recommendations are given to avoid the most common stability problems. New potentially stable structures are theoretically studied to demonstrate the future prospects of molecular superbases design.
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Affiliation(s)
- Andrey V. Kulsha
- Chemical Department, Belarusian State University, 14 Leningradskaya Str., 220006 Minsk, Belarus;
| | - Oleg A. Ivashkevich
- Research Institute for Physical Chemical Problems, Belarusian State University, 14 Leningradskaya Str., 220006 Minsk, Belarus
| | - Dmitry A. Lyakhov
- Computer, Electrical and Mathematical Science and Engineering Division, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; (D.A.L.); (D.M.)
| | - Dominik Michels
- Computer, Electrical and Mathematical Science and Engineering Division, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; (D.A.L.); (D.M.)
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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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7
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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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8
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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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9
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Menezes HNS, Júnior HCS, Ferreira GB. Ab initio investigation of the geometrical behavior in solution and electronic structure of the anion complexes [bis(1,3-dithiole-2-thione-4,5-dithiolate)M], for M = Bi(III), Sb(III), and Zn(II). J Mol Model 2024; 30:258. [PMID: 38976085 DOI: 10.1007/s00894-024-06052-6] [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: 03/01/2024] [Accepted: 06/27/2024] [Indexed: 07/09/2024]
Abstract
CONTEXT 1,3-Dithiole-2-thione-4,5-dithiolate (dmit) ligands are known for their conductive and optical properties. Dmit compounds have been assessed for use in sensor devices, information storage, spintronics, and optical material applications. Associations with various metallic centers endow dmit complexes with magnetic, optical, conductive, and antioxidant properties. Optical doping can facilitate the fabrication of magnetic conductor materials from ground-state nonmagnetic cations. While most studied complexes involve transition-metal centers due to their diverse chemistry, compounds with representative elements are less explored in the literature. This study investigated the structural and electronic properties of bisdmit complexes with representative Bi(III), Sb(III), and Zn(II) cations. AIMD calculations revealed two new geometries for Bi(III) and Zn(II) complexes, diverging from the isolated geometry typically used in quantum chemical calculations. The coordination of acetonitrile molecules to the cationic centers of the complexes resulted in unstable structures, while the dimerization of the complexes was stable. SA-CASSCF/NEVPT2 calculations were applied to the structures of the isolated complexes and stable dimers, confirming the multireference character of the electronic structure of the three systems and the multiconfigurational character of the Bi(III) complex. The electronic spectra simulated by the STEOM-DLPNO-CCSD calculations accurately reproduced the experimental UV‒Vis spectra indicating the participation of the isolated Bi(III) dmit complex and its dimeric form in solution. METHODOLOGY AIMD calculations of the dmit salts were conducted using the GFN2-xTB method with 60 explicit acetonitrile molecules as the solvent at 300 K for a total simulation time of 50.0 ps, with printing intervals of 0.5 fs. The final geometries were optimized employing the PBEh-3c compound method, incorporating implicit conductor-like polarizable continuum model (CPCM) solvation for acetonitrile. Local energy decomposition (LED) analysis at the DLPNO-CCSD(T)/Def2-TZVP level of theory was utilized to investigate the stability of the complex geometries identified by AIMD. The electronic structures of the complexes were assessed using the SA-CASSCF/NEVPT2/Def2-TZVP method to confirm the multiconfigurational and multireference nature of their electronic structures. Electronic spectra were analyzed using the STEOM-DLPNO-CCSD/Def2-TZVP method, with CPCM used to simulate an acetonitrile medium.
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Affiliation(s)
- Heloisa N S Menezes
- Departamento de Química Inorgânica, Instituto de Química, Universidade Federal Fluminense, Outeiro de S. João Batista s/n., Centro, Niterói, RJ, 24210-130, Brazil
| | - Henrique C S Júnior
- Programa de Pós-Graduação em Química, Instituto de Química, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, Agronomia, Porto Alegre, RS, 90650-001, Brazil
| | - Glaucio B Ferreira
- Departamento de Química Inorgânica, Instituto de Química, Universidade Federal Fluminense, Outeiro de S. João Batista s/n., Centro, Niterói, RJ, 24210-130, Brazil.
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10
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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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11
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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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12
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Mihrin D, Feilberg KL, Larsen RW. Self-Association and Microhydration of Phenol: Identification of Large-Amplitude Hydrogen Bond Librational Modes. Molecules 2024; 29:3012. [PMID: 38998964 PMCID: PMC11243154 DOI: 10.3390/molecules29133012] [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: 06/17/2024] [Accepted: 06/19/2024] [Indexed: 07/14/2024] Open
Abstract
The self-association mechanisms of phenol have represented long-standing challenges to quantum chemical methodologies owing to the competition between strongly directional intermolecular hydrogen bonding, weaker non-directional London dispersion forces and C-H⋯π interactions between the aromatic rings. The present work explores these subtle self-association mechanisms of relevance for biological molecular recognition processes via spectroscopic observations of large-amplitude hydrogen bond librational modes of phenol cluster molecules embedded in inert neon "quantum" matrices complemented by domain-based local pair natural orbital-coupled cluster DLPNO-CCSD(T) theory. The spectral signatures confirm a primarily intermolecular O-H⋯H hydrogen-bonded structure of the phenol dimer strengthened further by cooperative contributions from inter-ring London dispersion forces as supported by DLPNO-based local energy decomposition (LED) predictions. In the same way, the hydrogen bond librational bands observed for the trimeric cluster molecule confirm a pseudo-C3 symmetric cyclic cooperative hydrogen-bonded barrel-like potential energy minimum structure. This structure is vastly different from the sterically favored "chair" conformations observed for aliphatic alcohol cluster molecules of the same size owing to the additional stabilizing London dispersion forces and C-H⋯π interactions between the aromatic rings. The hydrogen bond librational transition observed for the phenol monohydrate finally confirms that phenol acts as a hydrogen bond donor to water in contrast to the hydrogen bond acceptor role observed for aliphatic alcohols.
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Affiliation(s)
- Dmytro Mihrin
- Department of Chemistry, Technical University of Denmark, Kemitorvet 206, 2800 Kongens Lyngby, Denmark
- DTU Offshore, Technical University of Denmark, Elektrovej 375, 2800 Kongens Lyngby, Denmark
| | - Karen Louise Feilberg
- DTU Offshore, Technical University of Denmark, Elektrovej 375, 2800 Kongens Lyngby, Denmark
| | - René Wugt Larsen
- Department of Chemistry, Technical University of Denmark, Kemitorvet 206, 2800 Kongens Lyngby, Denmark
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13
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Willrett J, Schmitt M, Zhuravlev V, Sellin M, Malinowski PJ, Krossing I. Synthesis and Characterization of a Copper Dinitrogen Complex Supported by a Weakly Coordinating Anion. Angew Chem Int Ed Engl 2024:e202405330. [PMID: 38859637 DOI: 10.1002/anie.202405330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/06/2024] [Accepted: 06/06/2024] [Indexed: 06/12/2024]
Abstract
We report the synthesis and full characterization of the copper dinitrogen complex [(η1-N2)Cu{Al(ORF)4}] 2 (RF=C(CF3)3) prepared by a cascade metathesis reaction of Ag[Al(ORF)4] with CuI-excess in iso-perfluorohexane (i-pfh) under N2 atmosphere. Title compound 2 features an extraordinarily high N2 stretching frequency at 2313/2314 cm-1 (IR/Raman) and was characterized by single-crystal and powder X-ray diffractometry. Quantum chemical charge displacement analysis based on natural orbitals of chemical valence (CD-NOCV) indicates that the copper-dinitrogen interaction is still governed by weak π-backdonation, but is significantly reduced compared to all literature-known transition metal dinitrogen complexes.
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Affiliation(s)
- Julie Willrett
- Institut für Anorganische und Analytische Chemie and Freiburger Materialforschungszentrum (FMF), Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Manuel Schmitt
- Institut für Anorganische und Analytische Chemie and Freiburger Materialforschungszentrum (FMF), Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
- Anorganisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Vadim Zhuravlev
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02097, Warsaw, Poland
| | - Malte Sellin
- Institut für Anorganische und Analytische Chemie and Freiburger Materialforschungszentrum (FMF), Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, 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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14
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Bensberg M, Reiher M. Uncertainty-Aware First-Principles Exploration of Chemical Reaction Networks. J Phys Chem A 2024; 128:4532-4547. [PMID: 38787736 PMCID: PMC11163430 DOI: 10.1021/acs.jpca.3c08386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 05/13/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024]
Abstract
Exploring large chemical reaction networks with automated exploration approaches and accurate quantum chemical methods can require prohibitively large computational resources. Here, we present an automated exploration approach that focuses on the kinetically relevant part of the reaction network by interweaving (i) large-scale exploration of chemical reactions, (ii) identification of kinetically relevant parts of the reaction network through microkinetic modeling, (iii) quantification and propagation of uncertainties, and (iv) reaction network refinement. Such an uncertainty-aware exploration of kinetically relevant parts of a reaction network with automated accuracy improvement has not been demonstrated before in a fully quantum mechanical approach. Uncertainties are identified by local or global sensitivity analysis. The network is refined in a rolling fashion during the exploration. Moreover, the uncertainties are considered during kinetically steering of a rolling reaction network exploration. We demonstrate our approach for Eschenmoser-Claisen rearrangement reactions. The sensitivity analysis identifies that only a small number of reactions and compounds are essential for describing the kinetics reliably, resulting in efficient explorations without sacrificing accuracy and without requiring prior knowledge about the chemistry unfolding.
