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1.
Inorg Chem ; 63(21): 9579-9587, 2024 May 27.
Artigo em Inglês | MEDLINE | ID: mdl-38374612

RESUMO

A family of rare-earth complexes [RE(III) = Y, La, Gd, Tb, Dy, and Er] with doubly reduced dibenzo[a,e]cyclooctatetraene (DBCOT) has been synthesized and structurally characterized. X-ray diffraction analysis confirms that all products of the [RE(DBCOT)(THF)4][RE(DBCOT)2] composition consist of the anionic sandwich [RE(DBCOT)2]- and the cationic counterpart [RE(DBCOT)(THF)4]+. Within the sandwich, two elongated π decks are slightly bent toward the metal center (avg. 7.3°) with a rotation angle of 35.9-37.6°. The RE(III) ion is entrapped between the central eight-membered rings of DBCOT2- in a η8 fashion. The trends in the RE-COT bond lengths are consistent with the variations of the ionic radii of RE(III) centers. The 1H NMR spectra of the diamagnetic Y(III) and La(III) analogues illustrate the distinct solution behavior for the cationic and anionic parts in this series. Magnetic measurements for the Dy analogue reveal single-molecule magnetism, which was rationalized by considering the effect of crystal-field splitting for both building units analyzed by electronic structure calculations.

2.
J Chem Inf Model ; 64(7): 2612-2623, 2024 Apr 08.
Artigo em Inglês | MEDLINE | ID: mdl-38157481

RESUMO

Structure-based drug discovery is a process for both hit finding and optimization that relies on a validated three-dimensional model of a target biomolecule, used to rationalize the structure-function relationship for this particular target. An ultralarge virtual screening approach has emerged recently for rapid discovery of high-affinity hit compounds, but it requires substantial computational resources. This study shows that active learning with simple linear regression models can accelerate virtual screening, retrieving up to 90% of the top-1% of the docking hit list after docking just 10% of the ligands. The results demonstrate that it is unnecessary to use complex models, such as deep learning approaches, to predict the imprecise results of ligand docking with a low sampling depth. Furthermore, we explore active learning meta-parameters and find that constant batch size models with a simple ensembling method provide the best ligand retrieval rate. Finally, our approach is validated on the ultralarge size virtual screening data set, retrieving 70% of the top-0.05% of ligands after screening only 2% of the library. Altogether, this work provides a computationally accessible approach for accelerated virtual screening that can serve as a blueprint for the future design of low-compute agents for exploration of the chemical space via large-scale accelerated docking. With recent breakthroughs in protein structure prediction, this method can significantly increase accessibility for the academic community and aid in the rapid discovery of high-affinity hit compounds for various targets.


Assuntos
Descoberta de Drogas , Ligação Proteica , Simulação de Acoplamento Molecular , Ligantes
3.
Cell Mol Life Sci ; 79(3): 179, 2022 Mar 06.
Artigo em Inglês | MEDLINE | ID: mdl-35253091

RESUMO

ATP synthases are unique rotatory molecular machines that supply biochemical reactions with adenosine triphosphate (ATP)-the universal "currency", which cells use for synthesis of vital molecules and sustaining life. ATP synthases of F-type (FOF1) are found embedded in bacterial cellular membrane, in thylakoid membranes of chloroplasts, and in mitochondrial inner membranes in eukaryotes. The main functions of ATP synthases are control of the ATP synthesis and transmembrane potential. Although the key subunits of the enzyme remain highly conserved, subunit composition and structural organization of ATP synthases and their assemblies are significantly different. In addition, there are hypotheses that the enzyme might be involved in the formation of the mitochondrial permeability transition pore and play a role in regulation of the cell death processes. Dysfunctions of this enzyme lead to numerous severe disorders with high fatality levels. In our review, we focus on FOF1-structure-based approach towards development of new therapies by using FOF1 structural features inherited by the representatives of this enzyme family from different taxonomy groups. We analyzed and systematized the most relevant information about the structural organization of FOF1 to discuss how this approach might help in the development of new therapies targeting ATP synthases and design tools for cellular bioenergetics control.


