The atmospheric oxidation of volatile organic compounds (VOCs) has an essential impact on Earth's climate. The oxidation of VOCs in indoor air also affects air quality and thereby human health. When the exchange rates between indoor and outdoor air are limited, the air conditions in indoor and outdoor atmospheres can be dramatically different, thus changing the oxidation mechanisms of the VOCs. Using theoretical methods, we study the gas-phase oxidation pathways of several atmospherically relevant VOCs under different conditions to elucidate some of these differences. Limonene is an important VOC emitted both indoors and outdoors in large quantities. In the pristine atmosphere, the oxidation of limonene is likely initiated by the hydroxyl radicals (OH). Under indoor or polluted conditions, the oxidation of limonene is more likely to be initiated by ozonolysis. The two initiation mechanisms lead to the formation of different peroxy (RO2) radicals. In the pristine atmosphere, the fast autoxidation pathways of limonene-derived RO2 radicals likely lead to the formation of highly oxygenated organic molecules, which can promote aerosol formation. Under indoor or polluted conditions with high NOx concentrations, bimolecular pathways forming ketones, aldehydes, or organic nitrates are more likely to outcompete the unimolecular autoxidation pathways. Reduced sulfur species is another important category of volatile organic compounds whose oxidation drives global cloud formation and precipitation. Calculations are performed on the oxidation mechanism of dimethyl disulfide (DMDS) and methanethiol (CH3SH) in the pristine atmosphere, with a focus on the CH3S radicals, which is an important intermediate for both of their oxidations. Many of the reactions show multireference characters and treating them with single-reference methods may cause large errors. The multireference character is generally more significant when the reactions involve the lone-pair electrons on the sulfur atom. The results indicate that both DMDS and CH3SH react with hydroxyl radicals forming mainly SO2 in the atmosphere, and methanesulfonic acid (MSA) formation from them is likely negligible. The knowledge obtained from DMDS and CH3SH oxidation is applied to the oxidation mechanism of dimethyl sulfide (DMS), the most important atmospheric reduced sulfur species, and some possible oxidation pathways are proposed.