Designing novel nicotinic agonists by searching a database of molecular shapes

Summary We introduce an approach by which novel ligands can be designed for a receptor if a pharmacophore geometry has been established and the receptor-bound conformations of other ligands are known. We use the shape-matching method of Kuntz et al. [J. Mol. Biol., 161 (1982) 269–288] to search a database of molecular shapes for those molecules which can fit inside the combined volume of the known ligands and which have interatomic distances compatible with the pharmacophore geometry. Some of these molecules are then modified by interactive modeling techniques to better match the chemical properties of the known ligands. Our shape database (about 5000 candidate molecules) is derived from a subset of the Cambridge Crystallographic Database [Allen et al., Acta Crystallogr., Sect. B,35 (1979) 2331–2339]. We show, as an example, how several novel designs for nicotinic agonists can be derived by this approach, given a pharmacophore model derived from known agonists [Sheridan et al., J. Med. Chem., 29 (1986) 889–906]. This report complements our previous report [DesJarlais et al., J. Med. Chem., in press], which introduced a similar method for designing ligands when the structure of the receptor is known.     

Comment on “Analytical evaluation for two-center nuclear attraction integrals over Slater type orbitals by using Fourier transform method” by S. ?zcan and E. ?ztekin (J. Math. Chem. DOI 10.1007/s10910-008-9398-z)

S. ?zcan and E. ?ztekin, (J. Math. Chem. doi:) published formulas for evaluating the two-center nuclear attraction integrals over Slater type orbitals. It is shown that the analytical relations for these integrals through the expansion coefficients of the electron charge density for the one-center case and the overlap integrals presented in Sect. 3 of this work can easily be derived by means of a simple algebra from the formulas published in our papers (I.I. Guseinov, J Mol Struct (Theochem) 417:117, 1997; J Math Chem 42:415, 2007 and B.A. Mamedov, Chin J Chem 22:545, 2004). It should be noted that the formulas of overlap integrals presented by E. ?ztekin et al., in previous paper (E. ?ztekin, M. Yavuz, Ş. Atalay, J Mol Struct (Theochem) 544:69, 2001) for the calculation of two-center nuclear attraction integrals also are obtained from our papers (see Comment: I.I. Guseinov, J Mol Struct (Theochem) 638:235, 2003).     

An iterative knowledge-based scoring function to predict protein-ligand interactions: II. Validation of the scoring function

We have developed an iterative knowledge-based scoring function (ITScore) to describe protein-ligand interactions. Here, we assess ITScore through extensive tests on native structure identification, binding affinity prediction, and virtual database screening. Specifically, ITScore was first applied to a test set of 100 protein-ligand complexes constructed by Wang et al. (J Med Chem 2003, 46, 2287), and compared with 14 other scoring functions. The results show that ITScore yielded a high success rate of 82% on identifying native-like binding modes under the criterion of rmsd < or = 2 A for each top-ranked ligand conformation. The success rate increased to 98% if the top five conformations were considered for each ligand. In the case of binding affinity prediction, ITScore also obtained a good correlation for this test set (R = 0.65). Next, ITScore was used to predict binding affinities of a second diverse test set of 77 protein-ligand complexes prepared by Muegge and Martin (J Med Chem 1999, 42, 791), and compared with four other widely used knowledge-based scoring functions. ITScore yielded a high correlation of R2 = 0.65 (or R = 0.81) in the affinity prediction. Finally, enrichment tests were performed with ITScore against four target proteins using the compound databases constructed by Jacobsson et al. (J Med Chem 2003, 46, 5781). The results were compared with those of eight other scoring functions. ITScore yielded high enrichments in all four database screening tests. ITScore can be easily combined with the existing docking programs for the use of structure-based drug design.     

