Ambers

In addition to shellac a number of other natural resins find use in modem industry. They include rosins, copals, kauri gum and pontianak. Such materials are either gums or very brittle solids and, although suitable as ingredients in surface coating formulations and a miscellany of other uses, are of no value in the massive form, i.e. as plastics in the most common sense of the word. 

One resin, however, can be considered as an exception to this. Although rarely recognised as a plastics material it can be fabricated into pipe mouthpieces, cigarette holders and various forms of jewellery. It may also be compression moulded and extraded. It is the fossil resin amber. 

Amber is of both historical and etymological interest as its property of attracting dust was known over 2000 years ago. From the Greek word for amber, elektron, has come the word electricity. Pliny in his works makes an interesting and informative dissertation on the occurrence and properties of amber. 

TABLE 20. Heats of formation and standard deviation (SD) (kcalmol-1) for enamines and aniline derivatives as calculated by the MM2 and MM3 force fields and observed by experiment44. Reproduced by permission of John Wiley Sons, Inc. from Ref. 44 

In the following equations, all parameters have their usual meanings unless otherwise noted. 

No specific parameterization of AMBER for amino, nitro or nitroso compounds has been published. However, several calculations with this force field are found in the literature and are discussed in Section II.D and in Section m of this chapter. 

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H02C(CH2)2C02H. Colourless prisms m.p. 182 C, b.p. 235°C. Occurs in amber, algae, lichens, sugar cane, beets and other plants, and is formed during the fermentation of sugar, tartrates, malates and other substances by a variety of yeasts, moulds and bacteria. Manufactured by the catalytic reduction of maleic acid or by heating 1,2-dicyanoethane with acids or alkalis. Forms an anhydride when heated at 235°C. Forms both acid and neutral salts and esters. Used in the manufacture of succinic anhydride and of polyesters with polyols. 

Electro - From Elektron a Greek word for amber. When amber was rubbed on cloth it attracted fluff. 

Uppar Spark Cti amber Chamber PhatQinultiplier Tebes... 

The Amber program of Professor Peter Kollman, University of California, San Francisco webpage... 

Fig. 1. The time evolution (top) and average cumulative difference (bottom) associated with the central dihedral angle of butane r (defined by the four carbon atoms), for trajectories differing initially in 10 , 10 , and 10 Angstoms of the Cartesian coordinates from a reference trajectory. The leap-frog/Verlet scheme at the timestep At = 1 fs is used in all cases, with an all-atom model comprised of bond-stretch, bond-angle, dihedral-angle, van der Waals, and electrostatic components, a.s specified by the AMBER force field within the INSIGHT/Discover program.

In this case, only two parameters (k and Iq) per atom pair are needed, and the computation of a quadratic function is less expensive. Therefore, this type of expression is used especially by biomolecular force fields (AMBER, CHARMM, GROMOS) dealing with large molecules like proteins, lipids, or DNA. 

It is noteworthy that it is not obligatory to use a torsional potential within a PEF. Depending on the parameterization, it is also possible to represent the torsional barrier by non-bonding interactions between the atoms separated by three bonds. In fact, torsional potentials and non-bonding 1,4-interactions are in a close relationship. This is one reason why force fields like AMBER downscale the 1,4-non-bonded Coulomb and van der Waals interactions. 

N is the number of point charges within the molecule and Sq is the dielectric permittivity of the vacuum. This form is used especially in force fields like AMBER and CHARMM for proteins. As already mentioned, Coulombic 1,4-non-bonded interactions interfere with 1,4-torsional potentials and are therefore scaled (e.g., by 1 1.2 in AMBER). Please be aware that Coulombic interactions, unlike the bonded contributions to the PEF presented above, are not limited to a single molecule. If the system under consideration contains more than one molecule (like a peptide in a box of water), non-bonded interactions have to be calculated between the molecules, too. This principle also holds for the non-bonded van der Waals interactions, which are discussed in Section 7.2.3.6. 

Modifications of the various versions of the AMBER parameter sets are implemented in numerous commercial and academic software packages. They are often referred to as AMBER. In every case, the user should read the documentation provided critically, and check the implementation by comparing the results of the implementation with original data. 

