Dynamics Simulations Of Aqueous Solutions Research Articles

Conformations of Low-Molecular-Weight Lignin Polymers in Water.

Low-molecular-weight lignin binds to cellulose during the thermochemical pretreatment of biomass for biofuel production, which prevents the efficient hydrolysis of the cellulose to sugars. The binding properties of lignin are influenced strongly by the conformations it adopts. Here, we use molecular dynamics simulations in aqueous solution to investigate the dependence of the shape of lignin polymers on chain length and temperature. Lignin is found to adopt collapsed conformations in water at 300 and 500 K. However, at 300 K, a discontinuous transition is found in the shape of the polymer as a function of the chain length. Below a critical degree of polymerization, Nc =15, the polymer adopts less spherical conformations than above Nc. The transition disappears at high temperatures (500 K) at which only spherical shapes are adopted. An implication relevant to cellulosic biofuel production is that lignin will self-aggregate even at high pretreatment temperatures.

Ca(2+) -complex stability of GAPAGPLIVPY peptide in gas and aqueous phase, investigated by affinity capillary electrophoresis and molecular dynamics simulations and compared to mass spectrometric results.

Strong, sequence-specific gas-phase bindings between proline-rich peptides and alkaline earth metal ions in nanoESI-MS experiments were reported by Lehmann etal. (Rapid Commun. Mass Spectrom. 2006, 20, 2404-2410), however its relevance for physiological-like aqueous phase is uncertain. Therefore, the complexes should also be studied in aqueous solution and the relevance of the MS method for binding studies be evaluated. A mobility shift ACE method was used for determining the binding between the small peptide GAPAGPLIVPY and various metal ions in aqueous solution. The findings were compared to the MS results and further explained using computational methods. While the MS data showed a strong alkaline earth ion binding, the ACE results showed nonsignificant binding. The proposed vacuum state complex also decomposed during a molecular dynamic simulation in aqueous solution. This study shows that the formed stable peptide-metal ion adducts in the gas phase by ESI-MS does not imply the existence of analogous adducts in the aqueous phase. Comparing peptide-metal ion interaction under the gaseous MS and aqueous ACE conditions showed huge difference in binding behavior.

Ab initio molecular dynamics simulation of aqueous solution of nitric oxide in different formal oxidation states

Ab initio molecular dynamics simulations were used to investigate the early chemical events involved in the dynamics of nitric oxide (NO), nitrosonium cation (NO+) and nitroxide anion (NO−) in aqueous solution. The NO+ ion is very reactive in aqueous solution having a lifetime of ∼4×10−13s, which is shorter than the value of 3×10−10s predicted experimentally. The NO+ reacts generating the nitrous acid as an intermediate and the NO2− ion as the final product. The dynamics of NO revealed the reversibly formation of a transient anion radical species HONO−.

Molecular structure and pronounced conformational flexibility of doxorubicin in free and conjugated state within a drug-peptide compound.

The search for targeted drug delivery systems requires the design of drug-carrier complexes, which could both reach the malignant cells and preserve the therapeutic substance activity. A promising strategy aimed at enhancing the uptake and reducing the systemic toxicity is to bind covalently the drug to a cell-penetrating peptide. To understand the structure-activity relationship in such preparations, the chemotherapeutic drug doxorubicin was investigated by unrestrained molecular dynamics simulations, supported by NMR, which yielded its molecular geometry in aqueous environment. Furthermore, the structure and dynamics of a conjugate of the drug with a cell-penetrating peptide was obtained from molecular dynamics simulations in aqueous solution. The geometries of the unbound compounds were characterized at different temperatures, as well as the extent to which they change after covalent binding and whether/how they influence each other in the drug-peptide conjugate. The main structural fragments that affect the conformational ensemble of every molecule were found. The results show that the transitions between different substructures of the three compounds require a modest amount of energy. At increased temperature, either more conformations become populated as a result of the thermal fluctuations or the relative shares of the various conformers equalize at the nanosecond scale. These frequent structural interconversions suggest expressed conformational freedom of the molecules. Conjugation into the drug-peptide compound partially immobilizes the molecules of the parent compounds. Nevertheless, flexibility still exists, as well as an effective intra- and intermolecular hydrogen bonding that stabilizes the structures. We observe compact packing of the drug within the peptide that is also based on stacking interactions. All this outlines the drug-peptide conjugate as a prospective building block of a more complex drug-carrier system.

