Kinetic isotope effects on thio-substituted biological phosphoryl transfer reactions from density-functional theory

Primary and secondary kinetic and equilibrium isotope effects are calculated with density-functional methods for the dianionic methanolysis of the native (unsubstituted) and thio-substituted ethylene phosphates.     

Squalenyl Hydrogen Sulfate Nanoparticles for Simultaneous Delivery of Tobramycin and an Alkylquinolone Quorum Sensing Inhibitor Enable the Eradication of P. aeruginosa Biofilm Infections

Elimination of pulmonary Pseudomonas aeruginosa (PA) infections is challenging to accomplish with antibiotic therapies, mainly due to resistance mechanisms. Quorum sensing inhibitors (QSIs) interfering with biofilm formation can thus complement antibiotics. For simultaneous and improved delivery of both active agents to the infection sites, self-assembling nanoparticles of a newly synthesized squalenyl hydrogen sulfate (SqNPs) were prepared. These nanocarriers allowed for remarkably high loading capacities of hydrophilic antibiotic tobramycin (Tob) and a novel lipophilic QSI at 30 % and circa 10 %, respectively. The drug-loaded SqNPs showed improved biofilm penetration and enhanced efficacy in relevant biological barriers (mucin/human tracheal mucus, biofilm), leading to complete eradication of PA biofilms at circa 16-fold lower Tob concentration than Tob alone. This study offers a viable therapy optimization and invigorates the research and development of QSIs for clinical use.     

A charge-scaling method to treat solvent in QM/MM simulations

 We present a method to treat the solvent efficiently in hybrid quantum mechanical/molecular mechanical simulations of chemical reactions in enzymes. The method is an adaptation of an approach developed for molecular-mechanical free-energy simulations. The charges of each of the exposed ionizable groups are scaled, and the system is simulated in the presence of a limited number of explicit solvent molecules to obtain a reasonable set of structures. Continuum electrostatics methods are then used to correct the energies. Variations in the procedure are discussed with an emphasis on modifications from the original protocol. We illustrate the method by applying it to the study of a hydrolysis reaction in a highly charged system comprising a complex between the base excision repair enzyme uracil-DNA glycosylase and double-stranded DNA. The resulting adiabatic reaction profile is in good agreement with experiment, in contrast to that obtained without scaling the charges. Received: 5 October 2001 / Accepted: 6 September 2002 / Published online: 28 February 2003 Contribution to the Proceedings of the Symposium on Combined QM/MM Methods at the 222nd National Meeting of the American Chemical Society, 2001 Correspondence to: M. Karplus e-mail: marci@tammy.harvard.edu     

Ugi Reaction on α-Phosphorated Ketimines for the Synthesis of Tetrasubstituted α-Aminophosphonates and Their Applications as Antiproliferative Agents

An Ugi three-component reaction using preformed α-phosphorated N-tosyl ketimines with different isocyanides in the presence of a carboxylic acid affords tetrasubstituted α-aminophosphonates. Due to the high steric hindrance, the expected acylated amines undergo a spontaneous elimination of the acyl group. The reaction is applicable to α-aryl ketimines bearing a number of substituents and several isocyanides. In addition, the densely substituted α-aminophosphonate substrates showed in vitro cytotoxicity, inhibiting the growth of carcinoma human tumor cell line A549 (carcinomic human alveolar basal epithelial cell).     

The Electronic Structure of the Al3− Anion: Is it Aromatic?

Multiconfigurational high‐level electronic structure calculations show that the ${{\rm Al}{{- \hfill \atop 3\hfill}}}$ ring‐like cluster anion has three close low‐lying electronic states of different spin, all of them having strong multiconfigurational character. The aromaticity of the cluster has, therefore, been studied by means of total electron delocalization and normalized multicenter electron delocalization indices evaluated from the multiconfigurational wave functions of each state. The lowest‐lying singlet and triplet states are found to be highly aromatic, whereas the next lowest‐lying state, the quintet state, has much less, though non‐negligible, aromatic character.     

Characterisation of hybrid xerogels synthesised in acid media using methyltriethoxysilane (MTEOS) and tetraethoxysilane (TEOS) as precursors

The mild synthetic conditions provided by the sol-gel process and the versatility of the colloidal state allow for the mixing of inorganic and organic components at the nanometre scale in virtually any ratio for the preparation of hybrid materials. Our interest in hybrid xerogels focuses on combining their porosity with other properties to prepare optic-fibre sensors. The specific aim of this paper is to synthesise hybrid xerogels in acid media using methyltriethoxysilane (MTEOS) and tetraethoxysilane (TEOS) as silica precursors and to investigate the effect of the MTEOS molar ratio on the structure and porous texture of xerogels. Gelation time exponentially increased as the MTEOS molar ratio increased. Increasing the MTEOS molar ratio yielded xerogels with lower density and lower particle size. The incorporation of MTEOS resulted in new FTIR bands at 1276 and 791 cm⁻¹, which was attributed to vibrational modes of methyl group. The band around 1092 cm⁻¹ associated with siloxane bonds shifted to lower wavenumbers and split into two bands. The ²⁹Si spectra only showed the Q ⁿ (n=2, 3, 4) signal in xerogels with 0% MTEOS and the T ⁿ (n=2, 3) signal in xerogels with 100% MTEOS; hybrid xerogels showed both Q and T signals. From XRD peaks at 2θ around 9°, we inferred that xerogels (>70% MTEOS) consisted of nanocrystalline CH₃–SiO_3/2 species. Increasing the MTEOS molar ratio produced xerogels with lower pore volumes and lower average pore size. The integration of methyl groups on the surface decreased the surface polarity and, in turn, the characteristic energy.     

