Kimyoviy kompyuter modellash




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ChemDraw, ChemWindow va IsisDraw programmalarida birikmalarning faqat ikki o’lchamli geometriyasi chizilishi mumkin. Bu programmalarda chizilgan geometriyalar qvant-kimyoviy hisoblashlarga yaroqsiz. Ammo, ChemOffice programmasi ikki o’lchamli birikma geometriyasini uch o’lchamli holatga o’tqaza

oladi (Get 3D Model → Edit 3D):

Umuman olganda, ChemOffice keng imkoniyatga ega, kimyogarlarga to’liq

ko’makchi vazifasini o’tay oladigan programma (pullik).

ChemOffice programmasi quyidagi tarkibiy qismlardan iborat:


  1. ChemDraw;

  2. Chem 3D;

  3. ChemFinder.

ChemDraw birikmalarning ikki o’lchamli tuzilish formulalarini chizish mumkin. Chizilgan strukturani nomlash mumkin (Structure→Convert Structure to Name) va nom asosida struktura chizish mumkin (Convert Name to Structure).
Foydalanilgan adabiyotlar:

  1. J.C.Cramer, Essentials ofcomputational chemistry. Theories and Models. Second Edition. John Wiley.2004.

  2. A.G.Eshimbetov, A.X.Xayitboyev, S.A.Maulyanov, H.S.Toshev. Kompyuter kimyosi. O’zMU. 2015. 112 b.

  3. Кларк Т. Компьютерная химия, М., Мир, 1990.

13-Ma’ruza

Masala yechishning tegishli uslubini tanlab olish. Masala va uning parametrlarini tuzishning asosiy qoidalari

Reja:


1.Tautomerlarni proton ko’chishini o’rganish

Hisoblashlar yordamida amin-imin, imin-enamin, keto-enol, laktam-laktim va boshqa tautomerlarning qaysi formasi barqarorligini va bir-biriga o’tish baryerini aniqlash mumkin. Mopac2012 programmasida o’tish holatini TS (Transition search) kalit so’zi, Gaussianda esa opt=ts kalit so’zi yordamida toppish mumkin. Undan tashqari, Mopac programmasida SADDLE kalit so’zi yordamida ham o’tish holatini topish mumkin. Firefly/Gamess programmasida RUNTYP=SADPOINT kalit so’zi yordamida o’tish holati topiladi. O’tish holati bir tautomer holatdan ikkinchi ikkinchi tautomer holatiga o’tishdagi energetic sathning maksimum holati:



Firefly programmasida AM1 usuli bilan timin molekulasining laktam va laktim holatlarining hosil bo’lish issiqligi (ΔHf) va umumiy energiyasi (Etotal) hamda bir-biriga o’tish baryeri (Ea) hisoblandi.



Laktam holat input fayli:


Laktim holat input fayli:



O’tish holatni topish input fayli quyidagicha:







Laktam

O’tish holati

Laktim

ΔHf =-61.10 kkal/mol

Etotal = -65.3284329945



ΔHf =-48.12 kkal/mol

Etotal = -65.33077570118



ΔHf = -48.39 kkal/mol

Etotal = -65.3081825516


Hosil bo’lish issiqligi kattaliklari 12.71 kkal/mol-ga laktam holat laktimga nisbatan barqaror ekanligini ko’rsatmoqda. Laktim holatdan lactam holatga o’tish baryeri Ea=0.27 kkal/mol. Laktam holatdan laktim holatga o’tish baryeri Ea=12.98 kkal/mol.

Konformatsion izlanishlar: ichki aylanish baryerini o’rganish

Etan molekulasi misolida metil guruhining ikkinchi metil guruhiga nisbatan ichki aylanishini qaraymiz. Buni Mopac programmasida bajarish juda qulay. Mopac z-matritsasi tuzish bo’limida ta’kidlanganidek, torsion bog’ uzunligi kattaligidan keyingi “1” soni “-1”qilib kiritilsa ushbu torsion burchakni berilgan nuqta (POINT) va qadam (STEP) asosida aylantirish hisoblashi bajariladi.



