On the Stability of Clathrate Hydrates Encaging Polar Guest Molecules: Contrast in the Hydrogen Bonds of Methylamine and Methanol Hydrates

Abstract

The stability of clathrate hydrates encaging highly polar guests has been investigated in order to explain the experimental observation that some amines form clathrate hydrates but alcohols act as inhibitor to hydrate formation. We choose methylamine and methanol as guest species and examine the stable structure, at which the total potential energy has a minimum value. At the local minima of those two hydrates, the potential energies of water-water and guest-water, and their hydrogen bonded networks are compared. It is found that methanol does not retain the host lattice structure, while the host-network structure is kept in the presence of methylamine. It is shown that the difference in the magnitude of the partial charge on the hydrogen atom between the hydroxyl and amino groups plays a much more significant role on the stability of both clathrate hydrates than the difference in molecular geometry. This is supported from the result of a methylamine-like model that has the same partial charges on the atoms in the hydrophilic site as methanol.     

Vibrational spectra of deuterated methane and water molecules in structure I clathrate hydrate from ab initio MD simulation

The deuteration of the lattice molecules in clathrate hydrates is a widely used experimental technique to clearly separate the vibrational modes. However, the effect of the deuteration on the vibrational spectra and molecular motions is not fully understood. Since the guest–host coupling may change the vibrational spectra, a detailed analysis of the vibrational spectra of deuterated clathrate hydrate is significant in the understanding of the mechanism of the vibrational shift. In this study, the vibrational spectra of the deuterated methane hydrates were calculated by ab initio molecular dynamics simulation. The intramolecular vibrational frequency of the methane in D₂O lattice and deuterated methane in H₂O lattice was calculated and compared with the pure methane hydrate. The bending, rocking and overtone of the bending mode was also reported. The effect of coupling of the rattling motions of guest and host molecules on the vibrational spectra was revealed.     

The thermal properties of binary structure sI clathrate hydrate from molecular dynamics simulation

In this work, we present temperature dependence of lattice parameter and normalised lattice parameter in the atmospheric pressure and 120 bar and also pressure dependence of unit cell volume and normalised unit cell volume at 150 and 250?K for variety guests with different size, polarity and guest–host hydrogen bonding capability such as trimethylene oxide (TMO), ethylene oxide (EO), formaldehyde (FA), cyclobutane (CB), cyclopropane (CP) and ethane (Et) in the large cages with CH₄ in small cages of sI clathrate hydrates by molecular dynamics simulations. The obtained values of lattice parameters for the guest species are compatible with the experimental values. These clathrate hydrates are simulated with TIP4P/ice four-site water potential. Herein, isobaric thermal expansivity and isothermal compressibility are calculated at a temperature range of 50–250?K and a wide pressure range. These structural properties have been compared for guests which they are isoelectronic and have similar masses but with different size and polarity. We use molecular dynamics simulations to relate microscopic guest properties, like guest–host hydrogen bonding to macroscopic sI clathrate hydrate properties. The temperature dependence of thermodynamic properties such as constant-volume and constant-pressure heat capacity is presented in the atmospheric pressure for these guest species.     

NMR diffusion as a novel tool for measuring the association constant between cyclodextrin and guest molecules

In this paper we introduce the use of diffusion measurements by nuclear magnetic resonance (NMR) spectroscopy for determining association constants of weak and very weak interactions between cyclodextrin and guest molecules, as long as both the free and complexed guest molecules are soluble to an extent that allows good sensitivity in the NMR experiment. The experimental setup and data analysis is discussed for three different guest molecules: L-phenylalanine, L-leucine and L-valine, representing different strengths of interaction. The underlying assumptions are discussed and the scope of the method (range of K(a) values, requirements to the guest molecule) are discussed. The method's main advantage is its general applicability independent of chromogenic or electrochemical properties of the guest molecule. Whereas calorimetric methods that exhibit a similar generality, are applicable mainly to strong interactions, NMR diffusion measurements are applicable to weaker interactions down to the theoretical limit of 1 M(-1), the upper limit for K(a) values to be determined by it is approximately 200. A further advantage of the method is the low amount of sample needed. The method is in principle applicable to any case of molecular recognition between a host and guest molecule leading to weak interactions.     

