Theoretical Studies on Coupled Electron and Proton Transfer in Cytochrome c Oxidase

The complexity of life is based on an effective energy transduction machinery, which has evolved during the last 3.5 billion years. In aerobic life, the utilization of the high oxidizing potential of molecular oxygen powers this machinery. Oxygen is safely reduced by a membrane bound enzyme, cytochrome c oxidase (CcO), to produce an electrochemical proton gradient over the mitochondrial or bacterial membrane. This gradient is used for energy-requiring reactions such as synthesis of ATP by F0F1-ATPase and active transport. In this thesis, the molecular mechanism by which CcO couples the oxygen reduction chemistry to proton-pumping has been studied by theoretical computer simulations. By building both classical and quantum mechanical model systems based on the X-ray structure of CcO from Bos taurus, the dynamics and energetics of the system were studied in different intermediate states of the enzyme. As a result of this work, a mechanism was suggested by which CcO can prevent protons from leaking backwards in proton-pumping. The use and activation of two proton conducting channels were also enlightened together with a mechanism by which CcO sorts the chemical protons from pumped protons. The latter problem is referred to as the gating mechanism of CcO, and has remained a challenge in the bioenergetics field for more than three decades. Furthermore, a new method for deriving charge parameters for classical simulations of complex metalloenzymes was developed.

Food aid and food production: A theoretical analysis

It has been claimed that food aid leads to permanent dependency as it depresses domestic food prices and thus farmers find it profitable to take land out of food production and into more lucrative activities. This paper develops two alternative scenarios under which the hypothesis about the damaging effect of food aid may not be true. Under the first scenario, it is argued that food production in developing countries is often low due to unfavourable trade policies and if food aid is tied to the removal of bias against the agricultural sector, food aid will not have any disincentive effect on food production. The second exercise argues that the revenue raised by the recipient government by selling aid could be used for R and D in agricultural production.

Theoretical calculations of base-base interactions in nucleic acids: II Stacking interactions in polynucleotides

Base-base interactions were computed for single- and double- stranded polynucleotides, for all possible base sequences. In each case, both right and left stacking arrangements are energetically possible. The preference of one over the other depends upon the base-sequence and the orientation of the bases with respect to helix-axis. Inverted stacking arrangement is also energetically possible for both single- and double-stranded polynucleotides. Finally, interaction energies of a regular duplex and the alternative structures3 were compared. It was found that the type II model3 is energetically more favourable than the rest.

Theoretical calculations of base-base interactions in nucleic acids: I Stacking interactions in free bases

Stacking interactions in free bases were computed on the basis of molecular association. The results of the calculations were compared with the stacking patterns observed in a few single crystals of nucleic acid components as examples. The following are the conclusions: (i) there can be two types of stacking pattern classified as normal and inverted types for any two interacting bases and both can be energetically favourable (ii) in both the types the stacking interaction is a combined effect of the overlap of the interacting bases and relative positions and orientations of the atomic centres of the two bases (iii) crystal symmetry and H-bonding interaction may influence stacking patterns.

Which One Is Preferred: Myers-Saito Cyclization of Ene-Yne-Allene or Garratt-Braverman Cyclization of Conjugated Bisallenic Sulfone? A Theoretical and Experimental Study

A competitive scenario between Myers-Saito (MS) and Garraff-Braverman (GB) cyclization has been created in a molecule. High-level computations indicate a preference for GB over MS cyclization. The activation energies for the rate-determining steps of the GB and MS cyclizations were found to be the same (24.4 kcal/mol) at the B3LYP/6-31G* level of theory; thus, from the kinetic point of view, both reactions are feasible. However, the main biradical intermediate GB2 of the GB reaction is 6.2 kcal/mol lower in energy than the biradical MS2, which is the main intermediate of MS reaction, so GB cyclization is thermodynamically favored over MS cyclization. To verify the prediction by computational techniques, bisenediynyl sulfones 1-4 and bisenediynyl sulfoxide 17 were synthesized. Under basic conditions, these molecules isomerized to a system possessing both the ene-yne-allene and the bisallenic sulfone. The isolation of only one product, identified as the corresponding naphthalene- or benzene-fused sulfone 8-11, indicated the occurrence of GB cyclization as the sole reaction pathway. No product corresponding to the MS cyclization pathway could be isolated. Though the theoretical prediction showed a preference for the GB pathway over the MS pathway, the exclusive preference for GB over MS cyclization is very striking. Further analysis showed that the intramolecular self-quenching nature of the GB pathway may play an important role in the complete preference for this reaction. Apart from the mechanistic studies, these sulfones showed DNA cleavage activity that had an inverse relation with the reactivity order. Our findings are important for the design of artificial DNA-cleaving agents.

