Competition STD NMR for the detection of high-affinity ligands and NMR-based screening

The reported competition STD NMR method combines saturation transfer difference (STD) NMR with competition binding experiments to allow the detection of high-affinity ligands that undergo slow chemical exchange on the NMR time-scale. With this technique, the presence of a competing high-affinity ligand in the compound mixture can be detected by the disappearance or reduction of the STD signals of a low-affinity indicator ligand. This is demonstrated on a BACE1 (beta-site amyloid precursor protein cleaving enzyme 1) protein-inhibitor system. This method can also be used to derive an approximate value, or a lower limit, for the dissociation constant of the potential ligand based on the reduction of the signal intensity of the STD indicator, which is illustrated on an HSA (human serum albumin) model system. This leads to important applications of the competition STD NMR method for lead discovery: it can be used (i) for compound library screening against a broad range of drug targets to identify both high- and low-affinity ligands and (ii) to rank order analogs rapidly and derive structure-activity relationships, which are used to optimize these NMR hits into viable drug leads.     

Towards Single-component Molecular Conductor [Ni(dmit)_2] by Charge Disproportionation:2[Ni(dmit)_2]~(-0.5)[Ni(dmit)_2]+[Ni(dmit)_2]~-

It was commonly thought that a molecular conductor or semiconductor should be composed of at least two components to make the conducting component in partially charged state. However, this idea became questionable by the recent report of the single-component molecular conductor [Ni(tmdt)2]1 as well as several reports about single-component molecular semiconductors such as [Ni(ptdt)2]2 and [Ni(C10H10S8)2]3. In fact, as early as 1985, [Ni(dmit)2] as a by-product in synthesizing TTF[Ni(dmit…     

Methodology for the calculation of the potential of mean force for a cation-pi complex in water.

We report potential of mean force (PMF) calculations on the interaction between the p-sulfonatocalix[4]arene and a monovalent cation (Cs(+)). It has been recently shown from microcalorimetry and (133)Cs NMR experiments that the association with Cs(+) is governed by favourable cation-pi interactions and is characterized by the insertion of the cation into the cavity of the macrocycle. We show that the PMF calculation based upon a classical model is not able to reproduce both the thermodynamic properties of association and the insertion of the cation. In order to take into account the different contributions of the cation-pi interactions, we develop a new methodology consisting of changing the standard PMF by an additional contribution resulting from quantum calculations. The calculated thermodynamic properties of association are thus in line with the microcalorimetry and (133)Cs NMR experiments and the structure of the complex at the Gibbs free-energy minimum shows the insertion of the cation into the cavity of the calixarene.     

Chemical deposition of semiconducting cadmium selenide quantum dots in thin film form and investigation of their optical and electrical properties

Cadmium selenide quantum dots with cubic crystal structure are chemically deposited in thin film form using selenosulfate as a precursor for selenide ions and ammonia buffer with double role: as a ligand and as a pH value controller. The optical band gap energies of as-deposited and thermally treated cadmium selenide thin films, calculated within the framework of parabolic approximation for the dispersion relation, on the basis of equations which arise from the Fermi's golden rule for electronic transitions from valence to conduction band, are 2.08 and 1.77 eV, correspondingly. The blue shift of band gap energy of 0.34 eV for as-deposited thin films with respect to the bulk value is due to the quantum size effects (i.e., nanocrystals behave as quantum dots) and this finding is in agreement with the theoretical predictions. During the thermal treatment the nanocrystals are sintered, the increase of crystal size being in correlation with the decrease of band gap energy. The annealed thin films are practically non-quantized. From the resistance-temperature measurements, on the basis of the dependence of ln(R/Ω) vs 1/T in the region of intrinsic conduction, the thermal band gap energy (at 0 K) of 1.85 eV was calculated.     

A new enzyme model for enantioselective esterases based on molecularly imprinted polymers

An efficient enzyme model exhibiting enantioselective esterase activity was prepared by using molecular imprinting techniques. The enantiomerically pure phosphonic monoesters 4 L and 5 L were synthesized as stable transition-state analogues. They were used as templates connected by stoichiometric noncovalent interactions to two equivalents of the amidinium binding site monomer 1. After polymerization and removal of the template, the polymers were efficient catalysts for the hydrolysis of certain nonactivated amino acid phenylesters (2 L, 2 D, 3 L, 3 D) depending on the template used. Imprinted catalyst IP4 (imprinted with 4 L) enhanced the hydrolysis of the corresponding substrate 2 L by a factor of 325 relative to that of a buffered solution. Relative to a control polymer containing the same functionalities, prepared without template 4 L, the enhancement was still about 80-fold, showing the highest imprinting effect up to now. In cross-selectivity experiments a strong substrate selectivity of higher than three was found despite small differences in the structure of the substrate and template. Plots of initial velocities of the hydrolysis versus substrate concentration showed typical Michaelis-Menten kinetics with saturation behavior. From these curves, the Michaelis constant K(M) and the catalytic constant k(cat) can be calculated. The enantioselectivity shown in these values is most interesting. The ratio of the catalytic efficiency k(cat)/K(M), between the hydrolysis of 2 L- and 2 D-substrate with IP4, is 1.65. This enantioselectivity derives from both selective binding of the substrate (K(M)L/K(M)D=0.82), and from selective formation of the transition state (k(cat)L/k(cat)D=1.36). Thus, these catalysts give good catalysis as well as high imprinting and substrate selectivity. Strong competitive inhibition is caused by the template used in imprinting. This behavior is also quite similar to the behavior of natural enzymes, for which these catalysts are good models.     

