Multiscale Modeling Unravels the Influence of Biomembranes on the Photochemical Properties of Embedded Anti-Oxidative Polyphenolic and Phenanthroline Chelating Dyes.

The embedding of caffeate methyl ester, the flavonoids luteolin and quercetin, and the o-phenanthroline and neocuproine in a liquid disordered lipid bilayer has been studied through extensive atomistic calculations. The location and the orientation of these bio-active antioxidants are explained and analyzed. While the two phenanthrolines strongly associate with the lipid tail region, the other three compounds are rather found among the head groups. The simulations showcase conformational changes of the flavonoids. Through the use of a hybrid quantum mechanics-molecular mechanics scheme and supported by a profound benchmarking of the electronic excited-state method for these compounds, the influence of the anisotropic environment on the compounds' optical properties is analyzed. Influences of surrounding water molecules and of the polar parts of the lipids on the transition dipole moments and excited-state dipole moments are weighted with respect to a change in conformation. The current study highlights the importance of the mapping of molecular interactions in model membranes and pinpoints properties, which can be biomedically used to discriminate and detect different lipid environments.

Methyl Radical in Clathrate Silica Voids. The Peculiar Physisorption Features of the Guest-Host Molecular Dynamics Interaction.

EPR line shape simulations of CH3/SiO2 clathrates and comparison to CH3/N2O and CH3/SiO2 experiments reveal the motional conditions of the CH3 radical up to the unusual regime of its stability, the high-temperature diffusional regime, at 300 K. In the low-temperature region, the CH3 in clathrates is found to rotate around the in-plane axes even at as low temperatures as 3.8 K. However, nonrotating methyls performing only libration about the C2-axes as well as around the C3-axis are also found, proving the existence of special sites in the clathrate voids that begin to accumulate a significant fraction of methyl radicals at temperatures below approximately 7 K. A distinctive feature in the spectrum anisotropy and line width temperature profiles is found nearby 25 K, which is interpreted as the radical physisorption inside the voids that occurs with the sample temperature lowering. The unusual increase of the CH3/SiO2 clathrate EPR spectral width with temperature over approximately 120 K has its origin in repeated angular momentum vector alterations due to frequent collisions with the clathrate void walls between periodical free rotation periods. This relaxation mechanism resembles to spin-rotation interaction known only for small molecular species in nonviscous fluids but unknown earlier for methyl hosted in solids.

Rotation Dynamics Do Not Determine the Unexpected Isotropy of Methyl Radical EPR Spectra.

A simple first-principles electronic structure computation, further qc (quantum chemistry) computation, of the methyl radical gives three equal hf (hyperfine) couplings for the three protons with the unpaired electron. The corresponding dipolar tensors were notably rhombic and had different orientations and regular magnitude components, as they should, but what the overall A-tensor was seen by the electron spin is a different story! The final g = (2.002993, 2.002993, 2.002231) tensor and the hf coupling results obtained in vacuum, at the B3LYP/EPRIII level of theory clearly indicate that in particular the above A = (-65.19, -65.19, 62.54) MHz tensor was axial to a first approximation without considering any rotational dynamics for the CH3. This approximation was not applicable, however, for the trifluoromethyl CF3 radical, a heavier and nonplanar rotor with very anisotropic hf coupling, used here for comparison. Finally, a derivation is presented explaining why there is actually no need for the CH3 radicals to consider additional rotational dynamics in order for the electron to obtain an axially symmetric hf (hyperfine) tensor by considering the simultaneous dipolar couplings of the three protons. An additional consequence is an almost isotropic A-tensor for the electron spin of the CH3 radical. To the best of our knowledge, this point has not been discussed in the literature before. The unexpected isotropy of the EPR parameters of CH3 was solely attributed to the rotational dynamics and was not clearly separated from the overall symmetry of the species. The present theoretical results allowed a first explanation of the "forbidden" satellite lines in the CH3 EPR spectrum. The satellites are a fingerprint of the radical rotation, helping thus in distinguishing the CH3 reorientation from quantum rotation at very low temperatures.

Anomalous EPR intensity distribution of the methyl radical quartet adsorbed on the surface of porous materials. Comparison with solid gas matrix isolation.

