2-Benzoyl-2-ethoxycarbonylvinyl-1 and 2-benzoylamino-2-methoxy-carbonylvinyl-1 as N-protecting groups in peptide synthesis. Their application in the synthesis of dehydropeptide derivatives containing N-terminal 3-heteroarylamino-2,3-dehydroalanine

Ethyl 2-benzoyl-3-dimethylaminopropenoate ( 6 ) and methyl 2-benzoylamino-3-dimethylaminopropenoate ( 46 ) were used as reagents for the protection of the amino group with 2-benzoyl-2-ethoxycarbonylvinyl-1 and 2-benzoylamino-2-methoxycarbonylvinyl groups in the peptide synthesis. Reactions of ethyl 2-benzoyl-3-dimethylaminopropenoate (6) with α-amino acids gave N-(2-benzoyl-2-ethoxycarbonylvinyl-1)-α-amino acids 13–19. These were coupled with various amino acid esters to form N-(2-benzoyl-2-ethoxycar-bonylvinyl-1)-protected dipeptide esters 20–31. The removal of 2-benzoyl-2-ethoxycarbonylvinyl-1 group, which was achieved by hydrazine monohydrochloride or hydroxylamine hydrochloride, afforded hydrochlo-rides of dipeptide esters 32–41 in high yields. Similarly, the substitution of the dimethylamino group in methyl 2-benzoylamino-3-dimethylaminopropenoate ( 46 ) by glycine gave N-(2-benzoylamino-2-methoxycar-bonylvinyl-1)glycine ( 47 ), which was coupled with glycine ethyl ester to give N-[N-(2-benzoylamino-2-methoxycarbonylvinyl-1)glycyl]glycine ethyl ester ( 48 ). Treatment of 48 with 2-arnino-4,6-dirnethylpyrimi-dine afforded N-[glycyl]glycine ethyl ester hydrochloride (34) in high yield. Amino acid esters and dipeptide esters were employed in the preparation of tri- 58-70, tetra- 71–82, and pentapeptide esters 83–85 containing N-terminal 3-heteroarylamino-2,3-dehydroalanine. 2-Chloro-4,6-dimethoxy-1,3,5-triazine was employed as a coupling reagent for the preparation of peptides 58–85.     

New dsDNA‐Binding Hybrid Molecules Combining an Unnatural Peptide and an Intercalating Moiety

In our search for new dsDNA‐binding ligands, combinatorial chemistry was first applied to select unnatural oligopeptides with moderate affinity for dsDNA. To enhance the binding affinity of a heptapeptide lead structure, Ac‐Arg‐Ual‐Sar‐Chi‐Chi‐Tal‐Arg‐NH₂ (K_d=4.9?10^?4 M ), the compound was conjugated to different heteropolyaromatic moieties by means of a variety of linker arms. Glycine, β‐alanine, glycyl‐glycine, glycyl‐β‐alanine, γ‐aminobutyric acid, and 6‐aminocaproic acid were used as spacers, representing different lengths and/or flexibilities. The intercalators coupled to the oligopeptide were acridine, fluorenone, anthracene, anthraquinone, and 3,8‐diamino‐5‐methyl‐6‐phenylphenantridinium (methidium). The binding capacities of these new hybrid molecules to dsDNA have been investigated by gel retardation and footprinting assays. The results show that, by conjugating the unnatural oligopeptide to intercalators, the affinity for dsDNA could be enhanced more than 100‐fold. For methidium‐β‐alanyl‐glycyl‐Arg‐Ual‐Sar‐Chi‐Chi‐Tal‐Arg‐NH₂ (K_d of 2.1?10^?6 M ), the interaction with dsDNA was dominated by the intercalator in such a way that the sequence specificity of the heptapeptide was changed. The interaction with dsDNA of hybrid molecules of other intercalators was mainly governed by the oligopeptide, since the sequence selectivity of the heptapeptide was conserved. In general, the linker arm glycine (shortest spacer) and glycine‐β‐alanine were preferred over β‐alanine, glycyl‐glycine and the more‐flexible spacers γ‐aminobutyric acid and 6‐aminocaproic acid. This way new hybrid molecules endowed with dsDNA affinities of ca. 10^?6 M and displaying different sequence selectivities have been developed. Therefore, combinations of such unnatural peptides with intercalators can be used to broaden the knowledge about the sequence‐selective recognition of dsDNA.     

