Understanding the Enzyme (S)-Norcoclaurine Synthase Promiscuity to Aldehydes and Ketones.

The (S)-norcoclaurine synthase from Thalictrum flavum (TfNCS) stereoselectively catalyzes the Pictet-Spengler reaction between dopamine and 4-hydroxyphenylacetaldehyde to give (S)-norcoclaurine. TfNCS can catalyze the Pictet-Spengler reaction with various aldehydes and ketones, leading to diverse tetrahydroisoquinolines. This substrate promiscuity positions TfNCS as a highly promising enzyme for synthesizing fine chemicals. Understanding carbonyl-containing substrates' structural and electronic signatures that influence TfNCS activity can help expand its applications in the synthesis of different compounds and aid in protein optimization strategies. In this study, we investigated the influence of the molecular properties of aldehydes and ketones on their reactivity in the TfNCS-catalyzed Pictet-Spengler reaction. Initially, we compiled a library of reactive and unreactive compounds from previous publications. We also performed enzymatic assays using nuclear magnetic resonance to identify some reactive and unreactive carbonyl compounds, which were then included in the library. Subsequently, we employed QSAR and DFT calculations to establish correlations between substrate-candidate structures and reactivity. Our findings highlight correlations of structural and stereoelectronic features, including the electrophilicity of the carbonyl group, to the reactivity of aldehydes and ketones toward the TfNCS-catalyzed Pictet-Spengler reaction. Interestingly, experimental data of seven compounds out of fifty-three did not correlate with the electrophilicity of the carbonyl group. For these seven compounds, we identified unfavorable interactions between them and the TfNCS. Our results demonstrate the applications of in silico techniques in understanding enzyme promiscuity and specificity, with a particular emphasis on machine learning methodologies, DFT electronic structure calculations, and molecular dynamic (MD) simulations.

Nitric Oxide Reacts Very Fast with Hydrogen Sulfide, Alcohols, and Thiols to Produce HNO: Revised Rate Constants.

The chemical reactivity of NO and its role in several biological processes seem well established. Despite this, the chemical reduction of •NO toward HNO has been historically discarded, mainly because of the negative reduction potential of NO. However, this value and its implications are nowadays under revision. The last reported redox potential, E'(NO,H+/HNO), at micromolar and picomolar concentrations of •NO and HNO, respectively, is between -0.3 and 0 V at pH 7.4. This potential implies that the one-electron-reduction process for NO is feasible under biological conditions and could be promoted by well-known biological reductants with reduction potentials of around -0.3 to -0.5 V. Moreover, the biologically compatible chemical reduction of •NO (nonenzymatic), like direct routes to HNO by alkylamines, aromatic and pseudoaromatic alcohols, thiols, and hydrogen sulfide, has been extensively explored by our group during the past decade. The aim of this work is to use a kinetic modeling approach to analyze electrochemical HNO measurements and to report for the first-time direct reaction rate constants between •NO and moderate reducing agents, producing HNO. These values are between 5 and 30 times higher than the previously reported keff values. On the other hand, we also showed that reaction through successive attack by two NO molecules to biologically compatible compounds could produce HNO. After over 3 decades of intense research, the •NO chemistry is still there, ready to be discovered.

Revisiting the Tropospheric OH-Initiated Unimolecular Decomposition of Chlorpyrifos and Chlorpyrifos-Methyl: A Theoretical Perspective.

