1
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Chan B, Karton A. The Bond Energy of the Carbon Skeleton in Polyaromatic Halohydrocarbon Molecules. Chemphyschem 2024:e202400234. [PMID: 39361551 DOI: 10.1002/cphc.202400234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/13/2024] [Indexed: 10/05/2024]
Abstract
We have investigated the thermochemical stability of the carbon skeleton in polycyclic aromatic (halo) hydrocarbons using a systematic collection of molecules (the PAHH343 set). With high-level quantum chemistry methods such as W1X-2, we have obtained chemically accurate (i. e.,±~5 kJ mol-1) "normalized carbon skeleton" bond energies. They are calculated by removing the C-H and C-X (X=F, Cl) bond energies from the total atomization energy, and then normalizing on a per-carbon basis. For species with isomeric halogen-substitution pattern, the energetic variation is generally small, though larger difference can also be seen due to structural distortion from steric repulsion. The skeleton energy becomes smaller with an increasing number of halogen atoms due to the withdrawal of electron density from the bonding orbitals, mainly through the σ-bonds. We have further assessed the performance of some low-cost quantum chemistry methods for the PAHH343 set. The deviations from reference values are largely systematic, and can thus be compensated for, yielding errors that are on average below 10 kJ mol-1. This provides the prospect for the study of an even wider range of PAHH and related systems.
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Affiliation(s)
- Bun Chan
- Graduate School of Engineering, Nagasaki University, Bunkyo 1-14, Nagasaki-shi, Nagasaki, 852-8521, Japan
| | - Amir Karton
- School of Science and Technology, University of New England, Armidale, NSW 2351, Australia
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2
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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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3
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Cao Y, Balduf T, Beachy MD, Bennett MC, Bochevarov AD, Chien A, Dub PA, Dyall KG, Furness JW, Halls MD, Hughes TF, Jacobson LD, Kwak HS, Levine DS, Mainz DT, Moore KB, Svensson M, Videla PE, Watson MA, Friesner RA. Quantum chemical package Jaguar: A survey of recent developments and unique features. J Chem Phys 2024; 161:052502. [PMID: 39092934 DOI: 10.1063/5.0213317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 07/12/2024] [Indexed: 08/04/2024] Open
Abstract
This paper is dedicated to the quantum chemical package Jaguar, which is commercial software developed and distributed by Schrödinger, Inc. We discuss Jaguar's scientific features that are relevant to chemical research as well as describe those aspects of the program that are pertinent to the user interface, the organization of the computer code, and its maintenance and testing. Among the scientific topics that feature prominently in this paper are the quantum chemical methods grounded in the pseudospectral approach. A number of multistep workflows dependent on Jaguar are covered: prediction of protonation equilibria in aqueous solutions (particularly calculations of tautomeric stability and pKa), reactivity predictions based on automated transition state search, assembly of Boltzmann-averaged spectra such as vibrational and electronic circular dichroism, as well as nuclear magnetic resonance. Discussed also are quantum chemical calculations that are oriented toward materials science applications, in particular, prediction of properties of optoelectronic materials and organic semiconductors, and molecular catalyst design. The topic of treatment of conformations inevitably comes up in real world research projects and is considered as part of all the workflows mentioned above. In addition, we examine the role of machine learning methods in quantum chemical calculations performed by Jaguar, from auxiliary functions that return the approximate calculation runtime in a user interface, to prediction of actual molecular properties. The current work is second in a series of reviews of Jaguar, the first having been published more than ten years ago. Thus, this paper serves as a rare milestone on the path that is being traversed by Jaguar's development in more than thirty years of its existence.
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Affiliation(s)
- Yixiang Cao
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Ty Balduf
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Michael D Beachy
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - M Chandler Bennett
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Art D Bochevarov
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Alan Chien
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Pavel A Dub
- Schrödinger, Inc., 9868 Scranton Road, Suite 3200, San Diego, California 92121, USA
| | - Kenneth G Dyall
- Schrödinger, Inc., 101 SW Main St., Suite 1300, Portland, Oregon 97204, USA
| | - James W Furness
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Mathew D Halls
- Schrödinger, Inc., 9868 Scranton Road, Suite 3200, San Diego, California 92121, USA
| | - Thomas F Hughes
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Leif D Jacobson
- Schrödinger, Inc., 101 SW Main St., Suite 1300, Portland, Oregon 97204, USA
| | - H Shaun Kwak
- Schrödinger, Inc., 101 SW Main St., Suite 1300, Portland, Oregon 97204, USA
| | - Daniel S Levine
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Daniel T Mainz
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Kevin B Moore
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Mats Svensson
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Pablo E Videla
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Mark A Watson
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, USA
| | - Richard A Friesner
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, USA
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4
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Bressanini D. Are There Atoms Inside Atomic Anions? H - and Li - Revisited. J Phys Chem A 2024; 128:4588-4592. [PMID: 38803162 DOI: 10.1021/acs.jpca.4c02319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Yes, atoms are still there. We show that the inner electrons of H- and Li- behave almost as if the outer electrons were not present and that the effect of electron correlation is such that the outer loosely bound electron tries to stay as close as possible to the nucleus but without interfering too much with the electronic distribution of the inner electrons in such a way that the electronic densities of H and Li are still recognizable inside the respective negative ions. We introduce the concept of partial electronic distribution, one for each electron: a particular decomposition of the electronic density. Equipped with this tool, we analyze the internal structure of the anions to recover the chemical intuition of an atomic negative ion on firm quantum mechanical grounds: that of an atom, almost unperturbed, with a loosely bound electron.
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Affiliation(s)
- Dario Bressanini
- Dipartimento di Scienza e Alta Tecnologia, Università degli Studi dell'Insubria, Via Valleggio 9, Como 22100, Italy
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5
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Bistoni G, Altun A, Wang Z, Neese F. Local Energy Decomposition Analysis of London Dispersion Effects: From Simple Model Dimers to Complex Biomolecular Assemblies. Acc Chem Res 2024; 57:1411-1420. [PMID: 38602396 PMCID: PMC11080063 DOI: 10.1021/acs.accounts.4c00085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/04/2024] [Accepted: 04/04/2024] [Indexed: 04/12/2024]
Abstract
ConspectusLondon dispersion (LD) forces are ubiquitous in chemistry, playing a pivotal role in a wide range of chemical processes. For example, they influence the structure of molecular crystals, the selectivity of organocatalytic transformations, and the formation of biomolecular assemblies. Harnessing these forces for chemical applications requires consistent quantification of the LD energy across a broad and diverse spectrum of chemical scenarios. Despite the great progress made in recent years in the development of experimental strategies for LD quantification, quantum chemical methods remain one of the most useful tools in the hand of chemists for the study of these weak interactions. Unfortunately, the accurate quantification of LD effects in complex systems poses many challenges for electronic structure theories. One of the problems stems from the fact that LD forces originate from long-range electronic dynamic correlation, and hence, their rigorous description requires the use of complex, highly correlated wave function-based methods. These methods typically feature a steep scaling with the system size, limiting their applicability to small model systems. Another core challenge lies in disentangling short-range from long-range dynamic correlation, which from a rigorous quantum mechanical perspective is not possible.In this Account, we describe our research endeavors in the development of broadly applicable computational methods for LD quantification in molecular chemistry as well as challenging applications of these schemes in various domains of chemical research. Our strategy lies in the use of local correlation theories to reduce the computational cost associated with complex electronic structure methods while providing at the same time a simple means of decomposition of dynamic correlation into its long-range and short-range components. In particular, the local energy decomposition (LED) scheme at the domain-based local pair natural orbital coupled cluster (DLPNO-CCSD(T)) level has emerged as a powerful tool in our research, offering a clear-cut quantitative definition of the LD energy that remains valid across a plethora of different chemical scenarios. Typical applications of this scheme are examined, encompassing protein-ligand interactions and reactivity studies involving many fragments and complex electronic structures. In addition, our research also involves the development of novel cost-effective methodologies, which exploit the LED definition of the LD energy, for LD energy quantification that are, in principle, applicable to systems with thousands of atoms. The Hartree-Fock plus London Dispersion (HFLD) scheme, correcting the HF interaction energy using an approximate CCSD(T)-based LD energy, is a useful, parameter-free electronic structure method for the study of LD effects in systems with hundreds of molecular fragments. However, the usefulness of the LED scheme reaches beyond providing an interpretation of the calculated DLPNO-CCSD(T) or DLPNO-MP2 interaction energies. For example, the dispersion energies obtained from the LED can be fruitfully used in order to parametrize semiempirical dispersion models. We will demonstrate this in the context of an emerging semiempirical method, namely, the Natural Orbital Tied Constructed Hamiltonian (NOTCH) method. NOTCH incorporates LED-derived LD energies and shows promising accuracy at a minimum amount of empiricism. Thus, it holds substantial promise for large and complex systems.
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Affiliation(s)
- Giovanni Bistoni
- Department
of Chemistry, Biology and Biotechnology, University of Perugia Via Elce di Sotto, 8, 06123 Perugia, Italy
| | - Ahmet Altun
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Zikuan Wang
- 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
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6
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Focke K, De Santis M, Wolter M, Martinez B JA, Vallet V, Pereira Gomes AS, Olejniczak M, Jacob CR. Interoperable workflows by exchanging grid-based data between quantum-chemical program packages. J Chem Phys 2024; 160:162503. [PMID: 38686818 DOI: 10.1063/5.0201701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/02/2024] [Indexed: 05/02/2024] Open
Abstract
Quantum-chemical subsystem and embedding methods require complex workflows that may involve multiple quantum-chemical program packages. Moreover, such workflows require the exchange of voluminous data that go beyond simple quantities, such as molecular structures and energies. Here, we describe our approach for addressing this interoperability challenge by exchanging electron densities and embedding potentials as grid-based data. We describe the approach that we have implemented to this end in a dedicated code, PyEmbed, currently part of a Python scripting framework. We discuss how it has facilitated the development of quantum-chemical subsystem and embedding methods and highlight several applications that have been enabled by PyEmbed, including wave-function theory (WFT) in density-functional theory (DFT) embedding schemes mixing non-relativistic and relativistic electronic structure methods, real-time time-dependent DFT-in-DFT approaches, the density-based many-body expansion, and workflows including real-space data analysis and visualization. Our approach demonstrates, in particular, the merits of exchanging (complex) grid-based data and, in general, the potential of modular software development in quantum chemistry, which hinges upon libraries that facilitate interoperability.
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Affiliation(s)
- Kevin Focke
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Matteo De Santis
- CNRS, UMR 8523-PhLAM-Physique des Lasers Atomes et Molécules, Univ. Lille, F-59000 Lille, France
| | - Mario Wolter
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Jessica A Martinez B
- CNRS, UMR 8523-PhLAM-Physique des Lasers Atomes et Molécules, Univ. Lille, F-59000 Lille, France
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, USA
| | - Valérie Vallet
- CNRS, UMR 8523-PhLAM-Physique des Lasers Atomes et Molécules, Univ. Lille, F-59000 Lille, France
| | | | - Małgorzata Olejniczak
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
| | - Christoph R Jacob
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
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7
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Zhang P, Yu ZX. Dynamically or Kinetically Controlled? Computational Study of the Mechanisms of Electrophilic Aminoalkenylation of Heteroaromatics with Keteniminium Ions. J Org Chem 2024; 89:4326-4335. [PMID: 38506441 DOI: 10.1021/acs.joc.3c02379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Quantum chemical calculations and molecular dynamics simulations were applied to study the electrophilic aminoalkenylation of heteroaromatics with keniminium ions. Post-transition state bifurcation (PTSB) was found in the electrophilic addition step for the aminoalkenylation of pyrroles and indoles, and the selectivity for these reactions was dynamically controlled. However, the aminoalkenylation of furan was kinetically controlled because no apparent PTSB was found in the electrophilic addition step. The substituents on the keteniminium ions can also affect the dynamic results for the aminoalkenylations to pyrroles: the C2-aminoalkenylated product is much more favored over the C3-aminoalkenylated product for keteniminium ions with electron-donating substituents, while the product ratio (C2 product/C3 product) decreased when stronger electron-withdrawing substituents were applied.
