Effects of Molecular Dynamics Thermostats on Descriptions of Chemical Nonequilibrium

Using NMR diffusion data to validate MD models of disordered proteins: Test case of N-terminal tail of histone H4

MD simulations can provide uniquely detailed models of intrinsically disordered proteins (IDPs). However, these models need careful experimental validation. The coefficient of translational diffusion Dtr, measurable by pulsed field gradient NMR, offers a potentially useful piece of experimental information related to the compactness of the IDP's conformational ensemble. Here, we investigate, both experimentally and via the MD modeling, the translational diffusion of a 25-residue N-terminal fragment from histone H4 (N-H4). We found that the predicted values of Dtr, as obtained from mean-square displacement of the peptide in the MD simulations, are largely determined by the viscosity of the MD water (which has been reinvestigated as a part of our study). Beyond that, our analysis of the diffusion data indicates that MD simulations of N-H4 in the TIP4P-Ew water give rise to an overly compact conformational ensemble for this peptide. In contrast, TIP4P-D and OPC simulations produce the ensembles that are consistent with the experimental Dtr result. These observations are supported by the analyses of the 15N spin relaxation rates. We also tested a number of empirical methods to predict Dtr based on IDP's coordinates extracted from the MD snapshots. In particular, we show that the popular approach involving the program HYDROPRO can produce misleading results. This happens because HYDROPRO is not intended to predict the diffusion properties of highly flexible biopolymers such as IDPs. Likewise, recent empirical schemes that exploit the relationship between the small-angle x-ray scattering-informed conformational ensembles of IDPs and the respective experimental Dtr values also prove to be problematic. In this sense, the first-principle calculations of Dtr from the MD simulations, such as demonstrated in this work, should provide a useful benchmark for future efforts in this area.

Further cautionary tales on thermostatting in molecular dynamics: Energy equipartitioning and non-equilibrium processes in gas-phase simulations

Molecular dynamics (MD) simulations of gas-phase chemical reactions are typically carried out on a small number of molecules near thermal equilibrium by means of various thermostatting algorithms. Correct equipartitioning of kinetic energy among translations, rotations, and vibrations of the simulated reactants is critical for many processes occurring in the gas phase. As thermalizing collisions are infrequent in gas-phase simulations, the thermostat has to efficiently reach equipartitioning in the system during equilibration and maintain it throughout the actual simulation. Furthermore, in non-equilibrium simulations where heat is released locally, the action of the thermostat should not lead to unphysical changes in the overall dynamics of the system. Here, we explore issues related to both obtaining and maintaining thermal equilibrium in MD simulations of an exemplary ion-molecule dimerization reaction. We first compare the efficiency of global (Nosé-Hoover and Canonical Sampling through Velocity Rescaling) and local (Langevin) thermostats for equilibrating a system of flexible compounds and find that of these three only the Langevin thermostat achieves equipartition in a reasonable simulation time. We then study the effect of the unphysical removal of latent heat released during simulations involving multiple dimerization events. As the Langevin thermostat does not produce the correct dynamics in the free molecular regime, we only consider the commonly used Nosé-Hoover thermostat, which is shown to effectively cool down the reactants, leading to an overestimation of the dimerization rate. Our findings underscore the importance of thermostatting for the proper thermal initialization of gas-phase systems and the consequences of global thermostatting in non-equilibrium simulations.

Simulations of the synthesis of boron-nitride nanostructures in a hot, high pressure gas volume

We performed nanosecond timescale computer simulations of clusterization and agglomeration processes of boron nitride (BN) nanostructures in hot, high pressure gas, starting from eleven different atomic and molecular precursor systems containing boron, nitrogen and hydrogen at various temperatures from 1500 to 6000 K. The synthesized BN nanostructures self-assemble in the form of cages, flakes, and tubes as well as amorphous structures. The simulations facilitate the analysis of chemical dynamics and we are able to predict the optimal conditions concerning temperature and chemical precursor composition for controlling the synthesis process in a high temperature gas volume, at high pressure. We identify the optimal precursor/temperature choices that lead to the nanostructures of highest quality with the highest rate of synthesis, using a novel parameter of the quality of the synthesis (PQS). Two distinct mechanisms of BN nanotube growth were found, neither of them based on the root-growth process. The simulations were performed using quantum-classical molecular dynamics (QCMD) based on the density-functional tight-binding (DFTB) quantum mechanics in conjunction with a divide-and-conquer (DC) linear scaling algorithm, as implemented in the DC-DFTB-K code, enabling the study of systems as large as 1300 atoms in canonical NVT ensembles for 1 ns time.

The fountain effect of ice-like water across nanotubes at room temperature

The well-known fountain effect of superfluid helium can directly convert heat to mechanical work by the transport of the superfluid across narrow channels under a temperature difference. But it is regarded as a unique feature of superfluids, only occurring below the temperature of 2.17 K. Here we report a peculiar fountain effect of ice-like water across nanotubes at room temperature. Based on molecular simulations, we observed fascinating ultrafast fountain flow across nanotubes from the cold side to the hot side under a small temperature difference, due to the near-dissipationless nature of ice-like ordered water inside the nanotubes. Water molecules exhibit collective behavior and spontaneously convert thermal energy from the surrounding into directed motion without dissipation. A surprising pressure difference of up to 256 bar is generated from a temperature difference of 23 K, almost reaching the thermodynamic limit. This finding is anticipated to provide a new protocol for power harvesting devices, heat engines and nanomotors.

