Consistent Assignment Of The Vibrations Of Chloro- And Bromobenzene Molecules And Their Deuterated Analogues

The consistency of the labelling and assignments of the vibrational frequencies of the chloro- and bromo- monosubstituted benzene molecules is investigated in their first electronically excited states (S$_{1}$). The assignments given utilise a recent nomenclature\footnote{A. M. Gardner and T. G. Wright, J. Chem. Phys., 135,114305 (2011)} discussed in a previous talk, allowing the ring-localised vibrations to be compared straightforwardly across different monohalosubstituted benzenes. For the S$_{1}$ state, one-colour resonance-enhanced multiphoton ionization (REMPI) spectroscopy was employed. The assignments of the frequencies include previous work but also the calculated wavenumbers for both fully hydrogenated monohalosubstituted benzenes (-\textit{h}$_{5}$) and the deuterated isotopologues (-\textit{d}$_{5}$) employing time-dependent density functional theory (TDDFT)

Spectroscopy of substituted benzene molecules

Consistent assignment of vibrational motions across substituted benzene derivatives is a long-standing desire amongst spectroscopists. In this thesis, the S1 electronic states of monohalosubstituted benzene molecules and their deuterated isotopologues are investigated, using resonance enhanced multiphoton ionisation spectroscopy. The observed vibrational bands are assigned using the Mi nomenclature proposed by Gardner and Wright where ring localised vibrations having the same atomic motion are given the same label, allowing straightforward comparisons of vibrational motions across monosubstituted benzene molecules to be achieved. Detailed investigation showed that it would not be possible to apply the same Mi nomenclature labels to the para disubstutited benzene derivatives owing to the different vibrational motions of mono- and disubstituted benzene molecules. As a consequence a new nomenclature, Di, for labelling the vibrational motions of para disubstituted benzene molecules is proposed in this work. The Di labelling scheme is based on the vibrations of the para difluorobenzene molecule. S0 state vibrations of symmetric and asymmetric para dihalobenzene species, para fluorotoluene and para xylene are studied in detail, showing that the ring localised vibrational motions of para disubstituted benzene species are being described by the same label

Assignment of the vibrations of the S0, S1, and D+0 states of perhydrogenated and perdeuterated isotopologues of chlorobenzene

We report vibrationally resolved spectra of the S1 ← S0 transition of chlorobenzene using resonance-enhanced multiphoton ionization spectroscopy. We study chlorobenzene-h5 as well as its perdeuterated isotopologue, chlorobenzene-d5. Changes in the form of the vibrational modes between the isotopologues and also between the S0 and S1 electronic states are discussed for each species. Vibrational bands are assigned utilizing quantum chemical calculations, previous experimental results, and isotopic shifts, including those between the 35Cl and 37Cl isotopologues. Previous work and assignments of the S1 spectra are discussed. Additionally, the vibrations in the ground state cation, D+0, are considered, since these have also been used by previous workers in assigning the excited neutral state spectra

Cytoplasmic glycoengineering of Apx toxin fragments in the development of Actinobacillus pleuropneumoniae glycoconjugate vaccines.

BACKGROUND: Actinobacillus pleuropneumoniae is the causative agent of porcine pleuropneumonia and represents a major burden to the livestock industry. Virulence can largely be attributed to the secretion of a series of haemolytic toxins, which are highly immunogenic. A. pleuropneumoniae also encodes a cytoplasmic N-glycosylation system, which involves the modification of high molecular weight adhesins with glucose residues. Central to this process is the soluble N-glycosyl transferase, ngt, which is encoded in an operon with a subsequent glycosyl transferase, agt. Plasmid-borne recombinant expression of these genes in E. coli results in the production of a glucose polymer on peptides containing the appropriate acceptor sequon, NX(S/T). However to date, there is little evidence to suggest that such a glucose polymer is formed on its target peptides in A. pleuropneumoniae. Both the toxins and glycosylation system represent potential targets for the basis of a vaccine against A. pleuropneumoniae infection. RESULTS: In this study, we developed cytoplasmic glycoengineering to construct glycoconjugate vaccine candidates composed of soluble toxin fragments modified by glucose. We transferred ngt and agt to the chromosome of Escherichia coli in order to generate a native-like operon for glycoengineering. A single chromosomal copy of ngt and agt resulted in the glucosylation of toxin fragments by a short glycan, rather than a polymer. CONCLUSIONS: A vaccine candidate that combines toxin fragment with a conserved glycan offers a novel approach to generating epitopes important for both colonisation and disease progression

