Structural isotopic effects in the smallest chiral amino acid: observation of a structural phase transition in fully deuterated alanine

A first study of possible changes instigated by deuteration in amino acids was carried out using neutron diffraction, inelastic neutron scattering, and Raman scattering in l-alanine, C2H4(NH2)COOH. Careful analysis of the structural parameters shows that deuteration of l-alanine engenders significant geometric changes as a function of temperature, which can be directly related to the observation of new lattice vibration modes in the Raman spectra. The combination of the experimental data suggests that C2D4(ND2)COOD undergoes a structural phase transition (or a structural rearrangement) at about 170 K. Considering that this particular amino acid is a hydrogen-bonded system with short hydrogen bonds (O...H approximately 1.8 A), we evoke the Ubbelohde effect to conclude that substitution of hydrogen for deuterium gives rise to changes in the hydrogen-bonding interactions. The structural differences suggest distinct relative stabilities for the hydrogenous and deuterated l-alanine.     

Water-soluble carbosilane dendrimers: synthesis biocompatibility and complexation with oligonucleotides; evaluation for medical applications

Novel amine- or ammonium-terminated carbosilane dendrimers of type nG-[Si{OCH2(C6H3)-3,5-(OCH2CH2NMe2)2}]x, nG-[Si{O(CH2)2N(Me)(CH2)2NMe2}]x and nG-[Si{(CH2)3NH2}]x or nG-[Si{OCH2(C6H3)-3,5-(OCH2CH2NMe3 +I-)2}]x, nG-[Si{O(CH2)2N(Me)(CH2)2NMe3 +I-}]x, and nG-[Si{(CH2)3NH3 +Cl-}]x have been synthesized and characterized up to the third generation by two strategies: 1) alcoholysis of Si--Cl bonds with amino alcohols and subsequent quaternization with MeI, and 2) hydrosilylation of allylamine with Si--H bonds of the dendritic systems and subsequent quaternization with HCl. Quaternized carbosilane dendrimers are soluble in water, although degradation is apparent due to hydrolysis of Si--O bonds. However, dendrimers containing Si--C bonds are water-stable. The biocompatibility of the second-generation dendrimers in primary cell cultures of peripheral blood mononuclear cells (PBMCs) and erythrocytes have been analyzed, and they show good toxicity profiles over extended periods. In addition, we describe a study on the interactions between the different carbosilane dendrimers and DNA oligodeoxynucleotides (ODNs) and plasmids along with a comparative analysis of their toxicity. They can form complexes with DNA ODNs and plasmids at biocompatible doses via electrostatic interaction. Also a preliminary transfection assay has been accomplished. These results demonstrate that the new ammonium-terminated carbosilane dendrimers are good base molecules to be considered for biomedical applications.     

Synthesis, crystal structure, spectroscopic and electrochemical characterization of the dinuclear complex {tetra-μ-[(±)-2-(p-methoxyphenoxy)-propionato-O,O′]bis(aqua)dicopper(II)}

Structural, electrochemical and spectroscopic data of a new dinuclear copper(II) complex with (±)-2-(p-methoxyphenoxy)propionic acid are reported. The complex {tetra-μ-[(±)-2-(p-methoxyphenoxy)propionato-O,O′]-bis(aqua)dicopper(II)} crystallizes in the monoclinic system, space group P2₁/n with a = 14.149(1) ?, b = 7.495(1) ?, c = 19.827(1) ?, β = 90.62(1) and Z = 4. X-ray diffraction data show that the two copper(II) ions are held together through four carboxylate bridges, coordinated as equatorial ligands in square pyramidal geometry. The coordination sphere around each copper ion is completed by two water molecules as axial ligands. Thermogravimetric data are consistent with such results. The ligand has an “L” type shape due to the angle formed by the β-carbon of the propionic chain and the linked p-methoxyphenoxy group. This conformation contributes to the occurrence of a peculiar structure of the complex. The complex retains its dinuclear nature when dissolved in acetonitrile, but it decomposes into the corresponding mononuclear species if dissolved in ethanol, according to the EPR measurements. Further, cyclic voltammograms of the complex in acetonitrile show that the dinuclear species maintains the same structure, in agreement with the EPR data in this solvent. The voltammogram shows two irreversible reduction waves at E _pc = −0.73 and −1.04 V vs. Ag/AgCl assigned to the Cu(II)/Cu(I) and Cu(I)/Cu° redox couples, respectively, and two successive oxidation waves at E _pa =− 0.01 and +1.41 V vs. Ag/AgCl, assigned to the Cu°/Cu(I) and Cu(I)/Cu(II) redox couples, respectively, in addition to the oxidation waves of the carboxylate ligand.     

