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Anita Dey Barsukova1 MIT Department of Mechanical Engineering, Cambridge, MA 02139 e-mail: anitadb1@mit.edu Ahmad Mujtaba Jebran1 MIT Department of Mechanical Engineering, Cambridge, MA 02139 e-mail: jebran@mit.edu Naomi Lynch MIT Department of Mechanical Engineering, Cambridge, MA 02139 e-mail: lynch.naomi@gmail.com Amit Galgali MIT Leaders for Global Operations, Cambridge, MA 02142 e-mail: amgalg@alum.mit.edu Andrea Moncada MIT Department of Mechanical Engineering, Cambridge, MA

Harold C. Simmons Comprehensive Cancer Center Bioinformatics Data Science Shared Resource Data Science Fellowship Agreement SCCC-DSSR This agreement is between the parties named below and the Director of SCCC-DSSR, Professor Jeon Lee. By signing this document, awardees (and their mentors, if applicable) acknowledge and agree to abide by the fellowship conditions listed below. Fellowship Awardee (Full Name

Harold C. Simmons Comprehensive Cancer Center Bioinformatics Data Science Shared Resource Data Science Collaboration Agreement SCCC-DSSR This agreement is between the DSSR user named below and the Director of SCCC-DSSR, Professor Jeon Lee. By signing this document, user acknowledges and agrees to the conditions listed below. DSSR collaborator (Full Name

#!/usr/bin/perl   open(FILE,  "accepted_hits_sorted.sam")  or  die("Unable  to  open  file");   open(OUTPUT,  ">final-­‐alignment.sam")  or  die("Unable  to  open  file");     use  strict;   my  $i;   my  $line;   my  $line1;   my  @group;   my  @sam_coord;   my  @sam_coord0;   my  @ID0;   my  @sam_coord1;   my  @ID1;   my  @record;   my  $j;   my  @as0;   my  @as;   my  $index;   my  $maxval;   my

Harold C. Simmons Comprehensive Cancer Center Bioinformatics Data Science Shared Resource Data Science On-Demand User Agreement SCCC-DSSR This agreement is between the DSSR client named below and the Director of SCCC-DSSR, Professor Jeon Lee. By signing this document, user acknowledges and agrees to the conditions listed below. DSSR client (Full Name

Oxidation of Unsaturated Systems 2 general reactivity patterns: X H X Yn+2 X+ Yn ++ OH simple example O A- Me2SCl+ S+ O + S + Cl- 2 electron oxidation 1 electron oxidation Xor -1 e- or X we will focus on oxidation of aromatic rings and enol/enolate systems Couple Eo Fe(III) + e- Fe(II) 0.77 V(V) + e- V(IV) 1.00 Tl(III) + 2 e- Th(I) 1.25 Pb(IV) + 2 e- Pb(II) 1.6-1.7 Mn(III) + e- 1.56Mn(II) Ce(IV) + e- Ce(III) 1.6 Reduction potentials of oxidants we will look at (bigger number

#!/usr/bin/perl     open(FILE1,  "Input.fastq")  or  die("Unable  to  open  file");   open(OUTPUT,  ">Output.fastq")  or  die("Unable  to  open  file");   use  strict;     my  $line;   my  @line;   my  $line1;   my  $seq0;   my  $junk;   my  $qual0;   my  $qual;   my  $seq;   my  $base;   my  $rest;   my  $newline;   my  @newline;   my  $n=1;   my  $m=1;   my  $newscore;   my  $restscore;   my

Substrate pKa's. Numbers are approximations for outside the range -2 - 16, but useful to know. For an extensive list, see http://www.chem.wisc.edu/areas/reich/pkatable/ Inorganics H2O DMSO CF3SO3H -14 HCl -8 H3O+ -2 H2O 16 NH4Cl 9 Organic X-H AcOH 5 12 O+ CH3Ph H -6 Me2OH+ -4 CH3SO3H -3 2 NH+ 5 3 N H O H 15 26 MeOH 16 28 17 29 NH3 36 38 41 EWG-CH NO2-CH3 10 17 O O 9 13 O EtO O 11 14 O EtO OEt O 13 16 O 20 27 O t-BuO 25 30 O Me2N 35 O S 3533PhOH 10 18

Oxidations at Carbon General references March, Advanced Org Chem, 1992, 1158-1238 Trost, Comp. Org. Syn. 1991, vol 7 Carey and Sundberg, Advanced Org Chem, part B, 615-664 Smith, Org Syn, Chap 3 H CH3 C(-IV) R CH3 C(-III) R CH2 OH C(-1) R CH OH RR H2 C R C(-II) R C O R C(0) R CH O C(+I) H CH2 OH C(-II) H CH O C(0) C(II) R COR O C(+III) H COH O C(+II) O C O C(+IV) RO COR O C(+IV) alkane RCH2M RCH2SiR3 RCH2X X=halide RCH2NR2 RCH2SR RCH2PR2 Acetal: RCH(OR)2

1 Ready; Catalysis Organometallics: Definitions Organometallics: Hard to define usefully and completely at the same time, but generally: Compounds containing metal-carbon bond(s). Fe Cl Ti Cl Cl ClFe NC NC CN CN CN CN K3 No question: Organometallic No question: Inorganic ???? Catalysis further complicates the issue: CH3 Br CH3 (HO)2B H3C + Me2N PCy2 PdL L H3C CH3 CH3 CH3 CH3 CH3 2% Pd(OAc)2 3% L CsF, rt L = Buchwald, JACS, 1998, 9722