Free-energy calculation of structure-H hydrates

A molecular-dynamics (MD) simulation of structure-H hydrates was performed under constant pressure and temperature with 6120 TIP4P water molecules, 900 OPLS-UA methane molecules, and 180 large molecular guest substance (LMGS) molecules. The LMGS molecules were represented in the form of a one-site Lennard-Jones (LJ) model using the LJ parameters sigma and epsilon. In order to clarify the thermodynamic stability of structure-H hydrates, we calculated the free-energy difference, changing on the sigma and epsilon only of the LMGS molecules. In this simulation, stable crystals of structure-H hydrates and a minimum value of DeltaG were obtained at sigma approximately 6.2 A and large values of epsilon. All simulations were performed using the special-purpose computer hardware MDGRAPE-2.     

The thermodynamic stability of clathrate hydrate. Encaging non-spherical propane molecules

The thermodynamic stability of a clathrate hydrate encaging non-spherical molecules has been investigated by examining the free energy of cage occupancy. In the present study, a generalized van der Waals and Platteeuw theory is extended to treat the rotational motion of guest molecules in clathrate hydrate cages. The vibrational free energy of both guest and host molecules is divided into harmonic and anharmonic contributions. The anharmonic free energy associated with the non-spherical nature of the guest molecules is evaluated as a perturbation from the spherical guest. Predicted thermodynamic properties are compared with measured values. It is shown that this anharmonic contribution is important in the free energy of the hindered rotation of the guests.     

Theoretical Investigation of the Fusion Process of Mono-Cages to Tri-Cages with CH4/C2H6 Guest Molecules in sI Hydrates

Owing to a stable and porous cage structure, natural gas hydrates can store abundant methane and serve as a potentially natural gas resource. However, the microscopic mechanism of how hydrate crystalline grows has not been fully explored, especially for the structure containing different guest molecules. Hence, we adopt density functional theory (DFT) to investigate the fusion process of structure I hydrates with CH₄/C₂H₆ guest molecules from mono-cages to triple-cages. We find that the volume of guest molecules affects the stabilities of large (5¹²6², L) and small (5¹², s) cages, which are prone to capture C₂H₆ and CH₄, respectively. Mixed double cages (small cage and large cage) with the mixed guest molecules have the highest stability and fusion energy. The triangular triple cages exhibit superior stability because of the three shared faces, and the triangular mixed triple cages (large-small-large) structure with the mixed guest molecules shows the highest stability and fusion energy in the triple-cage fusion process. These results can provide theoretical insights into the growth mechanism of hydrates with other mono/mixed guest molecules for further development and application of these substances.     

A host–guest strategy for converting the photodynamic agents from a singlet oxygen generator to a superoxide radical generator

Type-I photosensitizers (PSs) generate cytotoxic oxygen radicals by electron transfer even in a hypoxic environment. Nevertheless, the preparation of type-I PSs remains a challenge due to the competition of triplet–triplet energy transfer with O₂ (type-II process). In this work, we report an effective strategy for converting the conventional type-II PS to a type-I PS by host–guest complexation. Electron-rich pillar[5]arenes are used as an electron donor and macrocyclic host to produce a host–guest complex with the traditional electron-deficient type-II PS, an iodide BODIPY-based guest. The host–guest complexation promotes intermolecular electron transfer from the pillar[5]arene moiety to BODIPY and then to O₂ by the type-I process upon light-irradiation, leading to efficient generation of the superoxide radical (O₂⁻˙). The results of anti-tumor studies indicate that this supramolecular PS demonstrates high photodynamic therapy efficacy even under hypoxic conditions. This work provides an efficient method to prepare type-I PSs from existing type-II PSs by using a supramolecular strategy.

A supramolecular strategy is reported for converting the conventional photodynamic agents from a singlet oxygen generator to a superoxide radical generator by the host–guest interaction enhanced electron transfer.     

Guest-Host Interaction Study in Clathrate Hydrates Using Lattice Dynamics Simulation

Lattice dynamics simulation of several gas hydrates （helium, argon, and methane） with different occupancy rates has been performed using TIP3P potential model. Results show that the coupling between the guest and host is not simple as depicted by the conventional viewpoints. For clathrate hydrate enclosing small guest, the small cages are dominantly responsible for the thermodynamic stability of clathrate hydrates. And the spectrum of methane hydrate is studied compared with argon hydrate, then as a result, shrink effect from positive hydrogen shell is proposed.     

