Relativistic quantum crystallography of diphenyl- and dicyanomercury. Theoretical structure factors and Hirshfeld atom refinement

2019 ◽  
Vol 75 (5) ◽  
pp. 705-717 ◽  
Author(s):  
Lukáš Bučinský ◽  
Dylan Jayatilaka ◽  
Simon Grabowsky
Keyword(s):  
Population Analysis ◽  
Relativistic Quantum ◽  
Perfect Match ◽  
Relativistic Effects ◽  
Basis Set ◽  
Hydrogen Atoms ◽  
Mulliken Population ◽  
Theoretical Structure ◽  
Structure Factors ◽  
The Impact

Quantum crystallographic refinement of heavy-element-containing compounds is a challenge, because many physical effects have to be accounted for adequately. Here, the impact and magnitude of relativistic effects are compared with those of electron correlation, polarization through the environment, choice of basis set and treatment of thermal motion effects on the structure factors of diphenylmercury(II) [Hg(Ph)2] and dicyanomercury(II) [Hg(CN)2]. Furthermore, the individual atomic contributions to the structure factors are explored in detail (using Mulliken population analysis and the exponential decay of atomic displacement parameters) to compare the contributions of lighter atoms, especially hydrogen atoms, against mercury. Subsequently, relativistic Hirshfeld atom refinement (HAR) is validated against theoretical structure factors of Hg(Ph)2 and Hg(CN)2, starting from perturbed geometries, to test if the relativistic variant of HAR leads to multiple solutions. Generally, relativistic HAR is successful, leading to a perfect match with the reference geometries, but some limitations are pointed out.

Population Analysis with Hydrogen 2 p Polarization Functions Included in the INDO Basis Set

1980 ◽  
Vol 35 (12) ◽  
pp. 1350-1353
Author(s):  
J. C. Facelli ◽  
R. H. Contreras
Keyword(s):  
Ab Initio ◽  
Population Analysis ◽  
Basis Set ◽  
Ab Initio Methods ◽  
Mulliken Population Analysis ◽  
Indo Method ◽  
Hydrogen Atoms ◽  
Mulliken Population ◽  
Electron Population ◽  
Polarization Functions

Abstract Mulliken population analysis with 2p polarization functions included in the AO basis set of the INDO method has been performed for a set of molecules containing hydrogen as well as first row atoms. It is found that this enlargement of the basis set yields an increasing electron population in hydrogen atoms, in agreement with trends found in “ab initio” methods.

HgH2 meets relativistic quantum crystallography. How to teach relativity to a non-relativistic wavefunction

2021 ◽  
Vol 77 (1) ◽  
pp. 54-66
Author(s):  
Michal Podhorský ◽  
Lukáš Bučinský ◽  
Dylan Jayatilaka ◽  
Simon Grabowsky
Keyword(s):  
Systematic Error ◽  
Structure Factor ◽  
Relativistic Quantum ◽  
Relativistic Effects ◽  
X Ray ◽  
Structure Factors ◽  
Quantum Crystallography

The capability of X-ray constrained wavefunction (XCW) fitting to introduce relativistic effects into a non-relativistic wavefunction is tested. It is quantified how much of the reference relativistic effects can be absorbed in the non-relativistic XCW calculation when fitted against relativistic structure factors of a model HgH2 molecule. Scaling of the structure-factor sets to improve the agreement statistics is found to introduce a significant systematic error into the XCW fitting of relativistic effects.

Examination of the molecular properties of D-fructose and L-sorbose by abinitio LCAO-MO calculations

1984 ◽  
Vol 62 (8) ◽  
pp. 1506-1511 ◽  
Author(s):  
Walter A. Szarek ◽  
Sirkka-Liisa Korppi-Tommola ◽  
Olivier R. Martin ◽  
Vedene H. Smith Jr.
Keyword(s):  
Point Charge ◽  
Population Analysis ◽  
Sweet Taste ◽  
Molecular Properties ◽  
Intramolecular Interactions ◽  
Mo Calculations ◽  
Hydrogen Atoms ◽  
Mulliken Population ◽  
Hydroxyl Hydrogen ◽  
Lcao Mo

Abinitio SCF LCAO-MO calculations at the STO-3G level have been performed on β-D-fructopyranose (1) and α-L-sorbopyranose (2) using crystallographic data as the geometrical input. Molecular properties of 1 and 2 are discussed in terms of orbital energies, total energy, ionization potentials, Mulliken population analysis, and electrostatic potentials, with a particular emphasis on the possible consequences of these features as regards the sweet taste of these two ketoses. No correlation was found, for example, with the electrostatic, point-charge distribution since the calculated hydrogen-bonding abilities would lead to the prediction of 2 being sweeter than 1. On the other hand, non-bonded overlap populations between oxygen and hydroxyl-hydrogen atoms reveal the presence of intramolecular interactions, which may have a determinant influence on the taste of these molecules and which could explain why D-fructose is much sweeter than its epimer at C-5, namely, L-sorbose.

