Biomedical subjects

Dylan Jayatilaka

Publications and source records attributed to Dylan Jayatilaka.

7 recordsLinked to original sources

PubMed2006

Effective molecular polarizabilities and crystal refractive indices estimated from x-ray diffraction data.

Although it was proposed some time ago that (hyper)polarizabilities might be estimated from the results of x-ray charge density refinements, early results were unconvincing. In this work we show that the one particle density obtained from the usual multipole refinement model does not contain sufficient information to determine these response properties and instead pursue the "constrained wave function" approach of fitting to x-ray structure factors. Simplified sum-over-states expressions are derived for determining the dipole polarizability from these wave functions, and these clearly show that the earlier work ignored important two-electron expectation values for the dipole polarizability, and two- and three-electron terms for Beta, etc. Correction factors for the simplified sum-over-states polarizability tensors from the constrained wave function are obtained by calibration against coupled Hartree-Fock ab initio results to yield in-crystal effective polarizability tensors. Results obtained for benzene, urea, and 2-methyl-4-nitroaniline demonstrate that the effective molecular polarizabilities clearly include the effects of intermolecular interactions and electron correlation, especially for urea where the effects on the polarizability are known to be quite large. We also carefully consider the way in which the linear bulk susceptibility, chi((1)), and refractive indices are determined from the x-ray fitted polarizabilities, employing three models based on a rigorous treatment of the local field. Incorrect results are obtained for the sort of molecules that are of interest in nonlinear optical applications if the molecules are approximated by single point dipoles. In contrast, the use of Lorentz-factor tensors averaged over several sites yields excellent results, with refractive indices obtained using this model in remarkably good agreement with optical measurements extrapolated to zero frequency.

Aniline Compounds↗

PubMed2006

Determination of the orientational distribution and orientation factor for transfer between membrane-bound fluorophores using a confocal microscope.

Orientational fluorophores have been a useful tool in physical chemistry, biochemistry, and more recently structural biology due to the polarized nature of the light they emit and that fact that energy can be transferred between them. We present a practical scheme in which measurements of the intensity of emitted fluorescence can be used to determine limits on the mean and distribution of orientation of the absorption transition moment of membrane-bound fluorophores. We demonstrate how information about the orientation of fluorophores can be used to calculate the orientation factor kappa(2) required for use in FRET spectroscopy. We illustrate the method using images of AlexaFluor probes bound to MscL mechanosensitive transmembrane channel proteins in spherical liposomes.

Algorithms↗

PubMed2005

A flexible approach to the calculation of resonance energy transfer efficiency between multiple donors and acceptors in complex geometries.

Resonance energy transfer provides a practical way to measure distances in the range of 10-100 A between sites in biological molecules. Although the relationship between the efficiency of energy transfer and the distance between sites is well described for a single pair of fluorophores, the situation is more difficult when more than two fluorophores are present. Using a Monte Carlo calculation scheme, we demonstrate how resonance energy transfer can be used to measure distances between fluorophores in complex geometries. We demonstrate the versatility of the approach by calculating the efficiency of energy transfer for individual fluorophores randomly distributed in two and three dimensions, for linked pairs of donors and acceptors and pentameric structures of five linked fluorophores. This approach can be used to relate the efficiency of energy transfer to the distances between fluorophores, R0, molecular concentrations, laser power, and donor/acceptor ratios in ensembles of molecules or when many fluorophores are attached to a single molecule such as in multimeric proteins.

Algorithms↗

PubMed2004

Electron localization functions obtained from X-ray constrained Hartree-Fock wavefunctions for molecular crystals of ammonia, urea and alloxan.

Constrained Hartree-Fock wavefunctions in the superposition of isolated molecules model have been calculated from precise X-ray diffraction data on crystals of ammonia (NH(3)), urea [CO(NH(2))(2)] and alloxan [(CO)(4)(NH)(2)]. The X-ray constrained wavefunctions have been used to derive and examine 'electron localization' information, quantified by the true and approximate electron localization function (ELF), and the true and approximate Fermi hole mobility function (FHMF). The plots of the Fermi hole mobility function are the first to appear in the literature. The results are compared with corresponding isolated-molecule Hartree-Fock calculations to gauge the effect of the crystal environment on the isolated molecules. An error analysis is performed to indicate the features in the plots which are well determined from the experimental data. The results from all plots are broadly consistent, but the approximate ELF shows some artifacts relative to the true ELF.

