A theoretical study of the cohesion of noble gases on graphite

The interactions of the noble gases with a graphene sheet are investigated theoretically. The short range repulsive interaction between the noble gas and each carbon atom is described using Hartree-Fock atomic densities and a local density functional theory with the exchange functional corrected for the finite range of the interaction by introducing a Rae-type correction depending on the effective number of electrons. The long range interactions are introduced as the sum of the Axilrod-Teller triple-dipole interaction plus the dipole-dipole and dipole-quadrupole dispersive attractions damped according to the theory of Jacobi and Csanak. The energy arising from the interactions between the permanent quadrupoles on the carbon atoms with the dipole they induce on the noble gas is negligible, being nonzero only on account of the atomistic structure of graphene. The mobile and delocalized nature of the graphene pi electrons causes the effective number of electrons to be around 500 rather than that of 12 appropriate for a system of entirely localized interactions with individual carbon atoms. Inclusion of the Axilrod-Teller term is required to obtain reliable predictions for the binding energies and equilibrium geometries. Absorption of a noble gas atom is predicted to occur at the site above the center of a six membered ring although this is preferred over two other sites by only about 5 meV. The methods presented for generating all the potentials can be applied to derive the interactions between any ion and carbon atom in the wall of a single-walled nanotube. Knowledge of these interactions is required to study the alkali halide nanocrystals encapsulated in single-walled carbon nanotubes of current interest.     

The effect of atomic and extra-atomic relaxation on atomic binding energies

An equivalent-cores-relaxation model is given for calculating atomic binding energies from orbital energies using only ground-state atomic properties. The agreement with experiment is excellent for the noble gases. On the basis of present knowledge of atomic relaxation, the phenomenon of “extra-atomic relaxation”, in which electronic charge is attracted toward a hole-state atom, is shown to have an important effect in lowering atomic core-level binding energies in condensed phases. This will affect the interpretation of most core-level binding energies measured to date.     

Phase-shift studies of the imprisonment lifetime of cadmium(5 3P1) and the effect of the addition of noble gases

The imprisonment lifetime of Cd³P₁), measured by a phase-shift method was found to depend on the modulation frequency at 534 K. This frequency dependence is considered to correspond to the non-exponential decay after a pulsed excitation, and was analyzed on the basis of Milne's diffusion theory. The effect of the addition of noble gases was also examined, and it was found that noble gases scarcely deactivate the Cd(³P₁) atoms at 458 K.     

NMR spectroscopic study of noble gas binding into the engineered cavity of HPr(I14A) from Staphylococcus carnosus

Xenon binding into preexisting cavities in proteins is a well-known phenomenon. Here we investigate the interaction of helium, neon, and argon with hydrophobic cavities in proteins by NMR spectroscopy. 1H and 15N chemical shifts of the I14A mutant of the histidine-containing phosphocarrier protein (HPr(I14A)) from Staphylococcus carnosus are analyzed by chemical shift mapping. Total noble gas induced chemical shifts, Delta, are calculated and compared with the corresponding values obtained using xenon as a probe atom. This comparison reveals that the same cavity is detected with both argon and xenon. Measurements using the smaller noble gases helium and neon as probe atoms do not result in comparable effects. The dependence of amide proton and nitrogen chemical shifts on the argon concentration is investigated in the range from 10 mM up to 158 mM. The average dissociation constant for argon binding into the engineered cavity is determined to be about 90 mM.     

CO2加氢合成甲醇催化反应中CO的作用

研究了铜基催化剂上CO₂加氢合成甲醇反应中掺人CO的作用,结果表明,在原料中添加少量CO,甲醇的选择性提高38%,收率提高25%;TPD-MS和TPSR-MS结果表明,CO能抑制催化剂表面起逆水汽变换作用的活性位对CO₂的吸附,从而提高了CO₂加氢合成甲醇的选抒性.     

