Organic Synthesis in the Age of Computers

The computer affords four areas of interest to synthetic chemists: (1) storage and retrieval of information; (2) complex calculations of shape and reaction dynamics; (3) artificial intelligence (AI) to solve synthetic and analytical problems; (4) overall direction of multiple laboratory experiments. Our work began 30 years ago initiating molecular geometry calculations to match experimental results. The explosive growth of computer power since will be illustrated. Synthesis design (as AI) requires an efficient protocol to search huge trees. The SYNGEN program is based on simplification and systematization, first of skeletal dissection, then of structure and reaction characterization, for generation of optimal synthesis routes. The program will be be described and its future development outlined. Finally, a perspective on the future of all four areas will be sketched, noting the necessary attendant growth in systematic use by chemists and in sympathetic interfaces by software designers.     

Mapping of protein:protein contact surfaces by hydrogen/deuterium exchange,followed by on-line high-performance liquid chromatography-electrospray ionization Fourier-transform ion-cyclotron-resonance mass analysis

Furfural contents in adapted and follow-up infant formulas were measured by RP-HPLC. The evolution of furfural compound contents during storage (a year at 20 and 37 degrees C) was studied. 2-Furylmethylketone and 5-methyl-2-furaldehyde were not detectable in analysed samples. The differences in the furfural compounds at point zero between both infant formulas has to be ascribed to the differences in protein and iron contents. An increase in free 5-hydroxymethyl-2-furfuraldehyde (HMF), 2-furaldehyde (F) and HMF+F contents was observed in all samples, although the differences were not statistically significant. The storage temperature affected the total HMF content and the storage time affected the total HMF and F contents.     

Construction of a hybrid quadrupole/fourier transform ion cyclotron resonance mass spectrometer for versatile MS/MS above 10 kDa

Technological advancements including an open-cylindrical Penning trap with capacitively coupled ICR cell, selective ion accumulation with a resolving quadrupole, and a voltage gradient used during ion extraction from an octopole ion trap, have individually improved dynamic range and sensitivity in Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS). Documented here is a new instrument utilizing these technologies toward the robust detection and fragmentation of biomolecules >10 kDa. Up to 55-fold enhancement in ion population by selective ion accumulation combined with 10- to 20- fold signal-to-noise improvement by application of a DC voltage gradient to an accumulation octopole during the ion transfer event offers improved signal-to-noise (or speed) of MS/MS experiments, for proteins from Methanococcus jannaschii and Saccharomyces cerevisiae whole cell lysates. After external quadrupole filtering with a 40 m/z window, three proteins were fragmented (and identified) in parallel from the database of Methanococcus jannaschii. Electron capture dissociation (ECD) of an intact yeast protein provides extensive sequence information resulting in a high degree of localization for an N-terminal acetylation. Hybrid fragmentation, infrared multiphoton dissociation (IRMPD) followed by low energy electrons (ECD), with the electron source located laterally off the z-axis and external to the magnet bore, presents a strategy for identification of proteins by means of the sequence tag approach. Automated implementation of diverse MS(n) approaches in a Q-FTMS instrument promises to help realize "top-down" proteomics in the future.     

Tetranuclear manganese carboxylate complexes with a trigonal pyramidal metal topology via controlled potential electrolysis

Controlled potential electrolysis (CPE) procedures are described that provide access to complexes with a [Mn4(mu 3-O)3(mu 3-O2CR)]6+ core (3MnIII,MnIV) and a trigonal pyramidal metal topology, starting from species containing the [Mn4(mu 3-O)2]8+ core (4MnIII). [Mn4O2(O2CMe)6(py)2(dbm)2] (6): triclinic, P1, a = 10.868(3) A, b = 13.864(3) A, c = 10.625(3) A, alpha = 108.62(1) degrees, beta = 118.98(1) degrees, gamma = 89.34(2) degrees, V = 1307 A3, Z = 1, T = -131 degrees C, R (Rw) = 3.24 (3.70)%. [Mn4O2(O2CPh)6(py)(dbm)2] (8): monoclinic, P2(1)/c, a = 14.743(6) A, b = 15.536(8) A, c = 30.006(13) A, beta = 102.79(1) degrees, V = 6702 A3, Z = 4, T = -155 degrees C, R (Rw) = 4.32 (4.44)%. Both 6 and 8 contain a [Mn4O2]8+ core; 8 only has one py group, the fourth MnIII site being five-coordinate. (NBun4)[Mn4O2(O2CPh)7(dbm)2] (10) is available from two related procedures. CPE of 10 at 0.65 V vs ferocene in MeCN leads to precipitation of [Mn4O3(O2CPh)4(dbm)3] (11); similarly, CPE of 6 at 0.84 V in MeCN/CH2Cl2 (3:1 v/v) gives [Mn4O3(O2CMe)4(dbm)3] (12). Complex 11: monoclinic, P2(1)/n, a = 15.161(3) A, b = 21.577(4) A, c = 22.683(5) A, beta = 108.04(3) degrees, V = 7056 A3, Z = 4, T = -100 degrees C, R (wR2) = 8.63 (21.80)%. Complex 12: monoclinic, P2(1)/n, a = 13.549(2) A, b = 22.338(4) A, c = 16.618(2) A, beta = 103.74(1) degrees, V = 4885 A3, Z = 4, T = -171 degrees C, R (Rw) = 4.63 (4.45)%. Both 11 and 12 contain a [Mn4(mu 3-O)3(mu-O2CR)] core with a Mn4 trigonal pyramid (MnIV at the apex) and the RCO2- bridging the MnIII3 base. However, in 11, the carboxylate is eta 2,mu 3 with one O atom terminal to one MnIII and the other O atom bridging the other two MnIII ions, whereas in 12 the carboxylate is eta 1,mu 3, a single O atom bridging three MnIII ions. Variable-temperature, solid-state magnetic susceptibility studies on 11 and 12 show that, for both complexes, there are antiferromagnetic exchange interactions between MnIII/MnIV pairs, and ferromagnetic interactions between MnIII/MnIII pairs. In both cases, the resultant ground states of the complex is S = 9/2, confirmed by magnetization vs field studies in the 2.00-30.0 K and 0.50-50 kG temperature and field ranges, respectively.     

