1
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Heindel JP, Sami S, Head-Gordon T. Completely Multipolar Model as a General Framework for Many-Body Interactions as Illustrated for Water. J Chem Theory Comput 2024. [PMID: 39288266 DOI: 10.1021/acs.jctc.4c00812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2024]
Abstract
We introduce a general framework for many-body force fields, the Completely Multipolar Model (CMM), that utilizes multipolar electrical moments modulated by exponential decay of electron density as a common functional form for all terms of an energy decomposition analysis of intermolecular interactions. With this common functional form, the CMM model establishes well-formulated damped tensors that reach the correct asymptotes at both long- and short-range while formally ensuring no short-range catastrophes. CMM describes the separable EDA terms of dispersion, exchange polarization, and Pauli repulsion with short-ranged anisotropy, polarization as intramolecular charge fluctuations and induced dipoles, while charge transfer describes explicit movement of charge between molecules, and naturally describes many-body charge transfer by coupling into the polarization equations. We also utilize a new one-body potential that accounts for intramolecular polarization by including an electric field-dependent correction to the Morse potential to ensure that CMM reproduces all physically relevant monomer properties including the dipole moment, molecular polarizability, and dipole and polarizability derivatives. The quality of CMM is illustrated through agreement of individual terms of the EDA and excellent extrapolation to energies and geometries of an extensive validation set of water cluster data.
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Affiliation(s)
- Joseph P Heindel
- Kenneth S. Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Selim Sami
- Kenneth S. Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Teresa Head-Gordon
- Kenneth S. Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Departments of Bioengineering and Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
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2
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Pullanchery S, Kulik S, Schönfeldová T, Egan CK, Cassone G, Hassanali A, Roke S. pH drives electron density fluctuations that enhance electric field-induced liquid flow. Nat Commun 2024; 15:5951. [PMID: 39009573 PMCID: PMC11251051 DOI: 10.1038/s41467-024-50030-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 06/26/2024] [Indexed: 07/17/2024] Open
Abstract
Liquid flow along a charged interface is commonly described by classical continuum theory, which represents the electric double layer by uniformly distributed point charges. The electrophoretic mobility of hydrophobic nanodroplets in water doubles in magnitude when the pH is varied from neutral to mildly basic (pH 7 → 11). Classical continuum theory predicts that this increase in mobility is due to an increased surface charge. Here, by combining all-optical measurements of surface charge and molecular structure, as well as electronic structure calculations, we show that surface charge and molecular structure at the nanodroplet surface are identical at neutral and mildly basic pH. We propose that the force that propels the droplets originates from two factors: Negative charge on the droplet surface due to charge transfer from and within water, and anisotropic gradients in the fluctuating polarization induced by the electric field. Both charge density fluctuations couple with the external electric field, and lead to droplet flow. Replacing chloride by hydroxide doubles both the charge conductivity via the Grotthuss mechanism, and the droplet mobility. This general mechanism deeply impacts a plethora of processes in biology, chemistry, and nanotechnology and provides an explanation of how pH influences hydrodynamic phenomena and the limitations of classical continuum theory currently used to rationalize these effects.
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Affiliation(s)
- S Pullanchery
- Laboratory for fundamental BioPhotonics, Institute of Bioengineering (IBI), School of Engineering (STI), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - S Kulik
- Laboratory for fundamental BioPhotonics, Institute of Bioengineering (IBI), School of Engineering (STI), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - T Schönfeldová
- Laboratory for fundamental BioPhotonics, Institute of Bioengineering (IBI), School of Engineering (STI), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - C K Egan
- International Centre for Theoretical Physics, Trieste, Italy
| | - G Cassone
- Institute for Physical-Chemical Processes, Italian National Research Council (IPCF-CNR), Messina, Italy
| | - A Hassanali
- International Centre for Theoretical Physics, Trieste, Italy.
| | - S Roke
- Laboratory for fundamental BioPhotonics, Institute of Bioengineering (IBI), School of Engineering (STI), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
- Institute of Materials Science and Engineering (IMX), School of Engineering (STI), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
- Lausanne Centre for Ultrafast Science, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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3
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Tarek Ibrahim M, Wait E, Ren P. Quantum Mechanics Characterization of Non-Covalent Interaction in Nucleotide Fragments. Molecules 2024; 29:3258. [PMID: 39064837 PMCID: PMC11279843 DOI: 10.3390/molecules29143258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 07/03/2024] [Accepted: 07/06/2024] [Indexed: 07/28/2024] Open
Abstract
Accurate calculation of non-covalent interaction energies in nucleotides is crucial for understanding the driving forces governing nucleic acid structure and function, as well as developing advanced molecular mechanics forcefields or machine learning potentials tailored to nucleic acids. Here, we dissect the nucleotides' structure into three main constituents: nucleobases (A, G, C, T, and U), sugar moieties (ribose and deoxyribose), and phosphate group. The interactions among these fragments and between fragments and water were analyzed. Different quantum mechanical methods were compared for their accuracy in capturing the interaction energy. The non-covalent interaction energy was decomposed into electrostatics, exchange-repulsion, dispersion, and induction using two ab initio methods: Symmetry-Adapted Perturbation Theory (SAPT) and Absolutely Localized Molecular Orbitals (ALMO). These calculations provide a benchmark for different QM methods, in addition to providing a valuable understanding of the roles of various intermolecular forces in hydrogen bonding and aromatic stacking. With SAPT, a higher theory level and/or larger basis set did not necessarily give more accuracy. It is hard to know which combination would be best for a given system. In contrast, ALMO EDA2 did not show dependence on theory level or basis set; additionally, it is faster.
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Affiliation(s)
- Mayar Tarek Ibrahim
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA;
| | - Elizabeth Wait
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, TX 78712, USA;
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA;
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, TX 78712, USA;
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4
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Shen H, Head-Gordon M. Occupied-Virtual Orbitals for Chemical Valence with Applications to Charge Transfer in Energy Decomposition Analysis. J Phys Chem A 2024; 128:5202-5211. [PMID: 38900728 DOI: 10.1021/acs.jpca.4c02364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
In this article, we introduce the occupied-virtual orbitals for chemical valence (OVOCV). The OVOCVs can replace or complement the closely related idea of the natural orbitals for chemical valence (NOCV). The input is a difference density matrix connecting any initial single determinant to any final determinant, at a given molecular geometry, and a given one-particle basis. This arises in problems such as orbital rearrangement or charge transfer (CT) in energy decomposition analysis (EDA). The OVOCVs block-diagonalize the density difference operator into 2 × 2 blocks, which are spanned by one level that is filled in the initial state (the occupied OVOCV) and one that is empty (the virtual OVOCV). By contrast, the NOCVs fully diagonalize the density difference matrix and therefore are orbitals with mixed occupied-virtual character. Use of the OVOCVs makes it much easier to identify the donor and acceptor orbitals. We also introduce two different types of EDA methods with the OVOCVs and, most importantly, a charge decomposition analysis method that fixes the unreasonably large CT amount obtained directly from NOCV analysis. The square of the CT amount associated with each NOCV pair emerges as the appropriate value from the OVOCV analysis. When connecting the same initial and final states, this value is identical to the CT amount obtained from the independent absolutely localized molecular orbital (ALMO) complementary occupied-virtual orbital pair (COVP) analysis. The total, summed over all pairs, is also exactly the same as the independently suggested excitation number, as proved herein. Several examples are presented to compare NOCVs and OVOCVs: stretched H2+, a strong halogen bond between tetramethylthiourea and iodine, coordination of ethene in Zeise's salt, and binding in the Cp3La···C≡NCy complex.
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Affiliation(s)
- Hengyuan Shen
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Martin Head-Gordon
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
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5
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Cheng YH, Ho YS, Yang CJ, Chen CY, Hsieh CT, Cheng MJ. Electron Dynamics in Alkane C-H Activation Mediated by Transition Metal Complexes. J Phys Chem A 2024; 128:4638-4650. [PMID: 38832757 PMCID: PMC11182348 DOI: 10.1021/acs.jpca.4c01131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 05/15/2024] [Accepted: 05/28/2024] [Indexed: 06/05/2024]
Abstract
Alkanes, ideal raw materials for industrial chemical production, typically exhibit limited reactivity due to their robust and weakly polarized C-H bonds. The challenge lies in selectively activating these C-H bonds under mild conditions. To address this challenge, various C-H activation mechanisms have been developed. Yet, classifying these mechanisms depends on the overall stoichiometry, which can be ambiguous and sometimes problematic. In this study, we utilized density functional theory calculations combined with intrinsic bond orbital (IBO) analysis to examine electron flow in the four primary alkane C-H activation mechanisms: oxidative addition, σ-bond metathesis, 1,2-addition, and electrophilic activation. Methane was selected as the representative alkane molecule to undergo C-H heterolytic cleavage in these reactions. Across all mechanisms studied, we find that the CH3 moiety in methane consistently uses an electron pair from the cleaved C-H bond to form a σ-bond with the metal. Yet, the electron pair that accepts the proton differs with each mechanism: in oxidative addition, it is derived from the d-orbitals; in σ-bond metathesis, it resulted from the metal-ligand σ-bonds; in 1,2-addition, it arose from the π-orbital of the metal-ligand multiple bonds; and in electrophilic activation, it came from the lone pairs on ligands. This detailed analysis not only provides a clear visual understanding of these reactions but also showcases the ability of the IBO method to differentiate between mechanisms. The electron flow discerned from IBO analysis is further corroborated by results from absolutely localized molecular orbital energy decomposition analysis, which also helps to quantify the two predominant interactions in each process. Our findings offer profound insights into the electron dynamics at play in alkane C-H activation, enhancing our understanding of these critical reactions.
