Intrinsic folding of small peptide chains: spectroscopic evidence for the formation of beta-turns in the gas phase

Laser desorption of model peptides coupled to laser spectroscopic techniques enables the gas-phase observation of genuine secondary structures of biology. Spectroscopic evidence for the formation of beta-turns in gas-phase peptide chains containing glycine and phenylalanine residues establishes the intrinsic stability of these forms and their ability to compete with other stable structures. The precise characterization of local minima on the potential energy surface from IR spectroscopy constitutes an acute assessment for the state-of-the-art quantum mechanical calculations also presented. The observation of different types of beta-turns depending upon the residue order within the sequence is found to be consistent with the residue propensities in beta-turns of proteins, which suggests that the prevalence of glycine in type II and II' turns stems essentially from an energetic origin, already at play under isolated conditions.     

A new route to arglecin by metalation and cross coupling of pyrazines. Metalation of diazines. XII

The metalation of dihalogeno and halogenomethoxypyrazines was performed. The resulting pyrazines were submitted to a cross-coupling reaction with propargyl alcohol followed, after dehydration, by a catalytic reduction. This gives a new route to the synthesis of a key intermediate in the synthesis of arglecin.     

Transient rheology in a new type of Couette apparatus.

Summary Calculations are performed which concern a new type of air-bearing viscometer. The transient motions of the rotor are studied for Newtonian fluids, and some applications are described for non-Newtonian fluids. It is shown that the rise and relaxation motions may be generally well described by only one exponential function of the time.

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Zusammenfassung Es werden Rechnungen betreffend ein luftgelagertes Viskosimeter neuen Typs durchgeführt. Die nichtstationären Bewegungen des Rotors werden zuerst für newtonsche Flüssigkeiten untersucht, anschließend folgt eine Anwendung auf nicht-newtonsche Flüssigkeiten. Es wird gezeigt, daß sowohl die Anlauf- als auch die Relaxationsbewegung im allgemeinen hinreichend gut durch eine einzige Exponentialfunktion beschrieben werden kann.

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With 10 figures and 1 table     

Quantum chemical study of the photocoloration reaction in the napthoxazine series

Ab initio and semiempirical quantum mechanical calculations were performed to study the electronic spectra of spiroxazine photochromic compounds as well as the corresponding photoisomers. Ground-state geometries were optimized based on density functional theory (DFT). Excitation energies of the different forms were calculated using the time-dependent density functional theory (TD-DFT) method. Semiempirical calculations including configuration interactions were performed to detail the mechanism of ring opening in excited states. On the basis of the obtained potential energy profile, a complete mechanism of photocoloration able to clarify some experimental findings is provided. A correlation of the experimental quantum yield of photocoloration with the calculated properties as a function of substituent effects is proposed.     

Sterically congested uranyl complexes with seven-coordination of the UO2 unit: the peculiar ligation mode of nitrate in [UO2(NO3)2(Rbtp)] complexes

