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1.
J Chem Theory Comput ; 19(18): 6392-6401, 2023 Sep 26.
Artigo em Inglês | MEDLINE | ID: mdl-37669417

RESUMO

The use of mechanical forces at the molecular level has been shown to be an interesting tool for modulating different chemical and physical molecular properties. The so-called covalent mechanochemistry deals with the application of precise mechanical forces that induce specific changes in the structure, stability, reactivity, and other physical properties. The use of this kind of force to modulate photophysical properties and photochemical reactivity has also been studied. Nevertheless, the general problem of mechanical modulation of the energy gap between two electronic states has been addressed only with the development of simple theoretical models. Here, we develop and implement an algorithm providing the Largest energy Gap variation with Minimal mechanical Force (LGMF) that allows the determination of the optimal mechanical forces tuning the electronic energy gap, as well as to identify the maximum mechanical response of a molecular system to the application of any mechanical stimulus. The algorithm has been implemented for diverse molecular systems showing different degrees of flexibility. The phyton code of the algorithm is available in a public repository.

2.
J Org Chem ; 88(13): 8674-8689, 2023 Jul 07.
Artigo em Inglês | MEDLINE | ID: mdl-37341522

RESUMO

ß-cyclodextrin (ßCyD) derivatives equipped with aromatic appendages at the secondary face exhibit tailorable self-assembling capabilities. The aromatic modules can participate in inclusion phenomena and/or aromatic-aromatic interactions. Supramolecular species can thus form that, at their turn, can engage in further co-assembling with third components in a highly regulated manner; the design of nonviral gene delivery systems is an illustrative example. Endowing such systems with stimuli responsiveness while keeping diastereomeric purity and a low synthetic effort is a highly wanted advancement. Here, we show that an azobenzene moiety can be "clicked" to a single secondary O-2 position of ßCyD affording 1,2,3-triazole-linked ßCyD-azobenzene derivatives that undergo reversible light-controlled self-organization into dimers where the monomer components face their secondary rims. Their photoswitching and supramolecular properties have been thoroughly characterized by UV-vis absorption, induced circular dichroism, nuclear magnetic resonance, and computational techniques. As model processes, the formation of inclusion complexes between a water-soluble triazolylazobenzene derivative and ßCyD as well as the assembly of native ßCyD/ßCyD-azobenzene derivative heterodimers have been investigated in parallel. The stability of the host-guest supramolecules has been challenged against the competitor guest adamantylamine and the decrease of the medium polarity using methanol-water mixtures. The collective data support that the E-configured ßCyD-azobenzene derivatives, in aqueous solution, form dimers stabilized by the interplay of aromatic-aromatic and aromatic-ßCyD cavity interactions after partial reciprocal inclusion. Photoswitching to the Z-isomer disrupts the dimers into monomeric species, offering opportunity for the spatiotemporal control of the organizational status by light.


Assuntos
beta-Ciclodextrinas , Dimerização , Compostos Azo , Polímeros , Água
3.
Int J Mol Sci ; 24(3)2023 Jan 28.
Artigo em Inglês | MEDLINE | ID: mdl-36768842

RESUMO

After a sudden and first spread of the pandemic caused by the novel SARS-CoV-2 (Severe Acute Respiratory Syndrome-Coronavirus 2) wild-type strain, mutants have emerged which have been associated with increased infectivity, inducing surges in the contagions. The first of the so-called variants of concerns, was firstly isolated in the United Kingdom and later renamed Alpha variant. Afterwards, in the middle of 2021, a new variant appeared called Delta. The latter is characterized by the presence of point mutations in the Spike protein of SARS-CoV-2, especially in the Receptor Binding Domain (RBD). When in its active conformation, the RBD can interact with the human receptor Angiotensin-Converting Enzyme 2 (ACE2) to allow the entry of the virions into cells. In this contribution, by using extended all-atom molecular dynamic simulations, complemented with machine learning post-processing, we analyze the changes in the molecular interaction network induced by these different strains in comparison with the wild-type. On one hand, although relevant variations are evidenced, only limited changes in the global stability indicators and in the flexibility profiles have been observed. On the other hand, key differences were obtained by tracking hydrophilic and hydrophobic molecular interactions, concerning both positioning at the ACE2/RBD interface and formation/disruption dynamic behavior.