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Affiliation(s)
- Pan Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry, Peking University, Beijing 100871, China
| | - Zhi-Xiang Yu
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry, Peking University, Beijing 100871, China
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8
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Pracht P, Grimme S, Bannwarth C, Bohle F, Ehlert S, Feldmann G, Gorges J, Müller M, Neudecker T, Plett C, Spicher S, Steinbach P, Wesołowski PA, Zeller F. CREST-A program for the exploration of low-energy molecular chemical space. J Chem Phys 2024; 160:114110. [PMID: 38511658 DOI: 10.1063/5.0197592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 02/29/2024] [Indexed: 03/22/2024] Open
Abstract
Conformer-rotamer sampling tool (CREST) is an open-source program for the efficient and automated exploration of molecular chemical space. Originally developed in Pracht et al. [Phys. Chem. Chem. Phys. 22, 7169 (2020)] as an automated driver for calculations at the extended tight-binding level (xTB), it offers a variety of molecular- and metadynamics simulations, geometry optimization, and molecular structure analysis capabilities. Implemented algorithms include automated procedures for conformational sampling, explicit solvation studies, the calculation of absolute molecular entropy, and the identification of molecular protonation and deprotonation sites. Calculations are set up to run concurrently, providing efficient single-node parallelization. CREST is designed to require minimal user input and comes with an implementation of the GFNn-xTB Hamiltonians and the GFN-FF force-field. Furthermore, interfaces to any quantum chemistry and force-field software can easily be created. In this article, we present recent developments in the CREST code and show a selection of applications for the most important features of the program. An important novelty is the refactored calculation backend, which provides significant speed-up for sampling of small or medium-sized drug molecules and allows for more sophisticated setups, for example, quantum mechanics/molecular mechanics and minimum energy crossing point calculations.
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Affiliation(s)
- Philipp Pracht
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Christoph Bannwarth
- Institute for Physical Chemistry, RWTH Aachen University, Melatener Str. 20, 52056 Aachen, Germany
| | - Fabian Bohle
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Sebastian Ehlert
- AI4Science, Microsoft Research, Evert van de Beekstraat 354, 1118 CZ Schiphol, The Netherlands
| | - Gereon Feldmann
- Institute for Physical Chemistry, RWTH Aachen University, Melatener Str. 20, 52056 Aachen, Germany
| | - Johannes Gorges
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Marcel Müller
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Tim Neudecker
- Institute for Physical and Theoretical Chemistry, University of Bremen, 28359 Bremen, Germany
| | - Christoph Plett
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | | | - Pit Steinbach
- Institute for Physical Chemistry, RWTH Aachen University, Melatener Str. 20, 52056 Aachen, Germany
| | - Patryk A Wesołowski
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Felix Zeller
- Institute for Physical and Theoretical Chemistry, University of Bremen, 28359 Bremen, Germany
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9
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Baldinelli L, De Angelis F, Bistoni G. Unraveling Atomic Contributions to the London Dispersion Energy: Insights into Molecular Recognition and Reactivity. J Chem Theory Comput 2024; 20:1923-1931. [PMID: 38324509 DOI: 10.1021/acs.jctc.3c00977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
We present a general framework that enables quantification with atomic resolution of the overall London dispersion energy, which can be readily integrated with currently available energy decomposition schemes. This approach can be used to determine the contribution of individual atoms and functional groups to molecular recognition, conformational preferences, molecular stability, and reactivity. Its efficacy across diverse realms of molecular chemistry and biology is demonstrated with application to molecular balances in solution, asymmetric organocatalytic transformations, and a subcomplex of the F1FO ATP synthase.
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Affiliation(s)
- Lorenzo Baldinelli
- Dipartmento di Chimica, Biologia e Biotecnologie, Università Degli Studi Di Perugia, Via Elce di sotto, 8, Perugia 06123, Italy
| | - Filippo De Angelis
- Dipartmento di Chimica, Biologia e Biotecnologie, Università Degli Studi Di Perugia, Via Elce di sotto, 8, Perugia 06123, Italy
- Computational Laboratory for Hybrid/Organic Photovoltaics (CLHYO), Istituto CNR di Scienze e Tecnologie Chimiche "Giulio Natta" (CNR-SCITEC), Perugia 06123, Italy
- Department of Mechanical Engineering, College of Engineering, Prince Mohammad Bin Fahd University, Al Khobar 31952, Saudi Arabia
- SKKU Institute of Energy Science and Technology (SIEST), Sungkyunkwan University, Suwon 440-746, Korea
| | - Giovanni Bistoni
- Dipartmento di Chimica, Biologia e Biotecnologie, Università Degli Studi Di Perugia, Via Elce di sotto, 8, Perugia 06123, Italy
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10
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Tchakoua T, Jansen T, van Nies Y, van den Elshout RFA, van Boxmeer BAB, Poort SP, Ackermans MG, Beltrão GS, Hildebrand SA, Beekman SEJ, van der Drift T, Kaart S, Šantić A, Spuijbroek EE, Gerrits N, Somers MF, Kroes GJ. Constructing Mixed Density Functionals for Describing Dissociative Chemisorption on Metal Surfaces: Basic Principles. J Phys Chem A 2023; 127:10481-10498. [PMID: 38051300 PMCID: PMC10726370 DOI: 10.1021/acs.jpca.3c01932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
The production of a majority of chemicals involves heterogeneous catalysis at some stage, and the rates of many heterogeneously catalyzed processes are governed by transition states for dissociative chemisorption on metals. Accurate values of barrier heights for dissociative chemisorption on metals are therefore important to benchmarking electronic structure theory in general and density functionals in particular. Such accurate barriers can be obtained using the semiempirical specific reaction parameter (SRP) approach to density functional theory. However, this approach has thus far been rather ad hoc in its choice of the generic expression of the SRP functional to be used, and there is a need for better heuristic approaches to determining the mixing parameters contained in such expressions. Here we address these two issues. We investigate the ability of several mixed, parametrized density functional expressions combining exchange at the generalized gradient approximation (GGA) level with either GGA or nonlocal correlation to reproduce barrier heights for dissociative chemisorption on metal surfaces. For this, seven expressions of such mixed density functionals are tested on a database consisting of results for 16 systems taken from a recently published slightly larger database called SBH17. Three expressions are derived that exhibit high tunability and use correlation functionals that are either of the PBE GGA form or of one of two limiting nonlocal forms also describing the attractive van der Waals interaction in an approximate way. We also find that, for mixed density functionals incorporating GGA correlation, the optimum fraction of repulsive RPBE GGA exchange obtained with a specific GGA density functional is correlated with the charge-transfer parameter, which is equal to the difference in the work function of the metal surface and the electron affinity of the molecule. However, the correlation is generally not large and not large enough to obtain accurate guesses of the mixing parameter for the systems considered, suggesting that it does not give rise to a very effective search strategy.
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Affiliation(s)
- Théophile Tchakoua
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Tim Jansen
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Youri van Nies
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | | | - Bart A B van Boxmeer
- Faculty of Applied Engineering, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerpen, Belgium
| | - Saskia P Poort
- Department of Chemical Engineering, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Michelle G Ackermans
- Department of Chemical Engineering, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Gabriel Spiller Beltrão
- Department of Chemical Engineering, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Stefan A Hildebrand
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Steijn E J Beekman
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Thijs van der Drift
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Sam Kaart
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Anthonie Šantić
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Esmee E Spuijbroek
- Department of Chemical Engineering, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Nick Gerrits
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Mark F Somers
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Geert-Jan Kroes
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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11
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Shi B, Zen A, Kapil V, Nagy PR, Grüneis A, Michaelides A. Many-Body Methods for Surface Chemistry Come of Age: Achieving Consensus with Experiments. J Am Chem Soc 2023; 145:25372-25381. [PMID: 37948071 PMCID: PMC10683001 DOI: 10.1021/jacs.3c09616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 10/15/2023] [Accepted: 10/17/2023] [Indexed: 11/12/2023]
Abstract
The adsorption energy of a molecule onto the surface of a material underpins a wide array of applications, spanning heterogeneous catalysis, gas storage, and many more. It is the key quantity where experimental measurements and theoretical calculations meet, with agreement being necessary for reliable predictions of chemical reaction rates and mechanisms. The prototypical molecule-surface system is CO adsorbed on MgO, but despite intense scrutiny from theory and experiment, there is still no consensus on its adsorption energy. In particular, the large cost of accurate many-body methods makes reaching converged theoretical estimates difficult, generating a wide range of values. In this work, we address this challenge, leveraging the latest advances in diffusion Monte Carlo (DMC) and coupled cluster with single, double, and perturbative triple excitations [CCSD(T)] to obtain accurate predictions for CO on MgO. These reliable theoretical estimates allow us to evaluate the inconsistencies in published temperature-programed desorption experiments, revealing that they arise from variations in employed pre-exponential factors. Utilizing this insight, we derive new experimental estimates of the (electronic) adsorption energy with a (more) precise pre-exponential factor. As a culmination of all of this effort, we are able to reach a consensus between multiple theoretical calculations and multiple experiments for the first time. In addition, we show that our recently developed cluster-based CCSD(T) approach provides a low-cost route toward achieving accurate adsorption energies. This sets the stage for affordable and reliable theoretical predictions of chemical reactions on surfaces to guide the realization of new catalysts and gas storage materials.
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Affiliation(s)
- Benjamin
X. Shi
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, CB2 1EW Cambridge, U.K.
| | - Andrea Zen
- Dipartimento
di Fisica Ettore Pancini, Università
di Napoli Federico II, Monte S. Angelo, I-80126 Napoli, Italy
- Department
of Earth Sciences, University College London, Gower Street, WC1E 6BT London, U.K.
| | - Venkat Kapil
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, CB2 1EW Cambridge, U.K.
| | - Péter R. Nagy
- Department
of Physical Chemistry and Materials Science, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Müegyetem rkp. 3, H-1111 Budapest, Hungary
- HUN-REN-BME
Quantum Chemistry Research Group, Müegyetem rkp. 3, H-1111 Budapest, Hungary
- MTA-BME
Lendület Quantum Chemistry Research Group, Müegyetem rkp. 3, H-1111 Budapest, Hungary
| | - Andreas Grüneis
- Institute
for Theoretical Physics, TU Wien, Wiedner Hauptstraße 8-10/136, 1040 Vienna, Austria
| | - Angelos Michaelides
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, CB2 1EW Cambridge, U.K.
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12
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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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13
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Madabeni A, Orian L. The Key Role of Chalcogenurane Intermediates in the Reduction Mechanism of Sulfoxides and Selenoxides by Thiols Explored In Silico. Int J Mol Sci 2023; 24:ijms24097754. [PMID: 37175462 PMCID: PMC10178455 DOI: 10.3390/ijms24097754] [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: 03/23/2023] [Revised: 04/18/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
Sulfoxides and selenoxides oxidize thiols to disulfides while being reduced back to sulfides and selenides. While the reduction mechanism of sulfoxides to sulfides has been thoroughly explored experimentally as well as computationally, less attention has been devoted to the heavier selenoxides. In this work, we explore the reductive mechanism of dimethyl selenoxide, as an archetypal selenoxide and, for the sake of comparison, the reductive mechanism of dimethyl sulfoxide to gain insight into the role of the chalcogen on the reaction substrate. Particular attention is devoted to the key role of sulfurane and selenurane intermediates. Moreover, the capacity of these system to oxidize selenols rather than thiols, leading to the formation of selenyl sulfide bridges, is explored in silico. Notably, this analysis provides molecular insight into the role of selenocysteine in methionine sulfoxide reductase selenoenzyme. The activation strain model of chemical reactivity is employed in the studied reactions as an intuitive tool to bridge the computationally predicted effect of the chalcogen on the chalcogenoxide as well as on the chalcogenol.
