Synthesis,experimental and in silico studies of N‐fluorenylmethoxycarbonyl‐O‐tert‐butyl‐N‐methyltyrosine,coupled with CSD data: a survey of interactions in the crystal structures of Fmoc–amino acids

Recently, fluorenylmethoxycarbonyl (Fmoc) amino acids (e.g. Fmoc–tyrosine or Fmoc–phenylalanine) have attracted growing interest in biomedical research and industry, with special emphasis directed towards the design and development of novel effective hydrogelators, biomaterials or therapeutics. With this in mind, a systematic knowledge of the structural and supramolecular features in recognition of those properties is essential. This work is the first comprehensive summary of noncovalent interactions combined with a library of supramolecular synthon patterns in all crystal structures of amino acids with the Fmoc moiety reported so far. Moreover, a new Fmoc‐protected amino acid, namely, 2‐{[(9H‐fluoren‐9‐ylmethoxy)carbonyl](methyl)amino}‐3‐{4‐[(2‐hydroxypropan‐2‐yl)oxy]phenyl}propanoic acid or N‐fluorenylmethoxycarbonyl‐O‐tert‐butyl‐N‐methyltyrosine, Fmoc‐N‐Me‐Tyr(t‐Bu)‐OH, C₂₉H₃₁NO₅, was successfully synthesized and the structure of its unsolvated form was determined by single‐crystal X‐ray diffraction. The structural, conformational and energy landscape was investigated in detail by combined experimental and in silico approaches, and further compared to N‐Fmoc‐phenylalanine [Draper et al. (2015). CrystEngComm, 42 , 8047–8057]. Geometries were optimized by the density functional theory (DFT) method either in vacuo or in solutio. The polarizable conductor calculation model was exploited for the evaluation of the hydration effect. Hirshfeld surface analysis revealed that H…H, C…H/H…C and O…H/H…O interactions constitute the major contributions to the total Hirshfeld surface area in all the investigated systems. The molecular electrostatic potentials mapped over the surfaces identified the electrostatic complementarities in the crystal packing. The prediction of weak hydrogen‐bonded patterns via Full Interaction Maps was computed. Supramolecular motifs formed via C—H…O, C—H…π, (fluorenyl)C—H…Cl(I), C—Br…π(fluorenyl) and C—I…π(fluorenyl) interactions are observed. Basic synthons, in combination with the Long‐Range Synthon Aufbau Modules, further supported by energy‐framework calculations, are discussed. Furthermore, the relevance of Fmoc‐based supramolecular hydrogen‐bonding patterns in biocomplexes are emphasized, for the first time.     

Gas phase and solution state stability of complexes L…M, where M = Cu, Ni, or Zn and L = R−C(O)NHOH (R = H, NH2, CH3, CF3, or Phenyl)

The structure and gas-phase metal affinities (M = Cu²⁺, Ni²⁺, and Zn²⁺) of formohydroxamic acid derivatives R–C(O)NHOH (R = H, NH₂, CH₃, CF₃ and Phenyl) were studied using the B3LYP/6-311+G(d,p) method of DFT theory. In order to evaluate the conformational behavior of these systems in water, we carried out CPCM-SCRF optimization calculations at the B3LYP/6-311+G(d,p) levels of theory. The obtained optimized geometries and interaction affinities of the gas and solution phase were compared. The following order of stability was found for ionic complexes of the transition metals: Cu²⁺ > Ni(t)²⁺ > Zn²⁺. The same stability order would be expected according to the Irving–Williams order of stability constants. The high-spin complexes of the Ni²⁺ were more stable than the low-spin complexes. The solvent effect reduced the observed relative stability of individual metallic complexes of substituted hydroxamic acids.     

