Correlation Problems in Atomic and Molecular Systems. IV. Extended Coupled-Pair Many-Electron Theory and Its Application to the B<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">H</mml:mi></mml:mrow><mml:mrow><mml:mn>3</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math>Molecule

Paldus, Josef; Čı́žek, J.; Shavitt, Isaiah

doi:10.1103/physreva.5.50

Cited by 891 publications

(312 citation statements)

References 13 publications

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“…20,21 The QM description of base stacking in general requires application of electron-correlation techniques and diffuse-polarization basis sets of atomic orbitals. The present golden standard for basestacking computations is the CBS(T) method, 19 which is based on MP2 22 calculations with complete basis-set (CBS) extrapolation corrected for higher-order electron-correlation contributions using the CCSD(T) 23 Cizek method 24 with a medium-size basis set. In the present paper we have carried out an extensive QM characterization of stacked conformations of the uracil dimer, which is the smallest base stacking system found in nucleic acids.…”

Section: Introductionmentioning

confidence: 99%

Balance of Attraction and Repulsion in Nucleic-Acid Base Stacking: CCSD(T)/Complete-Basis-Set-Limit Calculations on Uracil Dimer and a Comparison with the Force-Field Description

Morgado

Jurečka

Svozil

et al. 2009

J. Chem. Theory Comput.

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Abstract:We have carried out reference quantum-chemical calculations for about 100 geometries of the uracil dimer in stacked conformations. The calculations have been specifically aimed at geometries with unoptimized distances between the monomers including geometries with mutually tilted monomers. Such geometries are characterized by a delicate balance between local steric clashes and local unstacking and had until now not been investigated using reference quantummechanics (QM) methods. Nonparallel stacking geometries often occur in nucleic acids and are of decisive importance, for example, for local conformational variations in B-DNA. Errors in the shortrange repulsion region would have a major impact on potential energy scans which were often used in the past to investigate local geometry variations in DNA. An incorrect description of such geometries may also partially affect molecular dynamics (MD) simulations in applications when quantitative accuracy is required. The reference QM calculations have been carried out using the MP2 method extrapolated to the complete basis-set limit and corrected for higher-order electron-correlation contributions using CCSD(T) calculations with a medium-sized basis set. These reference calculations have been used as benchmark data to test the performance of the DFT-D, SCS(MI)-MP2, and DFT-SAPT QM methods and of the AMBER molecular-mechanics (MM) force field. The QM methods show close to quantitative agreement with the reference data, albeit the DFT-D method tends to modestly exaggerate the repulsion of steric clashes. The force field in general also provides a good description of base stacking for the systems studied here. However, for geometries with close interatomic contacts and clashes, the repulsion effects are rather severely exaggerated. The discrepancy reported here should not affect the overall stability of MD simulations and qualitative applications of the force field. However, it may affect the description of subtle quantitative effects such as the local conformational variations in B-DNA. Preliminary calculations for two H-bonded uracil base pairs, including one with a C-H · · · O H-bond, indicate excellent performance of the tested QM methods for all intermonomer distances. The force field, on the other hand, is less satisfactory, especially in the repulsive regions.

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Section: Introductionmentioning

confidence: 99%

Balance of Attraction and Repulsion in Nucleic-Acid Base Stacking: CCSD(T)/Complete-Basis-Set-Limit Calculations on Uracil Dimer and a Comparison with the Force-Field Description

Morgado

Jurečka

Svozil

et al. 2009

J. Chem. Theory Comput.

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“…Exclusion of pair-excitations fulfils the orthogonality condition eq. (5). If the excitation operator contains both single and double excitations, the single excitations can be accounted for by addinĝ (11) to the double excitation operator.…”

Section: Theoretical Models For Dynamic Correlationmentioning

confidence: 99%

“…Computational studies are particularly desirable especially when experimental manipulations are limited or impossible. Conventional "ab initio" quantum chemistry tools used in thermochemistry are commonly based on different flavours of many-body perturbation theory and coupled cluster approaches [2][3][4][5][6][7][8][9]. Over the years, the CCSD(T) (Coupled Cluster Singles, Doubles and perturbative Triples) method has unfolded as one of the most reliable and accurate models for systems that are well-represented by a single electron configuration.…”

Section: Introductionmentioning

confidence: 99%

Benchmark of Dynamic Electron Correlation Models for Seniority-Zero Wave Functions and Their Application to Thermochemistry

Boguslawski

Tecmer

2017

J. Chem. Theory Comput.

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Wavefunctions restricted to electron-pair states are promising models to describe static/nondynamic electron correlation effects encountered, for instance, in bond-dissociation processes and transition-metal and actinide chemistry. To reach spectroscopic accuracy, however, the missing dynamic electron correlation effects that cannot be described by electron-pair states need to be included a posteriori. In this article, we extend the previously presented perturbation theory models with an Antisymmetric Product of 1-reference orbital Geminal (AP1roG) reference function that allow us to describe both static/nondynamic and dynamic electron correlation effects. Specifically, our perturbation theory models combine a diagonal and off-diagonal zero-order Hamiltonian, a single-reference and multi-reference dual state, and different excitation operators used to construct the projection manifold. We benchmark all proposed models as well as an a posteriori linearized coupled cluster correction on top of AP1roG against CR-CCSD(T) reference data for reaction energies of several closed-shell molecules that are extrapolated to the basis set limit. Moreover, we test the performance of our new methods for multiple bond breaking processes in the N2, C2, and BN dimers against MRCI-SD and MRCI-SD+Q reference data. Our numerical results indicate that the best performance is obtained from a linearized coupled cluster correction as well as second-order perturbation theory corrections employing a diagonal and off-diagonal zero-order Hamiltonian and a single-determinant dual state. These dynamic corrections on top of AP1roG allow us to reliably model molecular systems dominated by static/nondynamic as well as dynamic electron correlation.

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“…incorporated in the CCM via a correlation operator S, These are S I'll> = e I~> , which was f-erhaps first employed for spin-lattice systems by3 Roger and Hetherington, 7 who were primarily interested in the solid phases of He.…”

Section: The Model and Preliminariesmentioning

confidence: 99%

Correlations in Quantum Spin Chains and Lattices: A Fully Microscopic Many-Body Approach

Bishop

Parkinson

Xian

1992

Recent Progress in Many-Body Theories

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Correlation Problems in Atomic and Molecular Systems. IV. Extended Coupled-Pair Many-Electron Theory and Its Application to the BH3Molecule

Cited by 891 publications

References 13 publications

Balance of Attraction and Repulsion in Nucleic-Acid Base Stacking: CCSD(T)/Complete-Basis-Set-Limit Calculations on Uracil Dimer and a Comparison with the Force-Field Description

Balance of Attraction and Repulsion in Nucleic-Acid Base Stacking: CCSD(T)/Complete-Basis-Set-Limit Calculations on Uracil Dimer and a Comparison with the Force-Field Description

Benchmark of Dynamic Electron Correlation Models for Seniority-Zero Wave Functions and Their Application to Thermochemistry

Correlations in Quantum Spin Chains and Lattices: A Fully Microscopic Many-Body Approach

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