Simple cyclodextrin aldehydes as excellent artificial oxidases

Cyclodextrin based oxidases, with a ketone as functional group are well known as good artificial enzyme mimics (Fenger et al. Org Biomol Chem 7:933?C943; Marinescu and Bols Angew Chem Int Ed 45:4590?C4593; Bjerre et al. Eur J Org Chem 704?C710; Marinescu et al. J Am Chem Soc 127:17578?C17579). We here report a series of modified cyclodextrins, having aldehydes as functional groups. The aldehyde based artificial enzymes have, in most cases, better catalysis than the ketones, because of their powerful covalent binding of hydrogen peroxide. Among the modified cyclodextrins studied are mono and di aldehydes on the 6 positions, with or without methylated hydroxyl groups. The aldehyde functionality was also introduced close to the secondary side, by attaching ethoxy-2-al or propoxy-3-al to the 2 position. The modified cyclodextrins showed excellent enzymatic activity towards oxidation of different aminophenols, and 4-methoxy benzyl alcohol with hydrogen peroxide as a stoichiometric oxidant. Rate enhancements up to 4,600 were achieved for oxidation of 4-methoxy benzyl alcohol, where as oxidation of amines gave rate enhancements up to 3,400. The artificial oxidases catalyses oxidations under enzymatic conditions (water, pH 7, 25 °C), following Michaelis?CMenten kinetics. To confirm the enzyme activity, inhibition studies with sodium naphthalene-2-sulfonate were carried out. These studies showed competitive inhibition of the enzymes, verifying the cyclodextrins enzyme like character.     

Variable selection and specification of robust QSAR models from multicollinear data: arylpiperazinyl derivatives with affinity and selectivity for α<Subscript>2</Subscript>-adrenoceptors

Two QSAR models have been identified that predict the affinity and selectivity of arylpiperazinyl derivatives for alpha1 and alpha2 adrenoceptors (ARs). The models have been specified and validated using 108 compounds whose structures and inhibition constants (Ki) are available in the literature [Barbaro et al., J. Med. Chem., 44 (2001) 2118; Betti et al., J. Med. Chem., 45 (2002) 3603; Barbaro et al., Bioorg. Med. Chem., 10 (2002) 361; Betti et al., J. Med. Chem., 46 (2003) 3555]. One hundred and forty-seven predictors have been calculated using the Cerius 2 software available from Accelrys. This set of variables exhibited redundancy and severe multicollinearity, which had to be identified and removed as appropriate in order to obtain robust regression models free of inflated errors for the beta estimates - so-called bouncing betas. Those predictors that contained information relevant to the alpha2 response were identified on the basis of their pairwise linear correlations with affinity (-log Ki) for alpha2 adrenoceptors; the remaining variables were discarded. Subsequent variable selection made use of Factor Analysis (FA) and Unsupervised Variable Selection (UzFS). The data was divided into test and training sets using cluster analysis. These two sets were characterised by similar and consistent distributions of compounds in a high dimensional, but relevant predictor space. Multiple regression was then used to determine a subset of predictors from which to determine QSAR models for affinity to alpha2-ARs. Two multivariate procedures, Continuum Regression (the Portsmouth formulation) and Canonical Correlation Analysis (CCA), have been used to specify models for affinity and selectivity, respectively. Reasonable predictions were obtained using these in silico screening tools.     

Parallelized integral-direct CIS(D) calculations with multilayer fragment molecular orbital scheme

We have developed a parallelized integral-direct code of the perturbative doubles correction for configuration interaction with singles, proposed as CIS(D) by Head-Gordon et al. (Chem Phys Lett 219:21, 1994). The CIS(D) method provides the energy corrections both of the relaxation and differential correlation for the respective CIS excited states. The implementation of CIS(D) is based on our original algorithm for the second-order Møller–Plesset perturbation (MP2) calculations (Mochizuki et al. in Theor Chem Acc 112:442, 2004). There is no need to communicate bulky intermediate data among worker processes of the parallelized execution. This CIS(D) code is then incorporated into a developer version of ABINIT-MP program, in order to improve the overestimation in excitation energies calculated by the CIS method in conjunction with the multilayer fragment molecular orbital scheme (MLFMO-CIS) (Mochizuki et al. in Chem Phys Lett 406:283, 2005). The MLFMO-CIS(D) method is first used in evaluating the lowest n\(\pi^{*}\) excitation energy of the hydrated formaldehyde. The photoactive yellow protein (PYP) is the second target of MLFMO-CIS(D) calculation. Through these applications, it is shown that the CIS(D) correction improves the CIS results favorably.     

