1) Molekul aspirin/asetil salisilat (C9H8O4)

Compute properties

Stretch :0.8943

Bend : 21.7533

Stretch-Bend :0.1600

Torsion :-7.7430

Non-1,4 VDW :2.2354

1,4 VDW :6.5155

Dipole/Dipole :6.4368

Total : 30.2522

The steric energy for frame 1: 30.252 kcal/mole

25 cartesian coordinates

Atom X Y ZC(1) 0.48 -0.386 -0.019C(2) 0.625 -1.781 -0.038C(3) 1.87 -2.418 -0.04C(4) 3.039 -1.664 -0.03C(5) 2.94 -0.274 -0.02C(6) 1.687 0.356 -0.015C(7) 1.66 1.849 -0.006O(8) 2.71 2.482 -0.006O(9) 0.524 2.581 0.001O(11) -0.711 0.295 -0.014C(12) -1.941 -0.287 0.028O(13) -2.199 -1.467 0.082C(14) -3.006 0.794 0.009H(21) -0.239 -2.458 -0.056H(20) 1.93 -3.518 -0.053H(19) 4.024 -2.159 -0.034H(18) 3.875 0.31 -0.017H(10) 0.781 3.518 0.003H(15) -4.024 0.341 0.016H(16) -2.914 1.42 -0.907H(17) -2.912 1.445 0.907Lp(22) -0.703 0.716 -0.442Lp(23) -0.686 0.74 0.389Lp(24) 0.209 2.459 0.497Lp(25) 0.206 2.462 -0.494

21 internal coordinates

Atom Bond Atom

Bond Length

Angle atom

first angle

third atom

second angle Angle type

C(1) ― ― ― ― ― ― ―C(2) C(1) 1.403 ― ― ― ― ―C(6) C(1) 1.417 C(2) 115.668 ― ― ―C(3) C(2) 1.399 C(1) 123.006 C(6) 0.608 DihedralC(5) C(6) 1.403 C(1) 121.725 C(2) -0.466 Dihedral

O(11) C(1) 1.372 C(2) 125.712 C(6) 118.618 Pro-SC(4) C(3) 1.391 C(2) 120.116 C(1) -0.345 DihedralC(7) C(6) 1.493 C(1) 120.574 C(5) 117.701 Pro-RC(12) O(11) 1.362 C(1) 124.872 C(2) 2.814 DihedralH(21) C(2) 1.098 C(1) 122.147 C(3) 114.847 Pro-RO(9) C(7) 1.352 C(6) 123.829 C(1) 0.07 DihedralC(14) C(12) 1.518 O(11) 109.212 C(1) -179.618 DihedralH(20) C(3) 1.103 C(2) 120.2 C(4) 119.684 Pro-RH(19) C(4) 1.102 C(3) 120.518 C(5) 120.731 Pro-RH(18) C(5) 1.102 C(4) 117.912 C(6) 121.356 Pro-RLp(22) O(11) 0.6 C(1) 109.5 C(12) 109.5 Pro-RLp(23) O(11) 0.6 C(1) 109.5 C(12) 109.5 Pro-SO(8) C(7) 1.227 C(6) 120.025 O(9) 116.146 Pro-RO(13) C(12) 1.209 O(11) 127.71 C(14) 123.076 Pro-RH(10) O(9) 0.972 C(7) 107.455 C(6) -179.818 DihedralH(15) C(14) 1.114 C(12) 110.612 O(11) 178.553 DihedralH(16) C(14) 1.114 C(12) 110.62 H(15) 108.043 Pro-RH(17) C(14) 1.114 C(12) 110.333 H(15) 108.043 Pro-SLp(24) O(9) 0.6 C(7) 109.5 H(10) 109.5 Pro-RLp(25) O(9) 0.6 C(7) 109.5 H(10) 109.5 Pro-S

2) Molekul asam palmitat / asam heksadekanoat ((CH3(CH2)14COOH)

Compute properties

Adding lone pairs to O O(17)

Note: Some parameters are not finalized (Quality = 3).