The pattern of distribution of amino groups modulates the structure and dynamics of natural aminoglycosides: implications for RNA recognition

Aminoglycosides are clinically relevant antibiotics that participate in a large variety of molecular recognition processes involving different RNA and protein receptors. The 3-D structures of these policationic oligosaccharides play a key role in RNA binding and therefore determine their biological activity. Herein, we show that the particular NH2/NH3(+)/OH distribution within the antibiotic scaffold modulates the oligosaccharide conformation and flexibility. In particular, those polar groups flanking the glycosidic linkages have a significant influence on the antibiotic structure. A careful NMR/theoretical analysis of different natural aminoglycosides, their fragments, and synthetic derivatives proves that both hydrogen bonding and charge-charge repulsive interactions are at the origin of this effect. Current strategies to obtain new aminoglycoside derivatives are mainly focused on the optimization of the direct ligand/receptor contacts. Our results strongly suggest that the particular location of the NH2/NH3(+)/OH groups within the antibiotics can also modulate their RNA binding properties by affecting the conformational preferences and inherent flexibility of these drugs. This fact should also be carefully considered in the design of new antibiotics with improved activity.     

Synthesis,structural characterization and reactivity of copper(I)-nitrile complexes: Crystal and molecular structure of [Cu(BzCN)4][BF4]

Complexes of general formula [CuL₄][BF₄] (L = benzonitrile – PhCN 2 or phenylacetonitrile – BzCN 3) have been prepared and structurally characterized by NMR spectroscopy and X-ray crystallography. Their structure and reactivity have been compared to the well known [Cu(MeCN)₄][BF₄] (1). The ⁶³Cu line width and the ⁶³Cu chemical shift have been evaluated by varying the temperature and the concentration of the complex 2 in benzonitrile solutions. The phenylacetonitrile solutions of the complex 3 give extremely broad signals which are beyond detection. Accordingly, compound 3 has been studied by ⁶³Cu MAS NMR spectroscopy. The solution NMR data are consistent to the prevalence of dynamic equilibrium between tetra- and low-coordinated species in both complexes. The X-ray structure of 3 revealed that the copper(I) atom sits in a slightly distorted tetrahedral geometry, surrounded by four BzCN ligands.     

Electrochemical gating of single osmium molecules tethered to Au surfaces

The electrochemical study of electron transport between Au electrodes and the redox molecule Os[(bpy)₂(PyCH₂ NH₂CO-]ClO₄ tethered to molecular linkers of different length (1.3 to 2.9 nm) to Au surfaces has shown an exponential decay of the rate constant k _ET ⁰ with a slope β = 0.53 consistent with through bond tunneling to the redox center. Electrochemical gating of single osmium molecules in an asymmetric tunneling nano-gap between a Au(111) substrate electrode modified with the redox molecules and a Pt-Ir tip of a scanning tunneling microscope was achieved by independent control of the reference electrode potential in the electrolyte, E _ref ? E _s, and the tip-substrate bias potential, E _bias. Enhanced tunneling current at the osmium complex redox potential was observed as compared to the off resonance set point tunneling current with a linear dependence of the overpotential at maximum current vs. the E _bias. This corresponds to a sequential two-step electron transfer with partial vibration relaxation from the substrate Au(111) to the redox molecule in the nano-gap and from this redox state to the Pt-Ir tip according to the model of Kuznetsov and Ulstrup (J Phys Chem A 104: 11531, 2000). Comparison of short and long linkers of the osmium complex has shown the same two-step ET (electron transfer) behavior due to the long time scale in the complete reduction-oxidation cycle in the electrochemical tunneling spectroscopy (EC-STS) experiment as compared to the time constants for electron transfer for all linker distances, k _ET ⁰.     