Assuntos
Desenho de Fármacos , ATPases Translocadoras de Prótons/metabolismo , Trifosfato de Adenosina/metabolismo , Bactérias/metabolismo , Proteínas de Bactérias/antagonistas & inibidores , Proteínas de Bactérias/classificação , Proteínas de Bactérias/metabolismo , Cloroplastos/metabolismo , Eucariotos/metabolismo , Filogenia , Subunidades Proteicas/metabolismo , ATPases Translocadoras de Prótons/antagonistas & inibidores , ATPases Translocadoras de Prótons/classificação , Bibliotecas de Moléculas Pequenas/química , Bibliotecas de Moléculas Pequenas/metabolismo
4.
Int J Mol Sci ; 24(8)2023 Apr 17.
Artigo em Inglês | MEDLINE | ID: mdl-37108531

RESUMO

The aim of this study was to prepare and characterize the glasses made of x(Fe2O3∙V2O5)∙(100 - x)[P2O5∙CaO] with x ranging of 0-50%. The contribution of Fe2O3 and V2O5 amount on the structure of P2O5·CaO matrix was investigated. The vitreous materials were characterized by XRD (X-ray diffraction analysis), EPR (Electron Paramagnetic Resonance) spectroscopy, and magnetic susceptibility measurements. A hyperfine structure typical for isolated V4+ ions was noticed to all spectra containing low amount of V2O5. The XRD spectra show the amorphous nature of samples, apart x = 50%. An overlap of the EPR spectrum of a broad line without the hyperfine structure characteristic of clustered ions was observed with increasing V2O5 content. The results of magnetic susceptibility measurements explain the antiferromagnetic or ferromagnetic interactions expressed between the iron and vanadium ions in the investigated glass.


Assuntos
Ferro , Vanádio , Vanádio/química , Cálcio/química , Fosfatos de Cálcio/química , Fenômenos Magnéticos , Vidro/química
5.
Chemistry ; 28(9): e202104194, 2022 Feb 16.
Artigo em Inglês | MEDLINE | ID: mdl-34890088

RESUMO

Chemical reduction of pentacene (C22 H14 , 1) with Group 1 metals ranging from Li to Cs revealed that 1 readily undergoes a two-fold reduction to afford a doubly-reduced 12- anion in THF. With the help of 18-crown-6 ether used as a secondary coordinating agent, five π-complexes of 12- with different alkali metal counterions have been isolated and fully characterized. This series of complexes enables the first evaluation of alkali-metal ion binding patterns and structural changes of the 12- dianion based on the crystallographically confirmed examples. The difference in coordination of the smallest Li+ ion vs. heavier Group 1 congeners has been demonstrated. In addition, the use of benzo-15-crown-5 in the reaction of 1 with Na metal allowed the isolation of the unique solvent-separated ion product with a "naked" dianion, 12- . The detailed structural analyses of the series revealed the C-C bond alteration and core deformation of pentacene upon two-fold reduction and complexation. The negative charge localization at the central six-membered ring of 12- identified by theoretical calculations corroborates with the X-ray crystallographic results. Subsequent in-depth theoretical analysis provided a detailed description of changes in the electronic structure and aromaticity of pentacene upon reduction.

6.
Int J Mol Sci ; 22(13)2021 Jun 29.
Artigo em Inglês | MEDLINE | ID: mdl-34210014

RESUMO

Human serum transferrin (HST) is a glycoprotein involved in iron transport that may be a candidate for functionalized nanoparticles to bind and target cancer cells. In this study, the effects of the simple and doped with cobalt (Co) and copper (Cu) ferrihydrite nanoparticles (Fh-NPs, Cu-Fh-NPs, and Co-Fh-NPs) were studied by spectroscopic and molecular approaches. Fluorescence spectroscopy revealed a static quenching mechanism for all three types of Fh-NPs. All Fh-NPs interacted with HST with low affinity, and the binding was driven by hydrogen bonding and van der Waals forces for simple Fh-NPs and by hydrophobic interactions for Cu-Fh-NPs and Co-Fh-NPs binding, respectively. Of all samples, simple Fh-NPs bound the most to the HST binding site. Fluorescence resonance energy transfer (FRET) allowed the efficient determination of the energy transfer between HST and NPs and the distance at which the transfer takes place and confirmed the mechanism of quenching. The denaturation of the HST is an endothermic process, both in the case of apo HST and HST in the presence of the three types of Fh-NPs. Molecular docking studies revealed that Fh binds with a low affinity to HST (Ka = 9.17 × 103 M-1) in accord with the fluorescence results, where the interaction between simple Fh-NPs and HST was described by a binding constant of 9.54 × 103 M-1.


