Binding site optimisation for artificial enzymes by diffusion NMR of small molecules

A binding site optimisation protocol for the design of artificial enzymes based on "small molecule-small molecule" binding studies by diffusion NMR is presented. Since the reaction chosen was the hydrolysis of ester 1 ([4-(4-carboxy-1-oxobutyl)-aminobenzyl]-phenethyl ester), an analogous phosphonate ester 2 ([4-(4-carboxy-1-oxobutyl)-aminobenzyl]-phosphonic phenethyl ester) was selected as a suitable transition state analogue (TSA). The key objective of the NMR studies was to find a unit with functional groups capable of binding to the acidic sites of the TSA. Nine dipeptides, mainly with basic and hydroxyl groups, were used and their affinity to the TSA was studied by measuring the change in the diffusion coefficient, D(pep), upon binding by pulse field gradient NMR. The value of D(pep) at 298 K in D(2)O at pD 5, 7 and 10 was measured both in free solution, and mixtures containing one dipeptide and the TSA. As both components are low molecular weight species with M < 500, a TSA-to-dipeptide ratio of 10:1 was used to detect significant changes in D(pep). The results revealed that dipeptides with basic residues show higher affinity to the TSA than those with hydroxyl or aliphatic side chains in aqueous solutions. The dipeptide showing the most significant relative change in D(pep) was H-Arg-Arg-OH, and the binding constant was estimated to be 86 L M(-1) by measuring D(pep) at varying concentrations of the TSA. In addition, binding of the TSA to a new water-soluble polymer with a polyallylamine backbone and randomly distributed Arg-Arg binding sites was examined, and the binding constant was estimated to be > or =1500 L M(-1). As confirmed by further catalytic activity tests, polymers containing Arg-Arg as a binding site are capable of significant rate accelerations in the hydrolysis of ester 1.     

Cyclization of aroylacetic acids 2-carboxyphenylamides into 2-[(Z)-2-aryl-2-hydroxy-1-ethenyl]-4H-3,1-benzoxazin-4-ones. Crystal and molecular structure of 2-[(Z)-2-hydroxy-2-phenyl-1-ethenyl]-4H-3,1-benzoxazin-4-one

2-Carboxyphenylamides of aroylacetic acids undergo cyclization when treated with dehydrating agents to give 2-[(Z)-2-aryl-2-hydroxy-1-ethenyl]-4H-3,1-benzoxazin-4-ones. Crystal and molecular structure of the latter phenyl derivative was studied by X-ray crystallography. Original Russian Text ? E.S. Vostrov, A.A. Novikov, A.N. Maslivets, Z.G. Aliev, 2007, published in Zhurnal Organicheskoi Khimii, 2007, Vol. 43, No. 2, pp. 232–235.     

Raman spectra of aqueous lithium sulfate and potassium thiocyanate in strong electric fields

The effects of high-voltage pulsed discharge (HVPD) activation on the Raman spectra of saturated aqueous solutions of lithium sulfate (Li₂SO₄/H₂O) in the range of the ν₁(A) totally symmetric vibrations of the SO ₄ ^2? anion and on the spectra of potassium thiocyanate KSCN/H₂O in the region of the ν₁(C≡N) vibrations of the SCN^? anion have been studied. The temperature dependences of the width and frequency of the corresponding spectral lines have been investigated.     

Five-Membered 2,3-Dioxo Heterocycles: XLVI. Reaction of 5-Aryl-4-quinoxalinyl-2,3-dihydrofuran-2,3-diones with Aldehydes and Ketones. Molecular and Crystalline Structure of 5-(3-p-Tolylquinoxalin-2-yl)-4H-1,3-dioxine- 2-spiro-2'-adamantan-4-one

Aroyl(quinoxalinyl)ketenes generated by thermolysis of 5-aryl-4-(3-arylquinoxalin-2-yl)-2,3-di-hydrofuran-2,3-diones act as dienes in [4 + 2]-cycloaddition at the carbonyl group of aldehydes and ketones to afford 2-substituted 6-aryl-5-(3-arylquinoxalin-2-yl)-4H-1,3-dioxin-4-ones. The structure of 5-(3-p-tolylquino-xalin-2-yl)-4H-1,3-dioxine-2-spiro-2'-adamantan-4-one was proved by X-ray analysis.     

