Structure and hydrogen bond dynamics of water–dimethyl sulfoxide mixtures by computer simulations

Anomalous viscoelastic response of water-dimethyl sulfoxide solution and a molecular explanation of non-monotonic composition dependence of viscosity

Amphiphilic molecules such as dimethyl sulfoxide (DMSO) and its aqueous binary mixtures exhibit pronounced nonideality in composition dependence of several static and dynamic properties. We carry out detailed molecular dynamics simulations to calculate various properties including viscosity of the mixture and combine the results with a mode coupling theory analysis to show that this nonideality can be attributed to local structures that are stable on a short time scale but transient on a long time scale to maintain the large scale homogeneity of the solution. Although the existence of such quasistable structures has been deciphered from spectroscopy, a detailed characterization does not exist. We calculate stress-stress autocorrelation functions (SACFs) of water-DMSO binary mixtures. We employ two different models of water, SPC/E and TIP4P/2005, to check the consistency of our results. Viscosity shows a pronounced nonmonotonic composition dependence. The calculated values are in good agreement with the experimental results. Fourier transform of SACF provides frequency-dependent viscosity. The frequency-dependent viscosity (that is, viscoelasticity) is also found to be strongly dependent on composition. Viscoelasticity exhibits sharp peaks due to intramolecular vibrational modes of DMSO, which are also seen in the density of states. We evaluate the wavenumber dependent dynamic structure factor and wavenumber dependent relaxation time. The latter also exhibits a sharp nonmonotonic composition dependence. The calculated dynamic structure factor is used in mode coupling theory expression of viscosity to obtain a semiquantitative understanding of anomalous composition dependence of viscosity. Both the self-diffusion coefficients and rotational correlation times of water and DMSO molecules exhibit nonmonotonic composition dependence.

Ovalbumin-Loaded Gelation Microneedles Made of Predictive Formulation by Molecular Dynamics Simulation for Enhancement of Skin Immunization

Gelation microneedle (GMNs) based vaccinations with tumor antigens have been considered to be an attractive method for transcutaneous immunization because of their superior ability to deliver vaccines through the stratum corneum (SC) in a minimally invasive manner, which subsequently induces adaptive antitumor immunity. In this study, molecular dynamics (MD) uniaxial tension simulations were conducted to predict the formulation of poly(vinyl alcohol) (PVA; possesses high water solubility) and poly(methyl vinyl ether-altmaleic anhydride) (PMVEMA; possesses high mechanical strength) blend that has the strongest mechanical properties. To validate the accuracy of the Dreiding potential for these two polymers, their densities and Hildebrand solubility parameters were first predicted using MD simulations. These values exhibited good agreement with the corresponding experimental results, indicating the accuracy of the Dreiding potential for the polymers. Regarding the simulation results, the number density of H-bonds between PVA and PMVEMA was the highest at 50% PMVEMA, which can significantly enhance the mechanical strength of pristine PVA for enhanced skin immunization. In terms of further experimental validation, evidence from mechanical strength, solubility, in vitro porcine skin penetration tests, and in vivo immunization were consistent with our simulation predictions. In addition, our results indicated that delivery of ovalbumin (OVA) using GMN patches fabricated using PVA/PMVEMA (50%/50%) provided even stronger immune responses. Using this molecular simulation procedure, the optimal fraction of PVA/PMVEMA composite for the strongest mechanical properties can be rapidly predicted to reduce research time and costs in related experiments.

Moisture-induced crossover in the thermodynamic and mechanical response of hydrophilic biopolymer

The use of natural sustainable resources such as wood in green industrial processes is currently limited by our poor understanding of the impact of moisture on their thermodynamic and mechanical behaviors. Here, a molecular dynamics approach is used to investigate the physical response of a typical hydrophilic biopolymer in softwood hemicellulose-xylan-when subjected to moisture adsorption. A unique moisture-induced crossover is found in the thermodynamic and mechanical properties of this prototypical biopolymer with many quantities such as the heat of adsorption, heat capacity, thermal expansion and elastic moduli exhibiting a marked evolution change for a moisture content about 30 wt%. By investigating the microscopic structure of the confined water molecules and the polymer-water interfacial area, the molecular mechanism responsible for this crossover is shown to correspond to the formation of a double-layer adsorbed film along the amorphous polymeric chains. In addition to this moisture-induced crossover, many properties of the hydrated biopolymer are found to obey simple material models.

