Gaussianを用いた分子モデリングと量子化学計算

Transcript

1.   ǹïNjǝ4lȮȗȳȸȇǣ ŦlCoĹĔ
   ıįİĴĭĵĭıĵħİİĹįįĬİİĹĴį
   đıį^ź4lĹĔÍĉoăĎъ
   Ljź4lȌȫȰȵȺȌȱȸǧǝǰǧȑȣȘǿȀǼ-Ūlj
   ¿ÇŻ/ ŧÙioŻio¯ĨŬøȹ­©ȐȸȒȺ ¯Ĩ­©ȌȎȖȬăĎšŪDŽ2¯¤               
   
   ĪĜ
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   TX‰Þ Ďº
   ƟƎƦƝ
   3 'J     ;G),/I ¾ŃŠǧÉijɄŋµdzǵɆ
   DŽ ՄDžź4lăĎǧ4ťǦǎNjǡDZĹĔÍȌȫȰȵȺ ȌȱȸǧÝïǐ†ǒĽǮǴǷǡǎǵDžȉȸȢȰȺȒȞȺșǿ ȀǼǧŗÐǣ0ǦDžhËǥȑȣȘǿȀǼǐ/ŬǗǷǡNj ǭǙdžǘǏǘDžź4lǹuŅǣǙǶǣĸǢĸǞǡDZDž K”DžÊŖDžÍĩǥǤuŅǨŴ‚Ǧh{ǦǸǝǵDžMǶ ǬǑȌȫȰȵȺȌȱȸžÚDžïNjǶǬǑȑȣȘǿȀǼǧúĄ ǥŠ ǐ“ijǣǥǵDžǏǴžǹǔǡNjNjǧǏǸǏǴ ǥNjǣNjnj³LJDZhNjǣ–NjǭǙdžȹȹȹ
   ǃŻ️
   ĹĔĉoȹȌȫȰȵȺȌȱȸĉoǫǧĩšȹ¼
   ǃŻìŁǧ;ĚǣDžʉǧůôDžřiǥĹĔȉȎȘȹȹȹ
   
2. ¾ŃŠǧüú
   DŽŦlCoĹĔȥȶȇȲȬ  ǹïNjDž4lŌŚÚ ǎdzǪt‰×Ů°ÚǦdzǶ4lȮȗȳȸȇǧcĆDžsŰ ǧĹĔǦǎǔǶȩǾȸȘǹķľǙǶ
   •  :śüÌɃ
   – ȄȺȷȺșǹDZǣǦ ijǥɕǹDžǟǏǯ
   – 4lǧÊŖȹæ—ȹK”ǧłijěǦǟNjǡDžŦlC oǧŝïPĩǥĖ_ǣǜǧůôǦǟNjǡľ¶ǢǑǶ
   – 4lȮȗȳȸȇǧ ǹDZǣǦDž”ïǢǑǶ
   ċV1XƝŽ”rƌƭƬƊƚž
   ųlè›ǐǸǏǶ !  “ijǥ˜dǨDžc¾úǦGlȹ4lǧ6¼ÊŖ ȼŠÌȽǧǮ !  sŹȠȲȭȺȒǦdzǴǚDžđGìȼab initioȽúǦ ķǒǖǣǐǢǑǶ !  ųlè›ǏǴDž¹ŝǥÊŖDžȁȜȴȅȺDž4læ—Dž CoK”ǹ áǙǶǖǣǐǢǑǶ ȥȲȔȘȣȂȺȬǧfC ź!ǥȷȺȆȎȖȺȌȱȸǧġ¡ȹĕìǣDžĹĔȉȎȘ →DŽÒŎúp!ǥȭțȺȉǼPCDžȎȘȵȺȍȹȭȮȳ →DŽi4lęǦDZħǍnjǶìŁȹȑȣȘǿȀǼŬø
   6 ³óǤǧǥź'VøçĨňŊ§ĩŵ
   ńŢŧťţřŨŘŧŞţŢħŧţħňţŠŚŘŨŠŖťħŊťŗŞŧŖŠħňŚŧŝţř
   7 ŎŘŝťůřŞŢŜŚťŒÅm
   • hųlęǧSchrödinger³Č‹ ĤΨ=EΨ →GlÆǧŘBǹ`r(Born-OppenheimerŐ) →ąÓúþïǧäĵ DŽ1ųlǐGlÆǣǧųlǏǴNǔǶȩȖȸȌȯȴǧ ǢŘBȼƒbeŐDž1ųlŐǭǝǨéĐųlȮȗȴȽdž
   8 2 1 1 ˆ 2 1 ˆ( ) A i i A i i j i iA ij i i j i ij Z H r r h i r > > = − ∇ + + = + ∑ ∑∑ ∑∑ ∑ ∑∑ 1ųlȞȫȴȘțǼȸǣ ųlŭKøȩȖȸȌȯȴ
   
3. ŎŠŖŧŚťä(m
   • ųlÛBŮ° →ųlǧ¨ǦǟNjǡKuĊ—ǹâǝǙ →Ƞǿȳǧ¥<ǹâǝǙ
   •  m ƞ1, 2, …, 2nƟŻěVlžr 1 ,r 2 , …, r 2n ƞ¸ï
   9 ψ(1,2,!,2n) = φ1 (1) φ1 (1) φ2 (1) φ2 (1) ! φn (1) φn (1) φ1 (2) φ1 (2) φ2 (2) φ2 (2) ! φn (2) φn (2) ! ! ! ! ! ! ! φ1 (2n) φ1 (2n) φ2 (2n) φ2 (2n) ! φn (2n) φn (2n) φn φ2 φ1 2n ūÑųlŢĥǧɃŻȾųlŮ°φn (x)Ǩ4lŌŚ
   ¤Ó4Vƞ4VøĂƞo¯Ĩİĩ
   ļŧţšŞŘħŊťŗŞŧŖŠħħıŤūøĂƞ
   11 ƜƂŻƙƮƯƸƨƭƮŻƦƲƩŻƙƂŻƠƸƼƸƯƮƀŻ  ŻƉƅŻżƄƌƋƈŽŻƅƃƉƂ
   ¤Ó4Vƞ4VøĂƞo¯Ĩıĩ
   ļŧţšŞŘħŊťŗŞŧŖŠħIJřøĂƞ
   12 ƗƂŻƟƭƮưƪƀŻ  ŻƌƄŻżƅƃƄƇŽŻƄƊƆƌƂ
   4lŌŚǧƚƑƏƜŐDžƠƑƔĹĔ
