From crystalline tetrahydrofuran clathrate hydrate, THF-CH (THF ∙ 17H2O, cubic structure II), three distinct polyamorphs can be derived. First, THF-CH undergoes pressure-induced amorphization when pressurized to 1.3 GPa in the temperature range 77–140 K to a form which, in analogy to pure ice, may be called high-density amorphous (HDA). Second, HDA can be converted to a densified form, very-HDA (VHDA), upon heat-cycling at 1.8 GPa to 180 K. Decompression of VHDA to atmospheric pressure below 130 K produces the third, recovered amorphous (RA) form. Results from a compilation of neutron scattering experiments and molecular dynamics simulations provide a generalized picture of the structure of amorphous THF hydrates with respect to crystalline THF-CH and liquid THF ∙ 17H2O solution (~2.5 M). The calculated density of (only in situ observable) HDA and VHDA at 2 GPa and 130 K is 1.287 and 1.328 g/cm3, respectively, whereas that of RA (at 1 atm) is 1.081 g/cm3. Although fully amorphous, HDA is heterogeneous with two length scales for water-water correlations (less dense local water structure) and guest-water correlations (denser THF hydration structure). The hydration structure of THF is influenced by guest-host hydrogen bonding. THF molecules maintain a quasiregular array, reminiscent of the crystalline state, and their hydration structure (out to 5 Å) constitutes ~23 H2O. The local water structure in HDA is reminiscent of pure HDA-ice, featuring 5-coordinated H2O. In VHDA, this structure is maintained but the local water structure is densified to resemble pure VHDA-ice with 6-coordinated H2O. The hydration structure of THF in RA constitutes ~18 H2O and the water structure corresponds to a strictly 4-coordinated network, as in the liquid. Both VHDA and RA can be considered as homogeneous, solid solutions of THF and water. The local water structure of water-rich (1:17) amorphous CHs resembles most that of the corresponding amorphous water ices when compared to guest-rich CHs, e.g., Ar ∙ ~6H2O. The proposed significance of different contributions of water local environments presents a simple view to justify neutron structure factor features.

The Kirkwood-Buff integrals (KBIs) for one-component systems are calculated from either the pair correlation functions or from experimental macroscopic quantities. As in the case of mixtures, the KBIs provide important information on the local densities around a molecule. In the low density limit (rho -> 0) one can extract from the KBI some information on the strength of the intermolecular forces. No such information may be extracted from the KBIs at higher densities. We used experimental data on densities and isothermal compressibilities to calculate the KBIs for various liquids ranging from inert molecules, to hydrocarbons, alcohols, and liquid water.

The stochastic Eulerian-Lagrangian method (SELM) is used to simulate coarse-grained lipid membrane models under steady-state conditions and in shear flow. SELM is an immersed boundary method which combines the efficiency of particle-based simulations with the realistic solvent dynamics provided by fluctuating hydrodynamics. Membrane simulations in SELM are shown to give structural properties in accordance with equilibrium statistical mechanics and dynamic properties in agreement with previous simulations of highly detailed membrane models in explicit solvent. Simulations of sheared membranes are used to calculate surface shear viscosities and inter-monolayer friction coefficients. The membrane models are shown to be shear thinning under a wide range of applied shear rates.

We demonstrate the estimation of homonuclear dipolar couplings, and thereby internuclear distances, between half-integer spin quadrupolar nuclei by central-transition (CT) double-quantum (2Q) sideband nuclear magnetic resonance (NMR) spectroscopy. It is shown that the rotor-encoded sideband amplitudes from CT 2Q coherences in the indirect dimension of the two-dimensional NMR spectrum are sensitive probes of the magnitude of the homonuclear dipolar coupling, but are significantly less affected by other NMR parameters such as the magnitudes and orientations of the electric field gradient tensors. Experimental results of employing the R2(2)(1)R2(2)(-1) recoupling sequence to the (11)B spin pair of bis(catecholato)diboron resulted in an estimation of the internuclear B-B distance as (169.6 +/- 3) pm, i.e., with a relative uncertainty of +/- 2%, and in excellent agreement with the distance of 167.8 pm determined by single-crystal X-ray diffraction.

A single-step microwave (MW)-assisted protocol for the synthesis of MIL-101(Cr) and of MIL-101(Cr)-NH2 is described herein, based on the addition of NaF as the modulator instead of hydrofluoric acid to obtain the corresponding polymers in only 1 h with high crystallinity and yields (>70%, 0.5 g). Compared to classic solvothermal protocols (12-72 h, <30%), MW-assisted synthesis allowed shorter reaction time and improved yields, replacing N,N-dimethylformamide by water. Physicochemical properties of MIL-101(Cr)-NH2 and MIL-101(Cr) obtained through this MW-assisted procedure are more homogenous than those observed for the corresponding solvothermal counterparts, and interestingly, enhanced higher control over nanometric particle size (80-130 vs 400-1000 nm), lower polydispersity, and higher Brunauer-Emett-Teller surface area (2000-2700 vs 1800-2300 m2/g) were observed because of the better accessibility and diffusion of gases throughout the internal pores.& COPY; 2023 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

A combination of solid-state NMR methods for the extraction of shift and quadrupolar parameters for half-integer nuclei in the structurally complex NaMnO₂ Na-ion cathode material, under magic-angle spinning (MAS) is presented. We show that the integration of the Magic-Angle Turning experiment with Rotor-Assisted Population transfer can be used both to identify shifts and to extract a range of magnitudes for their quadrupolar coupling. We also demonstrate the applicability of the the two-dimensional one pulse (TOP) based double-sheared Satellite Transition Magic-Angle Spinning (TOP-STMAS) showing how it can yield a spectrum with separated shift and second-order quadrupolar anisotropies, which in turn can be used to analyse a quadrupolar lineshape free of bulk magnetic susceptibility induced shift dispersion and determine both isotropic shift and quadrupolar products. Combining all these experiments, the shift and quadrupolar parameters for all observed Na environments were extracted and yielded excellent agreement with the density functional theory (DFT) based models that were reported in previous literature. We expect these methods to open the door for new possibilities for solid-state NMR to probe half-integer quadrupolar nuclei in paramagnetic materials and other systems exhibiting large shift dispersion. 