The two inner lines of the EPR quartet of methyl radicals trapped in cryogenic gas matrices are superpositions of the inner transitions of an A-proton-spin quartet and an E-proton-spin doublet. Their intensity relative to the outer lines provides information on the population of the methyl-rotation quantum states. The above intensity ratio for the CH3 in solids is a challenging problem of the quantum dynamics and statistical thermodynamics. The influence of the quantum-mechanical/inertial rotation on the intensity distribution of the hf components of methyl radical on the surface of porous materials, e.g., silica gel, is investigated by EPR line shape simulations and compared with spectra of the radical isolated in the bulk of solid gas samples. The experimental part of this study includes the first in literature EPR observation of methyl radical in the bulk of N2O solid and provides new essential information on CH3 in CO2 and Ar matrices, thus, covering both strongly hindered and almost free rotation of the radical. We verify the observation of nonrotating methyl radicals in a N2O matrix, discovered earlier in cold CO2, give a thorough account of their EPR characteristics, and explore their formation at the inner surface of porous materials. Combination of a classical spin-Hamiltonian with employment of quantum effects due to nuclear spin-rotation coupling and the radical symmetry were used to interpret the experimental spectral observations. The cause of experimentally found unexpected contribution of the excited degenerate E-doublets to the EPR spectrum down to 4.2 K and A/E transition amplitude ratios sometimes as high as ca. 1:8 at liquid-N2 temperature is sought. The validity of Bose-Einstein quantum (BEq-) statistics of the spin rotation states in addition to the classical Maxwell-Boltzmann (Boltzmann) statistics was also assessed against experimental population A/E-ratio data. The BEq-statistics were not previously applied to similar systems. Furthermore, detailed consideration of the laboratory/free space rotational degeneracy and the planarity of methyl radical was also included in this work.

Inertial rotation and matrix interaction effects on the EPR spectra of methyl radicals isolated in 'inert' cryogenic matrices.

The CW-EPR lineshapes of methyl and small methyl-like radicals trapped in noble gas matrices at liquid He temperatures are substantially different from the expected classical EPR spectra. At low temperatures they show small or negligible anisotropy in studies using different experimental techniques and have a temperature dependence that differs from systems whose motional dynamics is diffusion controlled. At liquid He temperatures, before the Boltzmann statistics take over in the classical high temperature realm, the spectral intensities are dominated by quantum statistics. These properties, which were obtained experimentally at temperatures about 5 K and lower, and up to about 20 K, can be attributed to quantum effects of inertial rotary motion and its coupling to the nuclear spin of the radical. Methyl-like radicals have nuclear-exchange symmetry and contain the lightest possible isotopes, protons, and deuterons. In the ideal case of absent radical-matrix interaction, the methyl rotation about the central heavier carbon atom guaranties minimal moments of inertia. However, the theoretical interpretation of the above effects and other related quantum effects, as well as recognition of the important physics which lead to them, is not a simple matter. The literature accumulated on the subject over the years is successful but contains several unresolved questions. Recently obtained spectra of methyl radicals in Kr, N(2) and CO matrices, which are less inert than the smaller noble gas Ar, were shown to exhibit greater, but certainly slight, overall anisotropic spectral features while in earlier experimental studies the anisotropy was practically absent. Even gases of smaller radii such as Ne and H(2) at liquid He temperatures show interesting differences as hosts of methyl radicals compared to Ar. Investigation of other possible causes of this difference, not excluding the experimentally controlled ones related to the sample preparation and the MW power saturation of the CW-EPR measurement, were conducted in this work.

3D QSAR/CoMFA and CoMSIA studies on antileukemic steroidal esters coupled with conformationally flexible nitrogen mustards.

