Investigation of molecular polarizabilities and derivatives in halomethanes

The research undertaken was to obtain absolute Raman intensities for the symmetric stretching vibrations of the methyl halides, CH3X with (X=F, CI, Br), by experiment and theory. The intensities were experimentally measured using the Ar+ ion gas laser as excitation source, a Spex 14018 double monochromator and a RCA C-31034 photomultiplier tube as detector. These intensities arise from changes in the derivative of the polarizability (8 a'), with respect to vibration along a normal coordinate (8qi). It was intended that these derivatives obtained with respect to normal coordinates would be converted to derivatives with respect to internal coordinates, for a quantitative comparison with theory. Theoretical numerical polarizability derivatives for the stretching vibrations are obtained using the following procedure. A vibration was simulated in the molecule by increasi.ng and decreasing the respective bond by the amount ±o.oosA for the C-H bonds and ±o.oIA for the C-X (X=F, CI, Br) bond. The derivative was obtained by taking the difference in the polarizability for the equilibrium geometry and the geometry when a particular bond is changed. This difference, when divided by the amount of change in each bond and the number of bonds present results in the derivative of the polarizability with respect to internal coordinate i.e., !1u/!1r. These derivatives were obtained by two methods: I} ab initio molecular orbital calculation and 2} theory of atoms in molecules (AIM) analysis. Due to errors in the experimental setup only a qualitative analysis of the results was undertaken relative to the theory. Theoretically it is predicted that the symmetric carbonhalogen stretch vibrations are more intense than the respective carbon-hydrogen stretch, but only for the methyl chloride and bromide. The carbon fluorine stretch is less intense than the carbon-hydrogen stretch, a fact which is attributed to the small size and high electronegativity of the fluorine atom. The experimental observations are seen to agree qualitatively with the theory results. It is hoped that when the experiment is repeated, a quantitative comparison can be made. The analysis by the theory of atoms in molecules, along with providing polarizabilities and polarizability derivatives, gives additional information outlined below. The theory provides a pictorial description of the main factors contributing to the molecular polarizability and polarizability derivative. These contributions are from the charge transfer and atomic dipole terms i.e., transfer of charge from one atom to another and the reorganization of atomic electronic charge distribution due to presence of an electric field. The linear relationship between polarizability and molecular volume was also observed.

A fast atom bombardment mass spectrometry study of tris (3, 6-dioxaheptyl) amine-alkali metal halide complexes and hydrogen bonded complexes

The objective of this thesis was to demonstrate the potential of fast atom bombardment mass spectrometry (FABMS) as a probe of condensed phase systems and its possible uses for the study of hydrogen bonding. FABMS was used to study three different systems. The first study was aimed at investigating the selectivity of the ligand tris(3,6-dioxaheptyl) amine (tdoha) for the alkali metal cations. FABMS results correlated well with infrared and nmr data. Systems where a crown ether competed with tdoha for a given alkali metal cation were also investigated by fast atom bombardment. The results were found to correlate with the cation affinity of tdoha and the ability of the crown ether to bind the cation. In the second and third studies, H-bonded systems were investigated. The imidazole-electron donor complexes were investigated and FABMS results showed the expected H-bond strength of the respective complexes. The effects of concentration, liquid matrix, water content, deuterium exchange, and pre-ionization of the complex were also investigated. In the third system investigated, the abundance of the diphenyl sulfone-ammonium salt complexes (presumably H-bonded) in the FABMS spectrum were found to correlate with qualitative considerations such as steric hindrance and strength of ion pairs.

Elliptical orbital studies of H21 and H2 molecules /|nS. K. Gupta. -- 260 St. Catharines, Ont. : [s. n.],

Calculations are performed on the \S <:Jd ground states of d ' + the H and HC) molecules using a basis set of non-integral ~ ~ I elliptical orbitals. Different variational wavefunctions constructed i- for H~ involved one parameter to three par~~eter variation. In order to l"'educe the ntunber of parameters in most commonly 0- used basis orbitals set, the importance of the term (,+~) Y\ over the term ;u 'Where n is a variational pararneter and the value of cr may be given by boundary condition or cusp condition is outlined in Chapters II and III. It is found that the two parameter -+ ion for H~ including the ternl (~+~) , a- given by the bound~ condition, gives lower variational energies than any wavefunction published to date for small and moderate internuclear separations. c;. In order to find out the importance of the term (I +~ ) Y\ over ;U for the two electron problem, the variational energy is computed for the H~ molecule from unrestricted two parameter closed shell wavefunctions including the term U+ft)ion in one case and from the cusp condition in the second case. In order to take into account in-out correlation partially, open shell calculation for the ground state of the hydrogen molecule for R =1.4 (equilibrium internuclear separation) is perfonaed. The results are excellent.

