scholarly journals Hirshfeld atom like refinement with alternative electron density partitions

IUCrJ ◽  
2020 ◽  
Vol 7 (6) ◽  
pp. 1199-1215 ◽  
Author(s):  
Michał Leszek Chodkiewicz ◽  
Magdalena Woińska ◽  
Krzysztof Woźniak
Keyword(s):  
Quantum Chemistry ◽  
Electron Density ◽  
Structural Parameters ◽  
Accurate Determination ◽  
Basis Set ◽  
Hydrogen Atoms ◽  
Minimal Basis ◽  
Bond Lengths ◽  
Hartree Fock ◽  
Systematic Effects

Hirshfeld atom refinement is one of the most successful methods for the accurate determination of structural parameters for hydrogen atoms from X-ray diffraction data. This work introduces a generalization of the method [generalized atom refinement (GAR)], consisting of the application of various methods of partitioning electron density into atomic contributions. These were tested on three organic structures using the following partitions: Hirshfeld, iterative Hirshfeld, iterative stockholder, minimal basis iterative stockholder and Becke. The effects of partition choice were also compared with those caused by other factors such as quantum chemical methodology, basis set, representation of the crystal field and a combination of these factors. The differences between the partitions were small in terms of R factor (e.g. much smaller than for refinements with different quantum chemistry methods, i.e. Hartree–Fock and coupled cluster) and therefore no single partition was clearly the best in terms of experimental data reconstruction. In the case of structural parameters the differences between the partitions are comparable to those related to the choice of other factors. We have observed the systematic effects of the partition choice on bond lengths and ADP values of polar hydrogen atoms. The bond lengths were also systematically influenced by the choice of electron density calculation methodology. This suggests that GAR-derived structural parameters could be systematically improved by selecting an optimal combination of the partition and quantum chemistry method. The results of the refinements were compared with those of neutron diffraction experiments. This allowed a selection of the most promising partition methods for further optimization of GAR settings, namely the Hirshfeld, iterative stockholder and minimal basis iterative stockholder.

Nonadditive effects of polysubstitution in CH4 and CH3: a test of abinitio and semiempirical MO methods

1983 ◽  
Vol 61 (7) ◽  
pp. 1567-1572 ◽  
Author(s):  
N. Colin Baird
Keyword(s):  
Basis Set ◽  
Semiempirical Methods ◽  
Valence Shell ◽  
Bond Lengths ◽  
Hartree Fock ◽  
Nonadditive Effects ◽  
D Orbitals ◽  
Split Valence ◽  
Abinitio Calculations

The effects to the bond lengths and molecular energy of making multiple substitutions at the same carbon atom in methane and the methyl free radical are studied using various molecular orbital methods. All abinitio calculations were based upon the Hartree–Fock formalism (unrestricted in the case of free radicals) and employed the STO-3G (with d orbitals on chlorine), 3-21G, and 4-31G bases, the last both with and without a set of Gaussian d orbitals on the carbon. The semiempirical methods used were the MINDO/3 and MNDO methods of Dewar and co-workers; computations for polysubstituted ethanes by these two methods also arc reported. The abinito methods which use a split valence shell basis set account very well for the trends in bond lengths and heats of formation, at least when the polysubstituent is fluorine or hydroxyl. In contrast, the semiempirical calculations and the abinitio STO-3G results gave very poor results. Finally, the role of interactions between the AH bonds in a variety of hydrides AHn is illustrated using experimental energetics.

The simplified ab initio method calculation of linear polarizability

1973 ◽  
Vol 26 (5) ◽  
pp. 921 ◽  
Author(s):  
RD Brown ◽  
GR Williams
Keyword(s):  
Ab Initio ◽  
Small Molecules ◽  
Basis Set ◽  
Basis Sets ◽  
Orbital Method ◽  
Polarizability Anisotropy ◽  
Minimal Basis ◽  
Hartree Fock ◽  
Numerical Performance ◽  
Experimental Values

The simplified ab-initio molecular-orbital method described previously is particularly suited to the calculation of polarizabilities by the non-perturbative coupled Hartree-Fock technique. Trial calculations on CO and HF, for which comparison with corresponding ab-initio calculations is possible, show that the method gives an adequate numerical performance. Minimal basis set calculations in general tend to give values that are considerably too low because of inadequate flexibility of the basis and this is the origin of the large discrepancy between theory and experiment, especially for small molecules. ��� Results are also reported for N2O and O3. For these larger systems the SAI results with minimal basis sets are noticeably nearer experimental values. The polarizability anisotropy for N2O is particularly well reproduced by the SAI method. �

scholarly journals Dispersion Corrected r2SCAN Based Global Hybrid Functionals: r2SCANh, r2SCAN0, and r2SCAN50