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Affiliation(s)
| | | | - Chia-Jung Yang
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
| | - Chun-Yu Chen
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
| | - Chi-Tien Hsieh
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
| | - Mu-Jeng Cheng
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
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6
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Sterling AJ, Levine DS, Aldossary A, Head-Gordon M. Chemical Bonding and the Role of Node-Induced Electron Confinement. J Am Chem Soc 2024; 146:9532-9543. [PMID: 38532619 DOI: 10.1021/jacs.3c10633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
The chemical bond is the cornerstone of chemistry, providing a conceptual framework to understand and predict the behavior of molecules in complex systems. However, the fundamental origin of chemical bonding remains controversial and has been responsible for fierce debate over the past century. Here, we present a unified theory of bonding, using a separation of electron delocalization effects from orbital relaxation to identify three mechanisms [node-induced confinement (typically associated with Pauli repulsion, though more general), orbital contraction, and polarization] that each modulate kinetic energy during bond formation. Through analysis of a series of archetypal bonds, we show that an exquisite balance of energy-lowering delocalizing and localizing effects are dictated simply by atomic electron configurations, nodal structure, and electronegativities. The utility of this unified bonding theory is demonstrated by its application to explain observed trends in bond strengths throughout the periodic table, including main group and transition metal elements.
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Affiliation(s)
- Alistair J Sterling
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Daniel S Levine
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Abdulrahman Aldossary
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Martin Head-Gordon
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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7
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Nagy S, Richter D, Dargó G, Orbán B, Gémes G, Höltzl T, Garádi Z, Fehér Z, Kupai J. Cinchona-Based Hydrogen-Bond Donor Organocatalyst Metal Complexes: Asymmetric Catalysis and Structure Determination. ChemistryOpen 2024; 13:e202300180. [PMID: 38189585 PMCID: PMC11004460 DOI: 10.1002/open.202300180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/12/2023] [Indexed: 01/09/2024] Open
Abstract
In this study, we describe the synthesis of cinchona (thio)squaramide and a novel cinchona thiourea organocatalyst. These catalysts were employed in pharmaceutically relevant catalytic asymmetric reactions, such as Michael, Friedel-Crafts, and A3 coupling reactions, in combination with Ag(I), Cu(II), and Ni(II) salts. We identified several organocatalyst-metal salt combinations that led to a significant increase in both yield and enantioselectivity. To gain insight into the active catalyst species, we prepared organocatalyst-metal complexes and characterized them using HRMS, NMR spectroscopy, and quantum chemical calculations (B3LYP-D4/def2-TZVP), which allowed us to establish a structure-activity relationship.
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Affiliation(s)
- Sándor Nagy
- Department of Organic Chemistry and TechnologyBudapest University of Technology and EconomicsMűegyetem rkp. 31111BudapestHungary
- Euroapi Hungary Kft.Tó utca 1–51045BudapestHungary
| | - Dóra Richter
- Department of Organic Chemistry and TechnologyBudapest University of Technology and EconomicsMűegyetem rkp. 31111BudapestHungary
| | - Gyula Dargó
- Department of Organic Chemistry and TechnologyBudapest University of Technology and EconomicsMűegyetem rkp. 31111BudapestHungary
| | - Balázs Orbán
- ELKH-BME Computation Driven Chemistry Research GroupDepartment of Inorganic and Analytical ChemistryBudapest University of Technology and EconomicsMűegyetem rkp. 31111BudapestHungary
- Furukawa Electric Institute of TechnologyKésmárk utca 28/A1157BudapestHungary
| | - Gergő Gémes
- Department of Organic Chemistry and TechnologyBudapest University of Technology and EconomicsMűegyetem rkp. 31111BudapestHungary
| | - Tibor Höltzl
- ELKH-BME Computation Driven Chemistry Research GroupDepartment of Inorganic and Analytical ChemistryBudapest University of Technology and EconomicsMűegyetem rkp. 31111BudapestHungary
- Furukawa Electric Institute of TechnologyKésmárk utca 28/A1157BudapestHungary
| | - Zsófia Garádi
- Department of PharmacognosySemmelweis UniversityÜllői út. 261085BudapesHungary
| | - Zsuzsanna Fehér
- Department of Organic Chemistry and TechnologyBudapest University of Technology and EconomicsMűegyetem rkp. 31111BudapestHungary
| | - József Kupai
- Department of Organic Chemistry and TechnologyBudapest University of Technology and EconomicsMűegyetem rkp. 31111BudapestHungary
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8
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Chakraborty R, Talbot JJ, Shen H, Yabuuchi Y, Carsch KM, Jiang HZH, Furukawa H, Long JR, Head-Gordon M. Quantum chemical modeling of hydrogen binding in metal-organic frameworks: validation, insight, predictions and challenges. Phys Chem Chem Phys 2024; 26:6490-6511. [PMID: 38324335 DOI: 10.1039/d3cp05540j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
A detailed chemical understanding of H2 interactions with binding sites in the nanoporous crystalline structure of metal-organic frameworks (MOFs) can lay a sound basis for the design of new sorbent materials. Computational quantum chemical calculations can aid in this quest. To set the stage, we review general thermodynamic considerations that control the usable storage capacity of a sorbent. We then discuss cluster modeling of H2 ligation at MOF binding sites using state-of-the-art density functional theory (DFT) calculations, and how the binding can be understood using energy decomposition analysis (EDA). Employing these tools, we illustrate the connections between the character of the MOF binding site and the associated adsorption thermodynamics using four experimentally characterized MOFs, highlighting the role of open metal sites (OMSs) in accessing binding strengths relevant to room temperature storage. The sorbents are MOF-5, with no open metal sites, Ni2(m-dobdc), containing Lewis acidic Ni(II) sites, Cu(I)-MFU-4l, containing π basic Cu(I) sites and V2Cl2.8(btdd), also containing π-basic V(II) sites. We next explore the potential for binding multiple H2 molecules at a single metal site, with thermodynamics useful for storage at ambient temperature; a materials design goal which has not yet been experimentally demonstrated. Computations on Ca2+ or Mg2+ bound to catecholate or Ca2+ bound to porphyrin show the potential for binding up to 4 H2; there is precedent for the inclusion of both catecholate and porphyrin motifs in MOFs. Turning to transition metals, we discuss the prediction that two H2 molecules can bind at V(II)-MFU-4l, a material that has been synthesized with solvent coordinated to the V(II) site. Additional calculations demonstrate binding three equivalents of hydrogen per OMS in Sc(I) or Ti(I)-exchanged MFU-4l. Overall, the results suggest promising prospects for experimentally realizing higher capacity hydrogen storage MOFs, if nontrivial synthetic and desolvation challenges can be overcome. Coupled with the unbounded chemical diversity of MOFs, there is ample scope for additional exploration and discovery.
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Affiliation(s)
- Romit Chakraborty
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA 94720, USA.
| | - Justin J Talbot
- Department of Chemistry, University of California, Berkeley, CA 94720, USA.
| | - Hengyuan Shen
- Department of Chemistry, University of California, Berkeley, CA 94720, USA.
| | - Yuto Yabuuchi
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA 94720, USA.
| | - Kurtis M Carsch
- Department of Chemistry, University of California, Berkeley, CA 94720, USA.
| | - Henry Z H Jiang
- Department of Chemistry, University of California, Berkeley, CA 94720, USA.
| | - Hiroyasu Furukawa
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA 94720, USA.
| | - Jeffrey R Long
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA 94720, USA.
- Department of Chemical and Biomedical Engineering, University of California, Berkeley, CA 94720, USA
| | - Martin Head-Gordon
- Department of Chemistry, University of California, Berkeley, CA 94720, USA.
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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9
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Dasgupta S, Palos E, Pan Y, Paesani F. Balance between Physical Interpretability and Energetic Predictability in Widely Used Dispersion-Corrected Density Functionals. J Chem Theory Comput 2024; 20:49-67. [PMID: 38150541 DOI: 10.1021/acs.jctc.3c00903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
We assess the performance of different dispersion models for several popular density functionals across a diverse set of noncovalent systems, ranging from the benzene dimer to molecular crystals. By analyzing the interaction energies and their individual components, we demonstrate that there exists variability across different systems for empirical dispersion models, which are calibrated for reproducing the interaction energies of specific systems. Thus, parameter fitting may undermine the underlying physics, as dispersion models rely on error compensation among the different components of the interaction energy. Energy decomposition analyses reveal that, the accuracy of revPBE-D3 for some aqueous systems originates from significant compensation between dispersion and charge transfer energies. However, revPBE-D3 is less accurate in describing systems where error compensation is incomplete, such as the benzene dimer. Such cases highlight the propensity for unpredictable behavior in various dispersion-corrected density functionals across a wide range of molecular systems, akin to the behavior of force fields. On the other hand, we find that SCAN-rVV10, a targeted-dispersion approach, affords significant reductions in errors associated with the lattice energies of molecular crystals, while it has limited accuracy in reproducing structural properties. Given the ubiquitous nature of noncovalent interactions and the key role of density functional theory in computational sciences, the future development of dispersion models should prioritize the faithful description of the dispersion energy, a shift that promises greater accuracy in capturing the underlying physics across diverse molecular and extended systems.
