1
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Fuemmeler EG, Damle A, DiStasio RA. Selected Columns of the Density Matrix in an Atomic Orbital Basis I: An Intrinsic and Non-iterative Orbital Localization Scheme for the Occupied Space. J Chem Theory Comput 2023. [PMID: 37944142 DOI: 10.1021/acs.jctc.1c00801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
In this work, we extend the selected columns of the density matrix (SCDM) methodology [J. Chem. Theory Comput. 2015, 11, 1463-1469]─a non-iterative and real-space procedure for generating localized occupied orbitals for condensed-phase systems─to the construction of local molecular orbitals (LMOs) in systems described using non-orthogonal atomic orbital (AO) basis sets. In particular, we introduce three different theoretical and algorithmic variants of SCDM (referred to as SCDM-M, SCDM-L, and SCDM-G) that can be used in conjunction with the AO basis sets used in standard quantum chemistry codebases. The SCDM-M and SCDM-L variants are based on a pivoted QR factorization of the Mulliken and Löwdin representations of the density matrix and are tantamount to selecting a well-conditioned set of projected atomic orbitals (PAOs) and projected (symmetrically-) orthogonalized atomic orbitals, respectively, as proto-LMOs that can be orthogonalized to exactly span the occupied space. The SCDM-G variant is based on a real-space (grid) representation of the wavefunction, and therefore has the added flexibility of considering a large number of grid points (or δ functions) when selecting a set of well-conditioned proto-LMOs. A detailed comparative analysis across molecular systems of varying size, dimensionality, and saturation level reveals that the LMOs generated by these three non-iterative/direct SCDM variants are robust, comparable in orbital locality to those produced with the iterative Boys or Pipek-Mezey (PM) localization schemes, and completely agnostic toward any single orbital locality metric. Although all three SCDM variants are based on the density matrix, we find that the character of the generated LMOs can differ significantly between SCDM-M, SCDM-L, and SCDM-G. In this regard, only the grid-based SCDM-G procedure (like PM) generates LMOs that qualitatively preserve σ-π symmetry (in systems such as s-trans alkenes), and are well-aligned with chemical (i.e., Lewis structure) intuition. While the direct and standalone use of SCDM-generated LMOs should suffice for most chemical applications, our findings also suggest that the use of these orbitals as an unbiased and cost-effective (initial) guess also has the potential to improve the convergence of iterative orbital localization schemes, in particular for large-scale and/or pathological molecular systems.
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Affiliation(s)
- Eric G Fuemmeler
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Anil Damle
- Department of Computer Science, Cornell University, Ithaca, New York 14853, United States
| | - Robert A DiStasio
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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2
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Sepehri A, Li RR, Hoffmann MR. Riemannian Trust Region Method for Minimization of the Fourth Central Moment for Localized Molecular Orbitals. J Phys Chem A 2023. [PMID: 37285307 DOI: 10.1021/acs.jpca.3c01295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The importance of localized molecular orbitals (MOs) in correlation treatments beyond mean-field calculation and in the illustration of chemical bonding (and antibonding) can hardly be overstated. However, the generation of orthonormal localized occupied MOs is significantly more straightforward than obtaining orthonormal localized virtual MOs. Orthonormal MOs allow facile use of highly efficient group theoretical methods (e.g., graphical unitary group approach) for calculation of Hamiltonian matrix elements in multireference configuration interaction calculations (such as MRCISD) and in quasi-degenerate perturbation treatments, such as the Generalized Van Vleck Perturbation Theory. Moreover, localized MOs can elucidate qualitative understanding of bonding in molecules, in addition to high-accuracy quantitative descriptions. We adopt the powers of the fourth moment cost function introduced by Jørgensen and coworkers. Because the fourth moment cost functions are prone to having multiple negative Hessian eigenvalues when starting from easily available canonical (or near-canonical) MOs, standard optimization algorithms can fail to obtain the orbitals of the virtual or partially occupied spaces. To overcome this drawback, we applied a trust region algorithm on an orthonormal Riemannian manifold with an approximate retraction from the tangent space built into the first and second derivatives of the cost function. Moreover, the Riemannian trust region outer iterations were coupled to truncated Conjugate Gradient inner loops, which avoided any costly solutions of simultaneous linear equations or eigenvector/eigenvalue solutions. Numerical examples are provided on model systems, including the high-connectivity H10 set in 1-, 2-, and 3-dimensional arrangements, and on a chemically realistic description of cyclobutadiene (c-C4H4) and the propargyl radical (C3H3). In addition to demonstrating the algorithm on occupied and virtual blocks of orbitals, the method is also shown to work on the active space at the MCSCF level of theory.
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Affiliation(s)
- Aliakbar Sepehri
- Chemistry Department, University of North Dakota, Grand Forks, North Dakota 58202-9024, United States
| | - Run R Li
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| | - Mark R Hoffmann
- Chemistry Department, University of North Dakota, Grand Forks, North Dakota 58202-9024, United States
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3
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Koroleva EV, Kornoushenko YV, Karpenko AD, Bosko IP, Siniutsich JV, Ignatovich ZV, Andrianov AM. In silico design and computational evaluation of novel 2-arylaminopyrimidine-based compounds as potential multi-targeted protein kinase inhibitors: application for the native and mutant (T315I) Bcr-Abl tyrosine kinase. J Biomol Struct Dyn 2023; 41:4065-4080. [PMID: 35470777 DOI: 10.1080/07391102.2022.2062784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 04/02/2022] [Indexed: 10/18/2022]
Abstract
An integrated computational approach to drug discovery was used to identify novel potential inhibitors of the native and mutant (T315I) Bcr-Abl tyrosine kinase, the enzyme playing a key role in the pathogenesis of chronic myeloid leukemia (CML). This approach included i) design of chimeric molecules based on the 2-arylaminopyrimidine fragment, the main pharmacophore of the Abl kinase inhibitors imatinib and nilotinib used in the clinic for the CML treatment, ii) molecular docking of these compounds with the ATP-binding site of the native and mutant Abl kinase, iii) refinement of the ligand-binding poses by the quantum chemical method PM7, iv) molecular dynamics simulations of the ligand/Abl complexes, and v) prediction of the ligand/Abl binding affinity in terms of scoring functions of molecular docking, machine learning, quantum chemistry, and molecular dynamics. As a result, five top-ranking compounds able to effectively block the enzyme catalytic site were identified. According to the data obtained, these compounds exhibit close modes of binding to the Abl kinase active site that are mainly provided by hydrogen bonds and multiple van der Waals contacts. The identified compounds show high binding affinity to the native and mutant Abl kinase comparable with the one calculated for the FDA-approved kinase-targeted inhibitors imatinib, nilotinib, and ponatinib used in the calculations as a positive control. The results obtained testify to the predicted drug candidates against CML may serve as good scaffolds for the design of novel anticancer agents able to target the ATP-binding pocket of the native and mutant Abl kinase.Communicated by Ramaswamy H. Sarma.