Exploring volume, compressibility and hydration changes of folded proteins upon compression.

Understanding the physical basis of the structure, stability and function of proteins in solution, including extreme environmental conditions, requires knowledge of their temperature and pressure dependent volumetric properties. One physical-chemical property of proteins that is still little understood is their partial molar volume and its dependence on temperature and pressure. We used molecular dynamics simulations of aqueous solutions of a typical monomeric folded protein, staphylococcal nuclease (SNase), to study and analyze the pressure dependence of the apparent volume, Vapp, and its components by the Voronoi-Delaunay method. We show that the strong decrease of Vapp with pressure (βT = 0.95 × 10(-5) bar(-1), in very good agreement with the experimental value) is essentially due to the compression of the molecular volume, VM, ultimately, of its internal voids, V. Changes of the intrinsic volume (defined as the Voronoi volume of the molecule), the contribution of the solvent to the apparent volume, and of the contribution of the boundary voids between the protein and the solvent have also been studied and quantified in detail. The pressure dependences of the volumetric characteristics obtained are compared with the temperature dependent behavior of these quantities and with corresponding results for a natively unfolded polypeptide.

Conformation and dynamics of 8-Arg-vasopressin in solution.

Arginine-vasopressin was subjected to a long (11μs) molecular dynamics simulation in aqueous solution. Analysis of the results by DASH and principal components analyses revealed four main ring conformations that move essentially independently of the faster-moving tail region. Two of these conformations (labeled "saddle") feature well-defined β-turns in the ring and conserved transannular hydrogen bonds, whereas the other two ("open") feature neither. The conformations have been identified and defined and are all of sufficient stability to be considered candidates for biological conformations in their cognate receptors.

Transient Effects of Excluded Volume Interactions on the Translational Diffusion of Hydrodynamically Anisotropic Molecules.

We have investigated effects of excluded volume interactions on the translational diffusion of hydrodynamically anisotropic molecules. For that, we have performed rigid-body Brownian dynamics simulations of aqueous solutions of hen egg-white lysozyme (HEWL), at concentrations ranging from 1.25 mg/mL to 250 mg/mL and evaluated the lysozyme's self-diffusion. In the long time limit (above 1 μs), the protein's translational diffusion is isotropic, regardless the solution concentration. However, on the time scale of the order of up to hundreds of nanoseconds, the anisotropic translational diffusion is observed, with the transition time from the anisotropic to isotropic translational diffusion depending on the lysozyme concentration. The magnitude of the translational diffusion anisotropy in this transient regime is also concentration-dependent and steric interactions enhance the anisotropy. Moreover, steric interactions cause the anisotropy to be a nonmonotonic function of time. When the hydrodynamic anisotropy of the protein is neglected in Brownian dynamics simulations and its diffusion tensor is replaced with average translational and rotational diffusion coefficients, the lysozyme's translational dynamics in the long-time limit is similar to that in the case of the corresponding hydrodynamically anisotropic object. However, such a similarity is not observed below 1 μs and in this time regime the translational dynamics of lysozyme molecules modeled with isotropic diffusion coefficients substantially deviates from that derived from Brownian dynamics simulations of their hydrodynamically anisotropic counterparts.