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Affiliation(s)
- Saswata Dasgupta
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Etienne Palos
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Yuanhui Pan
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
- Materials Science and Engineering, University of California San Diego, La Jolla, California 92093, United States
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, United States
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10
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Zheng WF, Chen J, Qi X, Huang Z. Modular and diverse synthesis of amino acids via asymmetric decarboxylative protonation of aminomalonic acids. Nat Chem 2023; 15:1672-1682. [PMID: 37973941 DOI: 10.1038/s41557-023-01362-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 10/06/2023] [Indexed: 11/19/2023]
Abstract
Stereoselective protonation is a challenge in asymmetric catalysis. The small size and high rate of transfer of protons mean that face-selective delivery to planar intermediates is hard to control, but it can unlock previously obscure asymmetric transformations. Particularly, when coupled with a preceding decarboxylation, enantioselective protonation can convert the abundant acid feedstocks into structurally diverse chiral molecules. Here an anchoring group strategy is demonstrated as a potential alternative and supplement to the conventional structural modification of catalysts by creating additional catalyst-substrate interactions. We show that a tailored benzamide group in aminomalonic acids can help build a coordinated network of non-covalent interactions, including hydrogen bonds, π-π interactions and dispersion forces, with a chiral acid catalyst. This allows enantioselective decarboxylative protonation to give α-amino acids. The malonate-based synthesis introduces side chains via a facile substitution of aminomalonic esters and thus can access structurally and functionally diverse amino acids.
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Affiliation(s)
- Wei-Feng Zheng
- State Key Laboratory of Synthetic Chemistry, Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Jingdan Chen
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, China
| | - Xiaotian Qi
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, China.
| | - Zhongxing Huang
- State Key Laboratory of Synthetic Chemistry, Department of Chemistry, The University of Hong Kong, Hong Kong, China.
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11
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Bui S, Gil-Guerrero S, van der Linden P, Carpentier P, Ceccarelli M, Jambrina PG, Steiner RA. Evolutionary adaptation from hydrolytic to oxygenolytic catalysis at the α/β-hydrolase fold. Chem Sci 2023; 14:10547-10560. [PMID: 37799987 PMCID: PMC10548524 DOI: 10.1039/d3sc03044j] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/31/2023] [Indexed: 10/07/2023] Open
Abstract
Protein fold adaptation to novel enzymatic reactions is a fundamental evolutionary process. Cofactor-independent oxygenases degrading N-heteroaromatic substrates belong to the α/β-hydrolase (ABH) fold superfamily that typically does not catalyze oxygenation reactions. Here, we have integrated crystallographic analyses under normoxic and hyperoxic conditions with molecular dynamics and quantum mechanical calculations to investigate its prototypic 1-H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase (HOD) member. O2 localization to the "oxyanion hole", where catalysis occurs, is an unfavorable event and the direct competition between dioxygen and water for this site is modulated by the "nucleophilic elbow" residue. A hydrophobic pocket that overlaps with the organic substrate binding site can act as a proximal dioxygen reservoir. Freeze-trap pressurization allowed the structure of the ternary complex with a substrate analogue and O2 bound at the oxyanion hole to be determined. Theoretical calculations reveal that O2 orientation is coupled to the charge of the bound organic ligand. When 1-H-3-hydroxy-4-oxoquinaldine is uncharged, O2 binds with its molecular axis along the ligand's C2-C4 direction in full agreement with the crystal structure. Substrate activation triggered by deprotonation of its 3-OH group by the His-Asp dyad, rotates O2 by approximately 60°. This geometry maximizes the charge transfer between the substrate and O2, thus weakening the double bond of the latter. Electron density transfer to the O2(π*) orbital promotes the formation of the peroxide intermediate via intersystem crossing that is rate-determining. Our work provides a detailed picture of how evolution has repurposed the ABH-fold architecture and its simple catalytic machinery to accomplish metal-independent oxygenation.
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Affiliation(s)
- Soi Bui
- Randall Centre for Cell and Molecular Biophysics, King's College London London SE1 1UL UK
| | - Sara Gil-Guerrero
- Departamento de Química Física, University of Salamanca Salamanca 37008 Spain
| | - Peter van der Linden
- European Synchrotron Radiation Facility (ESRF), Partnership for Soft Condensed Matter (PSCM) 71 Avenue des Martyrs Grenoble 38000 France
| | - Philippe Carpentier
- European Synchrotron Radiation Facility (ESRF) 71 Avenue des Martyrs 38043 Grenoble France
- Université Grenoble Alpes, CNRS, CEA, Interdisciplinary Research Institute of Grenoble (IRIG), Laboratoire Chimie et Biologie des Métaux (LCBM) UMR 5249 17 Avenue des Martyrs 38054 Grenoble France
| | - Matteo Ceccarelli
- Department of Physics, University of Cagliari Monserrato 09042 Italy
- IOM-CNR Unità di Cagliari, Cittadella Universitaria Monserrato 09042 Italy
| | - Pablo G Jambrina
- Departamento de Química Física, University of Salamanca Salamanca 37008 Spain
| | - Roberto A Steiner
- Randall Centre for Cell and Molecular Biophysics, King's College London London SE1 1UL UK
- Department of Biomedical Sciences, University of Padova Italy
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12
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Horwitz MA, Dürr AB, Afratis K, Chen Z, Soika J, Christensen KE, Fushimi M, Paton RS, Gouverneur V. Regiodivergent Nucleophilic Fluorination under Hydrogen Bonding Catalysis: A Computational and Experimental Study. J Am Chem Soc 2023; 145:9708-9717. [PMID: 37079853 PMCID: PMC10161234 DOI: 10.1021/jacs.3c01303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
The controlled programming of regiochemical outcomes in nucleophilic fluorination reactions with alkali metal fluoride is a problem yet to be solved. Herein, two synergistic approaches exploiting hydrogen bonding catalysis are presented. First, we demonstrate that modulating the charge density of fluoride with a hydrogen-bond donor urea catalyst directly influences the kinetic regioselectivity in the fluorination of dissymmetric aziridinium salts with aryl and ester substituents. Moreover, we report a urea-catalyzed formal dyotropic rearrangement, a thermodynamically controlled regiochemical editing process consisting of C-F bond scission followed by fluoride rebound. These findings offer a route to access enantioenriched fluoroamine regioisomers from a single chloroamine precursor, and more generally, new opportunities in regiodivergent asymmetric (bis)urea-based organocatalysis.
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Affiliation(s)
- Matthew A Horwitz
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Alexander B Dürr
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Konstantinos Afratis
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Zijun Chen
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Julia Soika
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Kirsten E Christensen
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Makoto Fushimi
- Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-Chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Robert S Paton
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80528, United States
| | - Véronique Gouverneur
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
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13
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Aldossary A, Gimferrer M, Mao Y, Hao H, Das AK, Salvador P, Head-Gordon T, Head-Gordon M. Force Decomposition Analysis: A Method to Decompose Intermolecular Forces into Physically Relevant Component Contributions. J Phys Chem A 2023; 127:1760-1774. [PMID: 36753558 DOI: 10.1021/acs.jpca.2c08061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Computational quantum chemistry can be more than just numerical experiments when methods are specifically adapted to investigate chemical concepts. One important example is the development of energy decomposition analysis (EDA) to reveal the physical driving forces behind intermolecular interactions. In EDA, typically the interaction energy from a good-quality density functional theory (DFT) calculation is decomposed into multiple additive components that unveil permanent and induced electrostatics, Pauli repulsion, dispersion, and charge-transfer contributions to noncovalent interactions. Herein, we formulate, implement, and investigate decomposing the forces associated with intermolecular interactions into the same components. The resulting force decomposition analysis (FDA) is potentially useful as a complement to the EDA to understand chemistry, while also providing far more information than an EDA for data analysis purposes such as training physics-based force fields. We apply the FDA based on absolutely localized molecular orbitals (ALMOs) to analyze interactions of water with sodium and chloride ions as well as in the water dimer. We also analyze the forces responsible for geometric changes in carbon dioxide upon adsorption onto (and activation by) gold and silver anions. We also investigate how the force components of an EDA-based force field for water clusters, namely MB-UCB, compare to those from force decomposition analysis.
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Affiliation(s)
- Abdulrahman Aldossary
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley California 94720, United States
| | - Martí Gimferrer
- Institut de Química Computacional i Catàlsi and Departament de Química, Universitat de Girona, 17003 Girona, Catalonia Spain
| | - Yuezhi Mao
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, California 92182, United States
| | - Hongxia Hao
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley California 94720, United States
| | - Akshaya K Das
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley California 94720, United States
| | - Pedro Salvador
- Institut de Química Computacional i Catàlsi and Departament de Química, Universitat de Girona, 17003 Girona, Catalonia Spain
| | - Teresa Head-Gordon
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley California 94720, United States
| | - Martin Head-Gordon
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley California 94720, United States
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14
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Gamboa-Arancibia ME, Caro N, Gamboa A, Morales JO, González Casanova JE, Rojas Gómez DM, Miranda-Rojas S. Improving Lurasidone Hydrochloride's Solubility and Stability by Higher-Order Complex Formation with Hydroxypropyl-β-cyclodextrin. Pharmaceutics 2023; 15:pharmaceutics15010232. [PMID: 36678861 PMCID: PMC9861442 DOI: 10.3390/pharmaceutics15010232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/21/2022] [Accepted: 01/03/2023] [Indexed: 01/13/2023] Open
Abstract
The biopharmaceutical classification system groups low-solubility drugs into two groups: II and IV, with high and low permeability, respectively. Most of the new drugs developed for common pathologies present solubility issues. This is the case of lurasidone hydrochloride-a drug used for the treatment of schizophrenia and bipolar depression. Likewise, the stability problems of some drugs limit the possibility of preparing them in liquid pharmaceutical forms where hydrolysis and oxidation reactions can be favored. Lurasidone hydrochloride presents the isoindole-1,3-dione ring, which is highly susceptible to alkaline hydrolysis, and the benzisothiazole ring, which is susceptible to a lesser extent to oxidation. Herein, we propose to study the increase in the solubility and stability of lurasidone hydrochloride by the formation of higher-order inclusion complexes with hydroxypropyl-β-cyclodextrin. Several stoichiometric relationships were studied at between 0.5 and 3 hydroxypropyl-β-cyclodextrin molecules per drug molecule. The obtained products were characterized, and their solubility and stability were assessed. According to the obtained results, the formation of inclusion complexes dramatically increased the solubility of the drug, and this increased with the increase in the inclusion ratio. This was associated with the loss of crystalline state of the drug, which was in an amorphous state according to infrared spectroscopy, calorimetry, and X-ray analysis. This was also correlated with the stabilization of lurasidone by the cyclodextrin inhibiting its recrystallization. Phase solubility,1H-NMR, and docking computational characterization suggested that the main stoichiometric ratio was 1:1; however, we cannot rule out a 1:2 ratio, where a second cyclodextrin molecule could bind through the isoindole-1,3-dione ring, improving its stability as well. Finally, we can conclude that the formation of higher-order inclusion complexes of lurasidone with hydroxypropyl-β-cyclodextrin is a successful strategy to increase the solubility and stability of the drug.
