I am preparing new MD simulation system contains Na2SO4. The research is about the salt-out effect for protein in salt solution. I prefer to use AMBER for the simulation. I find an ECC force field for sulphate group, but not sure whether it's good or not.
Does anyone have experience to run MD simulation that contains Na2SO4?
Thanks,
Xiaoquan.
Mr. Sun,
Please find as attachment MM/MD using UFF. In addition the freq/otp test using the same theoretical level is presented below:
----------------------------
# UFF Opt Pop=(Minimal) Test
----------------------------
1/6=10,10=10,14=-1,18=10,38=1,56=1/1,3;
2/17=6,18=5,29=2/2;
3/5=2,11=9,12=1,25=1,30=1/1;
4/20=10,22=1001,24=1/2;
7/7=1/16;
1/6=10,10=10,14=-1,18=10/3(1);
99/12=1/99;
2/29=1/2;
3/5=2,11=9,12=1,25=1,30=1/1;
4/16=2,20=10,22=1001,24=1/2;
7/7=1/16;
1/6=10,10=10,14=-1,18=10/3(-4);
2/29=1/2;
99/12=1/99;
-----
NaSO4
-----
Symbolic Z-matrix:
Charge = -2 Multiplicity = 1
O 0 -1.77361 -0.49722 -0.97539
S 0 -0.28453 -0.12309 -0.55196
O 0 -0.24991 1.03618 0.59592
O 0 1.0318 0.28352 -1.50566
O 0 0.29297 -1.16757 0.70293
Na 0 1.69379 0.46417 0.48685
Na 0 -1.71216 -1.00226 1.03635
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
Berny optimization.
Initialization pass.
No Z-matrix variables, so optimization will use Cartesian coordinates.
Trust Radius=1.00D-01 FncErr=1.00D-07 GrdErr=1.00D-07
Number of steps in this run= 10 maximum allowed number of steps= 100.
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
------------------------------------------------------------------------
Z-MATRIX (ANGSTROMS AND DEGREES)
CD Cent Atom N1 Length/X N2 Alpha/Y N3 Beta/Z J
------------------------------------------------------------------------
1 1 O 0 -1.773605 -0.497223 -0.975388
2 2 S 0 -0.284531 -0.123093 -0.551956
3 3 O 0 -0.249908 1.036179 0.595917
4 4 O 0 1.031800 0.283524 -1.505661
5 5 O 0 0.292969 -1.167572 0.702927
6 6 Na 0 1.693787 0.464172 0.486847
7 7 Na 0 -1.712158 -1.002258 1.036346
------------------------------------------------------------------------
Z-Matrix orientation:
---------------------------------------------------------------------
Center Atomic Atomic Coordinates (Angstroms)
Number Number Type X Y Z
---------------------------------------------------------------------
1 8 0 -1.773605 -0.497223 -0.975388
2 16 0 -0.284531 -0.123093 -0.551956
3 8 0 -0.249908 1.036179 0.595917
4 8 0 1.031800 0.283524 -1.505661
5 8 0 0.292969 -1.167572 0.702927
6 11 0 1.693787 0.464172 0.486847
7 11 0 -1.712158 -1.002258 1.036346
---------------------------------------------------------------------
Distance matrix (angstroms):
1 2 3 4 5
1 O 0.000000
2 S 1.592674 0.000000
3 O 2.672447 1.631785 0.000000
4 O 2.959908 1.675595 2.574081 0.000000
5 O 2.745330 1.731812 2.272154 2.743977 0.000000
6 Na 3.883969 2.310354 2.029049 2.107356 2.161382
7 Na 2.075069 2.309492 2.547033 3.955293 2.039370
6 7
6 Na 0.000000
7 Na 3.748710 0.000000
Interatomic angles:
O1-S2-O3=111.9466 O1-S2-O4=129.8047 O1-O3-O4= 68.6592
O3-S2-O4=102.1994 O1-S2-O5=111.2689 O1-O3-O5= 66.884
O3-S2-O5= 84.9327 O1-O5-O4= 65.2602 O4-S2-O5=107.2666
O4-O3-O5= 68.6471 O1-S2-Na6=168.4741 O1-O3-Na6=110.6591
S2-O3-Na6= 77.4222 O1-O4-Na6= 98.6824 S2-O4-Na6= 74.3016
O3-Na6-O4= 76.9426 O1-O5-Na6=104.029 S2-O5-Na6= 71.8419
O3-Na6-O5= 65.5817 O4-Na6-O5= 79.9921 S2-O1-Na7= 76.8053
O1-Na7-O3= 69.7923 O3-S2-Na7= 78.4502 O4-O1-Na7=102.1115
O4-S2-Na7=165.7971 O4-O3-Na7=101.1295 O1-Na7-O5= 83.7044
S2-O5-Na7= 75.0315 O3-O5-Na7= 72.1916 O4-O5-Na7=110.699
Na6-S2-Na7=108.473 Na6-O3-Na7=109.4891 Na6-O5-Na7=126.3259
Stoichiometry Na2O4S(2-)
Framework group C1[X(Na2O4S)]
Deg. of freedom 15
Full point group C1 NOp 1
Largest Abelian subgroup C1 NOp 1
Largest concise Abelian subgroup C1 NOp 1
Standard orientation:
---------------------------------------------------------------------
Center Atomic Atomic Coordinates (Angstroms)
Number Number Type X Y Z
---------------------------------------------------------------------
1 8 0 -1.468749 1.229075 0.060536
2 16 0 -0.032796 0.546289 -0.031378
3 8 0 0.264469 -0.423221 1.247062
4 8 0 1.468139 1.237962 -0.307783
5 8 0 -0.094781 -0.927227 -0.939168
6 11 0 1.836566 -0.810232 0.024045
7 11 0 -1.911829 -0.796435 -0.022511
---------------------------------------------------------------------
Rotational constants (GHZ): 3.4828999 1.8548466 1.5025794
Isotopes: O-16,S-32,O-16,O-16,O-16,Na-23,Na-23
Standard basis: VSTO-3G (5D, 7F)
Warning: center 6 has no basis functions!
