Characterising the geometric diversity of functional groups in chemical databases

Summary We have developed a program, HookSpace, which provides a simplistic approach to assessing the diversity of molecular databases. The spatial relationship between pairs of intramolecular functional groups can be analysed in a variety of ways to provide both qualitative and quantitative measures of diversity. Results are described and contrasted for two commercially available databases and a combinatorial library of benzodiazepam derivatives. HookSpace highlights the main differences in molecular content of these data sets.     

Ab initio calculations on the multipole moments and dipole polarisabilities of the PO molecular ion (XΣ)

The potential energy, dipole, quadrupole and octopole moments and dipole polarisabilities have been calculated at CASSCF level for the ground X¹Σ⁺ state of the PO⁺ molecular ion as a function of internuclear distance. Most of the electrical properties have not previously been calculated and show rapid variations around 5 a.u. due to a perturbation. The calculated vibrational frequency of 1410.4 cm⁻¹ and the integrated IR absorption intensity of 984 cm² mol⁻¹ should lead towards the first observation of the vibrational spectrum.     

修正的分子连接性指数mL用于氯代苯、醇、酯的QSAR/QSRR研究

在分子拓扑理论的基础上,提出了1个改进的连接性指数气^mL并用气研究了氯代苯、醇、酯的正辛醇-水分配系数及气相色谱保留指数,^mL不仅对这些有机化合物有良好的结构选择性,而且与其正辛醇-水分配系数、气相色谱保留指数有良好的相关性;由方程得出的预测值与实验测定值之间能较好地吻合。     

Hierarchical clustering analysis of flexible GBR 12909 dialkyl piperazine and piperidine analogs

Pharmacophore modeling of large, drug-like molecules, such as the dopamine reuptake inhibitor GBR 12909, is complicated by their flexibility. A comprehensive hierarchical clustering study of two GBR 12909 analogs was performed to identify representative conformers for input to three-dimensional quantitative structure–activity relationship studies of closely-related analogs. Two data sets of more than 700 conformers each produced by random search conformational analysis of a piperazine and a piperidine GBR 12909 analog were studied. Several clustering studies were carried out based on different feature sets that include the important pharmacophore elements. The distance maps, the plot of the effective number of clusters versus actual number of clusters, and the novel derived clustering statistic, percentage change in the effective number of clusters, were shown to be useful in determining the appropriate clustering level.Six clusters were chosen for each analog, each representing a different region of the torsional angle space that determines the relative orientation of the pharmacophore elements. Conformers of each cluster that are representative of these regions were identified and compared for each analog. This study illustrates the utility of using hierarchical clustering for the classification of conformers of highly flexible molecules in terms of the three-dimensional spatial orientation of key pharmacophore elements.     

Synthesis and chemical diversity analysis of bicyclo[3.3.1]non-3-en-2-ones

Functionalized bicyclo[3.3.1]non-3-en-2-ones are obtained from commercially available phenols by a hypervalent iodine oxidation, enone epoxidation, epoxide thiolysis, and intramolecular aldol reaction sequence. Reaction optimization studies identified room temperature as well as microwave-mediated procedures, providing moderate to good yields (57-88%) in the thiophenol-mediated epoxide opening and intramolecular aldol reaction. In addition, the isolation of a key intermediate and in situ NMR studies supported the mechanistic hypothesis. The bicyclic ring products occupy novel chemical space according to ChemGPS and Chemaxon chemical diversity and cheminformatics analyses.     

Statistical Investigation into the Structural Complementarity of Natural Products and Synthetic Compounds

The potential of new natural products as an important source for the exploration and development of new drugs and crop protection products is a long way from being exhausted. The statistical analysis of the structures of the natural and synthetically derived compounds has shown conspicuous variations in structural types in the natural products derived from different natural sources, which can be utilized in the search for individual active substances. The occasionally voiced prepossession that natural products have already been sufficiently examined and therefore no more innovations are to be expected can definitely be rejected.     