Theoretical study of conformational disorder and selective adsorption of small organic molecules in the flexible metal-organic framework material MIL-53-Fe

Many of the potential applications for metal-organic framework (MOF) materials require molecular level understanding of their adsorption of small organic molecules, which are not readily accessible from experiment. Through high-level van der Waals corrected, hybrid density functional theory calculations, we elucidate the adsorption configurations of several, representative small organic guest molecules in an archetypal flexible MOF material, MIL-53-Fe. The predicted relative energies between low-energy adsorption configurations of 1,4-benzoquinone in MIL-53-Fe are in very good agreement with the thermal transition temperatures observed experimentally and suggest that thermodynamic factors govern the precise arrangements and loading of guests in the MOF host. Experimentally observed conformational disorder of small organic molecules in MIL-53-Fe is explained by predicted multiple low-energy adsorption configurations that are comparable with the thermal energy of the guests, kT. Finally, we show that the previously observed selective adsorption of pyridine and 2,6-lutidine molecules in water by MIL-53-Fe, can be rationalised through a careful analysis of the host–guest and guest–guest interactions and is controlled by thermodynamic factors.     

Dissociation mechanism of gas hydrates (I,II, H) of alkane molecules: a comparative molecular dynamics simulation

Employing NPT molecular dynamics method with consistent valence force field, the dissociation processes of sI, sII and sH gas hydrates are simulated at different temperatures and at a constant pressure of 100 MPa. The dissociation mechanisms of gas hydrates are revealed by analysing the structural snapshots, radial distribution functions and diffusion coefficients at different temperatures. As temperature increases, the diffusion rates of water molecules and guest molecules increase; thus the clathrate skeleton formed by water molecules with hydrogen bonds distorts and breaks down; meanwhile the guest molecules encapsulated in the water cavities are released. The size of guest molecules affects the dissociation behaviour of gas hydrate. In addition, the dissociation behaviour also relies on the structural phase of gas hydrates.     

Microbial Stabilization and Kinetic Enhancement of Marine Methane Hydrates

Abstract

In clathrate hydrates, a water host lattice encages small guest molecules in cavities. Methane hydrates are the most widespread in-situ clathrate in the permafrost and continental-shelf ocean regions, constituting a significant energy resource, and prompting recent marine-hydrate gas-production trials. Despite exciting engineering advances and a few marine-mimicking laboratory studies of methane-hydrate kinetics and stabilization, from microbial perspectives, little is known about a potential microbial origin of marine hydrates, nor their possible formation kinetics or potential stabilization by microbial sources. Here, for the first time, we show that an exported, extra-cytoplasmic porin – produced by a marine methylotrophic bacterium culture – provides the basis for kinetic enhancement and stabilization of methane hydrates under conditions simulating the seabed environment. We then identify the key protein at play, and we therefore suggest microbe-based stabilization of marine hydrates is evidently a property likely to be found in many marine bacteria. Our research opens the possibility of managing marine-hydrate deposits using microbiological strategies for environmental and societal benefit.     

Crystal structure of cyclomaltoheptaose (beta-cyclodextrin) complexes with p-aminobenzoic acid and o-aminobenzoic acid

Crystal structures of cyclomaltoheptaose (beta-cyclodextrin) complexes with p-aminobenzoic acid and o-aminobenzoic acid have been determined by single-crystal X-ray diffraction. The space group of the beta-cyclodextrin-p-aminobenzoic acid complex is P2(1) with a host:guest stoichiometry of 1:1, and that of the beta-cyclodextrin-o-aminobenzoic acid complex is P1 with a stoichiometry of 2:3. The different structures of the guest molecules lead to the different molecular packing structures of the two complexes. Intermolecular hydrogen-bond interactions are the main force that stabilize the supramolecular systems. In both crystals, there are water molecules located near the cavity rims and in interstices between molecules of beta-cyclodextrin participating in formation of intermolecular hydrogen bonds.     

