{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/72400"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/72400","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Direct QM/MM Simulations of the Excited State Dynamics of Retinal Protonated Schiff Base in Isolation and in Complex Environments","abstract":"Retinal Protonated Schiff Base (RPSB) is the chromophore employed by the rhodopsin family of proteins, which includes rhodopsin (Rh), bacteriorhodopsin (bR) and halorhodopsin (hR). Photoisomerization of RPSB from the all-trans to 13-cis conformation triggers ion transport across the cell membrane in hR and bR. Visual perception in the eye is initiated by RPSB isomerization from 11-cis to all-trans conformation in Rh. An important unresolved question is the role of the protein environment in altering the photochemical mechanism. We have investigated the detailed photochemical mechanism in RPSB using the full multiple spawning method to describe quantum mechanical effects of the nuclear degrees of freedom. Simulations are carried out in isolation as well as a solvated (methanol) and protein environments. A reparameterized multireference semiempirical method is used to describe the ground and excited electronic states of the chromophore and the environment is represented with an empirical force field (QM/MM). The potential energy surfaces and their couplings are determined "on the fly," i.e. simultaneously with the dynamic evolution. We compare our results in methanol and in protein environments (Rh, bR, and hR) to experimental results and find good agreement. The results from these simulations provide a much more complete picture of the role of complex environments in influencing photochemical mechanism and achieving bond selectivity in isomerization.","abstract_html":"Retinal Protonated Schiff Base (RPSB) is the chromophore employed by the rhodopsin family of proteins, which includes rhodopsin (Rh), bacteriorhodopsin (bR) and halorhodopsin (hR). Photoisomerization of RPSB from the all-trans to 13-cis conformation triggers ion transport across the cell membrane in hR and bR. Visual perception in the eye is initiated by RPSB isomerization from 11-cis to all-trans conformation in Rh. An important unresolved question is the role of the protein environment in altering the photochemical mechanism. We have investigated the detailed photochemical mechanism in RPSB using the full multiple spawning method to describe quantum mechanical effects of the nuclear degrees of freedom. Simulations are carried out in isolation as well as a solvated (methanol) and protein environments. A reparameterized multireference semiempirical method is used to describe the ground and excited electronic states of the chromophore and the environment is represented with an empirical force field (QM/MM). The potential energy surfaces and their couplings are determined "on the fly," i.e. simultaneously with the dynamic evolution. We compare our results in methanol and in protein environments (Rh, bR, and hR) to experimental results and find good agreement. The results from these simulations provide a much more complete picture of the role of complex environments in influencing photochemical mechanism and achieving bond selectivity in isomerization.","abstract_has_math":false,"creators":["Punwong, Chutintorn"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Biophysics and Computational Biology","degree_department":null,"school":null,"contributors":["Martinez, Todd J."],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2014,"date_issued":"2014-12-17T22:22:47Z","date_published":"2014-12-17T22:22:47Z","updated_at":"2026-07-22T22:26:06Z","subjects":["Chemistry, Physical","Biophysics, General"],"languages":[],"rights":[],"rights_urls":[],"identifier_entries":[{"key":"dc:identifier","label":"Identifier","values":["(UMI)AAI3363060"],"render_values":[{"text":"(UMI)AAI3363060","href":null,"code":true}]}]},"links":{"outbound_url":"http://hdl.handle.net/2142/72400","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Martinez, Todd J."]},{"key":"dc:creator","label":"Author","values":["Punwong, Chutintorn"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2014-12-17T22:22:47Z","10000-01-01","2009"]},{"key":"dc:type","label":"Dc Type","values":["text"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Biophysics and Computational Biology"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Dissertation"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Ph.D."