A “substance” is not a solid, tangible, thing - that is the everyday sense of the word; not the sense it has in the theological discussion of the sacraments, such as the Eucharist. A substance is a thing that exists without having to be a property of a thing so as to exist - for example, hair is a substance, while redness is a property of that substance - there can be hair that is not red, and redness cannot exist except as a property of a thing. As we are talking about metaphysics, and not chemistry, the two don’t collide: talk about the redness of red hair & the distinction between the substance & the properties (“accidents”, in technical terminology), is not affected by the fact that colour exists in a spectrum - metaphysics & chemistry may consider the same things, but, under incommensurable aspects; which is why there is no collision
“Substance” is the crucial word - the appearances of bread and wine remain after the consecration (which is effected by the power of the Holy Spirit of the same Christ, working through His minister the human priest); so what is seen, tasted, touched, has all the appearances of bread & wine - including toxicity, if they are poisoned. What has changed, is the reality to which the appearances properly belong - that-which-was-bread - has ceased to exist, so only the properties of bread endure.
And it is the reality which is the thing that changes - not the properties. The substantia “stat sub”, “stands under” the accidents - they manifest what it is, that stands under them, which would otherwise be unknowable. The substance of bread can’t be discovered by chemical analysis, neither can the substance of anything: they can be known, but not directly - only by their effects, such as taste, colour, chemistry, electro-magnetism - for the objection is answered by noting that the phenomena on which the objection is based, are themselves further accidents of the Gifts. As the appearance of the bread remains, it is to be expected that its sub-atomic properties will do so - & those properties are not properties of substance as substance*; they are properties of the substance particularised & known as bread.
As for NMR spectroscopy - that deals with appearances; not with substance. The same applies to Heisenberg’s Uncertainty principle - quantum mechanics has no bearing on substance, so the Church is not concerned with it. The same applies to Anton van Leeuwenhoek - what the dogma is about, and what these men investigated, are not the same aspects of reality.
If any of this is wrong, someone please correct it.
substance as substance* - what is called “substantia prima”, undifferentiated unindividualised substance which has not received any form.
Hope that helps ##