Force field development for actinyl ions via quantum mechanical calculations: an approach to account for many body solvation effects

Genome-Based Multi-Antigenic Epitopes Vaccine Construct Designing against Staphylococcus hominis Using Reverse Vaccinology and Biophysical Approaches

Staphylococcus hominis is a Gram-positive bacterium from the staphylococcus genus; it is also a member of coagulase-negative staphylococci because of its opportunistic nature and ability to cause life-threatening bloodstream infections in immunocompromised patients. Gram-positive and opportunistic bacteria have become a major concern for the medical community. It has also drawn the attention of scientists due to the evaluation of immune evasion tactics and the development of multidrug-resistant strains. This prompted the need to explore novel therapeutic approaches as an alternative to antibiotics. The current study aimed to develop a broad-spectrum, multi-epitope vaccine to control bacterial infections and reduce the burden on healthcare systems. A computational framework was designed to filter the immunogenic potent vaccine candidate. This framework consists of pan-genomics, subtractive proteomics, and immunoinformatics approaches to prioritize vaccine candidates. A total of 12,285 core proteins were obtained using a pan-genome analysis of all strains. The screening of the core proteins resulted in the selection of only two proteins for the next epitope prediction phase. Eleven B-cell derived T-cell epitopes were selected that met the criteria of different immunoinformatics approaches such as allergenicity, antigenicity, immunogenicity, and toxicity. A vaccine construct was formulated using EAAAK and GPGPG linkers and a cholera toxin B subunit. This formulated vaccine construct was further used for downward analysis. The vaccine was loop refined and improved for structure stability through disulfide engineering. For an efficient expression, the codons were optimized as per the usage pattern of the E coli (K12) expression system. The top three refined docked complexes of the vaccine that docked with the MHC-I, MHC-II, and TLR-4 receptors were selected, which proved the best binding potential of the vaccine with immune receptors; this was followed by molecular dynamic simulations. The results indicate the best intermolecular bonding between immune receptors and vaccine epitopes and that they are exposed to the host’s immune system. Finally, the binding energies were calculated to confirm the binding stability of the docked complexes. This work aimed to provide a manageable list of immunogenic and antigenic epitopes that could be used as potent vaccine candidates for experimental in vivo and in vitro studies.

Force Field Parameterization of Actinyl Molecular Cations Using the 12-6-4 Model

In this work, a set of 12-6-4 force fields (FFs) parameters were developed for the actinyl molecular cations, AnO2n+ (n = 1, 2), from uranium to plutonium for classical molecular dynamics (MD) for four water models: TIP3P, SPC/E, OPC3, and TIP4Pew. Such a non-bonded potential model taking into account the induced dipole between the metallic center and the surrounding molecules has shown better performances for various cations than the classic 12-6 non-bonded potentials. The parametrization method proposed elsewhere for metallic cations has been extended to these molecular cations. In contrast to the actinyl 12-6 FFs from the literature, the new models reproduce correctly both solvation and thermodynamic properties, thanks to the inclusion of the induced dipole term (C4). The transferability of such force fields was assessed by performing MD simulations of carbonato actinyl species, which are highly implicated in actinide migration or actinide extraction from seawater. A highly satisfying agreement was found when comparing the EXAFS signals computed from our MD simulation to the experimental ones. The set of FFs developed here opens new possibilities for the study of actinide chemistry.

Combining EXAFS and Computer Simulations to Refine the Structural Description of Actinyls in Water

EXAFS spectroscopy is one of the most used techniques to solve the structure of actinoid solutions. In this work a systematic analysis of the EXAFS spectra of four actinyl cations, [UO2]2+, [NpO2]2+, [NpO2]+ and [PuO2]2+ has been carried out by comparing experimental results with theoretical spectra. These were obtained by averaging individual contributions from snapshots taken from classical Molecular Dynamics simulations which employed a recently developed [AnO2]2+/+ -H2O force field based on the hydrated ion model using a quantum-mechanical (B3LYP) potential energy surface. Analysis of the complex EXAFS signal shows that both An-Oyl and An-OW single scattering paths as well as multiple scattering ones involving [AnO2]+/2+ molecular cation and first-shell water molecules are mixed up all together to produce a very complex signal. Simulated EXAFS from the B3LYP force field are in reasonable agreement for some of the cases studied, although the k= 6-8 Å-1 region is hard to be reproduced theoretically. Except uranyl, all studied actinyls are open-shell electron configurations, therefore it has been investigated how simulated EXAFS spectra are affected by minute changes of An-O bond distances produced by the inclusion of static and dynamic electron correlation in the quantum mechanical calculations. A [NpO2]+-H2O force field based on a NEVPT2 potential energy surface has been developed. The small structural changes incorporated by the electron correlation on the actinyl aqua ion geometry, typically smaller than 0.07 Å, leads to improve the simulated spectrum with respect to that obtained from the B3LYP force field. For the other open-shell actinyls, [NpO2]2+ and [PuO2]2+, a simplified strategy has been adopted to improve the simulated EXAFS spectrum. It is computed taking as reference structure the NEVPT2 optimized geometry and including the DW factors of their corresponding MD simulations employing the B3LYP force field. A better agreement between the experimental and the simulated EXAFS spectra is found, confirming the a priori guess that the inclusion of dynamic and static correlation refine the structural description of the open-shell actinyl aqua ions.