Based on density functional theory (DFT) electronic structure calculations with dispersion correction, we propose new reaction pathways in which no extra reaction step is necessary to account for the formation of 3,5,6-trichloro-2-pyridynol (TCP) within the process of tropospheric OH-initiated unimolecular decomposition of chlorpyrifos (CLP) and chlorpyrifos-methyl (CLPM). Chlorpyrifos and its analogous compound are among the most used organophosphorus pesticides worldwide, and their unimolecular decomposition in the troposphere is a dominant process of removal in the gas phase. The reaction pathways that we put forward have turned out to be the most exergonic ones among the three possible routes for the attack of the hydroxyl radical to the thiophosphoryl (P═S) bond of both CLP and CLPM. The results showed that the reaction is thermodynamically controlled with the formation of P-bonded adducts via a six-membered ring. The unimolecular decomposition of such reactive intermediates takes place with small energy barriers (less than 3 kcal mol-1) and is distinguished by hydrogen transfer to the nitrogen atom of the aromatic ring, resulting in the formation of 3,5,6-trichloro-2-pyridinol (TCP) and dialkyl phosphate radical (DAP·) product complexes in a single step.

NO/H2S "Crosstalk" Reactions. The Role of Thionitrites (SNO-) and Perthionitrites (SSNO-).

The redox chemistry of H2S with NO and other oxidants containing the NO group is discussed on a mechanistic basis because of the expanding interest in their biological relevance, with an eye open to the chemical differences of H2S and thiols RSH. We focus on the properties of two "crosstalk" intermediates, SNO- (thionitrite) and SSNO- (perthionitrite, nitrosodisulfide) based in the largely controversial status on their identity and chemistry in aqueous/nonaqueous media, en route to the final products N2O, NO2-, NH2OH/NH3, and S8. Thionitrous acid, generated either in the direct reaction of NO + H2S or through the transnitrosation of RSNO's (nitrosothiols) with H2S at pH 7.4, is best described as a mixture of rapidly interconverting isomers, {(H)SNO}. It is reactive in different competitive modes, with a half-life of a few seconds at pH 7.4 for homolytic cleavage of the N-S bond, and could be deprotonated at pH values of up to ca. 10, giving SNO-, a less reactive species than {(H)SNO}. The latter mixture can also react with HS-, giving HNO and HS2- (hydrogen disulfide), a S0(sulfane)-transfer reagent toward {(H)SNO}, leading to SSNO-, a moderately stable species that slowly decomposes in aqueous sulfide-containing solutions in the minute-hour time scale, depending on [O2]. The previous characterization of HSNO/SNO- and SSNO- is critically discussed based on the available chemical and spectroscopic evidence (mass spectrometry, UV-vis, 15N NMR, Fourier transform infrared), together with computational studies including quantum mechanics/molecular mechanics molecular dynamics simulations that provide a structural and UV-vis description of the solvatochromic properties of cis-SSNO- acting as an electron donor in water, alcohols, and aprotic acceptor solvents. In this way, SSNO- is confirmed as the elusive "yellow intermediate" (I412) emerging in the aqueous crosstalk reactions, in contrast with its assignment to polysulfides, HSn-. The analysis extends to the coordination abilities of {(H)SNO}, SNO-, and SSNO- into heme and nonheme iron centers, providing a basis for best unraveling their putative specific signaling roles.

Base Mechanism to the Hydrolysis of Phosphate Triester Promoted by the Cd2+/Cd2+ Active site of Phosphotriesterase: A Computational Study.

In the present work, density functional theory (DFT) calculations at the B3LYP/6-31+G(d) and including dispersion effects were used to investigate the hydrolysis of paraoxon, using a cluster model of the active site of Cd2+/Cd2+-phosphotriesterase (PTE) from Pseudomonas diminuta. The mechanism proposed here consist of (i) Exchange of the coordinated water molecule and coordination of the substrate to the more solvent exposed Cdß center in monodentate fashion, (ii) protonation of the µ-hydroxo bridge by the uncoordinated water molecule and in situ formation of the nucleophile, (iii) formation of a pentacoordinate intermediate with significant bond breaking to the leaving group and bond formation to the nucleophile, and (iv) protonation of the Asp301 residue and restoration of the active site through the coordination of another water molecule of the medium. The water molecules initially coordinated to the active site play a crucial role in stabilizing the transition states and the pentacoordinate intermediate. The reaction takes place in a two-step (AN + DN) mechanism, with energy barriers of 12.9 and 1.9 kcal/mol for the first and second steps, respectively, computed at the B3LYP-D3/6-311++G(2d,2p) level of theory, in excellent agreement with the experimental findings. Dispersion effects alone contribute to diminish the energy barriers as much as 26%. The base mechanism for the Cd2+/Cd2+-PTE proposed here, in conjunction with the agreement found with the experimental energetic value for the energy barrier, makes it a consistent and kinetically viable mechanistic proposal for the hydrolysis of phosphate triesters promoted by the Cd2+ substituted PTE enzyme.

