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1.
Int J Mol Sci ; 25(11)2024 May 27.
Article in English | MEDLINE | ID: mdl-38892021

ABSTRACT

Thyroxine (T4) is a drug extensively utilized for the treatment of hypothyroidism. However, the oral absorption of T4 presents certain limitations. This research investigates the efficacy of CO2 nanobubbles in water as a potential oral carrier for T4 administration to C57BL/6 hypothyroid mice. Following 18 h of fasting, the formulation was administered to the mice, demonstrating that the combination of CO2 nanobubbles and T4 enhanced the drug's absorption in blood serum by approximately 40%. To comprehend this observation at a molecular level, we explored the interaction mechanism through which T4 engages with the CO2 nanobubbles, employing molecular simulations, semi-empirical quantum mechanics, and PMF calculations. Our simulations revealed a high affinity of T4 for the water-gas interface, driven by additive interactions between the hydrophobic region of T4 and the gas phase and electrostatic interactions of the polar groups of T4 with water at the water-gas interface. Concurrently, we observed that at the water-gas interface, the cluster of T4 formed in the water region disassembles, contributing to the drug's bioavailability. Furthermore, we examined how the gas within the nanobubbles aids in facilitating the drug's translocation through cell membranes. This research contributes to a deeper understanding of the role of CO2 nanobubbles in drug absorption and subsequent release into the bloodstream. The findings suggest that utilizing CO2 nanobubbles could enhance T4 bioavailability and cell permeability, leading to more efficient transport into cells. Additional research opens the possibility of employing lower concentrations of this class of drugs, thereby potentially reducing the associated side effects due to poor absorption.


Subject(s)
Carbon Dioxide , Disease Models, Animal , Hypothyroidism , Thyroxine , Water , Animals , Hypothyroidism/drug therapy , Hypothyroidism/metabolism , Mice , Carbon Dioxide/chemistry , Water/chemistry , Mice, Inbred C57BL , Administration, Oral , Nanoparticles/chemistry , Drug Carriers/chemistry
2.
Polymers (Basel) ; 14(12)2022 Jun 07.
Article in English | MEDLINE | ID: mdl-35745887

ABSTRACT

Thermoelectric materials enable the direct conversion of thermal to electrical energy. One application of this is ambient heat energy harvesting where relatively stable temperature gradients existing between the inside and outside of a building could be utilized to produce electricity. Buildings can thus change from energy consumers to energy generators. This could ultimately help reduce the surface temperatures and energy consumption of buildings, especially in urban areas. In this paper, research work carried out on developing and characterizing a cement-based thermoelectric material is presented. Cement-based samples are doped with different metal oxides (Bi2O3 and Fe2O3) to enhance their thermoelectric properties, which are defined through their Seebeck coefficient, electrical conductivity and thermal conductivity. The study also discusses the positive impact of moisture content on the electrical conductivity.

3.
R Soc Open Sci ; 9(5): 212011, 2022 May.
Article in English | MEDLINE | ID: mdl-35619995

ABSTRACT

Modelling the inelastic scattering of electrons in water is fundamental, given their crucial role in biological damage. In Monte Carlo track-structure (MC-TS) codes used to assess biological damage, the energy loss function (ELF), from which cross sections are extracted, is derived from different semi-empirical optical models. Only recently have first ab initio results for the ELF and cross sections in water become available. For benchmarking purpose, in this work, we present ab initio linear-response time-dependent density functional theory calculations of the ELF of liquid water. We calculated the inelastic scattering cross sections, inelastic mean free paths, and electronic stopping power and compared our results with recent calculations and experimental data showing a good agreement. In addition, we provide an in-depth analysis of the contributions of different molecular orbitals, species and orbital angular momenta to the total ELF. Moreover, we present single-differential cross sections computed for each molecular orbital channel, which should prove useful for MC-TS simulations.

