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1.
J Chem Phys ; 153(11): 114117, 2020 Sep 21.
Artigo em Inglês | MEDLINE | ID: mdl-32962380

RESUMO

Many natural substances and drugs are radical scavengers that prevent the oxidative damage to fundamental cell components. This process may occur via different mechanisms, among which, one of the most important, is hydrogen atom transfer. The feasibility of this process can be assessed in silico using quantum mechanics to compute ΔGHAT ○. This approach is accurate, but time consuming. The use of machine learning (ML) allows us to reduce tremendously the computational cost of the assessment of the scavenging properties of a potential antioxidant, almost without affecting the quality of the results. However, in many ML implementations, the description of the relevant features of a molecule in a machine-friendly language is still the most challenging aspect. In this work, we present a newly developed machine-readable molecular representation aimed at the application of automatized ML algorithms. In particular, we show an application on the calculation of ΔGHAT ○.

2.
Inorg Chem ; 59(15): 10907-10919, 2020 Aug 03.
Artigo em Inglês | MEDLINE | ID: mdl-32658468

RESUMO

With a half-life of 7.45 days, silver-111 (ßmax 1.04 MeV, Eγ 245.4 keV [Iγ 1.24%], Eγ 342.1 keV [Iγ 6.7%]) is a promising candidate for targeted cancer therapy with ß- emitters as well as for associated SPECT imaging. For its clinical use, the development of suitable ligands that form sufficiently stable Ag+-complexes in vivo is required. In this work, the following sulfur-containing derivatives of tetraazacyclododecane (cyclen) have been considered as potential chelators for silver-111: 1,4,7,10-tetrakis(2-(methylsulfanyl)ethyl)-1,4,7,10-tetraazacyclododecane (DO4S), (2S,5S,8S,11S)-2,5,8,11-tetramethyl-1,4,7,10-tetrakis(2-(methylsulfanyl)ethyl)-1,4,7,10-tetraazacyclododecane (DO4S4Me), 1,4,7-tris(2-(methylsulfanyl)ethyl)-1,4,7,10-tetraazacyclododecane (DO3S), 1,4,7-tris(2-(methylsulfanyl)ethyl)-10-acetamido-1,4,7,10-tetraazacyclododecane (DO3SAm), and 1,7-bis(2-(methylsulfanyl)ethyl)-4,10,diacetic acid-1,4,7,10-tetraazacyclododecane (DO2A2S). Natural Ag+ was used in pH/Ag-potentiometric and UV-vis spectrophotometric studies to determine the metal speciation existing in aqueous NaNO3 0.15 M at 25 °C and the equilibrium constants of the complexes, whereas NMR and DFT calculations gave structural insights. Overall results indicated that sulfide pendant arms coordinate Ag+ allowing the formation of very stable complexes, both at acidic and physiological pH. Furthermore, radiolabeling, stability in saline phosphate buffer, and metal-competition experiments using the two ligands forming the strongest complexes, DO4S and DO4S4Me, were carried out with [111Ag]Ag+ and promising results were obtained.

3.
J Comput Chem ; 41(23): 2045-2054, 2020 Sep 05.
Artigo em Inglês | MEDLINE | ID: mdl-32656797

RESUMO

Methylmercury is a highly toxic compound and human exposure is mainly related to consumption of polluted fish and seafood. The inactivation of thiol-based enzymes, promoted by the strong affinity binding of electrophilic mercuric ions to thiol and selenol groups of proteins, is likely an important factor explaining its toxicity. A key role is played by the chemistry and reactivity of the mercury-chalcogens bond, particularly HgS and HgSe, which is the focus of this computational work (level of theory: (COSMO)-ZORA-BLYP-D3(BJ)/TZ2P). We analyze nine ligand-exchange model reactions (the so-called Rabenstein's reactions) involving an entering ligand (methylchalcogenolate) and a substrate (methylchalcogenolatemethylmercury). Trends in reaction and activation energies are discussed and a change in mechanism is reported for all cases when going from gas phase to water, that is, from a single-well potential energy surface (PES) to a canonical SN 2-like mechanism. The reasons accounting for the biochemically challenging and desired displacement of methylmercury from a seleno/thiol protein can be found already in these model reactions, as can be seen from the similarities of the ligand exchange reactions in solution in thermodynamics and kinetics.

