scholarly journals Density Functional Theory Study on Metal-Binding Energies for Human Serum Transferrin-Metal Complexes

2012 ◽  
Vol 2012 ◽  
pp. 1-5 ◽  
Author(s):  
Tetsuya Sakajiri ◽  
Hirofumi Yajima ◽  
Takaki Yamamura
Keyword(s):  
Density Functional Theory ◽  
Human Serum ◽  
Metal Binding ◽  
Density Functional ◽  
Conformational Transition ◽  
Binding Energies ◽  
Serum Transferrin ◽  
Functional Theory ◽  
Human Serum Transferrin ◽  
Solvation Energies

The absolute values of the metal-binding energies of human serum transferrin (Tf) N-lobe, |ΔE|, were calculated using the density functional theory and were found to increase in magnitude in the following order: Fe(III)>Ga(III)>Al(III)>Cu(II)>Zn(II)>Ni(II). The calculated energies were well correlated with the logarithmic values of the reported metal-binding constants of Tf, which had been experimentally determined, with a correlation coefficient of 0.96. In the estimation of the binding energies, the solvation energies (solvent effect) of free metal ions were a very important factor. The results provide a theoretical explanation for the binding of Fe(III) to Tf, which produces sufficient energy to induce a conformational transition of the Tf molecule, making it possible to interact with Tf receptor 1.

A Density Functional Theory Study of the Iron-Binding Site of Human Serum Transferrin

2004 ◽  
Vol 57 (12) ◽  
pp. 1219 ◽  
Author(s):  
David Rinaldo ◽  
Martin J. Field
Keyword(s):  
Human Serum ◽  
Binding Site ◽  
Conformational Changes ◽  
Metal Binding ◽  
Density Functional ◽  
Release Mechanism ◽  
Serum Transferrin ◽  
Iron Binding ◽  
Iron Release ◽  
Human Serum Transferrin

Human serum transferrin binds ferric ions with high affinity in the blood stream and releases them into cells by a process involving receptor-mediated endocytosis and a decrease in pH. The iron-release mechanism is unclear but protonation events and conformational changes are known to be important. In this study, we investigate properties of the iron-binding site theoretically. Our results suggest that an equatorial histidine could be in its histidinate form when bound to iron at neutral and high pH and that protonation of an axial tyrosine is a key event in iron release. Support for this mechanism from other metal-binding enzymes is also presented.

A DFT study of spherands containing five anisyl groups — Highly preorganized to bind the alkali metal

2006 ◽  
Vol 84 (8) ◽  
pp. 1045-1049 ◽  
Author(s):  
Shabaan AK Elroby ◽  
Kyu Hwan Lee ◽  
Seung Joo Cho ◽  
Alan Hinchliffe
Keyword(s):  
Density Functional Theory ◽  
Binding Energy ◽  
Density Functional ◽  
Ionic Radius ◽  
Binding Energies ◽  
Cavity Size ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
X Ray ◽  
Good Agreement

Although anisyl units are basically poor ligands for metal ions, the rigid placements of their oxygens during synthesis rather than during complexation are undoubtedly responsible for the enhanced binding and selectivity of the spherand. We used standard B3LYP/6-31G** (5d) density functional theory (DFT) to investigate the complexation between spherands containing five anisyl groups, with CH2–O–CH2 (2) and CH2–S–CH2 (3) units in an 18-membered macrocyclic ring, and the cationic guests (Li+, Na+, and K+). Our geometric structure results for spherands 1, 2, and 3 are in good agreement with the previously reported X-ray diffraction data. The absolute values of the binding energy of all the spherands are inversely proportional to the ionic radius of the guests. The results, taken as a whole, show that replacement of one anisyl group by CH2–O–CH2 (2) and CH2–S–CH2 (3) makes the cavity bigger and less preorganized. In addition, both the binding and specificity decrease for small ions. The spherands 2 and 3 appear beautifully preorganized to bind all guests, so it is not surprising that their binding energies are close to the parent spherand 1. Interestingly, there is a clear linear relation between the radius of the cavity and the binding energy (R2 = 0.999).Key words: spherands, preorganization, density functional theory, binding energy, cavity size.

