HyperChem7 (tiengViet)

Hng dn s dng HyperChem 7.04

Bi 1 Bt u s dng phn mmNhp chut vo biu tng HyperChem, mn hnh lm vic hin ln nh sau:

Thanh tiu (title bar)Biu din tn file ang biu din trn ca s. Nu cha lu file th tn s l untitled

Thanh cng c la chn (menu bar)Cha cc cng c tnh ton khc: File, Edit (hiu chnh), Build (xy dng), Databases (d liu), Setup (t phng php tnh), Compute (tnh ton), Annotations (ghi ch, din gii), cancel (thot), Script, v Help (tr gip).

Thanh biu tng cng c (tool bar)Cha cc cng c cho php ta v, chn, biu din, v di chuyn cc nguyn t, phn t. Phn bn phi thanh cng c c cha cc cng c gip ta ghi ch thm, lu nhanh, ct, dn, in, tr gip.

Mn lm vic (workspace)L ni biu din h phn t hin ti. 1


Dng hin trng tnh ton (status line)Cho ta bit thng tin nh l s nguyn t trong mt phn t, hin trng tnh ton, gi tr tnh ton

Tr gip (help)Cha cc hng dn thm cho ngi s dng.

Cch s dng chut:Mun thao tc trn cng c no ta ch vic nhp tri chut (L-Click) vo biu tng cng c . V d mun s dng cng c v, ta di chuyn biu tng chut n biu tng v nhp chut:

S dng bn phmThay v phi dng chut ta c th dng bn phm di chuyn n nhng la chn cn thit. V d m select menu ta nhn ng thi hai phm [Alt] + [S] ([Alt] v [S]). chn cc la chn khc trong hp thoi ta nhp tip vo k t tt c gch di trong mi la chn. V d chn tip select all ta nhp ch e trn bn phm.

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Cc phm tt khc:Ctrl + N Ctrl + O Ctrl + S Ctrl + X Ctrl + C Ctrl + V Alt + F4 Ctrl + D Ctrl + K Ctrl + L Ctrl + F Ctrl + B Spacebar F2 F9 Esc To trang lm vic mi M file Lu file (save) trong File menu Ct (cut) trong File menu Copy (copy) trong Edit menu Dn (paste) trong Edit menu Thot khi HyperChem Xo (delete) trong Annotations menu La chn tip (select next) trong Annotations menu La chn phn trc (select previous) trong Annotations menu Di chuyn tip (move forward) trong Annotations menu Di chuyn tr li (move backward) trong Annotations menu Di chuyn h phn t vo trung tm v biu din theo t l mn lm vic. Tr li kiu biu din lc trc (last rendering) trong Display menu Copy hnh nh (copy image) trong Edit menu Nh mc thot (cancel) trn thanh cng c

Cc cng c quan trng trn thanh cng c

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Cc thao tc trn HyperChem M mt file v d: V d m file c ui HIN.1. Di chuyn con tr chut n File trn thanh cng c. 2. Nhp tri chut (L-click) vo File mn hnh s hin ra nh sau:

3. Nhp tri chut vo Open. Mn hnh s hin ra nh sau:

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4. Nu mn hnh list vn cn cc cht khc, c th ko thanh trt tm kim.

ko thanh trt ta nhp tri biu tng chut vo thanh trt, gi nguyn nh th v r chut theo chiu mun ko. 5. Mun m file no ta ch cn nhp tri (L-click) chut vo file ri nhn tip vo nt Open trn list

Trn mn hnh s hin ra phn t cha trong file

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Cch s dng Display SettingsDisplay settings cha cc la chn biu din h phn t trn trang lm vic m Display menu ta thc hin nh sau 1. Nhp tri chut vo biu tng Display trn thanh cng c. Mn hnh khi hin ra nh sau:

S dng nhn (Labels)

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Hng dn s dng HyperChem 7.04 Nhp tri chut vo Labels trong Display. Hp thoi Labels hin ra vi cc la chn khc nhau, ta c th la chn hnh thc nhn biu hin ca cc nguyn t trong h.

Atoms None B tt c cc nhn. Symbol Biu tng nguyn t, v d C, O, N.. Name Tn ca nguyn t theo ngn hng d liu, v d CA, CB i vi cacbon alpha v beta. S th t to nguyn t. Number Type Kiu nguyn t, theo tc ng ca trng lc, v d CT i vi cacbon t din trong trng lc AMBER. Charge in tch thc ca nguyn t. Spin Tng spin thc (alpha-beta) ca mt nguyn t Poputation Mass Khi lng nguyn t Basis set Tp hp hm c bn p dng cho nguyn t Chirality R hoc S RMS Gradient Ga tr v hng ca vect bin thin m t trng lc trn mt nguyn t. Custom t tu chn. Residues None B tt c cc nhn. Name Tn hp phn, v d: TRP, ILE. Sequence Th t hp phn t hp phn ui N (Nteminus).1,2,3 Name+Seq C tn ln th t. Bonds

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Hng dn s dng HyperChem 7.04 None B tt c cc nhn Bond Length di lin kt gia cc nguyn t Bond Order Th t lin kt tnh ton theo c hc lng t.

Hnh thc biu din phn t:Ta hon ton c th biu din cc phn t khc nhau trong h.

Thay i hnh thc biu din:1. Nhp tri chut vo Rendering trong Display menu Hp thoi la chn hin ra nh sau:

Nhp tri chut vo mt trong nhng hnh thc biu din, v d chn Balls and Cylinders (kiu hnh cu v hnh tr) th trn m hnh cc nguyn t ca h c biu din di dng hnh cu, lin kt dng hnh tr nh sau:

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Ch : HyperChem cn c cc kiu biu din khc: - Sticks: Kiu que. - Balls : Kiu hnh cu. - Overlapping Spheres: Kiu hnh cu chng ln nhau. - Dots: Kiu chm. - Sticks & Dots: Kiu chm - gch.

t mu nn trang lm vic t mu nn trang lm vic ta lm nh sau: 1. Nhp tri chut tch chn Preferences trong File menu. 2. Tch chn mc Window Color trong hp thoi Preferences. Mu ngm nh cho trang lm vic ca HyperChem l mu en:

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Hng dn s dng HyperChem 7.04 3. Tch chn White ri nhp OK xem biu din mu nn ca mn lm vic. Mu nn lc ny l mu trng:

Ch : Nu ta t mu khc th nn s c mu khc: - Black: Mu en. - Blue: Mu xanh nc bin. - Green: Mu xanh da tri. - Cyan: Mu lc lam. - Red: Mu . - Violet: Mu ta. - Yellow: Mu vng. - White: Mu trng.

t mu sc lin kt trong phn t1. Tch chn Preferences trong File menu.

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2. Chn mc Bond Color trong hp thoi Preferences. Tch chn mu m ta mun t cho lin kt. V d ta chn mu en (Black). Hnh nh biu din trn mn lm vic s nh sau:

Ch : Tu theo ta chn mu no, lin kt s c biu din theo mu y. HyperChem ngm nh mu cho lin kt theo cc nguyn t, nh ta c th quan st d dng cc lin kt khc nhau, tuy nhin iu khng c li trong khi ta phi in en trng.

Mu sc ca nguyn tHyperChem ngm nh mu sc ca cc nguyn t c trng nh sau: Nguyn t Mu ngm nh 11

Hng dn s dng HyperChem 7.04 Cacbon Nit Oxy Flo Lu hunh Natri Kali St Coban ng Brom Iot Vng Tt c cc nguyn t cn li Lc lam Xanh Vng Vng Ta Ta Xanh Xanh l cy Vng Vng Mu trng

Ta c th t li mu sc biu din cc nguyn t theo su mu chun, cng vi mu trng v mu en. HyperChem s dng mt tp hp mu ngm nh. Nu ta thay i mu sc ca mt nguyn t, ta vn c th tr li vi mu ngm nh bng cch nhp vo Revert trong hp thoi sau:

t mu mi cho nguyn t ta lm nh sau: 1. Nhp tri chut chn Element color trong Display menu. 2. Nhp tri chut vo tn nguyn t mun i mu. 3. Nhp tri chut vo mu mun i. 4. Nhp OK chn. 5. tr li mu ngm nh nhp Revert.

t ch Copy hnh nh

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Hng dn s dng HyperChem 7.04 y l phn kh th v nu ta mun ly hnh nh ca HyperChem chuyn qua trnh ng dng khc, v d nh trnh Word ca Microsoft. 1. Nhp tri chut chn Preferences trong File menu. Chn mc Setup Image. Hnh nh hp thoi lc ny nh sau:

2. t cc la chn nh trn hnh v. Nhp OK chn. 3. Nhp F9 hoc nhp tri chut chn Copy Image trong Edit menu. 4. Nhp OK nu HyperChem t ra cu cnh bo no. C ca s mn lm vic ca HyperChem s c Copy. Nu ta dn qua Word th s thy nh sau:

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Ch : HyperChem cho ta nhiu la chn copy hnh nh. Top leve Copy c cc hp thoi v menu ko Window xung nu ta nhp vo Copy image (Ca s) thay v nhp F9. Workspace Ch Copy phn mn lm vic. HyperChem Copy c ca s lm vic HyperChem Full screen Copy c mn hnh, k c cc ca s khc. Bitmap Lu kiu file c ui .bmp. Dng File format mu chun. Thch hp lu cho biu (Kiu file) din phn t kiu hnh cu, cc biu ca tnh ton im n, tnh ton bn kinh nghim. RGB Bitmap Ging nh .bmp, dng 24 mu. Kh hn ch trong cc ng dng khc khng c ch 24 mu. Metafile File ui m rng l .wmf. Thch hp lu vi cc kiu biu din phn t nh Sticks, Ball and Cylinder, Dots v Stick & Dots. Detination(Ni File HyperChem lu nh c phn ui l t file) .bmp hay .wmf vo trong file. Clipboard Lu nh vo b nh tm thi, mi ln c mt nh. Color Tch chn lu hnh nh vi mu sc y , nu khng n ch c 14

Hng dn s dng HyperChem 7.04 dng en trng. Tch chn im tr chut c trong nh. Dng t tn v v tr file t nh.

Cursor Filename

Thot khi HyperChemC nhiu cch thot khi chng trnh lm vic 1. Nhp tri chut vo Exit trong Menu file 2. Nhp Alt + F4 c thm: Chng 1 trong HyperChem for Windows Reference Manual.

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Bi 2. V v hiu chnhV nguyn t v lin kt v nguyn t ta cn c bng la chn cc nguyn t.

C hai cch thc hin iu ny1. Nhp tri chut vo Default Element trong Menu Build. 1. Nhp lin tc hai ln chut tri (Double-click) vo cng c V

Bng la chn cc nguyn t hin ra nh sau: la chn nguyn t no ta ch vic nhp tri chut vo nguyn t . 2. Mun bit thuc tnh ca tng nguyn t ta ch vic nhp vo biu tng thuc tnh (Properties) trong thoi, bng cc thuc tnh ca nguyn t s xut hin.

Sau khi la chn nguyn t mun v, nhp tri chut ln mn lm vic ta s c nguyn t mun v. Mn hnh hin ra c dng nh sau:

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3. Mun v lin kt ta ch vic nhn nt tri chut v r t v tr ny n v tr khc mun v. Nu u kia l mt nguyn t khc th ta phi la chn nguyn t li sau cng nhn nt tri chut v r t v tr nguyn t ban u n v tr m nguyn t th hai mun biu din.

4. v phn t dng vng ta nhn v r chut ni cc nguyn t vi nhau.

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5. To lin kt i, ba bng cch nhp tri chut vo chnh lin kt . 6. To vng lin hp bng cch nhp lin tip hai ln chut tri vo lin kt vng c v. 7. Thm nhanh nhng nguyn t Hydro cn thiu trong phn t, nu c bng cch nhp lin tip hai ln chut tri vo biu tng cng c la chn trn thanh cng c.

Chn nguyn t (Selecting Atoms)Trong phn ny ta hc nhng k thut c bn la chn mt nguyn t, nhm nguyn t hay mt tp hp no ang biu din trn trang lm vic.

t cc hnh thc chn c mt s bc sau:1. Nhp tri chut vo Select menu. Trn mn hnh hin ra nh sau:

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2. Nu cc nguyn t cha c chn th hy nhp chut tri vo Atoms chn. Tip theo tt chn nhiu (Multiple Selections) bng cch nhp chut tri b du tch (). Khi ta tch chn Atoms, n v la chn nh nht chn nguyn t, vi cng c la chn, khi ta c th la chn cc nguyn t, lin kt v gc ring. Gii hn ny vn hot ng cho n khi ta chn Residures hoc Molecules. Ch : S dng la chn Atoms nu ta khng mun chn cc hp phn hay cc phn t.

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Chn nguyn t1. Nhp tri chut vo cng c la chn (select) trn thanh cng c, sau di chuyn con tr xung mn lm vic. 2. t con tr chut vo nguyn t mun chn v nhp tri chut. Nguyn t c chn s c khoanh vng sng hn cc nguyn t khc. 3. Mun chn lin kt no ta nhp tri chut vo lin kt . 4. Mun chn tt c cc nguyn t trong mn lm vic, ta thc hin bng cch di chuyn chut n khong trng ca trang lm vic v nhp phi chut (R-click)

Ch : nguyn t c la chn c m t trn dng hin trng: S ch th t to ra nguyn t trong phn t Atom number Tn nguyn t. Element name Tn nguyn t, xut hin khi chn nguyn t trong Atom name protein hoc amino axit. Trng lc p dng cho kiu nguyn t (amber, Force Field mm+, bio+ hoc opls). Kiu nguyn t Atom type in tch nguyn t Charge To ca nguyn t theo h to ca phn t. Atomic coordinates

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Chn nhm nguyn t chn mt nhm nguyn t ta dng kiu chn hnh ch nht 1. Nhp tri chut vo cng c la chn trn thanh cng c. 2. Nhp ng thi tri v phi chut, gia nh vy v r to hnh ch nht cha cc nguyn t mun chn. 3. Nh chut th tt c cc nguyn t trong hnh ch nht c chn

Chn thm mt nhm nguyn t1. Nhp tri chut tch chn Multiple select trong Select menu 2. R chut chn nhm nguyn t mi theo hnh ch nht nh trn.

