Interaction of formaldehyde with nucleic acids and their structural components in the presence of amines. II. Structure of adenine derivatives formed in the reaction with formaldehyde and primary amine

Two products of modified adenine have been isolated from reaction of adenine with a mixture of formaldehyde and methylamine; their structures have been demonstrated by UV, 1H NMR and mass spectra data. The formal scheme of reaction can be described as simultaneous or sequential cycloaddition of dimethylol derivatives of methylamine to two reaction's positions of the adenine residue. This results in the formation of a new partly or completely hydrogenated six-membered 1,3,5-triazine cycle which has the atoms of adenine nitrogen in its 1,3-positions and nitrogen of methylamine in 5-position. This is used as a model for discussing the peculiarities of DNA-formaldehyde interaction in the presence of amine.     

Reaction of iron(III)-polyaminocarboxylate complexes with hydrogen peroxide: Correlation between ligand structure and reactivity

Reactions of iron(III) complexes with five polyaminocarboxylates and hydrogen peroxide in an alkaline solution were investigated. Iron(III) complexes of which the ring including two nitrogen and iron atoms is five-membered formed a well-known stable side-on peroxo adduct. On the other hand, iron(III) complexes which have a six-membered ring formed a short-lived side-on peroxo adduct and then changed to iron(II) complex and superoxide. Electrochemical measurements showed that the redox potentials of the iron complexes having a six-membered ring are higher than those of the complexes having a five-membered ring. These results indicate that the chelate size is an important factor for tuning the redox potential of the iron center and for the reactivity toward hydrogen peroxide.     

Computational investigation of double nitrogen doping on graphene

Density functional theory (DFT) calculations were performed to study doping of two nitrogen atoms at different positions on a finite-sized graphene model of C₈₂H₂₄. We examined 21 structures of double nitrogen doped graphene to calculate their relative stabilities. The structure with two nitrogen atoms located apart is the most stable among the positional isomers considered in this study. For double nitrogen doping within a six-membered ring, the 1,4-position is more preferred than 1,3- or 1,2-positions for the finite-sized single layer graphene sheet. Our computational study supports the experimental observation of two nitrogen atoms at the 1,3- and 1,4-positions in a single six-membered ring of graphene. Furthermore, the structures with N-N bond are the least stable among two nitrogen doped graphene structures. The effects of nitrogen doping and the positions of two nitrogen atoms on the HOMO-LUMO energy gap of pristine graphene were analyzed.     

The effect of histidyl residues on the complexation of bis(imidazolyl) containing tripeptides with copper(II) ion

Copper(II) complexes of tripeptide derivatives of bis(imidazol-2-yl) group have been studied by potentiometric, UV-visible and EPR spectroscopic methods. The peptide molecules correspond to the amino acid sequence of collagen containing histidyl residues in different locations and were connected to the bis(imidazol-2-yl) group either on the C-termini (BOC-Pro-Leu-His-BIMA, BOC-His-Leu-Gly-BIMA) or on the N-termini (BIP-His-Ala-Gly-OEt, BIP-Ile-Ala-His-OMe). It was concluded that the imidazole nitrogen donor atoms of the bis(imidazol-2-yl) moiety are the primary metal binding sites, but the histidyl imidazole nitrogens in the side chains have also some effect on the stability and the coordination mode of the complexes. All ligands can coordinate tridentately to copper(II) ion forming a six-membered chelate and a macrochelate in the [CuL]2+ complexes, which results in a slight distortion in the coordination geometry of [CuL2]2+ complexes. The deprotonation and coordination of amide nitrogens, however, were not observed in any cases.     

Model studies on the coordination of copper in biological systems. The deprotonated peptide nitrogen as a potential binding site for copper(II)

