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The authentic evidence proves that Prophet Mohammad (peace be upon him and his Holy Progeny) did not die a natural death but he was killed by poison. The evidence is in Sunni and Shia books. In the Sunni books there is an authentic narration from Abdullah ibn Mas'ood.
The name 'Azra'il is used for the Angel of Death in a number of hadith, such as in Bihar al-Anwar, but not in the Qur'an.
A du'a transmitted from Imam al-Sadiq in which one prays for blessings on the angels includes praying for blessings on 'Azrail, the Angel of Death (allahumma salli 'ala Azra'il, malak al-mawt).
Interestingly, there is a variant of this du'a which calls him "malak al-rahmah" - the Angel of Mercy, although still describing him as taking people's souls. Perhaps this is because, for the believer, it is said that he will be kindly.
In any case, he is doing his job tirelessly and deserves blessings! :)
If you feel justified in invoking divine wrath against someone, prayer number 14 in al-Sahifah al-Sajjadiyah ("His supplication when suffering acts of wrongdoing") may suffice, especially when recited regularly until the situation is resolved, and sometimes these du'as also help as a coping mechanism to gain wisdom from difficulty.
Ziyarat Ashura and Dua Alqamah do not hurt in this regard either.
Allah knows best whether death itself is the best manifestation of His justice, as sometimes justice is better served by keeping someone alive for some time. Frequently, Allah delivers justice in a manner which we could not have expected or asked for.
Of course, sometimes someone may wish to pray for someone to die to be free of their tyranny.
It is generally considered bad form to pray for the death of one's biological parents or children, perhaps due to the intimate link, but of course one could pray for other things such as relocation.
Death is guaranteed for all people anyway.
Is the concept of soul identical to that of Nafs? If so, how can it be interpreted that every Nafs is to taste death? Aren't souls eternal?
In the Qur'an, when used alone, the word "nafs" is not really used as a synonym for soul (in the sense of the soul as a non-corporeal entity distinct from the body). Rather, it is usually used to refer to the complete self; for instance, in phrases like "bring yourselves" or "they deceive themselves".
(Of course, this distinction can be blurry based on how one perceives the nature of the soul and the relationship between the soul and the body.)
This is different from the use of the word "nafs" outside the Qur'an, in that "nafs" in other texts or discussions is often used to mean specifically the immaterial part of the human.
Therefore, when the Qur'an says "kullu nafsin dha'iqat al-mawt", it means that all people will taste death in a holistic sense, not specifically that all souls will.
However, since the soul and body experience things simultaneously, the soul will also taste the experience of death, just as it experiences other things occurring via the body.
If one understands death to mean "transfer from realm to realm", rather than "annihilation", then definitely the soul will experience transfer from realm to realm upon death.
Some say that we will have a different type of body as a vehicle for the soul in the barzakh and in the Hereafter. Therefore, if death is also understood to mean "transfer from one type of body to another", the soul will also taste death in that way.
So it is not incorrect to say that all souls will taste death; the usage of the word in the Qur'an is simply more expansive than that.
Note that compound phrases in the Qur'an such as nafs al-'ammarah (the bestial soul), nafs al-lawwamah (the blaming soul), and nafs al-mutma'innah (the content soul which God calls to Paradise) refer more to immaterial aspects of the human being.