The present invention provides protonated compounds having antiviral and antimicrobial activity. The invention also provides antimicrobial compositions comprising protonated compounds of the invention. The protonated compounds of the invention provide efficacious antimicrobial activity against resistant strains of bacteria and opportunistic fungi. The invention also provides antiviral compositions comprising compounds of the invention. Viruses that may be treated by compositions of the invention include, but are not limited to, HIV, HSV, CMV, HBV, HCV and influenza virus.