Platinum(IV) complexes with ethylenediamine-N,N′-diacetate diester (R2edda) ligands: Synthesis, characterization and in vitro antitumoral activity

The novel N,N-type bidentate ligand precursors, diethyl, dipropyl esters of ethylenediamine-N,N′-diacetic acid dihydrochloride (HOOCCH₂NHCH₂CH₂NHCH₂COOH · 2HCl, H₂edda · 2HCl), and the corresponding tetrachloroplatinum(IV) complexes, [PtCl₄(R₂edda)] · H₂O (ROOCCH₂NHCH₂CH₂NHCH₂COOR, R = Me, Et, n-Pr), were synthesized. The esters coordinated as bidentate ligands via both N donor atoms. The esters, as well as the complexes, have been characterized by infrared, ¹H and ¹³C NMR spectroscopy and elemental analysis. Solid state structures of both dimethyl and diethyl ester platinum(IV) complexes have been determined by X-ray crystallography. Quantum chemical calculations were performed in order to investigate diastereoselectivity in the formation of the platinum(IV) complexes. The in vitro cytotoxic evaluation of the investigated complexes in human tumor cell lines 1411HP, H12.1 (both testicular germ cell tumors), DLD-1 (colon carcinoma), 518A2 (melanoma), A549 (lung carcinoma) and liposarcoma showed a dose-dependent antiproliferative effect in all cell lines. Remarkably, the highest cytotoxic activity was observed in the cisplatin-resistant cell line 1411HP. In addition, at higher concentrations the treatment with these complexes led to the induction of apoptosis in all cell lines except for DLD-1.     

Low temperature infrared spectra of polyglycines and C--H...O==C hydrogen bonding in polyglycine II

Infrared spectra of polyglycines I and II obtained at ?170°C. have been compared with those obtained at room temperature. The changes in frequency of some of the C—H stretching bands are consistent with the earlier suggestion that C—H …? O?C hydrogen bonds are present in the structure of polyglycine II.     

15N-nmr spectroscopy. 20. Cis/trans isomerism and neighboring residue effects of proline-containing peptides

Five N-protected tetrapeptide esters of the structure Gly-Pro-X-X*-O-methyl were synthesized in such a way that one of the two variable amino acid residues (X) was isotopically enriched in ¹⁵N (denoted by*). The variable amino acids are glycine, alanine, leucine, valine, and phenylalanine. For the natural abundance ¹⁵N-nmr spectra of these tetrapeptide derivatives in methylene chloride only the signals of the Gly-Pro trans isomer were found. In a 2:1 mixture of acetone and dimethylsulfoxide, signals for both the cis and trans isomers were observed. Three of the five tetrapeptide derivatives show cis/trans splitting of all four nitrogen signals. The ¹⁵N-nmr spectra of Z-Pro-Pro-OH and of (D ,L -proline)_n were measured in a 2:1 mixture of acetone and dimethylsulfoxide as well as in water. The effects of solvents and neighboring residues and the influence of the cis/trans isomerism on the nmr spectra are discussed. The determination of the cis/trans equilibria and the assignment of the ¹⁵N-nmr signals of all oligopeptides were achieved by selective isotopic enrichment and by means of ¹³C-nmr spectra.     

Low-frequency vibrational spectra of some homopolypeptides in the solid state

Low-frequency Raman and far-infrared spectra of polyglycine, poly-L -alanine, and poly-L -valine have been measured. The Raman spectra exhibit an intense band near 100 cm^?1 for these homopolypeptides. Lattice calculations of the polyglycines are used to assign the intense Raman band to a rotary lattice mode. For homopolypeptides in the β conformation, an infrared band is observed whose frequency varies inversely with the square root of the mass of the peptide repeating unit. This infrared band is assigned to the hydrogen bond stretching lattice vibration.     

Amide I band of IR spectrum and structure of collagen and related polypeptides

The infrared amide I band of collagens (rat and cod skin) and related compounds (polyproline, polyglycine, and polytripeptides) was studied. Assignment of amide I-band components for polyproline II and polytripeptides (Gly-Pro-Pro)_n and (Gly-Pro-Gly)_n in the solid state and water solution was made. Three amide I components observed in the polypeptide spectra were attributed to three different peptide CO groups in each triplet. On the basis of this assignment, the interpretation of the amide I multicomponent structure in collagen and isomorphous oligo- and polypeptides was attempted. The ordering of intra- and intermolecular hydrogen bonds involving peptide CO groups in collagen and related compounds was discussed.     

