Physics Fiction In Crystallography

[faysunKle]

Simulating Crystallography With Simulated Electron Pathways (orbitals) On Simulated Atoms/Molecules. 

 

One can see often in scientific literature things like this: "If we actually knew how electrons are distributed and move in atoms we would have been able to know better how they bond to form compounds and find new improved materials without having to test hundreds (or even thousands) of combinations every day in labs around the world" Can scientists (possibly) simulate crystallography ? 

For the formation of the pattern of bright spots on the screen in crystallographic analysis it is commonly said. "In x-ray crystallography, the pattern of x-ray intensities (reflections) is formed (by constructive, partial, and destructive interference) of x-ray photons scattered by electron clouds of atoms within a crystal."   or similarly   "....a high-intensity x-ray beam is targeted on the sample crystal. X-rays diffract off the electrons in the atoms...." So with real samples they don't know where the electrons are and they calculate their position (and then the atoms) from the pattern created on the screen.   Further more "...producing an image from a diffraction pattern requires sophisticated mathematics and often an iterative process of modelling and refinement. In this process, the mathematically predicted diffraction patterns of an hypothesized or "model" structure are compared to the actual pattern generated by the crystalline sample........."  Can then scientists do directly the opposite, in other words if the position of the electrons is known can they simulate the pattern ?   If they can and since the pathways (orbitals} of the electrons in the atom can be animated, (a zillion of them off cource, an attempt is described below) then wouldn't be right to assume that electrons travel in real atoms the same way or in one of the ways as in the simulated atom when the pattern of the simulated crystallography matches that of the physical one.

About the simulation. It is believed that the size of the atom is of the order of 10^-10 and the size of the electron is of the order of 10^-18 so one could create a cube with sides of 10⁸ points ( one next to the other like the points of a line in computer graphics) and altogether  1024 points in this cube. At the initial stage, the simulation of the traveling of the electron, may be called animation. there will be no physics involved. It doesn't matter what makes electrons move the way they move, doesn't matter what forces act on them, the interest is on their " pathways" (orbitals).

Starting from one point let's say one of the 8 corners, lines are traced  to EACH  and EVERY other point in the cube, except to those to which traced  lines are considered by scientists impossible PATHS,  for  electrons to follow. (Like the ones to which electrons have to go through the nucleus to reach to or because it is almost accepted that electrons are found  away from the nucleus at the edges of the atom, to exclude whole regions close to the nucleus.) These lines will be the "ELEMENTAL PATHS" of "ELECTRON PATHWAYS" (orbitals) to be created.  So we start N (1024-1) "electron pathways".  From EACH and EVERYONE of ALL of these other (new) points to which the first series of  "ELEMENTAL PATHS" ended another series of lines (new  "ELEMENTAL PATHS" is traced to EVERY and ALL other points in the cube, so now there are another N "ELEMENTAL PATHS" for each of the N "ELEMENTAL PATHS" of the first round and  so N² "electron pathways".  Continuing this process again and again, N^zillion  continues "electron pathways" are created and stored and these will include all short of curves: circular, elliptical, saw like,vibrational, totally irregular, periodic and not. ( One may decide instead of taking all the points to take every 2,5 or 10 points. ) The process of creating "electron pathways" must stop SOMETIME and here the 4th dimension must be introduced, TIME, to get a number for the z in the N^zillion "electron pathways." Since scientists have counted times of chemical reactions and estimate the speed of electrons IN THE ATOMS at some percentage of the speed of light (e.g 1/3 or 2/3) they may use their intelligent guess for the "time" that "electrons" will travel along their "paths" in these simulated "electron pathways"  in the atom. Having then simulated "electron pathways" one may "create atoms" of 1,2,3....,10,.... electrons by combining all "electron pathways" stored by the previous procedure for each electron. So there will be (10^zillion)² combinations for a "two electron atom", (10^zillion)³ for a "three electron atom" etc. Off course again filters will be used on  "combined electron paths" some will be substructed, for example because two "electrons" are at the same place at the same time. Unfortunately when one creates "molecules" it has to be taken that "electrons" have adjusted their "pathways" to "bond" and can not find how "electrons" were distributed in "single isolated atoms".

