12‐ to 22‐Membered Bridged β‐Lactams as Potential Penicillin‐Binding Protein Inhibitors

As potential inhibitors of penicillin‐binding proteins (PBPs), we focused our research on the synthesis of non‐traditional 1,3‐bridged β‐lactams embedded into macrocycles. We synthesized 12‐ to 22‐membered bicyclic β‐lactams by the ring‐closing metathesis (RCM) of bis‐ω‐alkenyl‐3(S)‐aminoazetidinone precursors. The reactivity of 1,3‐bridged β‐lactams was estimated by the determination of the energy barrier of a concerted nucleophilic attack and lactam ring‐opening process by using ab initio calculations. The results predicted that 16‐membered cycles should be more reactive. Biochemical evaluations against R39 DD‐peptidase and two resistant PBPs, namely, PBP2a and PBP5, revealed the inhibition effect of compound 4d , which featured a 16‐membered bridge and the N‐tert‐butyloxycarbonyl chain at the C3 position of the β‐lactam ring. Surprisingly, the corresponding bicycle, 12d , with the PhOCH₂CO side chain at C3 was inactive. Reaction models of the R39 active site gave a new insight into the geometric requirements of the conformation of potential ligands and their steric hindrance; this could help in the design of new compounds.     

Interaction Modes and Absolute Affinities of α‐Amino Acids for Mn2+: A Comprehensive Picture

Manganese is involved as a cofactor in the activation of numerous enzymes as well as the oxygen‐evolving complex of photosystem II. Full understanding of the role played by the Mn²⁺ ion requires detailed knowledge of the interaction modes and energies of manganese with its various environments, a knowledge that is far from complete. To bring detailed insight into the local interactions of Mn in metallopeptides and proteins, theoretical studies employing first‐principles quantum mechanical calculations are carried out on [Mn‐amino acid]²⁺ complexes involving all 20 natural α‐amino acids (AAs). Detailed investigation of [Mn‐serine]²⁺_, [Mn‐cysteine]²⁺, [Mn‐phenylalanine]²⁺, [Mn‐tyrosine]²⁺, and [Mn‐tryptophan]²⁺ indicates that with an electron‐rich side chain, the most stable species involves interaction of Mn²⁺ with carbonyl oxygen, amino nitrogen, and an electron‐rich section of the side chain of the AA in its canonical form. This is in sharp contrast with aliphatic side chains for which a salt bridge is formed. For aromatic AAs, complexation to manganese leads to partial oxidation as well as aromaticity reduction. Despite multisite binding, AAs do not generate strong enough ligand fields to switch the metal to a low‐ or even intermediate‐spin ground state. The affinities of Mn²⁺ for all AAs are reported at the B3LYP and CCSD(T) levels of theory, thereby providing the first complete series of affinities for a divalent metal ion. The trends are compared with those of other cations for which affinities of all AAs have been previously obtained.     

Oxime Side‐Chain Cross‐Links in an α‐Helical Coiled‐Coil Protein: Structure,Thermodynamics, and Folding‐Templated Synthesis of Bicyclic Species

Covalent side‐chain cross‐links are a versatile method to control peptide folding, particularly when α‐helical secondary structure is the target. Here, we examine the application of oxime bridges, formed by the chemoselective reaction between aminooxy and aldehyde side chains, for the stabilization of a helical peptide involved in a protein–protein complex. A series of sequence variants of the dimeric coiled coil GCN4‐p1 bearing oxime bridges at solvent‐exposed positions were prepared and biophysically characterized. Triggered unmasking of a side‐chain aldehyde in situ and subsequent cyclization proceed rapidly and cleanly at pH 7 in the folded protein complex. Comparison of folding thermodynamics among a series of different oxime bridges show that the cross links are consistently stabilizing to the coiled coil, with the extent of stabilization sensitive to the exact size and structure of the macrocycle. X‐ray crystallographic analysis of a coiled coil with the best cross link in place and a second structure of its linear precursor show how the bridge is accommodated into an α‐helix. Preparation of a bicyclic oligomer by simultaneous formation of two linkages in situ demonstrates the potential use of triggered oxime formation to both trap and stabilize a particular peptide folded conformation in the bound state.     

