Ion spectroscopy: Where did it come from; where is it now; and where is it going?

The ASMS conference on ion spectroscopy brought together at Asilomar on October 16–20, 2009 a large group of mass spectrometrists working in the area of ion spectroscopy. In this introduction to the field, we provide a brief history, its current state, and where it is going. Ion spectroscopy of intermediate size molecules began with photoelectron spectroscopy in the 1960s, while electronic spectroscopy of ions using the photodissociation “action spectroscopic” mode became active in the next decade. These approaches remained for many years the main source of information about ionization energies, electronic states, and electronic transitions of ions. In recent years, high-resolution laser techniques coupled with pulsed field ionization and sample cooling in molecular beams have provided high precision ionization energies and vibrational frequencies of small to intermediate sized molecules, including a number of radicals. More recently, optical parametric oscillator (OPO) IR lasers and free electron lasers have been developed and employed to record the IR spectra of molecular ions in either molecular beams or ion traps. These results, in combination with theoretical ab initio molecular orbital (MO) methods, are providing unprecedented structural and energetic information about gas-phase ions.     

Entropy evaluation using the kinetic method: is it feasible?

The kinetic method is one of the most widely used experimental techniques for the measurement of thermochemical parameters by mass spectrometry. Recently it has been realized that it can also be used to determine reaction entropies, but the validity of this approach has not been established. This Perspective evaluates kinetic method plots in cases where there is a significant entropy difference between the competing fragmentation channels (i.e. between sample and reference compounds in the dissociating cluster ion). The concept underlying this study is to calculate mass spectra theoretically, based on known thermochemical parameters and as a function of experimental conditions. This can be done accurately using the RRKM-based MassKinetics software. The resulting mass spectra are then interpreted by the kinetic method, yielding DeltaH and DeltaS values. These values are, in turn, compared with the true values used to generate the calculated mass spectra. The results show that the reaction entropy difference between sample and reference has a very large influence on kinetic method plots. This should always be considered when studying energy-dependent mass spectra (using metastable ions or low- or high-energy collision-induced dissociation (CID)), even if only DeltaH is to be determined. Kinetic method plots are not strictly linear and this becomes a serious issue in the case of small molecules showing a large entropy effect. In such cases, results obtained at a low degree of excitation are more accurate. Energy and entropy effects can be evaluated in a relatively straightforward manner: first, the apparent Gibbs energy (DeltaG(app)) and effective temperature (T(eff)) are determined from kinetic method plots (intercept and slope, respectively), obtained from experiments using various degrees of excitation. Second, the resulting DeltaG(app) is plotted against T(eff), the slope yielding DeltaS while the intercept (extrapolation to zero temperature) yields DeltaH. This data evaluation yields more accurate results than alternative methods used in the literature. The resulting DeltaH values are fairly accurate, with errors, in most cases, <4 kJ mol(-1). On the other hand, DeltaS is systematically underestimated by 20-40%. Empirically scaling DeltaS values determined by the kinetic method by 1.35 results in a DeltaS value within 20% (or 10 J mol(-1) K(-1)) of the theoretical value.     

Weighted least-squares in calibration: what difference does it make?

In univariate calibration, an unknown concentration or amount x(0) is estimated from its measured response y(0) by comparison with a calibration data set obtained in the same way for known x values. The calibration function y = f(x) contains parameters obtained from a least-squares (LS) fit of the calibration data. Since minimum-variance estimation requires that the data be weighted inversely as their true variances, any other weighting leads to predictable losses of precision in the calibration parameters and in the estimation of x(0). Incorrect weighting also invalidates the apparent standard errors returned by the LS calibration fit. Both effects are studied using Monte Carlo calculations. For the strongest commonly encountered heteroscedasticity, proportional error (sigma(i) proportional, varianty(i)), neglect of weights yields as much as an order of magnitude precision loss for x(0) in the small x region, but only nominal loss in the calibration mid-range. Use of replicates gives great improvement at small x but can underperform unweighted regression in the mid-to-large x region. Variance function estimation approximates minimum-variance, even though the true variance functions are not well reproduced. A relative error test applied to the calibration data themselves is predisposed to favor 1/y(2) (or 1/x(2)) weighting, even if the data are homoscedastic. This predisposition weakens when replicate measurements are taken and disappears when the test is applied to an independent set of data. The distinction between a priori and a posteriori parameter standard errors is emphasized. Where feasible, the a priori approach permits reliable assignment of weights, application of a chi(2) test, and use of the normal distribution for confidence limits.     