Warning: center 7 has no basis functions!
There are 20 symmetry adapted basis functions of A symmetry.
Crude estimate of integral set expansion from redundant integrals=1.000.
Integral buffers will be 262144 words long.
Raffenetti 1 integral format.
Two-electron integral symmetry is turned on.
20 basis functions 60 primitive gaussians
17 alpha electrons 17 beta electrons
nuclear repulsion energy 102.6213856989 Hartrees.
UFF calculation of energy and first derivatives.
MO and density RWFs will be updated.
Recover connectivity from rwf.
EGHMM: NBAlg=1 ICut=1 CutNB= 1.43D+03
I= 2 IAn= 16 Valence= 6.
JB= 1 J= 1 IAn= 8 IBT= 1 Dist= 1.59D+00
JB= 2 J= 3 IAn= 8 IBT= 1 Dist= 1.63D+00
JB= 3 J= 4 IAn= 8 IBT= 1 Dist= 1.68D+00
JB= 4 J= 5 IAn= 8 IBT= 1 Dist= 1.73D+00
JB= 5 J= 6 IAn= 11 IBT= 2 Dist= 2.31D+00
JB= 6 J= 7 IAn= 11 IBT= 2 Dist= 2.31D+00
I= 5 IAn= 8 Valence= 3.
JB= 1 J= 2 IAn= 16 IBT= 1 Dist= 1.73D+00
JB= 2 J= 6 IAn= 11 IBT= 1 Dist= 2.16D+00
JB= 3 J= 7 IAn= 11 IBT= 1 Dist= 2.04D+00
I= 6 IAn= 11 Valence= 8.
JB= 1 J= 2 IAn= 16 IBT= 2 Dist= 2.31D+00
JB= 2 J= 3 IAn= 8 IBT= 1 Dist= 2.03D+00
JB= 3 J= 4 IAn= 8 IBT= 1 Dist= 2.11D+00
JB= 4 J= 5 IAn= 8 IBT= 1 Dist= 2.16D+00
I= 7 IAn= 11 Valence= 3.
JB= 1 J= 1 IAn= 8 IBT= 1 Dist= 2.08D+00
JB= 2 J= 2 IAn= 16 IBT= 2 Dist= 2.31D+00
JB= 3 J= 5 IAn= 8 IBT= 1 Dist= 2.04D+00
Convergence limit is 0.750E-04
Step NS ND Rises Max. Force RMS Force Max. Disp. RMS Disp. Energy Flag
1 1 0 F 0.12920336 0.05179489 0.08640587 0.03463828 0.9778235 ----
2 2 2 F 0.08121638 0.03347786 0.10797727 0.04594769 0.9478194 ----
3 3 3 F 0.03860882 0.01992295 0.08993591 0.04721400 0.9244963 ----
4 4 4 F 0.01717219 0.00986227 0.04305260 0.02348995 0.9107711 ----
5 5 5 F 0.01576786 0.00758545 0.03422483 0.01675615 0.9068965 ----
6 6 6 F 0.01589676 0.00712728 0.03783040 0.01759240 0.9043745 ----
7 2 1 F 0.01707623 0.00721655 0.02381593 0.01006480 0.9017692 ----
8 2 1 F 0.01807947 0.00745838 0.01258880 0.00519322 0.9002200 ----
9 2 1 F 0.01855894 0.00760078 0.01920178 0.00788193 0.8993990 ----
10 2 1 F 0.01919125 0.00781649 0.01663672 0.00677529 0.8981237 ----
11 2 1 F 0.01971719 0.00800450 0.01868558 0.00759208 0.8969983 ----
12 2 1 F 0.02020721 0.00820694 0.01832721 0.00743959 0.8957063 ----
13 2 1 F 0.02062375 0.00839797 0.01909350 0.00777132 0.8944093 ----
14 2 1 F 0.02099444 0.00858832 0.01921369 0.00785270 0.8930235 ----
15 2 1 F 0.02132532 0.00877476 0.01959593 0.00805482 0.8915921 ----
16 2 1 F 0.02163298 0.00896358 0.01980171 0.00819471 0.8900921 ----
17 2 1 F 0.02193457 0.00915852 0.02007243 0.00836993 0.8885332 ----
18 2 1 F 0.02224527 0.00936568 0.02030834 0.00853801 0.8869057 ----
19 2 1 F 0.02257823 0.00959035 0.02057702 0.00872709 0.8852069 ----
20 2 1 F 0.02294469 0.00983800 0.02085937 0.00892955 0.8834273 ----
21 2 1 F 0.02335365 0.01011340 0.02117648 0.00915504 0.8815575 ----
22 2 1 F 0.02381195 0.01042072 0.02152610 0.00940357 0.8795845 ----