X-ray and DFT Investigation of (E)-4-bromo-5-methoxy-2-((o-tolylimino)methyl)phenol Compound

2018 ◽  
pp. 454-461
Keyword(s):  
Density Functional ◽  
Theoretical Calculations ◽  
Population Analysis ◽  
Diffraction Method ◽  
Dft Method ◽  
Basis Set ◽  
X Ray Diffraction ◽  
Mulliken Population ◽  
Charge Delocalization ◽  
X Ray

(E)-4-bromo-5-methoxy-2-((o-tolylimino)methyl)phenol was investigated by experimental and theoretical methodologies. The solid state molecular structure was determined by X-ray diffraction method. All theoretical calculations were performed by density functional theory (DFT) method by using B3LYP/6-31G(d,p) basis set. The titled compound showed the preference of enol form, as supported by X-ray diffraction method. The geometric and molecular properties were compaired for both enol-imine and keto-amine forms for title compound. Stability of the molecule arises from hyperconjugative interactions, charge delocalization and intramolecular hydrogen bond has been analyzed using natural bond orbital (NBO) analysis. Mulliken population method and natural population analysis (NPA) have been studied. Also, condensed Fukui function and relative nucleophilicity indices calculated from charges obtained with orbital charge calculation methods (NPA). Molecular electrostatic potential (MEP) and non linear optical (NLO) properties are also examined.

scholarly journals The Hydrogen Passivated Graphene Cluster and its Stability - First Principle DFT (B3LYP) Levels of Approximation with the Basis Set 3-21G

2018 ◽  
Vol 1 (1) ◽  
pp. 5-10
Author(s):  
Debendra Baniya
Keyword(s):  
Binding Energy ◽  
Carbon Atom ◽  
State Energy ◽  
Population Analysis ◽  
Basis Set ◽  
Mulliken Population ◽  
B3lyp Level ◽  
Reported Data ◽  
Homo Lumo ◽  
Graphene Cluster

First-principles DFT (B3LYP) levels of calculations with the basis set 3-21G have been carried out in order to study the geometric stability and electronic properties of hydrogen passivated graphene (H-graphene) clusters(CN) (where N = 6, 10, 13, 16, 22, 24, 27, 30, 35, 37, 40, 42, 45, 47, 48, 50, 52, 54, 70 and 96) and perform the DOS spectrum on H-graphene (C16H10, C24H12, C30H14, C48H18, C70H22 and C96H24) using Mulliken population analysis by the Gaussian 03 W set of programs. The variations of ground state energy of graphene clusters are observed on sizes and corresponding number of carbon atoms. The binding energy per carbon atom is the function of carbon atoms for the number of carbon atoms less than 30 and saturated at carbon’s number 30 and more in the DFT (B3LYP) levels of approximation with the basis set 3-21G. The binding energy per carbon atom of a pure graphene sheet C32 is 8.03 eV/atom in the DFT (B3LYP) level of approximation with the choice of the basis set 3-21G, which is acceptable with previous reported data 7.91 eV/atom. The HOMO-LUMO gap in NBO is studied for some H-grapheneclustors C16H10, C24H12, C30H14, C48H18, C70H22 and C96H24.

Quantum Mechanical Study of Clean and H-Covered α-MoO3(100) Surface

2003 ◽  
Vol 02 (02) ◽  
pp. 245-256 ◽  
Author(s):  
A. Sayede ◽  
B. Khelifa ◽  
C. Mathieu ◽  
H. Aourag
Keyword(s):  
Electronic Properties ◽  
Density Functional ◽  
Population Analysis ◽  
Chemical Properties ◽  
Hydrogen Atoms ◽  
Mulliken Population ◽  
Hartree Fock ◽  
Mechanical Study ◽  
Quantum Mechanical Study ◽  
Local Electronic Structure

Structure and electronic properties of the α-MoO3(100) surface, as well as H adsorption on the α-MoO3(100) surface have been studied with periodic slab Hartree–Fock calculations. Gradient corrected density functional calculations have been performed in this study. The structure and electronic properties of the (100) surface are in agreement with experimental and previous theoretical results. Local electronic structure near the different surface oxygen sites are analyzed with Mulliken Population Analysis. The oxide is partially ionic and the symmetrically oxygens exhibit more ionic feature while the terminal oxygens are more covalent. Electrostatic potentials show broad negative minima above the terminal oxygen centers, which suggest that electrophilic adparticles, like H, resulting from surface reactions, will be attracted preferentially at these sites. The results of the H adsorption on the (100) surface are interpreted based on charge-transfer interactions between the surface and H species. It is found that terminal oxygen sites are the most stable binding site. Ionic relaxation of the α-MoO3(100) surface for the adsorption of hydrogen has no effect on the chemical properties and hydrogen atoms adsorbed favorably on the α-MoO3(100) surface at full coverage.

scholarly journals Corrosion Inhibition of Copper in 2M Nitric Acid Solution by 2-(Thiobenzyl)-5-Nitro-1H-Benzimidazole