   • GlŌŚ(AO)ǧĢğR(Linear Combination) GlŌŚχǧĢğRǢ4lŌŚǹıǸǙɃLCAO ȁȜȴȅȺ¼)ǹÖǰǶǝǰǦLCAOǧ4lč4ǹķǒ ķǒǬǑՄ³Č‹ǨHartree-Fock-Roothaan³Č‹ǣǥǵ DŽİ5F,S,cǐĂÿǐäǒǥǶǭǢĹĔǹĤǵőǙ →Īä«āǥeDŽself-consistent field(SCF)ĹĔ
   1 m i ri r r c φ χ = = ∑ ˆ E H d Ψ Ψ τ ∗ = ∫ ( ) 0 i i i − = F S c e xŬǙǶc‡Ů°ǧŠ
   f4ÚǦdzǶȁȜȴȅȺ¹vC
   ȁȜȴȅȺLÀǧȓȀȔȆDŽ→DŽMODž4læ— SCFǹķǒ³ÚŁǧŠ
   13
4. 'VøĂîÍĨŃŖťŧťŚŚĬŁţŘş§ĩƝƩƖƘsƪƭƬxO ź¤'Vƞ
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   ƖƜƛƜ
   ƚƢƛƜ
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   ɉÑ
   ƅƶŻŻŻŻŻŻŻŻƅƴŻŻŻƅƴŻŻƅƴŻ
   4lŌŚżƛƜŽŻƍŻƽ
   ŌŚȁȜȴȅȺƍŻ
   
   4lŌŚÚǧ4Ÿ
   •  ŴĞŹú³Ú non empirical –  ǙǬǡǧ4lč4ǹĀõǥǘǦİnj = ab initioÚǣDZZǩǷǶdž –  ªBÚDžŢĥŭþïǦdzǵDžLjųlþŮljǧAÄǹMǵŏ ǯǖǣǐǢǑDžęĠúǦʉǹǕǶǖǣǐǢǑǶdž –  ȑȣȘǿȀǼɃGaussian, Spartan, GAMESS, NWChemǥǤ •  EĞŹú³Ú semi-empirical –  !ųlǧǮǹMǵŸNjDžč4ǹȠȲȭȺȒCǘǝǵĀõǙǶ –  ȑȣȘǿȀǼɃMOPAC(AM1, PM3, MOZYMEÚǥǤ) •  ĞŹú³Ú empirical –  HückelŐǢǨDžπųlǧǮǹŸNjDžĞŹȠȲȭȺȒǹïNjǶ •  t‰×Ů°(DF)ÚDŽdensity functional –  ųlt‰ǹc¾f°ǣǘǝKohn-Sham³Č‹Ǧǘǝǐnjdžų lþŮǹºAúǦMǵŏǯǐDžĹĔȉȎȘǨHartree-FockŐ ǣTȉǢàǯdžՄDžûǺǦïNjǴǷǡNjǶdž
   15 ĝÖĤ»'VøçƞNjƶǛǝƸǢ
   •  ěVď6ºƞĠƯŻß'RƞěVƅƗƇƬh JƞPƚƍƘûƏƬǤ°ÈÏVǖDŽǝǥƝƩƖƘƀƬ
   –  û÷ęƞěVď6ºƞāTðǪ0»ěV½Đ
   –  ěVĉÜƞƶLjǝƹǢ©ƞûƒǪĝ0»ěV½Đ
   –  "ŃŁ§ƞŎľŁƞטƟŻuƐ¾ƞƶLjǝƹǢƞŒƝſƬǣ
   •  ěV½ĐƞÝzƝƩƬÑØ»ƜÐk<
   –  ňŰŠŠŚťĬŋŠŚŦŦŚŧƝƩƬ†0§ħňŋħŤŚťŧŨťŗŖŧŞţŢħŧŝŚţťŬǪŵ ŸĨňŋıĩŻŸǤňŋIJǥŻCŸǤňŋijǥ
   –  ĉÜď½µħľţŢśŞŜŨťŖŧŞţŢħńŢŧŚťŖŘŧŞţŢħĨľńǥǪŵ ſƪƮƝƒƭƓƭƞěV/öĉÜƯÝzŻSĉܧƚƧ@ơŵ ľńŎĨǧěV/öĉÜƣƙĩŻŻľńŎĿŻľńŎĿŏŻľńŎĿŏŌǡǡǡŁľń
   –  ×:ƺǛƾǀǢ§ħľţŨŤŠŚřħľŠŨŦŧŚťǪźljǔǝDžLJƱǠƢªÍVƯÛ ƫúƥźǩěV/öĉÜƣƙÝzƍƔľľŎĿĨŏĩƜƛ
   16 ³ÚŁDžc‡Ů°ęȼŒȽǦuǙǶǂ ĹĔȉȎȘǣu”Gl°
   •  ³ÚŁǣc‡Ů°ęǧŠ ǧǝǰǦǨɇ –  ĹĔǘǝNjęǨu”Gl°ǦLǭǞǡNjǶǏ –  ¼ǙǶĹĔ·ŭǦǎǗǭǶǏ –  ĴǝNjæ—ǹD4ǦĺŒǢǑǶǏ
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   =/
   (.E33N- A<5D"*1
   -0%)3 7?%)F
   ŴĞŹú4lŌŚÚ
   CCSD(T)/QZP +C9 < ~2 kcal/mol K
   N 7 5 K 6 MP2/DZP $+C9
   K
   N 5 K 10 B3LYP(DFT)/DZP $+C9
   K
   N 3K4 K 102K
   HF/SZ +19
   K
   N 4 K 102K
   EĞŹú4lŌŚÚ
   PM5,AM1,PM4,MNDO +19
   K
   N 3 K 10 MOZYME8
   +19
   K
   N 1.38 K 104 17 @Ŋè›ȼŢĥȽ°
   c‡Ů°ęǧiǑǗ
   