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Affiliation(s)
- Moritz Bensberg
- Department of Chemistry and Applied
Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Markus Reiher
- Department of Chemistry and Applied
Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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15
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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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16
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Abeywardane K, Goldsmith CF. Accurate Enthalpies of Formation for PFAS from First-Principles: Combining Different Levels of Theory in a Generalized Thermochemical Hierarchy. ACS PHYSICAL CHEMISTRY AU 2024; 4:247-258. [PMID: 38800729 PMCID: PMC11117692 DOI: 10.1021/acsphyschemau.3c00056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 05/29/2024]
Abstract
The enthalpies of formation are computed for a large number of per- and poly fluoroalkyl substances (PFAS) using a connectivity-based hierarchy (CBH) approach. A combination of different electronic structure methods are used to provide the reference data in a hierarchical manner. The ANL0 method, in conjunction with the active thermochemical tables, provides enthalpies of formation for smaller species with subchemical accuracy. Coupled-cluster theory with explicit correlations are used to compute enthalpies of formation for intermediate species, based upon the ANL0 results. For the largest PFAS, including perfluorooctanoic acid (PFOA) and heptafluoropropylene oxide dimer acid (GenX), coupled-cluster theory with local correlations is used. The sequence of homodesmotic reactions proposed by the CBH are determined automatically by a new open-source code, AutoCBH. The results are the first reported enthalpies of formation for the majority of the species. A convergence analysis and global uncertainty quantification confirm that the enthalpies of formation at 0 K should be accurate to within ±5 kJ/mol. This new approach is not limited to PFAS, but can be applied to many chemical systems.
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Affiliation(s)
- Kento Abeywardane
- Chemical Engineering Group, School
of Engineering, Brown University, Providence, Rhode Island 02912, United States
| | - C. Franklin Goldsmith
- Chemical Engineering Group, School
of Engineering, Brown University, Providence, Rhode Island 02912, United States
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17
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Pasik D, Frandsen BN, Meder M, Iyer S, Kurtén T, Myllys N. Gas-Phase Oxidation of Atmospherically Relevant Unsaturated Hydrocarbons by Acyl Peroxy Radicals. J Am Chem Soc 2024; 146:13427-13437. [PMID: 38712858 PMCID: PMC11389977 DOI: 10.1021/jacs.4c02523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
This study assesses the atmospheric impact of reactions between unsaturated hydrocarbons such as isoprene and monoterpenes and peroxy radicals containing various functional groups. We find that reactions between alkenes and acyl peroxy radicals have reaction rates high enough to be feasible in the atmosphere and lead to high molar mass accretion products. Moreover, the reaction between unsaturated hydrocarbons and acyl peroxy radicals leads to an alkyl radical, to which molecular oxygen rapidly adds. This finding is confirmed by both theoretical calculations and experiments. The formed perester peroxy radical may either undergo further H-shift reactions or react bimolecularly. The multifunctional oxygenated compounds formed through acyl peroxy radical + alkene reactions are potentially important contributors to particle formation and growth. Thus, acyl peroxy radical-initiated oxidation chemistry may need to be included in atmospheric models.
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Affiliation(s)
- Dominika Pasik
- Department of Chemistry, University of Helsinki, Helsinki 00014, Finland
- Institute for Atmospheric and Earth System Research, University of Helsinki, Helsinki 00014, Finland
| | - Benjamin N Frandsen
- Department of Chemistry, University of Helsinki, Helsinki 00014, Finland
- Aerosol Physics Laboratory, Tampere University, Tampere 33014, Finland
| | - Melissa Meder
- Institute for Atmospheric and Earth System Research, University of Helsinki, Helsinki 00014, Finland
| | - Siddharth Iyer
- Aerosol Physics Laboratory, Tampere University, Tampere 33014, Finland
| | - Theo Kurtén
- Department of Chemistry, University of Helsinki, Helsinki 00014, Finland
- Institute for Atmospheric and Earth System Research, University of Helsinki, Helsinki 00014, Finland
| | - Nanna Myllys
- Department of Chemistry, University of Helsinki, Helsinki 00014, Finland
- Institute for Atmospheric and Earth System Research, University of Helsinki, Helsinki 00014, Finland
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18
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Zheng Y, Ni Z, Wang Y, Li W, Li S. Analytical Gradient Using Cluster-in-Molecule RI-MP2 Method for the Geometry Optimizations of Large Systems. J Chem Theory Comput 2024; 20:3626-3636. [PMID: 38626287 DOI: 10.1021/acs.jctc.4c00087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2024]
Abstract
We present an efficient analytical energy gradient algorithm for the cluster-in-molecule resolution-of-identity second-order Møller-Plesset perturbation (CIM-RI-MP2) method based on the Lagrange multiplier method. Our algorithm independently constructs the Lagrangian formalism within each cluster, avoiding the solution of the coupled-perturbed Hartree-Fock (CPHF) equation for the whole system. Due to this feature, the computational cost of the CIM-RI-MP2 gradients is much lower than that of other local MP2 algorithms. Benchmark calculations of several molecules containing up to 312 atoms demonstrate the general applicability of our CIM-RI-MP2 gradient algorithm. The optimized structure of a 244-atom molecule using the CIM-RI-MP2 method with the cc-pVDZ basis set is in good agreement with the corresponding crystal structure. A single-point gradient calculation conducted for a molecular cage containing 972 atoms and 9612 basis functions takes 48 h on 25 nodes, utilizing a total of 600 CPU cores. The present CIM-RI-MP2 gradient program is applicable for obtaining the optimized geometries of large systems with hundreds of atoms.
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Affiliation(s)
- Yang Zheng
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, New Cornerstone Science Laboratory, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Zhigang Ni
- College of Material, Chemistry and Chemical Engineering, Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education, Hangzhou Normal University, Hangzhou 311121, P. R. China
| | - Yuqi Wang
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, New Cornerstone Science Laboratory, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Wei Li
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, New Cornerstone Science Laboratory, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Shuhua Li
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, New Cornerstone Science Laboratory, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
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19
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Remmerswaal WA, de Jong T, van de Vrande KNA, Louwersheimer R, Verwaal T, Filippov DV, Codée JDC, Hansen T. Backside versus Frontside S N2 Reactions of Alkyl Triflates and Alcohols. Chemistry 2024; 30:e202400590. [PMID: 38385647 DOI: 10.1002/chem.202400590] [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: 02/20/2024] [Accepted: 02/22/2024] [Indexed: 02/23/2024]
Abstract
Nucleophilic substitution reactions are elementary reactions in organic chemistry that are used in many synthetic routes. By quantum chemical methods, we have investigated the intrinsic competition between the backside SN2 (SN2-b) and frontside SN2 (SN2-f) pathways using a set of simple alkyl triflates as the electrophile in combination with a systematic series of phenols and partially fluorinated ethanol nucleophiles. It is revealed how and why the well-established mechanistic preference for the SN2-b pathway slowly erodes and can even be overruled by the unusual SN2-f substitution mechanism going from strong to weak alcohol nucleophiles. Activation strain analyses disclose that the SN2-b pathway is favored for strong alcohol nucleophiles because of the well-known intrinsically more efficient approach to the electrophile resulting in a more stabilizing nucleophile-electrophile interaction. In contrast, the preference of weaker alcohol nucleophiles shifts to the SN2-f pathway, benefiting from a stabilizing hydrogen bond interaction between the incoming alcohol and the leaving group. This hydrogen bond interaction is strengthened by the increased acidity of the weaker alcohol nucleophiles, thereby steering the mechanistic preference toward the frontside SN2 pathway.
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Affiliation(s)
- Wouter A Remmerswaal
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The, Netherlands
| | - Tjeerd de Jong
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The, Netherlands
| | - Koen N A van de Vrande
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The, Netherlands
| | - Rick Louwersheimer
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The, Netherlands
| | - Thomas Verwaal
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The, Netherlands
| | - Dmitri V Filippov
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The, Netherlands
| | - Jeroen D C Codée
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The, Netherlands
| | - Thomas Hansen
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The, Netherlands
- Department of Chemistry and Pharmaceutical Sciences, AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The, Netherlands
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20
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Meyer KAE, Garand E. The impact of solvation on the structure and electric field strength in Li +GlyGly complexes. Phys Chem Chem Phys 2024; 26:12406-12421. [PMID: 38623633 DOI: 10.1039/d3cp06264c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
To scrutinise the impact of electric fields on the structure and vibrations of biomolecules in the presence of water, we study the sequential solvation of lithium diglycine up to three water molecules with cryogenic infrared action spectroscopy. Conformer-specific IR-IR spectroscopy and H2O/D2O isotopic substitution experiments provide most of the information required to decipher the structure of the observed conformers. Additional confirmation is provided by scaled harmonic vibrational frequency calculations using MP2 and DFT. The first water molecule is shown to bind to the Li+ ion, which weakens the electric field experienced by the peptide and as a consequence, also the strength of an internal NH⋯NH2 hydrogen bond in the diglycine backbone. The strength of this hydrogen bond decreases approximately linearly with the number of water molecules as a result of the decreasing electric field strength and coincides with an increase in the number of conformers observed in our spectra. The addition of two water molecules is already sufficient to change the preferred conformation of the peptide backbone, allowing for Li+ coordination to the lone pair of the terminal amine group.
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Affiliation(s)
- Katharina A E Meyer
- University of Wisconsin-Madison, Department of Chemistry, 1101 University Ave, Madison, WI 53706, USA.
| | - Etienne Garand
- University of Wisconsin-Madison, Department of Chemistry, 1101 University Ave, Madison, WI 53706, USA.