Molecular dynamics simulation package with various force field implementations, special support for AMBER. Parallel version and Xll trajectory viewer available. http //ganter.chemie.uni-dortmund.de/MOSCITO/... 

United Atom force fieldsare used often for biological polymers. In th esc m oleciiles, a reduced ii nm ber of explicit h ydrogen s can have a notable effect on the speed of the calculation. Both the BlOn and OPLS force fields are United Atom force fields. AMBER con tain s both aU nited and an All Atom force field. 

Caution If you arc new Lo com pn taLion al chemisLry. do not use Unilcd ALoms for AMBER calciilalions. This TlypcrCh cm oplion is available for researchers who warn lo alter aiom types aiul parameters for this force field. 

TlypcrC hcm oilers four molecular mechanics force fields MM+, AMBER, BIO+, and OPES (sec References on page 106). To run a molecular mechanics calciilaLion. yon miisi lirsi choose a force Eeld. The following sections discuss considerations in choosing a force field. 

The force field ec uations for M.Vf+, AMBER, BlOg and OPES are similar in the types of terms they contain bond, angle, dihedral, van der Waals. and electrostatic. There are som e differences m the form s of the etinations that can al fect your ch oice of force field. 

Wofe." rh c BIO + force field is an im plern en lation oflheCH. ARMM (Chcmistry at H.ARvard MacromoIceular Mechanics ) force field developed in the group of Martin Karplusat Harvard University, l.ike. AMBER and OP1.S, it is primarily designed to explore rnacro-moleciilcs. 

Lsc th e force fields th at have dern on strated accuracy for particu lar molecules or simulations. For example, CiPLS reproduces physical properties in liquid simulations extremely well. MM+ reproduces the structure and thermodynamic properties of small, nonpolar molecules better than AMBER, BIO+, and OPLS. 

Also use constant dielectric Tor MM+aiul OPLS ciilciilatimis. Use the (lislance-flepeiident dielecinc for AMBER and BlO+to mimic the screening effects of solvation when no explicit solvent molecules are present. The scale factor for the dielectric permittivity, n. can vary from 1 to H(l. IlyperChem sets tt to 1. .5 for MM-r. Use 1.0 for AMBER and OPLS. and 1.0-2..5 for BlO-r. 

AMBER. BlO-t-. and OPLS calciilations use information on atomic charges. Atomic charges can come from these sources ... 

Hach molecular mechanics method has its own functional form MM+. AMBER, OPL.S, and BIO+. The functional form describes the an alytic form of each of th e term s in th e poteri tial. For exam pie, MM+h as both a quadratic and a cubic stretch term in th e poten tial whereas AMBER, OPES, and BIO+ have only c nadratic stretch term s, I h e functional form is referred to here as the force field. For exam pie, th e fun ction al form of a qu adratic stretch with force constant K, and equilibrium distance i q is ... 

Finally, each force field may have multiple parameter sets (the val-uesolT oand K. for example). Th e AMBER force field and AMBER set ol types may be used with, for example, the AMBER/2 or AMDER/3 set of param eters. 

The chemical environment foran atom m a molecule is probably niiit iie to th at molecule. Chem istry tries to find unify in g concepts an d the atom type Is on e of those unifying con cepts. For example, the AMBER force field defines five atom types for oxygens ... 

In principle, atom types eoiild be assoeiated wilh a partieiilar parameter set rather than the functional form or force field. In HyperChern, however, atoms types are rigorously lied to a force field . M.M-t, AMBER, OPTS, and BIO+. Each of the force fields has a... 

Xote that two dilTcren t environni cn is. although they migh t be dis-liiignisbcd by tests (such as for ether and ester) can share an atom type (such as OS), A rel inem en i of th e AMBER force field would use separate types for these two along with differen t parani eters for th e differen L types. 

This section descrihes IlyperChem s four force fields, MM-h AMBER, OPES, and BlO-h providing auxiliary information for all force field calculations. 

The AMBER (Assisted Model Building and Energy Refin emeni) is based on a force field developed for protein and nucleic acid computations by members of the Peter Kollman research group at the... 

The fiinctioiial form for electrostatic in teraction s m AMBER is identical with that shown in equation (2fi) on page 179. You normally use a dielectric scaling of D=1 with AMBER com bin ed with a constant functional form when solvent molecules are explicitly... 

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