4.
Phys Chem Chem Phys ; 22(6): 3455-3465, 2020 Feb 12.
Artigo em Inglês | MEDLINE | ID: mdl-31984980

RESUMO

We propose an approach to the evaluation of kinetic rates of elementary chemical reactions within Kramers' theory based on the definition of the reaction coordinate as a linear combination of natural, pseudo Z-matrix, internal coordinates of the system. The element of novelty is the possibility to evaluate the friction along the reaction coordinate, within a hydrodynamic framework developed recently [J. Campeggio et al., J. Comput. Chem. 2019, 40, 679-705]. This, in turn, allows to keep into account barrier recrossing, i.e. the transmission coefficient that is employed in correcting transition state theory evaluations. To test the capabilities and the flaws of the approach we use as case studies two archetypal SN2 reactions. First, we consider to the standard substitution of chloride ion to bromomethane. The rate constant at 295.15 K is evaluated to k/c⊖ = 2.7 × 10-6 s-1 (with c⊖ = 1 M), which compares well to the experimental value of 3.3 × 10-6 s-1 [R. H. Bathgate and E. A. Melwyn-Hughes, J. Chem. Soc 1959, 2642-2648]. Then, the method is applied to the SN2 reaction of methylthiolate to dimethyl disulfide in water. In biology, such an interconversion of thiols and disulfides is an important metabolic topic still not entirely rationalized. The predicted rate constant is k/c⊖ = 7.7 × 103 s-1. No experimental data is available for such a reaction, but it is in accord with the fact that the alkyl thiolates to dialkyl disulfides substitutions in water have been found to be fast reactions [S. M. Bachrach, J. M. Hayes, T. Dao and J. L. Mynar, Theor. Chem. Acc. 2002, 107, 266-271].

5.
J Chem Phys ; 152(3): 034201, 2020 Jan 21.
Artigo em Inglês | MEDLINE | ID: mdl-31968969

RESUMO

The nature of the photoexcited triplet state of free-base 5,10,15,20-tetrakis(4-sulfonatophenyl)porphyrin (H2TPPS4-) has been investigated by advanced Electron Paramagnetic Resonance (EPR) techniques combined with quantum chemical calculations. The zero-field splitting (ZFS) parameters, D and E, the orientation of the transition dipole moment in the ZFS tensor frame, and the proton hyperfine couplings have been determined by magnetophotoselection-EPR and pulse electron-nuclear double resonance spectroscopy. Both time-resolved and pulse experiments exploit the electron spin polarization of the photoexcited triplet state. Comparison of the magnetic observables with computational results, including CASSCF calculations of the ZFS interaction tensor, provides an accurate picture of the triplet-state electronic structure. The theoretical investigation has been integrated with a systematic analysis on the parent free-base porphyrin molecule to assess the effect of the sulfonatophenyl substituents on the magnetic tensors. Additionally, the magnetophotoselection effects are discussed in terms of tautomerization in the excited singlet state of H2TPPS4-.