4.
J Chem Phys ; 153(3): 034113, 2020 Jul 21.
Article in English | MEDLINE | ID: mdl-32716198

ABSTRACT

Knowledge of the electronic stopping curve for swift ions, Se(v), particularly around the Bragg peak, is important for understanding radiation damage. Experimentally, however, the determination of such a feature for light ions is very challenging, especially in disordered systems such as liquid water and biological tissue. Recent developments in real-time time-dependent density functional theory (rt-TDDFT) have enabled the calculation of Se(v) along nm-sized trajectories. However, it is still a challenge to obtain a meaningful statistically averaged Se(v) that can be compared to observations. In this work, taking advantage of the correlation between the local electronic structure probed by the projectile and the distance from the projectile to the atoms in the target, we devise a trajectory pre-sampling scheme to select, geometrically, a small set of short trajectories to accelerate the convergence of the averaged Se(v) computed via rt-TDDFT. For protons in liquid water, we first calculate the reference probability distribution function (PDF) for the distance from the proton to the closest oxygen atom, ϕR(rp→O), for a trajectory of a length similar to those sampled experimentally. Then, short trajectories are sequentially selected so that the accumulated PDF reproduces ϕR(rp→O) to increasingly high accuracy. Using these pre-sampled trajectories, we demonstrate that the averaged Se(vp) converges in the whole velocity range with less than eight trajectories, while other averaging methods using randomly and uniformly distributed trajectories require approximately ten times the computational effort. This allows us to compare the Se(vp) curve to experimental data and assess widely used empirical tables based on Bragg's rule.

5.
J Phys Chem Lett ; 11(13): 5108-5114, 2020 Jul 02.
Article in English | MEDLINE | ID: mdl-32515961

ABSTRACT

Metallic hollow nanoparticles exhibit interesting optical properties that can be controlled by geometrical parameters. Irradiation with femtosecond laser pulses has emerged recently as a valuable tool for reshaping and size modification of plasmonic metal nanoparticles, thereby enabling the synthesis of nanostructures with unique morphologies. In this Letter, we use classical molecular dynamics simulations to investigate the solid-to-hollow conversion of gold nanoparticles upon femtosecond laser irradiation. Here, we suggest an efficient method for producing hollow nanoparticles under certain specific conditions, namely that the particles should be heated to a maximum temperature between 2500 and 3500 K, followed by a fast quenching to room temperature, with cooling rates lower than 120 ps. Therefore, we describe the experimental conditions for efficiently producing hollow nanoparticles, opening a broad range of possibilities for applications in key areas, such as energy storage and catalysis.

6.
J Phys Condens Matter ; 32(4): 045701, 2020 Jan 23.
Article in English | MEDLINE | ID: mdl-31581146

ABSTRACT

Despite being the archetypal thermoelectric material, still today some of the most exciting advances in the efficiency of these materials are being achieved by tuning the properties of PbTe. Its inherently low lattice thermal conductivity can be lowered to its fundamental limit by designing a structure capable of scattering phonons over a wide range of length scales. Intrinsic defects, such as vacancies or grain boundaries, can and do play the role of these scattering sites. Here we assess the effect of these defects by means of molecular dynamics simulations. For this we purposely parametrize a Buckingham potential that provides an excellent description of the thermal conductivity of this material over a wide temperature range. Our results show that intrinsic point defects and grain boundaries can reduce the lattice conductivity of PbTe down to a quarter of its bulk value. By studying the size dependence we also show that typical defect concentrations and grain sizes realized in experiments normally correspond to the bulk lattice conductivity of pristine PbTe.

7.
Chem Sci ; 10(10): 2924-2929, 2019 Mar 14.
Article in English | MEDLINE | ID: mdl-30996870

ABSTRACT

Although solvent-free mechanochemical synthesis continues to gain ever greater importance, the molecular scale processes that occur during such reactions remain largely uncharacterised. Here, we apply computational modelling to indentations between particles of crystals of aspirin and meloxicam under a variety of conditions to mimic the early stages of their mechanochemical cocrystallisation reaction. The study also extends to the effects of the presence of small amounts of solvent. It is found that, despite the solid crystalline nature of the reactants and the presence of little or no solvent, mixing occurs readily at the molecular level even during relatively low-energy collisions. When indented crystals are subsequently drawn apart, a connective neck formed by a mixture of the reactant molecules is observed, suggesting plastic-like behaviour of the reacting materials. Overall the work reveals some striking new insights including (i) relatively facile mixing of crystals under solvent-free conditions, (ii) no appreciable local temperature increases, (iii) localised amorphisation at the contact region and neck of the reacting crystals, and (iv) small amounts of solvent have relatively little effect during this early stage of the reaction, suggesting that their accelerating effect on the reaction may be exerted at later stages.

