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Biomedical subjects

Carlos Alemán

Publications and source records attributed to Carlos Alemán.

At least 19 recordsLinked to original sources
PubMed2007

Contraction process of an electroactive actuator based on a one microsecond atomistic molecular dynamics simulation.

The contraction process of an electroactive actuator constituted by calix[4]arene units and quaterthiophene segments has been investigated at the microscopic level by using atomistic molecular dynamics simulations in dichloromethane solution using explicit solvent molecules. Results derived from a 1 mus trajectory of the oxidized and deprotonated actuator indicate that the contraction occurs through a non-concerted mechanism in which each actuating units present in the system behave independently. The efficiency of the contraction process can be reduced by the presence of secondary conformational transitions in the calix[4]arene scaffolds. Accordingly, the drastic reduction of the molecular length expected during the contraction process can be limited by such transitions, which involve the rotational isomerism of a phenolate ring. However, such type of conformational transitions does not compromise the actuator power due to its intrinsic capacity to adopt compact molecular arrangements. On the other hand, the rate of the contraction process is influenced by the presence of solvent molecules, which have been found to reduce it by a factor of about 1000.

Calixarenes↗
PubMed2006

Conformational isomerism of electroactive calix[4]arenes: influence of the electronic state in the flexibility of thiophene-containing calix[4]arene.

The cone-to-paco conformational isomerism of 11,23-bis(thiophen-5-yl)-26,28-dimethoxycalix[4]arene-25,27-diol, a calix[4]arene with thiophene substituents in para position with respect to the hydroxyl groups, has been investigated using ab initio and DFT quantum mechanical methods. This compound models a molecular device constituted by small oligomers of thiophene and calix[4]arene units, whose actuation mechanism is promoted by the conformational flexibility of the latter. To examine the influence of the electronic structure of this electroactive calix[4]arene, three different states have been considered: (i) neutral state; (ii) oxidized state, in which one electron is extracted from each thiophene ring; and (iii) oxidized-deprotonated state, in which the two hydroxyl groups of the oxidized compound are deprotonated. Results are discussed and compared with those obtained for the same molecule but without thiophene substituents, 25,27-dihydroxy-26,28-dimethoxycalix[4]arene. Although the influence of the thiophene substituents is negligible in the neutral state, they play a crucial role in the rotational isomerism of both the oxidized and deprotonated-oxidized states.

Journal Article↗
PubMed2006

Structure by design: from single proteins and their building blocks to nanostructures.

Nanotechnology realizes the advantages of naturally occurring biological macromolecules and their building-block nature for design. Frequently, assembly starts with the choice of a "good" molecule that is synthetically optimized towards the desired shape. By contrast, we propose starting with a pre-specified nanostructure shape, selecting candidate protein building blocks from a library and mapping them onto the shape and, finally, testing the stability of the construct. Such a shape-based, part-assembly strategy is conceptually similar to protein design through the combinatorial assembly of building blocks. If the conformational preferences of the building blocks are retained and their interactions are favorable, the nanostructure will be stable. The richness of the conformations, shapes and chemistries of the protein building blocks suggests a broad range of potential applications; at the same time, it also highlights their complexity. In this Opinion article, we focus on the first step: validating such a strategy against experimental data.

Drug Design↗
PubMed2006

Force-field parametrization of retro-inverso modified residues: development of torsional and electrostatic parameters.

Torsional and the electrostatic parameters for molecular mechanics studies of retro-inverso modified peptides have been developed using quantum mechanical calculations. The resulting parameters have been compared with those calculated for conventional peptides. Rotational profiles, which were obtained spanning the corresponding dihedral angle, were corrected by removing the energy contributions associated to changes in interactions different from torsion under study. For this purpose, the torsional energy associated to each point of the profiles was estimated as the corresponding quantum mechanical energy minus the bonding and nonbonding energy contributions produced by the perturbations that the variation of the spanned dihedral angle causes in the bond distances, bond angles and the other dihedral angles. These energies were calculated using force-field expressions. The corrected profiles were fitted to a three-term Fourier expansion to derive the torsional parameters. Atomic charges for retro-inverso modified residues were derived from the rigorously calculated quantum mechanical electrostatic potential. Furthermore, the reliability of electrostatic models based on geometry-dependent charges and fixed charges has been examined.

