1
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Chen T, Zhang C, Cheng L, Ng KB, Malbrunot-Ettenauer S, Flambaum VV, Lasner Z, Doyle JM, Yu P, Conn CJ, Zhang C, Hutzler NR, Jayich AM, Augenbraun B, DeMille D. Relativistic Exact Two-Component Coupled-Cluster Study of Molecular Sensitivity Factors for Nuclear Schiff Moments. J Phys Chem A 2024. [PMID: 39047199 DOI: 10.1021/acs.jpca.4c02640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Relativistic exact two-component coupled-cluster calculations of molecular sensitivity factors for nuclear Schiff moments (NSMs) are reported. We focus on molecules containing heavy nuclei, especially octupole-deformed nuclei. Analytic relativistic coupled-cluster gradient techniques are used and serve as useful tools for identifying candidate molecules that sensitively probe for physics beyond the Standard Model in the hadronic sector. Notably, these tools enable straightforward "black-box" calculations. Two competing chemical mechanisms that contribute to the NSM are analyzed, illuminating the physics of ligand effects on NSM sensitivity factors.
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Affiliation(s)
- Tianxiang Chen
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Chaoqun Zhang
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Lan Cheng
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Kia Boon Ng
- TRIUMF, 4004 Wesbrook Mall, Vancouver, BC V6T 2A3, Canada
| | - Stephan Malbrunot-Ettenauer
- TRIUMF, 4004 Wesbrook Mall, Vancouver, BC V6T 2A3, Canada
- Department of Physics, University of Toronto, Toronto M5S 1A7, Canada
| | - Victor V Flambaum
- School of Physics, University of New South Wales, Sydney 2052, Australia
| | - Zack Lasner
- Department of Physics, Harvard University, Cambridge, Massachusetts 02138, United States
- Harvard-MIT Center for Ultracold Atoms, Cambridge, Massachusetts 02138, United States
| | - John M Doyle
- Department of Physics, Harvard University, Cambridge, Massachusetts 02138, United States
- Harvard-MIT Center for Ultracold Atoms, Cambridge, Massachusetts 02138, United States
| | - Phelan Yu
- Division of Physics, Mathematics, and Astronomy, California Institute of Technology, Pasadena, California 91125, United States
| | - Chandler J Conn
- Division of Physics, Mathematics, and Astronomy, California Institute of Technology, Pasadena, California 91125, United States
| | - Chi Zhang
- Division of Physics, Mathematics, and Astronomy, California Institute of Technology, Pasadena, California 91125, United States
| | - Nicholas R Hutzler
- Division of Physics, Mathematics, and Astronomy, California Institute of Technology, Pasadena, California 91125, United States
| | - Andrew M Jayich
- Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - Benjamin Augenbraun
- Department of Chemistry, Williams College, 47 Lab Campus Drive, Williamstown, Massachusetts 01267, United States
| | - David DeMille
- Department of Physics, University of Chicago, Chicago, Illinois 60637, United States
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2
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Jackowski K, Wilczek M. Measurements of Nuclear Magnetic Shielding in Molecules. Molecules 2024; 29:2617. [PMID: 38893492 PMCID: PMC11173999 DOI: 10.3390/molecules29112617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/24/2024] [Accepted: 05/30/2024] [Indexed: 06/21/2024] Open
Abstract
The origin of nuclear magnetic shielding in diamagnetic molecules is discussed, pointing out various contributions to the shielding from electrons and the effects of intra- and intermolecular interactions. In NMR practice, chemical shifts are determined first as the measure of shielding in observed samples. The descriptions of shielding and chemical shifts are not fully consistent. Gas phase studies permit the withdrawal of intermolecular contributions from shielding and obtaining the magnetic shielding data in isolated molecules. The shielding determination in molecules is possible using at least three methods delivering the reference shielding standards for selected nuclei. The known shielding of one magnetic nucleus can be transferred to other nuclei if the appropriate nuclear magnetic moments are available with satisfactory accuracy. It is possible to determine the nuclear magnetic dipole moments using the most advanced ab initio shielding calculations jointly with the NMR frequencies measurements for small-sized isolated molecules. Helium-3 gas is postulated as all the molecules' primary and universal reference standard of shielding. It can be easily applied using common deuterium lock solvents as the secondary reference standards. The measurements of absolute shielding are available for everyone with the use of standard NMR spectrometers.
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Affiliation(s)
- Karol Jackowski
- Laboratory of NMR Spectroscopy, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland;
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3
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Zhang T, Banerjee S, Koulias LN, Valeev EF, DePrince AE, Li X. Dirac-Coulomb-Breit Molecular Mean-Field Exact-Two-Component Relativistic Equation-of-Motion Coupled-Cluster Theory. J Phys Chem A 2024; 128:3408-3418. [PMID: 38651293 DOI: 10.1021/acs.jpca.3c08167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
We present a relativistic equation-of-motion coupled-cluster with single and double excitation formalism within the exact two-component framework (X2C-EOM-CCSD), where both scalar relativistic effects and spin-orbit coupling are variationally included at the reference level. Three different molecular mean-field treatments of relativistic corrections, including the one-electron, Dirac-Coulomb, and Dirac-Coulomb-Breit Hamiltonian, are considered in this work. Benchmark calculations include atomic excitations and fine-structure splittings arising from spin-orbit coupling. Comparison with experimental values and relativistic time-dependent density functional theory is also carried out. The computation of the oscillator strength using the relativistic X2C-EOM-CCSD approach allows for studies of spin-orbit-driven processes, such as the spontaneous phosphorescence lifetime.
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Affiliation(s)
- Tianyuan Zhang
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Samragni Banerjee
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Lauren N Koulias
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Edward F Valeev
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - A Eugene DePrince
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| | - Xiaosong Li
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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4
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Rutskoy B, Ozerov G, Bezrukov D. The Role of Bond Functions in Describing Intermolecular Electron Correlation for Van der Waals Dimers: A Study of (CH 4) 2 and Ne 2. Int J Mol Sci 2024; 25:1472. [PMID: 38338750 PMCID: PMC10855067 DOI: 10.3390/ijms25031472] [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: 11/16/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
We present a study of the intermolecular interactions in van der Waals complexes of methane and neon dimers within the framework of the CCSD method. This approach was implemented and applied to calculate and examine the behavior of the contracted two-particle reduced density matrix (2-RDM). It was demonstrated that the region near the minimum of the two-particle density matrix correlation part, corresponding to the primary bulk of the Coulomb hole contribution, exerts a significant influence on the dispersion interaction energetics of the studied systems. As a result, the bond functions approach was applied to improve the convergence performance for the intermolecular correlation energy results with respect to the size of the atomic basis. For this, substantial acceleration was achieved by introducing an auxiliary basis of bond functions centered on the minima of the 2-RDM. For both methane and neon dimers, this general conclusion was confirmed with a series of CCSD calculations for the 2-RDM and the correlation energies.
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Affiliation(s)
- Bogdan Rutskoy
- National Research Centre “Kurchatov Institute”, Moscow 123182, Russia;
- Institute of Nuclear Physics and Technology, National Research Nuclear University “MEPhI” (Moscow Engineering Physics Institute), Moscow 115409, Russia
- Chemistry Department, M.V. Lomonosov Moscow State University, Moscow 119991, Russia;
| | - Georgiy Ozerov
- Chemistry Department, M.V. Lomonosov Moscow State University, Moscow 119991, Russia;
| | - Dmitry Bezrukov
- Chemistry Department, M.V. Lomonosov Moscow State University, Moscow 119991, Russia;
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5
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Yuan X, Halbert L, Pototschnig JV, Papadopoulos A, Coriani S, Visscher L, Pereira Gomes AS. Formulation and Implementation of Frequency-Dependent Linear Response Properties with Relativistic Coupled Cluster Theory for GPU-Accelerated Computer Architectures. J Chem Theory Comput 2024; 20:677-694. [PMID: 38193434 DOI: 10.1021/acs.jctc.3c00812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
We present the development and implementation of relativistic coupled cluster linear response theory (CC-LR), which allows the determination of molecular properties arising from time-dependent or time-independent electric, magnetic, or mixed electric-magnetic perturbations (within a common gauge origin for the magnetic properties) as well as taking into account the finite lifetime of excited states in the framework of damped response theory. We showcase our implementation, which is capable to offload the computationally intensive tensor contractions characteristic of coupled cluster theory onto graphical processing units, in the calculation of (a) frequency-(in)dependent dipole-dipole polarizabilities of IIB atoms and selected diatomic molecules, with a particular emphasis on the calculation of valence absorption cross sections for the I2 molecule; (b) indirect spin-spin coupling constants for benchmark systems such as the hydrogen halides (HX, X = F-I) as well the H2Se-H2O dimer as a prototypical system containing hydrogen bonds; and (c) optical rotations at the sodium D line for hydrogen peroxide analogues (H2Y2, Y = O, S, Se, Te). Thanks to this implementation, we are able to show the similarities in performance, but often the significant discrepancies, between CC-LR and approximate methods such as density functional theory. Comparing standard CC response theory with the flavor based upon the equation of motion formalism, we find that for valence properties such as polarizabilities, the two frameworks yield very similar results across the periodic table as found elsewhere in the literature; for properties that probe the core region, such as spin-spin couplings, on the other hand, we show a progressive differentiation between the two as relativistic effects become more important. Our results also suggest that as one goes down the periodic table, it may become increasingly difficult to measure pure optical rotation at the sodium D line due to the appearance of absorbing states.