8.
Int J Mol Sci ; 20(5)2019 Mar 05.
Article in English | MEDLINE | ID: mdl-30841600

ABSTRACT

Efficient charge transport has been observed in iodine-doped, iodide-based room-temperature ionic liquids, yielding high ionic conductivity. To elucidate preferred mechanistic pathways for the iodide ( I - )-to-triiodide ( I 3 - ) exchange reactions, we have performed 10 ns reactive molecular-dynamics calculations in the liquid state for 1-butyl-3-methylimidazolium iodide ([BMIM][I]) at 450 to 750 K. Energy-barrier distributions for the iodine-swapping process were determined as a function of temperature, employing a charge-reassignment scheme drawn in part from electronic-structure calculations. Bond-exchange events were observed with rate-determining energy barriers ranging from ~0.19 to 0.23 ± 0.06 eV at 750 and 450 K, respectively, with an approximately Arrhenius temperature dependence for iodine self-diffusivity and reaction kinetics, although diffusion dominates/limits the bond-exchange events. This charge transfer is not dissimilar in energetics to those in solid-state superionic conductors.


Subject(s)
Iodine Compounds/chemistry , Ionic Liquids/chemistry , Imidazoles/chemistry , Kinetics
9.
J Phys Chem B ; 123(7): 1537-1544, 2019 02 21.
Article in English | MEDLINE | ID: mdl-30694675

ABSTRACT

Ionizing radiation can excite the cellular medium to produce secondary electrons that can subsequently cause damage to DNA. The damage is believed to occur via dissociative electron attachment (DEA). In DEA, the electron is captured by a molecule in a resonant antibonding state and a transient negative ion is formed. If this ion survives against electron autodetachment, then bonds within the molecule may dissociate as energy is transferred from the electronic degrees of freedom into vibrational modes of the molecule. We present a model for studying the effect that transferring kinetic energy into the vibrational modes of a molecule in this way has on a DNA nucleobase. We show that when the base is in an aqueous environment, dissociation is affected by interactions with the surrounding water molecules. In particular, hydrogen bonding between the nucleobase and the solvent can suppress the dissociative channel.


Subject(s)
Solvents/chemistry , Thymine/chemistry , Density Functional Theory , Electrons , Hydrogen Bonding
10.
J Chem Phys ; 150(1): 015101, 2019 Jan 07.
Article in English | MEDLINE | ID: mdl-30621408

ABSTRACT

We present a first-principles molecular dynamics study of the effect of shock waves (SWs) propagating in a model biological medium. We find that the SW can cause chemical modifications through varied and complex mechanisms, in particular, phosphate-sugar and sugar-base bond breaks. In addition, the SW promotes the dissociation of water molecules, thus enhancing the ionic strength of the medium. Freed protons can hydrolyze base and sugar rings previously opened by the shock. However, many of these events are only temporary, and bonds reform rapidly. Irreversible damage is observed for pressures above 15-20 GPa. These results are important to gain a better understanding of the microscopic damage mechanisms underlying cosmic-ray irradiation in space and ion-beam cancer therapy.