5. ³óǤǨǥź]k¦Đ‹§ĨĿŁ§ĩ
   ńŢŧťţřŨŘŧŞţŢħŧţħĿŚŢŦŞŧŬħŁŨŢŘŧŞţŢŖŠħŏŝŚţťŬ
   18 ņţŝŢĬŎŝŖšħĨņŎĩħŒÅm
   •  ŒĭħņţŝŢƚŇĭħŅĭħŎŝŖšƝƩƬěV]kρĨrĩƝĐƏ ƬŒÅmħħ"RĈǒǃǠƽǗǝő œľ Ɲ]k¦Đ‹ħδE [ρǤrǥ]/δρǤrǥƅ²ƭƬ
   •  ñä¨0ЋƯěV‹nƝ^ƍƘ3nŸƯƧƗ ΨǧǸǵǦDž3Î+ǹDZǟρȼrȽǹǞǡDZdzNjŵ "ŃţŝŚŢŗŚťŜĬņţŝŢƞZ³ 19 ˆ H = − 1 2 ∇i 2 i ∑ + Z A r iA i ∑ A ∑ + 1 r ij j>i ∑ i ∑ = − 1 2 ∇i 2 i ∑ + ˆ V + ˆ G → − 1 2 ∇i 2 + ˆ V i ∑ + ρ( ! r ) r − " r d ! r ∫ + ˆ V XC (r) ŃţŝŚŢŗŚťŜĬņţŝŢƞZ³
   •  ÊZ³ǪĝÚĊNj¯yƞěV]kƚRĈ ǒǃǠƽǗǝǤZ‹Ĉ'ƯēƇǥƞďƝƟ^ƞ ĐƅſƬż
   •  ÊZ³ǪſƬRĈǒǃǠƽǗǝƝ^ƍƘŻñä ěV]kƞƶLjǝƹǢ¦Đ‹ǤƶLjǝƹǢǥƟŻ Nj¯yƞƶLjǝƹǢƩƫgƝĥƀƄſƬƀƟñ äěV]kƚNj¯yƞěV]kƅàƍƔƚ ƆƝĒƫËƍƀż
   •  "ųƯ!ÇďƙÆ'ƏƬƚěV‹ƝƜƫŻom »ƝŻƶLjǝƹǢƯěV]kƞ¦Đ‹ƚƍƘ‘ƈƬŵ E = E[ρǤrǥ] „½ĐǒǃǠƽǗǝǪ œľħ ĻħδE [ρǤrǥ]/δρǤrǥ 20 ƙƠÚǢǧƚƑƏƜŐDžƠƑƔĹĔ
   • GlŌŚ(AO)ǧĢğR(Linear Combination) GlŌŚχǧĢğRǢ4lŌŚǹıǸǙɃLCAO ȁȜȴȅȺ¼)ǹÖǰǶǝǰǦLCAOǧ4lč4ǹķǒ ķǒǬǑՄ³Č‹ǨHartree-Fock-Roothaan³Č‹ǣŸ DŽİ5F,S,cǐĂÿǐäǒǥǶǭǢĹĔǹĤǵőǙ →Īä«āǥeDŽself-consistent field(SCF)ĹĔ
   1 m i ri r r c φ χ = = ∑ ˆ E H d Ψ Ψ τ ∗ = ∫ ( ) 0 i i i − = F S c e xŬǙǶc‡Ů°ǧŠ
   f4ÚǦdzǶȁȜȴȅȺ¹vC
   .ųlȁȜȴȅȺȼ¨þŮȁȜȴȅȺȽǨ‘ǝ4lŌŚǹDZǣ Ǧ8'ǦķNjǡLÀ7rǙǶDŽ→DŽKSŌŚDž4læ— SCFǹķǒ³ÚŁǧŠ
   21
6. ŋŚťřŚŪƞǘƼǎƞƟƍƋ
   •  ĿŁŏîÍƟ ¿ƜƞƄǬ
   – ŅţŝŢħŋŚťřŚŪħŅŖŘţŗŴŦħŇŖřřŚť
   – UGƣƙƞĴƗƞŽšǤƊǥžǤōŨŢŜǥ
   22 ƘƂŻƝƂŻƝƪƵƩƪƹŻƦƲƩŻƙƂŻƠƨƭƱƮƩƷƀŻǀƘƦƨƳƧƿƶŻưƦƩƩƪƵŻƳƫŻƩƪƲƶƮƷƻŻƫƸƲƨƷƮƳƲƦư
   ƦƴƴƵƳƺƮƱƦƷƮƳƲƶŻƫƳƵŻƷƭƪŻƪƺƨƭƦƲƬƪƁƨƳƵƵƪưƦƷƮƳƲŻƪƲƪƵƬƻǁƂŻƗƲŻƒƪƲƶƮƷƻŻ ƔƸƲƨƷƮƳƲƦưŻơƭƪƳƵƻŻƦƲƩŻƗƷƶŻƏƴƴưƮƨƦƷƮƳƲŻƷƳŻƛƦƷƪƵƮƦưƶƎŻƣƂŻƣƦƲŻƒƳƵƪƲƀŻƑƂŻƣƦƲŻ ƏưƶƪƲƳƻƀŻƦƲƩŻƝƂŻƕƪƪƵưƮƲƬƶƀŻƓƩƶƂƀŻ   ŻżƅƃƃƄŽŻƄƾƅƃƂ
   VWN
   PW91 PBE LYP
   VS98 TPSS
   B3LYP PBE0
   EĞŹúƍŻƐƌƊƀŻƐƌƊƁƒƀŻƛƺężǝǣǍǩ ƛƃƉǨDžƝƐƓǹIJÏǘǝƛƃƈǣƐƌƊþŮǣ ƣƠƌƋ¨þŮǣƖƦƵƷƵƪƪƁƔƳƨƯ¨ǧ ȞǾȤȳȔșȽƀŻƛƃƉƁƅƤǥǤ
   ƩƇƮƭƬ„½Đ¦Đ‹
   •  ŇĿļĹħŎŠŖŧŚťƞœűīħőţŦşĬŒŞŠşĬʼnŨŦŖŞťĨőŒʼnĩ½Đ
   •  łłļĹħĽŚŘşŚķķ„īħŋŚťřŚŪĬŒŖŢŜİĸĸİĨŋŒĸİĩ„īħ ŋŚťřŚŪĬĽŨťşŚĬŀťŢŭŚťŝţśĨŋĽŀĩ„īħťŚũŋĽŀ„ǡǡǡīħ ŋŒĸݽĐīħŋĽŀ½ĐīħŇŚŚĬŔŖŢŜĬŋŖťťǤŇŔŋǥ½Đīħǧ Q‹ǏǟƻǞǂƽǎǤŊŋǥ½ĐƜƛ
   •  ǕǀłłļĹħũŖŢħőţţťŝŞŦĬŎŘŨŦŚťŞŖİĸĸķǤőŎĸķǥǕǀ„½ ĐīħŏŖţĬŋŚťřŚŪĬŎŧŖťţũŚťţũĬŎŘŨŦŚťŞŖǤŏŋŎŎǥǕǀ „½ĐħƜƛ
   •  ljƳǎǜǂdžĹħĽIJŇŔŋīħŋĽŀįħƊƞ‹WƟNJǛǕǢǀ‹