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Affiliation(s)
- Xiang Yuan
- Univ. Lille, CNRS, UMR 8523─PhLAM─Physique des Lasers Atomes et Molécules, F-59000 Lille, France
- Department of Chemistry and Pharmaceutical Sciences, Faculty of Science, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Loïc Halbert
- Univ. Lille, CNRS, UMR 8523─PhLAM─Physique des Lasers Atomes et Molécules, F-59000 Lille, France
| | - Johann Valentin Pototschnig
- Department of Chemistry and Pharmaceutical Sciences, Faculty of Science, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Anastasios Papadopoulos
- Department of Chemistry and Pharmaceutical Sciences, Faculty of Science, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Sonia Coriani
- DTU Chemistry─Department of Chemistry, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Lucas Visscher
- Department of Chemistry and Pharmaceutical Sciences, Faculty of Science, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
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6
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Zhang C, Lipparini F, Stopkowicz S, Gauss J, Cheng L. Cholesky Decomposition-Based Implementation of Relativistic Two-Component Coupled-Cluster Methods for Medium-Sized Molecules. J Chem Theory Comput 2024; 20:787-798. [PMID: 38198515 DOI: 10.1021/acs.jctc.3c01236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
A Cholesky decomposition (CD)-based implementation of relativistic two-component coupled-cluster (CC) and equation-of-motion CC (EOM-CC) methods using an exact two-component Hamiltonian augmented with atomic-mean-field spin-orbit integrals (the X2CAMF scheme) is reported. The present CD-based implementation of X2CAMF-CC and EOM-CC methods employs atomic-orbital-based algorithms to avoid the construction of two-electron integrals and intermediates involving three and four virtual indices. Our CD-based implementation extends the applicability of X2CAMF-CC and EOM-CC methods to medium-sized molecules with the possibility to correlate around 1000 spinors. Benchmark calculations for uranium-containing small molecules were performed to assess the dependence of the CC results on the Cholesky threshold. A Cholesky threshold of 10-4 is shown to be sufficient to maintain chemical accuracy. Example calculations to illustrate the capability of the CD-based relativistic CC methods are reported for the bond-dissociation energy of the uranium hexafluoride molecule, UF6, with up to quadruple-ζ basis sets, and the lowest excitation energy in the solvated uranyl ion [UO22+(H2O)12].
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Affiliation(s)
- Chaoqun Zhang
- Department of Chemistry, the Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, Pisa I-56124, Italy
| | - Stella Stopkowicz
- Fachrichtung Chemie, Universität des Saarlandes, Saarbrücken D-66123, Germany
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, P.O. Box 1033, Blindern, Oslo N-0315, Norway
| | - Jürgen Gauss
- Department Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, Mainz D-55128, Germany
| | - Lan Cheng
- Department of Chemistry, the Johns Hopkins University, Baltimore, Maryland 21218, United States
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7
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Zhang C, Zheng X, Liu J, Asthana A, Cheng L. Analytic gradients for relativistic exact-two-component equation-of-motion coupled-cluster singles and doubles method. J Chem Phys 2023; 159:244113. [PMID: 38153147 DOI: 10.1063/5.0175041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 11/20/2023] [Indexed: 12/29/2023] Open
Abstract
A first implementation of analytic gradients for spinor-based relativistic equation-of-motion coupled-cluster singles and doubles method using an exact two-component Hamiltonian augmented with atomic mean-field spin-orbit integrals is reported. To demonstrate its applicability, we present calculations of equilibrium structures and harmonic vibrational frequencies for the electronic ground and excited states of the radium mono-amide molecule (RaNH2) and the radium mono-methoxide molecule (RaOCH3). Spin-orbit coupling is shown to quench Jahn-Teller effects in the first excited state of RaOCH3, resulting in a C3v equilibrium structure. The calculations also show that the radium atoms in these molecules serve as efficient optical cycling centers.
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Affiliation(s)
- Chaoqun Zhang
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Xuechen Zheng
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Junzi Liu
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Ayush Asthana
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Lan Cheng
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, USA
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8
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Zhang J, Kriebel CN, Wan Z, Shi M, Glaubitz C, He X. Automated Fragmentation Quantum Mechanical Calculation of 15N and 13C Chemical Shifts in a Membrane Protein. J Chem Theory Comput 2023; 19:7405-7422. [PMID: 37788419 DOI: 10.1021/acs.jctc.3c00621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
In this work, we developed an accurate and cost-effective automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) method to calculate the chemical shifts of 15N and 13C of membrane proteins. The convergence of the AF-QM/MM method was tested using Krokinobacter eikastus rhodopsin 2 as a test case. When the distance threshold of the QM region is equal to or larger than 4.0 Å, the results of the AF-QM/MM calculations are close to convergence. In addition, the effects of selected density functionals, basis sets, and local chemical environment of target atoms on the chemical shift calculations were systematically investigated. Our results demonstrate that the predicted chemical shifts are more accurate when important environmental factors including cross-protomer interactions, lipid molecules, and solvent molecules are taken into consideration, especially for the 15N chemical shift prediction. Furthermore, with the presence of sodium ions in the environment, the chemical shift of residues, retinal, and retinal Schiff base are affected, which is consistent with the results of the solid-state nuclear magnetic resonance (NMR) experiment. Upon comparing the performance of various density functionals (namely, B3LYP, B3PW91, M06-2X, M06-L, mPW1PW91, OB95, and OPBE), the results show that mPW1PW91 is a suitable functional for the 15N and 13C chemical shift prediction of the membrane proteins. Meanwhile, we find that the improved accuracy of the 13Cβ chemical shift calculations can be achieved by the employment of the triple-ζ basis set. However, the employment of the triple-ζ basis set does not improve the accuracy of the 15N and 13Cα chemical shift calculations nor does the addition of a diffuse function improve the overall prediction accuracy of the chemical shifts. Our study also underscores that the AF-QM/MM method has significant advantages in predicting the chemical shifts of key ligands and nonstandard residues in membrane proteins than most widely used empirical models; therefore, it could be an accurate computational tool for chemical shift calculations on various types of biological systems.
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Affiliation(s)
- Jinhuan Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Clara Nassrin Kriebel
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Zheng Wan
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Man Shi
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Clemens Glaubitz
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
- New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai 200062, China
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9
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Kleine Büning JB, Grimme S. Computation of CCSD(T)-Quality NMR Chemical Shifts via Δ-Machine Learning from DFT. J Chem Theory Comput 2023. [PMID: 37262324 DOI: 10.1021/acs.jctc.3c00165] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
NMR spectroscopy undoubtedly plays a central role in determining molecular structures across different chemical disciplines, and the accurate computational prediction of NMR parameters is highly desirable. In this work, a new Δ-machine learning approach is presented to correct DFT-computed NMR chemical shifts using input features from the calculation and in addition highly accurate reference data at the CCSD(T)/pcSseg-2 level of theory with a basis set extrapolation scheme. The model is trained on a data set containing 1000 optimized and geometrically distorted structures of small organic molecules comprising most elements of the first three periods and containing data for 7090 1H and 4230 13C NMR chemical shifts. Applied to the PBE0/pcSseg-2 method, the mean absolute deviation (MAD) on the internal NMR shift test set is reduced by 81% for 1H and 92% for 13C at virtually no additional computational cost. For 12 different DFT functional and basis set combinations, the MAD of the ML-corrected NMR shifts ranges from 0.021 to 0.039 ppm (1H) and from 0.38 to 1.07 ppm (13C). Importantly, the new method consistently outperforms the simple and widely used linear regression correction technique. This behavior is reproduced on three different external benchmark sets, confirming the generality and robustness of the correction scheme, which can easily be applied in DFT-based spectral simulations.
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Affiliation(s)
- Julius B Kleine Büning
- Mulliken Center for Theoretical Chemistry, Clausius Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Clausius Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
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10
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Wong J, Ganoe B, Liu X, Neudecker T, Lee J, Liang J, Wang Z, Li J, Rettig A, Head-Gordon T, Head-Gordon M. An in-silico NMR laboratory for nuclear magnetic shieldings computed via finite fields: Exploring nucleus-specific renormalizations of MP2 and MP3. J Chem Phys 2023; 158:164116. [PMID: 37114707 PMCID: PMC10148725 DOI: 10.1063/5.0145130] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
We developed and implemented a method-independent, fully numerical, finite difference approach to calculating nuclear magnetic resonance shieldings, using gauge-including atomic orbitals. The resulting capability can be used to explore non-standard methods, given only the energy as a function of finite-applied magnetic fields and nuclear spins. For example, standard second-order Møller-Plesset theory (MP2) has well-known efficacy for 1H and 13C shieldings and known limitations for other nuclei such as 15N and 17O. It is, therefore, interesting to seek methods that offer good accuracy for 15N and 17O shieldings without greatly increased compute costs, as well as exploring whether such methods can further improve 1H and 13C shieldings. Using a small molecule test set of 28 species, we assessed two alternatives: κ regularized MP2 (κ-MP2), which provides energy-dependent damping of large amplitudes, and MP2.X, which includes a variable fraction, X, of third-order correlation (MP3). The aug-cc-pVTZ basis was used, and coupled cluster with singles and doubles and perturbative triples [CCSD(T)] results were taken as reference values. Our κ-MP2 results reveal significant improvements over MP2 for 13C and 15N, with the optimal κ value being element-specific. κ-MP2 with κ = 2 offers a 30% rms error reduction over MP2. For 15N, κ-MP2 with κ = 1.1 provides a 90% error reduction vs MP2 and a 60% error reduction vs CCSD. On the other hand, MP2.X with a scaling factor of 0.6 outperformed CCSD for all heavy nuclei. These results can be understood as providing renormalization of doubles amplitudes to partially account for neglected triple and higher substitutions and offer promising opportunities for future applications.