Preparation and characterization of biodegradable poly(lactic acid)‐ block‐poly(ε‐caprolactone) multiblock copolymer

Biodegradable copolymers of poly(lactic acid)‐block‐poly(ε‐caprolactone) (PLA‐b‐PCL) were successfully prepared by two steps. In the first step, lactic acid monomer is oligomerized to low molecular weight prepolymer and copolymerized with the (ε‐caprolactone) diol to prepolymer, and then the molecular weight is raised by joining prepolymer chains together using 1,6‐hexamethylene diisocyanate (HDI) as the chain extender. The polymer was carefully characterized by using ¹H‐NMR analysis, gel permeation chromatography (GPC), thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), and Fourier transform infrared spectroscopy (FTIR). The results of ¹H‐NMR and TGA indicate PLA‐b‐PCL prepolymer with number average molecular weights (M_n) of 4000–6000 were obtained. When PCL‐diols are 10 wt%, copolymer is better for chain extension reaction to obtain the polymer with high molecular weight. After chain extension, the weight average molecular weight can reach 250,000 g/mol, as determined by GPC, when the molar ratio of –NCO to –OH was 3:1. DSC curve showed that the degree of crystallization of PLA–PCL copolymer was low, even became amorphous after chain extended reaction. The product exhibits superior mechanical properties with elongation at break above 297% that is much higher than that of PLA chain extended products. Copyright © 2009 John Wiley & Sons, Ltd.     

Synthesis and Analysis of the Conformational Preferences of 5‐Aminomethyloxazolidine‐2,4‐dione Scaffolds: First Examples of β2‐ and β2, 2‐Homo‐Freidinger Lactam Analogues

Constrained peptidomimetic scaffolds are of considerable interest for the design of therapeutically useful analogues of bioactive peptides. We present the single‐step cyclization of (S)‐ or (R)‐α‐hydroxy‐β²‐ or α‐substituted‐α‐hydroxy‐β^{2, 2}‐amino acids already incorporated within oligopeptides to 5‐aminomethyl‐oxazolidine‐2,4‐dione (Amo) rings. These scaffolds can be regarded as unprecedented β²‐ or β^{2, 2}‐homo‐Freidinger lactam analogues, and can be equipped with a proteinogenic side chain at each residue. In a biomimetic environment, Amo rings act as inducers of extended, semi‐bent or folded geometries, depending on the relative stereochemistry and the presence of α‐substituents.     

Chromium Bis(anthracene‐η6) Complexes – A DFT Study

Chromium bisanthracene‐η⁶ complexes are considered within the framework of density functional theory using LANL2DZ and 6‐31+G(d) basis sets and B3LYP functional. The complexation with both the same types of rings of anthracene decks (AA‐ and BB‐type complexes) and with different rings (AB‐type complex) are considered. The optimized geometries and the associated quantum chemical properties are comparatively discussed for the both types of basis sets used. LANL2DZ basis set yielded some unreasonable results. B3LYP/6‐31+G(d) level of calculations yielded the stability order as AA > BB > AB. IR spectra of AA and BB‐type complexes resemble each other. The C–H frequencies are almost the same for both of the anthracene decks, whereas they differ in the case of AB‐type complex. UV/Vis spectra of the complexes all absorb above 500 nm. AA and AB‐type complexes in contrast to BB‐type display rather complex pattern. The NICS(0) values of various rings in the complexes considered are obtained and discussed.     