Assuntos
Enzima de Conversão de Angiotensina 2 , COVID-19 , Humanos , Enzima de Conversão de Angiotensina 2/genética , SARS-CoV-2/genética , COVID-19/genética , Aprendizado de Máquina , Simulação de Dinâmica Molecular , Ligação Proteica , Mutação , Glicoproteína da Espícula de Coronavírus/genética
4.
Phys Chem Chem Phys ; 25(6): 5007-5020, 2023 Feb 08.
Artigo em Inglês | MEDLINE | ID: mdl-36722876

RESUMO

We present a computational investigation of the absorption spectrum in water of 5,5-spirocyclopropyl-oxyluciferin (5,5-CprOxyLH), an analogue of the emitter compound responsible for the bioluminescence in fireflies. Several factors participate in determining the 5,5-CprOxyLH's spectral shape: (i) the contribution of the four close-energy excited states, which show significant non-adiabatic couplings, (ii) the flexible molecular structure and (iii) the specific interactions established with the surrounding environment, which strongly couple the protic solvent dynamics with the dye's spectral response. To tackle the challenge to capture and dissect the role of all these effects we preliminarily investigate the role of non-adiabatic couplings with quantum dynamics simulations and a linear vibronic coupling model in the gas phase. Then, we account for both the molecular flexibility and solvent interactions by resorting to a mixed quantum classical protocol, named Adiabatic Molecular Dynamics generalized Vertical Gradient (Ad-MD|gVG), which is built on a method recently proposed by some of us. It is rooted in the partition between stiff degrees of freedom of the dye, accounted for at the vibronic level within the harmonic approximation, and flexible degrees of freedom of the solute (and of the solvent), described classically through a sampling based on Molecular Dynamics (MD). Ad-MD|gVG avoids spurious effects arising in the excited state Hessians due to non-adiabatic couplings, and can therefore be applied to account for the contributions of the first four excited states to the 5,5-CprOxyLH absorption spectrum. The final simulated spectrum is in very good agreement with the experiment, especially when the MD is driven by a refined quantum-mechanically derived force-field. More importantly, the origin of each separate contribution to the spectral shape is appropriately accounted for, paving the way to future applications of the method to more complex systems or alternative spectroscopies, as emission or circular dichroism.

5.
J Org Chem ; 87(19): 12586-12595, 2022 10 07.
Artigo em Inglês | MEDLINE | ID: mdl-36166757

RESUMO

In this work, we demonstrate that the forbidden oxirane-type photoproduct (the cyclopropyl ketone photoproduct is the allowed one) of the oxa-di-π-methane photorearrangement can be obtained by mechanochemical control of the photoreactions. This control is achieved by the application of simple force pairs rationally chosen. By analyzing in detail the effect of the applied forces on this photoreaction, it comes to light that the mechanical action affects the diverse properties of the oxa-di-π-methane rearrangement, modifying all the steps of the reaction: (i) the initial ground-state conformers' distribution becomes affected; (ii) the new conformational population makes the triplet excitation process to be changed, responding to the magnitude of the applied force; (iii) the stability of the different intermediates along the triplet pathway also becomes affected, changing the dynamical behavior of the system and the reaction kinetics; and (iv) the intersystem crossing also becomes strongly affected, making the forbidden oxirane-type photoproduct to decay more efficiently to the ground state. All these changes provide a complex scenario where a detailed study of the effect of applied forces is necessary in order to predict its overall effect on the photoreactivity.


Assuntos
Cetonas , Metano , Compostos de Epóxi , Cetonas/química , Metano/química
6.
Pharmaceutics ; 14(5)2022 May 17.
Artigo em Inglês | MEDLINE | ID: mdl-35631655

RESUMO

Controlling the activity of a pharmaceutical agent using light offers improved selectivity, reduction of adverse effects, and decreased environmental build-up. These benefits are especially attractive for antibiotics. Herein, we report a series of photoreleasable quinolones, which can be activated using visible/NIR light (520-800 nm). We have used BODIPY photocages with strong absorption in the visible to protect two different quinolone-based compounds and deactivate their antimicrobial properties. This activity could be recovered upon green or red light irradiation. A comprehensive computational study provides new insight into the reaction mechanism, revealing the relevance of considering explicit solvent molecules. The triplet excited state is populated and the photodissociation is assisted by the solvent. The light-controlled activity of these compounds has been assessed on a quinolone-susceptible E. coli strain. Up to a 32-fold change in the antimicrobial activity was measured.