Comparison of different methods for calculating the paramagnetic relaxation enhancement of nuclear spins as a function of the magnetic field

The enhancement of the spin-lattice relaxation rate for nuclear spins in a ligand bound to a paramagnetic metal ion [known as the paramagnetic relaxation enhancement (PRE)] arises primarily through the dipole-dipole (DD) interaction between the nuclear spins and the electron spins. In solution, the DD interaction is modulated mostly by reorientation of the nuclear spin-electron spin axis and by electron spin relaxation. Calculations of the PRE are in general complicated, mainly because the electron spin interacts so strongly with the other degrees of freedom that its relaxation cannot be described by second-order perturbation theory or the Redfield theory. Three approaches to resolve this problem exist in the literature: The so-called slow-motion theory, originating from Swedish groups [Benetis et al., Mol. Phys. 48, 329 (1983); Kowalewski et al., Adv. Inorg. Chem. 57, (2005); Larsson et al., J. Chem. Phys. 101, 1116 (1994); T. Nilsson et al., J. Magn. Reson. 154, 269 (2002)] and two different methods based on simulations of the dynamics of electron spin in time domain, developed in Grenoble [Fries and Belorizky, J. Chem. Phys. 126, 204503 (2007); Rast et al., ibid. 115, 7554 (2001)] and Ann Arbor [Abernathy and Sharp, J. Chem. Phys. 106, 9032 (1997); Schaefle and Sharp, ibid. 121, 5387 (2004); Schaefle and Sharp, J. Magn. Reson. 176, 160 (2005)], respectively. In this paper, we report a numerical comparison of the three methods for a large variety of parameter sets, meant to correspond to large and small complexes of gadolinium(III) and of nickel(II). It is found that the agreement between the Swedish and the Grenoble approaches is very good for practically all parameter sets, while the predictions of the Ann Arbor model are similar in a number of the calculations but deviate significantly in others, reflecting in part differences in the treatment of electron spin relaxation. The origins of the discrepancies are discussed briefly.     

Synthesis, molecular modeling and biological activity of methyl and thiomethyl substituted pyrimidines as corticotropin releasing hormone type 1 antagonists

Four small, targeted libraries of differentially substituted amino pyrimidines were synthesized in moderate to good yields. Excellent regiochemistry was observed for substitution at C2/C4 with selectivity > 50:1 noted. All analogues were screened for their ability to interact with CRH1 and CRH2 receptors. In all instances only poor agonistic and/or antagonistic behaviour was noted at CRH2. However, several compounds were potent and selective CRH1 antagonists, most notably 13a Ki = 39 nM. Additionally we have utilized these data and that recently reported by others to refine our original CRH1 pharmacophore (J Med. Chem., 1999, 42, 2351-2357).     