Chiral discrimination of β‐3‐homo‐amino acids using the kinetic method

Chiral discrimination of seven enantiomeric pairs of β‐3‐homo‐amino acids was studied by using the kinetic method and trimeric metal‐bound complexes, with natural and unnatural α‐amino acids as chiral reference compounds and divalent metal ions (Cu²⁺ and Ni²⁺) as the center ions. The β‐3‐homo‐amino acids were selected for this study because, first of all, chiral discrimination of β‐amino acids has not been extensively studied by mass spectrometry. Moreover, these β‐3‐homo‐amino acids studied have different aromatic side chains. Thus, the emphasis was to study the effect of the side chain (electron density of the phenyl ring, as well as the difference between phenyl and benzyl side chains) for the chiral discrimination. The results showed that by the proper choice of a metal ion and a chiral reference compound, all seven enantiomeric pairs of β‐3‐homo‐amino acids could be differentiated. Moreover, it was noted that the β‐3‐homo‐amino acids with benzyl side chains provided higher enantioselectivity than the corresponding phenyl ones. However, increasing or decreasing the electron density of the aromatic ring by different substituents in both the phenyl and benzyl side chains had practically no role for chiral discrimination of β‐3‐homo‐amino acids studied. When copper was used as the central metal, the phenyl side chain containing reference molecules (S)‐2‐amino‐2‐phenylacetic acid (L ‐Phg) and (S)‐2‐amino‐2‐(4‐hydroxyphenyl)‐acetic acid (L ‐4′‐OHPhg) gave rise to an additional copper‐reduced dimeric fragment ion, [Cu^I(ref)(A)]⁺. The inclusion of this ion improved noticeably the enantioselectivity values obtained. Copyright © 2010 John Wiley & Sons, Ltd.     

Polyrotaxanes based on polyethers and β‐cyclodextrin

A polyrotaxane in which β‐cyclodextrins (β‐CDs) are threaded onto a polyether chain was prepared by polycondensation of a β‐CD/bisphenol A (BPA) inclusion complex with aromatic dihalides. Two dihalides, with and without a side chain, were used. This polycondensation results in a polyrotaxane (or pseudopolyrotaxane for polymers without stoppers) with a 1:1 threading ratio when the side chain is present and 2:3 when there is none. The long side chain prevents dethreading of the macrocycles. The best yield and a good threading ratio were obtained when the polycondensation was performed by liquid?solid phase transfer catalysis without solvent (L/S PTC) using 2,5‐bi(iodomethyl)‐4‐methoxy‐(1‐octyloxy)benzene as dihalide. The ¹H NMR and FTIR spectra show that the products consist of β‐CD and polyether. The 2D NOESY NMR spectrum shows that the polyether chains are included in the β‐CD cavity. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 4391–4399, 2009     

Structural transitions of nanocrystalline domains in regioregular poly(3‐hexyl thiophene) thin films

The effects of solution processing and thermal annealing on thin film morphology and crystalline structures of regioregular poly(3‐hexyl thiophene) (RR P3HT) are studied in terms of molecular weight (M_w). Using grazing‐incidence X‐ray diffraction, π‐conjugated planes in drop‐cast films from chloroform solutions are found to be preferentially oriented parallel to the substrates regardless of M_w. However, the mesoscale nanocrystalline morphology of the drop‐cast films is significantly affected by M_w, exhibiting a distinctive morphological transition from short nanorods to long nanofibrils above a critical number‐averaged M_w (～ 3.6 kDa). This is probably due to the change in a conformation change from an extended‐chain to a folded‐chain, as M_w of RR P3HT increases. In contrast, spin‐casting of high M_w RR P3HT produces less ordered films with a lower crystallinity and mixed parallel/perpendicular orientations of π‐conjugated planes. The crystallinity and parallel π‐conjugated orientation of RR P3HT in spin‐cast films could be improved by thermal treatments at high‐temperatures either (1) above the glass transition temperature or (2) above the melting temperature of RR 3PHT followed by recrystallization upon cooling under vacuum. However, the charge mobility of the spin‐cast films for a field‐effect transistor application is still lower than that of the drop‐cast films. This would be attributed to the chain oxidation and the development of distinct grain boundaries between RR P3HT nanofibrils during the thermal treatments. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 1303–1312, 2007     

Gas‐phase fragmentation of γ‐lactone derivatives by electrospray ionization tandem mass spectrometry

