scholarly journals The Redox-Active Tyrosine Is Essential for Proton Pumping in Cytochrome c Oxidase

2021 ◽  
Vol 9 ◽  
Author(s):  
Margareta R. A. Blomberg
Keyword(s):  
Free Energy ◽  
Energy Conservation ◽  
Density Functional ◽  
Reduction Process ◽  
Proton Pumping ◽  
Cellular Respiration ◽  
Tyrosyl Radical ◽  
Reduction Step ◽  
Redox Active ◽  
Enzyme Complexes

Cellular respiration involves electron transport via a number of enzyme complexes to the terminal Cytochrome c oxidase (CcO), in which molecular oxygen is reduced to water. The free energy released in the reduction process is used to establish a transmembrane electrochemical gradient, via two processes, both corresponding to charge transport across the membrane in which the enzymes are embedded. First, the reduction chemistry occurring in the active site of CcO is electrogenic, which means that the electrons and protons are delivered from opposite sides of the membrane. Second, the exergonic chemistry is coupled to translocation of protons across the entire membrane, referred to as proton pumping. In the largest subfamily of the CcO enzymes, the A-family, one proton is pumped for every electron needed for the chemistry, making the energy conservation particularly efficient. In the present study, hybrid density functional calculations are performed on a model of the A-family CcOs. The calculations show that the redox-active tyrosine, conserved in all types of CcOs, plays an essential role for the energy conservation. Based on the calculations a reaction mechanism is suggested involving a tyrosyl radical (possibly mixed with tyrosinate character) in all reduction steps. The result is that the free energy released in each reduction step is large enough to allow proton pumping in all reduction steps without prohibitively high barriers when the gradient is present. Furthermore, the unprotonated tyrosine provides a mechanism for coupling the uptake of two protons per electron in every reduction step, i.e. for a secure proton pumping.

Methods and models for studying mechanisms of redox-active enzymes

2005 ◽  
Vol 363 (1829) ◽  
pp. 847-860 ◽  
Author(s):  
Per E.M Siegbahn ◽  
Margareta R.A Blomberg
Keyword(s):  
Density Functional ◽  
Hybrid Methods ◽  
Proton Pumping ◽  
X Ray ◽  
Functional Methods ◽  
Redox Active ◽  
Chemical Studies ◽  
Quantum Chemical Studies ◽  
Exact Exchange ◽  
Stable Structures

Methods and models used in recent quantum chemical studies of redox-active enzymes are described. Only density functional methods are able to treat these systems with sufficient accuracy. For the most accurate of these methods, the so-called hybrid methods, a fraction of exact exchange is included and the deviation from experimental energies is usually not higher than 5 kcal mol −1 . The size of the models depends on the problem studied, but is usually in the range 60–100 atoms. To keep the optimized structures sufficiently close to the experimental ones, one atom in each amino acid residue is kept frozen to its position in the X-ray structure. Examples from different recent studies are given with emphasis on dioxygen evolution in photosystem II and proton pumping in cytochrome oxidase. The main advantage of using theoretical methods to study these systems is that short-lived intermediates and transition states can be investigated as easily as stable structures.

DFT study on the hydrolysis of metsulfuron-methyl: A sulfonylurea herbicide

2018 ◽  
Vol 17 (08) ◽  
pp. 1850050 ◽  
Author(s):  
Qiuhan Luo ◽  
Gang Li ◽  
Junping Xiao ◽  
Chunhui Yin ◽  
Yahui He ◽  
...  
Keyword(s):  
Free Energy ◽  
Water Molecule ◽  
Carbonyl Group ◽  
Energy Barrier ◽  
Density Functional ◽  
Free Energy Barrier ◽  
Functional Theory ◽  
Metsulfuron Methyl ◽  
Catalytic Role ◽  
Hydrolysis Of