Chn cc hp phn (Residures)Khi ta tch chn Residures, n v la chn nh nht chn cc hp phn. Hp phn phi c ngun gc t Databases menu hoc t ngn hng d liu Protein. HyperChem khng nhn ra nhng hp phn do ta v t cc nguyn t. Ch : Nu khng c hp phn no trong phn t th Residures hot ng nh Atoms. 21


chn hp phn ta c cc cch sau: 1. Nhp tri chut vo hp phn ta mun chn. Nu cng c la chn chn ln mt phn t, n s chn hp phn gn nht vi n. 2. Nhp phi chut vo hp phn b la chn n. 3. Chn Muiltiple trong Select menu chn nhiu m khng phi loi b bt k la chn no trc . 4. Nhp tri chut vo vng trng trn mn lm vic chn tt c cc nguyn t trong h phn t. Nhp phi chut vo vng trng mn lm vic loi b tt c cc la chn. Hp phn la chn c m t trn dng hin trng:

Number of residures selected Residure name and number

S th t to hp phn c th s l 0 cho tt c cc hp phn. y l tn v th t ni tip ca hp phn ta chn.

Chn c phn t (Molecules)Khi ta tch chn Molecules, n v la chn nh nht chn phn t ring. Hnh thc la chn ny hot ng cho n khi ta tch chn kiu chn khc. Cc kiu la chn phn t ging nh i vi la chn hp phn v la chn nguyn t: 1. Nhp tri chut ln mt phn t chn n. Nu cng c la chn gn hai phn t th n s chn phn t gn nht. 22


Loi b la chn1. Nhp phi chut vo nguyn t chn, nu khng mun chn nguyn t na. 2. Nhp phi chut vo gia lin kt nu mun khng chn lin kt . 3. Nhp phi chut vo khong trng trong trang lm vic loi b tt c cc nguyn t chn.

Mu sc biu din khi la chn

Tch chn mc Select Color trong hp thoi Preferences. Tch chn Thick line (ng m) th khi la chn cc ng biu din s la chn s m hn:

Ch : Khi ta chn cc mu khc th khi la chn phn la chn s c 23

Hng dn s dng HyperChem 7.04 kiu mu tng ng.

Chn phn b (Complement Selection)Ta thc hin chn phn b chn tt c nhng phn cha c chn v b la chn i vi phn chn. Cch thc hin l nhp vo Complement Selection trong Select menu.

Hp thoi la chn (Select Dialog Box) Ta thng quan tm n hp thoi la chn khi c s la chn c bit, v d nh ch chn nguyn t no hoc ch chn mt hp phn no .

By string

Chn nguyn t vi gi tr xc nh theo mt chui gi tr khc nhau. Nhp tri chut vo mt nt xem chui gi tr thch hp trong bn phi. Chui gi tr khc nhau m t tp hp cc nguyn t c th chn c nh sau: Atom Symbol Biu tng nguyn t quy c cho mi nguyn t, 24

Hng dn s dng HyperChem 7.04 nh l C, N, O, F Tn quy c cho mt nguyn t trong amino axit hoc nucleic axit. Ch p dng cho cho tn nh ngha trong cc mu i vi cc thnh phn ca phn t ln. V d l CA, 1HA, 2HA i vi cacbon alpha ni vi hydro. Kiu nguyn t trong c hc phn t nh l CT, HC Tn ca mt hp phn amino axit hoc nucleic axit, nh l GLY, ALA, Tp hp hm c bn tnh theo Ab initio hoc DFT quy cho nguyn t. V d: 6-31G*. S bt i xng, R hoc S, quy cho nguyn t bt i. Dy cc phn la chn c t tn trc . Dy ny gm c cc la chn nh trc nh l LINE, POINT v PLANE, c c cc tn theo biu tng nguyn t quy c nh l C, N, O, F Loi b phn la chn c t tn no khi list. Chn mt nguyn t theo mt gi tr xc nh t mt dy cc gi tr s khc nhau. Nhp tri chut vo mt nt chn kiu s mun chn sau nh gi tr s vo cc thch hp bn phi. Chn nguyn t theo s th t to ra n trong phn t. Chn hp phn theo s th t ni tip trong phn t. Theo th t to phn t. Theo khi lng nguyn t Theo s th t nguyn t trong bng h thng tun hon. Theo in tch nguyn t tnh trong c hc lng t. Chn theo cn bc hai bnh phng trung bnh ca gradient. Chn theo mt spin, da theo lng electron alpha (hng ln) v electrong beta(hng xung) 25

Atom Name

Atom Type Residue Name Basis Set Chirality Named Selection

Remove By Number

Atome Number Residue Number Molecule Number Atomic Mass Atomic Number Electric Charge RMS gradient Spin Population

Hng dn s dng HyperChem 7.04 Value Gi tr s dng t cho kiu la chn thch hp. For Molecule(s) Chn tt c cc phn t, nu khng tch th s gii hn theo list.

Chn theo chui (String)1. 2. 3. 4. 5. Chn Select trong Select menu. Nhp tri chut chn By String trong hp thoi. Nhp tri chut vo mt trong cc nt thch hp. Nhp tri chut vo mt trong cc gi tr biu din bn phi. Nhp OK chn.

Chn theo sChn Select trong Select menu. Chn By Number trong hp thoi. Tch chn vo nt thch hp chn. nh gi tr ph hp theo khong hoc xc nh. Nu tch chn For Molecule (s) xc nh mt tp hp hoc gii hn cc phn t. Nu khng tch chn tt c cc phn t l ngm nh. 6. Nhp OK chn. 1. 2. 3. 4. 5.

Tn phn la chn (Name Selection)t tn phn la chn gip ta d dng chn li chng vo ln sau. Tn phn la chn c th l: POINT, LINE, PLANE, REACTANT, PRODUCT, PLOT1, PLOT2, GHOST ATOMS, NMR ATOMS, QUANTUM ATOMS hoc tn do ta t (ti a 19 k t)

POINT LINE

Tm khi ca cc nguyn t chn. ng thng gia hai hay nhiu nguyn t, hoc l 26

Hng dn s dng HyperChem 7.04 trc qun tnh th nht. Mt phng to bi trc th nht v trc qun tnh th hai ca cc nguyn t chn Tn phn cc nguyn t cht phn ng. Dng tm trng thi chuyn tip trong phn ng. Ch hot ng khi ta chn mt na s nguyn t trn mn lm vic. Tn cc nguyn t ca sn phm. Dng tm trng thi chuyn tip. Hot ng ng thi vi Reactant. Tn cha mt tp hp ca 2, 3 hay 4 nguyn t cng xc nh mt di lin kt, mt gc lin kt hay mt xon lin kt xc nh s bin thin th nng trong khng gian mt chiu hoc hai chiu. Dng xc nh s bit thin th nng trong khng gian hai chiu. Cha tp hp cc nguyn t c coi l cc nguyn t m (ma) khi tnh ton Ab initio hoc DFT. Cha cc nguyn t c quy cho spin nhn v s dng trong tnh ton HyperNMR. Cha tp hp cc nguyn t c xc nh l cc nguyn t lng t trong s pha trng gia tnh ton c hc lng t v c hc phn t (MM/QM). Tn do ta t

PLANE REACTANT PRODUCT PLOT1

PLOT2 GHOST ATOMS NMR ATOMS QUANTUM ATOMS Other

Xo nguyn tXo mt nguyn t n hoc mt lin kt n 1. Nhp tri chut vo cng c v trn thanh cng c. 2. Nhp phi chut vo nguyn t hoc vo gia lin kt mun xo. Khi nguyn t hoc lin kt s bin mt.

Xo nhiu nguyn t1. Nhp tri chut vo cng c chn trn thanh cng c. 2. R chut chn nhng nguyn t mun xo. 3. Nhp tri chut vo Clear (xo sch) trong Edit menu. Hp thoi xut hin hi c thc s mun xo phn la chn khng. 4. Chn Yes nu mun xo. 5. Chn No nu khng mun xo.

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Copy nguyn t vo b nh tm thi (Clipboard)1. 2. 3. 4. Nhp tri chut vo cng c chn trn thanh cng c. Nhp tri chut vo lin kt hoc nguyn t mun chn. Chn Copy trong Edit menu. Chn Paste trong Edit menu. Mt bn copy ca cc nguyn t chn s c dn vo trong mn lm vic.

t in tch hnh thc cho nguyn t trong hTa hon ton c th t in tch hnh thc cho mt nguyn t no trong phn t. in tch hnh thc trong HyperChem nh sn l cc gi tr nguyn. N ta mun t in tch hnh thc cho nguyn t no th cch lm nh sau: 1. Chn nguyn t mun t in tch hnh thc. 2. Nhp tri chut chn Set Formal Charge trong Build menu. Hp thoi la chn xut hin nh sau:

Ta c th t in tch hnh thc thch hp cho nguyn t chn. 0-Neutral +1-Singly Positive -1-Singly Negative +2-Doubly Positive -2-Doubly Negative +3-Triply Positive -3-Triply Negative Trung tnh Dng mt m mt Dng hai m hai Dng ba m ba

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Hng dn s dng HyperChem 7.04 Nu nh nhiu nguyn t c chn th Set Formal Charge khng hot ng, khi ta c kiu t in tch khc. Ch : in tch hnh thc ch c ngha biu din, khng c gi tr tnh ton.

t in tch thcHyperChem c th tnh ton in tch ca tng nguyn t ring bit trong phn t, nhng ta cng c th t in tch theo mun. Cch lm nh sau: 1. Chn nguyn t hay nhm nguyn t mun t in tch. Hp thoi t in tch xut hin:

nh gi tr in tch thch hp m ta mun. Nhp OK chn. Khi cc nguyn t chn s c cng in tch m ta nh vo.

t khi lng nguyn tCch lm tng t nh t in tch nguyn t trn, bng cch nhp tri chut vo Set mass trong Build menu.

t di lin ktt di lin kt cho php ta t di lin kt chn theo mun. 1. Nhp chn lin kt mun t li di. 2. Nhp chn Set Bond Length trong Edit menu. nh gi tr mun t vo hp thoi la chn.

Nhp OK thc hin thay i di lin kt chn.

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Ch : Lin kt chn thay i khng c l lin kt trong vng. t gc lin kt Cch lm tng t nh t di lin kt trn, nhng ta phi chn gc lin kt v tch chn Set Bond Angle trong Edit menu m hp thoi la chn.

t xon lin ktTa cng thc hin nh cch t di lin kt trn, nhng ta phi chn bn nguyn t lin tip to gc xon mun thay i, tch chn Set Bond Torsion trong Edit menu.

t nhn ringTa c th ghi ch nhn tu cho nguyn t la chn, cch lm tng t nh t in tch nguyn t trn. Ta tch chn Set Custom Label trong Build menu m hp thoi v nh nhn m mnh mun vo .

t kiu nguyn t (Atom Type)Kiu nguyn t ch c ngha khi ta thc hin tnh ton theo c hc phn t, khng c gi tr g khi ta tnh ton bn kinh nghim. Kiu nguyn t cng c ngm nh theo cc thit lp nh sn nu ta khng thay i g. Ta khng nn t li kiu nguyn t nu khng r v n. Cch t kiu nguyn t nh cch t in tch trn, ta chn nguyn t mun t li kiu, tch chn Compile Type Rules trong Build menu. Hp thoi la chn xut hin v ta chn kiu nguyn t m mnh mong mun. c thm: Atom types trang 177- chng 11-quyn Computational Chemistry.

Thay i cc thuc tnh hnh hc Cng bc hnh hcVi cc kiu cng bc trong HyperChem gip ta un, thay i gc, di lin kt theo mong mun. Vic cng bc nh vy lun nh hng n tnh ton v kt qu cui cng. Tuy nhin HyperChem khng phi lc no cng

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Hng dn s dng HyperChem 7.04 cho ta c ngay hnh hc mong mun, v vy y l mt trong nhng cng c hu ch. Ch : Cng bc hnh hc ch hot ng khi mt nguyn t c chn. cng bc hnh hc ta lm nh sau: 1. Chn mt nguyn t trong h. 2. Tch chn Constrain Geometry trong Build menu. Hp thoi la chn xut hin:

3. Tch chn hnh thc cng bc m ta mun, nhp OK chn. 4. Loi b la chn nguyn t. 5. Nhp vo Model Build thc hin cng bc chn. Tt c cc gc lin kt ni vi nguyn t c chn s chu cng bc. Ch : Ta cng c th b nhng cng bc va thc hin bng cch tch chn Computed trong hp thoi cng bc v nhp vo Model Build trong Build Menu xy dng li cu trc theo trnh xy dng. Computed Linear Trigonal Tetrahedral Square Planar Bipyramidal Octahedral Khng cng bc. Trnh xy dng quyt nh hnh hc. Cng bc hai lin kt to gc 1800.. Cng bc to mt phng tam gic, mi cp lin kt to gc 1200. Cng bc to t din, mi cp lin kt to gc 109.470. Cng bc to mt phng, mi cp lin kt lin nhau to to gc 900. To hai chp tam gic chng ln nhau. To bt din.

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Cng bc di lin ktTa c th gii hn di lin kt theo mun. Cch lm nh sau: 1. Chn lin kt mun thay i di. 2. Nhp chn Constrain Bond Length trong Build menu. Hp thoi la chn xut hin:

3. Tch chn Other v nh gi tr di mong mun vo. Nhp OK chn. 4. B chn lin kt. 5. Nhp chn Model Build trong Build menu thc hin cng bc lin kt. Ch : Vic cng bc lin kt lun nh hng n tnh ton, ta ch nn t khi thy cn thit. loi b cng bc ta chn li lin kt, tch chn Computed trong hp thoi cng bc v thc hin nh vi cch cng bc trn.

Cng bc gc lin kt cng bc gc lin kt no ta lm nh sau: 1. Chn gc lin kt mun thay i. 2. Chn Constrain Bond Angle trong Build menu. 32

Hng dn s dng HyperChem 7.04 Hp thoi la chn xut hin:

3. Tch chn kiu gc mun thay i. Nhp OK chn. 4. B chn gc lin kt. 5. Nhp chn Model Build thc hin cng bc. Ch : Vic cng bc gc lin kt c nh hng n gi tr tnh ton. loi b cng bc ta lm tng t nh khi cng bc nhng tch chn Computed trong hp thoi la chn. Cc kiu la chn gc nh sau: Computed Linear Trigonal Tetrahedral Orthogonal Other Khng cng bc 1800 1200 109.470 900 Tu t gi tr t 3600 n +3600

Cng bc lin kt xonCch lm tng t nh kiu cng bc gc lin kt trn. Tuy nhin y ta phi chn lin kt xon gm t nht bn nguyn t. Hp thoi la chn cng bc nh sau:

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Cc kiu la chn: Computed Trans Cis Gauche+ GaucheOther Khng cng bc Cng bc 1800 00 600 -600 Tu gi tr t vo t 1800 n +1800

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Bi 3. To nhng phn t nh trong khng gian hai chiu (2D) v ba chiu (3D). Cch v phn t trong khng gian hai chiu. Hiu chnh lin kt v cc nguyn t. Biu din phn t trn khng gian ba chiu. Lu cu trc phn t.