Assessing the Efficiency of Polymeric Excipients by Atomistic Molecular Dynamics Simulations

We have performed all-atom molecular dynamics simulations of aqueous solutions of model oligomers of hydroxypropyl methylcellulose (HPMC) and hydroxypropyl methylcellulose acetate succinate (HPMCAS) excipients interacting with a representative poorly soluble active pharmaceutical ingredient (API), phenytoin. Simulations reveal formation of excipient-API complexes for some of the oligomers, which results in a reduction of API aggregation. API aggregation and diffusivity decreased with an increase in excipient content. Excipients form a "gel-like" phase spanning the simulation box beyond ∼10 wt %; API diffusivity within this gel phase is much smaller than API diffusivity without excipient, and decreases exponentially, by 5 orders of magnitude, with increased polymer concentration. Substantial differences are observed with variations in methyl, hydroxypropyl, acetate, and succinate substitution levels in the model oligomers and with the deprotonation state of succinate groups, with strongest interactions with hydrophobic phenytoin observed in the case of acetate substitution. These are used to develop quantitative measures of excipient-API interactions and excipient efficiency in the inhibition of API aggregation. We also find that for model oligomers based on Methocel E (manufactured by Dow Pharma & Food Solutions) chemistry, oligomers of length 10 monomers and simulation boxes of size 7 nm give results similar to those for longer oligomers and bigger boxes. The quantitative measures developed in this study are expected to prove useful as computational screening tools in excipient design.

Structure of a uranyl peroxo complex in aqueous solution from first-principles molecular dynamics simulations

Static ab initio and density-functional computations, as well as Car-Parrinello molecular dynamics simulations in aqueous solution are reported for [UO2(OH)(κ(2)-O2)(H2O)2](-) and [UO2(OH)2(κ(1)-O2H)(H2O)](-). Whereas the κ(1)-hydroperoxo isomer is found to be more stable than the κ(2)-peroxo form in the gas phase, the order of stability is reversed in explicit bulk solution. Based on free energies from thermodynamic integration (BLYP functional), the peroxo form is favoured by ca. 32 kJ mol(-1) in water. This stabilisation is discussed in terms of the hydration shells about the individual ligands and dipole moments of the complexes in water, and highlights the importance of explicit solute-solvent interactions and bulk solvation for the speciation of uranyl(vi) compounds.

Complexes between Poly(amido amine) Dendrimers and Poly(methacrlyic acid): Insight from Molecular Dynamics Simulations

SummaryIn this work we present results from fully atomistic molecular dynamics simulations of aqueous solutions of poly(amido amine) dendrimers and poly(methacrylic) acid in the dilute regime and at low ionic strength and physiological pH conditions, in which the polymeric components are charged. We have studied stoichiometric (1:1) and non‐stoichiometric (1:2) systems, comprised by dendrimers of two different generations and two different lengths of the linear polyelectrolyte. For all systems studied, a polymer‐rich and a solvent‐rich region is formed. The polymer‐rich region consists of aggregated complexes between the polymeric components bearing similarities to percolated structures met in physical hydrogels. We examine morphological characteristics of the two components as well as the degree of ionic pairing between the different ionic moieties, providing information regarding the degree of physical adsorption of the linear chains on the dendrimer's surface and that of the respective counterions on the oppositely charged monomers.

Generalized image charge solvation model for electrostatic interactions in molecular dynamics simulations of aqueous solutions

This paper extends the image charge solvation model (ICSM) [Y. Lin, A. Baumketner, S. Deng, Z. Xu, D. Jacobs, W. Cai, An image-based reaction field method for electrostatic interactions in molecular dynamics simulations of aqueous solutions, J. Chem. Phys. 131 (2009) 154103], a hybrid explicit/implicit method to treat electrostatic interactions in computer simulations of biomolecules formulated for spherical cavities, to prolate spheroidal and triaxial ellipsoidal cavities, designed to better accommodate non-spherical solutes in molecular dynamics (MD) simulations. In addition to the utilization of a general truncated octahedron as the MD simulation box, central to the proposed extension is an image approximation method to compute the reaction field for a point charge placed inside such a non-spherical cavity by using a single image charge located outside the cavity. The resulting generalized image charge solvation model (GICSM) is tested in simulations of liquid water, and the results are analyzed in comparison with those obtained from the ICSM simulations as a reference. We find that, for improved computational efficiency due to smaller simulation cells and consequently a less number of explicit solvent molecules, the generalized model can still faithfully reproduce known static and dynamic properties of liquid water at least for systems considered in the present paper, indicating its great potential to become an accurate but more efficient alternative to the ICSM when bio-macromolecules of irregular shapes are to be simulated.