HNO Is Produced by the Reaction of NO with Thiols.

Azanone (nitroxyl, HNO) is a highly reactive compound whose biological role is still a matter of debate. One possible route for its formation is NO reduction by biological reductants. These reactions have been historically discarded due to the negative redox potential for the NO,H+/HNO couple. However, the NO to HNO conversion mediated by vitamins C, E, and aromatic alcohols has been recently shown to be feasible from a chemical standpoint. Based on these precedents, we decided to study the reaction of NO with thiols as potential sources of HNO. Using two complementary approaches, trapping by a Mn porphyrin and an HNO electrochemical sensor, we found that under anaerobic conditions aliphatic and aromatic thiols (as well as selenols) are able to convert NO to HNO, albeit at different rates. Further mechanistic analysis using ab initio methods shows that the reaction between NO and the thiol produces a free radical adduct RSNOH•, which reacts with a second NO molecule to produce HNO and a nitrosothiol. The nitrosothiol intermediate reacts further with RSH to produce a second molecule of HNO and RSSR, as previously reported.

Water Solvent Effect on Theoretical Evaluation of 1H NMR Chemical Shifts: o-Methyl-Inositol Isomer.

In this paper, density functional theory calculations of nuclear magnetic resonance (NMR) chemical shifts for l-quebrachitol isomer, previously studied in our group, are reported with the aim of investigating in more detail the water solvent effect on the prediction of 1H NMR spectra. In order to include explicit water molecules, 20 water-l-quebrachitol configurations obtained from Monte Carlo simulation were selected to perform geometry optimizations using the effective fragment potential method encompassing 60 water molecules around the solute. The solvated solute optimized geometries were then used in B3LYP/6-311+G(2d,p) NMR calculations with PCM-water. The inclusion of explicit solvent in the B3LYP NMR calculations resulted in large changes in the 1H NMR profiles. We found a remarkable improvement in the agreement with experimental NMR profiles when the explicit hydrated l-quebrachitol structure is used in B3LYP 1H NMR calculations, yielding a mean absolute error (MAE) of only 0.07 ppm, much lower than reported previously for the gas phase optimized structure (MAE = 0.11 ppm). In addition, a very improved match between theoretical and experimental 1H NMR spectrum measured in D2O was achieved with the new hydrated optimized l-quebrachitol structure, showing that a fine-tuning of the theoretical NMR spectra can be accomplished once solvent effects are properly considered.

Phosphorane lifetime and stereo-electronic effects along the alkaline hydrolysis of phosphate esters.

Hybrid quantum mechanical/effective fragment potential (QM/EFP) calculations, in conjunction with the quantum theory of atoms in molecules (QTAIM) and energy decomposition analysis (EDA), were employed to investigate the reaction mechanism and stereo-electronic effects along the alkaline hydrolysis of the monoethyl phosphate dianion (MEP) and the diethylphosphate monoanion (DEP). Reactions proceed through a synchronous bimolecular ANDN mechanism for MEP and a stepwise (AN + DN) mechanism for DEP, with the formation of a phosphorane intermediate, having an overall reaction free energy and barrier of 11.5 and 43.0 kcal mol(-1), respectively. In addition, ab initio molecular dynamics simulations were performed to investigate the stability of the phosphorane pentacoordinate intermediate observed in the reaction of the phosphate diester. The phosphorane intermediate has a lifetime of ∼1 ps after which it decomposes into the corresponding alcohol and phosphate monoester dianion. Electrostatics governs the interaction between the nucleophile and the phosphate ester. However, some degree of covalence in the interaction starts to appear at distances shorter than 2.45 Šfor MEP and 2.63 Šfor DEP. For the monoester, the electrostatic repulsive terms are the dominant contributions for the formation of the transition state. On the other hand, for the phosphate diester, the formation of the P-OH bond is dominated by associative terms of electrostatic nature.

