Jordi Casanovas

Reviewing Extrapolation Procedures of the Electronic Properties on the π-Conjugated Polymer Limit

In this article, the extrapolation procedures of π-π* electronic transition energy on π-conjugated oligomers are reexamined. Different models, including the simplest coupled oscillator, the free electron, the Hückel approach, the molecular exciton model, and some specific fitting-functions, are compared using the transition energies derived from theoretical calculations on three thiophene-based oligomer series. Specifically, oligomers of up to 30 repeating units have been considered to include the saturation effects as a function of chain length. The coupled oscillator model of W. Kuhn and the fitting-function of Hirayama are the models that present the better suit on the transition energy interpolation as a function of chain length. Using only the first four oligomers of the series (n = 2 up to 8) yields an estimation of the transition energy on the polymer limit with an average error of ∼1.5%. The vertical and adiabatic ionization potential present a better fit with the Hückel model approach. Finally, implications of the environmental polarity on the electronic properties, molecular geometry, charge distribution, and aromaticity are shortly discussed.

Ab initio calculations of 29Si solid state NMR chemical shifts of silane and silanol groups in silica

Abstract We report the results of first principles density functional theory (DFT) calculations on the 1 H and 29 Si NMR chemical shifts of silane and hydroxyl groups in silica. The structure of the isolated ≡Si–H and ≡Si–OH or of the geminal =Si(H)2 and =Si(OH)2 defects has been fully optimized from mechanically embedded cluster models derived from crystalline α-quartz and the nuclear magnetic shielding properties have been determined according to the GIAO method. The computed 29 Si chemical shifts, δ( 29 Si) in ppm, are (in parenthesis the experimental values): ≡Si–OH −99 (−99), ≡Si–H −86 (−85), =Si(OH)2 −85 (−89), =Si–(H)2 −55 (−50).

Ab initio calculations on π‐stacked thiophene dimer, trimer, and tetramer: Structure, interaction energy, cooperative effects, and intermolecular electronic parameters

π‐Stacked complexes formed by two, three, and four thiophene rings have been investigated using abinitio quantum mechanical calculations. The relative orientation between the rings was investigated for each complex by exploring the corresponding potential energy surface at the MP2/6‐31+G(d,p) level, the inter‐ring distance, and the degree of tilting being examined in each case. Interaction energies were calculated at the MP2, MP3, MP4, and CCSD, levels of theory. Negligible or even slightly positive n‐body effects have been predicted for the stacked thiophene arrangements studied in this work. This is consequence of the cancellation of favorable induction contribution by the destabilizing dispersion component. On the other hand analysis of the optimized geometries obtained for the trimer and tetramer revealed that the orientation of the rings presents a preferred degree of periodicity. Finally, we found that the lowest transition energy decreases when the size of the complex increases, this feature being attributed to desestabilization of the HOMO and stabilization of the LUMO that occur simultaneously.

The Energy Landscape of a Selective Tumor-Homing Pentapeptide

Recently, a potentially powerful strategy based on phage-display libraries has been presented to target tumors via homing peptides attached to nanoparticles. The Cys-Arg-Glu-Lys-Ala (CREKA) peptide sequence has been identified as a tumor-homing peptide that binds to clotted plasmas proteins present in tumor vessels and interstitium. The aim of this work consists of mapping the conformational profile of CREKA to identify the bioactive conformation. For this purpose, a conformational search procedure based on modified simulated annealing combined with molecular dynamics was applied to three systems that mimic the experimentally used conditions: (i) the free peptide; (ii) the peptide attached to a nanoparticle; and (iii) the peptide inserted in a phage display protein. In addition, the free peptide was simulated in an ionized aqueous solution environment, which mimics the ionic strength of the physiological medium. Accessible minima of all simulated systems reveal a multiple interaction pattern involving the ionized side chains of Arg, Glu, and Lys, which induces a beta-turn motif in the backbone observed in all simulated CREKA systems.

Modeling biominerals formed by apatites and DNA

Different aspects of biominerals formed by apatite and DNA have been investigated using computer modeling tools. Firstly, the structure and stability of biominerals in which DNA molecules are embedded into hydroxyapatite and fluoroapatite nanopores have been examined by combining different molecular mechanics methods. After this, the early processes in the nucleation of hydroxyapatite at a DNA template have been investigated using molecular dynamics simulations. Results indicate that duplexes of DNA adopting a B double helix can be encapsulated inside nanopores of hydroxyapatite without undergoing significant distortions in the inter-strand hydrogen bonds and the intra-strand stacking. This ability of hydroxyapatite is practically independent of the DNA sequence, which has been attributed to the stabilizing role of the interactions between the calcium atoms of the mineral and the phosphate groups of the biomolecule. In contrast, the fluorine atoms of fluoroapatite induce pronounced structural distortions in the double helix when embedded in a pore of the same dimensions, resulting in the loss of its most relevant characteristics. On the other hand, molecular dynamics simulations have allowed us to observe the formation of calcium phosphate clusters at the surface of the B-DNA template. Electrostatic interactions between the phosphate groups of DNA and Ca2+ have been found to essential for the formation of stable ion complexes, which were the starting point of calcium phosphate clusters by incorporating from the solution.