Image Charge Solvation Model (ICSM) with Improved Boundary Conditions

In previous work the Image Charge Solvation Model (ICSM) [1] was introduced as an alternative way to simulate bulk properties of solutions. The ICSM consists of a spherical cavity of explicit solvent embedded in a continuum dielectric medium, and solves the electrostatic interactions accurately and more efficiently than the Particle Mesh Ewald (PME) method on large scales. In spite of the success of the model in simulating a pure water system, and extremely dilute ionic solutions [2], periodic boundary conditions create unphysical charge-charge correlations at finite ion concentrations. Although expanding the system size can reduce these extraneous correlations to negligible levels in principle, the PME method remains more efficient on large scales. In this work we re-evaluate the applied boundary conditions at the cavity wall to correct the problem at its origin, which is related to torques on water molecules due to the electrostatic reaction field [3]. Here, we apply a mean field force representing bulk media outside the cavity, and a self-correcting torque field is introduced to enforce translational symmetry. Our modified ICSM maintains accuracy, performs more efficiently than previously and removes the primary cause of spatial correlations between ions.[1] Y. Lin, A. Baumketner, S. Deng, Z. Xu, D. Jacobs, W. Cai, An image-based reaction field method for electrostatic interactions in molecular dynamics simulations of aqueous solutions. J. Chem. Phys. 131, (2009).[2] Y. Lin, A. Baumketner, W. Song, S. Deng, D. Jacobs, and W. Cai, Ionic solvation studied by image-charge reaction field method. J. Chem. Phys. 134, (2011).[3] W. Song, Y. Lin, A. Baumketner, S. Deng, W. Cai and D. Jacobs, Effect of the reaction field on molecular forces and torques revealed by an Image-Charge Solvation Model, Comm. Comp. Phys. 13:129-149 (2013).

Thermodynamic Study of Hydrolysis Reactions in Aqueous Solution from Ab Initio Potential and Molecular Dynamics Simulations

A procedure for the theoretical study of chemical reactions in solution by means of molecular dynamics simulations of aqueous solution at infinite dilution is described using ab initio solute‐solvent potentials and TIP3P water model to describe the interactions. The procedure is applied to the study of neutral hydrolysis of various molecules (HCONH2, HNCO, HCNHNH2, and HCOOCH3) via concerted and water‐assisted mechanisms. We used the solvent as a reaction coordinate and the free energy curves for the calculation of the properties related with the reaction mechanism, namely, reaction and activation energies.

ICSM: An order [formula omitted] method for calculating electrostatic interactions added to TINKER

We present an order N method for calculating electrostatic interactions that has been integrated into the molecular dynamics portion of the TINKER Molecular Modeling package. This method, introduced in a previous paper [Y. Lin, A. Baumketner, S. Deng, Z. Xu, D. Jacobs, W. Cai, An image-based reaction field method for electrostatic interactions in molecular dynamics simulations of aqueous solutions, J. Chem. Phys. 131 (2009) 154103] and termed the Image-Charge Solvation Model (ICSM), is a hybrid electrostatic approach that combines the strengths of both explicit and implicit representations of the solvent. A multiple-image method is used to calculate reaction fields due to the implicit part while the Fast Multipole Method (FMM) is used to calculate the Coulomb interactions for all charges, including the explicit part. The integrated package is validated through test simulations of liquid water. The results are compared with those obtained by the Particle Mesh Ewald (PME) method that is built in the TINKER package. Timing performance of TINKER with the integrated ICSM is benchmarked on bulk water as a function of the size of the system. In particular, timing analysis results show that the ICSM outperforms the PME for sufficiently large systems with the break-even point at around 30,000 particles in the simulated system.