Adsorbents with high capacity and selectivity for adsorption of CO2 are currently being investigated for applications in adsorption-driven separation of CO2 from flue gas. An adsorbent with a particularly high CO2-over-N-2 selectivity and high capacity was tested here. Zeolite ZK-4 (Si:Al similar to 1.3:1), which had the same structure as zeolite A (LTA), showed a high CO2 capacity of 4.85 mmol/g (273 K, 101 kPa) in its Na+ form. When approximately 26 at % of the extraframework cations were exchanged for K+ (NaK-ZK-4), the material still adsorbed a large amount of CO2 (4.35 mmol/g, 273 K, 101 kPa), but the N-2 uptake became negligible (<0.03 mmol/g, 273 K, 101 kPa). The majority of the CO2 was physisorbed on zeolite ZK-4 as quantified by consecutive volumetric adsorption measurements. The rate of physisorption of CO2 was fast, even for the highly selective sample. The molecular details of the sorption of CO2 were revealed as well. Computer modeling (Monte Carlo, molecular dynamics simulations, and quantum chemical calculations) allowed us to partly predict the behavior of fully K+ exchanged zeolite K-ZK-4 upon adsorption of CO2 and N-2 for Si:Al ratios up to 4:1. Zeolite K-ZK-4 with Si:Al ratios below 23:1 restricted the diffusion of CO2 and N-2 across the cages. These simulations could not probe the delicate details of the molecular sieving of CO2 over N-2. Still, this study indicates that zeolites NaK-ZK-4 and K-ZK-4 could be appealing adsorbents with high CO2 uptake (similar to 4 mmol/g, 101 kPa, 273 K) and a kinetically enhanced CO2-over-N-2 selectivity.

Cardiolipin is a key lipid component in many biological membranes. Proton conduction and proton−lipid interactions on the membrane surface are thought to be central to mitochondrial energy production. However, details on the cardiolipin headgroup structure are lacking and the protonation state of this lipid at physiological pH is not fully established. Here we present ab initio DFT calculations of the cardiolipin (CL) headgroup and its 2′-deoxy derivative (dCL), with the aim of establishing a connection between structure and acid−base equilibrium in CL. Furthermore, we investigate the effects of solvation on the molecular conformations. In our model, both CL and dCL showed a significant gap between the two pK_a values, with pK_a2 above the physiological range, and intramolecular hydrogen bonds were found to play a central role in the conformations of both molecules. This behavior was also observed experimentally in CL. Structures derived from the DFT calculations were compared with those obtained experimentally, collected for CL in the Protein Data Bank, and conformations from previous as well as new molecular dynamics simulations of cardiolipin bilayers. Transition states for proton transfer in CL were investigated, and we estimate that protons can exchange between phosphate groups with an approximate 4−5 kcal/mol barrier. Computed NMR and IR spectral properties were found to be in reasonable agreement with experimental results available in the literature.

Lipid shape and charge are connected with the physical properties and biological function of membranes. Cardiolipin, a double phospholipid with four chains and the potential of changing its charge with pH, is crucially connected with mitochondrial inner membrane shape, and recent experiments suggest that local pH changes allow highly curved local geometries. Here, we use a coarse grained molecular dynamics model to investigate the mechanical properties of cardiolipin bilayers, systematically varying the headgroup charge and composition in mixtures with zwitterionic DOPC or DOPE. Low cardiolipin charge, corresponding to low pH, was found to induce bending moduli on the order of kBT, and curved microdomains. On the length scale investigated, in contrast to continuum theoretical models, we found the area modulus and bending modulus to be inversely correlated for mixtures of cardiolipin and DOPC/DOPE, explainable by changes in the effective head group volume.

We present a strategy, referred to as “split network” analysis, for assessing the average network polymerization (r(F)) and mean number of bridging oxygen (BO) atoms ( (N) over bar (F)(BO)) for each individual network former F in multi-component oxide-based glasses, primarily targeting those involving Al, B, P and Si. This requires a priori knowledge about the parameters (r(F), (N) over bar (F)(BO)) of all network builders, but one, whose values are deduced by the split network procedure. We illustrate split-network concepts for establishing composition/structure/bioactivity correlations in Na-Ca-Si-P-O glasses. The cooperating influences on the bioactivity from the average polymerization degree of the silicate network and the amounts of orthophosphate and sodium ions are discussed.

Three two-dimensional (2D) NMR homonuclear correlation techniques invoking double-quantum (2Q) filtration of the central transitions of half-integer spins are evaluated numerically and experimentally. They correlate directly detected single-quantum (1Q) coherences in the t(2) domain with either of 1Q, two-spin 2Q or single-spin multiple-quantum coherence-evolutions in the indirect (t(1)) dimension. We employ experimental Na-23 and Al-22 NMR on sodium sulfite and the natural mineral sillimanite (SiAl2O5), in conjunction with simulated 2D spectra from pairs of dipolar-recoupled spins-3/2 and 5/2 at different external magnetic fields, to compare the correlation strategies from the viewpoints of 2D spectral resolution, signal sensitivity, implementational aspects and their relative merits for establishing internuclear proximities and quadrupolar tensor orientations.

