Unveiling the complex pattern of intermolecular interactions responsible for the stability of the DNA duplex

Altun, Ahmet; García-Ratés, Miquel; Neese, Frank; Bistoni, Giovanni

doi:10.1039/d1sc03868k

Cited by 18 publications

(18 citation statements)

References 100 publications

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“…Neither the PTE scheme nor the PTE(S) scheme involves explicit corrections to the equations to compute the CC excitations (T amplitudes). In the present study, we use the PTE(S) scheme, which has been recently implemented in ORCA 5.0 for open-shell systems, , to compute the solvation free energies both for the oxidized and reduced species. It is noted that the various approximate schemes show a high degree of consistency, and hence, the errors arising from the approximation of the solvation terms in the cluster equations must be very small, much smaller than the errors intrinsic in the implicit solvation schemes.…”

Section: Theory and Methodologymentioning

confidence: 99%

Ionization Energies and Redox Potentials of Hydrated Transition Metal Ions: Evaluation of Domain-Based Local Pair Natural Orbital Coupled Cluster Approaches

Bhattacharjee

Isegawa

García-Ratés

et al. 2022

J. Chem. Theory Comput.

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Hydrated transition metal ions are prototypical systems that can be used to model properties of transition metals in complex chemical environments. These seemingly simple systems present challenges for computational chemistry and are thus crucial in evaluations of quantum chemical methods for spin-state and redox energetics. In this work, we explore the applicability of the domain-based pair natural orbital implementation of coupled cluster (DLPNO-CC) theory to the calculation of ionization energies and redox potentials for hydrated ions of all first transition row (3d) metals in the 2+/3+ oxidation states, in connection with various solvation approaches. In terms of model definition, we investigate the construction of a minimally explicitly hydrated quantum cluster with a first and second hydration layer. We report on the convergence with respect to the coupled cluster expansion and the PNO space, as well as on the role of perturbative triple excitations. A recent implementation of the conductor-like polarizable continuum model (CPCM) for the DLPNO-CC approach is employed to determine self-consistent redox potentials at the coupled cluster level. Our results establish conditions for the convergence of DLPNO-CCSD(T) energetics and stress the absolute necessity to explicitly consider the second solvation sphere even when CPCM is used. The achievable accuracy for redox potentials of a practical DLPNO-based approach is, on average, 0.13 V. Furthermore, multilayer approaches that combine a higher-level DLPNO-CCSD(T) description of the first solvation sphere with a lower-level description of the second solvation layer are investigated. The present work establishes optimal and transferable methodological choices for employing DLPNO-based coupled cluster theory, the associated CPCM implementation, and cost-efficient multilayer derivatives of the approach for open-shell transition metal systems in complex environments.

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Section: Theory and Methodologymentioning

confidence: 99%

Ionization Energies and Redox Potentials of Hydrated Transition Metal Ions: Evaluation of Domain-Based Local Pair Natural Orbital Coupled Cluster Approaches

Bhattacharjee

Isegawa

García-Ratés

et al. 2022

J. Chem. Theory Comput.

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“…In addition, if combined with the LED scheme, the HFLD approach can be used to quantify the other physical contibutions to the interaction ( e.g ., electrostatic, exchange, and electronic preparation), as recently shown for the interaction of the base pairs in a DNA duplex model. 91 Thus, the open-shell variant of the HFLD scheme opens up unprecedented opportunities for the accurate quantification and analysis of NCIs in large and complex systems.…”

Section: Results and Discussionmentioning

confidence: 99%

“…Matching auxiliary basis sets were used in the SCF and correlation parts . As HFLD results show a very fast convergence with the basis set size (see the original HFLD paper, our DNA study, as well the PNO-SIZE sheet in the Supporting Information of this work), this basis set settings typically provide reasonably well-converged energetics. This cost-effective HFLD/NormalPNO*/def2-TZVP(-f) approach is denoted hereafter as HFLD*.…”