2021 ◽  
Author(s):  
Markus Bursch ◽  
Hagen Neugebauer ◽  
Sebastian Ehlert ◽  
Stefan Grimme
Keyword(s):  
Structural Parameters ◽  
Main Group ◽  
Basis Set ◽  
Generalized Gradient ◽  
Exchange Correlation ◽  
Hartree Fock ◽  
Exact Exchange ◽  
Hybrid Functionals ◽  
London Dispersion

The re-regularized semilocal meta generalized gradient approximation (meta-GGA) exchange-correlation functional r2SCAN [J. W. Furness, A. D. Kaplan, J. Ning, J. P. Perdew, and J. Sun, J. Phys. Chem. Lett. 11, 8208–8215 (2020)] is used to create the three global hybrid functionals with varying admixtures of Hartree–Fock exact exchange (HFX). The resulting exchange-correlation functionals r2SCANh (10% HFX), r2SCAN0 (25% HFX), and r2SCAN50 (50%HFX) are combined with the recent semi-classical D4 London dispersion correction. The new functionals are assessed for molecular geometries, general main-group, and metalorganic thermochemistry at 26 comprehensive benchmark sets including such as the large GMTKN55, ROST61, and IONPI19 sets. It is shown that a moderate admixture of HFX leads to overall mean percentual improvements of −11 (r2SCANh-D4), −16 (r2SCAN0-D4), and −1% (r2SCAN50-D4) regarding thermochemistry compared to the parental meta-GGA. For organometallic reaction energies and barriers, r2SCAN0-D4 even yields a mean improvement of −35%. The computation of structural parameters does not systematically profit from HFX admixture. Overall, the most promising combination r2SCAN0-D4 performs well for both main-group and organometallic thermochemistry. It yields deviations better or on par with other very well-performing global hybrid functionals such as PW6B95-D4 or PBE0-D4. Regarding systems prone to self-interaction errors (SIE4x4), r2SCAN0-D4 shows reasonable performance, reaching the quality of the range-separated ωB97X-V functional. Accordingly, r2SCAN0-D4 in combination with a sufficiently converged basis set (def2-QZVP(P)) represents a robust and reliable choice for general use in the calculation of thermochemical properties of both, main-group and organometallic chemistry.

scholarly journals Infrared Spectrum for the New Exobiological Nanomolecules Asi, Csi, Tsi and Gsi

2021 ◽  
pp. 25-31
Author(s):  
Ricardo Gobato ◽  
Alireza Heidari ◽  
Lauro Figueroa Valverde ◽  
Abhijit Mitra
Keyword(s):  
Infrared Spectrum ◽  
Quantum Chemistry ◽  
Ab Initio ◽  
Basis Sets ◽  
Minimal Basis ◽  
Hartree Fock ◽  
Standard Bases ◽  
Quantum Chemistry Calculations ◽  
Computational Calculations ◽  
Correlation Consistent

The core of the work is based on the replacement of carbon atoms by silicon atoms, on the basis of four standard bases of DNA: A, C, G and T (adenine, cytosine, guanine, thymine). Determining with minimum computational methods via ab initio Hartree-Fock methods, infrared spectrum and their peak absorbance frequencies. The option for simple replacement of carbon by silicon is due to the peculiar characteristics between both. Atomic interactions under non-carbon conditions were studied, with only the Hydrogen, Silicon, Nitrogen and Oxygen atoms, in CNTP, for the four standard bases of DNA, A, C, G and T, thus obtaining by quantum chemistry four new compounds, named here as: ASi, CSi, GSi and TSi. Computational calculations admit the possibility of the formation of such molecules, their existence being possible via quantum chemistry. Calculations obtained in the ab initio Unrestricted and Restrict Hartree-Fock method, (UHF and RHF) in the set of basis used Effective core potential (ECP) minimal basis, UHF CEP-31G (ECP split valance) and UHF CEP-121G (ECP triple-split basis), CC-pVTZ (Correlation-consistent valence-only basis sets triple-zeta) and 6-311G**(3df, 3pd) (Gaussian functions quadruple-zeta basis sets).