Stretch : 0.0000

Bend :8.1253

Stretch-Bend : -0.0000

Torsion : -1.5816

Non-1,4 VDW: -2.0468

1,4 VDW : 9.6872

Dipole/Dipole : 1.7836

Total : 25.9677

The steric energy for frame 1: 25.968 kcal/mole

52 cartesian coordinates

Atom X Y ZC(1) -9.807 0.332 0C(2) -8.495 1.105 0C(3) -7.328 0.126 0C(4) -6.016 0.899 0C(5) -4.849 -0.08 0C(6) -3.537 0.693 0C(7) -2.37 -0.286 0C(8) -1.058 0.487 0C(9) 0.109 -0.492 0C(10) 1.421 0.281 0C(11) 2.588 -0.698 0C(12) 3.9 0.075 0C(13) 5.067 -0.904 0C(14) 6.379 -0.131 0C(15) 7.546 -1.11 0C(16) 8.852 -0.356 0O(17) 9.833 -1.266 0O(19) 8.98 0.722 0.531H(20) -10.666 1.04 0H(21) -9.869 -0.313 0.905H(22) -9.869 -0.313 -0.905H(23) -8.442 1.743 0.91H(24) -8.442 1.743 -0.91H(25) -7.381 -0.513 -0.91H(26) -7.381 -0.513 0.91H(27) -5.963 1.537 0.91

H(28) -5.963 1.537 -0.91H(29) -4.902 -0.719 -0.91H(30) -4.902 -0.719 0.91H(31) -3.484 1.331 0.91H(32) -3.484 1.331 -0.91H(33) -2.423 -0.925 -0.91H(34) -2.423 -0.925 0.91H(35) -1.005 1.125 0.91H(36) -1.005 1.125 -0.91H(37) 0.056 -1.131 -0.91H(38) 0.056 -1.131 0.91H(39) 1.474 0.919 0.91H(40) 1.474 0.919 -0.91H(41) 2.535 -1.337 -0.91H(42) 2.535 -1.337 0.91H(43) 3.953 0.713 0.91H(44) 3.953 0.713 -0.91H(45) 5.014 -1.543 -0.91H(46) 5.014 -1.543 0.91H(47) 6.432 0.508 0.91H(48) 6.432 0.508 -0.91H(49) 7.497 -1.743 -0.914H(50) 7.497 -1.743 0.914H(18) 10.666 -0.766 0Lp(51) 9.798 -1.598 -0.499Lp(52) 9.798 -1.598 0.499

51 internal coordinates

Atom Bond Atom

Bond Length

Angle atom

first angle

third atom

second angle

Angle type

C(16) ― ― ― ― ― ― ―C(15) C(16) 1.509 ― ― ― ― ―C(14) C(15) 1.523 C(16) 110   ― ―C(13) C(14) 1.523 C(15) 109.5 C(16) 180 DihedralC(12) C(13) 1.523 C(14) 109.5 C(15) 180 DihedralC(11) C(12) 1.523 C(13) 109.5 C(14) 180 DihedralC(10) C(11) 1.523 C(12) 109.5 C(13) 180 DihedralC(9) C(10) 1.523 C(11) 109.5 C(12) 180 DihedralC(8) C(9) 1.523 C(10) 109.5 C(11) 180 DihedralC(7) C(8) 1.523 C(9) 109.5 C(10) 180 DihedralC(6) C(7) 1.523 C(8) 109.5 C(9) 180 DihedralC(5) C(6) 1.523 C(7) 109.5 C(8) 180 DihedralC(4) C(5) 1.523 C(6) 109.5 C(7) 180 DihedralC(3) C(4) 1.523 C(5) 109.5 C(6) 180 DihedralC(2) C(3) 1.523 C(4) 109.5 C(5) 180 DihedralC(1) C(2) 1.523 C(3) 109.5 C(4) 180 Dihedral

O(17) C(16) 1.338 C(15) 107.1 C(14) 180 DihedralO(19) C(16) 1.208 C(15) 122.5 O(17) 122 Pro-RH(18) O(17) 0.972 C(16) 106.1 C(15) 180 DihedralH(20) C(1) 1.113 C(2) 110 C(3) 180 DihedralH(21) C(1) 1.113 C(2) 110 H(20) 109 Pro-RH(22) C(1) 1.113 C(2) 110 H(20) 109 Pro-SH(23) C(2) 1.113 C(1) 109.41 C(3) 109.41 Pro-RH(24) C(2) 1.113 C(1) 109.41 C(3) 109.41 Pro-SH(25) C(3) 1.113 C(2) 109.41 C(4) 109.41 Pro-RH(26) C(3) 1.113 C(2) 109.41 C(4) 109.41 Pro-SH(27) C(4) 1.113 C(3) 109.41 C(5) 109.41 Pro-RH(28) C(4) 1.113 C(3) 109.41 C(5) 109.41 Pro-SH(29) C(5) 1.113 C(4) 109.41 C(6) 109.41 Pro-RH(30) C(5) 1.113 C(4) 109.41 C(6) 109.41 Pro-SH(31) C(6) 1.113 C(5) 109.41 C(7) 109.41 Pro-RH(32) C(6) 1.113 C(5) 109.41 C(7) 109.41 Pro-SH(33) C(7) 1.113 C(6) 109.41 C(8) 109.41 Pro-RH(34) C(7) 1.113 C(6) 109.41 C(8) 109.41 Pro-SH(35) C(8) 1.113 C(7) 109.41 C(9) 109.41 Pro-RH(36) C(8) 1.113 C(7) 109.41 C(9) 109.41 Pro-SH(37) C(9) 1.113 C(8) 109.41 C(10) 109.41 Pro-R