Journal Article↗

PubMed2003

Wave functions derived from experiment. V. Investigation of electron densities, electrostatic potentials, and electron localization functions for noncentrosymmetric crystals.

The constrained Hartree-Fock method using experimental X-ray diffraction data is extended and applied to the case of noncentrosymmetric molecular crystals. A new way to estimate the errors in derived properties as a derivative with respect to added Gaussian noise is also described. Three molecular crystals are examined: ammonia [NH(3)], urea [CO(NH(2))(2)], and alloxan [(CO)(4)(NH)(2)]. The energetic and electrical properties of these molecules in the crystalline state are presented. In all cases, an enhancement of the dipole moment is observed upon application of the experimental constraint. It is found that the phases of the structure factors are robustly determined by the constrained Hartree-Fock model, even in the presence of simulated noise. Plots of the electron density, electrostatic potential, and the electron localization function for the molecules in the crystal are displayed. In general, relative to the Hartree-Fock model, there is a depletion of charge around hydrogen atoms and lone pair regions, and a build-up of charge within the molecular framework near nuclei, directed along the bonds. The electron localization function plots reveal an increase in the pair density between vicinal hydrogen atoms.

Journal Article↗

PubMed2002

Wavefunctions derived from experiment. III. Topological analysis of crystal fragments.

A constrained wavefunction model has been used to extract a Hartree-Fock wavefunction for C2H2O4.4H2O from both low-angle (sin theta /lambda < 0.71 A-1, 571 reflections) and full (sin theta / lambda < 1.00 A-1, 968 reflections) experimental X-ray diffraction data for crystalline alpha-oxalic acid dihydrate (alpha-C2H2O4.2H2O) using polarized double-zeta and triple-zeta Gaussian basis sets. Properties obtained from the zero-flux partitioning of the total charge-density distribution derived from these wavefunctions, as well as from multipole refinement of the experimental data, are calculated and compared. This work represents the first calculation of integrated atomic properties derived from the fitting of Gaussian density functions to experimental X-ray diffraction data. In particular, atomic kinetic energies derived from experimental data are presented for the first time. The results obtained from the constrained (experimental) charge density show qualitatively similar properties to those obtained from conventional ab initio gas-phase calculations, though the quantitative differences are often substantial. The accuracy of integrated properties calculated using this procedure was established from the analysis of a wavefunction derived from simulated random-error diffraction data; that is, data obtained by adding normally distributed errors to the experimental structure factors. Analysis of this random-error wavefunction indicated that most topological properties are accurate to within approximately 5%, although the error is much larger for those properties that have a steep gradient in the region being evaluated [e.g. the value of V(2)rho(rb) at bond critical points] or are very small (e.g. the atomic dipole moment). Calculations of the constrained wavefunction using both the larger basis set and the complete set of experimental data yield results that agree quantitatively with the smaller calculations.

Journal Article↗

PubMed2002

Wavefunctions derived from experiment. IV. Investigation of the crystal environment of ammonia.

Constrained Hartree-Fock calculations have been performed to obtain wavefunctions that reproduce experimental X-ray structure-factor magnitudes for crystalline NH3 to within the limits of experimental error. Different model densities using both a single molecule and clusters of NH3 in the calculation of X-ray structure-factor magnitudes have been examined. The effects of the crystalline lattice on the experimental wavefunction of the NH3 unit can be reproducibly recovered. The construction of structure-factor magnitudes based on normally distributed random perturbations of the experimental values has also been used to gauge the accuracy of integrated atomic properties obtained from the wavefunctions, the point at which the constraint procedure should be terminated, and the approximate error in the experimental sigma(k) values.

Journal Article↗