6.
Redox Biol ; 28: 101328, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31574461

RESUMO

Ferroptosis is a form of cell death primed by iron and lipid hydroperoxides and prevented by GPx4. Ferrostatin-1 (fer-1) inhibits ferroptosis much more efficiently than phenolic antioxidants. Previous studies on the antioxidant efficiency of fer-1 adopted kinetic tests where a diazo compound generates the hydroperoxyl radical scavenged by the antioxidant. However, this reaction, accounting for a chain breaking effect, is only minimally useful for the description of the inhibition of ferrous iron and lipid hydroperoxide dependent peroxidation. Scavenging lipid hydroperoxyl radicals, indeed, generates lipid hydroperoxides from which ferrous iron initiates a new peroxidative chain reaction. We show that when fer-1 inhibits peroxidation, initiated by iron and traces of lipid hydroperoxides in liposomes, the pattern of oxidized species produced from traces of pre-existing hydroperoxides is practically identical to that observed following exhaustive peroxidation in the absence of the antioxidant. This supported the notion that the anti-ferroptotic activity of fer-1 is actually due to the scavenging of initiating alkoxyl radicals produced, together with other rearrangement products, by ferrous iron from lipid hydroperoxides. Notably, fer-1 is not consumed while inhibiting iron dependent lipid peroxidation. The emerging concept is that it is ferrous iron itself that reduces fer-1 radical. This was supported by electroanalytical evidence that fer-1 forms a complex with iron and further confirmed in cells by fluorescence of calcein, indicating a decrease of labile iron in the presence of fer-1. The notion of such as pseudo-catalytic cycle of the ferrostatin-iron complex was also investigated by means of quantum mechanics calculations, which confirmed the reduction of an alkoxyl radical model by fer-1 and the reduction of fer-1 radical by ferrous iron. In summary, GPx4 and fer-1 in the presence of ferrous iron, produces, by distinct mechanism, the most relevant anti-ferroptotic effect, i.e the disappearance of initiating lipid hydroperoxides.


Assuntos
Cicloexilaminas/farmacologia , Ferroptose/efeitos dos fármacos , Fenilenodiaminas/farmacologia , Antioxidantes/farmacologia , Morte Celular/efeitos dos fármacos , Cromatografia Líquida , Cicloexilaminas/química , Teoria da Densidade Funcional , Relação Dose-Resposta a Droga , Ferroptose/genética , Hidrogênio/química , Peroxidação de Lipídeos/efeitos dos fármacos , Peróxidos Lipídicos/metabolismo , Lipidômica/métodos , Lipídeos/química , Modelos Moleculares , Estrutura Molecular , Oxirredução , Fenilenodiaminas/química , Espectrometria de Massas em Tandem
7.
J Phys Chem B ; 123(39): 8232-8239, 2019 10 03.
Artigo em Inglês | MEDLINE | ID: mdl-31502466

RESUMO

An investigation of the photoexcited triplet state of chlorophyll (Chl) b has been carried out by means of electron nuclear double resonance, both in a frozen organic solvent and in a protein environment provided by the water-soluble chlorophyll protein of Lepidium virginicum. Density functional theory calculations have allowed the complete assignment of the observed hyperfine couplings corresponding to the methine protons and the methyl groups, leading to a complete picture of the spin density distribution of the triplet state in the tetrapyrrole macrocycle. The triplet-state properties of Chl b are found to be similar, in many respects, to those previously reported for Chl a, although some specificities have been highlighted. Concerning the spin density distribution, the differences are mainly localized on the carbon atoms close to the formyl group which, in Chl b, replaces the methyl group of Chl a.