23 2 1 F 0.02432407 0.01076322 0.02191426 0.00967872 0.8774938 ----
24 2 1 F 0.02489172 0.01114307 0.02233920 0.00998078 0.8752685 ----
25 2 1 F 0.02551325 0.01156098 0.02279885 0.01030982 0.8728901 ----
26 2 1 F 0.02618286 0.01201587 0.02328639 0.01066382 0.8703388 ----
27 2 1 F 0.02688960 0.01250439 0.02379172 0.01103924 0.8675942 ----
28 2 1 F 0.02761644 0.01302041 0.02430003 0.01143036 0.8646363 ----
29 2 1 F 0.02833932 0.01355455 0.02479208 0.01182936 0.8614474 ----
30 2 1 F 0.02902673 0.01409382 0.02524411 0.01222621 0.8580136 ----
31 3 1 F 0.02963985 0.01462145 0.02562857 0.01260894 0.8543272 ----
32 4 1 F 0.03013375 0.01511719 0.02591537 0.01296402 0.8503895 ----
33 2 1 F 0.03045991 0.01555803 0.02607365 0.01327705 0.8462130 ----
34 2 1 F 0.03074131 0.01591958 0.02614950 0.01353350 0.8418234 ----
35 2 1 F 0.03102695 0.01617794 0.02634991 0.01371966 0.8372605 ----
36 2 1 F 0.03091606 0.01631192 0.02625922 0.01382346 0.8325780 ----
37 3 2 F 0.03038687 0.01630539 0.03323150 0.01781332 0.8278413 ----
38 4 2 F 0.02980170 0.01607525 0.19171726 0.10317400 0.8217786 ----
39 5 2 F 0.02878656 0.01385845 0.16766917 0.08460782 0.8047671 ----
40 2 2 F 0.02246215 0.01049268 0.09620145 0.04538383 0.7923963 ----
41 3 3 F 0.01357126 0.00677907 0.04067304 0.02241268 0.7850440 ----
42 4 4 F 0.01257552 0.00521850 0.04794208 0.02824193 0.7824041 ----
43 5 1 F 0.01335603 0.00498820 0.01886082 0.00704413 0.7802271 ----
44 6 6 F 0.01238925 0.00435894 0.13130941 0.05375851 0.7795999 ----
45 7 1 F 0.02914465 0.00940142 0.03998868 0.01289946 0.7791093 ----
46 8 2 F 0.01488827 0.00525493 0.01688020 0.00596289 0.7777106 ----
47 9 5 F 0.00865201 0.00412006 0.04608099 0.02296066 0.7771605 ----
48 10 6 F 0.00752980 0.00298860 0.12216318 0.04390761 0.7756160 ----
49 11 6 F 0.00512556 0.00229148 0.04093266 0.01452267 0.7740253 ----
50 12 7 F 0.00386792 0.00172619 0.06504489 0.02369081 0.7735666 ----
51 13 9 F 0.00311236 0.00128607 0.01822743 0.00746807 0.7730675 ----
52 14 1 F 0.00288512 0.00110725 0.00411924 0.00158088 0.7729474 ----
53 15 8 F 0.00183964 0.00092313 0.03120260 0.01423046 0.7729183 ----
54 16 8 F 0.00127739 0.00068851 0.00577218 0.00268350 0.7727317 ----
55 17 9 F 0.00122061 0.00056599 0.02736963 0.01256331 0.7727013 ----
56 18 11 F 0.00076844 0.00034551 0.01267587 0.00589291 0.7726071 ----
57 2 1 F 0.00050078 0.00024837 0.00071538 0.00035480 0.7725863 ----
58 3 3 F 0.00040648 0.00016270 0.00258150 0.00120486 0.7725852 ----
59 4 4 F 0.00026957 0.00010858 0.00262710 0.00112009 0.7725831 ----
60 5 5 F 0.00016619 0.00007216 0.00111757 0.00054870 0.7725818 -+--
61 6 6 F 0.00015019 0.00006355 0.00105561 0.00050522 0.7725811 -+--
62 7 7 F 0.00014133 0.00005781 0.00162541 0.00074021 0.7725805 -+--
63 8 7 F 0.00012450 0.00005085 0.00133976 0.00055316 0.7725798 -+--
64 9 8 F 0.00010104 0.00004473 0.00549442 0.00230344 0.7725793 ++--
65 10 5 F 0.00004175 0.00002232 0.00031600 0.00015258 0.7725781 ====
Energy= 0.772578110285 NIter= 0.