Kinetic Isotope and Collision Energy Effects in the Dissociation of Chloride and Bromide Adducts of Aliphatic Alcohols, Benzaldehyde, and 2,4-Pentanedione

2003 ◽  
Vol 56 (5) ◽  
pp. 415 ◽  
Author(s):  
Rodinei Augusti ◽  
Xubin Zheng ◽  
M. Turowski ◽  
R. Graham Cooks
Keyword(s):  
Density Functional ◽  
Collision Energy ◽  
Basis Set ◽  
Cluster Ions ◽  
Basis Sets ◽  
Stable Form ◽  
Triple Quadrupole Mass Spectrometer ◽  
Hydrogen Atoms ◽  
Hartree Fock ◽  
Chloride Adduct

A tandem-in-space triple quadrupole mass spectrometer was used to measure kinetic isotopic effects (KIEs) for the dissociation of chloride and bromide adducts of several compounds that bind halide anions via either hydrogen bonds or by nucleophilic attachment. Two isotopomers of each adduct were simultaneously mass-selected in the first quadrupole and dissociated by collision with argon in the second quadrupole. The KIEs were measured by comparing the extents of dissociation of the lighter versus the heavier isotopomeric adducts. In most cases, lower collision energies and multiple collision conditions favoured larger KIE values, an expected feature of easily dissociated cluster ions considering zero-point energies (ZPEs). The larger chloride adduct of cyclohexanol gave greater KIEs compared with the smaller alcohols, a consequence of slower dissociation due to the larger number of degrees of freedom. Dissociation of the chloride adducts gave greater KIEs than the corresponding bromide adducts, a result that is also consistent with expectations based on ZPEs. Both the chloride and bromide adducts of 2,4-pentanedione, when dissociated at 6 eV collision energy under single-collision conditions, displayed normal KIEs (1.0460 ± 0.0012 and 1.0092 ± 0.0035 respectively). These and the alcohol results were correctly predicted by the ZPEs calculated using commonly applied ab initio Hartree–Fock (HF) and B3LYP density functional theory (DFT) methods with large basis sets (6–311 containing both polarization and diffuse functions). Geometry optimization calculations for the 2,4-pentanedione chloride adduct using either the Restricted Hartree–Fock (RHF) method with a 6–31G* basis set or using the more accurate 6–31++G** method showed that, in the most stable form, the chloride is bonded at multiple sites by a molecule of 2,4-pentanedione. In this structure, chloride binds weakly to both the methylene and the methyl hydrogen atoms. Collision-induced dissociation furnishes chloride and 2,4-pentanedione anion ([M – H]–) as competitive negatively charged products, which is consistent with the proposed structure. It is interesting that the intermolecular KIEs in this study tend to be normal, while intramolecular isotope effects in halides, notably of the type M1Cl+M2 are inverse, as a consequence of the lower ZPEs associated with the heavier isotopomers. The difference in the two systems is that the stronger bonds are found in the products in the case of M1Cl+M2 dissociation but in the reactants in the case of MCl– dissociation.

scholarly journals Hirshfeld atom refinement

IUCrJ ◽  
2014 ◽  
Vol 1 (5) ◽  
pp. 361-379 ◽  
Author(s):  
Silvia C. Capelli ◽  
Hans-Beat Bürgi ◽  
Birger Dittrich ◽  
Simon Grabowsky ◽  
Dylan Jayatilaka
Keyword(s):  
Hydrogen Atom ◽  
Diffraction Data ◽  
Iterative Procedure ◽  
Structural Parameters ◽  
X Ray Diffraction ◽  
Hydrogen Atoms ◽  
Electron Densities ◽  
X Ray ◽  
Bond Lengths ◽  
Better Than

Hirshfeld atom refinement (HAR) is a method which determines structural parameters from single-crystal X-ray diffraction data by using an aspherical atom partitioning of tailor-madeab initioquantum mechanical molecular electron densities without any further approximation. Here the original HAR method is extended by implementing an iterative procedure of successive cycles of electron density calculations, Hirshfeld atom scattering factor calculations and structural least-squares refinements, repeated until convergence. The importance of this iterative procedure is illustratedviathe example of crystalline ammonia. The new HAR method is then applied to X-ray diffraction data of the dipeptide Gly–L-Ala measured at 12, 50, 100, 150, 220 and 295 K, using Hartree–Fock and BLYP density functional theory electron densities and three different basis sets. All positions and anisotropic displacement parameters (ADPs) are freely refined without constraints or restraints – even those for hydrogen atoms. The results are systematically compared with those from neutron diffraction experiments at the temperatures 12, 50, 150 and 295 K. Although non-hydrogen-atom ADPs differ by up to three combined standard uncertainties (csu's), all other structural parameters agree within less than 2 csu's. Using our best calculations (BLYP/cc-pVTZ, recommended for organic molecules), the accuracy of determining bond lengths involving hydrogen atoms from HAR is better than 0.009 Å for temperatures of 150 K or below; for hydrogen-atom ADPs it is better than 0.006 Å2as judged from the mean absolute X-ray minus neutron differences. These results are among the best ever obtained. Remarkably, the precision of determining bond lengths and ADPs for the hydrogen atoms from the HAR procedure is comparable with that from the neutron measurements – an outcome which is obtained with a routinely achievable resolution of the X-ray data of 0.65 Å.

