Low-energy conformers of pamidronate and their intramolecular hydrogen bonds: a DFT and QTAIM study

Extensive DFT and ab initio calculations were performed to characterize the conformational space of pamidronate, a typical pharmaceutical for bone diseases. Mono-, di- and tri-protic states of molecule, relevant for physiological pH range, were investigated for both canonical and zwitterionic tautomers. Semiempirical PM6 method were used for prescreening of the single bond rotamers followed by geometry optimizations at the B3LYP/6-31++G(d,p) and B3LYP/6-311++G(d,p) levels. For numerous identified low energy conformers the final electronic energies were determined at the MP2/6-311++G(2df,2p) level and corrected for thermal effects at B3LYP level. Solvation effects were also considered via the COSMO and C-PCM implicit models. Reasonable agreement was found between bond lengths and angle values in comparison with X-ray crystal structures. Relative equilibrium populations of different conformers were determined from molecular partition functions and the role of electronic, vibrational and rotational degrees of freedom on the stability of conformers were analyzed. For no level of theory is a zwitterionic structure stable in the gas-phase while solvation makes them available depending on the protonation state. Geometrically identified intramolecular hydrogen bonds were analyzed by QTAIM approach. All conformers exhibit strong inter-phosphonate hydrogen bonds and in most of them the alkyl-amine side chain is folded on the P-C-P backbone for further hydrogen bond formation.

Computational study of the intramolecular proton transfer reactions of 3-hydroxytropolone (2,7-dihydroxycyclohepta-2,4,6-trien-1-one) and its dimers

The proton transfer reaction and dimerization processes of 3-hydroxytropolone (3-OHTRN) have been investigated using density functional theory (DFT) at the B3LYP/6–31+G** level. The influence of the solvent on the proton transfer reaction of 3-OHTRN was examined using the self-consistent isodensity polarized continuum model (SCI-PCM) with different dielectric constants (ε?=?4.9, CHCI₃; ε?=?32.63, CH₃OH; ε?=?78.39, H₂O). The intramolecular proton transfer reaction occurs more readily in the gas phase than in solution. Results also show that the stability of 3-OHTRN dimers in the gas phase is directly affected by the hydrogen bond length in the dimer structure.     

DFT and MP2 study of low barrier proton transfer in hydrazide schiff base tautomers via water bridges and in the gas

MP2 and DFT studies were performed on the tautomers of N′-ethylideneacetohydrazide in different environments including gas phase, continuum solvent and microhydrated environment. The ground electronic state structures of the tautomers were optimized at the MP2 and B3LYP levels of theory using 6-311++G(d,p), separately. The optimized geometries of the transition states of different tautomerism processes, which occur through the proton transfer (PT) reaction, were determined using the QST3 approach at the same levels of theory. The same stability order as T1Z〉 T1E〉 T2ZE〉 T2ZZ〉 T2EE〉 T2EZ〉 T6〉 T4E was found for the tautomers in the gas phase, continuum solvent and microhydrated environment for both B3LYP and MP2 levels of theory. In addition, the variations of the Gibbs free energies of tautomeric processes, the activation Gibbs free energies of the forward and reverse tautomeric processes with the polarity of the solvent (in continuum solvent model) and the number of water molecules (in microhydrated environment) were investigated. It was found that the reverse tautomeric process is more favorable in all considered environments thermodynamically and kinetically. In addition, it was shown that the rate constants of the reverse and forward considered tautomeric processes decrease with the solvent polarity in the continuum solvent model and the process becomes more difficult than the gas phase. The opposite trend is seen in the microhydrated environment.     

