The more clearer the stone, it will not give negative effects.
Except Rahu and Ketu gems i.e. Gomedh (Hessonite) and lahsuniya(cat's eye) no other gem can give negative effect. Only its positivity may be reduced or it may be ineffective.
There are 4 groups of planets possible in a horoscope(as per lordship of houses):
Group A : KENDRA - 1,4,7,10
Group B: TRIKONA - 1,5,9
Group C : TRISHDHAY - 3,6,11.....AND 8
Group D : NEUTRAL - 2,12
Group C is the most dangerous group for gem wearing. If any planet signifies 3,6,11,8 the gem related to it must NOT be worn.
RULE FOR GEM WEARING:
- PAAPI PLANET- If lord of Trishdhay + lord of trikona or kendra
- KEWAL PAAPI PLANET - If lord of Trishdhay
- ATI PAAPI - If lord of Trishdhay + 8th house
- Also remember that among Kendra houses 1<4<7<10
- Another rule on similar lines is that among Trikona houses 1<5<9 which means that 9th house is most powerful of all Trikona houses.
- Another rule on similar lines is that among Trishdhay houses 3<6<11 which means 3 is least malefic and 11 the most malefic in modern times of kaliyuga(since desire is the root of all evil)
- If planet signifies ATI PAAPI HOUSES - NO GEM OF THAT PLANET
- If planet signifies KEWAL PAAPI houses - check the forthcoming planetary dasas and antardasas of the native. If all the Upchaya houses / Improvement houses of profession are vibrating he can be suggested to wear stone of that planet. BEWARE that oncoming dasa/antardasa should not signify houses 8, 12 in which case the gem is not to be worn.
- If planet signifies PAAPI house then check the twin lordships of that planet. If one rashi or sign is falling in 3,6,11 and the other rashi or sign is falling in 1,4,7,10,5,9 then the MOOL TRIKON SIGN of that planet. By the above rule of UTTAROTAR BALI check which house is powerful.



In this horoscope Mercury is lord of 9th trikona house which is very positive but the other lordship is falling in 12th house which is a neutral house. In such case check the OCCUPYING PLACE of mercury and check its acoompanying planet. That will decide whether Mercury is positive or negative finally in this horoscope. Suppose its posited with Jupiter which is a functional malefic in this chart then Emerald cannot be suggested.
Apart from accompanying planets(SAHCHARYA) you should also check for which planets are aspecting Mercury (and their lorships) and also in which planet's star or nakshatra Mercury is posited in. This will tell finally whether Mercury stone is suited for the native or not.
NOTE: while considering the gem stone also take care that the bitter enemy of 8th house lord needs to be calculated (for that particular chart) and its stone should not be worn as it reduces the LONGEVITY of the native.