Amino Acids↗
PubMed2006

From peptide-based material science to protein fibrils: discipline convergence in nanobiology.

This paper illustrates the merits of convergence in nanobiology of two seemingly disparate fields, material science and computational biology. Traditionally, material science has been a discipline involving design and fabrication of synthetic polymers consisting of repeating units. Collaboration with synthetic organic chemists allowed design of new polymers, with a range of altered conformations. Yet, naturally occurring proteins are also materials. Their varied sequences and structures should enrich material science providing more complex shapes, scaffolds and chemical properties. For material scientists, the enhanced coverage of chemical space obtained by integrating proteins and synthetic organic chemistry through the introduction of non-natural residues allows a range of new useful potential applications.

Biocompatible Materials↗
PubMed2006

Concepts and schemes for the re-engineering of physical protein modules: generating nanodevices via targeted replacements with constrained amino acids.

Physically building complex multi-molecular structures from naturally occurring biological macromolecules has aroused a great deal of interest. Here we focus on nanostructures composed of re-engineered, natural 'foldamer' building blocks. Our aim is to provide some of the underlying concepts and schemes for crafting structures utilizing such conformationally relatively stable molecular components. We describe how, via chemical biology strategies, it is further possible to chemically manipulate the foldamer building blocks toward specific shape-driven structures, which in turn could be used toward potential-designed functions. We outline the criteria in choosing candidate foldamers from the vast biological repertoire, and how to enhance their stability through selected targeted replacements by non-proteinogenic conformationally constrained amino acids. These approaches combine bioinformatics, high performance computations and mathematics with synthetic organic chemistry. The resulting artificially engineered self-organizing molecular scale structures take advantage of nature's nanobiology toolkit and at the same time improve on it, since their new targeted function differs from that optimized by evolution. The major challenge facing nanobiology is to be able to exercise fine control over the performance of these target-specific molecular machines.

Combinatorial Chemistry Techniques↗
PubMed2006

De novo tubular nanostructure design based on self-assembly of beta-helical protein motifs.

We present an approach for designing self-assembled nanostructures from naturally occurring building block segments obtained from native protein structures. We focus on structural motifs from left-handed beta-helical proteins. We selected 17 motifs. Copies of each of the motifs are stacked one atop the other. The obtained structures were simulated for long periods by using Molecular Dynamics to test their ability to retain their organization over time. We observed that a structural model based on the self-assembly of a motif from E. coli galactoside acetyltransferase produced a very stable tube. We studied the interactions that help maintain the conformational stability of the systems, focusing on the role of specific amino acids at specific positions. Analysis of these systems and a mutational study of selected candidates revealed that the presence of proline and glycine residues in the loops of beta-helical structures greatly enhances the structural stability of the systems.

Acetyltransferases↗
PubMed2005

DFT-GIAO study of aryltetralin lignan lactones: conformational analyses and chemical shifts calculations.

The conformational properties of polygamain and morelensin, two aryltetralin lignan lactones, have been investigated in both the gas-phase and chloroform solution using DFT calculations at the B3LYP/6-311G(d,p) level. Results indicate that the conformation of polygamain is very rigid. Thus, the conformational flexibility of its five-membered rings is considerably restricted as reflects the pseudorotational parameters of the corresponding envelope conformations. On the other hand, morelensin shows a notable conformational flexibility, which is mainly due to its two methoxy groups. Accordingly, 16 minimum energy conformations with relative energies smaller than 2.4 kcal/mol were detected. Furthermore, chemical shifts for 13C nuclei have been calculated using the GIAO method, results being compared with experimental data. A good agreement was found for both polygamain and morelensin.