Dipole moment= 0.000000 0.000000 0.000000
***** Axes restored to original set *****
-------------------------------------------------------------------
Center Atomic Forces (Hartrees/Bohr)
Number Number X Y Z
-------------------------------------------------------------------
1 8 -0.000003917 0.000012456 -0.000025885
2 16 0.000007279 -0.000001504 0.000006231
3 8 -0.000016314 -0.000047104 0.000024905
4 8 -0.000004150 -0.000026109 0.000011726
5 8 0.000001492 0.000020998 0.000038153
6 11 0.000026542 0.000030053 -0.000040017
7 11 -0.000010933 0.000011211 -0.000015113
-------------------------------------------------------------------
Cartesian Forces: Max 0.000047104 RMS 0.000022316
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
Berny optimization.
Search for a local minimum.
Step number 1 out of a maximum of 10
All quantities printed in internal units (Hartrees-Bohrs-Radians)
Second derivative matrix not updated -- unit matrix used.
RFO step: Lambda=-1.04576450D-08.
Linear search not attempted -- first point.
TrRot= 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
Variable Old X -DE/DX Delta X Delta X Delta X New X
(Linear) (Quad) (Total)
X1 -2.35923 0.00000 0.00000 0.00000 0.00000 -2.35924
Y1 -1.57667 0.00001 0.00000 0.00001 0.00001 -1.57666
Z1 -1.49576 -0.00003 0.00000 -0.00003 -0.00003 -1.49579
X2 -0.70289 0.00001 0.00000 0.00001 0.00001 -0.70288
Y2 1.09401 0.00000 0.00000 0.00000 0.00000 1.09401
Z2 -1.39721 0.00001 0.00000 0.00001 0.00001 -1.39720
X3 -0.19216 -0.00002 0.00000 -0.00002 -0.00002 -0.19217
Y3 2.14441 -0.00005 0.00000 -0.00005 -0.00005 2.14436
Z3 1.46656 0.00002 0.00000 0.00002 0.00002 1.46659
X4 2.11887 0.00000 0.00000 0.00000 0.00000 2.11887
Y4 0.30272 -0.00003 0.00000 -0.00003 -0.00003 0.30269
Z4 -2.40052 0.00001 0.00000 0.00001 0.00001 -2.40051
X5 0.41700 0.00000 0.00000 0.00000 0.00000 0.41700
Y5 -1.29777 0.00002 0.00000 0.00002 0.00002 -1.29775
Z5 0.12585 0.00004 0.00000 0.00004 0.00004 0.12589
X6 3.57901 0.00003 0.00000 0.00003 0.00003 3.57904
Y6 0.75523 0.00003 0.00000 0.00003 0.00003 0.75526
Z6 1.31006 -0.00004 0.00000 -0.00004 -0.00004 1.31002
X7 -2.79861 -0.00001 0.00000 -0.00001 -0.00001 -2.79862
Y7 -1.31111 0.00001 0.00000 0.00001 0.00001 -1.31109
Z7 2.28220 -0.00002 0.00000 -0.00002 -0.00002 2.28218
Item Value Threshold Converged?
Maximum Force 0.000047 0.000450 YES
RMS Force 0.000022 0.000300 YES
Maximum Displacement 0.000047 0.001800 YES
RMS Displacement 0.000022 0.001200 YES
Predicted change in Energy=-5.228822D-09
Optimization completed.
-- Stationary point found.
-------------------
- Thermochemistry -
-------------------
Temperature 298.150 Kelvin. Pressure 1.00000 Atm.
Atom 1 has atomic number 8 and mass 15.99491
Atom 2 has atomic number 16 and mass 31.97207
Atom 3 has atomic number 8 and mass 15.99491
Atom 4 has atomic number 8 and mass 15.99491
Atom 5 has atomic number 8 and mass 15.99491
Atom 6 has atomic number 11 and mass 22.98977
Atom 7 has atomic number 11 and mass 22.98977
Molecular mass: 141.93127 amu.
Principal axes and moments of inertia in atomic units:
1 2 3
EIGENVALUES -- 592.78893 985.773091186.01113
X 1.00000 0.00000 0.00000
Y 0.00000 1.00000 0.00000
Z 0.00000 0.00000 1.00000
THIS MOLECULE IS AN ASYMMETRIC TOP.
ROTATIONAL SYMMETRY NUMBER 1.
WARNING-- ASSUMPTION OF CLASSICAL BEHAVIOR FOR ROTATION
MAY CAUSE SIGNIFICANT ERROR
ROTATIONAL TEMPERATURES (KELVIN) 0.14611 0.08786 0.07303
ROTATIONAL CONSTANTS (GHZ) 3.04449 1.83079 1.52169
3 IMAGINARY FREQUENCIES IGNORED.
Zero-point vibrational energy 37222.5 (Joules/Mol)
8.89638 (Kcal/Mol)
VIBRATIONAL TEMPERATURES: 69.92 277.37 352.37 404.11 499.80
(KELVIN) 589.67 664.94 668.22 1095.46 1422.44
1444.67 1464.64
Hi,
In a salt solution Na2SO4 would exist as ionic components. So if you are using the AMBER force field, you could safely employ the parameters for sodium ions and the sulphate group available. I hope this would help.