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21
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Huang GT, Yu JSK. Catalytic role of the enol ether intermediate in the intramolecular Stetter reaction: a computational perspective. Phys Chem Chem Phys 2024; 26:11833-11853. [PMID: 38567403 DOI: 10.1039/d3cp06051a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The intramolecular Stetter reaction catalyzed by a carbene is investigated by density functional theory (DFT) calculations and kinetic simulations. Catalyst 1 first reacts with aldehyde 2 to give the primary adduct (PA). The PA undergoes the intramolecular oxa-Michael reaction to irreversibly generate enol ether intermediate 9. The conversion of the enol ether to the Breslow intermediate (BI) requires the assistance of a base such as the PA. The next step involves formation of a carbon-carbon bond through the Michael addition, and expulsion of the catalyst generates the Stetter product 7. Calculations show that the catalytic cycle is composed of two irreversible processes: the first one involves the exergonic formation of the enol ether intermediate, while the second one is the conversion of the enol ether to the final product. Kinetic simulations using initial concentrations of [1]0 = 0.005 M and [2]0 = 0.025 M demonstrate that under a steady-state condition, 35% of the catalyst rests on the state of the enol ether (0.0018 M). The catalyst resting state therefore consists of the unbound form (the free catalyst) and its bound form (the enol ether species). According to variable time normalization analysis, the reaction exhibits a second-order dependence (first order in catalyst and first order in substrate), which agrees with experiments. The oxa-Michael reaction to form the enol ether is identified to be turnover limiting in the intramolecular Stetter reaction, which rationalizes the observed electronic effect of the Michael acceptor on the reactivity, as well as the measured isotope effect with respect to the aldehydic proton/deuteron. The base that participates in the BI formation has a significant effect on the build-up of the resting state 9 and the active catalyst concentration. In addition, the thermodynamic stability of the enol ether is found to depend on the tether length between the aromatic aldehyde and the Michael acceptor, as well as the chemical nature of the carbene catalyst. The favorability for the oxa-Michael reaction is therefore suggested to govern the reactivity of the intramolecular Stetter transformation.
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Affiliation(s)
- Gou-Tao Huang
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu City 300, Taiwan.
| | - Jen-Shiang K Yu
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu City 300, Taiwan.
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu City 300, Taiwan
- Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu City 300, Taiwan
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22
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Yu Y, Pan L, Sun Q, Wang J. The mechanism and kinetics of the atmospheric oxidation of CF 3(CF 2) 2CHCH 2 (HFC-1447fz) by hydroxyl radicals: ab initio investigation. Phys Chem Chem Phys 2024; 26:10989-10997. [PMID: 38526437 DOI: 10.1039/d3cp06149c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
The oxidation of 3,3,4,4,5,5,5-heptafluoro-1-pentene (HFC-1447fz) by hydroxyl radicals plays a crucial role in atmospheric conditions. By employing the CCSD(T)/cc-pVTZ//M06-2X/6-311++G(d,p) level of theory, the detailed reaction mechanism, kinetics and atmospheric implications of the degradation of HFC-1447fz by hydroxyl radicals were investigated. Compared to H-abstraction channels, the OH addition reaction is determined to be more favorable initial pathways in the degradation processes of HFC-1447fz. The overall rate coefficient of the degradation of HFC-1447fz by OH radicals is estimated to be 1.66 × 10-12 cm3 molecule-1 s-1 and the lifetime of HFC-1447fz is found to be 7 days at 298 K, which are in good agreement with the reported experimental results. The global warming potential (GWP) for HFC-1447fz on the 50, 100 and 500-year time horizons is estimated using the calculated rate coefficient. Furthermore, the mechanisms of the subsequent reactions of two OH-addition adducts have also been investigated. By TD-DFT calculations, it was found that eleven species can undergo photodissociation, while ten other species are photolytically stable under sunlight.
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Affiliation(s)
- Youqing Yu
- Green Intelligence Environmental School, Yangtze Normal University, Chongqing 408100, China.
| | - Li Pan
- Chongqing Medical and Health School, Chongqing 408100, China
| | - Qiyao Sun
- Green Intelligence Environmental School, Yangtze Normal University, Chongqing 408100, China.
| | - Jie Wang
- Green Intelligence Environmental School, Yangtze Normal University, Chongqing 408100, China.
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23
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Rummel L, Schreiner PR. Advances and Prospects in Understanding London Dispersion Interactions in Molecular Chemistry. Angew Chem Int Ed Engl 2024; 63:e202316364. [PMID: 38051426 DOI: 10.1002/anie.202316364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 12/03/2023] [Accepted: 12/05/2023] [Indexed: 12/07/2023]
Abstract
London dispersion (LD) interactions are the main contribution of the attractive part of the van der Waals potential. Even though LD effects are the driving force for molecular aggregation and recognition, the role of these omnipresent interactions in structure and reactivity had been largely underappreciated over decades. However, in the recent years considerable efforts have been made to thoroughly study LD interactions and their potential as a chemical design element for structures and catalysis. This was made possible through a fruitful interplay of theory and experiment. This review highlights recent results and advances in utilizing LD interactions as a structural motif to understand and utilize intra- and intermolecularly LD-stabilized systems. Additionally, we focus on the quantification of LD interactions and their fundamental role in chemical reactions.
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Affiliation(s)
- Lars Rummel
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
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24
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Li H, Mansoori Kermani M, Ottochian A, Crescenzi O, Janesko BG, Truhlar DG, Scalmani G, Frisch MJ, Ciofini I, Adamo C. Modeling Multi-Step Organic Reactions: Can Density Functional Theory Deliver Misleading Chemistry? J Am Chem Soc 2024; 146:6721-6732. [PMID: 38413362 DOI: 10.1021/jacs.3c12713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Many organic reactions are characterized by a complex mechanism with a variety of transition states and intermediates of different chemical natures. Their correct and accurate theoretical characterization critically depends on the accuracy of the computational method used. In this work, we study a complex ambimodal cycloaddition with five transition states, two intermediates, and three products, and we ask whether density functional theory (DFT) can provide a correct description of this type of complex and multifaceted reaction. Our work fills a gap in that most systematic benchmarks of DFT for chemical reactions have considered much simpler reactions. Our results show that many density functionals not only lead to seriously large errors but also differ from one another in predicting whether the reaction is ambimodal. Only a few of the available functionals provide a balanced description of the complex and multifaceted reactions. The parameters varied in the tested functionals are the ingredients, the treatment of medium-range and nonlocal correlation energy, and the inclusion of Hartree-Fock exchange. These results show a clear need for more benchmarks on the mechanisms of large molecules in complex reactions.
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Affiliation(s)
- Hanwei Li
- Chimie ParisTech, PSL Research University, CNRS, Institute of Chemistry for Life and Health Sciences, Paris F-75005, France
| | - Maryam Mansoori Kermani
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Alistar Ottochian
- Chimie ParisTech, PSL Research University, CNRS, Institute of Chemistry for Life and Health Sciences, Paris F-75005, France
| | - Orlando Crescenzi
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cinthia, Napoli 80126, Italy
| | - Benjamin G Janesko
- Department of Chemistry & Biochemistry, Texas Christian University, Fort Worth, Texas 76129, United States
| | - Donald G Truhlar
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | | | | | - Ilaria Ciofini
- Chimie ParisTech, PSL Research University, CNRS, Institute of Chemistry for Life and Health Sciences, Paris F-75005, France
| | - Carlo Adamo
- Chimie ParisTech, PSL Research University, CNRS, Institute of Chemistry for Life and Health Sciences, Paris F-75005, France
- Institut Universitaire de France, 103 Boulevard Saint Michel, Paris F-75005, France
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25
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Hillers-Bendtsen AE, Mikkelsen KV, Martinez TJ. Tensor Hypercontraction of Cluster Perturbation Theory: Quartic Scaling Perturbation Series for the Coupled Cluster Singles and Doubles Ground-State Energies. J Chem Theory Comput 2024; 20:1932-1943. [PMID: 38380846 DOI: 10.1021/acs.jctc.3c01038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Even though cluster perturbation theory has been shown to be a robust noniterative alternative to coupled cluster theory, it is still plagued by high order polynomial computational scaling and the storage of higher order tensors. We present a proof-of-concept strategy for implementing a cluster perturbation theory ground-state energy series for the coupled cluster singles and doubles energy with N4 computational scaling using tensor hypercontraction (THC). The reduction in computational scaling by two orders is achieved by decomposing two electron repulsion integrals, doubles amplitudes and multipliers, as well as selected double intermediates to the THC format. Using the outlined strategy, we showcase that the THC pilot implementations retain numerical accuracy to within 1 kcal/mol relative to corresponding conventional and density fitting implementations, and we empirically verify the N4 scaling.
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Affiliation(s)
| | - Kurt V Mikkelsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen Ø DK-2100, Denmark
| | - Todd J Martinez
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
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26
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Lapoot L, Jabeen S, Durantini AM, Greer A. Role of curvature in acridone for 1 O 2 oxidation of a natural product homoallylic alcohol: A novel iso-hydroperoxide intermediate. Photochem Photobiol 2024; 100:455-464. [PMID: 37602967 DOI: 10.1111/php.13843] [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: 06/05/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 08/22/2023]
Abstract
A density functional theoretical (DFT) study is presented, implicating a 1 O2 oxidation process to reach a dihydrobenzofuran from the reaction of the natural homoallylic alcohol, glycocitrine. Our results predict an interconversion between glycocitrine and an iso-hydroperoxide intermediate [R(H)O+ -O- ] that provides a key path in the chemistry which then follows. Formations of allylic hydroperoxides are unlikely from a 1 O2 'ene' reaction. Instead, the dihydrobenzofuran arises by 1 O2 oxidation facilitated by a 16° curvature of the glycocitrine ring imposed by a pyramidal N-methyl group. This curvature facilitates the formation of the iso-hydroperoxide, which is analogous to the iso species CH2 I+ -I- and CHI2 + -I- formed by UV photolysis of CH2 I2 and CHI3 . The iso-hydroperoxide is also structurally reminiscent of carbonyl oxides (R2 C=O+ -O- ) formed in the reaction of carbenes and oxygen. Our DFT results point to intermolecular process, in which the iso-hydroperoxide's fate relates to O-transfer and H2 O dehydration reactions for new insight into the biosynthesis of dihydrobenzofuran natural products.
