Conformational dependence of the intrinsic acidity of the aspartic acid residue sidechain in N-acetyl- -aspartic acid-N′-methylamide

The sidechain conformational potential energy hypersurfaces (PEHS) for the γ_L, β_L, α_L, and α_D backbone conformations of N-acetyl- -aspartate-N′-methylamide were generated. Of the 81 possible conformers initially expected for the aspartate residue, only seven were found after geometric optimizations at the B3LYP/6-31G(d) level of theory. No stable conformers could be located in the δ_L, _L, γ_D, δ_D, and _D backbone conformations. The ‘adiabatic’ deprotonation energies for the endo and exo forms of N-acetyl- -aspartic acid-N′-methylamide were calculated by comparing their optimized relative energies against those found for the seven stable conformers of N-acetyl- -aspartate-N′-methylamide. Sidechain conformational PEHSs were also generated for the estimation of ‘vertical’ deprotonation energies for both endo and exo forms of N-acetyl- -aspartic acid-N′-methylamide. All backbone–sidechain (N–H⁻O–C) and backbone–backbone (N–HO=C) hydrogen bond interactions were analyzed. A total of two backbone–backbone and four backbone–sidechain interactions were found for N-acetyl- -aspartate-N′-methylamide. The deprotonated sidechain of N-acetyl- -aspartate-N′-methylamide may allow the aspartyl residue to form strong hydrogen bond interactions (since it is negatively charged) which may be significant in such processes as protein–ligand recognition and ligand binding. As a primary example, the molecular geometry of the aspartyl residue may be important in peptide folding, such as that in the RGD tripeptide.     

Synthesis and characterization of complexes of lanthanide nitrates with N,N′-dinaphthyl-N,N′-diphenyl-3,6-dioxaoctanediamide

Solid complexes of lighter lanthanide nitrates with N,N′-dinaphthyl-N,N′-diphenyl-3,6-dioxaoctanediamide (DDD), Ln(NO₃)₃(DDD) (Ln = La---Nd, Sm) have been prepared in non-aqueous media. These complexes have been characterized by elemental analysis, conductivity measurements, IR spectra, electronic spectra and TG-DTA techniques. In all the complexes, DDD and NO₃⁻ are coordinated to the lanthanide ions as tetradentate and bidentate ligands, respectively. The differences in the IR and electronic spectra between these complexes and lanthanide nitrate complexes with N,N,N′,N′-tetraphenyl-3,6-dioxaoctanediamide (TDD) are discussed.     

Temperature dependence vapour pressure measurements of Mg(tmhd)2(tmeda) [(tmhd = 2,2,6,6-tetramethyl-3,5-heptanedione, tmeda = N,N,N′,N′-tetramethylethylenediamine]

The reaction between the magnesium β-diketonate complex Mg(tmhd)₂(H₂O)₂ and 1 equiv. of N,N,N′,N′-tetramethylethylenediamine (tmeda = Me₂NCH₂CH₂NMe₂) in hexane at room temperature yielded Mg(tmhd)₂(tmeda). The standard enthalpy of sublimation (83.2 ± 2.3 kJ mol⁻¹) and entropy of sublimation (263 ± 6.3 J mol⁻¹ K⁻¹) of Mg(tmhd)₂(tmeda) were obtained from the temperature dependence vapour pressure, determined by adopting a horizontal dual arm single furnace thermogravimetric analyser as a transpiration apparatus. From the observed melting point depression DTA, the standard enthalpy of fusion (58.3 ± 5.2 kJ mol⁻¹) was evaluated, using the ideal eutectic behaviour of Mg(tmhd)₂(tmeda) as a solvent with bis(2,4-pentanedionato)magnesium(II), Mg(acac)₂ as a non-volatile solute.     

A variety of oxidation products of antioxidants based on N,N′-substituted p-phenylenediamines

Electrochemical and spectroscopic (EPR, UV–Vis, IR) studies of the aromatic secondary amines N,N′-diphenyl-1,4-phenylenediamine (DPPD), N-phenyl-N′-isopropyl-p-phenylene diamine (IPPD), N-phenyl-N′-(α-methylbenzyl)-p-phenylenediamine (SPPD) and N-phenyl-N′-(1,3-dimethyl-butyl)-p-phenylenediamine (6PPD), which represent the most important group of antioxidants used in the rubber industry, are presented. During oxidation, all the compounds show reversible redox couples in acetonitrile/0.1 M TBABF₄. The first oxidation potential depends substantially on the R substituent at the –N′H– moiety. Very similar UV–VIS spectra of monocation radicals and dications for all the compounds were observed by applying anodic oxidation as well as oxidation by tert-butyl hydroperoxide both in air and in inert atmosphere. The samples with N′-bonded aliphatic carbon in the molecule (e.g. IPPD) heated in air undergo consecutive chemical reactions leading to the formation of –N′C– group. By the use of RO₂ radicals only very low concentration of nitroxide radicals was obtained. Very high concentration of nitroxide radicals was achieved using 3-chloroperbenzoic acid. In the oxidation of investigated aromatic secondary amines with powder PbO₂ no EPR spectra were observed and UV–Vis and IR studies indicate the rapid formation of the final dehydrogenated oxidation product.     

