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1.
J Phys Chem B ; 125(36): 10273-10281, 2021 Sep 16.
Artigo em Inglês | MEDLINE | ID: mdl-34472354

RESUMO

The excited state proton transfer (ESPT) reaction from the photoacid 8-hydroxypyrene-1,3,6-trisulfonic acid (HPTS or pyranine) to an acetate molecule has been investigated in explicit aqueous solution via excited state ab initio molecular dynamics simulations based on hybrid quantum/molecular mechanics (QM/MM) potentials. In all the trajectories, the direct proton transfer has been observed in the excited state within 1 ps. We find that the initial structural configuration extracted from the ground state distribution strongly affects the ESPT kinetics. Indeed, the relative orientation of the proton donor-acceptor pair and the presence of a water molecule hydrogen bonded to the phenolic acid group of the pyranine are the key factors to facilitate the ESPT. Furthermore, we analyze the vibrational fingerprints of the ESPT reaction, reproducing the blue shift of the acetate CO stretching (COac), from 1666 to 1763 cm-1 testifying the transformation of acetate to acetic acid. Finally, our findings suggest that the acetate CC stretching (CCac) is also sensitive to the progress of the ESPT reaction. The CCac stretching is indeed ruled by the two vibrational modes (928 and 1426 cm-1), that in the excited state are alternately activated when the proton is shared or bound to the donor/acceptor, respectively.

2.
Biomolecules ; 11(7)2021 07 16.
Artigo em Inglês | MEDLINE | ID: mdl-34356672

RESUMO

In the search for new therapeutic strategies to contrast SARS-CoV-2, we here studied the interaction of polydatin (PD) and resveratrol (RESV)-two natural stilbene polyphenols with manifold, well known biological activities-with Spike, the viral protein essential for virus entry into host cells, and ACE2, the angiotensin-converting enzyme present on the surface of multiple cell types (including respiratory epithelial cells) which is the main host receptor for Spike binding. Molecular Docking simulations evidenced that both compounds can bind Spike, ACE2 and the ACE2:Spike complex with good affinity, although the interaction of PD appears stronger than that of RESV on all the investigated targets. Preliminary biochemical assays revealed a significant inhibitory activity of the ACE2:Spike recognition with a dose-response effect only in the case of PD.


Assuntos
Enzima de Conversão de Angiotensina 2/metabolismo , COVID-19/tratamento farmacológico , Glucosídeos/farmacologia , Resveratrol/farmacologia , SARS-CoV-2/efeitos dos fármacos , Glicoproteína da Espícula de Coronavírus/metabolismo , Estilbenos/farmacologia , COVID-19/metabolismo , Descoberta de Drogas , Medicamentos de Ervas Chinesas/farmacologia , Inibidores Enzimáticos/farmacologia , Interações Hospedeiro-Patógeno/efeitos dos fármacos , Humanos , Simulação de Acoplamento Molecular , Ligação Proteica/efeitos dos fármacos , SARS-CoV-2/metabolismo
3.
J Phys Chem A ; 125(17): 3569-3578, 2021 May 06.
Artigo em Inglês | MEDLINE | ID: mdl-33900071

RESUMO

In this work, we simulate the excited state proton transfer (ESPT) reaction involving the pyranine photoacid and an acetate molecule as proton acceptor, connected by a bridge water molecule. We employ ab initio molecular dynamics combined with an hybrid quantum/molecular mechanics (QM/MM) framework. Furthermore, a time-resolved vibrational analysis based on the wavelet-transform allows one to identify two low frequency vibrational modes that are fingerprints of the ESPT event: a ring wagging and ring breathing. Their composition suggests their key role in optimizing the structure of the proton donor-acceptor couple and promoting the ESPT event. We find that the choice of the QM/MM partition dramatically affects the photoinduced reactivity of the system. The QM subspace was gradually extended including the water molecules directly interacting with the pyranine-water-acetate system. Indeed, the ESPT reaction takes place when the hydrogen bond network around the reactive system is taken into account at full QM level.