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MESH Headings
- Humans
- Adenosine Triphosphate/metabolism
- Antineoplastic Agents/chemistry
- Antineoplastic Agents/pharmacology
- Catalytic Domain
- Computer Simulation
- Drug Design
- Fusion Proteins, bcr-abl/antagonists & inhibitors
- Fusion Proteins, bcr-abl/genetics
- Hydrogen Bonding
- Imatinib Mesylate/pharmacology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/enzymology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Ligands
- Machine Learning
- Molecular Docking Simulation
- Molecular Dynamics Simulation
- Mutant Proteins/antagonists & inhibitors
- Mutant Proteins/genetics
- Mutation
- Protein Kinase Inhibitors/chemistry
- Protein Kinase Inhibitors/pharmacology
- Pyrimidines/chemistry
- Pyrimidines/pharmacology
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Affiliation(s)
- Elena V Koroleva
- Institute of Chemistry of New Materials, National Academy of Sciences of Belarus, Minsk, Republic of Belarus
| | - Yuri V Kornoushenko
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Republic of Belarus
| | - Anna D Karpenko
- United Institute of Informatics Problems, National Academy of Sciences of Belarus, Minsk, Republic of Belarus
| | - Ivan P Bosko
- United Institute of Informatics Problems, National Academy of Sciences of Belarus, Minsk, Republic of Belarus
| | - Julia V Siniutsich
- Institute of Chemistry of New Materials, National Academy of Sciences of Belarus, Minsk, Republic of Belarus
| | - Zhanna V Ignatovich
- Institute of Chemistry of New Materials, National Academy of Sciences of Belarus, Minsk, Republic of Belarus
| | - Alexander M Andrianov
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Republic of Belarus
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4
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Wang Z, Aldossary A, Head-Gordon M. Sparsity of the electron repulsion integral tensor using different localized virtual orbital representations in local second-order Møller-Plesset theory. J Chem Phys 2023; 158:064105. [PMID: 36792513 DOI: 10.1063/5.0134764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Utilizing localized orbitals, local correlation theory can reduce the unphysically high system-size scaling of post-Hartree-Fock (post-HF) methods to linear scaling in insulating molecules. The sparsity of the four-index electron repulsion integral (ERI) tensor is central to achieving this reduction. For second-order Møller-Plesset theory (MP2), one of the simplest post-HF methods, only the (ia|jb) ERIs are needed, coupling occupied orbitals i, j and virtuals a, b. In this paper, we compare the numerical sparsity (called the "ragged list") and two other approaches revealing the low-rank sparsity of the ERI. The ragged list requires only one set of (localized) virtual orbitals, and we find that the orthogonal valence virtual-hard virtual set of virtuals originally proposed by Subotnik et al. gives the sparsest ERI tensor. To further compress the ERI tensor, the pair natural orbital (PNO) type representation uses different sets of virtual orbitals for different occupied orbital pairs, while the occupied-specific virtual (OSV) approach uses different virtuals for each occupied orbital. Our results indicate that while the low-rank PNO representation achieves significant rank reduction, it also requires more memory than the ragged list. The OSV approach requires similar memory to that of the ragged list, but it involves greater algorithmic complexity. An approximation (called the "fixed sparsity pattern") for solving the local MP2 equations using the numerically sparse ERI tensor is proposed and tested to be sufficiently accurate and to have highly controllable error. A low-scaling local MP2 algorithm based on the ragged list and the fixed sparsity pattern is therefore promising.
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Affiliation(s)
- Zhenling Wang
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Abdulrahman Aldossary
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Martin Head-Gordon
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA
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5
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Whitten JL. Correction of Residual Errors in Configuration Interaction Electronic Structure Calculations. J Chem Phys 2022; 157:124101. [DOI: 10.1063/5.0098793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Methods for correcting residual energy errors of configuration interaction (CI) calculations of molecules and other electronic systems are discussed based on the assumption that the energy defect can be mapped onto atomic regions. The methods do not consider the detailed nature of excitations, but instead define a defect energy per electron that that is unique to a specific atom. Defect energy contributions are determined from calculations on diatomic and hydride molecules and then applied to other systems. Calculated energies are compared with experimental thermodynamic and spectroscopic data for a set of forty-one mainly organic molecules representing a wide range of bonding environments. The most stringent test is based on a severely truncated virtual space in which higher spherical harmonic basis functions are removed. The errors of the initial CI calculations are large, but in each case, including defect corrections brings calculated CI energies into agreement with experimental values. The method is also applied to a NIST compilation of coupled-cluster calculations that employ a larger basis set and no truncation of the virtual space. The corrections show excellent consistency with total energies in very good agreement with experimental values. An extension of the method is applied to dmsn states of Sc, Ti, V, Mn, Cr, Fe, Co, Ni and Cu, significantly improving the agreement of calculated transition energies with spectroscopic values.
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Affiliation(s)
- Jerry L Whitten
- North Carolina State University, North Carolina State University, United States of America
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6
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Saitow M, Uemura K, Yanai T. A local pair-natural orbital-based complete-active space perturbation theory using orthogonal localized virtual molecular orbitals. J Chem Phys 2022; 157:084101. [DOI: 10.1063/5.0094777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The multireference second-order perturbation theory (CASPT2) is known to deliver a quantitative description of various complex electronic states. Despite its near-size-consistent nature, the applicability of the CASPT2 method to large, real-life systems is mostly hindered by large computational and storage costs for the two-external tensors, such as two-electron integrals, amplitudes, and residuum. To this end, Menezes and co-workers developed a reduced-scaling CASPT2 scheme by incorporating the local pair-natural orbital (PNO) representation of the many-body wave functions using non-orthonormal projected atomic orbitals (PAOs) into the CASPT theory [F. Menezes et al., J. Chem. Phys. 145, 124115 (2016)]. Alternatively, in this paper, we develop a new PNO-based CASPT2 scheme using the orthonormal localized virtual molecular orbitals (LVMOs) and assess its performance and accuracy in comparison with the conventional PAO-based counterpart. Albeit the compactness, the LVMOs were considered to perform somewhat poorly compared to PAOs in the local correlation framework because they caused enormously large orbital domains. In this work, we show that the size of LVMO domains can be rendered comparable to or even smaller than that of PAOs by the use of the differential overlap integrals for domain construction. Optimality of the MOs from the CASSCF treatment is a key to reducing the LVMO domain size for the multireference case. Due to the augmented Hessian-based localization algorithm, an additional computational cost for obtaining the LVMOs is relatively minor. We demonstrate that the LVMO-based PNO-CASPT2 method is routinely applicable to large, real-life molecules such as Menshutkin SN2 reaction in a single-walled carbon nanotube reaction field.
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Affiliation(s)
- Masaaki Saitow
- Department of Chemistry, Graduate School of Science, Nagoya University, Furocho, Chikusa Ward, Nagoya, Aichi 464-8601, Japan
| | - Kazuma Uemura
- Department of Chemistry, Graduate School of Science, Nagoya University, Furocho, Chikusa Ward, Nagoya, Aichi 464-8601, Japan
| | - Takeshi Yanai
- Department of Chemistry, Graduate School of Science, Nagoya University, Furocho, Chikusa Ward, Nagoya, Aichi 464-8601, Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furocho, Chikusa Ward, Nagoya, Aichi 464-8601, Japan
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7
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Folkestad SD, Matveeva R, Høyvik IM, Koch H. Implementation of Occupied and Virtual Edmiston-Ruedenberg Orbitals Using Cholesky Decomposed Integrals. J Chem Theory Comput 2022; 18:4733-4744. [PMID: 35856495 PMCID: PMC9367017 DOI: 10.1021/acs.jctc.2c00261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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We present a trust-region optimization of the Edmiston–Ruedenberg
orbital localization function. The approach is used to localize both
the occupied and the virtual orbitals and is the first demonstration
of general virtual orbital localization using the Edmiston–Ruedenberg
localization function. In the Edmiston–Ruedenberg approach,
the sum of the orbital self-repulsion energies is maximized to obtain
the localized orbitals. The Cholesky decomposition reduces the cost
of transforming the electron repulsion integrals, and the overall
scaling of our implementation is . The optimization is performed with all
quantities in the molecular orbital basis, and the localization of
the occupied orbitals is often less expensive than the corresponding
self-consistent field (SCF) optimization. Furthermore, the occupied
orbital localization scales linearly with the basis set. For the virtual
space, the cost is significantly higher than the SCF optimization.
The orbital spreads of the resulting virtual Edmiston–Ruedenberg
orbitals are larger than for other, less expensive, orbital localization
functions. This indicates that other localization procedures are more
suitable for applications such as local post-Hartree–Fock calculations.