Simple theoretical analysis of the Einstein's photoemission from quantum confined superlattices

In this paper, we study the Einstein's photoemission from III-V, II-VI, IV-VI and HgTe/CdTe quantum well superlattices (QWSLs) with graded interfaces and quantum well effective mass superlattices in the presence of a quantizing magnetic field on the basis of newly formulated dispersion relations in the respective cases. Besides, the same has been studied from the afore-mentioned quantum dot superlattices and it appears that the photoemission oscillates with increasing carrier degeneracy and quantizing magnetic field in different manners. In addition, the photoemission oscillates with film thickness and increasing photon energy in quantum steps together with the fact that the solution of the Boltzmann transport equation will introduce new physical ideas and new experimental findings under different external conditions. The influence of band structure is apparent from all the figures and we have suggested three applications of the analyses of this paper in the fields of superlattices and microstructures.

Theoretical Investigation on the Effect of Different Nitrogen Donors on Intramolecular Se center dot center dot center dot N Interactions

The effect of different donor nitrogen atoms on the strength and nature of intramolecular Se center dot center dot center dot N interactions is evaluated for organoselenium compounds having N,N-dimethylaminomethyl (dime), oxazoline (oxa) and pyridyl (py) substituents. Quantum chemical calculations on three series of compounds [2-(dime)C6H4SeX (1a-g), 2-(oxa)C6H4SeX (2a-g), 2- (py)C6H4SeX (3-ag); X=Cl, Br, OH, CN, SPh, SePh, CH3] at the B3LYP/6-31G(d) level show that the stability of different conformers depends on the strength of intramolecular nonbonded Se center dot center dot center dot N interactions. Natural bond orbital (NBO), NBO deletion and atoms in molecules (AIM) analyses suggest that the nature of the Se center dot center dot center dot N interaction is predominantly covalent and involves nN ->sigma*(Se-X) orbital interaction. In the three series of compounds, the strength of the Se center dot center dot center dot N interaction decreases in the order 3>2>1 for a particular X, and it decreases in the order Cl > Br > OH>SPh approximate to CN approximate to SePh>CH3 for all the three series 1-3. However, further analyses suggest that the differences in strength of Se center dot center dot center dot N interaction in 1-3 is predominantly determined by the distance between the Se and N atoms, which in turn is an outcome of specific structures of 1, 2 and 3, and the nature of the donor nitrogen atoms involved has very little effect on the strength of Se center dot center dot center dot N interaction. It is also observed that Se center dot center dot center dot N interaction becomes stronger in polar solvents such as CHCl3, as indicated by the shorter r(Se center dot center dot center dot N) and higher E-Se center dot center dot center dot N values in CHCl3 compared to those observed in the gas phase.

Type II beta-turn conformation of pivaloyl-L-prolyl-a-aminoiso-butyryl-N-methylamide: Theoretical, spectroscopic and X-ray studies

Pivaloyl-L-Pro-Aib-N-methylamihdaes been shown to possess one intramolecular hydrogen bond in (CD&SO solution, by 'H-nmr methods, suggesting the existence of p-turns, with Pro-Aib as the corner residues. Theoretical conformational analysis suggests that Type II P-turn conformations are about 2 kcal mol-' more stable than Type 111 structures. A crystallographic study has established the Type I1 /%turn in the solid state. The molecule crystallizes in the space group P21 with a = 5.865 8, b = 11.421 A, c = 12.966 A, /3 = 97.55", and 2 = 2. The structure has been refined to a final R value of 0.061. The Type I1 p-turn conformation is stabilized by an intramolecular 4 - 1 hydrogen bond between the methylamide NH and the pivaloyl CO group. The conformational angles are @pro= -57.8", $pro = 139.3', @Aib = 61.4', and $Ajb = 25.1'. The Type 11 /%turn conformation for Pro-Aib in this peptide is compared with the Type I11 structures observed for the same segment in larger peptides.

