MENTHOR,a database system for the storage and retrieval of three-dimensional molecular structures and associated data searchable by substructural,biologic, physical,or geometric properties

Summary MENTHOR is a database system for the storage and retrieval of three-dimensional coordinate and charge information on molecules as well as of traditional biological and physical properties. Our molecular graphics system retrieves from MENTHOR structural information in individual molecules and receptor map/macromolecular binding site hypotheses. Substructural searches of MENTHOR are used to find starting coordinates for molecular modeling and traditional database searches of MENTHOR identify compounds for which modeling is needed. It also forms the data to be searched with ALLADDIN, our substructure/geometric search program. MENTHOR expedites molecular modeling by organizing previous work and facilitating transmission of information between individuals. Examples from modeling of D-2 receptor agonists are shown.     

Computer-aided design of formulated products

Formulated products represent a particular class of complex chemical products, and their design is typically based on experience and extensive experimentation. Although still at an early stage, and despite that their potential is not fully accessed and not fully used by the industry, computer-aided design (CAD) methods and tools offer many possibilities in the design of formulated products. The CAD methodology based on computerized models enables the formulation chemists to speed up the design process, without completely replacing experiments.In this work, we summarize previous studies in the field and present important elements of the CAD framework, emphasizing estimation methods for key target properties, link to specifications, and finally, some case studies will illustrate how the CAD framework can be used in practice for formulated products.     

Quantitative AES and XPS: convergence between theory and experimental databases

Experimental spectral databases have been recorded for AES and XPS using fully calibrated instruments. These instruments have been calibrated so that the spectra have the true shape and peak area intensities may be integrated to give absolute yields for AES and relative yields for XPS. Removal of all the backgrounds requires care but may be completed by using information from both databases. The resultant yields may be compared with theory. The correlations for AES are the more complex and involve the total intensities for all transitions originating in each shell. The correlations are excellent using significant changes to the traditional approach. These involve the use of the Casnati et al. ionisation cross section and the restriction of the number of electrons for use in the inelastic mean free path calculations to electrons of 14 eV or less binding energy in the s, p or d sub-shells. The average ratio of experiment to theory is 1.04 with a standard uncertainty of the mean of 4%. Results for XPS are excellent using Scofield’s ionisation cross section together with the above rules for the inelastic mean free path calculations. Improvements for certain elements are still needed for removing the inelastically scattered Auger and photoelectrons in both databases. To assist analysts in using such databases a simpler measure of Auger electron intensity is developed involving differential spectra broadened with a Gaussian function of 15–20 eV width. The peak-to-peak intensities from these broadened spectra are reasonably closely related to the peak area of the direct spectra except in a few exceptional cases. The unbroadened differential spectra show strong contributions from the spectrometer resolution and changes in the chemical state which are avoided by the spectral broadening. To simplify calculations for the analyst when studying homogeneous materials by AES and XPS, the relative sensitivity factors are re-defined to be for an average matrix instead of the pure element. This leads to a matrix-less equation for calculating compositions from the spectra.     

Line intensities of C2H2 in the 7.7 μm spectral region

Absolute intensities of 414 lines are measured in eight bands of the 7.7 μm spectral region of the ¹²C₂H₂ molecule, with an average accuracy of 5%. Vibrational transition dipole moment squared values and empirical Herman–Wallis coefficients are obtained in order to model the rotational dependence of the transition dipole moment squared, except for some forbidden bands for which smoothed values are given. These data are used to calculate a line list for atmospheric or astrophysical applications.     

Measurement of absolute line intensities in the ν5-ν4 band of C2H2 using SOLEIL synchrotron far infrared AILES beamline

Absolute intensities of about 120 lines of the ¹²C₂H₂ molecule are reported for the ν₄-ν₅ band between 65 and 192 cm^-1, with an average accuracy of 5%. Vibrational transition dipole moment squared values and empirical Herman-Wallis coefficients are obtained allowing modelling the rotational dependence of the transition dipole moment squared. Special care is taken to accurately determine an apparatus function for the Bruker IFS 125-HR coupled to the synchrotron SOLEIL far infrared AILES beamline in order to minimize its effects on the line parameter retrieval.     

New line intensity measurements for C2H2 around 7.7 μm and HITRAN format line list for applications

Absolute intensities of 467 lines are measured in 9 bands of the 7.7 μm spectral region of the ¹²C₂H₂ molecule, with an average accuracy of 5%. For each band, the vibrational transition dipole moment squared and Herman-Wallis coefficients are obtained in order to model the rotational dependence of the transition dipole moment squared. These results are used to calculate a line list for atmospheric or astrophysical applications. Merged in the line list set up in a previous work for the 8 strongest bands around 7.7 μm [5], these new data give now a quasi-exhaustive view of the ¹²C₂H₂ spectrum in the involved spectral region.     

Quantitative XPS: I. Analysis of X-ray photoelectron intensities from elemental data in a digital photoelectron database

An analysis of the correlation of theoretical predictions for photoelectron intensities is made with experimental data from an XPS digital database for 46 solid elements measured using a spectrometer with calibrated intensity and energy scales. This analysis covers single element samples measured for Al and Mg K X-rays. The spectral data are for widescans at 1 eV energy intervals with kinetic energies from 200 to 1506 eV using Al X-rays and to 1273 eV using Mg X-rays. In addition are narrow scans around the photoelectron peaks at 0.1 eV energy intervals. All spectra have the instrument intensity/energy response function removed so that the peak areas are proportional to the number of electrons emitted per steradian per incident K photon. Correlations are made for the ionisation cross sections of Scofield and the inelastic mean free paths given by the TPP-2M formula. The correlations are excellent, apart from a factor which may be associated with the background removal arising from the use of the Tougaard Universal cross section. These correlations lead directly to pure element relative sensitivity factors suitable for quantitative analysis. General equations are also provided to extract values for a new form of relative sensitivity factor for an average matrix. These average matrix relative sensitivity factors lead to simpler equations involving matrix factors that are effectively unity instead of the traditional values in the range 0.3 to 3.0.     

Theoretical calculations of self-broadening coefficients in the ν6 band of CH3Br

A semiclassical impact theory based upon the Anderson-Tsao-Curnutte formalism has been used to calculate the self-broadening coefficients in the ^PP-, ^PQ-, ^PR-, ^RP-, ^RQ- and ^RR-branches of the ν₆ band of ¹²CH₃⁷⁹Br and ¹²CH₃⁸¹Br near 10 μm. Comparisons have then been performed with the extensive set of previous measurements [3] (Jacquemart et al., 2007). The intermolecular potential used, involving the overwhelming electrostatic contributions, leads to larger results than the experimental data for middle J values. By arbitrarily limiting the integration of the differential cross-section to an impact parameter equal to 29 Å, quite satisfactory results have been obtained, and the J and K dependences are in reasonable agreement with those observed experimentally. The theoretical results are, on the whole, slightly larger for CH₃⁷⁹Br than for CH₃⁸¹Br and for same J and K initial states of the transitions they depend on the sub-branch considered. These differences and dependencies were not observed in the previous measurements due to scatter in the experimental data. Finally, the theoretical results obtained for all sub-branches of ¹²CH₃⁷⁹Br and ¹²CH₃⁸¹Br are given as supplementary materials of this paper.