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Affiliation(s)
- Lloyd Lapoot
- Department of Chemistry, Brooklyn College, City University of New York, Brooklyn, New York, USA
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, New York, USA
| | - Shakeela Jabeen
- Department of Chemistry, Brooklyn College, City University of New York, Brooklyn, New York, USA
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, New York, USA
| | - Andrés M Durantini
- Department of Chemistry, Brooklyn College, City University of New York, Brooklyn, New York, USA
- IDAS-CONICET, Departamento de Química, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Córdoba, Argentina
| | - Alexander Greer
- Department of Chemistry, Brooklyn College, City University of New York, Brooklyn, New York, USA
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, New York, USA
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, New York, USA
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27
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Karak P, Moitra T, Banerjee A, Ruud K, Chakrabarti S. Accidental triplet harvesting in donor-acceptor dyads with low spin-orbit coupling. Phys Chem Chem Phys 2024; 26:5344-5355. [PMID: 38268441 DOI: 10.1039/d3cp04904c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
We present an accidental mechanism for efficient intersystem crossing (ISC) between singlet and triplet states with low spin-orbit coupling (SOC) in molecules having donor-acceptor (D-A) moieties separated by a Sigma bond. Our study shows that SOC between the lowest singlet excited state and the higher-lying triplet states, together with nuclear motion-driven coupling of this triplet state with lower-lying triplet states during the free rotation about a Sigma bond, is one of the possible ways to achieve the experimentally observed ISC rate for a class of D-A type photoredox catalysts. This mechanism is found to be the dominant contributor to the ISC process with the corresponding rate reaching a maximum at a dihedral angle in the range of 72°-78° between the D-A moieties of 10-(naphthalen-1-yl)-3,7-diphenyl-10H-phenoxazine and other molecules included in the study. We have further demonstrated that the same mechanism is operative in a specific spirobis[anthracene]dione molecule, where the D and A moieties are interlocked near to the optimal dihedral angle, indicating the plausible effectiveness of the proposed mechanism. The present finding is expected to have implications in strategies for the synthesis of new generations of triplet-harvesting organic molecules.
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Affiliation(s)
- Pijush Karak
- Department of Chemistry, University of Calcutta, 92 A.P.C Road, Kolkata - 700009, West Bengal, India.
| | - Torsha Moitra
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø - The Arctic University of Norway, 9037 Tromsø, Norway.
| | - Ambar Banerjee
- Department of Physics and Astronomy, X-ray Photon Science, Uppsala University, Ångströmlaboratoriet, Lägerhyddsvägen 1, 75120, Uppsala, Sweden.
| | - Kenneth Ruud
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø - The Arctic University of Norway, 9037 Tromsø, Norway.
- Norwegian Defence Research Establishment, P.O.Box 25, 2027 Kjeller, Norway
| | - Swapan Chakrabarti
- Department of Chemistry, University of Calcutta, 92 A.P.C Road, Kolkata - 700009, West Bengal, India.
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28
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Groslambert L, Cornaton Y, Ditte M, Aubert E, Pale P, Tkatchenko A, Djukic JP, Mamane V. Affinity of Telluronium Chalcogen Bond Donors for Lewis Bases in Solution: A Critical Experimental-Theoretical Joint Study. Chemistry 2024; 30:e202302933. [PMID: 37970753 DOI: 10.1002/chem.202302933] [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: 09/09/2023] [Revised: 11/15/2023] [Accepted: 11/15/2023] [Indexed: 11/17/2023]
Abstract
Telluronium salts [Ar2 MeTe]X were synthesized, and their Lewis acidic properties towards a number of Lewis bases were addressed in solution by physical and theoretical means. Structural X-ray diffraction analysis of 21 different salts revealed the electrophilicity of the Te centers in their interactions with anions. Telluroniums' propensity to form Lewis pairs was investigated with OPPh3 . Diffusion-ordered NMR spectroscopy suggested that telluroniums can bind up to three OPPh3 molecules. Isotherm titration calorimetry showed that the related heats of association in 1,2-dichloroethane depend on the electronic properties of the substituents of the aryl moiety and on the nature of the counterion. The enthalpies of first association of OPPh3 span -0.5 to -5 kcal mol-1 . Study of the affinity of telluroniums for OPPh3 by state-of-the-art DFT and ab-initio methods revealed the dominant Coulombic and dispersion interactions as well as an entropic effect favoring association in solution. Intermolecular orbital interactions between [Ar2 MeTe]+ cations and OPPh3 are deemed insufficient on their own to ensure the cohesion of [Ar2 MeTe ⋅ Bn ]+ complexes in solution (B=Lewis base). Comparison of Grimme's and Tkatchenko's DFT-D4/MBD-vdW thermodynamics of formation of higher [Ar2 MeTe ⋅ Bn ]+ complexes revealed significant molecular size-dependent divergence of the two methodologies, with MBD yielding better agreement with experiment.
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Affiliation(s)
- Loïc Groslambert
- LASYROC, UMR 7177 CNRS, University of Strasbourg, 1 Rue Blaise Pascal, F-67000, Strasbourg, France
| | - Yann Cornaton
- LCSOM, UMR 7177 CNRS, Université de Strasbourg, 4 rue Blaise Pascal, F-67000, Strasbourg, France
| | - Matej Ditte
- Department of Physics and Materials Science, University of Luxembourg, L-1511, Luxembourg City, Luxembourg
| | | | - Patrick Pale
- LASYROC, UMR 7177 CNRS, University of Strasbourg, 1 Rue Blaise Pascal, F-67000, Strasbourg, France
| | - Alexandre Tkatchenko
- Department of Physics and Materials Science, University of Luxembourg, L-1511, Luxembourg City, Luxembourg
| | - Jean-Pierre Djukic
- LCSOM, UMR 7177 CNRS, Université de Strasbourg, 4 rue Blaise Pascal, F-67000, Strasbourg, France
| | - Victor Mamane
- LASYROC, UMR 7177 CNRS, University of Strasbourg, 1 Rue Blaise Pascal, F-67000, Strasbourg, France
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29
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Zeng JK, Wang HQ, Li HF, Zheng H, Zhang JM, Mei XJ, Zhang YH, Ding XL. Exploring the stability and aromaticity of rare earth doped tin cluster MSn 16- (M = Sc, Y, La). Phys Chem Chem Phys 2024; 26:2986-2994. [PMID: 38163990 DOI: 10.1039/d3cp04803a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Rare earth elements have high chemical reactivity, and doping them into semiconductor clusters can induce novel physicochemical properties. The study of the physicochemical mechanisms of interactions between rare earth and tin atoms will enhance our understanding of rare earth functional materials from a microscopic perspective. Hence, the structure, electronic characteristics, stability, and aromaticity of endohedral cages MSn16- (M = Sc, Y, La) have been investigated using a combination of the hybrid PBE0 functional, stochastic kicking, and artificial bee colony global search technology. By comparing the simulated results with experimental photoelectron spectra, it is determined that the most stable structure of these clusters is the Frank-Kasper polyhedron. The doping of atoms has a minimal influence on density of states of the pure tin system, except for causing a widening of the energy gap. Various methods such as ab initio molecular dynamics simulations, the spherical jellium model, adaptive natural density partitioning, localized orbital locator, and electron density difference are employed to analyze the stability of these clusters. The aromaticity of the clusters is examined using iso-chemical shielding surfaces and the gauge-including magnetically induced currents. This study demonstrates that the stability and aromaticity of a tin cage can be systematically adjusted through doping.
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Affiliation(s)
- Jin-Kun Zeng
- College of Information Science and Engineering, Huaqiao University, Xiamen, 361021, China.
| | - Huai-Qian Wang
- College of Information Science and Engineering, Huaqiao University, Xiamen, 361021, China.
- College of Engineering, Huaqiao University, Quanzhou, 362021, China
| | - Hui-Fang Li
- College of Engineering, Huaqiao University, Quanzhou, 362021, China
| | - Hao Zheng
- College of Information Science and Engineering, Huaqiao University, Xiamen, 361021, China.
| | - Jia-Ming Zhang
- College of Information Science and Engineering, Huaqiao University, Xiamen, 361021, China.
| | - Xun-Jie Mei
- College of Engineering, Huaqiao University, Quanzhou, 362021, China
| | - Yong-Hang Zhang
- College of Information Science and Engineering, Huaqiao University, Xiamen, 361021, China.
| | - Xun-Lei Ding
- Department of Mathematics and Physics, North China Electric Power University, Beijing, 102206, China
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30
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Pasik D, Iyer S, Myllys N. Cost-effective approach for atmospheric accretion reactions: a case of peroxy radical addition to isoprene. Phys Chem Chem Phys 2024; 26:2560-2567. [PMID: 38170853 DOI: 10.1039/d3cp04308h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
We present an accurate and cost-effective method for investigating the accretion reactions between unsaturated hydrocarbons and oxidized organic radicals. We use accretion between isoprene and primary, secondary and tertiary alkyl peroxy radicals as model reactions. We show that a systematic semiempirical transition state search can lead to better transition state structures than relaxed scanning with density functional theory with a significant gain in computational efficiency. Additionally, we suggest accurate and effective quantum chemical methods to study accretion reactions between large unsaturated hydrocarbons and oxidized organic radicals. Furthermore, we examine the atmospheric relevance of these types of reactions by calculating the bimolecular reaction rate coefficients and formation rates under atmospheric conditions from the quantum chemical reaction energy barriers.
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Affiliation(s)
- Dominika Pasik
- Department of Chemistry, University of Helsinki, Helsinki 00014, Finland.
- Institute for Atmospheric and Earth System Research, University of Helsinki, Helsinki 00014, Finland
| | - Siddharth Iyer
- Aerosol Physics Laboratory, Tampere University, Tampere FI-3720, Finland
| | - Nanna Myllys
- Department of Chemistry, University of Helsinki, Helsinki 00014, Finland.
