It is known from theoreticalstudies of supramolecular complexes of a variety of π-systems such as benzene, naphthalene and the DNA bases that a correct description of dispersion interactions is required already at the stage of geometry optimization. 63,120-122 It is widely recognized that Hartree–Fock calculations describe dispersion interactions rather poorly due to their neglect of correlation effects. Good results are often obtained already at the MP2 level. An overestimation of dispersion forces observed in some cases at this latter level can be remedied either through more highly correlated single reference approaches such as CCSD(T) 123 or through rescaling the MP2 correlation energies according to the SCS-MP2 procedure. 63,121,122 Unfortunately, gradient-corrected density functional methods such as BLYP and hybrid functionals such as Becke3LYP are not able to describe dispersion interactions correctly in a systematic fashion due the essentially local design of these functionals. 63,121,122 How far a correlated treatment is also required for the correct description of conformational properties of the catalysts under study here is investigated using catalyst 55 as a test case. A rigorous conformational search has first been performed for 55 and its acetyl intermediate by modified OPLS-AA force field, then the identified conformers were reoptimized at the B3LYP/6-31G(d) level of theory, identifying 24 conformers for neutral 55 and 54 conformers for the corresponding acetyl intermediate 55Ac. The potential of this level of theory was tested in earlier studies of the catalytic potential of pyridine bases. 10,71,83 Based on the Boltzmann-averaged enthalpies calculated at the B3LYP/6-311+G(d,p)//B3LYP/6- 31G(d) level approximately 30 conformations make a significant contribution (>1%) to the conformational ensemble at 298 K, the energetically most favorable conformer of 55Ac contributing 9.5%. The existence of stacked conformations in pyridinium cations can be determined in structural terms using the distance between the center of the pyridine ring and the center of the closest lying six membered aromatic ring (as indicated in Figure 5.2). This distance amounts to 5.20 Å in the most favorable conformer optimized at the B3LYP/6- 31G(d) level, which is not a π–π stacking structure and does not agree with the spectroscopic studies performed by Kawabata and coworkers. 17 Kawabata and coworkers have studied catalyst 55 and its acyl intermediate using 1 H NMR in CDCl 3 at 20 °C. Based on an analysis
Theoreticalstudies o f EPR g factors for 3d7 ions in cubic octahedral crystals, such as Co2+ in MgO and CaO crystals, have attracted interest for a long time [1 - 4]. In these crystals, the ground state o f the 3d7 ion is an orbital triplet 4T, (F). From the eigenfunctions
A. P. M azurek and G. Karpiriska • TheoreticalStudies on Molecular D eterm inants 473
each co m p o u n d in ex tended and hydrogen- b o n d ed form (w hen the solvent m olecule is re p resen ted by M ulliken point charge positioned at the nuclei) are given in colum n 1 of Table III. In each case, th e h y d rogen-bonded form is hydrated b e tte r th a n corresp o n d in g o p en ed form . The en- thalpic c o n trib u tio n enhances the hydrogen bond stren g th calculated in vacuum . Thus for neutral species stabilization energy due to intram olecular hydrogen bon d in g is increased in aqueous m e dium . H ow ever, th e o rd e r of the total stabilization energy is d ifferen t for un h y d rated molecules. The a -M e H A ap p e a re d to gain relatively less stabiliza tion due to h y d ratio n w hen changing from opened to h y d ro g en -b o n d ed conform ation. As rep o rted by R ashin (R ash in and N am boodiri, 1987) for som e system s a discrepancy was found betw een the calculated and experim ental values of hy dratio n enthalpy, p robably due to failure of the M ulliken p o p u latio n analysis to yield a charge distrib u tio n th a t correctly rep ro d u ces the dipole m om ent an d o th e r electrostatic p ro p erties of m o lecular systems. A t this point it becam e im portant to verify if the m eth o d itself, regardless of re p resen tatio n of charge distribution, can properly describe side chain structures of the studied com pounds, especially H A vs. a-M e H A . T herefore we also calculated h ydration enthalpies for m eth- ylam ine and ethylam ine. R esults p resen ted in Table II indicate th a t the in h eren t e rro r is im p lem en ted in the calculation, because the differ ence b etw een th e values of ex perim ental hy d ratio n en th alp ies of m ethylam ine and ethylam ine is ca. 2.2 kcal/m ol (last row o f Table II) (A ue et al., 1976). T he results suggest th a t for a -M eH A
