On the transferability of QTAIMC descriptors derived from X-ray diffraction data and DFT calculations: substituted hydropyrimidine derivatives (original) (raw)
Related papers
Future Medicinal Chemistry, 2011
The use of electron density-based molecular descriptors in drug research, particularly in quantitative structure–activity relationships/quantitative structure–property relationships studies, is reviewed. The exposition starts by a discussion of molecular similarity and transferability in terms of the underlying electron density, which leads to a qualitative introduction to the quantum theory of atoms in molecules (QTAIM). The starting point of QTAIM is the topological analysis of the molecular electron-density distributions to extract atomic and bond properties that characterize every atom and bond in the molecule. These atomic and bond properties have considerable potential as bases for the construction of robust quantitative structure–activity/property relationships models as shown by selected examples in this review. QTAIM is applicable to the electron density calculated from quantum-chemical calculations and/or that obtained from ultra-high resolution x-ray diffraction experimen...
Theoretical Chemistry Accounts, 2007
This paper overviews the work made by our group during the past 10-15 years on crystalline systems, semiconductor surfaces, molecular complexes and on materials of interest for technological applications, such as the defective silicon or the novel generation thermoelectric materials. Our main aim of extracting chemical insight into the analysis of electron densities and computed wave functions is illustrated through a number of examples. The recently proposed Source Function analysis is reviewed and a few of its more interesting applications are summarized. Software package developments, motivated by the need of a direct comparison with experiment or by the help these packages can provide for interpreting complex experimental outcomes, are described and future directions outlined. A particular emphasis is given to the TOPOND and TOPXD programs, which enable one to analyze theoretical and experimental crystalline densities using the rigorous framework of the Quantum Theory of Atoms in Molecules, due to Bader.
Crystallography Reports, 2005
Methods for calculating some properties of molecules and crystals from the electron density reconstructed from a precise X-ray diffraction experiment using the multipole model are considered. These properties include, on the one hand, the characteristics of the electron density and the inner-crystal electrostatic field and, on the other hand, the local electronic energies (kinetic, potential, total), the exchange energy density, the electron-pair localization function, the localized-orbital locator, the effective crystal potential, and others. It is shown that the integration of these characteristics over pseudoatomic volumes bounded by the surfaces of the zero flux of the electron density gradient makes it possible to characterize directly from an experiment the properties of molecules and crystals in terms of the atomic contributions. The computer program WinXPRO2004, realizing these possibilities, is briefly described.
Further Validation of Quantum Crystallography Approaches
Molecules, 2021
Quantum crystallography is a fast-developing multidisciplinary area of crystallography. In this work, we analyse the influence of different charge density models (i.e., the multipole model (MM), Hirshfeld atom refinement (HAR), and the transferable aspherical atom model (TAAM)), modelling of the thermal motion of hydrogen atoms (anisotropic, isotropic, and with the aid of SHADE or NoMoRe), and the type of radiation used (Mo Kα and Cu Kα) on the final results. To achieve this aim, we performed a series of refinements against X-ray diffraction data for three model compounds and compared their final structures, geometries, shapes of ADPs, and charge density distributions. Our results were also supported by theoretical calculations that enabled comparisons of the lattice energies of these structures. It appears that geometrical parameters are better described (closer to the neutron values) when HAR is used; however, bonds to H atoms more closely match neutron values after MM or TAAM ref...
Combining electronic structure and many-body theory with large databases: A method for predicting the nature of <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML">mml:mrowmml:mn4mml:mif states in Ce compounds
Physical Review Materials, 2017
Recent progress in materials informatics has opened up the possibility of a new approach to accessing properties of materials in which one assays the aggregate properties of a large set of materials within the same class in addition to a detailed investigation of each compound in that class. Here we present the first large scale investigation of electronic properties and correlated magnetism in Ce-based compounds accompanied by a systematic study of the electronic structure and 4f-hybridization function of a large body of Ce compounds. We systematically study the electronic structure and 4f-hybridization function of a large body of Ce compounds with the goal of elucidating the nature of the 4f states and their interrelation with the measured Kondo energy in these compounds. The hybridization function has been analyzed for more than 350 data sets (being part of the IMS data base) of cubic Ce compounds using electronic structure theory that relies on a full-potential approach. We demonstrate that the strength of the hybridization function, evaluated in this way, allows us to draw precise conclusions about the degree of localization of the 4f states in these compounds. The theoretical results are entirely consistent with all experimental information, relevant to the degree of 4f localization for all investigated materials. Furthermore, a more detailed analysis of the electronic structure and the hybridization function allows us to make precise statements about Kondo correlations in these systems. The calculated hybridization functions, together with the corresponding density of states, reproduce the expected exponential behavior of the observed Kondo temperatures and prove a consistent trend in real materials. This trend allows us to predict which systems may be correctly identified as Kondo systems. A strong anti-correlation between the size of the hybridization function and the volume of the systems has been observed. The information entropy for this set of systems is about 0.42. Our approach demonstrates the predictive power of materials informatics when a large number of materials is used to establish significant trends. This predictive power can be used to design new materials with desired properties. The applicability of this approach for other correlated electron systems is discussed.