 

[exchemist]

 

Simulating Crystallography With Simulated Electron Pathways (orbitals) On Simulated Atoms/Molecules. 

 

One can see often in scientific literature things like this: "If we actually knew how electrons are distributed and move in atoms we would have been able to know better how they bond to form compounds and find new improved materials without having to test hundreds (or even thousands) of combinations every day in labs around the world" Can scientists (possibly) simulate crystallography ? 

For the formation of the pattern of bright spots on the screen in crystallographic analysis it is commonly said. "In x-ray crystallography, the pattern of x-ray intensities (reflections) is formed (by constructive, partial, and destructive interference) of x-ray photons scattered by electron clouds of atoms within a crystal."   or similarly   "....a high-intensity x-ray beam is targeted on the sample crystal. X-rays diffract off the electrons in the atoms...." So with real samples they don't know where the electrons are and they calculate their position (and then the atoms) from the pattern created on the screen.   Further more "...producing an image from a diffraction pattern requires sophisticated mathematics and often an iterative process of modelling and refinement. In this process, the mathematically predicted diffraction patterns of an hypothesized or "model" structure are compared to the actual pattern generated by the crystalline sample........."  Can then scientists do directly the opposite, in other words if the position of the electrons is known can they simulate the pattern ?   If they can and since the pathways (orbitals} of the electrons in the atom can be animated, (a zillion of them off cource, an attempt is described below) then wouldn't be right to assume that electrons travel in real atoms the same way or in one of the ways as in the simulated atom when the pattern of the simulated crystallography matches that of the physical one.

About the simulation. It is believed that the size of the atom is of the order of 10^-10 and the size of the electron is of the order of 10^-18 so one could create a cube with sides of 10⁸ points ( one next to the other like the points of a line in computer graphics) and altogether  1024 points in this cube. At the initial stage, the simulation of the traveling of the electron, may be called animation. there will be no physics involved. It doesn't matter what makes electrons move the way they move, doesn't matter what forces act on them, the interest is on their " pathways" (orbitals).

Starting from one point let's say one of the 8 corners, lines are traced  to EACH  and EVERY other point in the cube, except to those to which traced  lines are considered by scientists impossible PATHS,  for  electrons to follow. (Like the ones to which electrons have to go through the nucleus to reach to or because it is almost accepted that electrons are found  away from the nucleus at the edges of the atom, to exclude whole regions close to the nucleus.) These lines will be the "ELEMENTAL PATHS" of "ELECTRON PATHWAYS" (orbitals) to be created.  So we start N (1024-1) "electron pathways".  From EACH and EVERYONE of ALL of these other (new) points to which the first series of  "ELEMENTAL PATHS" ended another series of lines (new  "ELEMENTAL PATHS" is traced to EVERY and ALL other points in the cube, so now there are another N "ELEMENTAL PATHS" for each of the N "ELEMENTAL PATHS" of the first round and  so N² "electron pathways".  Continuing this process again and again, N^zillion  continues "electron pathways" are created and stored and these will include all short of curves: circular, elliptical, saw like,vibrational, totally irregular, periodic and not. ( One may decide instead of taking all the points to take every 2,5 or 10 points. ) The process of creating "electron pathways" must stop SOMETIME and here the 4th dimension must be introduced, TIME, to get a number for the z in the N^zillion "electron pathways." Since scientists have counted times of chemical reactions and estimate the speed of electrons IN THE ATOMS at some percentage of the speed of light (e.g 1/3 or 2/3) they may use their intelligent guess for the "time" that "electrons" will travel along their "paths" in these simulated "electron pathways"  in the atom. Having then simulated "electron pathways" one may "create atoms" of 1,2,3....,10,.... electrons by combining all "electron pathways" stored by the previous procedure for each electron. So there will be (10^zillion)² combinations for a "two electron atom", (10^zillion)³ for a "three electron atom" etc. Off course again filters will be used on  "combined electron paths" some will be substructed, for example because two "electrons" are at the same place at the same time. Unfortunately when one creates "molecules" it has to be taken that "electrons" have adjusted their "pathways" to "bond" and can not find how "electrons" were distributed in "single isolated atoms".