Fragmentation reactions of β‐hydroxymethyl‐, β‐acetoxymethyl‐ and β‐benzyloxymethyl‐butenolides and the corresponding γ‐butyrolactones were investigated by electrospray ionization tandem mass spectrometry (ESI‐MS/MS) using collision‐induced dissociation (CID). This study revealed that loss of H₂O [M + H ?18]⁺ is the main fragmentation process for β‐hydroxymethylbutenolide (1) and β‐hydroxymethyl‐γ‐butyrolactone (2). Loss of ketene ([M + H ?42]⁺) is the major fragmentation process for protonated β‐acetoxymethyl‐γ‐butyrolactone (4), but not for β‐acetoxymethylbutenolide (3). The benzyl cation (m/z 91) is the major ion in the ESI‐MS/MS spectra of β‐benzyloxymethylbutenolide (5) and β‐benzyloxymethyl‐γ‐butyrolactone (6). The different side chain at the β‐position and the double bond presence afforded some product ions that can be important for the structural identification of each compound. The energetic aspects involved in the protonation and gas‐phase fragmentation processes were interpreted on the basis of thermochemical data obtained by computational quantum chemistry. Copyright © 2009 John Wiley & Sons, Ltd.     

RAFT Polymerization of N‐Isopropylacrylamide and Acrylic Acid under γ‐Irradiation in Aqueous Media

Summary: The ambient temperature (20 °C) reversible addition fragmentation chain transfer (RAFT) polymerization of N‐isopropylacrylamide (NIPAAm) and acrylic acid (AA) conducted directly in aqueous media under γ‐initiation (at dose rates of 30 Gy · h⁻¹) proceeds in a controlled fashion (typically, < 1.2) to near quantitative conversions and up to number‐average molecular weights of 2.5 × 10⁵ g · mol⁻¹ for PNIPAAm and 1.1 × 10⁵ g · mol⁻¹ for PAA via two water‐soluble trithiocarbonate chain transfer agents, i.e., S,S‐bis(α,α′‐dimethyl‐α″‐acetic acid)trithiocarbonate (TRITT) and 3‐benzylsulfanylthiocarbonylsulfanyl propionic acid (BPATT). The generated polymers are successfully chain extended, which suggests that the RAFT agents are stable throughout the polymerization process so that complex and well‐defined architectures can be obtained.

An increase of the monomer/CTA ratio leads to an increase of the molecular weight for the RAFT polymerization of NIPAAm under γ‐radiation in water using TRITT at ambient temperature.     

An inorganic–organic hybrid supramolecular framework based on the γ‐[Mo8O26]4− cluster and cobalt complex of aspartic acid: X‐ray structure and DFT study

A new inorganic–organic hybrid based on an aspartate functionalized polyoxomolybdate, [pentaaquacobalt(II)]‐μ‐aspartate‐[γ‐octamolybdate]‐μ‐aspartate‐[pentaaquacobalt(II)] tetrahydrate, [Co₂(C₄H₆NO₄)₂(γ‐Mo₈O₂₆)(H₂O)₁₀]·4H₂O ( 1 ), has been synthesized under hydrothermal conditions from the reaction of an Evans–Showell‐type polyoxometalate, (NH₄)₆[Co₂Mo₁₀H₄O₃₈], and l ‐aspartic acid. The complex exhibits a supramolecular three‐dimensional framework structure in the crystal lattice. Compound 1 was structurally characterized by elemental analyses, IR and UV–Vis (diffuse reflectance) spectroscopy and single‐crystal X‐ray diffraction. In this compound, aspartic acid acts as a bridge between the two Co atoms and the Mo centres, with the –CH₂COOH side chain directly linked to the Mo centre in γ‐[Mo₈O₂₆]^4? and the α‐carboxylate side chain bound to the Co centre. Commonly, the binding of transition‐metal complexes to POMs involves coordination of the metal to a terminal O atom of the POM so that 1 , with a bridging ligand between Mo and Co atoms, belongs to a separate class of hybrid materials. While the starting materials are both chiral and one might expect them to form a chiral hybrid, the decomposition of the chiral Evans–Showell‐type POM and its conversion to the centrosymmetric γ‐octamolybdate POM, plus the presence of two aspartate ligands centrosymmetrically placed on either side of the POM, leads to the formation of an achiral hybrid. We have studied energetically by means of density functional theory (DFT) calculations and using the Bader's `atoms‐in‐molecules' analysis the electrostatically enhanced hydrogen bonds (EEHBs) observed in the solid state of 1 , which are crucial for the formation of one‐dimensional supramolecular assemblies.     

