{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,25]],"date-time":"2026-03-25T01:49:51Z","timestamp":1774403391345,"version":"3.50.1"},"reference-count":70,"publisher":"AIP Publishing","issue":"4","funder":[{"name":"Russian Foundation for Basic Research","award":["mol_a 12-02-31374"],"award-info":[{"award-number":["mol_a 12-02-31374"]}]}],"content-domain":{"domain":["pubs.aip.org"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2013,1,28]]},"abstract":"<jats:p>We present a generalized version of the ITIM algorithm for the identification of interfacial molecules, which is able to treat arbitrarily shaped interfaces. The algorithm exploits the similarities between the concept of probe sphere used in ITIMand the circumsphere criterion used in the \u03b1-shapes approach, and can be regarded either as a reference-frame independent version of the former, or as an extended version of the latter that includes the atomic excluded volume. The new algorithm is applied to compute the intrinsic orientational order parameters of water around a dodecylphosphocholine and a cholic acid micelle in aqueous environment, and to the identification of solvent-reachable sites in four model structures for soot. The additional algorithm introduced for the calculation of intrinsic density profiles in arbitrary geometries proved to be extremely useful also for planar interfaces, as it allows to solve the paradox of smeared intrinsic profiles far from the interface.<\/jats:p>","DOI":"10.1063\/1.4776196","type":"journal-article","created":{"date-parts":[[2013,1,29]],"date-time":"2013-01-29T01:11:49Z","timestamp":1359421909000},"update-policy":"https:\/\/doi.org\/10.1063\/aip-crossmark-policy-page","source":"Crossref","is-referenced-by-count":87,"title":["The generalized identification of truly interfacial molecules (ITIM) algorithm for nonplanar interfaces"],"prefix":"10.1063","volume":"138","author":[{"given":"Marcello","family":"Sega","sequence":"first","affiliation":[{"name":"Tor Vergata University of Rome 1 , via della Ricerca scientifica 1, I-00133 Rome, Italy"}]},{"given":"Sofia S.","family":"Kantorovich","sequence":"additional","affiliation":[{"name":"Sapienza University of Rome 2 , p.le A. Moro 4, I-00188 Rome, Italy"},{"name":"Ural Federal University 3 , Lenin Ave. 51, 620083 Ekaterinburg, Russia"}]},{"given":"P\u00e1l","family":"Jedlovszky","sequence":"additional","affiliation":[{"name":"E\u00f6tv\u00f6s Lor\u00e1nd University 4 Laboratory of Interfaces and Nanosize Systems, Institute of Chemistry, , P\u00e1zm\u00e1ny stny 1\/a, H-1117 Budapest, Hungary ; , Szt. Gell\u00e9rt t\u00e9r 4, H-1111 Budapest, Hungary ; and , H-3300 Eger, Le\u00e1nyka u. 6, Hungary"},{"name":"MTA-BME Research Group of Technical Analytical Chemistry 4 Laboratory of Interfaces and Nanosize Systems, Institute of Chemistry, , P\u00e1zm\u00e1ny stny 1\/a, H-1117 Budapest, Hungary ; , Szt. Gell\u00e9rt t\u00e9r 4, H-1111 Budapest, Hungary ; and , H-3300 Eger, Le\u00e1nyka u. 6, Hungary"},{"name":"EKF Department of Chemistry 4 Laboratory of Interfaces and Nanosize Systems, Institute of Chemistry, , P\u00e1zm\u00e1ny stny 1\/a, H-1117 Budapest, Hungary ; , Szt. Gell\u00e9rt t\u00e9r 4, H-1111 Budapest, Hungary ; and , H-3300 Eger, Le\u00e1nyka u. 6, Hungary"}]},{"given":"Miguel","family":"Jorge","sequence":"additional","affiliation":[{"name":"Universidade do Porto 5 LSRE - Laboratory of Separation and Reaction Engineering - Associate Laboratory LSRE\/LCM, Faculdade de Engenharia, , Rua Dr. Roberto Frias, 4200-465 Porto, Portugal"}]}],"member":"317","published-online":{"date-parts":[[2013,1,28]]},"reference":[{"key":"2023062523342408000_c1","doi-asserted-by":"publisher","first-page":"166103","DOI":"10.1103\/PhysRevLett.91.166103","volume":"91","year":"2003","journal-title":"Phys. Rev. Lett."