Fluorinations with complex metal fluorides. Part 6 [1] fluorination of yridine and related compounds with caesium tetrafluorocobaltate(III) [2]

Pyridine has been fluorinated over caesium tetrafluorocobaltate(III) (CsCo^IIIF₄) at 300–400°C to give a mixture of undecafluoro-N-methylpyrrolidine, bis(trifluoromethyl)amine, pentafluoropyridine and several polyfluoropyridines; the product composition depended to some extent on the geometry of the reactor. The fluorinations of pentafluoropyridine, piperidine and undecafluoropiperidine were also investigated.     

Comparison of linear-scaling semiempirical methods and combined quantum mechanical/molecular mechanical methods for enzymic reactions. II. An energy decomposition analysis

QM/MM methods have been developed as a computationally feasible solution to QM simulation of chemical processes, such as enzyme-catalyzed reactions, within a more approximate MM representation of the condensed-phase environment. However, there has been no independent method for checking the quality of this representation, especially for highly nonisotropic protein environments such as those surrounding enzyme active sites. Hence, the validity of QM/MM methods is largely untested. Here we use the possibility of performing all-QM calculations at the semiempirical PM3 level with a linear-scaling method (MOZYME) to assess the performance of a QM/MM method (PM3/AMBER94 force field). Using two model pathways for the hydride-ion transfer reaction of the enzyme dihydrofolate reductase studied previously (Titmuss et al., Chem Phys Lett 2000, 320, 169-176), we have analyzed the reaction energy contributions (QM, QM/MM, and MM) from the QM/MM results and compared them with analogous-region components calculated via an energy partitioning scheme implemented into MOZYME. This analysis further divided the MOZYME components into Coulomb, resonance and exchange energy terms. For the model in which the MM coordinates are kept fixed during the reaction, we find that the MOZYME and QM/MM total energy profiles agree very well, but that there are significant differences in the energy components. Most significantly there is a large change (approximately 16 kcal/mol) in the MOZYME MM component due to polarization of the MM region surrounding the active site, and which arises mostly from MM atoms close to (<10 A) the active-site QM region, which is not modelled explicitly by our QM/MM method. However, for the model where the MM coordinates are allowed to vary during the reaction, we find large differences in the MOZYME and QM/MM total energy profiles, with a discrepancy of 52 kcal/mol between the relative reaction (product-reactant) energies. This is largely due to a difference in the MM energies of 58 kcal/mol, of which we can attribute approximately 40 kcal/mol to geometry effects in the MM region and the remainder, as before, to MM region polarization. Contrary to the fixed-geometry model, there is no correlation of the MM energy changes with distance from the QM region, nor are they contributed by only a few residues. Overall, the results suggest that merely extending the size of the QM region in the QM/MM calculation is not a universal solution to the MOZYME- and QM/MM-method differences. They also suggest that attaching physical significance to MOZYME Coulomb, resonance and exchange components is problematic. Although we conclude that it would be possible to reparameterize the QM/MM force field to reproduce MOZYME energies, a better way to account for both the effects of the protein environment and known deficiencies in semiempirical methods would be to parameterize the force field based on data from DFT or ab initio QM linear-scaling calculations. Such a force field could be used efficiently in MD simulations to calculate free energies.     

Distributed data parallel coupled-cluster algorithm: Application to the 2-hydroxypyridine/2-pyridone tautomerism

The recently developed parallel coupled-cluster algorithm of Rendell, Lee, and Lindh [Chem. Phys. Lett., 194 , 84 (1992)] is extended to allow four-indexed quantities containing one or two indices in the virtual orbital space to be stored across the global memory of distributed-memory parallel processors. Quantities such as the double-excitation amplitudes can now be distributed over multiple nodes, with blocks of data retrieved from remote nodes by the use of interrupt handlers. As an application of the new code, we have investigated the potential energy surface of the 2-hydroxypyridine/2-pyridone tautomers. Using large basis sets, the structure of each tautomer and the transition state connecting the two minima has been determined at the SCF level. The relative energy difference and the activation energy were then redetermined using the MP2, CCSD, and CCSD(T) methods. All calculations have been performed on Intel distributed-memory supercomputers. The largest coupled-cluster calculations contained over 2 million double-excitation amplitudes. © John Wiley & Sons, Inc.     

Infrared dispersion studies: Part 12: infrared dispersion of dichloro-, dibromo- and diiodomethane and their deuterated analogues

Absorption spectra and dispersion curves have been obtained for dichloro-, dibromo- and diiodomethane in the liquid phase between 500 and 20 cm^?1 using interferometric and Fourier spectroscopic techniques. The refractive index data extend existing information on these molecules to include all infrared active fundamental modes. Dispersion curves have also been obtained for deuterated dichloro- and dibromomethane, in the liquid phase, between 5000 and 450 cm^?1.The refractive indices have been used to calculate absolute band intensities, dipole moment derivatives and vibrational polarizations.     

