The nature of Ru-NO bonds in ruthenium tetraazamacrocycle nitrosyl complexes-a computational study

Ruthenium complexes including nitrosyl or nitrite complexes are particularly interesting because they can not only scavenge but also release nitric oxide in a controlled manner, regulating the NO-level in vivo. The judicious choice of ligands attached to the [RuNO] core has been shown to be a suitable strategy to modulate NO reactivity in these complexes. In order to understand the influence of different equatorial ligands on the electronic structure of the Ru-NO chemical bonding, and thus on the reactivity of the coordinated NO, we propose an investigation of the nature of the Ru-NO chemical bond by means of energy decomposition analysis (EDA), considering tetraamine and tetraazamacrocycles as equatorial ligands, prior to and after the reduction of the {RuNO}(6) moiety by one electron. This investigation provides a deep insight into the Ru-NO bonding situation, which is fundamental in designing new ruthenium nitrosyl complexes with potential biological applications.FAPESCCNPq [17.413/2009-0]CAPESFAPESB (Processo PPP039/2010)FAPESP (Processo 2006/53266-4

The nature of Ru-NO bonds in ruthenium tetraazamacrocycle nitrosyl complexes-a computational study

Ruthenium complexes including nitrosyl or nitrite complexes are particularly interesting because they can not only scavenge but also release nitric oxide in a controlled manner, regulating the NO-level in vivo. The judicious choice of ligands attached to the [RuNO] core has been shown to be a suitable strategy to modulate NO reactivity in these complexes. In order to understand the influence of different equatorial ligands on the electronic structure of the Ru-NO chemical bonding, and thus on the reactivity of the coordinated NO, we propose an investigation of the nature of the Ru-NO chemical bond by means of energy decomposition analysis (EDA), considering tetraamine and tetraazamacrocycles as equatorial ligands, prior to and after the reduction of the {RuNO}(6) moiety by one electron. This investigation provides a deep insight into the Ru-NO bonding situation, which is fundamental in designing new ruthenium nitrosyl complexes with potential biological applications.FAPESCCNPq [17.413/2009-0]CAPESFAPESB (Processo PPP039/2010)FAPESP (Processo 2006/53266-4

