Conformational analysis of methylphenidate: comparison of molecular orbital and molecular mechanics methods

Summary Methylphenidate (MP) binds to the cocaine binding site on the dopamine transporter and inhibits reuptake of dopamine, but does not appear to have the same abuse potential as cocaine. This study, part of a comprehensive effort to identify a drug treatment for cocaine abuse, investigates the effect of choice of calculation technique and of solvent model on the conformational potential energy surface (PES) of MP and a rigid methylphenidate (RMP) analogue which exhibits the same dopamine transporter binding affinity as MP. Conformational analysis was carried out by the AM1 and AM1/SM5.4 semiempirical molecular orbital methods, a molecular mechanics method (Tripos force field with the dielectric set equal to that of vacuum or water) and the HF/6-31G* molecular orbital method in vacuum phase. Although all three methods differ somewhat in the local details of the PES, the general trends are the same for neutral and protonated MP. In vacuum phase, protonation has a distinctive effect in decreasing the regions of space available to the local conformational minima. Solvent has little effect on the PES of the neutral molecule and tends to stabilize the protonated species. The random search (RS) conformational analysis technique using the Tripos force field was found to be capable of locating the minima found by the molecular orbital methods using systematic grid search. This suggests that the RS/Tripos force field/vacuum phase protocol is a reasonable choice for locating the local minima of MP. However, the Tripos force field gave significantly larger phenyl ring rotational barriers than the molecular orbital methods for MP and RMP. For both the neutral and protonated cases, all three methods found the phenyl ring rotational barriers for the RMP conformers/invertamers (denoted as cte, tte, and cta) to be: cte, tte> MP > cta. Solvation has negligible effect on the phenyl ring rotational barrier of RMP. The B3LYP/6-31G* density functional method was used to calculate the phenyl ring rotational barrier for neutral MP and gave results very similar to those of the HF/6-31G* method.     

Cu(II) in liquid ammonia: an approach by hybrid quantum-mechanical/molecular-mechanical molecular dynamics simulation.

To investigate the solvation structure of the Cu(II) ion in liquid ammonia, ab initio quantum-mechanical/molecular-mechanical (QM/MM) molecular dynamics (MD) simulations were carried out at Hartree Fock (HF) and hybrid density functional theory (B3 LYP) levels. A sixfold-coordinated species was found to be predominant in the HF case whereas five- and sixfold-coordinated complexes were obtained in a ratio 2:1 from the B3 LYP simulation. In contrast to hydrated Cu(II), which exhibits a typical Jahn-Teller distortion, the geometrical arrangement of ligand molecules in the case of ammonia can be described as a [2 + 4] ([2 + 3]) configuration with 4 (3) elongated copper-nitrogen bonds. First shell solvent exchange reactions at picosecond rate took place in both HF and B3 LYP simulations, again in contrast to the more stable sixfold-coordinated hydrate. NH3 ligands apparently lead to strongly accelerated dynamics of the Cu(II) solvate due to the "inverse" [2 + 4] structure with its larger number of elongated copper-ligand bonds. Several dynamical properties, such as mean ligand residence times or ion-ligand stretching frequencies, prove the high lability of the solvated complex.     

Partitioning behaviour of organic compounds between ionic liquids and supercritical fluids

Applications and prospects of two-phase, tuneable solvent systems composed of ionic liquids (ILs) and supercritical fluids with an emphasis on supercritical carbon dioxide (scCO(2)) are reviewed. The IL-scCO(2) biphasic systems have increasingly been used in diverse fields of chemistry and technology, and some examples of these applications are mentioned here. Rational design of such applications can obviously benefit from pertinent data on phase equilibria including the partition coefficients of the prospective products and reactants between the two phases. Therefore, a reliable technique to measure the limiting partition coefficients would be of value. Here, the pros and cons of supercritical fluid chromatography in this respect are discussed. An overview of methods for predictive thermodynamic modelling of binary (IL-scCO(2)) and ternary (solute-IL-scCO(2)) systems is also included.     

基于分子动力学模拟和连续介质模型的自由能计算方法*

近些年,基于分子动力学模拟和连续介质模型的自由能计算方法受到了越来越多的关注,其中MM/PBSA就是最具代表性的方法.在MM/PBSA中,体系的焓变采用分子力学(MM)的方法计算得到;溶剂效应中极性部分对自由能的贡献通过解Poisson-Boltzmann(PB)方程的方法计算得到;溶液效应中非极性部分对自由能的贡献则通过分子表面积(SA)计算得到.本文结合我们科研组的工作,就近几年MM/PBSA方法的最新进展做了较为详细的阐述,同时对MM/PBSA的发展前景进行了展望.     

The effect of hydration on the photo-deactivation pathways of 4-aminopyrimidine

The influence of water on the photo-deactivation process of 4-aminopyrimidine has been investigated by means of microsolvation and continuum solvation models. Two- and four-water models were used for the former purpose. Vertical excitations, stationary points on the first excited singlet surface, conical intersections (minima on the crossing seam) and reaction paths have been investigated at the state-averaged complete active space self-consistent field (CASSCF) and multistate CAS perturbation theory to second order (MS-CASPT2) levels of theory. A destabilizing effect of 0.2–0.3 eV has been observed for nπ∗ states while the ππ∗ state is almost unaffected. The two-water model gives already a good representation of hydration effects, especially when combined with the continuum model. A small enhancement of energy barriers (∼0.1 eV) is observed leading to the conclusion that the photodynamics of 4-aminopyrimidine should be affected only little by these solvent effects.     