The Partial Molar Volume and Heat Capacity of the Glycyl Group in Aqueous Solution at 25^C

The partial molar volumes, V₂ ^{^}, and the partial molar heat capacities, C_p,2 ^{^}, at infinite dilution have been determined for three new peptides of sequence seryl(glycyl)_xglycine, where x=0 to 2, in aqueous solution at 25^{^}C. Values for V₂ ^{^} at 25^°C have also been determined for two neutral peptide derivatives N-acetylglycylglycinamide and N-acetylglycylglycylglycinamide. These V₂ ^°; and C_p,2 ^°; results were used to estimate the partial molar volume and heat capacity of the backbone glycyl group, CH₂CONH, of proteins in aqueous solution at 25^°;C. The results obtained are compared with those calculated using partial molar data for alternative model compounds. The new glycyl group contributions are in excellent agreement with those currently used in our group additivity schemes for the calculation of the partial molar volumes and heat capacities of unfolded proteins.     

Oncinotine-Type Spermidine Alkaloids from Oncinotis tenuiloba. Transformation of N-acetyloncinotin-12-one to N,N′-diacetylinandenin-12-one

From extracts of Oncinotis tenuiloba STAPF , two novel polyamine alkaloids, oncinotin-11-one ( 5 ) and oncinotin-12-one ( 6 ), were isolated. Peracetylation of 6 provided the N-acetyl derivative 11 as well as N,N′-diacetylinandenin-10-en-12-one ( 12 ) due to a β-elimination-type side reaction resulting in ring enlargement of 11 (Scheme 1). Deuteration of 12 yielded 13 , showing the same retention time as N,N′-diacetylinandenin-12-one ( 14 ), when co-HPLC was performed together with different keto-isomeric N,N′-diacetylinandeninones. Structure elucidation was extended by Schmidt degradation of 6 and N,N′-diacetyl(10,11-²H₂)inandenin-12-one ( 13 ); the degradation products were identified by GC and ESI-MS. The structure of 5 was proposed on the basis of spectroscopic means. Comparison of the spectroscopic data of 5 with those obtained from synthetic material as well as co-HPLC of the N-acetyl derivative 20 together with the corresponding synthetic compound revealed the identity of the substances and confirmed the structure of 5 . Additionally, oncinotine ( 2 ) and neooncinotine ( 3 ) were isolated, separated, and identified with authentic samples by co-HPLC of their N-acetyl derivatives 8 and 9 , respectively.     

Conformation of tert‐butoxy­carbonyl­glycyl‐dehydro­alanyl‐glycine methyl ester in the crystalline state and calculated in the gas phase

tert‐Butoxy­carbonyl­glycyl‐dehydro­alanyl‐glycine methyl ester (systematic name: methyl {2‐[(tert‐butoxycarbonylamino)­acetamido]prop‐2‐enamido}acetate) (Boc⁰‐Gly¹‐ΔAla²‐Gly³‐OMe), C₁₃H₂₁N₃O₆, has been structurally characterized by single‐crystal X‐ray diffraction and by density functional theory (DFT) calculations at the B3LYP/6–311+G** level. The peptide chain in both the solid‐state and calculated structures adopts neither β nor γ turns. All amino acid residues in the tripeptide sequence are linked trans to each other. The bond lengths and valence angles of the amino acid units in the crystal structure and gas phase are comparable. However, the conformation of the third glycyl residue (Gly³) is different in the crystalline state and in the gas phase. It is stabilized in the calculated structure by an additional intra­molecular short contact between Gly³ NH and methyl ester COMe groups.     