Computational Study of [2.2]cyclophanes

Neste trabalho foram estudados computacionalmente os [2.2]ciclofanos ([2.2]paraciclofano (1), anti-[2.2]metaciclofano (2a), sin-[2.2]metaciclofano (2b) e [2.2]metaparaciclofano (3)), que são os [2n]ciclofanos mais simples, contendo dois anéis fenílicos conectados por duas pontes etilênicas. Os ciclofanos têm apresentado inúmeras aplicações importantes, podendo atuar como auxiliares em sínteses assimétricas e como catalisadores que simulam funções enzimáticas, apresentando seletividade em relação aos substratos. Eles são empregados tanto em químicab supramolecular quanto em áreas biomédicas. Estudos que empregam ressonância de spin eletrônico ou que investigam propriedades ópticas não-lineares dos [2.2]ciclofanos indicam que os mesmos apresentam interações transanulares, que ocorrem através de recobrimento direto entre orbitais pertencentes a anéis diferentes, through-space, ou através de recobrimento entre orbitais dos anéis e das pontes, through-bond. As interações transanulares possuem um papel fundamental na química dos ciclofanos, alterando o comportamento reacional destes compostos e as transições espectroscópicas. Apesar dos métodos de preparação de ciclofanos, desde os mais simples aos mais complexos, serem intensamente investigados, estudos computacionais, que busquem compreender as correlações entre tensão e aromaticidade, estrutura eletrônica e o mecanismo de ocorrência das interações transanulares, são raramente encontrados na literatura. Desse modo, o objetivo deste trabalho foi estudar as interações transanulares, bem como correlacionar as diferenças estruturais, a tensão sobre anéis e pontes, cargas atômicas, aromaticidade e os deslocamentos químicos, não apenas para os isômeros dos [2.2]ciclofanos, mas também seus derivados fluorados (perfluoração de um dos anéis dos [2.2]ciclofanos), bem como avaliar os efeitos de diversos substituintes (CN, Cl, C=O, NH2 e NO2) e da protonação na estrutura eletrônica do isômero [2.2]paraciclofano. As otimizações de geometria de 1, realizadas com diferentes métodos e conjuntos de funções de base, mostraram que os modelos MP2/6-31+G(d,p) e B3PW91/6-31+G(d,p) fornecem os melhores resultados em comparação com os dados de raios-x. Buscas conformacionais mostraram que 2a e 2b são confôrmeros com energias diferentes e que 3 possui dois confôrmeros degenerados. As energias relativas e de tensão das pontes, seguiram a mesma ordem, indicando que a tensão sobre as pontes e a repulsão entre as nuvens ? dos anéis aromáticos são determinantes para a estabilidade dos [2.2]ciclofanos. As reações isodésmicas indicaram que os anéis comportam-se como absorvedores de tensão. NICS e HOMA mostraram que apesar das perdas de planaridade dos anéis a aromaticidade é mantida. O método NBO confirmou que todos os [2.2]ciclofanos apresentam interações through-bond, mas apenas 2a e 2b apresentaram interações through-space significantes. A análise AIM mostrou que as interações transanulares observadas são do tipo camada fechada (iônica ou ligação de hidrogênio) e que estabilizam os [2.2]ciclofanos. Para os derivados fluorados as principais alterações geométricas observadas foram para os diedros das pontes. As reações isodésmicas revelaram que as tensões das pontes e as energias relativas são afetadas pela fluoração. Além disso, os anéis dos isômeros fluorados absorvem mais tensão que os anéis dos isômeros não fluorados. NICS e HOMA mostraram que a substituição por flúor aumenta a aromaticidade dos [2.2]ciclofanos. A análise NBO indicou que a perfluoração aumentou o número e a intensidade das interações through-space, mas as mesmas ficaram restritas principalmente aos derivados fluorados de 2a e 2b. A mesma análise evidenciou que há uma conjugação dos pares de elétrons dos átomos de flúor com o sistema ?. Por outro lado, a análise AIM sugeriu que a substituição não aumenta o número de interações through-space, mas confirmou a conjugação dos pares de elétrons dos átomos de flúor. Os demais substituintes empregados afetam os parâmetros geométricos do [2.2]paraciclofano (1) de maneira diferenciada. A análise particionada das reações isodésmicas mostrou que as tensões nos anéis e nas pontes dependem não apenas do substituinte empregado, mas também da posição da substituição. NICS e HOMA indicaram que a aromaticidade no anel não-substituído dos derivados substituídos é maior que em 1. A análise NBO revelou que a substituição e a protonação aumentam a ocorrência de interações transanulares through-space. O método AIM indicou a presença de interações transanulares apenas para o derivado substituído com NH2 e CN e para a espécie protonada. No entanto, tais interações apresentaram características de interações de camada fechada. com pequenas estabilizações. As cargas atômicas e os deslocamentos químicos