Alchemical prediction of hydration free energies for SAMPL

Hydration free energy calculations have become important tests of force fields. Alchemical free energy calculations based on molecular dynamics simulations provide a rigorous way to calculate these free energies for a particular force field, given sufficient sampling. Here, we report results of alchemical hydration free energy calculations for the set of small molecules comprising the 2011 Statistical Assessment of Modeling of Proteins and Ligands challenge. Our calculations are largely based on the Generalized Amber Force Field with several different charge models, and we achieved RMS errors in the 1.4-2.2 kcal/mol range depending on charge model, marginally higher than what we typically observed in previous studies (Mobley et al. in J Phys Chem B 111(9):2242-2254, 2007, J Chem Theory Comput 5(2):350-358, 2009, J Phys Chem B 115:1329-1332, 2011; Nicholls et al. in J Med Chem 51:769-779, 2008; Klimovich and Mobley in J Comput Aided Mol Design 24(4):307-316, 2010). The test set consists of ethane, biphenyl, and a dibenzyl dioxin, as well as a series of chlorinated derivatives of each. We found that, for this set, using high-quality partial charges from MP2/cc-PVTZ SCRF RESP fits provided marginally improved agreement with experiment over using AM1-BCC partial charges as we have more typically done, in keeping with our recent findings (Mobley et al. in J Phys Chem B 115:1329-1332, 2011). Switching to OPLS Lennard-Jones parameters with AM1-BCC charges also improves agreement with experiment. We also find a number of chemical trends within each molecular series which we can explain, but there are also some surprises, including some that are captured by the calculations and some that are not.     

Construction of 4D-QSAR Models for Use in the Design of Novel p38-MAPK Inhibitors

The p38-mitogen-activated protein kinase (p38-MAPK) plays a key role in lipopolysaccharide-induced tumor necrosis factor-alpha (TNF-alpha) and interleukin-1 (IL-1) release during the inflammatory process, emerging as an attractive target for new anti-inflammatory agents. Four-dimensional quantitative structure-activity relationship (4D-QSAR) analysis [Hopfinger et al., J. Am. Chem. Soc., 119 (1997) 10509] was applied to a series of 33 (a training set of 28 and a test set of 5) pyridinyl-imidazole and pyrimidinyl-imidazole inhibitors of p38-MAPK, with IC50 ranging from 0.11 to 2100 nM [Liverton et al., J. Med. Chem., 42 (1999) 2180]. Five thousand conformations of each analogue were sampled from a molecular dynamics simulation (MDS) during 50 ps at a constant temperature of 303 K. Each conformation was placed in a 2 angstroms grid cell lattice for each of three trial alignments. 4D-QSAR models were constructed by genetic algorithm (GA) optimization and partial least squares (PLS) fitting, and evaluated by leave-one-out cross-validation technique. In the best models, with three to six terms, the adjusted cross-validated squared correlation coefficients, Q2adj, ranged from 0.67 to 0.85. Model D (Q2adj = 0.84) was identified as the most robust model from alignment 1, and it is representative of the other best models. This model encompasses new molecular regions as containing pharmacophore sites, such as the amino-benzyl moiety of pyrimidine analogs and the N1-substituent in the imidazole ring. These regions of the ligands should be further explored to identify better anti-inflammatory inhibitors of p38-MAPK.     

The architecture and the Jones polynomial of polyhedral links

In this paper, we first recall some known architectures of polyhedral links (Qiu and Zhai in J Mol Struct (THEOCHEM) 756:163–166, 2005; Yang and Qiu in MATCH Commun Math Comput Chem 58:635–646, 2007; Qiu et al. in Sci China Ser B Chem 51:13–18, 2008; Hu et al. in J Math Chem 46:592–603, 2009; Cheng et al. in MATCH Commun Math Comput Chem 62:115–130, 2009; Cheng et al. in MATCH Commun Math Comput Chem 63:115–130, 2010; Liu et al. in J Math Chem 48:439–456 2010). Motivated by these architectures we introduce the notions of polyhedral links based on edge covering, vertex covering, and mixed edge and vertex covering, which include all polyhedral links in Qiu and Zhai (J Mol Struct (THEOCHEM) 756:163–166, 2005), Yang and Qiu (MATCH Commun Math Comput Chem 58:635–646, 2007), Qiu et al. (Sci China Ser B Chem 51:13–18, 2008), Hu et al. (J Math Chem 46:592–603, 2009), Cheng et al. (MATCH Commun Math Comput Chem 62:115–130, 2009), Cheng et al. (MATCH Commun Math Comput Chem 63:115–130, 2010), Liu et al. (J Math Chem 48:439–456, 2010) as special cases. The analysis of chirality of polyhedral links is very important in stereochemistry and the Jones polynomial is powerful in differentiating the chirality (Flapan in When topology meets chemistry. Cambridge Univ. Press, Cambridge, 2000). Then we give a detailed account of a result on the computation of the Jones polynomial of polyhedral links based on edge covering developed by Jin, Zhang, Dong and Tay (Electron. J. Comb. 17(1): R94, 2010) and, at the same time, by using this method we obtain some new computational results on polyhedral links of rational type and uniform polyhedral links with small edge covering units. These new computational results are helpful to judge the chirality of polyhedral links based on edge covering. Finally, we give some remarks and pose some problems for further study.     