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Affiliation(s)
- Jonathan Wong
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Brad Ganoe
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Xiao Liu
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Tim Neudecker
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Joonho Lee
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Jiashu Liang
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Zhe Wang
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Jie Li
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Adam Rettig
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA
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11
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Jackowski K, Słowiński MA. Searching for the Best Values of NMR Shielding and Spin-Spin Coupling Parameters: CH 4-nF n Series of Molecules as the Example. Molecules 2023; 28:molecules28031499. [PMID: 36771162 PMCID: PMC9919152 DOI: 10.3390/molecules28031499] [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: 12/24/2022] [Revised: 01/20/2023] [Accepted: 01/28/2023] [Indexed: 02/09/2023] Open
Abstract
Attempts at the theoretical interpretation of NMR spectra have a very long and fascinating history. Present quantum chemical calculations of shielding and indirect spin-spin couplings permit modeling NMR spectra when small, isolated molecules are studied. Similar data are also available from NMR experiments if investigations are performed in the gas phase. An interesting set of molecules is formed when a methane molecule is sequentially substituted by fluorine atoms-CH4-nFn, where n = 0, 1, 2, 3, or 4. The small molecules contain up to three magnetic nuclei, each with a one-half spin number. The spectral parameters of CH4-nFn can be easily observed in the gas phase and calculated with high accuracy using the most advanced ab initio methods of quantum chemistry. However, the presence of fluorine atoms makes the calculations of shielding and spin-spin coupling constants extremely demanding. Appropriate experimental 19F NMR parameters are good but also require some further improvements. Therefore, there is a real need for the comparison of existing NMR measurements with available state-of-the-art theoretical results for a better understanding of actual limits in the determination of the best shielding and spin-spin coupling values, and CH4-nFn molecules are used here as the exceptionally important case.
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12
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Karadakov PB, Stewart B, Cooper DL. Magnetic Shielding Analysis of Bonding in [1.1.1]Propellane. J Phys Chem A 2023; 127:861-869. [PMID: 36655346 PMCID: PMC9900594 DOI: 10.1021/acs.jpca.2c06450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The bonding in [1.1.1]propellane, bicyclo[1.1.0]butane, bicyclo[1.1.1]pentane, tetrahedrane, and cyclopropane is investigated by analyzing changes in the off-nucleus isotropic magnetic shielding within the space surrounding each of these molecules and, for [1.1.1]propellane, by examining also the diamagnetic and paramagnetic contributions to this shielding. Any shielding arising from the two "exo" sp3-like hybrid atomic orbitals on the bridgehead carbon atoms that have been used to support the idea of an inverted bond between these two atoms is found to be almost entirely contained within the [1.1.1]propellane cage and to contribute to a strongly shielded central region. This strongly shielded region suggests the establishment of a mainly covalent bonding interaction involving all carbon atoms that cannot be straightforwardly decomposed into contributions from individual carbon-carbon bonds. The emergence of the strongly shielding central region is traced by comparing the shielding variations in and around molecules with one three-membered carbon ring (cyclopropane), two fused three-membered carbon rings (bicyclo[1.1.0]butane), and three fused three-membered carbon rings ([1.1.1]propellane).
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Affiliation(s)
- Peter B. Karadakov
- Department
of Chemistry, University of York, Heslington, YorkYO10 5DD, U.K.,
| | - Ben Stewart
- Department
of Chemistry, University of York, Heslington, YorkYO10 5DD, U.K.
| | - David L. Cooper
- Department
of Chemistry, University of Liverpool, LiverpoolL69 7ZD, U.K.
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13
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Quantum Chemical Approaches to the Calculation of NMR Parameters: From Fundamentals to Recent Advances. MAGNETOCHEMISTRY 2022. [DOI: 10.3390/magnetochemistry8050050] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Quantum chemical methods for the calculation of indirect NMR spin–spin coupling constants and chemical shifts are always in progress. They never stay the same due to permanently developing computational facilities, which open new perspectives and create new challenges every now and then. This review starts from the fundamentals of the nonrelativistic and relativistic theory of nuclear magnetic resonance parameters, and gradually moves towards the discussion of the most popular common and newly developed methodologies for quantum chemical modeling of NMR spectra.
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14
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Lu Y, Wang Z, Wang F. Intermediate Hamiltonian Fock-space coupled-cluster theory for excitation energies, double ionization potentials, and double electron attachments with spin–orbit coupling. J Chem Phys 2022; 156:114111. [DOI: 10.1063/5.0076462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The intermediate Hamiltonian Fock-space coupled-cluster methods at the singles and doubles level (IHFSCCSD) for excitation energies in the (1p, 1h) sector, double ionization potentials in the (0p, 2h) sector, and double electron attachments in the (2p, 0h) sector of the Fock space are implemented based on the CCSD method with spin–orbit coupling (SOC) included in the post-Hartree–Fock treatment using a closed-shell reference in this work. The active space is chosen to contain those orbitals that have the largest contribution to principal ionized or electron-attached states obtained from the equation-of-motion coupled-cluster calculations. Both time-reversal symmetry and spatial symmetry are exploited in the implementation. Our results show that the accuracy of IHFSCCSD results is closely related to the active space, and the sufficiency of the active space can be assessed from the percentage of transitions within the active space. In addition, unreasonable results may be encountered when the ionized or electron-attached states with a somewhat larger contribution from double excitations are included to determine the active space and cluster operators in the (0p, 1h) or (1p, 0h) sector of the Fock space. A larger active space may be required to describe SO splitting reliably than that in the scalar-relativistic calculations in some cases. The IHFSCCSD method with SOC developed in this work can provide reliable results for heavy-element systems when a sufficient active space built upon the principal ionization potential/electron affinity states is adopted.
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Affiliation(s)
- Yanzhao Lu
- Institute of Atomic and Molecular Physics, Key Laboratory of High Energy Density Physics and Technology, Ministry of Education, Sichuan University, Chengdu 610065, People’s Republic of China
| | - Zhifan Wang
- College of Chemistry and Life Science, Chengdu Normal University, Chengdu 611130, People’s Republic of China
| | - Fan Wang
- Institute of Atomic and Molecular Physics, Key Laboratory of High Energy Density Physics and Technology, Ministry of Education, Sichuan University, Chengdu 610065, People’s Republic of China
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15
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Schattenberg CJ, Kaupp M. Extended Benchmark Set of Main-Group Nuclear Shielding Constants and NMR Chemical Shifts and Its Use to Evaluate Modern DFT Methods. J Chem Theory Comput 2021; 17:7602-7621. [PMID: 34797677 DOI: 10.1021/acs.jctc.1c00919] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
An extended theoretical benchmark set, NS372, for light main-group nuclear shieldings and NMR shifts has been constructed based on high-level GIAO-CCSD(T)/pcSseg-3//CCSD(T)/cc-pVQZ reference data. After removal of the large static-correlation cases O3, F3-, and BH from the statistical evaluations for the 17O, 19F, and 11B subsets, the benchmark comprises overall 372 shielding values in 117 molecules with a wide range of electronic-structure situations, containing 124 1H, 14 11B, 93 13C, 43 15N, 31 17O, 47 19F, 14 31P, and 6 33S shielding constants. The CCSD(T)/pcSseg-3 data are shown to be close to the basis-set and method limit and thus provide an excellent benchmark to evaluate more approximate methods, such as density functional approaches. This dataset has been used to evaluate Hartree-Fock (HF) and MP2, and a wide range of exchange-correlation functionals from local density approximation (LDA) to generalized gradient approximations (GGAs) and meta-GGAs (focusing on their current-density functional implementations), as well as global hybrid, range-separated hybrid, local hybrid, and double-hybrid functionals. Starting with absolute shielding constants, the DSD-PBEP86 double hybrid is confirmed to provide the highest accuracy, with an aggregate relative mean absolute error (rel. MAE) of only 0.9%, followed by MP2 (1.1%). MP2 and double hybrids only show larger errors for a few systems with the largest static-correlation effects. The double-hybrid B2GP-PLYP, the two local hybrids cLH12ct-SsirPW92 and cLH12ct-SsifPW92, and the current-density functional meta-GGA cB97M-V follow closely behind (all 1.5%), as do some further functionals, cLH20t and cMN15-L (both 1.6%), as well as B2PLYP and KT3 (both 2.0%). Functionals on the lower rungs of the usual ladder offer the advantage of lower computational cost and access to larger molecules. Closer examination also reveals the best-performing methods for individual nuclei in the test set. Different ways of treating τ-dependent functionals are evaluated. When moving from absolute shielding constants to chemical shifts, some of the methods can benefit from systematic error compensation, and the overall error range somewhat narrows. Further methods now achieve the 2% threshold of relative MAEs, including functionals based on TPSS (TPSSh, cmPSTS).
