Energetics of Radical Formation in Eumelanin Building Blocks: Implications for Understanding Photoprotection Mechanisms in Eumelanin.

The supramolecular structure of melanin pigments is characterized by a high concentration of radical species. Therefore, the energetics of the radical formation in melanin building blocks is key for understanding the structure and the electronic properties of the pigments at the molecular level. Nevertheless, the radical energetics of even the simplest melanin building blocks are largely unknown. In order to address this fundamental issue, the bond dissociation enthalpies (BDEs) for the melanin monomers 5,6-dihydroxy-1H-indole-2-carboxylic acid (DHICA), 1H-indole-5,6-diol (DHI), and 1H-indole-5,6-dione (IQ) were determined through high-accuracy ab initio quantum chemistry methods. Our results provide strong evidence of the importance on BDEs for explaining the experimentally observed dependence of the antioxidant properties of eumelanin pigments on the DHICA/DHI ratio, and the role that these two species play on the photoprotection mechanism.

A First-Principles Approach to the Dynamics and Electronic Properties of p-Nitroaniline in Water.

Born-Oppenheimer molecular dynamics of p-nitroaniline (PNA) in water was carried out and the electronic structure was investigated by time-dependent density functional theory. Hydrogen bonding involving the PNA nitro and amine groups and the water molecules leads to an ∼160 cm(-1) red shift of the ν(N-O) and ν(N-H) stretching frequencies relative to the gas phase species. Our estimate for the peak position of the charge transfer (CT) band in the absorption spectrum of PNA in water (∼3.5 eV) is in good agreement with experimental data (3.3 eV). We have investigated the specific role played by local hydrogen bonding and electrostatic interactions on the electronic absorption spectrum. It is shown that although electrostatic interactions play a major role for explaining the structure of the PNA CT band in water, the theoretical prediction of the observed red shift is improved by the explicit consideration of local hydrogen bonding of PNA to water. For isolated PNA, we predict that the dipole moment of the second excited state (S2) is 9.6 D greater than ground state (S0) dipole, which is in good agreement with experimental information (8.2-9.3 D). Calculation of charge transfer indexes for the two first excitations of PNA in water indicates that despite the feature that a small fraction of S1 states (<5%) may exhibit some CT character, CT states in solution are mainly associated with S2 ← S0 transitions.

Probing Lewis Acid-Base Interactions with Born-Oppenheimer Molecular Dynamics: The Electronic Absorption Spectrum of p-Nitroaniline in Supercritical CO2.

The structure and dynamics of p-nitroaniline (PNA) in supercritical CO2 (scCO2) at T = 315 K and ρ = 0.81 g cm(-3) are investigated by carrying out Born-Oppenheimer molecular dynamics, and the electronic absorption spectrum in scCO2 is determined by time dependent density functional theory. The structure of the PNA-scCO2 solution illustrates the role played by Lewis acid-base (LA-LB) interactions. In comparison with isolated PNA, the ν(N-O) symmetric and asymmetric stretching modes of PNA in scCO2 are red-shifted by -17 and -29 cm(-1), respectively. The maximum of the charge transfer (CT) absorption band of PNA in scSCO2 is at 3.9 eV, and the predicted red-shift of the π → π* electronic transition relative to the isolated gas-phase PNA molecule reproduces the experimental value of -0.35 eV. An analysis of the relationship between geometry distortions and excitation energies of PNA in scCO2 shows that the π → π* CT transition is very sensitive to changes of the N-O bond distance, strongly indicating a correlation between vibrational and electronic solvatochromism driven by LA-LB interactions. Despite the importance of LA-LB interactions to explain the solvation of PNA in scCO2, the red-shift of the CT band is mainly determined by electrostatic interactions.

A first principles approach to the electronic properties of liquid and supercritical CO2.

