F.J. Ramírez

Biogenic amines and polyamines: Similar biochemistry for different physiological missions and biomedical applications

Biogenic amines are organic polycations derived from aromatic or cationic amino acids. All of them have one or more positive charges and a hydrophobic skeleton. Nature has evolved these molecules to play different physiological roles in mammals, but maintains similar patterns for their metabolic and intracellular handling. As deduced from this review, many questions still remain to be solved around their biochemistry and molecular biology, blocking our aims to control the relevant pathologies in which they are involved (cancer and immunological, neurological, and gastrointestinal diseases). Advances in this knowledge are dispersed among groups working on different biomedical areas. In these pages, we put together the most relevant information to remark how fruitful it can be to learn from Nature and to take advantage of the biochemical similarities (keyprotein structures and their regulation data on metabolic interplays and binding properties) to generate new hypothesis and develop different biomedical strategies based on biochemistry and molecular biology of these compounds.

Efficient π electrons delocalization in α,α′‐dimethyl end‐capped oligothiophenes: A vibrational spectroscopic study

α,α′‐dimethyl substituted oligothiophenes with increasing chain length (from the dimer up to the hexamer) were recently synthesized by chemical methods. In this paper we have investigated the vibrational Fourier transform‐IR and Fourier transform‐Raman spectra of solid α,α′‐dimethyl substituted oligothiophenes in the neutral state. The data are consistent with the existence of a chain‐length dependent π electron delocalization: a large frequency dispersion with conjugation length is observed for some Raman and infrared active vibrational modes, particularly at the high‐energy side of the aromatic C=C stretching region. Vibrational assignments are proposed for the main vibrational features in the whole spectral range. This vibrational spectroscopic analysis of the solid samples thus becomes a tool for deriving information on the structure of these neutral materials in solution and in the doped state.

Fourier transform Raman study of the structural specificities on the interaction between DNA and biogenic polyamines.

Biogenic polyamines putrescine, spermidine, and spermine are essential molecules for proliferation in all living organisms. Direct interaction of polyamines with nucleic acids has been proposed in the past based on a series of experimental evidences, such as precipitation, thermal denaturation, or protection. However, binding between polyamines and nucleic acids is not clearly explained. Several interaction models have also been proposed, although they do not always agree with one another. In the present work, we make use of the Raman spectroscopy to extend our knowledge about polyamine-DNA interaction. Raman spectra of highly polymerized calf-thymus DNA at different polyamine concentrations, ranging from 1 to 50 mM, have been studied for putrescine, spermidine, and spermine. Both natural and heavy water were used as solvents. Difference Raman spectra have been computed by subtracting the sum of the separated component spectra from the experimental spectra of the complexes. The analysis of the Raman data has supported the existence of structural specificities in the interactions, at least under our experimental conditions. These specificities lead to preferential bindings through the DNA minor groove for putrescine and spermidine, whereas spermine binds by the major groove. On the other hand, spermine and spermidine present interstrand interactions, whereas putrescine presents intrastrand interactions in addition to exo-groove interactions by phosphate moieties.

Inversion of Supramolecular Helicity in Oligo‐p‐phenylene‐Based Supramolecular Polymers: Influence of Molecular Atropisomerism

The helical organization of oligo-p-phenylene-based organogelators has been investigated by atomic force microscopy, circular and vibrational circular dichroism, and Raman techniques. Whilst OPPs with more than two phenyl rings in the core self-assemble into left-handed helices, that with a biphenyl core shows an inversion of the supramolecular helicity depending on the formation conditions through the atropisomerism of the biphenyl central unit. The results presented herein outline a new example of kinetically controlled modulation of supramolecular helicity.

An interpretation of the vibrational spectra of insulating and electrically conducting poly(3-methylthiophene) aided by a theoretical dynamical model

It is shown that the relevant spectral features which arise in the infrared spectrum of poly(3‐methylthiophene) upon chemical doping or photoexcitation (i.e., in the electrically conducting form) can be properly explained by means of the effective conjugation coordinate (ECC) formalism. This theoretical dynamical model accounts for the intramolecular hopping of π electrons in the class of polyconjugated aromatic systems. A complete assignment for the infrared and Raman spectra of the polymer in the pristine state (i.e., in the insulating form) is proposed as the result of a theoretical vibrational potential function derived from semiempirical calculations on short oligomers. The dependence of the bandgap energy on the internal rotation about the inter‐ring single bond is analyzed theoretically in dimers as model molecules and the results are compared with experiments.