4.
J Phys Chem Lett ; 11(22): 9738-9744, 2020 Nov 19.
Artigo em Inglês | MEDLINE | ID: mdl-33141585

RESUMO

The development of efficient artificial leaves relies on the subtle combination of molecular assemblies able to absorb sunlight, converting light energy into electrochemical potential energy and finally transducing it into accessible chemical energy. The electronic design of these charge transfer molecular machines is crucial to build a complex supramolecular architecture for the light energy conversion. Here, we present an ab initio simulation of the whole decay pathways of a recently proposed artificial molecular reaction center. A complete structural and energetic characterization has been carried out with methods based on density functional theory, its time-dependent version, and a broken-symmetry approach. On the basis of our findings we provide a revision of the pathway only indirectly postulated from an experimental point of view, along with unprecedented and significant insights on the electronic and nuclear structure of intramolecular charge-separated states, which are fundamental for the application of this molecular assembly in photoelectrochemical cells. Importantly, we unravel the molecular driving forces of the various charge transfer steps, in particular those leading to the proton-coupled electron transfer final product, highlighting key elements for the future design strategies of such molecular assays.


Assuntos
Complexos de Coordenação/química , Fotossíntese , Teoria da Densidade Funcional , Transporte de Elétrons , Cinética , Ligantes , Simulação de Dinâmica Molecular , Oxirredução , Processos Fotoquímicos , Relação Estrutura-Atividade , Luz Solar
5.
Front Mol Biosci ; 7: 569990, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33195416

RESUMO

The Green Fluorescent Protein (GFP) is a widely studied chemical system both for its large amount of applications and the complexity of the excited state proton transfer responsible of the change in the protonation state of the chromophore. A detailed investigation on the structure of the chromophore environment and the influence of chromophore form (either neutral or anionic) on it is of crucial importance to understand how these factors could potentially influence the protein function. In this study, we perform a detailed computational investigation based on the analysis of ab-initio molecular dynamics simulations, to disentangle the main structural quantities determining the fine balance in the chromophore environment. We found that specific hydrogen bonds interactions directly involving the chromophore (or not), are correlated to quantities, such as the volume of the cavity in which the chromophore is embedded and that it is importantly affected by the chromophore protonation state. The cross-correlation analysis performed on some of these hydrogen bonds and the cavity volume, demonstrates a direct correlation among them and we also identified the ones specifically involved in this correlation. We also found that specific interactions among residues far in the space are correlated, demonstrating the complexity of the chromophore environment and that many structural quantities have to be taken into account to properly describe and understand the main factors tuning the active site of the protein. From an overall evaluation of the results obtained in this work, it is shown that the residues which a priori are perceived to be spectators play instead an important role in both influencing the chromophore environment (cavity volume) and its dynamics (cross-correlations among spatially distant residues).

6.
Phys Chem Chem Phys ; 22(39): 22645-22661, 2020 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-33015693

RESUMO

Vibrational analysis in solution and the theoretical determination of infrared and Raman spectra are of key importance in many fields of chemical interest. Vibrational band dynamics of molecules and their sensitivity to the environment can also be captured by these spectroscopies in their time dependent version. However, it is often difficult to provide an interpretation of the experimental data at the molecular scale, such as molecular mechanisms or the processes hidden behind them. In this work, we present a theoretical-computational protocol based on ab initio molecular dynamics simulations and a combination of normal-like (generalized) mode analysis of solute-solvent clusters with a wavelet transform, for the first time. The case study is the vibrational dynamics of N-methyl-acetamide (NMA) in water solution, a well-known model of hydration of peptides and proteins. Amide modes are typical bands of peptide and protein backbone, and their couplings with the environment are very challenging in terms of the accurate prediction of solvent induced intensity and frequency shifts. The contribution of water molecules surrounding NMA to the composition of generalized and time resolved modes is introduced in our vibrational analysis, showing unequivocally its influence on the amide mode spectra. It is also shown that such mode compositions need the inclusion of the first shell solvent molecules to be accurately described. The wavelet analysis is proven to be strongly recommended to follow the time evolution of the spectra, and to capture vibrational band couplings and frequency shifts over time, preserving at the same time a well-balanced time-frequency resolution. This peculiar feature also allows one to perform a combined structural-vibrational analysis, where the different strengths of hydrogen bond interactions can quantitatively affect the amide bands over time at finite temperature. The proposed method allows for the direct connection between vibrational modes and local structural changes, providing a link from the spectroscopic observable to the structure, in this case the peptide backbone, and its hydration layouts.