STRUCTURES, ELECTRONIC AND MAGNETIC PROPERTIES OF C20 FULLERENES DOPED TRANSITION METAL ATOMS M@C20 (M = Fe, Co, Ti, V)

2010 ◽  
Vol 21 (12) ◽  
pp. 1469-1477 ◽  
Author(s):  
M. SAMAH ◽  
B. BOUGHIDEN
Keyword(s):  
Density Functional Theory ◽  
Magnetic Moment ◽  
Density Functional ◽  
Binding Energies ◽  
Functional Theory ◽  
Magnetic Dipoles ◽  
Metal Atoms ◽  
Transition Metal Atoms ◽  
Semiconductor Behavior ◽  
Co Doped

Structures, binding energies, magnetic and electronic properties endohedrally doped C 20 fullerenes by metallic atoms ( Fe , Co , Ti and V ) have been obtained by pseudopotential density functional theory. All M @ C 20, except Co @ C 20, are more stable than the undoped C 20 cage. The magnetic moment values are 1 and 2μB. These values and semiconductor behavior give to these compounds interesting feature in several technological applications. Titanium doped C 20 has a same magnetic moment than the isolated Ti atom. Hybridization process in the Co doped C 20 fullerene is most strong than in other doped cages. Electrical and magnetic dipoles calculated in the iron doped C 20 are very strong compared with other clusters.

Research Optical Characteristics of H2S Molecule Adsorption on Agn (n=2,4,6) Clusters

2013 ◽  
Vol 321-324 ◽  
pp. 499-502
Author(s):  
Hong Zhou ◽  
Jun Feng Wang ◽  
Jun Qing Wen ◽  
Wei Bin Cheng ◽  
Jun Fei Wang
Keyword(s):  
Density Functional Theory ◽  
Infrared Spectrum ◽  
Density Functional ◽  
Global Minimum ◽  
Electronic States ◽  
Binding Energies ◽  
Optical Characteristics ◽  
Functional Theory ◽  
Calculation Results ◽  
Planar Geometries

Density-functional theory has been used to calculate the energetically global-minimum geometries and electronic states of AgnH2S (n=2, 4, 6) clusters. The lowest-energy structures of Ag2, Ag4, Ag6, Ag2H2S, Ag4H2S and Ag6H2S clusters were obtained, respectively. The calculation results show that the lowest-energy structures of Ag2, Ag4and Ag6clusters are planar geometries. The binding energies of Agn(n=2, 4, 6) clusters are gradually increasing in our calculations. Compare the infrared spectrum peaks of Ag4cluster with that of Ag6cluster, which show that the peaks shift to shortwave. After adsorption, we found that the peaks shift to shortwave by comparison.

scholarly journals Covalent Functionalization of Nickel Phosphide Nanocrystals with Aryl-Diazonium Salts

2021 ◽  
Author(s):  
Ian Murphy ◽  
Peter Rice ◽  
Madison Monahan ◽  
Leo Zasada ◽  
Elisa Miller ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Photoelectron Spectroscopy ◽  
Density Functional ◽  
Binding Energies ◽  
Diazonium Salts ◽  
Surface Functional Group ◽  
Covalent Functionalization ◽  
Substitution Pattern ◽  
Core Electron ◽  
Functional Theory

Covalent functionalization of Ni2P nanocrystals was demonstrated using aryl-diazonium salts. Spontaneous adsorption of aryl functional groups was observed, with surface coverages ranging from 20-96% depending on the native reactivity of the salt as determined by the aryl substitution pattern. Increased coverage was possible for low reactivity species using a sacrificial reductant. Functionalization was confirmed using thermogravimetric analysis, FTIR and X-ray photoelectron spectroscopy. The structure and energetics of this nanocrystal electrocatalyst system, as a function of ligand coverage, was explored with density functional theory calculations. The Hammett parameter of the surface functional group was found to linearly correlate with the change in Ni and P core-electron binding energies and the nanocrystal’s experimentally and computationally determined work-function. The electrocatalytic activity and stability of the functionalized nanocrystals for hydrogen evolution were also improved when compared to the unfunctionalized material, but a simple trend based on electrostatics was not evident. We used density functional theory to understand this discrepancy and found that H adsorption energies on the covalently functionalized Ni2P also do not follow the electrostatic trend and are predictive descriptors of the experimental results.