 

I think you have misunderstood the issue.

 

The problem in X-ray diffraction is how to work backwards from a diffraction pattern to the arrangement of atoms in the crystal that gives rise to it. This is where iterative modelling comes in. A model is made and the effect of x-rays impinging on the model is calculated and compared with experiment.

 

There is, however, no problem caused by the motion of electrons in their orbitals. It is an illusion to think that one can know the exact position within its orbital of an electron. This is intrinsically unknowable, and in fact meaningless, due to the Uncertainty Principle.

 

And in any case it doesn't matter because it is the "smeared out" electronic shape, distributed as it is within its orbital, which is the entity that diffracts the X-rays.

 

Also, (though this is a side issue) it is untrue that electrons cannot go up to the nucleus. Electrons in s orbitals, in other words in those orbitals with zero orbital angular momentum, do in fact go right up to the nucleus. You can see this on the graphs of the radial component of the electron's wave function for an s orbital, which can be found in any undergraduate chemistry textbook. In fact, the explanation of some periodic properties of the elements depends on this, as it is the source of what is called "shielding"of some valence electrons from the nuclear charge.

Edited January 24, 2017 by exchemist

[faysunKle]

NO NO NO      NO Uncertainty Principles HERE, PLEASE.  READ IT AGAIN, IF YOU HAVE TIME TO GET ITS ESSENCE. BUT IF YOU ARE A REAL RESEARCH SCIENTIST KEEP AWAY FROM Physics Fiction In Crystallography BECAUSE WE

NEED YOU TO FIND THE STRUCTURES OF OUR PROTEINS. YOU DON'T NEED INTELLECTUAL AMUSEMENT YOU DO INTELLECTUAL WORK.

 

[exchemist]

 

NO NO NO      NO Uncertainty Principles HERE, PLEASE.  READ IT AGAIN, IF YOU HAVE TIME TO GET ITS ESSENCE. BUT IF YOU ARE A REAL RESEARCH SCIENTIST KEEP AWAY FROM Physics Fiction In Crystallography BECAUSE WE

NEED YOU TO FIND THE STRUCTURES OF OUR PROTEINS. YOU DON'T NEED INTELLECTUAL AMUSEMENT YOU DO INTELLECTUAL WORK.

 

 

Ah, you mean this is really intended to be fiction? 

 

If so, perhaps the moderators should move it out of the Physics section.

 

I'll report it and ask them for you.

[OceanBreeze]

 

Simulating Crystallography With Simulated Electron Pathways (orbitals) On Simulated Atoms/Molecules. 

 

One can see often in scientific literature things like this: "If we actually knew how electrons are distributed and move in atoms we would have been able to know better how they bond to form compounds and find new improved materials without having to test hundreds (or even thousands) of combinations every day in labs around the world" Can scientists (possibly) simulate crystallography ? 

For the formation of the pattern of bright spots on the screen in crystallographic analysis it is commonly said. "In x-ray crystallography, the pattern of x-ray intensities (reflections) is formed (by constructive, partial, and destructive interference) of x-ray photons scattered by electron clouds of atoms within a crystal."   or similarly   "....a high-intensity x-ray beam is targeted on the sample crystal. X-rays diffract off the electrons in the atoms...." So with real samples they don't know where the electrons are and they calculate their position (and then the atoms) from the pattern created on the screen.   Further more "...producing an image from a diffraction pattern requires sophisticated mathematics and often an iterative process of modelling and refinement. In this process, the mathematically predicted diffraction patterns of an hypothesized or "model" structure are compared to the actual pattern generated by the crystalline sample........."  Can then scientists do directly the opposite, in other words if the position of the electrons is known can they simulate the pattern ?   If they can and since the pathways (orbitals} of the electrons in the atom can be animated, (a zillion of them off cource, an attempt is described below) then wouldn't be right to assume that electrons travel in real atoms the same way or in one of the ways as in the simulated atom when the pattern of the simulated crystallography matches that of the physical one.