7.
J Chem Theory Comput ; 16(11): 7033-7043, 2020 Nov 10.
Artigo em Inglês | MEDLINE | ID: mdl-33112132

RESUMO

The rapid growth of time-resolved spectroscopies and the theoretical advances in ab initio molecular dynamics (AIMD) pave the way to look at the real-time molecular motion following the electronic excitation. Here, we exploited the capabilities of AIMD combined with a hybrid implicit/explicit model of solvation to investigate the ultrafast excited-state proton transfer (ESPT) reaction of a super photoacid, known as QCy9, in water solution. QCy9 transfers a proton to a water solvent molecule within 100 fs upon the electronic excitation in aqueous solution, and it is the strongest photoacid reported in the literature so far. Because of the ultrafast kinetics, it has been experimentally hypothesized that the ESPT escapes the solvent dynamics control (Huppert et al., J. Photochem. Photobiol. A 2014, 277, 90). The sampling of the solvent configuration space on the ground electronic state is the first key step toward the simulation of the ESPT event. Therefore, several configurations in the Franck-Condon region, describing an average solvation, were chosen as starting points for the excited-state dynamics. In all cases, the excited-state evolution spontaneously leads to the proton transfer event, whose rate is strongly dependent on the hydrogen bond network around the proton acceptor solvent molecule. Our study revealed that the explicit representation at least of three solvation shells around the proton acceptor molecule is necessary to stabilize the excess proton. Furthermore, the analysis of the solvent molecule motions in proximity of the reaction site suggested that even in the case of the strongest photoacid, the ESPT is actually assisted by the solvation dynamics of the first and second solvation shells of the water accepting molecule.

8.
J Chem Theory Comput ; 16(10): 6007-6013, 2020 Oct 13.
Artigo em Inglês | MEDLINE | ID: mdl-32955870

RESUMO

We present a novel time-resolved vibrational analysis for studying photoinduced nuclear relaxation. Generalized modes velocities are defined from ab initio molecular dynamics and wavelet transformed, providing the time localization of vibrational signals in the electronic excited state. The photoexcited pyranine in aqueous solution is presented as a case study. The transient and sequential activation of the simulated vibrational signals is in good agreement with vibrational dynamics obtained from femtosecond stimulated Raman spectroscopy data.

9.
J Comput Chem ; 41(26): 2228-2239, 2020 10 05.
Artigo em Inglês | MEDLINE | ID: mdl-32770577

RESUMO

Solute-solvent interactions are proxies for understanding how the electronic density of a chromophore interacts with the environment in a more exhaustive way. The subtle balance between polarization, electrostatic, and non-bonded interactions need to be accurately described to obtain good agreement between simulations and experiments. First principles approaches providing accurate configurational sampling through molecular dynamics may be a suitable choice to describe solvent effects on solute chemical-physical properties and spectroscopic features, such as optical absorption of dyes. In this context, accurate energy potentials, obtained by hybrid implicit/explicit solvation methods along with employing nonperiodic boundary conditions, are required to represent bulk solvent around a large solute-solvent cluster. In this work, a novel strategy to simulate methanol solutions is proposed combining ab initio molecular dynamics, a hybrid implicit/explicit flexible solvent model, nonperiodic boundary conditions, and time dependent density functional theory. As case study, the robustness of the proposed protocol has been gauged by investigating the microsolvation and electronic absorption of the anionic green fluorescent protein chromophore in methanol and aqueous solution. Satisfactory results are obtained, reproducing the microsolvation layout of the chromophore and, as a consequence, the experimental trends shown by the optical absorption in different solvents.