Assuntos
Cobalto/química , Compostos Férricos/síntese química , Transferrina/química , Transferrina/metabolismo , Cobre/química , Compostos Férricos/química , Transferência Ressonante de Energia de Fluorescência , Humanos , Ligação de Hidrogênio , Modelos Moleculares , Simulação de Acoplamento Molecular , Nanopartículas , Ligação Proteica , Conformação Proteica , Espectrometria de Fluorescência , Termodinâmica
7.
Angew Chem Int Ed Engl ; 60(48): 25445-25453, 2021 Nov 22.
Artigo em Inglês | MEDLINE | ID: mdl-34554612

RESUMO

The stepwise chemical reduction of a molecular warped nanographene (WNG) having a negatively curved π-surface and defined C80 H30 composition with Cs metal used as the reducing and complexing agent allowed the isolation of three different reduced states with one, two, and three electrons added to its π-conjugated system. This provided a unique series of nanosized carbanions with increasing negative charge for in-depth structural analysis of consequences of controlled electron charging of non-planar nanographenes, using X-ray crystallographic and computational tools. The 3D molecular electrostatic potential (MEP) maps identified the negative charge localization at the central part of the WNG surface where selective coordination of Cs+ ions is confirmed crystallographically. In-depth theoretical investigation revealed a complex response of the WNG to the stepwise electron acquisition. The extended and contorted π-surface of the WNG undergoes subtle swinging distortions that are accompanied by notable changes in the electronic structure and site-dependent aromaticity of the resulting carbanions.

8.
J Am Chem Soc ; 142(52): 21634-21639, 2020 12 30.
Artigo em Inglês | MEDLINE | ID: mdl-33320644

RESUMO

High-valent transition metal-oxo, -peroxo, and -superoxo complexes are crucial intermediates in both biological and synthetic oxidation of organic substrates, water oxidation, and oxygen reduction. While high-valent oxygenated complexes of Mn, Fe, Co, and Cu are increasingly well-known, high-valent oxygenated Ni complexes are comparatively rarer. Herein we report the isolation of such an unusual high-valent species in a thermally unstable NiIII2(µ-1,2-peroxo) complex, which has been characterized using single-crystal X-ray diffraction and X-ray absorption, NMR, and UV-vis spectroscopies. Reactivity studies show that this complex is stable toward dissociation of oxygen but reacts with simple nucleophiles and electrophiles.

9.
J Comput Chem ; 41(2): 88-96, 2020 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-31495954

RESUMO

The comprehensive theoretical investigation of stability of functionalized corannulene cations [R-C20 H10 ]+ with respect to two alternative bond-breaking mechanisms, namely, homolytic or radical ([R-C20 H10 ]+ → R• + C20 H10 +• ) and heterolytic or cationic ([R-C20 H10 ]+ → R+ + C20 H10 ), was accomplished. The special focus was on the influence of the nature of R-group on the energetics of the bond cleavage. Detailed study of energetics of both mechanisms has revealed that the systems with small alkyl groups such as methyl tend to undergo bond breaking in accordance with homolytic mechanism. Subsequent elongation of the chain of the R-group resulted in shifting the paradigm, making heterolytic path more energetically favorable. Subsequent analysis of different components of the bonding between R-group and corannulene polyaromatic core helped to shed light on trends observed. In both mechanisms, the covalent contribution was found to be dominating, whereas ionic part contributes ~25-27%. Two leading components of ΔEorb , C20 H10 → R and R → C20 H10 , were identified with NOCV-EDA approach. While the homolytic pathway is best described as R → C20 H10 process, the heterolytic mechanism shows domination of the C20 H10 → R term. Surprisingly, the preparation energy (ΔEprep ) was identified as a key player in stability tendencies found. In other words, the relative stability of corresponding molecular fragments (here R-groups as the corannulene fragment remains the same for all systems) in their cationic or radical forms determine the preference given to a specific bond breaking path and, as consequence, the total stability of target functionalized cations. These conclusions were further confirmed by extending a set of R-groups to conjugated (allyl, phenyl), bulky (iPr, tBu), ß-silyl (CH2 SiH3 , CH2 SiMe3 ), and benzyl (CH2 Ph) groups. © 2019 Wiley Periodicals, Inc.