On functions and quantities derived from the experimental electron density
Acta Crystallographica Section A Foundations of Crystallography, 2004
Calculation of properties of molecules and crystals as obtained from a multipole electron-density model restored from the accurate X-ray diffraction data is considered. Electronic and exchange energy-density distributions are presented along with those of local temperature and local entropy. Integration of the local functions over atomic basins de®ned by the zero-¯ux condition allows properties of molecules and crystals to be expressed in terms of atomic contributions derived directly from X-ray diffraction experiments. Distributions of local Fermi momentum and one-electron potential are considered as well. The approach has been applied to diamond, sodium¯uoride, sodium chloride, solid chlorine, -oxalic acid dihydrate and YBa 2 Cu 3 O 6.98 .
Molecular Modeling and Electronic Structure Calculations
2017
This laboratory is designed to use the program GAMESS (General Atomic Molecular Electronic Structure System, developed in Gordon research group at Iowa State) through a website called nanoHUB (www.nanoHUB.org) to determine the geometric and electronic properties of numerous small molecules. GAMESS uses ab initio and semi-empirical calculations to determine these properties. Ab initio (“from first principles”) calculations solve the Schrödinger equation using the exact computational expression for the energy of the electrons. The particular ab initio method that we will use for this lab is called HartreeFock (HF). HF uses an approximate wavefunction to solve Schrödinger, so the resulting molecular properties are approximate, but for many applications the accuracy is adequate for interpreting experiments. Semi-empirical calculations use an approximate energy expression for the electrons, but solve for the exact wavefunction associated with this expression. Usually the energy expressio...
Journal of Computational Chemistry, 2009
This article compares molecular properties and atomic properties defined by the quantum theory of atoms in molecules (QTAIM) obtained from three underlying levels of theory: MP2(full), density functional theory (DFT) (B3LYP), and Hartree-Fock (H-F). The same basis set (6-31111G(d,p)) has been used throughout the study. The calculations and comparisons were applied to a set of 30 small molecules representing common fragments of biological molecules. The molecular properties investigated are the energies and the electrostatic moments (up to and including the quadrupoles), and the atomic properties include electron populations (and atomic charge), atomic dipolar and quadrupolar polarizations, atomic volumes, and corrected and raw atomic energies. The Cartesian distance between dipole vectors and the Frobenius distance between the quadrupole tensors calculated at the three levels of theory provide a measure of their correlation (or lack thereof). With the exception of energies (atomic and molecular), it is found that both DFT and H-F are in excellent agreement with MP2, especially with regards to the electrostatic mutipoles up to the quadrupoles, but DFT and MP2 agree better in almost all studied properties (with the exception of molecular geometries). QTAIM properties whether obtained from H-F, DFT(B3LYP), or MP2 calculations when used in the construction of empirical correlations with experiment such as quantitative structure-activity-(or property)-relationships (QSAR/QSPR) are equivalent (because the properties calculated at the three levels are very highly correlated among themselves with r 2 typically [0.95, and therefore preserving trends). These results suggest that the massive volume of results that were published in the older literature at the H-F level is valid especially when used to study trends or in QSAR or QSPR studies, and, as long as our test set of molecules is representative, there is no pressing need to re-evaluate them at other levels of theory except when inadequate basis sets were used by today's standards. Extensive tabulation of molecular and atomic properties at the three theoretical levels is available in the Supporting Information, including optimized geometries, molecular energies, virial ratios, molecular electrostatic moments up to and including hexadecapoles, atomic populations, atomic volumes, atomic electrostatic moments up to and including the quadrupoles, and atomic energies.