Modeling the Interactions between Peptide Functions and Cu(I): Formamide−Cu+ Reactions in the Gas Phase

Magnetic susceptibility anisotropy of myocardium imaged by cardiovascular magnetic resonance reflects the anisotropy of myocardial filament α-helix polypeptide bonds

BACKGROUND

A key component of evaluating myocardial tissue function is the assessment of myofiber organization and structure. Studies suggest that striated muscle fibers are magnetically anisotropic, which, if measurable in the heart, may provide a tool to assess myocardial microstructure and function.

METHODS

To determine whether this weak anisotropy is observable and spatially quantifiable with cardiovascular magnetic resonance (CMR), both gradient-echo and diffusion-weighted data were collected from intact mouse heart specimens at 9.4 Tesla. Susceptibility anisotropy was experimentally calculated using a voxelwise analysis of myocardial tissue susceptibility as a function of myofiber angle. A myocardial tissue simulation was developed to evaluate the role of the known diamagnetic anisotropy of the peptide bond in the observed susceptibility contrast.

RESULTS

The CMR data revealed that myocardial tissue fibers that were parallel and perpendicular to the magnetic field direction appeared relatively paramagnetic and diamagnetic, respectively. A linear relationship was found between the magnetic susceptibility of the myocardial tissue and the squared sine of the myofiber angle with respect to the field direction. The multi-filament model simulation yielded susceptibility anisotropy values that reflected those found in the experimental data, and were consistent that this anisotropy decreased as the echo time increased.

CONCLUSIONS

Though other sources of susceptibility anisotropy in myocardium may exist, the arrangement of peptide bonds in the myofilaments is a significant, and likely the most dominant source of susceptibility anisotropy. This anisotropy can be further exploited to probe the integrity and organization of myofibers in both healthy and diseased heart tissue.

Using the reaction force and the reaction electronic flux on the proton transfer of formamide derived systems

In this work, we present a theoretical study of the mechanism of double proton transfer in formamide, formamide-thioformamide and thioformamide dimers. The reaction mechanisms were analyzed in terms of the energy profile and novel concepts such as the reaction force profile and reaction electronic flux, along with local electronic properties such as NBO analysis. All systems were characterized computationally using DFT/B3LYP 6-311G** on Gaussian09. These results show that the electronic processes take place mostly in the transition state for all the systems; in the formamide and thioformamide dimers, electron transfer has a synchronic nature, while the electron transfer is asynchronic in the formamide-thioformamide dimer.

Atomic decomposition of conceptual DFT descriptors: application to proton transfer reactions

We present an atomic decomposition of the molecular energy, reaction force and reaction flux, which is based on Bader's atoms-in-molecules theory.

Modelling peptide-metal dication interactions: formamide-Ca2+ reactions in the gas phase

The collision induced dissociation of formamide-Ca(2+) complexes produced in the gas phase through nanoelectrospray ionization yields as main products ions [CaOH](+), [HCNH](+), [Ca(NH(2))](+), HCO(+) and [Ca(NH(3))](2+) and possibly [Ca(H(2)O)](2+) and [C,O,Ca](2+), the latter being rather minor. The mechanisms behind these fragmentation processes have been established by analyzing the topology of the potential energy surface by means of B3LYP calculations carried out with a core-correlated cc-pWCVTZ basis set. The Ca(2+) complexes formed by formamide itself and formimidic acid play a fundamental role. The former undergoes a charge separation reaction yielding [Ca(NH(2))](+) + HCO(+), and the latter undergoes the most favorable Coulomb explosion yielding [Ca-OH](+) + [HCNH](+) and is the origin of a multistep mechanism which accounts for the observed loss of water and HCN. Conversely, the other isomer of formamide, amino(hydroxyl)carbene, does not play any significant role in the unimolecular reactivity of the doubly charged molecular cation.