Thirty-eight antileukemic steroidal esters possessing conformationally flexible nitrogen mustards were studied, and the 3D QSAR/CoMFA and CoMSIA methodologies were applied in order to derive the correlation between their structure and the in vivo antileukemic activity. These compounds show significantly reduced toxicity and possibly increased bioavailability compared to free nitrogen mustards and therefore constitute potent antileukemic drugs. Both the CoMFA and CoMSIA studies gave similar results indicating that the steric effect and the hydrophobic/hydrophilic balance especially in the steroidal part of the molecules probably determined their bioactivity. Of paramount interest is the observation that the orientation of the alkylating part of the SMEs toward the surface of ring B of the steroidal skeleton was related with increased activity. Concerning the steroidal part, the presence of hydrophobic groups in rings B and D was found to be important for enhanced activity. Enhancement of antileukemic potency is further observed if hydrophilic/H-bond acceptor groups are present at the positions 7 and 17 of the steroidal skeleton. Leapfrog simulations provided novel compounds which lead our future synthetic endeavor for obtaining SMEs with optimum bioactivity.

Interactions of the dipeptide paralysin beta-Ala-Tyr and the aminoacid Glu with phospholipid bilayers.

Existing evidence points out that the biological activity of beta-Ala-Tyr may in part related to its interactions with the cell membranes. For comparative reasons the effects of Glu were also examined using identical techniques and conditions. In order to examine their thermal and dynamic effects on membrane bilayers a combination of DSC, Raman and solid state NMR spectroscopy on DPPC/water model membranes were applied and the results were compared. DSC data showed that Glu perturbs to a greater degree the model membrane compared to beta-Ala-Tyr. Thus, alteration of the phase transition temperature and half width of the peaks, abolishment of the pretransition and influence on the enthalpy of the phase transition were more pronounced in the Glu loaded bilayers. Raman spectroscopy showed that incorporation of Glu in DPPC/water bilayers increased the order in the bilayers in contrast to the effect of the dipeptide. Several structural and dynamical properties of the DPPC multilamellar bilayers with and without the dipeptide or Glu were compared using high resolution C-13 MAS (Magic Angle Spinning) spectra and spectral simulations of inhomogeneously broadened, stationary P-31 NMR lineshapes measured under CP (Cross-polarization) conditions. These methods revealed that the aminoacid Glu binds in the close realm of the phosphate in the hydrophilic headgroup of DPPC while beta-Ala-Tyr is located more deeply inside the hydrophobic zone of the bilayer. The P-31 NMR simulations indicated restricted fast rotary motion of the phospholipids about their long axes in the organized bilayer structure. Finally, by the applied methodologies it is concluded that the two molecules under study exert dissimilar thermal and dynamic effects on lipid bilayers, the Glu improving significantly the packing of the lipids in contrast to the smaller and opposite effect of the dipeptide.

3D-Quantitative structure-activity relationships of synthetic antileishmanial ring-substituted ether phospholipids.

The application of 2D-NMR spectroscopy and Molecular Modeling in determining the active conformation of flexible molecules in 3D-QSAR was demonstrated in the present study. In particular, a series of 33 flexible synthetic phospholipids, either 2-(4-alkylidene-cyclohexyloxy)ethyl- or omega-cycloalkylidene-substituted ether phospholipids were systematically evaluated for their in vitro antileishmanial activity against the promastigote forms of Leishmania infantum and Leishmania donovani by CoMFA and CoMSIA 3D-QSAR studies. Steric and hydrophobic properties of the phospholipids under study appear to govern their antileishmanial activity against both strains, while the electrostatic properties have no significant contribution. The acknowledgment of these important properties of the pharmacophore will aid in the rational design of new analogues with higher activity.

Influence of the anisotropic hyperfine interaction on the 14N ENDOR and the ESEEM orientation-disordered spectra.

The influence of the anisotropic hyperfine interaction on the 14N electron-nuclear double resonance/electron spin echo envelope modulation spectra is studied by approximate analytical and graphical methods for the case of the isotropic g-factor. The suggested determination of the modified characteristic directions of the magnetic field due to anisotropy enhances the insight in the structural details of the system and analytical solutions of the secular equation for these conditions are derived. The graphical method, previously used for the analysis of the orientation dependence of the 14N nuclear-transition frequencies in orientation-disordered samples for isotropic hyperfine interaction is extended to the case of arbitrary anisotropic hyperfine tensor. The above analytical and graphical methods are illustrated and tested against exact simulations in two practically important cases: (i) isotropic hyperfine interaction (hfi) exceeding other nuclear interactions in nuclear spin Hamiltonian. (ii) Cancellation of the isotropic part of the hfi.