V phn t trn khng gian hai chiu1. Nhp hai ln lin tip tri chut (Double-click) vo cng c v. Hp thoi la chn nguyn t s hin ra. 2. Tch (4) trong phn Allow Arbitrary Valence, v b tch trong phn Explicit Hydrogens. Nu ta khng b tch Explicit Hydrogens, th hydro lun t ng thm vo. 3. Chn nguyn t mun v, y ly v d chn Carbon.

4. Nhp tri chut, gi v r n cc im theo cng thc phn t mun v.

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Lu bc v vo trong mt FileTrc khi thc hin sa i bc v, ta hy lu bc v li. iu ny gip ta khng phi v li bc v ban u nu trong qu trnh chnh sa b hng.

Cch lu nh sau1. Nhp tri chut vo Save (lu) trong File menu. HyperChem s hin ln hp thoi c dng nh sau:

2. nh tn file m bn mun t vo mc File name. 3. t kiu ui HIN lu dng nh trong phn Save as type. 4. Nhp tri chut vo nt Save lu file. Lc ny hp thoi lu t ng thot v ta c c hnh nh phn t hin ti lu. 5. Nhng thao tc lc sau trn phn t v, mun lu ta ch vic nhp vo Save. Nu mun lu vo tn file khc th ta nhp vo Save as trong File menu.

Thay i hnh thc lin ktVic sa i gip ta c th biu din phn t c cha cc lin kt i, ba hay l to vng benzen. 1. Nhp tri chut vo cng c v. 2. to lin kt i ta ch vic nhp tri chut vo gia lin kt n to ra trc .

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3. To lin kt ba bng cch nhp tip tri chut vo lin kt i to ra.

4. Ch : Mun sa tr li thnh lin kt n ta ch vic ln lt nhp phi chut vo gia lin kt i, ba to ra.To vng benzen bng cch nhp lin tip hai ln tri chut vo mch vng.

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Biu din nguyn t di cc dng nhn khc nhauTa hon ton c th biu din cc nguyn t trn trang lm vic di dng biu tng, tn, in tch, khi lng ca n.

Cch biu din nhn nguyn t1.Nhp tri chut vo Labels trong Display menu.

Hp thoi nhn (label) hin ra nh sau: 38


2. Tch vo kiu nhn m ta mun biu din. 3. Nhp tri chut vo OK chn. Nu ta chn kiu biu tng (symbol) th trn mn lm vic cc nguyn t s c biu din di dng biu tng.

Chnh sa cc nguyn tNu trong phn t v, ta mun thay i nguyn t ny thnh nguyn t khc th cch lm nh sau. 1. Nhp hai ln tri chut vo cng c v trn thanh cng c. Bng cc nguyn t s hin ra. 2. Chn nguyn t mun thay th. V d chn oxi. 3. Nhp tri chut vo nguyn t mun thay th trong phn t v. V d nh cacbon.

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Nguyn t cacbon s c thay th bng nguyn t oxi.

Thm nhanh hydro cn thiu nhanh chng thm nhng hydro cn thiu trong phn t ta c th thc hin d dng, cu trc sau khi thm hydro nhanh s dng khng gian ba chiu. Cch lm nh sau. 1. Nhp tri chut chn Add H & Model Build trong Build menu.

HyperChem s thc hin biu din phn t ta v trn khng gian ba chiu v t ng thm nhng hydro cn thiu.

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Nu vn khng thy hydro xut hin th hy tch (4) chn Show Hydrogens trong Display menu.

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Bi 4. Dch chuyn, quay v biu din h phn t theo t l mn lm vic. Dch chuyn phn t theo cc trc. Quay phn t theo cc trc. Phng to, thu nh. Chuyn phn t thnh nhng lt nh theo trc z.

H to trong HyperChemHyperChem c hai h to biu din phn t: H to ca ngi quan st v h to phn t. Mi h to u c cc trc to Decac x, y v z.

H to phn t tu thuc vo phn t , do khi dch chuyn phn t th h to cng thay i theo. Cn h to ca ngi quan st l khng i trong HyperChem, n c biu din nh hnh trn. Trong HyperChem khi ta s dng cc cng c ta dng nhp tri chut dch chuyn, quay l thc hin theo h to ngi quan st, vic dch chuyn ny xy ra cho ton b h phn t. Ta dng phi chut dch chuyn, quay theo h to phn t. Vic dch chuyn ny ch xy ra i vi cc nguyn t, hp phn, phn t c chn.

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H to ca ngi quan stH to ca ngi quan st (Viewers Coordinate System) nh r v tr ca cc nguyn t lin h vi ta, ngi quan st. H to ca ngi quan st gn vi dng hnh hc mn hnh. Trc y thng ng, trc x nm ngang, trc z thng gc vi mt phng mn hnh. Trong h to ca ngi quan st, ta c th di chuyn phn t m khng lm thay i cc to nguyn t. Vi cc cng c trong HyperChem, ta dng tri chut dch chuyn cc phn t theo h to ca ngi quan st. Cc phn t dch chuyn nh ta nag thay i v tr quan st ca mnh. S dch chuyn nh hng ln ton b h phn t. Vi mt s hp thoi lc chn ca HyperChem, nh l Align Viewer (t thng ngi quan st), s dch chuyn l t ng theo to ca ngi quan st nu khng c nguyn t no c chn. Khi ta to mt phn t u tin, HyperChem t thng h to ca ngi quan st v h to ca phn t do cc trc x, y v z l tng ng nhau. Khi ta dch chuyn phn t, cc h to khng cn tng ng nhau na. Dng Align Viewer trong Edit menu dch chuyn h to ca ngi quan st n tng ng vi h to ca phn t. Khi ta lu h phn t vo file HIN, HyperChem cng lu c h to ca ngi quan st. Khi m li file ny ta s c ng h to lu.

H to ca phn tH to ca phn t gn lin vi h phn t v nh r to ca cc nguyn t, cc ta ny c s dng trong tt c cc tnh ton ho hc ca HyperChem. Ta c th xc nh to phn t ca bt k nguyn t no bng cch la chn nguyn t . To ca nguyn t c chn xut hin trn dng hin trng (status line). Vi cc cng c ca HyperChem, ta dch chuyn cc nguyn t theo h to phn t bng cch s dng nt phi chut. Vic dch chuyn ny ch tc ng ln cc nguyn t, hp phn, v cc phn t c chn. Cng c (Tool) Chc nng ca nt phi chut 43

Hng dn s dng HyperChem 7.04 Quay theo XY Ch quay khi c phn t c chn. Quay theo Z Ch quay c phn t hay nhnh c th quay c. Dch chuyn theo XY Dch chuyn cc nguyn t hay phn t chn.(a) Dch chuyn theo Z Dch chuyn cc nguyn t hay phn t chn.(a) a. Chc nng ca nt phi c gii hn cho ton b phn t nu Whole molecule translation trong mc Tool ca hp thoi Preferences (trong File menu) c tch chn. Vi cc hp thoi ca HyperChem, nh l Align Molecules, s dch chuyn t ng theo h to ca phn t.

Trc qun tnhi vi cc nguyn t hay c h phn t c chn, HyperChem c th tnh ton s chuyn ng theo qun tnh v c cc trc qun tnh. HyperChem bo s chuyn ng theo qun tnh trn dng hin trng v biu din cc trc qun tnh l cc ng nt t, c nh trong h to ca phn t. C ba s chuyn ng v ba trc (trc th nht, th hai v th ba) thc hin chc nng theo v tr v khi lng ca cc nguyn t. Cc trc qun tnh ph thuc vo h phn t v khng ph thuc vo h to ca ngi quan st ln h to ca phn t. Tch chn Show inertial Axes trong Display menu biu din cc trc qun tnh. C s trc dao (vung gc) v c nh s th t 1, 2 v 3 cho cc trc th nht, th hai v th ba ring. Cc trc vn hin trn mn lm vic cho n khi ta b tch Show inertial Axes trong Display menu. Trc qun tnh th nht thng biu th khong cch di nht qua h phn t, v trc qun tnh th ba biu th khong cch ngn nht.

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HyperChem dng cc trc qun tnh b tr cc phn t (Xem t phn t thng trc: Align Molecules) trn mn lm vic v khi nh r POINT, LINE v PLANE (xem phn chn: Select). Nhng s nh r ny l trong cc s hng ca cc trc qun tnh. in giao nhau ca cc trc qun tnh ti tm khi ca cc nguyn t chn. LINE Trc th hai ca cc nguyn t chn. (1) PLANE Mt phng hnh thnh t trc th nht v trc th hai, vung gc (trc giao) vi trc th ba ca cc nguyn t chn. (1) Trc th nht ng vi gi tr c trng nh nht trong s chuyn ng ca ma trn qun tnh. POINT

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t ch lm vic cho cc cng cTch chn Preferences trong File menu. Tch chn mc Tool trong hp thoi Preferences. Hnh nh hp thoi lc ny c dng nh sau:

Cc la chn gip ta trong qu trnh s dng cc cng c quay, phng to, dch chuyn trn mn lm vic. Gi tr t cho vic di chuyn chut t mp ny n mp i din trong mn lm vic. XY rotation Nu ta t l 360 th khi dch chuyn t mp ny n mp i din phn t s quay c 3600. Mc ny t c gi tr t > 0 n 36000. t c gi tr t > 0 n 36000. t c gi tr t > 0 n 1000A0. t c t l t > 0 n 1000 ln. t c di dch chuyn mt ct t > 0 n 1000A0. Khi tch chn, gip ta chuyn dch nhanh hnh nh h phn t. Nu ta tch chn mc ny th khi dng cng c hay hp thoi u dch chuyn c c phn t. Nu khng tch chn thi khi dch chuyn theo to ca phn t s ch dch chuyn c phn la chn trong phn t. (Dch chuyn quan st l nh nhau khi ta tch hay khng tch, ch c s khc nhau khi dch chuyn theo to phn t)

Z rotation Z translation Zoom Clip Fast translation Whole molecule translation

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Hng dn s dng HyperChem 7.04 Ch : Tng t ta cng t c ch cho cc cng c khi s dng bn phm bng cch t cc la chn trong mc Key ca hp thoi Preferences.

Nghch chuyn (Invert: chuyn (ho) thnh)Nghch chuyn tin hnh chuyn ho hnh hc phn t (nghch chuyn) qua mt im (POINT). POINT l tm khi ca mt hay nhiu nguyn t chn. S dng hp thoi Name Selection trong Select menu xc nh POINT. Nu to ca mt nguyn t l x, y v z (lin h vi POINT), Invert chuyn chng thnh x, -y v -z. Khi ta thit lp mt POINT, ta c th nghch chuyn bt k nguyn t no chn, hoc nu khng c la chn th s nghch chuyn c h phn t. Ch : Invert chuyn qua mu xm hot ng c khi h chn POINT trong Name Selection.

nghch chuyn cc nguyn t v phn t ta lm nh sau:1. Chn mt hoc nhiu nguyn t nh nghch chuyn POINT. 2. Chn Name Selection trong Select menu. Sau tch chn POINT trong hp thoi ny v nhp OK chn. 3. B chn tt c cc nguyn t. 4. Chn Invert trong Edit menu. Ch : Nu ta nghch chuyn cc nguyn t chn trong mt phn t HyperChem ch nghch chuyn cc nguyn t ny v c th bp mo cc lin kt ni vi cc nguyn t t phn ng yn ca phn t. Ta nn t Chirality trong hp thoi Labels d dng quan st s nghch chuyn. V d: nghch chuyn amino axit alanine. Khi carbon alpha l mt tm bt i, s nghch chuyn thay i s bt i ca nguyn t ny.

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Ta cng c th dng s nghch chuyn nghch chuyn cu hnh dng gh v dng thuyn.

Phn chiu (Reflect)Phn chiu tin hnh chuyn ho hnh hc phn t (s phn chiu) qua mt mt phng (PLANE). S chuyn ho phn t ny c th to ra mt hnh nh qua gng cc nguyn t hoc ton b phn t chn. Nu PLANE l mt phng XY, khi Reflect chuyn to ca nguyn t t x, y v z (lin h vi PLANE) thnh x, y v -z. S dng hp thoi Name Selection nh r PLANE. PLANE l mt phng c xc nh theo trc qun tnh th nht v th hai ca cc nguyn t. Phn chiu tc ng ln cc phn t c chn, hoc nu khng chn th n tc ng ln ton b h phn t. Nu cc nguyn t c phn chiu c mt hay nhiu tm bt i, HyperChem lm thay i s bt i ca chng. Ch : Phn chiu chuyn qua mu xm hot ng c khi h phn t c phn la chn vi tn l PLANE. Ta nn t Chirality trong hp thoi Labels d quan st s thay i.

phn chiu cc nguyn t v phn t ta lm nh sau:1. Chn t nht ba nguyn t phn chiu PLANE. 2. Chn Name Selection trong Select menu. Tch chn PLANE trong hp thoi v nhp OK chn. 3. B la chn cc nguyn t. 4. Chn Reflect trong Edit menu.

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Hng dn s dng HyperChem 7.04 V d: Phn chiu mt nhm bn ca cyclohexane:

Dch chuyn phn t theo trc xyTa c th dng cng c dch chuyn dch chuyn phn t n cc v tr trn mn hnh theo cc trc X v Y. Cch tin hnh nh sau 1. Nhp tri chut vo cng c dch chuyn. 2. Di chuyn con tr ln mn lm vic. 3. Nhp tri chut, gi v r phn t n v tr mi.

