On the modeling of arginine-bound carboxylates: a case study with Pyruvate Formate-Lyase

High level ab initio and density functional calculations have been employed to determine the most appropriate manner in which to truncate an arginine-bound carboxylate motif, using the substrate mechanism of Pyruvate Formate-Lyase as a case study. The results show that, both qualitatively and quantitatively, a neutral carboxylic acid provides a more realistic approximation to the salt bridge arrangement than does a bare anionic carboxylate substituent.     

Comparative study of the photochemistry of the azidopyridine 1-oxides

The photochemistry of azidopyridine 1-oxides was studied using an array of glass and matrix isolation techniques. As with room temperature, the photochemistry of 4-azidopyridine 1-oxide is dominated by triplet nitrene chemistry. However, in the case of the 3-azide, matrix photolysis indicates the formation of diazabicyclo[4.1.0]hepta-2,4,6-triene N-oxide and diazacycloheptatetraene N-oxide intermediates as well as triplet nitrene.     

Synthesis, crystal structure, infrared and Raman spectra of Sr4Cu3(AsO4)2(AsO3OH)4·3H2O and Ba2Cu4(AsO4)2(AsO3OH)3

The two new compounds, Sr₄Cu₃(AsO₄)₂(AsO₃OH)₄·3H₂O (1) and Ba₂Cu₄(AsO₄)₂(AsO₃OH)₃(2), were synthesized under hydrothermal conditions. They represent previously unknown structure types and are the first compounds synthesized in the systems SrO/BaO-CuO-As₂O₅-H₂O. Their crystal structures were determined by single-crystal X-ray diffraction [space group C2/c, a=18.536(4) Å, b=5.179(1) Å, c=24.898(5) Å, β=93.67(3)°, V=2344.0(8) Å³, Z=4 for 1; space group P4₂/n, a=7.775(1) Å, c=13.698(3) Å, V=828.1(2) Å³, Z=2 for 2]. The crystal structure of 1 is related to a group of compounds formed by Cu²⁺-(XO₄)³⁻ layers (X=P⁵⁺, As⁵⁺) linked by M cations (M=alkali, alkaline earth, Pb²⁺, or Ag⁺) and partly by hydrogen bonds. In 1, worth mentioning is the very short hydrogen bond length, D···A=2.477(3) Å. It is one of the examples of extremely short hydrogen bonds, where the donor and acceptor are crystallographically different. Compound 2 represents a layered structure consisting of Cu₂O₈ centrosymmetric dimers crosslinked by As1φ₄ tetrahedra, where φ is O or OH, which are interconnected by Ba, As2 and hydrogen bonds to form a three-dimensional network. The layers are formed by Cu₂O₈ centrosymmetric dimers of CuO₅ edge-sharing polyhedra, crosslinked by As1O₄ tetrahedra. Vibrational spectra (FTIR and Raman) of both compounds are described. The spectroscopic manifestation of the very short hydrogen bond in 1, and ABC-like spectra in 2 were discussed.     

Ultrafast intramolecular charge transfer with strongly twisted aminobenzonitriles: 4-(di-tert-butylamino)benzonitrile and 3-(di-tert-butylamino)benzonitrile

The newly synthesized aminobenzonitriles with two bulky amino substituents 4-(di-tert-butylamino)benzonitrile (DTABN) and 3-(di-tert-butylamino)benzonitrile (mDTABN) have strongly twisted amino groups in the ground state. From X-ray crystal analysis it is found that the amino twist angle theta of mDTABN equals 86.5 degrees , whereas a twist angle of around 75 degrees is deduced for DTABN from the extinction coefficient of its lowest-energy absorption band in n-hexane. Because of the electronic decoupling between the amino and benzonitrile groups caused by these large twist angles, the absorption of DTABN and mDTABN is relatively weak below 40000 cm-1, with extinction coefficients around 25 times smaller than those of the planar 4-(dimethylamino)benzonitrile (DMABN). DTABN as well as mDTABN undergo efficient intramolecular charge transfer (ICT) in the singlet excited state, in nonpolar (n-hexane) as well as in polar (acetonitrile) solvents. Their fluorescence spectra consist of an ICT emission band, without evidence for locally excited (LE) fluorescence. The occurrence of efficient ICT with mDTABN is different from the findings with all other N,N-dialkylaminobenzonitriles in the literature, for which ICT only appears with the para-derivative. From solvatochromic measurements, an ICT dipole moment of 17 D is determined for DTABN as well as for mDTABN, similar to that of DMABN. The picosecond fluorescence decays of DTABN (time resolution 3 ps) are effectively single exponential. Their decay time is equal to the ICT lifetime tau'0(ICT), which increases with solvent polarity from 0.86 ns in n-hexane to 3.48 ns in MeCN at 25 degrees C. The femtosecond excited-state absorption (ESA) spectra of DTABN in n-hexane and MeCN at 22 degrees C show a decay of the LE and a corresponding rise of the ICT absorption. The ICT reaction time is 70 fs in n-hexane and 60 fs in MeCN. DTABN and mDTABN may have a strongly twisted ICT state, similar to that of 6-cyanobenzoquinuclidine but different from that of DMABN.     

