Pairwise Distribution Function Research Articles

Molecular dynamics simulation study of sodium ion structure & dynamics in water in ionic liquids electrolytes using 1-butyl-3-methyl imidazolium tetrafluoroborate and 1-butyl-3-methyl imidazolium hexafluorophosphate

In this paper, we have performed an all-atom molecular dynamics simulation to understand the structure and dynamics of Na+ ions in water mixed Ionic liquids (Water in Ionic liquid). Two ionic liquid (IL) systems consist of (1) 1-butyl-3-methylimidazolium [BMIM] tetrafluoroborate [BF4] and (2) 1-butyl-3-methylimidazolium [BMIM] hexafluorophosphate [PF6] were considered in this work. We understand various inter-molecular structures and dynamic and thermodynamic behaviours of Na+ ions in the water-mixed IL systems. The water (H2O) mole fractions (x) varied from 0.33 to 0.71. The neat ILs [BMIM][BF4] and [BMIM][PF6] pairwise radial distribution functions show a decrease with an increase in x. The [BMIM][PF6] exhibits a strong coordination structure with Na+ ions across the entire range of x values. The rdf between the pairs of Na+-[PF6] presents a significant interaction compared to Na+ and [BF4]. The Na + ions manifested greater coordination with H2O In H2O-[BMIM][PF6] compared to H2O-[BMIM][BF4]. The self-diffusion coefficient (D) values of Na + ions increase with the rise in x in both ILs. The D values of Na + ions are 10-fold higher in [BMIM][BF4] than [BMIM][PF6]. The ionic conductivity values are higher for [BMIM][BF4]. Overall, this paper unveils molecular-level insights for understanding the behavior of Na+ ions in the water in ionic liquid systems.

Computational Reverse-Engineering Analysis for Scattering Experiments of Assembled Binary Mixture of Nanoparticles.

In this paper, we describe a computational method for analyzing results from scattering experiments on dilute solutions of supraparticles, where each supraparticle is created by the assembly of nanoparticle mixtures. Taking scattering intensity profiles and nanoparticle mixture composition and size distributions in each supraparticle as input, this computational approach called computational reverse engineering analysis for scattering experiments (CREASE) uses a genetic algorithm to output information about the structure of the assembled nanoparticles (e.g., real space pair correlation function, extent of nanoparticle mixing/segregation, sizes of domains) within a supraparticle. We validate this method by taking as input in silico scattering intensity profiles from coarse-grained molecular simulations of a binary mixture of nanoparticles, forming a close-packed structure and testing if our computational method can correctly reproduce the nanoparticle structure observed in those simulations. We test the strengths and limitations of our method using a variety of in silico scattering intensity profiles obtained from simulations of a spherical or a cubic supraparticle comprising binary nanoparticle mixtures with varying chemistries, with and without dispersity in sizes, that exhibit well-mixed to strongly segregated structures. The strengths of the presented method include its capability to analyze scattering intensity profiles even when the wavevector q range is limited, to handily provide all of the pairwise radial distribution functions, and to correctly determine the extent of segregation/mixing of the nanoparticles assembled in complex geometries.

Solvation Structures and Deactivation Pathways of Luminescent Isothiazole-Derived Nucleobases: tzA, tzG, and tzI.

The photophysical relaxation pathways of tzA, tzG, and tzI luminescent nucleobases were investigated with the MS-CASPT2 quantum-chemical method and double-ζ basis sets (cc-pVDZ) in gas and condensed phases (1,4-dioxane and water) with the sequential Monte Carlo/CASPT2 and free energy gradient (FEG) methods. Solvation shell structures, in the ground and excited states, were examined with the pairwise radial distribution function (G(r)) and solute-solvent hydrogen-bond networks. Site-specific hydrogen bonding analysis evidenced relevant changes between both electronic states. The three luminescent nucleobases share a common photophysical pattern, summarized as the lowest-lying 1(ππ*) bright state that is populated directly after the absorption of radiation and evolves barrierless to the minimum energy structure, from where the excess of energy is released by fluorescence. From the 1(ππ*)min region, the conical intersection with the ground state ((ππ*/GS)CI) is not accessible due to the presence of high energetic barriers. By combining the present results with those reported earlier by us for the pyrimidine fluorescent nucleobases, we present a comprehensive description of the photophysical properties of this important class of new fluorescent nucleosides.