The crystal structure, vibrational spectra, and thermal behavior of dilithium piperazinium(2+) selenate tetrahydrate and dilithium N,N′-dimethylpiperazinium(2+) selenate tetrahydrate

The crystal structure of dilithium piperazinium(2+) selenate tetrahydrate has been solved; this substance crystallizes in the triclinic space group , a=7.931(2) Å, b=7.974(2) Å, c=7.991(2) Å, α=106.99(2)°, β=101.83(2)°, γ=119.28(2)° Z=1, R=0.0280 for 1489 observed reflections. A similar compound, dilithium N,N′-dimethylpiperazinium(2+) selenate tetrahydrate crystallizes in a monoclinic system with space group P2₁/c and lattice parameters a=7.338(1) Å, b=8.792(2) Å, c=12.856(1) Å, β=92.04(2)°, Z=2, R=0.0334 for 1462 observed reflections. Both structures are centrosymmetric with center of symmetry in the center of eight membered ring formed with two SeO₄ tetrahedra and two LiO₄ tetrahedra connected through tops. The two remaining oxygens on each Li atom come from water molecules. The FTIR and FT Raman spectra of both natural and N,O-deuterated substances have been measured and studied. The thermoanalytical properties were studied using TG, DTG and DTA methods in the temperature range 293–873 K for piperazinium derivative and in the range 293–523 K for dimethylpiperazinium derivative. DSC measurements were carried out in the temperature range 95–343 K. No phase transition was found in this temperature region for either of the compounds.     

Application of α-chloroaldoxime O-methanesulfonates to one-pot synthesis of N,N′,N″-substituted guanidines via Tiemann rearrangement

A practical one-pot synthesis of N,N′,N″-trisubstituted guanidines via Tiemann rearrangement involving the reaction of α-chloroaldoxime O-methanesulfonates with alkyl amines is disclosed.     

Synthesis of some new N,N′-diarylsubstituted methylene-bis-dihydro-2H-1,3-benzoxazines

The synthesis of a new series of six-membered N,N′-diarylsubstituted methylene-bis-dihydro-2H-1,3-benzoxazines （5a-e） was achieved in excellent yields by Mannich-type condensation of N,N′-diarylsubstituted methylene-bis-o-hydroxybenzyl amines （4a- e） with formaldehyde in chloroform at reflux. These amines （4a-e） were obtained by the reduction of N, Nr-diarylsubstituted methylene-bis-o-hydroxybenzyl imines （3a-e） with NaBH4, which inturn were obtained by the condensation of methylene-bissalicylaldehyde （2） with various substituted arylamines.     

Mixed Monolayers of Amphiphilic Cyclodextrins and Phospholipids: II. Surface Potential–Area Behavior of Per-(6-amino-2,3-di-O-hexyl) β-CD Hydrochloride Salt and 1,2 Dipalmitoyl, 3-sn-Phosphatidic Acid Mixed Monolayers

The dielectric properties of mixed monolayers of per-(6-amino-2,3-di-O-hexyl) β-CD hydrochloride (NH₃-β-CD-OC6) and 1,2 dipalmitoyl, 3-sn-phosphatidic acid (DPPA) have been assessed using surface potential measurements at constant area. From the comparison of these surface potential (ΔV) versus surface density (δ) relationships with those of surface pressure (π) against surface density (δ) it was apparent that the increase in the NH₃-β-CD-OC6 content in mixed films gave rise to a gradual increase in the saturation value of the surface potential (ΔV_max). This potential for pure DPPA was found to be equal to 396 mV and for pure CD 554 mV. The ΔV_maxvalues reflect the onset of reorientation effects that arrive at molar areas before the collapse of these films. Independently of reorientation effects, the obtained results strongly indicate that the dipolar term contributing to the overall ΔVvalue was for NH₃-β-CD-OC6 due to the hydration of its NH⁺₃group. For both DPPA and NH₃-β-CD-OC6 molecules the contribution of the electric double layer (Ψ) was calculated and was found for DPPA and NH₃-β-CD-OC6 to be equal to −249 and +252 mV, respectively. These calculated Ψ values made possible the evaluation of dipole moments for NH₃-β-CD-OC6 and DPPA monolayers which revealed a marked difference in dipolar properties between these two film forming components. In contrast to DPPA which exhibited a decrease in the surface dipole moment (μ) with the decrease inA, NH₃-β-CD-OC6 displayed an increase in μwith the decrease inAforAvalues above 580 Ų. Below this value μdecreases with decreasing molecular area and this variation arises from a change in the polarity of the electric double layer arising from interactions with the complementary anion. The differences in dielectric properties between the two film forming molecules have been attributed to modification, during compression, in the structure of the interfacial water bound to the cyclodextrin.     

