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The brief positive emotional experience (i.e., affect) that accompanies smoking comes from the rapid neuromodulatory effects of nicotine in the glutamatergic and dopaminergic pathways propagating between the mesolimbic centers and the prefrontal cortex. This is the basis of addiction.
About a bad mood. One theory is that smoking increases the amount of deoxygenated hemoglobin in the blood in the prefrontal cortex. Simply put, your brain receives less oxygen than it should. That's where all the problems come from. The authors of the study also found that 30 minutes of intense physical activity after smoking can significantly reduce this harm. Smoking and exercising is still a perversion, but it's better than just smoking and sitting on your butt straight.
By the way, this is the latest research published just a few days ago, exactly to your question.
Monroe, Derek C., et al. “The effects of exercise on mood and prefrontal brain responses to emotional scenes in smokers.” Physiology & behavior 213 (2020): 112721.
It is also believed that after the initial pleasant effect of smoking, after some time there is an abstinence syndrome, i.e. craving for nicotine. Many people smoke to relieve stress and anxiety, but the paradox is that smoking often causes this anxiety or worsens the existing one. It turns out a vicious circle-you smoke to relieve tension, then it only increases, and what do you do? that's right, you smoke more and make it worse. You are fine as long as nicotine acts for a short time, as soon as its effect disappears, the withdrawal syndrome begins. Anxiety is one of its symptoms.