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Affiliation(s)
- María Elena Gamboa-Arancibia
- Facultad de Química y Biología, Universidad de Santiago de Chile, Av. Libertador Bernardo O’Higgins 3363, Estación Central, Santiago 9170022, Chile
- Correspondence: (M.E.G.-A.); (S.M.-R.); Tel.: +56-2-2-7181166 (M.E.G.-A.); +56-2-2-6618341 (S.-M.R.)
| | - Nelson Caro
- Centro de Investigación Austral Biotech, Facultad de Ciencias, Universidad Santo Tomas, Avenida Ejército 146, Santiago 8370003, Chile
| | - Alexander Gamboa
- Facultad de Química y Biología, Universidad de Santiago de Chile, Av. Libertador Bernardo O’Higgins 3363, Estación Central, Santiago 9170022, Chile
- Centro de Investigación Austral Biotech, Facultad de Ciencias, Universidad Santo Tomas, Avenida Ejército 146, Santiago 8370003, Chile
| | - Javier Octavio Morales
- Department of Pharmaceutical Science and Technology, School of Chemical and Pharmaceutical Sciences, University of Chile, Santiago 8380494, Chile
- Advanced Center for Chronic Diseases, Santiago 8380494, Chile
- Center of New Drugs for Hypertension, Santiago 8380494, Chile
| | | | - Diana Marcela Rojas Gómez
- Escuela de Nutrición y Dietética, Facultad de Medicina, Universidad Andrés Bello, Santiago 8370321, Chile
| | - Sebastián Miranda-Rojas
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andrés Bello, Av. República 275, Santiago 8370146, Chile
- Correspondence: (M.E.G.-A.); (S.M.-R.); Tel.: +56-2-2-7181166 (M.E.G.-A.); +56-2-2-6618341 (S.-M.R.)
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15
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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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16
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Chakraborty R, Carsch KM, Jaramillo DE, Yabuuchi Y, Furukawa H, Long JR, Head-Gordon M. Prediction of Multiple Hydrogen Ligation at a Vanadium(II) Site in a Metal-Organic Framework. J Phys Chem Lett 2022; 13:10471-10478. [PMID: 36326596 DOI: 10.1021/acs.jpclett.2c02844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Densifying hydrogen in a metal-organic framework (MOF) at moderate pressures can circumvent challenges associated with high-pressure compression. The highly tunable structural and chemical composition in MOFs affords vast possibilities to optimize binding interactions. At the heart of this search are the nanoscale characteristics of molecular adsorption at the binding site(s). Using density functional theory (DFT) to model binding interactions of hydrogen to the exposed metal site of cation-exchanged MFU-4l, we predict multiple hydrogen ligation of H2 at the first coordination sphere of V(II) in V(II)-exchanged MFU-4l. We find that the strength of this binding between the metal site and H2 molecules can be tuned by altering the halide counterion adjacent to the metal site and that the fluoride containing node affords the most favorable interactions for high-density H2 storage. Using energy decomposition analysis, we delineate electronic contributions that enable multiple hydrogen ligation and demonstrate its benefits for hydrogen adsorption and release at modest pressures.
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Affiliation(s)
- Romit Chakraborty
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California94720, United States
- Department of Chemistry, University of California, Berkeley, California94720, United States
| | - Kurtis M Carsch
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California94720, United States
- Department of Chemistry, University of California, Berkeley, California94720, United States
| | - David E Jaramillo
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California94720, United States
- Department of Chemistry, University of California, Berkeley, California94720, United States
| | - Yuto Yabuuchi
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California94720, United States
- Department of Chemistry, University of California, Berkeley, California94720, United States
| | - Hiroyasu Furukawa
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California94720, United States
- Department of Chemistry, University of California, Berkeley, California94720, United States
| | - Jeffrey R Long
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California94720, United States
- Department of Chemistry, University of California, Berkeley, California94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California94720, United States
- Department of Chemical and Biomedical Engineering, University of California, Berkeley, California94720, United States
| | - Martin Head-Gordon
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California94720, United States
- Department of Chemistry, University of California, Berkeley, California94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California94720, United States
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17
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Jia X, Wang Q, Huang F, Liu J, Wang W, Yang C, Sun C, Chen D. Cation Bridge Mediating Homo- and Cross-Coupling in Copper-Catalyzed Reductive Coupling of Benzaldehyde and Benzophenone. Inorg Chem 2022; 61:18033-18043. [DOI: 10.1021/acs.inorgchem.2c02392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Xinhua Jia
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, P. R. China
| | - Qiong Wang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, P. R. China
| | - Fang Huang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, P. R. China
| | - Jianbiao Liu
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, P. R. China
| | - Wenjuan Wang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, P. R. China
| | - Chong Yang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, P. R. China
| | - Chuanzhi Sun
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, P. R. China
| | - Dezhan Chen
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, P. R. China
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18
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Guo W, Hare SR, Chen SS, Saunders CM, Tantillo DJ. C-H Insertion in Dirhodium Tetracarboxylate-Catalyzed Reactions despite Dynamical Tendencies toward Fragmentation: Implications for Reaction Efficiency and Catalyst Design. J Am Chem Soc 2022; 144:17219-17231. [PMID: 36098581 DOI: 10.1021/jacs.2c07681] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rh-catalyzed C-H insertion reactions to form β-lactones suffer from post-transition state bifurcations, with the same transition states leading to ketones and ketenes via fragmentation in addition to β-lactones. In such a circumstance, traditional transition state theory cannot predict product selectivity, so we employed ab initio molecular dynamics simulations to do so and provide a framework for rationalizing the origins of said selectivity. Weak interactions between the catalyst and substrate were studied using energy decomposition and noncovalent interaction analyses, which unmasked an important role of the 2-bromophenyl substituent that has been used in multiple β-lactone-forming C-H insertion reactions. Small and large catalysts were shown to behave differently, with the latter providing a means of overcoming dynamically preferred fragmentation by lowering the barrier for the recombination of the product fragments in the grip of the large catalyst active site cavity.
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Affiliation(s)
- Wentao Guo
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Stephanie R Hare
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Shu-Sen Chen
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Carla M Saunders
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Dean J Tantillo
- Department of Chemistry, University of California, Davis, California 95616, United States
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19
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Hisada M, Shimizu D, Matsuda K. π-Expansion of 2,3,6,7-Tetraazanaphthalene with Two Embedded Heptagons: Highly Twisted Structure and Lone-Pair/π* Interaction in the Crystal. Org Lett 2022; 24:3707-3711. [PMID: 35561030 DOI: 10.1021/acs.orglett.2c01345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Synthesis and characterization of doubly diphenylene-fused 2,3,6,7-tetraazanaphthalene 1 are described. Single-crystal X-ray diffraction analysis showed the highly twisted structure of 1 with a degree of twisting of 13.0°/Å, which is one of the largest values for a π-system. In the crystal, molecules of 1 formed an orthogonal one-dimensional column with π-stacking of diphenylene moieties and a short intermolecular C···N distance due to lone-pair/π* interaction, which is a rare example of lone-pair/π* interaction in a supramolecular assembly.
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Affiliation(s)
- Masato Hisada
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Daiki Shimizu
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Kenji Matsuda
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
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20
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Kron KJ, Hunt JR, Dawlaty JM, Mallikarjun Sharada S. Modeling and Characterization of Exciplexes in Photoredox CO 2 Reduction: Insights from Quantum Chemistry and Fluorescence Spectroscopy. J Phys Chem A 2022; 126:2319-2329. [PMID: 35385660 DOI: 10.1021/acs.jpca.1c10658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Interactions between excited-state arenes and amines can lead to the formation of structures with a distinct emission behavior. These excited-state complexes or exciplexes can reduce the ability of the arene to participate in other reactions, such as CO2 reduction, or increase the likelihood of degradation via Birch reduction. Exciplex geometries are necessary to understand photophysical behavior and probe degradation pathways but are challenging to calculate. We establish a detailed computational protocol for calculation, verification, and characterization of exciplexes. Using fluorescence spectroscopy, we first demonstrate the formation of exciplexes between excited-state oligo-(p-phenylene) (OPP), shown to successfully carry out CO2 reduction, and triethylamine. Time-dependent density functional theory is employed to optimize the geometries of these exciplexes, which are validated by comparing both emission energies and their solvatochromism with the experiment. Excited-state energy decomposition analysis confirms the predominant role played by charge transfer interactions in the red shift of emissions relative to the isolated excited-state OPP*. We find that although the exciplex emission frequency depends strongly on solvent dielectric, the extent of charge separation in an exciplex does not. Our results also suggest that the formation of solvent-separated ionic radical states upon complete electron transfer competes with exciplex formation in higher-dielectric solvents, thereby leading to reduced exciplex emission intensities in fluorescence experiments.