   •  2ÖĤ»ĹħĽĸĶīħĽĸĶĬĿīħňūÑĨƔƚƂƠňįĵƟŻŋĽŀƯæ ƍƔňįĴƚĽĸĶ½ĐƚőŎĸķ„½ĐƚŃŖťŧťŚŚĬŁţŘş „ƞljƳǎǜǂdžǥīħňįĵĬıœƜƛź'Vď-ƝnƤ
   24 NjЋÑƞć}
   ŎŚŠŚŘŧŞţŢħţśħŗŖŦŞŦħŦŚŧ
   30 ’aNjĐ‹ÑźŦŞŢŜŠŚħŭŚŧŖħŎŕ
   •  N•»ƜÝƂŒĹħİƗƞħļŊħƯİƗƞNjЋƙ ûƏƬżħ
   – åħŎŏŊĬłħĨħĻıĵĩīħňńʼnńĬİ
   – FǪİīıīIJīĴħƞłŖŨŦŦLøĂĨłŏŊĩƞÚÒƞăƀ
   32
7. ’aNjЋÑƞBĢ«
   •  þgµƀƬNjЋÑƟŻN•»Ɲ°ÈƍƔ4VƯN ƝƍƘ{ƍƘſƬƔƦŻ'VƞěV¯yƯåƏƝƟħ śŠŚūŞŗŞŠŞŧŬħƅƄƜƫ ƍƀż®ƝŻ’aNjЋÑƝƟ ƞƩƁƜĚ«ƅſƬż
   İĭħİƗƞħļŊħƯİƗƞNjЋƙåƍƘƀƬżƗƣƫħļŊħƞiƅƫƯİƗ ƞøĂ‹ħĨŲĩħƙ*ĒƍƘƍƣƁƞƙŻbH1ƍƔŻƣƔƟ0qĈ' ƝçĘƜœÿƯ~ƗěV'fƯïüƙƆƜƀż
   ıĭħ'V#ƙûƒƍƘƀƬ4VƨěVƞpğƝƩƫ¡ƤƯ8ƈƬƔƦŻ ěV'fƅ°ÈƍƔ4VƞƧƞƚTƆƇ¹ƜƬP:ƝƧŻƒƞïüƅ EĚƙſƬż
   IJĭħĕƳƷǠƞƩƁƝ4Vƞ¯yƙƟÝƂƪƭƜƀƇƪƀĄŒƣƙiƇě Vƅ'fƏƬP:ƝƧŻěV'fƞïüƅEĚƙſƬż
   33 Ŷ¹ƜƬøĂ‹Ư~Ɨç‹ƞłŏŊƙ
   •  ıNjЋÑħĨřţŨŗŠŚħŭŚŧŖħĿŕĩ
   •  IJNjЋÑħĨŧťŞŤŠŚħŭŚŧŖħŏŕĩ
   •  ı4V¢NjЋÑīħIJ4V¢NjĐ ‹ÑħĨŦŤŠŞŧħũŖŠŚŢŘŚĩ
   – ˆá«ǪİƗƞħļŊħƯŻÚưƕ'fƯ~ƗƧƞŻiƅƖƔ 'fƯ~ƗƧƞƜƛŻıƗħĨſƬƀƟIJƗĩħƞNjЋƙ åƏżƗƣƫŻİƗƞħļŊħƯıƗħĨſƬƀƟIJƗĩħƞ¹ƜƬø Ă‹ħĨŲĩħƯ~ƗNjЋƙåƏżħ#¢Ɵ1X» ƝſƣƫĊèƙƜƀƞƙŻ’R¢ħĨ4V¢ĩħƕƈƯç ‹ƞNjЋƙcĎƍƔƧƞƅŻ4V¢NjƙſƬż
   – åħIJĬıİłīħijĬIJİłīħĵĬIJİłīħňńĿńĬijħĨı4V ¢NjЋÑĩħħħĵĬIJİİłĨIJ4V¢NjЋÑĩ
   34 '›NjЋÑ
   •  '›NjЋÑ
   – ˆá«ħěV'fƞo¯ƞçĘƌƝ^vƌƑƬƔƦƝŻ ƩƫSƜŒ<wƯ~ƗNjЋħĨ'›Đ‹Ż ŋţŠŖťŞŭŖŧŞţŢħŁŨŢŘŧŞţŢĩƯ.ƂƬżƂƠħľīʼnīŊħËƝħřħ Lƞ'›Đ‹ƯŻŃħƝƟħŤħLƞ'›Đ‹Ư`
   – åħħħŵ Êı?”đƞ4VƝ'›Đ‹Ư` ƍƔƧƞħŮħŮħŮħ ijĬIJİłŷĨijĬIJİłĨřĩĩīħĵĬIJİłŷĨĵĬIJİłĨřĩĩīħ ňńĿńĬijřĨňńĿńĬijĨřĩĩħŵ ƝŻŃħƝƧħŤħL'›Đ‹Ư.ƂƔƧƞħŮħŮħŮħ ijĬIJİłŷŷĨijĬIJİłĨřŤĩĩīħĵĬIJİłŷŷĨĵĬIJİłĨřŤĩĩīħ ňńĿńĬijŷĨňńĿńĬijĨřŤĩĩ
   35 'ŠNjЋÑ
   •  'ŠNjЋÑ
   – ˆá«ħƄƜƫiƅƖƔħĨłŁħƞøĂ‹ħűħĻħįĭįİħŸħįĭİ ħÅkĩħŦħLƨħŤħLƞ'ŠĐ‹ħĨřŞśśŨŦŚħśŨŢŘŧŞţŢĩħƯ. ƂƬż ƝƱLJƷǠƯ=ưƕÑƞîÍƝƮƭƬż
   – åŵ Êı?”đƞ4VƝħŤħLƞ'ŠĐ‹Ư.ƂƔƧƞħŮħŮħŮħ IJĬıİĪłīħĵĬIJİĪłŵ ƝŻŃħƝƧħŦħLƞ'ŠĐ‹Ư.ƂƔƧƞħŮħŮħŮħIJĬıİĪĪłīħ ĵĬIJİĪĪł
   36
8. ƒƞ
   •  ŋţŤŠŚħƞNjЋÑ
   – ÊIJ?”đƞ4VƝƞƤ'›Đ‹Ư` ƍƔƧƞħŮħŮħŮħ IJĬıİłĨŷĩħīħĵĬIJİłĨŷĩħħƜƛħ'›Đ‹ƚ'ŠĐ‹Ư Œ` ƍƔƧƞħŮħŮħŮħIJĬıİĪłŷīħĵĬIJİĪĪłŷħħƜƛ
   •  ěV½ĐƯµƀƬĖƞNjЋÑ
   – ľţťťŚŠŖŧŞţŢĬľţŢŦŞŦŧŚŢŧħŤţŠŖťŞŭŚřħũŖŠŚŢŘŚħŗŖŦŞŦħŦŚŧŦŮħŮħ ŮħŘŘĬŤőĿŕīħŘŘĬŤőŏŕīħŘŘĬŤőŌŕīħŘŘĬŤőĴŕīħŘŘĬŤőĵŕħ
   – ěV½ĐƞÝzŽƝÐkƩƇîÍƯäƜƂƬƩƁƝĎ ºƌƭƔNjЋÑ
   – S‹ƞ'›Đ‹ƅ ƖƘƀƬżƣƔŻ4V¢ƞ', ƯÕƄƇħĨĵƣƙĩƍƘƃƫŻÑØ»ƝNjЋƞTƆƌ ƯƉƘƀƇħ ƅ&–Ƭ
   37 å»ƜNjЋÑƞ
   38 (.E3>