4. Nu mun dch chuyn n to c th ta c th dng hp thoi la chn. C hai cch lm xut hin hp thoi ny: 49

Hng dn s dng HyperChem 7.04 - Nhp tri chut chn Translation trong Edit menu. - Nhp lin tip hai ln tri chut vo cng c dch chuyn. Hp thoi xut hin nh sau:

5. Nhp tri chut vo tng la chn dx, dy, dz v nh s thch hp vo . C th dch chuyn gia cc phn la chn khc nhau nh s bng cc nhp phm Tab trn bn phm. 6. Nhp OK chn sau khi nh cc s theo mun. Cc mc trong hp thoi dch chuyn:

Translate Viewer (chuyn dch quan st) dx dy dz Translate Selection (Chuyn phn la chn)

Dch chuyn ton b phn t trong mn lm vic, nhng cho php to cc nguyn t khng thay i. y ging nh dng nt tri chut vi cng c dch chuyn trn mn lm vic. Lng chuyn sang phi, A0. Lng chuyn ln trn, A0. Lng chuyn ra pha ngi quan st, A0. Chuyn tm khi ca cc nguyn t c chn n mt im mi, lm thay i to nguyn t. y ging nh dng phi chut vi cng c dch chuyn trn mn lm vic. Nu ch mt phn phn t c chn, v khng c tch chn Whole Molecule translation (trong mc Tool ca hp thoi Preferences) th HyperChem s ch dch chuyn phn la chn. POINT Dch chuyn phn t hoc cc nguyn t chn n POINT (im) xc nh trong hp thoi Name Selection. Origin Dch chuyn phn t hoc cc nguyn t chn n h to ban u. 50

Hng dn s dng HyperChem 7.04 Other Dch chuyn phn t hoc cc nguyn t chn n to mi do ta t.

Dch chuyn theo trc ZTrong HyperChem thit k cng c ta dch chuyn nhanh phn t theo trc XY ring v trc Z ring. Tuy nhin cch lm u ging nhau. Nhng hp thoi la chn c th to mun dch chuyn l nh nhau. Cng c dch chuyn nhanh theo trc Z c dng sau: Ch : a phn t dch chuyn tr li trung tm mn lm vic ta ch cn nhp vo phm trn bn phm. S dch chuyn ch c tc dng khi ta dch chuyn cng c sao cho phng dc theo cng c lun song song vi trc z ngm nh ca HyperChem, iu c ngha l ta phi dch chuyn cng c ln xung theo trc thng ng (trc Y).

S dng cng c phng toi khi phi xem chi tit v tr no trn phn t ta cn phng to v tr , cng c khi ta mun xem ton b h th li phi thu nh va phi. Do vic s dng cng c phng to, thu nh l cn thit.

Cch s dng cng c phng to (zoom tool)51

Hng dn s dng HyperChem 7.04 1. Nhn phm Shift ng thi nhp tri chut vo gn nh phi ca biu tng phng to, gi nh vy cho n khi phn t trn mn hnh nh nh mong mun. 2. phng to ta cng lm tng t nhng lc ny nhp tri chut vo gc di bn tri ca biu tng phng to. Phn t c phng to c dng nh:

Ch : ch s dng c vi phm Shift khi HyperChem trn my l ci t. i vi phn mm ch c copy gia cc my th khng thc hin c nh vy m ta phi dng cc phng php khc. Ta cng c th phng to hay thu nh bng cch iu khin trc tip chut hoc s dng hp thoi chn kch c c th. 1. Thao tc bng chut - Nhp tri chut vo biu tng phng to. - Di chuyn con tr xung mn lm vic. - Nhp tri chut v r theo phng to-nh ca biu tng phng to hay thu nh phn t. 2. S dng hp thoi - Ta nhp lin tip hai ln tri chut vo biu tng phng to trn thanh cng c hoc nhp vo Zoom trong Edit menu. Hp thoi la chn hin ra. - nh vo kch c m ta mun phng to hay thu nh. - Nhp OK chn. 52


+Zoom Factor: h s phng to.

t phn t tr li tm v biu din theo t lKhi mt h phn t c m t File, n c biu din tm mn lm vic theo kch c chun nh sn. Nhng do qu trnh thao tc lm lch v tr ban u ca n i. Nhng ta hon ton c th a n tr li tm mn lm vic vi t l chun nh sn.

Cch lm nh sau1. Nhp tri chut chn Scale to Fit trong Display menu, hoc nhp nt Spacebar trn bn phm. Phn t s c a tr li kch c ban u v n c t vo tm mn lm vic. Ch : Ta c th a phn t tr li tm vi kch c chun ban u bng cch chn gi tr 1 trong hp thoi ca cng c phng to.

Quay phn t theo phng XY quay phn t theo cc trc x, y ta dng cng c quay. Cch lm nh sau 1. Nhp tri chut vo cng c quay theo trc XY. 2. Di chuyn con tr xung mn lm vic. 3. Nhp tri chut, gi v r theo phng x, y m ta mun xoay phn t. Hnh nh trn mn hnh c dng nh sau:

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Quay phn t theo trc Z quay phn t theo trc z ta s dng cng c quay theo trc z.

Cch lm nh sau1. Nhp tri chut vo cng c quay theo trc z.

2. a con tr xung mn hnh. 3. Nhp tri chut v r qua tri hay phi xoay phn t theo mun.

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Hng dn s dng HyperChem 7.04 Ch : R chut theo chiu ln xung khng c tc dng g trong cch quay ny. Ta cng c th s dng hp thoi la chn quay. Vic ny thc hin bng cch nhp chn Rotate trong Edit menu hoc nhp lin tip hai ln tri chut vo cng c quay trn thanh cng c hp thoi la chn xut hin. Hp thoi la chn quay:

Rotate About

X Axis Y A xis Z Axis LINE Angle Apply to Molecules Viewer

Ta c th quay cc nguyn t la chn, hoc khng la chn, hoc c h phn t quanh mt trc theo h to ca ngi quan st hay h to phn t, hoc quanh mt LINE (ng). LINE l phn la chn c t tn ph thuc vo h phn t. Nu ta khng th quay cc nguyn t chn, HyperChem biu din mt dng thng tin trn thanh hin trng. L trc trong mt phng nm ngang ca mn hnh Trc trong mt phng thng ng ca mn hnh Trc vung gc vi mt phng mn hnh L tn ca phn la chn. Ta dng Name Selection t LINE chon h phn t. t gc quay. Gi tr thay i t 360 n +3600 Quay cc nguyn t chn hay ton b h phn t theo cc cch: Quay theo h to ca phn t, lm thay i to ca cc nguyn t. Quay theo h to ca ngi quan st, to ca cc nguyn t khng i.

Ct phn t thnh tng lt nh theo trc Z

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Hng dn s dng HyperChem 7.04 Vi cng c ct phn t theo trc z s gip cho ta quan st k hn bn trong phn t t nhng lt ct nh

Cch lm nh sau1. Xoay phn t bng cng c xoay sao cho khi ct ta d quan st.

2. Nhp hai ln tri chut vo cng c ct theo trc Z, hoc nhp tri chut vo Z Clip trong Edit menu.

Hp thoi la chn xut hin:

3. Ta c th ko thanh cun hoc chn ch s thch hp ct phn t theo mun. Sau khi chn ct xong ta nhp OK thc hin. Hnh nh phn t b ct v d nh sau:

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4. Mun ct tip ta thc hin nhp li vo cng c ct v thc hin nh trn. Ch : Ta cng c th thc hin ct phn t bng chut trn mn lm vic. Cch lm nh sau: 1. Nhp tri chut chn cng c ct theo trc Z trn thanh cng c v di chuyn cng c ct ln mn lm vic. 2. Nhp tri chut gi v r thng ng iu chnh v tr ct mt phng pha trc ca phn t. 3. Nhp Phi chut, gi v r thng ng iu chnh v tr ct mt sau ca phn t.

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Hng dn s dng HyperChem 7.04 4. Di chuyn chut t mp trn xung mp di mn lm vic ta s dch chuyn mt phng ct c khong 10A0 (Ngm nh). Ta c th xem dch chuyn trn dng hin trng bn di ca s HyperChem. Ch : a phn t tr li trng thi ban u ta ch vic nhp vo nt Spacebar trn bn phm.

Ch thch hp thoi Z Clip

System Slab

V tr xa nht ng trc v ng sau ca ton b phn t trn mn lm vic. V tr mt phng ct trc v sau gn vi ngi quan st.

Dng cc dng nm (Wedge) biu din lin kt trong khng gianHyperChem cho php ta biu din cc lin kt trong khng gian bng cch biu din lin kt di dng cc hnh nm. Cc hnh nm c s dng vi quy c nh sau:

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Cch thc hin nh sau: 1. Nhp chn Rendering trong Display menu, sau chn mc Sticks v tch chn Wedges, nhp OK ng hp thoi. 2. Nhp tri chut chn cng c v trn thanh cng c. 3. Nhn phm Shift trn bn phm ng thi nhp tri chut vo lin kt mun biu din cho n khi c dng mong mun. 4. Nhp lin tip hai ln tri chut vo cng c la chn trn thanh cng c dng trnh xy dng biu din li cu trc trong khng gian, nu mun.

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Bi 5. Xem thuc tnh cu trc phn tTrong bi ny ta hc cch o cc thuc tnh cu trc ca phn t nh l gc lin kt, di lin kt, gc vn

Xem thuc tnh ca nguyn t Cch lm nh sau:1. Nhp tri chut tch vo Atoms v b tch Multiple Selections trong Select menu. 2. Nhp tri chut vo cng c la chn trn thanh cng c. 3. Nhp tri chut vo nguyn t mun bit c tnh. Nguyn t c la chn s sng hn v c tnh ca phn t hin ra thanh hin trng bn di.

Dng hin trng cho ta bit s nguyn t, tn nguyn t, in tch nguyn t theo trng c hc phn t hin ti, to theo cc phng x, y v z.

o di lin ktTa hon ton c th xc nh c di cc lin kt trong phn t. Gi tr di ny trnh by trong dng hin trng bn di.

Cch o nh sau1. Nhp tri chut vo cng c la chn trn thanh cng c. 60

Hng dn s dng HyperChem 7.04 2. Nhp tri chut vo nguyn t th nht mun o ko n nguyn t th hai ri nh chut ra. Lin kt gia hai nguyn t s sng hn, di o c biu din dng hin trng. Ch : Sau khi thc hin tnh ton ti u h phn t ta c th bit c gi tr thuc tnh khc ca h bng cch nhp chn phn mun xem hoc xem thuc tnh c h (khng cn chn phn no) tip theo chn Propeties trong Computer menu. Mt hp thoi thuc tnh hnh hc xut hin trn mn lm vic, vi c h c th c c cc gi tr v nng lng ton phn, nhit hnh thnh, momen lng cc...

o gc lin kt o gc lin kt ta nhp tri chut vo nguyn t th nht v r n nguyn t th ba (theo th t lp thnh gc). Cch o gc lin kt 1. Nhp tri chut vo cng c la chn trn thanh cng c. 2. Nhp tri chut vo nguyn t th nht r n nguyn t th ba (theo th t to nn gc) ri nh chut.

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o gc vnTa c th o gc vn bng cch r chut chn hai phn t u v cui trong bn phn t to nn gc vn.

Cch lm nh sau1. Nhp tri chut vo cng c la chn trn thanh cng c. 2. Nhp tri chut vo phn t u r n phn t th t trong bn phn t to nn gc vn ri gii phng chut. Hnh nh v d nh sau:

3. Gi tr gc vn hin th trong dng tnh trng di. 62


o khong cch khng lin kt o khong cch khng lin kt ta lm nh sau1. Nhp tri chut tch vo Multiple Selections trong Select menu. Vic bt Multiple Selections cho php ta chn nhiu nhm, ngoi ra khi ta la chn nhm th hai th nhm th nht vn c chn. 2. Nhp tri chut vo cng c la chn trn thanh cng c. 3. Nhp phi chut vo phn trng trn mn lm vic. Vic ny gip ta hu b tt c cc la chn trc . 4. Nhp tri chut ln lt vo hai nguyn t khng lin kt. Khong cch gia chng hin th trn dng hin trng.

Lin kt Hydro gip ta xc nhn iu kin to lin kt hydro, HyperChem cho php ta tnh ton v biu din lin kt ny. Lin kt hydro c hnh thnh khi khong cch t hydro cho n nguyn t nhn b hn 3,2 A0.

biu din lin kt hydro ta lm nh sau1. 2. 3. 4. Nhp tri chut vo cng c la chn trn thanh cng c. Nhp phi chut vo vng trng trn trang lm vic. Nhp tri chut tch vo Show Hydrogen Bonds trong Display menu. Nhp tri chut chn Recompute H Bonds trong Display menu. HyperChem s biu din cc lin kt hydro nu c di dng ng nt t nh sau:

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Hng dn s dng HyperChem 7.04 Lin kt hydro khng t ng tnh ton ng thi vi qu trnh ti u hnh hc phn t. Do ta phi tnh lin kt hydro li mi khi cn thit.

Recompute Hydrogen BondsTnh ton li lin kt hydro xc nh cc lin kt hydro gia cc phn t chn hoc nu khng c s la chn, th n xc nh lin kt hydro gia tt c cc nguyn t trong h phn t. HyperChem to ra cc lin kt hydro nu khong cch gia cc hydro cho v nguyn t nhn b hn 3.2A0 v gc to bi lin kt cng ho tr t hydro cho n cc nguyn t nhn ln hn 1500. Tuy nhin ta cng c th thay i cc tiu chun ny.

Biu din momen lng ccKhi ta tch chn Show Dipole Moment, HyperChem s biu din momen lng cc tnh ton cho cc nguyn t c chn hoc cho c h phn t. Show Dipole Moment ch hot ng sau khi ta thc hin tnh ton im n. Momen lng cc biu din trn mn hnh dng ng nt t tm khi ca cc nguyn t chn. Dng hin trng cho bit tng gi tr ca momen lng cc v gi tr momen theo cc trc khc nhau theo n v Debye.

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Bi 6. Databases MenuTo chui PolypeptideNi cc hp phn li vi nhau Thm phn cn thiu cho chui Thay i hp phn v tr c bit

S dng hp thoi la chn cc Amino AxitHp thoi la chn cha cc hp phn amino axit c cu trc ho hc chun. Trong hp thoi ta chn cc cu hnh bc hai ca polypeptit (Xon apha, mng beta hay cc kiu gc khc ta t: gc Phi, Psi v Omega). Ta chn xy dng chui bt u t amino axit c im N cui (N-Terminus: ui nit). Trong hp thoi gm c: 20 amino axit chun. Hai kiu trung tnh v mt kiu proton ho ca histidine (Hid, Hie v His). pH sinh l, histidine c th mang in tch dng hoc trung ho tu thuc vo mi trng. Half-Cyx (bn Cystine) dng to lin kt ngang i sunfua. Mt nhm c im N cui (N-teminal: Ace). N ch c dng lm hp phn khi u cho chui. Mt nhm c im C cui (C-teminal: Nme). N ch c dng kt thc chui.