Synthesis and reactivity of metal-containing monomers

Acid and neutral Co^II, Cu^II, Ni^II, Zn^II, Fe^II, and Fe^III maleates, fumarates, and itaconates were obtained and characterized. The methods for their synthesis were optimized, and the valence state and coordination of metals were studied. Co^II and Fe^II hydrogen maleates, Co^II maleate, and Co^II fumarate were examined by X-ray diffraction analysis. The ligands based on unsaturated dicarboxylic acids can be mono-, bi-, and tetradentate, which results in the formation of acid salts, chain and three-dimensional coordination polymers, whose double bond is not involved in the coordination. The strong antiferromagnetic exchange (μ_elf=1.41 and 0.34 μ_B at 290 and 80 K, respectively) was detected in Cu^II itaconate. Based on the data of Mössbauer spectroscopy, the partial reduction of Fe^III to Fe^II during the synthesis of Fe^III maleate was shown to occur: δFe=0.43 and 1.27 mm s^?1, ΔE _Q=0.57 and 3.13 mm s^?1 and Γ=0.37 and 0.28 mm s^?1 atT=298 K for Fe^III and Fe^II, respectively.     

Synthesis and molecular structure of 3-(2-aryl-2-oxoethyl)-3-methoxy-2-oxo-2,3-dihydroimidazo-[1,2-<Emphasis Type="Italic">a</Emphasis>]pyridine hydrochlorides

Reactions between 2-pyridylamides of Z-4-aryl-2-hydroxy-4-oxobut-2-enoic acids with diazomethane have been used to synthesize 3-(2-aryl-2-oxoethyl)-3-methoxy-2-oxo-2,3-dihydroimidazo[1,2-a]pyridines, which form hydrochlorides with hydrochloric acid. The structure of the latter has been demonstrated by XRD for the hydrochloride of 3-methoxy-2-oxo-3-(2-phenyl-2-oxoethyl)-2,3-dihydroimidazo[1,2-a]pyridine. __________ Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 3, pp. 464–468, 2007.     

Interaction in the Yb2S3-In2S3 system

A T-x diagram is designed for the Yb₂S₃-In₂S₃ system using physicochemical methods. A complex chemical reaction occurs in the system to yield ternary compounds Yb₃InS₆ (S₁), YbInS₃ (S₂), Yb₃In₅S₁₂ (S₃), and YbIn₃S₆ (S₄). In₂S₃-based limited solid solutions are found. Phases S₁, S₃, and S₄ are formed by peritectic reactions at 1260, 1200, and 1100 K, respectively. Compound S₂ melts congruently at 1390 K. Compound S₃ crystallizes in monoclinic system (a = 10.90 Å, b = 21.01 Å, c = 3.846 Å, β = 96.2°). Compounds S₁ and S₄ crystallize in orthorhombic system (for S₁, a = 16.76 Å, b = 13.70 Å, c = 3.88 Å; for S₄, a = 3.86 Å, b = 11.64 Å, c = 20.98 Å, d _exp = 4.62 g/cm³). Compound S₂ crystallizes in cubic system (a = 10.68 Å).     

Dynamic mechanical analysis (DMA), 13c solid state nmr and micro-thermomechanical studies of historical parchment

DMA and solid state ¹³C NMR techniques were used to measure historical parchment samples within the framework of the project (MAP) Micro Analysis of Parchment (EC contract No. SMT4-96-2101) in collaboration with the School of Conservation in Copenhagen. DMA was used in both thermal scan and creep modes. Thermal scans provided information on the transitions associated with the collagen polymer. Microthermal analysis was also used to obtain information on the topography and thermal conductivity of sample areas of 100 μm. Localised heating enabled measurements of softening transitions in the sample. This behaviour is influenced by the chemical composition of parchment. 13C NMR provided information on the carbon atoms associated with the polypeptide chains of the collagen in parchment. The behaviour of samples immersed in water and measured in DMA creep mode was used to measure the shrinkage behaviour of the parchment samples. The different but complementary techniques provided a means for characterising the physicochemical state of parchment samples. This revised version was published online in July 2006 with corrections to the Cover Date.