Use Of Electron Density Research Articles

OC-0465: Evaluation of the use of electron density overrides in MR-Linac breast treatment planning

OC-0465: Evaluation of the use of electron density overrides in MR-Linac breast treatment planning

An electron density based analysis to establish the electronic adiabaticity of proton coupled electron transfer reactions.

Electrons and protons are the main actors in play in proton coupled electron transfer (PCET) reactions, which are fundamental in many biological (i.e., photosynthesis and enzymatic reactions) and electrochemical processes. The mechanism, energetics and kinetics of PCET reactions are strongly controlled by the coupling between the transferred electrons and protons. Concerted PCET reactions are classified according to the electronical adiabaticity degree of the process. To discriminate among different mechanisms, we propose a new analysis based on the use of electron density based indexes. We choose, as test case, the 3-Methylphenoxyl/phenol system in two different conformations to show how the proposed analysis is a suitable tool to discriminate between the different degree of adiabaticity of PCET processes. The very low computational cost of this procedure is extremely promising to analyze and provide evidences of PCET mechanisms ruling the reactivity of many biological and catalytic systems.

Macromolecular refinement by model morphing using non-atomic parameterizations.

Refinement is a critical step in the determination of a model which explains the crystallographic observations and thus best accounts for the missing phase components. The scattering density is usually described in terms of atomic parameters; however, in macromolecular crystallography the resolution of the data is generally insufficient to determine the values of these parameters for individual atoms. Stereochemical and geometric restraints are used to provide additional information, but produce interrelationships between parameters which slow convergence, resulting in longer refinement times. An alternative approach is proposed in which parameters are not attached to atoms, but to regions of the electron-density map. These parameters can move the density or change the local temperature factor to better explain the structure factors. Varying the size of the region which determines the parameters at a particular position in the map allows the method to be applied at different resolutions without the use of restraints. Potential applications include initial refinement of molecular-replacement models with domain motions, and potentially the use of electron density from other sources such as electron cryo-microscopy (cryo-EM) as the refinement model.

Multi-scale analysis of compressible fluctuations in the solar wind

Abstract. Compressible plasma turbulence is investigated in the fast solar wind at proton kinetic scales by the combined use of electron density and magnetic field measurements. Both the scale-dependent cross-correlation (CC) and the reduced magnetic helicity (σm) are used in tandem to determine the properties of the compressible fluctuations at proton kinetic scales. At inertial scales the turbulence is hypothesised to contain a mixture of Alfvénic and slow waves, characterised by weak magnetic helicity and anti-correlation between magnetic field strength B and electron density ne. At proton kinetic scales the observations suggest that the fluctuations have stronger positive magnetic helicities as well as strong anti-correlations within the frequency range studied. These results are interpreted as being characteristic of either counter-propagating kinetic Alfvén wave packets or a mixture of anti-sunward kinetic Alfvén waves along with a component of kinetic slow waves. Keywords. Interplanetary physics (MHD waves and turbulence)

Decoding X-ray observations from centres of galaxy clusters using MCMC

We correct for the use of electron densities instead of total gas density in the pressure fits which were used to derive the local free-fall times (t$_{\rm ff}$) in the original paper.

Monte Carlo Simulations of Site-Specific Radical Attack to DNA Bases

An atomistic biophysical model permitting the calculation of initial attacks to a 38-bp representation of B-DNA base moieties by water radicals is presented. This model is based on a previous radiation damage model developed by Aydogan et al. (Radiat. Res. 157, 38-44, 2002). Absolute efficiencies for radical attack to the 38-bp DNA molecule are calculated to be 41, 0.8 and 15% for hydroxyl radical ((.)OH), hydrogen radical (H(.)), and hydrated electron (e(aq))(,) respectively. Among the nucleobases, guanine is found to have the highest percentage (.)OH attack probability at 36%. Adenine, cytosine and thymine moieties have initial attack probabilities of 24, 18 and 22%, respectively. A systematic study is performed to investigate (.)OH attack probabilities at each specified attack site in four molecular models including free bases, single nucleotides, single base pairs, and the central eight base pairs of the 38-bp DNA molecule. Cytosine is the free base moiety for which the closest agreement is observed between the model prediction and the experimental data. The initial (.)OH attack probabilities for cytosine as the free base are calculated to be 72 and 28%, while experimental data are reported at 87 and 13% for the C5 and C6 positions on the base, respectively. In this study, we incorporated atomic charges to scale the site-specific (.)OH reaction rates at the individual atomic positions on the pyrimidine and purine bases. Future updates to the RIDNA model will include the use of electron densities to scale the reaction rates. With respect to reactions of the aqueous electron with DNA, a comparison of the initial distribution of electron attack sites calculated in this study and experimental results suggests an extremely rapid and extensive redistribution of the e(-)(aq) after their initial reactions with DNA.

Many-Electron Problem in Terms of the Density: From Thomas–Fermi to Modern Density-Functional Theory

In this paper we focus on the use of electron density and current-density as basic variables in describing a many-electron system. We start with a discussion of the seminal Thomas–Fermi theory and its extension by Bloch for time-dependent hamiltonians. We then present modern density-functional theory (for both time-independent and time-dependent hamiltonians) and approximations involved in implementing it. Also discussed is perturbation theory in terms of electron density and its use for calculating various response properties and related quantities. In particular, van der Waals coefficient C6is calculated using density and current density in time-dependent perturbation theory. Throughout the paper, results for alkali-metal clusters are presented to demonstrate the strength of density-based theories.

Use of electron densities in comparative molecular field analysis (CoMFA): O?H bond dissociation energies in phenols

The ability to successfully predict the bond dissociation energies of the phenol OH bond is important in medicinal chemistry for a variety of therapeutic applications. Previous reports utilized rigorous approaches with semi-empirical, ab initio and density functional theory, as well as more empirically based quantitative structure activity relationship (QSAR) approaches. Here we report the use of a three-dimensional quantitative structure activity relationship method incorporating electron densities computed using the Austin Method 1 (AM1) method followed by correlation of the electron density with the relative bond dissociation energies. The QSAR is determined for both the ground-state phenol as well as the singlet phenoxy radical with a set of compounds for which the bond dissociation energies have been measured. The model developed using the ground-state phenol model is more predictive. The coefficients of the QSAR have also been interpreted. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 75: 187–195, 1999

Gradient expansion correction to the Dirac exchange term in statistical models for the Na atom with shell structure

AbstractIn the study of the ground‐state binding energy of atoms, relatively more attention has been paid to the gradient expansion of the kinetic energy term of the Thomas–Fermi–Dirac model than to the gradient expansion of the exchange term of this model. Recently Shih and Shih, Murphy, and Wang have focused on this problem and calculated the first gradient expansion correction to the Dirac exchange term by making use of electron densities constructed from Hartree–Fock wave functions. In previous work, aimed to introduce the shell structure of atoms via a variational procedure using the energy density functional formalism, electron densities have been obtained for the Na atom within the Thomas–Fermi–Dirac model with and without the Weizsäcker and Hodges gradient expansion corrections to the kinetic energy term. In this paper we make use of the respective electron densities and calculate the first gradient expansion corrections to the Dirac exchange term. The results show that, for the Na atom, the magnitude of this correction is about 1% of the magnitude of the total binding energy.

Sensitivity of atomic interaction potentials to details of the electron distribution

Interaction energies as a function of internuclear separation have been computed for two argon atoms. Use of electron densities obtained from self-consistent field calculations gives appreciably higher interaction energies than those obtained from Thomas-Fermi-Dirac densities.