"Take from their wealth an alms..."
More than one authority reported from Ibn Abbas—may Allah be pleased with them both—that when [the believers who had stayed behind] were granted release, they departed and came with their wealth, saying: "O Messenger of Allah, this is our wealth, so give alms from it on our behalf and seek forgiveness for us." The Prophet, peace and blessings be upon him, replied: "I have not been commanded to take anything from your wealth." Then this verse was revealed, and he, peace and blessings be upon him, took a third of it, as stated in some reports.
Thus, the "alms" here does not refer to the obligatory alms (i.e., Zakat), because the Prophet was [initially] commanded to take it [without restriction]; rather, it is—as has been said—an expiation for their sins, as indicated by His Almighty’s saying: "that you may purify them thereby," meaning from the filth of lagging behind [in the expedition] that had stained them.
Al-Jubba'i holds that it refers to Zakat, and the Prophet, peace and blessings be upon him, was commanded to take it here to dispel the assumption that they were to be lumped in with the hypocrites, for [the alms of hypocrites] would not be accepted from them, as you have learned—and the matter of purification is simple. In any case, the pronoun in "their wealth" refers to these confessing individuals. It has also been said that, under the second interpretation, it refers to the owners of wealth in general, and the plural "wealth" is used to indicate that taking from all types of property is permissible.
The prepositional phrase [from their wealth] relates to "take." It is also permissible for it to relate to a suppressed constituent serving as a state (hal) for "alms." The letter ta in "you may purify them" (tuthahhiruhum) is for the second person [addressing the Prophet]. It has also been recited with a jussive sukūn as the response to the command, and in the nominative case, considering the clause as a state (hal) for the subject of "take," or as an adjective for "alms" (implying "by it"), based on the indication of what follows it, or as a new inception (isti'naf), as Abu al-Baqa' said. Regarding the possibility of it being an adjective, it is permissible that the ta be for the third person [the alms], with the feminine pronoun referring back to "alms," thus requiring no "by it." It has also been read as tutahhiruhum, from at-tahara, meaning to cleanse.
"And pray for them" (wa salli 'alayhim)—meaning, supplicate for them and seek forgiveness. The verb is connected with "upon" ('ala) because it carries the meaning of inclination, as it is derived from al-sulw (the inner part of the back). The literal linguistic meaning here is the one most immediately understood, and interpreting it as the funeral prayer is far-fetched, even if it is narrated from Ibn Abbas—may Allah be pleased with them both. For this reason, the verse is used as evidence for the recommendation of supplicating for those who give alms. Al-Shafi'i recommended that [the collector] say to the almsgiver: "May Allah reward you for what you gave, make it a purification for you, and bless you in what you have kept." Some said: It is obligatory for the Imam to supplicate when he takes [the alms]. Others said: It is obligatory for the obligatory alms (fard) and recommended for voluntary alms. Others said: It is obligatory for the Imam and recommended for the poor. The truth is that it is recommended in all cases.
"Indeed, your prayer is a source of serenity for them" is a justification for the command to pray. Sakan (serenity) is tranquility and that which the soul finds peace in, such as family or homeland. According to the first interpretation, the prayer is made the very essence of serenity and reassurance by way of hyperbole. According to the second, the meaning is to liken his prayer—peace and blessings be upon him—to a refuge, where one seeks shelter. The first is more appropriate: meaning, your supplication brings their souls to rest, their hearts to find absolute peace, and they trust that He—the Almighty—has accepted them. More than one of the seven [readers] read it as salawatuka (plural), in consideration of the number of those being prayed for.
"And Allah is All-Hearing"—hearing their confession of sin, their repentance, and their supplication—"All-Knowing" of the remorse and grief within their hearts for what they neglected, and of their sincerity in repentance and supplication. Or, He is All-Hearing, answering your prayer for them, and All-Knowing of what wisdom necessitates. In this case, the clause is a concluding summary (tadhil) for the justification, confirming its content. Under the first interpretation, it is a concluding summary for the preceding two verses, substantiating what is within them.