Recent advances in the UltraScan SOlution MOdeller(US-SOMO) hydrodynamic and small-angle scattering data analysis and simulation suite.

The UltraScan SOlution MOdeller (US-SOMO) is a comprehensive, public domain, open-source suite of computer programs centred on hydrodynamic modelling and small-angle scattering (SAS) data analysis and simulation. We describe here the advances that have been implemented since its last official release (#3087, 2017), which are available from release #3141 for Windows, Linux and Mac operating systems. A major effort has been the transition from the legacy Qt3 cross platform software development and user interface library to the modern Qt5 release. Apart from improved graphical support, this has allowed the direct implementation of the newest, almost two-orders of magnitude faster version of the ZENO hydrodynamic computation algorithm for all operating systems. Coupled with the SoMo-generated bead models with overlaps, ZENO provides the most accurate translational friction computations from atomic-level structures available (Rocco and Byron Eur Biophys J 44:417-431, 2015a), with computational times comparable with or faster than those of other methods. In addition, it has allowed us to introduce the direct representation of each atom in a structure as a (hydrated) bead, opening interesting new modelling possibilities. In the small-angle scattering (SAS) part of the suite, an indirect Fourier transform Bayesian algorithm has been implemented for the computation of the pairwise distance distribution function from SAS data. Finally, the SAS HPLC module, recently upgraded with improved baseline correction and Gaussian decomposition of not baseline-resolved peaks and with advanced statistical evaluation tools (Brookes et al. J Appl Cryst 49:1827-1841, 2016), now allows automatic top-peak frame selection and averaging.

Direct observation of the spatial distribution of primary cascade damage in tungsten

Recently we have presented direct experimental evidence for large defect clusters being formed in primary damage cascades in self-ion irradiated tungsten [Yi et al., EPL 110:36001 (2015)]. This large size is significant, as it implies that strong elastic interaction between the defects will affect their subsequent evolution, especially if defects are formed close together. Here we present a direct experimental observation of the separation between visible defects in self-ion irradiated tungsten, in the form of a 2d pairwise radial distribution function extracted from transmission electron micrographs (TEM). We also present a detailed analysis of the observed radial distribution function, and infer the probable size and shape of individual cascades. We propose and validate a simple exponential form for the spatial distribution of defects within a single cascade. The cascade statistics necessary have been acquired by developing an automated procedure for analysing black-dot damage in TEM micrographs. We confirm that the same model also produces a high-quality fit to the separation between larger defects observed in MD simulations. For the first time we present experimental evidence for the sub-nanometre-scale spatial distribution of defect clusters within individual cascades.

On the calculation of x-ray scattering signals from pairwise radial distribution functions

We derive a formulation for evaluating (time-resolved) x-ray scattering signals of solvated chemical systems, based on pairwise radial distribution functions, with the aim of this formulation to accompany molecular dynamics simulations. The derivation is described in detail to eliminate any possible ambiguities, and the result includes a modification to the atom-type formulation which to our knowledge is previously unaccounted for. The formulation is numerically implemented and validated.

Amino Acid Correlation Functions in Protein Structures.

Understanding the spatial folding of proteins from their amino acid sequences has an enormous potential in contemporary life sciences. The ability to predict secondary and tertiary structures from primary ones through the use of computers will enable a much faster and more efficient discovery of organic substances with therapeutic or otherwise bioactive potential, largely eliminating the need for synthesis and testing of large numbers of organic substances for physiological effects. Our manuscript presents an application of correlation function analysis, usually used to describe properties of liquids, to protein structures in order to elucidate statistically favored distances among amino acids. Pairwise distribution functions were calculated between C-alpha atoms of 20 amino acids in a large ensemble of Protein Data Bank structures. The correlation functions show characteristic distances in amino acid interactions. Different propensities for forming various secondary structure elements among all 210 possible amino acid pairs have been visualized and some have been interpreted. Notably, we found helices to be surprisingly common among certain pairs.