   #6E3&
   #2E3&
   ¹vc‡Ů°ęȼSZȽ
   ƠơƜƁƆƕ
   ȿ(c‡Ů°ęȼDZȽ
   ƉƁƆƄƕ
   ƉƁƆƄƕž
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   ƦƸƬƁƨƨƁƴƣƒƥ
   ɀ(c‡Ů°ęȼTZȽ
   ƉƁƆƄƄƕ
   ƉƁƆƄƄƕž
   ƉƁƆƄƄſƕž
   ƨƨƁƴƣơƥ
   ƦƸƬƁƨƨƁƴƣơƥ
   Ɂ(c‡Ů°ęȼQZȽ
   ƨƨƁƴƣƞƥ
   ƦƸƬƁƨƨƁƴƣƞƥ
   ƖƦƵƷƵƪƪƁƔƳƨƯÈů
   ǦŐǠǒ
   'V­wǤǧǥź4Věã
   ňţŠŚŘŨŠŖťħŤťţŤŚťŧŬħĹħļŧţšŞŘħŘŝŖťŜŚ
   39 ěV¨0Ћ"ěV]k
   •  ǒnjǙǞǢƽǚǠ헼ŋţŤŨŠŖŧŞţŢħļŢŖŠŬŦŞŦ
   – NjЋƞ‹ƞ ƞAƅN•
   
   •  ľŠŖŦŦħńħħńőħƞ'ģǤľĭħľťŖšŚťħıįįijǥ
   – ľŠŖŦŦħńħĹħÖĤ»ǤłŖŦŧŚŞŜŚťħŖŢřħňŖťŦŞŠŠŞħİĸķįǥ
   – ľŠŖŦŦħńńħĹħļŊ',ǤňŨŠŠŞşŚŢħİĸĴĴīħŇůŪřŞŢħİĸĶįīħʼnŋļǥ
   – ľŠŖŦŦħńńńħĹħĜěǒǃǠƽǗǝǤļŧţšŦħŞŢħňţŠŚŘŨŠŚīħŀŎŋǥ
   – ľŠŖŦŦħńőħĹħŗţŢřħţťřŚťħšŖŤŤŞŢŜħ#ħľŠŖŦŦħńńĮńńń
   40
9. ľŠŖŦŦħńń
   •  ňŨŠŠŞşŚŢħŋţŤŨŠŖŧŞţŢħļŢŖŠŬŦŞŦħĨňŋļĩ
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   – ĊƜƫÆ'ä(ƯŻİĮıƐƗ',
   •  ʼnŖŧŨťŖŠħŋţŤŨŠŖŧŞţŢħļŢŖŠŬŦŞŦħĨʼnŋļĩ
   – ěV3“‹Ư‹ƝƧƗ߬øĂƝ_p
   – ߬øĂƄƪ¥ƣƬěV]kä(ƙƟŻĝ^ìĠƅǦ
   – ňŋļƚ;Ɲ4VƝĉ'ź
   •  ŇůŪřŞŢħŋţŤŨŠŖŧŞţŢħļŢŖŠŬŦŞŦħ
   – ſƣƫƮƜƀƅŻļŊNjƯꚼä1ƍƘí—
   
   41 ľŠŖŦŦħńńń
   •  ļŧţšŦħŞŢħňţŠŚŘŨŠŚħĹħŽ'V#ƞ4VžƞŒ§
   – ěV]kt'ƯƖƘŻġM',
   ź"ħįħśŠŨūħŦŨťśŖŘŚźǤ[Ùǥħ
   – ĽţŢřħŘťŞŧŞŘŖŠħŤţŞŢŧħŹħƅ¥ƣƬ
   •  ŀŎŋěã
   – ňŨŠŠŞşŚŢěãƅƬěPƯŵ ƒƭƓƭƞ4V2qƝŵ Çď',ǡǍƲǂǃƲǠƻƍƘ%ĉ'
   – ľŃŀŇŋł§īħōŀŎŋ§ƜƛļňĽŀō-PƝąµƌƭƬ
   42 'V­wǤǨǥźƶLjǝƹǢŻ'V œÿŻ1X6vŻÀ£»­w
   ňţŠŚŘŨŠŖťħŤťţŤŚťŧŬĹħŀŢŚťŜŬīħšţŠŚŘŨŠŖťħŦŧťŨŘŧŨťŚīħŘŝŚšŞŘŖŠħťŚŖŘŧŞţŢīħ šŖŜŢŚŧŞŘħŤťţŤŚťŧŬ
   44 ƶLjǝƹǢƅÁƏƧƞ
   •  ƶLjǝƹǢ
   – ěVƶLjǝƹǢźŞŧŚťŖŧŞũŚƝíƇǤŎľŁîÍǥ
   – 'Vœÿƞ߶kħIJĬĵħǪź'V0ŻDùŻĀ
   •  ǒǃǠƽǗǝƶLjǝƹǢĞźŋţŧŚŢŧŞŖŠħŀŢŚťŜŬħ ŎŨťśŖŘŚħĨŋŀŎĩ
   – ±ǤƒƞI«ƞƶLjǝƹǢt'ǥƄƪŻb|’a«ŵ ŠţŘŖŠħšŞŢŞšŨšħƅ‚ÔƌƭŻƣƕ’YZƄ)ZƙƆƜƀ
   45
10. 'Vœÿƚ1X6v
    •  ’YZœÿ
    – N©0í—ƞטŻôƞ0‹ƅƜƀ¯y
    •  €«ŻĆįy
    – N©0í—ƞטŻôƞ0‹ƯǧƗ~Ɨ
    •  b|YZœÿƝĔƖƘƀƜƀƄǬ
    – ĉl헯čŽďƞňĿƜƛƙ‚ÔƍƘ¿ƄƦƬ
    •  'Vď-ǤŇţŢřţŢƞ'Š-ǥƞÝz
    – òö5›VǖǢǕǠDžƝ¶–ƏƬ
    –  ňŋıƞěV½ĐƞÝzŻ'Šæ Ĩ2ÖĤ»ĿŁŏƜƛĩ
    46 ěV/ö
    •  ǍǛǠƺǫƼǠdžǠƞK¼/öźũŚťŧŞŘŖŠħŚūŘŞŧŖŧŞţŢ
    – âŻøĂƶLjǝƹǢ©ƞďƞěVĆÄ
    •  $ČLeźŘţŢŞŘŖŠħŞŢŧŚťŦŚŘŧŞţŢ
    – 1X6vƝéƪƭƬ
    •  ĠďeźŞŢŧŚťŦŬŦŧŚšħŘťţŦŦŞŢŜ
    – N•»ƝƟÂ*ĆÄźǥĊĠĬĊĠĆÄ
