Guanidinium-Type resonance stabilization and its biological implications. I. the guanidine and extended-guanidine series

An unusual type of π-electron delocalization in Y-shaped molecules related to guanidine and its protonated form, the guanidinium ion, has been studied by ab initio methods at the STO -3G and 3-21G levels. Results are reported for tautomeric, rotameric, and protonated forms of the oxygen-substituted guanidine series (urea, carbamic, and carbonic acids); “extended-guanidine” (aminomethylene guanidine) including pseudocyclic forms; and simple ring systems in which the extended-guanidine group is incorporated (3-amino-1,2,4-triazole, 2,4-diaminopyrimidine). Both the guanidine and guanidinium type stabilizations have been characterized in terms of a number of structural and energetic parameters: degree of single/double bond character from bond lengths and π-bond orders, electron distributions, and protonation energies. The major finding is that the structural and energetic properties of the isolated extended-guanidinium group resemble those of the group when incorporated within 6-membered heterocyclic or heterobicyclic rings, although the details vary with the nature of the ring and possibility of reinforcement or interference with the substructure resonance from overall ring delocalization. The implications for stabilization of the protonated forms of some biologically important pteridines is discussed.     

4,5-Disubstituted cis-pyrrolidinones as inhibitors of 17β-hydroxysteroid dehydrogenase II. Part 1: Synthetic approach

17β-Hydroxysteroid dehydrogenase II (17β-HSD II) antagonists may provide an important way into preventing the onset of osteoporosis. The discovery of 4,5-disubstituted cis-pyrrolidinones as 17β-HSD II inhibitors led to the development of an efficient intramolecular Michael addition, followed by catalytic hydrogenation to obtain the desired cis configuration.     

Theoretical studies on pteridines. 2. Geometries,tautomer, ionization and reduction energies of substrates and inhibitors of dihydrofolate reductase

Ab initio SCF calculations with STO-3G and 3-21G basis sets are reported for approximately 85 pteridines of interest to the study of the reaction and inhibition mechanisms of dihydrofolate reductase. These include tautomeric, protonated, deprotonated, reduced and 6-substituted forms of the 2-amino-4-oxo- and 2,4-diamino-pteridines, many of which are not easily amenable to experimental investigation. Full geometry optimizations at the SCF/STO-3G level for 30 such pteridines have been performed. A step-wise computational protocol designed to identify the minimum level of theory necessary for reliable prediction of relative tautomer, reduction and ionization energies has been developed in an effort to minimize the cost of calculations for this reasonably large N-heterobicylic system. In general, SCF/STO-3G results were found to be inadequate while SCF/3-21G results obtained with STO-3G optimized geometries agreed with all available experimental evidence with the exception of the relative acidity of 6-methyl-7,8-dihydropterin. Correlation graphs relating experimental pK_a's to the calculated ionization energies are presented: these are of potential predictive value. An analysis is given of the importance of resonance substructures, such as the guanidinium and extended-guanidinium groups, in stabilizing some preferred tautomeric and ionized forms, and in explaining the observed geometry changes.     

Optimization of GC detector parameters using electronic pressure control

HP 5890 Series II Gas Chromatographs are equipped with prototype hardware enabling electronic pressure programming of all detector and carrier gases. A method of using electronic pressure control (EPC) to optimize detector performance (sensitivity, selectivity, and baseline stability) is demonstrated. With EPC, sample introduction, column separation, and detector performance can be optimized simultaneously without the classical trade-offs in performance. An example is also presented of the use of a new automated system which enables cool on-column injection into 250 or 320 μm columns without the need for a retention gap.     

Ratcheting motion of liquid drops on gradient surfaces

The motions of liquid drops of various surface tensions and viscosities were investigated on a solid substrate possessing a gradient of wettability. A drop of any size moves spontaneously on such a surface when the contact angle hysteresis is negligible; but it has to be larger than a critical size in order to move on a hysteretic surface. The hysteresis can, however, be reduced or eliminated with vibration that allows the drop to sample various metastable states, thereby setting it to the path of global energy minima. Significant amplification of velocity is observed with the frequency of forcing vibration matching the natural harmonics of drop oscillation. It is suggested that the main cause for velocity amplification is related to resonant shape fluctuation, which can be illustrated by periodically deforming and relaxing the drop at low frequencies.     

Adsorption and selectivity of carbon dioxide with methane and nitrogen in slit-shaped carbonaceous micropores: Simulation and experiment

We have used the grand canonical Monte Carlo method to study the adsorption and selectivity of mixtures of carbon dioxide with methane and nitrogen at high (i.e., ambient) temperatures in model slit pores with graphitic surfaces. Experimental data, including new high pressure measurements for carbon dioxide and methane on a non-porous graphitic standard, were used to test the potential models. The mixture simulations predict that carbon dioxide is preferentially adsorbed in both systems. The results are discussed in terms of competing energetic and entropic effects and the underlying molecular mechanisms.     