- Institute for Atmospheric and Earth System Research, University of Helsinki, Helsinki 00014, Finland
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31
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McNamee RE, Frank N, Christensen KE, Duarte F, Anderson EA. Taming nonclassical carbocations to control small ring reactivity. SCIENCE ADVANCES 2024; 10:eadj9695. [PMID: 38215201 PMCID: PMC10786418 DOI: 10.1126/sciadv.adj9695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 12/13/2023] [Indexed: 01/14/2024]
Abstract
Prediction of the outcome of ring opening of small organic rings under cationic conditions can be challenging due to the intermediacy of nonclassical carbocations. For example, the solvolysis of cyclobutyl or cyclopropylmethyl derivatives generates up to four products on nucleophilic capture or elimination via cyclopropylcarbinyl and bicyclobutonium ions. Here, we show that such reaction outcomes can be controlled by subtle changes to the structure of nonclassical carbocation. Using bicyclo[1.1.0]butanes as cation precursors, the regio- and stereochemistry of ring opening is shown to depend on the degree and nature of the substituents on the cationic intermediates. Reaction outcomes are rationalized using computational models, resulting in a flowchart to predict product formation from a given cation precursor.
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Affiliation(s)
| | | | | | - Fernanda Duarte
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
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32
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Wappett DA, Goerigk L. Exploring CPS-Extrapolated DLPNO-CCSD(T 1) Reference Values for Benchmarking DFT Methods on Enzymatically Catalyzed Reactions. J Phys Chem A 2024; 128:62-72. [PMID: 38124376 DOI: 10.1021/acs.jpca.3c05086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Domain-based local pair natural orbital coupled-cluster singles doubles with perturbative triples [DLPNO-CCSD(T)] is regularly used to calculate reliable benchmark reference values at a computational cost significantly lower than that of canonical CCSD(T). Recent work has shown that even greater accuracy can be obtained at only a small additional cost through extrapolation to the complete PNO space (CPS) limit. Herein, we test two levels of CPS extrapolation, CPS(5,6), which approximates the accuracy of standard TightPNO, and CPS(6,7), which surpasses it, as benchmark values to test density functional approximations (DFAs) on a small set of organic and transition-metal-dependent enzyme active site models. Between the different reference levels of theory, there are changes in the magnitudes of the absolute deviations for all functionals, but these are small and there is minimal impact on the relative rankings of the tested DFAs. The differences are more significant for the metalloenzymes than the organic enzymes, so we repeat the tests on our entire ENZYMES22 set of organic enzyme active site models [Wappett, D. A.; Goerigk, L. J. Phys. Chem. A 2019, 123, 7057-7074] to confirm that using the CPS extrapolations for the reference values has negligible impact on the benchmarking outcomes. This means that we can particularly recommend CPS(5,6) as an alternative to standard TightPNO settings for calculating reference values, increasing the applicability of DLPNO-CCSD(T) in benchmarking reaction energies and barrier heights of larger models of organic enzymes. DLPNO-CCSD(T1)/CPS(6,7) energies for ENZYMES22 are finally presented as updated reference values for the set, reflecting the recent improvements in the method.
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Affiliation(s)
- Dominique A Wappett
- School of Chemistry, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Lars Goerigk
- School of Chemistry, The University of Melbourne, Parkville, Victoria 3010, Australia
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33
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Luo Z, Zhou W, Jiang Y, Minakata D, Spinney R, Dionysiou DD, Liu J, Xiao R. Bimolecular versus Trimolecular Reaction Pathways for H 2O 2 with Hypochlorous Species and Implications for Wastewater Reclamation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:847-858. [PMID: 38153291 DOI: 10.1021/acs.est.3c06375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
The benchmark advanced oxidation technology (AOT) that uses UV/H2O2 integrated with hypochlorous species exhibits great potential in removing micropollutants and enhancing wastewater treatability for reclamation purposes. Although efforts have been made to study the reactions of H2O2 with hypochlorous species, there exist great discrepancies in the order of reaction kinetics, the rate constants, and the molecule-level mechanisms. This results in an excessive use of hypochlorous reagents and system underperformance during treatment processes. Herein, the titled reaction was investigated systematically through complementary experimental and theoretical approaches. Stopped-flow spectroscopic measurements revealed a combination of bi- and trimolecular reaction kinetics. The bimolecular pathway dominates at low H2O2 concentrations, while the trimolecular pathway dominates at high H2O2 concentrations. Both reactions were simulated using direct dynamics trajectories, and the pathways identified in the trajectories were further validated by high-level quantum chemistry calculations. The theoretical results not only supported the spectroscopic data but also elucidated the molecule-level mechanisms and helped to address the origin of the discrepancies. In addition, the impact of the environmental matrix was evaluated by using two waters with discrete characteristics, namely municipal wastewater and ammonium-rich wastewater. Municipal wastewater had a negligible matrix effect on the reaction kinetics of H2O2 and the hypochlorous species, making it a highly suitable candidate for this integration technique. The obtained in-depth reaction mechanistic insights will enable the development of a viable and economical technology for safe water reuse.
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Affiliation(s)
- Zonghao Luo
- Institute of Environmental Engineering, School of Metallurgy and Environment, Central South University, Changsha 410083, China
- Chinese National Engineering Research Center for Control and Treatment of Heavy Metal Pollution, Changsha 410083, China
| | - Wenjing Zhou
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, Queens, New York 11367, United States
| | - Ying Jiang
- Institute of Environmental Engineering, School of Metallurgy and Environment, Central South University, Changsha 410083, China
- Chinese National Engineering Research Center for Control and Treatment of Heavy Metal Pollution, Changsha 410083, China
| | - Daisuke Minakata
- Department of Civil and Environmental Engineering, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Richard Spinney
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Dionysios D Dionysiou
- Environmental Engineering and Science Program, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Jianbo Liu
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, Queens, New York 11367, United States
| | - Ruiyang Xiao
- Institute of Environmental Engineering, School of Metallurgy and Environment, Central South University, Changsha 410083, China
- Chinese National Engineering Research Center for Control and Treatment of Heavy Metal Pollution, Changsha 410083, China
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34
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Melnikov IN, Pivkina AN, Kiselev VG. New Mechanistic Insights into the Primary Thermolysis Reactions of 1,3,4,6-Tetranitrooctahydroimidazo-[4,5- d]imidazole (BCHMX) from Predictive Local Coupled Cluster Calculations. J Phys Chem A 2023; 127:10860-10871. [PMID: 38039193 DOI: 10.1021/acs.jpca.3c06352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2023]
Abstract
Theoretical studies of the decomposition mechanism of energetic materials quite often scrutinize only the primary thermolysis reactions. However, the secondary reactions are crucial, inter alia, for proper building of the combustion models and understanding the autocatalytic processes. In the present study, we applied predictive DLPNO-CCSD(T) calculations to elucidate the kinetics and decomposition mechanism of a novel promising energetic material, 1,3,4,6-tetranitrooctahydroimidazo [4,5-d] imidazole (BCHMX). We identified eight previously unknown BCHMX conformers, both cis and trans in accordance to the spatial position of the H atoms bonded to a carbon bridge. Among them, the relative enthalpies of cis isomers lie in the narrow range ∼10 kJ mol-1 rendering them thermally accessible in the course of decomposition. The radical N-NO2 bond cleavage via one of the novel conformers is the dominant primary decomposition channel of BCHMX with the kinetic parameters Ea = 168.4 kJ mol-1 and log(A, s-1) = 18.5. We also resolved several contradictory assumptions on the mechanism and key intermediates of BCHMX thermolysis. To get a deeper understanding of the decomposition mechanism, we examined a series of unimolecular and bimolecular secondary channels of BCHMX. Among the former reactions, the C-C bond unzipping followed by another radical elimination of a nitro group is the most energetically favorable pathway with an activation barrier ∼113 kJ mol-1. However, contrary to the literature assumptions, the bimolecular H atom abstraction from a pristine BCHMX molecule by a primary nitramine radical product, not the nitro one, followed by another NO2 radical elimination, is the most important bimolecular secondary thermolysis reaction of BCHMX at lower temperatures. The isokinetic temperature of the bimolecular and unimolecular secondary reactions is ∼620 K. Unimolecular reactions might be important in dilute solutions, where bimolecular reactions are suppressed. The secondary reactions considered in the present work might be pertinent in the case of related energetic nitramines (e.g., RDX, HMX, and CL-20).
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Affiliation(s)
- Igor N Melnikov
- Semenov Federal Research Center for Chemical Physics RAS, 4 Kosygina Str., 119991 Moscow, Russia
| | - Alla N Pivkina
- Semenov Federal Research Center for Chemical Physics RAS, 4 Kosygina Str., 119991 Moscow, Russia
| | - Vitaly G Kiselev
- Novosibirsk State University, 1 Pirogova Str., 630090 Novosibirsk, Russia
- Institute of Chemical Kinetics and Combustion SB RAS, 3 Institutskaya Str., 630090 Novosibirsk, Russia
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35
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Eisele NF, Rahrt R, Giachanou L, Shikho F, Koszinowski K. Gas-Phase Alkali-Metal Cation Affinities of Stabilized Enolates. Chemistry 2023; 29:e202302540. [PMID: 37752885 DOI: 10.1002/chem.202302540] [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: 08/04/2023] [Revised: 09/23/2023] [Accepted: 09/25/2023] [Indexed: 09/28/2023]
Abstract
The chemistry of alkali-metal enolates is dominated by ion pairing. To improve our understanding of the intrinsic interactions between the alkali-metal cations and the enolate anions, we have applied Cooks' kinetic method to determine relative M+ (M=Li, Na, K) affinities of the stabilized enolates derived from acetylacetone, ethyl acetoacetate, diethyl malonate, ethyl cyanoacetate, 2-cyanoacetamide, and methyl malonate monoamide in the gas phase. Quantum chemical calculations support the experimental results and moreover afford insight into the structures of the alkali-metal enolate complexes. The affinities decrease with increasing size of the alkali-metal cations, reflecting weaker electrostatic interactions and lower charge densities of the free M+ ions. For the different enolates, a comparison of their coordinating abilities is complicated by the fact that some of the free anions undergo conformational changes resulting in stabilizing intramolecular interactions. If these complicating effects are disregarded, the M+ affinities correlate with the electron density of the chelating functionalities, that is, the carbonyl and/or the nitrile groups of the enolates. A comparison with the known association constants of the corresponding alkali-metal enolates in solution points to the importance of solvation effects for these systems.