Spatially Heterogeneous Water Properties at Disordered Surfaces Decrease the Hydrophobicity of Nonpolar Self-Assembled Monolayers

Understanding the relationship between hydrophobicity and the properties of functionalized surfaces is vital to the design of materials that interact in aqueous environments. In this Letter, we use atomistic molecular dynamics simulations to investigate the effects of surface order on the hydrophobicity of self-assembled monolayers (SAMs) containing nonpolar ligands. We find that the interfacial hydrophobicity is highly correlated with SAM order and, strikingly, poorly correlated with the solvent-accessible surface area, which typically has been related to interfacial hydrophobicity. Analysis of spatial variations in both SAM and water properties reveals that the SAM-water interface is pinned near regions of disordered SAM surfaces with increased free volume, decreasing the overall interfacial hydrophobicity. Spatial variations in ligand end group positions at disordered SAM surfaces thus translate to spatial variations in hydrophobicity, yielding heterogeneous surface properties. These findings provide new insights into how surface order can alter the hydrophobicity of chemically uniform surfaces.

Intermolecular dynamics of ultraconfined interlayer water in tobermorite: influence on mechanical performance

Ultraconfined interlayer water within the tobermorite molecular structure is responsible for changes in the uniaxial tensile and compressive response of the family of tobermorites: 9, 11 and 14 Å. These confined interlayer water molecules are engaged in solvation of cations and anions within the tobermorite structure, which has been demonstrated through the intermolecular vibrational spectra and hydrogen bond lifetime of the water molecules. This study demonstrates that instead of ionization of water molecules (as proposed in an earlier study), breaking of hydrogen bonds of water is more plausible leading to solvation of ions within the molecular structure of tobermorite. A schematic of the coordinate covalent bonds between the water molecules and the cations and anions of the tobermorite structure has been proposed in this study.

Lysozyme-luteolin binding: molecular insights into the complexation process and the inhibitory effects of luteolin towards protein modification

In the proposed work, the complexation of bioactive flavonoid luteolin with hen egg white lysozyme (HEWL) along with its inhibitory influence on HEWL modification has been explored with the help of multi-spectroscopic and computational methods. The binding affinity has been observed to be moderate in nature (in the order of 10⁴ M^-1) and the static quenching mechanism was found to be involved in the fluorescence quenching process. The binding constant (K_b) shows a progressive increase with the increase in temperature from (4.075 ± 0.046 × 10⁴ M^-1) at 293 K to (6.962 ± 0.024 × 10⁴ M^-1) at 313 K under experimental conditions. Spectroscopic measurements along with molecular docking calculations suggest that Trp62 is involved in the binding site of luteolin within the geometry of HEWL. The positive changes in enthalpy (ΔH = +19.99 ± 0.65 kJ mol^-1) as well as entropy (ΔS = +156.28 ± 2.00 J K^-1 mol^-1) are indicative of the presence of hydrophobic forces that stabilize the HEWL-luteolin complex. The micro-environment around the Trp residues showed an increase in hydrophobicity as indicated by synchronous fluorescence (SFS), three dimensional fluorescence (3D) and red edge excitation (REES) studies. The % α-helix of HEWL showed a marked reduction upon binding with luteolin as indicated by circular dichroism (CD) and Fourier-transform infrared spectroscopy (FTIR) studies. Moreover, luteolin is situated at a distance of 4.275 ± 0.004 nm from the binding site as indicated by FRET theory, and the rate of energy transfer k_ET (0.063 ± 0.004 ns^-1) has been observed to be faster than the donor decay rate (1/τ_D = 0.606 ns^-1), which is indicative of the non-radiative energy transfer during complexation. Leaving aside the binding study, luteolin showed promising inhibitory effects towards the d-ribose mediated glycation of HEWL as well as towards HEWL fibrillation as studied by fluorescence emission and imaging studies. Excellent correlation with the experimental observations as well as precise location and dynamics of luteolin within the binding site has been obtained from molecular docking and molecular dynamics simulation studies.

