Fluorogenic sensing of CH3CO2- and H2PO4- by ditopic receptor through conformational change

Cyclo-bis-(urea-3,6-dichlorocarbazole) (1) forms a 1 : 2 complex with CH(3)CO(2)(-) and H(2)PO(4)(-) through hydrogen bonding with the two urea moieties, resulting in fluorescence enhancement via a combined photoinduced electron transfer (PET) and energy transfer mechanism. The binding mechanism involves a conformational change of the two urea receptors to a trans orientation after binding of the first anion, which facilitates the second interaction.     

Diketoacid HIV-1 integrase inhibitors: An ab initio study

The stable tautomeric forms of two representative arene-substituted diketoacid HIV-1 integrase inhibitors, 5-ClTEP and L-731,988, were investigated by B3LYP with 6-31G*, 6-31G(d,p), and 6-31+G(d,p) basis sets. Optimization with MP2/6-31G* was also performed for 5-ClTEP. The solvation effect was considered using a conductor-like screening model. With the density functional theory method, the trans diketo conformations are more stable than the cis conformers. The difference is 14 kJ mol(-1) for 5-ClTEP and 33 kJ mol(-1) for L-731,988. Two trans diketo structures were obtained. The difference between these two trans diketo structures is less than 4 kJ mol(-1) calculated at the B3LYP/6-311+G(3df,2p) level. Two enol forms prevail over the diketo tautomers and are calculated to have the same free energy. Because there is no barrier observed between these two enol forms, they can interchange easily such that a delocalized transition state is suggested to be the observed form. Contradictory to the results of the MP2 method that predicts a preference for the trans diketo forms, the B3LYP method predicts a preference for the enol tautomers, which is in agreement with the experimental results.     

Solid-state NMR study of ureidopyrimidinone model compounds

High-resolution (1)H and (15)N{(1)H} solid-state NMR experiments were conducted on two ureidopyrimidinone model compounds: dimeric 2-butylureido-6-methyl-4-pyrimidinone (1) and its bifunctional analogue N,N-1,6-hexanediyl(2-ureido-6-methyl-4-pyrimidinone) (4). High magic angle spinning rates and (1)H decoupling schemes were used to increase the proton spectral resolution. Upon heating 1 to 440 K, an increase in mobility was observed for non-hydrogen-bonded protons; the dimer remained in keto tautomeric form, which is capable of much stronger intermolecular hydrogen bonding than the enol tautomer. From these findings, it was concluded that this ureidopyrimidinone moiety should allow the design of strongly bonded molecular assemblies whose thermal stability compares favourably with that of conventional engineering polymers.     

Binding of inorganic oxoanions to macrocyclic ligands: effect of the degree of protonation on supramolecular assemblies formed by phosphate and [18]aneN(6)

Five macrocycle-oxoanion adducts have been isolated from aqueous solutions containing 1,4,7,10,13,16-hexaazacyclooctadecane ([18]aneN(6), L) and phosphoric acid whose pH had been adjusted to selected values in the 1-8 range. Four products, (H(6)L)(H(2)PO(4))(6).2H(3)PO(4) (1), (H(6)L)(H(2)PO(4))(6) (2), (H(4)L)(H(2)PO(4))(4).2H(2)O (4), and (H(4)L)(HPO(4))(2).7H(2)O (5) crystallized from aqueous solutions at pH 1, 3, 6, and 8, respectively, while (H(4)L)(H(2)PO(4))(4) (3) crystallized on diffusion of EtOH into an aqueous reaction mixture at pH 6. Single-crystal X-ray structure determinations enabled an examination of supramolecular interactions between protonated forms of [18]aneN(6), phosphoric acid and its conjugate bases, and water of solvation. The macrocycle adopts a variety of conformations in order to accommodate the supramolecular constructs formed by the oxoanions and solvent molecules as the relative proportions of interacting species are altered. At pH 1 and 3, the fully protonated macrocycle, [LH(6)](6+), is found with six H(2)PO(4)(-) anions. At pH 6 and 8, the tetraprotonated macrocycle, [LH(4)](4+), crystallizes with four H(2)PO(4)(-) and two HPO(4)(2)(-), respectively. Variations in the solute of crystallization are evident, with phosphoric acid being present at the lowest pH and water at pH 6 and 8. In 5, the seven unique water molecules form a string-of-pearls motif within which a new heptameric isomer, consisting of a water pentamer that uses a single water to interact with the other two unique water molecules, is found. Structures 1, 2, 4, and 5 exhibit eta-3 H-bonding of ammonium protons to a single oxygen of the guest phosphates located above and below the macrocyclic ring. In 3, two phosphate oxygens of the cavity anion interact with the macrocycle, one of which participates in eta-2 H-bonding with ammonium groups.     