NMR studies of strong hydrogen bond to fluoride ion

Systems such as MF/diol (M = alkali metal) and }1F/carboxylic acid were subjected to IH, I9F and 13C nmr study to investigate the nature of the very strong H-bonding of fluoride ions with these systems. Evidence indicates a strong H-bond in diol-fluoride systems (~H ~ -(56) kJ mol-I) which is stronger than most 'typical' H-bonds (~H = -(12-40) kJ mol-I), but weaker than that reported for carboxylic acid-fluoride systems (~H ~ -(120) kJ mol-I). Approximate fluoride H-bonded shifts (o(OH)OHF) were evaluated for MF/diol systems from IH chemical shift measurements. No direct correlation was observed between I9F chemical shift and H-bond strength. Thermodynamic parameters were calculated from temperature dependent IH and 19F shifts. Preliminary studies of BUn 4NF-acetylacetone by I9F nmr were conducted at low temperatures and a possible Jmax (ca. 400 Hz) is reported for the fluoride ion H-bonded to acetylacetone. Highfield shift for non-protonated carbons and downfield shift for protonated carbons were observed in carboxylic acid/KF systems. Significant decreas$in I3C TI due to strong H-bonding to fluoride ions were also detected in both diol and carboxylic acid systems. Anomalous results were obtained, such as increasing NOE with increasing temperature in neat 1,2-ethanediol (values above the theoretical maximum of 1.988) and in 1,2-ethanediol/KF. The large 13C NOE's for carboxy carbons in neat carboxylic acids which are. further enhanced by the addition of KF are also unusual.

The crystal and molecular structure of bis (pyridoxamine) copper (II) dinitrate monohydrate

The crystal structure of Cu(PM)2(N03hoH20 (where PM is pyridoxamine, CSHI2N202) has been determined from three dimensional x-ray diffraction data. The crystals are triclinic, space group pI, a = 14.248 (2), b = 8.568 (1), c = 9.319 (1) 1, a = 94.08 (1), e = 89.73 (1), y~~ 99.18 (1)°, z = 2, jl(MoK) = 10.90 em-I, Po = 1.61 g/cm3 and Pc = 1.61 g/em3• The structure a was solved by Patterson techniques from data collected on a Picker 4-circle diffractometer to 26max = 45°. All atoms, including hydrogens, have been located. Anisotropic thermal parameters have been refined for all nonhydrogen atoms. For the 2390 independent reflections with F ? 3cr(F) , R = 0.0408. The results presented here provide the first detailed structural information of a metal complex with PM itself. The copper atoms are located on centres of symmetry and each is chela ted by two PM zwitterions through the amino groups and phenolate oxygen atoms. The zwitterionic form found in this structure involves the loss of a proton from the phenolate group and protonation of the pyridine ring nitrogen atoms. The two independent Cu(PM)2 moieties are symmetrically bridged by a single oxygen atom from one of the nitrate groups. The second nitrate group is not coordinated to the copper atoms but is central to an extensive hydrogen bonding network involving the water molecule and uncoordinated functional groups of PM.

The crystal and molecular structure of thiamine hydroiodide /|nWilliam Edward Lee. -- 260 St. Catharines [Ont.] : Dept. of Chemistry, Brock University,

The x-ray crystal structure of thiamine hydroiodide,C1ZH18N40S12' has been determined. The unit cell parameters are a = 13.84 ± 0.03, o b = 7.44 ± 0.01, c = 20.24 ± 0.02 A, 8 = 120.52 ± 0.07°, space group P2/c, z = 4. A total of 1445 reflections having ,2 > 2o(F2), 26 < 40° were collected on a Picker four-circle diffractometer with MoKa radiation by the 26 scan technique. The structure was solved by the heavy atom method. The iodine and sulphur atoms were refined anisotropically; only the positional parameters were refined for the hydrogen atoms. Successive least squares cycles yielded an unweighted R factor of 0.054. The site of protonation of the pyrimidine ring is the nitrogen opposite the amino group. The overall structure conforms very closely to the structures of other related thiamine compounds. The bonding surrounding the iodine atoms is distorted tetrahedral. The iodine atoms make several contacts with surrounding atoms most of them at or near the van der Waal's distances A thiaminium tetrachlorocobaltate salt was produced whose molecular and crystal structure was j~dged to be isomorphous to thiaminium tetrachlorocadmate.

