5-Bromo-3-(indan-1-yl-oxy)pyridin-2-amine.

The title compound, C(14)H(13)BrN(2)O, was obtained by reaction of indan-1-yl methane-sulfonate with 2-amino-5-bromo-pyridin-3-ol in the presence of caesium carbonate. The indane ring system is approximately planar [all but one of the C atoms are coplanar within 0.03 Å, the latter atom being displaced by 0.206 (2) Šfrom the mean plane through the remaining atoms] and forms a dihedral angle of 58.41 (4)° with the pyridine ring. In the crystal, centrosymmetrically related mol-ecules are linked into dimers by N-H⋯N hydrogen bonds.

2-Chloro-4-(1H-pyrazol-1-yl)-5-(trifluoro-meth-yl)pyrimidine.

The reaction of 2,4-dichloro-5-(trifluoro-meth-yl)pyrimidine with 1H-pyrazole gave two structural isomers in a 1:1 ratio that were separable by chromatography. The title compound, C(8)H(4)ClF(3)N(4), was the first product to elute and was characterized in the present study to confirm that substitution by the pyrazolyl group had occurred at position 4. The mol-ecule (with the exception of the F atoms) is essentially planar, with a mean deviation of 0.034 Šfrom the least-squares plane through all non-H and non-F atoms. The bond angles in the pyrimidine ring show a pronounced alternating pattern with three angles, including those at the two N atoms being narrower, and the remaining three wider than 120°.

2-(6-Bromo-3-pyrid-yl)-8-methyl-imidazo[1,2-a]pyrazine.

The structure of the title compound, C(12)H(9)BrN(4), prepared by the reaction of 2-bromo-1-(6-bromo-3-pyrid-yl)ethanone with 2-amino-3-methyl-pyrazine indicates that the compound with the bromo-pyridyl substituent at position 2 of the imidazopyrazine fused-ring system represents the major product of this reaction. The plane of the pyridine ring forms a dihedral angle of 16.2 (2)° with the essentially planar (r.m.s. deviation = 0.006 Å) imidazopyrazine system. In the crystal, mol-ecules are linked by weak C-H⋯N inter-actions.

5-Bromo-1H-thieno[2,3-d]imidazole.

The crystal structure of the title compound, C(5)H(3)BrN(2)S, shows that bromination of 1H-thieno[2,3-d]imidazole with N-bromo-succinimide in acetonitrile occurs at position 5 of the bicyclic system. The mol-ecule is almost planar, with a mean deviation of 0.015 Šfrom the least-squares plane through all the non-H atoms. In the crystal, N-H⋯N hydrogen bonds link the mol-ecules into infinite C(4) chains running along [101].

trans-4-(2-Amino-5-bromo-6-methyl-pyrimidin-4-ylamino)-1-methyl-cyclo-hexa-nol.

The title compound, C(12)H(19)BrN(4)O, represents the minor component of the two products obtained in a series of transformations involving the Grignard reaction of tert-butoxy-carbonyl-protected 4-amino-cyclo-hexa-none with MeMgBr, and subsequent inter-action of the obtained amino-substituted cyclo-hexa-nol with 4-chloro-6-methyl-pyrimidin-2-amine followed by bromination with N-bromo-succinimide. The X-ray structure showed that this product represents a trans isomer with respect to the amino and hydr-oxy substituents in the cyclo-hexyl ring; the dihedral angle between the amino-pyrimidine plane and the (noncrystallographic) mirror plane of the substituted cyclo-hexyl fragment is 33.6 (3)°. Only two of the four potentially 'active' H atoms participate in inter-molecular N-H⋯O and O-H⋯N hydrogen bonds, linking the mol-ecules into layers parallel to the (10) plane.

6-Methyl-sulfanyl-4H-pyrimido[1,6-a]pyrimidin-4-one.

Reaction of 2-(methyl-sulfan-yl)pyrimidin-4-amine with the 5-(methoxy-vinyl-idene) derivative of Meldrum's acid and subsequent heating of the product in Dowtherm fluid yielded the title compound, C(8)H(7)N(3)OS, which was proven to contain a bicyclic 4H-pyrimido[1,6-a]pyrimidine system. All non-H atoms of the mol-ecule are coplanar within 0.15 Å. The bond-length distribution in the bicyclic core shows localization of the double bonds. The geometry of the intra-molecular S⋯O 1,5-contact [2.534 (2) Å] is consistent with the existence of an attractive inter-action.

2-Morpholino-4-oxo-4,5-dihydro-thio-phene-3-carbonitrile.

The title compound, C(9)H(10)N(2)O(2)S, was obtained from the treatment of ethyl 4-cyano-3-hydr-oxy-5-morpholinothio-phene-2-carboxyl-ate with concentrated HCl. The mean plane of the essentially planar dihydro-thio-phene ring is almost orthogonal to the mirror plane of the N-morpholine substituent, making a dihedral angle of 87.2 (2)°.