Lattice dynamics and vibrational spectra of pristine and doped polyconjugated polyfuran

The interpretation of the infrared and Raman spectra of polyconjugated polyfuran prepared by electroreduction of 2,5‐dibromofuran is presented as the result of lattice dynamical calculations. Geometries and vibrational force fields are derived from semiempirical calculations carried out on oligomers and the parameters are used for the polymer. Finally, it is shown that the infrared and Raman spectra of polyfuran pristine and doped are accounted for by effective conjugation coordinate theory, thus showing that this material also constitutes a polyconjugated material.

Vibrational study of aspartic acid and glutamic acid dipeptides

Abstract The infrared and Raman spectra of glutamic acid dipeptide and aspartic acid dipeptide as solid samples were registered and measured. A general assignment for the fundamental vibrations has been proposed in the basis of previous works about their monomers and other studies on the characteristic frequencies for the peptide linkage. A correlation between the assignments of the two peptides was also carried out, showing similar vibrational properties.

Self-Assembly Studies of a Chiral Bisurea-Based Superhydrogelator

A chiral bisurea-based superhydrogelator that is capable of forming supramolecular hydrogels at concentrations as low as 0.2 mM is reported. This soft material has been characterized by thermal studies, rheology, X-ray diffraction analysis, transmission electron microscopy (TEM), and by various spectroscopic techniques (electronic and vibrational circular dichroism and by FTIR and Raman spectroscopy). The expression of chirality on the molecular and supramolecular levels has been studied and a clear amplification of its chirality into the achiral analogue has been observed. Furthermore, thermal analysis showed that the hydrogelation of compound 1 has a high response to temperature, which corresponds to an enthalpy-driven self-assembly process. These particular thermal characteristics make these materials easy to handle for soft-application technologies.

Synthesis of the Smallest Axially Chiral Molecule by Asymmetric Carbon–Fluorine Bond Activation

Surprisingly, thecarbon backbones of 3 and 5adeviate by 4.4(3)8 and 4.6(2)8from the linearity that would be expected based on their sp-hybridized central carbon atoms (Figure 2). Furthermore, thetwo terminal F-C-H planes in5a have a torsion angle of91.9(2)8. The previously reported structures derived frommicrowave spectroscopy do not show the same distortions(Supporting Information, Table S2), because erroneously, therefinement was based on a constrained linear geometry.

Force field and normal coordinate calculations for glutamic acid

The MNDO-scaled harmonic force field of glutamic acid is obtained in the space of a set of non-redundant local-symmetrized internal coordinates. A set of scaling factors is transferred from aspartic acid. The theoretical vibrational frequencies for the fundamentals are successfully compared with the observed values, and the frequencies of the 15N and d4 isotopic derivatives are also calculated and compared with the experiments. These results and the description of the normal modes followed by mean of the potential energy distribution, agree with the previous assignments proposed for most of the observed bands, showing an extensive coupling among the bending and skeletal stretching coordinates. A GOOD prediction of a molecular force field is a powerful tool to use for the vibrational properties of a molecule in a large number of structural problems. Molecular orbital methods at both, semiempirical or ab initio levels, provide fundamental frequencies and quadratic force constants that deviate systematically from the observed values. In order to fit the theoretical results to the experiments, a set of well selected scaling factors can be used. In the last few years the semiempirical MNDO method provided us with harmonic force fields which reproduced successfully the vibrational frequencies of some amino acids such as glycine (1), glutamine (2) or aspartic acid (3). From these works we have built a set of scaling factors that can be applied to the force fields of other related molecules. In a recent paper (4) the infrared and Raman spectra of L-glutamic acid and its tSN and 2H isotopomers have been reported and a general assignment of their fundamentals have been proposed on the basis of the isotopic shifts measured. To support these assign- ments, in this paper we present a normal coordinate analysis for this amino acid. We have chosen the MNDO method (5) in order to transfer the scaling factors previously used for other amino acids. This semiempirical method has been extensively employed in a great number of vibrational calculations involving very different molecules. On the basis of the obtained results, we have reviewed the previous assignments.