Sulfonylureas are an important group of herbicides widely used for a range of weeds and grasses control particularly in cereals. However, some of them tend to persist for years in environments. Hydrolysis is the primary pathway for their degradation. To understand the hydrolysis behavior of sulfonylurea herbicides, the hydrolysis mechanism of metsulfuron-methyl, a typical sulfonylurea, was investigated using density functional theory (DFT) at the B3LYP/6-31[Formula: see text]G(d,p) level. The hydrolysis of metsulfuron-methyl resembles nucleophilic substitution by a water molecule attacking the carbonyl group from aryl side (pathway a) or from heterocycle side (pathway b). In the direct hydrolysis, the carbonyl group is directly attacked by one water molecule to form benzene sulfonamide or heterocyclic amine; the free energy barrier is about 52–58[Formula: see text]kcal[Formula: see text]mol[Formula: see text]. In the autocatalytic hydrolysis, with the second water molecule acting as a catalyst, the free energy barrier, which is about 43–45[Formula: see text]kcal[Formula: see text]mol[Formula: see text], is remarkably reduced by about 11[Formula: see text]kcal[Formula: see text]mol[Formula: see text]. It is obvious that water molecules play a significant catalytic role during the hydrolysis of sulfonylureas.

scholarly journals Free Energy of Metals from Quasi-Harmonic Models of Thermal Disorder

Metals ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 195
Author(s):  
Pavel A. Korzhavyi ◽  
Jing Zhang
Keyword(s):  
Free Energy ◽  
First Principles ◽  
Density Functional ◽  
Helmholtz Free Energy ◽  
Complex Materials ◽  
Predictive Capability ◽  
Temperature Dependent ◽  
Disordered Alloys ◽  
Thermal Disorder ◽  
Structure Calculations

A simple modeling method to extend first-principles electronic structure calculations to finite temperatures is presented. The method is applicable to crystalline solids exhibiting complex thermal disorder and employs quasi-harmonic models to represent the vibrational and magnetic free energy contributions. The main outcome is the Helmholtz free energy, calculated as a function of volume and temperature, from which the other related thermophysical properties (such as temperature-dependent lattice and elastic constants) can be derived. Our test calculations for Fe, Ni, Ti, and W metals in the paramagnetic state at temperatures of up to 1600 K show that the predictive capability of the quasi-harmonic modeling approach is mainly limited by the electron density functional approximation used and, in the second place, by the neglect of higher-order anharmonic effects. The developed methodology is equally applicable to disordered alloys and ordered compounds and can therefore be useful in modeling realistically complex materials.

scholarly journals DFT investigations on arylsulphonyl pyrazole derivatives as potential ligands of selected kinases

2020 ◽  
Vol 18 (1) ◽  
pp. 857-873
Author(s):  
Kornelia Czaja ◽  
Jacek Kujawski ◽  
Radosław Kujawski ◽  
Marek K. Bernard
Keyword(s):  
Free Energy ◽  
Molecular Orbital ◽  
Density Functional ◽  
Chemical Reactivity ◽  
Chemical Hardness ◽  
Free Energy Of Solvation ◽  
Fukui Functions ◽  
Reactivity Descriptors ◽  
Condensed Fukui Functions ◽  
Charge Partitioning

AbstractUsing the density functional theory (DFT) formalism, we have investigated the properties of some arylsulphonyl indazole derivatives that we studied previously for their biological activity and susceptibility to interactions of azoles. This study includes the following physicochemical properties of these derivatives: electronegativity and polarisability (Mulliken charges, adjusted charge partitioning, and iterative-adjusted charge partitioning approaches); free energy of solvation (solvation model based on density model and M062X functional); highest occupied molecular orbital (HOMO)–lowest occupied molecular orbital (LUMO) gap together with the corresponding condensed Fukui functions, time-dependent DFT along with the UV spectra simulations using B3LYP, CAM-B3LYP, MPW1PW91, and WB97XD functionals, as well as linear response polarisable continuum model; and estimation of global chemical reactivity descriptors, particularly the chemical hardness factor. The charges on pyrrolic and pyridinic nitrogen (the latter one in the quinolone ring of compound 8, as well as condensed Fukui functions) reveal a significant role of these atoms in potential interactions of azole ligand–protein binding pocket. The lowest negative value of free energy of solvation can be attributed to carbazole 6, whereas pyrazole 7 has the least negative value of this energy. Moreover, the HOMO–LUMO gap and chemical hardness show that carbazole 6 and indole 5 exist as soft molecules, while fused pyrazole 7 has hard character.

