Modified Neglect Of Diatomic Overlap Research Articles

Essential oils from fennel plants as valuable chemical products: gas chromatography–mass spectrometry, FTIR, quantum mechanical investigation, and antifungal activity

AbstractIn the present study, the biomass produced by fennel plants (Foeniculum vulgare Mill.) was converted to yield bioactive chemicals, and the hydrodistillation method was used to extract the essential oils (EOs) from both the leaves and the umbels. The antifungal activity of the EOs was tested using bioassay against the development of Fusarium oxysporum MW854649 and Alternaria solani MT279570. Molecular spectroscopic detection techniques were used to evaluate the EO products using gas chromatography–mass spectrometer (GC–MS) and Fourier transform infrared spectroscopy (FTIR). GC–MS equipped with single quadruple analyzers have been used to measure the electron ionization (EI) mass spectra of the primary constituents of fennel EOs at 70 eV. The main chemical compounds in the EO from leaves were anethole, estragole, D-limonene, trans-β-ocimene, and fenchone, with percentages of 37.94, 35.56, 17.46, 1.53, and 1.49%, respectively. The abundant compounds in the EO from umbels were estragole, anethole, D-limonene, fenchone, and γ-terpinene, with percentages of 51.18, 25.08, 12.22, 6.57, and 2.86%, respectively. EI mass spectral fragmentation of the major compounds D-limonene, estragole, anethole, and fenchone has been investigated. Umbels and leaf EOs at 5000 mg/L displayed the strongest suppression of fungal growth against A. solani, with values of 87.78% and 79.63%, respectively, compared to the positive control (94.44%). The EOs from umbels and leaves at 5000 mg/L showed the highest inhibition of fungal growth against F. oxysprium as compared to the positive control (94.44%), with values of 77.77% and 72.96%, respectively. All of the important ions—including a few distinctive fragment ions—have comprehensive fragmentation pathways defined. Based on EI, the main routes of fragmentation for the primary compounds have been identified. The existence of alkenes, aliphatic alcohols, ethers, carboxylic acids, ester compounds, alkanes, hydrogen-bonded alcohols, and phenols was demonstrated by the FTIR analysis of fennel EOs. On the other hand, the reactive behavior of the studied molecules has been investigated using two quantum mechanics method: the modified neglect of diatomic overlap (MNDO), a semi-empirical method, and the density functional theory (DFT)/B3LYP hybrid density functional method with the 6-311G (d, p) basis set in the ground state for gas phase. The optimum geometries have been obtained through the execution of computations and electrostatic potential. The obtained analytical and calculated results were then used to understand the activity of the studied EOs in further medical applications.

Mass Spectroscopic Analysis, MNDO Quantum Chemical Studies and Antifungal Activity of Essential and Recovered Oil Constituents of Lemon-Scented Gum against Three Common Molds

The present study described the possibility of using wood-treated oil-fungicide of lemon-scented gum (Corymbia citriodora) from newly emerged leaves and unripened fruits against the infestation of Fusarium culmorum, Rhizoctonia solani and Penicillium chrysogenum. Air-dried wood samples of Melia azedarach were treated with the extracted oils from leaves and unripened fruits from C. citriodora. The main chemical constituents identified in the essential oil (EO) from leaves were citronellal (55.31%), citronellol (21.03%) and isopulegol (10.79%), while in unripened fruits were α-pinene (17.86%), eudesmol (13.9%), limonene (9.19%), γ-terpinen (8.21%), and guaiol (7.88%). For recovered oils (ROs), the major components from leaves were D-limonene (70.23%), γ-terpinene (13.58%), β-pinene (2.40%) and isopregol (2.23%), while, 4-terpineol (21.35%), cis-β-terpineol, (19.33%), D-limonene (14.75%), and γ-terpinene (7.42%) represented the main components in fruits. EOs from leaves and fruits at the amounts of 100, 50 and 25 µL showed the highest inhibition percentage (IP) of 100% against F. culmorum and P. chrysogenum compared to control treatment, while at the amounts of 100, and 50 µL showed 100% IP of R. solani. Wood treated with ROs from leaves and fruits showed IPs of 96.66% and 93.33%, respectively, against the growth of R. solani. The mass spectra of the main components of C. citriodora leaves and fruits’ EOs have been recorded in electron ionization mode at 70 eV and fragmentation has been reported and discussed. On the other hand, different quantum parameters such as the heat of formation, ionization energy total energy, binding energy, electronic energy and dipole moment using the modified neglect of diatomic overlap (MNDO) semi-empirical method have been calculated.

