A parallel algorithm is described for the coupled-cluster singles and doubles method augmented with a perturbative correction for triple excitations [CCSD(T)] using the resolution-of-the-identity (RI) approximation for two-electron repulsion integrals (ERIs). The algorithm bypasses the storage of four-center ERIs by adopting an integral-direct strategy. The CCSD amplitude equations are given in a compact quasi-linear form by factorizing them in terms of amplitude-dressed three-center intermediates. A hybrid MPI/OpenMP parallelization scheme is employed, which uses the OpenMP-based shared memory model for intranode parallelization and the MPI-based distributed memory model for internode parallelization. Parallel efficiency has been optimized for all terms in the CCSD amplitude equations. Two different algorithms have been implemented for the rate-limiting terms in the CCSD amplitude equations that entail and -scaling computational costs, where and denote the number of correlated occupied and virtual orbitals, respectively. One of the algorithms assembles the four-center ERIs requiring and -scaling memory costs in a distributed manner on a number of MPI ranks, while the other algorithm completely bypasses the assembling of quartic memory-scaling ERIs and thus largely reduces the memory demand. It is demonstrated that the former memory-expensive algorithm is faster on a few hundred cores, while the latter memory-economic algorithm shows a better strong scaling in the limit of a few thousand cores. The program is shown to exhibit a near-linear scaling, in particular for the compute-intensive triples correction step, on up to 8000 cores. The performance of the program is demonstrated via calculations involving molecules with 24-51 atoms and up to 1624 atomic basis functions. As the first application, the complete basis set (CBS) limit for the interaction energy of the π-stacked uracil dimer from the S66 data set has been investigated. This work reports the first calculation of the interaction energy at the CCSD(T)/aug-cc-pVQZ level without local orbital approximation. The CBS limit for the CCSD correlation contribution to the interaction energy was found to be -8.01 kcal/mol, which agrees very well with the value -7.99 kcal/mol reported by Schmitz, Hättig, and Tew [ 2014, 16, 22167-22178]. The CBS limit for the total interaction energy was estimated to be -9.64 kcal/mol.
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FEBS Lett
January 2025
Allgemeine Botanik, Karlsruhe Institute of Technology, Joseph Kölreuter Institut für Pflanzenwissenschaften (JKIP), Karlsruhe, Germany.
Phytochromes are biliprotein photoreceptors found in bacteria, fungi, and plants. The soil bacterium Agrobacterium fabrum has two phytochromes, Agp1 and Agp2, which work together to control DNA transfer to plants and bacterial conjugation. Both phytochromes interact as homodimeric proteins.
View Article and Find Full Text PDFMagn Reson Chem
January 2025
Laboratório de Química Computacional e Modelagem Molecular (LQC-MM), Departamento de Química Inorgânica, Instituto de Química, Universidade Federal Fluminense (UFF), Niterói, Rio de Janeiro, Brazil.
We present a DFT-PCM NMR study of 3-indoleacetic acid (3-IAA), used as a working example, including explicit solvent molecules, named PCM-nCHCl, PCM-nDMSO (n = 0, 2, 4, 8, 14, 20, and 25), to investigate the dimer formation in solution. Apart from well-known cyclic (I) and open (II) acetic acid (AA) dimers, two new structures were located on DFT-PCM potential energy surface (PES) for 3-IAA named quasicyclic A (III) and quasicyclic B (IV), the last one having N-H…O hydrogen bond (instead of O-H…O). In addition, four other structures having π-π type interactions named V, VI, VII, and VIII were also obtained completing the sample on the PES.
View Article and Find Full Text PDFJ Comput Chem
January 2025
Department of Inorganic Chemistry, Faculty of Chemistry and Petroleum Sciences, Bu-Ali Sina University, Hamedan, Iran.
The strength and cooperative energy of chalcogen and dihydrogen bonds in some ABC triad systems of the types XHTe…NCH…HY (X = F, Cl, Br, I, H; Y = Li, Na, BeH, MgH) and FHCh…NCH…HNa (Ch = Te, Se, S) were computed and compared at several levels of theory. All resulting data showed that the strengths of chalcogen (Te…N) and dihydrogen (H…H) bonds increase in the order of H < I < Br < Cl < F, and Be < Mg < Li < Na, respectively. Then, the comparison of data for the FHTe…NCH…HY, FHSe…NCH…HNa, and FHS…NCH…HNa triads indicated that the interaction, stabilization, and cooperativity energies decrease in the order of Te > Se > S.
View Article and Find Full Text PDFCommun Chem
January 2025
Institute of Physics, Albert-Ludwig-University of Freiburg, Freiburg, Germany.
The interplay between attractive London dispersion forces and steric effects due to repulsive forces resulting from the Pauli principle often determines the geometry and stability of nanostructures. Aromatic polyimides (PI) and carbon nanotubes (CNT) were chosen as building blocks as two components in the hetero delocalized electron nanostructures. Two PIs, having the same diamine part and different linkage substituents between two phenyl rings of dianhydride part, one linked with ether bond (C-O-C) (OPI), the other with C-(CF3)2 (FPI), were investigated.
View Article and Find Full Text PDFNat Commun
January 2025
School of Environment, Tsinghua University, Beijing, 100084, P. R. China.
Modulation of electronic spin states in cobalt-based catalysts is an effective strategy for molecule activations. Crystalline-amorphous interfaces often exhibit unique catalytic properties due to disruptions of long-range order and alterations in electronic structure. However, the mechanisms of molecule activation and spin states at interfaces remain elusive.
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