This thesis deals with structural properties of unsaturated chlorhydrocarbons of general formulas C^H^Cl, C^H^Cl and as studied by microwave spectroscopy, electron diffraction and vibrational spectroscopic methods. The two former methods both give values of molecular structure parameters in gas phase, but due to different averages of the thermal motion the structures arrived at are not comparable. The link between the different structures is provided for by a reliable force field, derived from the observed fundamental vibrational energy transitions, on which the emphasis of this work lies.

The vibrational spectra of cis- and trans-monochlorobutadiene, cis, cis-, cis.trans- and trans,trans-dichlorobutadiene and of 4-chlorobuten- 3-yne were recorded in the medium and far infrared region and in Raman.

Assignment of the spectra was possible. Band contours of the spectra in the gaseous state as well as Raman polarization data were taken into account. Normal coordinate analyses were carried out with the help of a computer program, in which the estimated force field of the simplified valence type of each molecule, constructed of parameter values from similar molecules, is fitted to the observed frequencies. For the monochlorobutadienes, force fields of 22 diagonal and 8 off-diagonal elements, of which 17 values were kept fixed, succeeded in reproducing the observed fundamental frequencies. For the disubstituted butadienes, force fields of 29 parameters, 7 of which off-diagonal, were employed. Root-mean-square amplitudes of vibration and perpendicular amplitude correction coefficients for subsequent use in the refinement of electron diffraction data were also calculated.

In the chlorobutenyne case, the force field consisted of 27 parameters, 10 off-diagonal elements. The agreement between the observed frequencies and those calculated with the force field was very good.

In a series of Ba-based oxonitrido-silicate S-phases (Ba2AlxSi12-xN16-xO2+x) spanning a compositional range up to x approximate to 3, we examine the incorporation of Al and O by Si-29 and Al-27 magic-angle spinning (MAS) solid state nuclear magnetic resonance (NMR) and Al-27 triple-quantum MAS (3QMAS). The 3QMAS spectra reveal Al-27 signals from two distinct structural environments, assigned to AlN4 or AlN3O tetrahedra, respectively, and with their relative amounts depending on the S-phase substitution parameter x. Si-29 NMR show variable fractions of SiN4 and SiN3O environments. The NMR results accord overall with a structural substitution model for which O enters at one crystallographic position (occupied according to N4-xOx), in conjunction with a random Al for Si substitution at two distinct crystallographic positions. This leads to S-phase frameworks built from SiN4, SiN3O, AlN4 and AlN3O tetrahedra.

This survey presents six previously published papers dealing with time-resolved atomic and molecular spectroscopy with applications to the chemical composition of the solar atmosphere. Three methods of measuring mean lives of excited states have been used:

Beam-foil spectroscopy Beam-laser spectroscopy High-frequency deflection

The methods used to estimate the abundances of the chemical elements in the sun will also be outlined. The experimental work has been carried out at the Research Institute of Physics in Stockholm.

Our understanding of structure-function relationships in biological systems demands new and more sophisticated methods for examining molecular structure. This thesis presents an effort of methodology development for molecular structure determination by solid-state NMR spectroscopy and applications to biological systems.

Rotational Resonance NMR is established as a major tool for extracting molecular structural information in solids. Some further aspects of the technique are explored. The technique is applied to obtain the binding conformation of an inhibitor, TMPIP, bound to gastric H⁺/K⁺-ATPase, an ab heterodimer with a molecular weight of over 150 kDa.

A novel solid-state NMR method for the determination of the torsional angle of a ¹³C-labeled H-C-C-H moiety is developed. A detailed theoretical introduction of the method is presented. The technique has been applied to determine the H-C10-C11-H torsional angle of the retinylidene chromophore in bovine rhodopsin, a 41 kDa integral membrane protein, and its photo-intermediate metarhodopsin-I.

A new solid-state NMR method is developed. It may be used to estimate the Ramachandran ( angle in a protein backbone chain. A detailed theory is presented. It is demonstrated on an isotopically labeled tripeptide.

Small-angle X-ray scattering (SAXS) is used to demonstrate the presence of density fluctuations in ambient water on a physical length-scale of ≈1 nm; this is retained with decreasing temperature while the magnitude is enhanced. In contrast, the magnitude of fluctuations in a normal liquid, such as CCl4, exhibits no enhancement with decreasing temperature, as is also the case for water from molecular dynamics simulations under ambient conditions. Based on X-ray emission spectroscopy and X-ray Raman scattering data we propose that the density difference contrast in SAXS is due to fluctuations between tetrahedral-like and hydrogen-bond distorted structures related to, respectively, low and high density water. We combine our experimental observations to propose a model of water as a temperature-dependent, fluctuating equilibrium between the two types of local structures driven by incommensurate requirements for minimizing enthalpy (strong near-tetrahedral hydrogen-bonds) and maximizing entropy (nondirectional H-bonds and disorder). The present results provide experimental evidence that the extreme differences anticipated in the hydrogen-bonding environment in the deeply supercooled regime surprisingly remain in bulk water even at conditions ranging from ambient up to close to the boiling point.

