Effects of variable selection on CoMFA coefficient contour maps in a set of triazines inhibiting DHFR

Summary An example of a CoMFA study is described with the aim to discuss one of the major problems of this 3D QSAR method: lack of variable selection. It is shown that the use of nonrelevant energy parameters might produce CoMFA contour maps which poorly reflect the actual nature of the binding site and are in part statistical artefacts. The data set employed in our analysis comparises triazine inhibitors of dihydrofolate reductase (DHFR), isolated from chicken liver, which have already been the object of a QSAR study by other authors. Since three-dimensional structures of triazine-DHFR complexes are known, it was possible not only to reduce ambiguities in the superimposition of the ligands, but also to compare the resulting CoMFA contour maps with the enzyme active site.Supplementary material available: The Cartesian coordinates and the atomic charges of the PM3-optimized structures used in the CoMFA study are available as MOL2 files upon request.To whose memory this paper is dedicated.     

Factors influencing conformer equilibria in retro models of cisplatin-DNA adducts as revealed by moderately dynamic (N,N'-dimethyl-2,3-diaminobutane)PtG(2) retro models (G = a guanine derivative)

Typical cis-PtA(2)G(2) models of key DNA lesions formed by cis-type Pt anticancer drugs are very dynamic and difficult to characterize (A(2) = diamine or two amines; G = guanine derivative). Retro models have A(2) carrier ligands designed to decrease dynamic motion without eliminating any of three possible conformers with bases oriented head-to-tail (two: DeltaHT and LambdaHT) or head-to-head (one: HH). All three were found in NMR studies of eight Me(2)DABPtG(2) retro models (Me(2)DAB = N,N'-dimethyl-2,3-diaminobutane with S,R,R,S and R,S,S,R configurations at the chelate ring N, C, C, and N atoms, respectively; G = 5'-GMP, 3'-GMP, 5'-IMP, and 3'-IMP). The bases cant to the left (L) in (S,R,R,S)-Me(2)DABPtG(2) adducts and to the right (R) in (R,S,S,R)-Me(2)DABPtG(2) adducts. Relative to the case in which the bases are both not canted, canting will move the six-membered rings closer in to each other ("6-in" form) or farther out from each other ("6-out" form). Interligand interactions between ligand components near to Pt (first-first sphere communication = FFC) or far from Pt (second-sphere communication = SSC) influence stability. In typical cases at pH < 8, the "6-in" form is favored, although the larger six-membered rings of the bases are close. In minor "6-out" HT forms, the proximity of the smaller five-membered rings could be sterically favorable. Also, G O6 is closer to the sterically less demanding NH part of the Me(2)DAB ligand, possibly allowing G O6-NH hydrogen bonding. These favorable FFC effects do not fully compensate for possibly stronger FFC dipole effects in the "6-in" form. SSC, phosphate-N1H cis G interactions favor LambdaHT forms in 5'-GMP and 5'-IMP complexes and DeltaHT forms in 3'-GMP and 3'-IMP complexes. When SSC and FFC favor the same HT conformer, it is present at >90% abundance. In six adducts [four (S,R,R,S)-Me(2)DABPtG(2) and (R,S,S,R)-Me(2)DABPtG(2) (G = 3'-GMP and 3'-IMP)], the minor "6-out" HT form at pH approximately 7 becomes the major form at pH approximately 10, where G N1H is deprotonated, because the large distance between the negatively charged N1 atoms minimizes electrostatic repulsion and probably because the G O6-(NH)Me(2)DAB H-bond (FFC) is strengthened by N1H deprotonation. At pH approximately 10, phosphate-negative N1 repulsion is an unfavorable SSC term. This factor disfavors the LambdaHT R form of two (R,S,S,R)-Me(2)DABPtG(2) (G = 5'-GMP and 5'-IMP) adducts to such an extent that the "6-in" DeltaHT R form remains the dominant form even at pH approximately 10.     

Asymmetric Induction at C(β) and C(α) of N-Enoylsultams by Organomagnesium 1,4-Addition/Enolate Trapping

The 1,4-addition of alkylmagnesium chlorides to conjugated N-enoylsultams and subsequent ‘enolate trapping’ with aq. NH₄Cl or MeI/hexamethylphosphoric triamide generated centers of asymmetry at C(β) and/or at C(α) with good to excellent π-face defferentiation as demonstrated by the conversions 1 → 2 , 1 → 4 , and 8 → 9 . This holds also for the regioselective 1,4-addition of EtMgC1 to a dienoylsultam ( 15 → 16 ). Reactive conformations 1 ^≠, 8 ^≠, 13 , and 14 are postulated in agreement with X-ray evidence which also served for the structure determination of the product 9j .     

Structural researches on metal complexes with ligands containing the pyridoxal moiety: X-ray structure of chloro(N-pyridoxylidene-N′-salicyloylhydrazinato) copper(II) Monohydrate

Summary The x-ray crystal structure of the title complex is described Crystals are monoclinic, space groupP2₁/n, with unit-cell dimensions:a=18.070(2),b=13.471(2),c=6.788(2) Å,=94.70(1),Z=4. The structure was solved from diffractometer data by Patterson and Fourier methods and refined by least-squares techniques toR=5.0% for 2451 independent reflections. It consists of complex molecules, in which the copper atom square planar coordination comprises the chlorine atom, Cu-Cl=2.240(3) Å, and the organic ligand which acts as terdentate through the oxygen atom [Cu-O=1.948(3) Å] and a nitrogen atom, [Cu-N=1.933(5) Å] from the hydrazidic chain and the oxygen atom, [Cu-O = 1.894(4) Å] from the pyridoxal group.     