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Affiliation(s)
- Andrea Madabeni
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Laura Orian
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Via Marzolo 1, 35131 Padova, Italy
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14
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Zhang P, Yu ZX. Kinetic, Thermodynamic, and Dynamic Control in Normal vs. Cross [2 + 2] Cycloadditions of Ene-Keteniminium Ions: Computational Understanding, Prediction, and Experimental Verification. J Am Chem Soc 2023; 145:9634-9645. [PMID: 37075170 DOI: 10.1021/jacs.3c00685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
Almost all reported intramolecular [2 + 2] reactions of ene-keteniminium ions gave normal [2 + 2] products with a fused bicycle framework, but not cross [2 + 2] products with a bicyclo[3.1.1]heptane skeleton, a highly pursued bioisostere in pharmaceutical chemistry. How to rationalize this and design new cross [2 + 2] reactions? Theoretical studies using density functional theory, high-level ab initio single-point energy calculations, and molecular dynamics showed that this [2 + 2] reaction has all three patterns of regiochemical control: the reaction is controlled either kinetically, thermodynamically, or dynamically. A carbocation model of forming endo and exo carbocations has been proposed to rationalize the reaction outcomes, revealing that the tethers (between alkenes and keteniminium ions), substituents (on the alkenes), and alkene configurations in ene-keteniminium ions play critical roles. These understandings were further used to predict that introducing a substituent in the terminal position of alkene with a trans configuration in ene-keteniminium ions can realize the cross [2 + 2] reaction, which is dynamically controlled for alkyl substituents or kinetically controlled for aryl substituents. These and more other predictions were realized experimentally, and many cross [2 + 2] products with a bicyclo[3.1.1]heptane skeleton can be achieved. Both molecular dynamics and new experiments have also been applied to correct a key but misassigned [2 + 2] product reported in the literature, further supporting the insightful mechanisms reported here.
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Affiliation(s)
- Pan Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry, Peking University, Beijing 100871, China
| | - Zhi-Xiang Yu
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry, Peking University, Beijing 100871, China
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15
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Vuong VQ, Cevallos C, Hourahine B, Aradi B, Jakowski J, Irle S, Camacho C. Accelerating the density-functional tight-binding method using graphical processing units. J Chem Phys 2023; 158:084802. [PMID: 36859078 DOI: 10.1063/5.0130797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Acceleration of the density-functional tight-binding (DFTB) method on single and multiple graphical processing units (GPUs) was accomplished using the MAGMA linear algebra library. Two major computational bottlenecks of DFTB ground-state calculations were addressed in our implementation: the Hamiltonian matrix diagonalization and the density matrix construction. The code was implemented and benchmarked on two different computer systems: (1) the SUMMIT IBM Power9 supercomputer at the Oak Ridge National Laboratory Leadership Computing Facility with 1-6 NVIDIA Volta V100 GPUs per computer node and (2) an in-house Intel Xeon computer with 1-2 NVIDIA Tesla P100 GPUs. The performance and parallel scalability were measured for three molecular models of 1-, 2-, and 3-dimensional chemical systems, represented by carbon nanotubes, covalent organic frameworks, and water clusters.
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Affiliation(s)
- Van-Quan Vuong
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Caterina Cevallos
- School of Chemistry, University of Costa Rica, San José 11501-2060, Costa Rica
| | - Ben Hourahine
- SUPA, Department of Physics, The John Anderson Building, 107 Rottenrow East, Glasgow G4 0NG, United Kingdom
| | - Bálint Aradi
- Bremen Center for Computational Materials Science, Universität Bremen, Bremen, Germany
| | - Jacek Jakowski
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Stephan Irle
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Cristopher Camacho
- School of Chemistry, University of Costa Rica, San José 11501-2060, Costa Rica
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16
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Bannwarth C, Martínez TJ. SQMBox: Interfacing a semiempirical integral library to modular ab initio electronic structure enables new semiempirical methods. J Chem Phys 2023; 158:074109. [PMID: 36813714 DOI: 10.1063/5.0132776] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Ab initio and semiempirical electronic structure methods are usually implemented in separate software packages or use entirely different code paths. As a result, it can be time-consuming to transfer an established ab initio electronic structure scheme to a semiempirical Hamiltonian. We present an approach to unify ab initio and semiempirical electronic structure code paths based on a separation of the wavefunction ansatz and the needed matrix representations of operators. With this separation, the Hamiltonian can refer to either an ab initio or semiempirical treatment of the resulting integrals. We built a semiempirical integral library and interfaced it to the GPU-accelerated electronic structure code TeraChem. Equivalency between ab initio and semiempirical tight-binding Hamiltonian terms is assigned according to their dependence on the one-electron density matrix. The new library provides semiempirical equivalents of the Hamiltonian matrix and gradient intermediates, corresponding to those provided by the ab initio integral library. This enables the straightforward combination of semiempirical Hamiltonians with the full pre-existing ground and excited state functionality of the ab initio electronic structure code. We demonstrate the capability of this approach by combining the extended tight-binding method GFN1-xTB with both spin-restricted ensemble-referenced Kohn-Sham and complete active space methods. We also present a highly efficient GPU implementation of the semiempirical Mulliken-approximated Fock exchange. The additional computational cost for this term becomes negligible even on consumer-grade GPUs, enabling Mulliken-approximated exchange in tight-binding methods for essentially no additional cost.
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Affiliation(s)
- Christoph Bannwarth
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA and SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
| | - Todd J Martínez
- Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA and SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA
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17
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Hasanayn F, Holland PL, Goldman AS, Miller AJM. Lewis Structures and the Bonding Classification of End-on Bridging Dinitrogen Transition Metal Complexes. J Am Chem Soc 2023; 145:4326-4342. [PMID: 36796367 PMCID: PMC9983020 DOI: 10.1021/jacs.2c12243] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
The activation of dinitrogen by coordination to transition metal ions is a widely used and promising approach to the utilization of Earth's most abundant nitrogen source for chemical synthesis. End-on bridging N2 complexes (μ-η1:η1-N2) are key species in nitrogen fixation chemistry, but a lack of consensus on the seemingly simple task of assigning a Lewis structure for such complexes has prevented application of valence electron counting and other tools for understanding and predicting reactivity trends. The Lewis structures of bridging N2 complexes have traditionally been determined by comparing the experimentally observed NN distance to the bond lengths of free N2, diazene, and hydrazine. We introduce an alternative approach here and argue that the Lewis structure should be assigned based on the total π-bond order in the MNNM core (number of π-bonds), which derives from the character (bonding or antibonding) and occupancy of the delocalized π-symmetry molecular orbitals (π-MOs) in MNNM. To illustrate this approach, the complexes cis,cis-[(iPr4PONOP)MCl2]2(μ-N2) (M = W, Re, and Os) are examined in detail. Each complex is shown to have a different number of nitrogen-nitrogen and metal-nitrogen π-bonds, indicated as, respectively: W≡N-N≡W, Re═N═N═Re, and Os-N≡N-Os. It follows that each of these Lewis structures represents a distinct class of complexes (diazanyl, diazenyl, and dinitrogen, respectively), in which the μ-N2 ligand has a different electron donor number (total of 8e-, 6e-, or 4e-, respectively). We show how this classification can greatly aid in understanding and predicting the properties and reactivity patterns of μ-N2 complexes.
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Affiliation(s)
- Faraj Hasanayn
- Department
of Chemistry, American University of Beirut, Beirut 1107 2020, Lebanon,E-mail: (F.H.)
| | - Patrick L. Holland
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Alan S. Goldman
- Department
of Chemistry and Chemical Biology, Rutgers,
The State University of New Jersey, New Brunswick, New Jersey 08903, United States
| | - Alexander J. M. Miller
- Department
of Chemistry, University of North Carolina
at Chapel Hill, Chapel
Hill, North Carolina 27599-3290, United States,E-mail: (A.J.M.M.)
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18
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Tokmachev AM. Statistical Equivalence of Quantum Chemical Methods for Energy Distribution in Water Clusters. Chemphyschem 2023; 24:e202300019. [PMID: 36787108 DOI: 10.1002/cphc.202300019] [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: 01/09/2023] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/15/2023]
Abstract
Methods of quantum chemistry are instrumental in understanding molecular structures and properties. However, the results demonstrate significant variability, which is difficult to predict and rationalize. The fundamental question is whether some molecular systems exhibit properties invariant with respect to the computational method. The idea explored here is that collective properties of statistical ensembles should be more robust than characteristics of individual molecules and their arbitrary sets. This effect is demonstrated for the complete set of hydrogen-bond topologies of the dodecahedral water cluster (H2 O)20 . Non-Gaussian energy distributions produced by various methods have the same functional form despite strong differences in mean values and standard deviations. The conclusion is tested on methods of different complexity and origin employing a number of criteria. A linear mapping between the energies produced by different methods is discussed. The significance of the results is in establishing a collective equivalence property of quantum chemical methods.
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Affiliation(s)
- Andrey M Tokmachev
- National Research Center "Kurchatov Institute", Kurchatov Sq. 1, 123182, Moscow, Russia
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19
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Xue W, Liu H, Zhao B, Tang C, Xia BY, You B. Interheteromolecular Hyperconjugation Boosts (De)hydrogenation for Reversible H 2 Storage. CHEMSUSCHEM 2023; 16:e202201512. [PMID: 36321739 DOI: 10.1002/cssc.202201512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 10/27/2022] [Indexed: 06/16/2023]
Abstract
Interheteromolecular hyperconjugation is ubiquitous in organic systems, affecting bond length, dipole moments, conformations and so on, while its effect on (de)hydrogenation reactivity in a heterogeneous thermo-catalytic system has rarely been explored. Herein, the N-heterocycles containing a benzene ring and aliphatic chain [N-ethylcarbazole (NEC) and N-propylcarbazole (NPC)] were utilized to study the correlation between interheteromolecular hyperconjugation and catalytic (de)hydrogenation. Density functional theory calculations, variable-temperature 1 H nuclear magnetic resonance spectroscopy, and catalytic experiments showed that the presented hyperconjugation between NEC and NPC weakened the electron cloud density of aromatic rings and thus facilitated the reactivity with hydrogen featuring unpaired electrons. Therefore, an extremely low temperature of 80 °C was enough for the hydrogenation. Moreover, this interheteromolecular hyperconjugation was general in other N-heterocycles (e. g., N-methyindole and NPC) and was also effective to (de)deuterate as revealed by isotope experiments. This work expands the application of interheteromolecular hyperconjugation to heterogeneous thermocatalysis for reversible H2 storage.
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Affiliation(s)
- Wenjie Xue
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Material Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Hongxia Liu
- School of Chemistry and Chemical Engineering, Wuhan Textile University, Wuhan, 430200, China
| | - Binbin Zhao
- Department of Materials Science and Engineering, National University of Singapore, Singapore, 117575, Singapore
| | - Conghui Tang
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Material Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Bao Yu Xia
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Material Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Bo You
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Material Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
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20
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Shen H, Wang Z, Head-Gordon M. Generalization of ETS-NOCV and ALMO-COVP Energy Decomposition Analysis to Connect Any Two Electronic States and Comparative Assessment. J Chem Theory Comput 2022; 18:7428-7441. [PMID: 36399401 DOI: 10.1021/acs.jctc.2c00901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Energy decomposition analysis (EDA) is a useful tool for obtaining chemically meaningful insights into molecular interactions. The extended transition-state method with natural orbitals for chemical valence (ETS-NOCV) and the absolutely localized molecular orbital-based method with complementary occupied-virtual pairs (ALMO-COVP) are two successful EDA schemes. Working within ground-state generalized Kohn-Sham density functional theory (DFT), we extend these methods to perform EDA between any two electronic states that can be connected by a unitary transformation of density matrices. A direct proof that the NOCV eigenvalues are symmetric pairs is given, and we also prove that the charge and energy difference defined by ALMO are invariant under certain orbital rotations, allowing us to define COVPs. We point out that ETS is actually a 1-point quadrature to obtain the effective Fock matrix, and though it is reasonably accurate, it can be systematically further improved by adding more quadrature points. We explain why the calculated amount of transferred charge measured by ALMO-COVP is typically much smaller than that of ETS-NOCV and explain why the ALMO-COVP values should be preferred. While the two schemes are independent, ETS-NOCV and ALMO-COVP in fact give a very similar chemical picture for a variety of chemical interactions, including H-H+, the transition structure for the Diels-Alder reaction between ethene and butadiene, and two hydrogen-bonded complexes, H2O···F- and H2O···HF.