Investigation of the zinc(II) acetylacetonate/benzotriazole reaction system in the presence of bridging N,N′-ligands: Pentanuclear, enneanuclear and polymeric complexes

The reaction of Zn(acac)₂ with btaH (1,2,3-benzotriazole) in dmf yielded the pentanuclear complex [Zn₅(bta)₆(acac)₄(dmf)]·dmf (1·dmf). In the presence of pyrazine, the pentanuclear [Zn₅(bta)₆(acac)₄(dmf)]·3.7dmf (2·3.7dmf) and enneanuclear [Zn₉(bta)₁₂(acac)₆]·6dmf (3·6dmf) complexes were formed, whereas in the presence of 4,4′-bpy the 1D coordination polymer [Zn(acac)₂(4,4′-bpy)]_n (4) was isolated. The molecular structures of 1·dmf and 2·3.7dmf reveal that the [Zn₅] clusters consist of four Zn^II ions which span the corners of a tetrahedron and the fifth resides at its centre. The molecular structure of 3·6dmf reveals that the [Zn₉] clusters consist of two corner sharing tetrahedra and the structure can be described as the addition of two [Zn₅] clusters of 1·dmf and/or 2·3.7dmf followed by the simultaneous abstraction of [Zn(acac)₂] and dmf molecules; this alternative was accomplished by recrystallization of 1·dmf from dmf which yielded 3·6dmf. Each of the μ₃-κN:κN′:κN′′ benzotriazolate ligands in 1·dmf, 2·3.7dmf and 3·6dmf spans an edge of the tetrahedron. The molecular structure of 4 reveals mononuclear [Zn(acac)₂] units bridged via 4,4′-bpy molecules to 1D coordination polymer. Characteristic IR bands of the four complexes are discussed in terms of the coordination modes of the ligands and known structures.     

Heterometallic clusters arising from cubic Ni3M′O4 (M′=K and Na) entity: Solvothermal synthesis with/without the assistance of microwave

Solvothermal reaction assisted with microwave leads to the formation of two unique heterometallic cubic clusters [Ni₃M′(L)₃(OH)(CH₃CN)₃]₂·CH₃CN (M′=K for 1 and M′=Na for 2, where L is an anion of 2-[(2-hydroxy-3-methoxy-benzylidene)-amino]-ethanesulfonate) with higher efficiency, yields and purity than those without it. The 6-metallacrown-3 [Ni₃(OH)(L)₃]⁻ groups exhibit interesting ion trapping and self-assembly of size-different Na⁺ and K⁺ through form recognition and coordination activity in 1 and 2. The magnetic studies for 1 and 2 suggest that the {Ni₃M′O₄} (M′=K and Na) cores both display dominant ferromagnetic interactions from the nature of the binding modes of μ₃-O (oxidophenyl) and μ₃-OH.     

Neutron diffraction study of the β′ and γ phases of LiFeO2

The β, β′, γ and α phases of LiFeO₂, synthesized as powders, were annealed at different temperatures and characterized by X-ray measurements. The β′ and γ modifications were also studied by time-of-flight neutron diffraction (ISIS Facility, UK). The structure of the β′ phase was refined in the monoclinic C2/c space group (a=8.566(1), b=11.574(2), c=5.1970(5) Å, β=146.064(5)°) to wR_p=0.071–0.080 (data from four counter banks). Fe and Li atoms are ordered over two of the four independent sites, and partially disordered over the other two. The ordered Li has a distorted tetrahedral coordination. The γ structure was refined at RT (a=4.047(1), c=8.746(2) Å) and at 570 °C (a=4.082(3), c=8.822(6) Å) in the I4₁/amd symmetry, showing full order with Li in octahedral coordination at RT, and in a split-atom configuration at high temperature. On annealing, the β′ polymorph was found to transform to γ at 550 °C, thus suggesting that it is a metastable phase. Electrostatics is discussed as the driving force for the α→β′→γ ordering process of LiFeO₂.     

