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Non-covalent intermolecular interactions responsible for chiral discrimination have been investigated in the gas phase both in neutral and ionic complexes. Mass-selected resonant two-photon ionization (R2PI) as well as infrared depleted R2PI (IR-R2PI) techniques have been applied to investigate the role of fluorine substitution in the chiral recognition process between (R)-1-phenyl 1-ethanol (ER), (S)-1-(4-fluorophenyl)-ethanol (pFE S), (R)-1-phenyl-2,2,2-trifluoroethanol (FER) and the two enantiomers of butan-2-ol (BR/S), generated in a supersonic molecular beam. The results have been interpreted with the aid of theoretical predictions at the D-B3LYP/6-31G**level of theory. The diastereomeric complexes of ER and pFES with R- and S-butan-2-ol are structurally similar, and dispersive interactions between the aliphatic chain of the alcohol and the π system of the chromophore as well repulsive interactions are mainly responsible for chiral recognition. FER forms, predominantly with S-butan-2-ol, also stable complexes in which the alcohol is oriented away from the aromatic ring. The ionic complexes between pure enantiomers of the bis (diamido)-bridged basket resorcin[4]arene and cytarabine are generated in the gas phase by electrospray ionization and investigated by IRMPD. The proton-bound diastereomers show clearly different IRMPD spectra which, in light of ONIOM (B3LYP/6-31(d):UFF) calculations, are consistent with the occurrence of several isomeric structures, in which the N(3)-protonated guest is either accommodated inside the host cavity or outside it. The spectral differences are attributed to the effects of the intramolecular hydrogen bonding between the C(2′) -OH group and the aglycone oxygen atom of the nucleosidic guest upon repulsive interactions between the same oxygen atom and the aromatic rings of the host. © 2013 Accademia Nazionale dei Lincei.

Crystal structures are presented for two members of the homologous series of 1,2-dibromo-4,5-dialkoxybenzenes, viz. those with decyloxy and hexadecyloxy substituents, namely 1,2-dibromo-4,5-bis(decyloxy)benzene, C26H44Br2O2, (II), and 1,2-dibromo-4,5-bis(hexadecyloxy) benzene, C38H68Br2O2, (III). The relative influences which halogen bonding, pi-pi stacking and van der Waals interactions have on these structures are analysed and the results compared with those already found for the lightest homologue, 1,2-dibromo-4,5-dimethoxybenzene, (I) [Cukiernik, Zelcer, Garland & Baggio (2008). Acta Cryst. C64, o604-o608]. The results confirm that the prevalent interactions stabilizing the structures of (II) and (III) are van der Waals contacts between the aliphatic chains. In the case of (II), weak halogen C-Br center dot center dot center dot(Br-C)´ interactions are also present and contribute to the stability of the structure. In the case of (III), van der Waals interactions between the aliphatic chains are almost exclusive, weaker C-Br center dot center dot center dot pi interactions being the only additional interactions detected. The results are in line with commonly accepted models concerning trends in crystal stability along a homologous series (as measured by their melting points), but the earlier report for n = 1, and the present report for n = 10 and 16, are among the few providing single-crystal information validating the hypothesis. Fil: Fonrouge, Ana. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Industrias; Argentina; Fil: Cecchi, Florencia. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Industrias; Argentina; Fil: Alborés, Pablo. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Industrias; Argentina; Fil: Cukiernik, Fabio Daniel. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Industrias; Argentina; Fil: Baggio, Ricardo Fortunato. Comisión Nacional de Energía Atómica; Argentina