Detecting phase separation of freeze-dried binary amorphous systems using pair-wise distribution function and multivariate data analysis

The purpose of this study is to investigate the use of multivariate data analysis for powder X-ray diffraction-pair-wise distribution function (PXRD-PDF) data to detect phase separation in freeze-dried binary amorphous systems. Polymer-polymer and polymer-sugar binary systems at various ratios were freeze-dried. All samples were analyzed by PXRD, transformed to PDF and analyzed by principal component analysis (PCA). These results were validated by differential scanning calorimetry (DSC) through characterization of glass transition of the maximally freeze-concentrate solute (Tg'). Analysis of PXRD-PDF data using PCA provides a more clear 'miscible' or 'phase separated' interpretation through the distribution pattern of samples on a score plot presentation compared to residual plot method. In a phase separated system, samples were found to be evenly distributed around the theoretical PDF profile. For systems that were miscible, a clear deviation of samples away from the theoretical PDF profile was observed. Moreover, PCA analysis allows simultaneous analysis of replicate samples. Comparatively, the phase behavior analysis from PXRD-PDF-PCA method was in agreement with the DSC results. Overall, the combined PXRD-PDF-PCA approach improves the clarity of the PXRD-PDF results and can be used as an alternative explorative data analytical tool in detecting phase separation in freeze-dried binary amorphous systems.

Some new classes of stationary max-stable random fields

We present two new classes of stationary max-stable random fields. For the first class, we use the spectral representation due to Schlather (2002) and assume that the stationary process used in the representation is proportional to a power of a max-stable random field. We derive the finite dimensional distributions, explain the relationship between distributions of both max-stable random fields and give sufficient conditions for the sample paths to be γ-Hölder continuous functions for some γ∈(0,1). For the second class, we consider a multiplicative factor model and a Poisson–Voronoï tessellation of Rd to construct new max-stable random fields. We provide explicit expressions for the pairwise distribution function.

Thioredoxin, the Processivity Factor, Sequesters an Exposed Cysteine in the Thumb Domain of Bacteriophage T7 DNA Polymerase

Gene 5 protein (gp5) of bacteriophage T7 is a non-processive DNA polymerase. It achieves processivity by binding to Escherichia coli thioredoxin (trx). gp5/trx complex binds tightly to a primer-DNA template enabling the polymerization of hundreds of nucleotides per binding event. gp5 contains 10 cysteines. Under non-reducing condition, exposed cysteines form intermolecular disulfide linkages resulting in the loss of polymerase activity. No disulfide linkage is detected when Cys-275 and Cys-313 are replaced with serines. Cys-275 and Cys-313 are located on loop A and loop B of the thioredoxin binding domain, respectively. Replacement of either cysteine with serine (gp5-C275S, gp5-C313S) drastically decreases polymerase activity of gp5 on dA(350)/dT(25). On this primer-template gp5/trx in which Cys-313 or Cys-275 is replaced with serine have 50 and 90%, respectively, of the polymerase activity observed with wild-type gp5/trx. With single-stranded M13 DNA as a template gp5-C275S/trx retains 60% of the polymerase activity of wild-type gp5/trx. In contrast, gp5-C313S/trx has only one-tenth of the polymerase activity of wild-type gp5/trx on M13 DNA. Both wild-type gp5/trx and gp5-C275S/trx catalyze the synthesis of the entire complementary strand of M13 DNA, whereas gp5-C313S/trx has difficulty in synthesizing DNA through sites of secondary structure. gp5-C313S fails to form a functional complex with trx as measured by the apparent binding affinity as well as by the lack of a physical interaction with thioredoxin during hydroxyapatite-phosphate chromatography. Small angle x-ray scattering reveals an elongated conformation of gp5-C313S in comparison to a compact and spherical conformation of wild-type gp5.

Development of a ReaxFF Reactive Force Field for Ettringite and Study of its Mechanical Failure Modes from Reactive Dynamics Simulations