Effective targeting of proton transfer at ground and excited states of ortho-(2'-imidazolyl)naphthol constitutional isomers.

Steady-state and time-resolved spectroscopy and quantum chemical computational studies were employed to investigate ground and excited state proton transfer of a novel series of ortho-(1H-imidazol-2-yl)naphthol constitutional isomers: 1-(1H-imidazol-2-yl)naphthalen-2-ol (1NI2OH), 2-(1H-imidazol-2-yl)naphthalen-1-ol (2NI1OH) and 3-(1H-imidazol-2-yl)naphthalen-2-ol (3NI2OH). Proper Near Attack Conformations (NACs) involving a strong intramolecular hydrogen bond between the naphthol moiety and the ortho-imidazole group account for the highest ground state acidity of 2NI1OH compared with 1NI2OH and 3NI2OH. Moreover, ESIPT for 2NI1OH and 3NI2OH is further associated with planar chelate H-ring formation whereas 1NI2OH shows the highest ESIPT barrier and a noncoplanar imidazole group. In addition to energetic and structural requirements, the final state also depends on electronic configuration of the ESIPT product with the neutral 3NI2OH showing an ICT effect that correlates with the excited state pKa of the cationic species.

Photophysics and Excited State Reactions of [Ru(bpy)2dppn]2+: A Computational Study.

In this work, we used DFT and TD-DFT in the investigation of the structural parameters and photophysics of the complex [Ru(bpy)2dppn]2+ (dppn = benzo[i]-dipyrido[3,2- a:2',3'-c]phenazine) in water, and its suitability as a photosensitizer (PS) in photodynamic therapy (PDT). For that, the thermodynamics of electron transfer (ET) and energy transfer (ENT) reactions in the excited state with molecular oxygen and guanosine-5'-monophosphate (GMP) were investigated. The overall intersystem crossing (ISC) rate constant was approximately 1012 s-1, indicating that this process is highly favorable, and the triplet excited states are populated. The triplet excited states are known to lead to photoreactions between the PS and species of the medium or directly with nucleobases. Here, we show that the Rudppn complex can react favorably to oxidize the GMP and generate singlet oxygen. Furthermore, this complex can also act as an intercalator between DNA base pairs and undergo dual-channel reactions. It has been proposed that the T2 excited state is responsible for oxidizing the GMP, but we show that T1 is thermodynamically capable of undergoing the same reaction. In this sense, docking simulations were carried out to investigate further the interactions of the Rudppn complex with a DNA fragment.

New Hybrid Compound Candidate as Photothermal Agent Based on DPP Derivatives and Toluidine Blue: A Theoretical Perspective.

In this article, the synthesis of a new hybrid compound, candidate as photothermal agent, is proposed, based on TDPP (3,6-di(thiophene-2-yl)-2,5-dihydropyrrolo[3,4-c]pyrrole-1,4-dione) and toluidine blue. Electronic structure calculations at the DFT, TD-DFT and CCSD level of theories were performed to obtain ground and excited states molecular structures, photophysical properties and absorption spectrum of the hybrid and the starting compounds. Additionally, ADMET calculations were performed to predict the pharmacokinetic, metabolic and toxicity properties of the proposed compound. The results showed that the proposed compound is a strong candidate for photothermal agent since (1) it absorbs close to the near-infrared region, (2) it has low fluorescence and intersystem crossing rate constants, (3) it has accessible conical intersection with low energy barrier, (4) the compound shows lower toxicity than the well know compound toluidine blue, which is used in photodynamic therapy, (5) the compound does not show carcinogenic potential, and (6) it obeys the Lipinski's rule of five, used as a reference for the design of new pharmaceuticals.

