Investigate change in C=O radius from 1.65 to 1.70 in Reduce

[russell-taylor]

Who did it, when, and did they say why?

[russell-taylor]

None of the commit logs mention 1.65 or 1.7 in this context. None mention carbonyl or C=O.

[russell-taylor]

The relevant line in ElementInfo.cpp is: insert( 6, "C=O","carbon(carbonyl)", 1.70, 1.70, 1.80, 0.77, "white", 0); //** seems to help

[russell-taylor]

The log for ElementInfo.cpp has a likely entry on Oct 17 2012 by fheadd "merged in updated H bond-length definitions and related changes". Yep, that's the one. It changed it from 1.65 to 1.70. It did not change the "seems to help" comment, which had been there before. Here is the relevant portion of the commit:

+// changes in hydrogen VDW radii made to accompany changes in hydrogen bond-lengths in StdResH.cpp
 //    atno                          explRad implRad covRad mageColors flags
-insert( 0, "?",  "unknown",            1.00, 0.00, 0.00, "magenta", 0);
+insert( 0, "?",  "unknown",            1.05, 0.00, 0.00, "magenta", 0);
 insert( 0, "ignore", "ignore",         0.00, 0.00, 0.00, "magenta", IGNORE);

-insert( 1, "H",  "hydrogen",           1.17, 0.00, 0.30, "grey",   0);
-insert( 1, "Har","hydrogen(aromatic)", 1.00, 0.00, 0.30, "grey",   0);
-insert( 1, "Hpol","hydrogen(polar)",   1.00, 0.00, 0.30, "grey",   DONOR_ATOM);
+insert( 1, "H",  "hydrogen",           1.22, 0.00, 0.30, "grey",   0);
+// wba 100514  to 1.22 from 1.17
+insert( 1, "Har","hydrogen(aromatic)", 1.05, 0.00, 0.30, "grey",   0);
+// wba 100514  to 1.05 from 1.00
+insert( 1, "Hpol","hydrogen(polar)",   1.05, 0.00, 0.30, "grey",   DONOR_ATOM);
+// wba 100514  to 1.05 from 1.00
 insert( 1, "Ha+p",
-         "hydrogen(aromatic&polar)",   1.00, 0.00, 0.30, "grey",   DONOR_ATOM);
-
+         "hydrogen(aromatic&polar)",   1.05, 0.00, 0.30, "grey",   DONOR_ATOM);
+// wba 100514  to 1.05 from 1.00
 insert( 1, "HOd",
-         "hydrogen(omnidirectional)",  1.00, 0.00, 0.30, "grey",   DONOR_ATOM|HB_ONLY_DUMMY);
-
-insert( 6, "C",  "carbon",             1.75, 1.90, 0.77, "white",  0);
+         "hydrogen(omnidirectional)",  1.05, 0.00, 0.30, "grey",   DONOR_ATOM|HB_ONLY_DUMMY);
+// wba 100514  to 1.05 from 1.00
+insert( 6, "C",  "carbon",             1.70, 1.90, 0.77, "white",  0);
 insert( 6, "Car","carbon(aromatic)",   1.75, 1.90, 0.77, "white",  ACCEPTOR_ATOM);
-insert( 6, "C=O","carbon(carbonyl)",   1.65, 1.80, 0.77, "white",  0); //** seems to help
+insert( 6, "C=O","carbon(carbonyl)",   1.70, 1.80, 0.77, "white",  0); //** seems to help
 insert( 7, "N",  "nitrogen",           1.55, 1.70, 0.70, "sky",    0);
 insert( 7, "Nacc","nitrogen(acceptor)",1.55, 1.70, 0.70, "sky",    ACCEPTOR_ATOM);
 insert( 8, "O",  "oxygen",             1.40, 1.50, 0.66, "red",    ACCEPTOR_ATOM);