Fast Desalination by Multilayered Covalent Organic Framework (COF) Nanosheets

Covalent organic frameworks (COFs) are penetrated with uniform and ordered nanopores, implying their great potential in molecular/ion separations. As an imine-linked, stable COF, TpPa-1 is receiving tremendous interest for molecular sieving membranes. Theoretically, atomically thin TpPa-1 monolayers exhibit extremely high water permeance but unfortunately no rejection to ions because of its large pore size (∼1.58 nm). The COF monolayers tend to stack to form laminated multilayers, but how this stacking influences water transport and ion rejections remains unknown. Herein, we investigate the transport behavior of water and salt ions through multilayered TpPa-1 COFs by nonequilibrium molecular dynamics simulations. By analyzing both the interfacial and interior resistance for water transport, we reveal that with rising stacking number of COF multilayers exhibit increasing ion rejections at the expense of water permeance. More importantly, stacking in the offset eclipsed fashion significantly reduces the equivalent pore size of COF multilayers to 0.89 nm, and ion rejection is correspondingly increased. Remarkably, 25 COF monolayers stacked in this fashion give 100% MgCl₂ rejection, whereas water permeance remains 1 to 2 orders of magnitude higher than that of commercial nanofiltration membranes. This work demonstrates the rational design of fast membranes for desalination by tailoring stacking number and fashion of the COF monolayers.

Atomic Motif Recognition in (Bio)Polymers: Benchmarks From the Protein Data Bank

Rationalizing the structure and structure-property relations for complex materials such as polymers or biomolecules relies heavily on the identification of local atomic motifs, e.g., hydrogen bonds and secondary structure patterns, that are seen as building blocks of more complex supramolecular and mesoscopic structures. Over the past few decades, several automated procedures have been developed to identify these motifs in proteins given the atomic structure. Being based on a very precise understanding of the specific interactions, these heuristic criteria formulate the question in a way that implies the answer, by defining a list of motifs based on those that are known to be naturally occurring. This makes them less likely to identify unexpected phenomena, such as the occurrence of recurrent motifs in disordered segments of proteins, and less suitable to be applied to different polymers whose structure is not driven by hydrogen bonds, or even to polypeptides when appearing in unusual, non-biological conditions. Here we discuss how unsupervised machine learning schemes can be used to recognize patterns based exclusively on the frequency with which different motifs occur, taking high-resolution structures from the Protein Data Bank as benchmarks. We first discuss the application of a density-based motif recognition scheme in combination with traditional representations of protein structure (namely, interatomic distances and backbone dihedrals). Then, we proceed one step further toward an entirely unbiased scheme by using as input a structural representation based on the atomic density and by employing supervised classification to objectively assess the role played by the representation in determining the nature of atomic-scale patterns.

Self-Assembled and Size-Controllable Oligonucleotide Nanospheres for Effective Antisense Gene Delivery through an Endocytosis-Independent Pathway

The development of efficient gene delivery vectors has faced two major challenges, namely endo- and lysosomal escape and intracellular release. To address these problems, we developed an oligonucleotide (ON)-template-assisted polymerization approach to create ON nanospheres as gene vectors. Guanidinium-containing disulfide monomers were organized on the ON templates to increase their effective local concentrations. Consequently, ring-opening disulfide-exchange polymerization between monomers was accelerated, further facilitating the self-assembly of ON nanospheres. The size of these nanospheres was controlled by varying the length of the ON templates. Importantly, the nanospheres can be directly delivered into the cytosol through an endocytosis-independent pathway, which is followed by intracellular depolymerization in the reductive cytosolic environment to release the packaged ONs, resulting in efficient gene silencing. The ON nanospheres thus hold great promise as candidates for gene therapy.

Characterization of the Photophysical Behavior of DFHBI Derivatives: Fluorogenic Molecules that Illuminate the Spinach RNA Aptamer

( Z)-5-(3,5-Difluoro-4-hydroxybenzylidene)-2,3-dimethyl-3,5-dihydro-4 H-imidazol-4-one (DFHBI) and its analogues are fluorogenic molecules that bind the Spinach aptamer (a small RNA molecule), which was selected for imaging RNA. They are extremely weakly fluorescent in liquid solvents. It had been hypothesized that photoisomerization is a very efficient nonradiative process of deactivation. We show, consistent with the results of other studies, that if the isomerization is impeded, the fluorescence signal is enhanced significantly. In addition, we provide a thorough characterization of the photophysical behavior of DFHBI and its derivatives, notably that of ( Z)-5-(3,5-difluoro-4-hydroxybenzylidene)-2-methyl-3-((perfluorophenyl)methyl)-3,5-dihydro-4 H-imidazol-4-one (PFP-DFHBI) in various solvent environments. Solvent-dependent studies were performed with various mixtures of solvents. The results suggest that hydrogen bonding or strong interactions of the solvents with the phenolic-OH group change the absorption band near 420-460 nm and the nature of emission near 430 and 500 nm through various degrees of stabilization and the transformation between the neutral and the anionic species at both ground and excited states. These observations are confirmed by using a methoxy-substituted molecule (( Z)-5-(4-methoxybenzylidene)-2,3-dimethyl-3,5-dihydro-4 H-imidazol-4-one), where the 420-460 nm band is absent in the presence of methanol and the spectra are similar to those of PFP-DFHBI in noninteracting solvents, such as acetonitrile and dichloromethane. Thus, in addition to the major role of photoisomerization as a nonradiative process of deactivation of the excited state, the fluorescence of DFHBI-type molecules is very sensitively dependent upon the pH of the medium as well as upon solvent-specific interactions, such as hydrogen-bonding ability and polarity.