Since its introduction in the market in 2002, fondaparinux (Arixtra®) is a drug of choice in the anticoagulant therapy. Its structure corresponds to the heparin pentasaccharide sequence that mediates its interaction with the natural plasma inhibitor of coagulation, antithrombin. However, like heparin, its application is limited due its unique administration by parenteral route. The aim of this project is to develop an efficient oral delivery system for fondaparinux by association with a squalene derivative. Squalene, a natural precursor of cholesterol in sterol biosynthesis, is well-known for its excellent oral absorption (i.e. more than 60 %). In this context, two strategies were investigated. The first consisted in achieving a covalent coupling between fondaparinux and a squalene derivative according to the concept of “squalenoylation”. The second was to associate fondaparinux to a cationic squalenoyl derivative by non-covalent association.Experimental work showed that the first strategy was delicate to implement due to the difficulty to synthesize a fondaparinux-squalene bioconjugate and, the loss of the anticoagulant properties of fondaparinux. Because of these obstacles, the concept of "squalenoylation" was not suitable for this type of active molecule. In contrast, the second strategy has been very promising. It consisted in the formulation of a nanoparticulate delivery system by ion-pairing of fondaparinux and a cationic squalenoyl derivative. This approach permitted to highlight the self-assembly of these two compounds in water as monodisperse nanoparticles thanks to electrostatic and hydrophobic interactions. Furthermore, the oral absorption of fondaparinux was significantly increased with this new nanoparticulate system. This new squalene-based approach has shown its effectiveness in improving the oral administration of fondaparinux and could be a potential delivery system in the treatment of thromboembolic diseases.; Le fondaparinux (Arixtra®), anticoagulant de la classe des pentasaccharides de synthèse, est le premier inhibiteur d'origine synthétique, spécifique et indirect du facteur Xa de la coagulation. Il résulte de la synthèse chimique de l'unité pentasaccharidique des héparines, capable de se lier à l'antithrombine, une protéine endogène, inhibitrice de la coagulation. Cependant, son utilisation reste limitée par son administration uniquement possible par voie parentérale.L'objectif de ce travail de thèse est de développer une forme orale du fondaparinux en l'associant à un dérivé squalénique. Le squalène, terpénoïde naturel précurseur de la synthèse du cholestérol, possède une très bonne absorption orale (supérieure à 60 %). Dans ce contexte, deux stratégies d'association ont été développées: la première consistant à associer par liaison covalente le fondaparinux à un dérivé squalénique selon le concept de la « squalénisation » et la deuxième à associer par interactions non covalentes le fondaparinux à un dérivé squalénique cationique.Les travaux expérimentaux ont montré que la première stratégie était délicate à mettre en œuvre en raison d'une part de la difficulté à synthétiser un bioconjugué fondaparinux-squalène et d'autre part de la perte de l'activité anticoagulante du fondaparinux. En raison de ces obstacles, le concept de la « squalénisation » n'est pas adapté à ce type de molécule active. En revanche, la deuxième stratégie s'est montrée très prometteuse. Elle a consisté à formuler des nanoparticules par association non covalente du fondaparinux, chargé négativement, à un dérivé squalénique cationique. Cette approche a permis de mettre en évidence l’excellente capacité d'auto-assemblage en milieu aqueux de ces deux composés, liée à l’établissement de deux types d’interactions, électrostatiques et hydrophobes (entre les molécules de squalène). L'absorption orale du fondaparinux a été considérablement augmentée grâce à ce nouveau système nanoparticulaire. Cette nouvelle approche à base de squalène a ainsi montré son efficacité dans l'amélioration de l'administration orale du fondaparinux et pourrait représenter un système thérapeutique potentiel dans le traitement des maladies thromboemboliques.

Theoretical and compelling experimental evidence indicates that the interaction between an anion and an aromatic π system when the anion is directly above the ring face (“η6”-type anion–π), can be attractive. This may play an important role in the formation and recognition of biomolecular structures. We examined high-resolution structures of proteins and nucleic acids for the presence of “η6”-type anion–π. Though less frequent than its counterpart cation–π, “η6”-type anion–π is observed unambiguously, occurring in protein/nucleic acid loops and often involving conserved/coevolving sites in proteins, suggesting it plays an important role in macromolecular folding and function.

The development of Fourier transform microwave (FTMW) spectroscopy and — most notably — its combination with supersonic-jet expansion techniques allow for challenging investigations of larger and larger interesting molecular systems. Large isolated molecules studied by microwave (MW) spectroscopy include long carbon chains of astronomical interest, organic molecules containing two or more aromatic rings, small biomolecules, and transition metal complexes. Often, these systems are characterized by large-amplitude motions and multifolded conformational and tautomeric equilibria. Rotational spectra have been reported for many large molecular complexes, such as adducts of large organic and biological molecules with rare gases, water (or other small proton donors/acceptors), and oligomers and hetero adducts of large molecules. Some of these complexes have interaction energies that are in the intermediate regime between bonding and nonbonding (charge-transfer complexes), and some of them, involving chiral molecules, act as a guide to understanding molecular recognition. In addition, the rotational spectra of several carbonyl sulfide (OCS)Hen species have been measured (up to n = 39), providing useful data to model superfluidity. The potentiality of MW spectroscopy to obtain spectroscopic and chemical information on these systems is demonstrated by numerous investigations. Many interesting examples, most of them achieved in the last two decades, have been compiled here. Keywords: Fourier transform spectroscopy; supersonic expansions; long-chain molecules; astrophysical molecules; fused-ring molecules; transition metal complexes; biomolecules; molecular complexes; van der Waals complexes; molecular aggregation; molecular solvation; quantum solvation; oligomers; hydrogen bonding; noncovalent interaction; charge transfer; molecular recognition

