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1.
J Phys Chem A ; 123(50): 10730-10738, 2019 Dec 19.
Artigo em Inglês | MEDLINE | ID: mdl-31714777

RESUMO

Conceptual density functional theory has been applied to study the Himbert intramolecular arene/allene Diels-Alder reaction. The effect of substitutions at different positions on the kinetics of these reactions has been analyzed. Therefore, from the calculation of the activation energies of more than 27 reactions involving concerted mechanisms, the selectivity of these reactions can be predicted and rationalized with the aid of conceptual DFT descriptors. An application of the two concepts, natural population analysis (NBO) and the state-specific dual descriptor (SSDD) for evaluating substituent effects, allows the investigation of the different interactions that promote a reaction compared to another. The SSDDs computed for the transition state structures provide important information about charge transfer interactions during the chemical reaction. In our case, the SSDD results show that the substituents promoting Himbert reaction have the lowest excitation energies, a fact which facilitates the allene/arene interaction. The NBO results show that according to the nature of the substituent, the Himbert reaction stands as a normal-electron demand or reverse. Thus, the interactions favoring each reaction are mentioned. The geometric deformation observed in the case of OCH3 is at the origin to the emergence of other low interactions between diene and dienophile as well as a strong electronic delocalization stabilizing the arene moiety. The calculated synchronicity indexes show that the Himbert intramolecular Diels-Alder reactions are very synchronous.

2.
Chem Sci ; 10(1): 277-283, 2019 Jan 07.
Artigo em Inglês | MEDLINE | ID: mdl-30746081

RESUMO

By using a combination of readily accessible experimental and computational experiments in water, we explored the factors governing the association between polyanionic dyn[4]arene and a series of α,ω-alkyldiammonium ions of increasing chain length. We found that the lock-and-key concept based on the best match between the apolar and polar regions of the molecular partners failed to explain the observed selectivities. Instead, the dissection of the energetic and structural contributions demonstrated that the binding events were actually guided by two crucial solvent-related phenomena as the chain length of the guest increases: the expected decrease of the enthalpic cost of guest desolvation and the unexpected increase of the favourable enthalpy of complex solvation. By bringing to light the decisive enthalpic impact of complex solvation during the binding of polyelectrolytes by inclusion, this study may provide a missing piece to a puzzle that one day could display the global picture of molecular recognition in water.

3.
Talanta ; 195: 441-446, 2019 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-30625567

RESUMO

Deformulation of a commercial surfactant mixture using Raman spectroscopy and advanced chemometric tools have been investigated. Since the use of surfactants is drastically expanding, their fine identification and quantification are required for quality control and regulation. Dilution of the detergent mixtures combined with Raman spectroscopy for signal extraction tools allowed the extraction of the first information concerning the composition of the mixture. The raw materials identified were thus used in an experimental design to obtain a robust model for the determination of detergent composition. The combination of chemometric tools (independent component analysis and Partial Least Square) and spectroscopic methods provided pertinent information for detergent composition. This methodology can easily be transposed to the industrial world.

4.
J Mol Model ; 24(11): 327, 2018 Oct 29.
Artigo em Inglês | MEDLINE | ID: mdl-30370435

RESUMO

In this work, the nature of the chemical interactions between the metalloid atom (M = Si, Ge, As, Sb, Te, Po) and the nitrogen atoms in the bora-amidinate (bam) complexes (ClnM[PhB(NtBu)2]) are investigated, mainly via density-based indices. The descriptors used are derived using the quantum theory of atoms in molecules and natural orbitals for chemical valence approaches. It is shown that the strongest interaction is achieved with silicon. Indeed, it is generally the lightest metalloid in a particular group of the periodic table (i.e., Si, As, and Te for groups 14-16, respectively) that exhibits the strongest bond in the bam complex. This suggests that the atomic radius of the metalloid is a useful parameter for predicting the bonding strength. Extended transition state (ETS) decomposition results indicate that the interactions are more electrostatic than due to orbital interactions.