H(38) C(9) 1.113 C(8) 109.41 C(10) 109.41 Pro-SH(39) C(10) 1.113 C(9) 109.41 C(11) 109.41 Pro-RH(40) C(10) 1.113 C(9) 109.41 C(11) 109.41 Pro-SH(41) C(11) 1.113 C(10) 109.41 C(12) 109.41 Pro-RH(42) C(11) 1.113 C(10) 109.41 C(12) 109.41 Pro-SH(43) C(12) 1.113 C(11) 109.41 C(13) 109.41 Pro-RH(44) C(12) 1.113 C(11) 109.41 C(13) 109.41 Pro-SH(45) C(13) 1.113 C(12) 109.41 C(14) 109.41 Pro-RH(46) C(13) 1.113 C(12) 109.41 C(14) 109.41 Pro-SH(47) C(14) 1.113 C(13) 109.41 C(15) 109.41 Pro-RH(48) C(14) 1.113 C(13) 109.41 C(15) 109.41 Pro-SH(49) C(15) 1.113 C(14) 109.41 C(16) 108.8 Pro-RH(50) C(15) 1.113 C(14) 109.41 C(16) 108.8 Pro-S

3) Molekul asam amino arginin (C6H14N4O2)

Compute propertiesAdding lone pairs to N N(5)Adding lone pairs to N N(24)Adding lone pairs to O O(21)Pi System : 1 5 4 7Warning : Some parameters are guessed (Quality = 1).Stretch : 2.6331 Bend : 6.2556 Stretch-Bend :0.0491 Torsion :12.3694 Non-1,4 VDW :6.5212 1,4 VDW :7.7286 Dipole/Dipole :-2.6431 Total :32.9139 The steric energy for frame 1: 32.914 kcal/mole

30 cartesian coordinate

Atom X Y ZN(1) -4.827 -1.241 0.571C(4) -3.644 -0.382 0.571N(5) -3.644 0.878 0.571N(7) -2.309 -0.976 0.559C(9) -1.24 0.032 0.561C(12) 0.13 -0.634 0.549C(15) 1.215 0.435 0.551C(18) 2.585 -0.231 0.538C(20) 3.667 0.821 0.54O(21) 4.87 0.236 0.529O(23) 3.481 2.014 0.562N(24) 2.687 -1.08 -0.655H(2) -4.981 -1.916 -0.218H(3) -5.521 -1.172 1.356H(6) -2.684 1.228 0.571H(8) -2.151 -2.014 0.541H(10) -1.349 0.635 1.491H(11) -1.36 0.649 -0.358H(13) 0.229 -1.259 -0.367H(14) 0.239 -1.273 1.453H(16) 1.116 1.061 1.466H(17) 1.106 1.075 -0.354H(19) 2.705 -0.847 1.457H(22) 5.521 0.958 0.531H(25) 3.601 -1.531 -0.674H(26) 2.674 -0.495 -1.491Lp(27) -4.073 1.178 0.865Lp(28) 2.257 -1.498 -0.64Lp(29) 4.931 -0.087 0.027Lp(30) 4.937 -0.095 1.025

30 internal coordinates

Atom Bond Atom

Bond Length

Angle atom

first angle

third atom

second angle

Angle type

C(4) ― ― ― ― ― ― ―N(5) C(4) 1.26 ― ― ― ― ―N(1) C(4) 1.462 N(5) 126 ― ― ―N(7) C(4) 1.462 N(1) 119.999 N(5) 113.999 Pro-RH(2) N(1) 1.05 C(4) 119.733 N(5) 120 DihedralH(6) N(5) 1.022 C(4) 110 N(1) 180 DihedralC(9) N(7) 1.47 C(4) 112.667 N(1) 180 DihedralH(3) N(1) 1.05 C(4) 119.732 H(2) 120.532 Pro-R