2-Cys peroxiredoxins (2-Cys Prxs) are ubiquitous peroxidases with important roles in cellular antioxidant defense and hydrogen peroxide-mediated signaling. Post-translational modifications of conserved cysteines cause the transition from low to high molecular weight oligomers, triggering the functional change from peroxidase to molecular chaperone. However, it remains unclear how non-covalent interactions of 2-Cys Prx with metabolites modulate the quaternary structure. Here, we disclose that ATP and Mg2+ (ATP/Mg) promote the self-polymerization of chloroplast 2-Cys Prx (polypeptide 23.5 kDa) into soluble higher order assemblies (>2 MDa) that proceed to insoluble aggregates beyond 5mMATP. Remarkably, the withdrawal of ATP or Mg2+ brings soluble oligomers and insoluble aggregates back to the native conformation without compromising the associated functions. As confirmed by transmission electron microscopy, ATP/Mg drive the toroid-like decamers (diameter 13 nm) to the formation of large sphere-like particles (diameter ∼30 nm). Circular dichroism studies on ATP-labeled 2-Cys Prx reveal that ATP/Mg enhance the proportion of β-sheets with the concurrent decrease in the content of α-helices. In line with this observation, the formation of insoluble aggregates is strongly prevented by 2,2,2-trifluoroethanol, a cosolvent employed to induce α-helical conformations. We further find that the response of self-polymerization to ATP/Mg departs abruptly from that of the associated peroxidase and chaperone activities when two highly conserved residues, Arg129 and Arg152, are mutated. Collectively, our data uncover that non-covalent interactions of ATP/Mg with 2-Cys Prx modulate dynamically the quaternary structure, thereby coupling the non-redox chemistry of cell energy with redox transformations at cysteine residues. © 2011 by The American Society for Biochemistry and Molecular Biology, Inc. Fil:Aran, M. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Mora-García, S. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Wolosiuk, R.A. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina.

Molecular self-assembly is a powerful technique for developing novel nanostructures by using noncovalent interactions such as hydrogen bonding, hydrophobic, electrostatic, metal-ligand, p-p and van der Waals interactions. These interactions are highly dynamic and are often delicate due to their relatively weak nature. However, a sufficient number of these weak interactions can yield a stable assembly. In this work, we studied the mechanical properties of self-assembled peptide amphiphile nanostructures in the nanometre and micrometre scale. Hydrogen bonding, hydrophobic and electrostatic interactions promote self-assembly of peptide amphiphile molecules into nanofibers. Bundles of nanofibers form a three-dimensional network resulting in gel formation. The effect of the nanofiber network on the mechanical properties of the gels was analyzed by AFM, rheology and CD. Concentration and temperature dependent measurements of gel stiffness suggest that the mechanical properties of the gels are determined by a number of factors including the interfiber interactions and mechanical properties of individual nanofibers. We point out that the divergence in gel stiffness may arise from the difference in strength of interfiber bonds based on an energetic model of elastic rod networks, along with continuum mechanical models of bundles of rods. This finding differs from the results observed with traditional polymeric materials. Understanding the mechanisms behind the viscoelastic properties of the gels formed by self-assembling molecules can lead to development of new materials with controlled stiffness. Tissue engineering applications can especially benefit from these materials, where the mechanical properties of the extracellular matrix are crucial for cell fate determination. © The Royal Society of Chemistry 2011.

The connection of molecular monomers through non-covalent interaction (e.g. hydrogen bonding, π-π interaction, coordination bonding) enables the formation of supramolecular polymers. The major advantage of these bonds is their reversibility and consequently their ability to self-assembly or to disconnect depending on given conditions. This thesis examines the self-assembly through quadruple hydrogen bonding, which is strong and the resulting structures stable. Ureidopyrimidinon A and aromatic amines were always used as the starting compound for the preparation of monofunctional and bifunctional ureidopyrimidinones.

