Ab Initio Fragment Method for Calculating Molecular X-ray Diffraction

Northey, Thomas; Kirrander, Adam

doi:10.1021/acs.jpca.9b00621

Cited by 17 publications

(14 citation statements)

References 63 publications

(171 reference statements)

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“…In fact, the method of electron density calculation proposed within the original MFCC scheme (Gao et al, 2004) differs from that used in fragHAR, although they both divide the polypeptide into overlapping fragments in the same way. Quantum chemical calculations for elastic X-ray scattering with fragmentation were also recently applied by Northey & Kirrander (2019). Most fragmentation approaches focus on obtaining accurate energies, which are global properties, but in the case of HAR, the calculations provide electron density (a local property), making the fragmentation scheme for HAR less complicated.…”

Section: Introductionmentioning

confidence: 99%

Fragmentation and transferability in Hirshfeld atom refinement

Chodkiewicz¹,

Pawlędzio²,

Woińska³

et al. 2022

IUCrJ

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Hirshfeld atom refinement (HAR) is one of the most effective methods for obtaining accurate structural parameters for hydrogen atoms from X-ray diffraction data. Unfortunately, it is also relatively computationally expensive, especially for larger molecules due to wavefunction calculations. Here, a fragmentation approach has been tested as a remedy for this problem. It gives an order of magnitude improvement in computation time for larger organic systems and is a few times faster for metal–organic systems at the cost of only minor differences in the calculated structural parameters when compared with the original HAR calculations. Fragmentation was also applied to polymeric and disordered systems where it provides a natural solution to problems that arise when HAR is applied. The concept of fragmentation is closely related to the transferable aspherical atom model (TAAM) and allows insight into possible ways to improve TAAM. Hybrid approaches combining fragmentation with the transfer of atomic densities between chemically similar atoms have been tested. An efficient handling of intermolecular interactions was also introduced for calculations involving fragmentation. When applied in fragHAR (a fragmentation approach for polypeptides) as a replacement for the original approach, it allowed for more efficient calculations. All of the calculations were performed with a locally modified version of Olex2 combined with a development version of discamb2tsc and ORCA. Care was taken to efficiently use the power of multicore processors by simple implementation of load-balancing, which was found to be very important for lowering computational time.

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Section: Introductionmentioning

confidence: 99%

Fragmentation and transferability in Hirshfeld atom refinement

Chodkiewicz¹,

Pawlędzio²,

Woińska³

et al. 2022

IUCrJ

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“…to the more recent efforts by Kirrander and coworkers, who took into account these kinds of integrals in their ab initio X-ray diffraction (AIXRD) method [45][46][47]. In the next two subsections, we will describe two efficient strategies of computing the integrals represented by Eq.…”

Section: Fourier Transforms Of Basis Functions Productsmentioning

confidence: 99%

The Advent of Quantum Crystallography: Form and Structure Factors from Quantum Mechanics for Advanced Structure Refinement and Wavefunction Fitting

Grabowsky

Genoni

Thomas

et al. 2020

Structure and Bonding

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X-ray diffraction experiments contain much more information than the information usually exploited for structure determination. In quantum crystallography, quantum mechanical wavefunctions are used to extract that information about bonding and properties from the measured X-ray structure factors. Here we show how quantum mechanically derived structure factors and atomic form factors are constructed to allow the improved description of the diffraction experiment. Subsequently, we discuss the basics and the applications of the advanced structure refinement method Hirshfeld Atom Refinement and of the X-ray constrained wavefunction fitting technique.

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“…Over the years several research groups have faced this problem, from the initial efforts by McWeeny (1953), Chandler & Spackman (1978) and Barua & Weyrich (1986), to the more recent work of the Kirrander group in the context of the ab initio X-ray diffraction (AIXRD) method (Northey et al, 2014;Moreno Carrascosa et al, 2019;Northey & Kirrander, 2019). However, so far in this context the most efficient technique remains the one proposed by Jayatilaka (1994), who extended the McMurchie-Davidson (MD) recurrence relations used in quantum chemistry to evaluate molecular integrals (McMurchie & Davidson, 1978).…”

Section: Introductionmentioning

confidence: 99%

On the use of the Obara–Saika recurrence relations for the calculation of structure factors in quantum crystallography

Genoni¹

2020

Acta Cryst Sect A

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Modern methods of quantum crystallography are techniques firmly rooted in quantum chemistry and, as in many quantum chemical strategies, electron densities are expressed as two‐centre expansions that involve basis functions centred on atomic nuclei. Therefore, the computation of the necessary structure factors requires the evaluation of Fourier transform integrals of basis function products. Since these functions are usually Cartesian Gaussians, in this communication it is shown that the Fourier integrals can be efficiently calculated by exploiting an extension of the Obara–Saika recurrence formulas, which are successfully used by quantum chemists in the computation of molecular integrals. Implementation and future perspectives of the technique are also discussed.

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Ab Initio Fragment Method for Calculating Molecular X-ray Diffraction

Cited by 17 publications

References 63 publications

Fragmentation and transferability in Hirshfeld atom refinement

Fragmentation and transferability in Hirshfeld atom refinement

The Advent of Quantum Crystallography: Form and Structure Factors from Quantum Mechanics for Advanced Structure Refinement and Wavefunction Fitting

On the use of the Obara–Saika recurrence relations for the calculation of structure factors in quantum crystallography

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