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Affiliation(s)
- Hengyuan Shen
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California94720, United States
| | - Zhenling Wang
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California94720, United States
| | - Martin Head-Gordon
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California94720, United States
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21
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Weik M, Domratcheva T. Insight into the structural dynamics of light sensitive proteins from time-resolved crystallography and quantum chemical calculations. Curr Opin Struct Biol 2022; 77:102496. [PMID: 36462226 DOI: 10.1016/j.sbi.2022.102496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/14/2022] [Accepted: 10/14/2022] [Indexed: 12/03/2022]
Abstract
The structural dynamics underlying molecular mechanisms of light-sensitive proteins can be studied by a variety of experimental and computational biophysical techniques. Here we review recent progress in combining time-resolved crystallography at X-ray free electron lasers and quantum chemical calculations to study structural changes in photoenzymes, photosynthetic proteins, photoreceptors, and photoswitchable fluorescent proteins following photoexcitation.
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Affiliation(s)
- Martin Weik
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044 Grenoble, France.
| | - Tatiana Domratcheva
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia; Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany.
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22
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Daru J, Forbert H, Behler J, Marx D. Coupled Cluster Molecular Dynamics of Condensed Phase Systems Enabled by Machine Learning Potentials: Liquid Water Benchmark. PHYSICAL REVIEW LETTERS 2022; 129:226001. [PMID: 36493459 DOI: 10.1103/physrevlett.129.226001] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 09/05/2022] [Accepted: 10/05/2022] [Indexed: 06/17/2023]
Abstract
Coupled cluster theory is a general and systematic electronic structure method, but in particular the highly accurate "gold standard" coupled cluster singles, doubles and perturbative triples, CCSD(T), can only be applied to small systems. To overcome this limitation, we introduce a framework to transfer CCSD(T) accuracy of finite molecular clusters to extended condensed phase systems using a high-dimensional neural network potential. This approach, which is automated, allows one to perform high-quality coupled cluster molecular dynamics, CCMD, as we demonstrate for liquid water including nuclear quantum effects. The machine learning strategy is very efficient, generic, can be systematically improved, and is applicable to a variety of complex systems.
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Affiliation(s)
- János Daru
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Harald Forbert
- Center for Solvation Science ZEMOS, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Jörg Behler
- Universität Göttingen, Institut für Physikalische Chemie, Theoretische Chemie, Tammannstrasse 6, 37077 Göttingen, Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
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23
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Seeman JI, Tantillo DJ. Understanding chemistry: from "heuristic (soft) explanations and reasoning by analogy" to "quantum chemistry". Chem Sci 2022; 13:11461-11486. [PMID: 36320403 PMCID: PMC9575397 DOI: 10.1039/d2sc02535c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 09/06/2022] [Indexed: 12/02/2022] Open
Abstract
"Soft theories," i.e., "heuristic models based on reasoning by analogy" largely drove chemistry understanding for 150 years or more. But soft theories have their limitations and with the expansion of chemistry in the mid-20th century, more and more inexplicable (by soft theory) experimental results were being obtained. In the past 50 years, quantum chemistry, most often in the guise of applied theoretical chemistry including computational chemistry, has provided (a) the underlying "hard evidence" for many soft theories and (b) the explanations for chemical phenomena that were unavailable by soft theories. In this publication, we define "hard theories" as "theories derived from quantum chemistry." Both soft and hard theories can be qualitative and quantitative, and the "Houk quadrant" is proposed as a helpful categorization tool. Furthermore, the language of soft theories is often used appropriately to describe quantum chemical results. A valid and useful way of doing science is the appropriate use and application of both soft and hard theories along with the best nomenclature available for successful communication of results and ideas.
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Affiliation(s)
- Jeffrey I Seeman
- Department of Chemistry, University of Richmond Richmond VA 23173 USA
| | - Dean J Tantillo
- Department of Chemistry, University of California - Davis Davis CA 95616 USA
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24
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Lunghi A, Sanvito S. Computational design of magnetic molecules and their environment using quantum chemistry, machine learning and multiscale simulations. Nat Rev Chem 2022; 6:761-781. [PMID: 37118096 DOI: 10.1038/s41570-022-00424-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2022] [Indexed: 11/09/2022]
Abstract
Having served as a playground for fundamental studies on the physics of d and f electrons for almost a century, magnetic molecules are now becoming increasingly important for technological applications, such as magnetic resonance, data storage, spintronics and quantum information. All of these applications require the preservation and control of spins in time, an ability hampered by the interaction with the environment, namely with other spins, conduction electrons, molecular vibrations and electromagnetic fields. Thus, the design of a novel magnetic molecule with tailored properties is a formidable task, which does not only concern its electronic structures but also calls for a deep understanding of the interaction among all the degrees of freedom at play. This Review describes how state-of-the-art ab initio computational methods, combined with data-driven approaches to materials modelling, can be integrated into a fully multiscale strategy capable of defining design rules for magnetic molecules.
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25
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Lunghi A. Toward exact predictions of spin-phonon relaxation times: An ab initio implementation of open quantum systems theory. SCIENCE ADVANCES 2022; 8:eabn7880. [PMID: 35930642 PMCID: PMC9355363 DOI: 10.1126/sciadv.abn7880] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 06/23/2022] [Indexed: 05/28/2023]
Abstract
Spin-phonon coupling is the main driver of spin relaxation and decoherence in solid-state semiconductors at finite temperature. Controlling this interaction is a central problem for many disciplines, ranging from magnetic resonance to quantum technologies. Spin relaxation theories have been developed for almost a century but often use a phenomenological description of phonons and their coupling to spin, resulting in a nonpredictive tool and hindering our detailed understanding of spin dynamics. Here, we combine time-local master equations up to the fourth order with advanced electronic structure methods and perform predictions of spin-phonon relaxation time for a series of solid-state coordination compounds based on both transition metals and lanthanide Kramers ions. The agreement between experiments and simulations demonstrates that an accurate, universal, and fully ab initio implementation of spin relaxation theory is possible, thus paving the way to a systematic study of spin-phonon relaxation in solid-state materials.
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Affiliation(s)
- Alessandro Lunghi
- School of Physics, AMBER and CRANN Institute, Trinity College, Dublin 2, Ireland
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26
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Jaworski A, Hedin N. Electron correlation and vibrational effects in predictions of paramagnetic NMR shifts. Phys Chem Chem Phys 2022; 24:15230-15244. [PMID: 35703010 DOI: 10.1039/d2cp01206e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electronic structure calculations are fundamentally important for the interpretation of nuclear magnetic resonance (NMR) spectra from paramagnetic systems that include organometallic and inorganic compounds, catalysts, or metal-binding sites in proteins. Prediction of induced paramagnetic NMR shifts requires knowledge of electron paramagnetic resonance (EPR) parameters: the electronic g tensor, zero-field splitting D tensor, and hyperfine A tensor. The isotropic part of A, called the hyperfine coupling constant (HFCC), is one of the most troublesome properties for quantum chemistry calculations. Yet, even relatively small errors in calculations of HFCC tend to propagate into large errors in the predicted NMR shifts. The poor quality of A tensors that are currently calculated using density functional theory (DFT) constitutes a bottleneck in improving the reliability of interpretation of the NMR spectra from paramagnetic systems. In this work, electron correlation effects in calculations of HFCCs with a hierarchy of ab initio methods were assessed, and the applicability of different levels of DFT approximations and the coupled cluster singles and doubles (CCSD) method was tested. These assessments were performed for the set of selected test systems comprising an organic radical, and complexes with transition metal and rare-earth ions, for which experimental data are available. Severe deficiencies of DFT were revealed but the CCSD method was able to deliver good agreement with experimental data for all systems considered, however, at substantial computational costs. We proposed a more computationally tractable alternative, where the A was computed with the coupled cluster theory exploiting locality of electron correlation. This alternative is based on the domain-based local pair natural orbital coupled cluster singles and doubles (DLPNO-CCSD) method. In this way the robustness and reliability of the coupled cluster theory were incorporated into the modern formalism for the prediction of induced paramagnetic NMR shifts, and became applicable to systems of chemical interest. This approach was verified for the bis(cyclopentadienyl)vanadium(II) complex (Cp2V; vanadocene), and the metal-binding site of the Zn2+ → Co2+ substituted superoxide dismutase (SOD) metalloprotein. Excellent agreement with experimental NMR shifts was achieved, which represented a substantial improvement over previous theoretical attempts. The effects of vibrational corrections to orbital shielding and hyperfine tensor were evaluated and discussed within the second-order vibrational perturbation theory (VPT2) framework.
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Affiliation(s)
- Aleksander Jaworski
- Department of Materials and Environmental Chemistry, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - Niklas Hedin
- Department of Materials and Environmental Chemistry, Stockholm University, SE-106 91 Stockholm, Sweden.
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Shafei R, Maganas D, Strobel PJ, Schmidt PJ, Schnick W, Neese F. Electronic and Optical Properties of Eu 2+-Activated Narrow-Band Phosphors for Phosphor-Converted Light-Emitting Diode Applications: Insights from a Theoretical Spectroscopy Perspective. J Am Chem Soc 2022; 144:8038-8053. [PMID: 35471974 PMCID: PMC9100680 DOI: 10.1021/jacs.2c00218] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
In this work, we
present a computational protocol that is able
to predict the experimental absorption and emission spectral shapes
of Eu2+-doped phosphors. The protocol is based on time-dependent
density functional theory and operates in conjunction with an excited-state
dynamics approach. It is demonstrated that across the study set consisting
of representative examples of nitride, oxo-nitride, and oxide Eu2+-doped phosphors, the energy distribution and the band shape
of the emission spectrum are related to the nature of the 4f–5d
transitions that are probed in the absorption process. Since the 4f
orbitals are very nearly nonbonding, the decisive quantity is the
covalency of the 5d acceptor orbitals that become populated in the electronically excited state that leads
to emission. The stronger the (anti) bonding interaction between the
lanthanide and the ligands is in the excited state, the larger will
be the excited state distortion. Consequently, the corresponding emission
will get broader due to the vibronic progression that is induced by
the structural distortion. In addition, the energy separation of the
absorption bands that are dominated by states with valence 4f–5d
and a metal to ligand charge transfer character defines a measure
for the thermal quenching of the studied Eu2+-doped phosphors.
Based on this analysis, simple descriptors are identified that show
a strong correlation with the energy position and bandwidth of the
experimental emission bands without the need for elaborate calculations.
Overall, we believe that this study serves as an important reference
for designing new Eu2+-doped phosphors with desired photoluminescence
properties.
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Affiliation(s)
- Rami Shafei
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr 45470, Germany.,Department of Chemistry, Faculty of Science, Beni-Suef University, Salah Salem Str, Beni-Suef 62511, Egypt
| | - Dimitrios Maganas
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr 45470, Germany
| | - Philipp Jean Strobel
- Lumileds Phosphor Center Aachen, Lumileds (Germany) GmbH, Philipsstraße 8, Aachen 52068 , Germany
| | - Peter J Schmidt
- Lumileds Phosphor Center Aachen, Lumileds (Germany) GmbH, Philipsstraße 8, Aachen 52068 , Germany
| | - Wolfgang Schnick
- Department of Chemistry, University of Munich (LMU), Butenandtstraße 5-13, München 81377, Germany
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr 45470, Germany
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Rimola A, Balucani N, Ceccarelli C, Ugliengo P. Tracing the Primordial Chemical Life of Glycine: A Review from Quantum Chemical Simulations. Int J Mol Sci 2022; 23:4252. [PMID: 35457069 PMCID: PMC9030215 DOI: 10.3390/ijms23084252] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/08/2022] [Accepted: 04/09/2022] [Indexed: 12/28/2022] Open
Abstract
Glycine (Gly), NH2CH2COOH, is the simplest amino acid. Although it has not been directly detected in the interstellar gas-phase medium, it has been identified in comets and meteorites, and its synthesis in these environments has been simulated in terrestrial laboratory experiments. Likewise, condensation of Gly to form peptides in scenarios resembling those present in a primordial Earth has been demonstrated experimentally. Thus, Gly is a paradigmatic system for biomolecular building blocks to investigate how they can be synthesized in astrophysical environments, transported and delivered by fragments of asteroids (meteorites, once they land on Earth) and comets (interplanetary dust particles that land on Earth) to the primitive Earth, and there react to form biopolymers as a step towards the emergence of life. Quantum chemical investigations addressing these Gly-related events have been performed, providing fundamental atomic-scale information and quantitative energetic data. However, they are spread in the literature and difficult to harmonize in a consistent way due to different computational chemistry methodologies and model systems. This review aims to collect the work done so far to characterize, at a quantum mechanical level, the chemical life of Gly, i.e., from its synthesis in the interstellar medium up to its polymerization on Earth.
