Linear-Scaling Implementation of Multilevel Hartree-Fock Theory.
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ABSTRACT:
SUBMITTER: Goletto L
PROVIDER: S-EPMC8675138 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The ability to perform ab initio electronic structure calculations that scales linearly with the system size is one of the central aims in theoretical chemistry. In this study, the implementation of the divide-and-conquer (DC) algorithm, an algorithm with the potential to aid the achievement of true linear scaling within Hartree-Fock (HF) theory is revisited. Standard HF calculations solve the Roothaan-Hall equations for the whole system; in the DC-HF approach, the diagonalization of the Fock matrix is carried out on smaller subsystems. The DC algorithm for HF calculations was validated on polyglycines, polyalanines and eleven real three-dimensional proteins of up to 608 atoms in this work. We also found that a fragment-based initial guess using molecular fractionation with conjugated caps (MFCC) method significantly reduces the number of SCF cycles and even is capable of achieving convergence for some globular proteins where the simple superposition of atomic densities (SAD) initial guess fails.
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Project description:The X-ray constrained wavefunction (XC-WF) method proposed by Jayatilaka [Jayatilaka & Grimwood (2001) ▸, Acta Cryst. A57, 76-86] has attracted much attention because it represents a possible third way of theoretically studying the electronic structure of atoms and molecules, combining features of the more popular wavefunction- and DFT-based approaches. In its original formulation, the XC-WF technique extracts statistically plausible wavefunctions from experimental X-ray diffraction data of molecular crystals. A weight is used to constrain the pure Hartree-Fock solution to the observed X-ray structure factors. Despite the wavefunction being a single Slater determinant, it is generally assumed that its flexibility could guarantee the capture, better than any other experimental model, of electron correlation effects, absent in the Hartree-Fock Hamiltonian but present in the structure factors measured experimentally. However, although the approach has been known for long time, careful testing of this fundamental hypothesis is still missing. Since a formal demonstration is impossible, the validation can only be done heuristically and, to accomplish this task, X-ray constrained Hartree-Fock calculations have been performed using structure factor amplitudes computed at a very high correlation level (coupled cluster) for selected molecules in isolation, in order to avoid the perturbations due to intermolecular interactions. The results show that a single-determinant XC-WF is able to capture the electron correlation effects only partially. The largest amount of electron correlation is extracted when: (i) a large external weight is used (much larger than what has normally been used in XC-WF calculations using experimental data); and (ii) the high-order reflections, which carry less information on the electron correlation, are down-weighted (or even excluded), otherwise they would bias the fitting towards the unconstrained Hartree-Fock wavefunction.
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Project description:The counterpoise (CP) correction by Boys and Bernardi has been well accepted as a reliable strategy to account for basis set superposition error (BSSE) in intermolecular complexes. The behavior of the CP correction was thoroughly studied in individual molecules of molecular complexes. This work studies the performance of the CP correction in many-body clusters including three-body clusters of organic compounds in the 3B-69 dataset. Additionally, we used crystal structures of polymorphs of benzene, aspirin, and oxalyl dihydrazide (ODH) to construct a many-body cluster dataset, abbreviated as the MBC-36 dataset, consisting of two, four and eight molecules, and 16 molecules in the case of benzene. A series of Dunning's basis sets-cc-pXZ and aug-cc-pXZ (X = D and T)-were used to predict CP-corrected Hartree-Fock (HF) interaction energies of the 3B-69 and MBC-36 datasets. The CP-corrected interaction energies were found to be basis-set independent, whereas the non-CP corrected interaction energies were found not to a follow a smooth exponential fitting as previously found for electronic energies of individual molecules. This observation was attributed to the presence of non-additive induction forces in some clusters. Two 2 × 2 × 2 supercells of benzene polymorphs were constructed to explore the local nature of BSSE effects. A cut-off radius of 10 Å was demonstrated to be sufficient to fully recover these effects. Although the behavior of CP correction was found to be non-conventional in many-body clusters of organic compounds, the use of a small basis set such as cc-pVDZ showed excellent performance in the prediction of HF interaction energies.