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Affiliation(s)
- Caspar Jonas Schattenberg
- Technische Universität Berlin, Institut für Chemie, Theoretische Chemie/Quantenchemie, Sekr. C7, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Martin Kaupp
- Technische Universität Berlin, Institut für Chemie, Theoretische Chemie/Quantenchemie, Sekr. C7, Straße des 17. Juni 135, D-10623 Berlin, Germany
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16
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Gillhuber S, Franzke YJ, Weigend F. Paramagnetic NMR Shielding Tensors and Ring Currents: Efficient Implementation and Application to Heavy Element Compounds. J Phys Chem A 2021; 125:9707-9723. [PMID: 34723533 DOI: 10.1021/acs.jpca.1c07793] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present an efficient implementation of paramagnetic NMR shielding tensors and shifts in a nonrelativistic and scalar-relativistic density functional theory framework. For the latter, we make use of the scalar exact two-component Hamiltonian in its local approximation, and generally we apply the well established (multipole-accelerated) resolution of the identity approximation and the seminumerical exchange approximation. The perturbed density matrix of a paramagnetic NMR shielding calculation is further used to study the magnetically induced current density and ring currents of open-shell systems as illustrated for [U@Bi12]3-. [U@Bi12]3- features delocalized highest occupied molecular orbitals and sustains a net diatropic ring current of ca. 18 nA/T through the Bi12 torus similar to the all-metal aromatic heavy-element cluster [Th@Bi12]4-.
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Affiliation(s)
- Sebastian Gillhuber
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
| | - Yannick J Franzke
- Fachbereich Chemie, Philipps-Universität Marburg, 35032 Marburg, Germany
| | - Florian Weigend
- Fachbereich Chemie, Philipps-Universität Marburg, 35032 Marburg, Germany
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17
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Alagöz Y, Ünal A, Bozkaya U. Efficient implementations of the symmetric and asymmetric triple excitation corrections for the orbital-optimized coupled-cluster doubles method with the density-fitting approximation. J Chem Phys 2021; 155:114104. [PMID: 34551547 DOI: 10.1063/5.0061351] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Efficient implementations of the symmetric and asymmetric triple excitation corrections for the orbital-optimized coupled-cluster doubles (OCCD) method with the density-fitting approach, denoted by DF-OCCD(T) and DF-OCCD(T)Λ, are presented. The computational cost of the DF-OCCD(T) method is compared with that of the conventional OCCD(T). In the conventional OCCD(T) and OCCD(T)Λ methods, one needs to perform four-index integral transformations at each coupled-cluster doubles iterations, which limits its applications to large chemical systems. Our results demonstrate that DF-OCCD(T) provides dramatically lower computational costs compared to OCCD(T), and there are more than 68-fold reductions in the computational time for the C5H12 molecule with the cc-pVTZ basis set. Our results show that the DF-OCCD(T) and DF-OCCD(T)Λ methods are very helpful for the study of single bond-breaking problems. Performances of the DF-OCCD(T) and DF-OCCD(T)Λ methods are noticeably better than that of the coupled-cluster singles and doubles with perturbative triples [CCSD(T)] method for the potential energy surfaces of the molecules considered. Specifically, the DF-OCCD(T)Λ method provides dramatic improvements upon CCSD(T), and there are 8-14-fold reductions in nonparallelity errors. Overall, we conclude that the DF-OCCD(T)Λ method is very promising for the study of challenging chemical systems, where the CCSD(T) fails.
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Affiliation(s)
- Yavuz Alagöz
- Department of Chemistry, Hacettepe University, Ankara 06800, Turkey
| | - Aslı Ünal
- Department of Chemistry, Hacettepe University, Ankara 06800, Turkey
| | - Uğur Bozkaya
- Department of Chemistry, Hacettepe University, Ankara 06800, Turkey
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18
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Topological Analysis of Magnetically Induced Current Densities in Strong Magnetic Fields Using Stagnation Graphs. CHEMISTRY 2021. [DOI: 10.3390/chemistry3030067] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Stagnation graphs provide a useful tool to analyze the main topological features of the often complicated vector field associated with magnetically induced currents. Previously, these graphs have been constructed using response quantities appropriate for modest applied magnetic fields. We present an implementation capable of producing these graphs in arbitrarily strong magnetic fields, using current-density-functional theory. This enables us to study how the topology of the current vector field changes with the strength and orientation of the applied magnetic field. Applications to CH4, C2H2 and C2H4 are presented. In each case, we consider molecular geometries optimized in the presence of the magnetic field. The stagnation graphs reveal subtle changes to this vector field where the symmetry of the molecule remains constant. However, when the electronic state and symmetry of the corresponding equilibrium geometry changes with increasing field strength, the changes to the stagnation graph are extensive. We expect that the approach presented here will be helpful in interpreting changes in molecular structure and bonding in the strong-field regime.
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19
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Burger S, Lipparini F, Gauss J, Stopkowicz S. NMR chemical shift computations at second-order Møller-Plesset perturbation theory using gauge-including atomic orbitals and Cholesky-decomposed two-electron integrals. J Chem Phys 2021; 155:074105. [PMID: 34418917 DOI: 10.1063/5.0059633] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
We report on a formulation and implementation of a scheme to compute nuclear magnetic resonance (NMR) shieldings at second-order Møller-Plesset (MP2) perturbation theory using gauge-including atomic orbitals (GIAOs) to ensure gauge-origin independence and Cholesky decomposition (CD) to handle unperturbed and perturbed two-electron integrals. We investigate the accuracy of the CD for the derivatives of the two-electron integrals with respect to an external magnetic field and for the computed NMR shieldings, before we illustrate the applicability of our CD-based GIAO-MP2 scheme in calculations involving up to about 100 atoms and more than 1000 basis functions.
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Affiliation(s)
- Sophia Burger
- Department Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Jürgen Gauss
- Department Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany
| | - Stella Stopkowicz
- Department Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany
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20
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Liu J, Cheng L. Relativistic coupled‐cluster and equation‐of‐motion coupled‐cluster methods. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1536] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Junzi Liu
- Department of Chemistry The Johns Hopkins University Baltimore Maryland USA
| | - Lan Cheng
- Department of Chemistry The Johns Hopkins University Baltimore Maryland USA
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21
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Liu J, Zheng X, Asthana A, Zhang C, Cheng L. Analytic evaluation of energy first derivatives for spin-orbit coupled-cluster singles and doubles augmented with noniterative triples method: General formulation and an implementation for first-order properties. J Chem Phys 2021; 154:064110. [PMID: 33588557 DOI: 10.1063/5.0038779] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A formulation of analytic energy first derivatives for the coupled-cluster singles and doubles augmented with noniterative triples [CCSD(T)] method with spin-orbit coupling included at the orbital level and an implementation for evaluation of first-order properties are reported. The standard density-matrix formulation for analytic CC gradient theory adapted to complex algebra has been used. The orbital-relaxation contributions from frozen core, occupied, virtual, and frozen virtual orbitals to analytic spin-orbit CCSD(T) gradients are fully taken into account and treated efficiently, which is of importance to calculations of heavy elements. Benchmark calculations of first-order properties including dipole moments and electric-field gradients using the corresponding exact two-component property integrals are presented for heavy-element containing molecules to demonstrate the applicability and usefulness of the present analytic scheme.
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Affiliation(s)
- Junzi Liu
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Xuechen Zheng
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Ayush Asthana
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Chaoqun Zhang
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Lan Cheng
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, USA
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22
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Bozkaya U, Ünal A, Alagöz Y. Energy and analytic gradients for the orbital-optimized coupled-cluster doubles method with the density-fitting approximation: An efficient implementation. J Chem Phys 2020; 153:244115. [PMID: 33380091 DOI: 10.1063/5.0035811] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Efficient implementations of the orbital-optimized coupled-cluster doubles (or simply "optimized CCD," OCCD, for short) method and its analytic energy gradients with the density-fitting (DF) approach, denoted by DF-OCCD, are presented. In addition to the DF approach, the Cholesky-decomposed variant (CD-OCCD) is also implemented for energy computations. The computational cost of the DF-OCCD method (available in a plugin version of the DFOCC module of PSI4) is compared with that of the conventional OCCD (from the Q-CHEM package). The OCCD computations were performed with the Q-CHEM package in which OCCD are denoted by OD. In the conventional OCCD method, one needs to perform four-index integral transformations at each of the CCD iterations, which limits its applications to large chemical systems. Our results demonstrate that DF-OCCD provides dramatically lower computational costs compared to OCCD, and there are almost eightfold reductions in the computational time for the C6H14 molecule with the cc-pVTZ basis set. For open-shell geometries, interaction energies, and hydrogen transfer reactions, DF-OCCD provides significant improvements upon DF-CCD. Furthermore, the performance of the DF-OCCD method is substantially better for harmonic vibrational frequencies in the case of symmetry-breaking problems. Moreover, several factors make DF-OCCD more attractive compared to CCSD: (1) for DF-OCCD, there is no need for orbital relaxation contributions in analytic gradient computations; (2) active spaces can readily be incorporated into DF-OCCD; (3) DF-OCCD provides accurate vibrational frequencies when symmetry-breaking problems are observed; (4) in its response function, DF-OCCD avoids artificial poles; hence, excited-state molecular properties can be computed via linear response theory; and (5) symmetric and asymmetric triples corrections based on DF-OCCD [DF-OCCD(T)] have a significantly better performance in near degeneracy regions.