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Affiliation(s)
- Sarai Dery Folkestad
- Department of Chemistry, The Norwegian University of Science and Technology, Trondheim 7491, Norway
| | - Regina Matveeva
- Department of Chemistry, The Norwegian University of Science and Technology, Trondheim 7491, Norway
| | - Ida-Marie Høyvik
- Department of Chemistry, The Norwegian University of Science and Technology, Trondheim 7491, Norway
| | - Henrik Koch
- Department of Chemistry, The Norwegian University of Science and Technology, Trondheim 7491, Norway
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8
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Schäfer T, Gallo A, Irmler A, Hummel F, Grüneis A. Surface science using coupled cluster theory via local Wannier functions and in-RPA-embedding: The case of water on graphitic carbon nitride. J Chem Phys 2021; 155:244103. [PMID: 34972356 DOI: 10.1063/5.0074936] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A first-principles study of the adsorption of a single water molecule on a layer of graphitic carbon nitride is reported employing an embedding approach for many-electron correlation methods. To this end, a plane-wave based implementation to obtain intrinsic atomic orbitals and Wannier functions for arbitrary localization potentials is presented. In our embedding scheme, the localized occupied orbitals allow for a separate treatment of short-range and long-range correlation contributions to the adsorption energy by a fragmentation of the simulation cell. In combination with unoccupied natural orbitals, the coupled cluster ansatz with single, double, and perturbative triple particle-hole excitation operators is used to capture the correlation in local fragments centered around the adsorption process. For the long-range correlation, a seamless embedding into the random phase approximation yields rapidly convergent adsorption energies with respect to the local fragment size. Convergence of computed binding energies with respect to the virtual orbital basis set is achieved employing a number of recently developed techniques. Moreover, we discuss fragment size convergence for a range of approximate many-electron perturbation theories. The obtained benchmark results are compared to a number of density functional calculations.
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Affiliation(s)
- Tobias Schäfer
- Institute for Theoretical Physics, TU Wien, Wiedner Hauptstraße 8-10/136, A-1040 Vienna, Austria
| | - Alejandro Gallo
- Institute for Theoretical Physics, TU Wien, Wiedner Hauptstraße 8-10/136, A-1040 Vienna, Austria
| | - Andreas Irmler
- Institute for Theoretical Physics, TU Wien, Wiedner Hauptstraße 8-10/136, A-1040 Vienna, Austria
| | - Felix Hummel
- Institute for Theoretical Physics, TU Wien, Wiedner Hauptstraße 8-10/136, A-1040 Vienna, Austria
| | - Andreas Grüneis
- Institute for Theoretical Physics, TU Wien, Wiedner Hauptstraße 8-10/136, A-1040 Vienna, Austria
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9
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Trepte K, Schwalbe S, Liebing S, Schulze WT, Kortus J, Myneni H, Ivanov AV, Lehtola S. Chemical bonding theories as guides for self-interaction corrected solutions: Multiple local minima and symmetry breaking. J Chem Phys 2021; 155:224109. [PMID: 34911315 DOI: 10.1063/5.0071796] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Fermi-Löwdin orbitals (FLOs) are a special set of localized orbitals, which have become commonly used in combination with the Perdew-Zunger self-interaction correction (SIC) in the FLO-SIC method. The FLOs are obtained for a set of occupied orbitals by specifying a classical position for each electron. These positions are known as Fermi-orbital descriptors (FODs), and they have a clear relation to chemical bonding. In this study, we show how FLOs and FODs can be used to initialize, interpret, and justify SIC solutions in a common chemical picture, both within FLO-SIC and in traditional variational SIC, and to locate distinct local minima in either of these approaches. We demonstrate that FLOs based on Lewis theory lead to symmetry breaking for benzene-the electron density is found to break symmetry already at the symmetric molecular structure-while ones from Linnett's double-quartet theory reproduce symmetric electron densities and molecular geometries. Introducing a benchmark set of 16 planar cyclic molecules, we show that using Lewis theory as the starting point can lead to artifactual dipole moments of up to 1 D, while Linnett SIC dipole moments are in better agreement with experimental values. We suggest using the dipole moment as a diagnostic of symmetry breaking in SIC and monitoring it in all SIC calculations. We show that Linnett structures can often be seen as superpositions of Lewis structures and propose Linnett structures as a simple way to describe aromatic systems in SIC with reduced symmetry breaking. The role of hovering FODs is also briefly discussed.
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Affiliation(s)
- Kai Trepte
- SUNCAT Center for Interface Science and Catalysis, Stanford University, Menlo Park, California 94025, USA
| | - Sebastian Schwalbe
- Institute of Theoretical Physics, TU Bergakademie Freiberg, D-09599 Freiberg, Germany
| | - Simon Liebing
- Joint Institute for Nuclear Research Dubna, Bogoliubov Laboratory of Theoretical Physics, 141980 Dubna, Russia
| | - Wanja T Schulze
- Institute of Theoretical Physics, TU Bergakademie Freiberg, D-09599 Freiberg, Germany
| | - Jens Kortus
- Institute of Theoretical Physics, TU Bergakademie Freiberg, D-09599 Freiberg, Germany
| | - Hemanadhan Myneni
- Science Institute and Faculty of Physical Sciences, VR-III, University of Iceland, 107 Reykjavík, Iceland
| | - Aleksei V Ivanov
- Science Institute and Faculty of Physical Sciences, VR-III, University of Iceland, 107 Reykjavík, Iceland
| | - Susi Lehtola
- Molecular Sciences Software Institute, Blacksburg, Virginia 24061, USA
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10
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Abstract
We describe a robust method for determining Pipek-Mezey (PM) Wannier functions (WF), recently introduced by Jónsson et al. (J. Chem. Theor. Chem. 2017, 13, 460), which provide some formal advantages over the more common Boys (also known as maximally-localized) Wannier functions. The Broyden-Fletcher-Goldfarb-Shanno-based PMWF solver is demonstrated to yield dramatically faster convergence compared to the alternatives (steepest ascent and conjugate gradient) in a variety of one-, two-, and three-dimensional solids (including some with vanishing gaps) and can be used to obtain Wannier functions robustly in supercells with thousands of atoms. Evaluation of the PM functional and its gradient in periodic linear combination of atomic orbital representation used a particularly simple definition of atomic charges obtained by Moore-Penrose pseudoinverse projection onto the minimal atomic orbital basis. An automated "canonicalize phase then randomize" method for generating the initial guess for WFs contributes significantly to the robustness of the solver.
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Affiliation(s)
- Marjory C Clement
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Xiao Wang
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States.,Center for Computational Quantum Physics, Flatiron Institute, New York, New York 10010, United States
| | - Edward F Valeev
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
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11
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Kirchhoff B, Ivanov A, Skúlason E, Jacob T, Fantauzzi D, Jónsson H. Assessment of the Accuracy of Density Functionals for Calculating Oxygen Reduction Reaction on Nitrogen-Doped Graphene. J Chem Theory Comput 2021; 17:6405-6415. [PMID: 34550689 DOI: 10.1021/acs.jctc.1c00377] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Experimental studies of the oxygen reduction reaction (ORR) at nitrogen-doped graphene electrodes have reported a remarkably low overpotential, on the order of 0.5 V, similar to Pt-based electrodes. Theoretical calculations using density functional theory have lent support to this claim. However, other measurements have indicated that transition metal impurities are actually responsible for the ORR activity, thereby raising questions about the reliability of both the experiments and the calculations. To assess the accuracy of the theoretical calculations, various generalized gradient approximation (GGA), meta-GGA, and hybrid functionals are employed here and calibrated against high-level wave-function-based coupled-cluster calculations (CCSD(T)) of the overpotential as well as self-interaction corrected density functional calculations and published quantum Monte Carlo calculations of O adatom binding to graphene. The PBE0 and HSE06 hybrid functionals are found to give more accurate results than the GGA and meta-GGA functionals, as would be expected, and for a low dopant concentration, 3.1%, the overpotential is calculated to be 1.0 V. The GGA and meta-GGA functionals give a lower estimate by as much as 0.4 V. When the dopant concentration is doubled, the overpotential calculated with hybrid functionals decreases, while it increases in GGA functional calculations. The opposite trends result from different potential-determining steps, the *OOH species being of central importance in the hybrid functional calculations, while the reduction of *O determines the overpotential obtained in GGA and meta-GGA calculations. The results presented here are mainly based on calculations of periodic representations of the system, but a comparison is also made with molecular flake models that are found to give erratic results due to finite size effects and geometric distortions during energy minimization. The presence of the electrolyte has not been taken into account explicitly in the calculations presented here but is estimated to be important for definitive calculations of the overpotential.
