1
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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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2
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Carder HM, Occhialini G, Bistoni G, Riplinger C, Kwan EE, Wendlandt AE. The sugar cube: Network control and emergence in stereoediting reactions. Science 2024; 385:456-463. [PMID: 39052778 DOI: 10.1126/science.adp2447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Accepted: 06/07/2024] [Indexed: 07/27/2024]
Abstract
Stereochemical editing strategies have recently enabled the transformation of readily accessible substrates into rare and valuable products. Typically, site selectivity is achieved by minimizing kinetic complexity by using protecting groups to suppress reactivity at undesired sites (substrate control) or by using catalysts with tailored shapes to drive reactivity at the desired site (catalyst control). We propose "network control," a contrasting paradigm that exploits hidden interactions between rate constants to greatly amplify modest intrinsic biases and enable precise multisite editing. When network control is applied to the photochemical isomerization of hexoses, six of the eight possible diastereomers can be selectively obtained. The amplification effect can be viewed as a mesoscale phenomenon between the limiting regimes of kinetic control in simple chemical systems and metabolic regulation in complex biological systems.
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Affiliation(s)
- Hayden M Carder
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Gino Occhialini
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Giovanni Bistoni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
| | | | | | - Alison E Wendlandt
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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3
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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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4
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Beletsan OB, Gordiy I, Lunkov SS, Kalinin MA, Alkhimova LE, Nosach EA, Ilin EA, Bespalov AV, Dallakyan OL, Chamkin AA, Prolomov IV, Zaripov RA, Pershin AA, Protsenko BO, Rusalev YV, Oganov RA, Kovaleva DK, Mironov VA, Dotsenko VV, Genaev AM, Sharapa DI, Tikhonov DS. From a humorous post to a detailed quantum-chemical study: isocyanate synthesis revisited. Phys Chem Chem Phys 2024; 26:13850-13861. [PMID: 38656824 DOI: 10.1039/d3cp04654k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Isocyanates play an essential role in modern manufacturing processes, especially in polyurethane production. There are numerous synthesis strategies for isocyanates both under industrial and laboratory conditions, which do not prevent searching for alternative highly efficient synthetic protocols. Here, we report a detailed theoretical investigation of the mechanism of sulfur dioxide-catalyzed rearrangement of phenylnitrile oxide into phenyl isocyanate, which was first reported in 1977. The DLPNO-CCSD(T) method and up-to-date DFT protocols were used to perform a highly accurate quantum-chemical study of the rearrangement mechanism. An overview of various organic and inorganic catalysts has revealed other potential catalysts, such as sulfur trioxide and selenium dioxide. Furthermore, the present study elucidated how substituents in phenylnitrile oxide influence reaction kinetics. This study was performed by a self-organized collaboration of scientists initiated by a humorous post on the VK social network.
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Affiliation(s)
- Oleg B Beletsan
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Igor Gordiy
- ChemU Corporation Ltd, 17 17 Gr. Xenopoulou St., 3106 Limassol, Cyprus
| | - Sergey S Lunkov
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
- N. D. Zelinsky Institute of Organic Chemistry, Leninsky prosp. 47, 119991 Moscow, Russia
| | - Mikhail A Kalinin
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Larisa E Alkhimova
- Center for Nature-Inspired Engineering, University of Tyumen, 625003 Tyumen, Russia
- School of Natural Sciences, University of Tyumen, 625003 Tyumen, Russia
| | - Egor A Nosach
- Department of Fundamental Physical and Chemical Engineering, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Egor A Ilin
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
- N. D. Zelinsky Institute of Organic Chemistry, Leninsky prosp. 47, 119991 Moscow, Russia
| | - Alexandr V Bespalov
- Department of Chemistry and High Technologies, Kuban State University, 149 Stavropolskaya St., 350040 Krasnodar, Russia
| | - Olgert L Dallakyan
- Computational Material Science Laboratory, Department of Physics, Yerevan State University, 0025 Yerevan, Armenia
| | - Aleksandr A Chamkin
- A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, 119334 Moscow, Russia
| | - Ilya V Prolomov
- D. Mendeleev University of Chemical Technology of Russia, 125047 Moscow, Russia
- N. D. Zelinsky Institute of Organic Chemistry, Leninsky prosp. 47, 119991 Moscow, Russia
| | - Radion A Zaripov
- Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Andrey A Pershin
- Samara Branch of Lebedev Physical Institute, 443011 Samara, Russia
- Department of Physics, Samara University, 443086 Samara, Russia
| | - Bogdan O Protsenko
- The Smart Materials Research Institute, Southern Federal University, 344090 Rostov-on-Don, Russia
| | - Yury V Rusalev
- The Smart Materials Research Institute, Southern Federal University, 344090 Rostov-on-Don, Russia
| | - Ruslan A Oganov
- Department of Biochemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Diana K Kovaleva
- Department of Biochemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Vladimir A Mironov
- A. M. Butlerov Chemistry Institute, Kazan Federal University, 420008 Kazan, Russia
| | - Victor V Dotsenko
- Department of Chemistry and High Technologies, Kuban State University, 149 Stavropolskaya St., 350040 Krasnodar, Russia
- Faculty of Chemistry and Pharmacy, North-Caucasus Federal University, 355017 Stavropol, Russia
| | - Alexandr M Genaev
- N.N. Vorozhtsov Institute of Organic Chemistry, 630090 Novosibirsk, Russia.