We present numerical estimates of the leading two- and three-body dispersion energy terms in van der Waals interactions for a broad variety of molecules and solids. The calculations are based on London and Axilrod-Teller-Muto expressions where the required interatomic dispersion energy coefficients, C6 and C9, are computed "on the fly" from the electron density. Inter- and intramolecular energy contributions are obtained using the Tang-Toennies (TT) damping function for short interatomic distances. The TT range parameters are equally extracted on the fly from the electron density using their linear relationship to van der Waals radii. This relationship is empiricially determined for all the combinations of He-Xe rare gas dimers, as well as for the He and Ar trimers. The investigated systems include the S22 database of noncovalent interactions, Ar, benzene and ice crystals, bilayer graphene, C60 dimer, a peptide (Ala10), an intercalated drug-DNA model [ellipticine- d (CG) 2], 42 DNA base pairs, a protein (DHFR, 2616 atoms), double stranded DNA (1905 atoms), and 12 molecular crystal polymorphs from crystal structure prediction blind test studies. The two- and three-body interatomic dispersion energies are found to contribute significantly to binding and cohesive energies, for bilayer graphene the latter reaches 50% of experimentally derived binding energy. These results suggest that interatomic three-body dispersion potentials should be accounted for in atomistic simulations when modeling bulky molecules or condensed phase systems. © 2010 American Institute of Physics.

Difluoromethane (CH2F2) is an atmospheric pollutant presenting strong absorptions within the 8-12 μm atmospheric window, hence it can contribute to global warming. Its dimer, (CH2F2)2, is bound through weak hydrogen bonds (wHBs). Theoretically, wHBs are of paramount importance in biological systems, though their modeling at density functional theory (DFT) level requires dispersion correlations to be accounted for. In this work, the binding energy (3.1 ± 0.5 kcal mol(-1)) of (CH2F2)2 is experimentally derived from the foreign broadening coefficients of the monomer compound, collisionally perturbed by a range of damping gases. Measurements are carried out on CH2F2 ro-vibrational transitions by means of tunable diode laser spectroscopy. Six stationary points on the potential energy surface (PES) of the dimer are investigated at DFT level by using some of the last generation density functionals (DFs). The Minnesota M06 suite of functionals as well as range separated DFs and DFs augmented by the non-local (NL) van der Waals (vdW) dispersion corrections are considered. DFT results are compared to reference values at the estimated complete basis set (CBS) limit of CCSD(T) theory (coupled cluster with singles and doubles augmented by a perturbational estimate of connected triples) and to the experimental binding energy. The M06-2X, M06-HF, VV10, BLYP-NL, and B3LYP-NL DFs reproduce CCSD(T)/CBS binding energies with a mean absolute deviation

Mass spectrometry has in recent years been established as the standard method for protein identification and characterization in proteomics with excellent intrinsic sensitivity and specificity. Fourier transform ion cyclotron resonance is the mass spectrometric technique that provides the highest resolving power and mass accuracy, increasing the amount of information that can be obtained from complex samples. This thesis concerns how useful information on proteins of interest can be extracted from mass spectrometric data on different levels of protein structure and how to obtain this data experimentally. It was shown that it is possible to analyze complex mixtures of protein tryptic digests by direct infusion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry and identify abundant proteins by peptide mass fingerprinting. Coupling on-line methods such as liquid chromatography and capillary electrophoresis increased the number of proteins that could be identified in human body fluids. Protein identification was also improved by novel statistical methods utilizing prediction of chromatographic behavior and the non-randomness of enzymatic digestion. To identify proteins by short sequence tags, electron capture dissociation was implemented, improved and finally coupled on-line to liquid chromatography for the first time. The combined techniques can be used to sequence large proteins de novo or to localize and characterize any labile post-translational modification. New computer algorithms for the automated analysis of isotope exchange mass spectra were developed to facilitate the study of protein structural dynamics. The non-covalent interaction between HIV-inhibitory peptides and the oligomerization of amyloid β-peptides were investigated, reporting several new findings with possible relevance for development of anti-HIV drug therapies and understanding of fundamental mechanisms in Alzheimer’s disease.

In the development and application of dispersion-corrected density-functional theory, the effects of basis set incompleteness have been largely mitigated through the use of very large, nearly-complete basis sets. However, the use of such large basis sets makes application of these methods inefficient for large systems. In this work, we examine a series of basis sets, including Pople-style, correlation-consistent, and polarization-consistent bases, for their ability to efficiently and accurately predict non-covalent interactions when used in conjunction with the exchange-hole dipole moment (XDM) dispersion model. We find that the polarization-consistent 2 (pc-2) basis sets, and two modifications thereof with some diffuse functions removed, give performance of comparable quality to that obtained with aug-cc-pVTZ basis sets, while being roughly 12 to 23 times faster computationally. The behavior is explained, in part, by the role of diffuse functions in recovering small density changes in the intermolecular region. The general performance of the modified basis sets is tested by application of XDM to standard intermolecular benchmark sets at, and away from, equilibrium. © 2013 AIP Publishing LLC.