    – ƾnjǠĬøĂ½µħŦŤŞŢĬţťŗŞŧħŘţŨŤŠŞŢŜħƞÝz
    •  ƳƷǠ1ǒǃǠƽǗǝħńŋħƚěVëA-ħŀļ
    – ňŊƙƟ΍»ƝƟŻŃŊňŊƞøĂƶLjǝƹǢƞýÉ9ƚŵ ŇŐňŊƞøĂƶLjǝƹǢƞýÉ9ǤņţţŤšŖŢŦƞZ³ǥ
    – ĿŁƙƟŅŖŢŖşƞZ³ǤņŎøĂƖƘƩƀƞƄǬǥ
    51 ƒƞƞƾǑƺDžǝ
    •  õR>7'ħŞŢśťŖťŚřĺħńō
    – ǓƳƺǟ¨ġMŻ'V0ǖǢdžƝ¶–
    •  DùƾǑƺDžǝ
    – ǓƳƺǟ¨ġMŻDùǖǢdžƝ¶–
    RPƝ^ƏƬvÌ­w
    •  ™À£"ĦƾǑƺDžǝħŢŨŘŠŚŖťħšŖŜŢŚŧŞŘħ ťŚŦţŢŖŢŘŚĺħʼnňō
    •  ěVƾnjǠ"ĦƾǑƺDžǝħŚŠŚŘŧťţŢħŦŤŞŢħ ĨŤŖťŖšŖŜŢŚŧŞŘĩħťŚŦţŢŖŢŘŚĺħŀŎōħƣƔƟħŀŋō
    57 łļŐŎŎńļʼnµƞ[Ė
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    61
11. 62 GaussView νϡʔτϦΞϧ •  4lŠÌǧÊė •  File> New> Create MolGroup ²ǘNjBuilderǿǽȸșǿœ •  Element fragment ǹȆȳȔȆǘǡX¼ıǹıć •  Builderǿǽȸșǿ1ǢȆȳȔȆǙǶǣŠ ǘǝȣȲȇȭȸȘÊŖǐëǷ Ƕdž
    ȼȕȺȴȹȟȺǧÍĩȽ Inquire: 4lǧÊŖȠȲȭȺȒĹá Element Fragment: X¼ıǧıć Modeify Bond/Angle/Dihedral: Ring Fragment: íèÊŖ4lȖȸȥȵȺȘ ğRũȹğRĶȹ ŵĶǧȠȲȭȺȒģŲ R-group Fragment: qĩcȖȸȥȵȺȘ Add Valence: ÔěǣǘǡGl!ǹœ? Biological Fragment: ǼȫȝţȹDNAȖȸȥȵȺȘ Atom delete: “ijǥGlǧÞH
    ԋश1)m-ΞϛϊϑΣϊʔϧ(Ϟσϧ)ͷߏங •  File> New> Create MolGroup •  Ring Fragment ǹȆȳȔȆǘŻȖȸȥȵȺȘǏǴbenzeneǹŠ •  Builderǿǽȸșǿ1ǢȆȳȔȆǘbenzeneíǹıćǗǛǶ •  Element Fragment ǹȆȳȔȆǘDžNǏǴNitrogen Tetravalent(sp3) ǼǾȉȸDžOǏǴOxygen Tetravalent(sp3)ǼǾȉȸǹŠ
    $  Builderǿǽȸșǿ1ǢDžbenzeneíǧÔě ǧǢȆȳȔȆǙǶǣqĩcǦĥǑ¨ǸǶ $  File> Save ǏǴŻǀtest.gjfǁǣǘǡ$n $  File> Save Image ǭǝǨ Edit> Image Capture Ǣó*ǹȣǻǾȴǦ $nǙǶǖǣǐǢǑǶ(tiff, jpg, ps, bmp, png) ȼBuilderǢǧ"9ǥ¬³ÚȽ ~ȆȳȔȆ:Īñ^ō Ctrl+Z: Dzǵýǘ QȆȳȔȆ:ȏȺȬȹƒŵ^ō Ctrl+Y: DzǵýǘǧDzǵýǘ ȆȳȔȆ(~ȹQT·) ǭǝǨ Ctrl+~ȆȳȔȆ: ƒİċB
    63 ԋश2)ਫ෼ࢠͷߏங, Ұ఺ܭࢉ •  File> New> Create MolGroup •  Element Fragment ǹȆȳȔȆǘŻȖȸȥȵȺȘǏǴOǹŠ •  File> Save> ǀh2o.gjfǁŻǾȸȥȔȘȣǻǾȴǧ$n •  Calculate> Gaussian ĹĔÁǧĻr •  Edit ǹȆȳȔȆǘinputȣǻǾȴǹý¦ģŲ(Vi, XEmacsĒ)* %chk=h2o.chk ȓȀȔȆȩǾȸȘ(chk)ȣǻǾȴ¢r %mem=64MB ȭȮȳ %nproc=1 CPU° #P HF/STO-3G Pop=full DŽDŽȴȺȘȐȆȌȱȸ SCF=(Conver=8) test ȼďİȽ H2O single-point DŽDŽȍȱȤȒǾȘȴ ȼďİȽ 0 1 DŽDŽDŽųĬ(0:—)DžȎȢȸhŤ‰(1:ŤŶ) O H 1 B1 DŽDŽDŽDŽDŽDŽDŽDŽZ-matrix(1šŠÌ) H 1 B2 2 A1 ȼďİȽ B1 0.96 B2 0.96 DŽDŽDŽDŽDŽDŽDŽŻÊŖȠȲȭȺȒ A1 109.5 ȼďİȽ