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Affiliation(s)
- Kareesa J Kron
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089, United States
| | - Jonathan Ryan Hunt
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Jahan M Dawlaty
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Shaama Mallikarjun Sharada
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089, United States.,Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
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21
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Abstract
We review different models for introducing electric polarization in force fields, with special focus on methods where polarization is modelled at the atomic charge level. While electric polarization has been included in several force fields, the common approach has been to focus on atomic dipole polarizability. Several approaches allow modelling electric polarization by using charge-flow between charge sites instead, but this has been less exploited, despite that atomic charges and charge-flow is expected to be more important than atomic dipoles and dipole polarizability. A number of challenges are required to be solved for charge-flow models to be incorporated into polarizable force fields, for example how to parameterize the models and how to make them computational efficient.
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Affiliation(s)
- Frank Jensen
- Department of Chemistry, Aarhus University, Denmark.
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22
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Das AK, Liu M, Head-Gordon T. Development of a Many-Body Force Field for Aqueous Alkali Metal and Halogen Ions: An Energy Decomposition Analysis Guided Approach. J Chem Theory Comput 2022; 18:953-967. [DOI: 10.1021/acs.jctc.1c00537] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Akshaya Kumar Das
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Meili Liu
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Teresa Head-Gordon
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Departments of Bioengineering and Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
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23
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Li B, Xu H, Dang Y, Houk KN. Dispersion and Steric Effects on Enantio-/Diastereoselectivities in Synergistic Dual Transition-Metal Catalysis. J Am Chem Soc 2022; 144:1971-1985. [DOI: 10.1021/jacs.1c12664] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Bo Li
- Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Department of Chemistry, School of Science, Tianjin University, Tianjin 300072, China
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Hui Xu
- Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Department of Chemistry, School of Science, Tianjin University, Tianjin 300072, China
| | - Yanfeng Dang
- Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Department of Chemistry, School of Science, Tianjin University, Tianjin 300072, China
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
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24
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Ashraf A, Herbert JM, Muhammad S, Farooqi BA, Farooq U, Salman M, Ayub K. Theoretical Approach to Evaluate the Gas-Sensing Performance of Graphene Nanoribbon/Oligothiophene Composites. ACS OMEGA 2022; 7:2260-2274. [PMID: 35071915 PMCID: PMC8772315 DOI: 10.1021/acsomega.1c05863] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
Composite formation with graphene is an effective approach to increase the sensitivity of polythiophene (nPT) gas sensors. The interaction mechanism between gaseous analytes and graphene/nPT composite systems is still not clear, and density functional theory calculations are used to explore the interaction mechanism between graphene/nPT nanoribbon composites (with n = 3-9 thiophene units) and gaseous analytes CO, NH3, SO2, and NO2. For the studied analytes, the interaction energy ranges from -44.28 kcal/mol for (C54H30-3PT)-NO2 to -2.37 kcal/mol for (C54H30-3PT)-CO at the counterpoise-corrected ωB97M-V/def2-TZVPD level of theory. The sensing mechanism is further evaluated by geometric analysis, ultraviolet-visible spectroscopy, density of-states analysis, calculation of global reactivity indices, and both frontier and natural bond orbital analyses. The variation in the highest occupied molecular orbital/lowest unoccupied molecular orbital gap of the composite indicates the change in conductivity upon complexation with the analyte. Energy decomposition analysis reveals that dispersion and charge transfer make the largest contributions to the interaction energy. The graphene/oligothiophene composite is more sensitive toward these analytes than either component taken alone due to larger changes in the orbital gap. The computational framework established in the present work can be used to evaluate and design graphene/nPT nanoribbon composite materials for gas sensors.
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Affiliation(s)
- Ayesha Ashraf
- Department
of Chemistry and Biochemistry, The Ohio
State University, Columbus, Ohio 43210, USA
| | - John M. Herbert
- Department
of Chemistry and Biochemistry, The Ohio
State University, Columbus, Ohio 43210, USA
| | - Shabbir Muhammad
- Department
of Physics, College of Science, King Khalid
University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Bilal Ahmad Farooqi
- Institute
of Chemistry, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590 Pakistan
| | - Umar Farooq
- Institute
of Chemistry, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590 Pakistan
| | - Muhammad Salman
- Institute
of Chemistry, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590 Pakistan
| | - Khurshid Ayub
- Department
of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
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25
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Wang YN, Wang X, Li SJ, Lan Y. Carbene-enabled ether activation through the formation of oxonium: a theoretical view. Org Chem Front 2022. [DOI: 10.1039/d1qo01730f] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Here, we report a theoretical investigation of the reactivity and chemoselectivity of carbene-enabled ether activation.
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Affiliation(s)
- Ya-Nan Wang
- College of Chemistry, and Institute of Green Catalysis, Zhengzhou University, 100 Science Avenue, Zhengzhou 450001, Henan, P. R. China
| | - Xinghua Wang
- College of Chemistry, and Institute of Green Catalysis, Zhengzhou University, 100 Science Avenue, Zhengzhou 450001, Henan, P. R. China
| | - Shi-Jun Li
- College of Chemistry, and Institute of Green Catalysis, Zhengzhou University, 100 Science Avenue, Zhengzhou 450001, Henan, P. R. China
| | - Yu Lan
- College of Chemistry, and Institute of Green Catalysis, Zhengzhou University, 100 Science Avenue, Zhengzhou 450001, Henan, P. R. China
- School of Chemistry and Chemical Engineering, and Chongqing Key Laboratory of Theoretical and Computational Chemistry, Chongqing University, Chongqing 400030, P. R. China
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26
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Zech A, Head-Gordon M. Dissociation of HCl in water nanoclusters: an energy decomposition analysis perspective. Phys Chem Chem Phys 2021; 23:26737-26749. [PMID: 34846396 DOI: 10.1039/d1cp04587c] [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
As known, small HCl-water nanoclusters display a particular dissociation behaviour, whereby at least four water molecules are required for the ionic dissociation of HCl. In this work, we examine how intermolecular interactions promote the ionic dissociation of such nanoclusters. To this end, a set of 45 HCl-water nanoclusters with up to four water molecules is introduced. Energy decomposition analysis based on absolutely localized molecular orbitals (ALMO-EDA) is employed in order to study the importance of frozen interaction, dispersion, polarization, and charge-transfer for the dissociation. The vertical ALMO-EDA scheme is applied to HCl-water clusters along a proton-transfer coordinate varying the amount of spectator water molecules. The corresponding ALMO-EDA results show a clear preference for the dissociated cluster only in the presence of four water molecules. Our analysis of adiabatic ALMO-EDA results reveals a push-pull mechanism for the destabilization of the HCl bond based on the synergy between forward and backward charge-transfer.
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Affiliation(s)
- Alexander Zech
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA.
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA. .,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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27
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Smock SR, Alimento R, Mallikarjun Sharada S, Brutchey RL. Probing the Ligand Exchange of N-Heterocyclic Carbene-Capped Ag 2S Nanocrystals with Amines and Carboxylic Acids. Inorg Chem 2021; 60:13699-13706. [PMID: 34492763 DOI: 10.1021/acs.inorgchem.1c02018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
N-Heterocyclic carbenes (NHCs) are versatile L-type ligands that have been shown to stabilize coinage metal chalcogenide nanocrystals, such as Ag2S, remarkably well. However, very little research has been done on the interaction between NHC ligands and coinage metal chalcogenide nanocrystal surfaces and subsequent ligand exchange reactions. Herein, solution 1H nuclear magnetic resonance methods were used to monitor ligand exchange reactions on stoichiometric Ag2S nanocrystal platforms with various primary amine and carboxylic acid ligands. Despite the introduction of new ligands, the native NHC ligands remain tightly bound to the Ag2S nanocrystal surface and are not displaced at room temperature. Primary amine and carboxylic acid ligands demonstrated quantitative ligand exchange only after the samples had been heated with an excess incoming ligand, which implies a strong NHC-Ag binding energy. Density functional theory affirms that a model NHC ligand binds the strongest to a Ag12S6 cluster surface, followed by amine and carboxylic acid binding; computational analysis is therefore in line with the absence of NHC displacement observed in experiments. Both the bulky sterics of the C14-alkyl chains on the NHC and the high energies for the binding of NHC to the Ag2S surface contribute to the superior colloidal stability over conventional long-chain amine or carboxylic acid ligands (many months vs hours to days).
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Affiliation(s)
- Sara R Smock
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Ryan Alimento
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089, United States
| | - Shaama Mallikarjun Sharada
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States.,Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089, United States
| | - Richard L Brutchey
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
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28
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Hannigan MD, McNeil AJ, Zimmerman PM. Using JPP to Identify Ni Bidentate Phosphine Complexes In Situ. Inorg Chem 2021; 60:13400-13408. [PMID: 34405991 PMCID: PMC8937619 DOI: 10.1021/acs.inorgchem.1c01720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Identifying intermediates of Ni-containing reactions can be challenging due to the high reactivity of Ni complexes and their sensitivity toward air and moisture. Many Ni bidentate phosphine complexes are diamagnetic and can be analyzed in situ via 31P NMR spectroscopy, but the oxidation state of Ni is difficult to determine using 31P chemical shift analysis alone. The J-coupling between P atoms, JPP, has been proposed to correlate with oxidation state, but few investigations have looked at how JPP is affected by parameters such as length of the linker or identity of the phosphine or other ligands. The present investigation into the JPP values of Ni bidentate phosphine complexes with two-carbon and three-carbon linkers shows that the JPP values observed in 31P NMR spectra, |JPP|, are competent indicators of the oxidation state at Ni. For complexes with two-carbon linkers, |JPP| > 40 Hz is typical of Ni0 while |JPP| < 30 Hz is typical of NiII; this trend is reversed for complexes with three-carbon linkers. Additionally, the Lewis acidity of the Ni and Lewis basicity of the phosphine ligand affect JPP predictably. For example, increased P-to-Ni donation arising from more-donating phosphines or more-withdrawing ligands trans to the P atoms causes a more negative JPP. These results should enable the oxidation state of Ni and properties of ligands in Ni bidentate phosphine complexes to be determined in situ during reactions containing these species.