Electrogenic events associated with electron and proton transfers within the cytochrome b(6)/f complex

The kinetics and amplitude of the membrane potential changes associated with electron and proton transfers within the cytochrome b(6)/f (cyt b/f) complex (phase b) are measured in vivo in Chlamydomonas reinhardtii under anaerobic conditions. Upon saturating flash excitation, fast components in the membrane potential decay superimposed on phase b lead to an underestimation of the amplitude of this phase. In the FUD50 mutant strain, which lacks the ATP synthase, the decay of the membrane potential is slowed down compared to the wild type, and the kinetics and amplitude of phase b may be accurately determined. This amplitude corresponds to the transfer of at least 1.5 charges across the membrane per positive charge transferred to photosystem I, whatever the flash energy. This value largely exceeds that predicted by a Q-cycle process. Similar conclusions are reached using the wild type strain in the presence of 9 microM dicyclohexylcarbodiimide, which specifically inhibits the ATP synthase. It is concluded that a proton pumping process is operating in parallel with the Q-cycle, with a yield of approximately 0.5 proton pumped by cyt b/f complex turnover, irrespective of the flash energy.     

Combined DFT and electrostatics study of the proton pumping mechanism in cytochrome c oxidase

Cytochrome c oxidase is a redox-driven proton pump which converts atmospheric oxygen to water and couples the oxygen reduction reaction to the creation of a membrane proton gradient. The structure of the enzyme has been solved; however, the mechanism of proton pumping is still poorly understood. Recent calculations from this group indicate that one of the histidine ligands of enzyme's Cu_B center, His291, may play the role of the pumping element. In this paper, we report on the results of calculations that combined first principles DFT and continuum electrostatics to evaluate the energetics of the key energy generating step of the model—the transfer of the chemical proton to the binuclear center of the enzyme, where the hydroxyl group is converted to water, and the concerted expulsion of the proton from δ-nitrogen of His291 ligand of Cu_B center. We show that the energy generated in this step is sufficient to push a proton against an electrochemical membrane gradient of about 200 mV. We have also re-calculated the pK_a of His291 for an extended model in which the whole Fe_a3-Cu_B center with their ligands is treated by DFT. Two different DFT functionals (B3LYP and PBE0), and various dielectric models of the protein have been used in an attempt to estimate potential errors of the calculations. Although current methods of calculations do not allow unambiguous predictions of energetics in proteins within few pK_a units, as required in this case, the present calculation provides further support for the proposed His291 model of CcO pump and makes a specific prediction that could be targeted in the experimental test.     

Uncoupling of electron and proton transfers in the photocycle of bacterial reaction centers under high light intensity

Photosynthetic reaction centers produce and export oxidizing and reducing equivalents in expense of absorbed light energy. The formation of fully reduced quinone (quinol) requires a strict (1:1) stoichiometric ratio between the electrons and H(+) ions entering the protein. The steady-state rates of both transports were measured separately under continuous illumination in the reaction center from the photosynthetic bacterium Rhodobacter sphaeroides. The uptake of the first proton was retarded by different methods and made the rate-limiting reaction in the photocycle. As expected, the rate constant of the observed proton binding remained constant (7 s(-)(1)), but that of the cytochrome photooxidation did show a remarkably large increase from 14 to 136 s(-)(1) upon increase of the exciting light intensity up to 5 W/cm(2) (808 nm) at pH 8.4 in the presence of NiCl(2). This corresponds to about 20:1 (e(-):H(+)) stoichiometric ratio. The observed enhancement is linearly proportional to the light intensity and the rate constant of the proton uptake by the acceptor complex and shows saturation character with quinone availability. For interpretation of the acceleration of cytochrome turnover, an extended model of the photocycle is proposed. A fraction of photochemically trapped RC can undergo fast (>10(3) s(-)(1)) conformational change where the semiquinone loses its high binding affinity (the dissociation constant increases by more than 5 orders of magnitude) and dissociates from the Q(B) binding site of the protein with a high rate of 4000 s(-)(1). Concomitantly, superoxide is being produced. No H(+) ion is taken up, and no quinol is created by the photocycle which is operating in about 25% of the reaction centers at the highest light intensity (5500 s(-)(1)) and slowest proton uptake (3.5 s(-)(1)) used in our experiments. The possible physical background of the light-induced conformational change and the relationship between the energies of dissociation and redox changes of the quinone in the Q(B) binding sites are discussed.     

