scholarly journals Spin Density Topology

Molecules ◽  
2020 ◽  
Vol 25 (15) ◽  
pp. 3537 ◽  
Author(s):  
Giovanna Bruno ◽  
Giovanni Macetti ◽  
Leonardo Lo Presti ◽  
Carlo Gatti
Keyword(s):  
Density Gradient ◽  
Spin Density ◽  
Critical Points ◽  
Density Functional ◽  
Topological Analysis ◽  
Scalar Fields ◽  
Density Topology ◽  
Density Distributions ◽  
Topological Features ◽  
Electron Density Gradient

Despite its role in spin density functional theory and it being the basic observable for describing and understanding magnetic phenomena, few studies have appeared on the electron spin density subtleties thus far. A systematic full topological analysis of this function is lacking, seemingly in contrast to the blossoming in the last 20 years of many studies on the topological features of other scalar fields of chemical interest. We aim to fill this gap by unveiling the kind of information hidden in the spin density distribution that only its topology can disclose. The significance of the spin density critical points, the 18 different ways in which they can be realized and the peculiar topological constraints on their number and kind, arising from the presence of positive and negative spin density regions, is addressed. The notion of molecular spin graphs, spin maxima (minima) joining paths, spin basins and of their valence is introduced. We show that two kinds of structures are associated with a spin–polarized molecule: the usual one, defined through the electron density gradient, and the magnetic structure, defined through the spin density gradient and composed in general by at least two independent spin graphs, related to spin density maxima and minima. Several descriptors, such as the spin polarization index, are introduced to characterize the properties of spin density critical points and basins. The study on the general features of the spin density topology is followed by the specific example of the water molecule in the 3B1 triplet state, using spin density distributions of increasing accuracy.

Computational Investigation of the Asymmetry in Photosynthetic Reaction Center Models from First Principles

2020 ◽  
Author(s):  
Denis Artiukhin ◽  
Patrick Eschenbach ◽  
Johannes Neugebauer
Keyword(s):  
Spin Density ◽  
Reaction Center ◽  
Density Functional ◽  
Photosynthetic Reaction Center ◽  
Chem Phys ◽  
Molecular Structures ◽  
Error Characteristic ◽  
Molecular Systems ◽  
Density Distributions ◽  
The Asymmetry

We present a computational analysis of the asymmetry in reaction center models of photosystem I, photosystem II, and bacteria from <i>Synechococcus elongatus</i>, <i>Thermococcus vulcanus</i>, and <i>Rhodobacter sphaeroides</i>, respectively. The recently developed FDE-diab methodology [J. Chem. Phys., 148 (2018), 214104] allowed us to effectively avoid the spin-density overdelocalization error characteristic for standard Kohn–Sham Density Functional Theory and to reliably calculate spin-density distributions and electronic couplings for a number of molecular systems ranging from dimeric models in vacuum to large protein including up to about 2000 atoms. The calculated spin densities showed a good agreement with available experimental results and were used to validate reaction center models reported in the literature. We demonstrated that the applied theoretical approach is very sensitive to changes in molecular structures and relative orientation of molecules. This makes FDE-diab a valuable tool for electronic structure calculations of large photosynthetic models effectively complementing the existing experimental techniques.

Intra- and intermolecular interactions in small bioactive molecules: cooperative features from experimental and theoretical charge-density analysis

2006 ◽  
Vol 62 (4) ◽  
pp. 612-626 ◽  
Author(s):  
Parthapratim Munshi ◽  
Tayur N. Guru Row
Keyword(s):  
Salicylic Acid ◽  
Hydrogen Bonds ◽  
Intermolecular Interactions ◽  
Density Functional ◽  
Theoretical Calculations ◽  
Topological Analysis ◽  
Van Der Waals Interactions ◽  
Bioactive Molecules ◽  
Topological Features ◽  
Weak Intermolecular Interactions

The topological features of the charge densities, ρ(r), of three bioactive molecules, 2-thiouracil [2,3-dihydro-2-thioxopyrimidin-4(1H)-one], cytosine [4-aminopyrimidin-2(1H)-one] monohydrate and salicylic acid (2-hydroxybenzoic acid), have been determined from high-resolution X-ray diffraction data at 90 K. The corresponding results are compared with the periodic theoretical calculations, based on theoretical structure factors, performed using DFT (density-functional theory) at the B3LYP/6-31G** level. The molecules pack in the crystal lattices via weak intermolecular interactions as well as strong hydrogen bonds. All the chemical bonds, including the intra- and intermolecular interactions in all three compounds, have been quantitatively described by topological analysis based on Bader's quantum theory of `Atoms In Molecules'. The roles of interactions such as C—H...O, C—H...S, C—H...π and π...π have been investigated quantitatively in the presence of strong hydrogen bonds such as O—H...O, N—H...O and N—H...S, based on the criteria proposed by Koch and Popelier to characterize hydrogen bonds and van der Waals interactions. The features of weak intermolecular interactions, such as S...S in 2-thiouracil, the hydrogen bonds generated from the water molecule in cytosine monohydrate and the formation of the dimer via strong hydrogen bonds in salicylic acid, are highlighted on a quantum basis. Three-dimensional electrostatic potentials over the molecular surfaces emphasize the preferable binding sites in the structure and the interaction features of the atoms in the molecules, which are crucial for drug–receptor recognition.

