The molecular mechanism of stabilization of proteins by TMAO and its ability to counteract the effects of urea

Trimethylamine n-oxide (TMAO) is a naturally occurring osmolyte that stabilizes proteins and offsets the destabilizing effects of urea. To investigate the molecular mechanism of these effects, we have studied the thermodynamics of interaction between TMAO and protein functional groups. The solubilities of a homologous series of cyclic dipeptides were measured by differential refractive index and the dissolution heats were determined calorimetrically as a function of TMAO concentration at 25 degrees C. The transfer free energy of the amide unit (-CONH-) from water to 1 M TMAO is large and positive, indicating an unfavorable interaction between the TMAO solution and the amide unit. This unfavorable interaction is enthalpic in origin. The interaction between TMAO and apolar groups is slightly favorable. The transfer free energy of apolar groups from water to TMAO consists of favorable enthalpic and unfavorable entropic contributions. This is in contrast to the contributions for the interaction between urea and apolar groups. Molecular dynamics simulations were performed to provide a structural framework for the interpretation of these results. The simulations show enhancement of water structure by TMAO in the form of a slight increase in the number of hydrogen bonds per water molecule, stronger water hydrogen bonds, and long-range spatial ordering of the solvent. These findings suggest that TMAO stabilizes proteins via enhancement of water structure, such that interactions with the amide unit are discouraged.     

Unrestricted perfect pairing: the simplest wave-function-based model chemistry beyond mean field

The perfect pairing (PP) approximation from generalized valence bond theory is formulated in an unrestricted fashion for both closed- and open-shell systems using a coupled cluster ansatz. In the model chemistry proposed here, active electron pairs are correlated, but the unpaired or radical electrons remain uncorrelated, leading to a linear number of decoupled cluster amplitudes which can be solved for analytically. The alpha and beta spatial orbitals are variationally optimized independently. This minimal treatment of electron-electron correlation noticeably improves upon symmetry-breaking problems and other pathologies in Hartree-Fock (HF) theory and may be computed using the resolution of the identity approximation at only a factor of several times more effort than HF itself. PP also generally predicts improved molecular structures over HF. This compact, correlated wave function potentially provides a useful starting point for dynamical correlation corrections.     

Computational results on an algorithm for finding all vertices of a polytope

This paper provides answers to several questions raised by V. Klee regarding the efficacy of Mattheiss' algorithm for finding all vertices of convex polytopes. Several results relating to the expected properties of polytopes are given which indicate thatn-polytopes defined by large numbers of constraints are difficult to obtain by random processes, the expected value of the number of vertices of polytope is considerably less than Klee's least upper bound the expected performance of Mattheiss' algorithm is far better than Klee's upper bound would suggest.     

Rotational band crossings in the actinides

In the actinides bothi _13/2 protons andj _15/2 neutrons are close to the Fermi surface. At rapid rotation these high-j particles will unpair and align their orbital angular momentum along the axis of rotation giving rise tos-bands that cross the ground-state band. Coulomb excitation of the odd nuclei ₂₃₇ ⁹³ Np (established up to the 45/2⁺ state) and ₂₃₅ ⁹² U (established up to the 51/2^? state) provides specific information about these band crossings: From the saturating alignment of the odd high-j particle in both nuclei at intermediate rotational frequencies we find the aligned angular momentum of thei _13/2 protons-band to be 6.6? while the corresponding value for thej _15/2 neutrons-band is 5.5?. At more rapid rotation above ?ω=0.18 MeV we observe additional alignment in²³⁵U. This is ascribed to the interaction of the protons-band. From the gradual onset of the additional alignment we deduce that forZ=92 the protons-band interacts strongly with the ground-state band and from a comparison of the actual amount of alignment with the full value of 6.6? we estimate the crossing to occur around ?gw _c ^p =0.25 MeV.     

An examination of the validity of nonequilibrium molecular-dynamics simulation algorithms for arbitrary steady-state flows

Nonlinear-response theory of nonequilibrium molecular-dynamics simulation algorithms is considered under the imposition of an arbitrary steady-state flow field. It is demonstrated that the SLLOD and DOLLS algorithms cannot be used for general flows, although the SLLOD algorithm is rigorous for planar Couette flow. Following the same procedure used to establish SLLOD as the valid algorithm for planar Couette flow [D. J. Evans and E. P. Morriss, Phys. Rev. A 30, 1528 (1984)], it is demonstrated that the p-SLLOD algorithm is valid for arbitrary flows and produces the correct nonlinear response of the viscous pressure tensor.     

Absorption spectra and photochemistry of the toluene cation and benzyl radical in solid argon

Toluene diluted in argon subjected to continuous argon discharge radiation during condensation at 21 K revealed absorptions at 310.5 and 449.6 nm due to benzyl radical, and 317 nm due to a C₇7H₉ radical. A photosensitive 430 nm band, in agreement with photodissociation spectra of the toluene parent cation, is assigned to this species.     