Mass Spectral Fragmentation of Pelargonium graveolens Essential Oil Using GC–MS Semi-Empirical Calculations and Biological Potential

The volatile constituents of the essential oil of local Pelargonium graveolens growing in Egypt was investigated by gas chromatography–mass spectrometry (GC–MS), and the main constituents were citronellol (27.67%), cis-Menthone (10.23%), linalool (10.05%), eudesmol (9.40%), geraniol formate 6.87%, and rose oxide (5.77%), which represent the major components in the obtained GC total ion chromatogram. The structural determination of the main constitutes based on their electron ionization mass spectra have been investigated. The MS of these compounds are absolutely identical in mass values of peaks of fragment ions, where their relative intensities have minor differences. In the spectra of all studied compounds, the observed characteristic ions were [M-H2O]+ and [M-CH3]+. The latter has a structure with m/z 69, 83. Different quantum parameters were obtained using Modified Neglect of Diatomic Overlap (MNDO) semi-empirical method as total energy, binding energy, heat of formations, ionization energy, the energy of highest occupied molecular orbital (HOMO), the energy of the lowest unoccupied molecular orbital (LUMO), energy gap Δ, and dipole moment. The antibacterial and antifungal activities of P. graveolens essential oil and identified compounds were tested against wide collection of organisms. The individual identified compounds in the essential oil—citronellol, cis-Menthone, and linalool (except eudesmol)—showed comparable activity to antibiotics. The most active isolated compound was the citronellol and the lowest MIC was found against E. coli. The essential oil showed high antifungal effects and this activity was attributed to cis-Menthone, eudesmol, and citronellol (excluding linalool). cis-Menthone was the most active compound against selected fungi followed by the eudesmol The study recommends local P. graveolens and identified active compounds for further applications in the pharmaceutical industries.

Investigation of Empirical and Semi‐Empirical Charges to Study the Effects of Partial Charges on Quality and Prediction Accuracy in 3D‐QSAR

AbstractIn Quantitative Structure‐Activity Relationship (QSAR) studies, selection of an appropriate method to assign the partial charge is crucial to derive a reliable model. The prediction accuracy of 3D‐QSAR models depends mainly on the method by which the partial charges were calculated. Therefore, we are interested in examining the effects of empirical and semi‐empirical partial charges on 3D‐QSAR methods, Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Indices Analysis (CoMSIA). The feasibility and performance of these charges have been tested on Janus Kinase 2 inhibitors. Both empirical (Gasteiger‐Huckel, Del‐Re, Gasteiger Marsili, Huckel, Merck Molecular Force Field 94 (MMFF94), Pullman) and semi‐empirical (Austin Model 1 (AM1), Parameterized Model 3 (PM3), Recife Model 1 (RM1), and Modified Neglect of Diatomic Overlap (MNDO)) charges exhibited statistically significant quality. Among them, MMFF94, MNDO and AM1 charges yielded higher cross‐validation correlation coefficient (q2) values whereas Del‐Re and MMFF94 charges produced topmost predictive ability (r2pred). Overall, MMFF94 in CoMFA and MMFF94 and MNDO in CoMSIA models was found to be the best charges when both q2 and r2pred values were used as an evaluation criterion. Our results could provide an idea of selection of appropriate charge rather than using default charge to enhance the quality of 3D‐QSAR when prediction accuracy and predictive ability were employed.

An efficient implementation of semiempirical quantum-chemical orthogonalization-corrected methods for excited-state dynamics.

We present an efficient implementation of configuration interaction with single excitations (CIS) for semiempirical orthogonalization-corrected OMx methods and standard modified neglect of diatomic overlap (MNDO)-type methods for the computation of vertical excitation energies as well as analytical gradients and nonadiabatic couplings. This CIS implementation is combined with Tully's fewest switches algorithm to enable surface hopping simulations of excited-state nonadiabatic dynamics. We introduce an accurate and efficient expression for the semiempirical evaluation of nonadiabatic couplings, which offers a significant speedup for medium-size molecules and is suitable for use in long nonadiabatic dynamics runs. As a pilot application, the semiempirical CIS implementation is employed to investigate ultrafast energy transfer processes in a phenylene ethynylene dendrimer model.