10.
Phys Chem Chem Phys ; 22(12): 6716-6726, 2020 Mar 28.
Artigo em Inglês | MEDLINE | ID: mdl-32163075

RESUMO

In this study, a comprehensive theoretical investigation of both kinetic and thermodynamic stabilities was performed for dimeric dianionic systems (C20H10)22- and (C28H14)22-, neutralized by two alkali metal cations. The influence of the counterions was of primary interest. The impact of the additional/spectator ligand(s) was elucidated by considering adducts with four molecules of diglyme or two molecules of 18-crown-6 ether. Importantly, both types of systems - in the form of contact-ion pair (CIP) and solvent-separated ion pair (SSIP) - were considered. The SSIP set was augmented by the adduct, in which the dimeric dianionic species were neutralized with purely organic cations N(CH3)4+ and P(CH3)4+. Detailed analysis of the bonding revealed that the presence of the counterions made these systems thermodynamically stable. This finding is in sharp contrast with results obtained for isolated (PAH)22- systems, which were previously found to be thermodynamically unstable, but kinetically persistent. The introduction of the alkali metal cations to the system significantly increases the ionic term (ΔEelstat), whereas the repulsive ΔEPauli one was found to be substantially reduced. Considering that the orbital component (ΔEorb) exhibited only a moderate decrease and the preparation energy (ΔEprep) showed no changes, the above-mentioned changes in ΔEelstat and ΔEPauli provided a clear explanation for the increase of the thermodynamic stability of the target species. Importantly, a clear correlation between the size of the alkali metal cation and stability of the target dimeric product was established. Thermodynamic stability of the system rises with a decrease in the size of M+ due to enlargement of the ΔEorb. Evaluated energy barriers (as spin-crossing points between singlet and triplet energy surfaces) were found to be equal to +15.85 kcal mol-1 and +18.5 kcal mol-1 for [(Cs+)2{(C20H10)22-}] and [(Cs+)2{(C28H14)22-}], respectively, which is substantially higher than those calculated for isolated (PAH)22- systems (+10.00 kcal mol-1 for (C20H10)22- and +12.35 kcal mol-1 for (C28H14)22-). Thus, this study identified the presence of counterions as the key factor, which have a dramatic influence on the thermodynamic and kinetic stabilities of the aimed dianionic dimeric systems, which are formed by two curved polyaromatic monoanion-radicals.

11.
Int J Mol Sci ; 21(16)2020 Aug 13.
Artigo em Inglês | MEDLINE | ID: mdl-32823747

RESUMO

Inspired by the unusual shapes of the titration curve observed for many surfactants and mixed colloidal systems, we decided to extend the analysis to isothermal titration calorimetric curves (ITC) by paying special attention to potential structural changes in micellar aggregates. In this paper, we used isothermal titration calorimetry in conjunction with Scanning Transmission Electron Microscopy (STEM), Small-Angle Neutron Scattering (SANS) and X-ray Scattering (SAXS) methods support by Monte Carlo and semiempirical quantum chemistry simulations to confirm if the isothermal calorimetric curve shape can reflect micelle transition phenomena. For that purpose, we analysed, from the thermodynamic point of view, a group of cationic gemini surfactants, alkanediyl-α,ω-bis(dimethylalkylammonium) bromides. We proposed the shape of aggregates created by surfactant molecules in aqueous solutions and changes thereof within a wide temperature range. The results provide evidence for the reorganization processes and the relationship (dependence) between the morphology of the created aggregates and the conditions such as temperature, surfactant concentration and spacer chain length which affect the processes.