A surprisingly simple electrostatic model explains bent vs. linear structures in M+-RG2 species (M = group 1 metal, Li–Fr; RG = rare gas, He–Rn)

It is found that a simple electrostatic model involving competition between the attractive dispersive interaction and induced-dipole repulsion between the two RG atoms performs extremely well in rationalizing the M+-RG2 geometries, where M = Group 1 metal and RG = rare gas. The Li+-RG2 and Na+-RG2 complexes have previously been found to exhibit quasilinear or linear minimum energy geometries, with the Na+-RG2 complexes having an additional bent local minimum [A. Andrejeva, A. M. Gardner, J. B. Graneek, R. J. Plowright, W. H. Breckenridge and T. G. Wright, J. Phys. Chem. A, 2013, 117, 13578]. In the present work, the geometries for M = K–Fr are found to be bent. A simple electrostatic model explains these conclusions and is able to account almost quantitatively for the binding energy of the second RG atom, as well as the form of the angular potential, for all thirty six titular species. Additionally, results of population analyses are presented together with orbital contour plots; combined with the success of the electrostatic model, the expectation that these complexes are all physically bound is confirmed

Vibrations of the S1 state of fluorobenzene-h5 and fluorobenzene-d5 via resonance-enhanced multiphoton ionization (REMPI) spectroscopy

We report resonance-enhanced multiphoton ionization spectra of the isotopologues fluorobenzeneh5 and fluorobenzene-d5. By making use of quantum chemical calculations, the changes in the wavenumber of the vibrational modes upon deuteration are examined. Additionally, the mixing of vibrational modes both between isotopologues and also between the two electronic states is discussed. The isotopic shifts lead to dramatic changes in the appearance of the spectrum as vibrations shift in and out of Fermi resonance. Assignments of the majority of the fluorobenzene-d5 observed bands are provided, aided by previous results on fluorobenzene-h5

Consistent assignment of the vibrations of symmetric and asymmetric para-disubstituted benzene molecules

We give a description of the phenyl-ring-localized vibrational modes of the ground states of the para-disubstituted benzene molecules including both symmetric and asymmetric cases. In line with others, we quickly conclude that the use of Wilson mode labels is misleading and ambiguous; we conclude the same regarding the related ones of Varsányi. Instead we label the modes consistently based upon the Mulliken (Herzberg) method for the modes of para-difluorobenzene (pDFB). Since we wish the labelling scheme to cover both symmetrically- and asymmetrically-substituted molecules, we apply the Mulliken labelling under C2v symmetry. By studying the variation of the vibrational wavenumbers with mass of the substituent, we are able to identify the corresponding modes across a wide range of molecules and hence provide consistent assignments. Particularly interesting are pairs of vibrations that evolve from in- and out-of-phase motions in pDFB to more localized modes in asymmetric molecules. We consider the para isomers of the following: the symmetric dihalobenzenes, xylene, hydroquinone, the asymmetric dihalobenzenes, halotoluenes, halophenols and cresol

Resonance-enhanced multiphoton ionization (REMPI) spectroscopy of bromobenzene and its perdeuterated isotopologue: assignment of the vibrations of the S0, S1 and D0+ states of bromobenzene and the S0 and D0+ states of iodobenzene

