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Biomedical subjects

A Laaksonen

Publications and source records attributed to A Laaksonen.

At least 19 recordsLinked to original sources

Nucleation probability in binary heterogeneous nucleation of water-n-propanol vapor mixtures on insoluble and soluble nanoparticles.

Nucleation probabilities for binary heterogeneous nucleation have been measured quantitatively. Heterogeneous nucleation of binary n-propanol-water vapor mixtures on partially soluble 6.9-nm NaCl particles and on nonsoluble oxidized and nonoxidized 8-nm Ag particles at a constant nucleation temperature of 288 K (NaCl) or 285 K (Ag) has been investigated experimentally and theoretically. An expansion chamber was applied to generate supersaturated vapor mixtures. Number concentrations of particles activated to condensational growth were determined optically for various vapor phase activities at constant temperature. Nucleation probabilities have been measured as functions of the vapor phase activities for several n-propanol-water vapor mixing ratios. Beyond certain vapor phase activities a sharp onset of heterogeneous nucleation was observed both for NaCl and for Ag particles. For insoluble particle surfaces the theoretical slopes of the nucleation probability versus vapor phase activity curves were found to be somewhat steeper as compared to the experiment. On the other hand, for soluble particles the experimental slopes were found to be in satisfactory agreement with theory. The onset of the nucleation process is defined at an activity value where 50% of the particles were activated to condensational growth. Onset activities were obtained for various mixing ratios of the binary vapor mixtures. In the case of NaCl nuclei for n-propanol rich mixtures, the heterogeneous nucleation calculations based on a thermodynamically consistent version of Fletcher theory and an experimentally determined contact angle provide a reasonable approximation of the experimental data. However, it appears that the Fletcher theory is not applicable in the region of transition from n-propanol rich to water rich mixtures. Based on the Köhler theory of activation of soluble particles, a theory was formulated accounting for the presence of two condensable vapors and limited solubility of NaCl in water-propanol liquid mixtures. This approach provides a satisfactory description of the transition from activation of soluble particles to nucleation of vapors on insoluble particles. In the case of silver particles Fletcher theory with macroscopic experimental contact angles as well as with contact angle zero results in strong deviations from experimental data. A significant improvement was achieved by introducing fit contact angles, which are substantially lower than the macroscopic experimental values and may be considered as approximate values of the microscopic contact angles.

Journal Article↗

Soluble-insoluble transition in binary heterogeneous nucleation.

In this Letter, we report the first experimental study of binary heterogeneous gas-liquid nucleation. Onset activities were obtained for nucleation of various n-propanol-water vapor mixtures on 6.9 nm NaCl particles soluble in water and practically insoluble in n-propanol. The Fletcher theory of vapor nucleation on insoluble particles provided a reasonable approximation for n-propanol rich mixtures only, whereas the Köhler theory of activation of soluble particles worked only for water rich mixtures. A new theory was formulated providing a satisfactory description of the transition from activation of soluble particles to vapor nucleation on insoluble particles.

Journal Article↗

A TD-DFT study of the photochemistry of urocanic acid in biologically relevant ionic, rotameric, and protomeric forms.

The photochemistry of Urocanic acid, a chromophore present in human skin and linked to photoimmunosuppression and skin cancer, is investigated theoretically by means of time-dependent density functional theory. Extensive calculations are carried out for different ionic, rotameric, and protomeric forms of both the trans and cis form. Inclusion of solvation effects, here accounted for by means of a continuum solvent model, are found to be crucial for the correct description of the biologically relevant zwitterionic forms of the molecule. For the trans zwitterionic form, it is found that the planar form usually assumed in the literature is not stable, and that a realistic charge separation cannot be achieved in the gas phase. Calculated vertical excitation energies are in excellent agreement with available experimental data, with a weakly absorbing n --> pi transition around 4.0 eV, and strongly absorbing pi --> pi transitions at 4.5-4.9 eV. The debated intramolecular hydrogen bond is predicted to have a modest impact on the vertical spectra in solution, but improves agreement with experiment when included. In general, we also predict that different rotameric forms have very similar absorption spectra. In addition, we find a candidate absorbing state to link trans-urocanic acid to singlet oxygen production and subsequent photoaging of the skin.

Anions↗

Atomic charges in molecular mechanical force fields: a theoretical insight.