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Affiliation(s)
- Niklas F Eisele
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammannstraße 2, 37077, Göttingen, Germany
| | - Rene Rahrt
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammannstraße 2, 37077, Göttingen, Germany
| | - Lamprini Giachanou
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammannstraße 2, 37077, Göttingen, Germany
| | - Fadi Shikho
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammannstraße 2, 37077, Göttingen, Germany
| | - Konrad Koszinowski
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammannstraße 2, 37077, Göttingen, Germany
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36
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Verma P, Mukherjee M, Bhattacharya D, Haritan I, Dutta AK. Shape resonance induced electron attachment to cytosine: The effect of aqueous media. J Chem Phys 2023; 159:214303. [PMID: 38038205 DOI: 10.1063/5.0157576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 08/31/2023] [Indexed: 12/02/2023] Open
Abstract
We have investigated the impact of microsolvation on shape-type resonance states of nucleobases, taking cytosine as a case study. To characterize the resonance position and decay width of the metastable states, we employed the newly developed DLPNO-based EA-EOM-CCSD method in conjunction with the resonance via Padé (RVP) method. Our calculations show that the presence of water molecules causes a redshift in the resonance position and an increase in the lifetime for the three lowest-lying resonance states of cytosine. Furthermore, there are some indications that the lowest resonance state in isolated cytosine may get converted to a bound state in the presence of an aqueous environment. The obtained results are extremely sensitive to the basis set used for the calculations.
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Affiliation(s)
- Pooja Verma
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Madhubani Mukherjee
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, USA
| | - Debarati Bhattacharya
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Idan Haritan
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 3200003, Israel
- Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel
| | - Achintya Kumar Dutta
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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37
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Moe MM, Tsai M, Liu J. Effects of Intra-Base Pair Proton Transfer on Dissociation and Singlet Oxygenation of 9-Methyl-8-Oxoguanine-1-Methyl-Cytosine Base-Pair Radical Cations. Chemphyschem 2023; 24:e202300511. [PMID: 37738022 DOI: 10.1002/cphc.202300511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/18/2023] [Accepted: 09/22/2023] [Indexed: 09/23/2023]
Abstract
8-Oxoguanosine is the most common oxidatively generated base damage and pairs with complementary cytidine within duplex DNA. The 8-oxoguanosine-cytidine lesion, if not recognized and removed, not only leads to G-to-T transversion mutations but renders the base pair being more vulnerable to the ionizing radiation and singlet oxygen (1 O2 ) damage. Herein, reaction dynamics of a prototype Watson-Crick base pair [9MOG ⋅ 1MC]⋅+ , consisting of 9-methyl-8-oxoguanine radical cation (9MOG⋅+ ) and 1-methylcystosine (1MC), was examined using mass spectrometry coupled with electrospray ionization. We first detected base-pair dissociation in collisions with the Xe gas, which provided insight into intra-base pair proton transfer of 9MOG⋅+ ⋅ 1MC← → ${{\stackrel{ {\rightarrow} } { {\leftarrow} } } }$ [9MOG - HN1 ]⋅ ⋅ [1MC+HN3' ]+ and subsequent non-statistical base-pair separation. We then measured the reaction of [9MOG ⋅ 1MC]⋅+ with 1 O2 , revealing the two most probable pathways, C5-O2 addition and HN7 -abstraction at 9MOG. Reactions were entangled with the two forms of 9MOG radicals and base-pair structures as well as multi-configurations between open-shell radicals and 1 O2 (that has a mixed singlet/triplet character). These were disentangled by utilizing approximately spin-projected density functional theory, coupled-cluster theory and multi-referential electronic structure modeling. The work delineated base-pair structural context effects and determined relative reactivity toward 1 O2 as [9MOG - H]⋅>9MOG⋅+ >[9MOG - HN1 ]⋅ ⋅ [1MC+HN3' ]+ ≥9MOG⋅+ ⋅ 1MC.
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Affiliation(s)
- May Myat Moe
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, NY 11367, USA
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Ave., New York, NY 10016, USA
| | - Midas Tsai
- Department of Natural Sciences, LaGuardia Community College, 31-10 Thomson Ave., Long Island City, NY 11101, USA
| | - Jianbo Liu
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, NY 11367, USA
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Ave., New York, NY 10016, USA
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38
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Wu H, Engsvang M, Knattrup Y, Kubečka J, Elm J. Improved Configurational Sampling Protocol for Large Atmospheric Molecular Clusters. ACS OMEGA 2023; 8:45065-45077. [PMID: 38046341 PMCID: PMC10688134 DOI: 10.1021/acsomega.3c06794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/12/2023] [Accepted: 10/17/2023] [Indexed: 12/05/2023]
Abstract
The nucleation process leading to the formation of new atmospheric particles plays a crucial role in aerosol research. Quantum chemical (QC) calculations can be used to model the early stages of aerosol formation, where atmospheric vapor molecules interact and form stable molecular clusters. However, QC calculations heavily depend on the chosen computational method, and when dealing with large systems, striking a balance between accuracy and computational cost becomes essential. We benchmarked the binding energies and structures and found the B97-3c method to be a good compromise between the accuracy and computational cost for studying large cluster systems. Further, we carefully assessed configurational sampling procedures for targeting large atmospheric molecular clusters containing up to 30 molecules (approximately 2 nm in diameter) and proposed a funneling approach with highly improved accuracy. We find that several parallel ABCluster explorations lead to better guesses for the cluster global energy minimum structures than one long exploration. This methodology allows us to bridge computational studies of molecular clusters, which typically reach only around 1 nm, with experimental studies that often measure particles larger than 2 nm. By employing this workflow, we searched for low-energy configurations of large sulfuric acid-ammonia and sulfuric acid-dimethylamine clusters. We find that the binding free energies of clusters containing dimethylamine are unequivocally more stable than those of the ammonia-containing clusters. Our improved configurational sampling protocol can in the future be applied to study the growth and dynamics of large clusters of arbitrary compositions.
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Affiliation(s)
- Haide Wu
- Department of Chemistry, Aarhus
University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Morten Engsvang
- Department of Chemistry, Aarhus
University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Yosef Knattrup
- Department of Chemistry, Aarhus
University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Jakub Kubečka
- Department of Chemistry, Aarhus
University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Jonas Elm
- Department of Chemistry, Aarhus
University, Langelandsgade 140, 8000 Aarhus C, Denmark
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39
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Wang Y, Guo Y, Neese F, Valeev EF, Li W, Li S. Cluster-in-Molecule Approach with Explicitly Correlated Methods for Large Molecules. J Chem Theory Comput 2023; 19:8076-8089. [PMID: 37920973 DOI: 10.1021/acs.jctc.3c00627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
In this article, we present a series of explicitly correlated local correlation methods developed under the cluster-in-molecule (CIM) framework, including explicitly correlated second-order Møller-Plesset perturbation (MP2), coupled-cluster singles and doubles (CCSD), domain-based local pair natural orbital CCSD (DLPNO-CCSD), and DLPNO-CCSD with perturbative triples (DLPNO-CCSD(T)). In these methods, F12 correction is decomposed into contributions from each occupied local molecular orbital and then evaluated independently in a given cluster, which consists of a subset of localized orbitals. These newly developed methods allow F12 calculations of large molecules (up to 145 atoms for quasi-one-dimensional systems) on a single node. We use these methods to investigate the relative stability between extended and folded alkane C30H62, the relative stability of four secondary structures of a polyglycine Ace(Gly)10NH2, and the binding energies of two host-guest complexes. The results demonstrate that the combination of CIM with F12 methods is a promising way to investigate large molecules with small basis set errors.
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Affiliation(s)
- Yuqi Wang
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, New Cornerstone Science Laboratory, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Yang Guo
- Qingdao Institute for Theoretical and Computational Sciences, Shandong University, Qingdao, Shandong 266237, P. R. China
| | - Frank Neese
- Max Planck Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Edward F Valeev
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Wei Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, New Cornerstone Science Laboratory, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Shuhua Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, New Cornerstone Science Laboratory, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
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40
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Wappett D, Goerigk L. Benchmarking Density Functional Theory Methods for Metalloenzyme Reactions: The Introduction of the MME55 Set. J Chem Theory Comput 2023; 19:8365-8383. [PMID: 37943578 PMCID: PMC10688432 DOI: 10.1021/acs.jctc.3c00558] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 11/10/2023]
Abstract
We present a new benchmark set of metalloenzyme model reaction energies and barrier heights that we call MME55. The set contains 10 different enzymes, representing eight transition metals, both open and closed shell systems, and system sizes of up to 116 atoms. We use four DLPNO-CCSD(T)-based approaches to calculate reference values against which we then benchmark the performance of a range of density functional approximations with and without dispersion corrections. Dispersion corrections improve the results across the board, and triple-ζ basis sets provide the best balance of efficiency and accuracy. Jacob's ladder is reproduced for the whole set based on averaged mean absolute (percent) deviations, with the double hybrids SOS0-PBE0-2-D3(BJ) and revDOD-PBEP86-D4 standing out as the most accurate methods for the MME55 set. The range-separated hybrids ωB97M-V and ωB97X-V also perform well here and can be recommended as a reliable compromise between accuracy and efficiency; they have already been shown to be robust across many other types of chemical problems, as well. Despite the popularity of B3LYP in computational enzymology, it is not a strong performer on our benchmark set, and we discourage its use for enzyme energetics.