The electrochemical proton potential and the proton/electron ratio of the electron transport with fumarate in Wolinella succinogenes

The electrochemical proton potential across the cytoplasmic membrane ( ) as well as the H⁺ / e ratio, which were brought about by the electron transport of Wolinella succinogenes, was measured with the aim of understanding the mechanism of electron-transport-coupled phosphorylation in this anaerobic bacterium. (1) Inverted vesicles derived from the bacterial membrane were found to take up protons from the external medium on initiation of fumarate reduction by H₂. Proton uptake was dependent on the presence of K⁺ within the vesicles, was enhanced by the presence of valinomycin and DCCD and high internal buffer concentration, and was abolished by protonophores. The maximum H⁺ / e ratio slightly exceeded 1. (2) The vesicles accumulated thiocyanate in the steady state of fumarate reduction by H₂. The concentration ratio (internal / external) was close to 1000 at an external thiocyanate concentration below 10 μM. Under the same conditions the uptake of methylamine was negligible. Thiocyanate uptake was abolished by the presence of a protonophore. (3) Cells of W. succinogenes accumulated tetraphenylphosphonium cation (TPP) in the steady state of fumarate reduction with H₂ or formate. Under the same conditions the uptake of benzoic acid was negligible. From the amount of TPP taken up by the bacteria, the free internal concentration of TPP was evaluated according to the procedure of Zaritsky et al. (Zaritsky, A., Kihara, M. and MacNab, R.M. (1981) J. Membrane Biol. 63, 215–231). The concentration ratio (internal / external) was 700 in the absence and close to 1 in the presence of a protonophore or in the absence of external Na⁺. (4) The experimental results are consistent with the view that the energy transduction from electron transport to phosphorylation is done by means of the across the bacterial membrane.     

Factors influencing the energetics of electron and proton transfers in proteins. What can be learned from calculations

A protein structure should provide the information needed to understand its observed properties. Significant progress has been made in developing accurate calculations of acid/base and oxidation/reduction reactions in proteins. Current methods and their strengths and weaknesses are discussed. The distribution and calculated ionization states in a survey of proteins is described, showing that a significant minority of acidic and basic residues are buried in the protein and that most of these remain ionized. The electrochemistry of heme and quinones are considered. Proton transfers in bacteriorhodopsin and coupled electron and proton transfers in photosynthetic reaction centers, 5-coordinate heme binding proteins and cytochrome c oxidase are highlighted as systems where calculations have provided insight into the reaction mechanism.     

Factors influencing the energetics of electron and proton transfers in proteins. What can be learned from calculations

A protein structure should provide the information needed to understand its observed properties. Significant progress has been made in developing accurate calculations of acid/base and oxidation/reduction reactions in proteins. Current methods and their strengths and weaknesses are discussed. The distribution and calculated ionization states in a survey of proteins is described, showing that a significant minority of acidic and basic residues are buried in the protein and that most of these remain ionized. The electrochemistry of heme and quinones are considered. Proton transfers in bacteriorhodopsin and coupled electron and proton transfers in photosynthetic reaction centers, 5-coordinate heme binding proteins and cytochrome c oxidase are highlighted as systems where calculations have provided insight into the reaction mechanism.     

Investigation of the intermolecular proton transfer in the supersystems adenine-methanol/ethanol/i-propanol: MP2 and DFT levels study

Twelve H-bonded supersystems constructed between the adenine tautomers and methanol, ethanol, and i-propanol were studied at the B3LYP and MP2 levels of theory using 6-311G(d,p) and 6-311++G(d,p) basis functions. The thermodynamic parameters of the complex formations were calculated in order to estimate the exact stability of the supersystems. It was proven that the calculated energy barriers of the alcohol-assisted proton transfers are about 60% lower than those of the intramolecular proton transfers in adenine found earlier (Gu and Leszczynski in J Phys Chem A 103:2744–2750, 1999). Figure H-bonded complex between i-propanol and adenine     