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Affiliation(s)
- Uğur Bozkaya
- Department of Chemistry, Hacettepe University, Ankara 06800, Turkey
| | - Aslı Ünal
- Department of Chemistry, Hacettepe University, Ankara 06800, Turkey
| | - Yavuz Alagöz
- Department of Chemistry, Hacettepe University, Ankara 06800, Turkey
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23
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Chandy SK, Thapa B, Raghavachari K. Accurate and cost-effective NMR chemical shift predictions for proteins using a molecules-in-molecules fragmentation-based method. Phys Chem Chem Phys 2020; 22:27781-27799. [PMID: 33244526 DOI: 10.1039/d0cp05064d] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have developed an efficient protocol using our two-layer Molecules-in-Molecules (MIM2) fragmentation-based quantum chemical method for the prediction of NMR chemical shifts of large biomolecules. To investigate the performance of our fragmentation approach and demonstrate its applicability, MIM-NMR calculations are first calibrated on a test set of six proteins. The MIM2-NMR method yields a mean absolute deviation (MAD) from unfragmented full molecule calculations of 0.01 ppm for 1H and 0.06 ppm for 13C chemical shifts. Thus, the errors from fragmentation are only about 3% of our target accuracy of ∼0.3 ppm for 1H and 2-3 ppm for 13C chemical shifts. To compare with experimental chemical shifts, a standard protocol is first derived using two smaller proteins 2LHY (176 atoms) and 2LI1 (146 atoms) for obtaining an appropriate protein structure for NMR chemical shift calculations. The effect of the solvent environment on the calculated NMR chemical shifts is incorporated through implicit, explicit, or explicit-implicit solvation models. The expensive first solvation shell calculations are replaced by a micro-solvation model in which only the immediate interaction between the protein and the explicit solvation environment is considered. A single explicit water molecule for each amine and amide proton is found to be sufficient to yield accurate results for 1H chemical shifts. The 1H and 13C NMR chemical shifts calculated using our protocol give excellent agreement with experiments for two larger proteins, 2MC5 (the helical part with 265 atoms) and 3UMK (33 residue slice with 547 atoms). Overall, our target accuracy of ∼0.3 ppm for 1H and ∼2-3 ppm for 13C has been achieved for the larger proteins. The proposed MIM-NMR method is accurate and computationally cost-effective and should be applicable to study a wide range of large proteins.
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Affiliation(s)
- Sruthy K Chandy
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA.
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24
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Guo M, Wang Z, Wang F. Equation-of-motion coupled-cluster theory for double electron attachment with spin-orbit coupling. J Chem Phys 2020; 153:214118. [PMID: 33291924 DOI: 10.1063/5.0032716] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We report implementation of the equation-of-motion coupled-cluster (EOM-CC) method for double electron-attachment (DEA) with spin-orbit coupling (SOC) at the CC singles and doubles (CCSD) level using a closed-shell reference in this work. The DEA operator employed in this work contains two-particle and three-particle one-hole excitations, and SOC is included in post-Hartree-Fock treatment. Time-reversal symmetry and spatial symmetry are exploited to reduce computational cost. The EOM-DEA-CCSD method with SOC allows us to investigate SOC effects of systems with two-unpaired electrons. According to our results on atoms, double ionization potentials (DIPs), excitation energies (EEs), and SO splittings of low-lying states are calculated reliably using the EOM-DEA-CCSD method with SOC. Its accuracy is usually higher than that of EOM-CCSD for EEs or DIPs if the same target can be reached from single excitations by choosing a proper closed-shell reference. However, performance of the EOM-DEA-CCSD method with SOC on molecules is not as good as that for atoms. Bond lengths for the ground and the several lowest excited states of GaH, InH, and TlH are underestimated pronouncedly, although reasonable EEs are obtained, and splittings of the 3Σ- state from the π2 configuration are calculated to be too small with EOM-DEA-CCSD.
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Affiliation(s)
- Minggang Guo
- Institute of Atomic and Molecular Physics, Key Laboratory of High Energy Density Physics and Technology, Ministry of Education, Sichuan University, Chengdu 610065, People's Republic of China
| | - Zhifan Wang
- College of Chemistry and Life Science, Chengdu Normal University, Chengdu 611130, People's Republic of China
| | - Fan Wang
- Institute of Atomic and Molecular Physics, Key Laboratory of High Energy Density Physics and Technology, Ministry of Education, Sichuan University, Chengdu 610065, People's Republic of China
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25
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Dittmer A, Stoychev GL, Maganas D, Auer AA, Neese F. Computation of NMR Shielding Constants for Solids Using an Embedded Cluster Approach with DFT, Double-Hybrid DFT, and MP2. J Chem Theory Comput 2020; 16:6950-6967. [PMID: 32966067 PMCID: PMC7659039 DOI: 10.1021/acs.jctc.0c00067] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
In
this work, we explore the accuracy of post-Hartree–Fock
(HF) methods and double-hybrid density functional theory (DFT) for
the computation of solid-state NMR chemical shifts. We apply an embedded
cluster approach and investigate the convergence with cluster size
and embedding for a series of inorganic solids with long-range electrostatic
interactions. In a systematic study, we discuss the cluster design,
the embedding procedure, and basis set convergence using gauge-including
atomic orbital (GIAO) NMR calculations at the DFT and MP2 levels of
theory. We demonstrate that the accuracy obtained for the prediction
of NMR chemical shifts, which can be achieved for molecular systems,
can be carried over to solid systems. An appropriate embedded cluster
approach allows one to apply methods beyond standard DFT even for
systems for which long-range electrostatic effects are important. We find that an embedded
cluster should include at least one sphere of explicit neighbors around
the nuclei of interest, given that a sufficiently large point charge
and boundary effective potential embedding is applied. Using the pcSseg-3
basis set and GIAOs for the computation of nuclear shielding constants,
accuracies of 1.6 ppm for 7Li, 1.5 ppm for 23Na, and 5.1 ppm for 39K as well as 9.3 ppm for 19F, 6.5 ppm for 35Cl, 7.4 ppm for 79Br, and
7.5 ppm for 25Mg as well as 3.8 ppm for 67Zn
can be achieved with MP2. Comparing various DFT functionals with HF
and MP2, we report the superior quality of results for methods that
include post-HF correlation like MP2 and double-hybrid DFT.
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Affiliation(s)
- Anneke Dittmer
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Georgi L Stoychev
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Dimitrios Maganas
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Alexander A Auer
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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26
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Dietschreit JCB, Wagner A, Le TA, Klein P, Schindelin H, Opatz T, Engels B, Hellmich UA, Ochsenfeld C. Predicting
19
F NMR Chemical Shifts: A Combined Computational and Experimental Study of a Trypanosomal Oxidoreductase–Inhibitor Complex. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202000539] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Johannes C. B. Dietschreit
- Theoretical Chemistry Department of Chemistry University of Munich (LMU) Butenandtstr. 7 81377 Munich Germany
| | - Annika Wagner
- Dept. Chemistry Section Biochemistry Johannes Gutenberg-Universität Mainz 55128 Mainz Germany
- Centre for Biomolecular Magnetic Resonance (BMRZ) Goethe-University Frankfurt Max-von-Laue Str. 9 60438 Frankfurt Germany
| | - T. Anh Le
- Institute for Physical and Theoretical Chemistry University of Würzburg Emil-Fischer-Straße 42 97074 Würzburg Germany
| | - Philipp Klein
- Dept. Chemistry Section Organic Chemistry Johannes Gutenberg-Universität Mainz 55128 Mainz Germany
| | - Hermann Schindelin
- Institute of Structural Biology Rudolf Virchow Center for Experimental Biomedicine University of Würzburg 97080 Würzburg Germany
| | - Till Opatz
- Dept. Chemistry Section Organic Chemistry Johannes Gutenberg-Universität Mainz 55128 Mainz Germany
| | - Bernd Engels
- Institute for Physical and Theoretical Chemistry University of Würzburg Emil-Fischer-Straße 42 97074 Würzburg Germany
| | - Ute A. Hellmich
- Dept. Chemistry Section Biochemistry Johannes Gutenberg-Universität Mainz 55128 Mainz Germany
- Centre for Biomolecular Magnetic Resonance (BMRZ) Goethe-University Frankfurt Max-von-Laue Str. 9 60438 Frankfurt Germany
| | - Christian Ochsenfeld
- Theoretical Chemistry Department of Chemistry University of Munich (LMU) Butenandtstr. 7 81377 Munich Germany
- Max Planck Institute for Solid State Research 70569 Stuttgart Germany
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27
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Dietschreit JCB, Wagner A, Le TA, Klein P, Schindelin H, Opatz T, Engels B, Hellmich UA, Ochsenfeld C. Predicting 19 F NMR Chemical Shifts: A Combined Computational and Experimental Study of a Trypanosomal Oxidoreductase-Inhibitor Complex. Angew Chem Int Ed Engl 2020; 59:12669-12673. [PMID: 32239740 PMCID: PMC7496126 DOI: 10.1002/anie.202000539] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/22/2020] [Indexed: 02/02/2023]
Abstract
The absence of fluorine from most biomolecules renders it an excellent probe for NMR spectroscopy to monitor inhibitor-protein interactions. However, predicting the binding mode of a fluorinated ligand from a chemical shift (or vice versa) has been challenging due to the high electron density of the fluorine atom. Nonetheless, reliable 19 F chemical-shift predictions to deduce ligand-binding modes hold great potential for in silico drug design. Herein, we present a systematic QM/MM study to predict the 19 F NMR chemical shifts of a covalently bound fluorinated inhibitor to the essential oxidoreductase tryparedoxin (Tpx) from African trypanosomes, the causative agent of African sleeping sickness. We include many protein-inhibitor conformations as well as monomeric and dimeric inhibitor-protein complexes, thus rendering it the largest computational study on chemical shifts of 19 F nuclei in a biological context to date. Our predicted shifts agree well with those obtained experimentally and pave the way for future work in this area.
