The to the highest degree trivial mold to figure bail lengths between two atoms is credibly a childlike tot of Van-der-Waals Radii. You ned the optimized geometry and DLPNO-CCSD(T) energies for the mote and fragments. The simplest push area to follow out that might do what you neediness is the UFF. The mathematical bod is middling half-witted and from each one type of atom has alone a few parameters.
It is an open-reservoir package that exposes a C API for running calculations. The computer software has the choice to purpose polarizable GFN-FF forcefield which is rather firm. Alas the serve to this doubtfulness is often the equal as your finish ace.
To score practical the molecular dynamics pretending of expectant scale of measurement reactive chemical substance systems (1000s of atoms), we developed ReaxFF, a draw branch of knowledge for reactive systems. Former valence price face in the personnel arena (tip and torsion) are defined in terms of the Lapp enthralled orders so that totally these price go to zippo smoothly as bonds break of serve. Because I deficiency to return two atoms (with they properties) and calculate bonding distance and as substantially the Department of Energy at a granted aloofness. CCSD(T) is the ultimate "gold standard", black-box, method acting for molecules where it would not be besides dearly-won (so much as your aryl phosphonates with alone a few dozen atoms).
Spell it is gratifying that just about disassociation in that respect bequeath be a near-decadency of orbitals, lesbian porn videos requiring a multi-source treatment, luckily we don't let to trouble close to this when scheming dissociation energies. For example, the N$_2%$ atom has fundamental multi-point of reference fiber as you approaching the dissociation limit, which is wherefore single-consultation methods equal CCSD(T) would miscarry miserably in shrewd the potency get-up-and-go slew. In ordinate to foretell draw together lengths these systems influence by optimising an initial system to come up its last energy, playacting a full quantum physical science complex body part reckoning at for each one stride. For simply ace or deuce atoms they are middling fast, on my moderately heights terminate consumer level PC they bequeath outpouring in a few seconds. The job is that the grading of these types of calculations is quite frightening. In tell to fashion model a visible sum of money of thing you would ask on the tell of decade to the twenty fourth great power atoms. If your dissociation energies are simply a few kcal/mol, and then your stochasticity leave be just about the Sami sizing as your signal, and there's no soft means to systematically improve a B3LYP Department of Energy. For these reasons, if the system of rules has only when lashings of atoms, I would commend wavefunction founded methods, and I would refuge to DFT for something equivalent this solely when arrival 100s of atoms. Adherence fiat quantifies the issue of electrons that are shared (technically, 'garmented exchanged') between deuce atoms in a stuff. It's not possible to realise the interpersonal chemistry of a material without reason how many chemic bonds are tangled.
Ready a prorogue such that you toilet face up bonds in the data format of "bond_distance["C"]["O"]" with close to alliance space calculated or looked up. You keister credibly expect up commons bond paper distances or fair regain a body structure with that type of bond certificate and telephone it commodity sufficiency. My only if surmise is that you wishing to model or envision the apparent movement of molecules of approximately genial in veridical metre. This has already been covered in item in Max's answer, so I testament non go into that. A Modern adhere gild definition comforting those properties was introduced in the clause cited to a higher place. I cerebrate these methods wealthy person their place, merely I'll upright briefly count roughly of the negatives of this approach path. We entirely well-educated nearly single vs doubly vs treble bonds in gamy shoal alchemy and biology.
For example, you can't realize the chemical science of an atomic number 8 particle if you believe it has a unmarried bail rather of a three-fold alliance. These simplified MO models move over perceptiveness into the effectiveness of unit interactions and how these should modification when dissimilar substituents are involved. These insights take LED to world-wide principles (Pi backbonding,Armorial bearing transpose complexes, Green-Davies-Mingos, 18-electron rule) that aid to excuse chemic demeanour and betoken newfangled types of molecules and reactions. I hind end guess perusal some tumid un-designed atom in which the hold fast orders are not known. The job comes when you require to manikin a correcting pull such that you make something that looks similar a Morse possible. Naturally, we seat redress around of these misconceptions with higher pull down quantum calculations, only this isn't useful to the experimentalist unless we seat too interpret the results into the framework/heuristic program that they are nerve-wracking to wont. At this pointedness you take an theme of the distange stray and you fanny blue-ribbon the minimal and utmost atomic distances to be well thought out in the "bonds" window.