Computational Investigation of the Spin-Density Asymmetry in Photosynthetic Reaction Center Models from First Principles

2020 ◽  
Author(s):  
Denis Artiukhin ◽  
Patrick Eschenbach ◽  
Johannes Neugebauer
Keyword(s):  
Spin Density ◽  
Reaction Center ◽  
Density Functional ◽  
Cation Radical ◽  
Photosynthetic Reaction Center ◽  
Chem Phys ◽  
Molecular Structures ◽  
Error Characteristic ◽  
Molecular Systems ◽  
Density Distributions

We present a computational analysis of the spin-density asymmetry in cation radical states of reaction center models from photosystem I, photosystem II, and bacteria from Synechococcus elongatus, Thermococcus vulcanus, and Rhodobacter sphaeroides, respectively. The recently developed FDE-diab methodology [J. Chem. Phys., 148 (2018), 214104] allowed us to effectively avoid the spin-density overdelocalization error characteristic for standard Kohn–Sham Density Functional Theory and to reliably calculate spin-density distributions and electronic couplings for a number of molecular systems ranging from inner pairs of (bacterio)chlorophyll a molecules in vacuum to large protein including up to about 2000 atoms. The calculated spin densities show a good agreement with available experimental results and were used to validate reaction center models reported in the literature. Here we demonstrate that the applied theoretical approach is very sensitive to changes in molecular structures and relative orientation of molecules. This makes FDE-diab a valuable tool for electronic structure calculations of large photosynthetic models effectively complementing the existing experimental techniques.<br>

MAGNETIC COUPLING CONSTANTS AND SPIN DENSITY DISTRIBUTIONS FOR CYANO-BRIDGED Gd(III)-Fe(III) AND Gd(III)-Cr(III) COMPOUNDS: BROKEN-SYMMETRY AND DENSITY FUNCTIONAL THEORY CALCULATIONS

2005 ◽  
Vol 19 (15n17) ◽  
pp. 2538-2543 ◽  
Author(s):  
YI QUAN ZHANG ◽  
CHENG LIN LUO ◽  
ZHI YU
Keyword(s):  
Density Functional Theory ◽  
Spin Density ◽  
Spin Polarization ◽  
Density Functional ◽  
Population Analysis ◽  
Magnetic Coupling ◽  
Coupling Constants ◽  
Broken Symmetry ◽  
Functional Theory ◽  
Density Distributions

Magnetic coupling constants J for the complete structures of [ Gd(capro) 2( H 2 O )4 Cr(CN) 6]• H 2 O (capro represents caprolactam) (a) and trans-[ Fe(CN) 4(μ- CN )2 Gd ( H 2 O )4 (bpy) ]•4 H 2 O •1.5 bpy (b) have been calculated using hybrid density functional theory (DFT) B3LYP combined with a modified broken symmetry approach (BS). The calculated J value of -0.24 cm-1 for a is very close to the experimental -0.33 cm-1. They both show the antiferromagnetic interaction between Gd(III) and Cr(III) . For b, although the sign of the calculated J value of 4.24 cm-1 is different from that of the experimental -0.38 cm-1, the two values both show the weak magnetic coupling interaction between Gd(III) and Fe(III) . The spin density distributions are discussed on the basis of Mulliken population analysis. For complexes a and b, both transition metal ( Fe(III) or Cr(III) ) and rare earth Gd(III) display a spin polarization effect on the surrounding atoms, where a counteraction of the opposite polarization effects leads to a low spin density on the bridging ligand C1N1 . For the compounds Gd(III) - Cr(III) (a) and Gd(III) - Fe(III) (b) in the HS states, Cr(III) has stronger spin polarization influence on the bridging atoms than Fe(III) even causing the positive spin population on the bridging atom N1 .

scholarly journals Topological Analysis of Magnetically Induced Current Densities in Strong Magnetic Fields Using Stagnation Graphs