Synthetic and antimicrobial studies of N-substituted-pyrazoline-based new bisheterocycles

In the present study, the four series of N-acetyl/N-carbothioamide/N-carboxamide/N-phenyl-based new bispyrazolines have been synthesized. These symmetrical bisheterocyclic products were prepared efficiently from the ring-closure reactions of new bischalcones 2a-d with appropriate cyclizing agents (hydrazine hydrate, thiosemicarbazide, semicarbazide, and phenyl hydrazine) under the alkaline ethanolic conditions. The compounds 2a-d were obtained by treating hydroxyl-substituted chalcone 1 with various dihalogenated reagents (α,α′-dibromo-o/m/p-xylene and 4,4′-bischloromethyl-diphenyl) in anhydrous K₂CO₃/dry acetone/Bu₄N⁺I⁻ medium. The structures of all the newly synthesized products have been authenticated with the help of their IR, ¹H-NMR, ¹³C-NMR, and ESI-MS spectral data and their purity was corroborated with the help of elemental analysis and thin-layer chromatography results. The in vitro antimicrobial screening of the newly synthesized intermediates and final bisheterocycles has also been performed by using the serial tube dilution technique against the selected number of microorganisms. The final bisheterocycles revealed better antibacterial and antifungal potencies as compared to their corresponding bischalcones. Among the symmetrical bisheterocyclic products, N-acetyl and N-carbothioamide-substituted bispyrazolines were found to exhibit potential antimicrobial properties than the other products.     

Accurate prediction of vertical electronic transitions of Ni(II) coordination compounds via time dependent density functional theory

Time dependent density functional theory calculations are completed for five Ni(II) complexes formed by polydentate peptides to predict the electronic absorption spectrum. The ligands examined were glycyl‐glycyl‐glycine (GGG), glycyl‐glycyl‐glycyl‐glycine (GGGG), glycyl‐glycyl‐histidine (GGH), glycyl‐glycyl‐cysteine (GGC), and triethylenetetramine (trien). Fifteen functionals and two basis sets were tested. On the basis of the mean absolute percent deviation (MAPD), the ranking among the functionals is: HSE06 ∼ MPW1PW91 ∼ PBE0 > ω‐B97x‐D ∼ B3P86 ∼ B3LYP ∼ CAM‐B3LYP > PBE ∼ BLYP ∼ BP86 > TPSS > TPSSh > BHandHLYP > M06 ≫ M06‐2X. Concerning the basis sets, the triple‐ζ def2‐TZVP performs better than the double‐ζ LANL2DZ. With the functional HSE06 and basis set def2‐TZVP the MAPD with respect to the experimental λ_max is 1.65% with a standard deviation of 1.26%. The absorption electronic spectra were interpreted in terms of vertical excitations between occupied and virtual MOs based on Ni‐d atomic orbitals. The electronic structure of the Ni(II) species is also discussed.     

Synthesis of 1,3,4-thiadiazoles containing the trifluoromethyl group

The following compounds have been synthesized: 2-Amino-5-trifluoromethyl-1,3,4-thiadiazole; N-(5-trifluoromethyl - 1,3,4-thiadizol-2-yl)benzenesulfonamide; N¹-(5-trifluoromethyl-1,3,4-thiadiazol-2-yl)sulfanilamide, its N⁴-acetyl, N⁴-succinyl, and N⁴-pathalyl derivatives; o - m - and p-trifluoromethylbenzoylthiosemicarbazide, their corresponding 2-amino-1,3,4-thiadiazoles, their corresponding sulfanilamides, their N⁴-acetyl, N⁴-succinyl and N⁴-phthalyl derivatives; 3-o-trifluoromethylphenyl-4H-1,2,4-triazole-5-thiol. Preliminary in-vitro assays show that synthesized sulfanilamide derivatives have antibacterial activity against Staphylococcus aureus.     