5.
Chemphyschem ; 19(21): 2938-2946, 2018 11 05.
Artigo em Inglês | MEDLINE | ID: mdl-30238613

RESUMO

A new Zn-N4 -Schiff base L=((±)-trans-N,N'-Bis(2-aminobenzylidene)-1,2-diaminocyclohexane) complex was synthesized and fully characterized, showing an unexpected self-assembled double-stranded helicate structure. The X-ray crystal analysis of the Zn2 L2 complex ((C40 H44 N8 Zn2 ,CH2 Cl2 , a=14.2375(3) Å, b=16.7976(4) Å, c=16.1613(4) Å, monoclinic, P21 /n, Z=4) shows a centrosymmetrical structure in which zinc atoms are in distorted tetrahedral environments, revealing an M- (R, R) left-handed helicity in its asymmetric unit. However, it was observed that this dinuclear complex is thermodynamically unstable in the presence of small water amounts and undergoes demetallation into free N4-Schiff base ligand and ZnO nanoparticles. This hydrolysis process was thoroughly identified and monitored through detailed 1 H NMR, DOSY NMR analysis. The reaction mechanism of this demetallation event was elucidated by using the DFT method, involving an activation energy smaller than 13 kcal/mol. Besides, a theoretical mechanism of the demetallation process is given for the first time.

6.
Phys Chem Chem Phys ; 20(23): 16102-16116, 2018 Jun 13.
Artigo em Inglês | MEDLINE | ID: mdl-29855008

RESUMO

The present work studies theoretically the mechanisms involved in the fluorine substituent effect on the stereochemistry of Diels-Alder reactions. The case of R-butenone with cyclopentadiene is used for the purpose of modelling more general α-fluoro-α,ß-unsaturated carbonyl compounds, in catalyzed and uncatalyzed cases. A thorough analysis of the mechanism is performed using energy decomposition analysis (EDA) and conceptual DFT tools. It is shown that the endo conformation is privileged in all the studied cases with the exception of the α-fluorinated ketone. It is found that the endo selectivity of the non-fluorinated reactions is only due to the decrease of dispersion energy. On the other hand, the presence of a fluorine atom in the dienophile moieties increases remarkably the magnitude not only of the interaction energy between the reactants but that of the strain energy as well. Moreover, it is the strong destabilization strain energy occurring at the transition state of the endo pathway of the reaction cyclopentadiene/3-fluorobutenone that is mainly responsible for the exo selectivity. The effect of a Lewis acid catalyst on these reactions is also studied. The Lewis acid catalyst affects the activation energy of the studied Diels-Alder reactions but not their stereoselectivity. Furthermore, the dual descriptor results shed light onto the mechanism. Besides, natural bond orbital analysis (NBO) and determination of the condensed values of the state-specific dual descriptors (SSDD) are carried out to evaluate the donor-acceptor properties in these reactions. For the first time, a semiquantitative prediction of stereoselectivity due to substitutions of dienophile is obtained, thus complementing the previous interpretations (R. Hoffmann and R. B. Woodward, J. Am. Chem. Soc., 1965, 87, 4388; I. Fernández and F. M. Bickelhaupt, Chem. Soc. Rev., 2014, 43, 4953). Finally, since the role of dispersion forces is evidenced in some cases, a comparison between some popular exchange-correlation functionals is presented, assessing the performance of some standard functionals besides functionals with explicit dispersion corrections.