Effect of DMSO, urea and ethanol on hydration of stratum corneum model membrane based on short-chain length ceramide [AP]

Hydration of oriented multilamellar membrane based on ceramide [AP] in the DMSO, urea and ethanol aqueous solutions at various solute concentrations was investigated by neutron diffraction. Neither urea nor DMSO influence the repeat distance of the membrane and internal structure of bilayer at their mole concentration of up to 0.15 and 0.10, respectively. The d-spacing reduction effect of both compounds was observed at their concentrations of 0.2 for urea and 0.2 and 0.4 for DMSO. Compared to hydration in the pure water, both urea and DMSO slow down the swelling process, and this slowdown is more pronounced with increasing in their concentration. At concentration of 0.2, urea and DMSO induce the slight phase separation of the fully hydrated samples; at the highest used concentration of 0.6, DMSO induces the strong time-depend separation of the sample probably due to fluidization of lipid bilayers. Ethanol at a used molar concentration of 0.03 leads to dissolution of the sample.

Molecular Order Affects Interfacial Water Structure and Temperature-Dependent Hydrophobic Interactions between Nonpolar Self-Assembled Monolayers

Understanding how material properties affect hydrophobic interactions-the water-mediated interactions that drive the association of nonpolar materials-is vital to the design of materials in contact with water. Conventionally, the magnitude of the hydrophobic interactions between extended interfaces is attributed to interfacial chemical properties, such as the amount of nonpolar solvent-exposed surface area. However, recent experiments have demonstrated that the hydrophobic interactions between uniformly nonpolar self-assembled monolayers (SAMs) also depend on molecular-level SAM order. In this work, we use atomistic molecular dynamics simulations to investigate the relationship between SAM order, water structure, and hydrophobic interactions to explain these experimental observations. The SAM-SAM hydrophobic interactions calculated from the simulations increase in magnitude as SAM order increases, matching experimental observations. We explain this trend by showing that the molecular-level order of the SAM impacts the nanoscale structure of interfacial water molecules, leading to an increase in water structure near disordered SAMs. These findings are consistent with a decrease in the solvation entropy of disordered SAMs, which is confirmed by measuring the temperature dependence of hydrophobic interactions using both simulations and experiments. This study elucidates how hydrophobic interactions can be influenced by an interfacial physical property, which may guide the design of synthetic materials with fine-tuned interfacial hydrophobicity.

Cryopreservation of Hematopoietic Stem Cells: Emerging Assays, Cryoprotectant Agents, and Technology to Improve Outcomes

Hematopoietic stem cell (HSC) therapy is widely used to treat a growing number of hematological and non-hematological diseases. Cryopreservation of HSCs allows for cells to be transported from the site of processing to the site of clinical use, creates a larger window of time in which cells can be administered to patients, and allows sufficient time for quality control and regulatory testing. Currently, HSCs and other cell therapies conform to the same cryopreservation techniques as cells used for research purposes: cells are cryopreserved in dimethyl sulfoxide (DMSO) at a slow cooling rate. As a result, HSC therapy can result in numerous adverse symptoms in patients due to the infusion of DMSO. Efforts are being made to improve the cryopreservation of HSCs for clinical use. This review discusses advances in the cryopreservation of HSCs from 2007 to the present. The preclinical development of new cryoprotectants and new technology to eliminate cryoprotectants after thawing are discussed in detail. Additional cryopreservation considerations are included, such as cooling rate, storage temperature, and cell concentration. Preclinical cell assessment and quality control are discussed, as well as clinical studies from the past decade that focus on new cryopreservation protocols to improve patient outcomes.

