Yes, they must change, for the following reasons.
The dogma of transubstantiation teaches us that the substance of bread and wine change into the substance of the body and blood of Christ. The soul and Divinity of Christ also become present, simultaneously. But the accidents (including appearances) of the bread and wine remain the same. So the consecrated bread and wine still look, smell, and taste like bread and wine. But the substance has changed.
Fine. But the question is, Do the molecules change?
Suppose we answer, ‘No the molecules do not change, only the substance changes.’ This implies that the molecules are entirely accidents, and not at all substance, which further implies a duality to material objects, that they consist of molecules plus substance. This answer is untenable. For when God created the material universe, He created matter and spirit:
3. This one true God, by his goodness and almighty power, not with the intention of increasing his happiness, nor indeed of obtaining happiness, but in order to manifest his perfection by the good things which he bestows on what he creates, by an absolutely free plan, together from the beginning of time brought into being from nothing the twofold created order, that is the spiritual and the bodily, the angelic and the earthly, and thereafter the human which is, in a way, common to both since it is composed of spirit and body [Lateran Council IV, Constitution 1]. (First Vatican Council, Chapter 1, On God the Creator of all things).
God did not create a threefold order of spirit, matter, and substance. All created things are either spirit (e.g. angels), or matter (e.g.. material objects), or both (the human person is matter and spirit). The term substance describes what is essential to a thing; whereas accidents describe what is non-essential to a thing. Matter has accident and substance; spirit has accident and substance.
Accidents are non-essentials to a thing; they are not the thing itself, but qualities and properties of the thing. Accidents never exist by themselves. Substance is the essential nature of the thing itself. The Nature of God is substance without accident, so substance can exist by itself. Without substance, a thing does not exist. Accidents are of substance; substance is of itself.
Molecules cannot be entirely accidents, because molecules exist of themselves. A molecule is not a quality or property of something else. The appearance of a thing is accident (e.g. water as mist, as liquid, as ice, as a snowflake). The properties of a thing are accident (e.g. water as ice is solid, when melted, it is not; water as liquid is visible, as gas it is not). But the term molecule does not denote properties, but the entire material object, accidents and substance.
So if we say that at the consecration, the molecules of bread and wine do not change, we are essentially denying the dogma of Transubstantiation. Some foolish persons have make this claim, because they cannot accept that the Eucharistic Miracle is a true mystery, beyond our understanding.
We cannot say that molecules are only accidents, or only substance, or neither. The only tenable position is that molecules have both accidents and substance. Therefore, we must reasonably conclude that, when the consecration of bread and wine occurs, the molecules of the bread and wine change in their substance, but not in their accidents. To say otherwise is to deny transubstantiation.
All that is physical, including a human body, has substance. So when the substances of the bread and wine are changed into the substance of Christ’s body and blood, Christ is physically present. See also my previous article:
Ronald L. Conte Jr.
Roman Catholic theologian and Bible translator