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Affiliation(s)
- Björn Kirchhoff
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, Hjar∂arhagi 2, 107 Reykjavík, Iceland.,Institute of Electrochemistry, Ulm University, Albert-Einstein-Allee 47, 89081 Ulm, Germany
| | - Aleksei Ivanov
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, Hjar∂arhagi 2, 107 Reykjavík, Iceland
| | - Egill Skúlason
- Science Institute and Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, University of Iceland, Hjar∂arhagi 2, 107 Reykjavík, Iceland
| | - Timo Jacob
- Institute of Electrochemistry, Ulm University, Albert-Einstein-Allee 47, 89081 Ulm, Germany.,Helmholtz-Institute Ulm (HIU) Electrochemical Energy Storage, Helmholtz-Straβe 16, 89081 Ulm, Germany.,Karlsruhe Institute of Technology (KIT), P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Donato Fantauzzi
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, Hjar∂arhagi 2, 107 Reykjavík, Iceland
| | - Hannes Jónsson
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, Hjar∂arhagi 2, 107 Reykjavík, Iceland
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12
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Luo Z, Khaliullin RZ. Variable-Metric Localization of Occupied and Virtual Orbitals. J Chem Theory Comput 2021; 17:5568-5581. [PMID: 34370474 DOI: 10.1021/acs.jctc.1c00379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The key idea of the variable-metric approach to orbital localization is to allow nonorthogonality between orbitals while, at the same time, preventing them from becoming linearly dependent. The variable-metric localization has been shown to improve the locality of occupied nonorthogonal orbitals relative to their orthogonal counterparts. In this work, numerous localization algorithms are designed and tested to exploit the conceptual simplicity of the variable-metric approach with the goal of creating a straightforward and reliable localization procedure for virtual orbitals. The implemented algorithms include the steepest descent, conjugate gradient (CG), limited-memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS), and hybrid procedures as well as trust-region (TR) methods based on the CG and Cauchy-point subproblem solvers. Comparative analysis shows that the CG-based TR algorithm is the best overall method to obtain nonorthogonal localized molecular orbitals (NLMOs), occupied or virtual. The L-BFGS and CG algorithms can also be used to obtain NLMOs reliably but often at higher computational cost. Extensive tests demonstrate that the implemented methods allow us to obtain well-localized Boys-Foster (i.e., maximally localized Wannier functions) and Pipek-Mezey, orthogonal and nonorthogonal, and occupied and virtual orbitals for a variety of gas-phase molecules and periodic materials. The tests also show that virtual NLMOs, which have not been described before, are, on average, 13% (Boys-Foster) and 18% (Pipek-Mezey) more localized than their orthogonal counterparts.
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Affiliation(s)
- Ziling Luo
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal QC H3A 0B8, Canada
| | - Rustam Z Khaliullin
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal QC H3A 0B8, Canada
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Ivanov AV, Ghosh TK, Jónsson EÖ, Jónsson H. Mn Dimer Can Be Described Accurately with Density Functional Calculations When Self-Interaction Correction Is Applied. J Phys Chem Lett 2021; 12:4240-4246. [PMID: 33900768 DOI: 10.1021/acs.jpclett.1c00364] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Qualitatively incorrect results are obtained for the Mn dimer in density functional theory calculations using the generalized gradient approximation (GGA), and similar results are obtained from local density and meta-GGA functionals. The coupling is predicted to be ferromagnetic rather than antiferromagnetic, and the bond between the atoms is predicted to be an order of magnitude too strong and approximately an Ångstrøm too short. Explicit, self-interaction correction (SIC) applied to a commonly used GGA energy functional, however, provides close agreement with both experimental data and high-level, multireference wave function calculations. These results show that the failure is not due to a strong correlation but rather the single electron self-interaction that is necessarily introduced in estimates of the classical Coulomb and exchange-correlation energy when only the total electron density is used as the input. The corrected functional depends explicitly on the orbital densities and can, therefore, avoid the introduction of a self-Coulomb interaction. The error arises because of an overstabilization of bonding d-states in the minority spin channel resulting from an overestimate of the d-electron self-interaction in the semilocal exchange-correlation functionals. Since the computational effort in the SIC calculations scales with the system size in the same way as for regular semilocal functional calculations, this approach provides a way to calculate properties of Mn nanoclusters as well as biomolecules and extended solids, where Mn dimers and larger cluster are present, while multireference wave function calculations can only be applied to small systems.
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Affiliation(s)
- Aleksei V Ivanov
- Science Institute and Faculty of Physical Sciences, University of Iceland VR-III, 107 Reykjavík, Reykjavik, Iceland
- St. Petersburg State University, St. Petersburg 199034, Russia
| | - Tushar K Ghosh
- Science Institute and Faculty of Physical Sciences, University of Iceland VR-III, 107 Reykjavík, Reykjavik, Iceland
- Department of Applied Physics, Aalto University, Espoo FI-00076, Finland
| | - Elvar Ö Jónsson
- Science Institute and Faculty of Physical Sciences, University of Iceland VR-III, 107 Reykjavík, Reykjavik, Iceland
- Department of Applied Physics, Aalto University, Espoo FI-00076, Finland
| | - Hannes Jónsson
- Science Institute and Faculty of Physical Sciences, University of Iceland VR-III, 107 Reykjavík, Reykjavik, Iceland
- Department of Applied Physics, Aalto University, Espoo FI-00076, Finland
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14
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Francisco E, Costales A, Menéndez-Herrero M, Pendás ÁM. Lewis Structures from Open Quantum Systems Natural Orbitals: Real Space Adaptive Natural Density Partitioning. J Phys Chem A 2021; 125:4013-4025. [PMID: 33909423 PMCID: PMC8900138 DOI: 10.1021/acs.jpca.1c01689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Building chemical models from state-of-the-art electronic structure calculations is not an easy task, since the high-dimensional information contained in the wave function needs to be compressed and read in terms of the accepted chemical language. We have already shown ( Phys. Chem. Chem. Phys. 2018, 20, 21368) how to access Lewis structures from general wave functions in real space by reformulating the adaptive natural density partitioning (AdNDP) method proposed by Zubarev and Boldyrev ( Phys. Chem. Chem. Phys. 2008, 10, 5207). This provides intuitive Lewis descriptions from fully orbital invariant position space descriptors but depends on not immediately accessible higher order cumulant density matrices. By using an open quantum systems (OQS) perspective, we here show that the rigorously defined OQS fragment natural orbitals can be used to build a consistent real space adaptive natural density partitioning based only on spatial information and the system's one-particle density matrix. We show that this rs-AdNDP approach is a cheap, efficient, and robust technique that immerses electron counting arguments fully in the real space realm.
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Affiliation(s)
- Evelio Francisco
- Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Aurora Costales
- Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, 33006 Oviedo, Spain
| | - María Menéndez-Herrero
- Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Ángel Martín Pendás
- Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, 33006 Oviedo, Spain
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15
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Senjean B, Sen S, Repisky M, Knizia G, Visscher L. Generalization of Intrinsic Orbitals to Kramers-Paired Quaternion Spinors, Molecular Fragments, and Valence Virtual Spinors. J Chem Theory Comput 2021; 17:1337-1354. [PMID: 33555866 DOI: 10.1021/acs.jctc.0c00964] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Localization of molecular orbitals finds its importance in the representation of chemical bonding (and antibonding) and in the local correlation treatments beyond mean-field approximation. In this paper, we generalize the intrinsic atomic and bonding orbitals [G. Knizia, J. Chem. Theory Comput. 2013, 9, 11, 4834-4843] to relativistic applications using complex and quaternion spinors, as well as to molecular fragments instead of atomic fragments only. By performing a singular value decomposition, we show how localized valence virtual orbitals can be expressed on this intrinsic minimal basis. We demonstrate our method on systems of increasing complexity, starting from simple cases such as benzene, acrylic acid, and ferrocene molecules, and then demonstrate the use of molecular fragments and inclusion of relativistic effects for complexes containing heavy elements such as tellurium, iridium, and astatine. The aforementioned scheme is implemented into a standalone program interfaced with several different quantum chemistry packages.