We report vibrationally-resolved spectra of the S1 S0 transition of bromobenzene using resonance-enhanced multiphoton ionization (REMPI) spectroscopy. We study bromobenzene-h5 as well as its perdeuterated isotopologue, bromobenzene-d5. The form of the vibrational modes between the isotopologues and also between the S0 and S1 electronic states are discussed for each species, allowing assignment of the bands to be achieved and the activity between states and isotopologues to be established. Vibrational bands are assigned utilizing quantum chemical calculations, previous experimental results and isotopic shifts. Previous work and assignments of the S1 spectra are discussed. Additionally, the vibrations in the ground state cation, D0+, are considered, since these have also been used by previous workers in assigning the excited neutral state spectra. We also examine the vibrations of iodobenzene in the S0 and D0+ states and comment on previous assignments of these. In summary, we have been able to assign corresponding vibrations across the whole monohalobenzene series of molecules, in the S0, S1 and D0+ states, gaining insight into vibrational activity and vibrational couplings

Consistent assignment of the vibrations of symmetric and asymmetric ortho-disubstituted benzenes

The form of molecular vibrations, and changes in these, give valuable insights into geometric and electronic structure upon electronic excitation or ionization, and within families of molecules. Here, we give a description of the phenyl-ring-localized vibrational modes of the ground (S₀) electronic states of a wide range of ortho-disubstituted benzene molecules including both symmetrically- and asymmetrically-substituted cases. We conclude that the use of the commonly-used Wilson or Varsányi mode labels, which are based on the vibrational motions of benzene itself, is misleading and ambiguous. In addition, we also find the use of the Mi labels for monosubstituted benzenes [A. M. Gardner and T. G. Wright. J. Chem. Phys. 135 (2011) 114305], or the recently-suggested labels for para-disubstituted benzenes [A. Andrejeva, A. M. Gardner, W. D. Tuttle, and T. G. Wright, J. Molec. Spectrosc. 321, 28 (2016)] are not appropriate. Instead, we label the modes consistently based upon the Mulliken (Herzberg) method for the modes of ortho-difluorobenzene (pDFB) under Cs symmetry, since we wish the labelling scheme to cover both symmetrically- and asymmetrically-substituted molecules. By studying the vibrational wavenumbers from the same force field while varying the mass of the substituent, we are able to identify the corresponding modes across a wide range of molecules and hence provide consistent assignments. We assign the vibrations of the following sets of molecules: the symmetric o-dihalobenzenes, o-xylene and catechol (o-dihydroxybenzene); and the asymmetric o-dihalobenzenes, o-halotoluenes, o-halophenols and o-cresol. In the symmetrically-substituted species, we find a pair of in-phase and out-of-phase carbon-substituent stretches, and this motion persists in asymmetrically-substituted molecules for heavier substituents. When at least one of the substituents is light, then we find that these evolve into localized carbon-substituent stretches

Theoretical study of M+ RG2: (M+= Ca, Sr, Ba and Ra; RG= He–Rn)

Ab initio calculations were employed to investigate M+ RG2 species, where M+ = Ca, Sr, Ba and Ra and RG= He–Rn. Geometries have been optimized, and cuts through the potential energy surfaces containing each global minimum have been calculated at the MP2 level of theory, employing triple-ζ quality basis sets. The interaction energies for these complexes were calculated employing the RCCSD(T) level of theory with quadruple-ζ quality basis sets. Trends in binding energies, De, equilibrium bond lengths, Re, and bond angles are discussed and rationalized by analyzing the electronic density. Mulliken, natural population, and atoms-in-molecules (AIM) population analyses are presented. It is found that some of these complexes involving the heavier Group 2 metals are bent whereas others are linear, deviating from observations for the corresponding Be and Mg metal-containing complexes, which have all previously been found to be bent. The results are discussed in terms of orbital hybridization and the different types of interaction present in these species