Pharmacophore alignment search tool: influence of scoring systems on text-based similarity searching

The text-based similarity searching method Pharmacophore Alignment Search Tool is grounded on pairwise comparisons of potential pharmacophoric points between a query and screening compounds. The underlying scoring matrix is of critical importance for successful virtual screening and hit retrieval from large compound libraries. Here, we compare three conceptually different computational methods for systematic deduction of scoring matrices: assignment-based, alignment-based, and stochastic optimization. All three methods resulted in optimized pharmacophore scoring matrices with significantly superior retrospective performance in comparison with simplistic scoring schemes. Computer-generated similarity matrices of pharmacophoric features turned out to agree well with a manually constructed matrix. We introduce the concept of position-specific scoring to text-based similarity searching so that knowledge about specific ligand-receptor binding patterns can be included and demonstrate its benefit for hit retrieval. The approach was also used for automated pharmacophore elucidation in agonists of peroxisome proliferator activated receptor gamma, successfully identifying key interactions for receptor activation.     

FTIR and millimeter wave investigation of the 7 and 9 states of formic acid HCOOH and HCOOH

High resolution FTIR spectra of the two overlapping bands ν₇ and ν₉ of the ¹³C species of formic acid have been measured and analyzed. Rotational transitions in the millimeter wave region were measured and included in the analysis. As in the parent species, there is a strong Coriolis interaction between the 7¹ and 9¹ states. The corresponding IR bands of the parent species have been remeasured and new MMW transitions recorded. The analysis of the spectra for the two species provides an opportunity to consider a reduction of the Hamiltonian employed for the analysis of this type of interacting system of states. Parameters with low correlations could be obtained. Several interstellar features coincide with transitions predicted from these parameters.     

New analysis of the ν5 and 2ν9 bands of HNO3 by infrared and millimeter wave techniques: line positions and intensities

Nitric acid (HNO₃) plays an important role in the Earth’s atmosphere as a reservoir molecule of NO_x species. It has a strong infrared signature at 11 μm which is one of the most commonly used for the infrared retrieval of this species in the atmosphere since this spectral region coincides with an atmospheric window. It is therefore essential to have high quality spectral parameters in this spectral region. The main goal of this work is then to generate as reliable as possible line positions and intensities for the ν₅ and 2ν₉ cold bands centered at 879.1075 and 896.4467 cm⁻¹, respectively. In particular the existing line parameters need improvement in the wings of the 11 μm window in order to retrieve more accurately the CFC-11 (CCl₃F) and CFC-12 (CCl₂F₂) atmospheric species at ∼850 and ∼920 cm⁻¹, respectively. This work is also motivated by theoretical considerations. Very strong resonances couple indeed the 5¹ and 9² rotational levels. In addition the ν₉ mode (OH torsion) is a “large amplitude” motion, and torsional splittings affect both the v₉=2 and the v₅=1 rotational transitions. In the present study, these effects are accounted for simultaneously both for the line position and line intensity calculations. To calculate the line positions the Hamiltonian matrix accounts for the very strong Fermi and the weaker Coriolis interactions linking the 5¹⇔9² rotational levels, and the torsional effects are accounted for within the frame of the IAM (Internal Axis Method) approach. In addition, the v-diagonal blocks involve non-orthorhombic operators together with Watson’s type rotational operators. This means that the z-quantization axis deviates from the a inertial axis for both the 5¹ and 9² vibrational states. The line intensity calculations were performed accounting also for the axis switching effects. As far as the experimental line positions are concerned we have used the millimeter wave data available in the literature [J. Mol. Spectrosc., 175 (1996) 395; J. Mol. Spectrosc., 208 (2001) 121; and references therein], as well as new centimeter wave measurements performed in Kiel and new Fourier transform infrared spectra recorded in Giessen. For the line intensities we have used an extensive set of individual line intensities measured recently [J. Mol. Spectrosc., 218 (2003) 151]. All these experimental data were very satisfactorily reproduced using the theoretical model described above and an improved set of line positions and intensities was generated for the ν₅ and 2ν₉ bands allowing one to better model the HNO₃ absorption in the 11 μm spectral domain.     

Ground state spectrum of methylcyanide

The rotational spectrum of methylcyanide (acetonitrile) in the ground vibrational state was measured in the spectral region from 91 to 810 GHz using the Cologne and Tsukuba spectrometers operated in the Doppler-limited and sub-Doppler saturation layouts. The resolution of the saturation Lamb-dip measurements is estimated to be about 1 kHz at the best of circumstances and the measuring accuracy of 10-60 kHz depending very sensitively on the quality of the spectrum. In the cases of rotational transitions with the low quantum number J (J<18) and with a low difference of the rotational quantum numbers J−K, the resolved or partly resolved hyperfine structures of the rotational transitions were observed. Together with the most accurate data from the literature, the newly measured experimental data were analyzed using the traditional polynomial energy formula as well as the Padè approximant for the effective rotational Hamiltonian. The resulting rotational, centrifugal distortion, and hyperfine structure spectroscopic constants were obtained with a significantly higher accuracy than the ones listed in the literature. In addition, an anomalous accidental resonance was detected between the K=14 ground state levels and the K=12, +l levels in the excited v₈=1 vibrational state.     

Submillimeter-wave spectroscopy of HCN in excited vibrational states

Measurements of the rotational spectrum of HCN in excited vibrational states have been extended to higher-J values. The transitions reach J=8←7 around 710 GHz for most vibrational states studied in this investigation and J=22←21 near 2 THz for the (020) and (030) vibrational states. Using a pure sample of gaseous HCN at 350 K, selected states up to one quantum in the C–H stretching vibration at 3311.5 cm⁻¹ have been investigated. Even transitions having two quanta in the C–H stretch could be studied employing a glow discharge in a gas mixture of CH₄ and N₂. Molecular constants in 13 vibrational states have been obtained, several of which have been studied for the first time by rotational spectroscopy. The vibrational temperature in the discharge system is found to be about 1500 K for the stretching vibrational modes and about 600 K for the bending states.     

Millimeter-wave spectrum of Ne–CO: new measurements

The b-type rotational transitions of the van der Waals complex, Ne–CO have been measured using the intracavity OROTRON jet spectrometer in the frequency range of 80–115 GHz. The high sensitivity of this technique enabled us to detect all three Ne isotopic modifications of the complex, ²⁰Ne–CO, ²²Ne–CO, and ²¹Ne–CO in natural abundance. The observed and assigned transitions belong to the Q-branch of the K = 1–0 subband and include also R (0) and P (2) lines. The newly obtained data were analysed together with previously observed millimeter-wave b-type and microwave a-type rotational transitions.     

Assignment and Power Series Analysis of the FIR Fourier Transform Spectrum of Cyanamide Using a Multimolecule Ritz Program

The “Ritz” program, originally written for the analysis of the Fourier transform spectra of the methanol isotopomers and presented in previous papers, has been extended in order to analyze the spectra of other molecules. This program evaluates the term values involved in the assigned transitions by the Rydberg–Ritz combination principle, and can tackle such perturbations as Fermi-type resonances or Coriolis interactions. As a first application of the extended version, we present an investigation of the Fourier transform spectrum of cyanamide between 25 and 980 cm⁻¹. More than 16 000 lines have been assigned. Our Ritz database now comprises a list of more than 19 000 assigned lines (including of the microwave and FIR lines available in the JPL database) and more than 3900 term values. All of the lines presented in this paper correspond to transitions within the ground and first excited inversion levels of the ground vibrational state of the small-amplitude modes.