7.
Chemistry ; 23(52): 12845-12852, 2017 Sep 18.
Artigo em Inglês | MEDLINE | ID: mdl-28815856

RESUMO

Biogenic polyamines, which play a role in DNA condensation and stabilization, are ubiquitous and are found at millimolar concentration in the nucleus of eukaryotic cells. The interaction modes of three polyamines-putrescine (Put), spermine (Spm), and spermidine (Spd)-with a self-complementary 16 base pair (bp) duplex, are investigated by all-atom explicit-solvent molecular dynamics. The length of the amine aliphatic chain leads to a change of the interaction mode from minor groove binding to major groove binding. Through all-atom dynamics, noncovalent interactions that stabilize the polyamine-DNA complex and prefigure the reactivity, leading to the low-barrier formation of deleterious DNA-polyamine cross-links, after one-electron oxidation of a guanine nucleobase, are unraveled. The binding strength is quantified from the obtained trajectories by molecular mechanics generalized Born surface area post-processing (MM-GBSA). The values of binding free energies provide the same affinity order, Put

Assuntos
DNA/metabolismo , Poliaminas/metabolismo , Sítios de Ligação , DNA/química , Simulação de Dinâmica Molecular , Conformação de Ácido Nucleico , Poliaminas/química , Putrescina/química , Putrescina/metabolismo , Espermidina/química , Espermidina/metabolismo , Espermina/química , Espermina/metabolismo , Termodinâmica
8.
Sci Rep ; 7(1): 8885, 2017 08 21.
Artigo em Inglês | MEDLINE | ID: mdl-28827702

RESUMO

Nonsteroidal 2-arylproprionic acids are widely used, over-the-counter, anti-inflammatory drugs. Photosensitivity is a commonly overlooked adverse effect of these drugs. Based on the combined use of cell viability assays and molecular modeling, we prove and rationalize the photochemical pathways triggering photosensitization for two drugs, ibuprofen and ketoprofen. As its parent compound benzophenone, ketoprofen produces singlet oxygen, upon triplet manifold population. However, ibuprofen and ketoprofen photodissociate and hence may generate two highly reactive radicals. The formation of metastable aggregates between the two drugs and B-DNA is also directly probed by molecular dynamics. Our approach characterizes the coupled influence of the drug's intrinsic photochemistry and the interaction pattern with DNA. The photosensitization activity of nonsteroidal 2-arylproprionic acids, being added to gels and creams for topical use, should be crucially analyzed and rationalized to enact the proper preventive measures.


Assuntos
Morte Celular/efeitos dos fármacos , Morte Celular/efeitos da radiação , Ibuprofeno/farmacologia , Cetoprofeno/farmacologia , Fármacos Fotossensibilizantes/farmacologia , Raios Ultravioleta , Apoptose/efeitos dos fármacos , Linhagem Celular Tumoral , Sobrevivência Celular/efeitos dos fármacos , Sinergismo Farmacológico , Humanos , Ibuprofeno/química , Cetoprofeno/química , Modelos Moleculares , Estrutura Molecular , Fármacos Fotossensibilizantes/química , Relação Estrutura-Atividade , Raios Ultravioleta/efeitos adversos
9.
J Mol Model ; 23(8): 236, 2017 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-28735497

RESUMO

The regioselectivity of the 1,3-dipolar cycloaddition of a model nitrone with a set of dipolarophiles, presenting diverse electronic effects, is analyzed using conceptual density functional theory (DFT) methods. We deviate from standard approaches based on frontier molecular orbitals and formulations of the local hard/soft acid/base principle and use instead the dual descriptor. A detailed analysis is carried out to determine the influence of the way to calculate the dual descriptor, the computational procedure, basis set and choice of method to condensate the values of this descriptor. We show that the qualitative regioselectivity predictions depend on the choice of "computational conditions", something that indicates the danger of using black-box computational set-ups in conceptual DFT studies.