The preceding part [M. Eden, J. Non.-Cryst. Solids, 357, (2011) 1595-1602] introduced the “split network” strategy for estimating the network polymerization degree (r(A)) and mean number of bridging oxygen (BO) atoms ((N) over bar (A)(BO)) for a network former A, given that these parameters are known for all other network builders in the multi-component oxide glass. However, as the detailed ordering of BO and non-bridging oxygen (NBO) species is often difficult to assess experimentally, we summarize some “rules of thumb” for predicting the coordination number and tendency to accept NBO ions for Al(3+), B(3+), Si(4+) and P(5+) cations: they are helpful in scenarios devoid of experimental data. Using the parameters r and (N) over bar (BO), we present expressions for the BO/NBO distributions among tetrahedrally coordinated cations, as predicted from the binary and random models. Multinuclear (11)B, (27)Al and (29)Si solid-state NMR is exploited to derive the split network representations of a set of Na-Ca-(Al)-(B)-Si-O glasses. These results are subsequently used to gain structural insight into two commercial glass-wool fibers that constitute alumino-borosilicate networks modified by Na(+), K(+), Ca(2+) and Mg(2+) ions.

To study the effects of water on conformational dynamics of polyalcohols, Molecular Dynamics simulations of glycerol water liquid mixtures have been carried out at different concentrations: 42.9 and 60.0 wt 96 of glycerol, respectively. On the basis of the analysis of backbone conformer distributions, it is found that the surrounding water molecules have a large impact on the populations of the glycerol conformers. While the local structure of water in the liquid mixture is surprisingly close to that in pure liquid water, the behavior of glycerols can be divided into three different categories where roughly 25% of them occur in a structure similar to that in pure liquid of glycerol, ca. 25% of them exist as monomers, solvated by water, and the remaining 50% of glycerols in the mixture form H-bonded strings as. remains of the glycerol H-bond network. The typical glycerol H-bond network still exists even at the lower concentration of 40 wt % of glycerol. The microheterogeneity of water glycerol mixtures is analyzed using time-averaged distributions of the sizes of the water aggregates. At 40 wt % of glycerol, the cluster sizes from 3 to 10 water molecules are observed. The increase of glycerol content causes a depletion of clusters leading to smaller 3-5 molecule clusters domination. Translational diffusion coefficients have been calculated to study the dynamical behavior of both glycerol and water molecules. Rotational-reorientational motion is studied both in overall and in selected substructures on the basis of time correlation functions. Characteristic time scales for different motional modes are deduced on the basis of the calculated correlation times. The general conclusion is that the presence of water increases the overall mobility of glycerol, while glycerol slows the mobility of water.

The mu opioid receptor (mu OR), the principal target to control pain, belongs to the G protein-coupled receptors (GPCRs) family, one of the most highlighted protein families due to their importance as therapeutic targets. The conformational flexibility of GPCRs is one of their essential characteristics as they take part in ligand recognition and subsequent activation or inactivation mechanisms. It is assessed that the intrinsic mechanical properties of the mu OR, more specifically its particular flexibility behavior, would facilitate the accomplishment of specific biological functions, at least in their first steps, even in the absence of a ligand or any chemical species usually present in its biological environment. The study of the mechanical properties of the mu OR would thus bring some indications regarding the highly efficient ability of the mu OR to transduce cellular message. We therefore investigate the intrinsic flexibility of the mu OR in its apo-form using all-atom Molecular Dynamics simulations at the sub-microsecond time scale. We particularly consider the mu OR embedded in a simplified membrane model without specific ions, particular lipids, such as cholesterol moieties, or any other chemical species that could affect the flexibility of the mu OR. Our analyses highlighted an important local effect due to the various bendability of the helices resulting in a diversity of shape and volume sizes adopted by the mu OR binding site. Such property explains why the mu OR can interact with ligands presenting highly diverse structural geometry. By investigating the topology of the mu OR binding site, a conformational global effect is depicted: the correlation between the motional modes of the extra-and intracellular parts of mu OR on one hand, along with a clear rigidity of the central mu OR domain on the other hand. Our results show how the modularity of the mu OR flexibility is related to its preability to activate and to present a basal activity.

Amorphous order: Amorphous calcium carbonates (ACC) have an intrinsic structure relating to the crystalline polymorphs of calcite and vaterite. The proto-crystalline structures of calcite and vaterite (pc-ACC and pv-ACC) are analyzed by NMR (see picture), IR, and EXAFS spectroscopy, which shows that the structuring of ACC relates to the underlying pH-dependent equilibria.

We review the benefits of using Si-29 and H-1 magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy for probing the local structures of both bulk and surface portions of mesoporous bioactive glasses (MBGs) of the CaO-SiO2-(P2O5) system. These mesoporous materials exhibit an ordered pore arrangement, and are promising candidates for improved bone and tooth implants. We discuss experimental MAS NMR results from three MBGs displaying different Ca, Si and P contents: the Si-29 NMR spectra were recorded either directly by employing radio-frequency pulses to Si-29, or by magnetization transfers from neighbouring protons using cross polarization, thereby providing quantitative information about the silicate speciation present in the pore wall and at the MBG surface, respectively. The surface modifications were monitored for the three MBGs during their immersion in a simulated body fluid (SBF) for intervals between 30 min and one week. The results were formulated as a reaction sequence describing the interconversions between the distinct silicate species. We generally observed a depletion of Ca2+ ions at the MBG surface, and a minor condensation of the silicate-surface network over one week of SBF soaking.

We present a novel approach, that combines the traditional Ewald summation technique with the nonuniform Fast Fourier transform to calculate the electrostatic energies and forces in molecular computer simulations. The method can easily be implemented in existing simulation programs. We report here some results from our implementation, where we utilize widely available libraries, and demonstrate the accuracy, and expected computational complexity of our approach.

