Diastereomeric Xe chemical shifts in tethered cryptophane cages

Cryptophane cages serve as host molecules to a Xe atom. Functionalization of cryptophane-A has permitted the development of Xe as a biosensor. Synthetic routes used to prepare cryptophanes result in racemic mixtures of the chiral cages. In the preparation of a tethered cryptophane-A cage for biosensor applications, some achiral and chiral substituents such as left-handed amino acids have been used. When the substituent is achiral, the NMR signal of the Xe atom in the functionalized cage in solution is a single isotropic peak, since the Xe shielding tensor components in the R and L cages differ by no more than the signs of the off-diagonal elements. Chiral substituents can split the cage-encapsulated Xe NMR signal into one or more sets of doublets, depending on the number of asymmetric centers in the substituent. We carry out quantum mechanical calculations of Xe nuclear magnetic shielding for the Xe atom at the same strategic position within an L cryptophane-A cage, under the influence of chiral potentials that represent r or l substituents outside the cage. Calculations of the Xe shielding response in the Lr and Ll diastereomeric pairs permit the prediction of the relative order of the Xe chemical shifts in solutions containing the Rl and Ll diastereomers. Where the substituent itself possesses two chiral centers, comparison of the calculated isotropic shielding responses in the Llr, Lrl, Rll, and Lrr systems, respectively, permits the prediction of the Xe spectrum of diastereomeric systems in solutions containing Llr, Rlr, Lll, and Rll systems. Assignment of the peaks observed in the experimental Xe NMR spectra is therefore possible, without having to undertake the difficult synthetic route that produces a single optically pure enantiomer.     

Molecular reorientation dynamics and microscopic friction in liquids

Molecular rotation reorientation times are investigated using time resolved fluorescence depolarization studies of three solutes of similar size and shape (nile red, neutral nile blue and cationic nile blue) dissolved in alcohol and alkane solvents as well as an extensive compilation of previous results for neautral and charged solutes dissolved in non-polar, polar and associated solvents. A universal correlation is foung between reorientation time, solvent viscosity, and solute volume for solutes dissolved in alkanes, while strongly interacting solutes experience relatively enhanced friction, and non-polar solutes dissolved in alcohols experience reduced friction. The results are compared and contrasted with slip and stick hydrodynamic predictions, and used to develop empirical correlations, which can be used to predict molecular reorientation times with an uncetainty on the order of a factor of two in virtually any solute-solvent system.     

Interpreting protein structural dynamics from NMR chemical shifts

In this investigation, semiempirical NMR chemical shift prediction methods are used to evaluate the dynamically averaged values of backbone chemical shifts obtained from unbiased molecular dynamics (MD) simulations of proteins. MD-averaged chemical shift predictions generally improve agreement with experimental values when compared to predictions made from static X-ray structures. Improved chemical shift predictions result from population-weighted sampling of multiple conformational states and from sampling smaller fluctuations within conformational basins. Improved chemical shift predictions also result from discrete changes to conformations observed in X-ray structures, which may result from crystal contacts, and are not always reflective of conformational dynamics in solution. Chemical shifts are sensitive reporters of fluctuations in backbone and side chain torsional angles, and averaged (1)H chemical shifts are particularly sensitive reporters of fluctuations in aromatic ring positions and geometries of hydrogen bonds. In addition, poor predictions of MD-averaged chemical shifts can identify spurious conformations and motions observed in MD simulations that may result from force field deficiencies or insufficient sampling and can also suggest subsets of conformational space that are more consistent with experimental data. These results suggest that the analysis of dynamically averaged NMR chemical shifts from MD simulations can serve as a powerful approach for characterizing protein motions in atomistic detail.     

The chemical shifts of Xe in the cages of clathrate hydrate Structures I and II

We report, for the first time, a calculation of the isotropic NMR chemical shift of 129Xe in the cages of clathrate hydrates Structures I and II. We generate a shielding surface for Xe in the clathrate cages by quantum mechanical calculations. Subsequently this shielding surface is employed in canonical Monte Carlo simulations to find the average isotropic Xe shielding values in the various cages. For the two types of cages in clathrate hydrate Structure I, we find the intermolecular shielding values [sigma(Xe@5(12) cage)-sigma(Xe atom)]=-214.0 ppm, and [sigma(Xe@5(12)6(2) cage)-sigma(Xe atom)]=-146.9 ppm, in reasonable agreement with the values -242 and -152 ppm, respectively, observed experimentally by Ripmeester and co-workers between 263 and 293 K. For the 5(12) and 5(12)6(4) cages of Structure II we find [sigma(Xe@5(12) cage)-sigma(Xe atom)]=-206.7 ppm, and [sigma(Xe@5(12)6(4) cage)-sigma(Xe atom)]=-104.7 ppm, also in reasonable agreement with the values -225 and -80 ppm, respectively, measured in a Xe-propane type II mixed clathrate hydrate at 77 and 220-240 K by Ripmeester et al.     