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Affiliation(s)
| | - Annika Wagner
- Dept. ChemistrySection BiochemistryJohannes Gutenberg-Universität Mainz55128MainzGermany
- Centre for Biomolecular Magnetic Resonance (BMRZ)Goethe-University FrankfurtMax-von-Laue Str. 960438FrankfurtGermany
| | - T. Anh Le
- Institute for Physical and Theoretical ChemistryUniversity of WürzburgEmil-Fischer-Straße 4297074WürzburgGermany
| | - Philipp Klein
- Dept. ChemistrySection Organic ChemistryJohannes Gutenberg-Universität Mainz55128MainzGermany
| | - Hermann Schindelin
- Institute of Structural BiologyRudolf Virchow Center for Experimental BiomedicineUniversity of Würzburg97080WürzburgGermany
| | - Till Opatz
- Dept. ChemistrySection Organic ChemistryJohannes Gutenberg-Universität Mainz55128MainzGermany
| | - Bernd Engels
- Institute for Physical and Theoretical ChemistryUniversity of WürzburgEmil-Fischer-Straße 4297074WürzburgGermany
| | - Ute A. Hellmich
- Dept. ChemistrySection BiochemistryJohannes Gutenberg-Universität Mainz55128MainzGermany
- Centre for Biomolecular Magnetic Resonance (BMRZ)Goethe-University FrankfurtMax-von-Laue Str. 960438FrankfurtGermany
| | - Christian Ochsenfeld
- Theoretical ChemistryDepartment of ChemistryUniversity of Munich (LMU)Butenandtstr. 781377MunichGermany
- Max Planck Institute for Solid State Research70569StuttgartGermany
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28
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Bodenstein T, Kvaal S. A state-specific multireference coupled-cluster method based on the bivariational principle. J Chem Phys 2020; 153:024106. [PMID: 32668937 DOI: 10.1063/5.0009429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
A state-specific multireference coupled-cluster (MRCC) method based on Arponen's bivariational principle is presented, the bivar-MRCC method. The method is based on single-reference theory and therefore has a relatively straightforward formulation and modest computational complexity. The main difference from established methods is the bivariational formulation, in which independent parameterizations of the wave function (ket) and its complex conjugate (bra) are made. Importantly, this allows manifest multiplicative separability of the state (exact in the extended bivar-MRECC version of the method and approximate otherwise), and additive separability of the energy, while preserving polynomial scaling of the working equations. A feature of the bivariational principle is that the formal bra and ket references can be included as bivariational parameters, which eliminates much of the bias toward the formal reference. A pilot implementation is described, and extensive benchmark calculations on several standard problems are performed. The results from the bivar-MRCC method are comparable to established state-specific multireference methods. Considering the relative affordability of the bivar-MRCC method, it may become a practical tool for non-experts.
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Affiliation(s)
- Tilmann Bodenstein
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, N-0315 Oslo, Norway
| | - Simen Kvaal
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, N-0315 Oslo, Norway
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29
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Prokopiou G, Autschbach J, Kronik L. Assessment of the Performance of Optimally Tuned Range‐Separated Hybrid Functionals for Nuclear Magnetic Shielding Calculations. ADVANCED THEORY AND SIMULATIONS 2020. [DOI: 10.1002/adts.202000083] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Georgia Prokopiou
- Department of Materials and InterfacesWeizmann Institute of ScienceRehovot 76100 Israel
| | - Jochen Autschbach
- Department of ChemistryState University of New York at BuffaloBuffalo NY 14260‐3000 USA
| | - Leeor Kronik
- Department of Materials and InterfacesWeizmann Institute of ScienceRehovot 76100 Israel
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30
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White AF, Kin-Lic Chan G. Finite-temperature coupled cluster: Efficient implementation and application to prototypical systems. J Chem Phys 2020; 152:224104. [DOI: 10.1063/5.0009845] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Affiliation(s)
- Alec F. White
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Garnet Kin-Lic Chan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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31
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Matthews DA, Cheng L, Harding ME, Lipparini F, Stopkowicz S, Jagau TC, Szalay PG, Gauss J, Stanton JF. Coupled-cluster techniques for computational chemistry: The CFOUR program package. J Chem Phys 2020; 152:214108. [DOI: 10.1063/5.0004837] [Citation(s) in RCA: 214] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Devin A. Matthews
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, USA
| | - Lan Cheng
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Michael E. Harding
- Institut für Physikalische Chemie, Karlsruher Institut für Technologie (KIT), Kaiserstr. 12, D-76131 Karlsruhe, Germany
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Stella Stopkowicz
- Department Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany
| | - Thomas-C. Jagau
- Department of Chemistry, University of Munich (LMU), Butenandtstr. 5-13, D-81377 Munich, Germany
| | - Péter G. Szalay
- ELTE Eötvös Loránd University, Institute of Chemistry, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary
| | - Jürgen Gauss
- Department Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany
| | - John F. Stanton
- Quantum Theory Project, Departments of Chemistry and Physics, University of Florida, Gainesville, Florida 32611, USA
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32
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Gräfenstein J. Efficient calculation of NMR isotopic shifts: Difference-dedicated vibrational perturbation theory. J Chem Phys 2019; 151:244120. [PMID: 31893883 DOI: 10.1063/1.5134538] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
We present difference-dedicated second-order vibrational perturbation theory (VPT2) as an efficient method for the computation of nuclear magnetic resonance (NMR) isotopic shifts, which reflect the geometry dependence of the NMR property in combination with different vibration patterns of two isotopologues. Conventional calculations of isotopic shifts, e.g., by standard VPT2, require scanning the geometry dependence over the whole molecule, which becomes expensive rapidly as the molecule size increases. In DD-VPT2, this scan can be restricted to a small region around the substitution site. At the heart of DD-VPT2 is a set of localized vibration modes common to the two isotopologues and designed such that the difference between the vibration patterns is caught by a small subset of them (usually fewer than 10). We tested the DD-VPT2 method for a series of molecules with increasing size and found that this method provides results with the same quality as VPT2 and in good agreement with the experiment, with computational savings up to 95% and less numerical instabilities. The method is easy to automatize and straightforward to generalize to other molecular properties.
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Affiliation(s)
- Jürgen Gräfenstein
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96 Göteborg, Sweden
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33
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Koulias LN, Williams-Young DB, Nascimento DR, DePrince AE, Li X. Relativistic Real-Time Time-Dependent Equation-of-Motion Coupled-Cluster. J Chem Theory Comput 2019; 15:6617-6624. [DOI: 10.1021/acs.jctc.9b00729] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lauren N. Koulias
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - David B. Williams-Young
- Computational Research Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road MS 50A-3111, Berkeley, California 94720, United States
| | - Daniel R. Nascimento
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | - A. Eugene DePrince
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | - Xiaosong Li
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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34
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Zhou X, Cao Z, Wang F. Analytical energy gradients for ionized states using equation-of-motion coupled-cluster theory with spin-orbit coupling. J Chem Phys 2019; 150:154114. [PMID: 31005096 DOI: 10.1063/1.5088639] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Spin-orbit coupling (SOC) may have a significant effect on the structure and harmonic frequencies of particularly heavy p-block element compounds. However, reports on analytical energy gradients with SOC are scarce, especially for excited states. In this work, we implemented analytical energy gradients for ionized states using the equation-of-motion coupled-cluster (CC) theory at the CC singles and doubles level (EOM-IP-CCSD) with SOC. Effects of SOC on structure and harmonic frequencies as well as properties for both the ground and some excited states of open-shell compounds with one unpaired electron can be investigated efficiently with the present implementation. A closed-shell reference is required in the calculations, and SOC is included in post-Hartree-Fock treatment. Relativistic effective core potentials are employed in dealing with both scalar relativistic effects and SOC, and we treat perturbations that are even under time reversal in this work. Both time-reversal symmetry and double point group symmetry for D2h * and its subgroups are exploited in the implementation. The method is applicable to states which can be reached by removing one electron from a closed-shell reference state. The results of some open-shell cations indicate the importance of SOC on structures and harmonic frequencies of heavy element compounds.