Unexpected acidity enhancement triggered by AlH3 association to phosphines

The complexes formed by the interaction between a series of phosphines R-PH(2) (R = H, CH(3), c-C(3)H(5), C(6)H(5)) and AlH(3) have been investigated through the use of high-level G4 ab initio calculations. These very stable complexes behave as much stronger acids than the isolated phosphines. This dramatic acidity enhancement, which can be as high as 174 kJ mol(-1), results from a much greater stabilization of the anionic deprotonated species with respect to the neutral one, upon AlH(3) association. This effect depends quantitatively on the nature of the substituent R and is smaller for R = C(6)H(5) because of the conjugation of the P lone pair with the aromatic system. More unexpectedly, however, the phosphine-alane complexes, RPH(2):AlH(3), are more acidic than the corresponding phosphine-borane RPH(2):BH(3) analogues. This unexpected result is due to the enhanced stability of the anionic deprotonated species for complexes involving AlH(3), because the delocalization of the newly created P lone pair with the P-Al bonding density is more favorable when the Lewis acid is aluminum trihydride than when it is borane.

Modeling the interactions between peptide functions and Sr2+: formamide-Sr2+ reactions in the gas phase

The interactions between formamide, which can be considered a prototype of a peptide function, and Sr(2+) have been investigated by combining nanoelectrospray ionization/mass spectrometry techniques and G96LYP DFT calculations. For Sr an extended LANL2DZ basis set was employed, together with a 6-311+G(3df,2p) basis set expansion for the remaining atoms of the system. The observed reactivity seems to be dominated by the Coulomb explosion process yielding [SrOH](+) + [HNCH](+), which are the most intense peaks in the MS/MS spectra. Nevertheless, additional peaks corresponding to the loss of HNC and CO indicate that the association of Sr(2+) to water or to ammonia leads to long-lived doubly charged species detectable in the timescale of these experimental techniques. The topology of the calculated potential energy surface permits us to establish the mechanisms behind these processes. Although the interaction between the neutral base and Sr(2+) is essentially electrostatic, the polarization triggered by the doubly charged metal ion results in the activation of several bonds, and favors different proton transfer mechanisms required for the formation of the [SrOH](+), [SrOH(2)](2+) and [SrNH(3)](2+) products.

Can DFT methods correctly and efficiently predict the coordination number of copper(I) complexes? A case study

The coordination number of various experimentally known Cu(I) compounds is studied using density functional theory. Various basis sets are tested, aiming to establish a reliable level for prediction of the coordination number of these and other Cu(I) complexes. It is found that most levels exhibit correct trends, namely, the bulkier ligands demonstrate larger preference for coordination of two ligands. Proper absolute values are obtained when dispersion corrections are also included in the calculations. It is concluded that the fairly small modified 6-31+G* basis set due to Pulay represents a good compromise between accuracy and efficiency, followed by Balabanov and Peterson's all-electron aug-cc-pVDZ basis set. The overall energy is decomposed into various components whose relative contribution to the overall tendency of forming a complex with a particular coordination is examined. It is shown that two opposing contributions play a major role: the interaction energy of the ligand being added and the deformation energy of the copper's coordination sphere prior to the ligand addition. The former being a stabilizing contribution, leads to higher coordination numbers while the later, a destabilizing contribution, is shown to favor lower coordination numbers.

Theoretical survey of the potential energy surface of methyl nitrite + Cu+ reaction

The gas-phase reaction of methyl nitrite with Cu+ has been investigated using density functional theory. The geometries and energies of all the stationary points involved in the reaction have been investigated at the B3LYP/6-311+G(2df,2pd) level. Seven different structures of the encounter complexes could be formed when Cu+ attacking at different electronegative heteroatoms of trans and cis conformational isomers of methyl nitrite, in which the inner oxygen attacks account for the most stable complexes. Extensive conversions could take place for these complexes converting into each other. Various mechanisms leading to the loss of NO and HNO are analyzed in terms of the topology of the potential energy surface. The reaction proceeds exclusively from the inner oxygen attachments, followed by four different mechanisms, i.e., direct dissociation, direct H abstraction, N-O activation, and C-H activation, where the former two provide direct channels for the respective losses of NO and HNO, the third one accounts for both of the losses, and C-H activation is unlikely to be important due to the energetics.

Thermochemistry, bonding, and reactivity of Ni+ and Ni2+ in the gas phase

In this review, we present a general overview on the studies carried out on Ni(+-)- and Ni(2+)-containing systems in the gas phase since 1996. We have focused our attention in the determination of binding energies in parallel with an analysis of the structure and bonding of the complexes formed by the interaction of Ni(+) with one ligand, or in clusters where this metal ion binds several identical or different ligands. Solvation of Ni(2+) by different ligands is also discussed, together with the theoretical information available of doubly charged Ni-containing species. The final section of this review is devoted to an analysis of the gas-phase uni- and bimolecular reactivity of Ni(+) and Ni(2+) complexes.