confirmaram as mudanças na densidade eletrônica, observadas através do método AIM.In this work, the [2.2]cyclophanes ([2.2]paracyclophane (1), anti-[2.2]metacyclophane (2a), syn-[2.2]metacyclophane (2b) e [2.2]metaparacyclophane (3)), which are the simplest [2n] cyclophanes that contain two phenyl rings connected by two ethanediyl linkages, were studied computationally. Cyclophanes have presented several important applications, such as auxiliary in asymmetric synthesis, catalysts that simulate enzymatic functions, presenting selectivity in relation to the substrates. They are employed either in supramolecular chemistry or in biomedical areas. Studies that apply electron spin resonance or that investigate the non-linear optical properties of [2.2]cyclophanes, indicate that these compounds present transannular interactions, which occur through direct overlap of orbitals lying in different rings, throughspace, or through overlap between orbitals from rings and bridges, through-bond. The transannular interactions have a fundamental role in cyclophane chemistry, changing the reactional behavior of these compounds, and the spectroscopic transitions. Despite the fact that the well known methods of preparation, from the simplest to the most complex cyclophanes, have been studied intensively, computational studies that intent to comprehend the correlations between tension and aromaticity, electronic structure, and the mechanism of the transannular interactions are rarely found in the literature. Therefore, the aim of this work was not only to study the transannular interactions, correlating the structural differences, tension in rings and bridges, atomic charges, aromaticity, and chemical shifts of the [2.2]cyclophanes isomers but also to extent a similar treatment to the fluorinated derivatives. In addition, the effects of substituents such as (CN, Cl, C=O, NH2, and NO2) and the protonation on the electronic structure of [2.2]paracyclophane were also evaluated. The geometry optimizations of 1, carried out by using different methods and basis set, showed that the models MP2/6-31+G(d,p) and B3PW91/6-31+G(d,p) provide the best results in comparison with the x-ray data. Conformational searches showed that 2a and 2b are the conformers that present the same energy and the isomer 3 has two degenerated conformers. The strain energies of the bridges followed the same tendency as the relative energies, indicating that the tension on the bridges and the repulsions between the ? clouds of the aromatic rings are the key factors that determine the [2.2]cyclophane stabilities. The isodesmic reactions indicated that the rings are absorbents of tension. NICS and HOMA showed that the aromaticity of the rings is preserved despite the changes on the planarity. The NBO method confirmed that all [2.2]cyclophanes present through-bond interactions, but only 2a and 2b exhibit noteworthy through-space interactions. The AIM analysis pointed out that the transannular interactions behave as closed shell interactions (ionic or hydrogen bond), stabilizing the [2.2]cyclophanes. The main geometric changes, observed to the fluorinated derivatives, were those related with the dihedral angle of bridges. The isodesmic reactions pointed out that the tensions of bridges and the relative energies are affected by the fluorination. In addition, the fluorinated rings absorb more tension than the non-fluorinated rings. NICS and HOMA showed that the substitution by fluorine increases the aromaticity of the [2.2]cyclophanes. The NBO analysis indicated that the number of through-space interactions increase with the fluorination, but it is restrict to the derivatives of 2a and 2b. In addition, the same analysis pointed out a conjugation of the fluorine lone pairs with the ? system. On the other hand, the AIM analysis suggested that the substitution do not increase the number of through-space interactions, but confirmed the conjugation of the fluorine lone pairs. The other substituents can affect the geometric parameter of 1 noticeably. The partitioned analysis of isodesmic reactions showed that the tensions in bridges and rings not only depend on the substituents employed but also on the position of substitution. NICS and HOMA pointed out that the aromaticity is bigger in the non-substituted rings of [2.2]paracyclophane derivatives than in 1. The NBO analysis showed that the substitution and protonation increase the number of through-space interactions. AIM method indicated the transannular interactions occur only to the derivate substituted by NH2 and CN, and to the protonated specie. However, these interactions presented features of closed shell interactions with small stabilizations. The atomic charges and the chemical shifts confirmed the changes of the electronic density, observed through the AIM method