Refined Force Field for Liquid Sulfolane with Particular Emphasis to Its Transport Characteristics

An all-atom force field dedicated to capturing the properties of multifunctional sulfolane is necessary. In addition to being an excellent solvent and extractor, sulfolane is also a frequently investigated component for battery electrolytes in recent times. Given this, theoretically capturing its transport properties is essential. However, given the rather high shear viscosity of liquid sulfolane and its polar aprotic nature, formulating an appropriate non-polarizable force field for this compound remains a challenge. Starting from a generic force field, we report a refined force field for sulfolane which quantitatively captures its bulk properties, resulting in significantly improved estimates for self-diffusion constant and shear viscosity of sulfolane in comparison to force fields reported hitherto. Density, self-diffusion constant, and shear viscosity were determined between temperatures (303 and 398) K and at 1 bar pressure. All properties determined from the refined force field are in good agreement with experiments. The refined model employs atomic site charges obtained from the density-derived electrostatic and chemical (DDEC6) method for liquid sulfolane modeled using quantum density functional theory. Lennard-Jones parameters were refined using quantum potential energy scans. Despite possessing a large dipole moment, the large molecular size of sulfolane partially disrupts intermolecular dipolar ordering in liquid sulfolane. Molecular dipoles of near neighbor sulfolane, however, retain a partial preference for antiparallel orientation even at the highest temperatures investigated here.

Developing a camera-based 3D momentum imaging system capable of 1 Mhits/s

A camera-based three-dimensional (3D) imaging system with a superb time-of-flight (TOF) resolution and multi-hit capability was recently developed for electron/ion imaging [Lee et al. J. Chem. Phys. 141, 221101 (2014)]. In this work, we report further improvement of the event rate of the system by adopting an event-driven camera, Tpx3Cam, for detecting the 2D positions of electrons, while a high-speed digitizer provides highly accurate (∼30 ps) TOF information for each event at a rate approaching 1 Mhits/sec.

Molecular Dynamics Simulation Studies on Structure, Dynamics, and Thermodynamics of Uranyl Nitrate Solution at Various Acid Concentrations

The structural and dynamical characteristics of uranyl ions in an aqueous acidic environment are of immense importance in the field of nuclear fuel reprocessing. In view of that, the structural and dynamical behavior of the uranyl ion in water has been investigated by performing molecular dynamics (MD) simulations using different force fields. All the force fields have depicted similar structural and dynamical properties except the free energy of hydration where the Guilbaud-Wipff (GW) model performs well over the others. The calculated density using MD simulations is found to be in excellent agreement with the measured experimental density, which ensures the accuracy of the adopted GW force field. The calculated surface tension and shear viscosity are seen to be increased with uranyl nitrate concentrations. At a higher concentration of about 4.0 mol/L, the supersaturation effect has been captured by an inflection in the plot of surface tension and shear viscosity against concentration because of the solution heterogeneity, which was correlated by an inflection in the scattering intensity observed by performing the dynamic light scattering experiment. The binding mode of nitrate ions with the uranyl ion is found to be concentration-dependent, and at higher concentration, it is predominantly monodentate.

