Geometriniu savybiu aptikimas atviroje mau molekuliu duomenu - PowerPoint PPT Presentation

Geometriniu ˛ savybiu ˛ aptikimas atviroje mažu ˛ molekuliu ˛ duomenu ˛ baz˙ eje COD Andrius Merkys, Antanas Vaitkus, Mykolas Okuliˇ c-Kazarinas ir Saulius Gražulis Vilnius, 2016 Vilniaus universiteto Biotechnologijos institutas 1 / 1

Strukt¯ urin˙ ˛ baz˙ es mažu ˛ molekuliu ˛ duomenu es Crystallography Cambridge Inorganic Crystal Open Structural Structure Database Database Database (COD) (CSD) (ICSD) 350 000 i ˛rašu ˛ 800 000 i ˛rašu ˛ 180 000 i ˛rašu ˛ atvira prenumeruojama prenumeruojama 2016 m. vasario m˙ en. duomenys 2 / 1

Vandenilio talpa kristaluose in silico tyrimas COD duomenu ˛ baz˙ eje COD 8100961 Breternitz ir Gregory (2015) 3 / 1

Ar grafenas tik vienas toks? Dvimaˇ ciu ˛ alotropu ˛ paieška COD ir ICSD duomenu ˛ baz˙ ese C60 Hg Sm Nd Te2 La As2 C8 Br As4 Gd Bi2 Ba Sn I C16 COD 9010988 C2 P42 C8 Bi4 C60 Ga2 P4 Pr Sb4 In P2 COD (15 vnt.) ICSD (19 vnt.) Mounet et al. (rengiama) 4 / 1

˛ geometrin˙ es savyb˙ Molekuliu es 15 Frequency 10 30 25 5 20 Frequency 0 15 1.20 1.25 1.30 1.35 1.40 1.45 1.50 1.55 10 bond length 5 8 0 0 50 100 150 200 250 300 350 6 dihedral angle Frequency 4 2 0 120 125 130 135 140 angle size 5 / 1

Kristalo simetrijos atstatymas Pavyzdys: grafito sluoksnis, COD 1011060 6 / 1

˛ jungˇ Tarpatominiu ciu ˛ paieška Pavyzdys: grafito sluoksnis, COD 1011060 7 / 1

Simetriškai ekvivalenˇ ciu ˛ stebiniu ˛ atmetimas Pavyzdys: benzeno molekul˙ e, COD COD 2100348 8 / 1

˛ imˇ Stebiniu ciu ˛ aprašymas 15 150 H  H                 C 2i − 1 C 2i    n 10 Frequency 100 Frequency N N 50 5 0 0 1.30 1.35 1.40 1.45 1.50 1.20 1.25 1.30 1.35 1.40 1.45 1.50 1.55 bond length bond length 100 80 80 CH 3 N N 60 H 3 C CH 3 60 Frequency Frequency C N N C 40 40 20 20 0 0 1.30 1.35 1.40 1.45 1.50 1.30 1.35 1.40 1.45 1.50 bond length bond length 9 / 1

COD geometrijos naršykl˙ e http://www.crystallography.net/geometry order by class name (ascending) order by observation count (descending) To search for bond models, please enter one to two COD atom class names separated by ';'. Examples: C(CC)2;C(CC)2 c(cCH)2(H);c(cCH)2(H) To search for angle models, please enter three COD atom class names separated by ';'. To search for dihedral angle models, please enter four COD atom class names separated by ';'. Percent sign (%) can be used as a wildcard. 10 / 1

Paieška: poliino anglis-anglis jungties ilgis 11 / 1

Dõminanˇ ciu ˛ deskriptoriu ˛ pasirinkimas 12 / 1

˛ baz˙ Poliinu ˛ jungtys COD duomenu eje order by class name (ascending) order by observation count (descending) Distribution of C(CC)2 - C(CC)2 bonds Warning: models for this class are scheduled for recalculation, out-of-date models are presented here for reference only. Distribution Peaks BIC Log-likelihood cauchy 3 -2983.63250734474 1521.29969433851 cauchy 4 -2972.23756189253 1526.65851186221 cauchy 5 -2954.17602788954 1528.68403511053 cauchy 6 -2945.47851368168 1535.3915682564 cauchy 7 -2931.49848709219 1539.45784521146 cauchy 8 -2931.13696008285 1550.3333719566 cauchy 9 -2911.97656549846 1551.80946491421 cauchy 10 -2903.18311848377 1558.46903165667 cauchy 2 -2306.60210414815 1171.72820249042 gaussian 4 -2174.55991783404 1127.81968983297 gaussian 5 -2164.18853401055 1133.69028817103 gaussian 2 -1955.22813260451 996.041216718596 gaussian 3 -1947.4479559367 1003.2074186345 gaussian 1 -1773.73018669565 894.235953514359 cauchy 1 -1556.82925243875 785.785486385914 gaussian 6 NaN NaN gaussian 7 NaN NaN gaussian 8 NaN NaN gaussian 9 NaN NaN gaussian 10 NaN NaN Breaks: Min: Max: Histogram width: Show individual mixture components 13 / 1

˛ baz˙ Poliinu ˛ jungtys COD duomenu eje order by class name (ascending) order by observation count (descending) Distribution of C(CC)2 - C(CC)2 bonds Warning: models for this class are scheduled for recalculation, out-of-date models are presented here for reference only. Distribution Peaks BIC Log-likelihood cauchy 3 -2983.63250734474 1521.29969433851 cauchy 4 -2972.23756189253 1526.65851186221 � � C 2i − 1 C 2i n cauchy 5 -2954.17602788954 1528.68403511053 cauchy 6 -2945.47851368168 1535.3915682564 cauchy 7 -2931.49848709219 1539.45784521146 cauchy 8 -2931.13696008285 1550.3333719566 [ ] m C cauchy 9 -2911.97656549846 1551.80946491421 cauchy 10 -2903.18311848377 1558.46903165667 cauchy 2 -2306.60210414815 1171.72820249042 gaussian 4 -2174.55991783404 1127.81968983297 gaussian 5 -2164.18853401055 1133.69028817103 gaussian 2 -1955.22813260451 996.041216718596 gaussian 3 -1947.4479559367 1003.2074186345 gaussian 1 -1773.73018669565 894.235953514359 cauchy 1 -1556.82925243875 785.785486385914 gaussian 6 NaN NaN gaussian 7 NaN NaN gaussian 8 NaN NaN gaussian 9 NaN NaN gaussian 10 NaN NaN Breaks: Min: Max: Histogram width: Show individual mixture components 14 / 1

Tolimesni planai ◮ Atvira prieiga prie duomenu ˛ MySQL protokolu ◮ Periodiškas duomenu ˛ baz˙ es atnaujinimas ◮ Strukt¯ uru ˛-išskirˇ ciu ˛ pašalinimas iš imties 15 / 1

Pad˙ ekos VU Biotechnologijos COD Advisory Board institutas Daniel Chateigner Virginijus Šikšnys Robert T. Downs ( skyriaus ved˙ ejas ) Werner Kaminsky Armel Le Bail Saulius Gražulis Luca Lutterotti Antanas Vaitkus Peter Moeck Mykolas Okuliˇ c-Kazarinas Peter Murray-Rust Miguel Quirós 16 / 1

Aˇ ci¯ u už d˙ emesi ˛! http://en.wikipedia.org/wiki/Topaz http://www.crystallography.net/2207377.html A path to freedom: GNU → Linux → Ubuntu → MySQL → R → L A T X → TikZ → Beamer E