Conserved Water Networks Identification for Drug Design Using Density Clustering Approaches on Positional and Orientational Data.

This work describes the development and testing of a method for the identification and classification of conserved water molecules and their networks from molecular dynamics (MD) simulations. The conserved waters in the active sites of proteins influence protein-ligand binding. Recently, several groups have argued that a water network formed from conserved waters can be used to interpret the thermodynamic signature of the binding site. We implemented a novel methodology in which we apply the complex approach to categorize water molecules extracted from the MD simulation trajectories using clustering approaches. The main advantage of our methodology as compared to current state of the art approaches is the inclusion of the information on the orientation of hydrogen atoms to further inform the clustering algorithm and to classify the conserved waters into different subtypes depending on how strongly certain orientations are preferred. This information is vital for assessing the stability of water networks. The newly developed approach is described in detail as well as validated against known results from the scientific literature including comparisons with the experimental data on thermolysin, thrombin, and Haemophilus influenzae virulence protein SiaP as well as with the previous computational results on thermolysin. We observed excellent agreement with the literature and were also able to provide additional insights into the orientations of the conserved water molecules, highlighting the key interactions which stabilize them. The source code of our approach, as well as the utility tools used for visualization, are freely available on GitHub.

The influence of pH on UV/Vis spectra of gallic and ellagic acid: A combined experimental and computational study.

The pH dependence of the UV/Vis spectrum of gallic and ellagic acid was measured in a buffer-free solution to obtain reliable data at wavelengths bellow 230 nm. UV/Vis absorption spectra were also calculated for all possible ionised species of gallic and ellagic acid using time dependent density functional theory (TD-DFT). From pKa values of gallic and ellagic acid the molar fraction of different ionised species was calculated for each pH value. Finally, the simulated spectra at different pH values were obtained as a weighted average of spectra of neutral, once, twice, three-times, and four-times deprotonated species. The calculated spectra were then compared to the experimental spectra, and the peaks in the experimental spectrum were explained in the terms of main electronic transitions that results in the observed absorption bands. At low pH values the agreement between the experimental and calculated spectra was excellent. At near-neutral pH values the majority of the experimental spectra features were well reproduced in the calculated spectra. A satisfactory agreement between experimental and calculated spectrum at high pH values was also achieved by incorporating the calculated spectra of the oxidised species of gallic acid as well as ellagic acid spectra with one lactone ring open.

Dependence of the Fe(II)-Gallic Acid Coordination Compound Formation Constant on the pH.

One important property of tannins involves their ability to form coordination compounds with metal ions, which is vital for the bioavailability of these ions, as well as for the antibacterial and antioxidative activities of tannins. In this study, the pH dependence of interactions between gallic acid, one of the basic building blocks of tannins, and Fe(II) ions, was investigated using UV/Vis spectroscopy, in conjunction with density functional theory (DFT) calculations. Moreover, two models were developed to explain the processes taking place in the solution. The first model treated the reaction as a simple bimolecular process while the second also considered the protolytic equilibrium, which was proven very successful in discerning the pH dependence of formation constants, and whose assumptions were well supported by DFT calculations. We showed that the two-time deprotonated gallic acid species forms the coordination compound with Fe(II) ions in a 1:1 molar ratio. To gain better insight into the process, the coordination compound formation was also studied using various DFT functionals, which further supported the model results. Furthermore, due to the relatively low sample amounts needed, the methodology developed here will be useful to study compounds that are more difficult to isolate.

Antioxidative Action of Ellagic Acid-A Kinetic DFT Study.

Although one can find numerous studies devoted to the investigation of antioxidative activity of ellagic acid (EA) in the scientific literature, the mechanisms of its action have not yet been fully clarified. Therefore, further kinetic studies are needed to understand its antioxidative capacity completely. This work aims to reveal the underlying molecular mechanisms responsible for the antioxidative action of EA. For this purpose, its reactions with HO∙ and CCl3OO∙ radicals were simulated at physiological conditions using the quantum mechanics-based test for overall free-radical scavenging activity. The density functional theory in combination with the conductor-like polarizable continuum solvation model was utilized. With HO∙ radical EA conforms to the hydrogen atom transfer and radical adduct formation mechanisms, whereas sequential proton loss electron transfer mechanism is responsible for scavenging of CCl3OO∙ radical. In addition, compared to trolox, EA was found more reactive toward HO∙, but less reactive toward CCl3OO∙. The calculated rate constants for the reactions of EA with both free radicals are in a very good agreement with the corresponding experimental values.

