A comparison of different water models for melting point calculation of methane hydrate using molecular dynamics simulations

Molecular Dynamics Modeling Based Investigation of the Effect of Freezing Rate on Lysozyme Stability

PURPOSE

The stability of protein drug products frozen during fill finish operations is greatly affected by the freezing rate applied. Non-optimal freezing rates may lead to the denaturation of protein's complex macromolecular conformation. However, limited work has been done to address the effect of different freezing rates on protein stability at nano-scale level.

METHODS

The stability of a model protein, lysozyme, was investigated at atomic and molecular scale under varying freezing rates and moving ice-water interface. Ice seeding approach was adopted to initiate ice formation in this present simulation.

RESULTS

The faster freezing rate (11-12 K/490 ns) applied resulted in overall smaller ice fraction within the simulation box with a larger freeze-concentrated liquid (FCL) region. Consequently, the faster freezing rate better maintained protein stability with less secondary structure deviations, higher hydration level and structural compactness, and less fluctuations at individual residues than observed following slow (5-6 K/490 ns) and medium (7-8 K/490 ns) freezing rates. The present study also identified the residues near and within helices 3, 6, 7, and 8 dominate the structural instability of the lysozyme at 247 K freezing temperature.

CONCLUSIONS

For the first time, ice formation in therapeutic protein solution was studied "non-isothermally" at different freezing rates using molecular dynamics simulations. Thus, a good understanding of freezing rates on protein instability was revealed by applying the developed computational model.

Modeling Solution Behavior of Poly(N-isopropylacrylamide): A Comparison between Water Models

Water is known to play a fundamental role in determining the structure and functionality of macromolecules. The same crucial contribution is also found in the in silico description of polymer aqueous solutions. In this work, we exploit the widely investigated synthetic polymer poly(N-isopropylacrylamide) (PNIPAM) to understand the effect of the adopted water model on its solution behavior and to refine the computational setup. By means of atomistic molecular dynamics simulations, we perform a comparative study of PNIPAM aqueous solution using two advanced water models: TIP4P/2005 and TIP4P/Ice. The conformation and hydration features of an atactic 30-mer at infinite dilution are probed at a range of temperature and pressure suitable to detect the coil-to-globule transition and to map the P–T phase diagram. Although both water models can reproduce the temperature-induced coil-to-globule transition at atmospheric pressure and the polymer hydration enhancement that occurs with increasing pressure, the PNIPAM–TIP4P/Ice solution shows better agreement with experimental findings. This result can be attributed to a stronger interaction of TIP4P/Ice water with both hydrophilic and hydrophobic groups of PNIPAM, as well as to a less favorable contribution of the solvent entropy to the coil-to-globule transition.

A Molecular Dynamics Study of Monomer Melt Properties of Cyanate Ester Monomer Melt Properties

The objective of this work was to computationally predict the melting temperature and melt properties of thermosetting monomers used in aerospace applications. In this study, we applied an existing voids method by Solca. to examine four cyanate ester monomers with a wide range of melting temperatures. Voids were introduced into some simulations by removal of molecules from lattice positions to lower the free-energy barrier to melting to directly simulate the transition from a stable crystal to amorphous solid and capture the melting temperature. We validated model predictions by comparing melting temperature against previously reported literature values. Additionally, the torsion and orientational order parameters were used to examine the monomers’ freedom of motion to investigate structure–property relationships. Ultimately, the voids method provided reasonable estimates of melting temperature while the torsion and order parameter analysis provided insight into sources of the differing melt properties between the thermosetting monomers. As a whole, the results shed light on how freedom of molecular motions in the monomer melt state may affect melting temperature and can be utilized to inspire the development of thermosetting monomers with optimal monomer melt properties for demanding applications.

Structure and thermodynamics of empty clathrate hydrates below the freezing point of water

Recently prepared as a new H2O phase, ice XVI was obtained by degassing a Ne-sII clathrate hydrate under vacuum, however very little is known of that crystalline solid under temperatures (T ≤ 220 K) and pressures (p ≤ 5000 bar) relevant for the Earth's environment and geochemistry. In this work, atomically detailed calculations using long time-scale molecular simulations, seldom paralelled before, are employed to probe empty sII clathrate hydrates. It is found that the volumetric response to an applied pressure-temperature gradient is accurately described by the Parsafar and Mason equation of state with an accuracy of at least 99.7%. Structural deformation induced upon the crystals is interpreted by monitoring the unit cell length and isobaric thermal expansivity, whilst benchmarked against previous neutron diffraction measurements of ice XVI and hexagonal ice under room pressure conditions; a critical comparison is established with other sII guest occupied lattices (CH4, CO2 and CnH2n+2 with n = 2, 3, 4), often found in permafrost regions and in the margins of continental shelves. Such an analysis reveals that empty sII frameworks are slightly more stable to thermal deformation than their sI analogues and that hexagonal ice is the structurally most stable of the condensed H2O phases addressed here. Of paramount importance for the oil and natural gas industries, heat capacities obtained from enthalpy profiles are identical for the sI and sII empty clathrates up to 2000 bar and diverge by only ∼7.3% at 5000 bar. The canonical tetrahedral symmetry of water-bonded networks is analysed in terms of an angular and a distance order parameters, which are observed to decrease (increase) as pressure (temperature) increases (decreases). The results now being reported constitute a landmark for future studies dealing with high-pressure and very low-temperature conditions, characteristic of the Earth's permafrost environment and other planetary interiors, whilst contributing to expand our knowledge regarding the recently discovered ice XVI phase.