Tetra(μ3-hydroxo)hexa(μ2-carboxylato-O,O′)-bridged tetranuclear terbium(III) cubane complex

A novel tetranuclear terbium(III) complex [Tb₄(OH)₄(pybet)₆(H₂O)₈][Tb₄(OH)₄(pybet)₆(H₂O)₇ (NO₃)](ClO₄)₁₄·6H₂O has been synthesized and shown by X-ray crystallography to have a cubane-like Tb₄(μ₃-OH)₄(μ₂-carboxylato-O,O′)₆ core. The ligand pybet is pyridinoacetate, C₅H₅⁺N-CH₂CO₂⁻. Magnetic susceptibility data were measured for this Tb₄ complex in the range of 2.0–320 K and in fields of 1.0 G to 50.0 kG. It is concluded that either there is very weak antiferromagnetic exchange interaction (J = −0.015 cm⁻¹) or there is a small crystal-field splitting of the ⁷F₆ Tb^III ground state.     

Single-molecule magnets: site-specific ligand abstraction from [Mn12O12(O2CR)16(H2O)4] and the preparation and properties of [Mn12O12(NO3)4(O2CCH2Bu(t))12(H2O)4

Site-selective carboxylate abstraction has been achieved from [Mn(12)O(12)(O(2)CR)(16)(H(2)O)(4)] complexes by treatment with HNO(3) in MeCN. The reaction of the R = Ph or CH(2)Bu(t)() complexes with 4 equiv of HNO(3) gives [Mn(12)O(12)(NO(3))(4)(O(2)CR)(12)(H(2)O)(4)] (R = CH(2)Bu(t) (6) or Ph (7)) in analytical purity. Complex 6.MeNO(2) crystallizes in monoclinic space group C2/c with the following cell parameters at -168 degrees C: a = 21.280(5), b = 34.430(8), c = 33.023(8) A, beta = 104.61(1) degrees, V = 23413 A, and Z = 8. The four NO(3)(-) groups are not disordered and are bound in bridging modes at axial positions formerly occupied by bridging carboxylate groups. (1)H NMR spectroscopy in CD(2)Cl(2) and CDCl(3) shows retention of the solid-state structure on dissolution in these solvents. DC magnetic susceptibility (chi(M)) and magnetization (M) studies have been carried out in the 2.00-300 K and 1.0-7.0 T ranges. Fits of M/Nmu(B) versus H/T plots gave S = 10, g = 1.92, and D = -0.40 cm(-1), where D is the axial zero-field splitting parameter. AC magnetic susceptibility studies on 6 have been performed in the 1.70-10.0 K range in a 3.5 Oe field oscillating at frequencies up to 1500 Hz. Out-of-phase magnetic susceptibility (chi(M)' ') signals were observed in the 4.00-8.00 K range which were frequency-dependent. Thus, 6 displays the slow magnetization relaxation diagnostic of a single-molecule magnet (SMM). The data were fit to the Arrhenius law, and this gave the effective barrier to relaxation (U(eff)) of 50.0 cm(-1) (72.0 K) and a pre-exponential (1/tau(0)) of 1.9 x 10(8) s(-1). Complex 6 also shows hysteresis in magnetization versus DC field scans, and the hysteresis loops show steps at regular intervals of magnetic field, the diagnostic evidence of field-tuned quantum tunneling of magnetization. High-frequency EPR (HFEPR) spectroscopy on oriented crystals of complex 6 shows resonances assigned to transitions between zero-field split M(s) states of the S = 10 ground state. Fitting of the data gave S = 10, g = 1.99, D = -0.46 cm(-1), and B(4)(0) = -2.0 x 10(-5), where B(4)(0) is the quartic zero-field coefficient. The combined results demonstrate that replacement of four carboxylate groups with NO(3)(-) groups leads to insignificant perturbation of the magnetic properties of the Mn(12) complex. Complex 6 should now be a useful starting point for further reactivity studies, taking advantage of the good leaving group properties of the NO(3)(-) ligands.     