4-Chloro-7-hydr-oxy-6-methyl-1,7-naphthyridin-8(7H)-one.

The title compound, C(9)H(7)ClN(2)O(2), was prepared by reaction of methyl 4-chloro-3-(prop-1-yn-yl)picolinate with hydroxy-l-amine in MeOH/KOH solution. The two essentially planar mol-ecules which make up the asymmetric unit have almost identical geometries and and are linked into dimeric aggregates via pairs of O-H⋯O hydrogen bonds. These aggregates have almost perfect inversion symmetry; however, quite unusually, the inversion center of the dimer does not coincide with the crystallographic inversion center.

(3aS,7aS)-5-[(S)-3,3,3-Trifluoro-2-meth-oxy-2-phenyl-propano-yl]-2,3,4,5,6,7-hexa-hydro-1H-pyrrolo[3,4-c]pyridin-3(2H)-one monohydrate.

rac-Benzyl 3-oxohexa-hydro-1H-pyrrolo[3,4-c]pyridine-5(6H)-carboxyl-ate was separated by chiral chromatography, and one of the enanti-omers ([α](22) (D) = +10°) was hydrogenated in the presence of Pd/C in methanol, producing octa-hydro-3H-pyrrolo[3,4-c]pyridin-3-one. The latter was reacted with (2R)-3,3,3-trifluoro-2-meth-oxy-2-phenyl-propanoyl chloride [(R)-(-)-Mosher acid chloride], giving rise to the title compound, C(17)H(19)F(3)N(2)O(3)·H(2)O. The present structure established the absolute configuration of the pyrrolopiperidine fragment based on the known configuration of the (R)-Mosher acid chloride. The piperidine ring has a somewhat distorted chair conformation and is cis-fused with the five-membered envelope-shaped ring; the plane of the exocyclic amide bond is approximately orthogonal to the plane of the phenyl ring, making a dihedral angle of 82.31 (3)°. The water mol-ecule acts as an acceptor to the proton of the amino group in an N-H⋯O inter-action, and as a double proton donor in O-H⋯O hydrogen bonds, generating infinite bands along the a axis.

5-Chloro-N-[2-(1H-imidazol-4-yl)eth-yl]-N-methyl-7H-pyrrolo[2,3-d]pyrimidin-4-amine.

The title compound, C(12)H(13)ClN(6), was prepared by reaction of 4,5-dichloro-7H-pyrrolo[2,3-d]pyrimidine with 2-(1H-imid-azol-4-yl)-N-methyl-ethanamine, and the X-ray study confirmed that chloro-substituent in six-membered ring was replaced in the reaction. The exocyclic N atom environment is approximately coplanar with the pyrrolo[2,3-d]pyrimidine [corresponding dihedral angle is 5.5 (1)°], whereas the mean plane of the N-C-C-C link connecting with the imidazolyl ring is almost exactly orthogonal to the plane of the bicyclic system [dihedral angle = 91.6 (2)°]. The imidazolyl plane itself, however, forms a relatively small dihedral angle of 20.8 (1)° with the pyrrolo[2,3-d]pyrimidine plane. There are two independent N-H⋯N hydrogen bonds in the structure, which link mol-ecules into layers parallel to (03).

6-(2,6-Dimethyl-phen-yl)pyrido[2,3-d]pyrimidin-7-amine.

In the title compound, C(15)H(14)N(4), the pyrido[2,3-d]pyrimidine system is almost ideally planar (r.m.s. deviation 0.028 Å) with its mean plane almost orthogonal to the 2,6-dimethyl-phenyl plane. The dihedral angle formed by these planes [87.3 (2)°] is close to the predicted value (89.7°) obtained by mol-ecular-mechanics force-field calculations. Only one of the two active amine H atoms participates in hydrogen bonding, which links mol-ecules into centrosymmetric dimers.

(R)-N-Methyl-4-[2-(methyl-sulfan-yl)pyrimidin-4-yl]-1-(tetra-hydro-furan-3-yl)-1H-pyrazol-5-amine.

The chiral center at the substituted atom of the tetra-hydro-furanyl ring in the title compound, C(13)H(17)N(5)OS, has an R configuration. The methyl-sulfanylpyrimidine group and the pyrazole ring are almost coplanar [the maximum deviation from this plane is 0.070 (4) Å], the N-Me substituent being displaced from the methyl-sulfanylpyrimidine-pyrazole plane by 0.880 (4) Å. The secondary amine group participates in an intra-molecular hydrogen bond with the pyrimidine N atom in position 3.

(R)-4-[2-(Methyl-sulfanyl)pyrimidin-4-yl]-1-(tetra-hydro-furan-3-yl)-1H-pyrazol-5-amine.