Comparison of the scavenging capacities of phloroglucinol and 2,4,6-trihydroxypyridine towards HO˙ radical: a computational study.

In this work the scavenging capacities of biologically active phloroglucinol (1,3,5-trihydroxybenzene, THB-OH) and structurally similar 2,4,6-trihydroxypyridine (THP-OH) towards HO˙ were examined. This task was realized by means of density functional theory, through investigation of all favorable antioxidative pathways in two solvents of different polarity: benzene and water. It was found that in benzene both compounds conform to the hydrogen atom transfer (HAT) and radical adduct formation (RAF) mechanisms. In water, the mechanisms of antioxidative action of the investigated compounds are far more complex, especially those of THB-OH. This compound and HO˙ undergo all four investigated mechanisms: HAT, RAF, sequential proton loss electron transfer (SPLET), and single electron transfer-proton transfer (SET-PT). HAT, RAF and SPLET are operative mechanisms in the case of THP-OH. Independently of solvent polarity, both investigated compounds are more reactive towards HO˙ in comparison to Trolox. Our final remark is as follows: the electron-withdrawing effect of the nitrogen is stronger than the electron-donating effect of the OH groups in the molecule of THP-OH. As a consequence, THB-OH is more powerful antioxidant than THP-OH, thus implying that the presence of nitrogen decreases the scavenging capacity of the respective compound.

Antioxidative activity of chlorogenic acid relative to trolox in aqueous solution - DFT study.

Chlorogenic acid (5CQA) is a dietary polyphenol known for its high biological activity. Antioxidative behavior of 5CQA relative to trolox (Tx) toward the HO and CH3OO radicals in aqueous solution at pH = 7.4 was simulated using density functional theory. This is the first study where behavior of monoanion and dianion of 5CQA at physiological conditions is described. Both anionic forms undergo only hydrogen atom transfer (HAT) mechanism with CH3OO. With HO, anionic forms of 5CQA conform to the HAT, radical adduct formation, sequential proton loss electron transfer, and single electron transfer - proton transfer mechanisms. Contribution of dianion to scavenging HO is comparable to that of more abundant monoanion. The calculated rate constant for overall reaction of 5CQA with HO is in perfect agreement with the corresponding experimental value. In comparison to Tx, 5CQA is more reactive toward HO, but less reactive toward CH3OO.

Antioxidative mechanisms in chlorogenic acid.

Although chlorogenic acid (5CQA) is an important ingredient of various foods and beverages, mechanisms of its antioxidative action have not been fully clarified. Besides electron spin resonance experiment, this study includes thermodynamic and mechanistic investigations of the hydrogen atom transfer (HAT), radical adduct formation (RAF), sequential proton loss electron transfer (SPLET), and single electron transfer - proton transfer (SET-PT) mechanisms of 5CQA in benzene, ethanol, and water solutions. The calculations were performed using the M06-2X/6-311++G(d,p) level of theory and CPCM solvation model. It was found that SET-PT is not a plausible antioxidative mechanism of 5CQA. RAF pathways are faster, but HAT yields thermodynamically more stable radical products, indicating that in acidic and neutral media 5CQA can take either HAT or RAF pathways. In basic environment (e.g. at physiological pH) SPLET is the likely antioxidative mechanism of 5CQA with extremely high rate.

Comparative study of the antioxidative activities of caffeoylquinic and caffeic acids.

A detailed conformational analysis was performed to determine the most stable conformers of chlorogenic, cryptochlorogenic, and neochlorogenic acids. The simulated and experimental NMR spectra of caffeoylquinic acids are in excellent agreement. The bond dissociation enthalpies, proton affinities, electron transfer enthalpies, ionisation potentials, and proton dissociation enthalpies for these compounds and caffeic acid in benzene, methanol, and water were used for thermodynamic consideration of the major antioxidative mechanisms: HAT (Hydrogen Atom Transfer), SPLET (Sequential Proton-Loss Electron-Transfer), and SET-PT (Single Electron Transfer - Proton Transfer). All compounds are characterised with very similar values of each enthalpy, suggesting that they will exhibit comparable antioxidative activities. This assumption is in perfect accord with the experimental findings. It was suggested that HAT may be the predominant mechanism in nonpolar solvents, while HAT and SPLET are competitive pathways in polar media. All calculations were performed using the B3LYP-D2/6-311++G(d,p) and M06-2X/6-311++G(d,p) levels of theory and CPCM solvation model.

Synergic application of spectroscopic and theoretical methods to the chlorogenic acid structure elucidation.