A rapidly convergent simulation method: Mixed Monte Carlo/stochastic dynamics

Although Monte Carlo and molecular dynamics are the primary methods used for free energy simulations of molecular systems, their application to molecules that have multiple conformations separated by energy barriers of ≥ 3 kcal/mol is problematic because of slow rates of convergence. In this article we introduce a hybrid simulation method termed MC-SD which mixes Monte Carlo (MC) and stochastic dynamics (SD). This new method generates a canonical ensemble via alternating MC and SD steps and combines the local exploration strengths of dynamics with the barrier-crossing ability of large-step Monte Carlo. Using calculations on double-well potentials and long simulations (10⁸ steps of MC and 1 μs of SD) of the simple, conformationally flexible molecule n-pentane, we find that MC-SD simulations converage faster than either MC or SD alone and generate ensembles which are equivalent to those created by classical MC or SD. Using pure SD at 300 K, the conformational populations of n-pentane are shown to be poorly converged even after a full microsecond of simulation. © 1994 by John Wiley & Sons, Inc.     

MC(JBW): Simple but smart Monte Carlo algorithm for free energy simulations of multiconformational molecules

Many of the most common molecular simulation methods, including Monte Carlo (MC) and molecular or stochastic dynamics (MD or SD), have significant difficulties in sampling the space of molecular potential energy surfaces characterized by multiple conformational minima and significant energy barriers. In such cases improved sampling can be obtained by special techniques that lower such barriers or somehow direct search steps toward different low energy regions of space. We recently described a hybrid MC/SD algorithm [MC(JBW)/SD] incorporating such a technique that directed MC moves of selected torsion and bond angles toward known low energy regions of conformational space. Exploration of other degrees of freedom was left to the SD part of the hybrid algorithm. In the work described here, we develop a related but simpler simulation algorithm that uses only MC to sample all degrees of freedom (e.g., stretch, bend, and torsion). We term this algorithm MC(JBW). Using simulations on various model potential energy surfaces and on simple molecular systems (n-pentane, n-butane, and cyclohexane), MC(JBW) is shown to generate ensembles of states that are indistinguishable from the canonical ensembles generated by classical Metropolis MC in the limit of very long simulations. We further demonstrate the utility of MC(JBW) by evaluating the room temperature free energy differences between conformers of various substituted cyclohexanes and the larger ring hydrocarbons cycloheptane, cyclooctane, cyclononane, and cyclodecane. The results compare favorably with available experimental data and results from previously reported MC(JBW)/SD conformational free energy calculations. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1736–1745, 1998     

Conformational and electronic study of N‐acetyl‐L‐isoleucine‐N‐methylamide using DFT and IPCM calculations

A conformational and electronic study on N‐acetyl‐L ‐isoleucine‐N‐methylamide was carried out. All side‐chain as well as backbone conformations were explored for this compound. Multidimensional conformational analysis predicts 81 structures in the case of N‐acetyl‐L ‐isoleucine‐N‐methylamide, 53 relaxed structures were determined at the DFT (B3LYP/6‐31G(d)) level of theory. An exhaustive electronic study employing the atoms‐in‐molecules (AIM) method was carried out. In addition, the effects of three solvents (water, acetonitrile, and chloroform) were included in the calculations using the isodensity polarizable continuum model (IPCM) method. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Synthesis and characterization of novel poly(ester‐carbonate)s by copolymerization of trans‐4‐hydroxy‐L‐proline with cyclic carbonate

The melt ring‐opening/condensation reaction of trans‐4‐hydroxy‐N‐benzyloxycarbonyl‐L‐proline (N‐CBz‐Hpr) with cyclic carbonate [trimethylene carbonate (tri‐MC) or tetramethylene carbonate (tetra‐MC)] at a wide range of molar fractions in the feed produced new degradable poly(ester‐carbonate)s. The influence of reaction conditions such as polymerization time and temperature on the yield and inherent viscosity of the copolymers was investigated. The polymerizations were carried out in bulk at 140 °C with 1.5 wt % stannous octoate as a catalyst for 30 h. The poly(ester‐carbonate)s obtained were characterized by Fourier transform infrared spectroscopy, ¹H NMR, differential scanning calorimetry, gel permeation chromatography, and Ubbelohde viscometry. The copolymers synthesized exhibited moderate molecular weights with rather narrow molecular weight distributions. The values of the glass‐transition temperature (T_g) of the copolymers depend on the molar fractions of cyclic carbonate. For the poly(N‐CBz‐Hpr‐co‐tri‐MC) system, with a decreased tri‐MC content from 93 to 16 mol %, the T_g increased from ?10 to 60 °C. Similarly, for the poly(N‐CBz‐Hpr‐co‐tetra‐MC) system, when the tetra‐MC content decreased from 80 to 8 mol %, the T_g increased from ?18 to 52 °C. The relationship between the poly(N‐CBz‐Hpr‐co‐tri‐MC) T_g and the compositions was in approximation with the Fox equation. In vitro degradation of these poly(N‐CBz‐Hpr‐co‐tri‐MC)s was evaluated from weight‐loss measurements. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 41: 1435–1443, 2003     