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Affiliation(s)
- Bruno Senjean
- Instituut-Lorentz, Universiteit Leiden, P.O. Box 9506, 2300 RA Leiden, The Netherlands
| | - Souloke Sen
- Theoretical Chemistry, Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands
| | - Michal Repisky
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Gerald Knizia
- Department of Chemistry, The Pennsylvania State University, University Park, State College, Pennsylvania 16802, United States
| | - Lucas Visscher
- Theoretical Chemistry, Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands
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16
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Abstract
Two methods for estimating the correlation energy of molecules and other electronic systems are discussed based on the assumption that the correlation energy can be partitioned between atomic regions. In the first method, the electron density is expanded in terms of atomic contributions using rigorous electron repulsion bounds, and in the second method, correlation contributions are associated with basis function pairs. These methods do not consider the detailed nature of localized excitations but instead define a correlation energy per electron factor that is unique to a specific atom. The correlation factors are basis function dependent and are determined by configuration interaction (CI) calculations on diatomic and hydride molecules. The correlation energy estimates are compared with the results of high-level CI calculations for a test set of 27 molecules representing a wide range of bonding environments (average error of 2.6%). An extension based on truncated CI calculations in which d-type and hydrogen p-type functions are eliminated from the virtual space combined with estimates of dynamical correlation contributions using atomic correlation factors is discussed and applied to the dissociation of several molecules.
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Affiliation(s)
- Jerry L Whitten
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
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17
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Abstract
We introduce new and robust decompositions of mean-field Hartree-Fock and Kohn-Sham density functional theory relying on the use of localized molecular orbitals and physically sound charge population protocols. The new lossless property decompositions, which allow for partitioning one-electron reduced density matrices into either bond-wise or atomic contributions, are compared to alternatives from the literature with regard to both molecular energies and dipole moments. Besides commenting on possible applications as an interpretative tool in the rationalization of certain electronic phenomena, we demonstrate how decomposed mean-field theory makes it possible to expose and amplify compositional features in the context of machine-learned quantum chemistry. This is made possible by improving upon the granularity of the underlying data. On the basis of our preliminary proof-of-concept results, we conjecture that many of the structure-property inferences in existence today may be further refined by efficiently leveraging an increase in dataset complexity and richness.
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Affiliation(s)
- Janus J Eriksen
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
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18
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Schwalbe S, Fiedler L, Kraus J, Kortus J, Trepte K, Lehtola S. PyFLOSIC: Python-based Fermi–Löwdin orbital self-interaction correction. J Chem Phys 2020; 153:084104. [DOI: 10.1063/5.0012519] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Sebastian Schwalbe
- Institute of Theoretical Physics, TU Bergakademie Freiberg, Leipziger Str. 23, D-09599 Freiberg, Germany
| | - Lenz Fiedler
- Institute of Theoretical Physics, TU Bergakademie Freiberg, Leipziger Str. 23, D-09599 Freiberg, Germany
| | - Jakob Kraus
- Institute of Theoretical Physics, TU Bergakademie Freiberg, Leipziger Str. 23, D-09599 Freiberg, Germany
| | - Jens Kortus
- Institute of Theoretical Physics, TU Bergakademie Freiberg, Leipziger Str. 23, D-09599 Freiberg, Germany
| | - Kai Trepte
- Department of Physics, Central Michigan University, Mount Pleasant, Michigan 48859, USA
| | - Susi Lehtola
- Department of Chemistry, University of Helsinki, P.O. Box 55 (A. I. Virtasen Aukio 1), FI-00014 University of Helsinki, Finland
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Jiang H, Zimmerman PM. Charge transfer via spin flip configuration interaction: Benchmarks and application to singlet fission. J Chem Phys 2020; 153:064109. [DOI: 10.1063/5.0018267] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- Hanjie Jiang
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Paul M. Zimmerman
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
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20
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Andrianov AM, Kornoushenko YV, Karpenko AD, Bosko IP, Tuzikov AV. Computational discovery of small drug-like compounds as potential inhibitors of SARS-CoV-2 main protease. J Biomol Struct Dyn 2020; 39:5779-5791. [PMID: 32662333 PMCID: PMC7441783 DOI: 10.1080/07391102.2020.1792989] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A computational approach to in silico drug discovery was carried out to identify small drug-like compounds able to show structural and functional mimicry of the high affinity ligand X77, potent non-covalent inhibitor of SARS-COV-2 main protease (MPro). In doing so, the X77-mimetic candidates were predicted based on the crystal X77-MPro structure by a public web-oriented virtual screening platform Pharmit. Models of these candidates bound to SARS-COV-2 MPro were generated by molecular docking, quantum chemical calculations and molecular dynamics simulations. At the final point, analysis of the interaction modes of the identified compounds with MPro and prediction of their binding affinity were carried out. Calculation revealed 5 top-ranking compounds that exhibited a high affinity to the active site of SARS-CoV-2 MPro. Insights into the ligand - MPro models indicate that all identified compounds may effectively block the binding pocket of SARS-CoV-2 MPro, in line with the low values of binding free energy and dissociation constant. Mechanism of binding of these compounds to MPro is mainly provided by van der Waals interactions with the functionally important residues of the enzyme, such as His-41, Met-49, Cys-145, Met-165, and Gln-189 that play a role of the binding hot spots assisting the predicted molecules to effectively interact with the MPro active site. The data obtained show that the identified X77-mimetic candidates may serve as good scaffolds for the design of novel antiviral agents able to target the active site of SARS-CoV-2 MPro.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Alexander M Andrianov
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Republic of Belarus
| | - Yuri V Kornoushenko
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Republic of Belarus
| | - Anna D Karpenko
- United Institute of Informatics Problems, National Academy of Sciences of Belarus, Minsk, Republic of Belarus
| | - Ivan P Bosko
- United Institute of Informatics Problems, National Academy of Sciences of Belarus, Minsk, Republic of Belarus
| | - Alexander V Tuzikov
- United Institute of Informatics Problems, National Academy of Sciences of Belarus, Minsk, Republic of Belarus
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21
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Abstract
Spatially localized one-electron orbitals, orthogonal and non-orthogonal, are widely used in electronic structure theory to describe chemical bonding and speed up calculations. In order to avoid linear dependencies of localized orbitals, the existing localization methods either constrain orbital transformations to be unitary, that is, metric preserving, or, in the case of variable-metric methods, fix the centers of non-orthogonal localized orbitals. Here, we developed a different approach to orbital localization, in which these constraints are replaced with a single restriction that specifies the maximum allowed deviation from the orthogonality for the final set of localized orbitals. This reformulation, which can be viewed as a generalization of existing localization methods, enables one to choose the desired balance between the orthogonality and locality of the orbitals. Furthermore, the approach is conceptually and practically simple as it obviates the necessity in unitary transformations and allows one to determine optimal positions of the centers of non-orthogonal orbitals in an unconstrained and straightforward minimization procedure. It is demonstrated to produce well-localized orthogonal and non-orthogonal orbitals with the Berghold and Pipek--Mezey localization functions for a variety of molecules and periodic materials including large systems with nontrivial bonding.