Aromaticidade: evolução histórica do conceito e critérios quantitativos

In this paper the evolution of the concept of aromaticity is discussed. It considers not only historical aspects of the aromaticity concept but also the different criteria (theoretical and experimental) that have appeared to explain the properties of the aromatic compounds. The topics range from the isolation of benzene by Faraday (1825) until the modern criteria based on geometries, magnetic properties, resonance energy (RE), aromatic stabilization energy (ASE), topological analyses, and others. A chronological separation of issues concerning aromaticity was made, splitting the definitions before and after the appearance of the quantum chemistry. This work reviews the concept of aromaticity

Bond analysis in dihalogen–halide and dihalogen– dimethylchalcogenide systems

The bonding in mixed chalcogen/halogen three- body systems of general formula XI···Y (X = Cl, Br, I; Y = I–, EMe2; E = S, Se, Te) is theoretically examined by using different methodologies, namely: charge-displacement (CD) analysis, which quantifies the electronic flux throughout the whole ad- duct; the energy decomposition analysis combined with natural orbital for chemical valence (EDA-NOCV) method; and zeroth order symmetry adapted perturbation theory (SAPT0), where the latter two methods decompose the contributions of the interaction energy between XI and Y into physically meaningful terms. In the solid state, the distribution of the relative elonga- tions of the two bonds (δXI and δIY) in the three-body systems examined here can be rationalized in terms of only one com- mon equation derived from the bond-valence model. According to CD and EDA-NOCV, the charge transfer between the two fragments does not depend on the exact nature of the atoms involved, but only on the values of δXI and δIY, with a variability of 0.05 e, and on the total charge of the system. On the other hand, using the SAPT0 method and computing the polariza- tion-free value of the charge transfer between the two frag- ments, the results are the same for all of the systems with the same δXI and δIY, irrespectively not only of the nature of the atoms, but also of the total charge of the system (anionic and neutral)

Oxindole-Schiff base copper(II) complexes interactions with human serum albumin: Spectroscopic, oxidative damage, and computational studies

CD and EPR were used to characterize interactions of oxindole-Schiff base copper(II) complexes with human serum albumin (HSA). These imine ligands form very stable complexes with copper, and can efficiently compete for this metal ion towards the specific N-terminal binding site of the protein, consisting of the amino acid sequence Asp-Ala-His. Relative stability constants for the corresponding complexes were estimated from CD data, using the protein as competitive ligand, with values of log K(CuL) in the range 15.7-18.1, very close to that of [Cu(HSA)] itself, with log K(CuHSA) 16.2. Some of the complexes are also able to interfere in the a-helix structure of the protein, while others seem not to affect it. EPR spectra corroborate those results, indicating at least two different metal species in solution, depending on the imine ligand. Oxidative damage to the protein after incubation with these copper(II) complexes, particularly in the presence of hydrogen peroxide, was monitored by carbonyl groups formation, and was observed to be more severe when conformational features of the protein were modified. Complementary EPR spin-trapping data indicated significant formation of hydroxyl and carbon centered radicals, consistent with an oxidative mechanism. Theoretical calculations at density functional theory (DFT) level were employed to evaluate Cu(II)-L binding energies, L -> Cu(II) donation, and Cu(II) -> L back-donation, by considering the Schiff bases and the N-terminal site of HSA as ligands. These results complement previous studies on cytotoxicity, nuclease and pro-apoptotic properties of this kind of copper(II) complexes, providing additional information about their possibilities of transport and disposition in blood plasma. (C) 2009 Elsevier Inc. All rights reserved

A theoretical investigation on the aminolysis of pyromellitic and 1,4,5,8-naphthalenetetracarboxylic dianhydrides

Aniline aminolysis reaction of pyromellitic (PMDA) and 1,4,5,8-naphthalenetetracarboxylic (NTDA) dianhydrides is investigated by means of density functional theory (BP86-D3(BJ)/def2-TZVP). The concerted mechanism is shown to be more favorable for both substrates, in comparison to the stepwise one, with the aminolysis of PMDA presenting lower activation energy than the reaction of NTDA. This result is shown to be related to the lower ring tension in NTDA. Solvation also shows significant influence on the kinetics and thermodynamics of these reactions, as determined by two different methods, implicit with the universal solvation model SMD, and explicit with alchemical FEP molecular dynamics simulations. The comparison between SMD and FEP enables us to explore possible inaccuracies on the SMD model, and examine the suitability of the FEP approach as a physics-based method for the calculation of the solvent contribution in different reactions11471319CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO - CNPQFUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPESPFUNDAÇÃO DE AMPARO À PESQUISA E INOVAÇÃO DO ESTADO DE SANTA CATARINA - FAPESC140485/2017-1; 311963/2017-02010/18268-1não te