8.
ACS Omega ; 4(2): 4192-4205, 2019 Feb 28.
Artigo em Inglês | MEDLINE | ID: mdl-31459629

RESUMO

Novel silver(I), gold(I), and palladium(II) complexes were synthesized with bidentate heteroditopic carbene ligands that combine an imidazol-2-ylidene (nNHC) with a 1,2,3-triazol-5-ylidene (tzNHC) connected by a propylene bridge. The silver(I) and gold(I) complexes were dinuclear species, [M2(nNHC-tzNHC)2](PF6)2 (M = Ag or Au), with the two bidentate ligands bridging the metal centers, whereas in the palladium(II) complex [Pd(nNHC-tzNHC)2](PF6)2, the two ligands were chelated on the same metal center. Because of the presence of two different carbene units, isomers were observed for the gold(I) and palladium(II) complexes. The molecular structures of the head-to-tail isomer for gold(I) complexes, with a twisted or folded-syn conformation of the bridge between the carbene units, were determined by X-ray diffraction analysis. The study was completed with a systematic structural investigation through density functional theory (DFT) calculations. For palladium(II) species, the head-to-head form was structurally characterized. The dinuclear gold(I) complexes were emissive in the solid state in the blue region (PLQY up to 8%); time-dependent density functional theory (abbreviated as TD-DFT) calculations disclosed that the absorption bands have metal-to-ligand-charge-transfer character and evidenced that the emission occurs from the T1 level (phosphorescence).

9.
Biosensors (Basel) ; 9(2)2019 Apr 17.
Artigo em Inglês | MEDLINE | ID: mdl-30999661

RESUMO

Surface-enhanced Raman scattering (SERS) has become a powerful tool in chemical, material and life sciences, owing to its intrinsic features (i.e., fingerprint recognition capabilities and high sensitivity) and to the technological advancements that have lowered the cost of the instruments and improved their sensitivity and user-friendliness. We provide an overview of the most significant aspects of SERS. First, the phenomena at the basis of the SERS amplification are described. Then, the measurement of the enhancement and the key factors that determine it (the materials, the hot spots, and the analyte-surface distance) are discussed. A section is dedicated to the analysis of the relevant factors for the choice of the excitation wavelength in a SERS experiment. Several types of substrates and fabrication methods are illustrated, along with some examples of the coupling of SERS with separation and capturing techniques. Finally, a representative selection of applications in the biomedical field, with direct and indirect protocols, is provided. We intentionally avoided using a highly technical language and, whenever possible, intuitive explanations of the involved phenomena are provided, in order to make this review suitable to scientists with different degrees of specialization in this field.


Assuntos
Bactérias/isolamento & purificação , Técnicas Biossensoriais , DNA/análise , Proteínas/análise , Vírus/isolamento & purificação , Animais , Humanos , Análise Espectral Raman , Propriedades de Superfície
10.
Molecules ; 24(7)2019 Mar 30.
Artigo em Inglês | MEDLINE | ID: mdl-30935011

RESUMO

The interest in diphenyl ditelluride (Ph2Te2) is related to its strict analogy to diphenyl diselenide (Ph2Se2), whose capacity to reduce organic peroxides is largely exploited in catalysis and green chemistry. Since the latter is also a promising candidate as an antioxidant drug and mimic of the ubiquitous enzyme glutathione peroxidase (GPx), the use of organotellurides in medicinal chemistry is gaining importance, despite the fact that tellurium has no recognized biological role and its toxicity must be cautiously pondered. Both Ph2Se2 and Ph2Te2 exhibit significant conformational freedom due to the softness of the inter-chalcogen and carbon⁻chalcogen bonds, preventing the existence of a unique structure in solution. Therefore, the accurate calculation of the NMR chemical shifts of these flexible molecules is not trivial. In this study, a detailed structural analysis of Ph2Te2 is carried out using a computational approach combining classical molecular dynamics and relativistic density functional theory methods. The goal is to establish how structural changes affect the electronic structure of diphenyl ditelluride, particularly the 125Te chemical shift.


Assuntos
Derivados de Benzeno/química , Compostos Organometálicos/química , Telúrio/química , Espectroscopia de Ressonância Magnética/métodos , Conformação Molecular , Simulação de Dinâmica Molecular , Compostos Organosselênicos/química , Teoria Quântica , Relação Estrutura-Atividade , Termodinâmica
11.
Comput Struct Biotechnol J ; 17: 311-318, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30867894

