The aqueous solvation of sodium chloride: A Monte Carlo transition path sampling study

Discovering and Targeting Dynamic Drugging Pockets of Oncogenic Proteins: The Role of Magnesium in Conformational Changes of the G12D Mutated Kirsten Rat Sarcoma-Guanosine Diphosphate Complex

KRAS-G12D mutations are the one of most frequent oncogenic drivers in human cancers. Unfortunately, no therapeutic agent directly targeting KRAS-G12D has been clinically approved yet, with such mutated species remaining undrugged. Notably, cofactor Mg2+ is closely related to the function of small GTPases, but no investigation has been conducted yet on Mg2+ when associated with KRAS. Herein, through microsecond scale molecular dynamics simulations, we found that Mg2+ plays a crucial role in the conformational changes of the KRAS-GDP complex. We located two brand new druggable dynamic pockets exclusive to KRAS-G12D. Using the structural characteristics of these two dynamic pockets, we designed in silico the inhibitor DBD15-21-22, which can specifically and tightly target the KRAS-G12D-GDP-Mg2+ ternary complex. Overall, we provide two brand new druggable pockets located on KRAS-G12D and suitable strategies for its inhibition.

Nucleation of Helium in Liquid Lithium at 843 K and High Pressures

Fusion energy stands out as a promising alternative for a future decarbonised energy system. In order to be sustainable, future fusion nuclear reactors will have to produce their own tritium. In the so-called breeding blanket of a reactor, the neutron bombardment of lithium will produce the desired tritium, but also helium, which can trigger nucleation mechanisms owing to the very low solubility of helium in liquid metals. An understanding of the underlying microscopic processes is important for improving the efficiency, sustainability and reliability of the fusion energy conversion process. The spontaneous creation of helium droplets or bubbles in the liquid metal used as breeding material in some designs may be a serious issue for the performance of the breeding blankets. This phenomenon has yet to be fully studied and understood. This work aims to provide some insight on the behaviour of lithium and helium mixtures at experimentally corresponding operating conditions (843 K and pressures between 108 and 1010 Pa). We report a microscopic study of the thermodynamic, structural and dynamical properties of lithium–helium mixtures, as a first step to the simulation of the environment in a nuclear fusion power plant. We introduce a new microscopic model devised to describe the formation of helium droplets in the thermodynamic range considered. Our model predicts the formation of helium droplets at pressures around 109 Pa, with radii between 1 and 2 Å. The diffusion coefficient of lithium (2 Å2/ps) is in excellent agreement with reference experimental data, whereas the diffusion coefficient of helium is in the range of 1 Å2/ps and tends to decrease as pressure increases.

Microscopic Interactions of Melatonin, Serotonin and Tryptophan with Zwitterionic Phospholipid Membranes

The interactions at the atomic level between small molecules and the main components of cellular plasma membranes are crucial for elucidating the mechanisms allowing for the entrance of such small species inside the cell. We have performed molecular dynamics and metadynamics simulations of tryptophan, serotonin, and melatonin at the interface of zwitterionic phospholipid bilayers. In this work, we will review recent computer simulation developments and report microscopic properties, such as the area per lipid and thickness of the membranes, atomic radial distribution functions, angular orientations, and free energy landscapes of small molecule binding to the membrane. Cholesterol affects the behaviour of the small molecules, which are mainly buried in the interfacial regions. We have observed a competition between the binding of small molecules to phospholipids and cholesterol through lipidic hydrogen-bonds. Free energy barriers that are associated to translational and orientational changes of melatonin have been found to be between 10-20 kJ/mol for distances of 1 nm between melatonin and the center of the membrane. Corresponding barriers for tryptophan and serotonin that are obtained from reversible work methods are of the order of 10 kJ/mol and reveal strong hydrogen bonding between such species and specific phospholipid sites. The diffusion of tryptophan and melatonin is of the order of 10-7 cm2/s for the cholesterol-free and cholesterol-rich setups.