Subject(s)
Molecular Dynamics Simulation , Nucleotides/chemistry , Electrons , Pressure , Temperature , Water/chemistry
11.
J Phys Condens Matter ; 31(2): 025502, 2019 Jan 16.
Article in English | MEDLINE | ID: mdl-30521487

ABSTRACT

LiF doped with Mg and Ti is the most widely used thermoluminescent (TL) dosimeter for a large variety of applications. It has been argued that the Mg dopant is the most important defect in the TL process. Besides the common F-centre defects in LiF, optical absorption measurements have suggested the presence of Mg-related absorption bands at 380 nm (3.26 eV), and 310 nm (4.0 eV) when LiF:Mg is exposed to ionizing radiation, whose origin is not yet well understood. This work presents an investigation of the role of defects induced by Mg interstitials in LiF through electronic structure calculations. The calculations show that Mg interstitials induce a local lattice distortion characterized by the displacement of two opposite fluorine atoms, adjacent to the magnesium, away from their original sites by an average distance of 0.6 Å each, while the closest Li atoms are displaced by 0.1 Å. This defect introduces electronic states in the band-gap that can trap excess electrons produced during irradiation, thus enhancing the efficiency of the detector. Holes, on the other hand, are created and trapped in orbitals of mainly Mg-3s character. Additionally, the results suggest that irradiation can simultaneously remove a Li atom nearby a Mg interstitial; substitute a Li by a Mg atom or create a Li vacancy plus a Mg substitutional, giving rise to defects within the LiF gap that are more stable thermodynamically than the Mg interstitial itself. Interestingly, under irradiation the energy levels obtained for LiF:Mg-Lisub + e - (3.486 eV) and LiF:Mg + e - (4.224 eV) defects are very close to the experimental absorption bands.

12.
J Phys Condens Matter ; 29(38): 383001, 2017 Sep 27.
Article in English | MEDLINE | ID: mdl-28617676

ABSTRACT

DNA damage caused by irradiation has been studied for many decades. Such studies allow us to better assess the dangers posed by radiation, and to increase the efficiency of the radiotherapies that are used to combat cancer. A full description of the irradiation process involves multiple size and time scales. It starts with the interaction of radiation-either photons or swift ions-and the biological medium, which causes electronic excitation and ionisation. The two main products of ionising radiation are thus electrons and radicals. Both of these species can cause damage to biological molecules, in particular DNA. In the long run, this molecular level damage can prevent cells from replicating and can hence lead to cell death. For a long time it was assumed that the main actors in the damage process were the radicals. However, experiments in a seminal paper by the group of Leon Sanche in 2000 showed that low-energy electrons (LEE), such as those generated when ionising biological targets, can also cause bond breaks in biomolecules, and strand breaks in plasmid DNA in particular (Boudaiffa et al 2000 Science 287 1658-60). These results prompted a significant amount of experimental and theoretical work aimed at elucidating the role played by LEE in DNA damage. In this Topical Review we provide a general overview of the problem. We discuss experimental findings and theoretical results hand in hand with the aim of describing the physics and chemistry that occurs during the process of radiation damage, from the initial stages of electronic excitation, through the inelastic propagation of electrons in the medium, the interaction of electrons with DNA, and the chemical end-point effects on DNA. A very important aspect of this discussion is the consideration of a realistic, physiological environment. The role played by the aqueous solution and the amino acids from the histones in chromatin must be considered. Moreover, thermal fluctuations must be incorporated when studying these phenomena. Hence, a special place in this Topical Review is occupied by our recent first-principles molecular dynamics simulations that address the issue of how the environment favours or prevents LEEs from causing damage to DNA. We finish by summarising the conclusions achieved so far, and by suggesting a number of possible directions for further study.


Subject(s)
DNA Damage , DNA/chemistry , Electrons , Molecular Dynamics Simulation , Ions , Plasmids , Radiation, Ionizing
13.
J Phys Chem B ; 121(26): 6436-6441, 2017 07 06.
Article in English | MEDLINE | ID: mdl-28636376

ABSTRACT

Efficient charge transport has been observed in iodide-based room-temperature ionic liquids when doped with iodine. To investigate preferred pathways for the iodide (I-)-to-triiodide (I3-) exchange reaction and to clarify the origin of this high ionic conductivity, we have conducted electronic structure calculations in the crystal state of 1-butyl-3-methylimidazolium iodide ([BMIM][I]). Energy barriers for the different stages of the iodine-swapping process, including the reorientation of the I-···I3- moiety, were determined from minimum energy paths as a function of a reaction coordinate. Hirshfeld charges and structural parameters, such as bond lengths and angles, were monitored during the reaction. Several bond-exchange events were observed with energy barriers ranging from 0.17 to 0.48 eV and coinciding with the formation of a twisted I-···I3- complex. Striking similarities were observed in the mechanics and energetics of this charge-transfer process in relation to solid-state superionic conductors.

