ch3717

Question 1

force field

Answer 1

functional form and parameters set to describe the potential energy of a molecular system

Question 2

Ep of system

Answer 2

energy of a system is considered to have due to the positions of its components in space

Question 3

simple force field

Answer 3

bond stretching
angle bending
torsion
electrostatic
van der Waals

Question 4

bonded terms

Answer 4

bond stretching
angle bending
torsions

Question 5

non-bonded terms

Answer 5

electrostatic interactions

van der Waals

Question 6

electrostatic interactions

Answer 6

non-uniform charge distribution in a molecule, represented by fractional point charges

Question 7

van der waals

Answer 7

attraction due to dispersion
repulsion due to exchange replusion
Lennard-jones potential

Question 8

Lennard-jones potential

Answer 8

sigma - where passes through 0 on x
e - well depth
equilibrium distance when = minimum

Question 9

deficiencies in point charge model

Answer 9

lack of polarisability as charges not affected by the local electrostatic environment

Question 10

polarizability

Answer 10

modification in the charge distribution in an atom due to an applied electric field

Question 11

water models

Answer 11

set parameters used fro models water or aqueous soltions

Question 12

water molecules rigid

Answer 12

fixed bond length, angle and torsion

only account for non-bonded interactions

Question 13

3-site. model

Answer 13

charges on atom

Question 14

4-site model

Answer 14

charges on atom and one charge away from o

Question 15

5-site model

Answer 15

2 lone pairs with. charge

Question 16

6-site model

Answer 16

2 lon e pairs and charge away from o

Question 17

more accurate models of water

Answer 17

intramolecular flexibly

including polarizability

Question 18

potential energy surface

Answer 18

energy of the molecular system as a function of the nuclear coordinates

Question 19

potential energy surface

Answer 19

maxima - eclipsed
minima - staggered
transition state

Question 20

energy minimisatuon

Answer 20

minimum energy ofd a paerticujkar molecule

calculate energy at particular bond length, change bond length and measure new energy

Question 21

molecular dynamics

Answer 21

form of computer simulation where the atoms and molecules are allowed tov interact with eachothetr for a period of time

Question 22

phase space

Answer 22

define the state of a molecular system containing N atoms, 6N values are required 3 coordinates x,y,z and 3 momentum components px,py,pz per atom

Question 23

calculate tranjectory

Answer 23

have energy function
differentiate -dv/dx = force
newtons 2nd law to give a = f / m
integration of equations of motion give v and x
gives trajectory describing how x,v,a of particle vary with time

Question 24

particles experience a constant force

Answer 24

charged partible through uniform electric field

force on particle is not constant

Question 25

running an md simulation

Answer 25

``` establish initial configuration of system assign initial velocities calculated the force on each atom and new positions of atoms equilibrium phase production phase ```

Question 26

md used to

Answer 26

stimulate a reaction | calculate thermodynamic properties

Question 27

ensemble

Answer 27

collection of points in phase space, a collection of the mictrostates in the trajectory

Question 28

calculate thermodynamic properties

Answer 28

statistical mechanics | macroscopic property calculated as an average over a corresponding microscopic property

Question 29

microanonical ensemble

Answer 29

thermally isolated system - constant E, N, volume

Question 30

canonical ensemble

Answer 30

system exchanges energy with heat bath. temp constant, n and volume

Question 31

lead compound

Answer 31

molecule with pharmacological or biological activity can be used as a starting point for chemical. modicifaqtion to enhance its potency and selectivity

Question 32

agonist

Answer 32

enhance or normal activity as natural substrate

Question 33

antagonist

Answer 33

inhibits the effect of natural ligand

Question 34

inverse agonist

Answer 34

creates opposite of natural ligand

Question 35

drug activity

Answer 35

molecular binding of one molecule to the pocket (binding site) of anothwe

Question 36

docking

Answer 36

predict structure and stability of complex, formed by 2 interacting molecules ligand and protein

Question 37

search alogorithm

Answer 37

generation of plausible strujcutres

Question 38

scoring function

Answer 38

how strong it binds | calculate likelihood that the pose represents a favourable binding interaqction

Question 39

a good scoring function is

Answer 39

selective - distinguish between correct t and incorrect structures efficient - fast

Question 40

search algorithms

Answer 40

protein and ligand rigid bodies (6 degrees of freedom) ligand flexible both flexible

Question 41

QSAR

Answer 41

quantitive structural activity analysis | method that relates numerical properties of a drug molecule to its biological acitivty

Question 42

receptor flexability

Answer 42

bond lengths/angles do not affect there shape of molecule much - torsions

Question 43

qsar

Answer 43

v = f (p)

Question 44

pharmacophores

Answer 44

set of structural featured that is common to a series of active molecules, recognised by receptors and are responsible for drug activity

Question 45

pharmacophores - structural featrurws

Answer 45

h bond donors and acceptors, charged groups, aromaticity, hydrophobic groups

Question 46

3d pharmacophore

Answer 46

includes spatial relationship between pharmacophoric groups. relationships expressed as distances, torsio ns and angles

Question 47

pharmacophoric mapping

Answer 47

can determine 3d pharmacophoerws for a series of comppununs | assumes all active compounds bind in similar way

Question 48

de novo ligand design

Answer 48

design of new molecules