To explore mechanisms of B-incorporation in common chain silicates we have investigated synthetic diopside samples produced under boron-saturated conditions by ¹¹B and ²⁹Si magic-angle spinning (MAS) NMR and single-crystal NRA, FTIR, EMP and XRD/SREF techniques. Our samples contain 0.14–0.65 wt.% B₂O₃. NMR reveals that B is predominantly present in trigonal coordination in the clinopyroxene structure. This observation is supported by vibrational bands characteristic for B–O stretching in BO₃ groups in the range 1250–1400 cm⁻¹ in polarised single crystal FTIR-spectra. Single crystal structure refinements suggest that boron replaces Si at the T site. Combined, these results suggest that boron replacement for Si at the T-site leads to disruption of one of the T–O bonds of the nominal clinopyroxene structure resulting in replacement of SiO₄ tetrahedra by BO₃ groups. Our results show that high concentrations of boron can be incorporated in the nominally boron-free diopside. Elevated B-concentrations in the present calcic clinopyroxenes are accompanied by modifications of the diopside crystal structure involving the breaking of one T–O bond and simultaneous formation of vacancies at the octahedral M2 site. These structural modifications destabilize the structure and constitute thereby limiting factors for incorporating higher boron concentrations in diopside.

We report physical properties of density, glass transition temperature, Vickers hardness and refractive index for 15 La–Al–Si–O glasses within the compositional region 10–28 mol% La₂O₃, 11–30% Al₂O₃ and 45–78% SiO₂. The glass transition temperature varies only slightly between 871 and 883 °C. Both the density (3.25–4.33 g cm⁻³) and refractive index (1.59–1.70) display similar compositional dependencies and are primarily dictated by the La₂O₃ content. The hardness (6.4–9.0 GPa) increases with decreasing SiO₂ content and to a minor extent also with the amount of La₂O₃ of the glass. The physical properties, in particular the hardness, are discussed with reference to glass structure. The similarity in the observed properties between the present oxide-based glasses and those of analogous rare-earth (RE) element-containing RE–Si–(Al)–O–N oxynitride glasses is highlighted and discussed in relation to the apparent, but hitherto largely neglected, role of RE-ions to primarily control many enhanced physical properties of oxynitride glasses.

We report the glass-forming regions of the ternary Lu2O3–Al2O3–SiO2 and Sc2O3–Al2O3–SiO2 systems. The density, molarvolume, compactness, Vickers hardness, refractive index, aswell as the glass transition (Tg) and crystallization temperatureare compared for two series of RE–Al–Si–O (RE=La, Y, Lu,Sc) glasses that display a constant molar ratio n_Al/n_Si=1.00,whereas n_RE/n_Si is equal to either 0.62 or 0.94. Several glassproperties scale roughly linearly with the cation field strength(CFS) of the rare-earth (RE³⁺) ion, except for the Tg values ofthe Sc-bearing glasses that are significantly lower than expected.Magic-angle spinning ²⁹Si and ²⁷Al nuclear magneticresonance (NMR) reveal enhanced network disorder and increasedrelative populations of AlO5 and AlO6 polyhedra in thealuminosilicate glasses for increasing RE³⁺ CFS, but overallsimilar Si and Al local environments (chemical shifts and quadrupolarcouplings) in all samples associated with a constant n_RE/n_Si ratio, except for unexpectedly shielded ²⁹Si NMR signalsobserved from the Sc–Al–Si–O glasses.

By combining molecular dynamics (MD) simulations with Si-29 and Al-27 magic-angle spinning nuclear magnetic resonance (NMR) spectroscopy, we present a comprehensive structural report on rare-earth (RE) aluminosilicate (AS) glasses of the RE2O3-Al2O3-SiO2 (RE = Y, Lu) systems, where the latter is studied for the first time. The structural variations stemming from changes in the glass composition within each RE system as well as the effects of the increased cation field-strength (CFS) of Lu3+ relative to Y3+-are explored and correlated to measured physical properties, such as density, molar volume, glass transition temperature, and Vickers hardness (H-V). Si-29 NMR reveals a pronounced network ordering for an increase in either the RE or Al content of the glass. Al mainly assumes tetrahedral coordination, but significant AlO5 and AlO6 populations are present in all structures, with elevated amounts in the Lu-bearing glasses compared to their Y analogues. The MD-derived oxygen speciation comprises up to 3% of free O2- ions, as well as non-negligible amounts (4-19%) of O-[3] coordinations (oxygen triclusters). While the SiO4 groups mainly accommodate the nonbridging oxygen ions, a significant fraction thereof is located at the AlO4 tetrahedra, in contrast to the scenario of analogous alkali- and alkaline-earth metal-based AS glasses. The average coordination numbers (CNs) of Al and RE progressively increase for decreasing Si content of the glass, with the average CN of the RE3+ ions depending linearly on both the amount of Si and the fraction of AlO5 groups in the structure. The Vickers hardness correlates strongly with the average CN of Al, in turn dictated by the CFS and content of the RE3+ ions. This is to our knowledge the first structural rationalization of the well-known compositional dependence of H-V in RE bearing AS glasses.

By using solid-state O-17 NMR spectroscopy, we provide the first direct experimental evidence for bonds between Al and non-bridging oxygen (NBO) ions in aluminosilicate glasses based on rare-earth (RE) elements, where RE = {Lu, Sc, Y}. The presence of similar to 10% Al-NBO moieties out of all NBO species holds regardless of the precise glass composition, at odds with the conventional structural view that Al-NBO bonds are absent in highly polymerized and Si-rich aluminosilicate glass networks.

The structures of 15 La-Al-Si-O glasses, whose compositions span 11-28 mol% La2O3, 11-30 mol% Al2O3, and 45-78 mol% SiO2, are explored over both short and intermediate length-scales by using a combination of solid-state Al-27 magic-angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics (MD) simulations. MAS NMR reveals Al speciations dominated by AlO4 groups, with minor but significant fractions of AlO5 (5-10%) and AlO6 (less than or similar to 3%) polyhedra present in all La2O3-Al2O3-SiO2 glasses; the amounts of Al-[5] and Al-[6] coordinations increase for decreasing molar fraction of Si. The MD simulations reproduce this compositional trend, with the fractional populations of AlOp groups (p = 4, 5, 6) according well with the experimental results. The modeled La speciations mainly involve LaO6 and LaO7 polyhedra, giving a range of average La3+ coordination numbers between 6.0 and 6.6; the latter increases slightly for decreasing Si content of the sample. Besides the expected bridging and non-bridging O species, minor contributions of oxygen triclusters (<= 9%) and free O-2(-) ions (<= 4%) are observed in all MD data. The glass structures exhibit a pronounced Al/Si disorder; the MD simulations reveal essentially random SiO4-SiO4, SiO4-AlOp and AlOp-AlOq (p, q = 4, 5, 6) associations, including significant amounts of AlO4-AlO4 contacts, regardless of the n(Al)/n(Si) molar ratio of the glass. The strong violation of Al-[4]-Al-[4] avoidance is verified by 2D Al-27 NMR experimentation that correlates double-quantum and single-quantum coherences, here applied for the first time to aluminosilicate glasses, and evidencing AlOp-AlOq connectivities dominated by AlO4-AlO4 and AlO4-AlO5 pairs. The potential bearings from distinct fictive temperatures of the experimental and modeled glass structures are discussed.