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Affiliation(s)
- Dominique
A. Wappett
- School of Chemistry, The University
of Melbourne, Melbourne, Victoria 3010, Australia
| | - Lars Goerigk
- School of Chemistry, The University
of Melbourne, Melbourne, Victoria 3010, Australia
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41
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Neugebauer H, Pinski P, Grimme S, Neese F, Bursch M. Assessment of DLPNO-MP2 Approximations in Double-Hybrid DFT. J Chem Theory Comput 2023; 19:7695-7703. [PMID: 37862406 PMCID: PMC10653103 DOI: 10.1021/acs.jctc.3c00896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Indexed: 10/22/2023]
Abstract
The unfavorable scaling (N5) of the conventional second-order Møller-Plesset theory (MP2) typically prevents the application of double-hybrid (DH) density functionals to large systems with more than 100 atoms. A prominent approach to reduce the computational demand of electron correlation methods is the domain-based local pair natural orbital (DLPNO) approximation that is successfully used in the framework of DLPNO-CCSD(T). Its extension to MP2 [Pinski P.; Riplinger, C.; Valeev, E. F.; Neese, F. J. Chem. Phys. 2015, 143, 034108.] paved the way for DLPNO-based DH (DLPNO-DH) methods. In this work, we assess the accuracy of the DLPNO-DH approximation compared to conventional DHs on a large number of 7925 data points for thermochemistry and 239 data points for structural features, including main-group and transition-metal systems. It is shown that DLPNO-DH-DFT can be applied successfully to perform energy calculations and geometry optimizations for large molecules at a drastically reduced computational cost. Furthermore, PNO space extrapolation is shown to be applicable, similar to its DLPNO-CCSD(T) counterpart, to reduce the remaining error.
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Affiliation(s)
- Hagen Neugebauer
- Mulliken
Center for Theoretical Chemistry, Clausius Institute for Physical
and Theoretical Chemistry, University of
Bonn, Beringstraße 4, D-53115 Bonn, Germany
| | - Peter Pinski
- HQS
Quantum Simulations GmbH, Rintheimer Straße 23, D-76131 Karlsruhe, Germany
| | - Stefan Grimme
- Mulliken
Center for Theoretical Chemistry, Clausius Institute for Physical
and Theoretical Chemistry, University of
Bonn, Beringstraße 4, D-53115 Bonn, Germany
| | - Frank Neese
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Markus Bursch
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
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42
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Werner HJ, Hansen A. Accurate Calculation of Isomerization and Conformational Energies of Larger Molecules Using Explicitly Correlated Local Coupled Cluster Methods in Molpro and ORCA. J Chem Theory Comput 2023; 19:7007-7030. [PMID: 37486154 DOI: 10.1021/acs.jctc.3c00270] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
An overview of the approximations in the explicitly correlated local coupled cluster methods PNO-LCCSD(T)-F12 in Molpro and DLPNO-CCSD(T)F12 in ORCA is given. Options to select the domains of projected atomic orbitals (PAOs), pair natural orbitals (PNOs), and triples natural orbitals (TNOs) in both programs are described and compared in detail. The two programs are applied to compute isomerization and conformational energies of the ISOL24 and ACONFL test sets, where the former is part of the GMTKN55 benchmark suite. Thorough studies of basis set effects are presented for selected systems. These revealed large intramolecular basis set superposition effects that make it practically impossible to reliably determine the complete basis set (CBS) limits without including explicitly correlated terms. The latter strongly reduce the basis set dependence and at the same time also errors caused by the local domain approximations. On the basis of these studies, the PNO-LCCSD(T)-F12 method is applied to determine new reference energies for the above-mentioned benchmark sets. We are confident that our results should agree within a few tenths of a kcal mol-1 with the (unknown) CCSD(T)/CBS values, which therefore allowed us to define computational settings for accurate explicitly correlated local coupled cluster methods with moderate computational effort. With these protocols, especially PNO-LCCSD(T)-F12b/AVTZ', reliable reference values for comprehensive benchmark sets can be generated efficiently. This can significantly advance the development and evaluation of the performance of approximate electronic structure methods, especially improved density functional approximations or machine learning approaches.
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Affiliation(s)
- Hans-Joachim Werner
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstrasse 4, D-53115 Bonn, Germany
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43
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Martín-Fernández C, Ferrer M, Alkorta I, Montero-Campillo MM, Elguero J, Mandado M. Metastable Charged Dimers in Organometallic Species: A Look into Hydrogen Bonding between Metallocene Derivatives. Inorg Chem 2023; 62:16523-16537. [PMID: 37755334 DOI: 10.1021/acs.inorgchem.3c02355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
Multiply charged complexes bound by noncovalent interactions have been previously described in the literature, although they were mostly focused on organic and main group inorganic systems. In this work, we show that similar complexes can also be found for organometallic systems containing transition metals and deepen in the reasons behind the existence of these species. We have studied the structures, binding energies, and dissociation profiles in the gas phase of a series of charged hydrogen-bonded dimers of metallocene (Ru, Co, Rh, and Mn) derivatives isoelectronic with the ferrocene dimer. Our results indicate that the carboxylic acid-containing dimers are more strongly bonded and present larger barriers to dissociation than the amide ones and that the cationic complexes tend to be more stable than the anionic ones. Additionally, we describe for the first time the symmetric proton transfer that can occur while in the metastable phase. Finally, we use a density-based energy decomposition analysis to shine light on the nature of the interaction between the dimers.
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Affiliation(s)
| | - Maxime Ferrer
- Instituto de Química Médica (CSIC), Juan de la Cierva, 3, 28006 Madrid, Spain
- PhD Programme in Theoretical Chemistry and Computational Modelling, Doctoral School, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Ibon Alkorta
- Instituto de Química Médica (CSIC), Juan de la Cierva, 3, 28006 Madrid, Spain
| | - M Merced Montero-Campillo
- Departamento de Química (Módulo 13, Facultad de Ciencias), Campus de Excelencia UAM-CSIC, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - José Elguero
- Instituto de Química Médica (CSIC), Juan de la Cierva, 3, 28006 Madrid, Spain
| | - Marcos Mandado
- Departamento de Química Física, Universidade de Vigo, Lagoas-Marcosende s/n, 36310 Vigo, Spain
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44
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Gómez-Suárez A, Neumann CN. Stereochemistry in All Its Shapes and Forms: The 56 th Bürgenstock Conference. Angew Chem Int Ed Engl 2023; 62:e202309468. [PMID: 37590448 DOI: 10.1002/anie.202309468] [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: 07/04/2023] [Indexed: 08/19/2023]
Abstract
Acknowledging the crucial role of stereochemistry in fields as diverse as total synthesis, synthetic methodology, spectroscopy, and the study of the origin of life, the 56th SCS Conference on Stereochemistry, better known as the BÃ1/4rgenstock Conference, brought together a diverse range of chemistry expertise in Brunnen, Switzerland.
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Affiliation(s)
- Adrián Gómez-Suárez
- Organic Chemistry, Bergische Universität Wuppertal, Gaußstr. 20, 42119, Wuppertal, Germany
| | - Constanze N Neumann
- Department of Heterogeneous Catalysis, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
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45
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Martins GF, Castro TS, Ferreira DAC. Theoretical investigation of anion perfluorocubane. J Mol Model 2023; 29:319. [PMID: 37725189 DOI: 10.1007/s00894-023-05725-y] [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: 03/26/2023] [Accepted: 09/12/2023] [Indexed: 09/21/2023]
Abstract
CONTEXT In this work, we did a theoretical exploration of C8F8 (Ib) and its anion radical analogue (IIb) in this work. By investigating the thermochemistry of electron capture, we find that the free energy associated with the conversion of C8H8 (Ia) into its anion radical analogue IIa is of the order of + 92.83 kcal.mol-1, while the conversion of Ib into IIb is - 6.42 kcal.mol-1. Therefore, species IIb is thermodynamically more stable than its neutral analogue. Natural bond orbitals (NBO) analyses revealed that compound Ib exhibits a relative electronic stability as a function of intramolecular delocalisations of the type [Formula: see text] of the order of 2.70 kcal.mol-1. Similar delocalizations for Ia are energetically lower (1.45 kcal.mol-1). Topological analyses of compounds Ib and IIb indicate that the addition of an electron to Ib enhances the covalency of the C-C bond, as can be seen by the reduction in the ellipticity of the C-C bond. The opposite is observed for Ia, whose addition of the electron (leading to IIa) reduces the covalency of the C-C bond. By comparing the free and packaged forms of the species, it is found that, in the crystalline form, the system will present greater relative stability due to the dispersive interactions involved, as evidenced by non-covalent interactions (NCI) analysis. Finally, it was possible to verify that the manifestation of the current density with a lower paratropic and less antiaromatic character in Ib and IIb point to C8F8 as a strong candidate for electron capture. METHODS Geometry optimization calculations were carried out, for all monomer structures using the hybrid functional B3LYP-D3 and the 6-31+G(d,p) basis set. To determine the formation thermochemistry of the ions, electronic energy corrections was performed using the DLPNO-CCSD(T)/aug-cc-pVTZ/C method. Starting from the optimised forms, shielding, nuclear magnetic resonance (NMR) spectra employing gauge-independent atomic orbital (GIAO), and NBO calculations were performed for these monomers, using the PBE0 functional and the pCSseg-2 atomic basis set. The magnetochemical analysis of ring currents was performed using the GIMIC formalism. For the topological analysis, it was applied the combination DLPNO-CCSD(T)/aug-cc-pVTZ/C, previously used for correcting the electronic energy.