Regards
Chirodeep.
Mr. Sun,
Please find as attachment MM/MD using UFF. In addition the freq/otp test using the same theoretical level is presented below:
----------------------------
# UFF Opt Pop=(Minimal) Test
----------------------------
1/6=10,10=10,14=-1,18=10,38=1,56=1/1,3;
2/17=6,18=5,29=2/2;
3/5=2,11=9,12=1,25=1,30=1/1;
4/20=10,22=1001,24=1/2;
7/7=1/16;
1/6=10,10=10,14=-1,18=10/3(1);
99/12=1/99;
2/29=1/2;
3/5=2,11=9,12=1,25=1,30=1/1;
4/16=2,20=10,22=1001,24=1/2;
7/7=1/16;
1/6=10,10=10,14=-1,18=10/3(-4);
2/29=1/2;
99/12=1/99;
-----
NaSO4
-----
Symbolic Z-matrix:
Charge = -2 Multiplicity = 1
O 0 -1.77361 -0.49722 -0.97539
S 0 -0.28453 -0.12309 -0.55196
O 0 -0.24991 1.03618 0.59592
O 0 1.0318 0.28352 -1.50566
O 0 0.29297 -1.16757 0.70293
Na 0 1.69379 0.46417 0.48685
Na 0 -1.71216 -1.00226 1.03635
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
Berny optimization.
Initialization pass.
No Z-matrix variables, so optimization will use Cartesian coordinates.
Trust Radius=1.00D-01 FncErr=1.00D-07 GrdErr=1.00D-07
Number of steps in this run= 10 maximum allowed number of steps= 100.
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
------------------------------------------------------------------------
Z-MATRIX (ANGSTROMS AND DEGREES)
CD Cent Atom N1 Length/X N2 Alpha/Y N3 Beta/Z J
------------------------------------------------------------------------
1 1 O 0 -1.773605 -0.497223 -0.975388
2 2 S 0 -0.284531 -0.123093 -0.551956
3 3 O 0 -0.249908 1.036179 0.595917
4 4 O 0 1.031800 0.283524 -1.505661
5 5 O 0 0.292969 -1.167572 0.702927
6 6 Na 0 1.693787 0.464172 0.486847
7 7 Na 0 -1.712158 -1.002258 1.036346
------------------------------------------------------------------------
Z-Matrix orientation:
---------------------------------------------------------------------
Center Atomic Atomic Coordinates (Angstroms)
Number Number Type X Y Z
---------------------------------------------------------------------
1 8 0 -1.773605 -0.497223 -0.975388
2 16 0 -0.284531 -0.123093 -0.551956
3 8 0 -0.249908 1.036179 0.595917
4 8 0 1.031800 0.283524 -1.505661
5 8 0 0.292969 -1.167572 0.702927
6 11 0 1.693787 0.464172 0.486847
7 11 0 -1.712158 -1.002258 1.036346
---------------------------------------------------------------------
Distance matrix (angstroms):
1 2 3 4 5
1 O 0.000000
2 S 1.592674 0.000000
3 O 2.672447 1.631785 0.000000
4 O 2.959908 1.675595 2.574081 0.000000
5 O 2.745330 1.731812 2.272154 2.743977 0.000000
6 Na 3.883969 2.310354 2.029049 2.107356 2.161382
7 Na 2.075069 2.309492 2.547033 3.955293 2.039370
6 7
6 Na 0.000000
7 Na 3.748710 0.000000
Interatomic angles:
O1-S2-O3=111.9466 O1-S2-O4=129.8047 O1-O3-O4= 68.6592
O3-S2-O4=102.1994 O1-S2-O5=111.2689 O1-O3-O5= 66.884
O3-S2-O5= 84.9327 O1-O5-O4= 65.2602 O4-S2-O5=107.2666
O4-O3-O5= 68.6471 O1-S2-Na6=168.4741 O1-O3-Na6=110.6591
S2-O3-Na6= 77.4222 O1-O4-Na6= 98.6824 S2-O4-Na6= 74.3016
O3-Na6-O4= 76.9426 O1-O5-Na6=104.029 S2-O5-Na6= 71.8419
O3-Na6-O5= 65.5817 O4-Na6-O5= 79.9921 S2-O1-Na7= 76.8053
O1-Na7-O3= 69.7923 O3-S2-Na7= 78.4502 O4-O1-Na7=102.1115
O4-S2-Na7=165.7971 O4-O3-Na7=101.1295 O1-Na7-O5= 83.7044
S2-O5-Na7= 75.0315 O3-O5-Na7= 72.1916 O4-O5-Na7=110.699
Na6-S2-Na7=108.473 Na6-O3-Na7=109.4891 Na6-O5-Na7=126.3259
Stoichiometry Na2O4S(2-)
Framework group C1[X(Na2O4S)]
Deg. of freedom 15
Full point group C1 NOp 1
Largest Abelian subgroup C1 NOp 1
Largest concise Abelian subgroup C1 NOp 1
Standard orientation:
---------------------------------------------------------------------
Center Atomic Atomic Coordinates (Angstroms)
Number Number Type X Y Z
---------------------------------------------------------------------
1 8 0 -1.468749 1.229075 0.060536
2 16 0 -0.032796 0.546289 -0.031378
3 8 0 0.264469 -0.423221 1.247062
4 8 0 1.468139 1.237962 -0.307783
5 8 0 -0.094781 -0.927227 -0.939168
6 11 0 1.836566 -0.810232 0.024045
7 11 0 -1.911829 -0.796435 -0.022511
---------------------------------------------------------------------
Rotational constants (GHZ): 3.4828999 1.8548466 1.5025794
Isotopes: O-16,S-32,O-16,O-16,O-16,Na-23,Na-23
Standard basis: VSTO-3G (5D, 7F)
Warning: center 6 has no basis functions!