Thermal effects in guest–host systems: [Zn2(bdc)(S‐lac)(dmf)]•PhEtOH: A DSC and NMR study

Differential scanning calorimetry and nuclear magnetic resonance were used to investigate thermal effects in the guest–host systems where homochiral metal–organic sorbent [Zn₂(bdc)(S ‐lac)(dmf)] is considered as a host while 1‐phenylethanol enantiomers and their racemic mixture serve as guest molecules. A maximum energy gain from the guest–host interaction was observed in the system with the racemic mixture. The effect of host–guest recognition was revealed for the case of the host and guest having a similar type of chirality in the presence of antipode guest molecules.     

Surface and interlayer structure of vermiculite intercalated with methyl viologen

Molecular modeling using empirical force field revealed the differences between the surface and interlayer arrangement of the dye guest molecules in vermiculite intercalated with the divalent methyl viologen cation (MV²⁺). Conformation and anchoring of MV²⁺ cations on the silicate layer in the interlayer space of vermiculite host structure is different from that on the crystal surface. A preferential position has been found for the anchoring of guests on the silicate layer. Anyway the arrangement of guests in the interlayer space as well as on the crystal surface exhibits a high degree of disorder due to a certain flexibility in guest molecules arrangement and first of all due to the presence of water molecules in the interlayer space. The presence of water disturbs not only the regularity in guest positions and orientations but also in conformation of guest molecules in the interlayer space of the host structure.     

Selective binding of chiral molecules of cinchona alkaloid by beta- and gamma-cyclodextrins and organoselenium-bridged bis(beta-cyclodextrin)s

The inclusion complexation behavior of chiral members of cinchona alkaloid with beta- and gamma-cyclodextrins (1 and 2) and 6,6(')-trimethylenediseleno-bridged bis(beta-cyclodextrin) (3) was assessed by means of fluorescence and 2D-NMR spectroscopy. The spectrofluorometric titrations have been performed in aqueous buffer solution (pH 7.20) at 25.0 degrees C to determine the stability constants of the inclusion complexation of 1-3 with guest molecules (i.e., cinchonine, cinchonidine, quinine, and quinidine) in order to quantitatively investigate the molecular selective binding ability. The stability constants of the resulting complexes of 2 with guest molecules are larger than that of 1. As a result of cooperative binding, the stability constants of inclusion complexation of dimeric beta-cyclodextrin 3 with cinchonidine and cinchonine are higher than that of parent 1 by factor of 4.5 and 2.4, respectively. These results are discussed from the viewpoint of the size-fit and geometric complementary relationship between the host and guest.     

Rearrangement of the Hydrogen-Bonded Network of the Clathrate Hydrates Encaging Polar Guest

Abstract

Rearrangement process of the hydrogen-bonded network of clathrate hydrate of the polar guest ethylamine is examined by the molecular dynamics simulation. The hydrogen-bonded network rearrangements with reorientation of water or migration of water are observed in the 10 ns trajectories and analyzed in term of a representative connectivity pattern of a time zone longer than a time scale of vibrational motion of molecules. The most frequent rearrangement is the reorientation of single water molecule rotating 180° around its twofold axis in the network unlike Bjerrum's picture of molecular rotation in ice. Migration of water in the host lattice rarely occurs and very long time (several hundred pico second) is required to complete the rearrangement process since cooperative reorientation of many neighboring water is necessarily accompanied. The correlation of reorientational motion of water appears to decay not with the Debye type but rather with a power-law behavior.     

Tuning the binding of coumarin 6 with DNA by molecular encapsulators: effect of β‐cyclodextrin and C‐hexylpyrogallol[4]arene

We report in this paper that the binding of coumarin 6 (C6) to DNA can be tuned by complexing it with host structures, viz. β‐cyclodextrin (β‐CD) and C‐hexylpyrogallol‐4‐arene (C‐HPA). Because host molecules are used as carriers of small molecules onto target sites, the exposed part of the guest molecule needs to be found out, and the relationship between the host : guest ratio and the mode of binding with the target macromolecule, that is, the DNA needs to be analyzed, in order to comprehend the preferred binding moiety and tune the binding. In this paper, the formation of the inclusion complex of C6 with β‐CD and with C‐HPA is studied by UV‐visible, fluorescence, 2D rotating‐frame nuclear Overhauser effect correlation spectroscopy and diffusion‐ordered spectroscopy nuclear magnetic resonance spectra and molecular modeling. C6 forms a 1:1 complex with β‐CD and a 1:2 complex with C‐HPA. The studies on the protonation of C6 in the presence and the absence of the host molecules suggest that the chromone part of C6 is outside the β‐CD molecule, whereas it is fully covered by C‐HPA. The binding of C6 with calf thymus DNA (ctDNA) occurs through intercalation and hydrogen bonding, and the host–guest structures remain intact on binding with ctDNA. The oxygens of the C6 molecules are exposed when inside the host molecules and aid in the hydrogen bonding with DNA. Copyright © 2014 John Wiley & Sons, Ltd.     