Molecular Reorientational Dynamics of the Neat Ionic Liquid 1‐Butyl‐3‐methylimidazolium Hexafluorophosphate by Measurement of 13C Nuclear Magnetic Relaxation Data

The reorientational dynamics of the ionic liquid 1butyl‐3‐methylimidazolium hexafluorophosphate ([BMIM]PF₆) were studied over a wide range of temperatures by measurement of ¹³C spin–lattice relaxation rates and NOE factors. The reorientational dynamics were evaluated by performing fits to the experimental relaxation data. Thus, the overall reorientational motion was described by a Cole–Davidson spectral density with a Vogel–Fulcher–Tammann temperature dependence of the correlation times. The reorientational motion of the butyl chain was modelled by a combination of the latter model for the overall motion with a Bloembergen–Purcell–Pound spectral density and an Arrhenius temperature dependence for the internal motion. Except for C2 in the aromatic ring, an additional reduction of the spectral density by the Lipari–Szabo model had to be employed. This reduction is a consequence of fast molecular motions before the rotational diffusion process becomes effective. The C2 atom did not exhibit this reduction, because the librational motion of the corresponding C2? H vector is severely hindered due to hydrogen bonding with the hexafluorophosphate anion. The observed dynamic features of the [BMIM]⁺ cation confirm quantum‐chemical structures obtained in a former study.     

Intramolecular Dynamics and Molecular Structure of Europium(III) Chelate Complexes with Crown Ethers as Studied by NMR Spectroscopy

Earlier the intramolecular inversion of the 18-crown-6 molecules was found in the complex ion pairs [Ln(ptfa)₂ (18-crown-6)]⁺ [Ln(ptfa)₄]⁻ (H₂O)₄ where Ln = La(1), Ce (2), Pr (3), Nd (4), and ptfa is 1,1,1-trifluoro-5,5-dimethyl-2,4-hexanedione. In this work the peculiarities of the molecular structure and dynamics were studied for [Eu(ptfa)₂ (18-crown-6)]⁺ [Eu(ptfa)₄]⁻ (H₂O)₄ (5) by NMR spectroscopy techniques. Through VT-NMR spectra analysis the temperature dependence was obtained for the rate constant. The free energy ΔG^‡(320) of 18-crown-6 ring inversion activation was found to be 65 ± 5 kJ mol⁻¹ for 5 in CDCl₃. This result is comparable with the earlier data [S.P. Babailov and D.A. Mainichev: J. Inclusion Phenom. Macrocyclic Chem. 43, 187–193 (2002)] for complexes 2, 3, 4 in deuterated toluene (ΔG^‡(320)=65 ± 9, 64 ± 9, 64 ± 9 kJ mol⁻¹ respectively). It was found by relaxation NMR spectroscopy that the effective distance between Ln and protons of the crown molecule is 4.5 ± 0.2 Å. The analysis of structural parameters testifies that the crown ether and chelated anions are in the first coordination sphere of a Ln cation. Obtained geometrical parameters show that the complex cations of Eu, Ce and Pr have similar spatial structures.This revised version was published online in July 2005 with a corrected issue number.     

Intramolecular Nonbonded Interactions Between Oxygen and Group VIA Elements: An Ab Initio Molecular Orbital and Density Functional Theory Investigation of the Structures of HX—CH2—COOH (X=S,Se, and Te)

Ab initio molecular orbital and density functional methods have been used to study the potential energy surfaces of the substituted acetic acids HX—CH₂—COOH, where X is one of the Group VIA Chalcophiles S, Se, or Te. The various conformers adopted by these compounds provide information regarding the energetic importance of nonbonded and hydrogen bonding interactions involving oxygen atoms with different hybridizations. Density functional and ab initio molecular orbital methods yield similar structural and energetic trends for these compounds. Calculations show that the structure of the lowest-energy conformer of each of these acids has the X—C—C—O backbone substantially twisted from planarity, similar to that previously observed for the corresponding aldehydes, HX—CH₂—CHO. In the twisted acid structures the shortest distance is within about 0.1 Å of the sum of the X and O van der Waals radii, which reduces overcrowding of the lone pairs of electrons on these atoms. In conformers where the heavy atom backbone is planar, one of the distances is significantly shorter than the sum of the van der Waals radii, and the total molecular energy of these conformers is higher than that of the twisted forms. The variation of X—H vibrational frequencies among conformers reflects the extent of X—H hydrogen bonding, and indicates that formation of this hydrogen bond is not the dominant factor in determining the lowest-energy conformation. When X is oxygen (HO—CH₂—COOH), the lowest-energy conformer is also nonplanar, whereas for the corresponding aldehyde, HO—CH₂—CHO, the lowest-energy conformer is a planar structure with C_S symmetry. The conformational preferences of these simple species provide reference points for inter- and intramolecular interactions in more complex systems of biological interest.