Warning: center 7 has no basis functions!
There are 20 symmetry adapted basis functions of A symmetry.
Crude estimate of integral set expansion from redundant integrals=1.000.
Integral buffers will be 262144 words long.
Raffenetti 1 integral format.
Two-electron integral symmetry is turned on.
20 basis functions 60 primitive gaussians
17 alpha electrons 17 beta electrons
nuclear repulsion energy 102.6213856989 Hartrees.
UFF calculation of energy and first derivatives.
MO and density RWFs will be updated.
Recover connectivity from rwf.
EGHMM: NBAlg=1 ICut=1 CutNB= 1.43D+03
I= 2 IAn= 16 Valence= 6.
JB= 1 J= 1 IAn= 8 IBT= 1 Dist= 1.59D+00
JB= 2 J= 3 IAn= 8 IBT= 1 Dist= 1.63D+00
JB= 3 J= 4 IAn= 8 IBT= 1 Dist= 1.68D+00
JB= 4 J= 5 IAn= 8 IBT= 1 Dist= 1.73D+00
JB= 5 J= 6 IAn= 11 IBT= 2 Dist= 2.31D+00
JB= 6 J= 7 IAn= 11 IBT= 2 Dist= 2.31D+00
I= 5 IAn= 8 Valence= 3.
JB= 1 J= 2 IAn= 16 IBT= 1 Dist= 1.73D+00
JB= 2 J= 6 IAn= 11 IBT= 1 Dist= 2.16D+00
JB= 3 J= 7 IAn= 11 IBT= 1 Dist= 2.04D+00
I= 6 IAn= 11 Valence= 8.
JB= 1 J= 2 IAn= 16 IBT= 2 Dist= 2.31D+00
JB= 2 J= 3 IAn= 8 IBT= 1 Dist= 2.03D+00
JB= 3 J= 4 IAn= 8 IBT= 1 Dist= 2.11D+00
JB= 4 J= 5 IAn= 8 IBT= 1 Dist= 2.16D+00
I= 7 IAn= 11 Valence= 3.
JB= 1 J= 1 IAn= 8 IBT= 1 Dist= 2.08D+00
JB= 2 J= 2 IAn= 16 IBT= 2 Dist= 2.31D+00
JB= 3 J= 5 IAn= 8 IBT= 1 Dist= 2.04D+00
Convergence limit is 0.750E-04
Step NS ND Rises Max. Force RMS Force Max. Disp. RMS Disp. Energy Flag
1 1 0 F 0.12920336 0.05179489 0.08640587 0.03463828 0.9778235 ----
2 2 2 F 0.08121638 0.03347786 0.10797727 0.04594769 0.9478194 ----
3 3 3 F 0.03860882 0.01992295 0.08993591 0.04721400 0.9244963 ----
4 4 4 F 0.01717219 0.00986227 0.04305260 0.02348995 0.9107711 ----
5 5 5 F 0.01576786 0.00758545 0.03422483 0.01675615 0.9068965 ----
6 6 6 F 0.01589676 0.00712728 0.03783040 0.01759240 0.9043745 ----
7 2 1 F 0.01707623 0.00721655 0.02381593 0.01006480 0.9017692 ----
8 2 1 F 0.01807947 0.00745838 0.01258880 0.00519322 0.9002200 ----
9 2 1 F 0.01855894 0.00760078 0.01920178 0.00788193 0.8993990 ----
10 2 1 F 0.01919125 0.00781649 0.01663672 0.00677529 0.8981237 ----
11 2 1 F 0.01971719 0.00800450 0.01868558 0.00759208 0.8969983 ----
12 2 1 F 0.02020721 0.00820694 0.01832721 0.00743959 0.8957063 ----
13 2 1 F 0.02062375 0.00839797 0.01909350 0.00777132 0.8944093 ----
14 2 1 F 0.02099444 0.00858832 0.01921369 0.00785270 0.8930235 ----
15 2 1 F 0.02132532 0.00877476 0.01959593 0.00805482 0.8915921 ----
16 2 1 F 0.02163298 0.00896358 0.01980171 0.00819471 0.8900921 ----
17 2 1 F 0.02193457 0.00915852 0.02007243 0.00836993 0.8885332 ----
18 2 1 F 0.02224527 0.00936568 0.02030834 0.00853801 0.8869057 ----
19 2 1 F 0.02257823 0.00959035 0.02057702 0.00872709 0.8852069 ----
20 2 1 F 0.02294469 0.00983800 0.02085937 0.00892955 0.8834273 ----
21 2 1 F 0.02335365 0.01011340 0.02117648 0.00915504 0.8815575 ----
22 2 1 F 0.02381195 0.01042072 0.02152610 0.00940357 0.8795845 ----
