Tip

All input files can be downloaded: Files.

nddo

This option controls how to perform an NDDO (like AM1, PM3, etc.) calculation.

Options

charge

Value

An integer

Default

0

Define the total charge of the system.

spin2p1

Value

An integer

Default

1 for even number of electrons

2 for odd number of electrons

Define the spin multiplicity of the system, i.e., \(2S+1\), where \(S\) is the spin of the system. For example, to consider the singlet and triplet state, one should set spin2p1 to 1 and 3, respectively.

max_it

Value

A non-negative integer

Default

150

Define the maximum number of SCF iteration.

print_MO

Print molecular orbital coefficients. Without this, only molecular orbital energies and occupancies are printed.

use_hcore

Use the core Hamiltonian matrix as the initial guess. Without this, the superposition of atomic NDDO densities is used as the initial guess.

print_level

Value

PrintNone for restricted SCF (alpha and beta orbitals are restricted to be identical)

PrintEssentials for unrestricted SCF (alpha and beta orbitals are not necessarily identical)

PrintDetails for unrestricted SCF (alpha and beta orbitals are not necessarily identical)

Default

PrintEssentials

The information printing level.

density_cov

Value

A real number

Default

1.E-9

The density matrix convergence threshold for SCF calculations.

Theoretical Background

The NDDO (Neglect of Diatomic Differential Overlap) method is a semi-empirical quantum chemistry method that simplifies the calculation of electronic structures in molecules. It is based on the Hartree-Fock theory but introduces several approximations to reduce computational cost while maintaining reasonable accuracy for many systems. The following NDDO-based methods are implemented in Qbics:

mndo

am1

am1d

rm1

pm3

pm3d

pm6

pmo

pmow

Input Examples

Note that, in all examples below, you can change energy to opt to do geometry optimization, or md to do molecular dynamics.

Example: NDDO Geometry Optimization of Congo Red Anion

We perform an NDDO geometry optimization of the Congo Red anion, which is of charge -2. The input file is as follows:

nddo-1.inp
 1mol
 2    N     -1.54332513     -2.09816265      1.04511234
 3    C     -1.24833878     -0.93106019      0.36508274
 4    C     -2.25957296     -0.07865002     -0.14856083
 5    N     -3.66148390     -0.29307361     -0.15493448
 6    N     -4.18863626     -1.27534731      0.37531946
 7    C     -5.60908641     -1.45451288      0.28158560
 8    C     -6.44457282     -0.83932131     -0.67188202
 9    C     -7.79728533     -1.15798249     -0.73630174
10    C     -8.36065510     -2.08786360      0.14739783
11    C     -9.77016879     -2.45880897      0.04894333
12    C    -10.37218322     -2.63400200     -1.20423937
13    C    -11.70230579     -3.02737161     -1.30728487
14    C    -12.47656958     -3.25031163     -0.15160638
15    N    -13.86557539     -3.62919999     -0.14487415
16    N    -14.32966893     -4.17706047     -1.14625475
17    C    -15.69877226     -4.57627884     -1.20899537
18    C    -16.68973206     -4.15262107     -0.27475128
19    C    -18.01024266     -4.49443901     -0.39532055
20    S    -19.17268148     -3.86811281      0.81316397
21    O    -19.75454266     -5.01617220      1.39840350
22    O    -18.38630356     -3.10248890      1.70179250
23    O    -20.10356966     -3.11120162      0.06462974
24    C    -18.41112808     -5.32846881     -1.47222133
25    C    -19.77910594     -5.71132399     -1.62198661
26    C    -20.17834220     -6.53295026     -2.64390564
27    C    -19.22910471     -7.02196171     -3.56998588
28    C    -17.90832650     -6.66645352     -3.45632203
29    C    -17.46190253     -5.80234089     -2.41478734
30    C    -16.07656666     -5.41039373     -2.29229722
31    N    -15.13888043     -5.91803387     -3.19440229
32    C    -11.87474269     -3.05051931      1.11034028
33    C    -10.54202081     -2.66675984      1.20101906
34    C     -7.53790038     -2.67731355      1.11825020
35    C     -6.18479683     -2.37215059      1.18838640
36    C     -1.87591174      1.15335474     -0.77615212
37    C     -0.57261374      1.52889060     -0.93591287
38    S     -0.22263048      3.07410672     -1.76404123
39    C      0.45596204      0.67936168     -0.44539542
40    C      1.82678779      1.04190252     -0.60713363
41    C      2.83356234      0.24415341     -0.12687164
42    C      2.52009139     -0.95668533      0.54667961
43    C      1.20940505     -1.33293101      0.71264279
44    C      0.14025272     -0.53616115      0.21319920
45    H     -2.46523916     -2.46286272      0.99215794
46    H     -0.83173045     -2.78829762      1.08002006
47    H     -6.03185765     -0.10143589     -1.37897310
48    H     -8.43461236     -0.66688250     -1.48777738
49    H     -9.78049223     -2.47062911     -2.11801307
50    H    -12.14290958     -3.16255408     -2.30720734
51    H    -16.38964262     -3.50879982      0.57744179
52    H    -20.50886405     -5.32738427     -0.88397665
53    H    -21.23309870     -6.82252491     -2.75059996
54    H    -19.55988556     -7.69221994     -4.37548943
55    H    -17.19714755     -7.08561026     -4.18243768
56    H    -15.48438601     -6.05340540     -4.11792530
57    H    -14.24364693     -5.48258085     -3.17857290
58    H    -12.46209252     -3.20084844      2.03078572
59    H    -10.08787943     -2.51709145      2.19260752
60    H     -7.96893149     -3.40122514      1.82663096
61    H     -5.56169201     -2.85401081      1.95772702
62    H     -2.67308708      1.82553392     -1.15690810
63    H      2.05510061      1.99022309     -1.12996590
64    H      3.88606179      0.53247497     -0.25657336
65    H      3.33326449     -1.58194610      0.94036557
66    H      1.01518864     -2.26662032      1.25943530
67    O     -1.49324251      3.61129258     -2.06889525
68    O      0.51932929      3.83612909     -0.83254053
69    O      0.53967816      2.71626705     -2.90040345
70end
71
72nddo
73    charge -2
74    spin2p1 1
75end
76
77task
78    opt am1
79end

You can also change am1 to pm3, pm6, etc. to use other NDDO methods listed in the table above. The final geometry is shown below:

../_images/nddo-1.jpg