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m hp thoi cch lm nh sau1. Nhp tri chut vo Amino Acids trong Databases menu. Hp thoi Amino axit xut hin nh sau:

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Hng dn s dng HyperChem 7.04 Hp thoi Amino axit hin cho ti khi no ta nhp vo nt tt trn gc phi. - Ala Alanine, thuc cht bo trung tnh, khng cc. - Gly Glycine, trung tnh, c cc. - Ser Serine, trung tnh, c cc. - Thr Threorine, trung tnh, c cc. - Leu Leucine, trung tnh, thuc cht bo, khng cc. - Ile Isoleucine, trung tnh, thuc cht bo, khng cc. - Val Valine, trung tnh, thuc cht bo, khng cc. - Asn Asparagine, trung tnh, c cc. - Gln Glutamine, trung tnh, c cc. - Arg Arginine, tch in dng. - Hid Histidine, trung tnh, c hydro nit delta. - Hie Histidine, trung tnh, c hydro nit epsilon. - Hip, His Histidine, tch in dng, c hydro c nit delta v epsilon. - Trp Tryptophan, vng thm trung tnh, khng cc. - Phe Phenylalanine, vng thm trung tnh, khng cc. - Tyr Tyrosine, vng thm trung tnh, c cc. - Glu Axit Glutamic, tch in m. - Asp Axit Aspartic, tch in m. - Lys Lysine, tch in dng. - Pro Proline, trung tnh, khng cc. - Cys Cysteine, trung tnh, c cc. - Cyx Bn Cystine, trung tnh, c cc. Nu ly t file PDB ta s c hp phn Cystine y . - Met Methionine, trung tnh, khng cc. - Ace Acetyl, Nhm c im N cui (N-teminal). - Nme N-Methyl amino, Nhm c im C cui (C-teminal).

To dng v biu din chui PolypeptideCc chui Polypeptide thng c hnh dng rt phc tp. d dng trong vic to dng v quan st ta phi la chn hnh dng biu din thch hp c v mt ho hc ln kh nng quan st. Trong phn ny ta hc cch dng cu trc bc hai ca polypeptide. Ch : Ta khng thm bt hay sa i g cc hp phn bng cch dng cng c v. sa i ta s hc cc bc sau (xem Thay th monome trong hp phn bng amino axit khc; To ion lng cc).

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Hng dn s dng HyperChem 7.04 HyperChem ni kt cc hp phn li vi nhau theo th t ta chn chng. Khi nhp chn hp phn c C-teminal (cn gi l np bt: cap), n s ngn cn khng cho ni thm cc hp phn khc vo chui. Nu ta chn tip th mt chui khc s c hnh thnh. Khi ko di chui, ta c th thay i cc thuc tnh ca cc hp phn tip theo: - Cu trc bc hai(xon alpha, mng beta, hay cc gi tr do ta t Other) - Cu hnh ca lin kt peptit (Omega) - ng phn L hoc D ca mi hp phn.

Cch lm nh sau:1. Nhp tri chut chn Amino Acids trong Databaes menu. 2. Tch chn Beta sheet trong hp thoi Amino Acids. iu ny gip biu din cc gc vn phi v psi 1800. 3. t gc vn omega l 1800.

To chui1. Nhp tri chut ln lt vo cc amino axit m ta mun ni thm vo. V d nh sau: Arg-Pro-Pro-Gly-Phe-Ser-Pro-Phe-Arg. Ch : Ta khng s dng trnh xy dng (Model Builder) dng li ton b cu trc chui. Trnh xy dng s lm hng cu trc ti u ca phn t v khng th ly li chnh xc cu trc ban u. Tuy nhin ta c th dng trnh xy dng i vi cc nguyn t c chn no . Nu chui polypeptide khng c np bt, ta c th thm tip cc hp phn n hp phn c C-teminus. Nu ta thc hin to ion lng cc (Make Zwitterion), ta cng khng th thm cc hp phn c na, khi chn thm hp phn th mt chui khc s c xy dng. Hp phn ca chui c th c cu hnh bc hai khc nhau. Chui polypeptide c th cng c cu trc xon alpha, cu trc gp beta cng nh cc cu hnh chuyn ho khc.

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Xon Alpha (Alpha helix: xon c alpha) Mng beta (Beta sheet)

t chun cc gc vn Phi v Psi l -58 v -470 cho xon alpha, cng vi lin kt peptit chuyn tip (transpeptide) (Omega = 1800). t chun cc gc Phi v Psi cng l 1800 v cng t tm gp khc tm beta l 1800, cng vi mi lin kt peptit chuyn tip (Omega = 1800).

Other Chp nhn gi tr khng chun cho cc gc vn Phi, Psi v Omega. Phi Gc vn () ca C-N-C-C: Thay i t 360 n +3600 Psi Gc vn () ca N-C-C-N. Thay t 360 n +3600. Omega Gc vn lin kt peptit (),thng thay i t 170 n 69

Hng dn s dng HyperChem 7.04 1800. p dng cho hp phn amino axit tip theo. Thay i t 360 n +3600. Cho php ta chn ng phn lp th L thng thng (Khng i xng S) hoc ng phn lp th D (khng i xng R).

Isomer

Ch : Ta c th dch chuyn hp thoi amino axit trn mn hnh v s dng c cc cng c khc (v d nh t nhn trong Display menu).

To ion lng cc (Make Zwitterion)Trong dung dch c pH trung tnh, cc polypeptide tn ti di dng cc ion lng cc, cha cc nhm ui l -NH3+ v -COO-. Thc hin to ion lng tnh cho phn t polypeptide chn nhm chuyn cu trc theo file d liu thnh ion lng tnh. Nu khng c polypeptide no c chn th Make Zwitterion s thc hin cho tt c cc polypeptide trong h. Cc polypeptide thc hin c Make Zwitterion phi c nhm ui thng thng (-NH v -CO) ch khng phi l cc nhm np bt (cap: Ace v Nme). Khi ta dng chui peptit vi HyperChem, cc phn ui cha y (cn l -N-H v -C-O). Make Zwitterion chuyn i cc phn ui thnh NH3+ v -COO-.

Cch lm nh sau1. Chn none ( phn Atoms) trong hp thoi Labels d nhn. 2. Dch chuyn v quay phn t polypeptide gip ta d quan st.

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3. Nhp tri chut chn Make Zwitterion trong Databases menu. HyperChem s thm vo oxi cn thiu trn nguyn t C.

HyperChem cng thm c cc proton cn thiu vo nguyn t N.

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Hng dn s dng HyperChem 7.04 Ch : Cc hp phn amino axit trong file d liu (Trong Database hay File PDB) bao gm cc nguyn t vi phn din tch ring. Khi thc hin Make Zwitterion s lm thay i in tch nhm nguyn t ui (Teminal). N khng lm thay i in tch ca cc nhm bin ca cc amino axit (v d xem cc nhm bin axit, baz hay cc nhm imio C3H4N2).

B Ion cc ui (Remove Ionic Ends)B ion ui ngc li vi kt qu Make Zwitterion. iu ny tc l chuyn cc nhm NH3+ v -COO- trong polypeptide thnh NH v -CO.

Thay th mt monome trong hp phn bng mt amino axit khcTh t ca cc amino axit trong chui ng mt vai tr quan trng trong cu trc chui. Mi s thay i th t hay thay th mt monome ny bng mt monome khc u dn thay i cu trc v thuc tnh ca protein, do cng thay i chc nng ca n.

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Cch lm nh sauTrc tin cn phi bit tn v v tr amino axit hp phn cn thay th. 1. Nhp tri chut vo Labels trong Display menu. 2. Nhp tri chut tch chn Name + seq trong hp thoi Labels. Nhp OK mn hnh s hin ra nh sau.

3. Nhp tri chut tch chn Residues trong Select menu. 4. Nhp tri chut vo cng c la chn trn thanh cng c. 5. Nhp phi chut vo vng trng mn lm vic loi b tt c cc la chn c th c trc . 6. Nhp tri chut vo PHE 5. Hp phn ny s sng hn ln. 7. Nhp tri chut chn Mutate trong Databases menu.

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Ch : Mutate s khng hot ng nu ta cha tch chn Residues trong Select menu. 8. Trong hp thoi Mutate, ko thanh cun chn amino axit mun thay th. V d chn Thr.

iu ny c ngha l phenylalanine c thay th bng threonine:

Ch : Nh lu tn phn t m bn mi to bng mt tn thch hp. i vi nucleic axit ta cng lm tng t.

Cc Axit NucleicV c bn cch xy dng chui polycucleotide tng t nh cch xy dng polypeptide trn. Ta s dng cc Axit Nucleic xy dng chui polynucleotide (AND v ARN). Cc hp phn ny c cu trc ho hc chun.

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Hng dn s dng HyperChem 7.04 Trong hp thoi Nucleic Acids, ta c th chn cc cu trc bc hai cho cc hp phn thm vo (A, B, Z hoc cc kiu gc cu hnh khc m ta t). Ta c th to chui polynucleotide bt u t cc ui 5 hoc 3 bng cch nhp chn cc hp phn axit nucleic ny: - Bn deoxyribonucleotide (monophosphat) - Bn ribonucleotide (monophosphat) - Np bt (Cap) A 3 cn tr ko di chui thm. - Np bt A 5 cn tr ko di chui thm. Ch : Ta khng chnh sa cc hp phn bng cng c v. Ta c th thm bt hay chnh sa cc hp phn nh trng hp Amino axit trn. HyperChem ni kt cc hp phn li vi nhau theo th t ta chn cc hp phn, bt u t phn ui 5. y l trt t t nhin ca qu trnh tng hp AND v ARN. Nu ta mun xy dng chui bt u t ui 3 th phi tch chn Backward (ngc) trong hp thoi. Cc u bt (cap) ngn cn vic thm tip cc hp phn k c cc hp phn ui 5 v 3. Sau khi thm mt u bt, vic chn thm hp phn mi s to mt chui khc. Nu chui cha c u bt, ta c th thm c nhiu hp phn na cho n khi c u bt. Khi ko di chui, ta c th thay i thuc tnh ca cc hp phn tip theo m ta thm vo: - Cu hnh bc hai (A, B, Z hay cc kiu khc). - K c kiu gp 2 Endo (gp ni) hay 3 Endo cho vng ng. Kiu A ca AND thng cha ng deoxyribose dng C3-endo bn vng hn. Kiu B ca AND cha ng C2-endo. - Double-Stranded (Kt i thnh phn). Tch chn phn ny th khi nhp chn axit, ngoi axit ta chn cn c thm baz lin hp ca chnh n, gia chng c cu ni hydro vi nhau (Tch chn Recompute H Bonds trong Display menu xem lin kt hydro). HyperChem quan tm ch yu n cp baz; mt s lin kt trong hp phn lin hp c di lin kt khng ng v mt s cp baz cng khng c cc gc cun chnh xc. Ta cn phi ti u hnh hc li sa cc li trong cu trc.

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Hng dn s dng HyperChem 7.04 Ch : Khng s dng trnh xy dng (Model Builder) i vi polynucleotide xy dng. Trnh xy dng s lm hng hnh hc ca phn t v khng th xy dng li chnh xc c. Cc la chn ta t c nh hng n cc hp phn sau cho n khi ta thay i kiu la chn khc. Ta khng th thay i thuc tnh sau khi tch chn hp phn . Hp thoi Nucleic Acids c dng nh sau:

Cc kiu hp phn trong hp thoi nh sau: - dA Deoxyadenosine 5 monophosphate, hp phn ca AND. - dT Deoxythymindine 5 monophosphate, hp phn ca AND. - dC Deoxycytidine 5 monophosphate, hp phn ca AND. - dG Deoxyguanosine 5 monophosphate, hp phn ca DNA. - rA Adenosine 5 monophosphate, hp phn ca ARN. - rU Uridine 5 monophosphate, hp phn ca ARN. - rG Guanosine 5- monophosphate, hp phn ca ARN. - rC Cytidine 5 monophosphate, hp phn ca ARN. - 5CAP u bt kiu A (-OH) kt thc chui ui 5. - 3CAP u bt kiu A (-OH) kt thc chui ui 3. Cc la chn cho hp phn nh sau: Helix Form t cu hnh bc hai cho cc hp phn ca chui. (Kiu xon c) Mi dng xon c c gc vn, cun (s vng quay ca mi phn) v cao (Chiu cao ca mt vng) c trng ring. A Form Cu hnh xon phi trong AND kt i, kh nc, c (Kiu A) khong 11 hp phn mi vng.

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Hng dn s dng HyperChem 7.04 B Form (Kiu B) Z Form (Kiu Z) Other (Kiu khc) Cu hnh xon phi trong AND kt i, kh nc, vi khong 10 hp phn mi vng. Cu hnh xon phi ca AND kt i, vi khong 12 hp phn mi vng. Xen k cc hp phn (c nh s chn l: odd, even) trong mi phn ca Z AND c cc gc vn khc nhau. Nhn cc gi tr ta t cho gc vn trong lin kt khung chui polynuleotide.

-

Alpha Beta Gama Chi Delta Epsilon Zeta

() Gc vn. Nhn gi tr t 360 n +3600. () Gc vn. Nhn gi tr t 360 n +3600. () Gc vn. Nhn gi tr t 360 n +3600. () Gc vn. Nhn gi tr t 360 n +3600. () Gc vn. Nhn gi tr t 360 n +3600. () Gc vn. Nhn gi tr t 360 n +3600. () Gc vn. Nhn gi tr t 360 n +3600.

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- Sugar Form 2 Endo 3 Endo - Double Strand

- Backward

Cu hnh ca vng ribo. C2 l ngoi mt phng vng, trn cng mt phng nh C5. C3 l ngoi mt phng vng, trn cng mt phng nh C5. Khi phn ny c tch chn, HyperChem thm hp phn lin hp ca chnh n, theo quy tc cp baz ca Watson-Crick, v dng ln mt polynucleotide khng song song. Ta c th tch hoc khng tch dng cc phn t c baz kt i mt phn. Khi tch chn phn ny, HyperChem bt u xy dng chui t phn ui 3, thm dn cc hp phn n phn ui 5. iu ny ngc li vi qu trnh tng hp AND v ARN thng thng. Vic t nh vy nh hng n ton b chui, do ta phi t n trc khi bt u xy dng chui.

Ch : Ta vn c th s dng cc cng c khc khi hp thoi Nucleic Acids cn trn mn hnh.

Thm cc ion tri du (Add Counter Ions)

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Hng dn s dng HyperChem 7.04 Add Counter Ions t mt ion natri gn mt nhm photphat trn khung lin kt ca chui polynucleotide. Ion Na+ cch u mi oxy ca nhm photphat mt khong 1.688A0.