Theoretical study on the electronic, structural, properties and reactivity of a series of mono-, di-, tri- and tetrafluorothiophenes as monomers for new conducting polymers

Electrical and structural properties of mono-, di-, tri- and tetrafluorothiophenes and their radical cations have been studied using density functional theory and B3LYP method with 6-311++G** basis set. The effects of the number and position of the substituent of fluorine atoms on the properties of the thiophene ring have been studied using optimized structures obtained for these molecules and their radical cations. Vibrational frequencies, spin-density distribution, size and direction of dipole moment vector, ionization potential, electric polarizability, HOMO-LUMO gaps and NICS values of these compounds have been calculated as well. The analysis of these data showed that double bonds in 3-fluorothiophene are more delocalized and it is the best possible candidate monomer among all fluorothiophenes for the synthesis of corresponding conducting polymers with modified characteristics.     

Enhanced detectability of fluorinated derivatives of N,N-dialkylamino alcohols and precursors of nitrogen mustards by gas chromatography coupled to Fourier transform infrared spectroscopy analysis for verification of chemical weapons convention

N,N-Dialkylamino alcohols, N-methyldiethanolamine, N  -ethyldiethanolamine and triethanolamine are the precursors of VX type nerve agents and three different nitrogen mustards respectively. Their detection and identification is of paramount importance for verification analysis of chemical weapons convention. GC–FTIR is used as complimentary technique to GC–MS analysis for identification of these analytes. One constraint of GC–FTIR, its low sensitivity, was overcome by converting the analytes to their fluorinated derivatives. Owing to high absorptivity in IR region, these derivatives facilitated their detection by GC–FTIR analysis. Derivatizing reagents having trimethylsilyl, trifluoroacyl and heptafluorobutyryl groups on imidazole moiety were screened. Derivatives formed there were analyzed by GC–FTIR quantitatively. Of these reagents studied, heptafluorobutyrylimidazole (HFBI) produced the greatest increase in sensitivity by GC–FTIR detection. 60–125 folds of sensitivity enhancement were observed for the analytes by HFBI derivatization. Absorbance due to various functional groups responsible for enhanced sensitivity were compared by determining their corresponding relative molar extinction coefficients (ε^′_max${{\epsilon }^{\prime }}_{\text{max}}$) considering uniform optical path length. The RSDs for intraday repeatability and interday reproducibility for various derivatives were 0.2–1.1% and 0.3–1.8%. Limit of detection (LOD) was achieved up to 10–15 ng and applicability of the method was tested with unknown samples obtained in international proficiency tests.     

Relationship between the gas chromatographic behaviour and the molecular structure of hydrocarbon samples and various stationary phases Part I. Correlation of retention data and thermodynamic functions with chemical structure

Summary Retention parameters of different hydrocarbon classes were determined at 90–120°C on non-polar and medium-polar stationary phases. The specific retention volumes, and the thermodynamic functions of solution were calculated and the relationship between these data, the physicochemical properties and the chemical structure of the solutes (samples) and solvents (liquid phases) investigated.     

Quantum computation of the properties of helium using two-body and three-body intermolecular potentials: a molecular dynamics study

We have performed the molecular dynamics simulation to obtain energy, pressure, and self-diffusion coefficient of helium at different temperatures and densities using Lennard–Jones (LJ), Hartree–Fock dispersion-Individual damping (HFD-ID) potential, and the HFD-like potential which has been obtained with an inversion of viscosity data at zero pressure supplemented by quantum corrections following the Feynman–Hibbs approach. The contribution of three-body interactions using an accurate simple relationship reported by Wang and Sadus between two-body and three-body interactions has been also involved for non-effective potentials (HFD-ID and HFD-like) in simulation. Our results show a good agreement with corresponding experimental data. A comparison of our simulated results with other molecular simulations using different potentials is also included.     

Enhancing the detection sensitivity of trace analysis of pharmaceutical genotoxic impurities by chemical derivatization and coordination ion spray-mass spectrometry

Many pharmaceutical genotoxic impurities are neutral molecules. Trace level analysis of these neutral analytes is hampered by their poor ionization efficiency in mass spectrometry (MS). Two analytical approaches including chemical derivatization and coordination ion spray-MS were developed to enhance neutral analyte detection sensitivity. The chemical derivatization approach converts analytes into highly ionizable or permanently charged derivatives, which become readily detectable by MS. The coordination ion spray-MS method, on the other hand, improves ionization by forming neutral-ion adducts with metal ions such as Na⁺, K⁺, or NH₄⁺ which are introduced into the electrospray ionization source. Both approaches have been proven to be able to enhance the detection sensitivity of neutral pharmaceuticals dramatically. This article demonstrates the successful applications of the two approaches in the analysis of four pharmaceutical genotoxic impurities identified in a single drug development program, of which two are non-volatile alkyl chlorides and the other two are epoxides.     

