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Atès que és un problema que tenim tots els de "llengües romàniques" quan ens iniciem en la llengua anglesa n'he fet un article per tal deixar-ho el més clar possible..

1.-Hydrogen was substituted for oxygen. --> hydrogen was used
1.-Considerable disagreement exists regarding the extent of substitution of chlorine for hydrogen in given alkalies. --> disagreement over the use of chlorine rather than hydrogen

2.-Hydrogen was substituted by oxygen. --> oxigen was used

These are the patterns that that emerge in the usage of substitute:

1.- substitute A for B --> A takes the place of B --> use A
1.- substitute CAT for DOG --> CAT takes the place of DOG --> use CAT

1.- A was substituted for B --> A takes the place of B --> use A
1.- CAT was substituted for DOG --> CAT takes the place of DOG --> use CAT

2.- substitute A with/by B --> B takes the place of A --> use B
2.- substitute CAT with/by DOG --> DOG takes the place of CAT --> use DOG

2.- A was substituted with/by B --> B takes the place of A --> use B
2.- CAT was substituted with/by DOG --> DOG takes the place of CAT --> use DOG

- substitute X for sy/sg --> sy/sg is replaced by X => X replaces sy/sg => replace sy/sg with X

- substitute --> context tells:
I was substituted in the second half ... after I had broken my arm. --> I left, sy else took my place
I was substituted in the second half ... and 5 minutes later, during the closing minutes, I scored an equalizer. --> I came in to play

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To sum up:
CASE1.- when there is the preposition for with substitute, what comes after for is removed
CASE2.- with by and with, it is the other way around

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http://www.usingenglish.com/forum/threads/98412-substituted-by-substituted-fo-substitution-of-for