Computational Chemistry

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Chapter 3 Molecular Mechanics We don’t give a damn where the electrons are. Words to the author, from the president of a well-kn ...

and angles imposed by the manufacturer, and in the case of space-filling models atoms cannot be forced too closely together. The ...

follows easily from the number of unpaired electrons). An oxygen nucleus and two protons with the rightx, y, zcoordinates, enoug ...

the most widely-used method for computing the geometries and energies of large biological molecules like proteins and nucleic ac ...

The Bond Stretching Term The increase in the energy of a spring (remember that we are modelling the molecule as a collection of ...

The Nonbonded Interactions Term This represents the change in potential energy with distance apart of atoms A and B that are not ...

The potential energy curve for two nonpolar nonbonded atoms has the general form shown in Fig.3.6. A simple way to approximate t ...

and so s¼ 2 $^1 =^6 ðRAþRBÞ¼ 0 : 89 ðRAþRBÞ (3.7) Thusscan be calculated fromrminor estimated from the van der Waals radii. Sett ...

we might have chosen to approximateEstretchby the sum of a quadratic and a cubic term: Estretch¼kstretchðl$leqÞ^2 þkðl$leqÞ^3 Th ...

of ethane with stretching of the C/C bond, as calculated by the ab initio STO-3G method. The equilibrium bond length has been ta ...

Calculations on staggered butane gave for the C–C–C angle aeqðCCCÞ¼ 112 : 5  (3.16) kbendðCCCÞ¼ 0 :110 KJ mol$^1 deg$^2 (3.17) ...

and s¼ 3 : 85 Å (3.20) Summary of the Parameterization of the Forcefield Terms The four terms of Eq.3.1were parameterized to giv ...

(twistingporbitals out of alignment reduces their overlap) by performing a simple PPP molecular orbital calculation (Chapter 6 ) ...

For structure 1 X bonds EstretchðC$CÞ¼ 7 ) 1 ; 735 ð 1 : 538 $ 1 : 538 Þ^2 ¼ 0 Bond stretch contribution cf:structure withleq¼ 1 ...

P nonbond Enonbondðanti$CH 3 =CH 3 Þþ P nonbond Enonbondðgauche$CH 3 =CH 3 Þ ¼ 3 ) 4 : 7 3 : 85 3 : 931  12 $ 3 : 85 3 : 931 " ...

Etotal¼EstretchþEbendþEtorsion¼ 6 : 67 þ 0 þ 21 : 0 þ250 kJ mol$^1 ¼277 kJ mol$^1 So the relative energies are calculated to be ...

3.3.1 To Obtain Reasonable Input Geometries for Lengthier (Ab Initio, Semiempirical or Density Functional) Kinds of Calculations ...

RX, and a ketone, thesp^2 carbon of which corresponds to the incipient cationic carbon of the transition state. One may wish a m ...

believed (e.g. from quantum mechanical calculations on simple systems, or from chemical intuition) to approximate those in the t ...