Conducting Block Copolymer Nanowires Containing Regioregular Poly(3‐Hexylthiophene) and Polystyrene

Grignard Metathesis polymerization (GRIM) for the synthesis of regioregular poly(3‐alkylthiophenes) proceeds via a “living” chain growth mechanism. Due to the “living” nature of this polymerization regioregular poly(3‐alkylthiophenes) with predetermined molecular weight, narrow molecular weight distributions and desired chain end functionality are now readily available. Allyl terminated poly(3‐hexylthiophene) was successfully used as a precursor for the synthesis of di‐block copolymers containing polystyrene. The addition of “living” poly(styryl)lithium to the allyl terminated regioregular poly(3‐hexylthiophene) generated the di‐block copolymer. Poly(3‐hexylthiophene)‐b‐polystyrene was also synthesized by atom transfer radical polymerization. Integration of poly(3‐hexylthiophene) in di‐block copolymers with polystyrene leads to the formation of nanowire morphology and self‐ordered conducting nanostructured materials.     

Interactions of the “piano‐stool” [ruthenium(II) (η6‐arene)(en)CL]+ complexes with water and nucleobases; ab initio and DFT study

Piano stool ruthenium complexes of the composition [Ru(II)(η⁶‐arene)(en)Cl]^+/2+ (en = ethylenediamine) represent an emerging class of cisplatin‐analogue anticancer drug candidates. In this study, we use computational quantum chemistry to characterize the structure, stability and reactivity of these compounds. All these structures were optimized at DFT(B3LYP)/6‐31G(d) level and their single point properties were determined by the MP2/6‐31++G(2df,2pd) method. Thermodynamic parameters and rate constants were determined for the aquation process, as a replacement of the initial chloro ligand by water and subsequent exchange reaction of aqua ligand by nucleobases. The computations were carried out at several levels of DFT and ab initio theories (B3LYP, MP2 and CCSD) utilizing a range of bases sets (from 6‐31G(d) to aug‐cc‐pVQZ). Excellent agreement with experimental results for aquation process was obtained at the CCSD level and reasonable match was achieved also with the B3LYP/6‐31++G(2df,2pd) method. This level was used also for nucleobase‐water exchange reaction where a smaller rate constant for guanine exchange was found in comparison with adenine. Although adenine follows a simple replacement mechanism, guanine complex passes by a two‐step mechanism. At first, Ru‐O6(G) adduct is formed, which is transformed through a chelate TS2 to the Ru‐N7(G) final complex. In case of guanine, the exchange reaction is more favorable thermodynamically (releasing in total by about 8 kcal/mol) but according to our results, the rate constant for guanine substitution is slightly smaller than the analogous constant in adenine case when reaction course from local minimum is considered. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009     

Octyl 1‐(5‐tert‐butyl‐1H‐pyrazol‐3‐yl)‐2‐(4‐chlorophenyl)‐1H‐benzimidazole‐5‐carboxylate: complex sheets built from N—H...N,C—H...N and C—H...O hydrogen bonds

In the title compound, C₂₉H₃₅ClN₄O₂, the bond lengths provide evidence for aromatic delocalization in the pyrazole ring but bond fixation in the fused imidazole ring, and the octyl chain is folded, rather than adopting an all‐trans chain‐extended conformation. A combination of N—H...N, C—H...N and C—H...O hydrogen bonds links the molecules into sheets, in which the hydrogen bonds occupy the central layer with the tert‐butyl and octyl groups arranged on either side, such that the closest contacts between adjacent sheets involve only the octyl groups. Comparisons are made with the supramolecular assembly in some simpler analogues.     

A New Mechanism for β‐Lactamases: Class D Enzymes Degrade 1β‐Methyl Carbapenems through Lactone Formation

β‐Lactamases threaten the clinical use of carbapenems, which are considered antibiotics of last resort. The classical mechanism of serine carbapenemase catalysis proceeds through hydrolysis of an acyl‐enzyme intermediate. We show that class D β‐lactamases also degrade clinically used 1β‐methyl‐substituted carbapenems through the unprecedented formation of a carbapenem‐derived β‐lactone. β‐Lactone formation results from nucleophilic attack of the carbapenem hydroxyethyl side chain on the ester carbonyl of the acyl‐enzyme intermediate. The carbapenem‐derived lactone products inhibit both serine β‐lactamases (particularly class D) and metallo‐β‐lactamases. These results define a new mechanism for the class D carbapenemases, in which a hydrolytic water molecule is not required.     