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Affiliation(s)
- Matthew D Hannigan
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Anne J McNeil
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
- Macromolecular Science and Engineering Program, University of Michigan, 2800 Plymouth Road, Ann Arbor, Michigan 48109-2800, United States
| | - Paul M Zimmerman
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
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29
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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: 480] [Impact Index Per Article: 160.0] [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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30
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Lan Z, Mallikarjun Sharada S. A framework for constructing linear free energy relationships to design molecular transition metal catalysts. Phys Chem Chem Phys 2021; 23:15543-15556. [PMID: 34254089 DOI: 10.1039/d1cp02278d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A computational framework for ligand-driven design of transition metal complexes is presented in this work. We propose a general procedure for the construction of active site-specific linear free energy relationships (LFERs), which are inspired from Hammett and Taft correlations in organic chemistry and grounded in the activation strain model (ASM). Ligand effects are isolated and quantified in terms of their contribution to interaction and strain energy components of ASM. Scalar descriptors that are easily obtainable are then employed to construct the complete LFER. We successfully demonstrate proof-of-concept by constructing and applying an LFER to CH activation with enzyme-inspired [Cu2O2]2+ complexes. The key benefit of using ASM is a built-in compensation or error cancellation between LFER prediction of interaction and strain terms, resulting in accurate barrier predictions for 37 of the 47 catalysts examined in this study. The LFER is also transferable with respect to level of theory and flexible towards the choice of reference system. The absence of interaction-strain compensation or poor model performance for the remaining systems is a consequence of the approximate nature of the chosen interaction energy descriptor and LFER construction of the strain term, which focuses largely on trends in substrate and not catalyst strain.
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Affiliation(s)
- Zhenzhuo Lan
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA, USA.
| | - Shaama Mallikarjun Sharada
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA, USA. and Department of Chemistry, University of Southern California, Los Angeles, CA, USA
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31
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Grofe A, Gao J, Li X. Exact-two-component block-localized wave function: A simple scheme for the automatic computation of relativistic ΔSCF. J Chem Phys 2021; 155:014103. [PMID: 34241404 DOI: 10.1063/5.0054227] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Block-localized wave function is a useful method for optimizing constrained determinants. In this article, we extend the generalized block-localized wave function technique to a relativistic two-component framework. Optimization of excited state determinants for two-component wave functions presents a unique challenge because the excited state manifold is often quite dense with degenerate states. Furthermore, we test the degree to which certain symmetries result naturally from the ΔSCF optimization such as time-reversal symmetry and symmetry with respect to the total angular momentum operator on a series of atomic systems. Variational optimizations may often break the symmetry in order to lower the overall energy, just as unrestricted Hartree-Fock breaks spin symmetry. Overall, we demonstrate that time-reversal symmetry is roughly maintained when using Hartree-Fock, but less so when using Kohn-Sham density functional theory. Additionally, maintaining total angular momentum symmetry appears to be system dependent and not guaranteed. Finally, we were able to trace the breaking of total angular momentum symmetry to the relaxation of core electrons.
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Affiliation(s)
- Adam Grofe
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Jiali Gao
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China; Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, USA; and Beijing University Shenzhen Graduate School, Shenzhen 518055, China
| | - Xiaosong Li
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
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32
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First-principles study of hybrid nanostructures formed by deposited phthalocyanine/porphyrin metal complexes on phosphorene. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115948] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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33
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Mao Y, Loipersberger M, Horn PR, Das A, Demerdash O, Levine DS, Prasad Veccham S, Head-Gordon T, Head-Gordon M. From Intermolecular Interaction Energies and Observable Shifts to Component Contributions and Back Again: A Tale of Variational Energy Decomposition Analysis. Annu Rev Phys Chem 2021; 72:641-666. [PMID: 33636998 DOI: 10.1146/annurev-physchem-090419-115149] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Quantum chemistry in the form of density functional theory (DFT) calculations is a powerful numerical experiment for predicting intermolecular interaction energies. However, no chemical insight is gained in this way beyond predictions of observables. Energy decomposition analysis (EDA) can quantitatively bridge this gap by providing values for the chemical drivers of the interactions, such as permanent electrostatics, Pauli repulsion, dispersion, and charge transfer. These energetic contributions are identified by performing DFT calculations with constraints that disable components of the interaction. This review describes the second-generation version of the absolutely localized molecular orbital EDA (ALMO-EDA-II). The effects of different physical contributions on changes in observables such as structure and vibrational frequencies upon complex formation are characterized via the adiabatic EDA. Example applications include red- versus blue-shifting hydrogen bonds; the bonding and frequency shifts of CO, N2, and BF bound to a [Ru(II)(NH3)5]2 + moiety; and the nature of the strongly bound complexes between pyridine and the benzene and naphthalene radical cations. Additionally, the use of ALMO-EDA-II to benchmark and guide the development of advanced force fields for molecular simulation is illustrated with the recent, very promising, MB-UCB potential.
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Affiliation(s)
- Yuezhi Mao
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA;
| | - Matthias Loipersberger
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA;
| | - Paul R Horn
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA;
| | - Akshaya Das
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA; .,Department of Bioengineering and Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, USA
| | - Omar Demerdash
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA; .,Department of Bioengineering and Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, USA
| | - Daniel S Levine
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA;
| | - Srimukh Prasad Veccham
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA;
| | - Teresa Head-Gordon
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA; .,Department of Bioengineering and Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, USA
| | - Martin Head-Gordon
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA;
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34
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Mishra KK, Borish K, Singh G, Panwaria P, Metya S, Madhusudhan MS, Das A. Observation of an Unusually Large IR Red-Shift in an Unconventional S-H···S Hydrogen-Bond. J Phys Chem Lett 2021; 12:1228-1235. [PMID: 33492971 DOI: 10.1021/acs.jpclett.0c03183] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The S-H···S non-covalent interaction is generally known as an extremely unconventional weak hydrogen-bond in the literature. The present gas-phase spectroscopic investigation shows that the S-H···S hydrogen-bond can be as strong as any conventional hydrogen-bond in terms of the IR red-shift in the stretching frequency of the hydrogen-bond donor group. Herein, the strength of the S-H···S hydrogen-bond has been determined by measuring the red-shift (∼150 cm-1) of the S-H stretching frequency in a model complex of 2-chlorothiophenol and dimethyl sulfide using isolated gas-phase IR spectroscopy coupled with quantum chemistry calculations. The observation of an unusually large IR red-shift in the S-H···S hydrogen-bond is explained in terms of the presence of a significant amount of charge-transfer interactions in addition to the usual electrostatic interactions. The existence of ∼750 S-H···S interactions between the cysteine and methionine residues in 642 protein structures determined from an extensive Protein Data Bank analysis also indicates that this interaction is important for the structures of proteins.
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Affiliation(s)
- Kamal K Mishra
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune-411008, India
| | - Kshetrimayum Borish
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune-411008, India
| | - Gulzar Singh
- Department of Biology, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune-411008, India
| | - Prakash Panwaria
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune-411008, India
| | - Surajit Metya
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune-411008, India
| | - M S Madhusudhan
- Department of Biology, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune-411008, India
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune-411008, India
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35
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Cortés-Arriagada D. Elucidating the co-transport of bisphenol A with polyethylene terephthalate (PET) nanoplastics: A theoretical study of the adsorption mechanism. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 270:116192. [PMID: 33338957 DOI: 10.1016/j.envpol.2020.116192] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/25/2020] [Accepted: 11/26/2020] [Indexed: 05/20/2023]
Abstract
Polyethylene terephthalate (PET) is a possible key component of nanoplastics in water environments, which can migrate pollutants through co-transport. In this regard, the co-transport of endocrine disruptors (such as bisphenol A, BPA) by nanoplastics is of emergent concern because of its cytotoxicity/bioaccumulation effects in aquatic organisms. In this work, a computational study is performed to reveal the BPA adsorption mechanism onto PET nanoplastics (nanoPET). It is found that the outer surface of nanoPET has a nucleophilic nature, allowing to increase the mass transfer and intraparticle diffusion into the nanoplastic to form stable complexes by inner and outer surface adsorption. The maximum adsorption energy is similar (even higher) in magnitude with respect to nanostructured adsorbents such as graphene, carbon nanotubes, activated carbon, and inorganic surfaces, indicating the worrying adsorption properties of nanoPET. The adsorption mechanism is driven by the interplay of dispersion (38-49%) and electrostatics effects (43-50%); specifically, dispersion effects dominate the inner surface adsorption, while electrostatics energies dominate the outer surface adsorption. It is also determined that π-π stacking is not a reliable interaction mechanism for aromatics on nanoPET. The formed complexes are also highly soluble, and water molecules behave as non-competitive factors, establishing the high risk of nanoPET to adsorb and migrate pollutants in water ecosystems. Furthermore, the adsorption performance is decreased (but not inhibited) at high ionic strength in salt-containing waters. Finally, these results give relevant information for environmental risk assessment, such as quantitative data and interaction mechanisms for non-biodegradable nanoplastics that establish strong interactions with pollutants in water.