All of the above experimental approaches are contingent upon the availability of actual substrate samples, a point not easily reconciled with the realities of catalyst development projects. Theoretically calculated nucleophilicities offer the advantage that predictions can be made for compounds before their respective synthesis, thus avoiding the potential problem of synthesizing compounds of low (catalytic) activity. A number of theoreticalstudies on enantioselective catalysts have been carried out during the last decade. Most of these concern the rationalization of the stereochemical outcome of these reactions and involve either the full characterization of potential energy surfaces or the localization of the transition states of the selectivity-determining step.  In contrast, studies devoted to application of theoretical methods to the prediction of catalyst activity have received comparatively little attention. [22c,25,26] One of the theoretical approaches for predicting nucleophilic activity is based on the minimum values of the molecular electrostatic potential (MEP), which was evaluated by Campodonico et al. for a series of substituted pyridines. [25a] Significantly closer to the situation in catalytic processes are approaches involving the calculation of affinity values towards model electrophiles. Since most of the organocatalytic transformations involve nucleophilic attack on carbon, methyl cation affinities (MCA) can serve as the most simple model for a carbon basicity scale. [25b] Zipse et al. [25c] have compared experimental rates of the Michael addition reaction of methanol to acrylamide catalyzed by amine and phosphane nucleophiles with pK a values, proton and methyl cation affinities (calculated at MP2(FC)/6-
Knowledge of the biological significance of hy droxyl radical modified bases must be accom plished by theoreticalstudies concerning funda mental properties of such derivatives. This work deals with characteristics of energetic, structural and electrostatic properties of different tautom ers of the fapy-guanine and fapy-adenine. Since inter- molecular complex formation is strongly related to the tautom eric form this paper intend to find out the tautom ers succession of all potential tautom ers of fapy-A and fapy-G, which may occur in the DNA.
Nanoscience, a branch of material science where materials at nanometer size range are investigated, has found most central place in the field of re- search over the last decades. Both experimentalists and theoreticians have contributed for this field but contributions from theoreticians are growing rapidly. Nanoscience has started in early 1980’s and its major development was birth of cluster science and since then clusters and nanoparticles in the size range of some 10s to some 10 000s of atoms are studied extensively. These systems are of special interest because they have sizes in a range where quantum confinement or quantum-size effects (QSE) play important role for the unique, size dependent properties of these materials. Thus, the determination of the size dependent properties of these nano-particles and to find relation between size and properties is not easy for these systems. In experimental studies the clusters are rarely isolated, but instead they often interact with some other medium while theoreticalstudies deal with isolated clusters of a well defined size for which it is overwhelmingly complicated to determine the structure. The identification of the structure of the lowest total energy for a cluster of N atoms requires searching in a geometry space of 3N-6 dimensions, which for any but the smallest values of N hardly is possible.
