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Permeation of Organometallic Compounds through Phospholipid Membranes

von Dr. Raycho Yonchev

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[1.] Ry/Fragment 040 01 - Diskussion
Zuletzt bearbeitet: 2016-04-01 20:47:01 WiseWoman
Accelrys Inc. - Forcefield-Based Simulations 1998, BauernOpfer, Fragment, Gesichtet, Ry, SMWFragment, Schutzlevel sysop

Typus
BauernOpfer
Bearbeiter
Klgn
Gesichtet
Yes.png
Untersuchte Arbeit:
Seite: 40, Zeilen: 1 ff. (entire page)
Quelle: Accelrys Inc. - Forcefield-Based Simulations 1998
Seite(n): 54, 55, 36,, Zeilen: 54:16ff; 55:1ff; 36: 21ff
Ry 40 diss Eq.png

The first three terms in Equation (2.6) handle the internal coordinates of bonds, angles, and dihedrals. Term 3 is also used to maintain the correct chirality and tetrahedral nature of sp3 centers in the united-atom representation. In the united-atom representation, nonpolar hydrogen atoms are not represented explicitly, but are coalesced into the description of the heavy atoms to which they are bonded. Terms 4 and 5 account for the van der Waals and electrostatic interactions. The final term, 6, is an optional hydrogen- bond term that augments the electrostatic description of the hydrogen bond. This term adds only about 0.5 kcal.mol-1 to the hydrogen-bond energy in AMBER, so the bulk of the hydrogen-bond energy still arises from the dipole-dipole interaction of the donor and acceptor groups.

The atom types in AMBER are quite specific to amino acids and DNA bases. In the original publications, the atom types and charges are defined by means of diagrams of the amino acids and nucleotide bases.

Extensible Systematic Force Field (ESFF)

ESFF [50] was derived using a mixture of Density Functional Theory (DFT) calculations on dressed atoms to obtain polarizabilities, gas-phase and crystal structures, etc. The training set included primarily organic and organometallic compounds and a few inorganic compounds. The focus was on crystal structures and sublimation energies. The training set included models containing each element in the first 6 periods up to lead (Z = 82) (except for the inert gases), Sr, Y, Tc, La, and the lanthanides (except for Yb).

Parameters and charges are generated on the fly, based on the model configuration, the local environment, and the derived rules.


50. BIOSYM/MSI. InsightII, Release 95.0: Discover Program, versions 2.9.7 & 95.0/3.00; San Diego: Biosym/MSI, 1995.

[page 54]

Ry 40 source Eq.png

The first three terms in Eq. 19 handle the internal coordinates of bonds, angles, and dihedrals. Term 3 is also used to maintain the correct chirality and tetrahedral nature of sp3 centers in the united-atom representation. (In the united-atom representation, nonpolar hydrogen atoms are not represented explicitly, but are coalesced into the description of the heavy atoms to which they are bonded.) Terms 4 and 5 account for the van der Waals and electrostatic interactions.

The final term, 6, is an optional hydrogen-bond term that augments the electrostatic description of the hydrogen bond. This term adds only about 0.5 kcal mol-1 to the hydrogen-bond energy in AMBER, so the bulk of the hydrogen-bond energy still arises

[page 55]

from the dipole–dipole interaction of the donor and acceptor groups.

The atom types in AMBER are quite specific to amino acids and DNA bases. In the original publications, the atom types and charges are defined by means of diagrams of the amino acids and nucleotide bases.

[page 36]

ESFF, extensible systematic forcefield

Derivation

ESFF was derived using a mixture of DFT calculations on dressed atoms to obtain polarizabilities, gas-phase and crystal structures, etc. The training set included primarily organic and organometallic compounds and a few inorganic compounds. The focus was on crystal structures and sublimation energies. The training set included models containing each element in the first 6 periods up to lead (Z = 82) (except for the inert gases), Sr, Y, Tc, La, and the lanthinides (except for Yb).

Parameters and charges are generated on-the-fly, based on the model configuration, the local environment, and the derived rules.

Anmerkungen

A source is given, but it is not clear that the formulas and text are identical to the Accelrys-Documentation that was published three years later than the source given.

Sichter
(Klgn), WiseWoman


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