14.
PLoS One ; 12(3): e0171820, 2017.
Article in English | MEDLINE | ID: mdl-28267804

ABSTRACT

Water radiolysis by low-energy carbon projectiles is studied by first-principles molecular dynamics. Carbon projectiles of kinetic energies between 175 eV and 2.8 keV are shot across liquid water. Apart from translational, rotational and vibrational excitation, they produce water dissociation. The most abundant products are H and OH fragments. We find that the maximum spatial production of radiolysis products, not only occurs at low velocities, but also well below the maximum of energy deposition, reaching one H every 5 Å at the lowest speed studied (1 Bohr/fs), dissociative collisions being more significant at low velocity while the amount of energy required to dissociate water is constant and much smaller than the projectile's energy. A substantial fraction of the energy transferred to fragments, especially for high velocity projectiles, is in the form of kinetic energy, such fragments becoming secondary projectiles themselves. High velocity projectiles give rise to well-defined binary collisions, which should be amenable to binary approximations. This is not the case for lower velocities, where multiple collision events are observed. H secondary projectiles tend to move as radicals at high velocity, as cations when slower. We observe the generation of new species such as hydrogen peroxide and formic acid. The former occurs when an O radical created in the collision process attacks a water molecule at the O site. The latter when the C projectile is completely stopped and reacts with two water molecules.


Subject(s)
Cations/chemistry , Molecular Dynamics Simulation , Molecular Conformation , Water/chemistry
15.
Sci Rep ; 7: 45410, 2017 03 28.
Article in English | MEDLINE | ID: mdl-28350013

ABSTRACT

Irradiation of biological matter triggers a cascade of secondary particles that interact with their surroundings, resulting in damage. Low-energy electrons are one of the main secondary species and electron-phonon interaction plays a fundamental role in their dynamics. We have developed a method to capture the electron-phonon inelastic energy exchange in real time and have used it to inject electrons into a simple system that models a biological environment, a water chain. We simulated both an incoming electron pulse and a steady stream of electrons and found that electrons with energies just outside bands of excited molecular states can enter the chain through phonon emission or absorption. Furthermore, this phonon-assisted dynamical behaviour shows great sensitivity to the vibrational temperature, highlighting a crucial controlling factor for the injection and propagation of electrons in water.

16.
Environ Sci Technol ; 49(22): 13676-83, 2015 Nov 17.
Article in English | MEDLINE | ID: mdl-26513644

ABSTRACT

One of the main challenges faced by the nuclear industry is the long-term confinement of nuclear waste. Because it is inexpensive and easy to manufacture, cement is the material of choice to store large volumes of radioactive materials, in particular the low-level medium-lived fission products. It is therefore of utmost importance to assess the chemical and structural stability of cement containing radioactive species. Here, we use ab initio calculations based on density functional theory (DFT) to study the effects of (90)Sr insertion and decay in C-S-H (calcium-silicate-hydrate) in order to test the ability of cement to trap and hold this radioactive fission product and to investigate the consequences of its ß-decay on the cement paste structure. We show that (90)Sr is stable when it substitutes the Ca(2+) ions in C-S-H, and so is its daughter nucleus (90)Y after ß-decay. Interestingly, (90)Zr, daughter of (90)Y and final product in the decay sequence, is found to be unstable compared to the bulk phase of the element at zero K but stable when compared to the solvated ion in water. Therefore, cement appears as a suitable waste form for (90)Sr storage.