The crystal and molecular structure of 18-Crown-6 HgC12 and 18-Crown-6 Cdc12

Hg(18-Crown-6)C12 and Cd(18-Crown-6)C12 are isostructura1, space group Cl~ Z = 2. For the mercury compound, a = 10.444(2) A° , b = 11. 468(1) A° , c = 7.754(1) A° , a = 90.06(1)°, B = 82.20(1)°, Y = 90.07(1)°, Dobs = 1.87, Dca1c = 1.93, V = 920.05 13, R = 4.66%. For the cadmium compound, 000 a = 10.374(1) A, b = 11.419(2) A, c = 7.729(1) A, a = 89.95(1)°, B = 81.86(2)°, Y = 89.99(1)°, Dobs = 1.61, Dcalc = 1.64, V = 906.4613, R = 3.95%. The mercury and cadmium ions exhibit hexagonal bipyramidal coordination, with the metal ion located on a centre of symmetry in the plane of the oxygen atoms. The main differences between the two structures are an increase in the metal-oxygen distance and a reduction in the metalchloride distance when the central ion changes from Cd2+ to Hg2+. These differences may be explained in terms of the differences in hardness or softness of the metal ions and the donor atoms.

Mass spectrometric studies on aryltin compounds and alkali halides /

The fragmentation behavior of aryltin compounds [(p-ThAnis)nSnPh4.n (n=l-4); (p-ThAnis)3SnX (X=C1, Br, I); (o-CH30C6H4)3SnCl; Ph3Sn(o-pyr)] have been studied comparatively under EI and FAB ionization modes. Alkali halides were run under FAB mode. For the aryltin compounds, the effect of ligand type on the spectra have been explored in both EI and FAB modes. The fragmentation mechanisms have been examined with linked scans, such as fragment ion scans (B/E) and parent ion scans (B^/E). Ab Initio molecular orbital calculations were used to determine the structures of the fragments by comparing their relative stabilities. In the EI MS studies, negative ion EI mode has also been used for some of the aryltin compounds, to examine the possible ion molecule reactions under low pressures at 70eV. In the positive ion FAB MS studies, matrix optimization experiments have been carried out. Negative ion FAB experiments of all the compounds have been done in two different ways. Finally, the comparison of the two methods, EI MS and FAB MS, have been made.For alkali halides, the studies focused on the FAB MS behavior under different conditions. The intensities of cluster ions were reported, and the anomalies in the intensity distribution was also discussed.

ESI-MS[n] of anticancer pt[iv] organoamido complexes and their interactions with DNA-model compounds /

The general solution behaviour and" the major fragmentation pathways of the anticanceractive PtIV coordination complexes, trans, trans, cis, cis-[PtCIOH{N(pFC6F4) CH2h(pY)2] (1), trans, cis, cis-[Pt(OH)2{N(p-FC6F4)CH2h(Py)2] (2), trans, cis, cis-[Pt(OH)2{N(p-HC6F4)CH2h(Py)2] (3), trans, trans, cis, cis-[PtCIOH{N(pHC6F4) CH2h(Py)2] (4), and trans, trans, cis, cis-[PtOH(OCH3){N(p-HC6F4)CH2h(PY)2] (5) (Py = pyridine) have been deduced by positive-ion tandem-in-time ESI-MS. Overall, the acquired full-scan, positive-ion ESI-MS spectra of 2, 3, and 5 were characterized by the presence of relatively low-intensity [M+Nar and [M+Kt mass spectral peaks, whereas those of 1 and 4 were dominated by extremely intense [M+Hr peaks. Complexes 2 and 3 were also noted to form [2M+Ht and [2M+Nat dilneric cations. The source of Na + and K+ ions is believed to be the sample, the solvent systems used or the transport line carrying the sample solutions into the ES ion source. Further, the fragmentation pathway of all complexes studied was found to be almost identical with concurrent loss of py and H20 molecules, loss of a {N(p-YC6F4)CH2} (Y = F, H) group and/or concomitant release of the latter group and a py ligand being the most conunon. The photochemical degradation behaviour of 1 and 2 was also investigated using either fluorescent or ultraviolet light and some products of that degradation were positively identified. Altogether, light irradiation of solutions of both complexes resulted in cation cationisation, reductive-elimination, ligand-release, ligand-exchange and ligand-addition reactions. Finally, positive- and negative-ion ESI-MSn spectra of 5' -GMP, guanosine, inosine and products of their reactions with 1, 2,3, and 4 were also recorded. On the whole, full-scan ESI-MS spectra of the pure nucleobases revealed the presence of cationic and anionic species that are highly reflective of both their solution ionic composition and their propensity t9 form polymeric clusters. Analyses of mass spectra acquired from their reaction solutions with the aforementioned platinum complexes indicated very slow kinetics. However, all complexes investigated formed, to various degrees, Pt-nucleobase adducts with guanosine and inosine, but not with 5'-GMP. The products included species having coordination numbers of III, IV, V, and VI, among which the first-time· observed, coordinatively saturated, jive-coordinate PtlI-nucleobase complexes were of most interest. The latter complexes are presumably stabilized by 7tback- donation involving the filled d orbitals of the PtII centre and the empty pz· orbital of MeCN. All products, whose peaks appeared inlull-scan ESI-MS spectra, are believed to represent solution species rather than artifacts of gas-phase processes. Finally, negativeion ESI-MSn spectra recorded in reaction solutions of 1 and 4 with guanosine and of the latter complex with inosine revealed the negative-ion-ESI-MS first-time observed, noncovalent, nucleoside-chloride adducts, with the source of chloride anion being complexes 1 and 4 theillselves. In contrast, no such adducts were observed to form with Na25'-GMP or its protonated fonn. Few suggestions are offered for the possible cause(s) behind the absence of such adduct ions.