About the simulation. It is believed that the size of the atom is of the order of 10^-10 and the size of the electron is of the order of 10^-18 so one could create a cube with sides of 10⁸ points ( one next to the other like the points of a line in computer graphics) and altogether  1024 points in this cube. At the initial stage, the simulation of the traveling of the electron, may be called animation. there will be no physics involved. It doesn't matter what makes electrons move the way they move, doesn't matter what forces act on them, the interest is on their " pathways" (orbitals).

Starting from one point let's say one of the 8 corners, lines are traced  to EACH  and EVERY other point in the cube, except to those to which traced  lines are considered by scientists impossible PATHS,  for  electrons to follow. (Like the ones to which electrons have to go through the nucleus to reach to or because it is almost accepted that electrons are found  away from the nucleus at the edges of the atom, to exclude whole regions close to the nucleus.) These lines will be the "ELEMENTAL PATHS" of "ELECTRON PATHWAYS" (orbitals) to be created.  So we start N (1024-1) "electron pathways".  From EACH and EVERYONE of ALL of these other (new) points to which the first series of  "ELEMENTAL PATHS" ended another series of lines (new  "ELEMENTAL PATHS" is traced to EVERY and ALL other points in the cube, so now there are another N "ELEMENTAL PATHS" for each of the N "ELEMENTAL PATHS" of the first round and  so N² "electron pathways".  Continuing this process again and again, N^zillion  continues "electron pathways" are created and stored and these will include all short of curves: circular, elliptical, saw like,vibrational, totally irregular, periodic and not. ( One may decide instead of taking all the points to take every 2,5 or 10 points. ) The process of creating "electron pathways" must stop SOMETIME and here the 4th dimension must be introduced, TIME, to get a number for the z in the N^zillion "electron pathways." Since scientists have counted times of chemical reactions and estimate the speed of electrons IN THE ATOMS at some percentage of the speed of light (e.g 1/3 or 2/3) they may use their intelligent guess for the "time" that "electrons" will travel along their "paths" in these simulated "electron pathways"  in the atom. Having then simulated "electron pathways" one may "create atoms" of 1,2,3....,10,.... electrons by combining all "electron pathways" stored by the previous procedure for each electron. So there will be (10^zillion)² combinations for a "two electron atom", (10^zillion)³ for a "three electron atom" etc. Off course again filters will be used on  "combined electron paths" some will be substructed, for example because two "electrons" are at the same place at the same time. Unfortunately when one creates "molecules" it has to be taken that "electrons" have adjusted their "pathways" to "bond" and can not find how "electrons" were distributed in "single isolated atoms".

 

 

 

 

I gather this is some sort of spoof post, but I still find it interesting. I wasn’t aware of the diffraction scattering analysis method used in crystallography, until reading this post, so kudos for the information.

 

Now that I have read a bit, my understanding is the bright spots produced are the result of a reinforcement pattern coming from the electron clouds of multiple atoms, not from multiple electrons within an atom. The pattern so produced indicates the crystalline structure of the molecule, not the structure of atoms themselves.

 

So, your speculation about mapping the orbitals of electrons is indeed a fiction, although an interesting one.

 

Should you want to be taken a bit more seriously next time, I suggest you adopt a more precise usage of the word “Zillion” in estimating the number of orbital paths in your proposed simulation. Your usage of 10^Zillion is likely to cause heavy moderation on some forums (but not here!). May I suggest you follow the usage suggested by Conway and Guy?

Conway and Guy (1996) define the nth zillion as 10^(3n+3) in the American system (million=10^6, billion=10^9, trillion=10^(12), ...) and 10^(6n) in the British system (million=10^6, billion=10^(12), trillion=10^(18), ...).