Nu ta chn Add Counter Ions v sau thm cc hp phn khc, th ch cc hp phn u mi c ion tri du. Ta phi chn li Add Counter Ions li thm cc ion Na+ cho cc hp phn mi. Ch : loi b cc ion Na+ ta s dng chn cc ion mun loi b v dng Clear hoc Cut trong Edit menu. Nu ta lu h vo file HIN th cc ion tri du cng c lu. Dng tinh th (Crystal Builder) Crystal Builder l mt modun dng c, to v quan st cu trc tinh th trong HyperChem. Cc cu trc tinh th c th c lu, chnh sa hoc tnh ton nh bt k h no khc. Crystal Builder c cc tnh nng nh sau: - D dng xy dng cc tinh th nguyn t da trn cc kiu tinh th c bn: lp phng, t din, trc thoi (orthorhombic), hnh lng din (rhombohedral:c cc mt hnh thoi), su cnh, n t (monoclinic) v tam t (triclinic) - Cc cu trc mu nh l NaCl, CsCl, CaF2, PbS, MgO, ZnS - C th hiu chnh d liu nguyn t nh l vi to ca chng trc khi to tinh th. - C kh nng quan st cc mt khc nhau ca tinh th, xc nh ch s Miller. 79

Hng dn s dng HyperChem 7.04 - C kh nng c v vit cc file trong ngun d liu b tr bn ngoi.

Cc lnh s dng trong xy dng tinh thFile/new File/Open File/save None Xem dng a Xem dng cu Xo trng mn lm vic M file lu trc Lu kt qu trn mn lm vic Bt Stick trong Rendering Bt Disk trong Rendering Bt Sphere trong Rendering

Xem b mt tinh th HyperChem/Get t t bo n v t HyperChem HyperChem/Put Gi tinh th n HyperChem Tm tr gip

To tinh th kim loi NatriPhn ny minh ho cho ta cch to cu trc tinh th Natri 1. Khi ng HyperChem, tip theo tch chn Crystal trong Databases menu. 2. Trong mc Crystal Type, tch vo Cubic (lp phng) chn t bo n v dng lp phng.

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3. Nhp s t bo n v: 3x3x3 bng cch nh gi tr 3 vo trong ba tng ng. 4. Trong mc Unit Cell Parameters, nhp kch thc ca t bo cho Na: 4.225 cho u tin t a, b, c =. Gi tr ca b v c s c t ng t l 4.225. 5. nh s th t ca cc nguyn t trong t bo n v Na (bcc): 2 cho thch hp. 6. Nhp tri chut vo Edit Atom Date.. m hp thoi d liu nguyn t (Atom Data). 7. Trong hp thoi nn biu din s th t nguyn t l 1. Thay i tn nguyn t t - thnh NA1. i nguyn t thnh Na. 8. Nhn ln dng trn trong nt spin hoc nhp s 2 cho s th t nguyn t, d liu ca 2 nguyn t s c biu din. Thay i a, b v c t 0 n 0.5. Chuyn tn nguyn t t - thnh NA2. Nhp vo nt Close. 9. Nhp chn nt lnh: HyperChem/Put chuyn cu trc to c vo cho HyperChem, hoc ln lt nhn nt Toolbar i n khi cc cht lng mu xanh xut hin. 10. Tinh th natri 3x3x3 s xut hin trn mn lm vic ca HyperChem. 11. quan st mt phng tinh th [111], chn lnh View/Crystal Face trong Crystal Builder hoc nhp vo nt View trn thanh cng c. Mt hp thoi s xut hin. Nhp gi tr 1 cho cc h, k v l, nhp OK, v HyperChem s quay tinh th v t ct mt phng nhm biu din cho ta mt [111]. Dng lnh Display/Rendering trong HyperChem chuyn dng biu din nguyn t sang dng cu. 12. Lu t bo n v bng cch nhp lnh File/Save as (Nhp Save as trong File menu). nh tn mun lu vo mt file mi: NA.CSD. Nhp OK, v t bo n v c lu vo kiu D liu tinh th Cambridge.

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Hng dn s dng HyperChem 7.04 13. Lu ton b tinh th bng cch nhp vo ca s HyperChem v chn lnh File/Save as... Lu file vi tn mi l: NA.HIN.

To tinh th NaClPhn ny ta s hc cch to tinh th ca natri clorua. 1. Tch chn Crystal Builder bng cch nhp Crystals.. trong Database menu. 2. Nhn nt Samples.. vo hp thoi cu trc tinh th mu (Sample Crystal Structure) 3. Chn kiu tinh th NaCl bng cch nhp vo nt thch hp v nhn OK chn. 4. Nhp s t bo n v l: 3x3x3 bng cch nhp gi tr 3 vo trong ba hiu chnh. Khng nn hiu chnh g n tham s t bo n v: Trnh xy dng tinh th (Crystal Builder) t cc gi tr thch hp cho NaCl. 5. Chn lnh: HyperChem/Put gi cu trc cho HyperChem, hoc nhn nt Toolbar i khi c dung dch mu xanh xut hin. 6. Tinh th NaCl 3x3x3 s xut hin trn mn lm vic. 7. quan st mt phng tinh th [111], chn lnh View/Crystal Face trong Crystal Builder hoc nhp vo nt View trn thanh cng c. Mt hp thoi s xut hin. Nhp gi tr 1 cho cc h, k v l, nhp OK, v HyperChem s quay tinh th v t ct mt phng nhm biu din cho ta mt [111]. Dng lnh Display/Rendering trong HyperChem chuyn dng biu din nguyn t sang dng cu(nu mun).

Dng mt ct [111].

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Xy dng phn t ng (Sugar Builder)Trnh xy dng ng (Sugar Builder) cho php ta xy dng cu trc polysaccharite tng t nh xy dng chui amino axi hay chui axit nucleic. Ta c th to cc hp phn theo mun ch khng nht thit phi l saccharite (sacarit), v dng Sugar Builder ni kt cc hp phn li vi nhau. Cc tnh nng ca Sugar Builder - C 32 mu monosaccharite thng thng, bao gm c aldose v ketose, k c dng D, L, alpha, beta v dng xp xon (acyclic). - C kh nng thm cc nhm thng thng, k c OAc v Nac. - C kh nng to chui t cc mono hnh thnh nn chui polysaccharite. - Tham s ho trng lc AMBER cho chui (aldose). - C kh nng ni kt cc chui to cc nhnh. - C kh nng thm ln n 21 hp phn ca ngi s dng vo file d liu. To chui Phn ny minh ho cho ta cch to poly(1-4)--D-Glucose 1. Nhp tri chut chn Saccharides trong Database menu. 2. Dng lnh Add/Aldoses m hp thoi Aldoses. 3. Chn D v chn Dng phn D v anome . 4. Chn Glucoses to ra hp phn glucose trong HyperChem. 5. Chn kiu ni kt 1-4 bng cch chn n t list. 6. t v ln lt l 48.05 v -20. 7. Nhp tri chut lp i lp li vo Glucose cho n khi nhn c chui mong mun. 8. Chuyn ra mn hnh HyperChem v quan st chui mi to.

83


Dng chui polymer dng mt chui polyme, hy ch n kh nng xem phn t n trn mn lm vic c kh nng to chui khng. Nhng vic cn lm l xc nh phn u v phn ui ca phn t, ng thi xc nh gc vn, gc lin kt s c dng ni kt lp i lp li u vi ui cho n khi to thnh chui vi di mong mun. Trnh xy dng polyme ch xy dng cu trc ca polyme, n khng phn tch thuc tnh nh HyperChem thc hin i vi cc phn t khc. Khi cu trc polyme vi kch thc nh sn xy dng c, n to nn mt phn t bnh thng nh HyperChem quan tm. nh r monome. u v ui cc monome c th dng xy dng chui phi c mt u, xem nh l a v mt ui b. iu c ngha l monome phi c kiu, b-R-a. Bt k phn t no c t nht ba nguyn t u c th l mt monome. Polyme ho bng s tch Phn ng polyme ho l phn ng to ra s tch (ngng t) ca a-b. l: R-R-R-R bng cch lp i lp li

84


Nu gc vn R-R c xem l ngu nhin, khi u (a) v ui (b) phi c xc nh xy dng chui. Xc nh gc vn Khi tch a v b, hnh hc bn trong ca R c xem nh khng i. Tuy nhin, vn c s quay quanh lin kt R-R. C mt la chn cho qu trnh polyme ho ngu nhin, nt nm ngay bn phi. Kh nng khc na l gc c xc nh theo ngi s dng nh mt gi tr hng cho qu trnh ni kt. Trong trng hp ny ta cn xem xt thm n hnh hc ca lin kt RR. Tha nhn l a c ni vi nguyn t x ln lt ni vi x. Tng t, nguyn t b ni vi y v y ni vi y. C th, s ngng t monome l:

Trong trng hp, gc vn c xc nh l xon x-x-y-y. Mi nguyn t ny, a, b, x, x, y, y, c xc nh trong monome bng cc phn la chn c t tn. Nu chng khng c t tn, khi ta s thy dng bo li sau xut hin: V d:

Ta s xy dng mt polyme t monome 1-3 butadien. Phn t monome trng nh sau, y ta dng custom labels v ch thch ch ra cc phn la chn c t tn

85


Nu phn la chn c t tn ph hp c thc hin, khi nhp chn Polymers trong Databases menu. Hp thoi la chn nh sau xut hin:

Nhng la chn phi c thc hin t ngu nhin cc gc x-x-y-y hoc t cc gi tr hng xc nh. Hn na ta phi chn di ca chui polyme mun xy dng. Ch : Tch chn Branching Enabled ch khi cc nguyn t khc cng c t tn tng ng. V d cnh b ta t b cnh a t a Nu ta chn 300 cho gc xon v xy dng chui bng 20 n v. Ta s thu c cu trc nh sau:

86


To polyme cho cc monome khc Trong kiu mu trn ta c th s dng bt k monome no khc m ta mun vi iu kin ta xc nh chnh xc cc nguyn t cn c, a, b, x, x, y v y. Vi cc phn u v ui ngn, vic xc nh x v x c th trng vi vic xc nh y v y nhng iu khng thnh vn vi iu kin a, x v x (hoc b, y v y) xem nh l cc nguyn t lin kt ni tip nhau. Do , v d, x v y hoc x v b c th l cng mt nguyn t. Cc phn la chn c t tn a (hoc b) c th xem nh l mt nhm cc nguyn t, ch khng phi l mt nguyn t n, vi iu kin cc nguyn t ny lin kt vi x (hoc y) bng mt lin kt.

Cc bc tun t to Polyme nh sau (v d cho butadien) 1. V phn t Butadien ln mn lm vic. 87

Hng dn s dng HyperChem 7.04 2. Chn cng c la chn trn thanh cng c. 3. Chn nguyn t hydro u tin, tip theo chn Name Selection trong Select menu. 4. Chn mc Other, ri nh b vo . Tip theo ln lt chn cc nguyn t khc v nh tn theo th t nh hng dn trn. 5. Nhp chn Polymer.. trong Database menu, hp thoi la chn xut hin, hy nhp cc gi tr nh gc vn, s monome n v.. thch hp:

6. Nhp OK thc hin to chui polyme. Ch : Ta hon ton c th thc hin cc tnh ton kho st h polyme m mnh va to ra. Tuy nhin do polyme l phn t ln nn thng ngi ta ch kho st mt phn no ca h bng cch chn phn v thc hin tnh ton nh i vi cc phn t nh khc.

88


Bi 7. La chn v biu din mt nhm cc nguyn t trn mn lm vic To vng xon c. Chn nhm nguyn t. t nhn v t mu nhm nguyn t.

To vng xon c alpha.Ta hc cch to vng xon cho chui polypeptide.

Cch lm nh sau1. Nhp tri chut chn Amino Acids trong Databases menu. Hp thoi amino axit xut hin. 2. Nhp tri chut tch chn Alpha helix mc Conformation (hnh dng) 3. t gc Omega l 1800. 4. Nhp ln lt su ln tri chut vo Phe. 5. Nhp vo nt tt hp thoi. Cu trc ca chui xut hin nh sau:

(Cu trc ny c tt Show Hydrogens trong Display menu v c xoay n nh vy cho d nhn, vi cc bc trn ta s thu c 89

Hng dn s dng HyperChem 7.04 cng thc phn t nh vy nhng cha c xoay theo gc nhn thch hp). 6. Nu cu trc xut hin vn cn biu din cc nguyn t hydro th hy nhp tri chut b tch Show Hydrogens trong Display menu. 7. Xoay phn t n gc nhn thch hp.

t nhn cho u v ui chui nhn c r hn ta nn t nhn cho cc nguyn t N v C cc ui ca chui.

Cch lm nh sau1. Nhp tri chut tch vo Atoms v Multiple Selections trong Select menu. 2. Nhp tri chut vo cng c la chn trn thanh cng c. 3. Nhp tri chut nguyn t nit ui.

4. Nhp tri chut vo C ui cn li.

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5. Nhp tri chut chn Labels trong Display menu. Hp thoi Labels xut hin. 6. Nhp tri chut tch chn Symbol trong mc Atom ca hp thoi Labels v nhp OK la chn. Cc nguyn t N-ui v C-ui s c biu din di dng nhn biu tng (symbol) nh sau:

Chn lin kt khung nghin cu vng xon c alpha t nhin ca chui polypeptide, vic chn ny gip ta hnh dung d dng hn.

91

Hng dn s dng HyperChem 7.04 Bc u tin chn lin kt khung, ta c th thc hin mt trong hai cch sau: - Chn ng ngn nht gia hai im chn lm ui. - S dng Select Backbone (chn lin kt khung) trong Select menu.

Chn ng ngn nht gia hai ui chn.1. Nu cn thit nhp b tch Show hydrogn trong Display menu. 2. Nhp tri chut vo cng c la chn trn thanh cng c. 3. Nhp tri chut vo nguyn t C-ui chn v r n nguyn t Nui chn ri nh chut.

S dng lnh Select Backbone: 1. u tin, nhp tri chut vo cng c la chn trn thanh cng c. 2. Nhp phi chut vo vng trng trn mn lm vic. Vic lm ny gip loi b nhng la chn trc . 3. Nhp tri chut chn Select Backbone trong Select menu. Hnh nh lin kt khung s xut hin nh sau:

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T mu lin kt khung t mu lin kt khung ta lm nh sau1. Nhp tri chut chn Color trong Display menu. Hp thoi la chn mu s xut hin. 2. Nhp tri chut chn mu m ta mun biu din, v d chn mu vng (Yellow) v nhp OK chn. 3. Nhp phi chut vo vng trng mn lm vic. HyperChem s biu din khung lin kt dng mu vng.