7.
Int J Mol Sci ; 23(10)2022 May 23.
Artigo em Inglês | MEDLINE | ID: mdl-35628665

RESUMO

Inhibition of the papain-like protease (PLpro) of SARS-CoV-2 has been demonstrated to be a successful target to prevent the spreading of the coronavirus in the infected body. In this regard, covalent inhibitors, such as the recently proposed VIR251 ligand, can irreversibly inactivate PLpro by forming a covalent bond with a specific residue of the catalytic site (Cys111), through a Michael addition reaction. An inhibition mechanism can therefore be proposed, including four steps: (i) ligand entry into the protease pocket; (ii) Cys111 deprotonation of the thiol group by a Brønsted-Lowry base; (iii) Cys111-S- addition to the ligand; and (iv) proton transfer from the protonated base to the covalently bound ligand. Evaluating the energetics and PLpro conformational changes at each of these steps could aid the design of more efficient and selective covalent inhibitors. For this aim, we have studied by means of MD simulations and QM/MM calculations the whole mechanism. Regarding the first step, we show that the inhibitor entry in the PLpro pocket is thermodynamically favorable only when considering the neutral Cys111, that is, prior to the Cys111 deprotonation. For the second step, MD simulations revealed that His272 would deprotonate Cys111 after overcoming an energy barrier of ca. 32 kcal/mol (at the QM/MM level), but implying a decrease of the inhibitor stability inside the protease pocket. This information points to a reversible Cys111 deprotonation, whose equilibrium is largely shifted toward the neutral Cys111 form. Although thermodynamically disfavored, if Cys111 is deprotonated in close proximity to the vinylic carbon of the ligand, then covalent binding takes place in an irreversible way (third step) to form the enolate intermediate. Finally, due to Cys111-S- negative charge redistribution over the bound ligand, proton transfer from the initially protonated His272 is favored, finally leading to an irreversibly modified Cys111 and a restored His272. These results elucidate the selectivity of Cys111 to enable formation of a covalent bond, even if a weak proton acceptor is available, as His272.


Assuntos
Tratamento Farmacológico da COVID-19 , Prótons , Proteases Semelhantes à Papaína de Coronavírus , Humanos , Ligantes , Papaína/metabolismo , Peptídeo Hidrolases/metabolismo , SARS-CoV-2
8.
Inorg Chem ; 61(1): 328-337, 2022 Jan 10.
Artigo em Inglês | MEDLINE | ID: mdl-34923820

RESUMO

A family of ruthenium(II) complexes containing one 2,2'-biimidazole (bim) ligand and two polypyridyl (NN) ligands has been prepared and their photophysical and photochemical features have been tested in the presence of tenuazonic acid (TeA), a widespread food and feed mycotoxin of current concern. While not tested in in vivo studies, TeA and other secondary metabolites of Alternaria fungi are suspected to exert adverse effects on the human health, so sensors and rapid analytical procedures are required. It is well-known that 1,3-dicarbonyl compounds such as TeA are relatively easy to deprotonate (the pKa of TeA is 3.5), yielding an enolate anion stabilized by resonance. The chelating and hydrogen-donor features of bim allow simultaneous binding to the metal core and to the target ß-diketonate delocalized anion. Such a binding induces changes in the blue absorption (40 nm bathochromic shift), red luminescence intensity (>75% quenching), and triplet lifetime (0.2 µs decrease) of the Ru(NN)2(bim)2+ luminophore. Moreover, we have computationally rationalized, by time-dependent density functional theory, the structure of the different adducts of Ru-bim complexes with TeA and the electronic nature of the spectral absorption bands and their change upon the addition of TeA.

9.
Molecules ; 26(23)2021 Dec 05.
Artigo em Inglês | MEDLINE | ID: mdl-34885961

RESUMO

Nonlinear optical techniques as two-photon absorption (TPA) have raised relevant interest within the last years due to the capability to excite chromophores with photons of wavelength equal to only half of the corresponding one-photon absorption energy. At the same time, its probability being proportional to the square of the light source intensity, it allows a better spatial control of the light-induced phenomenon. Although a consistent number of experimental studies focus on increasing the TPA cross section, very few of them are devoted to the study of photochemical phenomena induced by TPA. Here, we show a design strategy to find suitable E/Z photoswitches that can be activated by TPA. A theoretical approach is followed to predict the TPA cross sections related to different excited states of various photoswitches' families, finally concluding that protonated Schiff-bases (retinal)-like photoswitches outperform compared to the others. The donor-acceptor substitution effect is therefore rationalized for the successful TPA activatable photoswitch, in order to maximize its properties, finally also forecasting a possible application in optogenetics. Some experimental measurements are also carried out to support our conclusions.