},{"key":"2023062523342408000_c2","doi-asserted-by":"publisher","first-page":"15442","DOI":"10.1021\/jp060440y","volume":"110","year":"2006","journal-title":"J. Phys. Chem. B"},{"key":"2023062523342408000_c3","doi-asserted-by":"publisher","first-page":"17612","DOI":"10.1021\/jp076178q","volume":"111","year":"2007","journal-title":"J. Phys. Chem. C"},{"key":"2023062523342408000_c4","doi-asserted-by":"publisher","first-page":"945","DOI":"10.1002\/jcc.20852","volume":"29","year":"2008","journal-title":"J. Comput. Chem."},{"key":"2023062523342408000_c5","doi-asserted-by":"publisher","first-page":"1954","DOI":"10.1021\/jp909219k","volume":"114","year":"2010","journal-title":"J. Phys. Chem. B"},{"key":"2023062523342408000_c6","doi-asserted-by":"publisher","first-page":"11169","DOI":"10.1021\/jp101035r","volume":"114","year":"2010","journal-title":"J. Phys. Chem. C"},{"key":"2023062523342408000_c7","doi-asserted-by":"publisher","first-page":"18656","DOI":"10.1021\/jp107378s","volume":"114","year":"2010","journal-title":"J. Phys. Chem. C"},{"key":"2023062523342408000_c8","doi-asserted-by":"publisher","first-page":"2999","DOI":"10.1021\/cr9904009","volume":"105","year":"2005","journal-title":"Chem. Rev."},{"key":"2023062523342408000_c9","doi-asserted-by":"publisher","first-page":"379","DOI":"10.1016\/0022-2836(71)90324-X","volume":"55","year":"1971","journal-title":"J. Mol. Biol."},{"key":"2023062523342408000_c10","doi-asserted-by":"publisher","first-page":"151","DOI":"10.1146\/annurev.bb.06.060177.001055","volume":"6","year":"1977","journal-title":"Annu. Rev. Biophys. Bioeng."},{"key":"2023062523342408000_c11","doi-asserted-by":"publisher","first-page":"548","DOI":"10.1107\/S0021889883010985","volume":"16","year":"1983","journal-title":"J. Appl. Cryst."},{"key":"2023062523342408000_c12","doi-asserted-by":"publisher","first-page":"709","DOI":"10.1126\/science.6879170","volume":"221","year":"1983","journal-title":"Science"},{"key":"2023062523342408000_c13","doi-asserted-by":"publisher","first-page":"351","DOI":"10.1016\/0022-2836(73)90011-9","volume":"79","year":"1973","journal-title":"J. Mol. Biol."},{"key":"2023062523342408000_c14","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/0022-2836(74)90570-1","volume":"82","year":"1974","journal-title":"J. Mol. Biol."},{"key":"2023062523342408000_c15","doi-asserted-by":"publisher","first-page":"303","DOI":"10.1073\/pnas.75.1.303","volume":"75","year":"1978","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2023062523342408000_c16","doi-asserted-by":"publisher","first-page":"537","DOI":"10.1016\/0022-2836(78)90201-2","volume":"119","year":"1978","journal-title":"J. Mol. Biol."},{"key":"2023062523342408000_c17","doi-asserted-by":"publisher","first-page":"411","DOI":"10.1016\/0022-2836(79)90268-7","volume":"132","year":"1979","journal-title":"J. Mol. Biol."},{"key":"2023062523342408000_c18","doi-asserted-by":"publisher","first-page":"1736","DOI":"10.1073\/pnas.77.4.1736","volume":"77","year":"1980","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2023062523342408000_c19","doi-asserted-by":"publisher","first-page":"74","DOI":"10.1107\/S0021889883009978","volume":"16","year":"1983","journal-title":"J. Appl. Cryst."},{"key":"2023062523342408000_c20","doi-asserted-by":"publisher","first-page":"1507","DOI":"10.1002\/bip.360220607","volume":"22","year":"1983","journal-title":"Biopolymers"},{"key":"2023062523342408000_c21","doi-asserted-by":"publisher","first-page":"1047","DOI":"10.1002\/jcc.540110907","volume":"11","year":"1990","journal-title":"J. Comput. Chem."},{"key":"2023062523342408000_c22","doi-asserted-by":"publisher","first-page":"868","DOI":"10.1002\/jcc.540120712","volume":"12","year":"1991","journal-title":"J. Comput. Chem."