Spectroscopic Observation of the Hydroxy Position in Butanol Hydrates and Its Effect on Hydrate Stability

In this study, we investigate the crystal structures and phase equilibria of butanols+CH₄+H₂O systems to reveal the hydroxy group positioning and its effects on hydrate stability. Four clathrate hydrates formed by structural butanol isomers are identified with powder X‐ray diffraction (PXRD). In addition, Raman spectroscopy is used to analyze the guest distributions and inclusion behaviors of large alcohol molecules in these hydrate systems. The existence of a free OH indicates that guest molecules can be captured in the large cages of structure II hydrates without any hydrogen‐bonding interactions between the hydroxy group of the guests and the water‐host framework. However, Raman spectra of the binary (1‐butanol+CH₄) hydrate do not show the free OH signal, indicating that there could be possible hydrogen‐bonding interactions between the guests and hosts. We also measure the four‐phase equilibrium conditions of the butanols+CH₄+H₂O systems.     

常见客体分子对笼型水合物晶格常数的影响

Natural gas hydrates are considered as ideal alternative energy resources for the future, and the relevant basic and applied research has become more attractive in recent years. The influence of guest molecules on the hydrate crystal lattice parameters is of great significances to the understanding of hydrate structural characteristics, hydrate formation/decomposition mechanisms, and phase stability behaviors. In this study, we test a series of artificial hydrate samples containing different guest molecules (e.g. methane, ethane, propane, iso-butane, carbon dioxide, tetrahydrofuran, methane + 2, 2-dimethylbutane, and methane + methyl cyclohexane) by a low-temperature powder X-ray diffraction (PXRD). Results show that PXRD effectively elucidates structural characteristics of the natural gas hydrate samples, including crystal lattice parameters and structure types. The relationships between guest molecule sizes and crystal lattice parameters reveal that different guest molecules have different controlling behaviors on the hydrate types and crystal lattice constants. First, a positive correlation between the lattice constants and the van der Waals diameters of homologous hydrocarbon gases was observed in the single-guest-component hydrates. Small hydrocarbon homologous gases, such as methane and ethane, tended to form sI hydrates, whereas relatively larger molecules, such as propane and iso-butane, generated sⅡ hydrates. The hydrate crystal lattice constants increased with increasing guest molecule size. The types of hydrates composed of oxygen-containing guest molecules (such as CO₂ and THF) were also controlled by the van der Waals diameters. However, no positive correlation between the lattice constants and the van der Waals diameters of guest molecules in hydrocarbon hydrates was observed for CO₂ hydrate and THF hydrate, probably due to the special interactions between the guest oxygen atoms and hydrate "cages". Furthermore, the influences of the macromolecules and auxiliary small molecules on the lengths of the different crystal axes of the sH hydrates showed inverse trends. Compared to the methane + 2, 2-dimethylbutane hydrate sample, the length of the a-axis direction of the methane + methyl cyclohexane hydrate sample was slightly smaller, whereas the length of the c-axis direction was slightly longer. The crystal a-axis length of the sH hydrate sample formed with nitrogen molecules was slightly longer, whereas the c-axis was shorter than that of the methane + 2, 2-dimethylbutane hydrate sample at the same temperature.     

Crystal lattice size and stability of type H clathrate hydrates with various large-molecule guest substances

To gain a better understanding of the effects of guest molecules on the lattice and stability of type H hydrates, we performed powder X-ray diffraction (PXRD) measurements and semiempirical molecular orbital calculations. The unit cell parameters and cohesive energies of various type H hydrates that contain methane (CH4) were analyzed. PXRD measurements indicated that an increase in the large-molecule guest volume caused the unit cell volume to increase. It was also indicated that a large-molecule guest substance caused the a-axis-direction of the unit cell to increase with little decrease in the c-axis direction. Calculations of cohesive energy by means of a semiempirical molecular orbital method indicated that the functional group and configuration of large-molecule guest substances affects the stability of type H hydrates. It was concluded that the icosahedron (5(12)6(8)) cages do not easily increase in length along the c-axis direction when larger guest molecules are used to form the hydrate, but the 5(12)6(8) cage and the layer of dodecahedron (5(12)) cages can easily increase in length along the a-axis direction due to interactions of the guest-host molecule.     