Molecular dynamics simulation of dual amino-functionalized imidazolium-based ionic liquids

In this work, the all-atom (AA) force fields were set up for three kinds of dual amino-functionalized imidazolium-based ionic liquids (ILs), composed by cations with different alkyl chain length and amino acid anion [Gly]⁻. The force field was based on our previous work and the default parameters were developed in this study. Molecular dynamics simulations were performed. Validation was carried out by comparing simulation densities with experimental data, and good agreement was obtained. Molar volume and heat capacity at constant pressure were predicted. Mean square displacements for these ILs were computed and these ILs were proved to move very slowly. It may be caused by hydrogen-bonded network between ions and the terminal azyl. To depict the microscopic structures of the ILs, many types of radial distribution functions were investigated. It is interesting to find that not only the cation and anion, but also the anions themselves will form hydrogen bonds.     

Molecular dynamics simulations of the surface tension of ionic liquids

We report molecular dynamics computer simulations of the surface tension and interfacial thickness of ionic liquid-vapor interfaces modeled with a soft core primitive model potential. We find that the surface tension shows an anomalous oscillatory behavior with interfacial area. This observation is discussed in terms of finite size effects introduced by the periodic boundary conditions employed in computer simulations. Otherwise we show that the thickness of the liquid-vapor interface increases with surface area as predicted by the capillary wave theory. Data on the surface tension of size-asymmetric ionic liquids are reported and compared with experimental data of molten salts. Our data suggest that the surface tensions of size-asymmetric ionic liquids do not follow a corresponding states law.     

Molecular structure and dynamics of liquids: aqueous urea solutions

In this review a multi-technical approach to the analysis of the structure and dynamics of the urea/water system is described. The reorientational movement of the solute molecule is investigated by the analysis of spectral band-shapes, as well as with the use of the optical Kerr effect (OKE) and molecular dynamics simulation (MDS). The effect of solute concentration on the structure and dynamics of the aqueous solutions (aggregation, orientational distribution, solvation...) is studied by molecular dynamics simulation and neutron scattering. The results obtained by other techniques are included to provide a critical analysis. Finally, the low-frequency Raman spectra of the system are interpreted on the basis of the semi-quantitative information obtained by molecular dynamics simulation.     

NO in Kr and Xe solids: Molecular dynamics and normal mode analysis

Molecular Dynamics Simulations of the shell dynamics and normal mode analysis (NMA) are carried out to study Rydberg photoexcitation of NO in Xe and Kr solids. In the case of the NO doped Kr system we have completed a previous study on shell dynamics by focusing only on the NMA, however, in the case of the NO doped Xe system we have carried out both studies: shell dynamics and NMA. For this purpose, we have used fitted Lennard–Jones potential parameters for NO(A²Σ⁺)–Kr and NO(A²Σ⁺)–Xe interactions since they have not been reported in literature. These parameters were fitted taking into account the match of simulation results to the available spectroscopic data. The dynamics of the Xe–NO matrix yielded a great dispersion in the trajectories and a slower medium response with respect to Kr–NO matrix. The NMA have allowed us to explain the immediate shell dynamics after photoexcitation, showing the validity of harmonic approximation of potentials. The results are shown comparatively with the rest of the studied matrices (Ar–NO and Ne–NO).     

Molecular dynamics simulation of phase separating binary liquids in cylindrical Couette flow

We use molecular dynamics simulations to study phase separation of a 50:50 (by volume) fluid mixture in a confined and curved (Taylor-Couette) geometry, consisting of two concentric cylinders. The inner cylinder may be rotated to achieve a shear flow. In nonsheared systems we observe that, for all cases under consideration, the final equilibrium state has a stacked structure. Depending on the lowest free energy in the geometry the stack may be either flat, with its normal in the z direction, or curved, with its normal in the r or theta direction. In sheared systems we make several observations. First, when starting from a prearranged stacked structure, we find that sheared gradient and vorticity stacks retain their character for the durations of the simulation, even when another configuration is preferred (as found when starting from a randomly mixed configuration). This slow transition to another configuration is attributed to a large free energy barrier between the two states. In case of stacks with a normal in the gradient direction, we find interesting interfacial waves moving with a prescribed angular velocity in the flow direction. Because such a wave is not observed in simulations with a flat geometry at similar shear rates, the curvature of the wall is an essential ingredient of this phenomenon. Second, when starting from a randomly mixed configuration, stacks are also observed, with an orientation that depends on the applied shear rate. Such transitions to other orientations are similar to observations in microphase separated diblock copolymer melts. At higher shear rates complex patterns emerge, accompanied by deviations from a homogeneous flow profile. The transition from steady stacks to complex patterns takes place around a shear rate 1/tau(dv), where tau(dv) is the crossover time from diffusive to viscous dominated growth of phase-separated domains, as measured in equilibrium simulations.     