'Second-generation' 1,2,3-triazole-based inhibitors of Porphyromonas gingivalis adherence to oral streptococci and biofilm formation

This study details the design, synthesis and bioassay of ‘click’ peptidomimetic compounds which inhibit the adherence of P. gingivalis to S. gordonii, a primary step toward pathogenic colonization of the subgingival pocket.

Several ‘second-generation’ click inhibitors of the multi-species biofilm propagated by the adherence of the oral pathogen Porphyromonas gingivalis to Streptococcus gordonii were synthesized and evaluated. The design of the structures was based on the results obtained with the first-generation diphenyloxazole ‘click’ inhibitors which bear suitable hydrophobic and polar groups within a dual scaffold molecule bearing a 1,2,3-triazole spacer. The structures of the synthetic targets reported herein now consist of a triazolyl(phenylsulfonylmethyl) and a triazolyl(phenylsulfinylmethyl) spacer which joins a 4,5-diphenyloxazole with both phenyl rings bearing lipophilic substituents. The triazolyl “linker” group is formed by a click reaction between the 4-azido(phenylsulfonyl/sulfinylmethyl) oxazoles and acetylenic components having aryl groups bearing hydrophobic substituents. The 1,3,5-trisubstituted-2,4,6-triazine scaffold of the most active click compounds were modeled after the structural motif termed the VXXLL nuclear receptor (NR) box. When substituted at the 3- and 5-positions with 2- and 4-fluorophenylamino and N,N-diethylamino units, the candidates bearing the 1,3,5-trisubstituted-2,4,6-triazine scaffold formed a substantial subset of the second-generation click candidates. Four of the click products, compounds 95, 111, 115 and 122 showed inhibition of the adherence of P. gingivalis to S. gordonii with an IC₅₀ range of 2.3–4.3 μM and only 111 exhibited cytotoxic activity against telomerase immortalized gingival keratinocytes at 60 μM. These results suggest that compounds 95, 115, 122, and possibly 111 represent the most suitable compounds to evaluate for activity in vivo.

Microscopic origin of the scattering pre-peak in aqueous propylamine mixtures: X-ray and neutron experiments versus simulations

The structure of aqueous propylamine mixtures is investigated through X-ray and neutron scattering experiments, and the scattered intensities compared with computer simulation data.

Structure and dynamic properties of stretched water in graphene nanochannels by molecular dynamics simulation: effects of stretching extent

Water confined in nanochannels can be stretched with the variation of external pressure, leading to the more disordered microstructure and higher diffusion coefficient than bulk water.

Investigating Interfacial Effects on Surface Nanobubbles without Pinning Using Molecular Dynamics Simulation

We investigated how the stability of aqueous argon surface nanobubbles on hydrophobic surfaces depends on gas adsorption, solid-gas interaction energy, and the bulk gas concentration using molecular dynamics simulation with the SPC/E water solvent. We observed stable surface nanobubbles without surface pinning sites for longer than 160 ns, contrary to previous findings using monoatomic Lennard-Jones solvent. In addition, the hydrophobicity of a substrate has an effect to reduce the requirement degree of oversaturation on water bulk. We found that the gas enrichment layer, gas adsorption monolayer on the hydrophobic substrate, and water hydrogen bonding near the interface are likely necessary conditions for nanobubble stability. We concluded that gas nanobubble stability does not necessarily require three-phase pinning sites.

Exploring Dynamics and Structure of Biomolecules, Cryoprotectants, and Water Using Molecular Dynamics Simulations: Implications for Biostabilization and Biopreservation

Successful stabilization and preservation of biological materials often utilize low temperatures and dehydration to arrest molecular motion. Cryoprotectants are routinely employed to help the biological entities survive the physicochemical and mechanical stresses induced by cold or dryness. Molecular interactions between biomolecules, cryoprotectants, and water fundamentally determine the outcomes of preservation. The optimization of assays using the empirical approach is often limited in structural and temporal resolution, whereas classical molecular dynamics simulations can provide a cost-effective glimpse into the atomic-level structure and interaction of individual molecules that dictate macroscopic behavior. Computational research on biomolecules, cryoprotectants, and water has provided invaluable insights into the development of new cryoprotectants and the optimization of preservation methods. We describe the rapidly evolving state of the art of molecular simulations of these complex systems, summarize the molecular-scale protective and stabilizing mechanisms, and discuss the challenges that motivate continued innovation in this field.