Cerium(IV), neptunium(IV), and plutonium(IV) 1,2-phenylenediphosphonates: correlations and differences between early transuranium elements and their proposed surrogates

The in situ hydrothermal reduction of Np(VI) to Np(IV) and Pu(VI) to Pu(IV) in the presence of 1,2-phenylenediphosphonic acid (PhP2) results in the crystallization of Np[C(6)H(4)(PO(3)H)(2)](2)·2H(2)O (NpPhP2) and Pu[C(6)H(4)(PO(3)H)(PO(3)H(2))][C(6)H(4)(PO(3)H)(PO(3))]·2H(2)O (PuPhP2), respectively. Similar reactions have been explored with Ce(IV) resulting in the isolation of the Ce(IV) phenylenediphosphonate Ce[C(6)H(4)(PO(3)H)(PO(3)H(2))][C(6)H(4)(PO(3)H)(PO(3))]·2H(2)O (CePhP2). Single crystal diffraction studies reveal that although all these three compounds all crystallize in the triclinic space group P1?, only PuPhP2 and CePhP2 are isotypic, whereas NpPhP2 adopts a distinct structure. In the cerium and plutonium compounds edge-sharing dimers of MO(8) polyhedra are bridged by the diphosphonate ligand to create one-dimensional chains. NpPhP2 also forms chains. However, the NpO(8) units are monomeric. The protonation of the ligands is also different in the two structure types. Furthermore, the NpO(8) polyhedra are best described as square antiprisms (D(4d)), whereas the CeO(8) and PuO(8) units are trigonal dodecahedra (D(2d)). Bond-valence parameters of R(o) = 1.972 and b = 0.538 have been derived for Np(4+) using a combination of the data reported in this work with that available in crystallographic databases. The UV-vis-NIR absorption spectra of NpPhP2 and PuPhP2 are also reported and used to confirm the tetravalent oxidation states.     

Molecular Structure of an Isocytosine Analog: Combined X-ray Structural and Computational Study of 2-Diethylamino-6-methyl-5-n-propyl-4(3H)-pyrimidinone

The structure of 2-diethylamino-6-methyl-5-n-propyl-4(3H)-pyrimidinone has been studied by X-ray crystallography and quantum-chemical calculations. X-ray analysis established that 2-diethylamino-6-methyl-5-n-propyl-4(3H)-pyrimidinone exists exclusively as the lactam tautomer protonated at the N3 ring nitrogen in the solid state. Crystals of 2-diethylamino-6-methyl-5-n-propyl-4(3H)-pyrimidinone are monoclinic (space group P2₁/n); the unit-cell dimensions are: a = 11.0460(8) Å, b = 5.0064(4) Å, c = 22.8358(17) Å, = = 90°, = 90.521(1)°. In the crystal, molecules of 2-diethylamino-6-methyl-5-n-propyl-4(3H)-pyrimidinone are assembled in planar centrosymmetric dimers by strong resonance-assisted N—H···O intermolecular hydrogen bonds from the NH group of one molecule to the C=O of the adjacent molecule (N—H···O distance 2.804 Å). Bond distances and angles are generally similar to those reported for the corresponding tautomer of isocytosine and derivatives. Quantum-chemical calculations on 2-diethylamino-6-methyl-5-n-propyl-4(3H)-pyrimidinone are also reported in order to estimate the relative energies of the possible tautomeric forms; ab initio and DFT results predict the coexistence of the N3 and AH tautomers in the gas phase. There is excellent correspondence between the crystal and the HF/6-311G** or B3LYP/6-31G* calculated structures of the N3 lactam form; the largest deviations between the experimental and computed structures are mostly the effects of strong intermolecular H bonds in the crystal.     

A pyrimidine-like nickel(II) DNA base pair

4-(2'-Pyridyl)-pyrimidinone deoxyriboside is synthesized and characterized as a DNA metallo base-pair; this novel nucleoside forms a self-pair in the presence of Ni(II) and stabilizes double helical DNA to the same extent as a G.C pair.     