Molecular beams and chemical dynamics at surfaces

The use of molecular beams to study chemical dynamics at surfaces is outlined. The techniques is briefly introduced and its applications are given in a few areas. Scattering experiments give detailed information about the first steps toward a chemical reaction at a surface. Beams with enhanced population of specific quantum states make an even more detailed analysis possible. Adsorption at surfaces can be studied very well using beam methods, especially in the case of activated processes. Beams can be used to grow novel structures. Beams allow the study of chemical reactions at surfaces, and in particular those where product are directly ejected into the gas phase, or where reactions take place upon impact. Finally the study of liquid surfaces is briefly introduced.     

Molecular potential-energy surfaces for chemical reaction dynamics

This paper reviews the construction of molecular potential-energy surfaces by an interpolation method which has been developed over the last several years. The method uses ab initio quantum chemistry calculations of the molecular electronic energy in an automated procedure to construct global potential- energy surfaces which can be used to simulate chemical reactions with either classical or quantum dynamics. The methodology is explained and several applications are presented to illustrate the approach. Received: 22 February 2002 / Accepted: 2 May 2002 / Published online: 6 November 2002 Correspondence to: M. A. Collins e-mail: collins@rsc.anu.edu.au Acknowledgements. The methods described in this overview are the result of collaborations with former members of my group, in particular with Josef Ischtwan, Meredith Jordon, Keiran Thompson and Ryan Bettens. I am also indebted for inspiration gained from many discussions with my colleagues Leo Radom and Donghui Zhang (National University of Singapore). This work has been supported by the Supercomputer Facility of the Australian National University and the Australian Partnership for Advanced Computing.     

Molecular recognition in molecular tweezers systems: quantum-chemical calculation of NMR chemical shifts

Quantum-chemical calculations for molecular tweezers systems are presented, where the focus is not only on the recognition process in the host-guest systems, but on the self aggregation of the tweezers host as well. Such intermolecular interactions influence the corresponding NMR spectra strongly by up to 6 ppm for proton chemical shifts, since ring-current effects are particularly important. The quantum-chemical results allow one to reliably assign the spectra and to gain information both on the structure and on the importance of intra- and intermolecular interactions. In addition, we study the accuracy of a variety of density functionals for describing the present host-guest systems, where we observe a considerable underestimation of ring-current effects on (1)H NMR chemical shifts at the density functional theory (DFT) level using smaller basis sets such as 6-31G**, so that larger bases like TZP are required. This stands in contrast to the behavior of the Hartree-Fock scheme, where small basis sets, such as 6-31G**, provide reliable (1)H NMR shieldings for molecular tweezers systems.     

Molecular dynamics and quantum chemical studies on nitroglycerine

A constant temperature molecular dynamics study has been performed on PM3 (RHF) geometry optimized nitroglycerine molecule. The dynamics was carried out by using MM+ method at 550 K which is above the explosion point of nitroglycerine. Some molecular orbital characteristics of nitroglycerine at elevated temperatures were computed.     

Molecular orbital calculation of Al and Mg Kα chemical shifts

The octahedral and tetrahedral coordination shifts of Mg and Al Kα were systematically measured using a high resolution spectrometer. To explain these shifts, we applied SCC-DV-Xα molecular orbital calculation to several cluster models. The results of the calculations agreed well with the observed shifts. The possibility of determining coordination by Mg or Al Kα shifts is confirmed after parameter survey of atomic distance.     

新型二肽类长链状化合物的分子动力学和量子化学研究

用分子动力学方法对5种新型肽类长链状化合物进行了构象研究,所得结果证明我们的构象搜索方法有效。分子L~3内的芳环堆积作用使整个分子具有特殊结构,这种结构特征可能使其具有特殊生物功能,该结果为药物分子设计提供了有用的信息。量子化学计算表明分子内形成的负电荷空穴,将使其易与受体结合。     

Frequency shifts of piezoelectric quartz crystals immersed in organic liquids

A piezoelectric quartz crystal oscillates in organic liquids. The frequency change (ΔF) depends on the density (d) and viscosity (η) according to ΔF = ad^1/2 + bη^1/2 — c, where a, b and c, are constants depending on the crystal.     

31P chemical shifts in N-aryliminotriphenylphosphoranes

³¹P chemical shifts in N-aryliminotriphenylphosphoranes and the corresponding N-methylated phosphonium salts are presented. They can be correlated with those theories of the bonding in phosphorus-nitrogen ylides which involve partial double bonding as a result of p^π–d^π overlap.