Light-induced reduction of bovine adrenodoxin via the covalently bound ruthenium(II) bipyridyl complex: intramolecular electron transfer and crystal structure

Bovine adrenodoxin (Adx) plays an important role in the electron-transfer process in the mitochondrial steroid hydroxylase system of the bovine adrenal cortex. Using electron paramagnetic resonance (EPR) spectroscopy, we showed that photoreduction of the [2Fe-2S] cluster of Adx via (4'-methyl-2,2'-bipyridine)bis(2,2'-bipyridine)ruthenium(II) [Ru(bpy)2(mbpy)] covalently attached to the protein surface can be used as a new approach to probe the "shuttle" hypothesis for the electron transfer by Adx. The 1.5 A resolution crystal structure of a 1:1 Ru(bpy)2(mbpy)-Adx(1-108) complex reveals the site of modification, Cys95, and allows to predict the possible intramolecular electron-transfer pathways within the complex. Photoreduction of uncoupled Adx, mutant Adx(1-108), and Ru(bpy)2(mbpy)-Adx(1-108) using safranin T as the mediating electron donor suggests that two electrons are transferred from the dye to Adx. The intramolecular photoreduction rate constant for the ruthenated Adx has been determined and is discussed according to the predicted pathways.     

DFT study on the structure and explosive properties of nitropyrazoles

Ab initio molecular orbital calculations at the B3LYP/aug-cc-pVDZ level have been carried out to explore the structure, stability, sensitivity and band gap of nitropyrazoles. Kamlet and Jacob equations were used to calculate the detonation velocity and detonation pressure of designed compounds. The explosive properties of polynitropyrazole-N-oxides appear to be higher compared with those of octanitrocubane and 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexa azaisowurtzitane. The sensitivity, heat of explosion, density, detonation velocity and detonation pressure are presumably related to the number and the relative positions of NO₂ groups on the pyrazole ring.     

Combined DFT and electrostatics study of the proton pumping mechanism in cytochrome c oxidase

Cytochrome c oxidase is a redox-driven proton pump which converts atmospheric oxygen to water and couples the oxygen reduction reaction to the creation of a membrane proton gradient. The structure of the enzyme has been solved; however, the mechanism of proton pumping is still poorly understood. Recent calculations from this group indicate that one of the histidine ligands of enzyme's CuB center, His291, may play the role of the pumping element. In this paper, we report on the results of calculations that combined first principles DFT and continuum electrostatics to evaluate the energetics of the key energy generating step of the model-the transfer of the chemical proton to the binuclear center of the enzyme, where the hydroxyl group is converted to water, and the concerted expulsion of the proton from delta-nitrogen of His291 ligand of CuB center. We show that the energy generated in this step is sufficient to push a proton against an electrochemical membrane gradient of about 200 mV. We have also re-calculated the pKa of His291 for an extended model in which the whole Fe(a3)-CuB center with their ligands is treated by DFT. Two different DFT functionals (B3LYP and PBE0), and various dielectric models of the protein have been used in an attempt to estimate potential errors of the calculations. Although current methods of calculations do not allow unambiguous predictions of energetics in proteins within few pKa units, as required in this case, the present calculation provides further support for the proposed His291 model of CcO pump and makes a specific prediction that could be targeted in the experimental test.     

Light and scanning electron microscopic study of the structure of the ostrich (Strutio camelus) tongue

The ostrich's tongue is situated in the posterior part of the oropharyngeal cavity and its length is only about a quarter of the beak cavity. The triangular shortened tongue has retained the usual division into the apex, the body and the root. There are no conical papillae between the body and the root of the tongue, and the presence of the flat fold with lateral processes sliding over the tongue root in the posterior part of the lingual body is a unique morphological feature. All lingual mucosa covers non-keratinised stratified epithelium, and the lamina propria of the mucosa is filled with mucous glands whose round or semilunar openings are found on both the dorsal and ventral surface of the tongue. The complex glands found in the lingual body are composed of alveoli and/or tubules. Moreover, simple tubular glands seen in the posterior part of the tongue root are an exception. Numerous observations have shown that the ostrich's tongue is a modified structure, though not a rudimentary one, whose main function is to produce the secretion moisturising the beak cavity surface and the ingested semidry plant food in this savannah species.     