Molecular structure,p<Emphasis Type="Italic">K</Emphasis>a,lipophilicity, solubility,absorption, polar surface area,and blood brain barrier penetration of some antiangiogenic agents

The methods of theoretical chemistry have been used to elucidate molecular properties of selected and novel antiangiogenic agents (semaxanib, sunitinib, N-methylsunitinib, sorafenib, motesanib, ABT-869, vatalanib, vandetanib, AEE 788, CP-547632, A-1, A-2, A-3, and A-4). The geometries and energies of these drugs have been computed using HF/6-31G(d), Becke3LYP/6-31G(d) and Becke3LYP/6-31++G(d,p) model chemistries. Wherever possible the most stable conformations of inhibitors studied are stabilized by means of intramolecular hydrogen bonds. Water has a remarkable effect on the geometry of the antiangiogenic agents studied. Computed partition coefficients (ALOGPS method) varied between 2.3 and 5. Compounds studied are described as lipophilic inhibitors. Semaxanib is inhibitor with lowest lipophilicity. The antiangiogenic agents studied are only slightly soluble in water; their computed solubility (log S) from interval between −3.4 and −5.4 is sufficient for fast absorption. Selection criteria for drug-like properties of VEGFR2 inhibitors investigated were designed. Based on these criteria, three compounds (A-2, A-3, and A-4) were selected for synthesis and biological testing for antianiogenic activity on VEGFR2 receptor.     

Non‐symmetric bent‐core mesogens with one terminal vinyl group

Two series of non‐symmetric banana‐shaped compounds, both with one alkyl and one alkenyl terminal tail, have been synthesized and studied. Both series were compared with the corresponding series with two saturated terminal alkyl tails. All the compounds have a bent central 1,3‐phenylene bis(4‐benzoyloxy)benzoate core; their mesophases were characterized by polarizing optical microscopy, differential scanning calorimetry, X‐ray diffraction and switching current response experiments. In all four series one of the terminal tails is varied from OC₈H₁₇ to OC₁₆H₃₃. The other terminal tails are OC₁₁H₂₃, O(CH₂)₉CH?=?CH₂, OC₁₀H₂₁ and O(CH₂)₈CH?=?CH₂. The short‐tailed compounds show monotropic or enantiotropic B₁ phases and the long‐tailed compounds the B₂ phase. The introduction of one terminal vinyl group slightly lowers the transition temperatures. The introduction of a second terminal vinyl group further suppresses the liquid crystalline properties. All compounds with B₂ phases have layer spacings that suggest a tilt of ～45° of the bent molecules in the layers, and their switching behaviour is antiferroelectric.     

Method for determination of methyl tert-butyl ether in gasoline by gas chromatography

A simple method for the determination of methyl tert-butyl ether (MTBE) in gasoline has been developed. The separation of MTBE from other analytes was controlled by the use of gas chromatography–mass spectrometry in the full scan mode using the characteristic primary, secondary and tertiary ions m/z 73, 57 and 43. The sample mass spectrum did not show any superimposition of other analytes. The separation from the common gasoline component 2-methylpentane was sufficient for reliable quantitation. An application of the developed conditions using gas chromatography with flame ionization detection was performed by the analysis of regular, euro super, super premium unleaded and ‘Optimax’ gasoline from petrol stations in the area of Frankfurt/Main, Germany. Regular unleaded gasoline shows an average MTBE content of 0.4% (w/w), whereas the MTBE content in euro super gasoline varies between 0.4 and 4.2% (w/w). The blending of MTBE to super premium has increased from 8.2% (w/w) in 1998 to 9.8% (w/w) on average in 1999. The recently introduced gasoline ‘Optimax’ shows an average MTBE content of 11.9% (w/w). The presented method might also be used for the analysis of other ethers, such as ethyl tert-butyl ether, which requires the use of another internal standard.     

Sensitive method for determination of methyl tert-butyl ether (MTBE) in water by use of headspace-SPME/GC-MS

A simple and rapid method for the determination of methyl tert-butyl ether (MTBE) in water by headspace-solid-phase microextraction (headspace-SPME) at sub-microg/L concentrations is described. On using a cooled SPME fiber coated with a 75-microm layer of poly(dimethylsiloxane)/carboxene and heating the sample to 35 degrees C, about 4 times more MTBE is extracted compared to SPME extraction with the fiber placed in the water sample. Stable analytical conditions with a detection limit of 10 ng/L are achieved. By use of a sample volume of 4 mL in a 10 mL vial, a sodium chloride content of 10% (w/w), and an extraction time of 30 min, the total time of an analytical cycle was optimized to 39 min. Precise linearity of R2>0.9991 and R2>0.9916 in the calibration range of 20-5000 ng/L and 20-100 ng/L, both in addition to blanks, respectively, and relative standard deviations of 10% (100 ng/L, long-term) and 11% (20 ng/L, short-term) are presented. The recovery is well within the accepted limits of 83-118% at a concentration of 100 ng/L and even close thereto at trace levels of 20 ng/L (96-125%). The data presented for a concentration of 100 ng/L are examined by statistical methods and show results for the T test at the 95% confidence level. Due to the large concentration range covered, the method is well suited for the monitoring of MTBE in the aquatic environment.     