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Affiliation(s)
- Xiaojun Zhou
- Institute of Atomic and Molecular Physics, Key Laboratory of High Energy Density Physics and Technology, Ministry of Education, Sichuan University, Chengdu, People's Republic of China
| | - Zhanli Cao
- School of Science, Xi'an University of Posts and Telecommunications, Xi'an 710121, People's Republic of China
| | - Fan Wang
- Institute of Atomic and Molecular Physics, Key Laboratory of High Energy Density Physics and Technology, Ministry of Education, Sichuan University, Chengdu, People's Republic of China
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35
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Asthana A, Liu J, Cheng L. Exact two-component equation-of-motion coupled-cluster singles and doubles method using atomic mean-field spin-orbit integrals. J Chem Phys 2019; 150:074102. [DOI: 10.1063/1.5081715] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Ayush Asthana
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Junzi Liu
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Lan Cheng
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, USA
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36
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Shee A, Saue T, Visscher L, Severo Pereira Gomes A. Equation-of-motion coupled-cluster theory based on the 4-component Dirac–Coulomb(–Gaunt) Hamiltonian. Energies for single electron detachment, attachment, and electronically excited states. J Chem Phys 2018; 149:174113. [DOI: 10.1063/1.5053846] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Avijit Shee
- Department of Chemistry, University of Michigan, 930 N. University, Ann Arbor, Michigan 48109-1055, USA
- Université de Lille, CNRS, UMR 8523—PhLAM—Physique des Lasers, Atomes et Molécules, F-59000 Lille, France
| | - Trond Saue
- Laboratoire de Chimie et Physique Quantiques, UMR 5626 CNRS—Université Toulouse III–Paul Sabatier, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Lucas Visscher
- Division of Theoretical Chemistry, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - André Severo Pereira Gomes
- Université de Lille, CNRS, UMR 8523—PhLAM—Physique des Lasers, Atomes et Molécules, F-59000 Lille, France
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37
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Rusakov YY, Rusakova IL. Relativistic heavy atom effect on 13 C NMR chemical shifts initiated by adjacent multiple chalcogens. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2018; 56:716-726. [PMID: 29412478 DOI: 10.1002/mrc.4720] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 01/21/2018] [Accepted: 01/23/2018] [Indexed: 06/08/2023]
Abstract
In this paper, we have investigated the cumulative peculiarity of the "heavy atom on light atom" effect on the 13 C NMR chemical shifts, initiated by the adjacent chalcogens. For this purpose, the most accurate hybrid computational scheme for the calculation of chemical shifts of carbon nuclei, directly bonded with several heavy chalcogens, is introduced and attested on the representative series of molecules. The best hybrid scheme combines the nonrelativistic coupled cluster-based approach with the different types of corrections, including vibrational, solvent, and relativistic. The dependences of the total relativistic corrections to carbon shielding constants in 2 series of model compounds, namely, X═13 C═Y (X, Y = O, S, Se, Te) and C(XH)m (YH)n (ZH)p (QH)s H1-m H1-n H1-p H1-s (X, Y, Z, Q = S, Se, Te and m, n, p, s = 0, 1), on the total atomic number of the adjacent chalcogens have been obtained.
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Affiliation(s)
- Yu Yu Rusakov
- A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033, Irkutsk, Russia
| | - I L Rusakova
- A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033, Irkutsk, Russia
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38
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Berkelbach TC. Communication: Random-phase approximation excitation energies from approximate equation-of-motion coupled-cluster doubles. J Chem Phys 2018; 149:041103. [DOI: 10.1063/1.5032314] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Timothy C. Berkelbach
- Department of Chemistry and James Franck Institute, University of Chicago, Chicago, Illinois 60637, USA
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39
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Stoychev GL, Auer AA, Neese F. Efficient and Accurate Prediction of Nuclear Magnetic Resonance Shielding Tensors with Double-Hybrid Density Functional Theory. J Chem Theory Comput 2018; 14:4756-4771. [DOI: 10.1021/acs.jctc.8b00624] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Georgi L. Stoychev
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr 45470, Germany
| | - Alexander A. Auer
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr 45470, Germany
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr 45470, Germany
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40
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Samanta PK, Blunt NS, Booth GH. Response Formalism within Full Configuration Interaction Quantum Monte Carlo: Static Properties and Electrical Response. J Chem Theory Comput 2018; 14:3532-3546. [DOI: 10.1021/acs.jctc.8b00454] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pradipta Kumar Samanta
- Institut für Theoretische Chemie, Universität Stuttgart, D-70569 Stuttgart, Germany
- Max Planck Institute for Solid State Research, D-70569 Stuttgart, Germany
| | - Nick S. Blunt
- University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - George H. Booth
- Department of Physics, King’s College London, Strand, London WC2R 2LS, United Kingdom
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41
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Bozkaya U, Sherrill CD. Analytic energy gradients for the coupled-cluster singles and doubles with perturbative triples method with the density-fitting approximation. J Chem Phys 2018; 147:044104. [PMID: 28764345 DOI: 10.1063/1.4994918] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
An efficient implementation of analytic gradients for the coupled-cluster singles and doubles with perturbative triples [CCSD(T)] method with the density-fitting (DF) approximation, denoted as DF-CCSD(T), is reported. For the molecules considered, the DF approach substantially accelerates conventional CCSD(T) analytic gradients due to the reduced input/output time and the acceleration of the so-called "gradient terms": formation of particle density matrices (PDMs), computation of the generalized Fock-matrix (GFM), solution of the Z-vector equation, formation of the effective PDMs and GFM, back-transformation of the PDMs and GFM, from the molecular orbital to the atomic orbital (AO) basis, and computation of gradients in the AO basis. For the largest member of the molecular test set considered (C6H14), the computational times for analytic gradients (with the correlation-consistent polarized valence triple-ζ basis set in serial) are 106.2 [CCSD(T)] and 49.8 [DF-CCSD(T)] h, a speedup of more than 2-fold. In the evaluation of gradient terms, the DF approach completely avoids the use of four-index two-electron integrals. Similar to our previous studies on DF-second-order Møller-Plesset perturbation theory and DF-CCSD gradients, our formalism employs 2- and 3-index two-particle density matrices (TPDMs) instead of 4-index TPDMs. Errors introduced by the DF approximation are negligible for equilibrium geometries and harmonic vibrational frequencies.
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Affiliation(s)
- Uğur Bozkaya
- Department of Chemistry, Hacettepe University, Ankara 06800, Turkey
| | - C David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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42
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Morzan UN, Alonso de Armiño DJ, Foglia NO, Ramírez F, González Lebrero MC, Scherlis DA, Estrin DA. Spectroscopy in Complex Environments from QM–MM Simulations. Chem Rev 2018; 118:4071-4113. [DOI: 10.1021/acs.chemrev.8b00026] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Uriel N. Morzan
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Diego J. Alonso de Armiño
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Nicolás O. Foglia
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Francisco Ramírez
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Mariano C. González Lebrero
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Damián A. Scherlis
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Darío A. Estrin
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
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43
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Wang Z, Wang F. Equation-of-motion coupled-cluster method for ionised states with spin-orbit coupling using open-shell reference wavefunction. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1439188] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Zhifan Wang
- School of Electronic Engineering, Chengdu Technological University, Chengdu, P. R.China
| | - Fan Wang
- Institute of Atomic and Molecular Physics, Sichuan University, Chengdu, P. R. China
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44
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Stoychev GL, Auer AA, Izsák R, Neese F. Self-Consistent Field Calculation of Nuclear Magnetic Resonance Chemical Shielding Constants Using Gauge-Including Atomic Orbitals and Approximate Two-Electron Integrals. J Chem Theory Comput 2018; 14:619-637. [DOI: 10.1021/acs.jctc.7b01006] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Georgi L. Stoychev
- Max Planck Institute for Chemical Energy Conversion, 45470 Mülheim an der Ruhr, Germany
| | - Alexander A. Auer
- Max Planck Institute for Chemical Energy Conversion, 45470 Mülheim an der Ruhr, Germany
| | - Róbert Izsák
- Max Planck Institute for Chemical Energy Conversion, 45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max Planck Institute for Chemical Energy Conversion, 45470 Mülheim an der Ruhr, Germany
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45
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Liu J, Shen Y, Asthana A, Cheng L. Two-component relativistic coupled-cluster methods using mean-field spin-orbit integrals. J Chem Phys 2018; 148:034106. [DOI: 10.1063/1.5009177] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Junzi Liu
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Yue Shen
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Ayush Asthana
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Lan Cheng
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, USA
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46
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Martínez FA, Aucar GA. Intermolecular magnetic interactions in stacked DNA base pairs. Phys Chem Chem Phys 2017; 19:27817-27827. [PMID: 28990030 DOI: 10.1039/c7cp04484d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The influence of pi-stacking on the magnetic properties of atoms that belong to adenine-thymine and guanine-cytosine pairs in sequences of three and five layers of DNA base pairs was analysed. As probes we used NMR spectroscopic parameters, which are among the most useful tools to learn about the transmission of magnetic interactions in molecules. Four DFT functionals were employed: B3LYP, BHANDLYP, KT2 and KT3, together with the SOPPA method. Besides, given that the number of non-hydrogen atoms of the supramolecular systems studied here is larger than 50 we applied a locally dense basis set scheme. Our results show that the piling up of a few Watson-Crick base pairs above and below a given pair modifies its NMR spectroscopic parameters by an amount that may be measurable and the percentage of variation does not depend on dispersion. We found that magnetic shieldings are more sensitive than J-couplings, and also that some atoms are more sensitive than others. Stacking affects the shielding of non-hydrogen atoms like nitrogens, that are donors in hydrogen bonds, HBs, and the carbons bonded to them. The amount of variation of these shieldings was found to be from 2% to 5% when the pairs are considered first as isolated, and then, placed in the middle of a sequence of three layers of base pairs. Such a variation becomes vanishingly small when the sequence contains more than three layers, showing that the stacking effect on NMR spectroscopic parameters has a local nature. We have also found a pattern for shieldings. First, equivalent atoms of similar monomers (thymine and adenine, or guanine and cytosine) have similar values of absolute shieldings in isolated pairs, and the amount of variation from isolated pairs to aggregates of a few pairs is also similar, meaning that equivalent atoms are affected in a similar manner by pi-stacking. Second, the hydrogen atoms which belong to hydrogen bonds are more sensitive to the piling up than the non-hydrogen atoms.