1H-nmr study of protected methionine homo-oligopeptides in helix-supporting environment

¹H-nmr spectra for a series of Boc-L -(Met)_n-OMe (n = 2–9) homo-oligopeptides have been observed in the helix-supporting solvent trifluoroethanol (TFE) at millimolar concentrations. Interfering solvent peaks were eliminated using two decoupling frequencies to selectively remove the methylene and hydroxyl protons of the solvent. Comparisons with specifically α-deuterated homo-oligopeptides gave complete assignments of the NH region of the Boc-Met_n-OMe oligomers up to the heptapeptide. Analysis of chemical shifts, coupling constants, and temperature dependence of chemical shifts suggests that up to the hexapeptide, similar structures exist in deuterochloroform and TFE. In contrast, nmr parameters at the heptapeptide for several internal residues differ in these solvents. These results suggest that a C₇ to α-helix transition may occur in TFE as the chain length of the methionine oligopeptides increases.     

The synthesis and use of a 15N and 2H isotopically-labelled derivative of the spin-trap 3, 5-dibromo-4-nitrosobenzenesulphonic acid

Summary

We report the synthesis and use of d₂-¹⁵N isotopically-labelled 3, 5-dibromo-4-nitrosobenzenesulphonic acid (DBNBS-d₂-¹⁵N, as its sodium salt), a spin-trap possessing several advantages over non-labelled DBNBS. The simplification in the electron paramagnetic resonance spectra of radical adducts of DBNBS-d₂-¹⁵N compared with those of DBNBS not only results in increased sensitivity, but also facilitates the assignment and analysis of complex spectra. An example of this simplification is given.     

Fluctuations of an alpha-helix.

Fluctuations in backbone dihedral angles in the α-helical conformation of homopolypeptides are studied based on an assumption that the conformational energy function of a polypeptide consisting of n amino-acid residues can be approximated by a 2n-dimensional parabola around the minimum point in the range of fluctuations. A formula is derived that relates 〈Δθ_iΔθ_j〉, the mean value of the product of deviations of dihedral angles ?_i and ψ_i (collectively designated by θ_i) from their energy minimum values, with a matrix inverse to the second derivative matrix F ,_n of the conformational energy function at the minimum point. A method of calculating the inverse matrix F _n^?1 explicitly is given. The method is applied to calculating 〈Δθ_iΔθ_j〉 for the α-helices of poly(L -alanine) and polyglycine. The autocorrelations 〈(Δ?_i)²〉 and 〈(Δψ_i)²〉 at 300°K are found to be about 66 deg² and 49 deg², respectively, for poly(L -alanine), and 84 deg² and 116 deg², respectively, for polyglycine. The length of correlations of fluctuations along the chain is found for both polypeptides to be about eight residues long.     

Bioremediation of Soil Contaminated with Diesel Using Inorganic Nitrogen Sources: Incorporating nth-Order Algorithm in the Evaluation of Process Kinetics

In the present study, we investigated the effects of inorganic nitrogen sources—(NPK fertilizer, 15:15:15), (urea fertilizer, 46:0:0), (NH₄)₂SO₄ as well as monitored natural attenuation on the bioremediation of diesel-polluted soil. At the end of the 6-week study, the highest degradation was recorded in soil amended with NPK fertilizer (95 ± 2.77%) while the least total petroleum hydrocarbon removal was observed in monitored natural attenuation (89 ± 2.91%). Nth-order kinetics effectively described three of the treatments out of the four treatment plans. These include urea amendment (r² = 0.9925, average relative error (ARE) = 1.45%, root mean square error (RMSE) = 0.038, k_n = (3.57 ± 0.61) × 10^?2, n = 1.33), NPK fertilizer amendment (r² = 0.9751, ARE = 3.241%, RMSE = 0.086, k_n = (8.04 ± 0.23) × 10^?1, n = 0.74), and monitored natural attenuation (r² = 0.9697, ARE = 2.77%, RMSE = 0.073, k_n = (1.57 ± 0.50) × 10^?2, n = 1.16). The values of n from the nth-order kinetics parameter estimation indicated that all the treatments resulted in diesel degradation that followed a first-order kinetics path. Thus, the outcome of kinetic modeling showed that nth-order can be used as validating tool when many kinetic orders are under consideration. The phytotoxicity assay with Zea mays showed that the treatments plans resulted in germination indices of 17–55%.     