1. A large number of potentially bidentate and tridentate amides, X-Y-CONH-Z, were used as model ligands to investigate the complex formation of Cu(II) with the deprotonated peptide nitrogen in biological molecules. A combination of potentiometric titration, spectrophotometry and electron paramagnetic resonance was applied to analyse the structure of the Cu(II) chelates formed at neurtal and basic pH. 2. By systematic variation of the primary binding function X, the ring size of the chelate, and the spatial properties of the C-terminal and N-terminal substituents, three classes of amide ligands could be established with reference to their capacity for Cu(II)-induced deprotonation of NHCO and metal binding. 3. Under physiological conditions of pH, peptide (class A) chelates are only formed by those bidentate amide ligands with X being an imidazole (sp2) nitrogen or a terminal (sp3) amino nitrogen. Mercaptide sulfur must also be considered to belong in this group of strong copper(II)-binding sites, but in our low-molecular-weight model ligands the redox equilibrium 2 Cu(II) + 2 RSH in equilibrium or formed from 2 CU(II) + RSSR + 2 H+ interferes, yielding insoluble Cu(I)-S polymers above pH 4. In addition to the unidentate binding strength of X, entropy effects play an important role. Depending on whether X is an imidazole or amino nitrogen, only five-membered or six-membered monocyclic chelate structures respectively cause coordination of the deprotonated peptide function. 4. Biuret (class B) Cu(II) chelates are only formed under non-physiological conditions at pH > 11.5 producing the well known violet chromophores CuIIN4(-). In general these complexes, which also include the Cu(II) biguanides, show a clearly resolved electron paramagnetic resonance spectrum with nitrogen superhyperfine structure. 5. A third class of peptide model ligands (class C) consists of those amides where the CuII-X bond does not provide enough thermodynamic stability. The binding site of these class C amides includes functional groups such as carboxylate (COO-), methionine sulfur (RSR'), aliphatic or aromatic hydroxyl (OH) and amide nitrogen (NHCO) itself. When X is a pyridine (sp2) nitrogen or an amino (sp3) nitrogen, NHCO deprotonation is only promoted in five-membered but not six-membered ring chelates. On the other hand, a combination of COO- and NH2, as in asparagine, will allow deprotonation of NHCO in the presence of Cu(II). And third, despite a pronounced unidentate affinity of the imidazole nitrogen for Cu(II), N-acetylhistamine acts as a class C amine, in contrast to imidazolylacetamide, which forms a stable Cu(II) peptide chelate. This difference in Cu binding is explained on the basis of space-filling models. These clearly demonstrate that in the case of the 2:1 complex of Cu(II) with N-acetylhistamine, the planarity of the ionised peptide function can not be retained in a square planar arrangement of the two amide ligands around the copper center.     

X-ray photoelectron spectroscopy of DNA-Pt complexes. Evidence of O6 (Gua)-N7 (Gua) chelation of DNA with cis- dichlorodiamine platinum(II).

The binding energies of nitrogen, oxygen, phosphorus, chlorine and Pt in several DNA - Pt (II) complexes are reported and discussed. The nitrogen band of DNA is slightly shifted upon complexation with Pt. Oxygen binding energies in the complexes studied clearly show that cis-Pt(NH3)2Cl2 forms a specific chelate N7(Gua) - O6 (Gua) with DNA as opposed to trans-Pt(NH3)2Cl2 and the other Pt compounds which react only with the N7(Gua) site of DNA.     

Alfalfa N2-fixation enhances the phosphorus uptake of walnut in interplantings

Walnut tree seedlings exhibited greater phosphorus (P) uptake from³²P-labelled hydroxyapatite when interplanted with alfalfa than with other walnuts, black locust, or orchard grass. Three mechanisms are proposed as possible explanations of this enhnaced P uptake by walnut. In this study, diffusion of solubilized apatite-P to the roots of walnut at points of walnut-alfalfa root intersection is believed to be the operative mechanism. Phosphorus is solubilized due to rhizosphere acidification of alfalfa during nitrogen fixation. These results underscore the interdependence of nutrient cycles. Enhancement of the phosphorus cycle through manipulation of the nitrogen cycle has important implications for world food and fiber production.     

Co-ordination compounds derived from dimethylhydrazones of cyclohexane-1,2-dione, 2-acetyl- and 2-benzoylpyridines and 4-bezoylpyridine

The 1,1-dimethylhydrazones of cyclohexane-1,2-dione (CDDMH), 2-acetylpyridine (APDMH) and 2-benzoylpyridine (2BPDMH) from tetrahedral complexes MX₂L (M = Co(II), Zn(II); X = Cl, Br) in which the ligand is chelating through the methylene nitrogen atoms (CDDMH) or one methylene and one pyridine nitrogen atom (APDMH, 2BPMDH). Octahedral complexes CoX₂L₂ (X = Cl, NCS; L = APDMH, 2BPDMH) have also been isolated but no tris-ligand complexes. The ligand 4-benzoylpyridine-dimethylhydrazone (4BPDMH) does not chelate but forms tetrahedral complexes MX₂(4BPDMH)₂ in which the unidentate ligand co-ordinates through the pyridine nitrogen atom.     