10.
Phys Chem Chem Phys ; 23(40): 22957-22971, 2021 Oct 20.
Artigo em Inglês | MEDLINE | ID: mdl-34636373

RESUMO

The identification of chemical compounds able to bind specific sites of the human/viral proteins involved in the SARS-CoV-2 infection cycle is a prerequisite to design effective antiviral drugs. Here we conduct a molecular dynamics study with the aim to assess the interactions of ivermectin, an antiparasitic drug with broad-spectrum antiviral activity, with the human Angiotensin-Converting Enzyme 2 (ACE2), the viral 3CLpro and PLpro proteases, and the viral SARS Unique Domain (SUD). The drug/target interactions have been characterized in silico by describing the nature of the non-covalent interactions found and by measuring the extent of their time duration along the MD simulation. Results reveal that the ACE2 protein and the ACE2/RBD aggregates form the most persistent interactions with ivermectin, while the binding with the remaining viral proteins is more limited and unspecific.


Assuntos
Enzima de Conversão de Angiotensina 2/metabolismo , Antivirais/metabolismo , Proteases 3C de Coronavírus/metabolismo , Proteases Semelhantes à Papaína de Coronavírus/metabolismo , Ivermectina/metabolismo , Enzima de Conversão de Angiotensina 2/química , Antivirais/química , Sítios de Ligação , Proteases 3C de Coronavírus/química , Proteases Semelhantes à Papaína de Coronavírus/química , Quadruplex G , Humanos , Ligação de Hidrogênio , Interações Hidrofóbicas e Hidrofílicas , Ivermectina/química , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Ligação Proteica , Domínios Proteicos , RNA/genética , RNA/metabolismo , SARS-CoV-2
11.
Chemistry ; 27(13): 4420-4429, 2021 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-33258498

RESUMO

Donor-acceptor Stenhouse adducts (DASAs) are playing an outstanding role as innovative and versatile photoswitches. Until now, all the efforts have been spent on modifying the donor and acceptor moieties to modulate the absorption energy and improve the cyclization and reversion kinetics. However, there is a strong dependence on specific structural modifications and a lack of predictive behavior, mostly owing to the complex photoswitching mechanism. Here, by means of a combined experimental and theoretical study, the effect of chemical modification of the π-bridge linking the donor and acceptor moieties is systematically explored, revealing the significant impact on the absorption, photocyclization, and relative stability of the open form. In particular, a position along the π-bridge is found to be the most suited to redshift the absorption while preserving the cyclization. However, thermal back-reaction to the initial isomer is blocked. These effects are explained in terms of an increased acceptor capability offered by the π-bridge substituent that can be modulated. This strategy opens the path toward derivatives with infra-red absorption and a potential anchoring point for further functionalization.

12.
Phys Chem Chem Phys ; 22(46): 26787-26795, 2020 Dec 07.
Artigo em Inglês | MEDLINE | ID: mdl-33211036

RESUMO

Different fungi lineages are known to emit light on Earth, mainly in tropical climates. Although the preparation of bioluminescent cell-free extracts allowed one to characterize the enzymatic requirements, the molecular mechanism underlying luminescence is still largely unknown and is based on the experimental putative assumption that a high-energy intermediate should be formed by reaction with O2 and formation of an endoperoxide. Here, we aim at determining, through state-of-the-art multiconfigurational quantum chemistry, the full mechanistic landscape leading from the endoperoxide to the emitting species, envisaging different possible pathways and proposing their viability. Especially, thermal CO2 detachment followed by excited-state peroxide opening (thermal-chemiluminescence) can compete with a parallel pathway, i.e., first excited-state endoperoxide opening, followed by CO2 detachment on the same excited-state (excited state-chemiluminescence). Clear differences in the energy supplies, as well as the possibility to directly populate the emitting species from the intersection seam between ground and excited states, land credence to a kinetically efficient thermal-chemiluminescent pathway, establishing for the first time a detailed description of fungal bioluminescence.