Molecular Recognition of a Peptide by the Nickel(II) Complex of 1,4,7,10‐Tetraazacyclododecane‐2,9‐dione

The nickel(II) complex of the macrocycle 1,4,7,10‐tetraazacyclododecane‐2,9‐dione (dota) was found to be efficient in the recognition of the dipeptide, glycyl‐glycine (Gly‐Gly) in aqueous solution. This (dota)Ni^II complex serves as a targeting molecule to form a stable ternary complex with the dipeptide at pH 8.3 in aqueous solution. The recognition constant (log K=19.20) and the recognition mechanism were investigated based on the potentiometric method. The single‐crystal of a six‐coordinated (dota)₂Ni^II complex is also reported.     

Hydrolysis of amides. Kinetics and mechanism of the basic hydrolysis of N-acylpyrroles,N-acylindoles and N-acylcarbazoles

The hydroxide ion catalyzed hydrolysis of N-formyl, N-acetyl and N-benzoylpyrroles, -indoles and -carbazoles has been studied in water at 25.0°. The rate constants of formation of the tetrahedral intermediate are strongly increased by releasing steric hindrance in the acyl portion as shown by the higher reactivity of N-formyl derivatives in comparison with N-acetyl and N-benzoyl derivatives.     

Kinetics and mechanism of interaction of dipeptide (glycyl–glycine) with ninhydrin in aqueous micellar media

The rates of reaction between ninhydrin and dipeptide glycyl–glycine (Gly–Gly) have been determined by studying the reaction spectrophotometrically at 70°C and pH 5.0 in aqueous and in aqueous cationic micelles of cetyltrimethylammonium bromide (CTAB). The reaction follows first‐ and fractional‐order kinetics, respectively, in [Gly–Gly] and [ninhydrin]. The observed rate constant is affected by [CTAB] changes and the maximum rate enhancement is ca. three‐fold. As the k_ψ ? [CTAB] profile shape is characteristic of bimolecular reactions catalyzed by micelles, the catalysis is explained in terms of the pseudo‐phase model of the micelles (proposed by Menger and Portnoy and developed by Bunton and Romsted). The presence of inorganic salts (NaCl, NaBr, Na₂SO₄) does not reveal any regular effect but the data with organic salts (NaBenz, NaSal) show an increase in the rate followed by a decrease. The kinetic data have been used to calculate the micellar binding constants K_S for Gly–Gly and K_N for ninhydrin and the respective values are 317 and 69 mol^?1 dm³. © 2006 Wiley Periodicals, Inc. Int J Chem Kinet 38: 643–650, 2006     

14N nuclear quadrupole resonance in N-acetyl amino acids

¹⁴N Nuclear quadrupole resonance (NQR) spectra of several N-acetyl amino acids and related compounds are reported and analyzed within the framework of the Townes and Dailey theory. The inductive effect of the chloroacetyl group on the nitrogen is discussed. A positive correlation between the π-σ_NC electron density at the nitrogen and the Taft inductive parameter σ* is observed, suggesting that the nitrogen π-charge density in the N-acetyl amino acids does not vary appreciably. NQR data for hippuric acid are compared to the ¹⁴N quadrupole parameters extracted from ENDOR data reported for X-irradiated hippuric acid.     