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Illinois at Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Chemistry, Physical","Biophysics, General"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["http://hdl.handle.net/2142/72400","(UMI)AAI3363060"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Retinal Protonated Schiff Base (RPSB) is the chromophore employed by the rhodopsin family of proteins, which includes rhodopsin (Rh), bacteriorhodopsin (bR) and halorhodopsin (hR). Photoisomerization of RPSB from the all-trans to 13-cis conformation triggers ion transport across the cell membrane in hR and bR. Visual perception in the eye is initiated by RPSB isomerization from 11-cis to all-trans conformation in Rh. An important unresolved question is the role of the protein environment in altering the photochemical mechanism. We have investigated the detailed photochemical mechanism in RPSB using the full multiple spawning method to describe quantum mechanical effects of the nuclear degrees of freedom. Simulations are carried out in isolation as well as a solvated (methanol) and protein environments. A reparameterized multireference semiempirical method is used to describe the ground and excited electronic states of the chromophore and the environment is represented with an empirical force field (QM/MM). The potential energy surfaces and their couplings are determined "on the fly," i.e. simultaneously with the dynamic evolution. We compare our results in methanol and in protein environments (Rh, bR, and hR) to experimental results and find good agreement. The results from these simulations provide a much more complete picture of the role of complex environments in influencing photochemical mechanism and achieving bond selectivity in isomerization.","Made available in DSpace on 2014-12-17T22:22:47Z (GMT). No. of bitstreams: 1 3363060.pdf: 3328236 bytes, checksum: 33f202eb651243a16d6f2bd8441148ad (MD5) Previous issue date: 2009","Embargo set by: Seth Robbins for item 72568 Lift date: Forever Reason: Restricted to the U of I community idenfinitely during batch ingest of legacy ETDs","Restricted to the U of I community idenfinitely during batch ingest of legacy ETDs","U of I Only","172 p.","Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 2009."]},{"key":"dc:title","label":"Title","values":["Direct QM/MM Simulations of the Excited State Dynamics of Retinal Protonated Schiff Base in Isolation and in Complex Environments"]}]}],"canonical_facts":{"dc:contributor":["Martinez, Todd J."],"dc:creator":["Punwong, Chutintorn"],"dc:date":["2014-12-17T22:22:47Z","10000-01-01","2009"],"dc:description":["Retinal Protonated Schiff Base (RPSB) is the chromophore employed by the rhodopsin family of proteins, which includes rhodopsin (Rh), bacteriorhodopsin (bR) and halorhodopsin (hR). Photoisomerization of RPSB from the all-trans to 13-cis conformation triggers ion transport across the cell membrane in hR and bR. Visual perception in the eye is initiated by RPSB isomerization from 11-cis to all-trans conformation in Rh. An important unresolved question is the role of the protein environment in altering the photochemical mechanism. We have investigated the detailed photochemical mechanism in RPSB using the full multiple spawning method to describe quantum mechanical effects of the nuclear degrees of freedom. Simulations are carried out in isolation as well as a solvated (methanol) and protein environments. A reparameterized multireference semiempirical method is used to describe the ground and excited electronic states of the chromophore and the environment is represented with an empirical force field (QM/MM). The potential energy surfaces and their couplings are determined "on the fly," i.e. simultaneously with the dynamic evolution. We compare our results in methanol and in protein environments (Rh, bR, and hR) to experimental results and find good agreement. The results from these simulations provide a much more complete picture of the role of complex environments in influencing photochemical mechanism and achieving bond selectivity in isomerization.","Made available in DSpace on 2014-12-17T22:22:47Z (GMT). No. of bitstreams: 1 3363060.pdf: 3328236 bytes, checksum: 33f202eb651243a16d6f2bd8441148ad (MD5) Previous issue date: 2009","Embargo set by: Seth Robbins for item 72568 Lift date: Forever Reason: Restricted to the U of I community idenfinitely during batch ingest of legacy ETDs","Restricted to the U of I community idenfinitely during batch ingest of legacy ETDs","U of I Only","172 p.","Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 2009."],"dc:identifier":["http://hdl.handle.net/2142/72400","(UMI)AAI3363060"],"dc:subject":["Chemistry, Physical","Biophysics, General"],"dc:title":["Direct QM/MM Simulations of the Excited State Dynamics of Retinal Protonated Schiff Base in Isolation and in Complex Environments"],"dc:type":["text"],"thesis:degree_discipline":["Biophysics and Computational Biology"],"thesis:degree_level":["Dissertation"],"thesis:degree_name":["Ph.D."],"thesis:institution_name":["University of Illinois at Urbana-Champaign"]},"updated_at":"2026-07-22T22:26:06Z"}