23 2 1 F 0.02432407 0.01076322 0.02191426 0.00967872 0.8774938 ----
24 2 1 F 0.02489172 0.01114307 0.02233920 0.00998078 0.8752685 ----
25 2 1 F 0.02551325 0.01156098 0.02279885 0.01030982 0.8728901 ----
26 2 1 F 0.02618286 0.01201587 0.02328639 0.01066382 0.8703388 ----
27 2 1 F 0.02688960 0.01250439 0.02379172 0.01103924 0.8675942 ----
28 2 1 F 0.02761644 0.01302041 0.02430003 0.01143036 0.8646363 ----
29 2 1 F 0.02833932 0.01355455 0.02479208 0.01182936 0.8614474 ----
30 2 1 F 0.02902673 0.01409382 0.02524411 0.01222621 0.8580136 ----
31 3 1 F 0.02963985 0.01462145 0.02562857 0.01260894 0.8543272 ----
32 4 1 F 0.03013375 0.01511719 0.02591537 0.01296402 0.8503895 ----
33 2 1 F 0.03045991 0.01555803 0.02607365 0.01327705 0.8462130 ----
34 2 1 F 0.03074131 0.01591958 0.02614950 0.01353350 0.8418234 ----
35 2 1 F 0.03102695 0.01617794 0.02634991 0.01371966 0.8372605 ----
36 2 1 F 0.03091606 0.01631192 0.02625922 0.01382346 0.8325780 ----
37 3 2 F 0.03038687 0.01630539 0.03323150 0.01781332 0.8278413 ----
38 4 2 F 0.02980170 0.01607525 0.19171726 0.10317400 0.8217786 ----
39 5 2 F 0.02878656 0.01385845 0.16766917 0.08460782 0.8047671 ----
40 2 2 F 0.02246215 0.01049268 0.09620145 0.04538383 0.7923963 ----
41 3 3 F 0.01357126 0.00677907 0.04067304 0.02241268 0.7850440 ----
42 4 4 F 0.01257552 0.00521850 0.04794208 0.02824193 0.7824041 ----
43 5 1 F 0.01335603 0.00498820 0.01886082 0.00704413 0.7802271 ----
44 6 6 F 0.01238925 0.00435894 0.13130941 0.05375851 0.7795999 ----
45 7 1 F 0.02914465 0.00940142 0.03998868 0.01289946 0.7791093 ----
46 8 2 F 0.01488827 0.00525493 0.01688020 0.00596289 0.7777106 ----
47 9 5 F 0.00865201 0.00412006 0.04608099 0.02296066 0.7771605 ----
48 10 6 F 0.00752980 0.00298860 0.12216318 0.04390761 0.7756160 ----
49 11 6 F 0.00512556 0.00229148 0.04093266 0.01452267 0.7740253 ----
50 12 7 F 0.00386792 0.00172619 0.06504489 0.02369081 0.7735666 ----
51 13 9 F 0.00311236 0.00128607 0.01822743 0.00746807 0.7730675 ----
52 14 1 F 0.00288512 0.00110725 0.00411924 0.00158088 0.7729474 ----
53 15 8 F 0.00183964 0.00092313 0.03120260 0.01423046 0.7729183 ----
54 16 8 F 0.00127739 0.00068851 0.00577218 0.00268350 0.7727317 ----
55 17 9 F 0.00122061 0.00056599 0.02736963 0.01256331 0.7727013 ----
56 18 11 F 0.00076844 0.00034551 0.01267587 0.00589291 0.7726071 ----
57 2 1 F 0.00050078 0.00024837 0.00071538 0.00035480 0.7725863 ----
58 3 3 F 0.00040648 0.00016270 0.00258150 0.00120486 0.7725852 ----
59 4 4 F 0.00026957 0.00010858 0.00262710 0.00112009 0.7725831 ----
60 5 5 F 0.00016619 0.00007216 0.00111757 0.00054870 0.7725818 -+--
61 6 6 F 0.00015019 0.00006355 0.00105561 0.00050522 0.7725811 -+--
62 7 7 F 0.00014133 0.00005781 0.00162541 0.00074021 0.7725805 -+--
63 8 7 F 0.00012450 0.00005085 0.00133976 0.00055316 0.7725798 -+--
64 9 8 F 0.00010104 0.00004473 0.00549442 0.00230344 0.7725793 ++--
65 10 5 F 0.00004175 0.00002232 0.00031600 0.00015258 0.7725781 ====
Energy= 0.772578110285 NIter= 0.