Electron-topological, energetic and π-electron delocalization analysis of ketoenamine-enolimine tautomeric equilibrium

The ketoenamine-enolimine tautometic equilibrium has been studied by the analysis of aromaticity and electron-topological parameters. The influence of substituents on the energy of the transition state and of the tautomeric forms has been investigated for different positions of chelate chain. The quantum theory of atoms in molecules method (QTAIM) has been applied to study changes in the electron-topological parameters of the molecule with respect to the tautomeric equilibrium in intramolecular hydrogen bond. Dependencies of the HOMA aromaticity index and electron density at the critical points defining aromaticity and electronic state of the chelate chain on the transition state (TS), OH and HN tautomeric forms have been obtained.     

Crystal and molecular structure of tris(propane-1,3-diamine)nickel(II) dinitrate complex

The title compound, [Ni(1,3-pn)₃](NO₃)₂, crystallizes in the orthorhombic space group Pbca with eight formula units in a cell of dimensions a = 17.146(8), b = 14.364(5) and c = 15.054(7). The structure was solved by the heavy-atom method and refined by least-squares calculations to R = 0.053 for 1439 counter data. It consists of discrete, slightly distorted octahedral [Ni(1,3-pn)₃]²⁺ cations and NO₃^? anions. One of the three six-membered chelate rings show a pronounced flattening unusual chair conformation. Magnetic and spectroscopic data agree to a lower stability of six-membered chelate rings, compared to five-membered chelate ones.     

Interaction of cisplatin with methionine- and histidine-containing peptides: competition between backbone binding,macrochelation and peptide cleavage

The pH- and time-dependent reaction of cis-[PtCl2(NH3)2] with the methionine- and histidine-containing peptides H-Gly-Met-OH, H-Gly-Gly-Met-OH, Ac-His-Gly-Met-OH, and Ac-His-(Ala)3-Met-OH at 313 K has been investigated by ion-pairing reverse phase HPLC and NMR spectroscopy. For equimolar solutions (c=0.8 mM, pH approximately equals 3 or 8.8), initial formation of the kinetically favored S-bound complex is followed by relatively rapid metallation of the neighboring methionine amide nitrogen NM to afford a kappa2NM,S six-membered chelate. The strong trans effect of the methionine S then favors facile NH3 substitution, leading to generation of tridentate complexes such as [Pt(H-Gly-MetH(-1)-OH)-kappa3NG,NM,S)(NH3)]+ or [Pt(H-Ac-His-GlyH(-1)-MetH(-1)-OH-kappa3NG,NM,S)(NH3)]. In the case of H-Gly-Gly-Met-OH, this reaction is accompanied by loss of a second NH3 ligand in alkaline solution to generate the tetradentate kappa4NG1,NG2,NM,S species. In contrast, cleavage of the backbone C(O)-N bond to the second metallated amide nitrogen after t>100 h is common to the tridentate complexes of the tri- and pentapeptides at pH<5. Although an imidazole-coordinated kappa2N3H,S macrochelate is formed throughout the whole range 2.5 < or = pH < or = 10 for Ac-His-Gly-Met-OH, it slowly decays (t=10-1000 h) to the thermodynamically more stable tridentate kappa3NG,NM,S complex. All major final products were separated and fully characterized by NMR and MS.     

Light,nitrogen, and phosphorus limitation of edaphic algae in a delaware salt marsh

The effects on edaphic algae associated with a pure stand of the cord grass, Spartina alterniflora Loisel of manipulating light intensity and additions of inorganic nitrogen and phosphorus as fertilizers to the marsh surface have been investigated for one year. The standing crop of edaphic algae as measured by chlorophyll a production was limited only by phosphorus supplies during fall and winter, by both phosphorus and nitrogen in spring, and only by nitrogen during the summer. Since the responses were in phase with the seasonal fluctuations in the concentration of nitrogen and phosphorus, it is concluded that the flood tide is the major source of nitrogen and phosphorus compounds for edaphic algal growth. Reduction in the quantity of light reaching the edaphic algae by Spartina cover is always a limiting factor for the standing crop. A gradient in the composition of the algal flora is directly related to light intensity, and indicates that this factor determines the relative contribution of diatoms and filamentous algae to the community. The interaction of light intensity and nutrients in regulating the production of edaphic algae and cord grass on the marsh under study over a yearly cycle has also been investigated.     