The development of radioactive glass surrogates for fallout debris

The production of glass that emulates fallout is desired by the nuclear forensics community for training and measurement exercises. The composition of nuclear fallout is complex, with widely varying isotopic compositions (Fahey et al., Proc Natl Acad Sci USA 107(47):20207–20212, 2010; Bellucci et al., Anal Chem 85:7588–7593, 2013; Wallace et al., J Radioanal Nucl Chem, 2013; Belloni et al., J Environ Radioact 102:852–862, 2011; Freiling, Science 139:1058–1059, 1963; Science 133:1991–1999, 1961; Bunney and Sam Government Report: Naval Ordinance Laboratory, White Oak, 1971). As the gaseous cloud traverses from hotter to cooler regions of the atmosphere, the processes of condensation and nucleation entrain environmental materials, vaporized nuclear materials and fission products. The elemental and isotopic composition of the fission products is altered due to chemical fractionation (i.e. the fission product composition that would be expected from fission of the original nuclear material is altered by differences in condensation rates of the elements); the fallout may be enriched or depleted in volatile or refractory fission products. This paper describes preliminary work to synthesize, irradiate and fractionate the fission product content of irradiated particulate glass using a thermal distillation 2 h after irradiation. The glass was synthesized using a solution-based polymerization of tetraethyl orthosilicate. (Izrael, Radioactive fallout after nuclear explosions and accidents, 2002) Uranium was incorporated into the glass particulate at trace concentrations during polymerization. The particulate was subjected to a short thermal neutron irradiation then heated to 1,273 K approximately 2 h after the end of irradiation. Fission products of ^{133, 134, 135}I, ^{132, 134}Te, ¹³⁵Xe, ¹³⁸Cs and ^{91, 92}Sr were observed to be distilled from the particulate. The results of these preliminary studies are discussed.     

On the efficiency of VBSCF algorithms,a comment on “An efficient algorithm for energy gradients and orbital optimization in valence bond theory”

We comment on the paper [Song et al., J. Comput. Chem. 2009, 30, 399]. and discuss the efficiency of the orbital optimization and gradient evaluation in the Valence Bond Self Consistent Field (VBSCF) method. We note that Song et al. neglect to properly reference Broer et al., who published an algorithm [Broer and Nieuwpoort, Theor. Chim. Acta 1988, 73, 405] to use a Fock matrix to compute a matrix element between two different determinants, which can be used for an orbital optimization. Further, Song et al. publish a misleading comparison with our VBSCF algorithm [Dijkstra and van Lenthe, J. Chem. Phys. 2000, 113, 2100; van Lenthe et al., Mol. Phys. 1991, 73, 1159] to enable them to favorably compare their algorithm with ours. We give detail timings in terms of different orbital types in the calculation and actual timings for the example cases. © 2012 Wiley Periodicals, Inc.     