High-level 2H/13C/15N labeling of proteins for NMR studies

Summary The protein human carbonic anhydrase II (HCA II) has been isotopically labeled with ²H, ¹³C and ¹⁵N for high-resolution NMR assignment studies and pulse sequence development. To increase the sensitivity of several key ¹H/¹³C/¹⁵N triple-resonance correlation experiments, ²H has been incorporated into HCA II in order to decrease the rates of ¹³C and ¹H_N T₂ relaxation. NMR quantities of protein with essentially complete aliphatic ²H incorporation have been obtained by growth of E. coli in defined media containing D₂O, [1,2-¹³C₂, 99%] sodium acetate, and [¹⁵N, 99%] ammonium chloride. Complete aliphatic deuterium enrichment is optimal for ¹³C and ¹⁵N backbone NMR assignment studies, since the ¹³C and ¹H_N T₂ relaxation times and, therefore, sensitivity are maximized. In addition, complete aliphatic deuteration increases both resolution and sensitivity by eliminating the differential ²H isotopic shift observed for partially deuterated CH_nD_m moieties.     

Cation-binding cyclic peptides with lipophilic tails

We have synthesized and characterized a series of cation-binding cyclic octapeptides which may function as potential ionophoric substances. The materials contain varying degrees of hydrophobic character, which was controlled systematically through the incorporation of N-alkylglycine residues where N-alkyl = methyl, n-hexyl, cyclohexyl, or n-decyl. The peptides reported include cyclo(Phe-Sar-Gly-Sar)₂, cyclo(Glu(OBzl)-Sar-Gly-Sar-Glu(OBzl)-Sar-Gly-(N-decyl)Gly), cyclo(Glu(OBzl)-Sar-Gly-(N-decyl)Gly)₂, cyclo(Glu(OBzl)-Sar-Gly-(N-hexyl)Gly)₂, cyclo(Glu(OBzl)-Sar-Gly-(N-cyclohexyl)Gly)₂, and the corresponding free diacid forms of the Glu-containing compounds. Using ¹³C- and ¹H-nmr spectra, we demonstrated that the mixture of cis/trans peptide bond-isomer conformers, characteristic of the free-peptide benzyl esters in solution, was converted to unique C₂-symmetric, presumably all-trans conformers on complexation with calcium ions. Cation-transport experiments, using the thick-liquid model of transport in a Pressman cell, established that these compounds transport a variety of cations and that one peptide examined in detail, cyclo(Glu(OBzl)-Sar-Gly-(N-decyl)Gly)₂ (selectivity Ca²⁺ > Na⁺ > K⁺ > Mn²⁺ > Cu²⁺ > Mg²⁺ > Co²⁺ > Zn²⁺), transports calcium about an order of magnitude more efficiently than magnesium.     

Isotopic signatures of N2O produced by ammonia-oxidizing archaea from soils

N₂O gas is involved in global warming and ozone depletion. The major sources of N₂O are soil microbial processes. Anthropogenic inputs into the nitrogen cycle have exacerbated these microbial processes, including nitrification. Ammonia-oxidizing archaea (AOA) are major members of the pool of soil ammonia-oxidizing microorganisms. This study investigated the isotopic signatures of N₂O produced by soil AOA and associated N₂O production processes. All five AOA strains (I.1a, I.1a-associated and I.1b clades of Thaumarchaeota) from soil produced N₂O and their yields were comparable to those of ammonia-oxidizing bacteria (AOB). The levels of site preference (SP), δ¹⁵N^bulk and δ¹⁸O -N₂O of soil AOA strains were 13–30%, −13 to −35% and 22–36%, respectively, and strains MY1–3 and other soil AOA strains had distinct isotopic signatures. A ¹⁵N-NH₄⁺-labeling experiment indicated that N₂O originated from two different production pathways (that is, ammonia oxidation and nitrifier denitrification), which suggests that the isotopic signatures of N₂O from AOA may be attributable to the relative contributions of these two processes. The highest N₂O production yield and lowest site preference of acidophilic strain CS may be related to enhanced nitrifier denitrification for detoxifying nitrite. Previously, it was not possible to detect N₂O from soil AOA because of similarities between its isotopic signatures and those from AOB. Given the predominance of AOA over AOB in most soils, a significant proportion of the total N₂O emissions from soil nitrification may be attributable to AOA.     