Volumetric and transport properties of binary liquid mixtures of N-methylacetamide with lactones at temperatures (303.15 to 318.15) K

The values of density (ρ), viscosity (η) and speed of sound (u) have been measured for binary liquid mixtures of γ-butyrolactone (GBL), δ-valerolactone (DVL), and ε-caprolactone (ECL) with N-methylacetamide (NMA) over the whole composition range at T = (303.15 to 318.15) K and atmospheric pressure. From these data, excess molar volume (V^E), deviation in viscosity (Δη), and deviation in isentropic compressibility (Δκ_s), are calculated. The results are fitted to a Redlich–Kister type polynomial equation to derive binary coefficients and standard deviations.     

Group 9 half-sandwich complexes containing the unique P,P′-diphenyl-1,4-diphospha-cyclohexane ligand: Synthesis, X-ray structure analyses and spectroscopic studies

We wish to report the synthesis and characterization of Group 9 metal complexes with the novel P,P′-diphenyl-1,4-diphospha-cyclohexane (dpdpc) ligand. The complexes are readily prepared by direct ligand substitution reactions from the dichloro-bridged binuclear complexes, [{η⁵-Cp*M(Cl)₂}₂]. The complexes include: [η⁵-Cp*Rh(Cl)₂]₂(μ-dpdpc) (1), [η⁵-Cp*Ir(Cl)₂]₂(μ-dpdpc) (2), and [η⁵-Cp*Rh(Cl)(dpdpc)]PF₆ (3). The structures for all three complexes are supported by ¹H, ¹³C{¹H}, and ³¹P{¹H} NMR spectroscopy as well as elemental analysis. The molecular structures of 1 and 3 have also been established by single-crystal X-ray analysis.     

Potential of ethylenediaminedi(o-hydroxyphenylacetic acid) and N,N′-bis(hydroxybenzyl)ethylenediamine-N,N′-diacetic acid for the determination of metal ions by capillary electrophoresis

Two aromatic polyaminocarboxylate ligands, ethylenediaminedi(o-hydroxyphenylacetic acid) (EDDHA) and N,N′-bis(hydroxybenzyl)ethylenediamine-N,N′-diacetic acid (HBED), were applied for the separation of transition and heavy metal ions by the ion-exchange variant of electrokinetic chromatography. EDDHA structure contains two chiral carbon centers. It makes it impossible to use the commercially available ligand. All the studied metal ions showed two peaks, which correspond to meso and rac forms of the ligand. The separation of metal–HBED chelates was performed using poly(diallyldimethylammonium) polycations in mixed acetate–hydroxide form. Simultaneous separation of nine single- and nine double-charged HBED chelates, including In(III), Ga(III), Co(II)–(III) and Mn(II)–(III) pairs demonstrated the efficiency of 40 000–400 000 theoretical plates. The separation of Co(III), Fe(III) complexes with different arrangements of donor groups and oxidation of Co(II), Mn(II), Fe(II) ions in reaction with HBED have been discussed.     

Synthesis, spectroscopic studies and nonlinear optical behavior of N,N′-bis(2-hydroxy-1-naphthylmethylidene)-1-methyl-1,2-diaminoethane-N,N′,O,O′-nickel(II)

A Schiff base complex N,N′-bis(2-hydroxy-1-naphthylmethylidene)-1-methyl-1,2- diaminoethane-N,N′,O,O′-nickel(II) has been synthesized. The title compound has been characterized by FT-IR and UV–vis spectroscopies. The UV–vis experiments indicate that the compound has solvatochromism in the UV region, implying non-zero molecular first hyperpolarizability. To investigate microscopic second-order nonlinear optical (NLO) behavior of the examined complex, the electric dipole moments (μ) and the first static hyperpolarizabilities (β) were computed using Finite Field second-order Møller Plesset (FF MP2) perturbation procedure. According to ab initio quantum mechanical calculations, the title complex exhibits non-zero β values, revealing microscopic second-order NLO behavior.     