Molecularly imprinted polyethersulfone microspheres for the binding and recognition of bisphenol A

BPA-imprinted polyethersulfone (PES) microspheres for the binding and recognition of bisphenol A (BPA) were fabricated by means of a liquid-liquid phase separation technique. The imprinted novel PES microspheres had a porous structure with a skin layer, under which was followed by a finger-like structure. The recognition experiments with the BPA-imprinted microspheres were carried out by applying the microspheres to various BPA solutions. In water, high binding amounts of BPA were observed in the range of 19-42 μmol/g capacity, but the recognition was low in the BPA water solution. With the increase of the concentration in BPA solution, the binding amounts and the recognition coefficient increased. However, 1,4-butylene glycol/water media showed high recognition of the imprinted microspheres with a low binding capacity of BPA. In addtion, with the increase of the BPA amounts in the PES solution used to prepare the imprinted microspheres, the specific recognition sites increased, and the recognition ability increased. Evidence revealed that microsphere recognition was effective for BPA due to the binding to specific recognition sites [S]_(sites). The imprinted microspheres showed the selectivity for BPA in the wine including BPA and other organic compounds. Charge transfer and special cavities could be employed to explain the mechanism.     

The binding selectivity of ADAR2's dsRBMs contributes to RNA-editing selectivity

ADAR2 is an RNA editing enzyme that deaminates adenosines in certain duplex structures. Here, we describe the role of its RNA binding domain, consisting of two copies of a common dsRNA binding motif (dsRBM), in editing site selectivity. ADAR2's dsRBMs bind selectively on a duplex RNA that mimics the Q/R editing site in the glutamate receptor B-subunit pre-mRNA. This selectivity is different from that of PKR's dsRBM I, indicating that dsRBMs from different proteins possess intrinsic binding selectivity. Using directed hydroxyl radical cleavage data, molecular models were developed that predict important recognition surfaces on the RNA for identified dsRBM binding sites. Blocking these surfaces by benzyl modification of guanosine 2-amino groups impeded RNA-editing, demonstrating a correlation between deamination efficiency by ADAR2 and selective binding by its dsRBMs. In addition, the editing activity of a mutant of ADAR2 lacking dsRBM I on N(2)-benzylguanosine-modified RNA suggests the location of the dsRBM I binding site that leads to editing at the GluR-B Q/R site.     

Molecularly imprinted hydrogel displaying reduced non‐specific binding and improved protein recognition

A novel approach for enhancing protein recognition in molecularly imprinted hydrogel (MIH) is presented. This approach was developed based on the hypothesis that the number of specific binding sites created in the previously described MIH is very small, thus attempts to enhance the capacity result in most cases in additional non‐specific binding and loss of selectivity. Thus, blocking the non‐specific binding sites could lead to higher capacities and better selectivity. To test this hypothesis, MIH interpenetrating networks designed to block non‐specific binding sites were synthesized using two separate stages of polymerization. Re‐binding of the template protein (lysozyme) and a competitor protein (cytochrome C) was measured, and the results were compared with the similar experiment performed using a control non‐imprinted hydrogel and a “conventional” MIH. The imprinting efficacy of the MIH interpenetrating network was found to be much higher than that of the controls. Furthermore, competitive adsorption assays have demonstrated the superiority of the new formulation.     

The response of a flame ionisation detector to pulses of noble gases in a gas chromatograph

Summary It has been confirmed that pulses of noble gases injected into the nitrogen carrier gas in a gas chromatograph produce responses from a flame ionisation detector. The responses are caused by a dual perturbation of the ‘blank’ signal resulting from trace impurities in the nitrogen. One type of perturbation is explicable from the theory of vacancy chromatography whilst the other, it is suggested, results from the influence of the noble gas on the net rate of production of charge carriers in the flame. This latter response can be used for gas hold up time measurements.     

Identification of strong DNA binding motifs for bleomycin

The bleomycins (BLMs) are clinically used antitumor antibiotics. Their mechanism of action is believed to involve oxidative cleavage of DNA and possibly also RNA degradation. DNA degradation has been studied extensively and shown to involve binding of an activated metallobleomycin to DNA, followed by abstraction of C4'-H from deoxyribose in the rate-limiting step for DNA degradation. It is interesting that while DNA and RNA degradation by activated Fe.BLM has been studied extensively, much less is known about the actual binding selectivity of BLM, that is, the obligatory step that precedes cleavage. Thus it is unclear whether cleavage specificity is defined by the binding event or whether cleavage occurs at a subset of preferred binding sites. With only a few exceptions, NMR binding studies have employed metalloBLMs such as Co.BLM and Zn.BLM whose therapeutic relevance is uncertain. A single biochemical study that compared DNA binding and cleavage directly also employed Co.BLM. It is logical to anticipate that preferred sites of DNA cleavage will occur at sites that are (a subset of) preferred DNA binding sites, but there are currently no data available relevant to this issue. Herein, we describe the development and implementation of a novel strategy to identify DNA motifs that bind BLM strongly.     