Layered inorganic/enzyme nanohybrids with selectivity and structural stability upon interacting with biomolecules

Effective intercalation of protein molecules within the galleries of montmorillonites can be achieved via simple space enlarging and exchange processes while retaining the native conformation of the guest protein and the multilayered structure of the bioinert host plates. The capacity of accommodating protein molecules in the galleries can be markedly larger than that governed by the Langmuir-type adsorption of protein molecules on the external surfaces of particles. The basal spacing in the multilayered structure of clay is abruptly enlarged when the extent of protein intercalation increases to a critical point. Beyond this critical point, the nanohybrids show well-preserved catalytic activity in hydrolyzing small substrates while establishing a barrier to interactions with large biomacromolecules. Furthermore, the structural stability of the inorganic/organic nanohybrids is enhanced such that neither exchange of biomolecules nor exfoliation of layered clay particles occurs when exposed to other proteins. The results indicate that, through the benign accommodation of protein species between the inorganic platelets, this nanoscaled manipulation of protein functions can be highly useful in developing new inorganic/enzyme nanohybrids for protein therapeutics and tissue engineering.     

Microhydration of caesium compounds: Cs,CsOH, CsI and Cs2I2 complexes with one to three H2O molecules of nuclear safety interest

The structure and properties of natural gas hydrates containing hydrocarbons, CO₂, and N₂ molecules were studied by using computational quantum chemistry methods via the density functional theory approach. All host cages involved in I, II, and H types structures where filled with hydrocarbons up to pentanes, CO₂ and N₂ molecules, depending on their size, and the structures of these host–guest systems optimized. Structural properties, vibrational spectra, and density of states were analyzed together with results from atoms-in-a-molecule and natural bond orbitals methods. The inclusion of dispersion terms in the used functional plays a vital role for obtaining reliable information, and thus, B97D functional was shown to be useful for these systems. Results showed remarkable interaction energies, not strongly affected by the type of host cage, with molecules tending to be placed at the center of the cavities when host cages and guest molecules cavities are of similar size, but with molecules approaching hexagonal faces for larger cages. Vibrational properties show remarkable features in certain regions, with shiftings rising from host-guest interactions, and useful patterns in the terahertz region rising from water surface vibrations strongly coupled with guest molecules. Likewise, calculations on crystal systems for the I and H types were carried out using a pseudopotential approach combined with Grimme’s method to take account of dispersion.

Theoretical tests of the mechanical protection strategy in protein nanomechanics

We provide theoretical tests of a novel experimental technique to determine mechanostability of proteins based on stretching a mechanically protected protein by single‐molecule force spectroscopy. This technique involves stretching a homogeneous or heterogeneous chain of reference proteins (single‐molecule markers) in which one of them acts as host to the guest protein under study. The guest protein is grafted into the host through genetic engineering. It is expected that unraveling of the host precedes the unraveling of the guest removing ambiguities in the reading of the force‐extension patterns of the guest protein. We study examples of such systems within a coarse‐grained structure‐based model. We consider systems with various ratios of mechanostability for the host and guest molecules and compare them to experimental results involving cohesin I as the guest molecule. For a comparison, we also study the force‐displacement patterns in proteins that are linked in a serial fashion. We find that the mechanostability of the guest is similar to that of the isolated or serially linked protein. We also demonstrate that the ideal configuration of this strategy would be one in which the host is much more mechanostable than the single‐molecule markers. We finally show that it is troublesome to use the highly stable cystine knot proteins as a host to graft a guest in stretching studies because this would involve a cleaving procedure. Proteins 2014; 82:717–726. © 2014 Wiley Periodicals, Inc.     