Characterization of Ascentis RP-Amide column: Lipophilicity measurement and linear solvation energy relationships

This study investigates lipophilicity determination by chromatographic measurements using the polar embedded Ascentis RP-Amide stationary phase. As a new generation of amide-functionalized silica stationary phase, the Ascentis RP-Amide column is evaluated as a possible substitution to the n  -octanol/water partitioning system for lipophilicity measurements. For this evaluation, extrapolated retention factors, log k^′_w$\text{log}{k^{\prime }}_w$, of a set of diverse compounds were determined using different methanol contents in the mobile phase. The use of n-octanol enriched mobile phase enhances the relationship between the slope (S  ) of the extrapolation lines and the extrapolated log k^′_w$\text{log}{k^{\prime }}_w$ (the intercept of the extrapolation), as well as the correlation between log P   values and the extrapolated log k^′_w$\text{log}{k^{\prime }}_w$ (1:1 correlation, r² = 0.966). In addition, the use of isocratic retention factors, at 40% methanol in the mobile phase, provides a rapid tool for lipophilicity determination. The intermolecular interactions that contribute to the retention process in the Ascentis RP-Amide phase are characterized using the solvation parameter model of Abraham. The LSER system constants for the column are very similar to the LSER constants of the n-octanol/water extraction system. Tanaka radar plots are used for quick visual comparison of the system constants of the Ascentis RP-Amide column and the n-octanol/water extraction system. The results all indicate that the Ascentis RP-Amide stationary phase can provide reliable lipophilic data.     

Binary mixed micelles of chiral sodium undecenyl leucinate and achiral sodium undecenyl sulfate: I. Characterization and application as pseudostationary phases in micellar electrokinetic chromatography

Sodium 10-undecenyl sulfate (SUS), sodium 10-undecenyl leucinate (SUL) and their five different mixed micelles at varied percent mole ratios were prepared. The critical micelle concentration (CMC), C₂₀, γ_CMC, partial specific volume, methylene group selectivity, mobilities and elution window were determined using a variety of analytical techniques. These surfactant systems were then evaluated as novel pseudostationary phases in micellar electrokinetic chromatography (MEKC). As a commonly used pseudostationary phase in MEKC, sodium dodecyl sulfate (SDS) was also evaluated. The CMC values of SUS and SUL were found to be 26 and 16 mM, respectively, whereas the CMC of mixed surfactants was found to be very similar to that of SUL. The C₂₀ values decreased dramatically as the concentration of SUL is increased in the mixed micelle. An increase in SUL content gradually increased the methylene group selectivity making the binary mixed surfactants more hydrophobic. Linear solvation energy relationships (LSERs) and free energy of transfer studies were also applied to predict the selectivity differences between the surfactant systems. The cohesiveness and the hydrogen bond acidic character of the surfactant systems were found to have the most significant influence on selectivity and MEKC retention. The SUS and SDS showed the strongest while SUL showed the weakest hydrogen bond donating capacity. The basicity, interaction with n and π-electrons of the solute and dipolarity/polarizability were the least significant factors in LSER model for the surfactant systems studied. Free energies of transfer of selected functional groups in each surfactant systems were also calculated and found to be in good agreement with the LSER data.     

Highly selective GC stationary phases consisting of binary mixtures of polymeric ionic liquids

GC stationary phases composed of binary mixtures of two polymeric ionic liquids (PILs), namely, poly(1‐vinyl‐3‐hexylimidazolium) bis[(trifluoromethyl)sulfonyl]imide (poly(ViHIm‐NTf₂))/poly(1‐vinyl‐3‐hexylimidazolium) chloride (poly(ViHIm‐Cl)) and poly(1‐vinyl‐3‐hexadecylimidazolium) bis[(trifluoromethyl)sulfonyl]imide (poly(ViHDIm‐NTf₂))/poly(1‐vinyl‐3‐hexadecylimidazolium) chloride (poly(ViHDIm‐Cl)), were evaluated in terms of their on‐set bleed temperature and separation selectivity. A total of six neat or binary PIL stationary phases were characterized using the solvation parameter model to investigate the effects of the polymeric cation and anion and PIL composition on the system constants of the resulting stationary phases. The hydrogen bond basicity of the mixed poly(ViHIm‐NTf₂)/poly(ViHIm‐Cl) stationary phases was enriched linearly with the increase in the poly(ViHIm‐Cl) content. Results revealed that tuning the composition of the stationary phase allowed for fine control of the retention factors and separation selectivity for alcohols and carboxylic acids as well as selected ketones, aldehydes, and aromatic compounds. A reversal of elution order was observed for particular classes of analytes when the weight percentage of the chloride‐based PIL was increased.