A force field of Li+^+ , Na+^+ , K+^+, Mg2+^{2+}, Ca2+^{2+}, Cl−^-, and SO42−_4^{2-} in aqueous solution based on the TIP4P/2005 water model and scaled charges for the ions

In this work, a force field for several ions in water is proposed. In particular, we consider the cations Li$^+$ , Na$^+$ , K$^+$, Mg$^{2+}$, Ca$^{2+}$ and the anions Cl$^-$, and SO$_4^{2-}$ . These ions were selected as they appear in the composition of seawater, and they are also found in biological systems. The force field proposed (denoted as Madrid-2019) is nonpolarizable, and both water molecules and sulfate anions are rigid. For water, we use the TIP4P/2005 model. The main idea behind this work is to further explore the possibility of using scaled charges for describing ionic solutions. Monovalent and divalent ions are modeled using charges of 0.85 and 1.7, respectively (in electron units). The model allows a very accurate description of the densities of the solutions up to high concentrations. It also gives good predictions of viscosities up to 3 m concentrations. Calculated structural properties are also in reasonable agreement with the experiment. We have checked that no crystallization occurred in the simulations at concentrations similar to the solubility limit. A test for ternary mixtures shows that the force field provides excellent performance at an affordable computer cost. In summary, the use of scaled charges, which could be regarded as an effective and simple way of accounting for polarization (at least to a certain extend), improves the overall description of ionic systems in water. However, for purely ionic systems, scaled charges will not adequately describe neither the solid nor the melt

In Silico Seawater

Many important processes affecting the Earth's climate are determined by the physical properties of seawater. Desalination of seawater is a significant source of drinking wate.Since the physical properties of seawater governing these processes depend on the molecular interactions among its components, a deeper knowledge of seawater at the molecular level is needed. However MD studies reporting the physical properties of seawater are currently lacking. This is probably due to the usual perception of the seawater composition being too complex to approach.This point of view ignores the fact that physical properties of seawater are dependent on a single parameter representing the composition, namely the salinity. This is because the relative proportions of any two major constituents of seasalt are always the same. An obstacle to performing MD simulations of seawater could have been the unavailability of a satisfactory force field representing the interactions between water molecules and dissolved substances. This drawback has recently been overcome with the proposal of the Madrid-2019 FF.Here we show for the first time that MD simulations of seawater are feasible. We have performed MD simulations of a system, the composition of which is close to the average composition of standard seawater and with the molecular interactions given by the Madrid-2019 force field. We are able to provide quantitative or semiquantitative predictions for a number of relevant physical properties of seawater for temperatures and salinities from the oceanographic range to those relevant to desalination processes. The computed magnitudes include static (density), dynamical (viscosity and diffusion coefficients), structural (ionic hydration, ion-ion distribution functions) and interfacial (surface tension) properties

Computation of Electrical Conductivities of Aqueous Electrolyte Solutions: Two Surfaces , One Property

In this work, we have computed electrical conductivities at ambient conditions of aqueous NaCl and KCl solutions by using the Einstein-Helfand equation. Common force fields (charge q = 1 e) do not reproduce the experimental values of electrical conductivities, viscosities and diffusion coefficients. Recently, we proposed the idea of using different charges to describe the Potential Energy Surface (PES) and the Dipole Moment Surface (DMS). In this work, we implement this concept. The equilibrium trajectories required to evaluate electrical conductivities (within linear response theory) were obtained by using scaled charges (with the value q = 0.75 e ) to describe the PES. The potential parameters were those of the Madrid-Transport force field, which describe accurately viscosities and diffusion coefficients of these ionic solutions. However, integer charges were used to compute the conductivities (thus describing the DMS). The basic idea is that although the scaled charge describes the ion-water interaction better, the integer charge reflects the value of the charge that is transported due to the electric field. The agreement obtained with experiments is excellent, as for the first time electrical conductivities (and the other transport properties) of NaCl and KCl electrolyte solutions are described with high accuracy for the whole concentration range up to their solubility limit. Finally, we propose an easy way to obtain a rough estimate of the actual electrical conductivity of the potential model under consideration using the approximate Nernst-Einstein equation, which neglects correlations between different ions

On the triplet structure of binary liquids

An approach to calculate the triplet structure of a simple liquid, that was proposed some years ago by Barrat, Hansen, and Pastore ͓Phys. Rev. Lett. 58, 2075 ͑1987͔͒ has been tested in the binary case. This approach is based on a factorization ansatz for the triplet direct correlation function c (3) ; the unknown factor function is determined via the sum rule relating c (3) and the pair direct correlation function which is the only input information of the system that is required in this formalism. We present an efficient and stable numerical algorithm which solves the six ͑partly coupled͒ integral equations for the unknown factor functions. Results are given for the case of a binary hard-sphere mixture and complemented by computer simulation data

On the triplet structure of binary liquids

An approach to calculate the triplet structure of a simple liquid, that was proposed some years ago by Barrat, Hansen, and Pastore ͓Phys. Rev. Lett. 58, 2075 ͑1987͔͒ has been tested in the binary case. This approach is based on a factorization ansatz for the triplet direct correlation function c (3) ; the unknown factor function is determined via the sum rule relating c (3) and the pair direct correlation function which is the only input information of the system that is required in this formalism. We present an efficient and stable numerical algorithm which solves the six ͑partly coupled͒ integral equations for the unknown factor functions. Results are given for the case of a binary hard-sphere mixture and complemented by computer simulation data

Stops making sense: translational trade-offs and stop codon reassignment

Background Efficient gene expression involves a trade-off between (i) premature termination of protein synthesis; and (ii) readthrough, where the ribosome fails to dissociate at the terminal stop. Sense codons that are similar in sequence to stop codons are more susceptible to nonsense mutation, and are also likely to be more susceptible to transcriptional or translational errors causing premature termination. We therefore expect this trade-off to be influenced by the number of stop codons in the genetic code. Although genetic codes are highly constrained, stop codon number appears to be their most volatile feature. Results In the human genome, codons readily mutable to stops are underrepresented in coding sequences. We construct a simple mathematical model based on the relative likelihoods of premature termination and readthrough. When readthrough occurs, the resultant protein has a tail of amino acid residues incorrectly added to the C-terminus. Our results depend strongly on the number of stop codons in the genetic code. When the code has more stop codons, premature termination is relatively more likely, particularly for longer genes. When the code has fewer stop codons, the length of the tail added by readthrough will, on average, be longer, and thus more deleterious. Comparative analysis of taxa with a range of stop codon numbers suggests that genomes whose code includes more stop codons have shorter coding sequences. Conclusions We suggest that the differing trade-offs presented by alternative genetic codes may result in differences in genome structure. More speculatively, multiple stop codons may mitigate readthrough, counteracting the disadvantage of a higher rate of nonsense mutation. This could help explain the puzzling overrepresentation of stop codons in the canonical genetic code and most variants