The title compound, C(12)H(15)N(5)OS, was obtained by reaction of 2-(2-(methyl-thio)pyrimidin-4-yl)-3-oxopropane-nitrile with (tetra-hydro-furan-3-yl)hydrazine dihydro-chloride, and the racemic product was subsequently separated by chiral chromatography (first peak; [α](D) (20) = +51.3°). The chiral center at the substituted atom of the tetra-hydro-furanyl group has an R-configuration. The pyrimidine and pyrazolyl rings are almost coplanar, their mean planes forming a dihedral angle of 6.4 (1)°. One of the H atoms of the amino group participates in an intra-molecular hydrogen bond with the pyrimidine N atom in position 3. The second H atom is involved in an inter-molecular hydrogen bond, which links the mol-ecules into an infinite chain.

tert-Butyl 4-(1-methyl-1H-pyrazol-5-yl)piperidine-1-carboxyl-ate.

The reaction of (E)-tert-butyl 4-[3-(dimethyl-amino)acrylo-yl]piperidine-1-carboxyl-ate with methyl-hydrazine leads to the formation of the title compound, C(14)H(23)N(3)O(2), with a 1-methyl-1H-pyrazol-5-yl substituent. The plane of the pyrazole ring forms a dihedral angle of 33.4 (1)° with the approximate mirror plane of the piperidine ring.

Methyl 3-[3-(ethoxy-carbon-yl)thio-ureido]-1H-pyrazole-5-carboxyl-ate.

The title compound, C(9)H(12)N(4)O(4)S, was proven to be the product of the reaction of methyl 5-amino-1H-pyrazole-3-carboxyl-ate with ethyl isothio-cyanato-carbonate. All non-H atoms of the mol-ecule are planar, the mean deviation from the least squares plane being 0.048 Å. The intra-molecular N-H⋯O bond involving the NH-group, which links the thio-urea and pyrazole fragments, closes a six-membered pseudo-heterocyclic ring, and two more hydrogen bonds (N-H⋯O with the participation of the pyrazole NH group and N-H⋯S involving the second thio-urea NH group) link the mol-ecules into infinite chains running along [10].

Racemic N-methyl-4-[2-(methyl-sulfan-yl)-pyrimidin-4-yl]-1-(tetra-hydro-furan-3-yl)-1H-pyrazol-5-amine.

The title compound, C(13)H(17)N(5)OS, was obtained by cyclo-addition of 2-[2-(methyl-sulfan-yl)pyrimidin-4-yl]-3-oxo-propane-nitrile with (tetra-hydro-furan-3-yl)hydrazine dihydro-chloride and subsequent N-methyl-ation of 4-[2-(methyl-sulfan-yl)-pyrimidin-4-yl]-1-(tetra-hydro-furan-2-yl)-1H-pyrazol-5-amine with methyl iodide. The two mol-ecules in the asymmetric unit have opposite absolute configurations and are related by a noncrystallographic inversion center. Both feature intra-mol-ecular N-H⋯N hydrogen bonds. The geometry of the mol-ecules is similar to that observed in the structure of a single enanti-omer of the title compound.

3-Amino-5-bromo-2-iodo-pyridine.

The reaction of 3-amino-5-bromo-pyridine with N-iodo-succinimide in the presence of acetic acid produces the title compound, C(5)H(4)BrIN, with an iodo substituent in position 2 of the pyridine ring. The crystal structure features rather weak inter-molecular N-H⋯N hydrogen bonds linking the mol-ecules into chains along the z axis of the crystal.

High-throughput preparative process utilizing three complementary chromatographic purification technologies.

A high-throughput process was developed in which wells in plates generated from parallel synthesis are automatically channeled to an appropriate purification technique using analytical data as a guide. Samples are directed to either of three fundamentally different preparative techniques: HPLC with UV-triggered fraction collection, supercritical fluid chromatography (SFC) with UV-triggered fraction collection, or HPLC with MS-triggered fraction collection. Automated analysis of the analytical data identifies the product compound mass and creates work lists based on chromatographic properties exhibited in the data so that each preparative instrument cherry picks the appropriate list of samples to purify when a preparative-scale plate is loaded.

High-throughput bioassay-guided fractionation: a technique for rapidly assigning observed activity to individual components of combinatorial libraries, screened in HTS bioassays.

In this paper, we describe an automated, high-throughput analytical tool for the unambiguous characterization of the active component(s) of a combinatorially derived reaction mixture. We call this technique high-throughput bioassay-guided fractionation (BGF). The novel aspects of this communication are the systematization of the BGF concept, the application of BGF to combinatorial chemistry, and the high-throughput nature of the identification technique. The identification of the active component in a well mixture is an essential step for subsequent resynthesis or isolation of the active component(s) or for removal of intractable wells from further consideration. We believe the technique described is also applicable to any mixture library, provided the expected component (or components) of each well is (are) known. Example mixture libraries would include collections of synthetic chemicals and collections of purified natural products. The mixture need not come from libraries produced using parallel synthesis. The BGF tool described herein allows full utilization of highly diverse combinatorial libraries, thereby obviating costly up-front purification or extensive prescreening characterization efforts.