Superexchange-like interaction of encaged molecular oxygen in nitrogen-doped water cages of clathrate hydrates

Clathrate hydrates are a highly prospective material in energy and environmental fields, but the inherent nature of inclusion phenomena occurring in the stacked water cages has not been completely resolved yet. Investigating the magnetism of guest molecules is a new experimental approach in clathrate hydrate research to open the possibility of icy magnetic applications as a novel material as well as to understand the unrevealed host-guest interactions in icy inclusion compounds. In this study, we observed an indirect spin coupling between encaged dioxygen molecules via a nonmagnetic water framework through the measurement of guest magnetization. This spin coupling is reminiscent of superexchange coupling between magnetic ions through intervening oxygens in antiferromagnetic oxides, such as MnO and CoO. Theoretical calculations revealed that OH(-) incorporated in the framework induced the mixing of perpendicular π* orbitals of two distant dioxygens and that ammonia doping into the hydrate cage leads to a longer lifetime of that orientation.     

Optimization of the GB/SA solvation model for predicting the structure of surface loops in proteins

Implicit solvation models are commonly optimized with respect to experimental data or Poisson-Boltzmann (PB) results obtained for small molecules, where the force field is sometimes not considered. In previous studies, we have developed an optimization procedure for cyclic peptides and surface loops in proteins based on the entire system studied and the specific force field used. Thus, the loop has been modeled by the simplified solvation function E(tot) = E(FF) (epsilon = 2r) + Sigma(i) sigma(i)A(i), where E(FF) (epsilon = nr) is the AMBER force field energy with a distance-dependent dielectric function, epsilon = nr, A(i) is the solvent accessible surface area of atom i, and sigma(i) is its atomic solvation parameter. During the optimization process, the loop is free to move while the protein template is held fixed in its X-ray structure. To improve on the results of this model, in the present work we apply our optimization procedure to the physically more rigorous solvation model, the generalized Born with surface area (GB/SA) (together with the all-atom AMBER force field) as suggested by Still and co-workers (J. Phys. Chem. A 1997, 101, 3005). The six parameters of the GB/SA model, namely, P(1)-P(5) and the surface area parameter, sigma (programmed in the TINKER package) are reoptimized for a "training" group of nine loops, and a best-fit set is defined from the individual sets of optimized parameters. The best-fit set and Still's original set of parameters (where Lys, Arg, His, Glu, and Asp are charged or neutralized) were applied to the training group as well as to a "test" group of seven loops, and the energy gaps and the corresponding RMSD values were calculated. These GB/SA results based on the three sets of parameters have been found to be comparable; surprisingly, however, they are somewhat inferior (e.g, of larger energy gaps) to those obtained previously from the simplified model described above. We discuss recent results for loops obtained by other solvation models and potential directions for future studies.     

Simulation of interaction forces between nanoparticles in the presence of Lennard-Jones polymers: freely adsorbing homopolymer modifiers

The force between two nanoscale colloidal particles dispersed in a solution of freely adsorbing Lennard-Jones homopolymer modifiers is calculated using the expanded grand canonical Monte Carlo simulation method. We investigate the effect of polymer chain length (N), nanoparticle diameter (sigma(c)), and colloid-polymer interaction energy (epsilon(cp)) on polymer adsorption (Gamma) and polymer-induced forces (F(P)(r)) between nanoparticles in the full thermodynamic equilibrium condition. There is a strong correlation between polymer adsorption and the polymer-mediated nanoparticle forces. When the polymer adsorption is weak, as in the case of smaller diameters and short polymer chain lengths (sigma(c) = 5, N = 10), the polymers do not have any significant effect on the bare nanoparticle interactions. The adsorbed amount increases with increasing particle diameter, polymer chain length, and colloid-polymer interaction energy. In general, for strong polymer-particle adsorption the polymer-governed force profiles between nanoparticles show short-range repulsion and long-ranged attraction, suggesting that homopolymers would not be ideal for achieving stabilization in nanoparticle dispersions. The attraction is likely due to bridging, as well as polymer segment-segment interactions. The location and magnitude of attractive minimum in the force profile can be controlled by varying N and epsilon(cp). The results show partial agreement and some marked differences with previous theoretical and experimental studies of forces in the limit of flat walls in an adsorbing polymer solution. The difference could be attributed to incorporation of long-ranged colloid-polymer potential in our simulations and the influence of the curvature of the nanoparticles.     