scholarly journals Including dispersion interactions in the ONETEP program for linear-scaling density functional theory calculations

2008 ◽  
Vol 465 (2103) ◽  
pp. 669-683 ◽  
Author(s):  
Quintin Hill ◽  
Chris-Kriton Skylaris
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Computational Cost ◽  
Density Functional Theory Calculations ◽  
Binding Energies ◽  
Molecular Structures ◽  
Dispersion Interactions ◽  
Biomolecular Systems ◽  
Functional Theory ◽  
High Level

While density functional theory (DFT) allows accurate quantum mechanical simulations from first principles in molecules and solids, commonly used exchange-correlation density functionals provide a very incomplete description of dispersion interactions. One way to include such interactions is to augment the DFT energy expression by damped London energy expressions. Several variants of this have been developed for this task, which we discuss and compare in this paper. We have implemented these schemes in the ONETEP program, which is capable of DFT calculations with computational cost that increases linearly with the number of atoms. We have optimized all the parameters involved in our implementation of the dispersion correction, with the aim of simulating biomolecular systems. Our tests show that in cases where dispersion interactions are important this approach produces binding energies and molecular structures of a quality comparable with high-level wavefunction-based approaches.

Binding Energies of Organic Charge-Transfer Complexes Calculated by First-Principles Methods

1998 ◽  
Vol 63 (8) ◽  
pp. 1223-1244 ◽  
Author(s):  
Cordula Rauwolf ◽  
Achim Mehlhorn ◽  
Jürgen Fabian
Keyword(s):  
Density Functional Theory ◽  
Charge Transfer ◽  
Ground State ◽  
Density Functional ◽  
Binding Energies ◽  
Basis Set ◽  
Dispersion Energy ◽  
Functional Theory ◽  
Basis Set Superposition Error ◽  
Donor And Acceptor

Weak interactions between organic donor and acceptor molecules resulting in cofacially-stacked aggregates ("CT complexes") were studied by second-order many-body perturbation theory (MP2) and by gradient-corrected hybrid Hartree-Fock/density functional theory (B3LYP exchange-correlation functional). The complexes consist of tetrathiafulvalene (TTF) and related compounds and tetracyanoethylene (TCNE). Density functional theory (DFT) and MP2 molecular equilibrium geometries of the component structures are calculated by means of 6-31G*, 6-31G*(0.25), 6-31++G**, 6-31++G(3df,2p) and 6-311G** basis sets. Reliable molecular geometries are obtained for the donor and acceptor compounds considered. The geometries of the compounds were kept frozen in optimizing aggregate structures with respect to the intermolecular distance. The basis set superposition error (BSSE) was considered (counterpoise correction). According to the DFT and MP2 calculations laterally-displaced stacks are more stable than vertical stacks. The charge transfer from the donor to the acceptor is small in the ground state of the isolated complexes. The cp-corrected binding energies of TTF/TCNE amount to -1.7 and -6.3 kcal/mol at the DFT(B3LYP) and MP2(frozen) level of theory, respectively (6-31G* basis set). Larger binding energies were obtained by Hobza's 6-31G*(0.25) basis set. The larger MP2 binding energies suggest that the dispersion energy is underestimated or not considered by the B3LYP functional. The energy increases when S in TTF/TCNE is replaced by O or NH but decreases with substitution by Se. The charge-transferred complexes in the triplet state are favored in the vertical arrangement. Self-consistent-reaction-field (SCRF) calculations predicted a gain in binding energy with solvation for the ground-state complex. The ground-state charge transfer between the components is increased up to 0.8 e in polar solvents.

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