Conformational structure of some trimeric and pentameric structural units of heparin

The molecular structure of trimeric units (D-E-F and F-G-H) and the pentamer D-E-F-G-H of heparin (sodium salts and their anionic forms) was studied using the B3LYP/6-31G(d) method. The equilibrium structure of the sodium salts of the trimers and pentamer investigated in the isolated state was determined by multidentate coordination of the sodium cations with oxygen atoms of the sulfate, carboxyl, and hydroxyl (hydroxymethyl) groups, respectively. The displacement of Na+ ions from the binding sites in the sodium salt of oligosaccharides studied resulted in the appreciable change of the overall conformation of the corresponding anion. Upon dissociation, a large change in both the position of the sulfate groups and the conformation across the glycosidic bonds was observed. The stable energy conformations around the glysosidic bonds found for the pentamer investigated are compared and discussed with the available experimental X-ray structural data for the structurally related heparin-derived pentasaccharides in cocrystals with proteins.     

Gas-phase and solution conformations of the alpha-L-iduronic acid structural unit of heparin

The IdoA2S structural unit of heparin (subunit G) may oscillate among the three conformations (4C1, 1C4, and 2So). Only the twisted boat conformation allowed the biologically active pentasaccharide unit of heparin (DEFGH) to bind to antithrombin. Our work reports, in detail, the results of systematic large-scale theoretical investigations of the three basic conformations (4C1, 1C4, and 2So) of the IdoA2S structural unit of heparin, its anionic forms, and its sodium salt using the B3LYP/6-311++G(d, p) and B3LYP/6-31+G(d) model chemistries. According to our calculations, the most stable structure of these molecules corresponds to the 2So skew-boat conformation. This form is also the most stable in a water solution. The 2So conformation of neutral molecules is not maintained in the anionic species. With anions, both 1C4 and 4C1 conformations are present. The relative stability of individual species of the substituted iduronic acid affects extra stabilization by means of intramolecular hydrogen bonds. The calculated macroscopic pKa of 1,4-DiOMe IdoA2S are as follows: pKa = 0.25 for the terminal C(2)-OSO3H group, pKa = 3.67 for the terminal C(5)-CO2H group, and pKa = 14.00 for the C(3)-OH hydroxyl group. The computed Gibbs interaction energies, DeltaGdegrees , for the reaction 1,4-DiOMe IdoA2S(2-) + 2Na+ <==> 1,4-DiOMe IdoA2SNa2 (4C1, 1C4, and 2So conformations) are negative and span a rather small energy interval (from -1244 to -1290 kJ mol(-1)).     

Loop grafting of Bacillus subtilis lipase A: inversion of enantioselectivity

Lipases are successfully applied in enantioselective biocatalysis. Most lipases contain a lid domain controlling access to the active site, but Bacillus subtilis Lipase A (LipA) is a notable exception: its active site is solvent exposed. To improve the enantioselectivity of LipA in the kinetic resolution of 1,2-O-isopropylidene-sn-glycerol (IPG) esters, we replaced a loop near the active-site entrance by longer loops originating from Fusarium solani cutinase and Penicillium purpurogenum acetylxylan esterase, thereby aiming to increase the interaction surface for the substrate. The resulting loop hybrids showed enantioselectivities inverted toward the desired enantiomer of IPG. The acetylxylan esterase-derived variant showed an inversion in enantiomeric excess (ee) from -12.9% to +6.0%, whereas the cutinase-derived variant was improved to an ee of +26.5%. The enantioselectivity of the cutinase-derived variant was further improved by directed evolution to an ee of +57.4%.