Ch biu din lin kt khung trn mn lm vic biu din mi lin kt khung ta lm nh sau1. Nhp tri chut chn Show Selection Only (ch biu din phn c chn) trong Display menu. Khi ch c phn lin kt khung v nhn ca n c biu din. 2. Nu mun khng xut hin c phn nhn th ta vo hp thoi Labels trong Display menu v chn none mc Atom ri nhp OK chn. Lc ny ch c lin kt khung c biu din trn mn lm vic. Ch : Nu nh ta th thc hin v d ny ngay cho lin kt khung c t mu trn th s khng cn g xut hin trn mn hnh, s d nh vy v trong phn trn hin th mu ta nhp phi chut ng ngha vi vic b tt c cc la chn.

Biu din lin kt nhnh (lin kt bin)93


biu din lin kt nhnh ta lm nh sau1. Quay v chuyn lin kt khung sao cho trc vng xon c lin kt khung hng ra ngoi mt phng mn hnh.

2. Nhp tri chut chn Show All trong Display menu. Mn hnh s hin ra nh sau:

Biu din cc nhm nguyn t khng chni khi ta mun chn v biu din cc phn cn li ca h phn t ch khng phi l phn la chn hin ti. Ta c th s dng Complement Selection (lu chn b xung) trong Select menu.

Cch lm nh sau94

Hng dn s dng HyperChem 7.04 1. Nhp tri chut chn Complement Selection trong Select menu. HyperChem s chn biu din tt c cc phn tr nhng phn c chn trc s dng bnh thng.

2. Nu ta nhp tip tri chut chn Show Selection Only trong Display menu th HyperChem s du lun phn lin kt chn trc. Ch : a phn t v trng thi bnh thng ta nhp tri chut chn Show All trong Display menu.

Chn theo hnh ch nht chn cc nguyn t theo hnh ch nht ba chiu ta lm nh sau1. 2. 3. 4. Chn Show Hydrogens v chn Show All trong Display menu. B tch nu c Select Sphere trong Select menu. Nhp tri chut vo cng c la chn trn thanh cng c. Nhp ng thi tri v phi chut gi nh vy v r ph ht nhng nguyn t mun chn vo hnh ch nht.

95


5. Nh chut v tr thch hp th tt c cc nguyn t trong hnh ch nht c chn s sng hn

Chn theo hnh cu chn cc nguyn t trong mt hnh cu ta lm nh sau1. Nhp tri chut vo cng c la chn trn thanh cng c. 2. Nhp phi chut vo khong trng trn mn lm vic b tt c cc la chn trc . 3. Nhp tri chut tch chn Select Sphere trong Select menu. 4. t con tr la chn vo mt nguyn t no c chn lm tm hnh cu

96


5. Nhp ng thi tri v phi chut, gi v r to mt hnh cu cha cc nguyn t mun chn. 6. Nh chut th tt c cc nguyn t trong phn hnh cu s sng hn.

Ch : nu ta chn mt im trng no lm tm th khi nhp v r chut s l kiu chn hnh ch nht ch khng phi kiu chn hnh cu.

t tn phn la chnHyperChem gip ta d dng t tn cc phn la chn v th c th d dng biu din li chng sau ny.

t tn phn la chn ta lm nh sau1. Chn Name Selection trong Select menu. Hp thoi Name Selection xut hin. 2. Nhp tri chut tch vo mc Other v nh tn ca nhm la chn ngay trng cnh .

3. Nhp OK chn. HyperChem s lu tt c phn la chn vi tn m ta nh vo, v d y l n_sub. 4. Nhp phi chut vo vng trng trn mn lm vic loi b la chn. 5. Nhp tri chut chn Select trong Select menu. 97

Hng dn s dng HyperChem 7.04 Hp thoi Select s hin ra. 6. Nhp tri chut chn Named Selection trong mc By String. 7. Nhp tri chut chn n_sub trong list cc tn bn cnh, nhp OK chn. Phn la chn vi tn tng ng s c chn tr li.

Chn lin kt vng chn vng lin kt ta lm nh sau1. Nhp tri chut chn cng c la chn trn thanh cng c. 2. Nhp phi chut vo vng trng trn mn lm vic b tt c cc la chn trc . 3. Nhp lin tip hai ln tri chut vo mt trong cc lin kt ca vng. Vng lin kt s c chn.

Ch : Nu tch chn Multiple Selection trong Select menu th ta c th chn c tt c cc lin kt vng.

98


Bi 8. Thao tc vi nhng phn t ln c v m cc file PDB. Biu din cc thuc tnh cu trc ca cc phn t ln. Biu din lin kt hydro Thay th cc monome. Quay lin kt nhnh Mt nt c trng quan trng ca HyperChem l kh nng thao tc bng tay v tnh ton thuc tnh ca cc phn t ln, nh l cc protein v nucleic acid. Ngoi kh nng xy dng v nghin cu cc phn t nh. By gi chng ta nghin cu cc phn t ln lu trong ngn hng d liu Protein Brookhaven (Brookhaven Protein Data Bank, PDB). Trong phn ny ta thc hnh trn trypsin, cht c ch tuyn tu (BPTI).

c ngun file d liu PDB .Cc file (PDB) trong ngn hng d liu Protein Brookhaven c phn ui m rng l .ent . HyperChem c th c cc file ny t cc ngun cung cp khc nhau. Cc file ny trc tin phi c chuyn t ngun gc n HyperChem.

m file PDB ta lm nh sau1. Nhp tri chut chn Open trong File menu. Hp thoi Open file xut hin. 2. Chuyn n th mc samples ca HyperChem. 3. Chn m th mc Pdb. 4. Chn phn ui m rng l Brookhaven PDB (*.ENT) trong mc Files of type. Cc file c ui ent hin ra. 5. Nhp tri chut chn pdb5pti.ent trong list file. Dng ch gii bn di (Comment) s cho bit s qua v ngun gc ca cht. 6. Nhp OK chn Mn lm vic s xut hin phn t nh sau

99


Trong h c c cc phn t nc. 7. Nu cu trc xut hin c c nhn ca cc nguyn t th ta nn chn none hp thoi Label trong Display menu d quan st. 8. Ta cng nn loi b biu din cc lin kt hydro tin quan st phn t.

Loi b cc phn t ncTrong phn ny ta hc cch loi b cc phn t nc bao quanh phn t BPTI (bovine pancreatic trypsin inhibitor) m ta ang nghin cu.

Cch lm nh sau1. Nhp tri chut chn Molecules trong Select menu. 2. Nhp tri chut vo cng c la chn trn thanh cng c. 3. Nhp tri chut vo phn t BPTI chn phn t ny. Phn t BPTI s sng hn ln 4. Nhp tri chut chn Complement Selection trong Select menu. Vic ny gip ta ch la chn cc phn t nc. 5. Nhp tri chut chn Clear trong Edit menu. Lc ny s c hp thoi hi ta c thc s mun xo cc nguyn t chn xut hin

6. Chn Yes. Cc phn t nc s b xo i v cu trc ca BPTI s xut hin trn mn lm vic nh sau: 100


Ch : trnh trng hp mun kho st cu trc BPTI trn m li phi loi b cc phn t nc khi m file PDB, ta nn lu cu trc hin ti vo mt tn khc khi m sn c. - Nhp tri chut chn Save as trong File menu. - nh tn mun lu vo mc File name v chn phn ui m rng l hin (HyperChem (*.HIN)). - Nhp Save chn HyperChem s lu li tn file m bn nh vo vi phn ui m rng l hin.

Biu din cu trc phn t Biu din cu trc chnh Biu din cu trc chnh ca phn t ta lm nh sau1. Nhp tri chut b tch Show Hydrogens trong Display menu. iu ny gip ta d quan st phn t hn. 2. Nhp tri chut chn Backbone trong Select menu. Lin kt khung s sng hn. 3. Nhp phm Spacebar trn bn phm. iu ny gip cho phn t c biu din ph hp vi t l mn hnh v cho php ta nhn r hn. 4. Nhp tri chut chn Show Selection Only trong Display menu.

101


Lc ny trn mn hnh ch biu din lin kt khung. 5. Nhp phi chut ln vng trng ca mn lm vic loi b la chn lin kt khung. Lin kt khung s tr v trng thi bnh thng. Ch : biu din li cc lin kt nhnh ta nhp tri chut chn Show All trong Display menu.

Biu din vng xon Alpha biu din vng xon Alpha ta lm nh sau1. Nhp tri chut tch chn Multiple Selections v Residues trong Select menu. 2. Nhp tri chut chn Select trong Select menu. Hp thoi Select xut hin. 3. Nhp tri chut tch chn Residue number trong mc By number. 4. nh s 47 vo mc value = v nhp OK chn. iu ny ng ngha vi SER 47 c chn. Vi cch ny gip ta d dng chn nhng monome hp phn c bit trong phn t. 5. Nhp tri chut chn Select trong Select menu m hp thoi Selecct mt ln na v nhp chn Residue number vi s ch 55. Ta thy trn mn hnh cc hp phn th 47 v 55 sng ln. 6. Nhp tri chut vo hp phn 47 v r n hp phn 55. iu ny gip cho cc hp phn t 47 n 55 c chn. Ta cng c th chn cc hp phn t 47 n 55 bng cch nh s 47 v 55 ln lt vo v tr value >= v * trong etilen.

Ti u trng thi c bn ca Etilen.By gi ta s c mt cht kh khn trong vic tnh ton thun tu l thuyt, v th phn ny s tm lc cho ta mt s ch dn.

to Etilen theo tp hp hm c bn STO-3G ta lm nh sau:1. Nhp tri chut chn New trong File menu. 2. B tch Explicit Hydrogens trong Build menu. 3. Chn cacbon trong hp thoi la chn nguyn t v v to lin kt i C = C. 4. Chn Add H & Model Build trong Build menu to ra etilen. 5. Chn Ab Initio trong Setup menu v chn Minimal (STO-3G) cho tp hp hm c bn. t Total charge = 0, Spin multiplity = 1, Spin pairing = RHF, Accelerate convergence = Yes (tch chn), v gi tr SCF Convergence Limit t thch hp l 0.0001. Nhp nt CI (Cofiguration Interaction) v t None ri nhp OK ln lt ng cc hp thoi.

ti u trng thi c bn ca etilen ta lm nh sau:1. Chn Geometry Optimization trong Compute menu. Tch chn phng php Polak-Ribiere v t gi tr 0.01 cho RMS gradient. Nhp OK ng hp thoi v bt u ti u. Ta s tm hnh hc c ti u ca etilen c di lin kt C-C l 1.31 A0, di lin kt C-H l 1.08 A0, v gc H-C-H l 115.70.

tnh nng lng tng tc ta lm nh sau:1. Chn Ab Initio trong Setup menu, nhn nt Options, v chn MP2 correlation energy. Nhp OK ng hp thoi ny li tr v mn lm vic. 2. Chn Single Point trong Compute menu.

223

Hng dn s dng HyperChem 7.04 Ta s tm nng lng SCF l -48364.64 kcal/mol v tng nng lng MP2 l -48438.61 kcal/mol trong bao gm c -74.97 kcal/mol nng lng tng tc. S khc nhau nh gia nng lng c ti u v nng lng tnh ton theo Single Point i khi c th xy ra.

Obital trng thi c bn ca Etilen quan st biu nng lng obital v cc obital ta lm nh sau:1. Chn Orbitals trong Compute menu. Nhp tri chut vo vng biu din cc vch mc nng lng obital, gi v r phng to cho n khi c th nhn cc vch mc c nh sau:

C hai obital c quy cho l obital c in y (HOMO) v obital * trng (LUMO) ca etilen. Cc trng thi kch thch thp nht ca etilen tng ng vi s chuyn mt electron t obital p n obital *. C ngha l t -> * (HOMO n LUMO) s chuyn dn n c hai trng thi mc n b kch thch, y cc electron kiu i nhau, v mt trng thi bi ba, y cc electron trong obital v * c spin song song. 2. Chn cc obital ny bng cch nhp tri chut vo n, v v biu obital. nh hng phn t etilen sao cho c th quan st c nh trong v d. y biu din obital *, sau khi phn t c t dc trc x bng cng c hiu chnh Align Molecules trong Edit menu.

224


CI v ph in t ca Etilen tnh ph ca Etilen ta lm nh sauNhp chn Ab Initio trong Setup menu. Nhp chn Minimal (STO-3G). Nhp vo nt Options. Nhp vo nt CI (Configuration Interaction). Tch chn Singly Excited. Chn Energy Criterion (Chun nng lng). nh gi tr 1000 cho Maximum Excitation Energy. Nhp ln lt OK tr li mn lm vic. Khi tin hnh tnh ton tng tc cu hnh (CI) kch thch n, n trn s lng ln cc th ca cc cu hnh. Cc cu hnh ny bao hm s kch thch mt electron t mt obital nh c n mt obital trng. Cn thit phi quyt nh c nhiu yu t nh th no lin quan n s trn. iu ny c th thc hin trn c s ca tt c cc kch thch c lin quan bao gm s lng c th cc obital khng nh c thp nht v obital nh c cao nht hoc trn c s chun nng lng kt hp vi s khc nhau v nng lng ca hai obital c lin quan. Chn gi tr 1000 s cho kt qu trong bao gm tt c cc cu hnh kch thch n trong CI (tng tc cu hnh). 7. Chn Single Point trong Compute menu. iu ny gip ta bt u tnh CI kt hp vi tnh ton im n. Khi tnh ton hon thnh, mc Electronic Spectrum s chuyn qua mu en v hot ng c. 8. Chn Electronic Spectrum trong Compute menu biu din ph nh sau: 1. 2. 3. 4. 5. 6.

225


Vch cao nht l 52.7 nm v n khng lin h g vi s chyn -> *. Mc chuyn nng lng thp nht (bc sng di nht) pha bn phi c bc sng l 3.3.7 nm v l s chuyn bi ba (triplet) -> *. Tt nhin, y c s cm (mt bng khng) khi tt c s chuyn l t singlet (bi mt, mc n) n triplet. Nng lng thp nht cho php chuyn 106.4 nm l s chuyn singlet -> *. Wavelength Zoom Oscillator Strength Pan Transition S ch gc cao bn tri v phi cho bit gii hn ph ang c biu din. Thanh trt phng to v thu nh gip d dng quan st biu din ph. T l ca cng dao ng (intensity). Thanh trt h tr quan st. Biu din s ca s chuyn, mc ca s chuyn c chn. S chuyn theo th t t bc sng di nht n bc sng ngn nht (tri qua phi). Ta c th chn mt s chuyn bng cch nh vo s ca s chuyn. Xc nh s suy bin ca trng thi kch thch theo s chuyn chn. L bi spin ton phn, 2S+1, y S l tng spin electron ca h. Mi electron khng kt i c spin l 1/2,. H v kn (singlet) c bi l 1, trng thi doublet, triplet ln lt c bi l 2 v 3. Bc sng (nm) ca s chuyn c chn. Lng khng th nguyn t l vi cng ca s chuyn c chn. 226

Degeneracy Spin multiplicity Wavelength Oscillator Strength

Hng dn s dng HyperChem 7.04 Copy Copy hnh nh hp thoi biu din ph vo trnh ng dng khc, vo b nh tm thi.