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Affiliation(s)
- Ziling Luo
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec QC H3A 0B8, Canada
| | - Rustam Z Khaliullin
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec QC H3A 0B8, Canada
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Wychowaniec JK, Patel R, Leach J, Mathomes R, Chhabria V, Patil-Sen Y, Hidalgo-Bastida A, Forbes RT, Hayes JM, Elsawy MA. Aromatic Stacking Facilitated Self-Assembly of Ultrashort Ionic Complementary Peptide Sequence: β-Sheet Nanofibers with Remarkable Gelation and Interfacial Properties. Biomacromolecules 2020; 21:2670-2680. [DOI: 10.1021/acs.biomac.0c00366] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jacek K. Wychowaniec
- School of Materials, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
- Manchester Institute of Biotechnology, Oxford Road, Manchester M13 9PL, United Kingdom
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
| | - Ronak Patel
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - James Leach
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Rachel Mathomes
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Vikesh Chhabria
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Yogita Patil-Sen
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Araida Hidalgo-Bastida
- Centre for Biosciences, Department of Life Science, Manchester Metropolitan University, Manchester, M1 5GD, United Kingdom
- Centre for Musculoskeletal Science and Sports Medicine, Manchester Metropolitan University, Manchester, M1 5GD, United Kingdom
- Centre for Advance Materials and Surface Engineering, Manchester Metropolitan University, Manchester, M1 5GD, United Kingdom
| | - Robert T. Forbes
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Joseph M. Hayes
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Mohamed A. Elsawy
- School of Materials, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
- Manchester Institute of Biotechnology, Oxford Road, Manchester M13 9PL, United Kingdom
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
- Leicester Institute of Pharmaceutical Innovation, Leicester School of Pharmacy, De Monfort University, The Gateway, Leicester LE1 9BH, United Kingdom
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23
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Lehtola S, Blockhuys F, Van Alsenoy C. An Overview of Self-Consistent Field Calculations Within Finite Basis Sets. Molecules 2020; 25:E1218. [PMID: 32182727 DOI: 10.3390/molecules25051218] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 02/12/2020] [Accepted: 02/17/2020] [Indexed: 11/17/2022] Open
Abstract
A uniform derivation of the self-consistent field equations in a finite basis set is presented. Both restricted and unrestricted Hartree-Fock (HF) theory as well as various density functional approximations are considered. The unitary invariance of the HF and density functional models is discussed, paving the way for the use of localized molecular orbitals. The self-consistent field equations are derived in a non-orthogonal basis set, and their solution is discussed also in the presence of linear dependencies in the basis. It is argued why iterative diagonalization of the Kohn-Sham-Fock matrix leads to the minimization of the total energy. Alternative methods for the solution of the self-consistent field equations via direct minimization as well as stability analysis are briefly discussed. Explicit expressions are given for the contributions to the Kohn-Sham-Fock matrix up to meta-GGA functionals. Range-separated hybrids and non-local correlation functionals are summarily reviewed.
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24
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Pokhilko P, Krylov AI. Effective Hamiltonians derived from equation-of-motion coupled-cluster wave functions: Theory and application to the Hubbard and Heisenberg Hamiltonians. J Chem Phys 2020; 152:094108. [DOI: 10.1063/1.5143318] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Pavel Pokhilko
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, USA
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, USA
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25
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Aquino FW, Shinde R, Wong BM. Fractional occupation numbers and self‐interaction correction‐scaling methods with the Fermi‐Löwdin orbital self‐interaction correction approach. J Comput Chem 2020; 41:1200-8. [DOI: 10.1002/jcc.26168] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 01/19/2020] [Indexed: 11/07/2022]
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26
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Schwalbe S, Trepte K, Fiedler L, Johnson AI, Kraus J, Hahn T, Peralta JE, Jackson KA, Kortus J. Interpretation and Automatic Generation of Fermi‐Orbital Descriptors. J Comput Chem 2019; 40:2843-2857. [DOI: 10.1002/jcc.26062] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 08/13/2019] [Accepted: 08/14/2019] [Indexed: 01/28/2023]
Affiliation(s)
- Sebastian Schwalbe
- TU Freiberg Institute of Theoretical Physics Leipziger Str. 23 D‐09599 Freiberg Germany
| | - Kai Trepte
- Department of Physics Central Michigan University Mount Pleasant Michigan 48859
| | - Lenz Fiedler
- TU Freiberg Institute of Theoretical Physics Leipziger Str. 23 D‐09599 Freiberg Germany
- Freiberg Instruments GmbH Delfter Str.6 D‐09599 Freiberg Germany
| | - Alex I. Johnson
- Department of Physics Central Michigan University Mount Pleasant Michigan 48859
| | - Jakob Kraus
- TU Freiberg Institute of Theoretical Physics Leipziger Str. 23 D‐09599 Freiberg Germany
| | - Torsten Hahn
- TU Freiberg Institute of Theoretical Physics Leipziger Str. 23 D‐09599 Freiberg Germany
| | - Juan E. Peralta
- Department of Physics Central Michigan University Mount Pleasant Michigan 48859
| | - Koblar A. Jackson
- Department of Physics Central Michigan University Mount Pleasant Michigan 48859
| | - Jens Kortus
- TU Freiberg Institute of Theoretical Physics Leipziger Str. 23 D‐09599 Freiberg Germany
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27
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Andrianov AM, Nikolaev GI, Kornoushenko YV, Usanov SA. Click chemistry in silico, docking, quantum chemical calculations, and molecular dynamics simulations to identify novel 1,2,4-triazole-based compounds as potential aromatase inhibitors. SN Appl Sci 2019; 1:1026. [DOI: 10.1007/s42452-019-1051-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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28
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Andrianov AM, Nikolaev GI, Kornoushenko YV, Xu W, Jiang S, Tuzikov AV. In Silico Identification of Novel Aromatic Compounds as Potential HIV-1 Entry Inhibitors Mimicking Cellular Receptor CD4. Viruses 2019; 11:v11080746. [PMID: 31412617 PMCID: PMC6723994 DOI: 10.3390/v11080746] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 07/31/2019] [Accepted: 08/01/2019] [Indexed: 12/13/2022] Open
Abstract
Despite recent progress in the development of novel potent HIV-1 entry/fusion inhibitors, there are currently no licensed antiviral drugs based on inhibiting the critical interactions of the HIV-1 envelope gp120 protein with cellular receptor CD4. In this connection, studies on the design of new small-molecule compounds able to block the gp120-CD4 binding are still of great value. In this work, in silico design of drug-like compounds containing the moieties that make the ligand active towards gp120 was performed within the concept of click chemistry. Complexes of the designed molecules bound to gp120 were then generated by molecular docking and optimized using semiempirical quantum chemical method PM7. Finally, the binding affinity analysis of these ligand/gp120 complexes was performed by molecular dynamic simulations and binding free energy calculations. As a result, five top-ranking compounds that mimic the key interactions of CD4 with gp120 and show the high binding affinity were identified as the most promising CD4-mimemic candidates. Taken together, the data obtained suggest that these compounds may serve as promising scaffolds for the development of novel, highly potent and broad anti-HIV-1 therapeutics.
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Affiliation(s)
- Alexander M Andrianov
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, 220141 Minsk, Belarus.
| | - Grigory I Nikolaev
- United Institute of Informatics Problems, National Academy of Sciences of Belarus, 220012 Minsk, Belarus
| | - Yuri V Kornoushenko
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, 220141 Minsk, Belarus
| | - Wei Xu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, 131 Dong An Road, Fuxing Building, Shanghai 200032, China
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, 131 Dong An Road, Fuxing Building, Shanghai 200032, China.
| | - Alexander V Tuzikov
- United Institute of Informatics Problems, National Academy of Sciences of Belarus, 220012 Minsk, Belarus.
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29
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Eskridge B, Krakauer H, Zhang S. Local Embedding and Effective Downfolding in the Auxiliary-Field Quantum Monte Carlo Method. J Chem Theory Comput 2019; 15:3949-3959. [DOI: 10.1021/acs.jctc.8b01244] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Brandon Eskridge
- Department of Physics, William & Mary, Williamsburg, Virginia 23187, United States
| | - Henry Krakauer
- Department of Physics, William & Mary, Williamsburg, Virginia 23187, United States
| | - Shiwei Zhang
- Department of Physics, William & Mary, Williamsburg, Virginia 23187, United States
- Center for Computational Quantum Physics, The Flatiron Institute, New York, New York 10010, United States
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30
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Krause C, Werner HJ. Scalable Electron Correlation Methods. 6. Local Spin-Restricted Open-Shell Second-Order Møller-Plesset Perturbation Theory Using Pair Natural Orbitals: PNO-RMP2. J Chem Theory Comput 2019; 15:987-1005. [PMID: 30571916 DOI: 10.1021/acs.jctc.8b01012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a (near) linear scaling implementation of high-spin open-shell Møller-Plesset perturbation theory using pair natural orbitals (PNO-RMP2). The theory is based on a new variant of open-shell MP2 which is fully spin-adapted and uses a single set of spin-free amplitudes, as in closed-shell MP2. This method, denoted SROMP2, is invariant to unitary orbital transformations within the closed, open, and virtual orbital subspaces. Accordingly, only a single set of PNOs per spatial orbital pair is needed, and the efficiency is similar to closed-shell calculations. The PNOs are obtained using a semicanonical approximation with large domains of projected atomic orbitals (PAOs). Linear scaling is achieved provided that the open-shell orbitals are local, and distant pairs are treated by multipole approximations. The method is efficiently parallelized. The convergence of ionization and reaction energies as a function of the PAO and PNO domain sizes is demonstrated and found to be very similar as for closed-shell calculations. The suitability of the PNOs for explicitly correlated PNO-RCCSD-F12 calculations is also tested. So far, this method is only simulated using a conventional program with appropriate projections to the PAO and PNO subspaces. It is demonstrated for radical stabilization energies as well as ionization potentials that the errors caused by the local domain approximations with our default thresholds are negligible.