2018 ◽  
Vol 3 (04) ◽  
pp. 54-63 ◽  
Author(s):  
Nagnonta Hippolyte Coulibaly ◽  
Yapi Serge Brou ◽  
Sagne Akpa ◽  
Juan Creus ◽  
Albert Trokourey
Keyword(s):  
Nitric Acid ◽  
Acid Solution ◽  
Molecular Orbital ◽  
Nitric Acid Solution ◽  
Energy Gap ◽  
Population Analysis ◽  
Basis Set ◽  
Adsorption Parameters ◽  
Mulliken Population ◽  
Reactivity Descriptors

Pickling with nitric acid is commonly practiced in industry for finishing metal surfaces. The use of inhibitors during the pickling operation is of very recent origin. The TBNBI inhibition effect on copper corrosion in 2M nitric acid solution was investigated by weight loss method in relation to the temperature (25 to 40°C) and inhibitor concentration range 10-4 to 5.10-3 M. The results show that TBNBI is a good inhibitor for copper and the inhibition efficiency increases with concentration of TBNBI but decreases with increase in temperature. The adsorption parameters (ΔGa0ds ,ΔHa0ds ,ΔSa0ds ) and the activation ones * * a a a (E ,ΔH ,ΔS ) for the corrosion process in inhibited and uninhibited nitric acid solution were also calculated using Arrhenius equations. It can be concluded that the adsorption of the compound is spontaneous and found to occur through both physisorption and chemisorption processes. The adsorbed film on copper surface was characterized using optic microscopy and Raman spectroscopy. The surface analysis confirmed the inhibition action of TBNBI. Quantum chemical calculations using Gaussian 09 at B3LYP level with 6-31G (d,p) basis set lead to obtain molecular descriptors such as EHOMO (energy of the highest occupied molecular orbital), ELUMO (energy of the lowest unoccupied molecular orbital), ΔE (energy gap) and μ (dipole moment). The global reactivity descriptors such as χ (electronegativity), η (hardness), S (softness) and ω (electrophilicity index) were derived using Koopman’s theorem and analyzed. We used the condensed Fukui function and softness indices, Mulliken population analysis for local reactivity study. The calculated results are consistent with the experimental data.

scholarly journals Crystal structure of new formamidinium triiodide jointly refined by single-crystal XRD, Raman scattering spectroscopy and DFT assessment of hydrogen-bond network features

2021 ◽  
Vol 77 (7) ◽  
pp. 692-695
Author(s):  
Artem A. Ordinartsev ◽  
Andrey A. Petrov ◽  
Konstantin A. Lyssenko ◽  
Andrey V. Petrov ◽  
Eugene A. Goodilin ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Raman Scattering ◽  
Population Analysis ◽  
Hydrogen Atoms ◽  
Mulliken Population ◽  
Triclinic Space Group ◽  
Raman Scattering Spectroscopy ◽  
Scattering Spectra ◽  
Bond Network ◽  
Raman Scattering Spectra

A novel triiodide phase of the formamidinium cation, CH5N2 +·I3 −, crystallizes in the triclinic space group P\overline{1} at a temperature of 110 K. The structure consists of two independent isolated triiodide ions located on inversion centers. The centrosymmetric character of I3 − was additionally confirmed by the observed pronounced peaks of symmetrical oscillations of I3 − at 115–116 cm−1 in Raman scattering spectra. An additional structural feature is that each terminal iodine atom is connected with three neighboring planar formamidinium cations by N—H...I hydrogen bonding with the N—H...I bond length varying from 2.81 to 3.08 Å, forming a deformed two-dimensional framework of hydrogen bonds. A Mulliken population analysis showed that the calculated charges of hydrogen atoms correlate well with hydrogen-bond lengths. The crystal studied was refined as a three-component twin with domain ratios of 0.631 (1):0.211 (1):0.158 (1).

Molecular Structural and Vibrational Spectroscopic Assignments of n5-(4-Methoxyphenyl)-3-(1-methylindol-3-yl)-isoxazole using DFT Theory Calculations

2019 ◽  
Vol 4 (3) ◽  
pp. 147-151
Author(s):  
J. Jani Matilda ◽  
T.F. Abbs Fen Reji
Keyword(s):  
Molecular Orbital ◽  
Density Functional ◽  
Population Analysis ◽  
Nbo Analysis ◽  
Basis Set ◽  
Atomic Charges ◽  
Dft Methods ◽  
Mulliken Population ◽  
B3lyp Method ◽  
Experimental Values

In an effort to evaluate and design fast, accurate density functional theory (DFT) methods for 5-(4- methoxyphenyl)-3-(1-methylindol-3yl)isoxazole compound was done using Gaussion’ 09 program package using B3LYP method with the 6-31G basis set, which has been successfully applied in order to derive the optimized geometry, bonding features, harmonic vibrational wave numbers, NBO analysis and Mulliken population analysis on atomic charges in the ground state. Optimized geometries of the molecule have been described and collate with the experimental values. The experimental atomic charges demonstrates adequate concurrence with the theoretical prediction from DFT. The theoretical spectra values have been interpreted and compared with the FT-IR spectra. The calculated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy gaps also confirm that charge transfer takes place within the molecule.

Sign in / Sign up

Export Citation Format

Share Document