The influence of local anesthetic lidocaine on electrostatic properties of a lipid membrane bilayer was studied by molecular dynamics simulations. The electrostatic dipole potential, charge densities, and orientations of the headgroup angle have been examined in presence of different amounts of charged or uncharged forms of lidocaine. Important differences of the membrane properties caused by the presence of the both forms of lidocaine are presented and discussed. Our simulations have shown that both charged and uncharged lidocaine cause almost the same increase of the dipole electrostatic potential in the middle of membrane though for different reasons. The increase, being about 90 mV for 9 mol % of lidocaine and 220 mV for 28 mol% of lidocaine, is of the size which may affect the functioning of voltage-gated ion channels.

The CHARMM force field for DMPC lipids was modified in order to improve agreement with experiment for a number of important properties of hydrated lipid bilayer. The modification consists in introduction of a scaling factor 0.83 for 1-4 electrostatic interactions (between atoms separated by three covalent bonds), which provides correct transgauche ratio in the alkane tails, and recalculation of the headgroup charges on the basis of HF/6-311(d,p) ab-initio computations. Both rigid TIP3P and flexible SPC water models were used with the new lipid model, showing similar results. The new model in a 75 ns simulation has shown a correct value of the area per lipid at zero surface tension, as well as good agreement with the experiment for the electron density, structure factor, and order parameters, including those in the headgroup part of lipids.

The present thesis concerns the interactions and dynamics of various types of smallmolecules in their liquid mixtures. The relationship between nuclear magneticrelaxation experiments, Molecular Dynamics simulations and dynamic models isexplored.Multinuclear magnetic relaxation was determined over the whole concentration rangein the components of the following binary mixtures: D^)-DMSO-dg, CD3CN-CDCI3 andCH3CN-H2O. Carbon-13 relaxation was measured in 1 mol% of sucrose and amethylated disaccharide in a 2:1 mixture of D2O-DMSO-dg, at variable temperatureoutside the extreme narrowing region. Nitrogen-14 relaxation was measured in 1 mol%of CHgCN in ^O-CHglCHg^OH as a function of the solvent mixture composition. Therotational correlation times were deduced from the relaxation rates. Self-diffusioncoefficients were also reported for the components of the CD3CN-CDCI3 system.Computer simulations were performed using the Molecular Dynamics method, and datacollected for the binary mixtures of CHgCN-CHClj and CH3CN-H2O over the wholeconcentration range. Radial distribution functions, pairwise interaction energies, andtime autocorrelation functions for the linear velocity, angular velocity andreorientation were reported.The NMR and MD-simulations data are not only directly compared, they are also usedto evaluate the applicability of diverse motional models. If a linear correlation withviscosity exists, the macroscopic hydrodynamic model is tested, possibly whileincluding some corrections for the molecular shape and boundary. However, this modelis seldom even seemingly correct for the small molecules of the present studies. Thediffusion model, where small angular displacements are assumed, is qualitativelyadequate in many cases. Nevertheless, some of the rotations are shown to be too far in theinertial limit to follow the diffusion model. The extended diffusion model, although itallows for rotations of arbitrary size, fails to describe the rotational motions in theacetonitrile/chloroform mixtures. The overall and internal motions of the twodisaccharides are described by the rotational diffusion model. A tentative attempt ismade to apply the continuum model of dielectric friction to acetonitrile in the mixedsolvent of water and 1-propanol.

A dense silica glass was prepared by consolidating a highly dispersed silicic acid powder (particle size < 10 nm) with the Spark Plasma Sintering (SPS) technique. The glass was characterized by ellipsometry, transmission electron microscopy (TEM), infrared reflectance and transmittance spectroscopy, as well as by Raman, UV-Vis-NIR and solid-state nuclear magnetic resonance (NMR) spectroscopy. The prototypic sample showed a transmittance of about 63% compared to silica glass in the UV-Vis spectral range. Based on the results of infrared transmittance spectroscopy this lower transparency is due to the comparably high water content, which is about 40 times higher than that in silica glass. H-1 magic-angle spinning (MAS) NMR confirmed an increase in hydroxyl groups in tie sample prepared by SPS relative to that of the conventional SiO2 reference glass. Aside from the comparably high water content, we conclude from the similarity of the IR-reflectance and the Si-29 MAS NMR spectra of the SPS sample and the corresponding spectra of the conventionally prepared silica glass, that the short- and medium-range order is virtually the same in both materials. Raman spectroscopy, however, Suggests that the number of three- and four-membered rings is significantly smaller in the SPS sample compared to the conventionally prepared sample. Based on these results we conclude that it is possible to prepare glasses by compacting amorphous powders by the SPS process. The SPS process may therefore enable the preparation of glasses with compositions inaccessible by conventional methods. 

