Kirkwood-Buff Analysis of Aqueous N-Methylacetamide and Acetamide Solutions. Modeled by the CHARMM Additive and Drude Polarizable Force Fields
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1 Supporting Information for Kirkwood-Buff Analysis of Aqueous N-Methylacetamide and Acetamide Solutions Modeled by the CHARMM Additive and Drude Polarizable Force Fields Bin Lin, 1 Pedro E. M. Lopes, 1 Benoît Roux, 2 Alexander D. MacKerell, Jr. 1 1 Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, 20 Penn Street HSFII, Baltimore, Maryland 21201, USA 2 Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, USA
2 Figure S1. Dihedral scan for the O6=C5- N7- C9 torsion of NMA. The energy at 0 is set to zero.
3 N cc Excess Coordination Number acetamide (ACEM) additive drude exp N cw N ww x c Figure S2. Excess coordination numbers as a function of mole fraction for the ACEM solutions.
4 Table S1. Vibrational data for ACEM a. Ab initio (MP2/6-31G*) Drude Mode frequency assignment % cont. frequency assignment % cont tcch tcch wnh bccn 100 tcn bccn wnh wco tcn tcn 96 wnh rco rco ncn wco wco wnh ncc ncc rch rnh 53 ncn rch 3 ' wco dch 3 as rch rnh dch 3 as rch 3 ' dch 3 s ncn bhnh dch 3 s rco' dch 3 s dch 3 as 36 ' rch dch 3 as dch 3 as rch 3 ' rch dch 3 as bhnh 76 ' rch bhnh dch 3 s ncc nco nco nch 3 s nch 3 s nch 3 as' nch 3 as nch 3 as' nch 3 as nch 3 as' nch 3 as nnht nnhc nnht nnhc nnhc nnht nnhc nnht rnh
5 a Frequencies in cm -1. Normal mode contributions determined with the MOLVIB module in CHARMM. Only modes contributing more than 20% are shown. n indicates a stretching mode, b indicates a bending mode, d indicates a deformation mode, t is used for torsional rotations and r is used for rocking modes. Ab initio data was obtained at the MP2/6-31G* level of theory and frequencies were scaled by (Scott and Radom, J. Phys. Chem. 1996, 100, ).
6 Table S2. Vibrational data for NMAa. Mode Ab initio (MP2/6-31G*) frequency assignment % cont tnch tcch tcn bcnc 56 bccn wnh Drude frequency assignment 51.7 tcch tnch tcn bccn rco bccn wco wco vcn rch3' vcc rch3 vnch3 rch3' rch3 rnh vcn dch3s dch3s dch3as' dch3as dch3as' dch3as rnh vco vch3s vch3s vch3as' vch3as vch3as' vch3as vnh % cont wnh wco bccn ncn rco wco wnh vcn vcc vcn rch3 rch3' rch3 rch3' rco dch3as dch3as' rch3' dch3as' rch3 dch3as rch3 dch3s dch3s vcc vco rnh vch3s vch3s vch3as vch3as vch3as' vch3as' vnh
7 a Frequencies in cm -1. Normal mode contributions determined with the MOLVIB module in CHARMM. Notations are the same as in Table S1. Ab initio data was obtained at the MP2/6-31G* level of theory and frequencies were scaled by (Scott and Radom, J. Phys. Chem. 1996, 100, ).
8 Table S3. Topology entries for NMA in CHARMM format. RESI NMA 0.000! N-methylacetamide!! Hl1 H! \ /! Hl2--CL--C---N! / \! Hl3 O Cc--Hc3 (typically cis to O)! / \! Hc1 Hc2! GROUP ATOM CL CD33C ALPHA THOLE ATOM HL1 HDA3A ATOM HL2 HDA3A ATOM HL3 HDA3A ATOM C CD2O1A ALPHA THOLE ATOM O OD2C1A ALPHA THOLE ATOM N ND2A ALPHA THOLE ATOM H HDP1A ATOM CC CD33C ALPHA THOLE ATOM HC1 HDA3A ATOM HC2 HDA3A ATOM HC3 HDA3A ATOM LPA LP ATOM LPB LP BOND HL1 CL HL2 CL HL3 CL BOND CL C C N N CC BOND C O N H BOND HC1 CC HC2 CC HC3 CC BOND O LPA O LPB IMPR C CL N O N C CC H LONEPAIR relative LPA O C CL distance 0.30 angle 91.0 dihe 0.0 LONEPAIR relative LPB O C CL distance 0.30 angle 91.0 dihe ANISOTROPY O C LPA LPB A A
9 Table S4. Topology entries for ACEM in CHARMM format. RESI ACEM 0.000! acetamide!! the amide charges listed below are used in asparagine and glutamine!! HL1 Ht (trans to O)! \ /! HL2--CL--C---N! / \! HL3 O Hc (cis to O)! GROUP ATOM CL CD33C ALPHA THOLE ATOM HL1 HDA3A ATOM HL2 HDA3A ATOM HL3 HDA3A ATOM C CD2O1A ALPHA THOLE ATOM O OD2C1A ALPHA THOLE ATOM N ND2A ALPHA THOLE ATOM HC HDP1A ATOM HT HDP1A ATOM LPA LP ATOM LPB LP BOND C N N Hc N Ht C O BOND C CL CL HL1 CL HL2 CL HL3 BOND O LPA O LPB IMPR C CL N O IMPR N HC HT C!from NMA LONEPAIR relative LPA O C CL distance 0.30 angle 91.0 dihe 0.0 LONEPAIR relative LPB O C CL distance 0.30 angle 91.0 dihe ANISOTROPY O C LPA LPB A A
10 Table S5. Internal parameters for NMA and ACEM in CHARMM format. BONDS K b : kcal/mol/å 2 B 0 : Å K b B 0 ND2A2 CD2O1A ND2A2 CD33C ND2A2 HDP1A OD2C1A CD2O1A CD2O1A CD33C CD33C HDA3A ND2A1 CD2O1A ND2A1 HDP1A ANGLES K theta : kcal/mol/rad 2 Theta 0 : degree K UB : kcal/mol/å 2 S 0 : Å K theta Theta 0 K UB S 0 CD2O1A ND2A2 CD33C CD2O1A ND2A2 HDP1A CD33C ND2A2 HDP1A ND2A2 CD2O1A OD2C1A ND2A2 CD2O1A CD33C OD2C1A CD2O1A CD33C ND2A2 CD33C HDA3A CD2O1A CD33C HDA3A CD2O1A ND2A1 HDP1A HDP1A ND2A1 HDP1A ND2A1 CD2O1A OD2C1A ND2A1 CD2O1A CD33C
11 DIHEDRALS K chi : kcal/mol n: multiplicity delta: degrees K chi n delta CD33C ND2A2 CD2O1A CD33C CD33C ND2A2 CD2O1A CD33C HDP1A ND2A2 CD2O1A CD33C CD2O1A ND2A2 CD33C HDA3A HDP1A ND2A2 CD33C HDA3A ND2A2 CD2O1A CD33C HDA3A OD2C1A CD2O1A CD33C HDA3A HDP1A ND2A1 CD2O1A OD2C1A HDP1A ND2A1 CD2O1A CD33C ND2A1 CD2O1A CD33C HDA3A IMPROPERS K psi : kcal/mol/å 2 PSI 0 : Å K psi PSI 0 CD2O1A CD33C ND2A2 OD2C1A ND2A2 CD2O1A CD33C HDP1A OD2C1A ND2A1 CD33C CD2O1A ND2A1 HDP1A HDP1A CD2O1A
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