10.
Nucleic Acids Res ; 45(7): 3654-3662, 2017 04 20.
Artigo em Inglês | MEDLINE | ID: mdl-28334906

RESUMO

DNA photolesions constitute a particularly deleterious class of molecular defects responsible for the insurgence of a vast majority of skin malignant tumors. Dimerization of two adjacent thymines or cytosines mostly gives rise to cyclobutane pyrimidine dimers (CPD) and pyrimidine(6-4)pyrimidone 64-PP as the most common defects. We perform all-atom classical simulations, up to 2 µs, of CPD and 64-PP embedded in a 16-bp duplex, which reveal the constrasted behavior of the two lesions. In particular we evidence a very limited structural deformation induced by CPD while 64-PP is characterized by a complex structural polymorphism. Our simulations also allow to unify the contrasting experimental structural results obtained by nuclear magnetic resonance or Förster Resonant Energy Transfer method, showing that both low and high bent structures are indeed accessible. These contrasting behaviors can also explain repair resistance or the different replication obstruction, and hence the genotoxicity of these two photolesions.


Assuntos
Reparo do DNA , Dímeros de Pirimidina/química , DNA de Forma B/química , Simulação de Dinâmica Molecular , Conformação de Ácido Nucleico
11.
Nucleic Acids Res ; 45(4): 2188-2195, 2017 02 28.
Artigo em Inglês | MEDLINE | ID: mdl-27986856

RESUMO

Oxidatively-generated interstrand cross-links rank among the most deleterious DNA lesions. They originate from abasic sites, whose aldehyde group can form a covalent adduct after condensation with the exocyclic amino group of purines, sometimes with remarkably high yields. We use explicit solvent molecular dynamics simulations to unravel the structures and mechanical properties of two DNA sequences containing an interstrand cross-link. Our simulations palliate the absence of experimental structural and stiffness information for such DNA lesions and provide an unprecedented insight into the DNA embedding of lesions that represent a major challenge for DNA replication, transcription and gene regulation by preventing strand separation. Our results based on quantum chemical calculations also suggest that the embedding of the ICL within the duplex can tune the reaction profile, and hence can be responsible for the high difference in yields of formation.


Assuntos
DNA/química , Simulação de Dinâmica Molecular , Conformação de Ácido Nucleico , Algoritmos , Modelos Moleculares , Estrutura Molecular
12.
Nucleic Acids Res ; 44(18): 8588-8599, 2016 Oct 14.
Artigo em Inglês | MEDLINE | ID: mdl-27587587

RESUMO

Clustered apurinic/apyrimidinic (AP; abasic) DNA lesions produced by ionizing radiation are by far more cytotoxic than isolated AP lesion entities. The structure and dynamics of a series of seven 23-bp oligonucleotides featuring simple bistranded clustered damage sites, comprising of two AP sites, zero, one, three or five bases 3' or 5' apart from each other, were investigated through 400 ns explicit solvent molecular dynamics simulations. They provide representative structures of synthetically engineered multiply damage sites-containing oligonucleotides whose repair was investigated experimentally (Nucl. Acids Res. 2004, 32:5609-5620; Nucl. Acids Res. 2002, 30: 2800-2808). The inspection of extrahelical positioning of the AP sites, bulge and non Watson-Crick hydrogen bonding corroborates the experimental measurements of repair efficiencies by bacterial or human AP endonucleases Nfo and APE1, respectively. This study provides unprecedented knowledge into the structure and dynamics of clustered abasic DNA lesions, notably rationalizing the non-symmetry with respect to 3' to 5' position. In addition, it provides strong mechanistic insights and basis for future studies on the effects of clustered DNA damage on the recognition and processing of these lesions by bacterial or human DNA repair enzymes specialized in the processing of such lesions.