The effects induced by spin-orbit coupling on the electronic states of Ni(II) complexes are studied with ab-initio and crystal field calculations.

The ab-initio calculations are performed in two steps, to separate the coulomb and the spin-orbit effects. The first step is an ordinary Cl calculation which provides excited states that are spin eigenfunctions. The second step is a spin-orbit coupled Cl of a selection of the previously created states. The spin-orbit coupling is described by an effective one-electron operator. Double group symmetry is used throughout to facilitate the analysis, and the experimental comparisons, of the spin-orbit states and the matrix elements.

The method is applied, and compared with experiments, on cubic Oh and orthorhombic Ö2h NiFg-. For the cubic form the calculated excited states are in excellent agreement. For the orthorhombic form comparison of the spin-orbit splitting, or zero field splitting, of the ground state shows that the calculated states are in correct order but a factor of two larger than the experimental energies.

To investigate the dependence of the zero-field splitting on the degree of distortion from octahedral symmetry and the type of ligand, a series of calculations with different ligands at different distances is performed.

Finally the possibility to parametrize the zero-field splitting as a function of the normal coordinate modes in octahedral symmetry is explored with crystal field and ab-initio calculations. The parameters for a generally distorted NiF4/6 complex are given and it is shown that crystal field calculations can be made to reproduce the ab-initio results at the expense of different scalings for the radial and the curvilinear modes.

Raman spectra from 600 to 1150 cm(-1) have been collected from wet-spun films of highly oriented CaDNA as a function of relative humidity (rh). Particular attention was paid to the Raman modes at 834 and 807 cm(-1); the presence of these modes indicates that the DNA backbone is in the B or A conformations. Though the B conformation is usually found only under conditions of high hydration in such wet-spun films, CaDNA is found to remain in the B conformation down to 75% rh. These results are consistent with the hypothesis that intermolecular bonds in ordered samples of DNA are critical for the stabilization of the A conformation of DNA.

The present thesis summarizes some aspects in the studies of molecular properties by combining molecular dynamics computer simulations and quantum mechanical calculations. Applications to water and related system are overviewed. 

First, method of combined quantum mechanical and molecular mechanical (QM/MM) calculations is outlined. Molecular dynamics simulations on water systems using combined QM/MM potentials are reviewed. In the simulations, the QM calculations are carried out at the ab initio Hartree-Fock level and TIP3P water models are used to represent the MM water molecules. The main focus of the studies is on the combined QM/MM coupling potentials. The simulation results show that the QM/MM coupling is very sensitive to the Lennard-Jones parameters used on the QM atoms. When the TIP3P Lennard-Jones parameters are used for the QM atoms, the QM/MM coupling is found to be too strong. However, when the LennardJones parameters on the QM atoms are optimized according to the corresponding QM/MM calculations of water dimer, the QM/MM coupling seems to be too weak. Therefore, we believe that the Lennard-Jones parameters on the QM atoms optimized from the corresponding QM/MM calculations for some molecular complexes cannot reliably be used in the simulation of the condensed phases. A modified QM/MM coupling for water systems is found by scaling down the MM charges appearing in the coupling potential. Studies show that the new QM/MM coupling potentials can be used satisfactorily in the combined Hartree-Fock QM/MM molecular simulations of water from ambient to supercritical conditions.

In the thesis, a self-consistent charge approach developed for the study of the electronic properties of a single molecule in condensed phases is also outlined. In the approach, only the Coulomb interaction between the molecules is considered. Therefore, it is suitable for the study of molecular properties in systems where Coulomb interaction is predominant, such as liquid water, methanol, etc. As an application, the electronic properties of water molecules in water clusters and liquid water are studied. The average water dipole moment in liquid water is found to be 2.65 D. Significant changes in quadrupole moment and polarizability are also found along the water plane in the direction perpendicular to the axis bisecting the H-O-H bond angle. A further theoretical derivation based on the interaction model is presented to find the atomic charge model suitable for the MM force fields. The derived charge model shows that the appropriate atomic charge corresponds to the average value of the electrostatic potential derived charge for an isolated molecule and that obtained for the molecule in the interaction system. Applications to liquid water and methanol show that the obtained charges are similar to those found in the widely used MM force field models, such as SPC, TIP3P, OPLS, etc.   