Competition/Cooperation between Humic Acid and Graphene Oxide in Uranyl Adsorption Implicated by Molecular Dynamics Simulations

Molecular dynamics (MD) simulations were performed to investigate the influence of curvature and backbone rigidity of an oxygenated surface, here graphene oxide (GO), on its adsorption of uranyl in collaboration with humic acid (HA). The planar curvature of GO was found to be beneficial in impeding the folding of HA. This, together with its rigidity that helps stabilize the extended conformation of HA, offered rich binding sites to interact with uranyl with only marginal loss of binding strength. According to our simulations, the interaction between uranyl and GO was mainly driven by electrostatic interactions. The presence of HA not only provided multiple sites to compete/cooperate with GO for adsorption of free uranyl but also interacted with GO acting as a "bridge" to connect uranyl and GO. The potential of mean force (PMF) profiles implied that HA significantly enhanced the interaction strength between uranyl and GO and stabilized the uranyl-GO complex. Meanwhile, GO could reduce the diffusion coefficients of uranyl and HA and retard their migrations in aqueous solution. This work provides theoretical hints on the GO-based remediation strategies for the sites contaminated by uranium or other heavy metal ions and oxygenated organic pollutants.

UO22+ structure in solvent extraction phases resolved at molecular and supramolecular scales: a combined molecular dynamics, EXAFS and SWAXS approach

We developed a polarizable force field for unraveling the UO₂²⁺ structure in both aqueous and solvent extraction phases.

A molecular dynamics investigation of actinyl–ligand speciation in aqueous solution

Actinyl ions (AnO₂ⁿ⁺), the form in which actinides are commonly found in aqueous solution, are important species in the nuclear fuel cycle.

Coordinated force generation of skeletal myosins in myofilaments through motor coupling

In contrast to processive molecular motors, skeletal myosins form a large motor ensemble for contraction of muscles against high loads. Despite numerous information on the molecular properties of skeletal myosin, its ensemble effects on collective force generation have not been rigorously clarified. Here we show 4 nm stepwise actin displacements generated by synthetic myofilaments beyond a load of 30 pN, implying that steps cannot be driven exclusively by single myosins, but potentially by coordinated force generations among multiple myosins. The simulation model shows that stepwise actin displacements are primarily caused by coordinated force generation among myosin molecules. Moreover, the probability of coordinated force generation can be enhanced against high loads by utilizing three factors: strain-dependent kinetics between force-generating states; multiple power stroke steps; and high ATP concentrations. Compared with other molecular motors, our findings reveal how the properties of skeletal myosin are tuned to perform cooperative force generation for efficient muscle contraction.

Skeletal muscle myosin forms large ensembles to generate force against high loads. Using optical tweezers and simulation Kaya et al. provide experimental evidence for cooperative force generation, and describe how the molecular properties of skeletal myosins are tuned for coordinated power strokes.

Dynamics of Humic Acid and Its Interaction with Uranyl in the Presence of Hydrophobic Surface Implicated by Molecular Dynamics Simulations

This work targeted a molecular level of understanding on the dynamics of humic acid (HA) and its interaction with uranyl in the presence of hydrophobic surface mimicked by a carbon nanotube (CNT), which also represents a potential intruder in the environment accompanying with the development of nanotechnology. In aqueous phase, uranyl and HA were observed to build close contact spontaneously, driven by electrostatic interaction, leading to a more compact conformation of HA. The presence of CNT unfolds HA via π-π interactions with the aromatic rings of HA without significant perturbation on the interaction strength between HA and uranyl. These results show that the hydrophilic uranyl and the hydrophobic CNT influence the folding behavior of HA in distinct manners, which represents two fundamental mechanisms that the folding behavior of HA may be modulated in the environment, that is, uranyl enhances the folding of HA via electrostatic interactions, whereas CNT impedes its spontaneous folding via van der Waals (vdW) interactions. The work also provides molecular level of evidence on the transformation of a hydrophobic surface into a hydrophilic one via noncovalent functionalization by HA, which in turn affects the migration of HA and the cations it binds to.

A classical force field for tetrahedral oxyanions developed using hydration properties: The examples of pertechnetate (TcO4(-)) and sulfate (SO4(2-))

Radioactive pertechnetate, (99)TcO4(-), is one of the most problematic ionic species in the context of the clean up and storage of nuclear waste. Molecular simulations can be used to understand the behavior of TcO4(-) in dilute aqueous solutions, providing reliable potentials are available. This work outlines the development of a new potential model for TcO4(-) and competing SO4(2-), optimized using their hydration properties, such as the Gibbs hydration free energy (calculated using Bennett's acceptance ratio method). The findings show that the TcO4(-) oxyanion has a very low hydration free energy (-202 kJ mol(-1)) compared to other anions (Cl(-), I(-), SO4(2-)) leading to fast water exchange dynamics and explaining its observed high mobility in the aqueous environment. Its hydrated structure, investigated using ion-water radial distribution functions, shows that it is unique amongst the other anions in that it does not possess well-defined hydration shells. Since contaminants and ubiquitous species in the aqueous environment are often present as tetrahedral oxyanions, it is proposed that the approach could easily be extended to a whole host of other species.

