Theory of chemical bonds in metalloenzymes III: Full geometry optimization and vibration analysis of ferredoxin-type [2Fe–2S] cluster

2006 ◽  
Vol 107 (1) ◽  
pp. 116-133 ◽  
Author(s):  
Mitsuo Shoji ◽  
Kenichi Koizumi ◽  
Takeshi Taniguchi ◽  
Yasutaka Kitagawa ◽  
Shusuke Yamanaka ◽  
...  
Keyword(s):  
Vibration Analysis ◽  
Geometry Optimization ◽  
Chemical Bonds ◽  
Full Geometry Optimization ◽  
Theory Of Chemical Bonds

Theory of chemical bonds in metalloenzymes XI: Full geometry optimization and vibration analysis of porphyrin iron-oxo species

2008 ◽  
Vol 108 (15) ◽  
pp. 2950-2965 ◽  
Author(s):  
Mitsuo Shoji ◽  
Hiroshi Isobe ◽  
Toru Saito ◽  
Yasutaka Kitagawa ◽  
Shusuke Yamanaka ◽  
...  
Keyword(s):  
Vibration Analysis ◽  
Geometry Optimization ◽  
Chemical Bonds ◽  
Full Geometry Optimization ◽  
Theory Of Chemical Bonds

scholarly journals ß-Cyclodextrin Inclusion Complexes with Catechol-Containing Antioxidants Protocatechuic Aldehyde and Protocatechuic Acid—An Atomistic Perspective on Structural and Thermodynamic Stabilities

Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3574
Author(s):  
Thammarat Aree
Keyword(s):  
Inclusion Complexes ◽  
Protocatechuic Acid ◽  
Inclusion Complexation ◽  
Geometry Optimization ◽  
Therapeutic Effects ◽  
Full Geometry Optimization ◽  
Oh Groups ◽  
X Ray ◽  
Protocatechuic Aldehyde ◽  
Crystal Contacts

Protocatechuic aldehyde (PCAL) and protocatechuic acid (PCAC) are catechol derivatives and have broad therapeutic effects associated with their antiradical activity. Their pharmacological and physicochemical properties have been improved via the cyclodextrin (CD) encapsulation. Because the characteristics of b-CD inclusion complexes with PCAL (1) and PCAC (2) are still equivocal, we get to the bottom of the inclusion complexation by an integrated study of single-crystal X-ray diffraction and DFT full-geometry optimization. X-ray analysis unveiled that PCAL and PCAC are nearly totally shielded in the b-CD wall. Their aromatic rings are vertically aligned in the b-CD cavity such that the functional groups on the opposite side of the ring (3,4-di(OH) and 1-CHO/1-COOH groups) are placed nearby the O6–H and O2–H/O3–H rims, respectively. The preferred inclusion modes in 1 and 2 help to establish crystal contacts of OH×××O H-bonds with the adjacent b-CD OH groups and water molecules. By contrast, the DFT-optimized structures of both complexes in the gas phase are thermodynamically stable via the four newly formed host–guest OH⋯O H-bonds. The intermolecular OH×××O H-bonds between PCAL/PCAC 3,4-di(OH) and b-CD O6–H groups, and the shielding of OH groups in the b-CD wall help to stabilize these antioxidants in the b-CD cavity, as observed in our earlier studies. Moreover, PCAL and PCAC in distinct lattice environments are compared for insights into their structural flexibility.

scholarly journals Theoretical Investigation of the Size Effect on the Oxygen Adsorption Energy of Coinage Metal Nanoparticles

2021 ◽  
Author(s):  
Amir H. Hakimioun ◽  
Elisabeth M. Dietze ◽  
Bart D. Vandegehuchte ◽  
Daniel Curulla-Ferre ◽  
Lennart Joos ◽  
...  
Keyword(s):  
Particle Size ◽  
Size Effect ◽  
Adsorption Energy ◽  
Single Point ◽  
Finite Size ◽  
Geometry Optimization ◽  
Oxygen Adsorption ◽  
Finite Size Effect ◽  
Full Geometry Optimization ◽  
Coinage Metal