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Affiliation(s)
- Christine Krause
- Institut für Theoretische Chemie , Universität Stuttgart , Pfaffenwaldring 55 , D-70569 Stuttgart , Germany
| | - Hans-Joachim Werner
- Institut für Theoretische Chemie , Universität Stuttgart , Pfaffenwaldring 55 , D-70569 Stuttgart , Germany
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31
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Abstract
Bond order quantifies the number of electrons dressed-exchanged between two atoms in a material and is important for understanding many chemical properties. Diatomic molecules are the smallest molecules possessing chemical bonds and play key roles in atmospheric chemistry, biochemistry, lab chemistry, and chemical manufacturing. Here we quantum-mechanically calculate bond orders for 288 diatomic molecules and ions. For homodiatomics, we show bond orders correlate to bond energies for elements within the same chemical group. We quantify and discuss how semicore electrons weaken bond orders for elements having diffuse semicore electrons. Lots of chemistry is effected by this. We introduce a first-principles method to represent orbital-independent bond order as a sum of orbital-dependent bond order components. This bond order component analysis (BOCA) applies to any spin-orbitals that are unitary transformations of the natural spin-orbitals, with or without periodic boundary conditions, and to non-magnetic and (collinear or non-collinear) magnetic materials. We use this BOCA to study all period 2 homodiatomics plus Mo2, Cr2, ClO, ClO−, and Mo2(acetate)4. Using Manz's bond order equation with DDEC6 partitioning, the Mo–Mo bond order was 4.12 in Mo2 and 1.46 in Mo2(acetate)4 with a sum of bond orders for each Mo atom of ∼4. Our study informs both chemistry research and education. As a learning aid, we introduce an analogy between bond orders in materials and message transmission in computer networks. We also introduce the first working quantitative heuristic model for all period 2 homodiatomic bond orders. This heuristic model incorporates s–p mixing to give heuristic bond orders of ¾ (Be2), 1¾ (B2), 2¾ (C2), and whole number bond orders for the remaining period 2 homodiatomics. Bond orders were computed for 288 diatomics, and a new bond order component analysis (BOCA) was applied to selected diatomics.![]()
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Affiliation(s)
- Taoyi Chen
- Department of Chemical & Materials Engineering
- New Mexico State University
- Las Cruces
- USA
| | - Thomas A. Manz
- Department of Chemical & Materials Engineering
- New Mexico State University
- Las Cruces
- USA
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32
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Cheng X, Jónsson E, Jónsson H, Weber PM. Reply to: "The diamine cation is not a chemical example where density functional theory fails". Nat Commun 2018; 9:5348. [PMID: 30559404 PMCID: PMC6297217 DOI: 10.1038/s41467-018-07683-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 11/06/2018] [Indexed: 11/09/2022] Open
Affiliation(s)
- Xinxin Cheng
- Department of Chemistry, Brown University, Providence, RI, 02912, United States.,The Hamburg Centre for Ultrafast Imaging (CUI), Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.,Max Planck Institute for the Structure and Dynamics of Matter (MPSD), Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Elvar Jónsson
- Faculty of Physical Sciences, VR-III, University of Iceland, 107, Reykjavík, Iceland
| | - Hannes Jónsson
- Department of Chemistry, Brown University, Providence, RI, 02912, United States.,Faculty of Physical Sciences, VR-III, University of Iceland, 107, Reykjavík, Iceland
| | - Peter M Weber
- Department of Chemistry, Brown University, Providence, RI, 02912, United States.
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33
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Affiliation(s)
- Qianli Ma
- Institute for Theoretical ChemistryUniversity of StuttgartStuttgartGermany
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34
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Abstract
From quantum atoms to electron counting the rs-AdNCP strategy: a Lewis structure through (nc,2e) functions.
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Affiliation(s)
- A. Martín Pendás
- Departamento de Química Física y Analítica
- Universidad de Oviedo
- Oviedo
- Spain
| | - E. Francisco
- Departamento de Química Física y Analítica
- Universidad de Oviedo
- Oviedo
- Spain
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35
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Huang C, Chi YC. Directly patching high-level exchange-correlation potential based on fully determined optimized effective potentials. J Chem Phys 2017; 147:244111. [PMID: 29289130 DOI: 10.1063/1.5003663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The key element in Kohn-Sham (KS) density functional theory is the exchange-correlation (XC) potential. We recently proposed the exchange-correlation potential patching (XCPP) method with the aim of directly constructing high-level XC potential in a large system by patching the locally computed, high-level XC potentials throughout the system. In this work, we investigate the patching of the exact exchange (EXX) and the random phase approximation (RPA) correlation potentials. A major challenge of XCPP is that a cluster's XC potential, obtained by solving the optimized effective potential equation, is only determined up to an unknown constant. Without fully determining the clusters' XC potentials, the patched system's XC potential is "uneven" in the real space and may cause non-physical results. Here, we developed a simple method to determine this unknown constant. The performance of XCPP-RPA is investigated on three one-dimensional systems: H20, H10Li8, and the stretching of the H19-H bond. We investigated two definitions of EXX: (i) the definition based on the adiabatic connection and fluctuation dissipation theorem (ACFDT) and (ii) the Hartree-Fock (HF) definition. With ACFDT-type EXX, effective error cancellations were observed between the patched EXX and the patched RPA correlation potentials. Such error cancellations were absent for the HF-type EXX, which was attributed to the fact that for systems with fractional occupation numbers, the integral of the HF-type EXX hole is not -1. The KS spectra and band gaps from XCPP agree reasonably well with the benchmarks as we make the clusters large.
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Affiliation(s)
- Chen Huang
- Department of Scientific Computing, Florida State University, Tallahassee, Florida 32306-4120, USA
| | - Yu-Chieh Chi
- Department of Scientific Computing, Florida State University, Tallahassee, Florida 32306-4120, USA
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36
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Abstract
Full configuration interaction (FCI) restricted to a pairing space yields size-extensive correlation energies but its cost scales exponentially with molecular size. Restricting the variational two-electron reduced-density-matrix (2-RDM) method to represent the same pairing space yields an accurate lower bound to the pair FCI energy at a mean-field-like computational scaling of O(r3) where r is the number of orbitals. In this paper, we show that localized molecular orbitals can be employed to generate an efficient, approximately size-extensive pair 2-RDM method. The use of localized orbitals eliminates the substantial cost of optimizing iteratively the orbitals defining the pairing space without compromising accuracy. In contrast to the localized orbitals, the use of canonical Hartree-Fock molecular orbitals is shown to be both inaccurate and non-size-extensive. The pair 2-RDM has the flexibility to describe the spectra of one-electron RDM occupation numbers from all quantum states that are invariant to time-reversal symmetry. Applications are made to hydrogen chains and their dissociation, n-acene from naphthalene through octacene, and cadmium telluride 2-, 3-, and 4-unit polymers. For the hydrogen chains, the pair 2-RDM method recovers the majority of the energy obtained from similar calculations that iteratively optimize the orbitals. The localized-orbital pair 2-RDM method with its mean-field-like computational scaling and its ability to describe multi-reference correlation has important applications to a range of strongly correlated phenomena in chemistry and physics.