Structural investigation of sparfloxacin drug using mass spec-trometry and MNDO semi-empirical molecular orbital calcu-lations

Sparfloxacin is a broad spectrum antibacterial fluoroquinolone against some microorganisms including gram-positive and gram-negative bacteria and exhibits moderate activity against anaerobes and mycobacteria. Sparfloxacin is well tolerated and the intake of food has no adverse effect on the pharmacokinetic features (Blondeau 1999, Stahlmann et al. 1998). For the medical important of this drug author have been study its structure by recording and investigate its electron ionization (EI) mass spectra at different electron energies 70 and 15 eV. Also, the chemical ionization (CI) mass spectrum has been recorded and investigated. The main fragmentation processes in EI and CI have elucidated and discussed. The main fragment ions in EI mass spectra are [M-C4H8N] + and fragment [M- C4H8N- CO2] +, while [MH- CO2]+ ion are the most fragment ion in CI mass spectrum. On the other hand, the molecular structure optimization of sparfloxacin was calculated using the modified neglect of diatomic overlap (MNDO) semi-empirical molecular orbital method. Also, the thermochemical data such as heat of formations, total energy, ionization energy, electron affinity and dipole moment have been calculated and discussed.

QUANTUM MECHANICAL STUDIES OF THE KINETICS, MECHANISMS AND THERMODYNAMICS OF THE GAS-PHASE THERMAL DECOMPOSITION OF ETHYLVINYL ETHER

The thermal decomposition of Ethyl Vinyl Ether was studied using Austin Model (AMI), Re-parameterized Austin Model (RMI), Parameterized Model 3 (PM#) and Modified Neglect of Diatomic Overlap (MNDO) Hamiltonian in the Semi-Empirical method, Hartree-Foch at 3-21G,6-31G*, 6-31G** level, and Density Functional method with Becke 3 Lee Yang Parr (B3LYP), 6-31G* in the Ab-initio method of calculation in Spartan '10. The geometric properties such as the bond length, dihedral, bond angles, heat of formation, atomic charges, and vibrational frequencies were obtained. The data were used to calculate the change in enthalpy delta H, entropy deltaS, free energy delta G, pre-exponential factor A, Rate, K at 624K, and the variation of rate, K with temperatures at 498K - 773K at temperature interval of 25K. It was observed that the values obtained are in good agreement with experimental values for both semi-empirical and ab-initio methods and according to Arrhenius Theory, calculated rate K, increases with an increase in temperature.

Diphenolic Schiff bases as corrosion inhibitors for aluminium in 0.1 M HCl: Potentiodynamic polarisation and EQCM investigations

The effects of novel synthesised two Schiff bases on the corrosion of aluminium in 0.1 M HCl were investigated using potentiodynamic polarisation and electrochemical quartz crystal microbalance measurements. Results show that inhibition efficiencies increase with increase in inhibitor concentration. This reveals that the inhibition occurs through adsorption of the inhibitor molecules on the metal surface. Adsorption of these inhibitors follows Temkin adsorption isotherm. The correlation between the inhibitor performances and their molecular structures has been investigated using quantum chemical parameters obtained by MNDO (modified neglect of diatomic overlap) semi-empirical method. Calculated quantum chemical parameters indicate that Schiff bases adsorbed on aluminium surface by chemical mechanism.

Second and third-order nonlinear optical properties and molecular parameters of azo chromophores: Semiempirical analysis

The static and frequency dependent average polarizability (〈 α〉), first- and second-hyperpolarizabilities (〈 β〉 and 〈 γ〉) and highest occupied molecular orbital (HOMO) and lowest occupied molecular orbital (LUMO) energies of nonlinear optical chromophores with nitro acceptors 1– 5 have been investigated by using the Austin Model 1 (AM1), Modified Neglect of Diatomic Overlap (MNDO), MNDO with d orbitals (MNDO-d), Parameterization Method 3 (PM3), Recife Model 1 (RM1) and Parameterization Method 6 (PM6) methods within a time-dependent Hartree–Fock (TDHF) approaches. The electronic properties of chromophores 1– 5 have been reported by employing two-state model calculated at Zerner's spectroscopic version of the Intermediate Neglect of Differential Overlap singly excited configuration interaction (ZINDO/S-SCI) method. Also, the molecular hardness ( η) and electronegativity ( χ) parameters have been obtained by using molecular frontier orbital energies. The 〈 α〉, 〈 β〉, 〈 γ〉 HOMO, LUMO energies, η and χ parameters have been investigated with respect to the choice of different semiempirical methods.