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Project description:The coupled-cluster (CC) singles and doubles with perturbative triples [CCSD(T)] method is frequently referred to as the "gold standard" of modern computational chemistry. However, the high computational cost of CCSD(T) [O(N7)], where N is the number of basis functions, limits its applications to small-sized chemical systems. To address this problem, efficient implementations of linear-scaling coupled-cluster methods, which employ the systematic molecular fragmentation (SMF) approach, are reported. In this study, we aim to do the following: (1) To achieve exact linear scaling and to obtain a pure ab initio approach, we revise the handling of nonbonded interactions in the SMF approach, denoted by LSSMF. (2) A new fragmentation algorithm, which yields smaller-sized fragments, that better fits high-level CC methods is introduced. (3) A modified nonbonded fragmentation scheme is proposed to enhance the existent algorithm. Performances of the LSSMF-CC approaches, such as LSSMF-CCSD(T), are compared with their canonical versions for a set of alkane molecules, CnH2n+2 (n = 6-10), which includes 142 molecules. Our results demonstrate that the LSSMF approach introduces negligible errors compared with the canonical methods; mean absolute errors (MAEs) are between 0.20 and 0.59 kcal mol-1 for LSSMF(3,1)-CCSD(T). For a larger alkanes set (L12), CnH2n+2 (n = 50-70), the performance of LSSMF for the second-order perturbation theory (MP2) is investigated. For the L12 set, various bonded and nonbonded levels are considered. Our results demonstrate that the combination of bonded level 6 with nonbonded level 2, LSSMF(6,2), provides very accurate results for the MP2 method with a MAE value of 0.32 kcal mol-1. The LSSMF(6,2) approach yields more than a 26-fold reduction in errors compared with LSSMF(3,1). Hence, we obtain substantial improvements over the original SMF approach. To illustrate the efficiency and applicability of the LSSMF-CCSD(T) approach, we consider an alkane molecule with 10,004 atoms. For this molecule, the LSSMF(3,1)-CCSD(T)/cc-pVTZ energy computation, on a Linux cluster with 100 nodes, 4 cores, and 5 GB of memory provided to each node, is performed just in ∼24 h. As a second test, we consider a biomolecular complex (PDB code: 1GLA), which includes 10,488 atoms, to assess the efficiency of the LSSMF approach. The LSSMF(3,1)-FNO-CCSD(T)/cc-pVTZ energy computation is completed in ∼7 days for the biomolecular complex. Hence, our results demonstrate that the LSSMF-CC approaches are very efficient. Overall, we conclude the following: (1) The LSSMF(m, n)-CCSD(T) methods can be reliably used for large-scale chemical systems, where the canonical methods are not computationally affordable. (2) The accuracy of bonded level 3 is not satisfactory for large chemical systems. (3) For high-accuracy studies, bonded level 5 (or higher) and nonbonded level 2 should be employed.
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Project description:ObjectiveThe present study aims to establish the relationship between the reported radical-scavenging activities of flavonoids and some enthalpy changes that may occur during flavonoids' reactions with free radicals.MethodEight flavonoids were chosen for the study on the basis of their structural merits and reported 1,1-diphenyl-2-picryl-hydrazyl scavenging activities. Enthalpy changes accompanying interconversions between selected conformations (including spin multiplicities) and homolytic dissociations were estimated.ResultsA novel relationship exists between the total enthalpy of reaction for the abstraction of two hydrogen atoms from flavonoids, their reported radical-scavenging activities and the enthalpy of the homolytic dissociation of hydrogen molecule (104.206 kcal mol(-1)). Only those flavonoids which could give up two hydrogen atoms with total enthalpy changes well below 104.206 kcal mol(-1) were active radical scavengers.DiscussionBy appealing to equilibrium dynamics, we demonstrated that, for flavonoids to be able to donate hydrogen atoms, the change in enthalpy accompanying the abstraction of two hydrogen atoms needs to be less than 104.206 kcal mol(-1). This condition does not seem to be restricted to flavonoids only but rather generally applicable to chian-breaking antioxidants.ConclusionThermodynamical relationships may be the most important factors governing the radical-scavenging reactions of flavonoids and possibly other compounds as well. Nevertheless, a more complete characterization of antioxidants would necessitate kinetic analysis.
| S-EPMC6837546 | biostudies-literature