Based on quantum theory of the Coulombic interactions between a molecule and its surrounding molecules, a theoretical derivation is presented to obtain an atomic charge model. The charge model shows that the appropriate atomic charge, used for example in molecular mechanical force fields, is simply the average value of the electrostatic potential (ESP) derived charge for an isolated molecule and that obtained for the molecule in the interaction system. Computational scheme to calculate the ESP derived atomic charges of a molecule in the interaction system is presented. The method is applied to two common liquids with associated hydrogen bonds: water and methanol. The obtained theoretical atomic charges are similar to those found in the common interaction potential models, such as: SPC, TIP3P, OPLS, etc. However, for methanol they differ considerably from those obtained using the restrained ESP method.

Journal Article↗

Spermine: an "invisible" component in the crystals of B-DNA. A grand canonical Monte Carlo and molecular dynamics simulation study.

The association of spermine(4+) (Spm(4+)), Mg(2+) and monovalent (M(+)) ions with DNA in crystal form, have been studied using grand canonical Monte Carlo (GCMC) and molecular dynamics (MD) computer simulations. GCMC calculations were used to calculate the distribution of Spm(4+), Mg(2+), and M(+) between the equilibrating solvent and the DNA crystal under conditions mimicking the crystal-growing protocols reported in a number of recent X-ray diffraction studies of DNA oligomers. The GCMC simulations show that the composition of ions neutralizing the negative charge of DNA can vary in a broad range. The GCMC simulations were used to provide appropriate conditions for subsequent 6 ns constant pressure and temperature MD simulations of DNA in a typical crystalline environment consisting of three DNA double helix decamers in a periodic hexagonal cell, containing 1200 water molecules, eight Spm(4+), 32 Na(+) and four Cl(-) ions. Based on the simulation results, it seems possible to give an explanation why spermine molecules are usually not detected in X-ray studies in spite of their high concentration in the preparatory samples used as the crystallizing agent. It appears that this flexible polyamine molecule has several binding modes, interacting in fairly irregular manner with different sites on DNA and showing no regular ordering in the DNA crystals. Ions of Na(+) and Spm(4+) compete with each other and with water molecules in binding to bases in the minor groove and they influence the structure of the DNA hydration shell in different ways.

Algorithms↗

Molecular dynamics simulations of alpha-D-Manp-(1-->3)-beta-D-Glcp-OMe in methanol and in dimethyl sulfoxide solutions.

Molecular dynamics simulations have been performed of the disaccharide alpha-D-Manp-(1-->3)-beta-D-Glcp-OMe in two different solvents, namely in methanol and in dimethyl sulfoxide. The conformation of the disaccharide is similar to that previously determined in water. The three-dimensional structure around the solute was investigated by geometric hydrogen bonding criteria, radial distribution functions, coordination number analysis, residence times for hydrogen bonds, and spatial distribution functions. Differences and similarities between methanol and the aprotic dimethyl sulfoxide as solvent are analyzed.

Carbohydrate Conformation↗

Surfactant effects and an order-disorder transition in binary gas-liquid nucleation

Density-functional theory is applied to the interaction site model to study gas-liquid nucleation in a partially immiscible binary system consisting of spherical Lennard-Jones atoms (monomers) and dumbbell molecules of two Lennard-Jones atoms (dimers). Increased interaction anisotropy between the dimer sites and monomers is shown to result in mutual enhancement of nucleation. Critical nuclei with a lamellar structure are observed at high dimer activities.

Journal Article↗

Spatial distribution functions as a tool in the analysis of ribonucleic acids hydration--molecular dynamics studies.

The spatial distribution functions (SDFs) determined as three-dimensional density distribution of hydrogen and oxygen atoms of water in a local coordinate system linked with RNA molecule are used to study details of the spatial structure of aqueous solution around selected parts of RNA duplexes: r(CGCGCG)2 and 2'-O-Me(CGCGCG)2. The influence of the 2'-O-methylation on the hydration pattern of RNA helical fragments is visualized at the atomic level.

Base Pairing↗

Topological and spatial aspects of the hydration of solutes of extreme solvation entropy.