Theoretical Investigation of Molecular and Electronic Structures of Buckminsterfullerene-Silicon Quantum Dot Systems

Density functional theory (DFT) and density functional tight binding (DFTB) molecular dynamics (DFTB/MD) simulations of embedding and relaxation of buckminsterfullerene C₆₀ molecules chemisorbed on (001) and (111) surfaces and inside bulk silicon lattice were performed. DFT calculations of chemisorbed fullerenes on both surfaces show that the C₆₀ molecule deformation was very small and the C₆₀ binding energies were roughly ∼4 eV. The charge analysis shows that the C₆₀ molecule charges on (001) and (111) surfaces were between -2 and -3.5 electrons, respectively, that correlates well with the number of C-Si bonds linking the fullerene molecule and the silicon surface. DFT calculations of the C₆₀ molecule inside bulk silicon confirm that the C₆₀ molecule remains stable with the deformation energy values of between 11 and 15 eV for geometries with different C₆₀ configurations. The formation of some C-Si bonds causes local silicon amorphization and corresponding electronic charge uptake on the embedded fullerene cages. Charge analysis confirms that a single C₆₀ molecule can accept up to 20 excessive electrons that can be used in practice, wherein the main charge contribution is located on the fullerene's carbon atoms bonded to silicon atoms. These DFT calculations correlate well with DFTB/MD simulations of the embedding process. In this process, the C₆₀ molecule was placed on the top of the Si(111) surface, and it was further exposed by a stream of silicon dimers, resulting in subsequent overgrowth by silicon.

Self-assembly of endohedral metallofullerenes: a decisive role of cooling gas and metal-carbon bonding

The endohedral metallofullerene (EMF) self-assembly process in Sc/carbon vapor in the presence and absence of an inert cooling gas (helium) is systematically investigated using quantum chemical molecular dynamics simulations. It is revealed that the presence of He atoms accelerates the formation of pentagons and hexagons and reduces the size of the self-assembled carbon cages in comparison with analogous He-free simulations. As a result, the Sc/C/He system simulations produce a larger number of successful trajectories (i.e. leading to Sc-EMFs) with more realistic cage-size distribution than simulations of the Sc/C system. The main Sc encapsulation mechanism involves nucleation of several hexagons and pentagons with Sc atoms already at the early stages of carbon vapor condensation. In such proto-cages, both Sc-C σ-bonds and coordination bonds between Sc atoms and the π-system of the carbon network are present. Sc atoms are thus rather labile and can move along the carbon network, but the overall bonding is sufficiently strong to prevent dissociation even at temperatures around 2000 kelvin. Further growth of the fullerene cage results in the encapsulation of one or two Sc atoms within the fullerene. In agreement with experimental studies, an extension of the simulations to Fe and Ti as the metal component showed that Fe-EMFs are not formed at all, whereas Ti is prone to form Ti-EMFs with small cage sizes, including Ti@C28-Td and Ti@C30-C2v(3).

The good, the bad and the user in soft matter simulations

Molecular dynamics (MD) simulations have become popular in materials science, biochemistry, biophysics and several other fields. Improvements in computational resources, in quality of force field parameters and algorithms have yielded significant improvements in performance and reliability. On the other hand, no method of research is error free. In this review, we discuss a few examples of errors and artifacts due to various sources and discuss how to avoid them. Besides bringing attention to artifacts and proper practices in simulations, we also aim to provide the reader with a starting point to explore these issues further. In particular, we hope that the discussion encourages researchers to check software, parameters, protocols and, most importantly, their own practices in order to minimize the possibility of errors. The focus here is on practical issues. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.

Fast Water Thermo-pumping Flow Across Nanotube Membranes for Desalination

Development of high-efficiency and low-cost seawater desalination technologies is critical to meet global water crisis. Here we report a fast water pumping method in which the water molecules in seawater are continuously pumped across nanotube membranes driven by a small temperature difference, opening the possibility of high-throughput small-scale desalination devices driven by low-grade thermal energy. Using molecular dynamics simulations, we show that an equivalent driving pressure of 5.3 MPa is achieved with a temperature difference of only 15 K. The remarkable water pumping ability is attributed to the asymmetric thermal fluctuation of water molecules. With this method, a 10 cm(2) nanotube membrane with 1.5 × 10(13) pores per cm(2) will produce freshwater with a flow rate of 7.77 L/h under a small temperature difference of 15 K.

Self-enhanced catalytic activities of functionalized graphene sheets in the combustion of nitromethane: molecular dynamic simulations by molecular reactive force field

Functionalized graphene sheet (FGS) is a promising additive that enhances fuel/propellant combustion, and the determination of its mechanism has attracted much interest. In the present study, a series of molecular dynamic simulations based on a reactive force field (ReaxFF) are performed to explore the catalytic activity (CA) of FGS in the thermal decay of nitromethane (NM, CH3NO2). FGSs and pristine graphene sheets (GSs) are oxidized in hot NM liquid to increase their functionalities and subsequently show self-enhanced CAs during the decay. The CAs result from the interatomic exchanges between the functional groups on the sheets and the NM liquid, i.e., mainly between H and O atoms. CA is dependent on the density of NM, functionalities of sheets, and temperature. The GSs and FGSs that originally exhibit different functionalities tend to possess similar functionalities and consequently similar CAs as temperature increases. Other carbon materials and their oxides can accelerate combustion of other fuels/propellants similar to NM, provided that they can be dispersed and their key reaction steps in combustion are similar to NM.