3α‐Hydroxytirucalla‐7,24‐dien‐21‐oic acid: a triterpene from Protium crenatum Sandwith

The crystal structure of the title compound, C₃₀H₄₈O₃, a triterpene extracted from the resin of Protium crenatum Sandwith, is reported. The aliphatic acidic side chain is attached to the tirucallene four‐ring system on its α‐face and is extended by 7.248 (5) Å in the `left‐hand' orientation.     

Synthesis,structural characterization and computational studies of catena‐poly[chlorido[μ3‐(pyridin‐1‐ium‐3‐yl)phosphonato‐κ3O:O′:O′′]zinc(II)]

Coordination polymers are constructed from two basic components, namely metal ions, or metal‐ion clusters, and bridging organic ligands. Their structures may also contain other auxiliary components, such as blocking ligands, counter‐ions and nonbonding guest or template molecules. The choice or design of a suitable linker is essential. The new title zinc(II) coordination polymer, [Zn(C₅H₅NO₃P)Cl]_n , has been hydrothermally synthesized and structurally characterized by single‐crystal X‐ray diffraction and vibrational spectroscopy (FT–IR and FT–Raman). Additionally, computational methods have been applied to derive quantitative information about interactions present in the solid state. The compound crystallizes in the monoclinic space group C 2/c . The four‐coordinated Zn^II cation is in a distorted tetrahedral environment, formed by three phosphonate O atoms from three different (pyridin‐1‐ium‐3‐yl)phosphonate ligands and one chloride anion. The Zn^II ions are extended by phosphonate ligands to generate a ladder chain along the [001] direction. Adjacent ladders are held together via N—H…O hydrogen bonds and offset face‐to‐face π–π stacking interactions, forming a three‐dimensional supramolecular network with channels. As calculated, the interaction energy between the neighbouring ladders is −115.2 kJ mol⁻¹. In turn, the cohesive energy evaluated per asymmetric unit‐equivalent fragment of a polymeric chain in the crystal structure is −205.4 kJ mol⁻¹. This latter value reflects the numerous hydrogen bonds stabilizing the three‐dimensional packing of the coordination chains.     

BaTiO3‐based nanolayers and nanotubes: First‐principles calculations

The first‐principles calculations using hybrid exchange‐correlation functional and localized atomic basis set are performed for BaTiO₃ (BTO) nanolayers and nanotubes (NTs) with the structure optimization. Both the cubic and the ferroelectric BTO phases are used for the nanolayers and NTs modeling. It follows from the calculations that nanolayers of the different ferroelectric BTO phases have the practically identical surface energies and are more stable than nanolayers of the cubic phase. Thin nanosheets composed of three or more dense layers of (0 1 0) and (0 1 ) faces preserve the ferroelectric displacements inherent to the initial bulk phase. The structure and stability of BTO single‐wall NTs depends on the original bulk crystal phase and a wall thickness. The majority of the considered NTs with the low formation and strain energies has the mirror plane perpendicular to the tube axis and therefore cannot exhibit ferroelectricity. The NTs folded from (0 1 ) layers may show antiferroelectric arrangement of Ti? O bonds. Comparison of stability of the BTO‐based and SrTiO₃‐based NTs shows that the former are more stable than the latter. © 2012 Wiley Periodicals, Inc.     

DFT study of 1‐D Li6Gd(BO3)3

Solid‐state calculations were performed with the program CASTEP to analyze some electronic structure features of the crystal compound Li₆Gd(BO₃)₃ (LIGDBO), which is known to be an efficient gamma radiation detector, in particular when doped with rare‐earth ions. The structure of this material displays a clear 1‐D preference, where chains of atoms are formed along one of the crystalline axes. These quasilinear chains are responsible for the energy transfer occurring in the system prior to the actual detection. To elucidate on some aspects of the former process, calculations based on a few cluster models were also carried out by means of the molecular program JAGUAR. One of our results corresponds to a theoretical absorption energy value close to that experimentally obtained. In our calculation, the absorption process seems to be associated with the formation of an excitonic magnon state. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003