Hnh hc v nng lng ca Etilen bi baDo trng thi kch thch thp nht ca etilen c trng thi spin khc (triplet) ch khng phi trng thi c bn (singlet), vi HyperChem ta c th tnh d dng v trc tip hm sng SCF ti u cho n. y khng phi l mt tnh ton n gin khi trng thi b kch thch c s i xng spin nh trng thi c bn v HyperChem hin ti khng c kh nng tnh trc tip trng thi singlet b kch thch cho etilen, ngoi thng tin c gi tr phng php CI cho trng thi c bn ra, nh l ta thc hin trn ra. Trng thi Triplet c th tnh ton c bng trc tip bng tnh ton SCF yu t n.

tnh hnh hc cho trng Etilen bi ba ta lm nh sau:1. To etilen chun theo trnh xy dng trn mn lm vic nu ta cha c. Khi ta tin hnh ti u hnh hc, hnh hc khi u hin ti khng ti hn v etilen ca ta c th l cu trc c ti u cho trng thi c bn theo STO-3G thu c t trc. 2. Chn mt gc vn trong etilen phng v khi chn Set Bond Torsion trong Edit menu i gc vn thnh 300. Nhng ngi ti u dn xut u tin theo HyperChem c th khng d dng tm thy s thun li ca s khng phng nu ta bt u vi mt cu hnh phng cho mt phn t. Ta ang gip cho s ti u i lch hng so vi mt cu trc khng phng. 3. Chn Ab Initio trong Setup menu v chn 3 (triplet) cho Spin Multiplicity v t UHF cho Spin Pairing. iu ny s tnh ton cho trng thi triplet electron khng cp i ch khng phi tnh bnh thng RHF cho trng thi c bn singlet electron cp i. t 0.0001 cho SCF convergence. S dng Minimal (STO-3G) Basis set v nhp OK tr li mn lm vic. 4. Chn Geometry optimization trong Compute menu. Tin hnh ti u vi RMS gradient l 0.01. S ti u mt mt lc kh lu. Tuy nhin kt qu l trng thi triplet c kch thch c xon n 900 so vi trng thi c bn. Lin kt i C C c dn rng n 1.49A0 so vi trng thi c bn l 1.31A0, ch yu, l lin kt i c ph v v gi li gn vi lin kt n. Khong cch C H cn li l 1.08A0 v gc H C H by gi l 117.80.

tnh nng lng kch thch on nhit ta lm nh sau:227

Hng dn s dng HyperChem 7.04 1. Chn AbInitio trong Setup menu, nhn nt Options, tch chn MP2 correlation energy. Nhp OK ng hp thoi thot ra mn lm vic. 2. Chn Single Point trong Compute menu. Nng lng SCF ca trng thi triplet kch thch c ti u l -48328.65 kcal/mol cao hn 35.99 kcal/mol (794.4 nm) so vi trng thi c bn singlet c ti u. y l nng lng kch thch on nhit o c t cc tiu nng lng ca mi trng thi. Nng lng tng tc MP2 trong trng thi triplet kch thch (-45.02 kcal/mol) b hn nhiu so vi trng thi c bn (-74.43 kcal/mol) do , di nh hng ca s tng tc, nng lng kch thch on nhit l 65.84 kcal/mol (434.3 nm). Nhng con s ny c th so snh vi nng lng kch thch cc im (91.14 kcal/mol hay 313.7 nm) tnh theo CI cho s chuyn ny. Nng lng kch thch cc im (ging nh hnh hc ca trng thi kch thch vi trng thi c bn) r rng cn phi ln hn nng lng kch thch on nhit.

kho st obital ca trng thi triplet ta lm nh sau:1. Chn Orbitals trong Compute menu. Phng to vo cc obital alpha xem biu nh sau:

Ch rng hai obital nh c v * xuy bin. Nhp vo cc obital ny chn v v biu tng ng kho st.

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Bi 17 Kh nng phn cc DFT ca H2 Tnh hm mt Chn hm tng tc trao i Thm trng in v tnh kh nng phn cc Thuyt hm mt (DFT) l phng php mi, n c nhiu im chung vi cc phng php tnh ton thun tu l thuyt. Phng php ny dng thuyt hm mt d on nng lng ph thuc vo mt . Phng php ny thay th cc th Hartree-Fock ca tnh ton thun tu l thuyt bng th tng tc trao i ca mt electron. L phng php chnh xc hn tnh ton thun tu l thuyt. Trong phn ny s gii thiu cho ta nhng bc c bn cn thit thc hin tnh ton DFT.

To H2 v to phn t hydro ta lm nh sau:1. Tch chn Explicit Hydrogens trong Build menu. 2. Chn Labels trong Display menu v tch chn Symbols. 3. Nhp tri chut vo cng c v trn thanh cng c v r v mt ng trn mn lm vic. Nu v sai th dng phi chut xo hnh nh va to.

4. Nhp tri chut vo Model Build trong Build menu to phn t hydro theo trnh xy dng vi di lin kt l 0.74 A0 quay dc theo trc Y. 229


By gi ta c mt phn t thc hin tnh ton. Ta s tin hnh tnh ton trn hnh hc ca trnh xy dng c di lin kt l 0.74 A0 mc d ta c th ti u hnh hc nu ta mun.

Chn th tng tc trao i biu th kiu tnh ton DFT ta mun thc hin cn lm nh sau: 1. Nhp chn Density Functional trong Setup menu. 2. Chn tp hp hm c bn 6-31G** nh trnh by di y. Kiu tp hphm c bn ny c thm hm phn cc kiu p cho cp tp hp hm c bn zeta 6-31G kiu s cho H2.

3. Nhp vo nt Options v chn cc la chn ngm nh sn nh bn diy:

Ring hi t ca SCF (1.0e-008) nn t nh hn bnh thng ( tnh kt qu SCF c chnh xc hn) khi ta gi nguyn cc gi tr khc. 4. Nhp vo nt Grid trong hp thoi Density Functional Method v chn Standard Grid #1 theo nh sn ca Pople v cc cng s.

230


Thuyt hm mt (DFT) i hi ta c lng cc yu t ma trn ca ton t Hamilton trong bt k phng php c hc lng t no. Trong trng hp DFT, cc s hng trong ton t Hamilton (cc th trao i v tng tc) c hnh thc hm qu phc tp c th khai thc cc cng thc gii tch cho cc tch phn thch hp. DFT ni chung i hi s tch phn tnh ton cc tch phn ny v iu ny ch cho ta phi chn mt li to biu din s tch phn ny. Standard Grid #1 l mt s ho hp gia chnh xc v phc tp (s cc im trn li). Nhiu im s cho cc tch phn chnh xc hn nhng s i hi nhiu thi gian tnh ton. 5. Nhp vo nt Exchange Corelation v tch chn c hm trao i ln hm tng tc. Chn phng php HCTH98 cho c hai.

Ta c th chn bt k hm trao i no kt hp vi bt k hm tng tc no hoc c th chn c s lin h nh c ti u theo cc tc gi. Nhiu trong s cc hm c pht trin vi s tha nhn chng s c s dng thnh tng i xc nh mc d HyperChem khng i hi iu ny. HyperChem cho php chn c lp cho trao i v chn c lp cho tng tc. Trong trng hp ca ta ta s chn c hai hm trao i v tng tc nh nhau (HCTH98) c nhm Handy thuc trng i hc Cambridge pht trin. Mt cht kinh nghim c l c gi tr s dng ch cho mt trong cc

231

Hng dn s dng HyperChem 7.04 cp hm. C chng ngi ta c th pht trin mt th trao i ti u nht trong chnh n m khng n s tng tc (hoc ngc li). Chn None trn l xt on ton din cho th tng tc khi tnh ton Hatree-Fock khng cha s tng tc. Tuy nhin chnj None chn s trao i l c vn ng ng mc d n lin quan n tnh ton Hatree.

Tnh ton DFT im n trong trng in. kho st ng dng ca trng in trn mn lm vic ta lm nh sau:1. Nhp chn Single Point tin hnh tnh ton DFT thiu s c mt ca trng in 0.74 A0. Ta thu c nng lng -743.850760 kcal/mol. 2. Nhp chn Show Dipole Moment trong Display menu. Momen lng cc bng khng (hoc gn khng) nh mong i. 3. Nhp chn Set Finite Field trong Setup menu v thm gi tr 0.001 cho trng in nh trnh by di y.

4. Nhp OK thm trng. 5. Nhp Single Point trong Compute menu tnh ton im n li nhng by gi c thm trng in c p dng. Ta thu c nng lng l -743.852747 kcal/mol b hn mt cht so vi khng c trng in. Momen lng cc trong trng in s khng bng khng. 6. Nhp vo Show Dipole Moment trong Display menu. Kt qa momen lng cc dc theo trc y l 0.16096 Debye hay l 0.16096/2.541765 = 0.00633 a.u. S phn cc dn n kt qa c momen lng cc theo trng p vo. Do , s phn cc dc theo trc y l 0.00633/0.001 = 6.33 n v nguyn t. Ta tin hnh tnh ton s lo lng hn ch v s phn cc ca H2 bng hm DFT hcth98. Tuy nhin, HyperChem cho php ta tnh trc tip s phn cc nh ta s thy sau y.

Tnh s cng phn cc

232


tnh s phn cc ta lm nh sau1. Nhp chn Set Finite Field trong Setup menu v b tch Electric ta t phn trc. 2. Nhp chn Density Functional trong Setup menu. Nhp vo nt Options v nhp tip vo Polarizabilities. Ta by gi c th yu cu tnh phn cc trong qu trnh tnh im n, t cc gi tr nh sau:

Dng gi tr 0.001 nh ta s dng trc y ch khng nn dng gi tr ngm nh 0.0005. Ga tr ngm nh l s ho hp gia chnh xc ca s thay i c th theo di c v gi tr chnh xc tuyt i ch trong gii hn trng bng khng p vo. 3. Nhp chn Single Point trong Compute menu tnh im n li nhng thi gian i hi nhiu hn. Tnh ton i hi mt 6 ln thi gian tnh ton khng c tnh s phn cc trong c tnh n c trng lc p vo cho cc trc X, Y v Z. xem kt qa tnh ton sau khi tnh ton hon thnh, nhp vo Properties trong Compute menu. Nhp vo Details xem y s cng.

Ta thy rng hp phn YY ch c gi tr l 6.33 nh tnh ton phn trn.

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Bi 18 Ch thch Thm ch thch cho phn t Chn, chnh sa v dch chuyn ch thch Th t lp ch thch theo trc Z, ghi ch thch vo lp ch thch. Phn ny s gii thiu cho ta bn kiu ch thch c bn-kiu ghi, kiu ng thng, elip (trn) v kiu ch nht. N gip ta lm cch no ghi ch v sa i kch c, mu sc v cc thuc tnh khc.

To mt h phn t to mt h phn t lm mu ta lm nh sau: 1. Chn Open trong File menu. 2. M chn file ethanol.hin m ta lu t trc (C th v trc tip trn trang lm vic cng c). Chn ball and cylinder mc Rendering ca Display menu. Hnh nh biu din trn m lm vic s c dng nh sau:

Ch thch kiu ch nhtCh thch kiu ch nht v elip c bn l nh nhau. Phn ny ch minh ho cho kiu ch thch ch nht. Bn hy th li vi kiu elip.

to v thao tc vi ch thch kiu ch nht ta lm nh sau1. Chn Options mun: trong Annotations menu v chn cc la chn mong

234


Tch chn nh trong hnh v. 2. Chn Color trong Annotations menu v chn mu xanh (blue). y s l mu sc ca bt k ng thng, elip hay ch nht no m ta v ra sau . 3. Nhp vo biu tng hnh ch nht trn thanh cng c. Ch l, sau khi ta nhp vo biu tng ny th khi chuyn ln mn lm vic chut cng c hnh dng ch nht. 4. t tr chut ln gc tri mn lm vic, nhp tri chut gi v r to hnh ch nht nh mong mun ri nh chut ra. Ch thch kiu ch nht khi xut hin nh sau:

Tt c phn t nm lp bn trong ri vi lp ch thch nm bn ngoi. Chnh v chn Annotation Layer in Front nn phn t ca ta b che mt. 5. Chn Options trong Annotations menu v b tch Annotation Layer in Front t lp ch thch ng sau, khi mn lm vic biu din nh sau: 235


6. Nhp chn cng c la chn trn thanh cng c v nhp tri chut vo ch thch ch nht chn ch thch ny. Ch nht ch thch s xut hin ng vin la chn mu (ngm nh l mu xanh). Nu cn thit loi b la chn ta ch vic nhp phi chut vo vng trng mn lm vic. Tng t ta cng c th chn phn t nh nhng bi trc. 7. Dng cng c dch chuyn v phng to iu chnh kch c v v tr ph hp. Ch , nu phn t cng c chn th n s c u tin i vi tc ng ca cc cng c. Nu ch ch thch c chn, th n s chu tc ng ca cng c phng to v cng c dch chuyn; cc cng c khc khng c tc dng vi n. 8. Ch chn hnh ch nht. 9. Chn Options trong Annotations menu v b tch Fill Circles and Rectangles. Nhp OK chn. 10. B la chn hnh ch nht. Ta s thy s lp y bin mt, thay vo l hnh nh nh sau:

236

Hng dn s dng HyperChem 7.04 11. Chn hnh ch nht li ln na v nhp chn Options trong Annotaions menu. Chn kiu ng thng (line type) l Dashed (Nt t). Ta s thy hnh ch nht lin trn chuyn thnh hnh nt t. Ch : - Hide Annotation layer: giu ch thch. - Fill Circles and Rectangles: Lm y ch thch (T y mu la chn) - Use Gravity on lines: Dng lc ht cho cc ng thng. - Line Width: rng ca ng. - Line type: Kiu ng: Solid (nt lin), Dashed (nt t), Dotted (chm chm), DashDotted (gch chm), DashDotDotted (gch chm chm).

Ch thch dng ng thngCh thch dng ng thng cng ging nh ch thch kiu elip v ch nht nhng khng c ch lm

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