Liposomes are proposed as drug delivery systems and can in principle be designed so as to cohere with specific tissue types or local environments. However, little detail is known about the exact mechanisms for drug delivery and the distributions of drug molecules inside the lipid carrier. In the current work, a coarse-grained (CG) liposome model is developed, consisting of over 2500 lipids, with varying degrees of drug loading. For the drug molecule, we chose hypericin, a natural compound proposed for use in photodynamic therapy, for which a CG model was derived and benchmarked against corresponding atomistic membrane bilayer model simulations. Liposomes with 21-84 hypericin molecules were generated and subjected to 10 microsecond simulations. Distribution of the hypericins, their orientations within the lipid bilayer, and the potential of mean force for transferring a hypericin molecule from the interior aqueous droplet through the liposome bilayer are reported herein.

Biological membranes are versatile in composition and host intriguing molecular processes. In order to be able to study these systems, an accurate model Hamiltonian or force field (FF) is a necessity. Here, we report the results of our extension of earlier developed all-atomistic FF parameters for fully saturated phospholipids that complements an earlier parameter set for saturated phosphatidylcholine lipids (J. Phys. Chem. B, 2012, 116, 3164-3179). The FF, coined Slipids (Stockholm lipids), now also includes parameters for unsaturated phosphatidylcholine and phosphatidylethanolamine lipids, e.g., POPC, DOPC, SOPC, POPE, and DOPE. As the extended set of parameters is derived with the same philosophy as previously applied, the resulting FF has been developed in a fully consistent manner. The capabilities of Slipids are demonstrated by performing long simulations without applying any surface tension and using the correct isothermal-isobaric (NPT) ensemble for a range of temperatures and carefully comparing a number of properties with experimental findings. Results show that several structural properties are very well reproduced, such as scattering form factors, NMR order parameters, thicknesses, and area per lipid. Thermal dependencies of different thicknesses and area per lipid are reproduced as well Lipid diffusion is systematically slightly underestimated, whereas the normalized lipid diffusion follows the experimental trends. This is believed to be due to the lack of collective movement in the relatively small bilayer patches used Furthermore, the compatibility with amino acid FFs from the AMBER family is tested in explicit transmembrane complexes of the WALP23 peptide with DLPC and DOPC bilayers, and this shows that Slipids can be used to study more complex and biologically relevant systems.

To be able to model complex biological membranes in a more realistic manner, the force field Slipids (Stockholm lipids) has been extended to include parameters for sphingomyelin (SM), phosphatidylglycerol (PG), phosphatidylserine (PS) lipids, and cholesterol. Since the parametrization scheme was faithful to the scheme used in previous editions of Slipids, all parameters are consistent and fully compatible. The results of careful validation of a number of key structural properties for one and two component lipid bilayers are in excellent agreement with experiments. Potentials of mean force for transferring water across binary mixtures of lipids and cholesterol were also computed in order to compare water permeability rates to experiments. In agreement with experimental and simulation studies, it was found that the permeability and partitioning of water is affected by cholesterol in lipid bilayers made of saturated lipids to the largest extent. With the extensions of Slipids presented here, it is now possible to study complex systems containing many different lipids and proteins in a fully atomistic resolution in the isothermic-isobaric (NPT) ensemble, which is the proper ensemble for membrane simulations.

An all-atomistic force field (FF) has been developed for fully saturated phospholipids. The parametrization has been largely based on high-level ab initio calculations in order to keep the empirical input to a minimum. Parameters for the lipid chains have been developed based on knowledge about bulk alkane liquids, for which thermodynamic and dynamic data are excellently reproduced. The FFs ability to simulate lipid bilayers in the liquid crystalline phase in a tensionless ensemble was tested in simulations of three lipids: 1,2-diauroyl-sn-glycero-3-phospocholine (DLPC), 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), and 1,2-dipalmitoyl-sn-glycero-3-phospcholine (DPPC). Computed areas and volumes per lipid, and three different kinds of bilayer thicknesses, have been investigated. Most importantly NMR order parameters and scattering form factors agree in an excellent manner with experimental data under a range of temperatures. Further, the compatibility with the AMBER FF for biomolecules as well as the ability to simulate bilayers in gel phase was demonstrated. Overall, the FF presented here provides the important balance between the hydrophilic and hydrophobic forces present in lipid bilayers and therefore can be used for more complicated studies of realistic biological membranes with protein insertions.

Free energy calculations are vital for our understanding of biological processes on an atomistic scale and can offer insight to various mechanisms. However, in some cases, degrees of freedom (DOFs) orthogonal to the reaction coordinate have high energy barriers and/or long equilibration times, which prohibit proper sampling. Here we identify these orthogonal DOFs when studying the transfer of a solute from water to a model membrane. Important DOFs are identified in bulk liquids of different dielectric nature with metadynamics simulations and are used as reaction coordinates for the translocation process, resulting in two- and three-dimensional space of reaction coordinates. The results are in good agreement with experiments and elucidate the pitfalls of using one-dimensional reaction coordinates. The calculations performed here offer the most detailed free energy landscape of solutes embedded in lipid bilayers to date and show that free energy calculations can be used to study complex membrane translocation phenomena.