Assuntos
Metanol/química , Modelos Químicos , Simulação de Dinâmica Molecular , Solventes/química , Água/química , Proteínas de Fluorescência Verde/química , Solubilidade
10.
J Comput Chem ; 41(20): 1835-1841, 2020 07 30.
Artigo em Inglês | MEDLINE | ID: mdl-32500950

RESUMO

Electrons and protons are the main actors in play in proton coupled electron transfer (PCET) reactions, which are fundamental in many biological (i.e., photosynthesis and enzymatic reactions) and electrochemical processes. The mechanism, energetics and kinetics of PCET reactions are strongly controlled by the coupling between the transferred electrons and protons. Concerted PCET reactions are classified according to the electronical adiabaticity degree of the process. To discriminate among different mechanisms, we propose a new analysis based on the use of electron density based indexes. We choose, as test case, the 3-Methylphenoxyl/phenol system in two different conformations to show how the proposed analysis is a suitable tool to discriminate between the different degree of adiabaticity of PCET processes. The very low computational cost of this procedure is extremely promising to analyze and provide evidences of PCET mechanisms ruling the reactivity of many biological and catalytic systems.


Assuntos
Elétrons , Fenóis/química , Prótons , Transporte de Elétrons , Fenóis/metabolismo
11.
Int J Biol Macromol ; 151: 1163-1172, 2020 May 15.
Artigo em Inglês | MEDLINE | ID: mdl-31747572

RESUMO

Among polyphenols, trans-resveratrol (tRES) and trans-polydatin (tPD) exert multiple biological effects, particularly antioxidant and antiproliferative. In this work, we have investigated the interaction of tPD with three cancer-related DNA sequences able to form G-quadruplex (G4) structures, as well as with a model duplex, and compared its behaviour with tRES. Interestingly, fluorescence analysis evidenced the ability of tPD to bind all the studied DNA systems, similarly to tRES, with tRES displaying a higher ability to discriminate G4 over duplex with respect to tPD. However, neither tRES nor tPD produced significant conformational changes of the analyzed DNA upon binding, as determined by CD-titration analysis. Computational analysis and biological data confirmed the biophysical results: indeed, molecular docking evidenced the stronger interaction of tRES with the promoter of c-myc oncogene, and immunoblotting assays revealed a reduction of c-myc expression, more effective for tRES than tPD. Furthermore, in vitro assays on melanoma cells proved that tPD was able to significantly reduce telomerase activity, and inhibit cell proliferation, with tRES producing higher effects than tPD.


Assuntos
DNA/química , Quadruplex G , Glucosídeos/química , Glucosídeos/farmacologia , Resveratrol/química , Resveratrol/farmacologia , Estilbenos/química , Estilbenos/farmacologia , Apoptose/efeitos dos fármacos , Linhagem Celular Tumoral , Proliferação de Células/efeitos dos fármacos , Humanos , Modelos Moleculares , Conformação Molecular , Proteínas Proto-Oncogênicas c-myc/genética , Proteínas Proto-Oncogênicas c-myc/metabolismo , Análise Espectral , Relação Estrutura-Atividade
12.
ACS Omega ; 4(1): 688-698, 2019 Jan 31.
Artigo em Inglês | MEDLINE | ID: mdl-31459356

RESUMO

The growing production of biodiesel as a promising alternative and renewable fuel led as the main problem the dramatic increase of its by-product: glycerol. Different strategies for glycerol derivatization have been reported so far, some more efficient or sustainable than others. Herein, we report a very promising and eco-friendly transformation of glycerol in nontoxic solvents and chemicals (i.e., solketal, ketals), proposing three new families of Fe(III) compounds capable of catalysing glycerol acetalization with unpublished turn over frequencies (TOFs), and adhering most of the principles of green chemistry. The comparison between the activity of complexes of formula [FeCl3(1-R)] (1-R = substituted pyridinimine), [FeCl(2-R,R')] (2-R,R' = substituted O,O'-deprotonated salens) and their corresponding simple salts reveals that the former are extremely convenient because they are able to promote solketal formation with excellent TOFs, up to 105 h-1. Satisfactory performances were shown with respect to the entire range of substrates, with results being competitive to those reported in the literature so far. Moreover, the experimental activity was supported by an accurate and complete ab initio study, which disclosed the fundamental role of iron(III) as Lewis acid in promoting the catalytic activity. The unprecedented high activity and the low loading of the catalyst, combined with the great availability and the good eco-toxicological profile of iron, foster future applications of this catalytic process for the sustainable transformation of an abundant by-product in a variety of chemicals.