Replica exchange dissipative particle dynamics method on threadlike micellar aqueous solutions

The self-assembly of surfactant molecules can spontaneously result in a variety of micelle morphologies, such as spherical micelles, threadlike micelles, and vesicles, and it is therefore crucial to predict and control the self-assembly to achieve a helpful process in the fields of materials chemistry and engineering. A dissipative particle dynamics (DPD) method used in a coarse-grained molecular simulation is applied to simulate various self-assembling soft matter systems because it can handle greater length and time scales than a typical molecular dynamics simulation (MD). It should be noted that the thorough sampling of a system is not assured at low temperatures because of large complex systems with coarse-grained representations. In this article, we demonstrate that the replica exchange method (REM) is very effective for even a DPD in which the energy barrier is comparatively lower than that of a MD. A replica exchange on DPD (REDPD) simulation for threadlike micellar aqueous solutions was conducted, and the values of the potential energy and the mean aggregation number were compared. As a result, the correct values and a self-assembled structure within a low-temperature range can only be obtained through the REDPD.

Molecular Dynamics Simulation of Methane Hydrate Decomposition in the Presence of Alcohol Additives

The decomposition process of methane hydrate in pure water and methanol aqueous solution was studied by molecular dynamics simulation. The effects of temperature and pressure on hydrate structure and decomposition rate are discussed. The results show that decreasing pressure and increasing temperature can significantly enhance the decomposition rate of hydrate. After adding a small amount of methanol molecules, bubbles with a diameter of about 2 nm are formed, and the methanol molecules are mainly distributed at the gas-liquid interface, which greatly accelerates the decomposition rate and gas-liquid separation efficiency. The radial distribution function and sequence parameter analysis show that the water molecules of the undecomposed hydrate with ordered ice-like configuration at a temperature of 275 K evolve gradually into a long-range disordered liquid structure in the dynamic relaxation process. It was found that at temperatures above 280 K and pressures between 10 atm and 100 atm, the pressure has no significant effect on hydrate decomposition rate, but when the pressure is reduced to 1 atm, the decomposition rate increases sharply. These findings provided a theoretical insight for the industrial exploitation of hydrates.

Factors Promoting the Formation of Clathrate-Like Ordering of Water in Biomolecular Structure at Ambient Temperature and Pressure

Clathrate hydrate forms when a hydrophobic molecule is entrapped inside a water cage or cavity. Although biomolecular structures also have hydrophobic patches, clathrate-like water is found in only a limited number of biomolecules. Also, while clathrate hydrates form at low temperature and moderately higher pressure, clathrate-like water is observed in biomolecular structure at ambient temperature and pressure. These indicate presence of other factors along with hydrophobic environment behind the formation of clathrate-like water in biomolecules. In the current study, we presented a systematic approach to explore the factors behind the formation of clathrate-like water in biomolecules by means of molecular dynamics simulation of a model protein, maxi, which is a naturally occurring nanopore and has clathrate-like water inside the pore. Removal of either confinement or hydrophobic environment results in the disappearance of clathrate-like water ordering, indicating a coupled role of these two factors. Apart from these two factors, clathrate-like water ordering also requires anchoring groups that can stabilize the clathrate-like water through hydrogen bonding. Our results uncover crucial factors for the stabilization of clathrate-like ordering in biomolecular structure which can be used for the development of new biomolecular structure promoting clathrate formation.

Molecular Insights into the Unusual Structure of an Antifreeze Protein with a Hydrated Core

The primary driving force for protein folding is the formation of a well-packed, anhydrous core. However, recently, the crystal structure of an antifreeze protein, maxi, has been resolved where the core of the protein is filled with water, which apparently contradicts the existing notion of protein folding. Here, we have performed standard molecular dynamics (MD) simulation, replica exchange MD (REMD) simulation, and umbrella sampling using TIP4P water at various temperatures (300, 260, and 240 K) to explore the origin of this unusual structural feature. It is evident from standard MD and REMD simulations that the protein is found to be stable at 240 K in its unusual state. The core of protein has two layers of semi-clathrate water separating the methyl groups of alanine residues from different helical strands. However, with increasing temperature (260 and 300 K), the stability decreases as the core becomes dehydrated, and methyl groups of alanine are tightly packed driven by hydrophobic interactions. Calculation of the potential of mean force by an umbrella sampling technique between a pair of model hydrophobes resembling maxi protein at 240 K shows the stabilization of second solvent-separated minima (SSM), which provides a thermodynamic rationale of the unusual structural feature in terms of weakening of the hydrophobic interaction. Because the stabilization of SSMs is implicated for cold denaturation, it suggests that the maxi protein is so designed by nature where the cold denatured-like state becomes the biologically active form as it works near or below the freezing point of water.