Fast and sensitive DNA analysis using changes in the FRET signals of molecular beacons in a PDMS microfluidic channel

A new DNA hybridization analytical method using a microfluidic channel and a molecular beacon-based probe (MB-probe) is described. A stem-loop DNA oligonucleotide labeled with two fluorophores at the 5′ and 3′ termini (a donor dye, TET, and an acceptor dye, TAMRA, respectively) was used to carry out a fast and sensitive DNA analysis. The MB-probe utilized the specificity and selectivity of the DNA hairpin-type probe DNA to detect a specific target DNA of interest. The quenching of the fluorescence resonance energy transfer (FRET) signal between the two fluorophores, caused by the sequence-specific hybridization of the MB-probe and the target DNA, was used to detect a DNA hybridization reaction in a poly(dimethylsiloxane) (PDMS) microfluidic channel. The azoospermia gene, DYS 209, was used as the target DNA to demonstrate the applicability of the method. A simple syringe pumping system was used for quick and accurate analysis. The laminar flow along the channel could be easily controlled by the 3-D channel structure and flow speed. By injecting the MB-probe and target DNA solutions into a zigzag-shaped PDMS microfluidic channel, it was possible to detect their sequence-specific hybridization. Surface-enhanced Raman spectroscopy (SERS) was also used to provide complementary evidence of the DNA hybridization. Our data show that this technique is a promising real-time detection method for label-free DNA targets in the solution phase. Figure FRET-based DNA hybridization detection using a molecular beacon in a zigzag-shaped PDMS microfluidic channel     

Skeletal and appendage diversity as design elements in the synthesis of a discovery library of nonaromatic polycyclic 5-iminooxazolidin-2-ones, hydantoins, and acylureas

Amino-acid derived cross-conjugated trienes were used as a starting point for the synthesis of a discovery library of over 200 polycyclic 5-iminooxazolidin-2-ones, hydantoins, and acylureas. The main feature of this library synthesis is a triple branching strategy, which provides efficient access to five skeletally diverse scaffolds. In addition, four sets of building blocks were applied in both a front end and a back end diversification strategy. Multiple fused rings were obtained by cyclization of diamides with phosgene and stereoselective Diels-Alder reactions with maleimides. The 5-iminooxazolidin-2-one scaffold was rearranged into the isomeric hydantoin scaffold through a sequence of ring-opening and ring-closing reactions.     

Estimation and analysis of the rheological properties of a perfluoropolyether through molecular dynamics simulation

Equilibrium and non-equilibrium molecular dynamics simulations of a perfluoropolyether C₈F₁₈O₄ are reported using an atomistic interaction potential. The bulk rheological properties of the perfluoropolyether are investigated through molecular dynamics simulations as a function of both temperature and shear rate. The effect of molecular structure on viscosity is explored in detail. The rotational relaxation time is reported as a function of temperature. Structural properties, including the mean-square end-to-end chain length, the mean-square radius of gyration of chains, and the distribution functions of bond lengths, bond angles, and bond torsional angles are collected and analyzed as functions of shear rate. After an initial plateau, both mean-square end-to-end chain length and mean-square radius of gyration decrease monotonically with increasing shear rate. The behaviors of the rheological and structural properties are explained through an analysis of the individual contributions due to bond stretching, bond bending, and bond torsion, as well as both intramolecular and intermolecular non-bonded interactions. A further analysis is possible through a meticulous breakdown of each contribution into a specific type of mode; e.g., the total bond stretching is comprised of CC, CO, and CF bond stretching terms. In this way, one can relate the shear viscosity to the specific chemical structure of C₈F₁₈O₄.     