13.
Phys Chem Chem Phys ; 21(7): 3606-3614, 2019 Feb 13.
Artigo em Inglês | MEDLINE | ID: mdl-30306981

RESUMO

In this work, excited state ab initio molecular dynamics together with a time resolved vibrational analysis is employed to shed light on the vibrational photoinduced dynamics of a well-known diarylethene molecule experiencing a ring opening reaction upon electronic excitation. The photoreactivity of diarylethenes is recognized to be controlled by a non-adiabatic intersection point between the ground and the first excited state surfaces. The computation of an energy scan, along a suitable reaction coordinate, allows us to identify the region of potential energy surfaces in which the ground (S0) and the first excited (S1) state are well separated. The adiabatic sampling of that region in S1 shows that in the first 3 picoseconds, the central CC bond, which is subject to break, oscillates in an antiphase with respect to the energy gap ΔE(S1 - S0). A multiresolution analysis based on the wavelet transform was then applied to the structural parameters extracted from the excited state dynamics. The wavelet maps show characteristic oscillations of the frequencies, mainly CC stretching and CCC bending localized on the central 4-ring moiety. Moreover, we have identified the main frequency (methyl wagging motion) involved in the modulation of these oscillations. The anharmonic coupling within a group of vibrational modes was therefore highlighted, in good agreement with experimental evidence. For the first time, a quantitative analysis of time resolved signals from a wavelet transform/ab initio molecular dynamics approach was performed.

14.
Biopolymers ; 109(10): e23225, 2018 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-30091460

RESUMO

Fe(III)-Mimochrome VI (MC6) is a recently reported artificial heme-peptide conjugate system with a high peroxidase-like activity. By design, its structure features a five-coordinated Fe(III)-deuteroporphyrin active site, embedded in a compact α-helix-heme-α-helix "sandwich" motif. Up to now, no detailed MC6 structural characterization is available. In this work we propose a theoretical investigation based on molecular dynamics (MD) simulations and hybrid quantum mechanics/molecular mechanics (QM/MM) optimizations, aimed to shed light on several Fe(III)-MC6 structural features and to validate the de novo designed fold. Key structural elements were analyzed to achieve indirect insight relevant to understand Fe(III)-MC6 catalytic performances in solution. Extensive MD simulations showed a partial stability of the "sandwich" fold in water solution. The smaller peptide chain bonded to the heme revealed a high conformational freedom, which promoted the exposition of the heme distal side to the solvent. Regarding the accessibility of water molecules, even in Fe(III)-MC6 "closed" structure the heme cavity appeared hydrated, suggesting an easy accessibility by exogenous ligands. Fe(III)-MC6 structure in both high and low spin states was then further characterized through hybrid QM/MM optimizations. In particular, an accurate description of the active site structure was obtained, allowing a direct comparison of Fe(III)-MC6 coordination environment with that observed in the Horseradish Peroxidase crystal structures. Our results suggest a structural similarity between Fe(III)-MC6 and the natural enzyme. This study supports the interpretation of data from experimental Fe(III)-MC6 structural and functional characterization and the rational design of new artificial mimics with improved catalytic performances.


Assuntos
Heme/química , Heme/metabolismo , Modelos Moleculares , Peroxidases/química , Peroxidases/metabolismo , Ligação de Hidrogênio , Ferro/química , Simulação de Dinâmica Molecular , Peptídeos/química , Estrutura Secundária de Proteína , Teoria Quântica , Água/química
15.
Chem Sci ; 9(5): 1126-1135, 2018 Feb 07.
Artigo em Inglês | MEDLINE | ID: mdl-29675157