Adducts of thianthrene- and phenoxathiin cation radical tetrafluoroborates to 1-alkynes. Structures and formation of 1-(5-thianthreniumyl)- and 1-(10-phenoxathiiniumyl)alkynes on alumina leading to alpha-ketoylides and alpha-ketols

[structure: see text] Thianthrene cation radical tetrafluoroborate (Th*+ BF4(-)) added to the terminal alkynes 1-pentyne, 1-hexyne, 1-heptyne, 1-octyne, 1-nonyne, and 1-decyne to form trans-1,2-bis(5-thianthreniumyl)alkene tetrafluoroborates (1-6). Similarly, addition of phenoxathiin cation radical tetrafluoroborate (PO*+ BF4(-)) to the same alkynes gave 1,2-bis(10-phenoxathiiniumyl)alkene tetrafluoroborates (7-12). The trans configuration of two of the adducts (1 and 4) was shown with X-ray crystallography. When solutions of 1-6 in chloroform were stirred with activated alumina, cis elimination of a proton and thianthrene (Th) occurred with the formation of 1-(5-thianthreniumyl)alkyne tetrafluoroborates (1a-6a). Similar treatment of 8-12 caused elimination of a proton and phenoxathiin (PO) with formation of 1-(10-phenoxathiiniumyl)alkene tetrafluoroborates (8a-12a). Stirring of 1a-6a with alumina for short periods of time caused their conversion into 5-[(alpha-keto)alkyl]thianthrenium ylides (1b-6b) and alpha-ketols, RC(O)CH2OH (1c-6c).     

Probing the solvent-induced tautomerism of a redox-active ureidopyrimidinone

A ferrocene-functionalised ureidopyrimidinone has been synthesised that can signal the solvent-induced tautomerism of the dimeric 4[1H]-pyrimidinone form to the monomeric 6[1H]-pyrimidinone form.     

Acetals of lactams and acid amides. 40. Synthesis and hydrolytic cleavage of one-ring and two-ring derivatives of 4-pyrimidinone

The reaction of 1-benzyl-5-cyano-6-dimethylaminomethylene-1, 6-dihydro-4-pyrimidinone with acid leads to 5-benzyl-1,2,7,8-tetrahydropyrido[4,3-d]pyrimidine-1,8-dione, whereas the reaction with ammonia leads to a mixture of 3-cyano-4-benzylamino-2-pyridone and 1-amino-5-benzyl-7,8-dihydropyrido[4,3-d]-pyrimidin-8-one. Heating of the latter in aqueous ethylene glycol is accompanied by recyclization to give 4-benzylamino-5,6-dihydropyrido[2,3-d]pyrimidin-5-one. The reaction of 1-benzyl-4-ditnethylaminomethylene-5-cyano-1,6-dihydro-6-pyrimidinone with ammonia leads to 1-amino-7-benzyl-7,8-dihydropyrido[4,3-d]-pyrimidin-8-one. The rate constants for cleavage of the pyrimidine ring in a number of 4-pyrimidinone derivatives were measured.See [1] for communication 39.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 4, pp. 532–537, April, 1984.     

The chemistry of 4-azido-2-pyrimidinone nucleosides revisited

Treatment of 4-azido-2-pyrimidinone nucleoside 1 with MeOH/K2CO3 or ammonium hydroxide led to derivatives 2 and 3, respectively. Both compounds derived from a nucleophilic addition at the modified base 2-position. These results contrast with the previously reported sensitivity of the 4-azido-2-pyrimidinone nucleoside 6-position to nucleophiles.     

Coordination chemistry of the water-soluble ligand TPPTP and formation of a [Mo(CO)5(m-TPPTP)] monolayer on an alumina surface

Phosphonate and phosphonic acid functionalized phosphine complexes of platinum(II) were prepared via direct reaction of the ligands with K2PtCl4 in water. Either cis or trans geometries were found depending on the nature of the ligand. The crystal structure of P(3-C6H4PO3H2)3.2H2O (6b) (triclinic, P1, a = 8.3501(6) A, b = 10.1907(6) A, c = 14.6529(14) A, alpha = 94.177(6) degrees, beta = 105.885(6) degrees, gamma = 108.784(5) degrees, Z = 2) shows a layered arrangement of the phosphonic acid. The phosphonodiamide complex cis-[PtCl2(P[4-C6H4PO[N(CH3]2]]3)2].3H2O (10) was synthesized in 89% yield and hydrolyzed to the phosphonic acid complex using dilute HCl. Aqueous phase and silica gel supported catalytic phosphonylation of phenyl triflate using palladium phosphine complexes was achieved. A molybdenum complex, Mo(CO)5[P3-C6H4PO3H2)3] (11), was synthesized in situ and grafted to an alumina surface. XPS, RBS, and AFM studies confirm the formation of a monolayer of 11 on the alumina surface.     