Ettringite is a hexacalcium aluminate trisulfate hydrate mineral that forms during Portland cement hydration. Its presence plays an important role in controlling the setting rate of the highly reactive aluminate phases in cement paste and has also been associated with severe cracking in cured hardened cement. To understand how it forms and how its properties influence those of hardened cement and concrete, we have developed a first-principles-based ReaxFF reactive force field for Ca/Al/H/O/S. Here, we report on the development of this ReaxFF force field and on its validation and application using reactive molecular dynamics (RMD) simulations to characterize and understand the elastic, plastic, and failure response of ettringite at the atomic scale. The ReaxFF force field was validated by comparing the lattice parameters, pairwise distribution functions, and elastic constants of an ettringite crystal model obtained from RMD simulations with those from experiments. The predicted results are in close agreement with published experimental data. To characterize the atomistic failure modes of ettringite, we performed stress-strain simulations to find that Ca-O bonds are responsible for failure of the calcium sulfate and tricalcium aluminate (C3A) column in ettringite during uniaxial compression and tension and that hydrogen bond re-formation during compression induces an increase in plastic strain beyond the material's stress-strain proportionality limit. These results provide essential insight into understanding the mechanistic role of this mineral in cement and concrete degradation, and the ReaxFF potential developed in this work serves as a fundamental tool to further study the kinetics of hydration in cement and concrete.

Polymorphic form of piroxicam influences the performance of amorphous material prepared by ball-milling

The objective of this study was to investigate the influence of the starting solid state form of piroxicam (anhydrate form I: PRXAH I vs form II: PRXAH II) on the properties of the resulting amorphous material. The second objective was to obtain further insight into the impact of critical factors like thermal stress, dissolution medium and storage conditions on the thermal behavior, solid state transformations and physical stability of amorphous materials. For analysis differential scanning calorimetry (DSC), Raman spectroscopy and X-ray powder diffractometry (XRPD) were used. Pair-wise distribution function (PDF) analysis of the XRPD data was performed. PDF analysis indicated that the recrystallization behavior of amorphous samples was influenced by the amount of residual order in the samples. The recrystallization behavior of amorphous samples prepared from PRXAH I showed similarity to the starting material, whereas the recrystallization behavior of amorphous samples prepared from PRXAH II resembled to that of the PRX form III (PRXAH III). Multivariate data analysis (MVDA) helped to identify that the influence of storage time and temperature was more pronounced in the case of amorphous PRX prepared from PRXAH I. Furthermore, the wet slurry experiments with amorphous materials revealed the recrystallization of amorphous material as PRXMH in the biorelevant medium.

Atomic Pairwise Distribution Function Analysis of the Amorphous Phase Prepared by Different Manufacturing Routes

Amlodipine besilate, a calcium channel antagonist, exists in several solid forms. Processing of anhydrate and dihydrate forms of this drug may lead to solid state changes, and is therefore the focus of this study. Milling was performed for the anhydrate form, whereas the dihydrate form was subjected to quench cooling thereby creating an amorphous form of the drug from both starting materials. The milled and quench cooled samples were, together with the crystalline starting materials, analyzed with X-ray powder diffraction (XRPD), Raman spectroscopy and atomic pair-wise distribution function (PDF) analysis of the XRPD pattern. When compared to XRPD and Raman spectroscopy, the PDF analysis was superior in displaying the difference between the amorphous samples prepared by milling and quench cooling approaches of the two starting materials.

Assessment of crystalline disorder in cryo-milled samples of indomethacin using atomic pair-wise distribution functions

The aim of this study was to investigate the usefulness of the atomic pair-wise distribution function (PDF) to detect the extension of disorder/amorphousness induced into a crystalline drug using a cryo-milling technique, and to determine the optimal milling times to achieve amorphisation. The PDF analysis was performed on samples of indomethacin obtained by cryogenic ball milling (cryo-milling) for different periods of time. X-ray powder diffraction (XRPD), differential scanning calorimetry (DSC), polarised light microscopy (PLM) and solid state nuclear magnetic resonances (ss-NMR) were also used to analyse the cryo-milled samples. The high similarity between the γ-indomethacin cryogenic ball milled samples and the crude γ-indomethacin indicated that milled samples retained residual order of the γ-form. The PDF analysis encompassed the capability of achieving a correlation with the physical properties determined from DSC, ss-NMR and stability experiments. Multivariate data analysis (MVDA) was used to visualize the differences in the PDF and XRPD data. The MVDA approach revealed that PDF is more efficient in assessing the introduced degree of disorder in γ-indomethacin after cryo-milling than MVDA of the corresponding XRPD diffractograms. The PDF analysis was able to determine the optimal cryo-milling time that facilitated the highest degree of disorder in the samples. Therefore, it is concluded that the PDF technique may be used as a complementary tool to other solid state methods and that further investigations are warranted to elucidate the capabilities of this technique.