RESUMO

We simulated an excited state proton transfer in green fluorescent protein by excited state ab initio dynamics, and examined the reaction mechanism in both the time and the frequency domain through a multi resolution wavelet analysis. This original approach allowed us, for the first time, to directly compare the trends of photoactivated vibrations to femtosecond stimulated Raman spectroscopy results, and to give an unequivocal interpretation of the role played by low frequency modes in promoting the reaction. We could attribute the main driving force of the reaction to an important photoinduced softening of the ring-ring orientational motion of the chromophore, thus permitting the tightening of the hydrogen bond network and the opening of the reaction pathway. We also found that both the chromophore (in terms of its inter-ring dihedral angle and phenolic C-O and imidazolinone C-N bond distances) and its pocket (in terms of the inter-molecular oxygen's dihedral angle of the chromophore pocket) relaxations are modulated by low frequency (about 120 cm-1) modes involving the oxygen atoms of the network. This is in agreement with the femtosecond Raman spectroscopy findings in the time-frequency domain. Moreover, the rate in proximity to the Franck Condon region involves a picosecond time scale, with a significant influence from fluctuations of nearby hydrogen bonded residues such as His148. This approach opens a new scenario with ab initio simulations as routinely used tools to understand photoreactivity and the results of advanced time resolved spectroscopy techniques.

16.
J Phys Chem A ; 122(11): 2884-2893, 2018 Mar 22.
Artigo em Inglês | MEDLINE | ID: mdl-29465236

RESUMO

Advances in time-resolved vibrational spectroscopy techniques provided a new stimulus for understanding the transient molecular dynamics triggered by the electronic excitation. The detailed interpretation of such time-dependent spectroscopic signals is a challenging task from both experimental and theoretical points of view. We simulated and analyzed the transient photorelaxation of the pyranine photoacid in aqueous solution, with special focus on structural parameters and low frequency skeleton modes that are possibly preparatory for the photoreaction occurring at later time, as suggested by experimental spectroscopic studies. To this aim, we adopted an accurate computational protocol that combines excited state ab initio molecular dynamics within an hybrid quantum mechanical/molecular mechanics framework and a time-resolved vibrational analysis based on the Wavelet transform. According to our results, the main nuclear relaxation on the excited potential energy surface is completed in about 500 fs, in agreement with experimental data. The rearrangement of C-C bonds occurs according to a complex vibrational dynamics, showing oscillatory patterns that are out of phase and modulated by modes below 200 cm-1. We also analyzed in both the ground and the excited state the evolution of some structural parameters involved in excited state proton transfer reaction, namely, those involving the pyranine and the water molecule hydrogen bonded to the phenolic O-H group. Both the hydrogen bond distance and the intermolecular orientation are optimized in the excited state, resulting in a tighter proton donor-acceptor couple. Indeed, we found evidence that collective low frequency skeleton modes, such as the out of plane wagging at 108 cm-1 and the deformation at 280 cm-1, are photoactivated by the ultrafast part of the relaxation and modulate the pyranine-water molecule rearrangement, favoring the preparatory step for the photoreactivity.

17.
J Mater Chem B ; 6(8): 1207-1215, 2018 Feb 28.
Artigo em Inglês | MEDLINE | ID: mdl-32254181

RESUMO

Synthetic receptors for biomacromolecules lack the supramolecular self-assembly behavior typical of biological systems. Here we propose a new method for the preparation of protein imprinted polymers based on the specific interaction of a peptide multi-functional block with a protein target. This peptide block contains a protein-binding peptide domain, a polymerizable moiety at the C-terminus and an environment-sensitive fluorescent molecule at the N-terminus. The method relies on a preliminary step consisting of peptide/protein supramolecular assembly, followed by copolymerization with the most common acrylate monomers (acrylamide, acrylic acid and bis-acrylamide) to produce a protein imprinted hydrogel polymer. Such a peptide block can function as an active assistant recognition element to improve affinity, and guarantees its effective polymerization at the protein/cavity interface, allowing for proper placement of a dye. As a proof of concept, we chose Bovine Serum Albumin (BSA) as the protein target and built the peptide block around a BSA binding dodecapeptide, with an allyl group as the polymerizable moiety and a dansyl molecule as the responsive dye. Compared to conventional approaches these hydrogels showed higher affinity (more than 45%) and imprinted sensitivity (about twenty fold) to the target, with a great BSA selectivity with respect to ovalbumin (α = 1.25) and lysozyme (α = 6.02). Upon protein binding, computational and experimental observations showed a blue shift of the emission peak (down to 440 nm) and an increase of fluorescence emission (twofold) and average lifetime (Δτ = 4.3 ns). Such an approach generates recognition cavities with controlled chemical information and represents an a priori method for self-responsive materials. Provided a specific peptide and minimal optimization conditions are used, such a method could be easily implemented for any protein target.