Subject(s)
Construction Materials , Radioactive Waste , Strontium Radioisotopes/chemistry , Calcium Compounds/chemistry , Nuclear Fission , Silicates/chemistry , Water/chemistry
17.
J Phys Chem Lett ; 6(15): 3091-7, 2015 Aug 06.
Article in English | MEDLINE | ID: mdl-26267207

ABSTRACT

Reactions that can damage DNA have been simulated using a combination of molecular dynamics and density functional theory. In particular, the damage caused by the attachment of a low energy electron to the nucleobase. Simulations of anionic single nucleotides of DNA in an aqueous environment that was modeled explicitly have been performed. This has allowed us to examine the role played by the water molecules that surround the DNA in radiation damage mechanisms. Our simulations show that hydrogen bonding and protonation of the nucleotide by the water can have a significant effect on the barriers to strand breaking reactions. Furthermore, these effects are not the same for all four of the bases.


Subject(s)
DNA/chemistry , Nucleotides/chemistry , Water/chemistry , DNA Damage/radiation effects , Hydrogen Bonding , Molecular Dynamics Simulation , Thermodynamics
18.
Phys Chem Chem Phys ; 16(44): 24350-8, 2014 Nov 28.
Article in English | MEDLINE | ID: mdl-25301285

ABSTRACT

Using first-principles molecular dynamics simulations, we have investigated the notion that amino acids can play a protective role when DNA is exposed to excess electrons produced by ionizing radiation. In this study we focus on the interaction of glycine with the DNA nucleobase thymine. We studied thymine-glycine dimers and a condensed phase model consisting of one thymine molecule solvated in amorphous glycine. Our results show that the amino acid acts as a protective agent for the nucleobase in two ways. If the excess electron is initially captured by the thymine, then a proton is transferred in a barrier-less way from a neighboring hydrogen-bonded glycine. This stabilizes the excess electron by reducing the net partial charge on the thymine. In the second mechanism the excess electron is captured by a glycine, which acts as a electron scavenger that prevents electron localization in DNA. Both these mechanisms introduce obstacles to further reactions of the excess electron within a DNA strand, e.g. by raising the free energy barrier associated with strand breaks.


Subject(s)
DNA/chemistry , Electrons , Glycine/chemistry , Thymine/chemistry , Computer Simulation , Models, Molecular , Radiation, Ionizing
19.
J Am Chem Soc ; 135(46): 17528-36, 2013 Nov 20.
Article in English | MEDLINE | ID: mdl-24156701

ABSTRACT

In a recent article (J. Am. Chem. Soc. 2011, 133, 20186) we investigated the initial spatial distribution of dry excess electrons in a series of room-temperature ionic liquids (RTILs). Perhaps unexpectedly, we found that in some alkylammonium-based systems the excess negative charge resided on anions and not on the positive cations. Following on these results, in the current paper we describe the time evolution of an excess electronic charge introduced in alkylammonium- and pyrrolidinium-based ionic liquids coupled with the bis(trifluoromethylsulfonyl)amide ([Tf2N(-)]) anion. We find that on a 50 fs time scale an initially delocalized excess electron localizes on a single [Tf2N(-)] anion which begins a fragmentation process. Low-energy transitions have a very different physical origin on the several femtoseconds time scale when compared to what occurs on the picosecond time scale. At time zero, these are intraband transitions of the excess electron. However after 40 fs when the excess electronic charge localizes on a single anion, these transitions disappear, and the spectrum is dominated by electron-transfer transitions between the fragments of the doubly charged breaking anion.

20.
Phys Rev Lett ; 108(21): 213201, 2012 May 25.
Article in English | MEDLINE | ID: mdl-23003250

ABSTRACT

The Born-Oppenheimer approximation is the keystone for molecular dynamics simulations of radiation damage processes; however, actual materials response involves nonadiabatic energy exchange between nuclei and electrons. In this work, time dependent density functional theory is used to calculate the electronic excitations produced by energetic protons in Al. We study the influence of these electronic excitations on the interatomic forces and find that they differ substantially from the adiabatic case, revealing a nontrivial connection between electronic and nuclear stopping that is absent in the adiabatic case. These results unveil new effects in the early stages of radiation damage cascades.

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