Isotope effects in the CO dimer: millimeter wave spectrum and rovibrational calculations of (12C18O)2

The millimeter wave spectrum of the isotopically substituted CO dimer, (12C18O)2, was studied with the Orotron jet spectrometer, confirming and extending a previous infrared study [A. R. W. McKellar, J. Mol. Spectrosc. 226, 190 (2004)]. A very dilute gas mixture of CO in Ne was used, which resulted in small consumption of 12C18O sample gas and produced cold and simple spectra. Using the technique of combination differences together with the data from the infrared work, six transitions in the 84-127 GHz region have been assigned. They belong to two branches, which connect four low levels of A+ symmetry to three previously unknown levels of A- symmetry. The discovery of the lowest state of A- symmetry, which corresponds to the projection K=0 of the total angular momentum J onto the intermolecular axis, identifies the geared bending mode of the 12C18O dimer at 3.607 cm(-1). Accompanying rovibrational calculations using a recently developed hybrid potential from ab initio coupled cluster [CCSD(T)] and symmetry-adapted perturbation theory calculations [G. W. M. Vissers et al., J. Chem. Phys. 122, 054306 (2005)] gave very good agreement with experiment. The isotopic dependence of the A+/A- energy splitting, the intermolecular separation R, and the energy difference of two ground state isomers, which change significantly when 18O or 13C are substituted into the normal (12C16O)2 isotopolog [L. A. Surin et al., J. Mol. Spectrosc. 223, 132 (2004)], was explained by these calculations. It turns out that the change in anisotropy of the intermolecular potential with respect to the shifted monomer centers of mass is particularly significant.     

Three-dimensional quantitative structure-activity relationships of steroid aromatase inhibitors

Summary Inhibition of aromatase, a cytochrome P450 that converts androgens to estrogens, is relevant in the therapeutic control of breast cancer. We investigate this inhibition using a three-dimensional quantitative structure-activity relationship (3D QSAR) method known as Comparative Molecular Field Analysis, CoMFA [Cramer III, R.D. et al., J. Am. Chem. Soc., 110 (1988) 5959]. We analyzed the data for 50 steroid inhibitors [Numazawa, M. et al., J. Med. Chem., 37 (1994) 2198, and references cited therein] assayed against androstenedione on human placental microsomes. An initial CoMFA resulted in a three-component model for log(1/K_i), with an explained variance r² of 0.885, and a cross-validated q² of 0.673. Chemometric studies were performed using GOLPE [Baroni, M. et al., Quant. Struct.-Act. Relatsh., 12 (1993) 9]. The CoMFA/GOLPE model is discussed in terms of robustness, predictivity, explanatory power and simplicity. After randomized exclusion of 25 or 10 compounds (repeated 25 times), the q² for one component was 0.62 and 0.61, respectively, while r² was 0.674. We demonstrate that the predictive r² based on the mean activity (Y_m) of the training set is misleading, while the test set Y_m-based predictive r² index gives a more accurate estimate of external predictivity. Using CoMFA, the observed differences in aromatase inhibition among C6-substituted steroids are rationalized at the atomic level. The CoMFA fields are consistent with known, potent inhibitors of aromatase, not included in the model. When positioned in the same alignment, these compounds have distinct features that overlap with the steric and electrostatic fields obtained in the CoMFA model. The presence of two hydrophobic binding pockets near the aromatase active site is discussed: a steric bulk tolerant one, common for C4, C6-alpha and C7-alpha substitutents, and a smaller one at the C6-beta region.     

Partition coefficients for the SAMPL5 challenge using transfer free energies

SAMPL challenges (Mobley et al. in J Comput Aided Mol Des 28:135–150, 2014; Skillman in J Comput Aided Mol Des 26:473–474, 2012; Geballe in J Comput Aided Mol Des 24:259–279, 2010; Guthrie in J Phys Chem B 113:4501–4507, 2009) provide excellent opportunities to assess theoretical approaches on new data sets with a goal of gaining greater insight towards protein and ligand modeling. In the SAMPL5 experiment, cyclohexane–water partition coefficients were determined using a vertical solvation scheme in conjunction with the SMD continuum solvent model. Several DFT functionals partnered with correlation consistent basis sets were evaluated for the prediction of the partition coefficients. The approach chosen for the competition, a B3PW91 vertical solvation scheme, yields a mean absolute deviation of 1.9 logP units and performs well at estimating the correct hydrophilicity and hydrophobicity for the full SAMPL5 molecule set.     

