Modal Model Identification with Unknown Nonstationary Base Motion

Techniques developed for structural identification are typically devoted to obtaining a model, parametrical or not, on the basis of information on the structural response and on the forcing action, both assumed as known from experimental tests. In many situations, however, it may be necessary, or simply useful, to refer only to the measured response. In this paper we describe the theoretical aspects of a technique we have recently developed to identify the modal model in the frequency domain when the input is unknown. To simplify, we refer to unknown nonstationary base motion, but many of our conclusions can be extended to different situations. We show that, from a theoretical point of view, the identification problem has a unique solution, for this kind of input, when at least three time histories are known, and this circumstance had never been pointed out before. Because the theoretical analysis furnishes only necessary conditions for the existence of a unique solution, an extensive numerical analysis is reported in the second part of the paper, which also shows the sensitivity of the identification procedure.     

Lights and Shadows on the Therapeutic Use of Antimicrobial Peptides

The emergence of antimicrobial-resistant infections is still a major concern for public health worldwide. The number of pathogenic microorganisms capable of resisting common therapeutic treatments are constantly increasing, highlighting the need of innovative and more effective drugs. This phenomenon is strictly connected to the rapid metabolism of microorganisms: due to the huge number of mutations that can occur in a relatively short time, a colony can “adapt” to the pharmacological treatment with the evolution of new resistant species. However, the shortage of available antimicrobial drugs in clinical use is also caused by the high costs involved in developing and marketing new drugs without an adequate guarantee of an economic return; therefore, the pharmaceutical companies have reduced their investments in this area. The use of antimicrobial peptides (AMPs) represents a promising strategy for the design of new therapeutic agents. AMPs act as immune defense mediators of the host organism and show a poor ability to induce antimicrobial resistance, coupled with other advantages such as a broad spectrum of activity, not excessive synthetic costs and low toxicity of both the peptide itself and its own metabolites. It is also important to underline that many antimicrobial peptides, due to their inclination to attack cell membranes, have additional biological activities, such as, for example, as anti-cancer drugs. Unfortunately, they usually undergo rapid degradation by proteolytic enzymes and are characterized by poor bioavailability, preventing their extensive clinical use and landing on the pharmaceutical market. This review is focused on the strength and weak points of antimicrobial peptides as therapeutic agents. We give an overview on the AMPs already employed in clinical practice, which are examples of successful strategies aimed at overcoming the main drawbacks of peptide-based drugs. The review deepens the most promising strategies to design modified antimicrobial peptides with higher proteolytic stability with the purpose of giving a comprehensive summary of the commonly employed approaches to evaluate and optimize the peptide potentialities.     

Selective Determination of Se4+ and Se6+ Using SPME and GC/MS

A method for the selective determination of Se⁴⁺ and Se⁶⁺ using solid phase microextraction (SPME) and GC/MS analysis is presented. Se⁴⁺ is selectively derivatized by reaction with 4,5-dichloro-1,2-phenylenediamine to form the corresponding piazselenolo complex, extracted by the SPME fiber, and determined by GC/MS. The RSD at a 5 μg/L concentration was 9.88% and the theoretical detection limit 6 ng/L. The method was employed to test real matrices; tap and river water were analyzed before and after spiking giving a recovery rate of 102% in river water and 97% in tap water.     

Improving performance of polarizable continuum model for study of large molecules in solution

We present a new implementation of the polarizable continuum model (PCM) that significantly improves its performance, especially for large solutes. This approach avoids the separation between electronic and nuclear sources in the calculation of the solvation charges, allowing the extension of iterative procedures to all the PCM versions [dielectric (D), conductor (C), and integral equation formalism (IEF)], so that the best method and/or algorithm can be selected, depending on the system at hand. In particular, the new balanced two-term iterative procedure with total charges avoids any nonlinear computational step and memory occupation. Furthermore, it also shows a good convergence for the C-PCM and IEF-PCM versions, which were quite problematic for the conventional separate charges approach. Also, first and second analytical derivatives are available in this context for Hartree–Fock and Kohn–Sham models. A number of examples are analyzed; they show that the new algorithms couple fully satisfactory numerical accuracy with remarkable computational efficiency. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1186–1198, 1999     