Assuntos
Dióxido de Carbono/química , Catecóis/química , Fungos/química , Peróxidos/química , Pironas/química , Teoria da Densidade Funcional , Luminescência , Modelos Químicos , Oxigênio/química
13.
J Proteome Res ; 19(11): 4291-4315, 2020 11 06.
Artigo em Inglês | MEDLINE | ID: mdl-33119313

RESUMO

The emergence in late 2019 of the coronavirus SARS-CoV-2 has resulted in the breakthrough of the COVID-19 pandemic that is presently affecting a growing number of countries. The development of the pandemic has also prompted an unprecedented effort of the scientific community to understand the molecular bases of the virus infection and to propose rational drug design strategies able to alleviate the serious COVID-19 morbidity. In this context, a strong synergy between the structural biophysics and molecular modeling and simulation communities has emerged, resolving at the atomistic level the crucial protein apparatus of the virus and revealing the dynamic aspects of key viral processes. In this Review, we focus on how in silico studies have contributed to the understanding of the SARS-CoV-2 infection mechanism and the proposal of novel and original agents to inhibit the viral key functioning. This Review deals with the SARS-CoV-2 spike protein, including the mode of action that this structural protein uses to entry human cells, as well as with nonstructural viral proteins, focusing the attention on the most studied proteases and also proposing alternative mechanisms involving some of its domains, such as the SARS unique domain. We demonstrate that molecular modeling and simulation represent an effective approach to gather information on key biological processes and thus guide rational molecular design strategies.


Assuntos
Antivirais , Infecções por Coronavirus , Desenho de Fármacos , Simulação de Acoplamento Molecular , Pandemias , Pneumonia Viral , Glicoproteína da Espícula de Coronavírus , Betacoronavirus , COVID-19 , Infecções por Coronavirus/tratamento farmacológico , Infecções por Coronavirus/virologia , Humanos , Simulação de Dinâmica Molecular , Pneumonia Viral/tratamento farmacológico , Pneumonia Viral/virologia , SARS-CoV-2 , Glicoproteína da Espícula de Coronavírus/química , Glicoproteína da Espícula de Coronavírus/genética , Glicoproteína da Espícula de Coronavírus/metabolismo , Proteínas não Estruturais Virais/química , Proteínas não Estruturais Virais/genética , Proteínas não Estruturais Virais/metabolismo , Internalização do Vírus
14.
J Phys Chem Lett ; 11(21): 9272-9281, 2020 Nov 05.
Artigo em Inglês | MEDLINE | ID: mdl-33085491

RESUMO

Since the end of 2019, the coronavirus SARS-CoV-2 has caused more than 1000000 deaths all over the world and still lacks a medical treatment despite the attention of the whole scientific community. Human angiotensin-converting enzyme 2 (ACE2) was recently recognized as the transmembrane protein that serves as the point of entry of SARS-CoV-2 into cells, thus constituting the first biomolecular event leading to COVID-19 disease. Here, by means of a state-of-the-art computational approach, we propose a rational evaluation of the molecular mechanisms behind the formation of the protein complex. Moreover, the free energy of binding between ACE2 and the active receptor binding domain of the SARS-CoV-2 spike protein is evaluated quantitatively, providing for the first time the thermodynamics of virus-receptor recognition. Furthermore, the action of different ACE2 ligands is also examined in particular in their capacity to disrupt SARS-CoV-2 recognition, also providing via a free energy profile the quantification of the ligand-induced decreased affinity. These results improve our knowledge on molecular grounds of the SARS-CoV-2 infection and allow us to suggest rationales that could be useful for the subsequent wise molecular design for the treatment of COVID-19 cases.


Assuntos
Betacoronavirus/metabolismo , Ligantes , Peptidil Dipeptidase A/metabolismo , Glicoproteína da Espícula de Coronavírus/metabolismo , Enzima de Conversão de Angiotensina 2 , Sítios de Ligação , COVID-19 , Infecções por Coronavirus/patologia , Infecções por Coronavirus/virologia , Diosmina/química , Diosmina/metabolismo , Humanos , Simulação de Dinâmica Molecular , Pandemias , Peptidil Dipeptidase A/química , Plicamicina/química , Plicamicina/metabolismo , Pneumonia Viral/patologia , Pneumonia Viral/virologia , Ligação Proteica , Domínios Proteicos , SARS-CoV-2 , Glicoproteína da Espícula de Coronavírus/química , Termodinâmica
15.
J Org Chem ; 85(8): 5503-5510, 2020 04 17.
Artigo em Inglês | MEDLINE | ID: mdl-32202422

