UT theoretical chemistry code forum

I'm looking at a hydrocarbon system with 13 C, 21 H and 5 O and a proton which should give a total of 138 electrons. However, the result that I get is:

# X Y Z CHARGE MIN DIST ATOMIC VOL
--------------------------------------------------------------------------------
1 -2.8736 1.5091 2.5185 4.0320 1.1785 382.0967
2 -1.0120 3.2106 3.3124 4.0365 1.1665 313.0553
3 -3.8001 -0.3061 4.2096 4.0416 1.1737 453.5009
4 -0.2915 4.6339 2.0131 0.9572 0.6111 940.7051
5 -5.2613 -1.6241 3.6088 0.9516 0.6050 1047.8329
6 -0.0725 3.0908 5.7838 4.0427 1.1893 139.7258
7 -2.8632 -0.4185 6.6772 4.0310 1.1923 219.4731
8 1.3677 4.4313 6.3864 0.9506 0.6163 448.7597
9 -3.6047 -1.8273 7.9825 0.9535 0.6022 377.0400
10 -0.9820 1.2738 7.4932 4.0118 1.1953 88.9573
11 -3.6077 1.6017 0.5988 0.9562 0.6436 443.9385
12 4.2271 -0.8357 9.7309 3.2710 0.2510 81.7178
13 5.8477 1.0512 10.6449 4.0237 1.1383 269.8683
14 5.1365 -2.7020 8.0884 4.0355 1.1422 201.2395
15 5.1584 2.4769 11.9540 0.9506 0.6148 601.8406
16 3.8543 -4.1554 7.4042 0.9373 0.5957 539.4015
17 8.3791 1.0709 9.8804 4.0303 1.1819 671.3970
18 7.6780 -2.6762 7.3565 4.0216 1.1879 618.1911
19 9.6341 2.5361 10.5951 0.9572 0.6140 1163.6041
20 8.3774 -4.1327 6.0828 0.9534 0.6217 1784.6215
21 9.3054 -0.7869 8.2391 4.0239 1.1535 802.3202
22 11.2783 -0.7646 7.6597 0.9629 0.6526 498.4286
23 0.0337 1.1291 10.1599 3.4560 0.2586 89.7304
24 1.0051 2.8754 10.6892 0.9477 0.6144 300.1689
25 -1.4917 0.7993 11.5162 0.9378 0.6201 418.9087
26 1.7282 -1.0296 10.5381 7.4810 1.7895 132.1738
27 0.8210 -3.5413 12.5975 0.3651 0.2401 14.9749
28 0.2423 -4.9221 13.7114 7.1418 1.3258 614.3092
29 1.0553 -4.6603 15.3276 0.3911 0.2510 152.3894
30 0.6831 -7.2144 12.7586 0.3647 0.3471 14.1173
31 0.9139 -9.1020 11.8853 7.1420 1.3522 955.3907
32 -0.1921 -10.4392 12.7427 0.3482 0.2379 17.6803
33 2.6612 -9.6402 11.9910 0.3745 0.2686 721.9821
34 -1.8460 -12.5625 13.9173 7.1256 1.3507 1029.3696
35 -3.4554 -12.8067 13.0860 0.3870 0.2557 567.9527
36 -2.2525 -12.3267 15.6836 0.4005 0.2736 127.9238
37 -5.5447 8.6399 8.3275 7.1461 1.3048 1469.1010
38 -4.6387 7.1955 7.6780 0.4228 0.2300 47.5718
39 -4.9037 10.0286 7.3325 0.4323 0.2278 225.2913
--------------------------------------------------------------------------------
VACUUM CHARGE: 0.0000
VACUUM VOLUME: 0.0000
NUMBER OF ELECTRONS: 101.9963


And so I get the wrong number of total electrons and the sum of charges is four rather than one. Does this have to do with the .cube file that I'm using or is there some other problem?

Thanks for your help.

Likely the 1s electrons for C and O are not treated explicitly, so that 36 electrons will be missing from what you expect.

Is this true even if I'm using a standard gaussian basis set? I thought these were explicitly all-electron.

At any rate, do you have any idea why the total charge on the system is +4 rather than +1?

Thanks for your help.

I count 13 x (4e for C) + 21 x (1e for H) + 5 x (6e for O) = 103 , and you have a total charge of 102, so it is overall +1.

I see, but the partial charges (once the valence of 4 for carbon, six for oxygen and 1 for hydrogen has been subtracted) equals 4. Shouldn't those sum to one as well?

I just don't understand any residual problems. There is no distinction between the valence and core charges in the Bader analysis. With the reasonable assumption that the 1s electrons are not treated explicitly in your calculation, the total number of electrons makes sense. Please think about what I have written and try to make sense of it -- I think I have given the explanation that you need.

[quote="graeme"]I just don't understand any residual problems. There is no distinction between the valence and core charges in the Bader analysis. With the reasonable assumption that the 1s electrons are not treated explicitly in your calculation, the total number of electrons makes sense. Please think about what I have written and try to make sense of it -- I think I have given the explanation that you need.[/quote]

I understand why the total number of electrons is correct given the electrons treated explicitly and the +1 charge of the system. I still don't see why the partial charges shouldn't be expected to sum to one. Aren't they meant to represent how charge is distributed in the system? Am I looking in the wrong file for the Bader partial charges?

I very much appreciate your help with my posts, but this is the most important question in terms of how I use these results for my research.

The Bader analysis only considers the electronic charge. You must subtract the nuclear charge from the electronic charge in order to get the partial charges. Then, they sum to +1.