Hydrophobic Surface Enhances Electrostatic Interaction in Water

A high dielectric constant is one of the peculiar properties of liquid water, indicating that the electrostatic interaction between charged substances is largely reduced in water. We show by molecular dynamics simulation that the dielectric constant of water is decreased near the hydrophobic surface. We further show that the decrease in the dielectric constant is due to both the decreased water density and the reduced water dipole correlation in the direction perpendicular to the surface. We finally demonstrate that electrostatic interaction in water is actually strengthened near the hydrophobic surface.

Role of hydrogen bonding in hysteresis observed in sorption-induced swelling of soft nanoporous polymers

Hysteresis is observed in sorption-induced swelling in various soft nanoporous polymers. The associated coupling mechanism responsible for the observed sorption-induced swelling and associated hysteresis needs to be unraveled. Here we report a microscopic scenario for the molecular mechanism responsible for hysteresis in sorption-induced swelling in natural polymers such as cellulose using atom-scale simulation; moisture content and swelling exhibit hysteresis upon ad- and desorption but not swelling versus moisture content. Different hydrogen bond networks are examined; cellulose swells to form water-cellulose bonds upon adsorption but these bonds do not break upon desorption at the same chemical potential. These findings, which are supported by mechanical testing and cellulose textural assessment upon sorption, shed light on experimental observations for wood and other related materials.

Dynamical crossover of water confined within the amphiphilic nanocores of aggregated amyloid β peptides

It is believed that the self-assembly of amyloid beta (Aβ) peptides in the brain is the cause of Alzheimer's disease. Atomistic molecular dynamics simulations of aqueous solutions of Aβ protofilaments of different sizes at room temperature have been carried out to explore the dynamic properties of water confined within the core and at the exterior surface of the protofilaments. Attempts have been made to understand how the non-uniform distortion of the protofilaments associated with their structural crossover influences the diffusivity and the hydrogen bonding environment of the confined water molecules. In contrast to the homogeneous solvent dynamical environment at the exterior surface, the calculations revealed heterogeneously restricted motions of water confined within the distorted cores of the protofilaments. Importantly, it is demonstrated that the structural crossover of the aggregates observed for the decamer is associated with a dynamical transition of water confined within its core. A direct one-to-one correlation between the heterogeneously restricted core water motions and the kinetics of the breaking and formation of hydrogen bonds quantitatively demonstrated that a modified hydrogen bond arrangement within the cores of higher order Aβ protofilaments is the origin behind the crossover in core water mobility. A fraction of the water molecules forming short-lived water-water hydrogen bonds within the core of the crossover protofilament decamer are believed to diffuse away easily from the core and thus play a crucial role in further growth of the protofilament by facilitating the binding of new peptide monomers.

How do glycerol and dimethyl sulphoxide affect local tetrahedral structure of water around a nonpolar solute at low temperature? Importance of preferential interaction

Glycerol and dimethyl sulphoxide (DMSO) have vital roles in cryoprotection of living cells, tissues, etc. The above action has been directly linked with disruption of hydrogen (H-) bond structure and dynamics of water by these cosolvents at bulk region and around various complex units, such as peptide, amino acid, protein, and lipid membrane. However, the disruption of the local structure of the water solvent around a purely hydrophobic solute is still not studied extensively. The latter is also important in the context of stabilization of protein from cold denaturation. Through all-atom molecular dynamics simulation, we have investigated the comparative effect of glycerol and DMSO on the orientational order of water around a nonpolar solute at -5 °C. A steady reduction of the tetrahedral order of water is observed at bulk (>10 Å distance from the solute) and solute interface (<5.5 Å distance from the solute) with increasing the cosolvent concentration. Contrasting roles of glycerol and DMSO have been evidenced. While DMSO affects the H-bond structure of the interfacial water more than that of the bulk water, glycerol affects the water structure almost uniformly at all regions around the solute. Furthermore, while glycerol helps to retain water molecules at the interface, DMSO significantly reduces the water content in that region. We have put forward a plausible mechanism for these contrasting roles of these cosolvents. The solute-cosolvent hydrophobic-interaction-induced orientational alignment of an interfacial cosolvent molecule determines whether the involvement of the cosolvent molecules in H-bonding with solvent water in the interface is akin to the bulk region or not.