RESUMO

Zolpidem (N,N-Dimethyl-2-[6-methyl-2-(4-methylphenyl)imidazo[1,2-a]pyridin-3-yl]acetamide) is a well-known drug for the treatment of sleeping disorders. Recent literature reports on positive effects of zolpidem therapy on improving renal damage after cisplatin and on reducing akinesia without sleep induction. This has been ascribed to the antioxidant and neuroprotective capacity of this molecule, and tentatively explained according to a generic structural similarity between zolpidem and melatonin. In this work, we investigate in silico the antioxidant potential of zolpidem as scavenger of five ROSs, acting via hydrogen atom transfer (HAT) mechanism; computational methodologies based on density functional theory are employed. For completeness, the analysis is extended to six metabolites. Thermodynamic and kinetic results disclose that indeed zolpidem is an efficient radical scavenger, similarly to melatonin and Trolox, supporting the biomedical evidence that the antioxidant potential of zolpidem therapy may have a beneficial effect against oxidative injury, which is emerging as an important etiopathogenesis in numerous severe diseases, including psychiatric disorders.

12.
ChemistryOpen ; 8(2): 143-154, 2019 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-30740289

RESUMO

Half-sandwich RhI compounds display good catalytic activity toward alkyne [2+2+2] cycloadditions. A peculiar structural feature of these catalysts is the coordination of the metal to an aromatic moiety, typically a cyclopentadienyl anion, and, in particular, the possibility to change the bonding mode easily by the metal slipping over this aromatic moiety. Upon modifying the ancillary ligands, or proceeding along the catalytic cycle, hapticity changes can be observed; it varies from η5, if the five metal-carbon distances are identical, through η3+η2, in the presence of allylic distortion, and η3, in the case of allylic coordination, to η1, if a σ metal-carbon bond forms. In this study, we present the slippage span model, derived with the aim of establishing a relationship between slippage variation during the catalytic cycle, quantified in a novel and rigorous way, and the performance of catalysts in terms of turnover frequency, computed with the energy span model. By collecting and comparing new data and data from the literature, we find that the highest performance is associated with the smallest slippage variation along the cycle.

13.
Phys Chem Chem Phys ; 20(43): 27592-27599, 2018 Nov 07.
Artigo em Inglês | MEDLINE | ID: mdl-30371693

RESUMO

Chalcogen-π interactions occur between a covalently bound chalcogen atom that enters into a non-covalent interaction with an unsaturated moiety, a bonding motif found in various structures, such as, proteins. In this work, we have systematically explored and analyzed chalcogen-π interactions in model systems X2DA (with D = O, S, Se, Te; X = halogen; A = acetylene, ethylene and 2-butyne), using relativistic density functional theory (DFT). The nature and trends in stability of the chalcogen-π bonds are analyzed and interpreted in terms of quantitative MO theory in combination with a matching canonical energy decomposition analysis (EDA) scheme. We find that chalcogen-π bonds increase in strength as the X-D electronegativity difference becomes greater. Moreover, 2-butyne was found to participate in the strongest non-covalent interaction due to enhanced orbital interactions.

14.
Phys Chem Chem Phys ; 20(32): 20874-20885, 2018 Aug 15.
Artigo em Inglês | MEDLINE | ID: mdl-30066704

RESUMO

The reactivity of diselenides and ditellurides of general formula (RX)2 (X = Se, Te; R = H, CH3, Ph) toward hydrogen peroxide was studied through a computational approach based on accurate Density Functional Theory (DFT) calculations. The aliphatic and aromatic dichalcogenides have been chosen in light of their activity in glutathione peroxidase (GPx)-like catalytic cycles and their promising features as efficient antioxidant compounds. The reaction products, the energetics and the mechanistic details of these oxidations are discussed. Analogous disulfides are included in our analysis for completeness. We find that the barrier for oxidation of dichalcogenides decreases from disulfides to diselenides to ditellurides. On the other hand, variation of the substituents at the chalcogen nucleus has relatively little effect on the reactivity.


