Theoretical description of nuclear quadrupole coupling in light diatomic molecules

A practical procedure for calculation of nuclear quadrupole coupling constants for light diatomic molecules is discussed. The procedure is based on a molecular wave function that explicitly describes nuclear motion. The approach is capable of yielding quadrupole coupling constants for excited rovibrational levels of diatomic molecules in their ground and excited electronic states. An application of the procedure to the X¹Σ⁺_g and B¹Σ⁺_u states of HD and D₂ is presented.     

The dielectric constant of water: influence of the quadrupole moment

We examine the suggestion that the very high dielectric constant of water is associated with the absence of a significant component of the quadrupole tensor along the direction of the dipole moment. We find that although ?_zz ≈ 0, there is a large “effective axial” moment ?^eff_zz.     

The temperature dependence of radiation sensitivity of large molecules

The change in radiation sensitivity with temperature is quantitatively the same for biological macromolecules and synthetic polymers. The mechanism(s) for this effect is (are) due to secondary processes occurring after the primary ionization and are associated with the presence of free radicals.     

Circular dichroism of large molecules

The circular dichroism of molecules, which are large compared to the wavelength of light, is considered. Explicit expressions are obtained for the circular dichroism and absorption of an exciton dimer and of a free particle on a helix. The dimensions are described for which the dipole approximation for the optical properties fails.     

Rotational-state-specific guiding of large molecules

A beam of polar molecules can be focused and transported through an ac electric quadrupole guide. At a given ac frequency, the transmission of the guide depends on the mass-to-dipole-moment (m/μ) ratio of the molecular quantum state. Here we present a detailed characterization of the m/μ selector, using a pulsed beam of benzonitrile (C(6)H(5)CN) molecules in combination with rotational quantum state resolved detection. The arrival time distribution as well as the transverse velocity distribution of the molecules exiting the selector are measured as a function of ac frequency. The μ/Δμ resolution of the selector can be controlled by the applied ac waveforms and a value of up to 20 can be obtained with the present setup. This is sufficient to exclusively transmit benzonitrile molecules in quantum states with the same m/μ value as the absolute ground state. The operation characteristics of the m/μ selector are in quantitative agreement with the outcome of trajectory simulations.     

Electric quadrupole polarizabilities of nuclear magnetic shielding in some small molecules

Computational procedures, based on (i) the Ramsey common origin approach and (ii) the continuous transformation of the origin of the quantum mechanical current density-diamagnetic zero (CTOCD-DZ), were applied at the Hartree-Fock level to determine electric quadrupole polarizabilities of nuclear magnetic shielding for molecules in the presence of a nonuniform electric field with a uniform gradient. The quadrupole polarizabilities depend on the origin of the coordinate system, but values of the magnetic field induced at a reference nucleus, determined via the CTOCD-DZ approach, are origin independent for any calculations relying on the algebraic approximation, irrespective of size and quality of the (gaugeless) basis set employed. On the other hand, theoretical estimates of the induced magnetic field obtained by single-origin methods are translationally invariant only in the limit of complete basis sets. Calculations of electric quadrupole polarizabilities of nuclear magnetic shielding are reported for H(2), HF, H(2)O, NH(3), and CH(4) molecules.     

Electrospray tandem quadrupole fragmentation of quinolone drugs and related ions. On the reversibility of water loss from protonated molecules

Selected reaction monitoring (SRM) of quinolone drugs showed different sensitivities in aqueous solution vs. biological extract. The authors suggested formation of two singly protonated molecules with different behavior, one undergoing loss of H(2)O and the other loss of CO(2), so that SRM transitions might depend on the ratios of these forms generated by the electrospray. These surprising results prompted us to re-examine several quinolone drugs and some simpler compounds to further elucidate the mechanisms. We find that the relative contributions of loss of H(2)O vs. loss of CO(2) in tandem mass spectrometric (MS/MS) experiments depend not only on molecular structure and collision energy, but also, in certain cases, on the cone voltage. We further find that many product ions formed by loss of H(2)O can reattach a water molecule in the collision cell, whereas ions formed by loss of CO(2) do not. Since reattachment of H(2)O can occur after water loss in the cone region and prior to selection of the precursor ion, this effect leads to the dependence of MS/MS spectra on the cone voltage used in creating the precursor ion, which explains the formerly observed effect on SRM ratios. Our results support the earlier conclusion that varying amounts of two ions of the same m/z value are responsible for problems in the analysis of these drugs, but the origin is in dehydration/rehydration reactions. Thus, SRM transitions for certain complex compounds may be comparable only when monitored under equivalent ion-forming conditions, including the voltage used in the production of the protonated molecules in the electrospray ionization (ESI) source.     

The mobility of water molecules through gas hydrates

Crystal growth simulations of gas hydrates have suggested that hydrate cages may occasionally be occupied by H(2)O rather than guest molecules, leaving interstitial defects within the hydrate crystal. Further inspection of the behavior of these interstitial H(2)O molecules has revealed that they are relatively highly mobile entities within a gas hydrate. In this paper, we report these observations and examine the molecular mechanisms responsible for the transport of these interstitial molecules through hydrate crystals. Four distinct pathways for the H(2)O molecule transport between cages are found, each facilitated by the presence of empty cages. The relative richness of the observed behavior of interstitial defects suggests that interstitial diffusion could be an important mechanism for the mass transport of H(2)O molecules through gas hydrates.     