We propose an effective and straightforward way of including atomic polarization in simulations of the partitioning of small molecules in inhomogenous media based on classical molecular dynamics with non-polarizable force fields. The approach presented here takes advantage of the relatively fast sampling of phase space obtained with additive force fields by adding the polarization effects afterwards. By using pre-polarized charges for the polar and non-polar phases together with a polarization correction term the effects of atomic polarization are effectively taken into account. The results show a clear improvement compared to using the more common setup with one set of charges obtained from gas phase ab initio calculations. It is shown that when proper measures are taken into account computer simulations with non-polarizable force fields are able to accurately determine water-membrane partitioning and preferential location of small molecules in the membrane interior. We believe that the approach presented here can be useful in rational drug design and in investigations of molecular mechanisms of anesthetic or toxic action.

An approach to a straightforward reparametrization of the general AMBER force field (GAFF) for small organic solutes and druglike compounds is presented. The parametrization is based on specific pair interactions between the solvent and the solute, namely, the interactions between the constituting atoms of the solute and the oxygen of water were tuned in order to reproduce experimental hydration free energies for small model compounds. The key of the parametrization was to abandon the Lorentz-Berthelot combination rules for the van der Waals interactions. These parameters were then used for larger solutes in order to validate the newly derived pair interactions. In total close to 600 hydration free energies are computed, ranging from simple alkanes to multifunctional drug compounds, and compared to experimental data. The results show that the proposed parameters work well in describing the interactions between the solute and the solvent and that the agreement in absolute numbers is good. This modified version of GAFF is a good candidate for computing and predicting hydration free energies on a large scale, which has been a long-sought goal of computational chemists and can be used in rational drug design.

Free energies of solvation (Delta G) in water and n-octanol have been computed for common drug molecules by molecular dynamics simulations with an additive fixed-charge force field. The impact of the electrostatic interactions was investigated by computing the partial atomic charges with four methods that all fit the charges from the quantum mechanically determined electrostatic potential (ESP). Due to the redistribution of electron density that occurs when molecules are transferred from gas phase to condensed phase, the polarization impact was also investigated. By computing the partial atomic charges with the solutes placed in a conductor-like continuum, the charges were effectively polarized to take the polarization effects into account. No polarization correction term or similar was considered, only the partial atomic charges. Results show that free energies are very sensitive to the choice of atomic charges and that Delta G can differ by several k(B)T depending on the charge computing method. Inclusion of polarization effects makes the solutes too hydrophilic with most methods and in vacuo charges make the solutes too hydrophobic. The restrained-ESP methods together with effectively polarized charges perform well in our test set and also when applied to a larger set of molecules. The effect of water models is also highlighted and shows that the conclusions drawn are valid for different three-point models. Partitioning between an aqueous and a hydrophobic phase is also described better if the two environment's polarization is taken into account, but again the results are sensitive to the charge calculation method. Overall, the results presented here show that effectively polarized charges can improve the description of solvating a drug-like molecule in a solvent and that the choice of partial atomic charges is crucial to ensure that molecular simulations produce reliable results.

Accurate estimation of protein-carbohydrate binding energies using computational methods is a challenging task. Here we report the use of expanded ensemble molecular dynamics (EEMD) simulation with double decoupling for estimation of binding energies of hevein, a plant lectin with its monosaccharide and disaccharide ligands GlcNAc and (GlcNAc)(2), respectively. In addition to the binding energies, enthalpy and entropy components of the binding energy are also calculated. The estimated binding energies for the hevein-carbohydrate interactions are within the range of +/- 0.5 kcal of the previously reported experimental binding data. For comparison, binding energies were also estimated using thermodynamic integration, molecular dynamics end point calculations (MM/GBSA) and the expanded ensemble methodology is seen to be more accurate. To our knowledge, the method of EEMD simulations has not been previously reported for estimating biomolecular binding energies.

The physical mechanism of the folding and unfolding of chromatin is fundamentally related to transcription but is incompletely characterized and not fully understood. We experimentally and theoretically studied chromatin compaction by investigating the salt-mediated folding of an array made of 12 positioning nucleosomes with 177 bp repeat length. Sedimentation velocity measurements were performed to monitor the folding provoked by addition of cations Na⁺, K⁺, Mg²⁺, Ca²⁺, spermidine³⁺, Co(NH₃)₆³⁺, and spermine⁴⁺. We found typical polyelectrolyte behavior, with the critical concentration of cation needed to bring about maximal folding covering a range of almost five orders of magnitude (from 2 μM for spermine⁴⁺ to 100 mM for Na⁺). A coarse-grained model of the nucleosome array based on a continuum dielectric description and including the explicit presence of mobile ions and charged flexible histone tails was used in computer simulations to investigate the cation-mediated compaction. The results of the simulations with explicit ions are in general agreement with the experimental data, whereas simple Debye-Hückel models are intrinsically incapable of describing chromatin array folding by multivalent cations. We conclude that the theoretical description of the salt-induced chromatin folding must incorporate explicit mobile ions that include ion correlation and ion competition effects.

The paper reviews our current studies on the experimentally induced cation compaction and aggregation in solutions of DNA and nucleosome core particles and the theoretical modelling of these processes using coarse-grained continuum models with explicit mobile ions and with all-atom molecular dynamics (MD) simulations. Recent experimental results on DNA condensation by cationic oligopeptides and the effects of added salt are presented. The results of MD simulations modelling DNA–DNA attraction due to the presence of multivalent ions including the polyamine spermidine and fragments of histone tails, which exhibit bridging between adjacent DNA molecules, are discussed. Experimental data on NCP aggregation, using recombinantly prepared systems are summarized. Literature data and our results of studying of the NCP solutions are compared with predictions of coarse-grained MD simulations, including the important ion correlation as well as bridging mechanisms. The importance of the results to chromatin folding and aggregation is discussed.