Synthesis, Characterization and Biological Evaluation of New Manganese Metal Carbonyl Compounds That Contain Sulfur and Selenium Ligands as a Promising New Class of CORMs

Three new manganese carbonyl compounds with heavy atom donors were synthesized and their potential use as photoCORMS was evaluated. Interestingly, all compounds had an elusive binding mode, in which the ligands adopted a κ2-X coordination (where X = S or Se), confirmed both by X-ray crystallography and IR spectroscopy. The stability of the title compounds in the dark was determined by monitoring the changes in the UV spectra of the compounds in both dichloromethane and acetonitrile. These studies show that in coordinating solvents there is an exchange of the bromide bonded to the metal centre by a solvent molecule, which is evidenced by the changes in the UV and IR spectra and by DFT analysis. EDA and natural bond order analyses were conducted to evaluate the influence of the heavy atom donors in the first coordination sphere of the compounds. Photoexcitation at 380 nm demonstrated that all compounds showed release of all three COs, as seen in the photoproducts detected by IR spectroscopy. Furthermore, CO release was observed when the photoCORMs were incubated with living cells, and we observed a CO-dependent inhibition of cell viability.Funded under the Brazilian governmental agencies CNPq (PVE - 400210/2014-2), CNPq, and CERSusChem GSK/FAPESP (grant 2014/50249-8) grants for A. Neves, A. L. Braga, A. L. Amorim and R. A. Peralta, CAPES (Finance Code 001). We also thank the FAPESC, EU Horizon 2020 programme, Marie Skłodowska-Curie ITN GA no. 675007 and TWINN-2017 ACORN, GA no. 807281, the Royal Society (UF110046 and URF\R\180019 to G. J. L. B.), FCT Portugal (iFCT IF/00624/2015 to G. J. L. B. and PhD studentship SFRH/BD/115932/2016 to A. G.), and an ERC StG (GA no. 676832) for funding

How does the acidic milieu interfere in the capability of ruthenium nitrosyl complexes to release nitric oxide?

The nitric oxide (NO) molecule is involved in a large number of biological routes. Thus, there is increasing interest in improving the understanding of the NO release mechanisms. One of the traditional NO release mechanisms involves (i) [Ru(NO)(NH3)5]3+ + e− → [Ru(NO)(NH3)5]2+ and (ii) [Ru(NO)(NH3)5]2+ + H2O → [Ru(H2O)(NH3)5]2+ + NO chemical reactions. Another possibility is associated with light irradiation: (iii) [Ru(NO)(NH3)5]3+ + H2O + hν → [Ru(H2O)(NH3)5]3+ + NO, aided by the Ru(dπ) → π*(NO) electronic transition, which decreases the π back-donation process in the Ru–NO chemical bond. The influence of the acid environment in which these chemical reactions typically occur experimentally has been explored in (iv) [Ru(NO)(NH3)5]2+ + H3O+ → [Ru(HNO)(NH3)5]3+ + H2O; and (v) [Ru(HNO)(NH3)5]3+ + H2O → [Ru(H2O)(NH3)5]3+ + HNO reactions. Reaction (v), supported by eight explicit water molecules, is the most propitious to occur. The HNO charge obtained from the atomic polar tensor scheme is close to zero. The methods of quantum theory of atoms in molecules and non-covalent interactions reveal that the HNO leaving group interacts with two water molecules through partially covalent or ionic chemical bonds. The HNO → NO conversion after the release from ruthenium molecules is thermodynamically feasible. The electronic spectrum of the structure [Ru(HNO)(NH3)5]3+ has, unlike the [Ru(NO)(NH3)5]3+ molecule, the Ru(dπ) → π*(NO) transition with an appropriate absorbance. Therefore, the proton increases the capability of ruthenium complexes to release nitric oxide after the chemical reduction reaction or the light-supported chemical reaction443773779CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO - CNPQCOORDENAÇÃO DE APERFEIÇOAMENTO DE PESSOAL DE NÍVEL SUPERIOR - CAPESFUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPESPFUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DO RIO GRANDE DO SUL - FAPERGS001; 2011/07623-8; 2017/24856; 22019/00543-0; 2013/08293-7306297/2018-3; 311963/2017-0; 303581/2018-2Não temNão temThis study was financed in part by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior – Brasil (CAPES) Finance Code 001. RLTP, RPO, GCGS and NHM thank grants 2011/07623-8, 2017/24856-2, 2019/00543-0, and 2013/08293-7 São Paulo Research Foundation (FAPESP) for the financial support. GN and MJP thank the Rio Grande do Sul Research Foundation (FAPERGS), National Council for Scientific and Technological Development (CNPq, 306297/2018-3). GFC and NHM thank CNPq (311963/2017-0, and 303581/2018-2, respectively) for the research fellowship. JCG thanks CALSIMLAB under the public grant ANR-11-LABX-0037-01, overseen by the French National Research Agency (ANR) as part of the Investissements d'Avenir program (reference: ANR-11-IDEX-0004-02

