I am not addressing Quantum Physics... to that end I must admit I am insufficient in my knowledge. I was addressing God's Sovereignty.
Admitedly, I too was a little confused as to what you were asking Ruiz as the O/P Title is "Do molecules have free will".
Even at that, technically speaking, molecules can not have "free will" in that free wil implies intellect, emotion and the ability to reason and make decisions.
Here is a passage of Scripture which gives evidence to that end:
Acts 5:1 But a certain man named Ananias, with Sapphira his wife, sold a possession,
2 And kept back part of the price, his wife also being privy to it, and brought a certain part, and laid it at the apostles' feet.
3 But Peter said, Ananias, why hath Satan filled thine heart to lie to the Holy Ghost, and to keep back part of the price of the land?
4 Whiles it remained, was it not thine own? and after it was sold, was it not in thine own power? why hast thou conceived this thing in thine heart? thou hast not lied unto men, but unto God.
5 And Ananias hearing these words fell down, and gave up the ghost: and great fear came on all them that heard these things.
6 And the young men arose, wound him up, and carried him out, and buried him.
In the context of creation there is at least one Scripture that is a possibility:
Hebrews 1:1 God, who at sundry times and in divers manners spake in time past unto the fathers by the prophets,
2 Hath in these last days spoken unto us by his Son, whom he hath appointed heir of all things, by whom also he made the worlds;
3 Who being the brightness of his glory, and the express image of his person, and upholding all things by the word of his power, when he had by himself purged our sins, sat down on the right hand of the Majesty on high;
This could be a general statement concerning the fact that the material universe not only requires an ex nihilo creation but a constant "upholding" which again IMO means that God constantly maintains the laws and principles of the ongoing existence of this material universe and has not simply left it to it's own.
This would therefore mean that the material universe is bound by the law(s) of God (Thermodyamics, etc) and therefore there is no true "randomness" or "free will" in terms of matter (molecules).
On the other end of the spectrum:
Psalm 147:4 He telleth the number of the stars; he calleth them all by their names.
The advances of man (Hubble telescope) have shown that there are upwards of 100 billion galaxies each containing upwards of 100 billion stars, yet God has named each of them which implies an intimate knowledge of each.
Simply awesome, though "awesome" does not touch the magnificense of the glory of God reflected in the material universe from electrons to pulsars.
But, as I had previously stated, when it comes to adverse circumstances in my seemingly infintesimal and insignificant life, I draw comfort from the fact that He knows all about it and cares.
1 Peter 5
6 Humble yourselves therefore under the mighty hand of God, that he may exalt you in due time:
7 Casting all your care upon him; for he careth for you.
Psalm 111:1 Praise ye the LORD. I will praise the LORD with my whole heart, in the assembly of the upright, and in the congregation.
2 The works of the LORD are great, sought out of all them that have pleasure therein.
3 His work is honourable and glorious: and his righteousness endureth for ever.
4 He hath made his wonderful works to be remembered: the LORD is gracious and full of compassion.
Romans 14:8 For whether we live, we live unto the Lord; and whether we die, we die unto the Lord: whether we live therefore, or die, we are the Lord's.
MY God bless you brother and your friend, I have prayed for her.
HankD