As W.C. Fields famously said “If you can't dazzle them with brilliance, baffle them with bullshit.”

[exchemist]

I gather this is some sort of spoof post, but I still find it interesting. I wasn’t aware of the diffraction scattering analysis method used in crystallography, until reading this post, so kudos for the information.

 

Now that I have read a bit, my understanding is the bright spots produced are the result of a reinforcement pattern coming from the electron clouds of multiple atoms, not from multiple electrons within an atom. The pattern so produced indicates the crystalline structure of the molecule, not the structure of atoms themselves.

 

So, your speculation about mapping the orbitals of electrons is indeed a fiction, although an interesting one.

 

Should you want to be taken a bit more seriously next time, I suggest you adopt a more precise usage of the word “Zillion” in estimating the number of orbital paths in your proposed simulation. Your usage of 10^Zillion is likely to cause heavy moderation on some forums (but not here!). May I suggest you follow the usage suggested by Conway and Guy?

Conway and Guy (1996) define the nth zillion as 10^(3n+3) in the American system (million=10^6, billion=10^9, trillion=10^(12), ...) and 10^(6n) in the British system (million=10^6, billion=10^(12), trillion=10^(18), ...).

As W.C. Fields famously said “If you can't dazzle them with brilliance, baffle them with bullshit.”

 

The interesting thing to me about this - which I had not previously thought about -  is that the scattering is due to valence shell electrons and is treated as elastic scattering by a free electron (Thomson scattering).

 

The valence electrons are not really free of course, being in either covalent bonds or bound in the outer shell of ions, but can be treated as if they are free because the energy of the X-rays is so much greater than the binding energy, i.e. the bonding can't affect much how they resonate in synch with the radiation. 

 

(X-rays themselves originate from electronic excitation of the inner shells, not the valence shells, of atoms and are consequently of far higher energy.) 

 

So, as you say a spoof post, but nonetheless thought-provoking :)

[Maine farmer]

 

NO NO NO      NO Uncertainty Principles HERE, PLEASE.  READ IT AGAIN, IF YOU HAVE TIME TO GET ITS ESSENCE. BUT IF YOU ARE A REAL RESEARCH SCIENTIST KEEP AWAY FROM Physics Fiction In Crystallography BECAUSE WE

NEED YOU TO FIND THE STRUCTURES OF OUR PROTEINS. YOU DON'T NEED INTELLECTUAL AMUSEMENT YOU DO INTELLECTUAL WORK.

 

 

I am not a real research scientist (nor a fake one) , but I can't see any way to avoid the Uncertainty Principle.

[faysunKle]

I gather this is some sort of spoof post, but I still find it interesting. I wasn’t aware of the diffraction scattering analysis method used in crystallography, until reading this post, so kudos for the information.

 

Now that I have read a bit, my understanding is the bright spots produced are the result of a reinforcement pattern coming from the electron clouds of multiple atoms, not from multiple electrons within an atom. The pattern so produced indicates the crystalline structure of the molecule, not the structure of atoms themselves.

 

So, your speculation about mapping the orbitals of electrons is indeed a fiction, although an interesting one.

 

Should you want to be taken a bit more seriously next time, I suggest you adopt a more precise usage of the word “Zillion” in estimating the number of orbital paths in your proposed simulation. Your usage of 10^Zillion is likely to cause heavy moderation on some forums (but not here!). May I suggest you follow the usage suggested by Conway and Guy?

Conway and Guy (1996) define the nth zillion as 10^(3n+3) in the American system (million=10^6, billion=10^9, trillion=10^(12), ...) and 10^(6n) in the British system (million=10^6, billion=10^(12), trillion=10^(18), ...).

As W.C. Fields famously said “If you can't dazzle them with brilliance, baffle them with bullshit.”

 

 

 

And they can figure out the atom to atom identity of a molecule from this pseudo-assumption ?