On the recognition of chloride, bromide and nitrate anions by anthracene-squaramide conjugated compounds: a computational perspective

Anion recognition is widely used in several biological fields. Squaramide derived compounds appear as potential structures to recognize anions. Here, the bond mechanisms between the chloride (Cl-), bromide (Br-) and nitrate (NO3-) anions and anthracene-squaramide conjugated compounds are elucidated considering the influence of the: (i) number, (ii) nature, and (iii) position of the substituents: trifluoromethyl (-CF3) and nitro (-NO2). Energy decomposition analysis (EDA) shows that the interactions between Cl-, Br- and NO3- and anthracene-squaramide have an attractive interaction energy supported predominantly by electrostatic energy followed by orbital contribution. Molecular electrostatic potential (MEP) surfaces imply electrostatic interactions between Cl-, Br- and the oxygen atom from NO3- and the hydrogen atoms from N-H and C-H bonds present in the squaramide structure, and an aryl group, respectively. Cl- interacts with the receptors more strongly than Br-. The NO3- recognition is less attractive than those presented by Cl- and Br-, in agreement with the hardness-softness features of these anions. Importantly, one and, mostly, two group substitutions, -H -> -CF3 or -NO2, favor the recognition of Cl-, Br- and NO3- due to the increase of the polarization in the receptor-NHMIDLINE HORIZONTAL ELLIPSISanion interaction. The -NO2 group promotes a larger effect relative to the -CF3 ligand. The -NO2 ligand positioned at the largest distance conceivable to the benzene-NH group promotes the lowest interference in the N-HMIDLINE HORIZONTAL ELLIPSISCl- interaction. These results provide information to design receptors with a larger capability to recognize anions.CoordenacAo de Aperfeicoamento de Pessoal de Nivel Superior - Brasil (CAPES) Finance 001 Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP) 2011/07623-8 2017/24856-2 2019/19175-1 National Council for Scientific and Technological Development (CNPq) 313648/2018-2 Foundation for Research Support of the State of Rio Grande do Sul (FAPERGS) National Council for Scientific and Technological Development (CNPq) 306297/2018-3 430364/2018-0 LabEx CALSIMLAB ANR-11-LABX-0037-01 ANR-11-IDEX-0004-02 Comision Nacional de Investigacion Cientifica y Tecnologica (CONICYT) CONICYT FONDECYT 1181121 Centers of Excellence with Basal/Conicyt Financing FB0807 National Council for Scientific and Technological Development (CNPq) 311963/2017-