Section: Computational Detailsmentioning

confidence: 99%

“… 88 Therefore, this cost-effective approach can be used to study intermolecular interactions accurately in large and complex (bio-)molecular systems. For example, a recent combined HFLD/LED study 91 on a large DNA duplex model (1001 atoms and 13 998 contracted basis functions) provided an in-depth characterization of the key inter- and intra-strand interactions responsible for the stability of human DNA.…”

Section: Introductionmentioning

confidence: 99%

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Open-Shell Variant of the London Dispersion-Corrected Hartree–Fock Method (HFLD) for the Quantification and Analysis of Noncovalent Interaction Energies

Altun

Neese

Bistoni

2022

J. Chem. Theory Comput.

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The London dispersion (LD)-corrected Hartree–Fock (HF) method (HFLD) is an ab initio approach for the quantification and analysis of noncovalent interactions (NCIs) in large systems that is based on the domain-based local pair natural orbital coupled-cluster (DLPNO-CC) theory. In the original HFLD paper, we discussed the implementation, accuracy, and efficiency of its closed-shell variant. Herein, an extension of this method to open-shell molecular systems is presented. Its accuracy is tested on challenging benchmark sets for NCIs, using CCSD(T) energies at the estimated complete basis set limit as reference. The HFLD scheme was found to be as accurate as the best-performing dispersion-corrected exchange-correlation functionals, while being nonempirical and equally efficient. In addition, it can be combined with the well-established local energy decomposition (LED) for the analysis of NCIs, thus yielding additional physical insights.

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“…The development of reduced-scaling quantum chemical methods became a significant part of the recent research effort. In particular, for coupled cluster approaches, the local domain-based methods have been introduced and successfully applied on large systems ( [1,57]). Our implementation is inspired by [1].…”

Section: Dlpno Ccsd(t)mentioning

confidence: 99%

TAMM: Tensor Algebra for Many-body Methods

Mutlu¹,

Panyala²,

Gawande³

et al. 2022

Preprint

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Tensor contraction operations in computational chemistry consume significant fractions of computing time on large-scale computing platforms. The widespread use of tensor contractions between large multi-dimensional tensors in describing electronic structure theory has motivated the development of multiple tensor algebra frameworks targeting heterogeneous computing platforms. In this paper, we present Tensor Algebra for Many-body Methods (TAMM), a framework for productive and performance-portable development of scalable computational chemistry methods. The TAMM framework decouples the specification of the computation and the execution of these operations on available high-performance computing systems. With this design choice, the scientific application developers (domain scientists) can focus on the algorithmic requirements using the tensor algebra interface provided by TAMM whereas high-performance computing developers can focus on various optimizations on the underlying constructs such as efficient data distribution, optimized scheduling algorithms, efficient use of intra-node resources (e.g., GPUs). The modular structure of TAMM allows it to be extended to support different hardware architectures and incorporate new algorithmic advances. We describe the TAMM framework and our approach to sustainable development of tensor contraction-based methods in computational chemistry applications. We present case studies that highlight the ease of use as well as the performance and productivity gains compared to other implementations.

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Unveiling the complex pattern of intermolecular interactions responsible for the stability of the DNA duplex

Abstract: Herein, we provide new insights into the intermolecular interactions responsible for the intrinsic stability of the duplex structure of a large portion of human B-DNA by using advanced quantum mechanical...

Cited by 18 publications

References 100 publications

Ionization Energies and Redox Potentials of Hydrated Transition Metal Ions: Evaluation of Domain-Based Local Pair Natural Orbital Coupled Cluster Approaches

Ionization Energies and Redox Potentials of Hydrated Transition Metal Ions: Evaluation of Domain-Based Local Pair Natural Orbital Coupled Cluster Approaches

Open-Shell Variant of the London Dispersion-Corrected Hartree–Fock Method (HFLD) for the Quantification and Analysis of Noncovalent Interaction Energies

TAMM: Tensor Algebra for Many-body Methods

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