18.
J Comput Chem ; 38(14): 1084-1092, 2017 05 30.
Artigo em Inglês | MEDLINE | ID: mdl-28409849

RESUMO

The performances, in the description of excited state potential energy surfaces, of several density functional approximations representative of the currently most applied exchange correlation functionals' families have been tested with respect to post Hartree-Fock references (here Symmetry Adapted Cluster-Configuration Interaction results). An experimentally well-characterized intermolecular proton transfer reaction has been considered as test case. The computed potential energy profiles were analyzed both in the gas phase and in toluene solution, here represented as a polarizable continuum model. The presence of intermolecular (dark) and intramolecular (bright) charge transfer excited states, whose polarity strongly differs along the reaction pathway, makes clear that only subtle compensation between spurious electronic effects-related to the incorrect asymptotic behavior of the functional-and solvent stabilization of polar states leads to the overall correct description of this excited state reaction when using global hybrids with low percentage of Hartree Fock exchange. © 2017 Wiley Periodicals, Inc.

19.
J Phys Chem Lett ; 7(24): 5015-5021, 2016 Dec 15.
Artigo em Inglês | MEDLINE | ID: mdl-27973871

RESUMO

We simulated for the first time the oxygen-oxygen bond formation in a synthetic calcium-tetra manganese complex recently developed by Zhang and co-workers. In spite of promising structural similarities to the native oxygen evolving complex (OEC) in Photosystem II, several uncertainties on the mimic stability in water and on its potential catalytic activity still persist. Here, we characterized at density functional theory level the electronic and structural features of the Sn states of the complex, along with the oxygen-oxygen bond formation reaction, proposing a reasonable model for the hydrate complex. As a main finding, both the synthetic compound and the natural OEC show very close energetic barriers for the oxo-oxyl coupling process, suggesting that key electronic features of the natural OEC reactivity are well reproduced. This result strongly encourages the use of this synthetic complex in combination with other molecular assemblies for the design of successful artificial leaves.

20.
J Chem Theory Comput ; 12(10): 4925-4933, 2016 Oct 11.
Artigo em Inglês | MEDLINE | ID: mdl-27571168

RESUMO

We simulated the intrinsic reaction path of the Green Fluorescent Protein (GFP) proton shuttle in both the ground state (S0) and first singlet excited state (S1), accounting for the main energetic and steric effects of the protein in a convenient model including the chromophore, the crystallographic water, and the residues directly involved in the proton transfer event. We adopted density functional theory (DFT) and time-dependent density functional theory (TD-DFT) levels to define the potential energy surfaces of the two electronic states, and we compared results obtained by the Damped Velocity Verlet and the Hessian-based Predictor-Corrector integrators of the intrinsic reaction coordinate, which gave a comparable and consistent picture of the mechanism. We show that, at S1, the GFP proton transfer becomes favored, with respect to S0, as suggested by the experimental evidence. As an important finding, this change is strictly related to the rearrangement of the hydrogen bond network composing the reaction path, which, in S1, relaxes to a tighter and planar configuration, as a consequence of the photoinduced relaxation in the GFP chromophore structure, thus prompting more effectively for the proton shuttle. Therefore, we give an unprecedented direct proof of the key role played by the photoinduced structural relaxation of the GFP on the chromophore photoacidity, validating, in particular, the hypothesis of Fang and co-workers [Nature 2009, 462, 200].


Assuntos
Proteínas de Fluorescência Verde/química , Proteínas de Fluorescência Verde/metabolismo , Ligação de Hidrogênio , Modelos Moleculares , Prótons , Teoria Quântica , Termodinâmica , Água/química
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