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Affiliation(s)
- Fernando A Martínez
- Instituto de Modelado e Innovación Tecnológica, CONICET, and Departamento de Física - Facultad de Ciencias Exactas y Naturales, UNNE, Avda Libertad 5460, W3404AAS, Corrientes, Argentina.
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47
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Sun Q, Berkelbach TC, Blunt NS, Booth GH, Guo S, Li Z, Liu J, McClain JD, Sayfutyarova ER, Sharma S, Wouters S, Chan GK. P
y
SCF: the Python‐based simulations of chemistry framework. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1340] [Citation(s) in RCA: 529] [Impact Index Per Article: 75.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Qiming Sun
- Division of Chemistry and Chemical EngineeringCalifornia Institute of Technology Pasadena CA USA
| | - Timothy C. Berkelbach
- Department of Chemistry and James Franck InstituteUniversity of Chicago Chicago IL USA
| | - Nick S. Blunt
- Chemical Science DivisionLawrence Berkeley National Laboratory Berkeley CA USA
- Department of ChemistryUniversity of California Berkeley CA USA
| | - George H. Booth
- Department of PhysicsKing's College London, Strand London UK
| | - Sheng Guo
- Division of Chemistry and Chemical EngineeringCalifornia Institute of Technology Pasadena CA USA
- Department of ChemistryPrinceton University Princeton NJ USA
| | - Zhendong Li
- Division of Chemistry and Chemical EngineeringCalifornia Institute of Technology Pasadena CA USA
| | - Junzi Liu
- Institute of Chemistry Chinese Academy of Sciences Beijing China
| | - James D. McClain
- Division of Chemistry and Chemical EngineeringCalifornia Institute of Technology Pasadena CA USA
- Department of ChemistryPrinceton University Princeton NJ USA
| | - Elvira R. Sayfutyarova
- Division of Chemistry and Chemical EngineeringCalifornia Institute of Technology Pasadena CA USA
- Department of ChemistryPrinceton University Princeton NJ USA
| | - Sandeep Sharma
- Department of Chemistry and BiochemistryUniversity of Colorado Boulder Boulder CO USA
| | | | - Garnet Kin‐Lic Chan
- Division of Chemistry and Chemical EngineeringCalifornia Institute of Technology Pasadena CA USA
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48
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Rusakov YY, Rusakova IL, Krivdin LB. On the significant relativistic heavy atom effect on 13C NMR chemical shifts of β- and γ-carbons in seleno- and telluroketones. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1350292] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Yuriy Yu. Rusakov
- A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russian Federation
| | - Irina L. Rusakova
- A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russian Federation
| | - Leonid B. Krivdin
- A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russian Federation
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Perera A, Gauss J, Verma P, Morales JA. Benchmark coupled-cluster g-tensor calculations with full inclusion of the two-particle spin-orbit contributions. J Chem Phys 2017; 146:164104. [PMID: 28456206 DOI: 10.1063/1.4979680] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
We present a parallel implementation to compute electron spin resonance g-tensors at the coupled-cluster singles and doubles (CCSD) level which employs the ACES III domain-specific software tools for scalable parallel programming, i.e., the super instruction architecture language and processor (SIAL and SIP), respectively. A unique feature of the present implementation is the exact (not approximated) inclusion of the five one- and two-particle contributions to the g-tensor [i.e., the mass correction, one- and two-particle paramagnetic spin-orbit, and one- and two-particle diamagnetic spin-orbit terms]. Like in a previous implementation with effective one-electron operators [J. Gauss et al., J. Phys. Chem. A 113, 11541-11549 (2009)], our implementation utilizes analytic CC second derivatives and, therefore, classifies as a true CC linear-response treatment. Therefore, our implementation can unambiguously appraise the accuracy of less costly effective one-particle schemes and provide a rationale for their widespread use. We have considered a large selection of radicals used previously for benchmarking purposes including those studied in earlier work and conclude that at the CCSD level, the effective one-particle scheme satisfactorily captures the two-particle effects less costly than the rigorous two-particle scheme. With respect to the performance of density functional theory (DFT), we note that results obtained with the B3LYP functional exhibit the best agreement with our CCSD results. However, in general, the CCSD results agree better with the experimental data than the best DFT/B3LYP results, although in most cases within the rather large experimental error bars.
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Affiliation(s)
- Ajith Perera
- Department of Chemistry and Biochemistry, Texas Tech University, P.O. Box 41061, Lubbock, Texas 79409-1061, USA
| | - Jürgen Gauss
- Institut für Physikalische Chemie, Universität Mainz, D-55099 Mainz, Germany
| | - Prakash Verma
- Department of Chemistry and Biochemistry, Texas Tech University, P.O. Box 41061, Lubbock, Texas 79409-1061, USA
| | - Jorge A Morales
- Department of Chemistry and Biochemistry, Texas Tech University, P.O. Box 41061, Lubbock, Texas 79409-1061, USA
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Babaei M, Jones IC, Dayal K, Mauter MS. Computing the Diamagnetic Susceptibility and Diamagnetic Anisotropy of Membrane Proteins from Structural Subunits. J Chem Theory Comput 2017; 13:2945-2953. [PMID: 28418668 DOI: 10.1021/acs.jctc.6b01251] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The behavior of large, complex molecules in the presence of magnetic fields is experimentally challenging to measure and computationally intensive to predict. This work proposes a novel, mixed-methods approach for efficiently computing the principal magnetic susceptibilities and diamagnetic anisotropy of membrane proteins. The hierarchical primary (amino acid), secondary (α helical and β sheet), and tertiary (α helix and β barrel) structure of transmembrane proteins enables analysis of a complex molecule using discrete subunits of varying size and resolution. The proposed method converts the magnetic susceptibility tensor for all protein subunits to a unit coordinate system and sums them to build the magnetic susceptibility tensor for the membrane protein. Using this approach, we calculate the diamagnetic anisotropy for all transmembrane proteins of known structure and investigate the effect of different subunit resolutions on the resulting predictions of diamagnetic anisotropy. We demonstrate that amino acid residues with aromatic side groups exhibit higher diamagnetic anisotropies. On average, high percentages of aromatic amino acid subunits, a β barrel tertiary structure, and a small volume are correlated with high volumetric diamagnetic anisotropy. Finally, we demonstrate that accounting for the spatial position of the residues with respect to one another is critical to accurately computing the magnetic properties of the complex protein molecule.
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Affiliation(s)
- Mahnoush Babaei
- Department of Civil and Environmental Engineering, Carnegie Mellon University , 5000 Forbes Ave., Pittsburgh, Pennsylvania 15213, United States
| | - Isaac C Jones
- Department of Civil and Environmental Engineering, Carnegie Mellon University , 5000 Forbes Ave., Pittsburgh, Pennsylvania 15213, United States
| | - Kaushik Dayal
- Department of Civil and Environmental Engineering, Carnegie Mellon University , 5000 Forbes Ave., Pittsburgh, Pennsylvania 15213, United States
| | - Meagan S Mauter
- Department of Civil and Environmental Engineering, Carnegie Mellon University , 5000 Forbes Ave., Pittsburgh, Pennsylvania 15213, United States.,Department of Engineering and Public Policy, Carnegie Mellon University , 5000 Forbes Ave., Pittsburgh, Pennsylvania 15213, United States
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