Solution Conformation and Thermodynamic Characteristics of RNA Binding by the Splicing Factor U2AF65

The U2 auxiliary factor large subunit (U2AF65) is an essential pre-mRNA splicing factor for the initial stages of spliceosome assembly. Tandem RNA recognition motifs (RRM)s of U2AF65 recognize polypyrimidine tract signals adjacent to 3' splice sites. Despite the central importance of U2AF65 for splice site recognition, the relative arrangement of the U2AF65 RRMs and the energetic forces driving polypyrimidine tract recognition remain unknown. Here, the solution conformation of the U2AF65 RNA binding domain determined using small angle x-ray scattering reveals a bilobal shape without apparent interdomain contacts. The proximity of the N and C termini within the inter-RRM configuration is sufficient to explain the action of U2AF65 on spliceosome components located both 5' and 3' to its binding site. Isothermal titration calorimetry further demonstrates that an unusually large enthalpy-entropy compensation underlies U2AF65 recognition of an optimal polyuridine tract. Qualitative similarities were observed between the pairwise distance distribution functions of the U2AF65 RNA binding domain and those either previously observed for N-terminal RRMs of Py tract-binding protein that lack interdomain contacts or calculated from the high resolution coordinates of a U2AF65 deletion variant bound to RNA. To further test this model, the shapes and RNA interactions of the wild-type U2AF65 RNA binding domain were compared with those of U2AF65 variants containing either Py tract-binding protein linker sequences or a deletion within the inter-RRM linker. Results of these studies suggest inter-RRM conformational plasticity as a possible means for U2AF65 to universally identify diverse pre-mRNA splice sites.

Structural Analysis of a Periplasmic Binding Protein in the Tripartite ATP-independent Transporter Family Reveals a Tetrameric Assembly That May Have a Role in Ligand Transport

Several bacterial solute transport mechanisms involve members of the periplasmic binding protein (PBP) superfamily that bind and deliver ligand to integral membrane transport proteins in the ATP-binding cassette, tripartite tricarboxylate transporter, or tripartite ATP-independent (TRAP) families. PBPs involved in ATP-binding cassette transport systems have been well characterized, but only a few PBPs involved in TRAP transport have been studied. We have measured the thermal stability, determined the oligomerization state by small angle x-ray scattering, and solved the x-ray crystal structure to 1.9 A resolution of a TRAP-PBP (open reading frame tm0322) from the hyperthermophilic bacterium Thermotoga maritima (TM0322). The overall fold of TM0322 is similar to other TRAP transport related PBPs, although the structural similarity of backbone atoms (2.5-3.1 A root mean square deviation) is unusually low for PBPs within the same group. Individual monomers within the tetrameric asymmetric unit of TM0322 exhibit high root mean square deviation (0.9 A) to each other as a consequence of conformational heterogeneity in their binding pockets. The gel filtration elution profile and the small angle x-ray scattering analysis indicate that TM0322 assembles as dimers in solution that in turn assemble into a dimer of dimers in the crystallographic asymmetric unit. Tetramerization has been previously observed in another TRAP-PBP (the Rhodobacter sphaeroides alpha-keto acid-binding protein) where quaternary structure formation is postulated to be an important requisite for the transmembrane transport process.

Structure and UV−Vis Spectrum of C60 Fullerene in Ethanol: A Sequential Molecular Dynamics/Quantum Mechanics Study

A molecular dynamics simulation combined with semiempirical quantum mechanics calculations has been performed to investigate the structure, dynamical, and electronic properties of pure C60 in liquid ethanol. The behavior of the fullerene alcoholic solution was obtained by using the NPT ensemble under ambient conditions, including one C60 fullerene immersed in 1000 ethanol molecules. Our analyzed center-of-mass pairwise radial distribution function indicated that, on average, there are 32, 72, 132, and 187 ethanol molecules around, respectively, the first, second, third, and fourth solvation shells of the C60 molecule. To investigate the UV-vis transition energies of C60 in the presence of ethanol, we have considered constituents of the time uncorrelated supramolecular structures of the first solvation shell, i.e., clusters of C60@{EtOH}32 types. The semiempirical calculations were performed at the intermediate neglect of differential overlap level with configuration interaction singles (INDO/CIS). Our results have pointed out that the characteristic C60 UV-vis absorbance peaks are slightly shifted to longer wavelengths, as compared to the isolated molecule. These findings are in connection with the weak donor-acceptor character of the interactions involving electron lone pairs of oxygen atoms on the solvent and the fullerene surface.