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Affiliation(s)
- Diego Cortés-Arriagada
- Programa Institucional de Fomento a La Investigación, Desarrollo e Innovación. Universidad Tecnológica Metropolitana. Ignacio Valdivieso, 2409, San Joaquín, Santiago, Chile.
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36
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Veccham SP, Lee J, Mao Y, Horn PR, Head-Gordon M. A non-perturbative pairwise-additive analysis of charge transfer contributions to intermolecular interaction energies. Phys Chem Chem Phys 2021; 23:928-943. [DOI: 10.1039/d0cp05852a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A non-perturbative scheme for complete decomposition of energy and charge associated with charge transfer interaction into pairwise additive components.
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Affiliation(s)
| | - Joonho Lee
- Department of Chemistry
- University of California
- Berkeley
- USA
- Chemical Sciences Division
| | - Yuezhi Mao
- Department of Chemistry
- University of California
- Berkeley
- USA
- Chemical Sciences Division
| | - Paul R. Horn
- Department of Chemistry
- University of California
- Berkeley
- USA
- Chemical Sciences Division
| | - Martin Head-Gordon
- Department of Chemistry
- University of California
- Berkeley
- USA
- Chemical Sciences Division
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37
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Grofe A, Zhao R, Wildman A, Stetina TF, Li X, Bao P, Gao J. Generalization of Block-Localized Wave Function for Constrained Optimization of Excited Determinants. J Chem Theory Comput 2020; 17:277-289. [PMID: 33356213 DOI: 10.1021/acs.jctc.0c01049] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The block-localized wave function method is useful to provide insights on chemical bonding and intermolecular interactions through energy decomposition analysis. The method relies on block localization of molecular orbitals (MOs) by constraining the orbitals to basis functions within given blocks. Here, a generalized block-localized orbital (GBLO) method is described to allow both physically localized and delocalized MOs to be constrained in orbital-block definitions. Consequently, GBLO optimization can be conveniently tailored by imposing specific constraints. The GBLO method is illustrated by three examples: (1) constrained polarization response orbitals through dipole and quadrupole perturbation in a water dimer complex, (2) the ground and first excited-state potential energy curves of ethene about its C-C bond rotation, and (3) excitation energies of double electron excited states. Multistate density functional theory is used to determine the energies of the adiabatic ground and excited states using a minimal active space (MAS) comprising specifically charge-constrained and excited determinant configurations that are variationally optimized by the GBLO method. We find that the GBLO expansion that includes delocalized MOs in configurational blocks significantly reduces computational errors in comparison with physical block localization, and the computed ground- and excited-state energies are in good accordance with experiments and results obtained from multireference configuration interaction calculations.
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Affiliation(s)
- Adam Grofe
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, Jilin 130023, China.,Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China.,Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Ruoqi Zhao
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, Jilin 130023, China.,Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Andrew Wildman
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Torin F Stetina
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Xiaosong Li
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Peng Bao
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Jiali Gao
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China.,Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States.,Beijing University Shenzhen Graduate School, Shenzhen 518055, China
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38
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Mao Y, Loipersberger M, Kron KJ, Derrick JS, Chang CJ, Sharada SM, Head-Gordon M. Consistent inclusion of continuum solvation in energy decomposition analysis: theory and application to molecular CO 2 reduction catalysts. Chem Sci 2020; 12:1398-1414. [PMID: 34163903 PMCID: PMC8179122 DOI: 10.1039/d0sc05327a] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 11/26/2020] [Indexed: 12/13/2022] Open
Abstract
To facilitate computational investigation of intermolecular interactions in the solution phase, we report the development of ALMO-EDA(solv), a scheme that allows the application of continuum solvent models within the framework of energy decomposition analysis (EDA) based on absolutely localized molecular orbitals (ALMOs). In this scheme, all the quantum mechanical states involved in the variational EDA procedure are computed with the presence of solvent environment so that solvation effects are incorporated in the evaluation of all its energy components. After validation on several model complexes, we employ ALMO-EDA(solv) to investigate substituent effects on two classes of complexes that are related to molecular CO2 reduction catalysis. For [FeTPP(CO2-κC)]2- (TPP = tetraphenylporphyrin), we reveal that two ortho substituents which yield most favorable CO2 binding, -N(CH3)3 + (TMA) and -OH, stabilize the complex via through-structure and through-space mechanisms, respectively. The coulombic interaction between the positively charged TMA group and activated CO2 is found to be largely attenuated by the polar solvent. Furthermore, we also provide computational support for the design strategy of utilizing bulky, flexible ligands to stabilize activated CO2 via long-range Coulomb interactions, which creates biomimetic solvent-inaccessible "pockets" in that electrostatics is unscreened. For the reactant and product complexes associated with the electron transfer from the p-terphenyl radical anion to CO2, we demonstrate that the double terminal substitution of p-terphenyl by electron-withdrawing groups considerably strengthens the binding in the product state while moderately weakens that in the reactant state, which are both dominated by the substituent tuning of the electrostatics component. These applications illustrate that this new extension of ALMO-EDA provides a valuable means to unravel the nature of intermolecular interactions and quantify their impacts on chemical reactivity in solution.
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Affiliation(s)
- Yuezhi Mao
- Department of Chemistry, University of California at Berkeley Berkeley CA 94720 USA
| | | | - Kareesa J Kron
- Mork Family Department of Chemical Engineering and Material Science, University of Southern California Los Angeles CA 90089 USA
| | - Jeffrey S Derrick
- Department of Chemistry, University of California at Berkeley Berkeley CA 94720 USA
| | - Christopher J Chang
- Department of Chemistry, University of California at Berkeley Berkeley CA 94720 USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory Berkeley CA 94720 USA
- Department of Molecular and Cell Biology, University of California Berkeley Berkeley CA 94720 USA
| | - Shaama Mallikarjun Sharada
- Mork Family Department of Chemical Engineering and Material Science, University of Southern California Los Angeles CA 90089 USA
- Department of Chemistry, University of Southern California Los Angeles CA 90089 USA
| | - Martin Head-Gordon
- Department of Chemistry, University of California at Berkeley Berkeley CA 94720 USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory Berkeley CA 94720 USA
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39
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Clarifying the quantum mechanical origin of the covalent chemical bond. Nat Commun 2020; 11:4893. [PMID: 32994392 PMCID: PMC7524788 DOI: 10.1038/s41467-020-18670-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 08/28/2020] [Indexed: 11/08/2022] Open
Abstract
Lowering of the electron kinetic energy (KE) upon initial encounter of radical fragments has long been cited as the primary origin of the covalent chemical bond based on Ruedenberg's pioneering analysis of H[Formula: see text] and H2 and presumed generalization to other bonds. This work reports KE changes during the initial encounter corresponding to bond formation for a range of different bonds; the results demand a re-evaluation of the role of the KE. Bonds between heavier elements, such as H3C-CH3, F-F, H3C-OH, H3C-SiH3, and F-SiF3 behave in the opposite way to H[Formula: see text] and H2, with KE often increasing on bringing radical fragments together (though the total energy change is substantially stabilizing). The origin of this difference is Pauli repulsion between the electrons forming the bond and core electrons. These results highlight the fundamental role of constructive quantum interference (or resonance) as the origin of chemical bonding. Differences between the interfering states distinguish one type of bond from another.
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40
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Xi Y, Su B, Qi X, Pedram S, Liu P, Hartwig JF. Application of Trimethylgermanyl-Substituted Bisphosphine Ligands with Enhanced Dispersion Interactions to Copper-Catalyzed Hydroboration of Disubstituted Alkenes. J Am Chem Soc 2020; 142:18213-18222. [DOI: 10.1021/jacs.0c08746] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Yumeng Xi
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Division of Chemical Sciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Bo Su
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Xiaotian Qi
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Shayun Pedram
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Peng Liu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - John F. Hartwig
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Division of Chemical Sciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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41
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Kron KJ, Gomez SJ, Mao Y, Cave RJ, Mallikarjun Sharada S. Computational Analysis of Electron Transfer Kinetics for CO 2 Reduction with Organic Photoredox Catalysts. J Phys Chem A 2020; 124:5359-5368. [PMID: 32491858 DOI: 10.1021/acs.jpca.0c03065] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present a fundamental description of the electron transfer (ET) step from substituted oligo(p-phenylene) (OPP) radical anions to CO2, with the larger goal of assessing the viability of underexplored, organic photoredox routes for utilization of anthropogenic CO2. This work varies the electrophilicity of para-substituents to OPP and probes the dependence of rate coefficients and interfragment interactions on the substituent Hammett parameter, σp, using constrained density functional theory (CDFT) and energy decomposition analysis (EDA). Large electronic couplings across substituents indicates an adiabatic electron transfer process for reactants at contact. As one might intuitively expect, free energy changes dominate trends in ET rate coefficients in most cases, and rates increase with substituent electron-donating ability. However, we observe an unexpected dip in rate coefficients for the most electron-donating groups, due to the combined impact of flattening free energies and a steep increase in reorganization energies. Our analysis shows that, with decreasing σp, flattening OPP LUMO levels lower the marginal increase in free energy. EDA reveals trends in electrostatics and charge transfer interactions between the catalyst and substrate fragments that influence free energy changes across substituents. Reorganization energies do not exhibit a direct dependence on σp and are largely similar across systems, with the exception of substituents containing lone pairs of electrons that exhibit significant deformation upon electron transfer. Our study therefore suggests that while a wide range of ET rates are observed, there is an upper limit to rate enhancements achievable by only tuning the substituent electrophilicity.