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Affiliation(s)
- Guilherme Ferreira Martins
- Instituto de Química, Laboratório de Dinâmica e Reatividade Molecular, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Asa Norte, Brasília-DF, CEP, 70910-900, Brazil
| | - Thiago Sampaio Castro
- Instituto de Química, Laboratório de Dinâmica e Reatividade Molecular, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Asa Norte, Brasília-DF, CEP, 70910-900, Brazil
- Instituto Federal do Tocantins-Campus Gurupi, Gurupi, TO, CEP, 77410-470, Brazil
| | - Daví Alexsandro Cardoso Ferreira
- Instituto de Química, Laboratório de Dinâmica e Reatividade Molecular, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Asa Norte, Brasília-DF, CEP, 70910-900, Brazil.
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46
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Semidalas E, Martin JML. Correlation Consistent Basis Sets for Explicitly Correlated Theory: The Transition Metals. J Chem Theory Comput 2023; 19:5806-5820. [PMID: 37540641 PMCID: PMC10500978 DOI: 10.1021/acs.jctc.3c00506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Indexed: 08/06/2023]
Abstract
We present correlation consistent basis sets for explicitly correlated (F12) calculations, denoted VnZ(-PP)-F12-wis (n = D,T), for the d-block elements. The cc-pVDZ-F12-wis basis set is contracted to [8s7p5d2f] for the 3d-block, while its ECP counterpart for the 4d and 5d-blocks, cc-pVDZ-PP-F12-wis, is contracted to [6s6p5d2f]. The corresponding contracted sizes for cc-pVTZ(-PP)-F12-wis are [9s8p6d3f2g] for the 3d-block elements and [7s7p6d3f2g] for the 4d and 5d-block elements. Our VnZ(-PP)-F12-wis basis sets are evaluated on challenging test sets for metal-organic barrier heights (MOBH35) and group-11 metal clusters (CUAGAU-2). In F12 calculations, they are found to be about as close to the complete basis set limit as the combination of standard cc-pVnZ-F12 on main-group elements with the standard aug-cc-pV(n+1)Z(-PP) basis sets on the transition metal(s). While our basis sets are somewhat more compact than aug-cc-pV(n+1)Z(-PP), the CPU time benefit is negligible for catalytic complexes that contain only one or two transition metals among dozens of main-group elements; however, it is somewhat more significant for metal clusters.
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Affiliation(s)
- Emmanouil Semidalas
- Department of Molecular Chemistry
and Materials Science, Weizmann Institute
of Science, 7610001 Reḥovot, Israel
| | - Jan M. L. Martin
- Department of Molecular Chemistry
and Materials Science, Weizmann Institute
of Science, 7610001 Reḥovot, Israel
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47
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Benny J, Liu J. Spin-orbit charge transfer from guanine and 9-methylguanine radical cations to nitric oxide radicals and the induced triplet-to-singlet intersystem crossing. J Chem Phys 2023; 159:085102. [PMID: 37638623 DOI: 10.1063/5.0160921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/08/2023] [Indexed: 08/29/2023] Open
Abstract
Nitric oxide (●NO) participates in many biological activities, including enhancing DNA radiosensitivity in ionizing radiation-based radiotherapy. To help understand the radiosensitization of ●NO, we report reaction dynamics between ●NO and the radical cations of guanine (a 9HG●+ conformer) and 9-methylguanine (9MG●+). On the basis of the formation of 9HG●+ and 9MG●+ in the gas phase and the collisions of the radical cations with ●NO in a guided-ion beam mass spectrometer, the charge transfer reactions of 9HG●+ and 9MG●+ with ●NO were examined. For both reactions, the kinetic energy-dependent product ion cross sections revealed a threshold energy that is 0.24 (or 0.37) eV above the 0 K product 9HG (or 9MG) + NO+ asymptote. To interrogate this abnormal threshold behavior, the reaction potential energy surface for [9MG + NO]+ was mapped out at closed-shell singlet, open-shell singlet, and triplet states using density functional and coupled cluster theories. The results showed that the charge transfer reaction requires the interaction of a triplet-state surface originating from a reactant-like precursor complex 3[9MG●+(↑)⋅(↑)●NO] with a closed-shell singlet-state surface evolving from a charge-transferred complex 1[9MG⋅NO+]. During the reaction, an electron is transferred from π∗(NO) to perpendicular π∗(9MG), which introduces a change in orbital angular momentum. The latter offsets the change in electron spin angular momentum and facilitates intersystem crossing. The reaction threshold in excess of the 0 K thermochemistry and the low charge-transfer efficiency are rationalized by the vibrational excitation in the product ion NO+ and the kinetic shift arising from a long-lived triplet intermediate.
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Affiliation(s)
- Jonathan Benny
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, New York 11367, USA
- The Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Ave., New York, New York 10016, USA
| | - Jianbo Liu
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, New York 11367, USA
- The Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Ave., New York, New York 10016, USA
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48
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Corzo HH, Hillers-Bendtsen AE, Barnes A, Zamani AY, Pawłowski F, Olsen J, Jørgensen P, Mikkelsen KV, Bykov D. Corrigendum: Coupled cluster theory on modern heterogeneous supercomputers. Front Chem 2023; 11:1256510. [PMID: 37654900 PMCID: PMC10466216 DOI: 10.3389/fchem.2023.1256510] [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: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 09/02/2023] Open
Abstract
[This corrects the article DOI: 10.3389/fchem.2023.1154526.].
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Affiliation(s)
| | | | | | - Abdulrahman Y. Zamani
- Department of Chemistry and Biochemistry and Center for Chemical Computation and Theory, University of California, Merced, CA, United States
| | - Filip Pawłowski
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL, United States
| | - Jeppe Olsen
- Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Poul Jørgensen
- Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Kurt V. Mikkelsen
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Dmytro Bykov
- Oak Ridge National Laboratory, Oak Ridge, TN, United States
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49
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Stošek J, Semrád H, Mazal C, Munzarová M. Mechanistic Analysis of Alkyne Haloboration: A DFT, MP2, and DLPNO-CCSD(T) Study. J Phys Chem A 2023; 127:6135-6146. [PMID: 37489760 PMCID: PMC10405270 DOI: 10.1021/acs.jpca.3c00607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 06/23/2023] [Indexed: 07/26/2023]
Abstract
Stereocontrol of the alkyne haloboration reaction has received attention in many experimental but few theoretical studies. Here we present a detailed quantum-chemical study of mechanisms leading to Z versus E isomers of haloboration products, considering acetylene and propyne combined with BCl3, BBr3, and BI3. Calculations using B3LYP-D3, MP2, and DLPNO-CCSD(T) methods are used to study polar reactions between the alkyne and BX3 in the absence and presence of an additional halide anion whose content in the reaction mixture can be controlled experimentally. The formation of anti-haloboration products via radical mechanisms is also explored, namely, by adding BX3 to (Z)-halovinyl radical. For the anti-haloboration of propyne, the radical route is prohibited by the regiochemistry of the initiating halopropenyl radical, while the polar route is unlikely due to a competitive allene generation. In contrast, energetically accessible routes exist for both syn- and anti-bromoboration of acetylene; hence, careful control of reaction conditions is necessary to steer the stereochemical outcome. Methodologically, MP2 results correspond better to the DLPNO-CCSD(T) energies than the B3LYP-D3 results in terms of both reaction barrier heights and relative ordering of energetically close stationary points.
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Nees S, Beer H, Just P, Teichmeier LM, Christoffer LE, Guljam A, Kushik, Braunschweig H, Hering-Junghans C. On the Reactivity of Mes*P(PMe 3 ) towards Aluminum(I) Compounds - Evidence for the Intermediate Formation of Phosphaalumenes. Chempluschem 2023; 88:e202300078. [PMID: 36824017 DOI: 10.1002/cplu.202300078] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 02/25/2023]
Abstract
Phosphaalumenes are the heavier isoelectronic analogs of alkynes and have eluded facile synthesis until recently. We have reported that the combination of a phosphinidene transfer agent, Ar TerP(PMe3 ) (Ar Ter=2,6-Ar2 -C6 H3 ), with (Cp*Al)4 (Cp*=C5 (CH3 )5 ) afforded the phosphaalumenes Ar TerPAlCp* as isolable, violet, thermally stable compounds. In here we describe attempts to utilize Mes*P(PMe3 ) (Mes*=2,4,6-tBu3 -C6 H2 ) as a phosphinidene source in combination with different Al(I) precursors, namely Dip NacnacAl (Dip Nacnac=HC[C(Me)NDip]2 , Dip=2,6-iPr2 -C6 H3 ), (Cp*Al)4 and Cp3t Al (Cp3t =1,2,4-tBu3 -C5 H2 ). In all cases the formation of phosphaalumenes was not observed, however, their intermediate formation is indicated by formation of the dimer [Cp*Al(μ-PMes*)]2 (2) and C-H-bond activation products along the putative P=Al bond, giving unusual 1,2-P,Al-tetrahydronaphtalene derivatives 1 and 4, clearly underlining the role the sterically demanding group on phosphorus plays in these transformations. The reactivity studies are supported by theoretical studies, demonstrating a thermodynamic preference for the C-H activation products. Additionally, we show that there are potential pitfalls in the synthesis of Cp*2 AlH, the precursor to make (Cp*Al)4 and give recommendations how to circumvent these.
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Affiliation(s)
- Samuel Nees
- Institut für Anorganische Chemie, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
- Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Henrik Beer
- Leibniz-Institut für Katalyse e.V. (LIKAT), Albert-Einstein-Straße 29a, 18059, Rostock, Germany
| | - Philip Just
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059, Rostock, Germany
| | - Leon M Teichmeier
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059, Rostock, Germany
| | - Leif E Christoffer
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059, Rostock, Germany
| | - Ailina Guljam
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059, Rostock, Germany
| | - Kushik
- Leibniz-Institut für Katalyse e.V. (LIKAT), Albert-Einstein-Straße 29a, 18059, Rostock, Germany
| | - Holger Braunschweig
- Institut für Anorganische Chemie, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
- Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
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