The packaging of genomic DNA into chromatin in the eukaryotic cell nucleus demands extensive compaction. This requires attractive nucleosome-nucleosome interactions to overcome repulsion between the negatively charged DNA segments as well as other constraints. At the same time, DNA must be dynamically accessible to the cellular machinery that operates on it. Recent progress in the experimental characterisation of the higher order structure and dynamics of well-defined chromatin fibres has stimulated the attempts at theoretical description of chromatin and the nucleosome. Here we review the present status of chromatin Modelling, with particular emphasis on coarse-grained computer simulation models, the role of electrostatic interactions, and discuss future perspectives in the field.

Computer modeling of very large biomolecular systems, such as long DNA polyelectrolytes or protein-DNA complex-like chromatin cannot reach all-atom resolution in a foreseeable future and this necessitates the development of coarse-grained (CG) approximations. DNA is both highly charged and mechanically rigid semi-flexible polymer and adequate DNA modeling requires a correct description of both its structural stiffness and salt-dependent electrostatic forces. Here, we present a novel CG model of DNA that approximates the DNA polymer as a chain of 5-bead units. Each unit represents two DNA base pairs with one central bead for bases and pentose moieties and four others for phosphate groups. Charges, intra-and inter-molecular force field potentials for the CG DNA model were calculated using the inverse Monte Carlo method from all atom molecular dynamic (MD) simulations of 22 bp DNA oligonucleotides. The CG model was tested by performing dielectric continuum Langevin MD simulations of a 200 bp double helix DNA in solutions of monovalent salt with explicit ions. Excellent agreement with experimental data was obtained for the dependence of the DNA persistent length on salt concentration in the range 0.1-100 mM. The new CG DNA model is suitable for modeling various biomolecular systems with adequate description of electrostatic and mechanical properties.

The positively charged N-terminal histone tails play a crucial role in chromatin compaction and are important modulators of DNA transcription, recombination, and repair. The detailed mechanism of the interaction of histone tails with DNA remains elusive. To model the unspecific interaction of histone tails with DNA, all-atom molecular dynamics (MD) simulations were carried out for systems of four DNA 22-mers in the presence of 20 or 16 short fragments of the H4 histone tail (variations of the 16-23 a. a. KRHRKVLR sequence, as well as the unmodified fragment a. a. 13-20, GGAKRHRK). This setup with high DNA concentration, explicit presence of DNA-DNA contacts, presence of unstructured cationic peptides (histone tails) and K+ mimics the conditions of eukaryotic chromatin. A detailed account of the DNA interactions with the histone tail fragments, K+ and water is presented. Furthermore, DNA structure and dynamics and its interplay with the histone tail fragments binding are analysed. The charged side chains of the lysines and arginines play major roles in the tailmediated DNA-DNA attraction by forming bridges and by coordinating to the phosphate groups and to the electronegative sites in the minor groove. Binding of all species to DNA is dynamic. The structure of the unmodified fully-charged H4 16-23 a. a. fragment KRHRKVLR is dominated by a stretched conformation. The H4 tail a. a. fragment GGAKRHRK as well as the H4 Lys16 acetylated fragment are highly flexible. The present work allows capturing typical features of the histone tail-counterionDNA structure, interaction and dynamics.

Relaxation theory for paramagnetic systems is reviewed in a historical perspective and different principal aspects covered. The emphasis is on the post-Solomon–Bloembergen–Morgan developments of the last two decades. Experimental methods and protocols are presented briefly. Illustrative examples of experimental spin-lattice and spin-spin relaxation rates as a function of temperature and magnetic field are provided for transition metal and lanthanide complexes. Novel experiments and applications for metalloproteins are also mentioned. Finally, some joint investigations of variable-field paramagnetic relaxation enhancement and ESR spectral lineshapes are presented

Electron Spin Resonance (ESR) spectroscopy and Nuclear Magnetic Relaxation Dispersion (NMRD) experiments are reported for propylene glycol solutions of the nitroxide radical: 4-oxo-TEMPO-d(16) containing N-15 and N-14 isotopes. The NMRD experiments refer to H-1 spin-lattice relaxation measurements in a broad frequency range (10 kHz-20 MHz). A joint analysis of the ESR and NMRD data is performed. The ESR lineshapes give access to the nitrogen hyperfine tensor components and the rotational correlation time of the paramagnetic molecule. The NMRD data are interpreted in terms of the theory of paramagnetic relaxation enhancement in solutions of nitroxide radicals, recently presented by Kruk et al. [J. Chem. Phys. 138, 124506 (2013)]. The theory includes the effect of the electron spin relaxation on the H-1 relaxation of the solvent. The H-1 relaxation is caused by dipole-dipole interactions between the electron spin of the radical and the proton spins of the solvent molecules. These interactions are modulated by three dynamic processes: relative translational dynamics of the involved molecules, molecular rotation, and electron spin relaxation. The sensitivity to rotation originates from the non-central positions of the interacting spin in the molecules. The electronic relaxation is assumed to stem from the electron spin-nitrogen spin hyperfine coupling, modulated by rotation of the radical molecule. For the interpretation of the NMRD data, we use the nitrogen hyperfine coupling tensor obtained from ESR and fit the other relevant parameters. The consistency of the unified analysis of ESR and NMRD, evaluated by the agreement between the rotational correlation times obtained from ESR and NMRD, respectively, and the agreement of the translation diffusion coefficients with literature values obtained for pure propylene glycol, is demonstrated to be satisfactory.