Addition of 1 or 2 molar equiv of Rbtp [Rbtp = 2,6-bis(5,6-dialkyl-1,2,4-triazin-3-yl)pyridine; R = Me, Pr ( n )] to UO 2(OTf) 2 in anhydrous acetonitrile gave the neutral compounds [UO 2(OTf) 2(Rbtp)] [R = Me ( 1), ( n )Pr ( 2)] and the cationic complexes [UO 2(Rbtp) 2][OTf] 2 [R = Me ( 3), Pr ( n ) ( 4)], respectively. No equilibrium between the mono and bis(Rbtp) complexes or between [UO 2(Rbtp) 2][OTf] 2 and free Rbtp in acetonitrile was detected by NMR spectroscopy. The crystal structures of 1 and 3 resemble those of their terpyridine analogues, and 3 is another example of a uranyl complex with the uranium atom in the unusual rhombohedral environment. In the presence of 1 molar equiv of Rbtp in acetonitrile, UO 2(NO 3) 2 was in equilibrium with [UO 2(NO 3) 2(Rbtp)] and the formation of the bis adduct was not observed, even with an excess of Rbtp. The X-ray crystal structures of [UO 2(NO 3) 2(Rbtp)] [R = Me ( 5), Pr ( n ) ( 6)] reveal a particular coordination geometry with seven coordinating atoms around the UO 2 fragment. The large steric crowding in the equatorial girdle forces the bidentate nitrate ligands to be almost perpendicular to the mean equatorial plane, inducing bending of the UO 2 fragment. The dinuclear oxo compound [U(CyMe 4btbp) 2(mu-O)UO 2(NO 3) 3][OTf] ( 7), which was obtained fortuitously from a 1:2:1 mixture of U(OTf) 4, CyMe 4btbp, and UO 2(NO 3) 2 [CyMe 4btbp = 6,6'-bis-(3,3,6,6-tetramethyl-cyclohexane-1,2,4-triazin-3-yl)-2,2'-bipyridine] is a very rare example of a mixed valence complex involving covalently bound U (IV) and U (VI) ions; its crystal structure also exhibits a seven coordinate uranyl moiety, with one bidentate nitrate group almost parallel to the UO 2 fragment. The distinct structural features of [UO 2(kappa (2)-NO 3) 2(Mebtp)], with its high coordination number and a noticeable bending of the UO 2 fragment, and of [UO 2(kappa (2)-NO 3)(kappa (1)-NO 3)(terpy)], which displays a classical geometry, were analyzed by Density Functional Theory, considering the bonding energy components and the molecular orbitals involved in the interaction between the uranyl, nitrate, and Mebtp or terpy moieties. The unusual geometry of the Mebtp derivative with the seven coordinating atoms around the UO 2 fragment was found very stable. In both the Mebtp and terpy complexes, the origin of the interaction appears to be primarily steric (Pauli repulsion and electrostatic); this term represents 62-63% of the total bonding energy while the orbital term contributes to about 37-38%.     

Ultrasoft pseudopotentials for lanthanide solvation complexes: core or valence character of the 4f electrons

The 4f electrons of lanthanides, because of their strong localization in the region around the nucleus, are traditionally included in a pseudopotential core. This approximation is scrutinized by optimizing the structures and calculating the interaction energies of Gd(3+)(H(2)O) and Gd(3+)(NH(3)) microsolvation complexes within plane wave Perdew-Burke-Ernzerhof calculations using ultrasoft pseudopotentials where the 4f electrons are included either in the core or in the valence space. Upon comparison to quantum chemical MP2 and CCSD(T) reference calculations it is found that the explicit treatment of the 4f electrons in the valence shell yields quite accurate results including the required small spin polarization due to ligand charge transfer with only modest computational overhead.     

Toward accurate solvation dynamics of lanthanides and actinides in water using polarizable force fields: from gas-phase energetics to hydration free energies

In this contribution, we focused on the use of polarizable force fields to model the structural, energetic, and thermodynamical properties of lanthanides and actinides in water. In a first part, we chose the particular case of the Th(IV) cation to demonstrate the capabilities of the AMOEBA polarizable force field to reproduce both reference ab initio gas-phase energetics and experimental data including coordination numbers and radial distribution functions. Using such model, we predicted the first polarizable force field estimate of Th(IV) solvation free energy, which accounts for −1,638 kcal/mol. In addition, we proposed in a second part of this work a full extension of the SIBFA (Sum of Interaction Between Fragments Ab initio computed) polarizable potential to lanthanides (La(III) and Lu(III)) and to actinides (Th(IV)) in water. We demonstrate its capabilities to reproduce all ab initio contributions as extracted from energy decomposition analysis computations, including many-body charge transfer and discussed its applicability to extended molecular dynamics and its parametrization on high-level post-Hartree–Fock data.     

Atomic charges for molecular dynamics calculations

Atomic charges obtained with the fit of the ab initio electrostatic potential suffers of several defects, for instance, chemical meaning is not insured. We have employed a method recently put forward for deriving atomic charges which addresses the issue of chemical meaning and conformational transferability to N,N-dibutylacetamide and ethylenediaminetetraacetate. The charges have been used in molecular dynamics calculations where the interaction with a metallic cation is considered. We found structural parameters for the complexes in good agreement with the available experimental results.     

Ab initio CI study and vibronic analysis of the photoelectron spectra of formaldoxime

The photoelectron spectrum of formaldoximie, CH₂NOH, has been re-investigated with higher resolution and interpreted by, means of ab initio SCF Cl calculations. Calculations have confirmed that the states increase in energy as π₁ < n₁ < π₂ < n₂ and have shown the existence of a shake-up peak at ≈15 eV. The calculation of Franck-Condon factors allowed the interpretation of the observed vibrational structure.