Atoms heavy

Referring to figure Bl.8.5 the radii of the tliree circles are the magnitudes of the observed structure amplitudes of a reflection from the native protein, and of the same reflection from two heavy-atom derivatives, dl and d2- We assume that we have been able to detemiine the heavy-atom positions in the derivatives and hl and h2 are the calculated heavy-atom contributions to the structure amplitudes of the derivatives. The centres of the derivative circles are at points - hl and - h2 in the complex plane, and the three circles intersect at one point, which is therefore the complex value of The phases for as many reflections as possible can then be... 

Figure Bl.8.5. Pp Pdl and Fdl are the measured stnicture amplitudes of a reflection from a native protein and from two heavy-atom derivatives. and are the heavy atom contributions. The pomt at which the tliree circles intersect is the complex value of F. ...

Heavy-atom relativistic effects influence these shifts. 

Often a degree of freedom moves very slowly for example, a heavy-atom coordinate. In that case, a plausible approach is to use a sudden approximation, i.e. fix that coordinate and do reduced dimensionality quantum-dynamics simulations on the remaining coordinates. A connnon application of this teclmique, in a three-dimensional case, is to fix the angle of approach to the target [120. 121] (see figure B3.4.14). 

Zeng Y, Biczok L and Linschitz H 1992 External heavy atom induced phosphorescence emission of fullerenes the energy of triplet Cgg J. Phys. Chem. 96 5237-9... 

These elecironic configuraiions are formal ihe orbitals in these heavy atoms are so close in energy that actual electronic configurations are very difficult to determine. 

Temperature also determines step size. An acceptable time step for room temperature simulations is about 0..5-1 fs for All Atom system s or for sim Illation s that do not con strain hydrogen atoms. For United Atom systems or systems containing only heavy atoms, you can use steps of 1-2 fs. 

You can use multiple basis sets in a single inoleeular system. I ti e Apply Basis E3et m HyperChem applies the currently selected basis set to the selected atom s or to all the atom s in IlypcrChem if th ere is no current selection. For example, some heavy atoms might have a b-1 IG basis set (s and p only) while other heavy atoms m igh t use a 6-151 CE basis set (with d-orbitals). Th is is an iiii usual but flexible option for ah miiro calculalioiis. 

For XH bonds, where X isany heavy atom, the hydrogen electron den sity is ri ot th ough t to be cen tered at th e position of th e hydrogen n ueleus but displaced alon g th e bon d sorn ewhat, towards X. The MM+ force field reduces the XH bond length by a factor of 0.9 I 5 strictly for th e purposes of calculatin g van der Waals in teraction s with hydrogen atoms. 

Unlike semiempirical methods that are formulated to completely neglect the core electrons, ah initio methods must represent all the electrons in some manner. However, for heavy atoms it is desirable to reduce the amount of computation necessary. This is done by replacing the core electrons and their basis functions in the wave function by a potential term in the Hamiltonian. These are called core potentials, elfective core potentials (ECP), or relativistic effective core potentials (RECP). Core potentials must be used along with a valence basis set that was created to accompany them. As well as reducing the computation time, core potentials can include the effects of the relativistic mass defect and spin coupling terms that are significant near the nuclei of heavy atoms. This is often the method of choice for heavy atoms, Rb and up. 

Correlated and relativistic quantum mechanical calculations give the highest possible accuracy and are necessary for heavy atoms or correlation-sensitive systems. 

The Schrodinger equation is a nonreiativistic description of atoms and molecules. Strictly speaking, relativistic effects must be included in order to obtain completely accurate results for any ah initio calculation. In practice, relativistic effects are negligible for many systems, particularly those with light elements. It is necessary to include relativistic effects to correctly describe the behavior of very heavy elements. With increases in computer capability and algorithm efficiency, it will become easier to perform heavy atom calculations and thus an understanding of relativistic corrections is necessary. 

The use of RECP s is often the method of choice for computations on heavy atoms. There are several reasons for this The core potential replaces a large number of electrons, thus making the calculation run faster. It is the least computation-intensive way to include relativistic effects in ah initio calculations. Furthermore, there are few semiempirical or molecular mechanics methods that are reliable for heavy atoms. Core potentials were discussed further in Chapter 10. 

Calculations at the 6-31G and 6-31G level provide, in many cases, quantitative results considerably superior to those at the lower STO-3G and 3-21G levels. Even these basis sets, however, have deficiencies that can only be remedied by going to triple zeta (6-31IG basis sets in HyperChem) or quadruple zeta, adding more than one set of polarization functions, adding f-type functions to heavy atoms and d-type functions to hydrogen, improving the basis function descriptions of inner shell electrons, etc. As technology improves, it will be possible to use more and more accurate basis sets. 

Because of fhe presence of heavy atoms in many inorganic molecules fhere may be several low-wavenumber vibrations. For tins reason if is generally more importanf fhan for organic molecules fo obfain fhe far-infrared or Raman spectrum. 

Geometric properties are quite sensitive to the basis set chosen, including the presence or absence of polarization functions (additional s and -type functions on H and on heavy atoms). 

The foHowing conclusions apply to organic molecules of about 25 heavy atoms (- 60 atoms total), assuming use of medium-size basis sets (3—2IG ) ... 

Hydrogen bond geometries may be reproduced or predicted fairly weH with reasonable, but sometimes underestimated heavy atom—heavy atom distances radial dependence of the hydrogen bond may be in error. 

In addition to the processes that can compete with fluorescence within the molecule itself, external actions can rob the molecule of excitation energy. Such an action or process is referred to as quenching. Quenching of fluorescence can occur because the dye system is too warm, which is a very common phenomenon. Solvents, particularly those that contain heavy atoms such as bromine or groups that ate detrimental to fluorescence in a dye molecule, eg, the nitro group, ate often capable of quenching fluorescence as ate nonfluorescent dye molecules. 

The aim of this work is the development of pyrene determination in gasoline and contaminated soils. For this purpose we used room temperature phosphorescence (RTP) in micellar solutions of sodium dodecylsulphate (SDS). For pyrene extraction from contaminated soils hexane was used. Then exttacts earned in glass and dried. After that remains was dissolved in SDS solution in the presence of sodium sulphite as deoxygenation agent and thallium (I) nitrate as heavy atom . For pyrene RTP excitation 337 nm wavelength was used. To check the accuracy of the procedures proposed for pyrene determining by RTP, the pyrene concentrations in the same gasoline samples were also measured by GC-MS. 

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