The first-principles calculation of non-covalent (particularly dispersion) interactions between molecules is a considerable challenge. In this work we studied the binding energies for ten small non-covalently bonded dimers with several combinations of correlation methods (MP2, coupled-cluster single double, coupled-cluster single double (triple) (CCSD(T))), correlation-consistent basis sets (aug-cc-pVXZ, X D, T, Q), two-point complete basis set energy extrapolations, and counterpoise corrections. For this work, complete basis set results were estimated from averaged counterpoise and non-counterpoise-corrected CCSD(T) binding energies obtained from extrapolations with aug-cc-pVQZ and aug-cc-pVTZ basis sets. It is demonstrated that, in almost all cases, binding energies converge more rapidly to the basis set limit by averaging the counterpoise and non-counterpoise corrected values than by using either counterpoise or non-counterpoise methods alone. Examination of the effect of basis set size and electron correlation shows that the triples contribution to the CCSD(T) binding energies is fairly constant with the basis set size, with a slight underestimation with CCSD(T)aug-cc-pVDZ compared to the value at the (estimated) complete basis set limit, and that contributions to the binding energies obtained by MP2 generally overestimate the analogous CCSD(T) contributions. Taking these factors together, we conclude that the binding energies for non-covalently bonded systems can be accurately determined using a composite method that combines CCSD(T)aug-cc-pVDZ with energy corrections obtained using basis set extrapolated MP2 (utilizing aug-cc-pVQZ and aug-cc-pVTZ basis sets), if all of the components are obtained by averaging the counterpoise and non-counterpoise energies. With such an approach, binding energies for the set of ten dimers are predicted with a mean absolute deviation of 0.02 kcalmol, a maximum absolute deviation of 0.05 kcalmol, and a mean percent absolute deviation of only 1.7, relative to the (estimated) complete basis set CCSD(T) results. Use of this composite approach to an additional set of eight dimers gave binding energies to within 1 of previously published high-level data. It is also shown that binding within parallel and parallel-crossed conformations of naphthalene dimer is predicted by the composite approach to be 9 greater than that previously reported in the literature. The ability of some recently developed dispersion-corrected density-functional theory methods to predict the binding energies of the set of ten small dimers was also examined. © 2011 American Institute of Physics.

The focus of the present work is to shed light on possible modifications of the molecular properties of polysaccharide hydrogels induced by the establishment of specific non-covalent interactions during the loading of a guest compound inside the gel phase. With this aim, a case study of the encapsulation of caffeine (Caf) inside cyclodextrin-based hydrogels, namely, cyclodextrin nanosponges (NS), is systematically investigated here by using UV Raman scattering experiments. The UV Raman spectra of the hydrogels, analysed as a function of temperature, concentration of the guest molecule loaded in the gel phase and pH, prove particularly informative both on the structural rearrangements of the hydrophobic/hydrophilic groups of the polymeric network and on the breaking/formation of specific guest–matrix interactions. Analysis of the temperature dependence of dynamical parameters, i.e., the dephasing time associated with specific vibrational modes of the polymer backbone, enables the proposal of a molecular picture in which the loading of Caf in NS hydrogels tends to favour access of the water solvent to the more hydrophobic portions of the polymer matrix, which is in turn reflected in a marked increase in the solvation of the whole system. The achievements of this work appear of interest with respect to the design of new possible strategies for controlling the diffusion/release of bioactive molecules inside hydrogel networks, besides corroborating the potential of UV Raman scattering experiments to give new molecular insights into complex phenomena affecting hydrogel phases.

Aerolysin, a virulence factor secreted by Aeromonas hydrophila, is representative of a group of β-sheet toxins that must form stable homooligomers in order to be able to insert into biological membranes and generate channels. Electron microscopy and image analysis of two-dimensional membrane crystals had previously revealed a structure with 7-fold symmetry et al. (1992) EMBO J. 11, 2457–2463]. However, this unusual et al. (1992) EMBO J. 11, 2457–2463]. However, this unusual molecularity of the channel remained to be confirmed by an independent method since low-resolution electron crystallography had led to artefactual data for other pore-forming toxins. In this study, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) was used to measure the mass of the aerolysin oligomer preparation. A mass of 333 850 Da was measured, fitting very well with a heptameric complex (expected mass: 332 300 Da). These results confirm the earlier evidence that the aerolysin oligomer is a heptamer and also show that MALDI-TOF mass spectrometry could be a valuable tool to study non-covalent association of proteins.