Assuntos
Antioxidantes/química , Peróxido de Hidrogênio/química , Compostos Organometálicos/química , Selênio/química , Telúrio/química , Catálise , Dissulfetos/química , Glutationa Peroxidase/química , Modelos Moleculares , Estrutura Molecular , Compostos Organosselênicos/química , Oxirredução , Termodinâmica
15.
Chemphyschem ; 19(14): 1766-1773, 2018 07 17.
Artigo em Inglês | MEDLINE | ID: mdl-29635782

RESUMO

The intramolecular oxidative coupling converting a bis-acetylene complex of formula CpM (C2 H2 )2 (Cp=C5 H5- ; M=Co, Rh, Ir) into a 16-electron metallacycle is studied in silico. This reaction is paradigmatic in acetylene [2+2+2] cycloaddition to benzene catalyzed by CpM fragments, being the step with the highest activation energy, and thus affecting the whole catalysis. Our activation strain and quantitative molecular orbital (MO) analyses elucidate the mechanistic details and reveal why cobalt performs better than rhodium and iridium catalysts outlining general principles for rational design of catalysts to be used in these processes.

16.
Dalton Trans ; 47(3): 935-945, 2018 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-29260150

RESUMO

Treatment of the tricationic gold(iii) [Au(MeImCH2ImMe)2](PF6)3 complex 1-3PF6 (Im = imidazol-2-ylidene) with excess halides affords complexes 1-3X (X = Cl, Br, and I), resulting from counter anion PF6-/X- exchange. The 1H chemical shift of the CH3 groups and particularly that of the CH2 linker in DMSO-d6 are different in the three complexes, thus suggesting selective XHC interactions. Complex 13+ can therefore be used as a halide sensor in DMSO and water. The host-guest interaction between the tricationic gold(iii) complex and the halides Cl-, Br- and I- in solution and in the solid state has been investigated by means of NMR titration experiments, DFT calculations and X-ray structure analysis. The electrostatic interaction between the halides and the triple formal positive charge on the metal centre, together with the CHX hydrogen bonding between the NHC ligand and halides, contributes to the formation of stable supramolecular aggregates in solution and in the solid state. The complexing properties of 13+ are strongly influenced by the nature of the solvent. Formation of the 1 : 1 and 1 : 2 species (1X2+ and 1X2+) is observed in DMSO-d6, while that of only the 1 : 1 aggregates (1X2+) is observed in D2O (X = Cl, Br, and I). Moreover, the selectivity towards the various halides is reversed in the two solvents, being in the order Cl- > Br- > I- in DMSO-d6 and I- > Br- > Cl- in D2O. The formation constants of the species 1X2+ and 1X2+ in DMSO and 1X2+ in water have been determined by fitting the NMR titration curves.

17.
Chemphyschem ; 18(21): 2990-2998, 2017 Nov 03.
Artigo em Inglês | MEDLINE | ID: mdl-28837255

RESUMO

The oxidation by H2 O2 of the human phospholipid hydroperoxide glutathione peroxidase (GPx4), used as a model peroxidase selenoenzyme, as well as that of its cysteine (Cys) and tellurocysteine (Tec) mutants, was investigated in silico through a combined classic and quantum mechanics approach to assess the role of the different chalcogens. To perform this analysis, new parameters for selenocysteine (Sec) and tellurocysteine (Tec) were accurately derived for the AMBER ff14SB force field. The oxidation represents the initial step of the antioxidant activity of GPx, which catalyzes the reduction of H2 O2 and organic hydroperoxides by glutathione (GSH). A mechanism involving a charge-separation intermediate is feasible for the Cys and Sec enzymes, leading from the initial thiol/selenol form to sulfenic/selenenic acid, whereas for the Tec mutant a direct oxidation pathway is proposed. Activation strain analyses, performed for Cys-GPx and Sec-GPx, provided insight into the rate-accelerating effect of selenium as compared to sulfur and the role of specific amino acids other than Cys/Sec that are typically conserved in the catalytic pocket.