Density functional theory predicts the barriers for radical fragmentation in solution

[reaction: see text] N-Methoxypyridyl radicals formed by one-electron reduction of the corresponding cationic heterocycles undergo N-O bond cleavage. Experimental activation free energies for a series of these bond fragmentations are compared to corresponding barriers determined from electronic structure calculations. The DFT barriers agree well with those from experiment, being smaller than the latter values by an average value of ca. 1 kcal/mol, for rate constants varying over almost 3 orders of magnitude, or within ca. 3 kcal/mol over 8 orders of magnitude of rate constant. For a model compound, the B3PW91/6-31+G hybrid density functional method is also found to be in good agreement with the MCSCF-MRMP2 method. One of the reactions is found by DFT to have no minimum for the reactant radical, consistent with a truly barrierless reaction.     

Synthesis, structure and spectroscopy of new thiopyrone and hydroxypyridinethione transition-metal complexes

The coordination chemistry of several O,S mixed donor ligands, namely thiopyrone and hydroxypyridinethione chelators, with a variety of middle and late first-row transition-metal ions is described. Complexes of 3-hydroxy-2-methyl-4-thiopyrone (thiomaltol) with cobalt(II), copper(II) and zinc(II); 3-hydroxy-1,2-dimethyl-4(1H)-pyridinethione (3,4-HOPTO) with iron(III), nickel(II), copper(II) and zinc(II); and 3-hydroxy-1-methyl-2(1H)-pyridinethione (3,2-HOPTO) with iron(III), nickel(II), copper(II) and zinc(II) have been synthesized and characterized. The structures, absorbance spectroscopy, cyclic voltammetry and superconducting quantum interferometer device (SQUID) measurements of selected metal complexes, as well as ligand protonation constants, are reported. Most of the metal complexes show coordination geometries indicative of a strong trans influence by the O,S chelators. The data presented herein provide the most detailed study of the transition-metal coordination chemistry of both thiopyrone and hydroxypyridinethione O,S donor ligands to date, and provide the basis for the investigation of these ligands in realm of biological inorganic chemistry.     

Evaluation and optimization of electron capture dissociation efficiency in fourier transform ion cyclotron resonance mass spectrometry

Electron capture dissociation (ECD) efficiency has typically been lower than for other dissociation techniques. Here we characterize experimental factors that limit ECD and seek to improve its efficiency. Efficiency of precursor to product ion conversion was measured for a range of peptide (∼15% efficiency) and protein (∼33% efficiency) ions of differing sizes and charge states. Conversion of precursor ions to products depends on electron irradiation period and maximizes at ∼5–30 ms. The optimal irradiation period scales inversely with charge state. We demonstrate that reflection of electrons through the ICR cell is more efficient and robust than a single pass, because electrons can cool to the optimal energy for capture, which allows for a wide range of initial electron energy. Further, efficient ECD with reflected electrons requires only a short (∼500 μs) irradiation period followed by an appropriate delay for cooling and interaction. Reflection of the electron beam results in electrons trapped in or near the ICR cell and thus requires a brief (∼50 μs) purge for successful mass spectral acquisition. Further electron irradiation of refractory precursor ions did not result in further dissociation. Possibly the ion cloud and electron beam are misaligned radially, or the electron beam diameter may be smaller than that of the ion cloud such that remaining precursor ions do not overlap with the electron beam. Several ion manipulation techniques and use of a large, movable dispenser cathode reduce the possibility that misalignment of the ion and electron beams limits ECD efficiency.     

The 'hybrid cell': a new compensated infinity cell for larger radius ion excitation in Fourier transform ion cyclotron resonance mass spectrometry

A new 'hybrid' ion cyclotron resonance (ICR) trap is proposed and analyzed by computer simulations. The trap is basically a hybrid of a segmented end cap (Infinity) and capacitively coupled cylindrical cell, with additional electrodes placed at the center of each end cap. The new trap produces an on-axis electric field z-profile similar to that of the Infinity cell or capacitively coupled open cylindrical cell during ion excitation. Simion simulations demonstrate that, during detection, appropriate changes of the potentials applied to the two new sets of electrodes produce a radial electric field z-profile that more closely approaches that for an ideal axial three-dimensional quadrupolar potential at high post-excitation ICR orbital radius, for improved signal-to-noise ratio and resolving power, and minimal m/z-discrimination.