15N-nmr spectroscopy. 33. Assignments of isotactic and syndiotactic sequences in poly(D,L-amino acids)

¹⁵N-enriched (D ,L -Leu)_n, (γ-OMe-D ,L -Glu)_n, (D ,L -Val)_n, and (D ,L -Phe)_n were prepared, 40.55-MHz ¹⁵N-nmr spectra were measured in various solvents. The signal patterns depend strongly on the nature of the solvent, yet in most cases at least four signals are resolved, representing the four enantiomeric pairs of triads L -L -L (D -D -D ), L -D -L (D -L -D ), L -L -D (D -D -L ), and D -L -L (L -D -D ). Numerous copolypeptides of the general structure (A)_n-B*-(A)_m (the asterisk denotes 40–50% ¹⁵N enrichment) were synthesized and measured as models for syndiotactic sequences in the spectra of poly(D ,L -amino acids). In this way unambiguous assignments for both isotactic and syndiotactic trials were obtained. A spectroscopic rule was established: “isotactic sequences absorb downfield of syndiotactic ones.” Furthermore, the spectra of various types of stereocopolypeptides such as (L -Leu/L -Val)_n and (L -Leu/D -Val)_n were investigated, including the ternary systems (L -Leu/L -Ala/D -Ala)_n (L -Leu/L -Ala/Gly)_n, (L -Leu/D -Ala/Gly)_n, (L -Val/L -Ala/Gly)_n, and (L -Val/D -Ala/Gly)_n. All copolymerization of D - and L -amino acid NCAs investigated in this work showed a low degree of stereoselectivity.     

Synthesis, characterization and X-ray crystal structure of [Re(L4)(CO)3]Br · 2CH3OH (L4 = N,N-bis[(2-diphenylphosphino)ethyl]methoxyethylamine): A model compound for novel cationic Tc(I)-tricarbonyl radiotracers useful for heart imaging

This report describes synthesis and evaluation of cationic complexes, [^99mTc(CO)₃(L)]⁺ (L = N-methoxyethyl-N,N-bis[2-(bis(3-ethoxypropyl)phosphino)ethyl]amine (L1), N-[(15-crown-5)-2-yl]-N,N-bis[2-(bis(3-ethoxypropyl)phosphino)ethyl]amine (L2) and N-[(18-crown-6)-2-yl]-N,N-bis[2-(bis(3-ethoxypropyl)phosphino)ethyl]amine (L3)) as potential radiotracers for heart imaging. Preliminary results from biodistribution studies in female adult BALB-c mice indicated that the cationic ^99mTc(I)-tricarbonyl complex, [^99mTc(CO)₃(L2)]⁺, has a significant localization in the heart at 60 min post-injection. To understand the coordination chemistry of these bisphosphine ligands with the ^99mTc(I)-tricarbonyl core, we prepared [Re(CO)₃(L4)]Br (L4: N,N-bis[(2-diphenylphosphino)ethyl]methoxyethylamine) as a model compound. [Re(CO)₃(L4)]Br has been characterized by elemental analysis, IR, ESI-MS, NMR (¹H, ¹³C, ¹H-¹H COSY, and ¹H-¹³C HMQC) methods, and X-ray crystallography. In solid state, [Re(CO)₃(L4)]⁺ has a distorted octahedron coordination geometry with PNP occupying one facial plane. The chelator backbone adopts a “chair” conformation with phosphine-P atoms at equatorial positions and the amine-N at the apical site. In solution, [Re(CO)₃(L4)]⁺ is able to maintain its cationic nature with no dissociation of carbonyl ligands or any of the three PNP donors.     