ChemInform Abstract: Pericyclic Reactions of 2-Pyrones with Nonconjugated Dienes. Conformational Analysis of the Double Diels-Alder Adducts by Molecular Mechanics Calculation.

Pericyclic reactions of 5-methoxycarbonyl-2-pyrone (Ic) with nonconjugated dienes (IIa-j) were investigated. The diene (Ic) reacted readily with IIa-j to give [4+2]π cycloadducts (IIIa-j) that lost carbon dioxide to afford intramolecular double Diels-Alder (DDA) adducts (V). The structures of these adducts were determined from spectral evidence. The reactivity of the addends and the regiochemistry of the primary adducts are discussed on the basis of modified neglect of diatomic overlap (MNDO) calculation data. The relative stability of the twistene- and isotwistene- type compounds and the conformation of some isotwistene-type compounds are discussed on the basis of the molecular mechanics (MM2) calculation data.

Part 3. Theoretical study on some amino acids and their potential activity as corrosion inhibitors for mild steel in HCl

Quantum chemical parameters, namely energy of the highest occupied molecular orbital, energy of the lowest unoccupied molecular orbital, energy gap, dipole moment, total energy, total electronic energy, core–core repulsion, ionisation potential, cosmo area, cosmo volume and other quantum descriptors [calculated from PM6, PM3, AM1, RM1 and modified neglect of diatomic overlap (MNDO) Hamiltonians], have been used to predict the corrosion inhibition potential of asparagine, aspartic acid, glutamine and glutamic acid. The results obtained indicate that the trend for the variation of the inhibition efficiencies of the compound is in the order: glutamine>asparagine>aspartic acid>glutamic acid. There is a strong agreement between some quantum chemical parameters and the experimental inhibition efficiencies. In order to establish the sites for electrophilic and nucleophilic attacks, condensed Fukui function, condensed softness and relative nucleophilicity/electrophilicity were considered. The results reveal that the sites for nucleophilic attacks in aspartic acid and glutamine are at the nitrogen atom (N5) but at the carbon atom (C3) for asparagine and glutamic acid. The sites for electrophilic attacks are at the oxygen atom (O9, for aspartic acid), carbon atom (C6, for asparagine), oxygen atom (O10, for glutamic acid) and nitrogen atom (N9, for glutamine).

Oxygen defect in silicon studied by semi-empirical calculations

The atomic and electronic structure of interstitial oxygen in bulk silicon is studied by a semi-empirical Hartree--Fock technique. The calculations are performed in real space on a hydrogen terminated cluster in combination with a new parameterization of oxygen within the framework of the modified neglect of diatomic overlap (MNDO) technique. We find that the results on the silicon cluster are in good agreement with experiment as well as with the results of ab initio calculations. Moreover, the various charge states of the oxygen have been analyzed. It has been found that interstitial oxygen in both neutral and double negative charge state forms a stable configuration but the single negative state forms an instable configuration with a strong level in the band gap at E v +0.55 eV.

Theoretical Study of Reaction Paths and Transition States on Conversion Methane into C 2 Hydrocarbons Through Plasma

The direct synthesis of C 2 hydrocarbons (ethylene, acetylene and ethane) from methane is one of the most important task in C 1 chemistry. Higher conversion of methane and selectivity to C 2 hydrocarbons can be realized through plasma reaction. In order to explore the reaction process and mechanism, the possible reaction paths (1)–(4) were proposed on coupling reaction of methane through plasma and studied theoretically using semi-PM3 method [PM3 is parameterization method of modified neglect of diatomic overlap (MNDO)] including determining the transition state, calculating the activation energy and thermodynamic state functions and analyzing the bond order and intrinsic reaction coordinate. The reaction heat results indicate that the reactions (2) and (4) are exothermic, while reactions of (1) and (3) are endothermic. The activation energy results show that activation energy for reactions (1) and (2) was much lower than that of reaction paths (3) and (4). Therefore, paths (1) and (2) is the favorable reaction path energetically. More interestingly by comparing the intrinsic reaction coordinated (IRC) of the reaction paths (1) and (2), it is found that the variations of bond lengths in reaction path (1) has a crucial effect on the potential energy, while in reaction path (2), the adjustment of the system geometry also contributes to the whole potential energy of the system.