Dipole moment= 0.000000 0.000000 0.000000
***** Axes restored to original set *****
-------------------------------------------------------------------
Center Atomic Forces (Hartrees/Bohr)
Number Number X Y Z
-------------------------------------------------------------------
1 8 -0.000003917 0.000012456 -0.000025885
2 16 0.000007279 -0.000001504 0.000006231
3 8 -0.000016314 -0.000047104 0.000024905
4 8 -0.000004150 -0.000026109 0.000011726
5 8 0.000001492 0.000020998 0.000038153
6 11 0.000026542 0.000030053 -0.000040017
7 11 -0.000010933 0.000011211 -0.000015113
-------------------------------------------------------------------
Cartesian Forces: Max 0.000047104 RMS 0.000022316
GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
Berny optimization.
Search for a local minimum.
Step number 1 out of a maximum of 10
All quantities printed in internal units (Hartrees-Bohrs-Radians)
Second derivative matrix not updated -- unit matrix used.
RFO step: Lambda=-1.04576450D-08.
Linear search not attempted -- first point.
TrRot= 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
Variable Old X -DE/DX Delta X Delta X Delta X New X
(Linear) (Quad) (Total)
X1 -2.35923 0.00000 0.00000 0.00000 0.00000 -2.35924
Y1 -1.57667 0.00001 0.00000 0.00001 0.00001 -1.57666
Z1 -1.49576 -0.00003 0.00000 -0.00003 -0.00003 -1.49579
X2 -0.70289 0.00001 0.00000 0.00001 0.00001 -0.70288
Y2 1.09401 0.00000 0.00000 0.00000 0.00000 1.09401
Z2 -1.39721 0.00001 0.00000 0.00001 0.00001 -1.39720
X3 -0.19216 -0.00002 0.00000 -0.00002 -0.00002 -0.19217
Y3 2.14441 -0.00005 0.00000 -0.00005 -0.00005 2.14436
Z3 1.46656 0.00002 0.00000 0.00002 0.00002 1.46659
X4 2.11887 0.00000 0.00000 0.00000 0.00000 2.11887
Y4 0.30272 -0.00003 0.00000 -0.00003 -0.00003 0.30269
Z4 -2.40052 0.00001 0.00000 0.00001 0.00001 -2.40051
X5 0.41700 0.00000 0.00000 0.00000 0.00000 0.41700
Y5 -1.29777 0.00002 0.00000 0.00002 0.00002 -1.29775
Z5 0.12585 0.00004 0.00000 0.00004 0.00004 0.12589
X6 3.57901 0.00003 0.00000 0.00003 0.00003 3.57904
Y6 0.75523 0.00003 0.00000 0.00003 0.00003 0.75526
Z6 1.31006 -0.00004 0.00000 -0.00004 -0.00004 1.31002
X7 -2.79861 -0.00001 0.00000 -0.00001 -0.00001 -2.79862
Y7 -1.31111 0.00001 0.00000 0.00001 0.00001 -1.31109
Z7 2.28220 -0.00002 0.00000 -0.00002 -0.00002 2.28218
Item Value Threshold Converged?
Maximum Force 0.000047 0.000450 YES
RMS Force 0.000022 0.000300 YES
Maximum Displacement 0.000047 0.001800 YES
RMS Displacement 0.000022 0.001200 YES
Predicted change in Energy=-5.228822D-09
Optimization completed.
-- Stationary point found.
-------------------
- Thermochemistry -
-------------------
Temperature 298.150 Kelvin. Pressure 1.00000 Atm.
Atom 1 has atomic number 8 and mass 15.99491
Atom 2 has atomic number 16 and mass 31.97207
Atom 3 has atomic number 8 and mass 15.99491
Atom 4 has atomic number 8 and mass 15.99491
Atom 5 has atomic number 8 and mass 15.99491
Atom 6 has atomic number 11 and mass 22.98977
Atom 7 has atomic number 11 and mass 22.98977
Molecular mass: 141.93127 amu.
Principal axes and moments of inertia in atomic units:
1 2 3
EIGENVALUES -- 592.78893 985.773091186.01113
X 1.00000 0.00000 0.00000
Y 0.00000 1.00000 0.00000
Z 0.00000 0.00000 1.00000
THIS MOLECULE IS AN ASYMMETRIC TOP.
ROTATIONAL SYMMETRY NUMBER 1.
WARNING-- ASSUMPTION OF CLASSICAL BEHAVIOR FOR ROTATION
MAY CAUSE SIGNIFICANT ERROR
ROTATIONAL TEMPERATURES (KELVIN) 0.14611 0.08786 0.07303
ROTATIONAL CONSTANTS (GHZ) 3.04449 1.83079 1.52169
3 IMAGINARY FREQUENCIES IGNORED.
Zero-point vibrational energy 37222.5 (Joules/Mol)
8.89638 (Kcal/Mol)
VIBRATIONAL TEMPERATURES: 69.92 277.37 352.37 404.11 499.80
(KELVIN) 589.67 664.94 668.22 1095.46 1422.44
1444.67 1464.64
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