Metalation of Biginelli compounds. A general unprecedented route to C-6 functionalized 4-aryl-3,4-dihydropyrimidinones

4-Aryl-6-methyl-3,4-dihydro-2(1H)-pyrimidinone esters (DHPMs) readily undergo metalation at the C-6 methyl (vinylogous ester) position on treatment with lithium diisopropylamide at -10 degrees C. The resulting anion intermediates can be treated with electrophilic reagents to afford functionalized DHPMs that have been chemically elaborated mainly at the C-6 position. Di- and trianion formation is also possible at both the vinylogous methyl and NH positions when reactions are performed with excess equivalents of the base.     

Vibrational spectra and conformations of chloromethyldimethyl- and tris(chloromethyl)phosphine oxides

A study was carried out on the IR spectra of (CH₃)₂P(O)CH₂Cl and (CH₂Cl)₂PO. The frequencies and forms of the normal modes were calculated. The molecular mechanics method was used to calculate the energy of the various conformations of these molecules. (CH₃)₂P(O)CH₂Cl in the liquid and solution is a mixture of trans and gauche conformations, while (CH₂Cl)₃PO is a mixture of trans,gauche,gauche, trans,gauche,gauche, and gauche,gauche,gauche conformations.S. M. Kirov Kazan Chemical Engineering Institute and A. E. Arbuzov Institute of Organic and Physical Chemistry, Kazan Branch, Academy of Sciences of the USSR. Translated from Zhurnal Strukturnoi Khimii, Vol. 30, No. 6, pp. 38–46, November–December, 1989.     

Two isotypic transition metal germanophosphates M(II)4(H2O)4[Ge(OH)2(HPO4)2(PO4)2] (M(II) = Fe, Co): synthesis, structure, Mössbauer spectroscopy, and magnetic properties

Synthetic, structural, thermogravimetric, M?ssbauer spectroscopic, and magnetic studies were performed on two new isotypic germanophosphates, M(II)(4)(H(2)O)(4)[Ge(OH)(2)(HPO(4))(2)(PO(4))(2)] (M(II) = Fe, Co), which have been prepared under hydro-/solvo-thermal conditions. Their crystal structures, determined from single crystal data, are built from zigzag chains of M(II)O(6)-octahedra sharing either trans or skew edges interconnected by [GeP(4)O(14)(OH)(4)](8-) germanophosphate pentamers to form three-dimensional neutral framework structure. The edge-sharing M(II)O(6)-octahedral chains lead to interesting magnetic properties. These two germanophosphates exhibit a paramagnetic to antiferromagnetic transition at low temperatures. Additionally, two antiferromagnetic ordering transitions at around 8 and 6 K were observed for cobalt compound while only one at 19 K for the iron compound. Low-dimensional magnetic correlations within the octahedral chains are also observed. The divalent state of Fe in the iron compound determined from the M?ssbauer study and the isothermal magnetization as well as thermal analyses are discussed.     

Photoisomerization and photochemistry of matrix-isolated 3-furaldehyde

3-Furaldehyde (3FA) was isolated in an argon matrix at 12 K and studied using FTIR spectroscopy and quantum chemistry. The molecule has two conformers, with trans and cis orientation of the O=C-C=C dihedral angle. At the B3LYP/6-311++G(d,p) level of theory, the trans form was computed to be ca. 4 kJ mol(-1) more stable than the cis form. The relative stability of the two conformers was explained using the natural bond orbital (NBO) method. In fair agreement with their calculated relative energies and the high barrier of rotamerization (ca. 34 kJ mol(-1) from trans to cis), the trans and cis conformers were trapped in an argon matrix from the compound room temperature gas phase in proportion ~7:1. The experimentally observed vibrational signatures of the two forms are in a good agreement with the theoretically calculated spectra. Broad-band UV-irradiation (λ > 234 nm) of the matrix-isolated compound resulted in partial trans → cis isomerization, which ended at a photostationary state with the trans/cis ratio being ca. 1.85:1. This result was interpreted based on results of time-dependent DFT calculations. Irradiation at higher energies (λ > 200 nm) led to decarbonylation of the compound, yielding furan, cyclopropene-3-carbaldehyde, and two C(3)H(4) isomers: cyclopropene and propadiene.     