Investigation into the relationships between molecular chaperones, mitochondrial antioxidant enzymes, and endothermic vertebrate longevity

The maximum lifespan (MLSP) of endothermic vertebrates can range from as little as a year to over two centuries, yet the underlying phenotype of aging is very similar amongst this group of organisms. One organelle that may be important in the phenotype of aging is the mitochondrion. When damaged, this organelle is thought to contribute to many of the neurodegenerative diseases of aging. For this thesis, mitochondria from brain tissues of 7 mammalian and 2 avian species were isolated to assess whether the antioxidant glutathione system and major molecular chaperone, HSP60, is correlated to species MLSP. Furthermore, HSP60, and the major endoplasmic reticulum chaperone, GRP78, were measured under basal conditions, and following the introduction of an oxidative stress (hydrogen peroxide) in cultured mammalian myoblasts from 10 different species. My results indicate that the enzymes involved in the glutathione defense system are not correlated to species MLSP in brain mitochondria; however HSP60 levels are indeed higher in the longer-lived species. HSP60 levels are also higher at the basal level in cultured mammalian myoblasts and after 1 hour of hydrogen peroxide exposure. GRP78 induction is not correlated to species MLSP at the basal level or following hydrogen peroxide exposure. Therefore, these results suggest that HSP60 is a correlate of longevity in endothermic vertebrate species, but neither the glutathione antioxidant defense system, nor GRP78, correlates to species longevity.

Mirroring Enzymes: The Role of H-Bonding In HQuin-BAM Catalyzed Asymmetric Aza-Henry Reactions: A DFT Study into the Reactivity, Mechanism, and Origins of Selectivity

The exact mechanistic understanding of various organocatalytic systems in asymmetric reactions such as Henry and aza-Henry transformations is important for developing and designing new synthetic organocatalysts. The focus of this dissertation will be on the use of density functional theory (DFT) for studying the asymmetric aza-Henry reaction. The first part of the thesis is a detailed mechanistic investigation of a poorly understood chiral bis(amidine) (BAM) Brønsted acid catalyzed aza-Henry reaction between nitromethane and N-Boc phenylaldimine. The catalyst, in addition to acting as a Brønsted base, serves to simultaneously activate both the electrophile and the nucleophile through dual H-bonding during C-C bond formation and is thus essential for both reaction rate and selectivity. Analysis of the H-bonding interactions revealed that there was a strong preference for the formation of a homonuclear positive charge-assisted H-bond, which in turn governed the relative orientation of substrate binding. Attracted by this well-defined mechanistic investigation, the other important aspect of my PhD research addressed a detailed theoretical analysis accounting for the observed selectivity in diastereoselective versions of this reaction. A detailed inspection of the stereodetermining C-C bond forming transition states for monoalkylated nitronate addition to a range of electronically different aldimines, revealed that the origins of stereoselectivity were controlled by a delicate balance of different factors such as steric, orbital interactions, and the extent of distortion in the catalyst and substrates. The structural analysis of different substituted transition states established an interesting dependency on matching the shape and size of the catalyst (host molecule) and substrates (guest molecules) upon binding, both being key factors governing selectivity, in essence, offering an analogy to positive cooperative binding effect of catalytic enzymes and substrates in Nature. In addition, both intra-molecular (intra-host) and inter-molecular (host-guest, guest-guest) stabilizing interactions play a key role to the high π-facial selectivity. The application of dispersion-corrected functionals (i.e., ωB97X-D and B3LYP-D3) was essential for accurately modeling these stabilizing interactions, indicating the importance of dispersion effects in enantioselectivity. As a brief prelude to more extensive future studies, the influence of a triflate counterion on both reactivity and selectivity in this reaction was also addressed.