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Affiliation(s)
- Kareesa J Kron
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089, United States
| | - Samantha J Gomez
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089, United States.,Bravo Medical Magnet High School, Los Angeles, California 90033, United States
| | - Yuezhi Mao
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Robert J Cave
- Department of Chemistry, Harvey Mudd College, Claremont, California 91711, United States
| | - Shaama Mallikarjun Sharada
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089, United States.,Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
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42
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Mao Y, Levine DS, Loipersberger M, Horn PR, Head-Gordon M. Probing radical-molecule interactions with a second generation energy decomposition analysis of DFT calculations using absolutely localized molecular orbitals. Phys Chem Chem Phys 2020; 22:12867-12885. [PMID: 32510096 DOI: 10.1039/d0cp01933j] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Intermolecular interactions between radicals and closed-shell molecules are ubiquitous in chemical processes, ranging from the benchtop to the atmosphere and extraterrestrial space. While energy decomposition analysis (EDA) schemes for closed-shell molecules can be generalized for studying radical-molecule interactions, they face challenges arising from the unique characteristics of the electronic structure of open-shell species. In this work, we introduce additional steps that are necessary for the proper treatment of radical-molecule interactions to our previously developed unrestricted Absolutely Localized Molecular Orbital (uALMO)-EDA based on density functional theory calculations. A "polarize-then-depolarize" (PtD) scheme is used to remove arbitrariness in the definition of the frozen wavefunction, rendering the ALMO-EDA results independent of the orientation of the unpaired electron obtained from isolated fragment calculations. The contribution of radical rehybridization to polarization energies is evaluated. It is also valuable to monitor the wavefunction stability of each intermediate state, as well as their associated spin density profiles, to ensure the EDA results correspond to a desired electronic state. These radical extensions are incorporated into the "vertical" and "adiabatic" variants of uALMO-EDA for studies of energy changes and property shifts upon complexation. The EDA is validated on two model complexes, H2O˙F and FH˙OH. It is then applied to several chemically interesting radical-molecule complexes, including the sandwiched and T-shaped benzene dimer radical cation, complexes of pyridine with benzene and naphthalene radical cations, binary and ternary complexes of the hydroxyl radical with water (˙OH(H2O) and ˙OH(H2O)2), and the pre-reactive complexes and transition states in the ˙OH + HCHO and ˙OH + CH3CHO reactions. These examples suggest that this second generation uALMO-EDA is a useful tool for furthering one's understanding of both energetic and property changes associated with radical-molecule interactions.
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Affiliation(s)
- Yuezhi Mao
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California at Berkeley, Berkeley, CA 94720, USA.
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43
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Removal of arsenic from water using iron-doped phosphorene nanoadsorbents: A theoretical DFT study with solvent effects. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.112958] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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44
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Ortega DE, Cortés-Arriagada D. Exploring the Nature of Interaction and Stability between Water-Soluble Arsenic Pollutants and Metal–Phosphorene Hybrids: A Density Functional Theory Study. J Phys Chem A 2020; 124:3662-3671. [DOI: 10.1021/acs.jpca.0c00532] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Daniela E. Ortega
- Centro Integrativo de Biologı́a y Quı́mica Aplicada (CIBQA), Universidad Bernardo OHiggins, Santiago 8370854, Chile
| | - Diego Cortés-Arriagada
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Ignacio Valdivieso, 2409, San Joaquín, Santiago 8940577, Chile
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45
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Tappan BA, Chen K, Lu H, Sharada SM, Brutchey RL. Synthesis and Electrocatalytic HER Studies of Carbene-Ligated Cu 3-xP Nanocrystals. ACS APPLIED MATERIALS & INTERFACES 2020; 12:16394-16401. [PMID: 32174101 DOI: 10.1021/acsami.0c00025] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
N-heterocyclic carbenes (NHCs) are an important class of ligands capable of making strong carbon-metal bonds. Recently, there has been a growing interest in the study of carbene-ligated nanocrystals, primarily coinage metal nanocrystals, which have found application as catalysts for numerous reactions. The general ability of NHC ligands to positively affect the catalytic properties of other types of nanocrystal catalysts remains unknown. Herein, we present the first carbene-stabilized Cu3-xP nanocrystals. Inquiries into the mechanism of formation of NHC-ligated Cu3-xP nanocrystals suggest that crystalline Cu3-xP forms directly as a result of a high-temperature metathesis reaction between a tris(trimethylsilyl)phosphine precursor and an NHC-CuBr precursor, the latter of which behaves as a source of both the carbene ligand and Cu+. To study the effect of the NHC surface ligands on the catalytic performance, we tested the electrocatalytic hydrogen evolving ability of the NHC-ligated Cu3-xP nanocrystals and found that they possess superior activity to analogous oleylamine-ligated Cu3-xP nanocrystals. Density functional theory calculations suggest that the NHC ligands minimize unfavorable electrostatic interactions between the copper phosphide surface and H+ during the first step of the hydrogen evolution reaction, which contributes to the superior performance of NHC-ligated Cu3-xP catalysts as compared to oleylamine-ligated Cu3-xP catalysts.
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Affiliation(s)
- Bryce A Tappan
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Keying Chen
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Haipeng Lu
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Shaama Mallikarjun Sharada
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089, United States
| | - Richard L Brutchey
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
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Egan CK, Bizzarro BB, Riera M, Paesani F. Nature of Alkali Ion–Water Interactions: Insights from Many-Body Representations and Density Functional Theory. II. J Chem Theory Comput 2020; 16:3055-3072. [DOI: 10.1021/acs.jctc.0c00082] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Colin K. Egan
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Brandon B. Bizzarro
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Marc Riera
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
- Materials Science and Engineering, University of California San Diego, La Jolla, California 92093, United States
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, United States
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47
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Chen J, Chan B, Shao Y, Ho J. How accurate are approximate quantum chemical methods at modelling solute-solvent interactions in solvated clusters? Phys Chem Chem Phys 2020; 22:3855-3866. [PMID: 32022044 PMCID: PMC7394230 DOI: 10.1039/c9cp06792b] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In this paper, the performance of a wide range of DFT methods is assessed for the calculation of interaction energies of thermal clusters of a solute in water. Three different charge states (neutral, proton transfer transition state and zwitterion) of glycine were solvated by 1 to 40 water molecules as sampled from molecular dynamics simulations. While some ab initio composite methods that employ insufficiently large basis sets incurred significant errors even for a cluster containing only 5 water molecules relative to the W1X-2 benchmark, the DLPNO-CCSD(T)/CBS and DSD-PBEP86 (triple zeta basis set) levels of theory predicted very accurate interaction energies. These levels of theory were used to benchmark the performance of 16 density functionals from different rungs of Jacob's Ladder. Of the Rung 4 functionals examined, the ωB97M-V and ωB97X-V functionals stood out for predicting absolute interaction energies in 40-water clusters with mean absolute deviations (MAD) ∼4 kJ mol-1. The B3LYP-D3(BJ) functional performed exceptionally well with a MAD ∼1.7 kJ mol-1 and is the overall best performing method. Calculations of relative interaction energies allow for cancellation of systematic errors, including basis set truncation and superposition errors, and the ωB97M-V and B3LYP-D3(BJ) double zeta basis set calculations yielded relative interaction energies that are within ∼3 kJ mol-1 of the benchmark. The ONIOM approximation provides another strategy for accelerating the calculation of accurate absolute interaction energies provided that the calculations have converged with respect to the size of the "high-level-layer".
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Affiliation(s)
- Junbo Chen
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Bun Chan
- Graduate School of Engineering, Nagasaki University, Bunkyo-Machi 1-14, Nagasaki 852-8521, Japan.
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - Junming Ho
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia.
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48
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Loipersberger M, Mao Y, Head-Gordon M. Variational Forward–Backward Charge Transfer Analysis Based on Absolutely Localized Molecular Orbitals: Energetics and Molecular Properties. J Chem Theory Comput 2020; 16:1073-1089. [DOI: 10.1021/acs.jctc.9b01168] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Matthias Loipersberger
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Yuezhi Mao
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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49
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Rossomme E, Lininger CN, Bell AT, Head-Gordon T, Head-Gordon M. Electronic structure calculations permit identification of the driving forces behind frequency shifts in transition metal monocarbonyls. Phys Chem Chem Phys 2020; 22:781-798. [DOI: 10.1039/c9cp04643g] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Our direct DFT decomposition of CO frequency shifts updates the paradigm for metal carbonyl binding.
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Affiliation(s)
- Elliot Rossomme
- Kenneth S. Pitzer Center for Theoretical Chemistry
- Department of Chemistry
- University of California
- Berkeley
- USA
| | - Christianna N. Lininger
- Chemical Sciences Division
- Lawrence Berkeley National Laboratory
- Berkeley
- USA
- Department of Chemical and Biomolecular Engineering
| | - Alexis T. Bell
- Chemical Sciences Division
- Lawrence Berkeley National Laboratory
- Berkeley
- USA
- Department of Chemical and Biomolecular Engineering
| | - Teresa Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry
- Department of Chemistry
- University of California
- Berkeley
- USA
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry
- Department of Chemistry
- University of California
- Berkeley
- USA
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50
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Veccham SP, Lee J, Head-Gordon M. Making many-body interactions nearly pairwise additive: The polarized many-body expansion approach. J Chem Phys 2019; 151:194101. [DOI: 10.1063/1.5125802] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Srimukh Prasad Veccham
- Department of Chemistry, University of California, Berkeley, California 94720 USA, and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Joonho Lee
- Department of Chemistry, University of California, Berkeley, California 94720 USA, and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Martin Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720 USA, and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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