Bifurcate hydrogen bonds. Interaction of intramolecularly H-bonded systems with Lewis bases

The structure and the hydrogen bonding in the systems formed by the intramolecularly H-bonded systems, namely, maltol (3-hydroxy-2-methyl-4-pyrone), 5, 2,4,6-trinitrophenol, 6, acetylacetone enol, 7, with Lewis bases, phosgene, 8, dioxane, 9, and DMSO, 10, have been studied by density functional theory (B3LYP) and MP2 using the 6-311G* basis set. The continuum solvent effect was simulated by IEF-PCM model. The hydrogen bond analysis using the atoms in molecules (AIM) method was applied by using the MP2(full)/6-311++G** electron density to establish the nature of the bifurcate hydrogen bond (BHB) in these systems as well as contributory factors for its stabilization. The nature of interaction in the intermolecular H-complexes formed by compounds 5- 7 with the Lewis bases 8- 10 was shown to depend on the strength of the intramolecular hydrogen bond O...H and the strength of the base. The critical values of the CO...H and NO...H angles for which the formation of BHB is possible, have been determined.     

Use of 73Ge NMR spectroscopy for the study of electronic interactions

The lack of understanding of the structural and electronic factors that affect the often difficult to observe germanium resonance has been a major deterrent to studies of bonding interactions at germanium. We utilized the symmetrical system GeR 4 to determine what structural factors inherent in the R group affect the shape and position of the (73)Ge resonance. The (73)Ge resonances of symmetrical tetrakis germanium compounds of the type GeR 4 (R = alkyl, aryl), GeX 4 (X = F, Cl, Br, I), Ge(OR) 4 (R = alkyl, methoxyalkyl, dimethylaminoalkyl), Ge(NR 2) 4 (R = alkyl), and Ge(SR) 4 (R = alkyl, dimethylaminoalkyl) were examined for evidence of intramolecular coordination. Although many of these compounds have sharp resonances due to idealized tetrahedral symmetry with relatively long relaxation times, others have broad or no observable resonances due to fast quadrupolar relaxation. We hypothesize that the perturbation of symmetry by even weak Lewis interactions or conformational changes causes broadening of the resonance before the interaction can become sufficiently strong to cause the significant low-frequency shift generally associated with hypercoordination in most nuclei. Intermolecular coordination to GeCl 4 is believed to be responsible for the low-frequency shifts in (73)Ge resonances and the associated changes in peak widths in mixtures with bases such as tributylphosphine oxide (TBPO) and triethylphosphine oxide (TEPO). Adduct formation with these bases is confirmed by broad (31)P resonances that are resolved into five peaks at -40 degrees C. The exchange-broadened resonances due to the 1:1 and 1:2 TEPO adducts are also observed at -40 degrees C in the (73)Ge spectrum. Thus, relatively strong bonding to the germanium in GeCl 4 results in both low-frequency shifts and broadening of the resonance. The broad (73)Ge resonances that occur in some compounds may be in part due to exchange as well as quadrupolar relaxation.     

A Single Methylene Group in Oligoalkylamine‐Based Cationic Polymers and Lipids Promotes Enhanced mRNA Delivery

The development of chemically modified mRNA holds great promise as a new class of biologic therapeutics. However, the intracellular delivery and endosomal escape of mRNA encapsulated in nanoparticles has not been systematically investigated. Here, we synthesized a diverse set of cationic polymers and lipids from a series of oligoalkylamines and subsequently characterized their mRNA delivery capability. Notably, a structure with an alternating alkyl chain length between amines showed the highest transfection efficiency, which was linked to a high buffering capacity in a narrow range of pH 6.2 to 6.5. Variation in only one methylene group resulted in enhanced mRNA delivery to both the murine liver as well as porcine lungs after systemic or aerosol administration, respectively. These findings reveal a novel fundamental structure–activity relationship for the delivery of mRNA that is independent of the class of mRNA carrier and define a promising new path of exploration in the field of mRNA therapeutics.     

Manifestation of side-chain interactions in solution properties of “loose” PI-graft-PMMA molecular brushes

The molecular properties of polymer brushes composed of polyimide with polymerization degree 50 and loosely grafted poly(methyl methacrylate) chains of variable length (PI-graft-PMMA) were studied by viscometry, dynamic light scattering, and equilibrium electro-optical Kerr effect methods in a diluted solution. It was established that the intrinsic viscosity and hydrodynamic dimension of PI-graft-PMMA copolymers increase when the electro-optical Kerr constant decreases with the elongation of PMMA side chains in the range of 40–110 monomer units. The observed difference in the solution properties of the copolymers was explained by their side-chain interactions in spite of a large distance between the neighboring grafting points typical of “loose brushes.” A strong effect of the chain rigidity and dipole structure on solution properties of the studied samples was demonstrated. The Kuhn segment lengths for PI-graft-PMMA copolymers were estimated to vary in the range 3.8–12.1?nm.     

Synthesis of Calcium(II) Amidinate Precursors for Atomic Layer Deposition through a Redox Reaction between Calcium and Amidines

We have prepared two new Ca^II amidinates, which comprise a new class of ALD precursors. The syntheses proceed by a direct reaction between Ca metal and the amidine ligands in the presence of ammonia. Bis(N,N′‐diisopropylformamidinato)calcium(II) ( 1 ) and bis(N,N′‐diisopropylacetamidinato)calcium(II) ( 2 ) adopt dimeric structures in solution and in the solid state. X‐ray crystallography revealed asymmetry in one of the bridging ligands to afford the structure [(η²‐L)Ca(μ‐η²:η²‐L)(μ‐η²:η¹‐L)Ca(η²‐L)]. These amidinate complexes showed unprecedentedly high volatility as compared to the widely employed and commercially available Ca^II precursor, [Ca₃(tmhd)₆]. In CaS ALD with 1 and H₂S, the ALD window was approximately two times wider and lower in temperature by about 150 °C than previously reported with [Ca₃(tmhd)₆] and H₂S. Complexes 1 and 2 , with their excellent volatility and thermal stability (up to at least 350 °C), are the first homoleptic Ca^II amidinates suitable for use as ALD precursors.