1-Phenyl-1,2-dicarba-closo-dodecaborane, 1-Ph-1,2-closo-C(2)B(10)H(11). Synthesis, Characterization, and Structure As Determined in the Gas Phase by Electron Diffraction, in the Crystalline Phase at 199 K by X-ray Diffraction, and by ab Initio Computations

The compound 1-phenyl-1,2-dicarba-closo-dodecaborane(12), 1-C(6)H(5)-1,2-closo-C(2)B(10)H(11) (1), has been synthesized and characterized by a complete assignment of its (11)B NMR spectrum via (11)B{(1)H}/(11)B{(1)H} (COSY), (1)H{(11)B(selective)} and (1)H{(11)B}/(1)H{(11)B} (COSY) spectroscopy. An electron- and X-ray diffraction investigation of 1, complemented by ab initio calculations, has been undertaken. The gas-phase electron-diffraction (GED) data can be fitted by several models describing conformations which differ in the position of the phenyl ring with respect to the carborane cage. Local symmetries ofC(2)(v)() and D(6)(h)() for the 1,2-C(2)B(10) and C(6) moieties, respectively, were adopted in the GED model in order to simplify the problem. In addition, constraints among the close-lying C-C and B-B bonds were employed. However, even though such simplifications led to satisfactory refinements (R(G) = 0.069-0.071), a unique, definitive solution could not be gained. The (C-C)(mean), (C-B)(mean) and (B-B)(mean) bond lengths,r(a), are ca. 1.44, 1.72, and 1.78 ?, respectively. The C(6) hexagon, with r(a)(C-C) = ca. 1.394 ?, either eclipses the C(1)-C(2) vector (overall C(s)() symmetry) or more or less eclipses the C(1)-B(4) cluster bond (overall C(1) symmetry). In contrast, in the solid at 199 K, the ring lies at a position intermediate between the two GED positions, as determined by X-ray crystallography [C(8)H(16)B(10), monoclinic P2(1)/a: a = 12.047(3) ?, b = 18.627(4) ?, c = 12.332(5) ?, beta = 110.09(4) degrees, Z = 8]. The C-B distances span the range 1.681(6)-1.743(5) ?, and B-B lengths lie between 1.756(6) and 1.795(6) ?. A similar conformation was found for the theoretical (RHF/6-31G level) structure which was fully optimized in C(1) symmetry. The r(e) distances are consistent with the dimensions derived in the experimental studies. IGLO calculations of the (11)B chemical shifts, in addition to SCF single-point energies of the GED structures, further support these observations.     

Importance of matrix: Analyte ratio for buffer tolerance using 2,5-dihydroxybenzoic acid as a matrix in matrix-assisted laser desorption/ionization-fourier transform mass spectrometry and matrix-assisted laser desorption/ionization-time of flight

Many biological samples destined for matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) contain buffers. The presence of these buffers often inhibits the ability to obtain spectra. Here, the results of a study of the effects of six different buffers on spectra of three representative small proteins are reported utilizing 2,5-dihydroxybenzoic acid as matrix. These proteins, bovine insulin, cytochrome c, and bovine albumin have masses from ～5000 to 66,000 Da. Three different sample preparation techniques were investigated: aerospray, dried-drop, and acetone redeposition. Both MALDI Fourier transform and time-of-flight mass spectrometry results show that buffer tolerance of MALDI-MS samples depends upon several factors, including the relative amount of the buffer in the MALDI matrix, as well as the identity of the specific buffer. Furthermore, the rate at which buffer tolerance decreases as buffer concentration is increased varies from buffer to buffer. The current results reveal that, at very high matrix:analyte ratios, buffer tolerance of MALDI is dramatically greater than concluded in previous literature reports.     

Redefinition of rubisco carboxylase reaction reveals origin of water for hydration and new roles for active-site residues

Crystallographic, mutagenesis, kinetic, and computational studies on Rubisco over three decades have revealed much about its catalytic mechanism and the role played by several active-site residues. However, key questions remain unanswered. Specific details of the carboxylase and oxygenase mechanisms, required to underpin the rational re-engineering of Rubisco, are still speculative. Here we address critical gaps in knowledge with a definitive comprehensive computational investigation of the mechanism of carboxylase activity at the Rubisco active site. Density functional theory calculations (B3LYP/6-31G(d,p)) were performed on active-site fragment models of a size up to 77 atoms, not previously possible computationally. All amino acid residues suspected to play roles in the acid-base chemistry in the multistep reaction, and interacting directly with the central Mg (2+) atom and the reactive moiety of substrate and intermediates, were included. The results provide a firm basis for us to propose a novel mechanism for the entire sequence of reactions in the carboxylase catalysis and to define precise roles for the active-site residues, singly and in concert. In this mechanism, the carbamylated LYS201 plays a more limited role than previously proposed but is crucial for initiating the reaction by acting as a base in the enolization. We suggest a wider role for HIS294, with involvement in the carboxylation, hydration, and C2-C3 bond-scission steps, consistent with the suggestion of Harpel et al. (1998) but contrary to the consensus view of Cleland et al. (1998). In contrast to the common assumption that the water molecule for the hydration step comes from within the active site, we propose that the Mg-coordinated water is not dissociated at the start of the gas-addition reaction but rather remains coordinated and is used for the hydration of the C3 carbon atom. New roles are also proposed for LYS175, GLU204, and HIS294. The mechanism suggests roles in the gas-addition step for residues in three spatially distinct regions of the active site, HIS294 and LYS334 in the C-terminal domain of the large subunit (LSU), but also hitherto unsuspected roles for a cluster of three residues (ASN123, GLU60, and TYR20) in the N-terminal domain of the partner LSU of the dimer containing the active site. Our new mechanism is supported by existing experimental data, provides new convincing interpretations of previously puzzling data, and allows new insights into mutational strategies for improving Rubisco activity.