Synthetic creatinine receptor: imprinting of a Lewis acidic zinc(II)cyclen binding site to shape its molecular recognition selectivity

Molecularly imprinted polymers (MIPs) from polymerizable Lewis acidic zinc(II)cyclen complexes and ethylene glycol dimethyl acrylate have been prepared. For the imprinting process the template molecule creatinine is reversibly coordinated to the zinc atom. The high strength of this interaction allows analyte binding to the MIP from aqueous solution with high affinity. Its pH dependence is used for controlled guest release with nearly quantitative analyte recovery rate. The binding capacity and selectivity profile of the MIP remains constant through several pH controlled binding and release cycles. MIPs missing a suitable metal binding site showed no significant affinity for thymine or creatinine. Flavin adsorbs nonspecifically to all polymers. The imprinting process reverses the binding selectivity of zinc(II)cyclen for creatinine and thymine from 1:34 in homogeneous solution to 3.5:1 in the MIP. Scatchard plot analysis of creatinine binding isotherms reveals uniform binding of the imprint, with fits indicating a one-site model; however, similar analysis for thymine indicate high and low affinity sites. This corresponds to unrestricted coordination sites freely accessible for thymine, e.g., at the polymer surface, and misshaped imprinted sites, which still can accommodate thymine. More than 50% of all binding sites exclusively bind creatinine and are not accessible to thymine. The binding properties of a copolymer of polymerizable zinc(II)cyclen and ethylene glycol dimethyl acrylate missing the creatinine template, which match the binding selectivity of the complex in solution, confirm that the origin of altered selectivities is the imprinting process. With binding ability at physiological pH, the MIPs are applicable for tasks in medicinal diagnostics or biotechnology. Imprinted zinc(II)cyclen complexes provide, like a metalloenzyme binding motif, high binding affinity by reversible coordination while the surrounding macromolecule determines binding selectivity.     

The roles of template complexation and ligand binding conditions on recognition in bupivacaine molecularly imprinted polymers

A model for the molecular basis for ligand recognition in bupivacaine imprinted methacrylic acid-ethylene glycol dimethacrylate co-polymers has been developed based upon a series of (1)H-NMR studies in conjunction with HPLC and radioligand binding analyses. (1)H-NMR studies indicated that functional monomer-template complexes survive the polymerisation process, at least up until the stage of gelation. Polymers were synthesised and characterised by surface area analysis (BET), FT-IR and SEM. A combination of zonal and frontal chromatographic studies in aqueous and non-polar media indicate that selectivity arises from a combination of hydrophobic and electrostatic interactions. However, in the concentration regime employed for LC-based studies, ligand recognition in aqueous media was shown to be predominantly non-specific and hydrophobic in character. Radioligand binding studies, in lower ligand binding concentration regimes, permitted closer examination of the higher affinity binding sites. It was shown that the presence of a polar modifier in a non-polar solvent, or an organic modifier in water, produced enhanced selectivity. Variable temperature studies showed that the temperature of binding influences selectivity as well as the apparent number of sites available and that this effect is different in organic and aqueous environments. This indicates that the system studied is more complex in character than is generally appreciated. A comparison of the techniques employed here indicates that although chromatographic studies provide a valuable first-round screen for polymer-ligand selectivities, the level of detail obtainable using radioligand binding studies (lower concentrations and true equilibrium binding) makes them superior for detailed evaluations of molecularly imprinted polymers.     