Synthesis of multivalent N-acetyl lactosamine modified quantum dots for the study of carbohydrate and galectin-3 interactions

Ternary core/shell CdSeS/ZnS-QDs coated with N-acetyl lactosamine was prepared as a fluorescent probe to study the interactions of N-acetyl lactosamine and galectin-3. The synthesis of N-acetyl lactosamine was achieved through the ‘azidoiodoglycosylation’ method. The amount of ligand coated on QDs was determined by ¹H NMR and ICP-OES. The interactions between carbohydrates and galectin-3 were measured using SPR. The results revealed that the affinity of galectin-3 with di- and multivalent N-acetyl lactosamine increased 20 and 184-fold, respectively. The prepared glyco-QDs could be used as an efficient fluorescent probe to study carbohydrates and galectin-3 interactions.     

Gas-phase thermolysis of N-cyanomethyl-N-ethyl aniline,N-cyanomethyl-N-ethyl-p-anisidine,and N-cyanomethyl-N-ethyl-p-nitroaniline

N-cyanomethyl-N-ethyl aniline (CEAN) and N-cyanomethyl-N-ethyl-p-anisidine (CEPA) have been thermolyzed in a stirred-flow reactor, in the range of 510–560 °C, pressures of 7–11 torr and residence times of 0.5–0.9 s, using toluene as carrier gas. N-cyanomethyl-N-ethyl-p-nitroaniline (ECNA) was thermolyzed at 640°C and 13% conversion. Ethylene and HCN formed in 43% yield each as products from all three starting materials. Phenyl methanaldimine and p-anisidyl methanaldimine were also products of CEAN and CEPA, respectively. The consumption of CEAN and CEPA showed first-order kinetics for a three-fold increase of reactant inflow and initial conversions of up to 40 percent. The following Arrhenius equations were obtained from the rate coefficients for the production of ethylene: CEAN: k=10^15.10±0.74 exp(−238±11 kJ/mol·RT); CEPA: k=10^15.61±0.29 exp(−246±4 kJ/mol·RT). The results are explained by means of radical, nonchain thermolysis mechanisms. The thermochemistry of relevant reaction steps has been estimated from thermochemical parameters calculated by using the semiempirical AM1 method. © 1998 John Wiley & Sons, Inc. Int J Chem Kinet: 30: 451–456, 1998     

Capillary electrophoresis applied for the determination of acidity constants and limiting electrophoretic mobilities of ionizable herbicides including glyphosate and its metabolites and for their simultaneous separation

Thermodynamic acidity constants and limiting ionic mobilities were determined for polyprotic non-chromophore analytes using capillary electrophoresis with capacitively coupled contactless conductivity detection. It was not necessary to work with buffers of identical ionic strength as ionic strength effects on effective electrophoretic mobilities were corrected by modeling during data evaluation (software AnglerFish). The mobility data from capillary electrophoresis coupled to conductivity detection were determined in the pH range from 1.25 to 12.02 with a high resolution (36 pH steps). With this strategy, thermodynamic acidity constants and limiting ionic mobilities for various acidic herbicides were determined, sometimes for the first time. The model analytes included glyphosate, its metabolites, and its acetylated derivates (aminomethyl phosphonic acid, glyoxylic acid, sarcosine, glycine, N-acetyl glyphosate, N-acetyl aminomethyl phosphonic acid, hydroxymethyl phosphonic acid). The obtained data were used in simulations to optimize separations by capillary electrophoresis. Simulations correlated very well to experimental results. With the new method, the separation of glyphosate from interfering components like phosphate in beer samples was possible.     

Determining sulfamonomethoxine and its acetyl/hydroxyl metabolites in chicken plasma under organic solvent-free conditions

A quantitative technique is described for a sample preparation followed by high performance liquid chromatography method for the simultaneous determination of sulfamonomethoxine and its metabolites, N ⁴-acetyl SMM and 2,6-dihydroxy SMM, in chicken plasma. The average recoveries, analytical total time, and limits of quantitation were ≥80% (relative standard deviations (SD) ≤6%), <30 min sample-1 (12 samples in 2 h), and ≤0.09 μg ml⁻¹, respectively. The procedure, performed under 100% aqueous conditions, uses no organic solvents and toxic reagents at all and is, therefore, harmless to the environment and humans.