Deterministic global optimization in ab-initio quantum chemistry

A large number of problems in ab-initio quantum chemistry involve finding the global minimum of the total system energy. These problems are traditionally solved by numerical approaches equivalent to local optimization. While these approaches are relatively efficient, they do not provide guarantees of global optimality unless a starting point sufficiently close to the global minimum is known apriori. Due to the enormous amount of computational effort required to solve these problems, more mathematically rigorous alternatives have so far received very little attention. Taking the above issue into consideration, this paper explores the use of deterministic global optimization in the context of Hartree-Fock theory, an important mathematical model applied in many quantum chemistry methods. In particular, it presents a general purpose approach for generating linear relaxations for problems arising from Hartree-Fock theory. This was then implemented as an extension to the ${{\tt COUENNE}}$ (Convex Over and Under ENvelopes for Nonlinear Estimation) branch and bound mixed integer non-linear programs solver. Proof of concept calculations that simultaneously optimise the orbital coefficients and the location of the nuclei in closed-shell Hartree-Fock calculations are presented and discussed.     

Precise mass measurement of a double-stranded 500 base-pair (309 kDa) polymerase chain reaction product by negative ion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry

Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICRMS) has been used to determine the mass of a double-stranded 500 base-pair (bp) polymerase chain reaction (PCR) product with an average theoretical mass of the blunt-ended (i.e. unadenylated) species of 308 859.35 Da. The PCR product was generated from the linearized bacteriophage Lambda genome which is a double-stranded template. Utilization of ethanol precipitation in tandem with a rapid microdialysis step to purify and desalt the PCR product was crucial to obtain a precise mass measurement. The PCR product (0.8 pmol/μL) was electrosprayed from a solution containing 75% acetonitrile, 25 mM piperidine, and 25 mM imidazole and was infused at a rate of 200 nL/min. The average molecular mass and the corresponding precision were determined using the charge-states ranging from 172 to 235 net negative charges. The experimental mass and corresponding precision (reported as the 95% confidence interval of the mean) was 309 406 +/- 27 Da (87 ppm). The mass accuracy was compromised due to the fact that the PCR generates multiple products when using Taq polymerase due to the non-template directed 3'-adenylation. This results in a mixture of three PCR products with nearly identical mass (i.e. blunt-ended, mono-adenylated and di-adenylated) with unknown relative abundances that were not resolved in the spectrum. Thus, the experimental mass will be a weighted average of the three species which, under our experimental conditions, reflects a nearly equal concentration of the mono- and di-adenylated species. This report demonstrates that precise mass measurements of PCR products up to 309 kDa (500 bp) can be routinely obtained by ESI-FTICR requiring low femtomole amounts. Copyright 1999 John Wiley & Sons, Ltd.     

Measuring inter-pulse intervals in sperm whale clicks: consistency of automatic estimation methods

Sperm whale clicks are characterized by a multi-pulsed structure. The time lag between consecutive pulses, i.e., the inter-pulse interval (IPI), is related to the size of the sound production organ such that its measurement provides a means to acoustically estimate the size of individual whales. Due to off-axis effects the identification of pulses is, however, not always straightforward, and automatic measurement methods provide not only more objective estimation, but may also facilitate IPI estimation in cases where single click measurements are ambiguous. In particular, averaging measurements over a time series of clicks from the same whale could enhance the discrimination of time invariant pulses. The authors developed two automatic methods of automatic IPI measurement based on waveform and autocorrelation averaging and compared their accuracy and consistency with other previously used methods. Manual measurement by an experienced operator provided the most self-consistent estimates. The autocorrelation averaging technique had the best overall performance of the automated methods achieving a very similar performance to manual measurement. On some recordings cepstrum averaging methods converged when autocorrelation did not. Therefore, applying both of these automated methods and choosing the best of the two are recommended.     

The structures,binding energies and vibrational frequencies of Ca3 and Ca4 — An application of the CCSD(T) method

Summary The Ca₃ and Ca₄ metallic clusters have been investigated using state-of-the-artab initio quantum mechanical methods. Large atomic natural orbital basis sets have been used in conjunction with the singles and doubles coupled-cluster (CCSD) method, a coupled-cluster method that includes a perturbational estimate of connected triple excitations, denoted CCSD(T), and the multireference configuration interaction (MRCI) method. The equilibrium geometries, binding energies and harmonic vibrational frequencies have been determined with each of the methods so that the accuracy of the coupled-cluster methods may be assessed. Since the CCSD(T) method reproduces the MRCI results very well, cubic and quartic force fields of Ca₃ and Ca₄ have been determined using this approach and used to evaluate the fundamental vibrational frequencies. The infrared intensities of both thee mode of Ca₃ and thet ₂ mode of Ca₄ are found to be small. The results obtained in this study are compared and contrasted with those from our earlier studies on small Be and Mg clusters.Dedicated to Prof. Klaus Ruedenberg on the occasion of his 70th birthday