Benzofurans↗
PubMed2005

Systematic evaluation of the conformational properties of aliphatic omega-methoxy methyl esters.

[structure: see text] A systematic conformational study of omega-methoxy methyl esters, CH(3)O-(CH2)n-COO-CH3 with n = 3 and 4, has been performed using quantum mechanical calculations at the MP2 level. Calculations have been carried out in both gas phase and chloroform solution, a polarizable continuum solvation model being used to represent the latter. Results have been compared with those recently obtained for the analogues omega-hydroxy acids, HO-(CH2)n-COOH with n = 3 and 4. The compounds with n = 3 clearly favor coiled conformations, the population expected for extended and semiextended conformations being very low. However, for compounds with n = 4 the minimum energy extended and semiextended structures become considerably more stable. The overall results indicate that the conformational preferences of the central aliphatic segment of omega-methoxy methyl esters and omega-hydroxy acids are not influenced by the formation of intramolecular O-H...O hydrogen bonds.

Journal Article↗
PubMed2005

Reliability of the density functional approximation to describe the charge transfer and electrostatic complexes involved in the modeling of organic conducting polymers.

Both the intermolecular interaction energies and the geometries for M... thiophene, M... pyrrole, M(n+)... thiophene, and M(n+)... pyrrole (with M = Li , Na, K, Ca, and Mg; and M(n+) = Li+, Na+, K+, Ca2+, and Mg2+) have been estimated using four commonly used density functional theory (DFT) methods: B3LYP, B3PW91, PBE, and MPW1PW91. Results have been compared to those provided by HF, MP2, and MP4 conventional ab initio methods. The PBE and MPW1PW91 are the only DFT methods able to provide a reasonable description of the M...pi complexes. Regarding M(n+)...pi complexes, the four DFT methods have been proven to be adequate in the prediction of these electrostatically stabilized systems, even though they tend to overestimate the interaction energies.

Journal Article↗
PubMed2005

Unusually high pyramidal geometry of the bicyclic amide nitrogen in a complex 7-azabicyclo[2.2.1]heptane derivative: Theoretical analysis using a bottom-up strategy.

The high pyramidalization of the bicyclic amide nitrogen found in the crystal structure of a dipeptide incorporating (1S,2S,4R)-N-benzoyl-2-phenyl-7-azabicyclo[2.2.1]heptane-1-carboxylic acid has been investigated using quantum mechanical calculations. More specifically, a bottom-up strategy based on the study of model molecules of progressive complexity has been used. First, an appropriate quantum mechanical method has been selected by examining the distortion of the amide bond in three simple model molecules. Next, the amide distortion induced by the norbornane ring has been evaluated by considering three different 7-azabicyclo[2.2.1]heptane amides. After this, the suitability of quantum mechanical calculations to predict the effect of the substituents on the pyramidalization of the bicyclic amide nitrogen has been investigated by comparing experimental and theoretical parameters for a number of compounds. Finally, the factors responsible for amide distortion in the (1S,2S,4R)-N-benzoyl-2-phenyl-7-azabicyclo[2.2.1]heptane-1-carboxylic acid derivative have been elucidated using a hierarchical approach. For this purpose, several derivatives were generated by removing or modifying the substituents attached to the 7-azanorbornane system. Results have been discussed in terms of intramolecular specific interactions.

Amides↗
PubMed2005

Systematic evaluation of the conformational properties of aliphatic omega-hydroxy acids.