Copper-biomolecule complexes in the gas phase. The ternary way

This review deals with copper complexes of a variety of organic and bioorganic molecules that have been produced as gas-phase ions by electrospray and other ionization methods and studied experimentally by mass spectrometry and theoretically by ab initio and density functional theory computations. Ternary complexes of Cu((II)) allow one to modify the oxidation state and coordination sphere of the copper ion and thus induce novel fragmentations that involve redox and radical-based reactions. Structure elucidation, distinction, and quantitation of leucine and isoleucine isomers in peptides, distinction of enantiomers in chiral compounds, and sensitive detection of antibiotics are some of the highlights of mass spectrometry of ternary copper complexes. Binary copper complexes are mainly represented by Cu((I)) species in which the copper ion displays the properties of a weak Lewis acid.

Structural Effect on the Stability of (Pyridine)2Cu+ Complexes in the Gas Phase: Nature of the Bond between Copper(I) Ion and Neutral Molecules

Free energy changes (DeltaG degrees , copper cation basicity) for the reaction L(2)Cu(+) = Cu(+) + 2L were obtained in the gas phase for substituted pyridines based on the measurement of ligand-exchange equilibria in a Fourier transform ion cyclotron resonance (FT-ICR) spectrometer. For 3- and 4-substituted pyridines, the relative copper cation basicities (DeltaCCB[L(2)Cu(+)]) were linearly correlated with the corresponding gas-phase proton basicities (DeltaGB) with a slope of 1.01. On the basis of a linear relationship between the calculated copper cation basicities of dimeric and monomeric complexes at MP2/6-311+G(2p,2d)//B3LYP/6-311G*, DeltaCCB[L(2)Cu(+)](calcd) = 1.54DeltaCCB[LCu(+)](calcd), the substituent effect on the DeltaCCB for the first ligand was estimated to be 0.66 times smaller than the corresponding DeltaGB. A comparison with the corresponding results for other Lewis cation basicity of the pyridine system showed that the magnitude of the substituent effect decreases in the order H(+) (1.00) > Me(3)Si(+) (0.95) > Cl(+) (0.83) > Cu(+) (0.66) > Li(+) (0.47). This change was associated with the natural charges at the Lewis cation moiety and the natural atomic orbital (NAO) bond order of the M+-N bond of the complex ion, indicating the decrease in covalent character of the M(+)-N bond in this order. Furthermore, when a variety of neutral bases such as amines, carbonyl compounds, and ethers were included in a comparison between CCB[L(2)Cu(+)] and GB, it was found that there is a good linear relationship with significant deviations of small molecules and bulky tributylamine, which is attributed to their different steric environment at the binding sites from others, while there is no simple linear relationship with the lithium cation basicities (LCB). The similarity of the substituent effect between CCB[L(2)Cu(+)] and GB reflects the covalent character in the Cu(+) interaction. In conclusion, although the ionic (ion-dipole interaction) nature of the Cu(+) interaction results in a smaller substituent effect than that for the protonation, the covalent nature also plays an important role in the Cu(+) interaction with neutral molecules.

Monosodium glutamate in its anhydrous and monohydrate form: differentiation by Raman spectroscopies and density functional calculations

Monosodium glutamate (MSG), a common flavor enhancer, is detected in aqueous solutions by Raman and surface-enhanced Raman (SERS) spectroscopies at the micromolar level. The presence of different species, such as protonated and unprotonated MSG, is demonstrated by concentration and pH dependent Raman and SERS experiments. In particular, the symmetric bending modes of the amino group and the stretching modes of the carboxy moiety are employed as marker bands. The protonation of the NH(2) group at acidic pH values, for example, is detected in the Raman spectra. From the measured SERS spectra, a strong chemical interaction of MSG with the colloidal particles is deduced and a geometry of MSG adsorbed on the silver surface is proposed. In order to assign the observed Raman bands, calculations employing density functional theory (DFT) were performed. The calculated geometries, harmonic vibrational wavenumbers and Raman scattering activities for both MSG forms are in good agreement with experimental data. The set of theoretical data enables a complete vibrational assignment of the experimentally detected Raman spectra and the differentiation between the anhydrous and monohydrate forms of MSG.