RESUMO

Fungal bioluminescence is a fascinating natural process, standing out for the continuous conversion of chemical energy into light. The structure of fungal oxyluciferin (light emitter) was proposed in 2017, being different and more complex than other oxyluciferins. The complexity of fungal oxyluciferin arises from diverse equilibria such as keto/enol tautomerization or deprotonation equilibria of four titratable groups. For this reason, still some crucial details of its structure remain unexplored. To obtain further structural information, a combined experimental and computational study of natural and three synthetic fungal oxyluciferin analogues has been performed. Here, we state the most stable chemical form of fungal oxyluciferin regarding its keto and enol tautomers, in the ground and excited states. We propose the (3Z,5E)-6-(3,4-dihydroxyphenyl)-4-hydroxy-2-oxohexa-3,5-dienoic acid form as the light emitter (fluorescent state) in water solution. Moreover, we show that chemical modifications on fungal oxyluciferin can affect the relative stability of the conformers. Furthermore, we show the clear effect of pH on emission. General conclusions about the role of these titratable groups in emission modulation have been drawn, such as the key role of dihydroxyphenyl deprotonation. This study is key to further analyze the properties of fungal bioluminescence and propose novel synthetic analogues.


Assuntos
Vaga-Lumes , Fungos , Animais , Concentração de Íons de Hidrogênio , Água
16.
Phys Chem Chem Phys ; 22(1): 82-91, 2019 Dec 18.
Artigo em Inglês | MEDLINE | ID: mdl-31802096

RESUMO

Firefly oxyluciferin is the chemical product of bioluminescence responsible for light emission. Experiments have already shown that different analogues of natural oxyluciferin, exhibit different emission colours. In particular, the structure of natural oxyluciferin has been modified by atom or group substitutions. However, a rationalization of the origin of the bioluminescence emission colour modulation of these analogues has still not been reported. For these reasons, the aim of this study is to explain the influence of structural modifications within the natural oxyluciferin on the colour modulation of bioluminescence. To do this, natural firefly oxyluciferin and three synthetic analogues whose experimental bioluminescence spectra are red- and blue-shifted compared to the natural one were studied. The absorption and emission transition energies have been calculated at the Time-dependent density functional theory (TD-DFT) level using both quantum mechanics (QM) and quantum mechanics/molecular mechanics (QM/MM) methods. Moreover, the solvent (water using the PCM model) and the protein surrounding effect have also been considered. The predicted emission spectra are in quite good agreement with the available experimental spectra, validating the methodology followed in this study. In particular, it was demonstrated that using the QM/MM approach, and considering explicitly the protein environment, the experimental bioluminescence spectra can be reproduced. Furthermore, this study shows that the substitution within the oxyluciferin structure causes a change of its electronic distribution and energies of the HOMO and LUMO orbitals involved in the vertical transitions, leading to different light emission colours. This work will promote future studies focused on luciferin mutations guided by the prediction of their bioluminescence emission spectra.

17.
Molecules ; 24(9)2019 Apr 26.
Artigo em Inglês | MEDLINE | ID: mdl-31035516

RESUMO

deMon2k is a readily available program specialized in Density Functional Theory (DFT) simulations within the framework of Auxiliary DFT. This article is intended as a tutorial-review of the capabilities of the program for molecular simulations involving ground and excited electronic states. The program implements an additive QM/MM (quantum mechanics/molecular mechanics) module relying either on non-polarizable or polarizable force fields. QM/MM methodologies available in deMon2k include ground-state geometry optimizations, ground-state Born-Oppenheimer molecular dynamics simulations, Ehrenfest non-adiabatic molecular dynamics simulations, and attosecond electron dynamics. In addition several electric and magnetic properties can be computed with QM/MM. We review the framework implemented in the program, including the most recently implemented options (link atoms, implicit continuum for remote environments, metadynamics, etc.), together with six applicative examples. The applications involve (i) a reactivity study of a cyclic organic molecule in water; (ii) the establishment of free-energy profiles for nucleophilic-substitution reactions by the umbrella sampling method; (iii) the construction of two-dimensional free energy maps by metadynamics simulations; (iv) the simulation of UV-visible absorption spectra of a solvated chromophore molecule; (v) the simulation of a free energy profile for an electron transfer reaction within Marcus theory; and (vi) the simulation of fragmentation of a peptide after collision with a high-energy proton.