Assuntos
Dano ao DNA , DNA/química , Conformação de Ácido Nucleico , Sequência de Bases , Reparo do DNA , DNA Liase (Sítios Apurínicos ou Apirimidínicos)/metabolismo , Humanos , Simulação de Dinâmica Molecular , Fatores de Tempo
13.
J Phys Chem Lett ; 7(19): 3760-3765, 2016 Oct 06.
Artigo em Inglês | MEDLINE | ID: mdl-27612215

RESUMO

In the present contribution, the interaction between damaged DNA and repair enzymes is examined by means of molecular dynamics simulations. More specifically, we consider clustered abasic DNA lesions processed by the primary human apurinic/apyrimidinic (AP) endonuclease, APE1. Our results show that, in stark contrast with the corresponding bacterial endonucleases, human APE1 imposes strong geometrical constraints on the DNA duplex. As a consequence, the level of recognition and, hence, the repair rate is higher. Important features that guide the DNA/protein interactions are the presence of an extended positively charged region and of a molecular tweezers that strongly constrains DNA. Our results are on very good agreement with the experimentally determined repair rate of clustered abasic lesions. The lack of repair for one particular arrangement of the two abasic sites is also explained considering the peculiar destabilizing interaction between the recognition region and the second lesion, resulting in a partial opening of the molecular tweezers and, thus, a less stable complex. This contribution cogently establishes the molecular bases for the recognition and repair of clustered DNA lesions by means of human endonucleases.


Assuntos
Reparo do DNA , DNA Liase (Sítios Apurínicos ou Apirimidínicos)/metabolismo , DNA/metabolismo , Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Sítios de Ligação , DNA/química , DNA Liase (Sítios Apurínicos ou Apirimidínicos)/química , Humanos , Simulação de Dinâmica Molecular , Conformação de Ácido Nucleico , Estrutura Terciária de Proteína , Especificidade por Substrato
14.
Chemistry ; 22(35): 12358-62, 2016 Aug 22.
Artigo em Inglês | MEDLINE | ID: mdl-27440482

RESUMO

Oxidatively generated DNA lesions are numerous and versatile, and have been the subject of intensive research since the discovery of 8-oxoguanine in 1984. Even for this prototypical lesion, the precise mechanism of formation remains elusive due to the inherent difficulties in characterizing high-energy intermediates. We have probed the stability of the guanine endoperoxide in B-DNA as a key intermediate and determined a unique activation free energy of around 6 kcal mol(-1) for the formation of the first C-O covalent bond upon the attack of singlet molecular oxygen ((1) O2 ) on the central guanine of a solvated 13 base-pair poly(dG-dC), described by means of quantum mechanics/molecular mechanics (QM/MM) simulations. The B-helix remains stable upon oxidation in spite of the bulky character of the guanine endoperoxide. Our modeling study has revealed the nature of the versatile (1) O2 attack in terms of free energy and shows a sensitivity to electrostatics and solvation as it involves a charge-separated intermediate.


Assuntos
DNA de Forma B/química , Guanina/análogos & derivados , Polidesoxirribonucleotídeos/química , Oxigênio Singlete/química , Pareamento de Bases , DNA de Forma B/metabolismo , Guanina/química , Simulação de Dinâmica Molecular , Oxirredução
16.
Phys Chem Chem Phys ; 18(2): 982-90, 2016 Jan 14.
Artigo em Inglês | MEDLINE | ID: mdl-26662022

RESUMO

In this paper, we show that trans effects in octahedral complexes can primarily be related to differences in the ability, for a given ligand, to cede electron density to the metal cation under the influence of the ligand at the trans position. Using tools from conceptual DFT or from related paradigms, we highlight these effects on a set of representative examples and further provide the basis for a computational trans effect scale. This quantification notably retrieves the experimental trans orienting series.

17.
Nucleic Acids Res ; 44(1): 56-62, 2016 Jan 08.
Artigo em Inglês | MEDLINE | ID: mdl-26656495

RESUMO

The reaction of singlet molecular oxygen with purine DNA bases is investigated by computational means. We support the formation of a transient endoperoxide for guanine and by classical molecular dynamics simulations we demonstrate that the formation of this adduct does not affect the B-helicity. We thus identify the guanine endoperoxide as a key intermediate, confirming a low-temperature nuclear magnetic resonance proof of its existence, and we delineate its degradation pathway, tracing back the preferential formation of 8-oxoguanine versus spiro-derivates in B-DNA. Finally, the latter oxidized 8-oxodGuo product exhibits an almost barrierless reaction profile, and hence is found, coherently with experience, to be much more reactive than guanine itself. On the contrary, in agreement with experimental observations, singlet-oxygen reactivity onto adenine is kinetically blocked by a higher energy transition state.