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5
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Boča R, Imrich R, Štofko J, Vranovičová B, Rajnák C. Molecular properties of linear amino acids in water. Amino Acids 2024; 56:5. [PMID: 38300332 PMCID: PMC10834582 DOI: 10.1007/s00726-023-03365-3] [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: 09/06/2023] [Accepted: 12/13/2023] [Indexed: 02/02/2024]
Abstract
Four linear amino acids of increased separation of the carboxyl and amino groups, namely glycine (aminoacetic acid), β-alanine (3-aminopropanoic acid), GABA (4-aminobutanoic acid) and DAVA (5-aminopentanoic acid), have been studied by quantum chemical ab initio and DFT methods including the solvent effect in order to get electronic structure and molecular descriptors, such as ionisation energy, electron affinity, molecular electronegativity, chemical hardness, electrophilicity index, dipole moment, quadrupole moment and dipole polarizability. Thermodynamic functions (zero-point energy, inner energy, enthalpy, entropy, and the Gibbs energy) were evaluated after the complete vibrational analysis at the true energy minimum provided by the full geometry optimization. Reaction Gibbs energy allows evaluating the absolute redox potentials on reduction and/or oxidation. The non-local non-additive molecular descriptors were compared along the series showing which of them behave as extensive, varying in match with the molar mass and/or separation of the carboxyl and amino groups. Amino acidic forms and zwitterionic forms of the substances were studied in parallel in order to compare their relative stability and redox properties. In total, 24 species were investigated by B3LYP/def2-TZVPD method (M1) including neutral molecules, molecular cations and molecular anions. For comparison, MP2/def2-TZVPD method (M2) with full geometry optimization and vibrational analysis in water has been applied for 12 species; analogously, for 24 substances, DLPNO-CCSD(T)/aug-cc-pVTZ method (M3) has been applied in the geometry obtained by MP2 and/or B3LYP. It was found that the absolute oxidation potential correlates with the adiabatic ionisation energy; the absolute reduction potential correlates with the adiabatic electron affinity and the electrophilicity index. In order to validate the used methodology with experimental vertical ionisation energies and vibrational spectrum obtained in gas phase, calculations were done also in vacuo.
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Affiliation(s)
- Roman Boča
- Faculty of Health Sciences, University of SS Cyril and Methodius, 91701, Trnava, Slovakia.