The ester group: how hydrofluoroalkane-philic is it?

Pressurized metered-dose inhalers (pMDIs) have been recognized as potential devices for the delivery of systemically acting drugs, including biomolecules, to and through the lungs. Therefore, the development of novel excipients capable of imparting stability to suspension formulations in hydrofluoroalkane (HFA) propellants is of great relevance because many of the drugs of interest are poorly soluble in HFAs. In this work, we use ab initio calculations and chemical force microscopy (CFM) to determine the HFA-philicity of the biodegradable and biocompatible ester moiety quantitatively. The complementary information obtained from the binding energy calculations and adhesion force measurements are used to gain microscopic insight into the relationship between the chemistry of the moiety of interest and its solvation in HFA. A lactide (LA)-based copolymer surfactant was synthesized and characterized, and its ability to stabilize a dispersion of micronized budesonide in HFA227 was demonstrated. These results corroborate the ab initio calculations and CFM and show that the LA-based moiety is a suitable candidate for enhancing the stability of dispersions in HFA-based pMDIs.     

How Sensitive is the Amide I Vibration of the Polypeptide Backbone to Electric Fields?

Site‐selective isotopic labeling of amide carbonyls offers a nonperturbative means to introduce a localized infrared probe into proteins. Although this strategy has been widely used to investigate various biological questions, the dependence of the underlying amide I vibrational frequency on electric fields (or Stark tuning rate) has not been fully determined, which prevents it from being used in a quantitative manner in certain applications. Herein, through the use of experiments and molecular dynamics simulations, the Stark tuning rate of the amide I vibration of an isotopically labeled backbone carbonyl in a transmembrane α‐helix is determined to be approximately 1.4 cm^?1/(MV/cm). This result provides a quantitative basis for using this vibrational model to assess local electric fields in proteins, among other applications. For instance, by using this value, we are able to show that the backbone region of a dipeptide has a surprisingly low dielectric constant.     

NHC-catalysed benzoin condensation – is it all down to the Breslow intermediate?

The Breslow catalytic cycle describing the benzoin condensation promoted by N-heterocyclic carbenes (NHC) as proposed in the late 1950s has since then been tried by generations of physical organic chemists. Emphasis has been laid on proofing the existence of an enaminol like structure (Breslow intermediate) that explains the observed umpolung of an otherwise electrophilic aldehyde. The present study is not focusing on spectroscopic elucidation of a thiazolydene based Breslow intermediate but rather tries to clarify if this key-intermediate is indeed directly linked with the product side of the overall reaction. The here presented EPR-spectroscopic and computational data provide a fundamentally different view on how the benzoin condensation may proceed: a radical pair could be identified as a second key-intermediate that is derived from the Breslow-intermediate via an SET process. These results highlight the close relationship to the Cannizarro reaction and oxidative transformations of aldehydes under NHC catalysis.     

Polymer modeling: where has it been and where is it going?

The development of the area of polymer modeling often referred to as molecular modeling has been reviewed from its early beginnings to the present day. Key forces influencing the development include computational power, algorithmic advances and access to computational resources. The desire to apply modeling techniques to predict the properties of increasingly complex polymer-containing systems, taken in conjunction with a number of current limitations discussed in this brief review, is expected to define in part some essential future developments.     

The Tolman length: is it positive or negative?

By means of a large-scale molecular dynamics simulation, we show that the Tolman length, although positive, is much smaller in magnitude than previously reported. We found that the range of interparticle interaction can significantly affect the magnitude of the Tolman length. When the range of interaction is longer than five molecular diameters, the Tolman length is on the order of a few hundredths of the molecular diameter, rather than a few tenths known previously.     

Hydrogen exchange mass spectrometry: what is it and what can it tell us?

Proteins are undoubtedly some of the most essential molecules of life. While much is known about many proteins, some aspects still remain mysterious. One particularly important aspect of understanding proteins is determining how structure helps dictate function. Continued development and implementation of biophysical techniques that provide information about protein conformation and dynamics is essential. In this review, we discuss hydrogen exchange mass spectrometry and how this method can be used to learn about protein conformation and dynamics. The basic concepts of the method are described, the workflow illustrated, and a few examples of its application are provided.     