AN EVALUATION OF QUANTUM CHEMICAL CALCULATIONS OF REACTION ENERGIES FOR CATALYTIC ACTIVATION PROCESSES: THE ACTIVATION OF PROPANE BY A RHODIUM CATALYST REVISITED

2012 ◽  
Vol 11 (02) ◽  
pp. 297-312 ◽  
Author(s):  
WILLIAN R. ROCHA ◽  
ÉDER S. XAVIER ◽  
JÚLIO C. S. DA SILVA ◽  
ROBERTA P. DIAS ◽  
HÉLIO F. DOS SANTOS ◽  
...  
Keyword(s):  
Ab Initio ◽  
Density Functional ◽  
Structural Parameters ◽  
Relative Energy ◽  
Basis Set ◽  
Geometrical Parameters ◽  
Computationally Efficient ◽  
Hartree Fock ◽  
Rhodium Atom ◽  
Reaction Energies

In this paper we report the state of the art CCSD(T)//MP2 ab initio calculations for the activation of propane by cyclopentadienyl carbonyl rhodium, (Cp)Rh(CO) , using the effective core potential of Hay and Wadt (LANL2DZ) for rhodium atom and the correlated consistent polarized valence double-ξ basis set (cc-pVDZ) for C , H and O atoms. The CCSD(T) energy values are used as reference to assess the effect of electron correlation on the reaction energies, as well as the performance of density functional theory (DFT) energy values using various functionals. An investigation on the accuracy of DFT results is relevant since their use in calculations involving large molecular systems is a computationally efficient strategy that enables us to tackle important problems in organometallics field and supramolecular chemistry. Our results for the small model system show that all DFT functionals used here correctly predict the CCSD(T) energy pattern and also reproduce very satisfactorily the MP2 geometrical parameters. The BP86, PBE1PBE and PW91 functionals exhibited the best agreement with structural parameters and relative energy values as compared with ab initio post-Hartree–Fock results, showing a potential use in theoretical investigations on larger systems.

scholarly journals Photocrosslinked Alginate-Methacrylate Hydrogels with Modulable Mechanical Properties: Effect of the Molecular Conformation and Electron Density of the Methacrylate Reactive Group

Materials ◽  
2020 ◽  
Vol 13 (3) ◽  
pp. 534 ◽  
Author(s):  
Fernanda Araiza-Verduzco ◽  
Eustolia Rodríguez-Velázquez ◽  
Harold Cruz ◽  
Ignacio A. Rivero ◽  
Delvis R. Acosta-Martínez ◽  
...  
Keyword(s):  
Mechanical Properties ◽  
Electron Density ◽  
Polymer Chain ◽  
Density Functional ◽  
Molecular Conformation ◽  
Structural Parameters ◽  
Density Functional Theory Method ◽  
Proton Nuclear Magnetic Resonance ◽  
Hydrogen Atoms ◽  
Tissue Replacement

Hydrogels for load-bearing biomedical applications, such as soft tissue replacement, are required to be tough and biocompatible. In this sense, alginate-methacrylate hydrogels (H-ALGMx) are well known to present modulable levels of elasticity depending on the methacrylation degree; however, little is known about the role of additional structural parameters. In this work, we present an experimental-computational approach aimed to evaluate the effect of the molecular conformation and electron density of distinct methacrylate groups on the mechanical properties of photocrosslinked H-ALGMx hydrogels. Three alginate-methacrylate precursor macromers (ALGMx) were synthesized: alginate-glycidyl methacrylate (ALGM1), alginate-2-aminoethyl methacrylate (ALGM2), and alginate-methacrylic anhydride (ALGM3). The macromers were studied by Fourier-transform infrared spectroscopy (FTIR), proton nuclear magnetic resonance (1H-NMR), and density functional theory method (DFT) calculations to assess their molecular/electronic configurations. In parallel, they were also employed to produce H-ALGMx hydrogels, which were characterized by compressive tests. The obtained results demonstrated that tougher hydrogels were produced from ALGMx macromers presenting the C=C reactive bond with an outward orientation relative to the polymer chain and showing free rotation, which favored in conjunction the covalent crosslinking. In addition, although playing a secondary role, it was also found that the presence of acid hydrogen atoms in the methacrylate unit enables the formation of supramolecular hydrogen bonds, thereby reinforcing the mechanical properties of the H-ALGMx hydrogels. By contrast, impaired mechanical properties resulted from macromer conditions in which the C=C bond adopted an inward orientation to the polymer chain accompanied by a torsional impediment.

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