Self‐Assembly of Tetraphenylalanine Peptides

Three different tetraphenylalanine (FFFF) based peptides that differ at the N- and C-termini have been synthesized by using standard procedures to study their ability to form different nanoassemblies under a variety of conditions. The FFFF peptide assembles into nanotubes that show more structural imperfections at the surface than those formed by the diphenylalanine (FF) peptide under the same conditions. Periodic DFT calculations (M06L functional) were used to propose a model that consists of three FFFF molecules defining a ring through head-to-tail NH3(+)⋅⋅⋅(-)OOC interactions, which in turn stack to produce deformed channels with internal diameters between 12 and 16 Å. Depending on the experimental conditions used for the peptide incubation, N-fluorenylmethoxycarbonyl (Fmoc) protected FFFF self-assembles into a variety of polymorphs: ultra-thin nanoplates, fibrils, and star-like submicrometric aggregates. DFT calculations indicate that Fmoc-FFFF prefers a parallel rather than an antiparallel β-sheet assembly. Finally, coexisting multiple assemblies (up to three) were observed for Fmoc-FFFF-OBzl (OBzl = benzyl ester), which incorporates aromatic protecting groups at the two peptide terminals. This unusual and noticeable feature is attributed to the fact that the assemblies obtained by combining the Fmoc and OBzl groups contained in the peptide are isoenergetic.

Application of 1-aminocyclohexane carboxylic acid to protein nanostructure computer design

Conformationally restricted amino acids are promising candidates to serve as basic pieces in redesigned protein motifs which constitute the basic modules in synthetic nanoconstructs. Here we study the ability of constrained cyclic amino acid 1-aminocyclohexane-1-carboxylic acid (Ac6c) to stabilize highly regular beta-helical motifs excised from naturally occurring proteins. Calculations indicate that the conformational flexibility observed in both the ring and the main chain is significantly higher than that detected for other 1-aminocycloalkane-1-carboxylic acids (Acnc, where n refers to the size of the ring) with smaller cycles. Incorporation of Ac6c into the flexible loops of beta-helical motifs indicates that the stability of such excised building blocks as well as the nanoassemblies derived from them is significantly enhanced. Thus, the intrinsic Ac6c tendency to adopt folded conformations combined with the low structural strain of the cyclohexane ring confers the ability to both self-adapt to the beta-helix motif and to stabilize the overall structure by absorbing part of its conformational fluctuations. Comparison with other Acnc residues indicates that the ability to adapt to the targeted position improves considerably with the ring size, i.e., when the rigidity introduced by the strain of the ring decreases.

Water absorbed by polyaniline emeraldine tends to organize, forming nanodrops

Interactions, in terms of both binding energies and microscopic organization, of water molecules absorbed by hydrophilic polyaniline emeraldine base have been investigated using quantum mechanical calculations, molecular dynamics simulation, FTIR spectroscopy, and (1)H NMR. From an enthalpic point of view, water molecules interact more favorably with imine nitrogen atoms than with amine ones, even though the latter are entropically favored with respect to the former because of their two binding sites. Quantum mechanical results show that interaction energies of water molecules reversibly absorbed but organized individually around a binding site range from 3.0 to 6.3 kcal/mol, which is in good agreement with activation energies of 3-5 kcal/mol previously determined by thermodynamic measurements. The irreversible absorption of water to produce C-OH groups in rings of diimine units has been examined considering a three steps process in which water molecules act as both acidic and nucleophilic reagent. Although calculations predict that the whole process is disfavored by 5-8 kcal/mol only, FTIR and (1)H NMR detected the existence of reversibly absorbed water but not of C-OH groups. Both the binding energies and the structural information provided by molecular dynamics simulations have been used to interpret the existence of two types of physisorbed water molecules: (i) those that interact individually with polymer chains and (ii) those immersed in nanodrops that are contained within the polymeric matrix. The binding energies calculated for these two types of water molecules are fully consistent with the thermodynamic activation energies previously reported.

A First Principle Analysis of the Structure of Oligoanilines Doped with Alkylsulfonic Acids

The interaction of polyaniline with alkylsulfonate dopants have been investigated at the atomic level using quantum mechanical methods. Calculations have been performed on complexes formed by dopant molecules with an alkyl group ranging from methyl to nonyl and model oligoanilines of different sizes. The stabilization provided by the formation of the alkylsulfonate...oligoaniline complexes (70-90 kcal/mol) is significantly higher than that found for conventional hydrogen bonds (5-12 kcal/mol) but lower than that obtained for methylsulfate...alkylammonium and methylsulfate...Na(+) systems (120-135 kcal/mol). On the other hand, the influence of size of the alkyl group contained in the dopant on the interaction is practically negligible, whereas, in opposition, the number of aniline units used to represent polyaniline significantly affects the energetics of the interaction. Specifically, the interaction energy of an alkyl-dopant molecule and an infinite polyaniline chain has been predicted to be around -65 kcal/mol. The overall results allow the conclusion that the interaction between alkylsulfonate dopants and polyaniline is a very local phenomenon.

29Si solid state NMR of hydroxyl groups in silica from first principle calculations

Abstract We report the results of first principles Hartree-Fock (HF) and density functional theory (DFT) calculations on the 1 H, 29 Si and 17 O NMR chemical shifts of hydroxyl groups in silica. The structure of the isolated or SiOH of the geminal Si(OH) 2 groups has been fully optimized from cluster models derived from crystalline α-quartz and the nuclear magnetic shielding properties have been determined according to the GIAO method. Quantitative agreement with the available experimental data has been obtained at the DFT level.