Study of the Polymer Length Dependence of the Single Chain Transition Temperature in Syndiotactic Poly(N-isopropylacrylamide) Oligomers in Water

Aqueous solutions of poly(N-isopropylacrylamide) (PNIPAM) exhibit a temperature responsive change in conformation. When the temperature is increased, the polymer transitions from an extended coil conformation to a collapsed structure. We performed molecular dynamics simulations of aqueous solutions of single chain, syndiotactic PNIPAM oligomers over a wide range of temperatures and varying degrees of polymerization to elucidate the effect of oligomer length on the single chain transition temperature, T1. We have reproduced recent measurements of the transition temperature increasing with decreasing oligomer chain length. Examination of the chain structure reveals that conformations above T1 bend to bring hydrophobic segments together to shield them from the water. The constraints of the dihedral dynamics require elevated temperatures for shorter chains to bend sharply enough in order to undergo the transition. This result is confirmed by calculations of the solvent accessible surface area, which shows an ...

Inclusion complexes of Schiff bases as phytogrowth inhibitors

This article details the preparation, characterization and phytotoxic evaluation of several Schiff base inclusion complexes obtained from β-cyclodextrin and p-sulfonic acid calix[6]arene. The inclusion complexes (1:1 molar ratio) were prepared by mixing a 5 mmol L−1 aqueous solution (containing 1 % DMSO) of Schiff bases (guests) with aqueous solution (containing 1 % DMSO) of 5 mmol L−1 of β-cyclodextrin or p-sulfonic acid calix[6]arene (hosts). The host–guest systems were characterized via a series of NMR experiments. The ability of the complexes to interfere with the radicle elongation of Sorghum bicolor (dicotyledonous species) and Cucumis sativus (monocotyledonous species) was evaluated. After 48 h, the inclusion complexes inhibited the radicle elongation of both species from 11 to 56 %. The formation of inclusion complexes was also investigated theoretically by molecular dynamics simulations in aqueous solution through implicit approach. Based on the experimental observation, the phytotoxic activity evaluated can be attributed to the formation of host–guest systems. This was supported by the theoretical findings based on stable interaction energy analyses for all the studied supramolecular systems.

Structure and Dynamics of Aqueous Solutions of Electrolytes in Confined Space

We perform isothermal-isobaric molecular dynamics simulations of aqueous solutions of potassium and chloride ions with varying tube diameter. An equilibrium state is attained within 1 ns, but the relaxation time to equilibrium is dependent on the initial arrangement of ions. When the tube diameter is larger than 1 nm, ions exchange their axial positions in few tens of picosecond to be the most stable configuration in which counterions are lined up alternately. However, ions in a tube narrower than 1 nm cannot exchange the mutual positions in axial-coordinate within an order of nano second. The axial self-diffusion coefficients are also examined. It is found that they increase with increasing the tube size once an equilibrium is attained. These results suggest the partial hydration and dehydration play a certain role in diffusion of the electrolytes in confined space like tubes and channels.