Simulation studies of ionic liquids: Orientational correlations and static dielectric properties

The ionic liquids BMIM+I-, BMIM+BF4-, and BMIM+PF6- were simulated by means of the molecular dynamics method over a time period of more than 100 ns. Besides the common structural analysis, e.g., radial distribution functions and three dimensional occupancy plots, a more sophisticated orientational analysis was performed. The angular correlation functions g(00)110(r) and g(00)101(r) are the first distance dependent coefficients of the pairwise orientational distribution function g(rij,Omega1,Omega2,Omega12). These functions help to interpret the three dimensional plot and reveal interesting insights into the local structure of the analyzed ionic liquids. Furthermore, the collective network of ionic liquids can be characterized by the Kirkwood factor Gkappa(r) [J. Chem. Phys. 7, 911 (1939)]. The short-range behavior (r<10 A) of this factor may be suitable to predict the water miscibility of the ionic liquid. The long-range limit of Gkinfinity is below 1 which demonstrates the strongly coupled nature of the ionic liquid networks. In addition, this factor relates the orientational structure and the dielectric properties of the ionic liquids. The static dielectric constant epsilon(omega=0) for the simulated system is 8.9-9.5. Since in ionic liquids the very same molecule contributes to the total dipole moment as well as carries a net charge, a small, but significant contribution of the cross term between the total dipole moment and the electric current to epsilon(omega=0) is observed.

Theoretical calculations of the structure and UV–vis absorption spectra of hydrated C 60 fullerene

A combined Monte Carlo simulation with semiempirical quantum mechanics calculations has been performed to investigate the structure of hydrated fullerene (C 60HyFn) and the influence of hydration on its UV–vis spectra. The statistical information of the C 60 fullerene aqueous solution (C 60FAS) is obtained from NPT ensemble including one C 60 fullerene immerses in 898 water molecules. To obtain an efficient ensemble average, the auto-correlation function of the energy has been calculated. The analyzed center-of-mass pair-wise radial distribution function indicates that, on average, there are 65 and 151 water molecules around the first and second hydration shells, respectively, of a single C 60 molecule. To calculate the average UV–vis transition energies of C 60HyFn, only the statistically uncorrelated configurations are used in the quantum mechanical calculations (INDO/CIS). These involve hundreds of supramolecular structures containing one C 60 fullerene surrounded by the first hydration shell. The calculated average transitions at 268 and 350 nm are in very good agreement with the experimental prediction.

Ni 3+ adsorbate dynamics on a NiO(0 0 1) surface

We present results concerning the dynamical behavior of a Ni 3+ adsorbate on a NiO(0 0 1) surface obtained by molecular dynamics simulations. In a first place, we examined at low temperature the position of the Ni 3+ ion as an adatom on the surface and the corresponding modification of its local environment as reflected on the pair-wise radial distribution function. The calculation of the vibrational properties of the adatom by means of the phonon local density of states (LDOS) shows that there is an anisotropic behavior both in the two principal in-plane directions as well as in the direction normal to the surface in accordance with the structural results. We compare the phonon LDOS of the Ni 3+ adatom with the corresponding results for the Ni 2+ adatom and the Ni 2+ surface cations. Static energetic calculations are indicative that the exchange of the Ni 3+ ion with a surface Ni 2+ ion could be favorable. Such a behavior is confirmed by results observed at temperatures higher than 700 K where the Ni 3+ adsorbate is located on a substitutional position on the surface and not on adatom position. The exchange takes place through simple or double exchange mechanisms. The structural and dynamical behavior of the Ni 3+ ion at the substitution position was investigated in the temperature range 700–2000 K through the calculation of the pair distribution function, the relaxed interlayer relative position (RIRP), mean-square displacements (MSDs) and phonon LDOS. Results show that in comparison with the Ni 2+ surface ions the Ni 3+ ion at substitution position is more tightly bound especially in the direction normal to the surface as is indicated by the local structure and the contraction it presents as well as its phonon LDOS. As temperature increases the binding of the Ni 3+ ion becomes less important as reflected on the physical properties mentioned above.