| | - Richard Imrich
- Faculty of Health Sciences, University of SS Cyril and Methodius, 91701, Trnava, Slovakia
| | - Juraj Štofko
- Faculty of Health Sciences, University of SS Cyril and Methodius, 91701, Trnava, Slovakia
| | - Beáta Vranovičová
- Faculty of Natural Sciences, University of SS Cyril and Methodius, 91701, Trnava, Slovakia
| | - Cyril Rajnák
- Faculty of Natural Sciences, University of SS Cyril and Methodius, 91701, Trnava, Slovakia
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6
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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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7
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Petrov AI. Quantum chemical modeling of the thermodynamics of the formation of Au(III), Pd(II), and Pt(II) chloride complexes. J Mol Model 2022; 28:391. [DOI: 10.1007/s00894-022-05381-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 11/08/2022] [Indexed: 11/18/2022]
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8
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Wang Y, Ni Z, Neese F, Li W, Guo Y, Li S. Cluster-in-Molecule Method Combined with the Domain-Based Local Pair Natural Orbital Approach for Electron Correlation Calculations of Periodic Systems. J Chem Theory Comput 2022; 18:6510-6521. [PMID: 36240189 DOI: 10.1021/acs.jctc.2c00412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The cluster-in-molecule (CIM) method was extended to systems with periodic boundary conditions (PBCs) in a previous work (PBC-CIM) [J. Chem. Theory Comput.2019, 15, 2933], which is able to compute the electronic structures of periodic systems at second-order Møller-Plesset perturbation theory (MP2) and coupled cluster singles and doubles (CCSD) levels. However, the high computational costs of CCSD with respect to the size of clusters limit the usage of PBC-CIM to crystals with small or medium unit cells. In this work, we further develop the PBC-CIM method by employing the domain-based local pair natural orbital (DLPNO) methods for the electron correlation calculations of clusters to reduce the computational costs. The combined approach allows CCSD with perturbative triples, denoted as CCSD(T), to be computationally available for accurate descriptions of periodic systems. The distant-pair correction is also implemented to improve the accuracy of PBC-CIM. As in the molecular cases, the distant pair correction significantly improves the accuracy of various PBC-CIM methods with few additional costs. The PBC-CIM-DLPNO-CCSD(T) approach has been applied to investigate the optimized lattice parameter of the cubic LiCl crystal and two adsorption problems (CO on the NaCl(100) surface and H2O on the h-BN surface). The results show that the CIM-DLPNO-CCSD(T) method offers accurate and efficient descriptions for the studied systems. Another application to the cohesive energy of the acetic acid crystal reveals that large basis sets are necessary for reliable calculations on the cohesive energies of molecular crystals.
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Affiliation(s)
- Yuqi Wang
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing210023, 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, Hangzhou311121, P. R. China
| | - Frank Neese
- Max Planck Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der RuhrD-45470, Germany
| | - Wei Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing210023, P. R. China
| | - Yang Guo
- Qingdao Institute for Theoretical and Computational Sciences, Shandong University, Qingdao, Shandong266237, P. R. China
| | - Shuhua Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing210023, P. R. China
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9
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King NJ, Brown A. Intermolecular Interactions of Pyrene and Its Oxides in Toluene Solution. J Phys Chem A 2022; 126:4931-4940. [PMID: 35882012 DOI: 10.1021/acs.jpca.2c02666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this work, the conformer-rotamer ensemble sampling tool (CREST), with the underlying semiempirical GFN2-xtb method, was used for automated geometry exploration of the homodimers of pyrene, pyrene-4,5-dione, and pyrene-4,5,9,10-tetraone, along with the heterodimer of pyrene and pyrene-4,5,9,10-tetraone. Geometries and energies of the dimers were further refined at the ωB97X-D4/def2-TZVP level of theory, both in the gas phase and in toluene solution. Computations in solution were handled using the CPCM (conductor-like polarizible continuum model) and SMD (solvation model based on density) models. Two previously unidentified pyrene-homodimer conformations were identified, and the effects of oxidation on the geometries and energies of dimerization were explored; in general, oxidation leads to stronger intermolecular interactions and decreased solubility in toluene. For selected dimers, DLPNO-CCSD(T)/cc-pVTZ/SMD(Toluene) energies were determined at the DFT geometries and illustrated the accuracy of the ωB97X-D4 approach, with an MAD of 1.47 kJ/mol.
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Affiliation(s)
- Nathanael J King
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Alex Brown
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
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10
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Bruno G, de Souza B, Neese F, Bistoni G. Can domain-based local pair natural orbitals approaches accurately predict phosphorescence energies? Phys Chem Chem Phys 2022; 24:14228-14241. [PMID: 35649286 DOI: 10.1039/d2cp01623k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Since the discovery of the peculiar conducting and optical properties of aromatics, many efforts have been made to characterize and predict their phosphorescence. This physical process is exploited in modern Organic Emitting Light Diodes (OLEDs), and it is also one of the processes decreasing the efficiency of Dye-sensitized solar cells (DSSCs). Herein, we propose a computational strategy for the accurate calculation of singlet-triplet gaps of aromatic compounds, which provides results that are in excellent agreement with available experimental data. Our approach relies on the domain-based local pair natural orbital (DLPNO) variant of the "gold standard" CCSD(T) method. The convergence of our results with respect to the key technical parameters of the calculation, such as the basis set used, the approximations employed in the perturbative triples correction, and the dimension of the PNOs space, was thoroughly discussed.