H-1 relaxation dispersion of decalin and glycerol solutions of nitroxide radicals, 4-oxo-TEMPO-d(16)-N-15 and 4-oxo-TEMPO-d(16)-N-14 was measured in the frequency range of 10 kHz-20 MHz (for H-1) using STELAR Field Cycling spectrometer. The purpose of the studies is to reveal how the spin dynamics of the free electron of the nitroxide radical affects the proton spin relaxation of the solvent molecules, depending on dynamical properties of the solvent. Combining the results for both solvents, the range of translational diffusion coefficients, 10(-9)-10(-11) m(2)/s, was covered (these values refer to the relative diffusion of the solvent and solute molecules). The data were analyzed in terms of relaxation formulas including the isotropic part of the electron spin - nitrogen spin hyperfine coupling (for the case of N-14 and N-15) and therefore valid for an arbitrary magnetic field. The influence of the hyperfine coupling on H-1 relaxation of solvent molecules depending on frequency and time-scale of the translational dynamics was discussed in detail. Special attention was given to the effect of isotope substitution (N-14/N-15). In parallel, the influence of rotational dynamics on the inter-molecular (radical - solvent) electron spin - proton spin dipole-dipole coupling (which is the relaxation mechanism of solvent protons) was investigated. The rotational dynamics is of importance as the interacting spins are not placed in the molecular centers. It was demonstrated that the role of the isotropic hyperfine coupling increases for slower dynamics, but it is of importance already in the fast motion range (10(-9)m(2)/s). The isotope effects is small, however clearly visible; the H-1 relaxation rate for the case of N-15 is larger (in the range of lower frequencies) than for N-14. It was shown that when the diffusion coefficient decreases below 5 x 10(-11) m(2)/s electron spin relaxation becomes of importance and its role becomes progressively more significant when the dynamics slows done. As far as the influence of the rotational dynamics is concerned, it was show that this process is of importance not only in the range of higher frequencies (like for diamagnetic solutions) but also at low and intermediate frequencies.

The Swedish slow motion theory [Nilsson and Kowalewski, J. Magn. Reson. 146, 345 (2000)] applied so far to Nuclear Magnetic Relaxation Dispersion (NMRD) profiles for solutions of transition metal ion complexes has been extended to ESR spectral analysis, including in addition g-tensor anisotropy effects. The extended theory has been applied to interpret in a consistent way (within one set of parameters) NMRD profiles and ESR spectra at 95 and 237 GHz for two Gd(III) complexes denoted as P760 and P792 (hydrophilic derivatives of DOTA-Gd, with molecular masses of 5.6 and 6.5 kDa, respectively). The goal is to verify the applicability of the commonly used pseudorotational model of the transient zero field splitting (ZFS). According to this model the transient ZFS is described by a tensor of a constant amplitude, defined in its own principal axes system, which changes its orientation with respect to the laboratory frame according to the isotropic diffusion equation with a characteristic time constant (correlation time) reflecting the time scale of the distortional motion. This unified interpretation of the ESR and NMRD leads to reasonable agreement with the experimental data, indicating that the pseudorotational model indeed captures the essential features of the electron spin dynamics.

Theoretical calculations are performed on a model zeolite A where sodium ions have successively been exchanged with potassium. Using both isolated cluster and periodic DFT calculations, we made an attempt to explain how the chemisorbed carbonate species in the material contribute to the exceptionally high CO2 over N-2 selectivity of nearly 200 found in recent experiments [Liu et al. [1]] with the zeolite NaKA as adsorbent to capture and separate carbon dioxide from a gas mixture containing nitrogen. We have shown that the high carbonate forming at the potassium positions in the 8R windows (KII) results in a larger 8R window diameter potentially enhancing the CO2 uptake if adsorption is measured for individual gases.

Raman spectroscopy is used to probe the nature of the hydrogen bonds which hold the water of hydration to DNA. The approximate to 3450cm(-1) molecular O-H stretching mode shows that the first six water molecules per base pair of the primary hydration shell are very strongly bound to the DNA. The observed shift in the peak position of this mode permits a determination of the length of the hydrogen bonds for these water molecules. These hydrogen bonds appear to be about 0.3 angstrom shorter than the hydrogen bonds in bulk water. The linewidth of this mode shows no significant changes above water contents of about 15 water molecules per base pair. This technique of using a vibrational spectroscopy to obtain structural information about the hydration shells of DNA could be used to study the hydration shells of other biomolecules.

The effects of laser irradiation on the surface microstructure and optical properties of ZnO films deposited on glass substrates were investigated experimentally and compared with those of thermal annealing. X-ray diffraction (XRD) and atomic force microscopy (AFM) measurements showed that the irradiation treatment with an Ar+ laser of 514 nm for 5 min improves the crystalline quality of ZnO thin films through increasing the grain size and enhancing the c-axis orientation, with the effects similar to those of the thermal annealing at 500 degrees C for 1 h. Laser irradiation was found to be more effective both for the relaxation of the residual compressive stress in the as-grown films and for the modification of the surface morphology. A significant increase in the UV absorption and a widening in the optical band-gap of the films were also observed after laser irradiation.

ZnO thin films were prepared by radio frequency (RF) reactive magnetron sputtering at varying deposition conditions. The effects of RF power (from 40 to 90 W) and substrate temperature (from 100 to 200 degrees C) on the grain growth behavior, surface morphology evolution, and the structural and optical properties of the films were investigated. Atomic force microscopy (AFM) measurements confirmed that the grain size and surface roughness depend mainly on the RF power and increase with increasing it at the initial deposition stage of 5 s, and are strongly affected by the substrate temperature and increase with increasing it at the final deposition stage of 45 min. The influence of both the deposition parameters on the surface structure of the ZnO films at different deposition stages and the mechanism concerning this influence were discussed. The X-ray diffraction (XRD) and optical absorption spectra analysis indicated that all the films deposited for 45 min are in the state of the compressive stress and exhibit polycrystalline nature with the (002) preferential orientation, and they have high optical transparency in the visible range and sharp absorption edges around the wavelength 360 nm corresponding to the ZnO exciton. With the increase of the RF power and substrate temperature, the grain size increases, the residual compressive stress relaxes, and the optical band gaps broaden. In comparison with the RF power, the substrate temperature has more evident influence on the microstructure of the ZnO thin films.