Aytaylik H7-C2-C1-H4 torsion burchakni C2-C1 o’qi atrofida aylantirish kerak. Ushbu torsion burchak 59.99° ekanligini z-matritsadan ko’rishimiz mumkin. Torsion burchakdan (59.9989 -dan) keyingi 1 soni (aylanaga olingan) muqobillash jarayonida ushbu torsion burchakni ham muqobillash kerakligini bildiradi. Ushbu 1 soni oldiga “-” ishorasini qo’ysak programma “Reaction coordinate calculation” hisoblashi amalga oshirilishini tushunadi.


Bu hisoblashni to’liq bajarish uchun “Coordinate reaction set” qismida qadamlar soni va gradus ko’rsatiladi. 0-360° oraliqda har 10° qadam bilan aylantirib ko’rish maqsadida 36 nuqtani (POINT=36) tanladik.





Hisoblash natijalari –jadvalda va –rasmda keltirilgan. Ichki aylanish energiyasining torsion burchakka bog’liqlik diagrammasi potensial sathida uchta maksimum va uchta minimumni ko’rishimiz mumkin. Energetik minimum nuqtalari 60, 180 va 300 (yani -60) graduslarda to’g’ri keladi. Energetik sathning maksimum holatlari esa 0, 120 va 240 (yani -120) graduslarda kuzatiladi.



Hisoblash natijalari

Hisoblash natijasi

Tahrirdan keyin

59.99890 -17.414450

60 -17.41

0

-16,16


69.99890 -17.334331


70 -17.33

10

-16,25

79.99890 -17.113046

80 -17.11

20

-16,49

89.99890 -16.804777

90 -16.80

30

-16,8

99.99890 -16.489038

100 -16.49

40

-17,11

109.99890 -16.252817

110 -16.25

50

-17,33

119.99890 -16.165217

120 -16.16

60

-17,41

129.99890 -16.252737

130 -16.25

70

-17,33

139.99890 -16.488789

140 -16.49

80

-17,11

149.99890 -16.804467

150 -16.80

90

-16,8

159.99890 -17.112846

160 -17.11

100

-16,49

169.99890 -17.334266

170 -17.33

110

-16,25

179.99890 -17.414446

180 -17.41

120

-16,16

189.99890 -17.334301

190 -17.33

130

-16,25

199.99890 -17.112908

200 -17.11

140

-16,49

209.99890 -16.804545

210 -16.80

150

-16,8

219.99890 -16.488869

220 -16.49

160

-17,11

229.99890 -16.252786

230 -16.25

170

-17,33

239.99890 -16.165234

240 -16.16

180

-17,41

249.99890 -16.252783

250 -16.25

190

-17,33

259.99890 -16.488965

260 -16.49

200

-17,11

269.99890 -16.804700

270 -16.80

210

-16,8

279.99890 -17.112982

280 -17. 11

220

-16,49

289.99890 -17.334293

290 -17.33

230

-16,25

299.99890 -17.414445

300 -17.41

240

-16,16

309.99890 -17.334302

310 -17.33

250

-16,25

319.99890 -17.112930

320 -17.11

260

-16,49

329.99890 -16.804625

330 -16.80

270

-16,8

339.99890 -16.488973

340 -16.49

280

-17,11

349.99890 -16.252825

350 -16.25

290

-17,33

359.99890 -16.165221

360 -16.16

300

-17,41

369.99890 -16.252772

10 -16.25

310

-17,33

379.99890 -16.488895

20 -16.49

320

-17,11

389.99890 -16.804546

30 -16.80

330

-16,8

399.99890 -17.112867

40 -17.11

340

-16,49

409.99890 -17.334271

50 -17.33

350

-16,25


Torsion burchakning ichki aylanish energiyasiga bog’liqlik diagrammasi



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