Theoretical studies on the conformations and properties of phenylazonaphthalenes

The conformations of phenylazo‐2‐naphthalene (I) and phenylazo‐1‐naphthalene (II) have been studied using ab initio methods and density functional theory. The rotational potential energy surfaces about the C N bonds were calculated for both the trans and the cis forms at the PM3 and HF/STO‐3G levels. The PM3 method was found to be incapable for locating the energy minima correctly. The geometries of rotamers obtained from the HF/STO‐3G surface were fully optimized at the HF/6‐31G* and B3LYP/6‐31G* levels. Single‐point MP2/6‐31G* calculations have also been carried out at the HF/6‐31G* geometries. The vibrational spectra, standard thermodynamic functions, heats of formation, and equilibrium molar fractions have been obtained. According to the calculated results, I is comparatively more stable than II. The trans forms have much lower energies than the cis forms, implying that I and II mainly exist in the trans planar forms. The energy gap (ΔE) between the frontier molecular orbitals (MOs) of the cis forms are about 0.7 eV higher than those of the trans ones, indicating that change in geometry from trans to cis form will cause a hypsochromic effect. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 79: 25–33, 2000     

具有新结构类型的化合物Csln[PO3(OH)]2的合成与结构

水热法合成了新结构类型化合物CsIn[P03(0H)]2,并通过单晶X-射线衍射表征结构.标题化合物空间群为P121/c1(No.14),晶体学参数为:M=439.69,mP56,a=0.532 86(6)nm,b=0.91653(7)nm,c=1.478 39(14)nm,β=93.849(9).,V=0.7204(1)nm3,Z=4,Dx=4.054 g·cm-3,μ=8.713 mm-1,F(000)=800,R1= 0.0325,wR2=0.0874.在该化合物中,2个In06八面体和4个PO4四面体形成交连的六元环柱,并沿a轴方向形成近六方密堆积并连接成Cs+离子占据的十二元环结构隧道,六元环和十二元环连接构筑了三维网络结构.与类似化学计量比化合物Na2In2[PO3(0H)]4·H2O比较,标题化合物中十二元环的形成明显取决于隧道阳离子的大小,其拓扑构造可看作扩展的6,3-网格连接,化合物RbIn[PO3(0H)]2与之同构.     

DNA cleavage by the photocontrolled cooperation of Zn(II) centers in an azobenzene-linked dizinc complex

We synthesized a new photoactive dinuclear zinc(II) complex by linking two zinc centers with a ligand containing an azobenzene chromophore and investigated the DNA cleavage activities of its trans and cis forms. The trans structure of the dinuclear zinc complex was determined by X-ray crystallography, where each zinc center is situated in an octahedral coordination environment comprised of three nitrogen atoms from the ligand and three oxygen atoms from two nitrate ions. The dinuclear zinc complex containing the azobenzene chromophore was photoisomerizable between the trans and cis forms. The binding affinities of the trans and cis complexes with calf thymus (CT)-DNA were similar. Although the DNA cleavage activity of the trans complex was negligible, the cis complex was able to cleave DNA. We attribute the efficient activity of the cis complex to the cooperation of the two closely located zinc centers and the inactivity of the trans complex to the two metal centers positioned far away from each other. The DNA cleavage activity of the cis complex exhibited a pH-dependent bell-shaped profile, which has been observed in the hydrolytic cleavage of DNA by zinc complexes. The DNA cleavage activity was not inhibited by a major groove binder, methyl green, but decreased significantly by a minor groove binder, 4',6-diamidino-2-phenylindole, indicating that the dinuclear zinc complex binds to the minor groove of DNA. The present work shows the importance of the cooperation of two zinc ions for hydrolytic DNA cleavage, which can be photoregulated by linking the two metal centers with a photoisomerizable spacer, such as an azobenzene chromophore.     

Adducts of thianthrene- and phenoxathiin cation radical salts with symmetrical alkynes. Structure and formation of cumulenes on alumina leading to alpha-diketones, alpha-hydroxyalkynes, and alpha-acetamidoalkynes

[reaction: see text] Thianthrene cation radical tetrafluoroborate (Th*+ BF4-) added to 2-butyne, 3-hexyne, 4-octyne, and 5-decyne in MeCN to form trans bisadducts R(Th+)C=C(Th+)R, where R = Me, Et, Pr, Bu (7a-d). Phenoxathiin cation radical tetrafluoroborate (PO*+ BF4-) added similarly to the last three alkynes to form adducts R(PO+)C=C(PO+)R, 8b-d. Cyclic monoadducts were not found. The trans structures of 7 and 8 were deduced with X-ray crystallography (7c) and NMR spectroscopy. When solutions of adducts in CHCl3 and MeCN were deposited on activated alumina, elimination of thianthrene (Th) and phenoxathiin (PO) occurred almost quantitatively. Detailed studies with (7b-d) indicated that a cumulene (15) was formed by the elimination of Th and that 15 was subsequently converted into small amounts of other products. In CHCl3, these products were the respective alkyne, thianthrene 5-oxide, an alpha-diketone (11), an alpha-hydroxyalkyne (12), and hydrogen. The same products were formed in MeCN along with an alpha-acetamidoalkyne (13). The formation of 15 and products derived from it is explained and was confirmed by preparation and reactions of 2,3,4-hexatriene.