AbstractThis study evaluates the finite size effect on the oxygen adsorption energy of coinage metal (Cu, Ag and Au) cuboctahedral nanoparticles in the size range of 13 to 1415 atoms (0.7–3.5 nm in diameter). Trends in particle size effects are well described with single point calculations, in which the metal atoms are frozen in their bulk position and the oxygen atom is added in a location determined from periodic surface calculations. This is shown explicitly for Cu nanoparticles, for which full geometry optimization only leads to a constant offset between relaxed and unrelaxed adsorption energies that is independent of particle size. With increasing cluster size, the adsorption energy converges systematically to the limit of the (211) extended surface. The 55-atomic cluster is an outlier for all of the coinage metals and all three materials show similar behavior with respect to particle size. Graphic Abstract

First Principles Investigation of the Stability and the Chemical Behavior of Hydrogen in ThCoH4

2011 ◽  
Vol 66 (3) ◽  
pp. 269-274
Author(s):  
Samir F. Matar
Keyword(s):  
Negative Charge ◽  
Geometry Optimization ◽  
Full Geometry Optimization ◽  
Intermetallic Matrix ◽  
Charge Analysis ◽  
The Stability ◽  
The One ◽  
Site Selective ◽  
Bader Charge Analysis ◽  
Positively Charged

We address the changes in the electronic structure brought by the insertion of hydrogen into ThCo leading to the experimentally observed ThCoH4. Full geometry optimization positions the hydrogen in three sites stabilized in the expanded intermetallic matrix. From a Bader charge analysis, hydrogen is found to be in a narrow iono-covalent (~−0.6) to covalent (~−0.3) bonding which should enable site-selective desorption. The overall chemical picture shows a positively charged Thδ+ with the negative charge redistributed over a complex anion {CoH4}δ− with δ~1.8. Nevertheless this charge transfer remains far from the one in the more ionic hydridocobaltate anion CoH54− in Mg2CoH5, due to the largely electropositive character of Mg.

scholarly journals Distinctive Supramolecular Features of β-Cyclodextrin Inclusion Complexes with Antidepressants Protriptyline and Maprotiline: A Comprehensive Structural Investigation

2021 ◽  
Vol 14 (8) ◽  
pp. 812
Author(s):  
Thammarat Aree
Keyword(s):  
Inclusion Complexes ◽  
Density Functional ◽  
Water Solubility ◽  
Geometry Optimization ◽  
Binding Constants ◽  
Basis Set ◽  
Full Geometry Optimization ◽  
Basis Set Superposition Error ◽  
X Ray ◽  
Molecular Stability

Depression, a global mental illness, is worsened due to the coronavirus disease 2019 (COVID-2019) pandemic. Tricyclic antidepressants (TCAs) are efficacious for the treatment of depression, even though they have more side effects. Cyclodextrins (CDs) are powerful encapsulating agents for improving molecular stability, water solubility, and lessening the undesired effects of drugs. Because the atomic-level understanding of the β-CD–TCA inclusion complexes remains elusive, we carried out a comprehensive structural study via single-crystal X-ray diffraction and density functional theory (DFT) full-geometry optimization. Here, we focus on two complexes lining on the opposite side of the β-CD–TCA stability spectrum based on binding constants (Kas) in solution, β-CD–protriptyline (PRT) 1—most stable and β-CD–maprotiline (MPL) and 2—least stable. X-ray crystallography unveiled that in the β-CD cavity, the PRT B-ring and MPL A-ring are aligned at a nearly perfect right angle against the O4 plane and primarily maintained in position by intermolecular C–H···π interactions. The increased rigidity of the tricyclic cores is arising from the PRT -CH=CH- bridge widens, and the MPL -CH2–CH2- flexure narrows the butterfly angles, facilitating the deepest and shallower insertions of PRT B-ring (1) and MPL A-ring (2) in the distorted round β-CD cavity for better complexation. This is indicated by the DFT-derived complex stabilization energies (ΔEstbs), although the complex stability orders based on Kas and ΔEstbs are different. The dispersion and the basis set superposition error (BSSE) corrections were considered to improve the DFT results. Plus, the distinctive 3D arrangements of 1 and 2 are discussed. This work provides the first crystallographic evidence of PRT and MPL stabilized in the β-CD cavity, suggesting the potential application of CDs for efficient drug delivery.