On the contribution of vibrational anharmonicity to the binding energies of water clusters

The second-order vibrational perturbation theory method has been used together with the B3LYP and MP2 electronic structure methods to investigate the effects of anharmonicity on the vibrational zero-point energy (ZPE) contributions to the binding energies of (H2O)n, n = 2-6, clusters. For the low-lying isomers of (H2O)6, the anharmonicity correction to the binding energy is calculated to range from -248 to -355 cm(-1). It is also demonstrated that although high-order electron correlation effects are important for the individual vibrational frequencies, they are relatively unimportant for the net ZPE contributions to the binding energies of water clusters.     

Quantitative description of the hydrophobic effect: the enthalpic contribution

A new method of experimental determination of the hydrophobic effect enthalpy is proposed. The method is based on regarding the hydration enthalpy as the sum of the nonspecific hydration enthalpy, specific hydration enthalpy, and the hydrophobic effect enthalpy. The hydrophobic effect enthalpies of noble and simple substance gases, alkanes, arenes, and normal aliphatic alcohols are determined. For the noble gases and alkanes, the hydrophobic effect enthalpy is found to be negative and independent of the size of molecule. For aromatic hydrocarbons, it is positive and grows up with the size of the hydrocarbon. The hydrophobic effect enthalpies of normal aliphatic alcohols are determined by assuming that the specific interaction enthalpies of alcohols in water and in methanol are equal. The hydrophobic effect enthalpy values for the aliphatic alcohols (-10.0 +/- 0.9 kJ.mol(-1)) were found to be close to the alkanes hydrophobic effect enthalpies (-10.7 +/- 1.5 kJ.mol(-1)).     

The use of ESI-MS to probe the binding of divalent cations to calmodulin

Proteins have evolved with distinct sites for binding particular metal ions. This allows metalloproteins to perform a myriad of specialized tasks with conformations tailor-made by the combination of its primary sequence and the effect on this of the ligated metal ion. Here we investigate the selectivity of the calcium trigger protein calmodulin for divalent metal ions. This ubiquitous and highly abundant protein exists in equilibrium between its apo and its holo form wherein four calcium ions are bound. Amongst its many functions, calmodulin modulates the calcium concentration present in cells, but this functional property renders it a target for competition from other metal ions. We study the competition posed by four other divalent cations for the calcium binding sites in calmodulin using electrospray ionization mass spectrometry (ESI-MS). We have chosen two other group II cations Mg²⁺, Sr²⁺, and two heavy metals Cd²⁺, Pb²⁺. The ease with which each of these metals binds to apo and to holo CaM[4Ca] is described. We find that each metal ion has different properties with respect to calmodulin binding and competition with calcium. The order of affinity for apo CaM is Ca²⁺ ≫ Sr²⁺ ∼ Mg²⁺ > Pb²⁺ ∼ Cd²⁺. In the presence of calcium the affinity alters to Pb²⁺ > Ca²⁺ > Cd²⁺ > Sr²⁺ > Mg²⁺. Once complexes have been formed between the metal ions and protein (CaM:[xM]) we investigate whether the structural change which must accompanies calcium ligation to allow target binding takes place for a given CaM:[xM] system. We use a 20 residue target peptide, which forms the CaM binding site within the enzyme neuronal nitric-oxide synthase. Our earlier work (Shirran et al. 2005) [1] has demonstrated the particular selectivity of this system for CaM:4Ca²⁺. We find that along with Ca²⁺ only Pb²⁺ forms complexes of the form CaM:4M²⁺:nNOS. This work demonstrates the affinity for calcium above all other metals, but also warns about the ability of lead to replace calcium with apparent ease.     

A molecular dynamics study of chloride binding by the cryptand SC24

The capture of chloride from water by the tetraprotonated form of the spherical macrotricyclic molecule SC24 was studied using molecular dynamics simulation methods. This model ionophore represents a broad class of molecules which remove ions from water. Two binding sites for the chloride were found, one inside and one outside the ligand. These sites are separated by a potential energy barrier of approximately 20 kcal mol⁻¹. The major contribution to this barrier comes from dehydration of the chloride. The large, unfavorable dehydration effect is compensated for by an increase in electrostatic attraction between the oppositely charged chloride and cryptand, and by energetically favorable rearrangements of water structure. Additional assistance in crossing the barrier and completing the dehydration of the ion is provided by the shift of three positively charged hydrogen atoms of the cryptand towards the chloride. This structural flexibility of the cryptand, leads to a decrease in the energy barrier, whereas, its structural rigidity is partially responsible for its selectivity.     