Failure of molecular dynamics to provide appropriate structures for quantum mechanical description of the aqueous chloride ion charge-transfer-to-solvent ultraviolet spectrum

The lowest band in the charge-transfer-to-solvent ultraviolet absorption spectrum of aqueous chloride ion is studied by experiment and computation. Interestingly, the experiments indicate that at concentrations up to at least 0.25 M, where calculations indicate ion pairing to be significant, there is no notable effect of ionic strength on the spectrum. The experimental spectra are fitted to aid comparison with computations. Classical molecular dynamic simulations are carried out on dilute aqueous Cl-, Na+, and NaCl, producing radial distribution functions in reasonable agreement with experiment and, for NaCl, clear evidence of ion pairing. Clusters are extracted from the simulations for quantum mechanical excited state calculations. Accurate ab initio coupled-cluster benchmark calculations on a small number of representative clusters are carried out and used to identify and validate an efficient protocol based on time-dependent density functional theory. The latter is used to carry out quantum mechanical calculations on thousands of clusters. The resulting computed spectrum is in excellent agreement with experiment for the peak position, with little influence from ion pairing, but is in qualitative disagreement on the width, being only about half as wide. It is concluded that simulation by classical molecular dynamics fails to provide an adequate variety of structures to explain the experimental CTTS spectrum of aqueous Cl-.

Efficient sampling of high-energy states by machine learning force fields

A method extending the range of applicability of machine-learning force fields is proposed. It relies on biased subsampling of the high-energy states described by the predefined coordinate(s).

Grand Canonical Monte Carlo coupled multiscale simulation for electrochemical and solvent parameters of silver halide systems in water

Grand Canonical Monte Carlo methods in conjunction with continuum Multiscale simulation to estimate the hydration energies and surface potentials of silver halides as demonstrated elsewhere is employed by incorporating random distribution of molecules, nearest neighbor distances and hydration numbers. The extent of dehydration during each step and the corresponding variation in the hydration numbers are evaluated, assuming the validity of hard spheres. These estimates are then employed to deduce the redox potential of the reaction viz. 2AgX(solution)⇔2Ag(solid)+X2(gas). The dependence of these values on the nature of the halides and solvation characteristics is indicated.

Exploring the Mechanisms of Reactions in Solution from Transition Path Sampling Molecular Dynamics Simulations

Recent advances in molecular dynamics simulations of rare reaction events and aggregation processes are reviewed. Therein the central focus is dedicated to employing the transition path sampling method to study reactions in solution. We describe systematic approaches for generating initial transition pathways and efficient strategies for computationally feasible exploration of further transition routes. The unprejudiced study of reaction mechanisms is illustrated for reactions in aqueous solution and other complex systems. Transition path sampling allows very detailed investigation of solvent effects. Apart from stabilization of reactant, transition, or product state ensembles, this also includes the role of the solvent as a heat bath and as a putative reaction partner. The latter issue is of particular importance for reactions in aqueous solutions, which involve proton-transfer steps that may be assisted by water molecules via the Grotthuss mechanism.

Dissolution of NaCl nanocrystals: an ab initio molecular dynamics study

NaCl nanocrystal dissolution was investigated in atomistic detail revealing a difference in the solvation of two different ionic species.

Monte Carlo simulation of electrodeposition of copper: a multistep free energy calculation

Electrodeposition of copper (Cu) involves length scales of a micrometer or even less. Several theoretical techniques such as continuum Monte Carlo, kinetic Monte Carlo (KMC), and molecular dynamics have been used for simulating this problem. However the multiphenomena characteristics of the problem pose a challenge for an efficient simulation algorithm. Traditional KMC methods are slow, especially when modeling surface diffusion with large number of particles and frequent particle jumps. Parameter estimation involving thousands of KMC runs is very time-consuming. Thus a less time-consuming and novel multistep continuum Monte Carlo simulation is carried out to evaluate the step wise free energy change in the process of electrochemical copper deposition. The procedure involves separate Monte Carlo codes employing different random number criterion (using hydrated radii, bare radii, hydration number of the species, redox potentials, etc.) to obtain the number of species (CuCl(2) or CuSO(4) or Cu as the case may be) and in turn the free energy. The effect of concentration of electrolyte, influence of electric field and presence of chloride ions on the free energy change for the processes is studied. The rate determining step for the process of electrodeposition of copper from CuCl(2) and CuSO(4) is also determined.