On the optimal surfmer addition profile in emulsion polymerisation

In this work, the optimal surfmer feeding profile for stabilizing a high-solid-content acrylic latex with a non-ionic alkenyl functional ^TMMaxemul 5011 was calculated. For this purpose, the model developed by de la Cal and Asua (J. Polym. Sci., Part A: Polym. Chem. 39 (2001) 585) was used. It was observed that, in spite of the low reactivity of the surfmer, it was possible to increase substantially the surfmer conversion using an optimal surfmer addition policy. To cite this article: E. Aramendia et al., C. R. Chimie 6 (2003).     

Spectroscopic characterization of the binding and isomerization cycle of Brooker’s merocyanine with α-, β-, and γ-cyclodextrins

Complexes of Brooker’s merocyanine dye with α-, β- and γ-cyclodextrin (CD) have been characterized to determine the relative strength and thermodynamics of binding, as well as the effect of binding on the protolytic-photochemical isomerization cycle of the dye. It was found that the dye binds most tightly to β-CD, with a binding equilibrium constant of 430 M^?1, in agreement with previous results (Hamasaki et al. J. Incl. Phenom. Mol. Rec. Chem. 13, 349–359 (1992)), while α-CD and γ-CD complexes have a binding constant of approximately 110 M^?1 and 70 M^?1, respectively, determined using absorbance and fluorescence spectroscopy. The isomerization cycle for the dye in α- and γ-CD complexes was found to be the same as for the free dye. Complexation with β-CD, however, resulted in depressed trans-to-cis photoisomerization in acidic conditions followed by spontaneous cis-to-trans isomerization (with the addition of base). Thermodynamic results also indicated differences between α-CD (ΔS° = ?48 J K^?1) and β-CD (ΔS° =  +12 J K^?1) complexes. There was no temperature dependence observed for the γ-CD complexes. These results can be justified in terms of the location of the dye molecule within the cyclodextrin cavity for each of the complexes.     

IBIsCO: a molecular dynamics simulation package for coarse-grained simulation

IBIsCO is a parallel molecular dynamics simulation package developed specially for coarse-grained simulations with numerical potentials derived by the iterative Boltzmann inversion (IBI) method (Reith et al., J Comput Chem 2003, 24, 1624). In addition to common features of molecular dynamics programs, the techniques of dissipative particle dynamics (Groot and Warren, J Chem Phys 1997, 107, 4423) and Lowe-Andersen dynamics (Lowe, Europhys Lett 1999, 47, 145) are implemented, which can be used both as thermostats and as sources of friction to compensate the loss of degrees of freedom by coarse-graining. The reverse nonequilibrium molecular dynamics simulation method (Müller-Plathe, Phys Rev E 1999, 59, 4894) for the calculation of viscosities is also implemented. Details of the algorithms, functionalities, implementation, user interfaces, and file formats are described. The code is parallelized using PE_MPI on PowerPC architecture. The execution time scales satisfactorily with the number of processors.     

Synthesis and Insecticidal Activity of New 4-Hydroxy-2H-1-benzopyran-2-one Derivatives

Several stable and storable anticoagulant rodenticides involving both merits of acute and chronic rodenticides have been synthesized (Holbrook et al. in Arch Intern Med 165:1095–1106, 2005; Baglin et al. in Br J Haematol 132:277–285, 2006). The structures of synthesized compounds were confirmed by IR, ¹H NMR. The compounds were also evaluated for their anticoagulant and acute biologic activity (Lipton et al., JAMA 252:3004–3005, 3).