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Affiliation(s)
- Giovanna Bruno
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | | | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Giovanni Bistoni
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany.,Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, Italy.
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11
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Neese F. Software update: The
ORCA
program system—Version 5.0. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1606] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Frank Neese
- Max Planck Institut für Kohlenforschung Mülheim an der Ruhr Germany
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12
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Bhattacharjee S, Isegawa M, Garcia-Ratés M, Neese F, Pantazis DA. Ionization Energies and Redox Potentials of Hydrated Transition Metal Ions: Evaluation of Domain-Based Local Pair Natural Orbital Coupled Cluster Approaches. J Chem Theory Comput 2022; 18:1619-1632. [PMID: 35191695 PMCID: PMC8908766 DOI: 10.1021/acs.jctc.1c01267] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
![]()
Hydrated transition
metal ions are prototypical systems that can
be used to model properties of transition metals in complex chemical
environments. These seemingly simple systems present challenges for
computational chemistry and are thus crucial in evaluations of quantum
chemical methods for spin-state and redox energetics. In this work,
we explore the applicability of the domain-based pair natural orbital
implementation of coupled cluster (DLPNO-CC) theory to the calculation
of ionization energies and redox potentials for hydrated ions of all
first transition row (3d) metals in the 2+/3+ oxidation states, in
connection with various solvation approaches. In terms of model definition,
we investigate the construction of a minimally explicitly hydrated
quantum cluster with a first and second hydration layer. We report
on the convergence with respect to the coupled cluster expansion and
the PNO space, as well as on the role of perturbative triple excitations.
A recent implementation of the conductor-like polarizable continuum
model (CPCM) for the DLPNO-CC approach is employed to determine self-consistent
redox potentials at the coupled cluster level. Our results establish
conditions for the convergence of DLPNO-CCSD(T) energetics and stress
the absolute necessity to explicitly consider the second solvation
sphere even when CPCM is used. The achievable accuracy for redox potentials
of a practical DLPNO-based approach is, on average, 0.13 V. Furthermore,
multilayer approaches that combine a higher-level DLPNO-CCSD(T) description
of the first solvation sphere with a lower-level description of the
second solvation layer are investigated. The present work establishes
optimal and transferable methodological choices for employing DLPNO-based
coupled cluster theory, the associated CPCM implementation, and cost-efficient
multilayer derivatives of the approach for open-shell transition metal
systems in complex environments.
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Affiliation(s)
- Sinjini Bhattacharjee
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Miho Isegawa
- International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Miquel Garcia-Ratés
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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13
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Altun A, Garcia-Ratés M, Neese F, Bistoni G. Unveiling the complex pattern of intermolecular interactions responsible for the stability of the DNA duplex. Chem Sci 2021; 12:12785-12793. [PMID: 34703565 PMCID: PMC8494058 DOI: 10.1039/d1sc03868k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/26/2021] [Indexed: 01/21/2023] Open
Abstract
Herein, we provide new insights into the intermolecular interactions responsible for the intrinsic stability of the duplex structure of a large portion of human B-DNA by using advanced quantum mechanical methods. Our results indicate that (i) the effect of non-neighboring bases on the inter-strand interaction is negligibly small, (ii) London dispersion effects are essential for the stability of the duplex structure, (iii) the largest contribution to the stability of the duplex structure is the Watson-Crick base pairing - consistent with previous computational investigations, (iv) the effect of stacking between adjacent bases is relatively small but still essential for the duplex structure stability and (v) there are no cooperativity effects between intra-strand stacking and inter-strand base pairing interactions. These results are consistent with atomic force microscope measurements and provide the first theoretical validation of nearest neighbor approaches for predicting thermodynamic data of arbitrary DNA sequences.
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Affiliation(s)
- Ahmet Altun
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 D-45470 Mülheim an der Ruhr Germany
| | - Miquel Garcia-Ratés
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 D-45470 Mülheim an der Ruhr Germany
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 D-45470 Mülheim an der Ruhr Germany
| | - Giovanni Bistoni
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 D-45470 Mülheim an der Ruhr Germany
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