scholarly journals First-Principles Study of Mechanical and Thermodynamic Properties of Binary and Ternary CoX (X = W and Mo) Intermetallic Compounds

Materials ◽  
2021 ◽  
Vol 14 (6) ◽  
pp. 1404
Author(s):  
Yunfei Yang ◽  
Changhao Wang ◽  
Junhao Sun ◽  
Shilei Li ◽  
Wei Liu ◽  
...  
Keyword(s):  
Free Energy ◽  
Thermodynamic Properties ◽  
Gibbs Free Energy ◽  
Density Functional ◽  
Vibrational Entropy ◽  
Functional Theory ◽  
Lattice Constants ◽  
The Density Functional Theory ◽  
Ductile Behavior ◽  
Pseudo Potential

In this study, the structural, elastic, and thermodynamic properties of DO19 and L12 structured Co3X (X = W, Mo or both W and Mo) and μ structured Co7X6 were investigated using the density functional theory implemented in the pseudo-potential plane wave. The obtained lattice constants were observed to be in good agreement with the available experimental data. With respect to the calculated mechanical properties and Poisson’s ratio, the DO19-Co3X, L12-Co3X, and μ-Co7X6 compounds were noted to be mechanically stable and possessed an optimal ductile behavior; however, L12-Co3X exhibited higher strength and brittleness than DO19-Co3X. Moreover, the quasi-harmonic Debye–Grüneisen approach was confirmed to be valid in describing the temperature-dependent thermodynamic properties of the Co3X and Co7X6 compounds, including heat capacity, vibrational entropy, and Gibbs free energy. Based on the calculated Gibbs free energy of DO19-Co3X and L12-Co7X6, the phase transformation temperatures for DO19-Co3X to L12-Co7X6 were determined and obtained values were noted to match well with the experiment results.

POSSIBILITY OF MOLECULAR-SWITCH WITH CONTROLLED HYDROGEN BOND: UTILITY OF COMBINATION OF 2,2′-BIIMIDAZOLE AND REDOX-ACTIVE LIGAND

2005 ◽  
Vol 04 (01) ◽  
pp. 333-344 ◽  
Author(s):  
HIROTOSHI MORI ◽  
EISAKU MIYOSHI
Keyword(s):  
Density Functional ◽  
Molecular Level ◽  
Molecular Switch ◽  
Vibration Band ◽  
Functional Theory ◽  
Inorganic Molecule ◽  
Redox Active Ligand ◽  
Active Ligand ◽  
Redox Active ◽  
Stretching Vibration

A new inorganic molecule [ Co(Hbim) ( C 6 H 4 O 2)( NH 3)2]2 that can be used as a new optically durable molecular switch was theoretically designed in the framework of density functional theory. Three stable minima, belonging to 1 A g , 5 A 1, and 9 A g states, were found in the complex. Theoretically predicted infrared spectra of the complexes showed that a strong peak of NH stretching vibration is observed at 2690, 2120, and 2770 cm -1 in the 1 A g , 5 A 1, and 9 A g states, respectively. The apparent red shift of the NH stretching vibration band in the 5 A 1 state make it possible to distinguish the electronic state from others (1 A g and 9 A g ). This means that the complex can be used as a molecular level switch whose memory can be stably read by IR light without any photoreaction process; namely, without memory degradation.

scholarly journals Application of reference-modified density functional theory: Temperature and pressure dependences of solvation free energy

2017 ◽  
Vol 39 (4) ◽  
pp. 202-217 ◽  
Author(s):  
Tomonari Sumi ◽  
Yutaka Maruyama ◽  
Ayori Mitsutake ◽  
Kenji Mochizuki ◽  
Kenichiro Koga
Keyword(s):  
Density Functional Theory ◽  
Free Energy ◽  
Density Functional ◽  
Solvation Free Energy ◽  
Functional Theory ◽  
Temperature And Pressure
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