Simultaneous analysis of pesticides from different chemical classes by using a derivatisation step and gas chromatography-mass spectrometry

This work presents a new method to analyse simultaneously by GC–MS 31 pesticides from different chemical classes (2,4 D, 2,4 MCPA, alphacypermethrin, bifenthrin, bromoxynil, buprofezin, carbaryl, carbofuran, clopyralid, cyprodinil, deltamethrin dicamba, dichlobenil, dichlorprop, diflufenican, diuron, fenoxaprop, flazasulfuron, fluroxypyr, ioxynil, isoxaben, mecoprop-P, myclobutanil, oryzalin, oxadiazon, picloram, tau-fluvalinate tebuconazole, triclopyr, trifluralin and trinexapac-p-ethyl). This GC–MS method will be applied to the analysis of passive samplers (Tenax^® tubes and SPME fiber) used for the evaluation of the indoor and outdoor atmospheric contamination by non-agricultural pesticides. The method involves a derivatisation step for thermo-labile or polar pesticides. Different agents were tested and MtBSTFA (N-(t-butyldimethylsilyl)-N-methyltrifluoroacetamide), a sylilation agent producing very specific fragments [M−57], was retained. However, diuron could not be derivatised and the isocyanate product was used for identification and quantification. Pesticides which did not need a derivatisation step were not affected by the presence of the derivatisation agent and they could easily be analysed in mixture with derivatised pesticides. The method can be coupled to a thermal-desorption unit or to SPME extraction for a multiresidue analysis of various pesticides in atmospheric samples.     

On the importance of the nature of the ionic liquids in the selective simultaneous separation of the substrates and products of a transesterification reaction through supported ionic liquid membranes

Previously, we reported the selective simultaneous separation of the substrates and products of a transesterification reaction (vinyl butyrate, 1-butanol, butyl butyrate, and butyric acid) through supported liquid membranes (SLMs) based on two ionic liquids (ILs): 1-butyl-3-methylimidazolium hexafluorophosphate, [bmim⁺][PF₆⁻], and 1-octyl-3-methylimidazolium hexafluorophosphate, [omim⁺][PF₆⁻]. The significant differences observed in the selectivity values, attributed to the different nature of the ionic liquid phase used, led us to further investigate this matter.     

Inhibitors of prolyl endopeptidase: Characterization of the pharmacophoric pattern using conformational analysis and 3D-QSAR

Summary A structure-activity study has been carried out on several compounds known as inhibitors of the serine protease prolyl endopeptidase. Conformational analysis has been done using different molecular mechanics methods such as molecular dynamics, or a randomized conformational search method. The conformers obtained were classified using geometric and energetic criteria. A pattern recognition analysis was done in order to divide conformers according to families. The resulting dominant families, for all compounds investigated, showed very similar geometric features. Based on the lowest energy conformers obtained after randomized conformational analysis, a 3D-QSAR model was established using the CoMFA approach. The validity of this model was verified by prediciting correctly the activity of other molecules not used in the construction of this model.     

Characterization of a discontinuous epitope of the HIV envelope protein gp120 recognized by a human monoclonal antibody using chemical modification and mass spectrometric analysis

A subset of the neutralizing anti-HIV antibodies recognize epitopes on the envelope protein gp120 of the human immunodeficiency virus. These epitopes are exposed during conformational changes when gp120 binds to its primary receptor CD4. Based on chemical modification of lysine and arginine residues followed by mass spectrometric analysis, we determined the epitope on gp120 recognized by the human monoclonal antibody 559/64-D, which was previously found to be specific for the CD4 binding domain. Twenty-four lysine and arginine residues in recombinant full-length glycosylated gp120 were characterized; the relative reactivities of two lysine residues and five arginine residues were affected by the binding of 559/64-D. The data show that the epitope is discontinuous and is located in the proximity of the CD4-binding site. Additionally, the reactivities of a residue that is located in the secondary receptor binding region and several residues distant from the CD4 binding site were also altered by Ab binding. These data suggest that binding of 559/64-D induced conformational changes which result in altered surface exposure of specific amino acids distant from the CD4-binding site. Consequently, binding of 559/64-D to gp120 affects not only the CD4-binding site, which is recognized as the epitope, but appears to have a global effect on surface exposed residues of the full-length glycosylated gp120.     

Synthesis of the pentasaccharide repeating unit of the O-antigen of Escherichia coli O175 using one-pot glycosylations and its conformational analysis

Synthesis of a pentasaccharide repeating unit of the cell wall O-antigenic polysaccharide of enteroaggregative Escherichia coli O175 has been achieved using one-pot, three components [1+2+2] block glycosylations. The intermediate steps were good yielding and satisfactory stereoselectivity was observed in the glycosylations. The synthesized pentasaccharide was subjected to conformational analysis in aqueous environment using 2D ROESY NMR spectral analysis in conjugation with molecular dynamics (MD) simulation technique.