Exploring the Synthetic Potential of γ-Lactam Derivatives Obtained from a Multicomponent Reaction—Applications as Antiproliferative Agents

A study on the reactivity of 3-amino α,β-unsaturated γ-lactam derivatives obtained from a multicomponent reaction is presented. Key features of the substrates are the presence of an endocyclic α,β-unsaturated amide moiety and an enamine functionality. Following different synthetic protocols, the functionalization at three different positions of the lactam core is achieved. In the presence of a soft base, under thermodynamic conditions, the functionalization at C-4 takes place where the substrates behave as enamines, while the use of a strong base, under kinetic conditions, leads to the formation of C-5-functionalized γ-lactams, in the presence of ethyl glyoxalate, through a highly diastereoselective vinylogous aldol reaction. Moreover, the nucleophilic addition of organometallic species allows the functionalization at C-3, through the imine tautomer, affording γ-lactams bearing tetrasubstituted stereocenters, where the substrates act as imine electrophiles. Taking into account the advantage of the presence of a chiral stereocenter in C-5 substituted γ-lactams, further diastereoselective transformations are also explored, leading to novel bicyclic substrates holding a fused γ and δ-lactam skeleton. Remarkably, an example of a highly stereoselective formal [3+3] cycloaddition reaction of chiral γ-lactam substrates is reported for the synthesis of 1,4-dihidropyridines, where a non-covalent attractive interaction of a carbonyl group with an electron-deficient arene seems to drive the stereoselectivity of the reaction to the exclusive formation of the cis isomer. In order to unambiguously determine the substitution pattern resulting from the diverse reactions, an extensive characterization of the substrates is detailed through 2D NMR and/or X-ray experiments. Likewise, applications of the substrates as antiproliferative agents against lung and ovarian cancer cells are also described.     

The Bond Order of C2 from a Strictly N‐Representable Natural Orbital Energy Functional Perspective

The bond order of the ground electronic state of the carbon dimer has been analyzed in the light of natural orbital functional theory calculations carried out with an approximate, albeit strictly N‐representable, energy functional. Three distinct solutions have been found from the Euler equations of the minimization of the energy functional with respect to the natural orbitals and their occupation numbers, which expand upon increasing values of the internuclear coordinate. In the close vicinity of the minimum energy region, two of the solutions compete around a discontinuity point. The former, corresponding to the absolute minimum energy, features two valence natural orbitals of each of the following symmetries, σ, σ*, π and π*, and has three bonding interactions and one antibonding interaction, which is very suggestive of a bond order large than two but smaller than three. The latter, features one σ–σ* linked pair of natural orbitals and three degenerate pseudo‐bonding like orbitals, paired each with one triply degenerate pseudo‐antibonding orbital, which points to a bond order larger than three. When correlation effects, other than Hartree–Fock for example, between the paired natural orbitals are accounted for, this second solution vanishes yielding a smooth continuous dissociation curve. Comparison of the vibrational energies and electron ionization energies, calculated on this curve, with their corresponding experimental marks, lend further support to a bond order for C ₂ intermediate between acetylene and ethylene.     

Fluorene‐based rib waveguides with optimized geometry for long‐term amplified spontaneous emission stability

Amongst the different optoelectronic applications of conjugated polymers, waveguide amplifiers and optically pumped lasers are those requiring larger photochemical stability, owing to the large irradiation conditions under operation. In this context, suitable waveguide optimization enabling the reduction of amplified spontaneous emission (ASE) threshold values appears as important as synthetic chemistry protocols to promote polymer robustness against photo‐oxidation. In this work, we develop rib waveguides with different geometries based on four different fluorene‐based compounds and assess the influence of rib confinement on ASE properties. We observe ASE threshold values as low as 8.9 × 10^?4 mJ cm^?2, being among the lowest threshold values reported so far on blue emitting polymer/oligomer waveguides. We demonstrate that the enhanced ASE efficiency on some of these rib waveguides leads to a fivefold increase in operation lifetime respect to spin‐coated slab waveguides, thus confirming the impact of waveguide geometry on ASE operation stability. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2015 , 53, 1040–1045     

Hybrid QM/MM study of thio effects in transphosphorylation reactions

Results of a series of hybrid quantum mechanical/molecular mechanical (QM/MM) activated dynamics simulations of thio effects in the transphosphorylation (methanolysis) of a 2'-ribose, 5'-methyl phosphate-diester under basic conditions are presented. Single and double substitutions in the nonbridging oxygen positions exhibit thio effects in accord with experimental data and show the existence of a stable intermediate. Thio substitution at the 2' and 5' positions resulted in reactions having a single transition state with increased and decreased free energy barriers, respectively, relative to the unsubstituted reaction. In all of the reactions except for the 5' substitution, the rate-limiting step corresponds to exocyclic cleavage. In the 5' substitution reaction, the rate-limiting step corresponds to endocyclic cleavage and shows a considerable reverse thio effect, in accord with experimental observations of phosphates with enhanced leaving groups. Thio substitution at the 3' position results in a mild reverse thio effect that arises from electronic stabilization of the dianionic transition state. The results presented here provide an important step toward the development and application of new hybrid QM/MM methods that, combined with experiment, may provide a detailed picture of the molecular mechanisms of RNA catalysis.