Calculation of Excited State Internal Conversion Rate Constant Using the One-Effective Mode Marcus-Jortner-Levich Theory.

In this article, the one-effective mode Marcus-Jortner-Levich (MJL) theory and the classical Marcus theory for electron transfer were applied to estimate the internal conversion rate constant, kIC, of organic molecules and a Ru-based complex, all belonging to the Marcus inverted region. For this, the reorganization energy was calculated using the minimum energy conical intersection point to account for more vibrational levels, correcting the density of states. The results showed good agreement with experimental and theoretically determined kIC, with a small overestimation by the Marcus theory. Also, molecules less dependent on the solvent effects, like benzophenone, presented better results than molecules with an expressive dependence, like 1-aminonaphthalene. Moreover, the results suggest that each molecule possesses unique normal modes leading to the excited state deactivation that does not necessarily match the X-H bond stretching, as previously suggested.

Synthesis, magnetostructural correlation, and catalytic promiscuity of unsymmetric dinuclear copper(II) complexes: models for catechol oxidases and hydrolases.

Herein, we report the synthesis and characterization, through elemental analysis, electronic spectroscopy, electrochemistry, potentiometric titration, electron paramagnetic resonance, and magnetochemistry, of two dinuclear copper(II) complexes, using the unsymmetrical ligands N',N',N-tris(2-pyridylmethyl)-N-(2-hydroxy-3,5-di-tert-butylbenzyl)-1,3-propanediamin-2-ol (L1) and N',N'-bis(2-pyridylmethyl)-N,N-(2-hydroxybenzyl)(2-hydroxy-3,5-di-tert-butylbenzyl)-1,3-propanediamin-2-ol (L2). The structures of the complexes [Cu(2)(L1)(µ-OAc)](ClO(4))(2)·(CH(3))(2)CHOH (1) and [Cu(2)(L2)(µ-OAc)](ClO(4))·H(2)O·(CH(3))(2)CHOH (2) were determined by X-ray crystallography. The complex [Cu(2)(L3)(µ-OAc)](2+) [3; L3 = N-(2-hydroxybenzyl)-N',N',N-tris(2-pyridylmethyl)-1,3-propanediamin-2-ol] was included in this study for comparison purposes only (Neves et al. Inorg. Chim. Acta2005, 358, 1807-1822). Magnetic data show that the Cu(II) centers in 1 and 2 are antiferromagnetically coupled and that the difference in the exchange coupling J found for these complexes (J = -4.3 cm(-1) for 1 and J = -40.0 cm(-1) for 2) is a function of the Cu-O-Cu bridging angle. In addition, 1 and 2 were tested as catalysts in the oxidation of the model substrate 3,5-di-tert-butylcatechol and can be considered as functional models for catechol oxidase. Because these complexes possess labile sites in their structures and in solution they have a potential nucleophile constituted by a terminal Cu(II)-bound hydroxo group, their activity toward hydrolysis of the model substrate 2,4-bis(dinitrophenyl)phosphate and DNA was also investigated. Double electrophilic activation of the phosphodiester by monodentate coordination to the Cu(II) center that contains the phenol group with tert-butyl substituents and hydrogen bonding of the protonated phenol with the phosphate O atom are proposed to increase the hydrolase activity (K(ass.) and k(cat.)) of 1 and 2 in comparison with that found for complex 3. In fact, complexes 1 and 2 show both oxidoreductase and hydrolase/nuclease activities and can thus be regarded as man-made models for studying catalytic promiscuity.