A gadolinium(III) complex of a carboxylic-phosphorus acid derivative of diethylenetriamine covalently bound to inulin, a potential macromolecular MRI contrast agent

A novel conjugate of a polysaccharide and a Gd(III) chelate with potential as contrast agent for magnetic resonance imaging (MRI) was synthesized. The structure of the chelate was derived from H5DTPA by replacing the central pendant arm by a phosphinic acid functional group, which was covalently bound to the polysaccharide inulin. On the average, each monosaccharide unit of the inulin was attached to approximately one (0.9) chelate moiety. The average molecular weight is 23110 and the average number of Gd3+ ions per molecule is 24. The ligand binds the Gd3+ ion in an octadentate fashion via three nitrogen atoms, four carboxylate oxygen atoms, and one P-O oxygen atom, and its first coordination sphere is completed by a water molecule. This compound shows promising properties for application as a contrast agent for MRI thanks to a favorable residence lifetime of this water molecule (170 ns at 298 K), a relatively long rotational correlation time (866 ps at 298 K), and the presence of two water molecules in the second coordination sphere of the Gd3+ ion. Furthermore, its stability toward transmetalation with Zn(II) is as high as that of the clinically used [Gd(DTPA)(H2O)]2-.     

Structural diversity of neutral bis-(β-iminoaldehyde) complexes of nickel(II)

Series of Ni^II and Cu^II complexes with dianionic [N₂O₂] ligands were synthesized and characterised applying spectroscopic and X-ray diffraction techniques. The ligands were obtained by 1:2 condensation of ethylene- and propylenediamine with malonic aldehyde derivatives (R² = H, R¹ = H or OCH₃). Although the molecular formulae of the complexes are quite similar, the X-ray investigations have proved a significant structural diversity in the solid state. Among others, we found some simple nearly planar molecules stacked in the crystal lattice with electron density of six-membered rings delocalised over the chelate rings as well as some very complex polymeric or nickel acetate bridged trinuclear complexes. The coordination of the nickel ion by surrounding oxygen and nitrogen atoms is square-planar in the simplest case and octahedral in the most complex one. Small topological differences in similar molecules generate completely different crystal structures.From magnetic studies, a small, negative value of J obtained confirms the occurrence of weak antiferromagnetic interactions between the Ni^II ions in polymeric chain of the propylenediamine dialdehyde substituted derivative.     

A study on the structures of the substituted (aminomethyl)lithium and (thiomethyl)lithium compounds

The structures of substituted (aminomethyl)lithium and (thiomethyl)lithium compounds have been examined. Geometric parameters, charge densities, bond orders, dipole moments and heats of formation for all the members of the two series of monomers and dimers of the units LiCN(R)2 and LiCSR where R=H, CH3(Me), C6H5(Ph) have been calculated. The structures of the three complex compounds containing the same units; [[Li(CH2SMe)(THF)]X], [Li2(CH2SPh)2(THF)4] and [Li2(CH2NPh2)2(THF)3] have also been modeled. Geometry optimizations have been performed with the semiempirical PM3 method. The molecular orbital calculations have been carried out by a self-consistent field method using the restricted Hartree-Fock formalism. Comparisons have been made with the corresponding properties of methyl lithium monomer and dimer. The results show that in all of the nitrogen-containing monomers, the C-Li bonds weaken and the Li-C-H(N) angles decrease due to the coordination of lithium with nitrogen. Substitution of hydrogen atoms by methyl or phenyl groups decreases the Li-N coordination. In the sulfur-containing compounds, sulfur behaves similarly to nitrogen but the changes are smaller because the 3p lone-pair orbital of sulfur is higher in energy than the 2p lone-pair of nitrogen. All the dimers of nitrogen/sulfur-containing methyl lithium derivatives form six-membered rings in which the Li-N(S) coordination is greater than the one in the corresponding monomers. Dimerization reactions have been found to be exothermic and the formation of all the dimers is favored. The results obtained for the three complex structures are comparable to the experimental results reported in the literature.Keywords:     

Nutrient ratios, differential retention, and the effect on nutrient limitation in a deep oligotrophic lake

Nutrient ratios have been related to nutrient limitation of algal growth in lakes. Retention of nutrients in lakes, by sedimentation and by denitrification, reduces the nutrient concentrations in the water column, thereby enhancing nutrient limitation. Differential retention of nitrogen and phosphorus alters their ratios in lakes and thereby contributes to determine whether nitrogen or phosphorus limits algal growth. We examined the relationships between differential nutrient retention, nutrient ratios, and nutrient limitation in Lake Brunner, a deep oligotrophic lake. The observed retention of nitrogen (20%) and phosphorus (47%) agreed with predictions by empirical equations from literature. As a result of differential retention with a much larger proportion of phosphorus retained than that of nitrogen, the nitrogen:phosphorus ratio was higher in the lake (69) than in the inflows (46). While the mean ratio in the inflows suggested no or only moderate phosphorus limitation, the lake appeared to be severely phosphorus limited. Combining empirical equations from literature that predict nitrogen and phosphorus retention suggests that the nitrogen:phosphorus ratio is enhanced by greater retention of phosphorus compared to nitrogen only in deep lakes with relatively short residence times, such as Lake Brunner. In contrast, in most lakes differential retention is expected to result in lower nitrogen:phosphorus ratios.     