Unexpected effect of charge density of the aromatic guests on the stability of calix[6]arene-phenol host-guest complexes

The pi-pi interaction-based inclusion complexation of calix[6]arene hexasulfonate as host with neutral aromatic guest molecules was studied in aqueous media. To vary the electron density on the guest's aromatic rings, the phenol parent compound was functionalized in the para-position with different electron-withdrawing groups, such as NO2 and Cl, as well as H and CH3 groups. To study the interaction between calixarene and the guests, PL, DSC, and quantum-chemical methods were used. The results indicate 1:1 stoichiometry for all examined host-guest complexes. Although the enthalpy change predicts strong interaction between the host and the guest, the Gibbs free energy change of the complex formation is small, resulting in a relatively low complex stability. This property is due to the high and negative entropy change during the complex formation. Comparing the thermodynamic parameters observed on the series of the guests, we observed a decrease of the enthalpy change when the electron density on the guest's aromatic ring increased. However, the Gibbs free energy and therefore, the stability of the complexes increased when the enthalpy change lowered. These unexpected results are based on the enthalpy-entropy compensation effect and probably due to the quite different entropy change related to the high and low electron density on the aromatic rings of different guest molecules. Using molecular dynamic calculations, a redistribution of the electron density of calixarene rings, followed by the reordering of the solvent molecules, was identified as a background of this unexpected entropy change at molecular level.     

Autocorrelation functions of a fluid of molecules interacting through steeply repulsive and attractive forces

A new method is presented for an extension of Enskog's approximation for the evaluation of the autocorrelation functions of a fluid, and this approach is used to evaluate these functions when the interaction between the molecules includes both steeply repulsive and steeply attractive forces. Consequently the correlation functions depend upon the temperature in a nontrivial way. As an example, the method is applied to calculate the velocity and force autocorrelation functions of a fluid when the molecules interact through the specific potential, V(r)=4epsilon[(sigma/r)2n-(sigma/r)n] when the parameter n is large. There is a relationship between this model and the "sticky sphere" one which is exploited in the theoretical computations. The results obtained from the theory are compared with molecular dynamics simulation for n=72 and 144 and for a range of temperatures from T=epsilon/kB down to epsilon/3kB. The two approaches agree very well for a range of state points, especially at short times. At later times the theory predicts a more oscillatory behavior than the simulation especially at very low reduced temperatures.     

Molecular dynamics study of the stability of methane structure H clathrate hydrates

Molecular dynamics simulations are used to study the stability of structure H (sH) methane clathrate hydrates in a 3 x 3 x 3 sH unit cell replica. Simulations are performed at experimental conditions of 300 K and 2 GPa for three methane intermolecular potentials. The five small cages of the sH unit cell are assigned methane guest occupancies of one and large cage guest occupancies of one to five are considered. Radial distribution functions, unit cell volumes, and configurational energies are studied as a function of large cage CH(4) occupancy. Free energy calculations are carried out to determine the stability of clathrates for large cage occupancies. Large cage occupancy of five is the most stable configuration for a Lennard-Jones united-atom potential and the Tse-Klein-McDonald potential parametrized for condensed methane phases and two for the most stable configuation for the Murad and Gubbins potential.     

The conversion process of hydrocarbon hydrates into CO2 hydrates and vice versa: thermodynamic considerations

Microscopy, confocal Raman spectroscopy and powder X-ray diffraction (PXRD) were used for in situ investigations of the CO(2)-hydrocarbon exchange process in gas hydrates and its driving forces. The study comprises the exposure of simple structure I CH(4) hydrate and mixed structure II CH(4)-C(2)H(6) and CH(4)-C(3)H(8) hydrates to gaseous CO(2) as well as the reverse reaction, i.e., the conversion of CO(2)-rich structure I hydrate into structure II mixed hydrate. In the case of CH(4)-C(3)H(8) hydrates, a conversion in the presence of gaseous CO(2) from a supposedly more stable structure II hydrate to a less stable structure I CO(2)-rich hydrate was observed. PXRD data show that the reverse process requires longer initiation times, and structural changes seem to be less complete. Generally, the exchange process can be described as a decomposition and reformation process, in terms of a rearrangement of molecules, and is primarily induced by the chemical potential gradient between hydrate phase and the provided gas phase. The results show furthermore the dependency of the conversion rate on the surface area of the hydrate phase, the thermodynamic stability of the original and resulting hydrate phase, as well as the mobility of guest molecules and formation kinetics of the resulting hydrate phase.     