Chemistry ◽  
2021 ◽  
Vol 3 (3) ◽  
pp. 916-934
Author(s):  
Tom J. P. Irons ◽  
Adam Garner ◽  
Andrew M. Teale
Keyword(s):  
Magnetic Field ◽  
Vector Field ◽  
Magnetic Fields ◽  
Density Functional ◽  
Strong Field ◽  
Topological Analysis ◽  
Equilibrium Geometry ◽  
Strong Magnetic Fields ◽  
Topological Features ◽  
Current Densities

Stagnation graphs provide a useful tool to analyze the main topological features of the often complicated vector field associated with magnetically induced currents. Previously, these graphs have been constructed using response quantities appropriate for modest applied magnetic fields. We present an implementation capable of producing these graphs in arbitrarily strong magnetic fields, using current-density-functional theory. This enables us to study how the topology of the current vector field changes with the strength and orientation of the applied magnetic field. Applications to CH4, C2H2 and C2H4 are presented. In each case, we consider molecular geometries optimized in the presence of the magnetic field. The stagnation graphs reveal subtle changes to this vector field where the symmetry of the molecule remains constant. However, when the electronic state and symmetry of the corresponding equilibrium geometry changes with increasing field strength, the changes to the stagnation graph are extensive. We expect that the approach presented here will be helpful in interpreting changes in molecular structure and bonding in the strong-field regime.

scholarly journals Computational Investigation of the Spin-Density Asymmetry in Photosynthetic Reaction Center Models from First Principles

2020 ◽  
Author(s):  
Denis Artiukhin ◽  
Patrick Eschenbach ◽  
Johannes Neugebauer
Keyword(s):  
Spin Density ◽  
Reaction Center ◽  
Density Functional ◽  
Cation Radical ◽  
Photosynthetic Reaction Center ◽  
Chem Phys ◽  
Molecular Structures ◽  
Error Characteristic ◽  
Molecular Systems ◽  
Density Distributions

We present a computational analysis of the spin-density asymmetry in cation radical states of reaction center models from photosystem I, photosystem II, and bacteria from Synechococcus elongatus, Thermococcus vulcanus, and Rhodobacter sphaeroides, respectively. The recently developed FDE-diab methodology [J. Chem. Phys., 148 (2018), 214104] allowed us to effectively avoid the spin-density overdelocalization error characteristic for standard Kohn–Sham Density Functional Theory and to reliably calculate spin-density distributions and electronic couplings for a number of molecular systems ranging from inner pairs of (bacterio)chlorophyll a molecules in vacuum to large protein including up to about 2000 atoms. The calculated spin densities show a good agreement with available experimental results and were used to validate reaction center models reported in the literature. Here we demonstrate that the applied theoretical approach is very sensitive to changes in molecular structures and relative orientation of molecules. This makes FDE-diab a valuable tool for electronic structure calculations of large photosynthetic models effectively complementing the existing experimental techniques.<br>

A density functional study of copper hydroxonitrate: size effects and spin density topology

Polyhedron ◽  
2001 ◽  
Vol 20 (11-14) ◽  
pp. 1305-1309 ◽  
Author(s):  
C Massobrio ◽  
Y Pouillon ◽  
P Rabu ◽  
M Drillon
Keyword(s):  
Spin Density ◽  
Size Effects ◽  
Density Functional ◽  
Functional Study ◽  
Density Topology ◽  
Density Functional Study

A Combined ab initio and Density Functional Study of the Electronic Structure of Thymine and 2-Thiothymine Radicals

2003 ◽  
Vol 68 (12) ◽  
pp. 2322-2334 ◽  
Author(s):  
Robert Vianello ◽  
Zvonimir B. Maksić
Keyword(s):  
Ab Initio ◽  
Spin Density ◽  
Density Functional ◽  
Radical Cations ◽  
Functional Study ◽  
Theory Approach ◽  
Functional Theory ◽  
Adiabatic Ionization Potential ◽  
Highest Occupied Molecular Orbital ◽  
Positively Charged

The electronic and energetic properties of thymine (1) and 2-thiothymine (2) and their neutral and positively charged radicals are considered by a combined ab initio and density functional theory approach. It is conclusively shown that ionization of 1 and 2 greatly facilitates deprotonation of the formed radical cations thus making the proton transfer between charged and neutral precursor species thermodynamically favourable. The adiabatic ionization potential of 1 and 2 are analysed. It appears that ADIP(1) is larger than ADIP(2) by 10 kcal/mol, because of greater stability of the highest occupied molecular orbital (HOMO) of the former. It is also shown beyond any doubt that the spin density in neutral and cationic radical of 2 is almost exclusively placed on the σ-3p AO of sulfur implying that these two systems represent rather rare sigma-radicals. In contrast, the spin density of radicals of 1 is distributed over their π-network.

Sign in / Sign up

Export Citation Format

Share Document