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Cisplatin (left) and transplatin (right). Color coding: Pt = gray, Cl = green, N = blue, and H = white.
Source publication
Long in the making, computational chemistry for the masses [J. Chem. Educ. 1996, 73, 104] is finally here. Our brief review on various free and open source software (FOSS) quantum chemistry packages points out the existence of software offering a wide range of functionality, all the way from approximate semiempirical calculations with tight-binding...
Contexts in source publication
Context 1
... Supporting Information includes step-by-step guidelines for installing xtb and using it to study structures, conformations, energetics, and molecular orbitals of inorganic and organic molecules. Calculations on pharmaceutically relevant cisplatin and transplatin molecules shown in figure 2 are briefly summarized here to showcase the basic use of xtb. Cisplatin, cis-[Pt(NH 3 ) 2 Cl 2 ], is a chemotherapy medication used in cancer treatments whose stereoisomer, transplatin, trans-[Pt(NH 3 ) 2 Cl 2 ], is ineffective in cancer treatment. ...
Context 2
... four highest occupied MOs (HOMOs) and the lowest unoccupied MO (LUMO) of cisplatin as obtained from NWChem (PBE0/def2-TZVP) and xtb (GFN2-xTB). The color code for the nuclei is the same as in figure 2, while red and blue denote positive and negative orbital amplitudes, respectively (note that the overall sign of the orbital can be freely chosen). The isovalue used for the orbitals is 0.04 electrons/Bohr 3 . ...
Citations
... From this library we access LDA-PW [50], PBEsol [51], and r 2 SCAN [22]. The used codes are Open-Source codes, meaning they are freely available to anyone [52,53]. Open-Source codes enable faster code development, re-usable concepts, and versatile tool-boxes. ...
We briefly review the analysis of the energy spectrum, the envelope eigenfunctions of electron, hole and exciton states, and the direct interband light absorption in cone-shaped and spheroidal impenetrable quantum dots. We apply high-order finite element method and calculation schemes of Kantorovich method in comparison with the adiabatic approximation (in the strong size quantization limit) for solving boundary-value problems that describe axially symmetric quantum dots. We demonstrate the efficiency of the algorithms and software by benchmark calculations of spectral and optical characteristics of the cone-shaped and spheroidal quantum dots and crossing points in their spectra.KeywordsCone-shaped and Spheroidal quantum dotsEnergy spectraCrossing pointsLight absorptionFinite element methodKantorovich methodAdiabatic approximation
... All input parameters are listed in Tab. 3 Given these input parameters, extra properties of the system have to be calculated. At first, the lattice vectors R of the unit cell can be built. ...
In this master thesis an educational Python-based plane wave DFT code using the modern DFT++ pragmas has been successfully implemented. The implementation has been tested and offers reproducible and comparable results to various plane wave codes, e.g., JDFTx and PWDFT.jl. Additional features have been implemented and tested, e.g., the calculation of dipole moments to further investigate the properties of orbitals and densities.
It has been found that the handling of the Coulomb potential in plane wave codes is important for calculating SIC energies. The usage of a periodic or a truncated Coulomb potential does not change the total energy of the system, but the resulting SIC energies will change.
The creation of FLOs has been successfully implemented and tested. The implementation includes an interface to the FOD generator PyCOM. The FLO generation uses a novel idea that utilizes the features of plane waves that allow shifts in reciprocal space. The properties of calculated FLOs have been illustrated.
The effect of various domain restrictions on the SIC energies have been discussed. While the current implementation does not allow large speed-ups, a convergence of SIC energies has been found for domains that truncate the real space using spherical and cuboidal domains. This shows that a subset of sampling points can be used to accurately calculate SIC energies. It has been shown that the mesh error of the total density can be used as a measurement of the numerical quality for the SIC energies.
Recently, Trepte et al. [J. Chem. Phys., vol. 155, 2021] pointed out the importance of analyzing dipole moments in the Fermi-Löwdin orbital (FLO) self-interaction correction (SIC) for cyclic, planar molecules. In this manuscript, the effect of the molecular and electronic geometries on dipole moments and polarizabilities is discussed for non-cyclic molecules. Computed values are presented for water, formaldehyde, and nitromethane. Continuing the work of Schwalbe et al. [J. Chem. Phys. vol. 153, (2020)], we reconfirm that systematic numerical parameter studies are essential to obtain consistent results in density functional theory (DFT) and SIC. In agreement with Trepte et al. [J. Chem. Phys., vol. 155, 2021], DFT agrees well with experiment for dipole moments, while SIC slightly overestimates them. A Linnett double-quartet electronic geometry is found to be energetically preferred for nitromethane.KeywordsDFTFLO-SICdipolepolarizabilities