Assuntos
Biocatálise , Calcogênios/metabolismo , Glutationa Peroxidase/metabolismo , Domínio Catalítico , Calcogênios/química , Glutationa Peroxidase/química , Humanos , Peróxido de Hidrogênio/química , Peróxido de Hidrogênio/metabolismo , Simulação de Dinâmica Molecular , Oxirredução
18.
Chemistry ; 23(10): 2405-2422, 2017 Feb 16.
Artigo em Inglês | MEDLINE | ID: mdl-27935210

RESUMO

The oxidation of organic phenylselenides by H2 O2 is investigated in model compounds, namely, n-butyl phenyl selenide (PhSe(nBu)), bis(phenylselanyl)methane (PhSeMeSePh), diphenyl diselenide (PhSeSePh), and 1,2-bis(phenylselanyl)ethane (PhSeEtSePh). Through a combined experimental (1 H and 77 Se NMR) and computational approach, we characterize the direct oxidation of monoselenide to selenoxide, the stepwise double oxidation of PhSeMeSePh that leads to different diastereomeric diselenoxides, the complete oxidation of the diphenyldiselenide that leads to selenium-selenium bond cleavage, and the subsequent formation of the phenylseleninic product. The oxidation of PhSeEtSePh also results in the formation of phenylseleninic acid along with 1-(vinylseleninyl)benzene, which is derived from a side elimination reaction. The evidence of a direct mechanism, in addition to an autocatalytic mechanism that emerges from kinetic studies, is discussed. By considering our observations of diselenides with chalcogen atoms that are separated by alkyl spacers of different length, a rationale for the advantage of diselenide versus monoselenide catalysts is presented.

19.
Chemistry ; 22(48): 17204-17214, 2016 Nov 21.
Artigo em Inglês | MEDLINE | ID: mdl-27868323

RESUMO

We present a novel pulsed electron paramagnetic resonance (EPR) spectroscopic ruler to test the performance of a recently developed spin-labeling method based on the photoexcited triplet state (S=1). Four-pulse electron double resonance (PELDOR) experiments are carried out on a series of helical peptides, labeled at the N-terminal end with the porphyrin moiety, which can be excited to the triplet state, and with the nitroxide at various sequence positions, spanning distances in the range 1.8-8 nm. The PELDOR traces provide accurate distance measurements for all the ruler series, showing deep envelope modulations at frequencies varying in a progressive way according to the increasing distance between the spin labels. The upper limit is evaluated and found to be around 8 nm. The PELDOR-derived distances are in excellent agreement with theoretical predictions. We demonstrate that high sensitivity is acquired using the triplet state as a spin label by comparison with Cu(II)-porphyrin analogues. The new labeling approach has a high potential for measuring nanometer distances in more complex biological systems due to the properties of the porphyrin triplet state.

20.
J Phys Chem A ; 120(25): 4389-400, 2016 Jun 30.
Artigo em Inglês | MEDLINE | ID: mdl-27267296

RESUMO

The General AMBER Force Field (GAFF) has been extended to describe a series of selenium and tellurium diphenyl dichalcogenides. These compounds, besides being eco-friendly catalysts for numerous oxidations in organic chemistry, display peroxidase activity, i.e., can reduce hydrogen peroxide and harmful organic hydroperoxides to water/alcohols and as such are very promising antioxidant drugs. The novel GAFF parameters are tested in MD simulations in different solvents and the (77)Se NMR chemical shift of diphenyl diselenide is computed using structures extracted from MD snapshots and found in nice agreement with the measured value in CDCl3. The whole computational protocol is described in detail and integrated with in-house code to allow easy derivation of the force field parameters for analogous compounds as well as for Se/Te organocompounds in general.


Assuntos
Derivados de Benzeno/química , Modelos Moleculares , Compostos Organometálicos/química , Compostos Organosselênicos/química , Conformação Molecular , Teoria Quântica , Termodinâmica
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