Assuntos
Modelos Teóricos , Simulação de Dinâmica Molecular , Teoria Quântica , Algoritmos
18.
Molecules ; 24(8)2019 Apr 20.
Artigo em Inglês | MEDLINE | ID: mdl-31009993

RESUMO

The emitted color in fireflies' bioluminescent systems depends on the beetle species the system is extracted from and on different external factors (pH, temperature…) among others. Controlling the energy of the emitted light (i.e., color) is of crucial interest for the use of such bioluminescent systems. For instance, in the biomedical field, red emitted light is desirable because of its larger tissue penetration and lower energies. In order to investigate the influence of the protein environment and the AMP protonation state on the emitted color, the emission spectra of the phenolate-keto and phenolate-enol oxyluciferin forms have been simulated by means of MD simulations and QM/MM calculations, considering: two different protein conformations (with an open or closed C-terminal domain with respect to the N-terminal) and two protonation states of AMP. The results show that the emission spectra when considering the protein characterized by a closed conformation are blue-shifted compared to the open conformation. Moreover, the complete deprotonation of AMP phosphate group (AMP2-) can also lead to a blue-shift of the emission spectra but only when considering the closed protein conformation (open form is not sensitive to changes of AMP protonation state). These findings can be reasoned by the different interactions (hydrogen-bonds) found between oxyluciferin and the surrounding (protein, AMP and water molecules). This study gets partial insight into the possible origin of the emitted color modulation by changes of the pH or luciferase conformations.


Assuntos
Monofosfato de Adenosina/química , Vaga-Lumes/química , Luminescência , Conformação Proteica , Animais , Ligação de Hidrogênio , Simulação de Dinâmica Molecular , Estrutura Molecular , Análise Espectral
19.
Inorg Chem ; 58(8): 5314-5324, 2019 Apr 15.
Artigo em Inglês | MEDLINE | ID: mdl-30943022

RESUMO

Following the track of the useful titanocene [Ti(η5-C5H5)2Cl] reagent in organic synthesis, the related half-sandwich titanium(III) derivatives [Ti(η5-C5R5)Cl2] are receiving increasing attention in radical chemistry of many catalyzed transformations. However, the structure of the active titanium(III) species remains unknown in the literature. Herein, we describe the synthesis, crystal structure, and electronic structure of titanium(III) aggregates of composition [{Ti(η5-C5Me5)Cl2} n]. The thermolysis of [Ti(η5-C5Me5)Cl2Me] (1) in benzene or hexane at 180 °C results in the clean formation of [{Ti(η5-C5Me5)Cl(µ-Cl)}2] (2), methane, and ethene. The treatment of 1 with excess pinacolborane in hexane at 65 °C leads to a mixture of 2 and the paramagnetic trimer [{Ti(η5-C5Me5)(µ-Cl)2}3] (3). The X-ray crystal structures of compounds 2 and 3 show Ti-Ti distances of 3.267(1) and 3.219(12) Å, respectively. Computational studies (CASPT2//CASSCF and BS DFT methods) for dimer 2 reveal a singlet ground state and a relatively large singlet-triplet energy gap. Nuclear magnetic resonance spectroscopy of 2 in aromatic hydrocarbon solutions and DFT calculations for several [{Ti(η5-C5Me5)Cl2} n] aggregates are consistent with the existence of an equilibrium between the diamagnetic dimer [{Ti(η5-C5Me5)Cl(µ-Cl)}2] and a paramagnetic tetramer [{Ti(η5-C5Me5)(µ-Cl)2}4] in solution. In contrast, complex 2 readily dissolves in tetrahydrofuran to give a green-blue solution from which blue crystals of the mononuclear adduct [Ti(η5-C5Me5)Cl2(thf)] (4) were grown.

20.
J Phys Chem Lett ; 10(5): 1063-1067, 2019 Mar 07.
Artigo em Inglês | MEDLINE | ID: mdl-30707586

RESUMO

We report theoretical and experimental evidence showing that photochemical reactivity of a chromophore can be modified by applying mechanical forces via molecular force probes. This mechanical action permits us to modulate main photochemical properties, such as fluorescence yield, excited-state lifetime, or photoisomerization quantum yield. The effect of molecular force probes can be rationalized in terms of simple mechanochemical models, establishing a qualitative framework for understanding the mechanical control of photoreactivity in stilbenes.

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