The importance of computational methods for the investigation of biological systems, has drasti- cally increased over the last decades. The ability of computational simulations to provide detailed information on structural and dynamic properties of molecular systems at the atomic level, makes it a valuable tool to uncover structure-function relationships. Furthermore, computer simula- tions can be helpful for the interpretation of experimental data, which mostly reflect macroscopic properties of the system, while the underlying microscopic processes often remain uncertain. For the red light absorbing phytochrome photoreceptors, as introduced in the previous chapter, numerous experimental studies have been done over the last decades for various members of this protein family from many different organisms. The ultimate goal of all those studies is to fully understand all the microscopic processes, which occur during the photocycle. However, most of the molecular events involved are still not fully understood, and despite the numerous studies in this field, the elucidation of the photointerconversion mechanism is still a matter of debate. A recent breakthrough in phytochrome research was the resolution of the three-dimensional struc- ture of several phytochrome fragments from crystallographic [15, 46, 47] and NMR spectroscopic [45, 48] studies, which revealed detailed insight to the structure at an atomic level. Such exper- imentally derived structures are also of utmost importance for theoretical investigations, since they provide reasonable starting geometries for molecular modelling and simulations. However, questions about dynamic properties and explicit environmental effect of molecular systems at an atomic level at room temperature can mostly not be adressed by experimental techniques. Such information, however, are of particular importance for structure-function relationships in phy- tochromes, since the highly flexible cofactors undergo conformational and configurational changes in a complex protein environment. To fully understand these processes, a detailed picture of the dynamics at the atomic level is a requirement. With a proper empirical force field avail- able, computational molecular simulations on the nanosecond time scale are known to generally deliver accurate conformations and dynamic properties of protein systems at room temperature [49, 50, 51].
Because of the experimental setup, the cross sections of the specimens were stress-free surfaces during the whole experiment. The chemical reaction front propagation was observed at these stress-free surfaces. Strictly speaking, one cannot use either a plane strain or a plane stress simplification in order to find the stresses at the reaction front. Neverthe- less, since one can find a kinetic equation for the interface movement for both plane stress and plane strain formulations in a closed form, we solve the model problem in this paper in both formulations, assuming that the real behavior may be somewhat ‘‘in between.’’ This gives the opportunity to fit the theoretical prediction with the experimental results, as described in the ‘‘Fitting the Model Parameters’’ section. Based on the fitted data, we further obtain an estimate for the diffusion coeffi- cient and for the chemical reaction kinetic constant. Consider an elastic layer with a cross section in the xy-coordinate plane and the plane reaction front propagating in the y-direction from y ¼ 0 to y ¼ H where H is the layer thickness and h is the current reaction front position (Fig. 17). The storage tem- perature in the oven is T and the reference temper- ature is T 0 , h ¼ T T 0 .
Polymeric structures like the diamond nanowires 79 are of particular interest for future applications as similar structures like diamond itself are used industrially.  For this reason several polymeric hydrocarbon structures were proposed in recent studies (Figure 7). Minyaev et al. theoretically investigated polyprismane structures such as 80, 81 and 82 and showed their thermodynamic stability.  These structures are especially intriguing because of the inverted, pyramidal configuration of the contained carbon atoms. The group of Crespi suggested novel hydrocarbon nanowires which promise high stiffness, high stability and insulating properties.  The suggested structures consist of cyclohexane rings in chair and boat conformations in 83 or exclusively in the boat conformation as in 84. The polymer 85, built up only of cyclohexane rings in the twist-boat conformation, was proposed by Barua et al. and was named polytwistane.  This polymer displays helical chirality due to the D 2 - symmetry of the constituting twist-boat cyclohexane rings and was also shown to be thermodynamically stable. All of these structures have not yet been realized experimentally but the example of graphane 86 illustrates that a theoretical compound can rapidly become reality. From the first mention of the structure of graphane 86 in the literature in 2003  over the prediction of its stability and some properties in 2007  to the experimental realization in 2009  it took only six years. The success of this project shows that it is worthwhile to pursue also ambitious aims in hydrocarbon chemistry.
ferroelectric energy harvesting is identified, optimally exploit- ing the potentials of re- and depolarization. In a real harvesting process, issues like residual stresses due to domain switching will effectively reduce the idealized efficiency as stress relief inevitably goes hand in hand with a waste of previously gained polarization. A model-based optimization, however, provides process parameters yielding best figures of merit under largely realistic conditions, and suggests a modification of the basic concept introducing two more process steps, finally generating even better harvesting efficiencies. Numerical studies further demonstrate the impact of various material parameters, sup- porting an appropriate choice of ferroelectric material for har- vesting applications. After all, exploiting the ferroelectric and elastic effects in a piezoelectric energy harvester may consid- erably improve figures of merit. The price to pay will probably be a reduced durability of the device, which has been indicated in the simulations considering induced residual stress.
