I found an article written by Toni Coleman about what chemistry is and I find that the explanation is an acceptable one. It's important to have a basic knowledge of what real chemistry consists of.
Chemistry has two components: the physical attraction, where a person will feel breathless, excited and weak in the knees, palms sweat, heart races and bondy tingles with nervous anticipation when meeting this person and the other dimension is the values, beliefs, personalities and worldview of this person.
Physical attraction can be so strong to overcome the rational thinking to find out the other party's character and views. Take a step back fro a minute and find out who the other party actually is before going deeper into a relationship. Actually, its all in the mind. It'll be better to use both heart and mind to find out if the other party has initial suitability.
Of the two components, I feel the latter holds a greater percentage in the makeup of chemistry but physical attraction does play a part too.
"Spiritual affinity" is what Kahlil Gibran defines the latter. It's the hidden element of chemistry. It's when two beings meet and connect on a deeper level. It can only be felt in the heart and soul. It's about friendship, respect and humor and the feelings of warmth and contentment that come when you are in his/her presence. This "deeper level" is made up of the family, surroundings one grow up in, values being imbued into and other factors tangible and intangible. Even if you can connect on this deeper level but will one be able to accept it is another story. It all boils down back to the basics. Maybe each individual's "basic" criteria is different but I would feel that some of the basics are happiness, food, enjoyment, care and concern, stability, focus, sincere, honest and supportive. Only when one has the basics, then it is possible to look out for other things in life.
It's time to think what is your basic if you've not done it.