Stability of a guest protein depends on stability of a host protein in insertional fusion

Insertional fusion between host and guest protein domains has been employed to create multi-domain protein complexes displaying integrated and coupled functionalities. The effects of insertional fusion on the stability of a guest protein are however rather controversial. In the study described here, we examined whether the stability of inserted TEM1 beta-lactamase (BLA), as a guest protein, might be affected by the stability of a maltodextrin-binding protein (MBP), as a host protein. Our results indicate that expression levels and in vitro stability of the BLA domain were significantly higher when inserted into thermophilic MBP from Pyrococcus furiosus (PfMBP) compared to mesophilic MBP from Escherichia coli (EcMBP). Moreover, insertion into PfMBP at selected sites was found to improve thermal stability of the BLA domain without compromise in expression levels and BLA activity. Kinetic stabilization during prolonged thermal denaturation of the BLA domain was not guaranteed by insertion into PfMBP, but rather relied on the insertion sites. Taken together, we provide evidence that (i) the stability of the guest protein depended on the stability of the host protein in insertional fusion and (ii) insertion into PfMBP, at least at selected locations, can serve as a novel method of improving protein thermal stability.     

Concomitant Pseudopolymorphs of 10-Deacetyl Baccatin III

Three new solvates [mono-dimethyl sulfoxide (mono-DMSO), mono-dimethyl acetamide (mono-DMA) and mono-dimethyl formamide (mono-DMF)] of 10-Deacetyl baccatin III, were generated by slow evaporation in DMSO, DMF, and DMSO/DMA (1:1) solvent systems respectively. Two concomitant forms mono-DMSO(a new form) and di-DMSO (a known form) were obtained in the DMSO solvent system. Yet two other concomitant forms mono-DMA (a new form) and di-DMSO (a known form) were obtained in DMSO/DMA (1:1) solvent system. A fourth solvate mono-DMF (a new form) was crystallized in unimolar ratio using DMF as a solvent. These solvates were characterized using powder X-ray diffraction, differential scanning calorimeter, thermogravimetric analysis (TGA), and spectroscopic [¹³C solid-state nuclear magnetic spectroscopy, solution ¹H NMR, and Fourier transform infrared] techniques. The interactions between host and guest molecules were elucitated by single-crystal X-ray diffraction data. In all the cases, guest molecules are connected to the host molecules by O–H···O hydrogen bonds. A remarkable difference in the desolvation onset temperatures of di- and mono-DMSO solvates was observed which was also featured by a corresponding weight loss during TGA analysis.     

C.P.-M.A.S. 13C-N.M.R. study of some solid-state inclusion complexes of cyclomalto-oligosaccharides with para-substituted benzenes

Cross polarisation—magic-angle sample spinning ¹³C-n.m.r. spectral have been measured in the solid state for p-nitrophenol, p-iodophenol, and their inclusion complexes with cyclomaltohexaose, cyclomaltoheptaose, and methylated cyclomaltohexaose. Analysis of the line-shapes of the resonances and the dipolar-dephasing experiments indicate that the guest molecules undergo motion in the host cavities, whereas the host molecules are almost static. The mode and rate of guest motion depend on the size of the cavity.     

Size makes a difference: Chiral recognition in complexes of fenchone with cyclodextrins studied by means of NMR titration

Gibbs energies of complex formation between enantiomers of bicyclic terpenoid, fenchone, and naturally occurring cyclodextrins, βCD and γCD, were determined by means of ¹³C and ¹H nuclear magnetic resonance (NMR) titration data. These results were compared with the corresponding data obtained previously for the diastereomeric fenchone/αCD complexes. The size of the inner cavity of host molecules significantly influences stoichiometry, association constants, and enantiomeric differentiation of the studied complexes. These complementary data allow us to discuss qualitatively the influence of the host size on the guest–host interactions. A method of the simultaneous use of titration data collected for several resonances of different isotopes in the determination of association constants was worked out and thoroughly analyzed. Comparison of the results of global data analyses with weighted means of individual ones revealed that both these approaches are equally trustworthy.