Unveiling the peculiar hydrogen bonding behavior of solvated N-heterocyclic carbenes

After fitting a molecular mechanical force field for imidazol-2-ylidenes, MD simulations revealed carbene–carbene and three-center hydrogen bonds of carbenes. The practical importance of these structures is also highlighted.

Dispelling some myths about the CO2 solubility in ionic liquids

ILs are not very good solvents for CO₂. The apparent high solubility results from their high M_w and not from any special capability to dissolve CO₂.

Molecular dynamics simulation study of distribution and dynamics of aqueous solutions of uranyl ions: the effect of varying temperature and concentration

Investigating the characteristics of actinyl ions has been of great interest due to their direct relevance in the nuclear fuel cycle. All-atom molecular dynamics simulations have been employed to study the orientational structure and dynamics of aqueous solutions of uranyl ions of various concentrations. The orientational structure of water around a uranyl ion has been thoroughly investigated by calculating different orientational probability distributions corresponding to different molecular axes of water. The orientational distribution of water molecules in the first coordination shell of a uranyl ion is found to be markedly different from that in bulk water. Analysis of counterion distribution around the uranyl ion reveals the presence of nitrate ions along with water molecules in the first solvation shell. From the comparison of the number of coordinated water and nitrate ions at various uranyl nitrate concentrations, it is evident that these two species compete for occupying the first solvation shell of the uranyl ion. Orientational dynamics of water molecules about different molecular axes of water in the vicinity of uranyl ions have also been investigated and decreasing orientational mobility of water with increasing uranyl concentration has been found. However, it is observed that the orientational dynamics remains more or less the same whether we consider all the water molecules in the aqueous solution or only the solvation shell water molecules. The effect of temperature on the translational and orientational characteristics of the aqueous uranyl solutions has also been studied in detail.

Uranyl Solvation by a Three-Dimensional Reference Interaction Site Model

We report an implementation of the three-dimensional reference interaction site model (3D RISM) that in particular addresses the treatment of the long-range Coulomb field of charged species, represented by point charges and/or a distributed charge density. A comparison of 1D and 3D results for atomic ions demonstrates a reasonable accuracy, even for a moderate size of the unit cell and a moderate grid resolution. In an application to uranyl complexes with 4-6 explicit aqua ligands and an implicit bulk solvent modeled by RISM, we show that the 3D technique is not susceptible to the deficiencies of the 1D technique exposed in our previous work [Li, Matveev, Krüger, Rösch, Comp. Theor. Chem. 2015, 1051, 151]. The 3D method eliminates the artificial superposition of explicit aqua ligands and the RISM medium and predicts essentially the same values for uranyl and uranyl-water bond lengths as a state-of-the-art polarizable continuum model. With the first solvation shell treated explicitly, the observables are nearly independent of the order of the closure relationship used when solving the set of integral equations for the various distribution functions. Furthermore, we calculated the activation barrier of water exchange with a hybrid approach that combines the 3D RISM model for the bulk aqueous solvent and a quantum mechanical description (at the level of electronic density functional theory) of uranyl interacting with explicitly represented water molecules. The calculated result agrees very well with experiment and the best theoretical estimates.

Dynamics of actinyl ions in water: a molecular dynamics simulation study

The dynamics of actinyl ions (AnO₂ⁿ⁺) in aqueous solutions is important not only for the design of advanced separation processes but also for understanding the fate of actinides in the environment.

Insights into the Intramolecular Properties ofη6-Arene-Ru-Based Anticancer Complexes Using Quantum Calculations

The factors that determine the stability and the effects of noncovalent interaction on theη6-arene ruthenium anticancer complexes are determined using DFT method. The intramolecular and intra-atomic properties were computed for two models of these half-sandwich ruthenium anticancer complexes and their respective hydrated forms. The results showed that the stability of these complexes depends largely on the network of hydrogen bonds (HB), strong nature of charge transfer, polarizability, and electrostatic energies that exist within the complexes. The hydrogen bonds strength was found to be related to the reported anticancer activities and the activation of the complexes by hydration. The metal–ligand bonds were found to be closed shell systems that are characterised by high positive Laplacian values of electron density. Two of the complexes are found to be predominantly characterised by LMCT while the other two are predominately characterised by MLCT.