Theory of chemical bonds in metalloenzymes II: Hybrid-DFT studies in iron-sulfur clusters

2005 ◽  
Vol 105 (6) ◽  
pp. 628-644 ◽  
Author(s):  
M. Shoji ◽  
K. Koizumi ◽  
Y. Kitagawa ◽  
S. Yamanaka ◽  
T. Kawakami ◽  
...  
Keyword(s):  
Chemical Bonds ◽  
Dft Studies ◽  
Iron Sulfur Clusters ◽  
Iron Sulfur ◽  
Theory Of Chemical Bonds

Substitution effects and electronic properties of the azo dye (1-phenylazo-2-naphthol) species: a TD-DFT electronic spectra investigation

2015 ◽  
Vol 93 (5) ◽  
pp. 509-517 ◽  
Author(s):  
Lakhdar Mansouri ◽  
Bachir Zouchoune
Keyword(s):  
Electronic Spectra ◽  
Geometry Optimization ◽  
Energy Difference ◽  
Point Of View ◽  
Substitution Effects ◽  
Spectral Position ◽  
Full Geometry Optimization ◽  
Small Energy ◽  
Perfect Agreement ◽  
Td Dft

DFT/B3LYP and ab initio Hartree–Fock calculations with full geometry optimization have been carried out on hydrazo and azo forms of 1-phenylazo-2-naphthol and their substituted derivatives. The predicted geometries show that a small energy difference of 1.8 kcal/mol might tune the equilibrium between both forms. Depending on the electron donating and electron accepting of the different used substituents (CF3, NH2, CH3, Cl, and NO2), the various obtained isomers show small energy differencies between meta and para substitution except for the NH2 one, indicating the coexistence of the tautomers in solution. The ortho(C12) position was found to be the less favored substitution in all cases, while the second ortho(C16) position for different substituents provides isomers competing with the most stable meta and para ones. The obtained results suggest that a judicious choice in the substituents’ use on the phenyl ring should lead to stabilization. The TD-DFT theoretical study performed on the optimized geometry allowed us to identify quite clearly the spectral position and the nature of the different electronic transitions according to their molecular orbital localization, hence, reproducing the available UV-Vis spectra. The increase in the wavelength values is in perfect agreement with red shifts and the ΔE (ELUMO – EHOMO) decreasing. Thus, from the point of view of both substitution and the used solvent, the obtained electronic spectra appear to behave quite differently.

Ab initio studies on amides: conformational preferences of formimide and barriers to interconversion of the conformers

1980 ◽  
Vol 33 (8) ◽  
pp. 1635 ◽  
Author(s):  
L Radom ◽  
NV Riggs
Keyword(s):  
Ground State ◽  
Room Temperature ◽  
Geometry Optimization ◽  
Basis Set ◽  
Partial Geometry ◽  
Electrostatic Repulsion ◽  
Full Geometry Optimization ◽  
Vapour State ◽  
Conformational Preferences ◽  
Model Transition

Formimide (diformamide), the parent of the diacylamines, is capable of existing in three basic ground-state conformations about the N-C bonds. Full geometry optimization with the STO-3G basis set predicts that all three conformers are fully coplanar, that the E,E (1) and E,Z(3) conformers are of similar energy, and that the Z,Z (2) conformer is of somewhat higher energy (by 11 kJ mol-1); 4-31G evaluation of the energies suggests that (2) is by far the least stable and that (1) is of higher energy than (3) by 6.5 kJ mol-1. Analysis of the calculated charge distribution suggests that (2) is destabilized by electrostatic repulsion. These results are consistent with experimental conclusions that planar (3) is strongly preferred in the vapour state at room temperature and that (2) has not been observed in the vapour state or in solution. Partial geometry optimization with the STO-3G basis set of model transition states for internal rotation suggests a barrier height of 52 kJ mol-1 (72 kJ mol-1 when evaluated with the 4-31G basis set) for the conversion (3) → (1).

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