Assuntos
Calorimetria , Micelas , Temperatura , Simulação por Computador , Teoria da Densidade Funcional , Cinética , Método de Monte Carlo , Difração de Nêutrons , Polímeros/química , Espalhamento a Baixo Ângulo , Tensoativos/química , Água/química
12.
Angew Chem Int Ed Engl ; 59(24): 9624-9630, 2020 Jun 08.
Artigo em Inglês | MEDLINE | ID: mdl-32166883

RESUMO

A known trinuclear structure was used to design the heterobimetallic mixed-valent, mixed-ligand molecule [CoII (hfac)3 -Na-CoIII (acac)3 ] (1). This was used as a template structure to develop heterotrimetallic molecules [CoII (hfac)3 -Na-FeIII (acac)3 ] (2) and [NiII (hfac)3 -Na-CoIII (acac)3 ] (3) via isovalent site-specific substitution at either of the cobalt positions. Diffraction methods, synchrotron resonant diffraction, and multiple-wavelength anomalous diffraction were applied beyond simple structural investigation to provide an unambiguous assignment of the positions and oxidation states for the periodic table neighbors in the heterometallic assemblies. Molecules of 2 and 3 are true heterotrimetallic rather than a statistical mixture of two heterobimetallic counterparts. Trinuclear platform 1 exhibits flexibility in accommodating a variety of di- and trivalent metals, which can be further utilized in the design of molecular precursors for the NaMM'O4 functional oxide materials.

13.
Acc Chem Res ; 51(6): 1541-1549, 2018 06 19.
Artigo em Inglês | MEDLINE | ID: mdl-29874040

RESUMO

The need for advanced energy storage technologies demands the development of new functional materials. Novel carbon-rich and carbon-based materials of different structural topologies attract significant attention in this regard. Attractive systems include a unique class of bowl-shaped polycyclic aromatic hydrocarbons that map onto fullerene surfaces and are thus often referred to as fullerene fragments, buckybowls, or π-bowls. Importantly, carbon bowls are able to acquire multiple electrons in stepwise reduction reactions producing sets of successively reduced carbanions. The resulting negatively charged π-bowls exhibit unique supramolecular assembly and metal intercalation patterns that only recently have begun to be uncovered. First, we have resolved the long-standing mystery behind the supramolecular structure formed by a highly reduced fullerene fragment called corannulene (C20H104-) with multiple lithium ions, using X-ray crystallography coupled with NMR spectroscopy and theoretical calculations. This work provided a new paradigm for lithium ion intercalation between the curved carbon π-surfaces and facilitated understanding of the lithium ion storage mechanism in carbonaceous matrices. Next, we have initiated a new research direction, an investigation of the mixed alkali metal reduction reactions using bowl-shaped corannulene as a remarkable multielectron reservoir and unique ligand with open convex and concave π-surfaces. As a result, we have revealed the cooperative effect of lithium with heavier Group 1 metals in reduction and self-assembly processes of corannulene. Moreover, we have discovered a new class of organometallic supramolecules having heterometallic cores with high nuclearity and charge such as Li3M36+ and LiM56+ (M = K, Rb, and Cs) sandwiched between two tetrareduced corannulene decks. The resulting triple-decker supramolecular assemblies, fully characterized by X-ray diffraction and spectroscopic methods, were found to exhibit a record ability of the highly charged corannulene π-surfaces to be fully engaged in intercalation of multiple metal ions. Based on this unique ability, curved π-ligands with extended carbon frameworks are expected to show remarkable potential for alkali metal storage compared to flat polycyclic arenes. Notably, a previously unseen mode of internal lithium binding revealed in the heterobimetallic sandwiches is accompanied by unprecedented negative shifts (up to -25 ppm) in 7Li NMR spectra. Based on in-depth analysis of NMR data, augmented by DFT calculations, we have rationalized the observed experimental trends and proposed the mechanism of stepwise alkali metal substitution reactions. Furthermore, we have correlated the origin of the record 7Li NMR shifts with unique electronic structures of these novel supramolecular aggregates. Herein we present comprehensive analysis of unusual structural and electronic features of remarkable heterometallic self-assemblies formed by tetrareduced corannulene, using a wealth of our recent experimental and computational results. This work uncovers unique potential of highly negatively charged bowl-shaped π-ligands for new supramolecular chemistry and materials chemistry applications.