Catalytic and bulk solvent effects on proton transfer: Formamide as a case study

Structural, thermodynamic, and kinetic aspects of the tautomerization of formamide through direct and solvent-assisted proton transfer have been investigated. Both specific and bulk effects of the solvent play a role in determining the overall result so that only a mixed discrete-continuum model is sufficiently reliable. Structural modifications induced by the solvent are significant, but have only a slight effect on thermodynamic and kinetic quantities. The same remarks apply to the vibrational shifts induced by the solvent. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 1993–2000, 1997     

Semi-Rigid (Aminomethyl) Piperidine-Based Pentadentate Ligands for Mn(II) Complexation

Two pentadentate ligands built on the 2-aminomethylpiperidine structure and bearing two tertiary amino and three oxygen donors (three carboxylates in the case of AMPTA and two carboxylates and one phenolate for AMPDA-HB) were developed for Mn(II) complexation. Equilibrium studies on the ligands and the Mn(II) complexes were carried out using pH potentiometry, ¹H-NMR spectroscopy and UV-vis spectrophotometry. The Mn complexes that were formed by the two ligands were more stable than the Mn complexes of other pentadentate ligands but with a lower pMn than Mn(EDTA) and Mn(CDTA) (pMn for Mn(AMPTA) = 7.89 and for Mn(AMPDA-HB) = 7.07). ¹H and ¹⁷O-NMR relaxometric studies showed that the two Mn-complexes were q = 1 with a relaxivity value of 3.3 mM⁻¹ s⁻¹ for Mn(AMPTA) and 3.4 mM⁻¹ s⁻¹ for Mn(AMPDA-HB) at 20 MHz and 298 K. Finally, the geometries of the two complexes were optimized at the DFT level, finding an octahedral coordination environment around the Mn²⁺ ion, and MD simulations were performed to monitor the distance between the Mn²⁺ ion and the oxygen of the coordinated water molecule to estimate its residence time, which was in good agreement with that determined using the ¹⁷O NMR data.     

Exploring Orthogonality between Halogen and Hydrogen Bonding Involving Benzene

The concept of orthogonality between halogen and hydrogen bonding, brought out by Ho and coworkers some years ago, has become a widely accepted idea within the chemists’ community. While the original work was based on a common carbonyl oxygen as acceptor for both interactions, we explore here, by means of M06-2X, M11, ωB97X, and ωB97XD/aug-cc-PVTZ DFT calculations, the interdependence of halogen and hydrogen bonding with a shared π-electron system of benzene. The donor groups (specifically NCBr and H₂O) were placed on either or the same side of the ring, according to a double T-shaped or a perpendicular geometry, respectively. The results demonstrate that the two interactions with benzene are not strictly independent on each other, therefore outlining that the orthogonality between halogen and hydrogen bonding, intended as energetical independence between the two interactions, should be carefully evaluated according to the specific acceptor group.     

The Self-Assembly of a Lipophilic Deoxyguanosine Derivative and the Formation of a Liquid-Crystalline Phase in Hydrocarbon Solvents

The lipophilic 3′,5′-di-O-decanoyl-2′-deoxyguanosine ( 1 ) in CHCl₃ undergoes extensive self-assembly, mediated by H-bonding between the guanine bases, to give ribbon-like aggregates. X-Ray investigation of the platelets obtained from CHCl₃ reveals a disordered fibre-like structure consisting of stacks of the ribbon-like aggregates. The aggregates are completely different from the columnar structures, based on G-quartets, which are the building blocks of the mesophases formed by deoxyguanosine oligonucleotides in H₂O. In pure hydrocarbons or in CHCl₃/hydrocarbons, 1 forms a lyotropic liquid-crystalline phase.