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Affiliation(s)
- Kade Head-Marsden
- Department of Chemistry and The James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA
| | - David A Mazziotti
- Department of Chemistry and The James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA
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37
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Lehtola S, Parkhill J, Head-Gordon M. Orbital optimisation in the perfect pairing hierarchy: applications to full-valence calculations on linear polyacenes. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1342009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Susi Lehtola
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - John Parkhill
- Department of Chemistry, University of Notre Dame, Notre Dame, IN, United States
| | - Martin Head-Gordon
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Chemistry, University of California, Berkeley, CA, United States
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38
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Affiliation(s)
- Hongyang Li
- Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, State Key Laboratory of Rare Earth Materials Chemistry and Applications, College of Chemistry and Molecular Engineering, and Center for Computational Science and Engineering, Peking University, Beijing 100871, People’s Republic of China
| | - Wenjian Liu
- Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, State Key Laboratory of Rare Earth Materials Chemistry and Applications, College of Chemistry and Molecular Engineering, and Center for Computational Science and Engineering, Peking University, Beijing 100871, People’s Republic of China
| | - Bingbing Suo
- Institute of Modern Physics, Northwest University, Xi’an 710069, People’s Republic of China
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39
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Affiliation(s)
- Elvar Ö. Jónsson
- COMP
Centre of Excellence and Department of Applied Physics, Aalto University School of Science, P.O. Box 11100, FI-00076 Aalto,
Espoo, Finland
| | - Susi Lehtola
- COMP
Centre of Excellence and Department of Applied Physics, Aalto University School of Science, P.O. Box 11100, FI-00076 Aalto,
Espoo, Finland
- Chemical
Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Martti Puska
- COMP
Centre of Excellence and Department of Applied Physics, Aalto University School of Science, P.O. Box 11100, FI-00076 Aalto,
Espoo, Finland
| | - Hannes Jónsson
- COMP
Centre of Excellence and Department of Applied Physics, Aalto University School of Science, P.O. Box 11100, FI-00076 Aalto,
Espoo, Finland
- Faculty
of Physical Sciences, University of Iceland, 107 Reykjavík, Iceland
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40
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Lehtola S, Parkhill J, Head-Gordon M. Cost-effective description of strong correlation: Efficient implementations of the perfect quadruples and perfect hextuples models. J Chem Phys 2016; 145:134110. [DOI: 10.1063/1.4964317] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Susi Lehtola
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - John Parkhill
- Department of Chemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, Indiana 46556, USA
| | - Martin Head-Gordon
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- Department of Chemistry, University of California, Berkeley, California 94720, USA
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41
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Molina A, Smereka P, Zimmerman PM. Exploring the relationship between vibrational mode locality and coupling using constrained optimization. J Chem Phys 2016; 144:124111. [PMID: 27036431 DOI: 10.1063/1.4944743] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The use of alternate coordinate systems as a means to improve the efficiency and accuracy of anharmonic vibrational structure analysis has seen renewed interest in recent years. While normal modes (which diagonalize the mass-weighted Hessian matrix) are a typical choice, the delocalized nature of this basis makes it less optimal when anharmonicity is in play. When a set of modes is not designed to treat anharmonicity, anharmonic effects will contribute to inter-mode coupling in an uncontrolled fashion. These effects can be mitigated by introducing locality, but this comes at its own cost of potentially large second-order coupling terms. Herein, a method is described which partially localizes vibrations to connect the fully delocalized and fully localized limits. This allows a balance between the treatment of harmonic and anharmonic coupling, which minimizes the error that arises from neglected coupling terms. Partially localized modes are investigated for a range of model systems including a tetramer of hydrogen fluoride, water dimer, ethene, diphenylethane, and stilbene. Generally, partial localization reaches ∼75% of maximal locality while introducing less than ∼30% of the harmonic coupling of the fully localized system. Furthermore, partial localization produces mode pairs that are spatially separated and thus weakly coupled to one another. It is likely that this property can be exploited in the creation of model Hamiltonians that omit the coupling parameters of the distant (and therefore uncoupled) pairs.
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Affiliation(s)
- Andrew Molina
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, USA
| | - Peter Smereka
- Department of Applied Mathematics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Paul M Zimmerman
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, USA
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42
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Lehtola S, Jónsson EÖ, Jónsson H. Effect of Complex-Valued Optimal Orbitals on Atomization Energies with the Perdew–Zunger Self-Interaction Correction to Density Functional Theory. J Chem Theory Comput 2016; 12:4296-302. [DOI: 10.1021/acs.jctc.6b00622] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Susi Lehtola
- COMP
Centre of Excellence and Department of Applied Physics, Aalto University School of Science, P.O. Box 11000, FI-00076 Aalto, Espoo, Finland
- Chemical
Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Elvar Ö. Jónsson
- COMP
Centre of Excellence and Department of Applied Physics, Aalto University School of Science, P.O. Box 11000, FI-00076 Aalto, Espoo, Finland
| | - Hannes Jónsson
- COMP
Centre of Excellence and Department of Applied Physics, Aalto University School of Science, P.O. Box 11000, FI-00076 Aalto, Espoo, Finland
- Faculty
of Physical Sciences, University of Iceland, 107 Reykjavík, Iceland
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43
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44
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Abstract
A self-interaction corrected density functional is used to describe the ground state of the CH3CN(-) ion that includes a dipole bound electron with large spatial extent and low binding energy. Without the correction, some commonly used density functionals based on the generalized gradient approximation as well as hybrid functionals fail to give a bound ground state of the anion. A negative HOMO orbital energy of magnitude 0.013 eV is obtained using the self-interaction corrected PBE functional in good correspondence with the experimentally estimated binding energy of 0.019 eV. The dipole bound electron polarizes the CH3CN molecule and increases its dipole moment by 7% to 4.2 D. Because the computational effort increases slowly with system size, as the number of electrons cubed, the results presented here point to a viable approach to theoretical studies of dipole bound electrons in large and complex systems such as molecular clusters, biological systems, and solvated electrons.
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Affiliation(s)
- Yao Zhang
- Department of Chemistry, Brown University , Providence, Rhode Island 02912, United States
| | - Peter M Weber
- Department of Chemistry, Brown University , Providence, Rhode Island 02912, United States
| | - Hannes Jónsson
- Faculty of Physical Sciences, University of Iceland , 107 Reykjavík, Iceland
- Department of Applied Physics, Aalto University , Espoo FIN-00076, Finland
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45
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Affiliation(s)
- Ida-Marie Høyvik
- Department
of Chemistry, The Norwegian University of Science and Technology, Høgskoleringen 5, 7491 Trondheim, Norway
| | - Poul Jørgensen
- qLEAP
Center for Theoretical Chemistry, Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
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46
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Lehtola S, Jónsson H. Correction to Variational, Self-Consistent Implementation of the Perdew–Zunger Self-Interaction Correction with Complex Optimal Orbitals. J Chem Theory Comput 2015; 11:5052-3. [DOI: 10.1021/acs.jctc.5b00806] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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47
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Zimmerman PM, Molina AR, Smereka P. Orbitals with intermediate localization and low coupling: Spanning the gap between canonical and localized orbitals. J Chem Phys 2015; 143:014106. [DOI: 10.1063/1.4923084] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Paul M. Zimmerman
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Andrew R. Molina
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Peter Smereka
- Department of Mathematics, University of Michigan, Ann Arbor, Michigan 48109, USA
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48
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49
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Affiliation(s)
- Chenyang Zhang
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, School of Chemistry and Chemical Engineering, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210093, People’s Republic of China
| | - Shuhua Li
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, School of Chemistry and Chemical Engineering, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210093, People’s Republic of China
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50
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Lehtola S, Jónsson H. Variational, Self-Consistent Implementation of the Perdew–Zunger Self-Interaction Correction with Complex Optimal Orbitals. J Chem Theory Comput 2014; 10:5324-37. [DOI: 10.1021/ct500637x] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Susi Lehtola
- COMP
Centre of Excellence and Department of Applied Physics, P.O. Box 11100, FI-00076 Aalto University, Espoo, Finland
| | - Hannes Jónsson
- COMP
Centre of Excellence and Department of Applied Physics, P.O. Box 11100, FI-00076 Aalto University, Espoo, Finland
- Faculty
of Physical Sciences, University of Iceland, Reykjavík, Iceland
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