Theoretical Studies of Hard Filling in Loop Heat Pipes

Loop heat pipe is a passive two-phase heat transport device that is gaining importance as a part of spacecraft thermal control systems and also in applications (such as in avionic cooling and submarines). Hard fill of a loop heat pipe occurs when the compensation chamber is full of liquid. A theoretical study is undertaken to investigate the issues underlying the loop beat pipe hard-fill phenomenon. The results of the study suggest that the mass of charge and the presence of a bayonet have significant impact on the loop heat pipe operation. With a largern mass of charge, a loop heat pipe hard fills at a lower heat load. As the heat load increases, there is a steep rise in the loop heat pipe operating temperature. In a loop heat pipe with a saturated compensation chamber, and also in a hard-filled loop heat pipe without a bayonet, the temperature of the compensation chamber and that of the liquid core are nearly equal. When a loop heat pipe with a bayonet hard fills, the compensation chamber and the evaporator core temperatures are different.

A theoretical model for the magnetic helicity of solar active regions

Active regions on the solar surface are known to possess magnetic helicity, which is predominantly negative in the northern hemisphere and positive in the southern hemisphere. Choudhuri et al. [Choudhuri, A.R. On the connection between mean field dynamo theory and flux tubes. Solar Phys. 215, 31–55, 2003] proposed that the magnetic helicity arises due to the wrapping up of the poloidal field of the convection zone around rising flux tubes which form active regions. Choudhuri [Choudhuri, A.R., Chatterjee, P., Nandy, D. Helicity of solar active regions from a dynamo model. ApJ 615, L57–L60, 2004] used this idea to calculate magnetic helicity from their solar dynamo model. Apart from getting broad agreements with observational data, they also predict that the hemispheric helicity rule may be violated at the beginning of a solar cycle. Chatterjee et al. [Chatterjee, P., Choudhuri, A.R., Petrovay, K. Development of twist in an emerging magnetic flux tube by poloidal field accretion. A&A 449, 781–789, 2006] study the penetration of the wrapped poloidal field into the rising flux tube due to turbulent diffusion using a simple 1-d model. They find that the extent of penetration of the wrapped field will depend on how weak the magnetic field inside the rising flux tube becomes before its emergence. They conclude that more detailed observational data will throw light on the physical conditions of flux tubes just before their emergence to the photosphere.

CsrA interacting small RNAs in Haemophilus spp genomes: a theoretical analysis

The csrA is a carbon storage regulator gene that encodes a protein with multiple RNA interaction sites. Bacterial non-coding small RNAs like csrB, csrC and their counterparts in diverse bacterial genus are identified to control the regulatory activities of CsrA and its orthologs. An attempt has been made in this study to identify 'novel' non-coding small RNAs that are involved in the regulatory activities of csrA gene. All CsrA-interacting small RNAs are computationally fingerprinted to have multiple occurrence of 7-nucleotide CsrA interacting repeats [CAGGA(U/A/C)G] along with a 18-nucleotide upstream binding site. However, in several of the genomes like Haemophilus spp, the upstream binding site is not identified. The current methodology overcomes this difficulty by identifying small RNA-specific orphan transcriptional units within the intergenic regions of the genome. The results could identify all known CsrA-interacting small RNAs in E. coli, Vibrio cholerae and Pseudomonas aeruginosa genomes and additionally has picked six new possible CsrA-interacting small RNA regions in E. coli. Our computational analysis indicates that known rygD and rprA sRNAs in E. coli could possibly interact with CsrA proteins. The study is extended to three of the Haemophilus genomes that could identify seven new possible CsrA interacting small RNAs.