Cucurbiturils mimicked by low polarizability solvents with pre-formed cavities: an empirical model to predict hydrocarbon selectivity

Relative binding affinities of a series of nine rigid hydrocarbons towards the cavity formed by a portion of the inner wall of cucurbit[8]uril (CB[8]) and a positive auxiliary guest were determined by competitive ¹⁹F NMR titrations in deuterium oxide. The corresponding free binding energies were corrected by the hydrocarbon computed solvation energies to obtain their free energies of transfer from the gas phase to the CB[8]/auxiliary guest cavity. These energies correlate linearly with the hydrocarbon static polarizabilities, thereby suggesting that the selectivity is driven, perhaps exclusively, by dispersive interactions between the hydrocarbons and the tailor-made cavity, regardless of the degree of unsaturation of the guests. The free energies of transfer also correlate linearly with the energy released upon introduction of the hydrocarbon into a pre-formed cavity extruded from a solvent (benzene) selected to mimic the polarity and polarizability of the CB[8]/auxiliary probe cavity – and this, with a unity slope. Among other features, this empirical model also accurately predicts the relative binding affinities of various rigid hydrocarbons to CB[6] and CB[7], as well as noble gases to CB[5], when the macrocycles are mimicked with pre-formed cavities in perfluorohexane or perfluorohexane/benzene mixtures, both being notoriously non-polar and non-polarizable environments.

Mimicking cucurbiturils with low polarizability solvents and pre-formed cavities allows the in silico prediction of their selectivities towards hydrocarbons and noble gases in aqueous solution.     

First-second shell interactions in metal binding sites in proteins: a PDB survey and DFT/CDM calculations

The role of the second shell in the process of metal binding and selectivity in metalloproteins has been elucidated by combining Protein Data Bank (PDB) surveys of Mg, Mn, Ca, and Zn binding sites with density functional theory/continuum dielectric methods (DFT/CDM). Peptide backbone groups were found to be the most common second-shell ligand in Mg, Mn, Ca, and Zn binding sites, followed (in decreasing order) by Asp/Glu, Lys/Arg, Asn/Gln, and Ser/Thr side chains. Aromatic oxygen- or nitrogen-containing side chains (Tyr, His, and Trp) and sulfur-containing side chains (Cys and Met) are seldom found in the second coordination layer. The backbone and Asn/Gln side chain are ubiquitous in the metal second coordination layer as their carbonyl oxygen and amide hydrogen can act as a hydrogen-bond acceptor and donor, respectively, and can therefore partner practically every first-shell ligand. The second most common outer-shell ligand, Asp/Glu, predominantly hydrogen bonds to a metal-bound water or Zn-bound histidine and polarizes the H-O or H-N bond. In certain cases, a second-shell Asp/Glu could affect the protonation state of the metal ligand. It could also energetically stabilize a positively charged metal complex more than a neutral ligand such as the backbone and Asn/Gln side chain. As for the first shell, the second shell is predicted to contribute to the metal selectivity of the binding site by discriminating between metal cations of different ionic radii and coordination geometries. The first-shell-second-shell interaction energies decay rapidly with increasing solvent exposure of the metal binding site. They are less favorable but are of the same order of magnitude as compared to the respective metal-first-shell interaction energies. Altogether, the results indicate that the structure and properties of the second shell are dictated by those of the first layer. The outer shell is apparently designed to stabilize/protect the inner-shell and complement/enhance its properties.     

Calculation of the Viscosity of Simple Fluids Based on the Rainwater‐Friend Theory

Viscosities of noble gases have been calculated over a wide temperature‐pressure range. Simple and accurate Tang‐Toennies potential of the noble gases are used in the Chapman‐Enskog calculation of the zero density viscosity and in the Rainwater‐Friend theory to determine the initial density dependence of the viscosity. At densities beyond the range of the theory (up to 46 mol.dm^?3), a variant of the residual viscosity is developed. A correlation function for the calculation of viscosity over the whole range of density is presented. A comparison of the calculated and experimental values of the viscosity yields an average absolute deviation of 1.5%.