    2 1 3 4 bond angle dihedral 64 O1 H3 H2 B2 A1 B1 ȼGJFȣǻǾȴǧç’Ƚ ȹ#İ(ȴȺȘȐȆȌȱȸ)Ǩ°İǦǸǝǞǡDZÊ ǸǥNjdž ȹi±m/v±mǧßaP ȹȄȺȷȺșŭǧďùǨNjǒǟǢDZÊǸǥNj ȹďİǨ“ŷ *additional keyword ǏǴǧĻrDZPĩ
    ݁Ռ2)OutputͷදࣔͱՄࢹԽ –  GlųĬǣȊȪȳǧıć •  File> Open> ǀh2o.logǁ •  Results> Charges •  Displayǿǽȸșǿǧ Show Charge NumberǦȓȀȔȆ •  Results> Summary ȊȪȳǧıć
    $  MODž.ųlt‰ǧıć $  File> Open> ǀh2o.fchkǁ $  Edit> MOs> Visualize ıćǗǛǝNjMOǹŠ  updateǹȆȳȔȆǙǶǣ§óǢǑǶ $  Results> Surfaces $  Cube Actions> New Cube> Total density Surface Actions> New Surface ȼMOǧËLJǥıć³ÚȽ BuilderǿǽȸșǿǢQȆȳȔȆ > Display Format > Surface Mesh(ȭȔȌȰıć)DžSolid(ȑȳȔș)DžTransparent(EŔ¶ıć) 65 $  ĹĔǧsİ+fchkȣǻǾȴǫǧf¨ $  prompt> g09 h2o.gjf prompt> formchk h2o.chk
12. ԋश3)ਫ෼ࢠͷߏ଄࠷దԽ –  InputȣǻǾȴǧ%Ï •  File> Open> ǀh2o.gjfǁ •  File> Save> ǀh2o_opt.gjfǁ 8UǢ$nǙǶ •  Calculate> Gaussian •  Edit> ǧ4ēǹ%Ï ȼlogȣǻǾȴǣchk(fchk)ȣǻǾȴǧŜNjȽ logȣǻǾȴǦǨDžĹĔřČǣ4lÊŖDžȁȜȴȅȺDžMO#°DžGlųĬDžJÈlȮȺȭȸȘǥǤǧĹ ĔğÄǐ3>ǗǷǶdžǖǧeR(OPTȄȺȷȺș)ǦǨDžÊŖ¹ŝCǧŕǧÊŖDZ3>ǦVǭǷǶdž chk(fchk)ȣǻǾȴǦǨMOǦŮǙǶ˜dDZVǭǷǶǧǢDž¹ĝÊŖǧMOǹıćǗǛǝNjǣǑǦïNjǶdž
    %chk=h2o_opt.chkȓȀȔȆȩǾȸȘȣǻǾȴ¢r %mem=64MB ȭȮȳ %nproc=1 CPU° #P OPT HF/STO-3G Pop=full SCF=(Conver=10) test ȼďİȽ H2O optimization ȍȱȤȒǾȘȴ ȼďİȽ ȹȹȹȹȹȹ ȹȹȹȹȹȹ
    $  ¹ŝCÊŖǧıć $  File> Open> ǀh2o_opt.logǁ ǿǽȸșǿšǦNJǶRead Intermediate geometriesǦȓȀȔȆ $  Results> Optimization $  Results> Summary 66 ԋश4)ਫ෼ࢠͷج४ৼಈղੳ –  ¹ŝCÊŖǏǴǧInputǧœ •  File> Open> ǀh2o_opt.logǁ =^ǧ¹ĝÊŖǹĿǮŏǯ •  File> Save> ǀh2o_freq.gjfǁ •  Calculate> Gaussian •  Edit> ǧ3ēǹ%Ï ȼprÊŖǏǤnjǏǧȓȀȔȆȽ cã£BķÃǏǴǨDžʼngWL(IR)ǎdzǪȲȪȸȎȧȆȘȴǧWLÛũǣŒ‰ǐÖǰǴǷǶdž ȁȜȴȅȺǐprǥÊŖǹïNjǥǔǷǩĹĔğÄǦ™YǨǥNjdžǭǝDžÊŖ¹ŝCǢïNjǝĹĔÚ/ c‡Ů°ǣöǥǶĹĔȵȦȴǹïNjǡDZNjǔǥNjdžDZǘņȼįȽǧ£B°ǐğÄǦëǷǷǩDžǜǧÊŖ ǐprŭȼşċè›ȽǢNJǶǖǣǹćǙ→prǥc‡è›ǧÊŖǢǨǥNjȻȻ
    %chk=h2o_freq.chkȓȀȔȆȩǾȸȘȣǻǾȴ¢r %mem=64MB ȭȮȳ %nproc=1 CPU° #P FREQ HF/STO-3G Pop=full SCF=(Conver=10) test ȼďİȽ H2O frequency ȍȱȤȒǾȘȴ ȼďİȽ ȹȹȹȹȹȹ ȹȹȹȹȹȹ