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Affiliation(s)
- Albert Rimola
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Catalonia, Spain
| | - Nadia Balucani
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy;
- Osservatorio Astrosico di Arcetri, Largo E. Fermi 5, 50125 Firenze, Italy
| | - Cecilia Ceccarelli
- CNRS, Institut de Planétologie et d’Astrophysique de Grenoble (IPAG), Université Grenoble Alpes, 38000 Grenoble, France;
| | - Piero Ugliengo
- Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS) Centre, Università degli Studi di Torino, Via P. Giuria 7, 10125 Torino, Italy;
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29
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Sim E, Song S, Vuckovic S, Burke K. Improving Results by Improving Densities: Density-Corrected Density Functional Theory. J Am Chem Soc 2022; 144:6625-6639. [PMID: 35380807 DOI: 10.1021/jacs.1c11506] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Density functional theory (DFT) calculations have become widespread in both chemistry and materials, because they usually provide useful accuracy at much lower computational cost than wavefunction-based methods. All practical DFT calculations require an approximation to the unknown exchange-correlation energy, which is then used self-consistently in the Kohn-Sham scheme to produce an approximate energy from an approximate density. Density-corrected DFT is simply the study of the relative contributions to the total energy error. In the vast majority of DFT calculations, the error due to the approximate density is negligible. But with certain classes of functionals applied to certain classes of problems, the density error is sufficiently large as to contribute to the energy noticeably, and its removal leads to much better results. These problems include reaction barriers, torsional barriers involving π-conjugation, halogen bonds, radicals and anions, most stretched bonds, etc. In all such cases, use of a more accurate density significantly improves performance, and often the simple expedient of using the Hartree-Fock density is enough. This Perspective explains what DC-DFT is, where it is likely to improve results, and how DC-DFT can produce more accurate functionals. We also outline challenges and prospects for the field.
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Affiliation(s)
- Eunji Sim
- Department of Chemistry, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul 03722, Korea
| | - Suhwan Song
- Department of Chemistry, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul 03722, Korea
| | - Stefan Vuckovic
- Institute for Microelectronics and Microsystems (CNR-IMM), Via Monteroni,Campus Unisalento, 73100 Lecce, Italy.,Department of Chemistry & Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Faculty of Science, Vrije Universiteit, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands
| | - Kieron Burke
- Departments of Chemistry and of Physics, University of California, Irvine, California 92697, United States
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Xu S, Liang J, Cao S, He R, Yin G, Wang QD. A Hierarchical Theoretical Study of the Hydrogen Abstraction Reactions of H 2/C 1-C 4 Molecules by the Methyl Peroxy Radical and Implications for Kinetic Modeling. ACS OMEGA 2022; 7:8675-8685. [PMID: 35309437 PMCID: PMC8928341 DOI: 10.1021/acsomega.1c06683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/18/2022] [Indexed: 06/14/2023]
Abstract
The hydrogen atom abstraction by the methyl peroxy radical (CH3O2) is an important reaction class in detailed chemical kinetic modeling of the autoignition properties of hydrocarbon fuels. Systematic theoretical studies are performed on this reaction class for H2/C1-C4 fuels, which is critical in the development of a base model for large fuels. The molecules include hydrogen, alkanes, alkenes, and alkynes with a carbon number from 1 to 4. The B2PLYP-D3/cc-pVTZ level of theory is employed to optimize the geometries of all of the reactants, transition states, and products and also the treatments of hindered rotation for lower frequency modes. Accurate benchmark calculations for abstraction reactions of hydrogen, methane, and ethylene with CH3O2 are performed by using the coupled cluster method with explicit inclusion of single and double electron excitations and perturbative inclusion of triple electron excitations (CCSD(T)), the domain-based local pair-natural orbital coupled cluster method (DLPNO-CCSD(T)), and the explicitly correlated CCSD(T)-F12 method with large basis sets. Reaction rate constants are computed via conventional transition state theory with quantum tunneling corrections. The computed rate constants are compared with literature values and those employed in detailed chemical kinetic mechanisms. The calculated rate constants are implemented into the recently developed NUIGMECH1.1 base model for kinetic modeling of ignition properties.
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Affiliation(s)
- Shenying Xu
- Faculty
of Materials and Chemical Engineering, Yibin
University, Yibin, Sichuan 644000, People’s Republic of China
| | - Jinhu Liang
- Faculty
of Materials and Chemical Engineering, Yibin
University, Yibin, Sichuan 644000, People’s Republic of China
- School
of Environment and Safety Engineering, North
University of China, Taiyuan 030051, People’s Republic
of China
| | - Shutong Cao
- School
of Environment and Safety Engineering, North
University of China, Taiyuan 030051, People’s Republic
of China
| | - Ruining He
- School
of Environment and Safety Engineering, North
University of China, Taiyuan 030051, People’s Republic
of China
| | - Guoliang Yin
- Faculty
of Materials and Chemical Engineering, Yibin
University, Yibin, Sichuan 644000, People’s Republic of China
| | - Quan-De Wang
- Jiangsu
Key Laboratory of Coal-Based Greenhouse Gas Control and Utilization,
Low Carbon Energy Institute, China University
of Mining and Technology, Xuzhou 221008, People’s Republic
of China
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31
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Wang Y, Liao W, Wang Y, Jiao L, Yu ZX. Mechanism and Stereochemistry of Rhodium-Catalyzed [5 + 2 + 1] Cycloaddition of Ene-Vinylcyclopropanes and Carbon Monoxide Revealed by Visual Kinetic Analysis and Quantum Chemical Calculations. J Am Chem Soc 2022; 144:2624-2636. [PMID: 35130434 DOI: 10.1021/jacs.1c11030] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Previously, we developed a rhodium-catalyzed [5 + 2 + 1] cycloaddition of ene-vinylcyclopropanes (ene-VCPs) and carbon monoxide to synthesize eight-membered carbocycles. The efficiency of this reaction can be appreciated from its application in the synthesis of several natural products. Herein we report the results of a 15-year investigation into the mechanism of the [5 + 2 + 1] cycloaddition by applying visual kinetic analysis and high-level quantum chemical calculations at the DLPNO-CCSD(T)//BMK level. According to the kinetic measurements, the resting state of the catalyst possesses a dimeric structure (with two rhodium centers) whereas the active catalytic species is monomeric (with one rhodium center). The catalytic cycle consists of cyclopropane cleavage (the turnover-limiting step), alkene insertion, CO insertion, reductive elimination, and catalyst transfer steps. Other reaction pathways have also been considered but then have been ruled out. The steric origin of the diastereoselectivity (cis versus trans) was revealed by comparing the alkene insertion transition states. In addition, how the double-bond configuration of the VCPs (Z versus E) affects the substrate reactivity and the origins of chemoselectivity ([5 + 2 + 1] versus [5 + 2]) were also investigated. The present study will provide assistance in understanding other carbonylative annulations catalyzed by transition metals.
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Affiliation(s)
- Yi Wang
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry, Peking University, Beijing 100871, People's Republic of China
| | - Wei Liao
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry, Peking University, Beijing 100871, People's Republic of China
| | - Yuanyuan Wang
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry, Peking University, Beijing 100871, People's Republic of China
| | - Lei Jiao
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry, Peking University, Beijing 100871, People's Republic of China
| | - Zhi-Xiang Yu
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry, Peking University, Beijing 100871, People's Republic of China
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Hu Y, Wang H, Ji Y, Li H, Fan Q, King RB, Schaefer HF. Binuclear Alkyne Manganese Carbonyls: Their Rearrangements to Allene, Allyl, and Vinylcarbene Derivatives by Hydrogen Migration from Methyl Substituents. Eur J Inorg Chem 2021. [DOI: 10.1002/ejic.202100375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yucheng Hu
- School of Science, Key Laboratory of High Performance Scientific Computation Xihua University Chengdu 610039 China
| | - Huijie Wang
- School of Science, Key Laboratory of High Performance Scientific Computation Xihua University Chengdu 610039 China
| | - Yupin Ji
- School of Science, Key Laboratory of High Performance Scientific Computation Xihua University Chengdu 610039 China
| | - Huidong Li
- School of Science, Key Laboratory of High Performance Scientific Computation Xihua University Chengdu 610039 China
- Center for Computational Quantum Chemistry University of Georgia Athens Georgia 30602 USA
| | - Qunchao Fan
- School of Science, Key Laboratory of High Performance Scientific Computation Xihua University Chengdu 610039 China
| | - R. Bruce King
- Center for Computational Quantum Chemistry University of Georgia Athens Georgia 30602 USA
| | - Henry F. Schaefer
- Center for Computational Quantum Chemistry University of Georgia Athens Georgia 30602 USA
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33
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Jaworski A, Hedin N. Local energy decomposition analysis and molecular properties of encapsulated methane in fullerene (CH 4@C 60). Phys Chem Chem Phys 2021; 23:21554-21567. [PMID: 34550137 DOI: 10.1039/d1cp02333k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Methane has been successfully encapsulated within cages of C60 fullerene, which is an appropriate model system to study confinement effects. Its chemistry and physics are also relevant for theoretical model descriptions. Here we provide insights into intermolecular interactions and predicted spectroscopic responses of the CH4@C60 complex and compared them with results from other methods and with data from the literature. Local energy decomposition analysis (LED) within the domain-based local pair natural orbital coupled cluster singles, doubles, and perturbative triples (DLPNO-CCSD(T)) framework was used, and an efficient protocol for studies of endohedral complexes of fullerenes is proposed. This approach allowed us to assess energies in relation to electronic and geometric preparation, electrostatics, exchange, and London dispersion for the CH4@C60 endohedral complex. The calculated stabilization energy of CH4 inside the C60 fullerene was -13.5 kcal mol-1 and its magnitude was significantly larger than the latent heat of evaporation of CH4. Evaluation of vibrational frequencies and polarizabilities of the CH4@C60 complex revealed that the infrared (IR) and Raman bands of the endohedral CH4 were essentially "silent" due to the dielectric screening effect of C60, which acted as a molecular Faraday cage. Absorption spectra in the UV-vis domain and ionization potentials of C60 and CH4@C60 were predicted. They were almost identical. The calculated 1H/13C NMR shifts and spin-spin coupling constants were in very good agreement with experimental data. In addition, reference DLPNO-CCSD(T) interaction energies for complexes with noble gases (Ng@C60; Ng = He, Ne, Ar, Kr) were calculated. The values were compared with those derived from supramolecular MP2/SCS-MP2 calculations and estimates with London-type formulas by Pyykkö and coworkers [Phys. Chem. Chem. Phys., 2010, 12, 6187-6203], and with values derived from DFT-based symmetry-adapted perturbation theory (DFT-SAPT) by Hesselmann & Korona [Phys. Chem. Chem. Phys., 2011, 13, 732-743]. Selected points at the potential energy surface of the endohedral He2@C60 trimer were considered. In contrast to previous theoretical attempts with the DFT/MP2/SCS-MP2/DFT-SAPT methods, our calculations at the DLPNO-CCSD(T) level of theory predicted the He2@C60 trimer to be thermodynamically stable, which is in agreement with experimental observations.
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Affiliation(s)
- Aleksander Jaworski
- Department of Materials and Environmental Chemistry, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - Niklas Hedin
- Department of Materials and Environmental Chemistry, Stockholm University, SE-106 91 Stockholm, Sweden.