The electronic absorption spectra of liquid and supercritical CO2 (scCO2) are investigated by coupling a many-body energy decomposition scheme to configurations generated by Born-Oppenheimer molecular dynamics. A Frenkel exciton Hamiltonian formalism was adopted and the excitation energies were calculated with time dependent density functional theory. A red-shift of ∼ 0.2 eV relative to the gas-phase monomer is observed for the first electronic absorption maximum in liquid and scCO2. The origin of this shift, which is not very dependent on deviations from the linearity of the CO2 molecule, is mainly related to polarization effects. However, the geometry changes of the CO2 monomer induced by thermal effects and intermolecular interactions in condensed phase lead to the appearance of an average monomeric electric dipole moment〈µã€‰= 0.26 ± 0.04 D that is practically the same at liquid and supercritical conditions. The predicted average quadrupole moment for both liquid and scCO2 is〈Θ〉= - 5.5 D Å, which is increased by ∼ -0.9 D Å relative to its gas-phase value. The importance of investigating the electronic properties for a better understanding of the role played by CO2 in supercritical solvation is stressed.

Ab initio calculation of the electronic absorption spectrum of liquid water.

The electronic absorption spectrum of liquid water was investigated by coupling a one-body energy decomposition scheme to configurations generated by classical and Born-Oppenheimer Molecular Dynamics (BOMD). A Frenkel exciton Hamiltonian formalism was adopted and the excitation energies in the liquid phase were calculated with the equation of motion coupled cluster with single and double excitations method. Molecular dynamics configurations were generated by different approaches. Classical MD were carried out with the TIP4P-Ew and AMOEBA force fields. The BLYP and BLYP-D3 exchange-correlation functionals were used in BOMD. Theoretical and experimental results for the electronic absorption spectrum of liquid water are in good agreement. Emphasis is placed on the relationship between the structure of liquid water predicted by the different models and the electronic absorption spectrum. The theoretical gas to liquid phase blue-shift of the peak positions of the electronic absorption spectrum is in good agreement with experiment. The overall shift is determined by a competition between the O-H stretching of the water monomer in liquid water that leads to a red-shift and polarization effects that induce a blue-shift. The results illustrate the importance of coupling many-body energy decomposition schemes to molecular dynamics configurations to carry out ab initio calculations of the electronic properties in liquid phase.

Structure and electronic properties of a benzene-water solution.

Electronic properties of benzene in water were investigated by a sequential quantum mechanical/molecular dynamics approach. Emphasis was placed on the analysis of the structure, polarization effects, and ionization spectrum. By adopting a polarizable model for both benzene and water the structure of the benzene-water solution is in good agreement with data from first principles molecular dynamics. Further, strong evidence that water molecules acquire enhanced orientational order near the benzene molecule is found. Upon hydration, the quadrupole moment of benzene is not significantly changed in comparison with the gas-phase value. We are also reporting results for the dynamic polarizability of benzene in water. Our results indicate that the low energy behaviour of the dynamic polarizability of gas-phase and hydrated benzene is quite similar. Outer valence Green's function calculations for benzene in liquid water show a splitting of the gas-phase energy levels associated with the 1e(1g)(π), 2e(2g), and 2e(1u) orbitals upon hydration. Lifting of the orbitals degeneracy and redshift of the outer valence bands is related to symmetry breaking of the benzene structure in solution and polarization effects from the surrounding water molecules.

Electronic excitation of Cl- in liquid water and at the surface of a cluster: a sequential Born-Oppenheimer molecular dynamics/quantum mechanics approach.

A sequential molecular dynamics/quantum mechanics approach is applied to investigate the electronic excitation of Cl(-) in liquid water and in a water cluster. Time-dependent density functional theory (TDDFT) and equation-of-motion coupled-cluster with single and double excitations (EOM-CCSD) are used to calculate the excitation energies from Born-Oppenheimer molecular dynamics configurations. The selected configurations include a quantum system with the Cl(-) anion and a number of explicit water molecules (n(w)) as well as an embedding background defined by fractional point charges on the remaining water molecules. Our results indicate that for both the liquid and the cluster environments the excited electron is delocalized on the hydrogen atoms of the first hydration shell and in a nearby cavity. Convergence of the charge-transfer-to-solvent (CTTS) energy with the number of water molecules is observed for a quantum system embedded in the polarizing charge background for n(w) > or = 3. Furthermore, we find that the CTTS energy of Cl(-) in both solution and cluster environments is very similar. The predicted CTTS energy threshold for the ionic solution (approximately 6.6 +/- 0.3 eV) is in good agreement with experiment (6.8 and 7.1 eV).