14.
Chemistry ; 25(62): 14140-14147, 2019 Nov 07.
Artigo em Inglês | MEDLINE | ID: mdl-31390107

RESUMO

One-electron reduction of corannulene, C20 H10 , with Li metal in diglyme resulted in crystallization of [{Li+ (diglyme)2 }4 (C20 H10 .- )2 (C20 H10 -C20 H10 )2- ] (1), as revealed by single-crystal X-ray diffraction. This hybrid product contains two corannulene monoanion-radicals along with a dianionic dimer, crystallized with four Li+ ions wrapped by diglyme molecules. The dimeric (C20 H10 -C20 H10 )2- anion provides the first crystallographically confirmed example of spontaneous radical dimerization for C20 H10 .- . The C-C bond length between the two C20 H10 .- bowls of 1.588(5) Šis consistent with the single σ-bond character of the linker. The trans-disposition of two bowls in the centrosymmetric (C20 H10 -C20 H10 )2- dimer is observed with the torsion angle around the central C-C bond of 180°. Comprehensive theoretical analysis of formation/decomposition processes of the dimeric dianion has been carried out in order to evaluate the nature of bonding and energetics of the C20 H10 .- coupling. It is found that such σ-bonded dimers are thermodynamically unstable due to large preparation energy and repulsive Pauli component of the bonding, but kinetically persistent due to a high energy barrier provided by the existing spin-crossing point.

15.
Eur Biophys J ; 48(3): 285-295, 2019 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-30923869

RESUMO

ß-Lactoglobulin is one of the most notable representatives of the lipocalin family of proteins that are mainly involved in the transportation of small hydrophobic molecules. Therefore, the conformation stability of these proteins represents an important step for several industrial applications. In this study, the ß-lactoglobulin (ß-lg) conformation stability in solution was studied as a function of the protein concentration, pH, NaCl and temperature when the protein concentration is significantly higher in the buffer solution. Using small-angle X-ray and neutron scattering methods (SANS and SAXS), it was shown that ß-lg forms dimeric structures in 50 mM HEPES buffer under various conditions of the medium. At pH 5.9, ß-lg preserves its dimeric form in the high protein concentration range of 10-40 mg/mL. However, the conformation swelled with the addition of 50 mM NaCl in the system with 20 mg/mL ß-lg concentration. Further increase of NaCl concentration leads to a decrease of the radius of gyration of the ß-lg dimer. At pH below 5.9 where the protein is positively charged, ß-lg dimer preserves its conformation, and only an increase of the radius of gyration was attested by SAXS as the acidity of the medium increased to pH 3.6. This supports and adds to the findings presented above regarding the stability of ß-lg dimer in 50 mM HEPES buffer in D2O. Furthermore, at neutral and alkaline pH, the values of both radius of gyration and maximum particle dimension decrease by increasing the pH of the medium.


Assuntos
Lactoglobulinas/química , Espalhamento a Baixo Ângulo , Animais , Bovinos , Relação Dose-Resposta a Droga , Concentração de Íons de Hidrogênio , Interações Hidrofóbicas e Hidrofílicas , Modelos Moleculares , Difração de Nêutrons , Conformação Proteica/efeitos dos fármacos , Estabilidade Proteica/efeitos dos fármacos , Cloreto de Sódio/farmacologia , Temperatura , Difração de Raios X
16.
Photochem Photobiol Sci ; 18(7): 1793-1805, 2019 Jul 10.
Artigo em Inglês | MEDLINE | ID: mdl-31116222

RESUMO

Light-Oxygen-Voltage (LOV) domains are conserved parts of photoreceptors in plants, bacteria and fungi that bind flavins as chromophores and detect blue light. In the past, LOV domain variants have been developed as fluorescent reporter proteins (called flavin-based fluorescent proteins; FbFPs), which due to their ability to fluoresce under anaerobic conditions, fast folding kinetics and a small size of ∼12-16 kDa are a promising reporter system for quantitative real-time analysis of biological processes. Here, we present a small thermostable flavin-based fluorescent protein CagFbFP derived from a soluble LOV domain-containing histidine kinase from the thermophilic bacterium Chloroflexus aggregans. CagFbFP is composed of 107 amino acids with a molecular weight of 11.6 kDa and consists only of the conserved LOV core domain. The protein is thermostable with a melting point of about 68 °C. It crystallizes easily and its crystals diffract to 1.07 Å. Both the crystal structure and small angle scattering data show that the protein is a dimer. Unexpectedly, glutamine 148, which in LOV photoreceptor proteins is the key residue responsible for signal transduction, occupies two conformations. Molecular dynamics simulations show that the two conformations interconvert rapidly. The crystal structure of the wild-type Chloroflexus aggregans LOV domain determined at 1.22 Å resolution confirmed the presence of two alternative conformations of the glutamine 148 side chain. Overall, this protein, due to its stability and ease of crystallization, appears to be a promising model for ultra-high resolution structural studies of LOV domains and for application as a fluorescent reporter.