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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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Tantillo DJ, Laconsay CJ. Melding of Experiment and Theory Illuminates Mechanisms of Metal-Catalyzed Rearrangements: Computational Approaches and Caveats. SYNTHESIS-STUTTGART 2021. [DOI: 10.1055/s-0040-1720451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
AbstractThis review summarizes approaches and caveats in computational modeling of transition-metal-catalyzed sigmatropic rearrangements involving carbene transfer. We highlight contemporary examples of combined synthetic and theoretical investigations that showcase the synergy achievable by integrating experiment and theory.1 Introduction2 Mechanistic Models3 Theoretical Approaches and Caveats3.1 Recommended Computational Tools3.2 Choice of Functional and Basis Set3.3 Conformations and Ligand-Binding Modes3.4 Solvation4 Synergy of Experiment and Theory – Case Studies4.1 Metal-Bound or Free Ylides?4.2 Conformations and Ligand-Binding Modes of Paddlewheel Complexes4.3 No Metal, Just Light4.4 How To ‘Cope’ with Nonstatistical Dynamic Effects5 Outlook
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37
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Klahn EA, Damgaard-Møller E, Krause L, Kibalin I, Gukasov A, Tripathi S, Swain A, Shanmugam M, Overgaard J. Quantifying magnetic anisotropy using X-ray and neutron diffraction. IUCRJ 2021; 8:833-841. [PMID: 34584744 PMCID: PMC8420765 DOI: 10.1107/s2052252521008290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 08/11/2021] [Indexed: 06/13/2023]
Abstract
In this work, the magnetic anisotropy in two iso-structural distorted tetrahedral Co(II) complexes, CoX 2tmtu2 [X = Cl(1) and Br(2), tmtu = tetra-methyl-thio-urea] is investigated, using a combination of polarized neutron diffraction (PND), very low-temperature high-resolution synchrotron X-ray diffraction and CASSCF/NEVPT2 ab initio calculations. Here, it was found consistently among all methods that the compounds have an easy axis of magnetization pointing nearly along the bis-ector of the compression angle, with minute deviations between PND and theory. Importantly, this work represents the first derivation of the atomic susceptibility tensor based on powder PND for a single-molecule magnet and the comparison thereof with ab initio calculations and high-resolution X-ray diffraction. Theoretical ab initio ligand field theory (AILFT) analysis finds the d xy orbital to be stabilized relative to the d xz and d yz orbitals, thus providing the intuitive explanation for the presence of a negative zero-field splitting parameter, D, from coupling and thus mixing of d xy and . Experimental d-orbital populations support this interpretation, showing in addition that the metal-ligand covalency is larger for Br-ligated 2 than for Cl-ligated 1.
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Affiliation(s)
- Emil Andreasen Klahn
- Department of Chemistry, Aarhus University, Langelandsgade 140, Aarhus C 8000, Denmark
| | - Emil Damgaard-Møller
- Department of Chemistry, Aarhus University, Langelandsgade 140, Aarhus C 8000, Denmark
| | - Lennard Krause
- Department of Chemistry, Aarhus University, Langelandsgade 140, Aarhus C 8000, Denmark
| | - Iurii Kibalin
- LLB, CEA, CE de Saclay, Gif sur Yvette 91191, France
| | - Arsen Gukasov
- LLB, CEA, CE de Saclay, Gif sur Yvette 91191, France
| | - Shalini Tripathi
- Department of Chemistry, IIT Bombay, Powai, Mumbai, Maharashtra 400076, India
| | - Abinash Swain
- Department of Chemistry, IIT Bombay, Powai, Mumbai, Maharashtra 400076, India
| | | | - Jacob Overgaard
- Department of Chemistry, Aarhus University, Langelandsgade 140, Aarhus C 8000, Denmark
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Epifanovsky E, Gilbert ATB, Feng X, Lee J, Mao Y, Mardirossian N, Pokhilko P, White AF, Coons MP, Dempwolff AL, Gan Z, Hait D, Horn PR, Jacobson LD, Kaliman I, Kussmann J, Lange AW, Lao KU, Levine DS, Liu J, McKenzie SC, Morrison AF, Nanda KD, Plasser F, Rehn DR, Vidal ML, You ZQ, Zhu Y, Alam B, Albrecht BJ, Aldossary A, Alguire E, Andersen JH, Athavale V, Barton D, Begam K, Behn A, Bellonzi N, Bernard YA, Berquist EJ, Burton HGA, Carreras A, Carter-Fenk K, Chakraborty R, Chien AD, Closser KD, Cofer-Shabica V, Dasgupta S, de Wergifosse M, Deng J, Diedenhofen M, Do H, Ehlert S, Fang PT, Fatehi S, Feng Q, Friedhoff T, Gayvert J, Ge Q, Gidofalvi G, Goldey M, Gomes J, González-Espinoza CE, Gulania S, Gunina AO, Hanson-Heine MWD, Harbach PHP, Hauser A, Herbst MF, Hernández Vera M, Hodecker M, Holden ZC, Houck S, Huang X, Hui K, Huynh BC, Ivanov M, Jász Á, Ji H, Jiang H, Kaduk B, Kähler S, Khistyaev K, Kim J, Kis G, Klunzinger P, Koczor-Benda Z, Koh JH, Kosenkov D, Koulias L, Kowalczyk T, Krauter CM, Kue K, Kunitsa A, Kus T, Ladjánszki I, Landau A, Lawler KV, Lefrancois D, Lehtola S, Li RR, Li YP, Liang J, Liebenthal M, Lin HH, Lin YS, Liu F, Liu KY, Loipersberger M, Luenser A, Manjanath A, Manohar P, Mansoor E, Manzer SF, Mao SP, Marenich AV, Markovich T, Mason S, Maurer SA, McLaughlin PF, Menger MFSJ, Mewes JM, Mewes SA, Morgante P, Mullinax JW, Oosterbaan KJ, Paran G, Paul AC, Paul SK, Pavošević F, Pei Z, Prager S, Proynov EI, Rák Á, Ramos-Cordoba E, Rana B, Rask AE, Rettig A, Richard RM, Rob F, Rossomme E, Scheele T, Scheurer M, Schneider M, Sergueev N, Sharada SM, Skomorowski W, Small DW, Stein CJ, Su YC, Sundstrom EJ, Tao Z, Thirman J, Tornai GJ, Tsuchimochi T, Tubman NM, Veccham SP, Vydrov O, Wenzel J, Witte J, Yamada A, Yao K, Yeganeh S, Yost SR, Zech A, Zhang IY, Zhang X, Zhang Y, Zuev D, Aspuru-Guzik A, Bell AT, Besley NA, Bravaya KB, Brooks BR, Casanova D, Chai JD, Coriani S, Cramer CJ, Cserey G, DePrince AE, DiStasio RA, Dreuw A, Dunietz BD, Furlani TR, Goddard WA, Hammes-Schiffer S, Head-Gordon T, Hehre WJ, Hsu CP, Jagau TC, Jung Y, Klamt A, Kong J, Lambrecht DS, Liang W, Mayhall NJ, McCurdy CW, Neaton JB, Ochsenfeld C, Parkhill JA, Peverati R, Rassolov VA, Shao Y, Slipchenko LV, Stauch T, Steele RP, Subotnik JE, Thom AJW, Tkatchenko A, Truhlar DG, Van Voorhis T, Wesolowski TA, Whaley KB, Woodcock HL, Zimmerman PM, Faraji S, Gill PMW, Head-Gordon M, Herbert JM, Krylov AI. Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package. J Chem Phys 2021; 155:084801. [PMID: 34470363 PMCID: PMC9984241 DOI: 10.1063/5.0055522] [Citation(s) in RCA: 513] [Impact Index Per Article: 171.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange-correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear-electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an "open teamware" model and an increasingly modular design.
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Affiliation(s)
- Evgeny Epifanovsky
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | | | | | - Joonho Lee
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Yuezhi Mao
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - Pavel Pokhilko
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Alec F. White
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Marc P. Coons
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Adrian L. Dempwolff
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Zhengting Gan
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Diptarka Hait
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Paul R. Horn
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Leif D. Jacobson
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | | | - Jörg Kussmann
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Adrian W. Lange
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Ka Un Lao
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Daniel S. Levine
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - Simon C. McKenzie
- Research School of Chemistry, Australian National University, Canberra, Australia
| | | | - Kaushik D. Nanda
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | | | - Dirk R. Rehn
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Marta L. Vidal
- Department of Chemistry, Technical University of Denmark, Kemitorvet Bldg. 207, DK-2800 Kgs Lyngby, Denmark
| | | | - Ying Zhu
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Bushra Alam
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Benjamin J. Albrecht
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | | | - Ethan Alguire
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Josefine H. Andersen
- Department of Chemistry, Technical University of Denmark, Kemitorvet Bldg. 207, DK-2800 Kgs Lyngby, Denmark
| | - Vishikh Athavale
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Dennis Barton
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg, Luxembourg
| | - Khadiza Begam
- Department of Physics, Kent State University, Kent, Ohio 44242, USA
| | - Andrew Behn
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Nicole Bellonzi
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Yves A. Bernard
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | | | - Hugh G. A. Burton
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Abel Carreras
- Donostia International Physics Center, 20080 Donostia, Euskadi, Spain
| | - Kevin Carter-Fenk
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | | | - Alan D. Chien
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | | - Vale Cofer-Shabica
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Saswata Dasgupta
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Marc de Wergifosse
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Jia Deng
- Research School of Chemistry, Australian National University, Canberra, Australia
| | | | - Hainam Do
- School of Chemistry, University of Nottingham, Nottingham, United Kingdom
| | - Sebastian Ehlert
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Beringstr. 4, 53115 Bonn, Germany
| | - Po-Tung Fang
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | | | - Qingguo Feng
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44240, USA
| | - Triet Friedhoff
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - James Gayvert
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Qinghui Ge
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Gergely Gidofalvi
- Department of Chemistry and Biochemistry, Gonzaga University, Spokane, Washington 99258, USA
| | - Matthew Goldey
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Joe Gomes
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - Sahil Gulania
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Anastasia O. Gunina
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | | | - Phillip H. P. Harbach
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Andreas Hauser
- Institute of Experimental Physics, Graz University of Technology, Graz, Austria
| | | | - Mario Hernández Vera
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Manuel Hodecker
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Zachary C. Holden
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Shannon Houck
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Xunkun Huang
- Department of Chemistry, Xiamen University, Xiamen 361005, China
| | - Kerwin Hui
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Bang C. Huynh
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Maxim Ivanov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Ádám Jász
- Stream Novation Ltd., Práter utca 50/a, H-1083 Budapest, Hungary
| | - Hyunjun Ji
- Graduate School of Energy, Environment, Water and Sustainability (EEWS), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Hanjie Jiang
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Benjamin Kaduk
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Sven Kähler
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Kirill Khistyaev
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Jaehoon Kim
- Graduate School of Energy, Environment, Water and Sustainability (EEWS), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Gergely Kis
- Stream Novation Ltd., Práter utca 50/a, H-1083 Budapest, Hungary
| | | | - Zsuzsanna Koczor-Benda
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Joong Hoon Koh
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Dimitri Kosenkov
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Laura Koulias
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | | | - Caroline M. Krauter
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Karl Kue
- Institute of Chemistry, Academia Sinica, 128, Academia Road Section 2, Nangang District, Taipei 11529, Taiwan
| | - Alexander Kunitsa
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Thomas Kus
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | | | - Arie Landau
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Keith V. Lawler
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Daniel Lefrancois
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | | | - Run R. Li
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | - Yi-Pei Li
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Jiashu Liang
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Marcus Liebenthal
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | - Hung-Hsuan Lin
- Institute of Chemistry, Academia Sinica, 128, Academia Road Section 2, Nangang District, Taipei 11529, Taiwan
| | - You-Sheng Lin
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Fenglai Liu
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | | | | | - Arne Luenser
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Aaditya Manjanath
- Institute of Chemistry, Academia Sinica, 128, Academia Road Section 2, Nangang District, Taipei 11529, Taiwan
| | - Prashant Manohar
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Erum Mansoor
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Sam F. Manzer
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Shan-Ping Mao
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | | | - Thomas Markovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Stephen Mason
- School of Chemistry, University of Nottingham, Nottingham, United Kingdom
| | - Simon A. Maurer
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Peter F. McLaughlin
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | | | - Jan-Michael Mewes