Dynamic polarizability, Cauchy moments, and the optical absorption spectrum of liquid water: a sequential molecular dynamics/quantum mechanical approach.

The dynamic polarizability and optical absorption spectrum of liquid water in the 6-15 eV energy range are investigated by a sequential molecular dynamics (MD)/quantum mechanical approach. The MD simulations are based on a polarizable model for liquid water. Calculation of electronic properties relies on time-dependent density functional and equation-of-motion coupled-cluster theories. Results for the dynamic polarizability, Cauchy moments, S(-2), S(-4), S(-6), and dielectric properties of liquid water are reported. The theoretical predictions for the optical absorption spectrum of liquid water are in good agreement with experimental information.

Study of doubly charged alkaline earth metal and 3-azidopropionitrile complexes by electrospray ionization mass spectrometry.

The present work describes a study of the complexation of calcium and magnesium by 3-azidopropionitrile by means of electrospray ionization mass spectrometry (ESI-MS). Complexes were obtained from solutions of calcium and magnesium salts of the type CaX2 and MgX2 (where X = Cl or NO3) in water and methanol/water. The complexes detected were mainly double positively charged, with various stoichiometries not depending on the solvent, since water and 3-azidopropionitrile were always the main ligands. Solvation with methanol was not observed unlike in a previous study of complexation of nickel and cobalt by 3-azidopropionitrile. The complex ions [M(II)Az4(H2O)](2+), [M(II)Az5](2+) (where M = Ca and Mg) are the most abundant for both metals, and both counter ions. Tandem mass spectrometric (MS/MS) analysis showed that, under collision-induced dissociation (CID) conditions, the most important processes occurring were loss of neutral ligands and the replacement of 3-azidopropionitrile by water. A complex species containing reduced alkaline earth metal was due to radical loss, resulting from homolytic cleavage in the azide ligand. Some terminal ions, in the fragmentation sequences, point to the nitrile group as the coordination site in the 3-azidopropionitrile. Density functional theory (DFT) calculations confirmed this coordination site and proved that 3-azidopropionitrile behaves as a monodentate ligand in the systems under study. Moreover, the theoretical study proved that the presence of water ligand introduces stability through a hydrogen bond established between the water molecule and one nitrogen atom of the azido group. In addition, the strong dipole moment of 3-azidopropionitrile (4.76 D), which is mainly related to presence of the nitrile group, favors the stabilization of the metal-ligand complexes through charge-dipole interactions and the coordination of the metal to the nitrile group.

Energetics of the allyl group.

Aiming to improve our understanding of the stability of radicals containing the allylic moiety, carbon-hydrogen bond dissociation enthalpies (BDEs) in propene, isobutene, 1-butene, (E)-2-butene, 3-metylbut-1-ene, (E)-2-pentene, (E)-1,3-pentadiene, 1,4-pentadiene, cyclohexene, 1,3-cyclohexadiene, and 1,4-cyclohexadiene have been determined by quantum chemistry calculations. The BDEs in cyclohexene, 1,3-cyclohexadiene, and 1,4-cyclohexadiene have also been obtained by time-resolved photoacoustic calorimetry. The theoretical study involved a DFT method as well as ab initio complete basis-set approaches, including the composite CBS-Q and CBS-QB3 procedures, and basis-set extrapolated coupled-cluster calculations (CCSD(T)). By taking the C(sp3)-H BDE in propene as a reference, we have concluded that one methyl group bonded to C3 in propene (i.e., 1-butene) leads to a decrease of 12 kJ mol(-1) and that a second methyl group bonded to C3 (3-methylbut-1-ene) further decreases the BDE by 8 kJ mol(-1). When the methyl group is bonded to C2 in propene (isobutene), an increase of 7 kJ mol(-1) is observed. Finally, a methyl group bonded to C1 in propene (2-butene) has essentially no effect (-1 kJ mol(-1)). While this trend can be rationalized in terms of stabilization of the corresponding radical (through hyperconjugation and pi-delocalization), the BDE values observed for the dienes can only be understood by considering the thermodynamic stabilities of the parent compounds.