Cluster chemistry: XVI. Synthesis and crystal structure of AuFe3(μ3-HCNBut)(CO)9(PPh3), an AuFe3 butterfly cluster

The reaction between AuCl(PPh₃ and [Fe(μ₃-HCNBu^t)(CO)₉]^? gives AuFe₃(μ₃-HCNBu^t)(CO)₉(PPh₃), crystals of which are triclinic, space group P$\text{1}$, with a 12.815(3), b 16.265(4), c 19.106(3) Å, α 67.15(3), β 73.46(2), γ 73.12(2)° and Z = 4. The comlex contains an AuFe₃ “butterfly” cluster, the Fe₃ face of which is bridged by the HCNBu^t ligand bonded in the (2σ + π) mode on the side opposite to the Au(PPh₃) moiety, which, contrary to expectation based on the analogy with H, bridges the two Fe atoms σ-bonded to N, and π-bonded to the CN group. The AuFe₂/Fe₃ dihedral angles in the two independent molecules differ significantly, with values of 110.9 and 132.1°.     

Evaluation of protocols for reproducible electrospray in-source collisionally induced dissociation on various liquid chromatography/mass spectrometry instruments and the development of spectral libraries

Mass spectral libraries provide a tool for identifying unknown compounds using both molecular weight and fragmentation information. Mass spectrometers with electrospray ionisation (ESI) and atmospheric chemical ionisation (ApCI) sources have the capability to produce data of this type using in-source collisionally induced dissociation (CID), and in-source CID libraries can be created. Due to the variation in electrospray source design from different instrument manufacturers, the production of reproducible in-source CID spectra that can be used in libraries for all instrument types is not a trivial task. To date, the evaluation of the production of in-source CID libraries has tended to focus on similar instruments from one manufacturer. The studies have also tended to focus on specific compound classes, with a limited molecular weight range.This report describes the findings from the investigation of protocols for the creation of mass spectral libraries using ESI in-source CID on six instruments from four different manufacturers. The overall goal was to create a spectral library for the identification of unknowns. The library could then be applied across all manufacturers' electrospray instruments.Two different experimental protocols were attempted. The first used a tuning compound to establish standard ESI source conditions, with fixed fragmentation potentials. The second involved the attenuation of the [M + H](+) ion to a known degree. A diverse range of compounds (pharmaceutical, photographic, pesticides) was tested to establish the reproducibility of the spectra on the six instruments. Both protocols produced spectra on the various instruments that in many cases were very similar. In other examples, the spectra differed not only in their relative ion abundances, but also in terms of the spectral content. Important observations regarding the effect of ion source design are also reported.The degree of spectral reproducibility was calculated off-line by comparing the five most abundant ions (20% for each ion that matches) from each spectrum on each instrument. This approach was adopted, as we do not possess a software package that met our requirements for spectral comparison. Match factors (% fit) were calculated by comparing each spectrum against the spectra recorded for the same compound and then for all other compounds, on each instrument. The % fit values derived by the off-line approach gave a clear view of the spectral reproducibility from instrument to instrument and also discriminated the spectra of the various compounds from each other. The applicability of this approach was tested using a blind trial in which several compounds were presented as unknowns, their in-source CID spectra recorded and the five-ion approach used for identification.     

Model complexes for metallated polythiophenes: gold(I) and palladium(II) complexes of bis(diphenylphosphino)oligothiophenes

The preparations of two new phosphinothiophene ligands, 3,3'-bis(diphenylphosphino)-2,2'-bithiophene (dppbt; 1) and 3,3' "-dihexyl-3',3' '-bis(diphenylphosphino)-2,5':2',2' ':5' ',2' "-quaterthiophene (hdppqt; 2) are reported. Oxidation of 1 gives 3,3'-bis(diphenylphosphine oxide)-2,2'-bithiophene (3), and the crystal structure of this compound was determined. Pd(II) and Au(I) complexes of these ligands have been synthesized and characterized. Crystal structures of [(dppbt)PdCl(2)] (1-Pd), [(hdppqt)PdCl(2)] (2-Pd), [(dppbt)(AuCl)(2)] (1-Au), and [(hdppqt)(AuCl)(2)] (2-Au) were obtained. [(dppbt)(AuCl)(2)] crystallized in two solid-state forms; crystals grown from CH(2)Cl(2)/Et(2)O show a gold-gold interaction of 3.3221(4) A, but from CH(2)Cl(2)/toluene, the molecule crystallizes as a toluene adduct (1-Au-tol) and does not show any gold-gold interaction. All the complexes were characterized via UV-vis spectroscopy and cyclic voltammetry, and the effect of the metal on the energy of the pi-pi transition and oxidation potential was determined. These data are correlated to the interannular torsion angles in the oligothienyl groups from the crystal structure studies.     

Vibrational population distribution of ground state BaO formed by the reaction Ba + O2

The vibrational population distribution of X ¹Σ(υ′' = 0 through ν′' = 7) BaO formed in the reaction Ba + O₂ at 0.3 torr has been measured by laser induced photoluminescence intensities. On the basis of the assumed similarity between the Ba + O₂ and Ba + N₂O reactions, these data suggest that a population inversion may exist between A ¹Σ(ν′ = 1) and X ¹Σ(υⁿ = 7) BaO formed in the latter reaction at ≈ 16 torr.