Assuntos
Modelos Teóricos , Purinas/química , Oxigênio Singlete/química , DNA/química , Simulação de Dinâmica Molecular , Oxirredução , Teoria Quântica
18.
Chemphyschem ; 16(15): 3151-5, 2015 Oct 26.
Artigo em Inglês | MEDLINE | ID: mdl-26289662

RESUMO

Proton transfer (PT) from protonated pyridine to water molecules is observed after excitation of microhydrated protonated pyridine (Py) clusters PyH(+) (H2 O)n (n=0-5) is induced by a single collision with an Ar atom at high incident velocity (95×10(3)  m s(-1) ). Besides the fragmentation channel associated with the evaporation of water molecules, the charged-fragment mass spectrum shows competition between the production of the PyH(+) ion (or its corresponding charged fragments) and the production of H(+) (H2 O) or H(+) (H2 O)2 ions. The increase in the production of protonated water fragments as a function of the number of H2 O molecules in the parent cluster ion as well sd the observation of a stable H(+) (H2 O)2 fragment, even in the case of the dissociation of PyH(+) (H2 O)2 , are evidence of the crucial role of PT in the relaxation process, even for a small number of solvating water molecules.


Assuntos
Piridinas/química , Água/química , Prótons , Solubilidade
19.
Chemistry ; 21(32): 11509-16, 2015 Aug 03.
Artigo em Inglês | MEDLINE | ID: mdl-26133111

RESUMO

The main chromophore of (6-4) photoproducts, namely, 5-methyl-2-pyrimidone (Pyo), is an artificial noncanonical nucleobase. This chromophore has recently been reported as a potential photosensitizer that induces triplet damage in thymine DNA. In this study, we investigate the spectroscopic properties of the Pyo unit embedded in DNA by means of explicit solvent molecular-dynamics simulations coupled to time-dependent DFT and quantum-mechanics/molecular-mechanics techniques. Triplet-state transfer from the Pyo to the thymine unit was monitored in B-DNA by probing the propensity of this photoactive pyrimidine analogue to induce a Dexter-type triplet photosensitization and subsequent DNA damage.


Assuntos
Dano ao DNA/efeitos dos fármacos , DNA/efeitos dos fármacos , DNA/efeitos da radiação , Desoxirribonucleosídeos/química , Desoxirribonucleosídeos/farmacologia , Transtornos de Fotossensibilidade/induzido quimicamente , Fármacos Fotossensibilizantes/química , Fármacos Fotossensibilizantes/farmacologia , DNA/química , Transferência de Energia , Estrutura Molecular , Processos Fotoquímicos
20.
Phys Chem Chem Phys ; 17(14): 9359-68, 2015 Apr 14.
Artigo em Inglês | MEDLINE | ID: mdl-25760399

RESUMO

The electron density changes from reactants towards the transition state of a chemical reaction is expressed as a linear combination of the state-specific dual descriptors (SSDD) of the corresponding reactant complexes. Consequently, the SSDD can be expected to bear important resemblance to the so-called natural orbitals for chemical valence (NOCV), introduced as the orbitals that diagonalize the deformation density matrix of interacting molecules. This agreement is shown for three case studies: the complexation of a Lewis acid with a Lewis base, a SN2 nucleophilic substitution reaction and a Diels-Alder cycloaddition reaction. As such, the SSDD computed for reactant complexes are shown to provide important information about charge transfer interactions during a chemical reaction.


Assuntos
Elétrons , Ácidos de Lewis/química , Teoria Quântica , Modelos Moleculares , Conformação Molecular
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