The hydration of charged Lennard-Jones spheres by simple point charge water is considered. Molecular dynamics and expanded ensemble simulations were used to compare the hydration structures surrounding solutes with extreme solvation entropy. The variations in the solvation entropy were analyzed in terms of changes in the spatial and topological structure of the hydration shells. The solvation entropy was found to be maximal for solutes that can replace water molecules in the hydrogen-bond network. Further, using a Kirkwood-type factorization, the solvation entropy was expanded as a sum over the partial n-body distribution functions. The two-body solute-water contribution to the solvation entropy was found to exceed the full solvation entropy for solutes with low charge, whereas the converse is true for the other solutes. This is consistent with the idea that water-water correlations are enhanced by solvation of, for example, noble gases, whereas they are disrupted by solvation of ions. Further, the orientational and radial parts of the two-body solute-water entropy were calculated as functions of the charge of the solute. The orientational part has a single maximum, whereas the radial part maintains the bimodal form of the full solvation entropy.

Journal Article↗

A molecular dynamics computer simulation study of nucleotide analogues. Comparison of the hydration pattern of dithymidine phosphate with those of the dithymidine methylphosphonate diastereomers.

The hydration pattern of thymidyl(3'->5') thymidine 1 and those of Rp and Sp diastereomers of the corresponding methylphosphonate analogue 2, have been studied using Molecular Dynamics (MD) computer simulation. It was found that the methylphosphonate modification leads to significant changes in the coordination of water molecules around the internucleotidic linkage and these, in turn, affect the hydration pattern of other parts of the molecule. The most notable differences between Rp and Sp diastereomers 2a and 2b were found to occur at the deoxyribose moieties of the nucleosid-5'-yl units.

Computer Simulation↗

Molecular dynamics simulations of DNA in solutions with different counter-ions.

Molecular dynamics simulations of the [d(ATGCAGTCAG]2 fragment of DNA, in water and in the presence of three different counter-ions (Li+, Na+ and Cs+) are reported. Three-dimensional hydration structure and ion distribution have been calculated using spatial distribution functions for a detailed picture of local concentrations of ions and water molecules around DNA. According to the simulations, Cs+ ions bind directly to the bases in the minor groove, Na+ ions bind prevailing to the bases in the minor groove through one water molecule, whereas Li+ ions bind directly to the phosphate oxygens. The different behavior of the counter-ions is explained by specific hydration structures around the DNA and the ions. It is proposed how the observed differences in the ion binding to DNA may explain different conformational behavior of DNA. Calculated self-diffusion coefficients for the ions agree well with the available NMR data.

Cesium↗

Visualization of solvation structures in liquid mixtures.

Spatial distribution functions of atomic densities. SDFs, have been proposed as a natural starting point for analysis of local molecular structure in liquids and solutions. The local structure in these systems is often complex and this is reflected in the fact that SDFs can be difficult to visualize. Among the different methods that can be used to visualize SDFs we discuss 3D isodensity surfaces, cross-sections, and 'comic book' animations. We also discuss the possibility of a simultaneous visualization of SDFs and other 3D fields, such as the electron density. These techniques are all intended to emphasize and bring out aspects of SDFs that promote a further understanding of the local molecular structure. OpenGL-based software has been used under X-Windows to implement these techniques, and we argue that high-quality molecular graphics need not be expensive. Data from a molecular dynamics simulation of an equimolar binary mixture of water and acetonitrile have been used to illustrate the discussion.

Computer Graphics↗

Hydration of cytidine, 2'-deoxycytidine and their phosphate salts in the aqueous solutions. A molecular dynamics computer simulation study.

To compare the hydration pattern of the cytidine (Cyd) and 2'-deoxycytidine (dCyd) in the aqueous solutions at the level of microscopic interactions. Molecular Dynamics (MD) computer simulations have been undertaken. The results indicate that the hydration of the heterocyclic base moiety in cytidine and 2'-deoxycytidine has a hydrophobic character. None of the three potential Watson-Crick base pair centres hydrogen bonds with the water molecules and the formation of something akin to a clathrate cage structure of water around base moieties of nucleosides in the aqueous solution is suggested. In contrast, the hydration of Cyd and dCyd sugar moieties shows a hydrophilic character and the three-dimensional networks of H-bonds involving all hydrophilic centres are formed differently around the ribose and 2'-deoxyribose. The sugar hydroxyl groups participate in the hydrogen bonding with water both as H-donor and as H-acceptor. Their donor-acceptor abilities have been evaluated and compared. The coordination numbers, the geometrical data of the first hydration shell, and the number of hydrogen bonds have been calculated. The changes in the pattern of hydration with the increased concentration of nucleosides and upon nucleoside protonation are discussed. The analysis of the pairwise interaction energies are also presented.

Computer Simulation↗