A systematic conformational study of omega-hydroxy acids, HO-(CH(2))(n)()-COOH with n ranging from 2 to 5, has been performed using quantum mechanical calculations at the MP2 level. To distinguish between intrinsic and environmentally induced conformational preferences, calculations have been carried out in both gas phase and chloroform solution, a polarizable continuum solvation model being used to represent the latter. Results indicate a consistent conformational behavior, as reflects the feature that the lowest energy minimum for n = 2, 3, 4, and 5 corresponds to the g+g-t, g+g+g-t, g-g+g+g-t, and g+g-g+g+g-t conformations, respectively. Furthermore, the stability of the extended and semi-extended conformations increases systematically with the size of the central aliphatic segment. The relationship between the size of the aliphatic segment and the stability of folded conformations is analyzed and discussed.

Journal Article↗
PubMed2005

Acid-base and electronic structure-dependent properties of Hoechst 33342.

An ab initio quantum mechanical study of the bis-benzimidazole derivative Hoechst 33342 is presented. Specifically, we report on the molecular geometry, proton affinity, gas-phase basicity, hydration, pKa, and molecular interaction potential map of Hoechst 33342 and the forms obtained by its protonation and deprotonation. Results have been compared with those obtained for Hoechst 33258 to analyze the influence of the chemical structure on the properties of this bis-benzimidazole derivative. Finally, the connection of some theoretical predictions with experimental evidences has been examined.

Benzimidazoles↗
PubMed2004

Theoretical strategy to provide atomistic models of comblike polymers: a generation algorithm combined with configurational bias Monte Carlo.

A computational strategy to model the amorphous phase of comblike polymers is presented. The strategy, denoted SuSi/CB (CB-configurational bias), combines the strength of an algorithm recently developed to generate reliable microstructures of dense amorphous polymers, which is based on a random search of energy minima, and configurational bias Monte Carlo method. The influence of different parameters used to define the characteristics of SuSi/CB on both the reliability of the generated structures and the computational effort has been examined in detail. Finally, we have modeled and characterized the supramolecular organization of poly(octadecyl acrylate) in the amorphous state.

Journal Article↗
PubMed2004

Performance of SuSi: a method for generating atomistic models of amorphous polymers based on a random search of energy minima.

The performance of a recently developed method to generate representative atomistic models of amorphous polymers has been investigated. This method, which is denoted SuSi, can be defined as a random generator of energy minima. The effects produced by different parameters used to define the size of the system and the characteristics of the generation algorithm have been examined. Calculations have been performed on poly(L,D-lactic) acid (rho = 1.25 g/cm3) and nylon 6 (rho = 1.084 g/cm(3)), which are important commercial polymers.

Algorithms↗
PubMed2004

Impact of the solvent on the conformational isomerism of calix[4]arenes: a study based on continuum solvation models.

The influence of solvation on the conformational isomerism of calix[4]arene and p-tert-butylcalix[4]arene has been investigated by using the continuum model reported by Miertus, Scrocco, and Tomasi (MST). The quantum mechanical (QM) and semiclassical (SC) formalisms of the MST model have been considered for two different solvents (chloroform and water). The suitability of the QM-MST and SC-MST methods has been examined by comparison with previous results derived from classical molecular dynamics (MD) simulations with explicit solvent molecules. The application of the continuum model to the solute configurations generated by using in vacuo classical MD simulations provides a fast strategy to evaluate the effects of the solvent on the conformational preferences of calixarenes. These encouraging results allow us to propose the use of continuum models to solutes with complex molecular structures, which are traditionally studied by MD simulations.

Journal Article↗
PubMed2004

Thermal stability of the secondary structure of poly(alpha,L-glutamate) in self-assembled complexes as studied by molecular dynamics in chloroform solution.

The thermal stability of the self-assembled complexes formed by alkyltrimethylammonium surfactants and poly(alpha,l-glutamate) is investigated in dilute chloroform solution by molecular dynamics simulations. By applying temperatures ranging from 300 to 500 K, we observed an extraordinary stability of the alpha-helix adopted by the polypeptide during a total of 48 ns. The multiple electrostatic interactions formed between the surfactant chains and the polyanion play a crucial role in this stability since they are responsible for the inaccessibility of the solvent molecules to the helix even at high temperatures.

Chloroform↗