Isotope-edited proton NMR study on the structure of a pepsin/inhibitor complex

A general approach is illustrated for providing detailed structural information on large enzyme/inhibitor complexes using NMR spectroscopy. The method involves the use of isotopically labeled ligands to simplify two-dimensional NOE spectra of large molecular complexes by isotope-editing techniques. With this approach, the backbone and side-chain conformations (at the P2 and P3 sites) of a tightly bound inhibitor of porcine pepsin have been determined. In addition, structural information on the active site of pepsin has been obtained. Due to the sequence homology between porcine pepsin and human renin, this structural information may prove useful for modeling renin/inhibitor complexes with the ultimate goal of designing more effective renin inhibitors. Moreover, this general approach can be applied to study other biological systems of interest such as other enzyme/inhibitor complexes, ligands bound to soluble receptors, and enzyme/substrate interactions.     

Redox control of proton transfers in membrane b-type cytochromes: an absorption and resonance Raman study on bis(imidazole) and bis(imidazolate) model complexes of iron-protoporphyrin

Optical absorption spectra and resonance Raman (RR) spectra, obtained with Soret excitation, are reported for bis(imidazole) and bis(imidazolate) complexes of iron(II)- and iron(III)-protoporphyrin IX, prepared in aqueous conditions. Perdeuteration experiments on the axial ligands permitted the assignment of the symmetric Fe-(ligand)₂ stretching mode of Fe[x]PP(L)₂ to RR bands at 203 (x = II; L = ImH), 212 (x = II; L = Im^–), 201 (x = III; L = ImH) and 226 cm^–1 (x = III; L = Im^–). These frequency differences indicate a strengthening of the axial bonds when the imidazole deprotonations occur. The larger difference observed for the ferric derivatives reflects the stronger -donor capability of the Im^– anion for iron(III) over iron(II). For the ferrous derivatives, the frequencies of several skeletal porphyrin modes (₄, ₁₀, ₁₁ and ₃₈) are downshifted by 2–10 cm^–1 upon deprotonation of the ligands. This effect corresponds to an increased back-bonding from the metal atom to the porphyrin ring when the axial ligand decreases its -acid strength. Bringing further support to this interpretation, an inverse linear relationship is established between the frequencies of (Fe(Il)-L₂) and ₁₁. This correlation is expected to monitor the overall H-bonding state of histidine ligands of reduced cytochromes b. On the other hand, absorption measurements have characterized large pK_a differences for the sequential imidazole ionizations of Fe[x]PP(ImH)₂ in aqueous cetyltrimethylammonium bromide (9.0 and 10.8 for x = 111; 13.0 and 14.1 for x = II). These titrations show that Fe(II)PP(Im^–)₂ and Fe(III)PP(ImH)₂ are good proton-acceptor and proton-donor, respectively, and suggest a model by which heme, located in a favorable environment inside a cytochrome, could couple a cycle of electron transfer with a proton transfer. Based on sequence data and structural models, it is further proposed that, in several membrane cytochromes b (b, b ₆, b ₅₅₉), a positively charged amino acid residue and an imidazolate ligand of the ferriheme could form an ion pair involved in a redox control of proton transfer.Abbreviations RR resonance Raman - EPR electron paramagnetic resonance - PP protoporphyrin IX - ImH imidazole - Im^– imidazolate - Im* imidazole or imidazolate - 1MeIm 1-methylimidazole - HisH histidine - His^– histidinate - CTABr cetyltrimethylammonium bromide - NaDS sodium dodecylsulphate - VLP very low potential - LP low potential - HP high potential