High-pressure preparation, crystal structure, and properties of the new rare-earth oxoborate β-Dy2B4O9

In this work we report about a new rare-earth oxoborate β-Dy₂B₄O₉ synthesized under high-pressure/high-temperature conditions from Dy₂O₃ and boron oxide B₂O₃ in a B₂O₃/Na₂O₂ flux with a walker-type multianvil apparatus at 8 GPa and 1000°C. Single crystal X-ray structure determination of β-Dy₂B₄O₉ revealed: , a=616.2(1) pm, b=642.8(1) pm, c=748.5(1) pm, α=102.54(1)°, β=97.08(1)°, γ=102.45(1)°, Z=2, R1=0.0151, wR₂=0.0475 (all data). The compound exhibits a new structure type which is built up from bands of linked BO₃- (Δ) and tetrahedral BO₄-groups (□). The Dy³⁺-cations are positioned in the voids between the bands. According to the conception of fundamental building blocks β-Dy₂B₄O₉ can be classified with the notation 2Δ6□:Δ3□=4□=3□Δ. Furthermore we report about temperature-resolved in situ powder diffraction measurements and IR-spectroscopic investigations on β-Dy₂B₄O₉.     

The stereochemistry of the dichlorocobalt(III) complexes with (2S,5S,9S)- and (2S,5R,9S)-trimethyltriethylenetetraamines

Dichlorocobalt(III) complexes of (2S,5S,9S)-trimethyltriethylenetetraamine (L₁) and (2S,5R,9S)-trimethyltriethylenetetraamine (L₂) have been prepared. Both L₁ and L₂ coordinate to the cobalt(III) ion to give three isomers: Λ-cis-α, Δ-cis-β, trans isomers for L₁ and Δ-cis-α, Δ-cis-β, trans isomers for L₂. Each of the trans-dichloro complexes of the two ligands have been isomerized stereospecifically to the cis-α-dichloro complex in methanol, and each of the cis-α-dichloro complexes stereospecifically to the trans-diaqua complex in water. Both the geometrical and optical inversions took place at the same time in the observed stereospecific isomerizations.     

Stability Enhancement of a Dimeric HER2-Specific Affibody Molecule through Sortase A-Catalyzed Head-to-Tail Cyclization

Natural backbone-cyclized proteins have an increased thermostability and resistance towards proteases, characteristics that have sparked interest in head-to-tail cyclization as a method to stability-enhance proteins used in diagnostics and therapeutic applications, for example. In this proof-of principle study, we have produced and investigated a head-to-tail cyclized and HER2-specific Z_HER2:342 Affibody dimer. The sortase A-mediated cyclization reaction is highly efficient (>95%) under optimized conditions, and renders a cyclic Z_HER3:342-dimer with an apparent melting temperature, T_m, of 68 °C, which is 3 °C higher than that of its linear counterpart. Circular dichroism spectra of the linear and cyclic dimers looked very similar in the far-UV range, both before and after thermal unfolding to 90 °C, which suggests that cyclization does not negatively impact the helicity or folding of the cyclic protein. The cyclic dimer had an apparent sub-nanomolar affinity (K_d ~750 pM) to the HER2-receptor, which is a ~150-fold reduction in affinity relative to the linear dimer (K_d ~5 pM), but the anti-HER2 Affibody dimer remained a high-affinity binder even after cyclization. No apparent difference in proteolytic stability was detected in an endopeptidase degradation assay for the cyclic and linear dimers. In contrast, in an exopeptidase degradation assay, the linear dimer was shown to be completely degraded after 5 min, while the cyclic dimer showed no detectable degradation even after 60 min. We further demonstrate that a site-specifically DyLight 594-labeled cyclic dimer shows specific binding to HER2-overexpressing cells. Taken together, the results presented here demonstrate that head-to-tail cyclization can be an effective strategy to increase the stability of an Affibody dimer.     

Characterization of anomeric differences of ammonium-bound monomeric and dimeric complex ions of 1α- and 1β-azido-pentofuranosyl derivates by kinetic method

Relative stabilities (ΔG^c) of ammonium-bound monomers and dimers of anomeric β- -pentofuranosyl 1α- and 1β-azide derivates are determinate using the kinetic method by measuring relative rates of competitive collision-induced dissociations of dimeric [ANH₄B]⁺ and trimeric [A₂NH₄B]⁺ or [ANH₄B₂]⁺ cluster ions. Comparison between calculated ammonium affinities (AAs) and relative stabilities (ΔG^c) of ammonium-bound monomers shows qualitative correlations between both thermochemical quantities, but in two examples the activation barrier differences of competitive fragmentation channels cause a large disparity between both thermochemical data. Therefore, the most stable ammonium-bound monomers of the anomeric lα- and lβ-2,3,5-tri-O-benzyl-β- -arabino-pento-furanosyl azides possess the lowest ammonium affinities and the highest relative stabilities. Two different relative stabilities measured for the same ammonium-bound homo- or hetero-dimers indicate dissimilar activated barriers of trimers transition states for dimer formations. The activated barriers of trimers depend on the relative stabilities of ammonium-bound monomer within the trimeric cluster ions.