N4-Phenyl-substituted 2-acetylpyridine thiosemicarbazones: cytotoxicity against human tumor cells, structure-activity relationship studies and investigation on the mechanism of action.

N(4)-Phenyl 2-acetylpyridine thiosemicarbazone (H2Ac4Ph; N-(phenyl)-2-(1-(pyridin-2-yl)ethylidene)hydrazinecarbothioamide) and its N(4)-ortho-, -meta- and -para-fluorophenyl (H2Ac4oFPh, H2Ac4mFPh, H2Ac4pFPh), N(4)-ortho-, -meta- and -para-chlorophenyl (H2Ac4oClPh, H2Ac4mClPh, H2Ac4pClPh), N(4)-ortho-, -meta- and -para-iodophenyl (H2Ac4oIPh, H2Ac4mIPh, H2Ac4pIPh) and N(4)-ortho-, -meta- and -para-nitrophenyl (H2Ac4oNO(2)Ph, H2Ac4mNO(2)Ph, H2Ac4pNO(2)Ph) derivatives were assayed for their cytotoxicity against human malignant breast (MCF-7) and glioma (T98G and U87) cells. The compounds were highly cytotoxic against the three cell lineages (IC(50): MCF-7, 52-0.16 nM; T98G, 140-1.0 nM; U87, 160-1.4 nM). All tested thiosemicarbazones were more cytotoxic than etoposide and did not present any haemolytic activity at up to 10(-5)M. The compounds were able to induce programmed cell death. H2Ac4pClPh partially inhibited tubulin assembly at high concentrations and induced cellular microtubule disorganization.

Theoretical investigation of [Ru(bpy)2(HAT)]2+ (HAT = 1,4,5,8,9,12-hexaazatriphenylene; bpy = 2,2'-bipyridine): Photophysics and reactions in excited state.

In this article, Density Functional Theory based calculations, including dispersion corrections, PBE0(D3BJ)/Def2-TZVP(-f), were performed to elucidate the photophysics of the [Ru(bpy)2(HAT)]2+ complex in water. In addition, the thermodynamics of the charge and electron transfer excited state reactions of this complex with oxygen, nitric oxide and Guanosine-5'-monophosphate nucleotide (GMP) were investigated. The first singlet excite state, S1, strongly couples with the second and third triplet excited states (T2 and T3) giving rise to a high intersystem crossing rate of 6.26 × 1011 s-1 which is ∼106 greater than the fluorescence rate decay. The thermodynamics of the excited reactions revealed that all electron transfer reactions investigated are highly favorable, due mainly to the high stability of the triply charged radical cation 2PS•3+ species formed after the electron has been transferred. Excited state electron transfer from the GMP nucleotide to the complex is also highly favorable (ΔGsol = -92.6 kcal/mol), showing that this complex can be involved in the photooxidation of DNA, in line with experimental findings. Therefore, the calculations allow to conclude that the [Ru(bpy)2(HAT)]2+ complex can act in Photodynamic therapy through both mechanisms type I and II, through electron transfer from and to the complex and triplet-triplet energy transfer, generating ROS, RNOS and through DNA photooxidation. In addition, the work also opens a perspective of using this complex for the in-situ generation of the singlet nitroxyl (1NO-) species, which can have important applications for the generation of HNO and may have, therefore, important impact for physiological studies involving HNO.

C-H bond activation of methane in aqueous solution: a hybrid quantum mechanical/effective fragment potential study.