Low-temperature reactions of some atomic ions with molecules of large quadrupole moment: C6F6 and c-C6H12

Reactions of He⁺,C⁺ and N⁺ ions with C₆F₆, and c-C₆H₆ were examined at 27, 68 and 297 K using both CRESU and SIFT techniques. Within the experimental uncertainties, all of the rate coefficients are found to be temperature-independent in this range. The results are discussed in relation to the most recent theoretical models describing the influence of the quadrupole moment on the temperature dependence of ion-molecule reaction rate coefficients.     

Do large molecules ionize?

A possible mechanism for the ionization or lack thereof in large molecules is discussed. The experimental observation is that the ionization efficiency rapidly decreases with increasing weight, whether one uses electron impact, single-photon or multi-photon ionization. Possible mechanisms for this decline in the yield of ions are considered. It is suggested that in larger molecules ionization occurs through the intermediate formation of charge pairs which can ionize in a unimolecular-like fashion due to an energy fluctuation. A more probable route is however for the charge pairs to recombine. Possible experimental tests of the proposed mechanism are considered and a scaling law for the mass-dependence is derived and shown to fit the available data.     

Visualization of large elongated DNA molecules

Long and linear DNA molecules are the mainstream single‐molecule analytes for a variety of biochemical analysis within microfluidic devices, including functionalized surfaces and nanostructures. However, for biochemical analysis, large DNA molecules have to be unraveled, elongated, and visualized to obtain biochemical and genomic information. To date, elongated DNA molecules have been exploited in the development of a number of genome analysis systems as well as for the study of polymer physics due to the advantage of direct visualization of single DNA molecule. Moreover, each single DNA molecule provides individual information, which makes it useful for stochastic event analysis. Therefore, numerous studies of enzymatic random motions have been performed on a large elongated DNA molecule. In this review, we introduce mechanisms to elongate DNA molecules using microfluidics and nanostructures in the beginning. Secondly, we discuss how elongated DNA molecules have been utilized to obtain biochemical and genomic information by direct visualization of DNA molecules. Finally, we reviewed the approaches used to study the interaction of proteins and large DNA molecules. Although DNA‐protein interactions have been investigated for many decades, it is noticeable that there have been significant achievements for the last five years. Therefore, we focus mainly on recent developments for monitoring enzymatic activity on large elongated DNA molecules.     

Fractional mass values of large molecules

From the standpoint of relative molecular mass (RMM) determination by mass spectrometry, the average relative molecular masses of organic molecules in the range over 2000 daltons are significantly influenced both by the fractional masses of the constituent elements and by natural variations in isotopic abundance. Differences between monoisotopic RMM and relative atomic mass (RAM) based RMM tend characteristically to differ between major classes of biomolecules primarily because of molar carbon content, the difference between polypeptides and nucleic acids being about 4 daltons at M_r = 25 000. Considering terrestrial sources alone, variations in the isotopic abundance of carbon lead to differences of about 10–25 ppm in average molecular mass, which is significant with respect to present mass measurement capability in the region up to several thousand daltons. Comments are made concerning the calculation of average RMM values horn isotopic probability profiles versus those from RAMs.     

On the photoionization of large molecules

There is no apparent limit to the size of a molecule for which photoionization can occur. It is argued that it is difficult to obtain useful photoionization mass spectra of peptides (above ～ 2000 u), proteins, and oligonucleotides, because of the high internal energy of these polar molecules as a result of the desorption event and because vibrationally excited radical cations readily fragment. Evidence to support this hypothesis is presented from the 118-nm single-photon ionization (SPI) mass spectra of the cyclic decapeptide gramicidin S and of fullerenes, from null SPI results with the linear peptides substance P and gramicidin D and oligonucleotides, and from a variety of data found in the literature. The literature data include mass spectra from jet-cooled peptides, perfluorinated polyethers, collisional ionization of small neutral peptides, and the ultraviolet photoelectron spectroscopy of polymeric solids.     

The reactions of energetic tritium atoms with water molecules

Hard sphere excitation functions are derived for the reactions of T atoms with H₂O molecules, and the results compared with the available experimental data.     

The calculation of indirect nuclear spin-spin coupling constants in large molecules

We present calculations of indirect nuclear spin-spin coupling constants in large molecular systems, performed using density functional theory. Such calculations, which have become possible because of the use of linear-scaling techniques in the evaluation of the Coulomb and exchange-correlation contributions to the electronic energy, allow us to study indirect spin-spin couplings in molecules of biological interest, without having to construct artificial model systems. In addition to presenting a statistical analysis of the large number of short-range coupling constants in large molecular systems, we analyse the asymptotic dependence of the indirect nuclear spin-spin coupling constants on the internuclear separation. In particular, we demonstrate that, in a sufficiently large one-electron basis set, the indirect spin-spin coupling constants become proportional to the inverse cube of the internuclear separation, even though the diamagnetic and paramagnetic spin-orbit contributions to the spin-spin coupling constants separately decay as the inverse square of this separation. By contrast, the triplet Fermi contact and spin-dipole contributions to the indirect spin-spin coupling constants decay exponentially and as the inverse cube of the internuclear separation, respectively. Thus, whereas short-range indirect spin-spin coupling constants are usually dominated by the Fermi contact contribution, long-range coupling constants are always dominated by the negative diamagnetic spin-orbit contribution and by the positive paramagnetic spin-orbit contribution, with small spin-dipole and negligible Fermi contact contributions.