Donchev et al. 10.1073/pnas.0602982103.

Supporting Information

Files in this Data Supplement:

Supporting Figure 6
Supporting Text
Supporting Table 4
Supporting Table 5





Supporting Figure 6

Fig. 6

. Dependence of energy of water homodimers on intermolecular distance. In each conformation set the distance R between the closest atoms was varied while maintaining the fixed orientation of the monomers shown (Insets). Curves correspond to QMPFF2 results; markers represent results of QM calculations.



Table 4. QMPFF2 atom types found in proteins

Name

Definition

Name

Definition

C3

Alkyl carbon

NA

Nitrogen as in pyrrole

HC3

Alkyl hydrogen

HNA

Hydrogen on pyrrole nitrogen

O1

Alcohol oxygen

SE

Sulfur in thioethers

HO1

Hydrogen on alcohol oxygen

S1

Thiol sulfur

N2

Nitrogen in aliphatic amines

HS1

H on thiol sulfur

HN2

Hydrogen on sp3 nitrogen

N=

General sp2 nitrogen

C=

General sp2 carbon

HN=

Hydrogen on sp2 nitrogen

HC=

Hydrogen on sp2 carbon

N+

Quaternary nitrogen

NE=

Nitrogen in amides

HN+

Hydrogen on quaternary nitrogen

HNE=

Hydrogen on amide nitrogen

O2-

Charged oxygen in carboxyl

O=

General sp2 oxygen

N3=+

Guanidinium nitrogen

CA

Carbon in aromatic ring

HN3+

Hydrogen on guanidinium nitrogen

HCA

Hydrogen on aromatic carbon

N2A+

Imidazolium nitrogen

NA=

Nitrogen as in pyridine

H2A+

Hydrogen on imidazoleum nitrogen





Table 5. QMPFF2 additional atom types

Name

Definition

Name

Definition

OW

Oxygen in water

N2=+

Amidinium nitrogen

HW

Hydrogen in water

HN2=+

Hydrogen on amidinium nitrogen

Li+

Lithium cation

OA

Oxygen in aromatic ring

Na+

Sodium cation

N3A+

Aromatic nitrogen in resonance structures containing three nitrogens (formal charge +1/3)

Mg++

Magnesium cation

H3A+

Hydrogen on N3A+ nitrogen

Ca++

Calcium cation

SA

Sulfur in aromatic ring

F-

Fluorine anion

F

Fluorine

Cl-

Chlorine anion

Cl

Chlorine

Br-

Bromine anion

Br

Bromine

OE

Ether oxygen

S6

Hexavalent sulfur

C4

Carbon in methane

P5

Pentavalent phosphorus

HC4

Hydrogen in methane

Cº

sp-carbon

N3

Nitrogen in ammonia

HCº

Hydrogen on sp carbon

HN3

Hydrogen in ammonia

Nº

sp-nitrogen

S2

Sulfur in dihydrosulfide

N5

Quinquivalent nitrogen

HS2

Hydrogen in dihydrosulfide

N1A+

Charged aromatic nitrogen as in methylpyridinium

N1=+

Nitrogen in H2N=CH2

O-

Deprotonated hydroxyl oxygen

HN1=+

Hydrogen on nitrogen in H2N=CH2