yields. [60,68] To improve atom eﬃciency, they used the concept of mediator recycling in later studies. The recycling was possible in two distinct approaches. The first approach was the application of an aryl iodide containing ionic liquid (Scheme 1.3). This approach brought two advantages. The product could be separated from the mediator after the reaction by simple extraction with organic solvents. Furthermore, due to the bulkiness of the mediator, reduction of the iodine(III) was not a severe problem and thus an undivided cell could be used.  The second approach made use of polystyrene bound aryl iodides in combination with chloride as co- mediator for the fluorination of benzylcarbonothioates yielding benzyl fluorides. In this case the mediator could be recycled simply by filtration. Within 10 recycling cycles, they didn’t observe any deterioration of the mediator activity.  The last literature known example for an in-cell use of iodine(III) compounds as mediators has been reported by Hara in which they fluorinated 1,3-dicarbonyls following the procedure of Fuchigami. [70,71] Astonishingly, all other reported applications of iodine(III) as electrochemical mediator have been done in an ex-cell manner which strongly diminishes the benefits of electrochemistry.  One such example for the ex-cell use is shown in Scheme 1.4, in which an ionic iodine(III) reagent was synthesised electrochemically (using hexafluoro-iso-propanolate or trifluoroethoxylate as ligands) and subsequently reacted with imines yielding benzoxazoles. 
than measurements on the sieve tube membrane hydraulic conductivity, L 1 , as they can be obtained from combining translocation velocity and turgor pressure gradients data. The review of Milburn (1975) on pressure flow hypothesis over the experimental work done up to that time found that k/ ranged from 0.58 to 9.7210 -10 m 2 .s -1 .Pa -1 . Most of the combined studies were performed on tree species. From the fewer studies of herbaceous, Milburn (1975) pointed out the values were smaller compared with those for trees. How- ever, due to different methodologies and the limited range of species studied, that differ- ence might not be real. The anatomy and structure of sieve tubes data are well suited to being used in Hagen–Poiseuille equation. This made its application on phloem transport almost universal and convincing to a lot of authors. Its simplicity and ease of interpreta- tion also contributed. Perhaps its most powerful feature was the fact that it allows anat- omy, physiology and structural data for different plant species, i.e. sieve tube element lumen, sieve plate pore dimensions and density, together with phloem sap viscosity, as equations (2.7) and (2.14) show, to be related to measured turgor pressure gradients and velocity. In this way, Tyree, Christy & Ferrier (1974) estimated k/ to vary between 0.2
This section presents the results of numerical simulations aimed at designing a gas cell suitable for an adiabatic release scheme at FLASHForward , the beam-driven plasma ac- celerator experiment at DESY . The CFD software Open ∇ FOAM ®  was used to simulate gas flow into capillary targets designed in computer-aided design (CAD) software. Full ion- ization was assumed to translate the gas density n 0 into the plasma density n e . The results were evaluated with the help of a numerical model that probes a plasma density profile for the quality of its plasma-to-vacuum transition in terms of adiabatic release of electrons. The studies consider only matched beams as described in Sec.1.2.2, where β matched = √ 2γ/k p , with the plasma wavenumber k p as defined in Eq. (84). The beam extraction is investigated by means of an ordinary differential equation (ODE) for monoenergetic beams in an ideal system, where Eq. (92) defines the focusing parameter. This implies that the change in plasma density happens on a length scale much longer than the plasma wavelength. The single-particle equa- tion of motion is given by Eq. (93), where the focusing parameter K = K(s) depends only on the longitudinal position.