Ab Initio Molecular Dynamics Studies of Ionic Dissolution and Precipitation of Sodium Chloride and Silver Chloride in Water Clusters, NaCl(H2O)n and AgCl(H2O)n,n = 6, 10, and 14

An ab initio molecular dynamics method was used to compare the ionic dissolution of soluble sodium chloride (NaCl) in water clusters with the highly insoluble silver chloride (AgCl). The investigations focused on the solvation structures, dynamics, and energetics of the contact ion pair (CIP) and of the solvent-separated ion pair (SSIP) in NaCl(H(2)O)(n) and AgCl(H(2)O)(n) with cluster sizes of n = 6, 10 and 14. We found that the minimum cluster size required to stabilize the SSIP configuration in NaCl(H(2)O)(n) is temperature-dependent. For n = 6, both configurations are present as two distinct local minima on the free-energy profile at 100 K, whereas SSIP is unstable at 300 K. Both configurations, separated by a low barrier (<10 kJ mol(-1)), are identifiable on the free energy profiles of NaCl(H(2)O)(n) for n = 10 and 14 at 300 K, with the Na(+)/Cl(-) pairs being internally solvated in the water cluster and the SSIP configuration being slightly higher in energy (<5 kJ mol(-1)). In agreement with the low bulk solubility of AgCl, no SSIP minimum is observed on the free-energy profiles of finite AgCl(H(2)O)(n) clusters. The AgCl interaction is more covalent in nature, and is less affected by the water solvent. Unlike NaCl, AgCl is mainly solvated on the surface in finite water clusters, and ionic dissolution requires a significant reorganization of the solvent structure.

Solvation of sodium-chloride ion pair in water cluster at atmospheric conditions: Grand canonical ensemble Monte Carlo simulation

Open statistical ensemble simulations are used to study the mechanism of nucleation of atmospheric water on sodium-chloride ion pair in a wide range of temperature and relative humidity values. The extended simple point-charge model is used for water molecules. Ions-water nonadditive interactions are taken into account by introducing the mutual polarization of ions and water in the field of each other. Gibbs free-energy variations are calculated from Na+-Cl- pair-correlation function and used as a criterion for determining the possible stable states of the cluster. In this relation, it was found that the dissociation of ion pairs in water clusters occurs even at vapor pressures of only a few millibars. In the conditions under consideration solvent-separated ion-pair states are found to be more probable than contact ion-pair configurations. The susceptibilities of water and ions are found to play an essential role in the stabilization of ions at large separations. The structure of ion-induced clusters is analyzed in terms of binary correlation functions. The non-pair interactions influence essentially the structure of ion solvation shells. The results of simulation show that the separation of the charges in water clusters containing simple ions can take place under atmospheric conditions.

Dissolution dynamics of NaCl nanocrystal in liquid water

The dissolution dynamics of a NaCl nanocrystal in liquid water was studied using molecular dynamics simulations. The dissolution process was found to start with a Cl(-) ion at a corner site, followed by a Na(+) ion nearby. Both show directional preference in the dissolution path. An ion sequence with alternating charge, i.e., Cl(-), Na(+), Cl(-), Na(+), etc. was found to dominate the dissolution process. This image can be understood from the ionic hydration structures and the Coulomb interaction between the ions.

A simple simulation methodology for estimation of dehydration energies and surface potentials of concentrated NaCl solutions

A novel simulation procedure for estimating the dehydration energies of NaCl solutions spanning a wide range of concentrations, which incorporates ionic and molecular sizes, ion-pair formation, etc., is proposed on geometric and phenomenological considerations. The extent of dehydration during each movement of the hydrated molecule is evaluated using the expected and actual displacement of the species and mean nearest-neighbor distances. The interdependence between the size of the simulation box, number of molecules, and electrolyte concentration is pointed out.

Transition path sampling study of flip-flop transitions in model lipid bilayer membranes

The microscopic dynamics of lipids in biomembranes is of special relevance in the study of chemical reactions produced in cells. The mechanism of the exchange of a model lipid molecule between both sides of a flexible bilayer membrane or flip-flop in an aqueous environment has been studied by computer simulation using the recently developed transition path sampling technique, since flip-flop transitions are infrequent events of the lipid dynamics. In addition, structural changes in the membrane have been investigated at ambient conditions and for increasing temperature. Our results highlight the cooperative effort of the whole system in order to allow a lipid molecule to cross the bottleneck in configuration space associated with the transition state of the flip-flop event. Within the time interval of the transition, all molecules of the system significantly change the frequency of their molecular motions.