Investigation of inter-ion interactions in N,N,N',N'-tetramethylethylenediammonium dithiocyanate via experimental and theoretical charge density studies

The crystal structure of the N,N,N',N'-tetramethylethylenediammonium dithiocyanate salt has been examined by experimental charge density studies from high-resolution X-ray diffraction data. The corresponding results are compared with multipole refinements, using theoretical structure factors obtained from a periodic density functional theory calculation at the B3LYP level with a 6-31G** basis set. The salt crystallizes in space group P (1) over bar and contains only a single ion pair with an inversion center in the cation. The salt has thus one unique classical N+-H center dot center dot center dot(NCS)(-) hydrogen bond but also has six other weaker interactions: four C-H center dot center dot center dot S, one C-H center dot center dot center dot N, and one C-H center dot center dot center dot C-pi. The nature of all these interactions has been examined topologically using Bader's quantum theory of "atoms in molecules" and all eight of the Koch-Popelier criteria. The experimental and theoretical approaches agree well and both show that the inter-ion interactions, even in this simplest of systems, play an integrated and complex role in the packing of the ions in the crystal. Electrostatic potential maps are derived from experimental charge densities. This is the first time such a system has been examined in detail by these methods.

Estimation of thermal breakdown voltage of HVDC cables - A theoretical framework

The insulation in a dc cable is subjected to both thermal and electric stress at the same time. While the electric stress is generic to the cable, the temperature rise in the insulation is, by and large, due to the Ohmic losses in the conductor. The consequence of this synergic effect is to reduce the maximum operating voltage and causes a premature failure of the cable. The authors examine this subject in some detail and propose a comprehensive theoretical formulation relating the maximum thermal voltage (MTV) to the physical and geometrical parameters of the insulation. The heat flow patterns and boundary conditions considered by the authors here and those found in earlier literature are provided. The MTV of a dc cable is shown to be a function of the load current apart from the resistance of the insulation. The results obtained using the expressions, developed by the authors, are compared with relevant results published in the literature and found to be in close conformity.

On the mechanical behavior of compacted pack ice : A theoretical and numerical investigation

Pack ice is an aggregate of ice floes drifting on the sea surface. The forces controlling the motion and deformation of pack ice are air and water drag forces, sea surface tilt, Coriolis force and the internal force due to the interaction between ice floes. In this thesis, the mechanical behavior of compacted pack ice is investigated using theoretical and numerical methods, focusing on the three basic material properties: compressive strength, yield curve and flow rule. A high-resolution three-category sea ice model is applied to investigate the sea ice dynamics in two small basins, the whole Gulf Riga and the inside Pärnu Bay, focusing on the calibration of the compressive strength for thin ice. These two basins are on the scales of 100 km and 20 km, respectively, with typical ice thickness of 10-30 cm. The model is found capable of capturing the main characteristics of the ice dynamics. The compressive strength is calibrated to be about 30 kPa, consistent with the values from most large-scale sea ice dynamic studies. In addition, the numerical study in Pärnu Bay suggests that the shear strength drops significantly when the ice-floe size markedly decreases. A characteristic inversion method is developed to probe the yield curve of compacted pack ice. The basis of this method is the relationship between the intersection angle of linear kinematic features (LKFs) in sea ice and the slope of the yield curve. A summary of the observed LKFs shows that they can be basically divided into three groups: intersecting leads, uniaxial opening leads and uniaxial pressure ridges. Based on the available observed angles, the yield curve is determined to be a curved diamond. Comparisons of this yield curve with those from other methods show that it possesses almost all the advantages identified by the other methods. A new constitutive law is proposed, where the yield curve is a diamond and the flow rule is a combination of the normal and co-axial flow rule. The non-normal co-axial flow rule is necessary for the Coulombic yield constraint. This constitutive law not only captures the main features of forming LKFs but also takes the advantage of avoiding overestimating divergence during shear deformation. Moreover, this study provides a method for observing the flow rule for pack ice during deformation.