Simultaneous determination of stable isotopically labelled l-histidine and urocanic acid in human plasma by stable isotope dilution mass spectrometry

A capillary gas chromatographic—mass spectrometric method for the simultaneous determination of stable isotopically labelled l-histidine (l-[3,3-²H₂,1′,3′-¹⁵N₂]histidine, l-His-[M + 4]) and urocanic acid ([3-²H,1′,3′-¹⁵N₂]urocanic acid, UA-[M + 3]) in human plasma was developed using dl-[2,3,3,5′-²H₄,2′-¹³C,1′,3′-¹⁵N₂]histidine (dl-His-[M + 7]) and [2,3,5′-²H₃,2′-¹³C,1′,3′-¹⁵N₂]urocanic acid (UA-[M + 6]) as internal standards. l-Histidine and urocanic acid were derivatized to ^αN-(trifluoroacetyl)-^imN-(ethoxycarbonyl)-l-histidine n-butyl ester and ^imN-(ethoxycarbonyl)urocanic acid n-butyl ester. Quantification was carried out by selected ion monitoring of the molecular ions of the respective derivatives of l-His-[M + 4], dl-His-[M + 7], UA-[M + 3] and UA-[M + 6]. The sensitivity, specificity, precision and accuracy of the method were demonstrated to be satisfactory for measuring plasma concentrations of l-His-[M + 4] and UA-[M + 3] following administration of trace amounts of l-His-[M + 4] to humans.     

Unusual conformational transitions of leucine-containing basic polytripeptides

The conformational transitions of synthetic basic polytripeptides (Lys-Leu-Gly)_n, (A₂bu-Leu-Gly)_n, (Lys-Leu-Ala)_n, and (A₂bu-Leu-Ala)_n induced by high salt concentrations and elevated pH were investigated by CD, ir, and ¹H-nmr spectroscopy, sedimentation analysis, viscometry, and light scattering. Sheet aggregates of chains in a conformation similar to the polyglycine II (polyproline II) helix, bound together by hydrogen bonds, are the most probable form of (Lys-Leu-Gly)_n and also, partly, of (A₂bu-Leu-Gly)_n in a high-pH or high-salt solutions. The conformation (Lys-Leu-Ala)_n, in a low-salt concentration, is an α-helix. Since (A₂bu-Leu-Ala)_n is disordered under similar conditions, it appears that this α-helix is stabilized by hydrophobic interactions between Lys and Leu side chains. In a high concentration of water structure-making ions, CD data for (Lys-Leu-Ala)_n indicate distortion of the α-helix, with a parallel increase in the average molecular weight corresponding to trimer formation. Hydrodynamic data are consistent with a model of bundles of three closely touching spherocylinders. (A₂bu-Leu-Ala)_n shows a limited tendency to α-helix formation.     

Exploring cycad foliage as an archive of the isotopic composition of atmospheric nitrogen

Molecular nitrogen (N₂) constitutes the majority of Earth's modern atmosphere, contributing ~0.79 bar of partial pressure (pN₂). However, fluctuations in pN₂ may have occurred on 10⁷–10⁹ year timescales in Earth's past, perhaps altering the isotopic composition of atmospheric nitrogen. Here, we explore an archive that may record the isotopic composition of atmospheric N₂ in deep time: the foliage of cycads. Cycads are ancient gymnosperms that host symbiotic N₂‐fixing cyanobacteria in modified root structures known as coralloid roots. All extant species of cycads are known to host symbionts, suggesting that this N₂‐fixing capacity is perhaps ancestral, reaching back to the early history of cycads in the late Paleozoic. Therefore, if the process of microbial N₂ fixation records the δ¹⁵N value of atmospheric N₂ in cycad foliage, the fossil record of cycads may provide an archive of atmospheric δ¹⁵N values. To explore this potential proxy, we conducted a survey of wild cycads growing in a range of modern environments to determine whether cycad foliage reliably records the isotopic composition of atmospheric N₂. We find that neither biological nor environmental factors significantly influence the δ¹⁵N values of cycad foliage, suggesting that they provide a reasonably robust record of the δ¹⁵N of atmospheric N₂. Application of this proxy to the record of carbonaceous cycad fossils may not only help to constrain changes in atmospheric nitrogen isotope ratios since the late Paleozoic, but also could shed light on the antiquity of the N₂‐fixing symbiosis between cycads and cyanobacteria.     