Gas-phase ion chemistry in organometallic systems

This review essentially deals with positive ion/molecule reactions occurring in gas-phase organometallic systems, and encompasses a period of time of approximately 7 years, going from 1997 to early 2004. Following the example of the excellent review by Eller & Schwarz (1991; Chem Rev 91:1121-1177), in the first part, results of reaction of naked ions are presented by grouping them according to the neutral substrate, while in the second part, ligated ions are grouped according to the different ligands. Whenever possible, comparison among similar studies is attempted, and general trends of reactivities are evidenced.

Biomimetic Assembly of Polypeptide-Stabilized CaCO3 Nanoparticles

In this paper, we report a simple polypeptide-directed strategy for fabricating large spherical assembly of CaCO(3) nanoparticles. Stepwise growth and assembly of a large number of nanoparticles have been observed, from the formation of an amorphous liquidlike CaCO(3)-polypeptide precursor, to the crystallization and stabilization of polypeptide-capped nanoparticles, and eventually, the spherical assembly of nanoparticles. The "soft" poly(aspartate)-capping layer binding on a nanoparticle surface resulted in the unusual soft nature of nanoparticle assembly, providing a reservoir of primary nanoparticles with a moderate mobility, which is the basis of a new strategy for reconstructing nanoparticle assembly into complex nanoparticle architectures. Moreover, the findings of the secondary assembly of nanoparticle microspheres and the morphology transformation of nanoparticle assembly demonstrate a flexible and controllable pathway for manipulating the shapes and structures of nanoparticle assembly. In addition, the combination of the polypeptide with a double hydrophilic block copolymer (DHBC) allows it to possibly further control the shape and complexity of the nanoparticle assembly. A clear perspective is shown here that more complex nanoparticle materials could be created by using "soft" biological proteins or peptides as a mediating template at the organic-inorganic interface.

Role of Barium(II) in the Determination of the Absolute Configuration of Chiral Amines by 1H NMR Spectroscopy

The assignment of the absolute configuration of alpha-chiral primary amines by complexation of their MPA derivatives with Ba2+ and NMR analysis of the changes generated is presented. All that is required is (a) the derivatization of the amine of unknown configuration with one enantiomer of the auxiliary reagent (MPA), either (R) or (S)-alpha-methoxyphenylacetic acid, (b) the recording of the 1H NMR spectrum of the resulting amide in MeCN-d3, (c) the addition of Ba(ClO4)2 to the NMR tube, and (d) the recording of a second spectrum after a few minutes of shaking. The above steps take a few minutes and are followed by an analysis of the shifts (measured as Deltadelta(Ba)) produced on the L1 and L2 substituents of the amine by the addition of Ba2+ and their comparison with those expected from the conformational changes produced by the complexation. The conformational changes initiated by complexation have been subjected to NMR and CD studies, which showed that the formation of the complex shifts the equilibrium from an antiperiplanar (AP) to a synperiplanar (SP) form, leading to an increase of the shielding by the phenyl group of MPA of the substituent of the amine located on the same side. In addition, theoretical calculations [density functional theory (DFT)] provide further support for the formation, structure, and stability of the complexes. The general applicability of this method and the trustworthiness of the resulting configurational assignment were guaranteed with a series of amines of known absolute configuration and varied structures, used as test compounds. The method proposed is simple, fast, and inexpensive, and it requires a very small amount of sample, only one derivatization, and the recording of just two 1H NMR spectra at room temperature. A graphical guide to simplify the application of this method is included.

Unusual Chemistry of the Complex Mg•+(2-Fluoropyridine) Activated by the Photoexcitation of Mg•+

The photochemistry of a gas-phase complex, Mg*(+)(2-fluoropyridine), has been studied in the spectral range of approximately 230-440 nm with a molecular beam coupled with a time-of-flight mass spectrometer. Surprisingly rich chemistry has been observed. Aside from the evaporative photofragment, Mg*(+), an abundant photoproduct, C(4)H(4)*(+), is observed after the electronic excitation of Mg(+). The formation of this photoproduct is associated with the loss of a stable species, CN[bond]Mg[bond]F. Also identified in this work are reactive pathways that occur with the elimination of HCN, HF, or MgF from the complex. The observed photoreactions have been examined in detail using quantum mechanics methods. A distinct structural feature of the complex is the direct attachment of Mg*(+) to the N atom of fluoropyridine due to the strong electrostatic interaction. The key to the rich photochemistry is the formation of the FMg(+)(C(5)H(4)N) intermediate, through facile fluorine migration. Plausible photoreaction mechanisms have been proposed. These mechanisms account for the evolution of the energized complex with the pre-defined structure en route to the target photoproducts that we have detected.