A theory of nuclear spin relaxation in paramagnetic complexes, allowing for the electron spin relaxation to be in the slow motion regime, is presented. The lattice i3 described in terms of the electron Zeeman interaction, a zero field splitting (ZFS) and a Markov operator for the relevant classical degrees of freedom. Several dynamic models for the motions in the lattice are discussed.

A reorientation model which includes only isotropic rotational diffusion of the complex is presented. Based on this model numerical calculations of nuclear spin-spin and spin-lattice relaxation rates are reported for electron spin systems (S=3/2 and S=5/2) coupled to the nuclear spin system via dipole-dipole and scalar spin-spin interaction.

The nuclear magnetic relaxation of protons in Ni(II) hexa-aquo complexes is discussed in detail. Three different dynamic models for the transient ZFS-interaction are presented. It is found that at least two different models is consistent with the available experimental data . A combined distortion-reorientation model for the ZFS-interaction is presented.

Within the slow motion theory the so called quadrupolar dip is discussed and numerical calculations is presented for the case of ^H-'^ spin pairs.

Analytical expressions for NMR lineshape of spin 5/2 and 7/2 nuclei are derived assuming quadrupolar relaxation and non-extreme narrowing conditions. The effects of both chemical exchange and dynamic shifts are included in the description.

Coarse-grained Langevin molecular dynamics computer simulations were conducted for systems that mimic solutions of nucleosome core particles (NCPs). The NCP was modeled as a negatively charged spherical particle representing the complex of DNA and the globular part of the histones combined with attached strings of connected charged beads modeling the histone tails. The size, charge, and distribution of the tails relative to the core were built to match real NCPs. Three models of NCPs were constructed to represent different extents of covalent modification on the histone tails: (nonmodified) recombinant (rNCP), acetylated (aNCP), and acetylated and phosphorylated (paNCP). The simulation cell contained 10 NCPs in a dielectric continuum with explicit mobile counterions and added salt. The NCP-NCP interaction is decisively dependent on the modification state of the histone tails and on salt conditions. Increasing the monovalent salt concentration (KCl) from salt-free to physiological concentration leads to NCP aggregation in solution for rNCP, whereas NCP associates are observed only occasionally in the system of aNCPs. In the presence of divalent salt (Mg²⁺), rNCPs form dense stable aggregates, whereas aNCPs form aggregates less frequently. Aggregates are formed via histone-tail bridging and accumulation of counterions in the regions of NCP-NCP contacts. The paNCPs do not show NCP-NCP interaction upon addition of KCl or in the presence of Mg²⁺. Simulations for systems with a gradual substitution of K⁺ for Mg²⁺, to mimic the Mg²⁺ titration of an NCP solution, were performed. The rNCP system showed stronger aggregation that occurred at lower concentrations of added Mg²⁺, compared to the aNCP system. Additional molecular dynamics simulations performed with a single NCP in the simulation cell showed that detachment of the tails from the NCP core was modest under a wide range of salt concentrations. This implies that salt-induced tail dissociation of the histone tails from the globular NCP is not in itself a major factor in NCP-NCP aggregation. The approximation of coarse-graining, with respect to the description of the NCP as a sphere with uniform charge distribution, was tested in control simulations. A more detailed description of the NCP did not change the main features of the results. Overall, the results of this work are in agreement with experimental data reported for NCP solutions and for chromatin arrays.

The description of the reorientational dynamics of flexible molecules is a challenging task, in particular when the rates of internal and global motions are comparable. The commonly used simple mode-decoupling models are based on the assumption of statistical independence between these motions. This assumption is not valid when the time scale separation between their rates is small, a situation that was found to arise in oligosaccharides in the context of certain internal motions. To make possible the interpretation of NMR spin relaxation data from such molecules, we developed a comprehensive approach generally applicable to flexible rotators with one internal degree of freedom. This approach integrates a stochastic description of coupled global tumbling and internal torsional motion, quantum chemical calculations of the local potential and the local geometry at the site of the restricted torsion, and hydrodynamics-based calculations of the diffusive properties. The method is applied to the disaccharide -D-Glcp-(16)--D-[6-¹³C]-Manp-OMe dissolved in a DMSO-d₆/D₂O cryosolvent. The experimental NMR relaxation parameters, associated with the ¹³CH₂ probe residing at the glycosidic linkage, include ¹³C T₁ and T₂ and ¹³C-{¹H} nuclear Overhauser enhancement (NOE) as well as longitudinal and transverse dipole-dipole cross-correlated relaxation rates, acquired in the temperature range of 253–293 K. These data are predicted successfully by the new theory with only the H–C–H angle allowed to vary. Previous attempts to fit these data using mode-decoupling models failed.