Although chlorogenic acid (5-O-caffeoylquinic acid, 5CQA) is a dietary polyphenol known for its pharmacological and nutritional properties, its structural features have not been completely elucidated. This is the first study whose aim is to contribute to clarification of the 5CQA structure by comparing the experimental and simulated IR, Raman, (1)H NMR, (13)C NMR, and UV spectra. For this purpose, a comprehensive conformational analysis of 5CQA was performed to reveal its most stable conformations in the gas-state and solution (DMSO and methanol). The lowest-energy conformers were used to predict the spectra at two levels of theory: B3LYP-D3/and M06-2X/6-311+G(d,p) in combination with the CPCM solvation model. Both methods provide very good agreement between all experimental and simulated spectra, thus indicating correct arrangement of the atoms in the 5CQA molecule. The quinic moiety is characterized with directed hydrogen bonds, where the carboxylic hydrogen is not oriented towards the carbonyl oxygen of the carboxylic group, but towards the oxygen of the proximate hydroxyl group. In the gas-state the lowest-energy conformers are characterized with the O4H4⋯O9' hydrogen bond, whereas in the solvated state the structures with the O4H4⋯O10' hydrogen bond prevail. Knowing the fine structural details, i.e. the proper conformation of 5CQA, provides a solid base for all further investigations related to this compound.

Application of Time-Dependent Density Functional and Natural Bond Orbital Theories to the UV-vis Absorption Spectra of Some Phenolic Compounds.

The UV-vis properties of 22 natural phenolic compounds, comprising anthraquinones, neoflavonoids, and flavonoids were systematically examined. The time-dependent density functional theory (TDDFT) approach in combination with the B3LYP, B3LYP-D2, B3P86, and M06-2X functionals was used to simulate the UV-vis spectra of the investigated compounds. It was shown that all methods exhibit very good (B3LYP slightly better) performance in reproducing the examined UV-vis spectra. However, the shapes of the Kohn-Sham molecular orbitals (MOs) involved in electronic transitions were misleading in constructing the MO correlation diagrams. To provide better understanding of redistribution of electron density upon excitation, the natural bond orbital (NBO) analysis was applied. Bearing in mind the spatial and energetic separations, as well as the character of the π bonding, lone pair, and π* antibonding natural localized molecular orbitals (NLMOs), the "NLMO clusters" were constructed. NLMO cluster should be understood as a part of a molecule characterized with distinguished electron density. It was shown that all absorption bands including all electronic transitions need to be inspected to fully understand the UV-vis spectrum of a certain compound, and, thus, to learn more about its UV-vis light absorption. Our investigation showed that the TDDFT and NBO theories are complementary, as the results from the two approaches can be combined to interpret the UV-vis spectra. Agreement between the predictions of the TDDFT approach and those based on the NLMO clusters is excellent in the case of major electronic transitions and long wavelengths. It should be emphasized that the approach for investigation of UV-vis light absorption based on the NLMO clusters is applied for the first time.

Local aromaticity in naphtho-annelated fluoranthenes: can the five-membered rings be more aromatic than the six-membered rings?

All Kekulé-structure-based theories predict that the central five-membered ring in fluoranthene and naphtho-annelated fluoranthenes is nonaromatic. In the present work, a detailed study of the local aromaticity in a series of naphtho-annelated fluoranthene derivatives was performed by means of the following aromaticity indices: the energy effect (ef), bond resonance energy (BRE), multicenter delocalization indices (MCI), harmonic oscillator model of aromaticity (HOMA) index, nucleus-independent chemical shifts (NICS), and ring current maps. It was found that, according to the ef, BRE, MCI, and HOMA values, the pentagonal rings in some naphtho-annelated fluoranthenes can be even more aromatic than some hexagonal rings in the respective molecules. The magnetic indices do not support the results obtained by the energetic, electron delocalization, and geometrical aromaticity indices.

Ring currents in benzo- and benzocyclobutadieno-annelated biphenylene derivatives.

The effect of benzo and benzocyclobutadieno annelation on the current density induced in a series of biphenylene derivatives is examined at the B3LYP/cc-pVDZ level of theory, by using the CTOCD-DZ method. Angular benzo annelation increases, whereas linear benzo annelation decreases the intensity of paratropic (antiaromatic) current density along the four-membered ring of biphenylene. The opposite effect is found for benzocyclobutadieno annelation. It is shown that the extent of local aromaticity of the four-membered ring in biphenylene congeners can vary from highly antiaromatic to nonaromatic, as a result of different modes of annelation.