Connector Effect in Electroluminescent Properties of Poly(p‐phenylene vinylene) Derivatives Containing Triazole Chromophores

AbstractSummary: We report the thermal, optical, electrochemical and electroluminescent properties of four polymers P1–P4 consisting of hole‐transporting [1,4‐bis(hexyloxy)‐2,5‐distyrylbenzene;DSB] and electron‐transporting [4‐(4‐(hexyloxy)phenyl)‐3,5‐diphenyl‐4H‐1,2,4‐triazole; TAZ] fluorophores linked by four kinds of connectors: (1) ether spacers, (2) single bonds, (3) 1,4‐phenylenes, and (4) 1,4‐divinylbenzenes. These polymers are soluble in common organic solvents such as chloroform, N‐methylpyrrolidone (NMP) and CH2Cl2CH2Cl2 and exhibit good thermal stability with decomposition temperatures higher than 340 °C. Compounds M1–M3 containing a TAZ or DSB core were employed as a model to study the optical properties of the polymers. The photoluminescence (PL) spectral maxima of P1–P4 in CHCl3 were spread over a wide range, from 453 nm to 501 nm, depending upon the chemical structures of the connectors. In the film state, the PL maxima shifted bathochromically from 464nm to 538 nm, which can be attributed to the formation of excimers. From the optimized semiempirical modified neglect of diatomic overlap (MNDO) calculations, the adjacent benzene rings between DSB and TAZ chromophores in P2 and P3 twist about 81–89° which is significantly different from P4 (circa 0°). The effect of the twisted connector architectures on optical and electrochemical properties for P1–P4 is discussed. The electroluminescences of P1–P4 and corresponding Commission Internationale de l'Eclairage (C.I.E.) coordinates are also depicted to indicate that incorporating different connectors to these polymers changed their color from blue, to green, to the yellow region.The C.I.E. 1931 diagram of lights emitted from the PLED devices (ITO/PEDOT:PSS/P1–P4/Al).magnified imageThe C.I.E. 1931 diagram of lights emitted from the PLED devices (ITO/PEDOT:PSS/P1–P4/Al).

Efficient Multipole Model and Linear Scaling of NDDO-Based Methods

Fast growth of computational costs with that of the system's size is a bottleneck for the applications of traditional methods of quantum chemistry to polyatomic molecular systems. This problem is addressed by the development of linear (or almost linear) scaling methods. In the semiempirical domain, it is typically achieved by a series of approximations to the self-consistent field (SCF) solution. By contrast, we propose a route to linear scalability by modifying the trial wave function itself. Our approach is based on variationally determined strictly local one-electron states and a geminal representation of chemical bonds and lone pairs. A serious obstacle previously faced on this route were the numerous transformations of the two-center repulsion integrals characteristic for the neglect of diatomic differential overlap (NDDO) methods. We pass it by replacing the fictitious charge configurations usual for the NDDO scheme by atomic multipoles interacting through semiempirical potentials. It ensures invariance of these integrals and improves the computational efficiency of the whole method. We discuss possible schemes for evaluating the integrals as well as their numerical values. The method proposed is implemented for the most popular modified neglect of diatomic overlap (MNDO), Austin model 1 (AM1), and PM3 parametrization schemes of the NDDO family. Our calculations involving well-justified cutoff procedures for molecular interactions unequivocally show that the proposed scheme provides almost linear scaling of computational costs with the system's size. The numerical results on molecular properties certify that our method is superior with respect to its SCF-based ancestors.

Theoretical study of the structural effects of polymethylene amines on corrosion inhibition of iron in acid solutions

Quantum chemical calculations were performed on azacyclo C5 to C14 amines, open chain C6 to C14 amines and phenylazacyclo C5 to C14 amines. Inspection of the calculated parameters and corrosion inhibition efficiencies were made to observe any clear links, which might exist between the two. Possible correlations between experimental inhibition efficiencies and parameters such as dipole moment ( μ), highest occupied ( E HOMO) and lowest unoccupied ( E LUMO) molecular orbitals and the differences between them, HOMO–LUMO gap ( Δ), as well as some structural characteristics were investigated. The models of the inhibitors were optimized with the Modified Neglect of Diatomic Overlap (MNDO) method. The Quantitative Structure Activity Relationship (QSAR) approach has been used and a composite index of some quantum chemical parameters were constructed in order to characterize the inhibition performance of the tested molecules. The inhibition effect of polymethylene amines is closely related to orbital energies and/or energy gap and dipole moment.