Atmospheric chemistry of dimethyl phosphonate, dimethyl methylphosphonate, and dimethyl ethylphosphonate

Rate constants for the reactions of OH radicals and NO3 radicals with dimethyl phosphonate [DMHP, (CH3O)2P(O)H], dimethyl methylphosphonate [DMMP, (CH3O)2P(O)CH3], and dimethyl ethylphosphonate [DMEP, (CH3O)2P(O)C2H5] have been measured at 296 +/- 2 K and atmospheric pressure using relative rate methods. The rate constants obtained for the OH radical reactions (in units of 10(-12) cm3 molecule(-1) s(-1)) were as follows: DMHP, 4.83 +/- 0.25; DMMP, 10.4 +/- 0.6; and DMEP, 17.0 +/- 1.0, with a deuterium isotope effect of k(OH + DMMP)/k(OH + DMMP-d9) = 4.8 +/- 1.2. The rate constants obtained for the NO3 radical reactions (in units of 10(-16) cm3 molecule(-1) s(-1)) were as follows: DMHP, < 1.4; DMMP, 2.0 +/- 1.0; and DMEP, 3.4 +/- 1.4. Upper limits to the rate constants for the O3 reactions of < 8 x 10(-20) cm3 molecule(-1) s(-1) for DMHP and < 6 x 10(-20) cm3 molecule(-1) s(-1) for DMMP and DMEP were determined. Products of the reactions of OH radicals with DMHP, DMMP, and DMEP were investigated in situ using atmospheric pressure ionization mass spectrometry (API-MS) and, for the DMMP and DMEP reactions, Fourier transform infrared (FT-IR) spectroscopy. API-MS analyses showed the formation of products of molecular weight 96 and 126, attributed to CH3OP(O)(H)OH and (CH3O)2P(O)OH, respectively, from DMHP; of molecular weight 110, attributed to CH3OP(O)(CH3)OH, from DMMP; and of molecular weight 124 and 126, attributed to CH3OP(O)(C2H5)OH and (CH3O)2P(O)OH, respectively, from DMEP. FT-IR analyses showed formation (values given are % molar yields) of the following: from DMMP, CO, 54 +/- 6; CO2, 5 +/- 1 in dry air; HCHO, 3.9 +/- 0.7; HC(O)OH, < 1.4 in dry air; RONO2, approximately 4; and formate ester, approximately 8; and from DMEP, CO, 50 +/- 7; CO2, 11 +/- 4; CH3CHO, 18 +/- 8; HCHO, < 7; HC(O)OH, < 6; RONO2, < or = 5; and formate ester, 5.0 +/- 1.5. Possible reaction mechanisms are discussed.     

Fragmentation of carbohydrate anomeric alkoxyl radicals. Synthesis of highly functionalized chiral vinyl sulfones

The reaction of derivatives of 3-acetyl-d-glucal, 3-acetyl-l-rhamnal, 3-acetyl-d-galactal, and 3-acetyl-d-lactal with sodium benzenesulfinate in acid medium catalyzed by HgSO₄ afforded diastereoisomeric mixtures of the corresponding 2,3-dideoxy-3-(phenylsulfonyl)-hexopyranoses through a Ferrier rearrangement. The anomeric alkoxyl radical fragmentation of these γ-hydroxy sulfones using the system (diacetoxyiodo)benzene and iodine gave vinyl sulfones with structures of 1,2-dideoxy-4-O-formyl-2-(phenylsulfonyl)-pent-1-enitol and configurations d-erythro, l-erythro, and d-threo at the two stereogenic centers.     

Thermo gravimetric analysis of supramolecular complexes of p-tert-butylcalix[6]arene and ammonium cations: crystal structure of diethylammonium complex

Thermo gravimetric analysis of ammonium-p-tert-butylcalix[6]arene salts were carried out to determine the stoichiometry of the inclusion compounds and the temperature of leaving of the ammonium cation, as amine, from the solid phase by a reverse proton transfer reaction to calixarene. The chain length of the amine molecules and their relative basicity order are the main factors which determine the decomplexation temperatures for the ammonium salts of piperidinium, diethylammonium, ethylenediammonium, morpholinium, s-butylammonium, butylammonium, hexylammonium and triethylammonium salts of p-tert-butylcalix[6]arene anion. The solid state structure of bis-diethylammonium-p-tert-butylcalix[6]arene dianion is reported. The calix moiety adopts a 1,2,3 alternate conformation, with one ammonium as exo-calix and other as endo-calix, with an intricate array of hydrogen bonds between phenol, phenolate and ammonium cations.