13C NMR studies of hydrocarbon guests in synthetic structure H gas hydrates: experiment and computation

(13)C NMR chemical shifts were measured for pure (neat) liquids and synthetic binary hydrate samples (with methane help gas) for 2-methylbutane, 2,2-dimethylbutane, 2,3-dimethylbutane, 2-methylpentane, 3-methylpentane, methylcyclopentane, and methylcyclohexane and ternary structure H (sH) clathrate hydrates of n-pentane and n-hexane with methane and 2,2-dimethylbutane, all of which form sH hydrates. The (13)C chemical shifts of the guest atoms in the hydrate are different from those in the free form, with some carbon atoms shifting specifically upfield. Such changes can be attributed to conformational changes upon fitting the large guest molecules in hydrate cages and/or interactions between the guests and the water molecules of the hydrate cages. In addition, powder X-ray diffraction measurements revealed that for the hexagonal unit cell, the lattice parameter along the a-axis changes with guest hydrate former molecule size and shape (in the range of 0.1 ?) but a much smaller change in the c-axis (in the range of 0.01 ?) is observed. The (13)C NMR chemical shifts for the pure hydrocarbons and all conformers were calculated using the gauge invariant atomic orbital method at the MP2/6-311+G(2d,p) level of theory to quantify the variation of the chemical shifts with the dihedral angles of the guest molecules. Calculated and measured chemical shifts are compared to determine the relative contribution of changes in the conformation and guest-water interactions to the change in chemical shift of the guest upon clathrate hydrate formation. Understanding factors that affect experimental chemical shifts for the enclathrated hydrocarbons will help in assigning spectra for complex hydrates recovered from natural sites.     

Excess Gibbs potential model for multicomponent hydrogen clathrates

A new thermodynamic calculation procedure is introduced to predict the equilibrium conditions of multicomponent gas hydrates containing hydrogen. This new approach utilizes an excess Gibbs potential term to account for second- or higher-order water-cavity distortions due to the presence of multiple guest species. The excess Gibbs potential describes changes in reference chemical potentials according to different compositions of guest mixtures in the hydrate phase. To determine the equilibrium conditions of multicomponent gas hydrates, the excess Gibbs potential term is incorporated to the Lee-Holder model along with the Zele-Lee-Holder cell distortion model. For binary gas hydrates between hydrogen and the other gas molecule, the predicted equilibrium pressure deviates within 10-20% from the experimental value. For the ternary and quaternary mixture hydrates, the model prediction is reasonably good but its error increases with increasing pressure and temperature under the presence of THF.     

DFT-B3LYP and SMD study on the interactions between aza-, diaza-, and triaza-12-crown-4 (A n -12-crown-4, n = 1, 2, 3) with Na+ in the gas phase and acetonitrile solution

B3LYP/6-311G level of theory is used to study the interactions between aza-, diaza-, and triaza- 12-crown-4 ligands as host molecules and Na⁺ ion as a guest species. Minimum energy structures, complexes binding energies, basis set superposition errors, and various thermodynamic parameters of free ligands, ion, and complexes have been calculated based on the proposed level of theory. A simple thermodynamic cycle with and without different acetonitrile cluster sizes inside the cavity of Na⁺, has been used to calculate the stability constants of aza-12-crown-4 complex. All solvation free energy estimations have been done with using SMD model. Results show that with introducing more acetonitrile molecules in the cavity of guest species, the absolute deviation is reduced. In addition, a good linear correlation between experimental complex formation constants and binding energies of complexes has been obtained. Calculated results, which are in agreement with the experimental data, predict that the interaction energy of triaza- is more than diaza-12-crown-4, which in turn is greater than aza-12-crown-4 with Na⁺ ion.     

Physical properties of soft repulsive particle fluids

Molecular dynamics computer simulation has been applied to inverse power or soft-sphere fluids, in which the particles interact through the soft-sphere pair potential, phi(r) = epsilon(sigma/r)(n), where n measures the steepness or stiffness of the potential, and epsilon and sigma are a characteristic energy and distance, respectively. The focus of the study is on very soft particles with n values down to 4 considered, at densities up to and along the fluid-solid co-existence density. It is shown that in the soft-particle limit the local structure is dominated by the lengthscale associated with the average nearest neighbour distance of a random structure, which is proportional, variantrho(-1/3) and increasingly only very weakly dependent on n. This scaling is also manifest in the behaviour of the average energy per particle with density. The self-diffusion coefficient and shear viscosity are computed along the fluid-solid co-existence line as a function of n, for the first time. The product Deta(s) steadily increases with softness for n < 10, whereas the modified Stokes-Einstein relationship of Zwanzig, Deta(s)/rho(1/3), where rho is the number density, is within statistics constant over the same softness range. This is consistent with our observation that the static properties are determined by a characteristic lengthscale (i.e., l) which is proportional, variantrho(-1/3) in the soft-particle limit. The high frequency elastic moduli of these fluids are examined, which reveals that the mechanical properties become more 'rubbery' as the particles get softer.