Hiral effects of single‐wall carbon nanotube fluorination and hydrogenation

AbstractThe results of calculations of the electronic and energy characteristics of atomic hydrogen and fluorine adsorption processes on an external surface of single‐wall hiral carbon nanotubes (n,m) are represented. Molecular cluster model within a framework of quantum chemical semiempirical schemes modified neglect of diatomic overlap (MNDO) and parametric method 3 (PM3) has been used. Sorption properties of (4,1), (4,2), (4,3), (5,1), (5,3), (5,4), (6,1), (6,2), (6,3), (6,4), and (6,5) tubes have been considered. Periodical behavior of the chemical bond and activation energies as nanotube diameter functions has been found. It appeared that (4,2), (4,3), and (5,1) nanotubes show more effective adsorption processes and (5,3), (5,4), (6,2), and (6,3) tubes are not advantageous for the chemisorptions. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004

Modified neglect of diatomic overlap parametrization of oxygen: A cluster study of oxygen defects in silicon

We present a parametrization of oxygen within the framework of the modified neglect of diatomic overlap (MNDO) technique. The atomic structure and formation energy of a oxygen defect in silicon are studied as a test of the reparametrized MNDO technique. We find that the geometry and the associated formation energy are in good agreement with experiment as well as with results of ab initio calculations. Even the calculations based on the MNDO technique are by 2 or 3 orders of magnitude less expensive than ab initio calculations.

High Birefringence Isothiocyanato Tolane Liquid Crystals

The phase transition temperatures, birefringence and visco-elastic coefficient of several high birefringence isothiocyanato tolane compounds were evaluated. The polarizability of these compounds was calculated by the Austin Model 1 (AM1) and Modified Neglect of Diatomic Overlap (MNDO) methods. Using these compounds, we have formulated a eutectic mixture exhibiting a wide nematic range and high figure of merit.

Coupling of electron and proton transport in photosynthetic membranes: molecular mechanism

Using the method of Modified Neglect of Diatomic Overlap (MNDO), the electronic structure of plastoquinol (PQH 2) and plastoquinone (PQ) in neutral, singly (PQ −) and doubly (PQ 2−) reduced states is studied. The conformational analysis performed on these molecules shows that in the lowest energy conformation, the angle between the first link of the tail backbone and the ring plane of neutral and singly reduced PQ and plastoquinol is nearly the same and differs by 15° from that of doubly reduced PQ. Nevertheless, for all states of plastoquinone and for plastoquinol, the total energy changes by less than 0.2 eV when the studied angle is varied from 0° to 180°. As in Rhodobacter sphaeroides, the oxygen of the PQ ring is reported to form a hydrogen bond with a nitrogen in the ring of Histidine (His) L 190. The energy of the PQ–His complex was calculated for different redox states of PQ and for several values of the distance between the molecules (N–O distance from 0.2 to 0.5 nm). For every considered complexes, the total energy dependence on the proton position on the line connecting the N and O atoms was determined, to see if the hydrogen bond is formed. It is shown that for only singly reduced PQ this dependence has a symmetric two-well form, i.e. the hydrogen bond is formed. For neutral and doubly reduced PQ, the curve is also two-well but asymmetric, so that the proton is bound to His or to PQ, correspondingly. On the basis of these results, we propose the following scheme of electron–proton coupling. Negatively charged oxygens of PQ form H-bonds with proton donor groups of the surrounding protein and fix PQ in its pocket. While the negative charges of oxygens increase after quinone reduction, protons shift to PQ oxygens and form strong hydrogen bonds with them. Upon second PQ reduction, protons are torn away from surrounding amino acids and form covalent bonds with the quinol. Resulting PQH 2 detaches from its binding place and is replaced by a neutral PQ. The lacking protons on amino acids in the Q B pocket are replaced by a step-by-step transfer from the stroma bulk through the proton channels.