Spectrophotometric determination of noble metals with tin(II) in bromide solutions

In presence of tin(II) bromide, noble metals give coloured products which are suitable for spcctrophotometric determinations. The colours are red (platinum), yellow-orange (rhodium), yellow-brown (palladium), yellow (iridium) and violet (gold) They are extracted, except for gold, with isoamyl alcohol Platinum, rhodium and palladium can be separated from irdium, and rhodium and platinum from palladium. Rhodium and platinum can be determined simultaneously.     

Azobenzene complexes of dicyclopentadienyltitanium and dicyclopentadienylvanadium

Reactions of azobenzene with dicarbonyldicyclopentadienyltitanium(II), Ti(π-C₅H₅)₂(CO)₂, and dicyclopentadienylvanadium(II), V(π-C₅H₅)₂, have yielded the corresponding dicyclopentadienylmetal-azobenzene complexes.     

The EPR study of dialkyl nitroxides as probes to investigate the exchange of solutes between micellar and water phases

An EPR investigation of the kinetics of the exit, k ^-, and entrance, k ⁺, processes in micelles of sodium dodecyl sulfate, hexadecyltrimethylammonium bromide and polyoxyethylene(6)decanol of a family of para-substituted benzyl tert -butyl nitroxides and para-substituted benzyl hydroxyalkyl nitroxides is reported. The inclusion of nitroxide probes in the hydrophobic environment of the micelle gives rise to a reduction of the value of both nitrogen and β-proton splittings, with the result that the resonance fields for the M_I(2H _β ) = ±1lines of the free and included species are significantly different. The rate constants were obtained by analyzing the EPR line shape variations as function of surfactant concentration and temperature. The experimental value of k ⁺ obtained from the study of benzyl tert-butyl nitroxide indicates that the association reaction is very close to being controlled by diffusion. The value of the exit rate, k ^-, instead, depends on the probe hydrocarbon chain length. A comparison of our results with those obtained by luminescence quenching techniques is also reported.     

High-intensity ultrasound and microwave, alone or combined, promote Pd/C-catalyzed aryl-aryl couplings

Pd-catalyzed homo- and cross-couplings of boronic acids and aryl halides were successfully carried out both in aqueous media under high-intensity ultrasound (US) and in DME under microwave (MW). Heterogeneous catalysis with Pd/C was employed, avoiding phosphine ligands and phase-transfer catalysts. In a trial series involving 15 different iodo- and bromoaryls and 7 boronic acids, both energy sources drastically reduced reaction times affording biaryls in acceptable to good yields. With palladium(II) acetate as catalyst, electron-deficient aryl chlorides also reacted, affording a few biaryls in acceptable yields. Ullmann-type zinc-mediated homocoupling of iodo- and bromoaryls in the presence of Pd/C under CO₂ atmosphere was achieved in aqueous media under US, though not under MW. Suzuki homo- and cross-couplings were also carried out in a new reactor developed in our laboratory, featuring combined US and MW irradiation, further improving a green synthetic method.     

Novel chiral three-dimensional iron(III) compound exhibiting magnetic ordering at T(c) = 40 K

The preparation and crystal structure determination of the iron(III) compound of formula [(NH(4))(2)[Fe(2)O(ox)(2)Cl(2)].2H(2)O](n) (1) (ox = oxalate dianion) are reported here. Complex 1 crystallizes in the orthorhombic system, space group Fdd2, with a = 14.956(7) A, b = 23.671(9) A, c = 9.026(4) A, and Z = 8. The structure of complex 1 consists of the chiral anionic three-dimensional network [Fe(2)O(ox)(2)Cl(2)](2-) where the iron(III) ions are connected by single oxo and bisbidentate oxalato groups. The metal-metal separations through these bridging ligands are 3.384(2) and 5.496(2) A, respectively. Ammonium cations and crystallization water molecules are located in the helical pseudohexagonal tunnels defined by iron atoms. The longest iron-iron distance in the pseudohexagonal tunnel is 15.778(2) A whereas the shortest one is 8.734(2) A. The iron atoms are hexacoordinated: a terminal chloro ligand and five oxygen atoms, that of the oxo group and four from two cis coordinated oxalate ligands, build a distorted octahedral environment around the metal atom. The Fe-O(oxo) bond distance [1.825(2) A] is significantly shorter than the Fe(III)-O(ox) [average value 2.103(4) A] and Fe(III)-Cl bond distances [2.314(2) A]. Magnetic susceptibility measurements of 1 in the temperature range 2.0-300 K reveal the occurrence of a susceptibility maximum at 195 K and a transition toward a magnetically ordered state in the lower temperature region with T(c) = 40 K. The strong antiferromagnetic coupling through the oxo bridge (J = -46.4 cm(-1), the Hamiltonian being H = -JS(A).S(B)) accounts for the susceptibility maximum whereas a weak spin canting of approximately 0.3 degrees due to the antisymmetric magnetic exchange within the chiral three-dimensional network is responsible for the magnetic ordering. The values of coercive field (H(c)) and remnant magnetization (M(r)) obtained from the hysteresis loop of 1 at 5 K are 4000 G and 0.016 micro(B).