Simultaneous nitrification,denitrification, and phosphorus removal in a lab-scale sequencing batch reactor

Simultaneous nitrification and denitrification (SND) via the nitrite pathway and anaerobic-anoxic-enhanced biological phosphorus removal (EBPR) are two processes that can significantly reduce the energy and COD demand for nitrogen and phosphorus removal. The combination of these two processes has the potential of achieving simultaneous nitrogen and phosphorus removal with a minimal requirement for COD. A lab-scale sequencing batch reactor (SBR) was operated in alternating anaerobic-aerobic mode with a low dissolved oxygen (DO) concentration (0.5 mg/L) during the aerobic period, and was demonstrated to accomplish nitrification, denitrification, and phosphorus removal. Under anaerobic conditions, COD was taken up and converted to polyhydroxyalkanoates (PHAs), accompanied by phosphorus release. In the subsequent aerobic stage, PHA was oxidized and phosphorus was taken up to <0.5 mg/L by the end of the cycle. Ammonia was also oxidized during the aerobic period, but without accumulation of nitrite or nitrate in the system, indicating the occurrence of simultaneous nitrification and denitrification. However, off-gas analysis showed that the final denitrification product was mainly nitrous oxide (N(2)O), not N(2). Further experimental results demonstrated that nitrogen removal was via nitrite, not nitrate. These experiments also showed that denitrifying glycogen-accumulating organisms (DGAOs), rather than denitrifying polyphosphate-accumulating organisms (DPAOs), were responsible for the denitrification activity.     

Preparation,characterization, and antitumor activity of new cisplatin analogues with 1-methyl-4-(methylamino)piperidine: crystal structure of [PtII(1-methyl-4-(methylamino) piperidine)(oxalate)

A series of new platinum(II) complexes of the type [Pt(II)(mmap)X] (where mmap, 1-methyl-4-(methylamino)piperidine and X, 1,1-cyclobutanedicarboxylato (CBDCA), oxalato, malonato, methylmalonato, dimethylmalonato, ethylmalonato, diethylmalonato or 2,3-naphthalene dicarboxylato (NDCA)) have been synthesized and characterized by elemental analysis, infrared (IR), and 13C and 195Pt nuclear magnetic resonance (NMR) spectroscopy. The crystal structure of the analogue [Pt(II)(mmap)(oxalate)] was determined using the single crystal X-ray diffraction method. Based upon a total of 4964 collected reflections, we determined that the compound crystallizes in the monoclinic space group P2(1)/c (with a=11.890(2) A, b=9.6695(19) A, c=9.875(2) A, beta=102.03(3) degrees, Z=4, and R=0.0428). In this complex, platinum has a slightly distorted square planar geometry with the two adjacent corners being occupied by two nitrogen atoms of the mmap ligand, whereas the remaining cis positions are occupied by two oxygen atoms of the oxalate molecule. The mmap ligand is in a boat conformation and forms six-membered chelating rings as well as the oxalate molecule forms five-membered chelating rings with platinum. The complexes were evaluated for their cytotoxic potential against the sensitive A2780 tumor model and cisplatin-resistant clone derived in vitro from potential cells.     

Boron complexes derived from the condensation reaction of 3-aminophenylboronic acid and 1,3-diketones

The structural analogy of 1,3-dicarbonyl compounds with 2-hydroxybenzencarbonyl compounds allowed to do an analysis towards the reactivity with 3-aminophenylboronic acid, in order to evaluate the synthesis of macrocyclic boron compounds having calixarene like structures. The results indicate that the chelate form is preferred over the reaction of the amino group with carbonyl groups. Thus the reaction of 1,3-diketones (1,3-diphenyl-1,3-propanedione, 1-phenyl-1,3-butanedione and 2,4-pentanedione) with 3-aminophenylboronic acid using methanol or propanol as solvent medium, afforded the six-membered boron chelates as the only product.     

Studies on the control of the cell cycle in cultured plant cells

Summary Patterns of cell cycle arrest or temporal modification have been investigated using suspension cultures ofAcer pseudoplatanus under nutrient limiting and nutrient starvation conditions. The results of nitrogen, phosphorous and carbohydrate starvation have been compared and contrasted with reference to the Principal Control Point hypothesis ofVan't Hof andKovacs (1972). Whilst cells suffering phosphorus or carbohydrate starvation arrest in the G 1 and G 2 phases in the approximate ratio of 4 to 1, nitrogen starved cells accumulate virtually exclusively in G 1.