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Stefanie A. Mewes
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Pierpaolo Morgante
- Department of Chemistry, Florida Institute of Technology, Melbourne, Florida 32901, USA
| | - J. Wayne Mullinax
- Department of Chemistry, Florida Institute of Technology, Melbourne, Florida 32901, USA
| | | | | | - Alexander C. Paul
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Suranjan K. Paul
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Fabijan Pavošević
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Zheng Pei
- School of Electrical and Computer Engineering, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - Stefan Prager
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Emil I. Proynov
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Ádám Rák
- Stream Novation Ltd., Práter utca 50/a, H-1083 Budapest, Hungary
| | - Eloy Ramos-Cordoba
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Bhaskar Rana
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Alan E. Rask
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Adam Rettig
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Ryan M. Richard
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Fazle Rob
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Elliot Rossomme
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Tarek Scheele
- Institute for Physical and Theoretical Chemistry, University of Bremen, Bremen, Germany
| | - Maximilian Scheurer
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Matthias Schneider
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Nickolai Sergueev
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44240, USA
| | - Shaama M. Sharada
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Wojciech Skomorowski
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - David W. Small
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Christopher J. Stein
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Yu-Chuan Su
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Eric J. Sundstrom
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Zhen Tao
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Jonathan Thirman
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Gábor J. Tornai
- Stream Novation Ltd., Práter utca 50/a, H-1083 Budapest, Hungary
| | - Takashi Tsuchimochi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Norm M. Tubman
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - Oleg Vydrov
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Jan Wenzel
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Jon Witte
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Atsushi Yamada
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44240, USA
| | - Kun Yao
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Sina Yeganeh
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Shane R. Yost
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Alexander Zech
- Department of Physical Chemistry, University of Geneva, 30, Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - Igor Ying Zhang
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Xing Zhang
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Yu Zhang
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Dmitry Zuev
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Alán Aspuru-Guzik
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Alexis T. Bell
- Department of Chemical Engineering, University of California, Berkeley, California 94720, USA
| | - Nicholas A. Besley
- School of Chemistry, University of Nottingham, Nottingham, United Kingdom
| | - Ksenia B. Bravaya
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Bernard R. Brooks
- Laboratory of Computational Biophysics, National Institute of Health, Bethesda, Maryland 20892, USA
| | - David Casanova
- Donostia International Physics Center, 20080 Donostia, Euskadi, Spain
| | | | - Sonia Coriani
- Department of Chemistry, Technical University of Denmark, Kemitorvet Bldg. 207, DK-2800 Kgs Lyngby, Denmark
| | | | | | - A. Eugene DePrince
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | - Robert A. DiStasio
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Barry D. Dunietz
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44240, USA
| | - Thomas R. Furlani
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260, USA
| | - William A. Goddard
- Materials and Process Simulation Center, California Institute of Technology, Pasadena, California 91125, USA
| | | | - Teresa Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | | | | | - Yousung Jung
- Graduate School of Energy, Environment, Water and Sustainability (EEWS), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Andreas Klamt
- COSMOlogic GmbH & Co. KG, Imbacher Weg 46, D-51379 Leverkusen, Germany
| | - Jing Kong
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Daniel S. Lambrecht
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | | | | | - C. William McCurdy
- Department of Chemistry, University of California, Davis, California 95616, USA
| | - Jeffrey B. Neaton
- Department of Physics, University of California, Berkeley, California 94720, USA
| | - Christian Ochsenfeld
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - John A. Parkhill
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Roberto Peverati
- Department of Chemistry, Florida Institute of Technology, Melbourne, Florida 32901, USA
| | - Vitaly A. Rassolov
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA
| | | | | | | | - Ryan P. Steele
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
| | - Joseph E. Subotnik
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Alex J. W. Thom
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Alexandre Tkatchenko
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg, Luxembourg
| | - Donald G. Truhlar
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Troy Van Voorhis
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Tomasz A. Wesolowski
- Department of Physical Chemistry, University of Geneva, 30, Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - K. Birgitta Whaley
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - H. Lee Woodcock
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, USA
| | - Paul M. Zimmerman
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Shirin Faraji
- Zernike Institute for Advanced Materials, University of Groningen, 9774AG Groningen, The Netherlands
| | | | - Martin Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - John M. Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA,Author to whom correspondence should be addressed:
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Stoll C, Atanasov M, Bandemehr J, Neese F, Pietzonka C, Kraus F, Karttunen AJ, Seibald M, Heymann G, Huppertz H. Coexistence of Two Different Distorted Octahedral [MnF 6 ] 3- Sites in K 3 [MnF 6 ]: Manifestation in Spectroscopy and Magnetism. Chemistry 2021; 27:9801-9813. [PMID: 33830547 PMCID: PMC8362050 DOI: 10.1002/chem.202005496] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Indexed: 11/28/2022]
Abstract
As a consequence of the static Jahn-Teller effect of the 5 E ground state of MnIII in cubic structures with octahedral parent geometries, their octahedral coordination spheres become distorted. In the case of six fluorido ligands, [MnF6 ]3- anions with two longer and four shorter Mn-F bonds making elongated octahedra are usually observed. Herein, we report the synthesis of the compound K3 [MnF6 ] through a high-temperature approach and its crystallization by a high-pressure/high-temperature route. The main structural motifs are two quasi-isolated, octahedron-like [MnF6 ]3- anions of quite different nature compared to that met in ideal octahedral MnIII Jahn-Teller systems. Owing to the internal electric field of Ci symmetry dominated by the next-neighbour K+ ions acting on the MnIII sites, both sites, the pseudo-rhombic (site 1) and the pseudo-tetragonally elongated (site 2) [MnF6 ]3- anions are present in K3 [MnF6 ]. The compound was characterized by single-crystal and powder X-ray diffraction, and magnetometry as well as by FTIR, Raman, and ligand field spectroscopy. A theoretical interpretation of the electronic structure and molecular geometry of the two Mn sites in the lattice is given by using a vibronic coupling model with parameters adjusted from multireference ab-initio cluster calculations.
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Affiliation(s)
- Christiane Stoll
- Universität InnsbruckInstitut für AllgemeineAnorganische und Theoretische ChemieInnrain 80–826020InnsbruckAustria
| | - Mihail Atanasov
- Max-Planck-Institut für KohlenforschungKaiser-Wilhelm-Platz 145470Mülheim an der RuhrGermany
- Institute of General and Inorganic ChemistryBulgarian Academy of SciencesAkad. G. Bontchev Street, Bl.111113SofiaBulgaria
| | - Jascha Bandemehr
- Philipps-Universität MarburgFachbereich ChemieAnorganische ChemieFluorchemieHans-Meerwein-Straße 435032MarburgGermany
| | - Frank Neese
- Max-Planck-Institut für KohlenforschungKaiser-Wilhelm-Platz 145470Mülheim an der RuhrGermany
| | - Clemens Pietzonka
- Philipps-Universität MarburgFachbereich ChemieAnorganische ChemieFluorchemieHans-Meerwein-Straße 435032MarburgGermany
| | - Florian Kraus
- Philipps-Universität MarburgFachbereich ChemieAnorganische ChemieFluorchemieHans-Meerwein-Straße 435032MarburgGermany
| | - Antti J. Karttunen
- Department of Chemistry and Materials ScienceAalto University00076AaltoFinland
| | - Markus Seibald
- OSRAM Opto Semiconductors GmbHMittelstetter Weg 286830SchwabmünchenGermany
| | - Gunter Heymann
- Universität InnsbruckInstitut für AllgemeineAnorganische und Theoretische ChemieInnrain 80–826020InnsbruckAustria
| | - Hubert Huppertz
- Universität InnsbruckInstitut für AllgemeineAnorganische und Theoretische ChemieInnrain 80–826020InnsbruckAustria
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40
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Guo Y, Sivalingam K, Neese F. Approximations of density matrices in N-electron valence state second-order perturbation theory (NEVPT2). I. Revisiting the NEVPT2 construction. J Chem Phys 2021; 154:214111. [PMID: 34240991 DOI: 10.1063/5.0051211] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Over the last decade, the second-order N-electron valence state perturbation theory (NEVPT2) has developed into a widely used multireference perturbation method. To apply NEVPT2 to systems with large active spaces, the computational bottleneck is the construction of the fourth-order reduced density matrix. Both its generation and storage become quickly problematic beyond the usual maximum active space of about 15 active orbitals. To reduce the computational cost of handling fourth-order density matrices, the cumulant approximation (CU) has been proposed in several studies. A more conventional strategy to address the higher-order density matrices is the pre-screening approximation (PS), which is the default one in the ORCA program package since 2010. In the present work, the performance of the CU, PS, and extended PS (EPS) approximations for the fourth-order density matrices is compared. Following a pedagogical introduction to NEVPT2, contraction schemes, as well as the approximations to density matrices, and the intruder state problem are discussed. The CU approximation, while potentially leading to large computational savings, virtually always leads to intruder states. With the PS approximation, the computational savings are more modest. However, in conjunction with conservative cutoffs, it produces stable results. The EPS approximation to the fourth-order density matrices can reproduce very accurate NEVPT2 results without any intruder states. However, its computational cost is not much lower than that of the canonical algorithm. Moreover, we found that a good indicator of intrude states problems in any approximation to high order density matrices is the eigenspectra of the Koopmans matrices.
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Affiliation(s)
- Yang Guo
- Qingdao Institute for Theoretical and Computational Sciences, Shandong University, Qingdao, Shandong 266237, China
| | - Kantharuban Sivalingam
- 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
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41
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Zheng K, Li D, Jiang L, Li X, Xie C, Feng L, Qin J, Qian S, Pang Q. Revisiting stacking interactions in tetrathiafulvalene and selected derivatives using tight-binding quantum chemical calculations and local coupled-cluster method. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2021; 77:311-320. [PMID: 34096512 DOI: 10.1107/s2052520621003085] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 03/23/2021] [Indexed: 06/12/2023]
Abstract
The engineering of supramolecular architectures needs accurate descriptions of the intermolecular interactions in crystal structures. Tetrathiafulvalene (TTF) is an effective building block used in the construction of promising functional materials. The parallel packing of the neutral TTF-TTF system was studied previously using the high-level quantum chemical method, advancing it as a valuable model system. The recently developed tight-binding quantum chemical method GFN2-xTB and local coupled-cluster method DLPNO-CCSD(T) were used to investigate the stacking interactions of TTF and selected derivatives deposited in the Cambridge Structural Database. Using the interaction energy of the TTF-TTF dimer calculated at the CCSD(T)/CBS level as the reference, the accuracies of the two methods are investigated. The energy decomposition analysis within the DLPNO-CCSD(T) framework reveals the importance of dispersion interaction in the TTF-related stacking systems. The dispersion interaction density plot vividly shows the magnitude and distribution of the dispersion interaction, providing a revealing insight into the stacking interactions in crystal structures. The results show that the GFN2-xTB and DLPNO-CCSD(T) methods could achieve accuracy at an affordable computational cost, which would be valuable in understanding the nature of parallel stacking in supramolecular systems.