Assuntos
Proteínas de Bactérias/química , Chloroflexus/metabolismo , Flavinas/química , Proteínas Luminescentes/química , Sequência de Aminoácidos , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Cristalografia por Raios X , Proteínas Luminescentes/genética , Proteínas Luminescentes/metabolismo , Peso Molecular , Estrutura Terciária de Proteína , Proteínas Recombinantes/biossíntese , Proteínas Recombinantes/química , Proteínas Recombinantes/isolamento & purificação , Espalhamento a Baixo Ângulo , Alinhamento de Sequência , Espectrometria de Fluorescência , Temperatura de Transição , Difração de Raios X
17.
J Comput Chem ; 39(28): 2385-2396, 2018 Oct 30.
Artigo em Inglês | MEDLINE | ID: mdl-30306575

RESUMO

In this study, the first comprehensive theoretical investigation of the stability of functionalized fullerene-based cations [R-C60 ]+ and its relationship with the nature of the attached R-group was performed. C60 -Fullerene core was functionalized with an alkyl group of different length (R = (CH2 )n CH3 , where n = 0-9). This set was further complemented by bulky isopropyl and tert-butyl and conjugated phenyl groups. A detailed study of the relative stability of target cationic species was accompanied by in-depth investigation of their electronic structure and aromaticity using a large set of descriptors of different nature. The stability of target species was considered with respect to two alternative and competing mechanisms of bond breaking, namely, heterolytic ([R-C60 ]+ → R+ + C60 ) and homolytic ([R-C60 ]+ → R• + C60 +• ) ones. The transformation of strained sp2 -carbon atom in unperturbed C60 -fullerene to nonconstrained tetrahedral sp3 -type in functionalized derivatives was found to be the driving force for the formation of its functionalized cations. In spite of the fact that all systems under consideration were found to be corresponding to local minima on corresponding potential energy surfaces, the functionalization of C60 -core with the smallest and simplest methyl group resulted in most stable compound, as evaluated by bonding energy between R+ and fullerene fragment (in the light of both mechanisms). Subsequent elongation of the alkyl chain or introducing bulky groups led to notable decrease of the bonding energy and, as consequence, of the stability within the framework of heterolytic bond cleavage, whereas homolytic pathway assumes opposite-slight increase of stability along with lengthening of the R-group. The orbital interaction (ΔEorb ) was identified as the main driving force for these trends. In general, the homolytic path was found to be dominating for small-length R-groups such as those with n = 0 and 1. At n = 2, heterolytic and homolytic pathways are equally probable (the difference in corresponding bonding energies is about 1 kcal/mol). However, when the alkyl chain becomes longer (n = 3-9), the cationic bond cleavage appears as the most energetically favorable. © 2018 Wiley Periodicals, Inc.

18.
Chemistry ; 24(14): 3455-3463, 2018 Mar 07.
Artigo em Inglês | MEDLINE | ID: mdl-29328530

RESUMO

Molecular and electronic structure, reduction electron transfer and coordination abilities of a polycyclic aromatic hydrocarbon (PAH) having a planar naphtho-group fused to the corannulene bowl have been investigated for the first time using a combination of theoretical and experimental tools. A direct comparison of naphtho[2,3-a]corannulene (C28 H14 , 1) with parent corannulene (C20 H10 , 2) revealed the effect of framework topology change on electronic properties and aromaticity of 1. The presence of two reduction steps for 1 was predicted theoretically and confirmed experimentally. Two reversible one-electron reduction processes with the formal reduction potentials at -2.30 and -2.77 V versus Fc+/0 were detected by cyclic voltammetry (CV) measurements, demonstrating accessibility of the corresponding mono- and dianionic states of 1. The products of the singly and doubly reduced napththocorannulene were prepared using chemical reduction with Group 1 metals and isolated as sodium and rubidium salts. Their X-ray diffraction study revealed the formation of "naked" mono- and dianions crystallized as solvent-separated ion products with one or two sodium cations as [Na+ (18-crown-6)(THF)2 ][C28 H14- ] and [Na+ (18-crown-6)(THF)2 ]2 [C28 H142- ] (3⋅THF and 4⋅THF, respectively). The dianion of 1 was also isolated as a contact-ion complex with two rubidium countercations, [{Rb+ (18-crown-6)}2 (C28 H142- )] (5⋅THF). The structural consequences of adding one and two electrons to the carbon framework of 1 are compared for 3, 4 and 5. Changes in aromaticity and charge distribution stemming from the stepwise electron acquisition are discussed based on DFT computational study.