In this study, we investigated the C-H bond activation of methane catalyzed by the complex [PtCl(4)](2-), using the hybrid quantum mechanical/effective fragment potential (EFP) approach. We analyzed the structures, energetic properties, and reaction mechanism involved in the elementary steps that compose the catalytic cycle of the Shilov reaction. Our B3LYP/SBKJC/cc-pVDZ/EFP results show that the methane activation may proceed through two pathways: (i) electrophilic addition or (ii) direct oxidative addition of the C-H bond of the alkane. The electrophilic addition pathway proceeds in two steps with formation of a σ-methane complex, with a Gibbs free energy barrier of 24.6 kcal mol(-1), followed by the cleavage of the C-H bond, with an energy barrier of 4.3 kcal mol(-1) . The activation Gibbs free energy, calculated for the methane uptake step was 24.6 kcal mol(-1), which is in good agreement with experimental value of 23.1 kcal mol(-1) obtained for a related system. The results shows that the activation of the C-H bond promoted by the [PtCl(4)](2-) catalyst in aqueous solution occurs through a direct oxidative addition of the C-H bond, in a single step, with an activation free energy of 25.2 kcal mol(-1), as the electrophilic addition pathway leads to the formation of a σ-methane intermediate that rapidly undergoes decomposition. The inclusion of long-range solvent effects with polarizable continuum model does not change the activation energies computed at the B3LYP/SBKJC/cc-pVDZ/EFP level of theory significantly, indicating that the large EFP water cluster used, obtained from Monte Carlo simulations and analysis of the center-of-mass radial pair distribution function, captures the most important solvent effects.

Theoretical Investigation of the 4,5-Dibromorodamine Methyl Ester (TH9402) Photosensitizer Used in Photodynamic Therapy: Photophysics, Reactions in the Excited State, and Interactions with DNA.

Photosensitizer (PS) molecules play a critical role in photodynamic therapy of cancer and the understanding of the molecular mechanism involved in the photophysics of these compounds, and their reactions in the excited state are, therefore, of great interest for the development of this technique. In this article, the photophysics of the cationic PS 4,5-dibromorodamine methyl ester (TH9402), its electron- and energy-transfer reactions in the excited triplet state, with molecular oxygen, nitric oxide, guanosine-5'-monophosphate (GMP), and guanine, and the interaction with DNA were evaluated. Time-dependent density functional theory calculations at the TPSSh/Def2-TZVP//B3LYP/Def2-TZVP level of theory in water solution reveals that the PS has a bright S1 state 2.33 eV above the ground state that produces a fluorescent rate constant of 5.40 × 107 s-1, calculated using Fermi's golden rule within a path integral formalism. Once excited to the bright state, the main intersystem crossing (ISC) channel involves the coupling with the T2 state just below S1 (S1 → T2 → T1) with an overall ISC rate constant of 10.1 × 107 s-1, in good agreement with the experimental data. Excited-state reaction thermodynamics, computed at the M06-2X/Def2-TZVP//B3LYP/Def2-TZVP level of theory in water, showed that from all the excited-state electron-transfer reactions studied, only the transfer from GMP to the PS is thermodynamically favorable, independent of the protonation state of guanosine, which indicates a possible DNA photo-oxidation mechanism for the PS. Triplet-triplet energy-transfer reactions from TH9402 to molecular oxygen, producing reactive singlet oxygen, and to the deprotonated guanosine, producing 3GMP2-, are also thermodynamically favorable, with ΔG = -2.0 and -24.0 kcal//mol, respectively. However, the energy transfer to the monoprotonated guanosine is not favorable, (ΔG = 36.1), suggesting that in the DNA double-strand environment, this energy-transfer process may not be observed. The results show that the PS can act through electron transfer and triplet-triplet energy-transfer reactions involved in mechanism types I and II in photodynamic therapy. Interactions of TH9402 with the d(AGACGTCT)2 octanucleotide revealed that the PS can intercalate between the d(GpC)-d(CpG) base pairs in three different orientations and, upon intercalation, the π → π* transition of the PS shows a bathochromic shift up to 90 nm and up to 60% decrease in intensity. Interactions through groove binding showed a smaller bathochromic shift of 52.2 nm and a 56% decrease in intensity of the main transition band.

Computational insights into the reactivity of chlorpyrifos and chlorpyrifos-methyl toward singlet oxygen.