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Affiliation(s)
- Kang Zheng
- School of Life Sciences, Shandong University of Technology, 266 Xincun West Road, Zibo, Shandong 255049, People's Republic of China
| | - Danping Li
- School of Life Sciences, Shandong University of Technology, 266 Xincun West Road, Zibo, Shandong 255049, People's Republic of China
| | - Liu Jiang
- School of Life Sciences, Shandong University of Technology, 266 Xincun West Road, Zibo, Shandong 255049, People's Republic of China
| | - Xiaowei Li
- School of Materials Science and Engineering, Shandong University of Technology, 266 Xincun West Road, Zibo, Shandong 255049, People's Republic of China
| | - Changjian Xie
- School of Life Sciences, Shandong University of Technology, 266 Xincun West Road, Zibo, Shandong 255049, People's Republic of China
| | - Ling Feng
- School of Life Sciences, Shandong University of Technology, 266 Xincun West Road, Zibo, Shandong 255049, People's Republic of China
| | - Jie Qin
- School of Life Sciences, Shandong University of Technology, 266 Xincun West Road, Zibo, Shandong 255049, People's Republic of China
| | - Shaosong Qian
- School of Life Sciences, Shandong University of Technology, 266 Xincun West Road, Zibo, Shandong 255049, People's Republic of China
| | - Qiuxiang Pang
- School of Life Sciences, Shandong University of Technology, 266 Xincun West Road, Zibo, Shandong 255049, People's Republic of China
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42
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Barone V, Alessandrini S, Biczysko M, Cheeseman JR, Clary DC, McCoy AB, DiRisio RJ, Neese F, Melosso M, Puzzarini C. Computational molecular spectroscopy. ACTA ACUST UNITED AC 2021. [DOI: 10.1038/s43586-021-00034-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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43
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Rasouli Z, Irani M, Jafari S, Ghavami R. Study of interaction of metal ions with methylthymol blue by chemometrics and quantum chemical calculations. Sci Rep 2021; 11:6465. [PMID: 33742047 PMCID: PMC7979746 DOI: 10.1038/s41598-021-85940-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/21/2020] [Indexed: 11/08/2022] Open
Abstract
In this study, we determine the acidity constants of methylthymol blue (MTB) and association constants of its complexes with the ZnII, CuII, and FeII metal ions (MIs), through theoretical and experimental means. The complexes were characterized using UV-Visible absorption spectroscopy combined with soft/hard chemometrics methods and quantum chemical calculations. Quantum chemical calculations revealed that electronic transitions in the UV-Visible spectra of MTB have mixed n → π* and π → π* characters. The results of molar ratio and multivariate curve resolution alternating least squares (MCR-ALS) revealed the formation of successive 1:2 and 1:1 complexes (MI:MTB) for the ZnII and CuII systems. However, the formation of successive 1:1 and 2:1 complexes are suggested for FeII by the molar ratio and MCR-ALS. The majority of transitions observed in the UV-Visible spectra of the Zn(MTB) and Cu(MTB) complexes have ligand-to-ligand charge transfer (LLCT) characters. However, the transitions in the UV-Visible spectrum of the Fe(MTB) complex have LLCT and metal-to-ligand charge transfer (MLCT) characters. For the Fe2(MTB) complex, the lowest energy transition of has an LLCT character. However, its higher energy transitions are a mixture of LLCT, MLCT, and metal-to-metal charge transfer (MMCT) characters. The correlation between experimental and computed wavelengths revealed that the 1:1 complexes of ZnII and CuII prefer square pyramidal geometries. However, the FeII complexes always show octahedral geometry.
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Affiliation(s)
- Zolaikha Rasouli
- Chemometrics Laboratory, Chemistry Department, Faculty of Science, University of Kurdistan, P.O. Box 416, 66177-15175, Sanandaj, Iran
| | - Mehdi Irani
- Theoretical Chemistry Laboratory, Chemistry Department, Faculty of Science, University of Kurdistan, P.O. Box 416, 66177-15175, Sanandaj, Iran
| | - Sonia Jafari
- Theoretical Chemistry Laboratory, Chemistry Department, Faculty of Science, University of Kurdistan, P.O. Box 416, 66177-15175, Sanandaj, Iran
| | - Raouf Ghavami
- Chemometrics Laboratory, Chemistry Department, Faculty of Science, University of Kurdistan, P.O. Box 416, 66177-15175, Sanandaj, Iran.
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44
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Welsh ID, Crittenden DL. New atoms-in-molecules dispersion models for use in ab initio derived force fields. J Chem Phys 2021; 154:094118. [PMID: 33685181 DOI: 10.1063/5.0037157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Recently, substantial research efforts have gone into bridging the accuracy-efficiency gap between parameterized force field models and quantum chemical calculations by extracting molecule-specific force fields directly from ab initio data in a robust and automated manner. One of the challenging aspects is deriving localized atomic polarizabilities for pairwise distributed dispersion models. The Tkatchenko-Scheffler model is based upon correcting free-atom C6 coefficients according to the square of the ratio of the atom-in-molecule volume to the free-atom volume. However, it has recently been shown that a more accurate relationship can be found if static atomic polarizabilities are also taken into account. Using this relationship, we develop two modified Tkatchenko-Scheffler dispersion models and benchmark their performance against SAPT2+3 reference data and other commonly used dispersion models.
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Affiliation(s)
- Ivan D Welsh
- School of Physical and Chemical Sciences, University of Canterbury, Christchurch, New Zealand
| | - Deborah L Crittenden
- School of Physical and Chemical Sciences, University of Canterbury, Christchurch, New Zealand
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45
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Investigating reactivity and electronic structure of copper(II)-polypyridyl complexes and hydrogen peroxide. Inorganica Chim Acta 2021. [DOI: 10.1016/j.ica.2020.120168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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46
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Halbertal D, Finney NR, Sunku SS, Kerelsky A, Rubio-Verdú C, Shabani S, Xian L, Carr S, Chen S, Zhang C, Wang L, Gonzalez-Acevedo D, McLeod AS, Rhodes D, Watanabe K, Taniguchi T, Kaxiras E, Dean CR, Hone JC, Pasupathy AN, Kennes DM, Rubio A, Basov DN. Moiré metrology of energy landscapes in van der Waals heterostructures. Nat Commun 2021; 12:242. [PMID: 33431846 PMCID: PMC7801382 DOI: 10.1038/s41467-020-20428-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 12/02/2020] [Indexed: 01/29/2023] Open
Abstract
The emerging field of twistronics, which harnesses the twist angle between two-dimensional materials, represents a promising route for the design of quantum materials, as the twist-angle-induced superlattices offer means to control topology and strong correlations. At the small twist limit, and particularly under strain, as atomic relaxation prevails, the emergent moiré superlattice encodes elusive insights into the local interlayer interaction. Here we introduce moiré metrology as a combined experiment-theory framework to probe the stacking energy landscape of bilayer structures at the 0.1 meV/atom scale, outperforming the gold-standard of quantum chemistry. Through studying the shapes of moiré domains with numerous nano-imaging techniques, and correlating with multi-scale modelling, we assess and refine first-principle models for the interlayer interaction. We document the prowess of moiré metrology for three representative twisted systems: bilayer graphene, double bilayer graphene and H-stacked MoSe2/WSe2. Moiré metrology establishes sought after experimental benchmarks for interlayer interaction, thus enabling accurate modelling of twisted multilayers.
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Affiliation(s)
- Dorri Halbertal
- Department of Physics, Columbia University, New York, NY, USA.
| | - Nathan R Finney
- Department of Mechanical Engineering, Columbia University, New York, NY, USA
| | - Sai S Sunku
- Department of Physics, Columbia University, New York, NY, USA
| | | | | | - Sara Shabani
- Department of Physics, Columbia University, New York, NY, USA
| | - Lede Xian
- Max Planck Institute for the Structure and Dynamics of Matter and Center Free-Electron Laser Science, Luruper. Chaussee 149, 22761, Hamburg, Germany
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, 523808, China
| | - Stephen Carr
- Department of Physics, Harvard University, Cambridge, MA, 02138, USA
- Brown University, Providence, RI, 02912, USA
| | - Shaowen Chen
- Department of Physics, Columbia University, New York, NY, USA
- Department of Physics, Harvard University, Cambridge, MA, 02138, USA
| | - Charles Zhang
- Department of Physics, Columbia University, New York, NY, USA
- Department of Physics, University of California at Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Lei Wang
- Department of Physics, Columbia University, New York, NY, USA
- National Laboratory of Solid-State Microstructures, School of Physics and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, China
| | - Derick Gonzalez-Acevedo
- Department of Physics, Columbia University, New York, NY, USA
- Department of Physics, Harvard University, Cambridge, MA, 02138, USA
| | | | - Daniel Rhodes
- Department of Physics, Columbia University, New York, NY, USA
- Department of Materials Science and Engineering, University of Winsconsin-Madison, Madison, WI, 53706, USA
| | | | | | - Efthimios Kaxiras
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
| | - Cory R Dean
- Department of Physics, Columbia University, New York, NY, USA
| | - James C Hone
- Department of Mechanical Engineering, Columbia University, New York, NY, USA
| | | | - Dante M Kennes
- Max Planck Institute for the Structure and Dynamics of Matter and Center Free-Electron Laser Science, Luruper. Chaussee 149, 22761, Hamburg, Germany
- Institut fur Theorie der Statistischen Physik, RWTH Aachen University, 52056, Aachen, Germany
| | - Angel Rubio
- Max Planck Institute for the Structure and Dynamics of Matter and Center Free-Electron Laser Science, Luruper. Chaussee 149, 22761, Hamburg, Germany
- Center for Computational Quantum Physics, Flatiron Institute, New York, NY, 10010, USA
| | - D N Basov
- Department of Physics, Columbia University, New York, NY, USA
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47
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Dorofeeva OV, Ryzhova ON. Accurate estimation of enthalpies of formation for C-, H-, O-, and N-containing compounds using DLPNO-CCSD(T1)/CBS method. Struct Chem 2021. [DOI: 10.1007/s11224-020-01681-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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48
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Engel EA. Identification of synthesisable crystalline phases of water – a prototype for the challenges of computational materials design. CrystEngComm 2021. [DOI: 10.1039/d0ce01260b] [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
We discuss the identification of experimentally realisable crystalline phases of water to outline and contextualise some of the diverse building blocks of a computational materials design process.
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Affiliation(s)
- Edgar A. Engel
- TCM Group
- Cavendish Laboratory
- University of Cambridge
- Cambridge CB3 0HE
- UK
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49
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Zhou TP, Zhong F, Wu Y, Liao RZ. Regioselectivity and stereoselectivity of intramolecular [2 + 2] photocycloaddition catalyzed by chiral thioxanthone: a quantum chemical study. Org Biomol Chem 2021; 19:1532-1540. [DOI: 10.1039/d0ob02330b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Chiral photosensitizer-catalyzed stereoselective olefin cyclization has shown its significance in organic synthesis.
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Affiliation(s)
- Tai-Ping Zhou
- Key Laboratory of Materials Chemistry for Energy Conversion and Storage
- Ministry of Education
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica
- Hubei Key Laboratory of Materials Chemistry and Service Failure
- School of Chemistry and Chemical Engineering
| | - Fangrui Zhong
- Key Laboratory of Materials Chemistry for Energy Conversion and Storage
- Ministry of Education
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica
- Hubei Key Laboratory of Materials Chemistry and Service Failure
- School of Chemistry and Chemical Engineering
| | - Yuzhou Wu
- Key Laboratory of Materials Chemistry for Energy Conversion and Storage
- Ministry of Education
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica
- Hubei Key Laboratory of Materials Chemistry and Service Failure
- School of Chemistry and Chemical Engineering
| | - Rong-Zhen Liao
- Key Laboratory of Materials Chemistry for Energy Conversion and Storage
- Ministry of Education
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica
- Hubei Key Laboratory of Materials Chemistry and Service Failure
- School of Chemistry and Chemical Engineering
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50
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Fan Z, Hu Y, Li H, Fu J, Fan Q, King RB, Schaefer HF. Agostic Hydrogens in 1‐Norbornyl Metal Cyclopentadienyl Structures. Eur J Inorg Chem 2020. [DOI: 10.1002/ejic.202000714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Zhixiang Fan
- School of Science Key Laboratory of High Performance Scientific Computation Xihua University 610039 Chengdu China
| | - Yuchen Hu
- School of Science Key Laboratory of High Performance Scientific Computation Xihua University 610039 Chengdu China
| | - Huidong Li
- School of Science Key Laboratory of High Performance Scientific Computation Xihua University 610039 Chengdu China
- Department of Chemistry and Center for Computational Chemistry University of Georgia 30602 Athens Georgia USA
| | - Jia Fu
- School of Science Key Laboratory of High Performance Scientific Computation Xihua University 610039 Chengdu China
| | - Qunchao Fan
- School of Science Key Laboratory of High Performance Scientific Computation Xihua University 610039 Chengdu China
| | - R. Bruce King
- Department of Chemistry and Center for Computational Chemistry University of Georgia 30602 Athens Georgia USA
| | - Henry F. Schaefer
- Department of Chemistry and Center for Computational Chemistry University of Georgia 30602 Athens Georgia USA
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