How stable actually is the planar ‘triangular’ benzene dication?

Quantum chemical calculations indicate that the kinetic stability of an earlier proposed elegant planar ‘triangular’ benzene dication 1a is very low. The kinetic stability of its methylated derivative 2a is even lower.     

Analysis of the singlet-triplet splitting computed by the density functional theory-broken-symmetry method: is it an exchange coupling constant?

We derive an analytical expression of the density functional theory (DFT)-broken-symmetry (BS) estimation J(BS) of the singlet-triplet gap at the "3 sites-4 electrons" level, that is, two S = (1)/(2) metallic sites + one diamagnetic bridge orbital. As originally designed by Noodleman and Davidson (Chem. Phys.1986, 109, 131), J(BS) contains the residual ferromagnetic contribution, single ligand-to-metal and metal-to-metal charge-transfer terms, but no double ligand-to-metal charge-transfer terms or intra/interligand spin-polarization terms. As revealed by the present analysis, the triplet and BS states computed by DFT differ, not only perturbatively (as expected) because of the various physical mechanisms involved (i.e., differential charge-transfer terms) but mainly because of a spurious and unphysical symmetry breaking of the bridge orbitals in the BS state. We examine the consequences of such a difference by deriving two analytical expressions of the exchange coupling constant, one from the BS orbitals designed to match J(BS) and another one from triplet orbitals only. Following and extending on the first paper in the series (J. Phys. Chem. A 2010, 114, 6149), we propose a simple procedure to extract appropriate parameters filling in our analytical expressions. Moreover, we derive the equivalent "3 sites-4 electrons" exchange coupling constant in the configuration-interaction approach, J(CI), for the purpose of comparison. These analytical expressions have been applied to various copper dimers and compared to experimental values.     

New bioorganic reagents: evolved cyclohexanone monooxygenase--why is it more selective?

Four mutants of the cyclohexanone monooxygenase (CHMO) evolved as catalysts for Baeyer-Villiger oxidation of 4-hydroxycyclohexanone were investigated as catalysts for a variety of 4-substituted and 4,4-disubstituted cyclohexanones. Several excellent catalytic matches (mutant/substrate) were identified. The most important, however, is the finding that, in a number of cases, a mutant with a single exchange, Phe432Ser, was shown to be as robust and more selective as a catalyst than the wild-type CHMO. All biotransformations were performed on a laboratory scale, allowing full characterization of the products. The absolute configurations of two products were established. A model suggesting a possible role of the 432 serine residue in enantioselectivity control is proposed.     

The indirect through-space F-F coupling in peri-difluoronaphthalene: is it anisotropic?

The (1)H, (19)F and (13)C spectra have been obtained of a sample of peri-difluoronaphthalene dissolved in the nematic liquid crystalline solvent ZLI 1695. The (13)C satellite spectra from the six, single-(13)C isotopomers at natural abundance in both the (1)H and (19)F spectra were identified and analysed to yield a set of residual total, anisotropic spin-spin couplings, T(ij). This was achieved by first obtaining residual (13)C-(19)F and (13)C-(1)H couplings from a proton-encoded, (13)C detected, local field 2D spectrum. The 45 values of T(HH), T(HF) and T(CH) were used to obtain the structure of the molecule, and then to estimate whether there is a significant contribution from the component along the magnetic field, J, of the anisotropic, electron-mediated, spin-spin coupling tensors for (13)C-(19)F and (19)F-(19)F pairs. It is found that there is strong evidence for a significant contribution of J to T(FF) but not for the (13)C-(19)F pairs.     

The Electronic Structure of the Al3− Anion: Is it Aromatic?

Multiconfigurational high‐level electronic structure calculations show that the ${{\rm Al}{{- \hfill \atop 3\hfill}}}$ ring‐like cluster anion has three close low‐lying electronic states of different spin, all of them having strong multiconfigurational character. The aromaticity of the cluster has, therefore, been studied by means of total electron delocalization and normalized multicenter electron delocalization indices evaluated from the multiconfigurational wave functions of each state. The lowest‐lying singlet and triplet states are found to be highly aromatic, whereas the next lowest‐lying state, the quintet state, has much less, though non‐negligible, aromatic character.