Rationale for the opposite stereochemistry of the major monoadducts and interstrand crosslinks formed by mitomycin C and its decarbamoylated analogue at CpG steps in DNA and the effect of cytosine modification on reactivity

Mitomycin C (MMC) is a potent antitumour agent that forms a covalent bond with the 2-amino group of selected guanines in the minor groove of double-stranded DNA following intracellular reduction of its quinone ring and opening of its aziridine moiety. At some 5'-CG-3' (CpG) steps the resulting monofunctional adduct can evolve towards a more deleterious bifunctional lesion, which is known as an interstrand crosslink (ICL). MMC reactivity is enhanced when the cytosine bases are methylated (5 MC) and decreased when they are replaced with 5-F-cytosine (5FC) whereas the stereochemical preference of alkylation changes upon decarbamoylation. We have studied three duplex oligonucleotides of general formula d(CGATAAXGCTAACG) in which X stands for C, 5MC or 5FC. Using a combination of molecular dynamics simulations in aqueous solution, quantum mechanics and continuum electrostatics, we have been able to (i) obtain a large series of snapshots that facilitate an understanding in atomic detail of the distinct stereochemistry of monoadduct and ICL formation by MMC and its decarbamoylated analogue, (ii) provide an explanation for the altered reactivity of MMC towards DNA molecules containing 5MC or 5FC, and (iii) show the distinct accommodation in the DNA minor groove of the different covalent modifications, particularly the most cytotoxic C1α and C1β ICLs.

Polarizable Force Fields and Polarizable Continuum Model: A Fluctuating Charges/PCM Approach. 1. Theory and Implementation.

We present a combined fluctuating charges-polarizable continuum model approach to describe molecules in solution. Both static and dynamic approaches are discussed: analytical first and second derivatives are shown as well as an extended lagrangian for molecular dynamics simluations. In particular, we use the polarizable continuum model to provide nonperiodic boundary conditions for molecular dynamics simulations of aqueous solutions. The extended lagrangian method is extensively discussed, with specific reference to the fluctuating charge model, from a numerical point of view by means of several examples, and a rationalization of the behavior found is presented. Several prototypical applications are shown, especially regarding solvation of ions and polar molecules in water.

Molecular Dynamics Simulations of CXCL-8 and Its Interactions with a Receptor Peptide, Heparin Fragments, and Sulfated Linked Cyclitols

CXCL-8 (Interleukin 8) is a CXC chemokine with a central role in the human immune response. We have undertaken extensive in silico analyses to elucidate the interactions of CXCL-8 with its various binding partners, which are crucial for its biological function. Sequence and structure analyses showed that residues in the thirdq β-sheet and basic residues in the heparin binding site are highly variable, while residues in the second β-sheet are highly conserved. Molecular dynamics simulations in aqueous solution of dimeric CXCL-8 have been performed with starting geometries from both X-ray and NMR structures showed shearing movements between the two antiparallel C-terminal helices. Dynamic conservation analyses of these simulations agreed with experimental data indicating that structural differences between the two structures at quaternary level arise from changes in the secondary structure of the N-terminal loop, the 3(10)-helix, the 30s, 40s, and 50s loops and the third β-sheet, resulting in a different interhelical separation. Nevertheless, the observation of these different states indicates that CXCL-8 has the potential to undergo conformational changes, and it seems likely that this feature is relevant to the mode of binding of glycosaminoglycan (GAG) mimetics such as cyclitols. Simulations of the receptor peptide fragment-CXCL-8 complex identified several specific interactions of the receptor peptide with CXCL-8 that could be exploited in the structure-based design of competitive peptides and nonpeptidic molecules targeting CXCL-8 for combating inflammatory diseases. Simulations of the CXCL-8 dimer complexed with a 24-mer heparin fragment and of the CXCL-8-receptor peptide complex revealed that Arg60, Lys64, and Arg68 in the dimer bind to cyclitols in a horseshoe pattern, defining a region which is spatially distinct from the receptor binding site. There appears to be an optimum number of sulfates and an optimum length of alkyl spacers required for the interaction of cyclitol inhibitors with the dimeric form of CXCL-8. Calculation of the binding affinities of cyclitol inhibitors reflected satisfactorily the ranking of experimentally determined inhibitory potencies. The findings of these molecular modeling studies will help in the search for inhibitors which can modulate various CXCL-8 biological activities and serve as an excellent model system to study CXC-inhibitor interactions.