Lp(27) N(5) 0.6 C(4) 120 H(6) 120 Pro-RC(12) C(9) 1.523 N(7) 110.74 C(4) 180 DihedralH(8) N(7) 1.05 C(4) 122.665 C(9) 124.665 Pro-RC(15) C(12) 1.523 C(9) 109.5 N(7) 180 DihedralH(10) C(9) 1.113 N(7) 107.5 C(12) 109.41 Pro-RH(11) C(9) 1.113 N(7) 107.5 C(12) 109.41 Pro-SC(18) C(15) 1.523 C(12) 109.5 C(9) 180 DihedralH(13) C(12) 1.113 C(9) 109.41 C(15) 109.41 Pro-RH(14) C(12) 1.113 C(9) 109.41 C(15) 109.41 Pro-SC(20) C(18) 1.509 C(15) 109.9 C(12) 180 DihedralH(16) C(15) 1.113 C(12) 109.41 C(18) 109.41 Pro-RH(17) C(15) 1.113 C(12) 109.41 C(18) 109.41 Pro-SO(21) C(20) 1.338 C(18) 109.9 C(15) 180 DihedralN(24) C(18) 1.468 C(15) 108.8 C(20) 110.74 Pro-RH(19) C(18) 1.113 C(15) 109.39 C(20) 107.9 Pro-SO(23) C(20) 1.208 C(18) 125.298 O(21) 124.798 Pro-RH(22) O(21) 0.972 C(20) 106.1 C(18) 180 DihedralH(25) N(24) 1.02 C(18) 109.47 C(15) 180 DihedralH(26) N(24) 1.02 C(18) 109.47 H(25) 104.5 Pro-RLp(28) N(24) 0.6 C(18) 109.5 H(25) 109.5 Pro-SLp(29) O(21) 0.6 C(20) 109.5 H(22) 109.5 Pro-RLp(30) O(21) 0.6 C(20) 109.5 H(22) 109.5 Pro-S

A. Dihedral Angle

Dihedral angle: The angle between two planes, where each plane is defined by three atoms. In

most common use, the angle between two bonds. In the Newman projection shown, the dihedral

angle between the Cl–C and H–C bonds is 60o (they are gauche), where as the dihedral angle

between the two C–Cl bonds is 180o (they are anti–periplanar).

Sudut dihedral: Sudut antara dua pesawat, di mana setiap pesawat ditetapkan oleh tiga atom.

Dalam penggunaan yang paling umum, sudut antara dua ikatan. Dalam proyeksi Newman

ditampilkan, sudut dihedral antara ikatan Cl-C dan H-C adalah 60o (mereka adalah gauche),

sedangkan sudut dihedral antara dua ikatan C-Cl adalah 180o (mereka anti-periplanar).

(Sumber: http://www.chem.ucla.edu/harding/IGOC/D/dihedral_angle.html)

Dihedral angels of four atom

The structure of a molecule can be defined with high precision by the dihedral angles between three successive chemical bond vectors (Figure 2). The dihedral angle   varies only the distance between the first and fourth atoms; the other interatomic distances are constrained by the chemical bond lengths and bond angles.

Struktur molekul dapat didefinisikan dengan keakuratan yang tinggi dengan sudut dihedral antara tiga vektor ikatan kimia yang berurutan (Gambar 2). Sudut dihedral bervariasi hanya jarak antara pertama dan keempat atom; jarak interatomik lainnya dibatasi oleh panjang ikatan kimia dan sudut ikatan.

To visualize the dihedral angle of four atoms, it's helpful to look down the second bond vector (Figure 3), which is equivalent to the Newman projection in chemistry. The first atom is at 6 o'clock, the fourth atom is at roughly 2 o'clock and the second and third atoms are located in the center. The second bond vector is coming out of the page. The dihedral angle   is the counterclockwise angle made by the vectors   (red) and   (blue). When the fourth atom eclipses the first atom, the dihedral angle is zero; when the atoms are exactly opposite (as in Figure 2), the dihedral angle is 180°.

Untuk memvisualisasikan sudut dihedral dari empat atom, sangat membantu bila kita melihat ke bawah vektor obligasi kedua (Gambar 3), yang setara dengan proyeksi Newman dalam kimia. Atom pertama

adalah pukul 6, atom keempat adalah pada sekitar 02:00 dan atom kedua dan ketiga berada di tengah. Vektor obligasi kedua yang keluar dari halaman. Sudut dihedral adalah sudut berlawanan yang dibuat oleh vektor (merah) dan (biru). Ketika atom keempat eclipses atom pertama, sudut dihedral adalah nol; ketika atom yang persis berlawanan (seperti pada Gambar 2), sudut dihedral adalah 180 °.

(Sumber: http://en.wikipedia.org/wiki/Dihedral_angle#Alternative_definitions)

Gambar 2

Gambar 4Gambar 3

B. Pro –S Angle