Complexation of transition metals by 3-azidopropionitrile. An electrospray ionization mass spectrometry study.

Most complexes of azides and transition metals involve the N(3)(-) azide anion as a ligand other than an organic azide. Complexes of organic azides with metals are involved in biological applications and in the deposition of nitrenes on metal surfaces, producing nitride layers for semi-conductors preparation; this makes the study of these interactions an important issue. This work describes a study of the complexation of nickel and cobalt by 3-azidopropionitrile by means of electrospray ionization mass spectrometry (ESI-MS). Complexes were obtained from solutions of NiCl(2) and CoCl(2) in methanol/water. In the case of nickel, other NiX(2) salts were investigated (where X = Br or NO(3)) and other solvents were also studied (notably ethanol/water). All complexes detected were single positively charged, with various stoichiometries, some resulted from the fragmentation of the ligand, the loss of N(2), and HCN being quite common. The most abundant cations observed were [Ni(II)AzAzX](+), where X = Cl, Br, NO(3). Some of the complexes showed solvation with methanol/ethanol/water. Metal reduction was observed in complexes where a radical was lost, resulting from the homolytic cleavage of a metal-nitrogen bond. Collision induced dissociation (CID) experiments followed by tandem mass spectrometry (MS-MS) analysis were not absolutely conclusive about the coordination site. However, terminal ions observed from the fragmentation routes were explained by a proposed gas-phase mechanism. Density functional theory calculations were carried out and provided structures for some complexes, pointing to the possibility of 3-azidopropionitrile acting as a mono- or a bidentate ligand.

Conformational and orientational guidance of the analgesic dipeptide kyotorphin induced by lipidic membranes: putative correlation toward receptor docking.

The analgesic dipeptide kyotorphin (L-Tyr-L-Arg) and an acylated kyotorphin derivative were studied by a combination of theoretical (molecular dynamics simulation and quantum mechanics methods) and experimental (fluorescence and infrared spectroscopies) approaches both in solution and in model systems of membranes. At biological pH the peptides have a neutral net charge. Nevertheless, their phenolic rings interact with phospholipid molecules (partition coefficient varies from 6 x 10(2) to 2 x 10(4), depending on the lipid and pH used) despite being exposed to the aqueous bulk medium. The lowest energy transition dipole moment is displaced from the normal to the lipid bilayer by 20 degrees on average. The observed extensive interaction, pK(a), precise location, and well-defined orientation in membranes combined with the ability to discriminate rigid raftlike membrane domains suggest that kyotorphin meets the structural constraints needed for receptor-ligand interaction. The acylated kyotorphin derivative mimics kyotorphin properties and represents a promising way for entrapment in a drug carrier and transport across the blood-brain barrier.

Filipin orientation revealed by linear dichroism. Implication for a model of action.

The organization of the polyene antibiotic filipin in membranes containing cholesterol is a controversial matter of debate. Two contradictory models exist, one suggesting a parallel and the other perpendicular organization of filipin with respect to the plane of the membrane. UV-vis linear dichroism, ATR-FTIR, and fluorescence anisotropy decay techniques were combined to study the orientation of filipin in model systems of membranes composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) or 1,2-palmitoyl-sn-glycero-3-phosphocholine (DPPC) with and without cholesterol. Filipin's orientation is determined by the presence/absence of cholesterol when it is inserted in gel crystalline phase model membranes. When cholesterol (33%) is present in DPPC bilayers, filipin stands perpendicular to the membrane surface as expected in "pore-forming" models. At variance, absence of cholesterol leaves filipin in an essentially random organization in the lipidic matrix. In liquid crystalline phase bilayers (POPC) filipin's orientation is perpendicular to the membrane surface even in absence of cholesterol. Thus filipin's activity/organization depends not only on cholesterol presence but also in the lipid phase domain it is inserted in. These findings were combined with spectroscopy and microscopy data in the literature, solving controversial matters of debate.