    $  cã£BȮȺșDžIRȎȧȆȘȴǧıć $  File> Open> ǀh2o_freq.logǁ ğÄǧĿǮŏǮ $  Results> Vibrations 67 ԋश5)ਫ෼ࢠͷ࣓֩ؾःṭఆ਺ 68 –  InputȣǻǾȴǧ%Ï •  File> Open> ǀh2o_opt.logǁ ¹ŝCÊŖǹĿǮŏǯ •  File> Save> ǀh2o_nmr.gjfǁ •  Calculate> Gaussian •  Edit> ǧ3ēǹ%Ï %chk=h2o_nmr.chkȓȀȔȆȩǾȸȘȣǻǾȴ¢r %mem=256MB ȭȮȳ %nproc=1 CPU° #P NMR=GIAO HF/6-31G(d) Pop=full SCF=(Conver=8) test ȼďİȽ H2O NMR tensor ȍȱȤȒǾȘȴ ȼďİȽ ȹȹȹȹȹȹ ȹȹȹȹȹȹ
    $  NMRȎȧȆȘȴıćDžcãæňǧ¢r $  File> Open> ǀh2o_nmr.logǁ ğÄǧĿǮŏǮ $  Results> NMR Element> H Reference> TMS HF/6-31G(d) ȼĹĔʉDžcãæňǣǧÒŎǦǟNjǡȽ ÆąÓŞĮr°ǨDžīǦcãæňǣǧ€ǣǘǡ‘ǴǷǶ(ɅCoȌȣȘDžppmF)džGaussViewǦ ǨTMS(ȖȘȲȭȓȴȌȲȸ)ǧĹĔ)ǐ ǰï™ǗǷǡNjǡDžHF/6-31G(d) ǣ B3LYP/6-311+G(2d,p) ǧĹĔȵȦȴǢǧCoȌȣȘǹĴčDZǶǖǣǐǢǑǶdžąe nǧæ—ǹÖǰǶc‡Ů°ȹ³ÚŁǦǟ NjǡǨ°hǒǧńŁǐNJǶdžD4ǥȵȦȴǢ¹ŝCǗǷǝÊŖǏsŹÊŖǹïNjǶǖǣǹǎkǰǙǶdž
    ǪƿǍDžƴƵƱƞć}Ż²[ÑƢ ƞąµƚĒ·
    69
13. ◦ਿ৿ެҰ1ɼ઒ล߂೭1ɼ௕ඌल࣮2ɼ੢઒ਗ਼2
 ʢ1ۚ৓େֶࣾձ෱ࢱֶ෦ɾ2ۚ୔େֶେֶӃࣗવՊֶݚڀՊʣ
    Ϧϯࢷ࣭εϑΟϯΰϛΤϦϯ෼ࢠͷߏ଄ ͱIRεϖΫτϧʹؔ͢Δཧ࿦తݚڀ Fig.1: Chemical structure of sphingomyelin and the truncated model.            
                                      
                           head group interface hydrophobic group truncated model (Sphingomyelin) (acyl chain) (sphingosine) (phosphocholine) head group interface hydrophobic group truncated model (Dihydrosphingomyelin) (acyl chain) (sphingosine) (phosphocholine) Fig.2: Truncated model of sphingomyelin and Ca2+ starting positions of geometry optimization.       
       (II) (I) 1-(II)Ca2+ 2-(II)Ca2+ ഑࠲ؒͷΤωϧΪʔࠩ͸ ྵ఺ΤωϧΪʔิਖ਼ޙͷ શΤωϧΪʔͷࠩ ΔEtot+ZPE (E1 – E2 ) Fig.3: Optimized structures by using B3LYP/6-31G(d,p); (1,2) sphingomyelin, and (1’,2’) dihydrosphingomyelin. 1 2 2’ ΔE = –4.070 kcal/mol 1’ ΔE = –7.4536 kcal/mol
14. Fig.4: Calculated IR spectrum of (a)1 and (b)1-(II)Ca2+ by B3LYP/6-31G(d,p), without scaling. O—H !@
    a) 3699 cm-1 b) 3744 cm-1 C=O !@
    a) 1717 cm-1 b) 1752 cm-1  
    H-:!@
    a) 1572 cm-1 b) 1522 cm-1 Fig.5: Calculated IR spectrum of (a)2 and (b)2-(II)Ca2+ by B3LYP/6-31G(d,p), without scaling. O—H !@
    a) 3544 cm-1 b) 3683 cm-1 C=O !@
    a) 1763 cm-1 b) 1641 cm-1  
    H-:!@
    a) 1541 cm-1 b) 1609 cm-1 +dǖDŽǝƙƞ'Vď-ǐǠǁǓǢƺ
    92 .1( E Q
    
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