Theoretical evidence that Cu(I) complexation promotes degradation of S-nitrosothiols

The degradation of S-nitrosothiols (RSNOs) to release NO is believed to be catalyzed by CuI ions, but the mechanism remains unclear. Kinetic experiments have shown that decomposition rates vary significantly with the chemical nature of the RSNO considered. On the basis of first-principles calculations, the catalytic role of CuI ion is investigated for the decomposition of S-nitrosocysteine and its N-acetylated and ethyl ester derivatives, and for S-nitrosohomocysteine. This preliminary study focuses on the CuI-RSNO intermediates involved in the decomposition pathway. The model chemistry has been validated by comparing calculated CuI-ligand binding energies and S-N bond homolysis energies with available experimental data. Calculations show that the formation of CuI-RSNO intermediates results in weakening of the S-N bond and strengthening of the N-O bond, which would promote S-N bond breaking and NO release from S-nitrosothiols.

Absolute configuration of secondary alcohols by 1H NMR: in situ complexation of alpha-methoxyphenylacetic acid esters with barium(II)

A novel methodology that allows the assignment of the absolute configuration of chiral secondary alcohols by NMR using only one derivative is presented. All that is needed is (a) the derivatization of the alcohol of unknown configuration with one enantiomer--either the (R)- or the (S)--of alpha-methoxyphenylacetic acid (MPA), (b) the recording of the 1H NMR spectrum of the resulting ester in MeCN-d3, and (c) addition of a barium(II) salt [i.e. Ba(ClO4)2] to the NMR tube till saturation and recording of a second spectrum. The assignment of the R/S configuration to the alcohol takes a few minutes and consists on the comparison of the signs of the shifts (Deltadelta(Ba)) produced by addition of the barium(II) with those predicted for the (R) and the (S) enantiomers in accordance to a simplified model that reflects the conformational changes produced by the complexation with barium and their consequences in the chemical shifts. These conformational changes are based on experimental NMR and CD results showing that the formation of a barium(II) complex with the MPA ester moves the conformational equilibrium between syn- (sp) and anti-periplanar (ap) forms toward the most stable ones (sp), and that this leads to the increase of the shielding caused by the MPA phenyl group on a certain substituent of the alcohol. In addition, ab initio Hartree-Fock (HF) and density functional theory (DFT) calculations provide further evidence on the formation, structure, and stability of the complexes with Ba2+, Mg2+, and the influence of the solvent. The general applicability of this methodology and the reliability of the configurational assignment were assured by the study of about twenty alcohols of known configuration and diverse structural features. Its scope and limitations have also being established and other representative cations (i.e. Li+, Rb+, Cs+, Mg2+, Ca2+, Sc3+, V3+, Zn2+) were also evaluated. The procedure proposed is simple, fast, and cheap because it requires a very small amount of sample, only one derivatization, and the recording of only two 1H NMR spectra at rt. A graphical guide to facilitate the application of this new method is included at the end of the paper.

Computational chemistry: a useful (sometimes mandatory) tool in mass spectrometry studies

In this review, we present a brief summary of the theoretical methods most frequently used in gas-phase ion chemistry. In subsequent sections, the performance of these methods is analyzed, paying attention to the reliability of geometries, vibrational frequencies, energies, and entropies. The possible pathologies of the different methods, in the form of instabilities of the wave function or spin contamination problems, are discussed. Several examples are presented to illustrate the usefulness of ab initio or density functional theory (DFT) methods to predict the existence of elusive molecules and/or to characterize non-conventional structures, and to rationalize the charge redistributions normally associated with ion-molecule interactions and which result in bond-weakening or bond-reinforcement effects. Finally, the role of non-classical structures in ion-molecule interactions is also illustrated with different examples.