A complete mechanism for the •OH-initiated atmospheric decomposition of the pesticides chlorpyrifos and chlorpyrifos-methyl is proposed, incorporating additional studies on the competing reaction with singlet oxygen. The computational study is based on density functional theory (DFT) at the double-hybrid functional level to treat static correlation in the calculations of energy barriers. Reaction of the P-bonded intermediate with 1O2 has a small energy barrier of ~ 2 kcal mol-1, generating the Oxone compound and the HOSO• radical, with a reaction free energy of - 49.8 kcal/mol for the chlorpyrifos reaction pathway. Direct reaction of the pesticides with singlet oxygen is unlikely to happen due to the exceedingly high energy barrier of ~ 52 kcal/mol. However, in aqueous solution, the activation energy reduces dramatically and changes the reaction thermodynamics, making it kinetically accessible and thermodynamically viable.

Electronic structure and mechanism for the uptake of nitric oxide by the Ru(iii) antitumor complex NAMI-A.

Nitric oxide (NO) has well known vasodilation effects in living organisms and its participation in the metastasis of cancer cells through the angiogenesis process has been demonstrated experimentally. Therefore, the uptake of NO has become one focus of investigation to produce anti-metastatic drugs. In this article we have investigated the uptake of NO by the ruthenium based metallodrug trans-tetrachloride(dimethylsulfoxide)imidazole ruthenate(iii) [Im]trans-[RuCl4(Im)(DMSO)], known as New Anti-tumor Metastasis Inhibitor-A (NAMI-A). Electronic structure calculations using Density Functional Theory, DFT, and State-Averaged Complete Active Space Self Consistent Field, SA-CASSCF, with second order perturbation theory corrections, NEVPT2 were carried out to investigate the mechanism involved in the uptake of NO by the Ru-based anticancer metallodrug NAMI-A. The calculations revealed that the reaction takes place at the triplet potential energy surface, with the singlet surface being ∼15 kcal mol-1 shifted to higher energies, and there is a surface crossing to form the most stable singlet product after the reaction takes place at the triplet surface. The spin pairing and electron transfer from the nitric oxide to the metallic fragment takes place at the region of the minimum energy crossing point between the two surfaces. The Ru-NO bond in the {Ru-NO}6 product has ∼10% of the RuIII-NO0 character. The SA-CASSCF/NEVPT2 calculations revealed that the uptake of NO by NAMI-A has a small energy barrier of ∼8 kcal mol-1 and, therefore a rate constant of 11.3 × 106 s-1 at 300 K. In addition, the reaction is thermodynamically favorable, with a Gibbs free energy of ∼30 kcal mol-1. These results show that the uptake of nitric oxide by the NAMI-A complex is kinetically and thermodynamically feasible in biological medium and, therefore, gives support to the anti-angiogenesis theory associated to the mode of action of NAMI-A and other related compounds.

Non-structural protein 5 (NS5) as a target for antiviral development against established and emergent flaviviruses.

Flaviviruses are among the most critical pathogens in tropical regions and cause a growing number of severe diseases in developing countries. The development of antiviral therapeutics is crucial for managing flavivirus outbreaks. Among the ten proteins encoded in the flavivirus RNA, non-structural protein 5, NS5, is a promising drug target. NS5 plays a fundamental role in flavivirus replication, viral RNA methylation, RNA polymerization, and host immune system evasion. Most of the NS5 inhibitor candidates target NS5 active sites. However, the similarity of NS5 activity sites with human enzymes can cause side effects. Identifying new allosteric sites in NS5 can contribute enormously to antiviral development. The NS5 structural characterization enabled exploring new regions, such as the residues involved in MTase-RdRp interaction, NS5 oligomerization, and NS5 interaction with other viral and host-cell proteins. Targeting NS5 critical interactions might lead to new compounds and overcomes the toxicity of current NS5-inhibitor candidates.