Monte carlo computation of the supercoiling energy,the sedimentation constant,and the radius of gyration of unknotted and knotted circular DNA

Closed random Gaussian polygonal chains of N (6 < N < 150) bonds of equal length b and thickness d have been generated on a computer. The knot type, the writhing number w, the radius of gyration, and the average of the inverse of the distance between two apices have been determined for each chain. For all the studied knot types—0, 3₁, 4₁, 5₁, and 5₂—the probability density of finding a given w is Gaussian. The Gaussian is centered about 0 for the amphichiral knots. Therefore, for long circular DNAs, the contribution to the supercoiling energy, which depends on w only, may be considered as purely entropic and may be expressed as ARTw²/N, in agreement with previous semiempirical considerations. The parameter A increases with chain thickness, it decreases as N gets larger but rapidly reaches a plateau. Comparison with experimental data from the literature would suggest that the ratio of the writhing to the constraint increases with ionic strength. The ratio of sedimentation constant of the supercoiled DNA to the sedimentation constant of the nicked DNA varies as N^1/4 (w/N)², and therefore depends on the writhing density and on the length of the DNA.     

Basic polypeptides as histone models. Synthesis, conformation, and interaction with DNA of statistical copolymers (Lys x,Ala y)n.

Statistical copolymers (Lys^x,Ala^y)_n were synthesized by copolymerization of N-carboxyanhydrides of L -amino acids. The conformation of copolymers in aqueous solutions was investigated using circular dichroism (CD). Calculations based on the CD data showed that polymers (Lys^x,Ala^y)_n can exhibit a random conformation, an α-helix, and a β-structure in various ratios. CD spectra of complexes of copolymers with DNA prepared by gradual dialysis from a high ionic strength to 0.15 M NaCl can be correlated with the copolymer conformation in medium and high ionic strength. For copolymers forming an α-helix and β-structure, these spectra show resemblance with similar spectra of complexes of those histones that are able to exhibit ordered conformations.     

Mixotrophic chain elongation with syngas and lactate as electron donors

Feeding microbial communities with both organic and inorganic substrates can improve sustainability and feasibility of chain elongation processes. Sustainably produced H₂, CO₂, and CO can be co-fed to microorganisms as a source for acetyl-CoA, while a small amount of an ATP-generating organic substrate helps overcome the kinetic hindrances associated with autotrophic carboxylate production. Here, we operated two semi-continuous bioreactor systems with continuous recirculation of H₂, CO₂, and CO while co-feeding an organic model feedstock (lactate and acetate) to understand how a mixotrophic community is shaped during carboxylate production. Contrary to the assumption that H₂, CO₂, and CO support chain elongation via ethanol production in open cultures, significant correlations (p < 0.01) indicated that relatives of Clostridium luticellarii and Eubacterium aggregans produced carboxylates (acetate to n-caproate) while consuming H₂, CO₂, CO, and lactate themselves. After 100 days, the enriched community was dominated by these two bacteria coexisting in cyclic dynamics shaped by the CO partial pressure. Homoacetogenesis was strongest when the acetate concentration was low (3.2 g L⁻¹), while heterotrophs had the following roles: Pseudoramibacter, Oscillibacter, and Colidextribacter contributed to n-caproate production and Clostridium tyrobutyricum and Acidipropionibacterium spp. grew opportunistically producing n-butyrate and propionate, respectively. The mixotrophic chain elongation community was more efficient in carboxylate production compared with the heterotrophic one and maintained average carbon fixation rates between 0.088 and 1.4 g CO₂ equivalents L⁻¹ days⁻¹. The extra H₂ and CO consumed routed 82% more electrons to carboxylates and 50% more electrons to carboxylates longer than acetate. This study shows for the first time long-term, stable production of short- and medium-chain carboxylates with a mixotrophic community.