19.
Chemphyschem ; 19(19): 2579-2588, 2018 10 05.
Artigo em Inglês | MEDLINE | ID: mdl-29920888

RESUMO

The first comprehensive and systematic theoretical exploration of the bonding nature and energetics of the interactions between Ag(I) cation and a wide set of π-ligands was accomplished. This set ranges from simple ethylene and aromatic benzene to planar and curved polyaromatic molecules and to closed-cage C60 -fullerene. Simultaneous application of two energy decomposition schemes based on different ideas, namely, NBO-NEDA and EDA-NOCV, allowed shedding light on the nature of the bonding and its energetics. Importantly, our results unambiguously indicate that reliable results can be obtained only if using more than one theoretical approach. All methods clearly revealed the importance and even domination of the ionic contribution of the bonding in all adducts, except for those of C60 -fullerene, in which the covalent component was found to be the largest. Subsequent decomposition of the orbital term onto components showed that it consists of two major parts: (i) ligand-to-metal (π(C=C)→s(Ag), L→M) and (ii) metal-to-ligand (M→L) terms, with significant domination of the former. Interestingly, while the L→M component is essentially the same for all systems considered, the nature of the M→L one depends on the coordination site of the polycyclic aromatic hydrocarbons (PAH). In most of adducts, the M→L can be described as dxy (Ag)→π* (C=C) donation, whereas for systems [Ag-spoke-C12 H8 ]+ and [Ag-spoke-C20 H10 ]+ it corresponds to the dz2 (Ag)→π* (C=C) type of interaction. As a result, the coordination mode in such complexes is switched from η2 -type to η1 . Thus, the nature of the bonding, its energetics and even coordination mode in adducts of unsaturated hydrocarbons with late transition metal cations should be considered as a function of many components, which primarily includes the topology and aromaticity of the (poly)aromatic molecules.

20.
Inorg Chem ; 57(9): 5183-5193, 2018 May 07.
Artigo em Inglês | MEDLINE | ID: mdl-29668269

RESUMO

Homoleptic complexes [Fe(L n)]X2 (L1 = 1,1'-(α,α'- o-xylyl)-2,2'-biimidazole, L2 = 1,1'-(α,α'-3,4-dibromo- o-xylyl)-2,2'-biimidazole, L3 = 1,1'-(α,α'-2,5-dimethoxy- o-xylyl)-2,2'-biimidazole; X = BF4- or ClO4-) were synthesized by direct reactions of the Fe(II) precursor salts and bidentate ligands L1, L2, or L3. All mononuclear complexes undergo gradual temperature-driven spin-crossover (SCO) between the high-spin (HS, S = 2) and low-spin (LS, S = 0) states. Complexes with ligands L1 and L2 synthesized in methanol exhibit complete SCO with the midpoint of the LS↔HS conversion varying from 233 to 313 K, while complexes with ligand L3, crystallized from an ethanol/dichloromethane mixture, exhibit incomplete SCO with the residual HS/LS ratio of ∼1:4 for [Fe(L3)3](BF4)2 and ∼1:1 for [Fe(L3)3](ClO4)2. Complexes with L1 can also be recrystallized from ethanol/dichloromethane, in which case they exhibit very gradual and incomplete SCO, similar to those of the complexes with L3. The differences in magnetic behavior have been traced back to peculiarities of molecular packing observed in the corresponding crystal structures. Density-functional theoretical calculations provide justification to the SCO behavior of these complexes, as compared to the HS-only behavior observed for the parent [Fe(bim)3]2+ complex with nonalkylated 2,2'-biimidazole (bim).

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