Resistance of water transport in carbon nanotube membranes

Carbon nanotube (CNT) membranes have long been considered as next-generation membranes due to superfast water transport inside tubes. However, a large pressure loss occurs at the pore mouth, and consequently water transport through the whole tubes is significantly retarded. To find out the reason behind this, we conduct systematic non-equilibrium molecular dynamics (NEMD) simulations on water transport through CNT membranes with various tube diameters and lengths. The whole transport resistance is contributed by the interfacial and interior parts, and the interfacial contribution plays a dominating role in short tubes and only can be ignored when the tube length reaches a scale of several micrometers. With regard to the origin of the interfacial resistance, the hydrogen bonding rearrangement (HBR) effect accounts for at least 45%, and the rest is attributed to the geometrical or steric crowding of water molecules near the pore mouth. To reduce the dominant interfacial resistance, we change the shape of the pore mouth from plate to hourglass by mimicking the aquaporin water channels. The interfacial resistance is thus decreased by >27%. It is also found that the reduction is originated from the optimized HBR rather than the subdued steric crowding of water molecules near the pore mouth.

Equilibration and analysis of first-principles molecular dynamics simulations of water

First-principles molecular dynamics (FPMD) simulations based on density functional theory are becoming increasingly popular for the description of liquids. In view of the high computational cost of these simulations, the choice of an appropriate equilibration protocol is critical. We assess two methods of estimation of equilibration times using a large dataset of first-principles molecular dynamics simulations of water. The Gelman-Rubin potential scale reduction factor [A. Gelman and D. B. Rubin, Stat. Sci. 7, 457 (1992)] and the marginal standard error rule heuristic proposed by White [Simulation 69, 323 (1997)] are evaluated on a set of 32 independent 64-molecule simulations of 58 ps each, amounting to a combined cumulative time of 1.85 ns. The availability of multiple independent simulations also allows for an estimation of the variance of averaged quantities, both within MD runs and between runs. We analyze atomic trajectories, focusing on correlations of the Kohn-Sham energy, pair correlation functions, number of hydrogen bonds, and diffusion coefficient. The observed variability across samples provides a measure of the uncertainty associated with these quantities, thus facilitating meaningful comparisons of different approximations used in the simulations. We find that the computed diffusion coefficient and average number of hydrogen bonds are affected by a significant uncertainty in spite of the large size of the dataset used. A comparison with classical simulations using the TIP4P/2005 model confirms that the variability of the diffusivity is also observed after long equilibration times. Complete atomic trajectories and simulation output files are available online for further analysis.

Influence of Cholesterol on the Dynamics of Hydration in Phospholipid Bilayers

We investigate the dynamics of interfacial waters in dipalmitoylphosphatidylcholine (DPPC) bilayers upon the addition of cholesterol, by molecular dynamics simulations. Our data reveal that the inclusion of cholesterol modifies the membrane aqueous interfacial dynamics: waters diffuse faster, their rotational decay time is shorter, and the DPPC/water hydrogen bond dynamics relaxes faster than in the pure DPPC membrane. The observed acceleration of the translational water dynamics agrees with recent experimental results, in which, by means of NMR techniques, an increment of the surface water diffusivity is measured upon the addition of cholesterol. A microscopic analysis of the lipid/water hydrogen bond network at the interfacial region suggests that the mechanism underlying the observed water mobility enhancement is given by the rupture of a fraction of interlipid water bridge hydrogen bonds connecting two different DPPC molecules, concomitant to the formation of new lipid/solvent bonds, whose dynamics is faster than that of the former. The consideration of a simple two-state model for the decay of the hydrogen bond correlation function yielded excellent results, obtaining two well-separated characteristic time scales: a slow one (∼250 ps) associated with bonds linking two DPPC molecules, and a fast one (∼15 ps), related to DPPC/solvent bonds.

Investigation of Nonlinear Output-Input Microwave Power of DMSO-Ethanol Mixture by Molecular Dynamics Simulation

The nonlinear response of output-input microwave power for DMSO-ethanol mixture, which was exhibited as the direct evidence of non-thermal effect in experiment, was investigated by molecular dynamics simulation. Effects of microwave field on the mixture were evaluated from the alteration in structure, transport, hydrogen bonding dynamics and intermolecular interaction energy. Increasing the strength of the microwave field did not lead to any markedly conformational change, but decrease the diffusion coefficient. Prolonged hydrogen bonding lifetimes, which caused by the redistribution of microwave energy, was also detected. Distinct threshold effect was observed, which was consistent with the behavior in the experiment.