},{"key":"2023062523342408000_c23","doi-asserted-by":"publisher","first-page":"349","DOI":"10.1002\/jcc.540140309","volume":"14","year":"1993","journal-title":"J. Comput. Chem."},{"key":"2023062523342408000_c24","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1002\/(SICI)1096-987X(19990130)20:2&lt;217::AID-JCC4&gt;3.0.CO;2-A","volume":"20","year":"1999","journal-title":"J. Comput. Chem."},{"key":"2023062523342408000_c25","doi-asserted-by":"publisher","first-page":"1118","DOI":"10.1021\/ja00291a006","volume":"107","year":"1985","journal-title":"J. Am. Chem. Soc."},{"key":"2023062523342408000_c26","doi-asserted-by":"publisher","first-page":"63","DOI":"10.1016\/0022-2836(84)90231-6","volume":"178","year":"1984","journal-title":"J. Mol. Biol."},{"key":"2023062523342408000_c27","doi-asserted-by":"publisher","first-page":"1247","DOI":"10.1080\/00268978700102951","volume":"62","year":"1987","journal-title":"Mol. Phys."},{"key":"2023062523342408000_c28","doi-asserted-by":"publisher","first-page":"641","DOI":"10.1080\/00268978800100453","volume":"64","year":"1988","journal-title":"Mol. Phys."},{"key":"2023062523342408000_c29","doi-asserted-by":"publisher","first-page":"402","DOI":"10.1002\/jcc.540120314","volume":"12","year":"1991","journal-title":"J. Comput. Chem."},{"key":"2023062523342408000_c30","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1002\/jcc.540130102","volume":"13","year":"1992","journal-title":"J. Comput. Chem."},{"key":"2023062523342408000_c31","doi-asserted-by":"publisher","first-page":"463","DOI":"10.1016\/S1093-3263(02)00203-6","volume":"21","year":"2003","journal-title":"J. Mol. Graphics Modell."},{"key":"2023062523342408000_c32","doi-asserted-by":"publisher","first-page":"551","DOI":"10.1109\/TIT.1983.1056714","volume":"29","year":"1983","journal-title":"IEEE Trans. Inf. Theory"},{"key":"2023062523342408000_c33","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1145\/174462.156635","volume":"13","year":"1994","journal-title":"ACM Trans. Graphic."},{"key":"2023062523342408000_c34","first-page":"256","article-title":"Measuring proteins and voids in proteins","volume-title":"Proceedings of the 28th Annual Hawaii International Conference on System Sciences, Los Alamitos, California, 1995","year":"1995"},{"key":"2023062523342408000_c35","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1002\/(SICI)1097-0134(19981001)33:1&lt;1::AID-PROT1&gt;3.0.CO;2-O","volume":"33","year":"1998","journal-title":"Proteins"},{"key":"2023062523342408000_c36","doi-asserted-by":"publisher","first-page":"046709","DOI":"10.1103\/PhysRevE.79.046709","volume":"79","year":"2009","journal-title":"Phys. Rev. E"},{"key":"2023062523342408000_c37","first-page":"1395","volume-title":"Handbook of Discrete and Computational Geometry","author":"Goodman","year":"2004"},{"key":"2023062523342408000_c38","first-page":"793","volume":"7","year":"1934","journal-title":"Izv. Akad. Nauk SSSR, Otd. Mat. Estest. Nauk"},{"key":"2023062523342408000_c39","volume-title":"Spatial Tessellations: Concepts and Applications of Voronoi Diagrams","year":"2000"},{"key":"2023062523342408000_c40","doi-asserted-by":"publisher","first-page":"223","DOI":"10.1016\/0020-0190(79)90074-7","volume":"9","year":"1979","journal-title":"Inf. Process. Lett."},{"key":"2023062523342408000_c41","doi-asserted-by":"publisher","first-page":"469","DOI":"10.1145\/235815.235821","volume":"22","year":"1996","journal-title":"ACM Trans. Math. Softw."},{"key":"2023062523342408000_c42","doi-asserted-by":"publisher","first-page":"509","DOI":"10.1145\/361002.361007","volume":"18","year":"1975","journal-title":"Commun. ACM"},{"key":"2023062523342408000_c43","doi-asserted-by":"publisher","first-page":"397","DOI":"10.1145\/356789.356797","volume":"11","year":"1979","journal-title":"ACM Comput. Surv."},{"key":"2023062523342408000_c44","doi-asserted-by":"publisher","first-page":"926","DOI":"10.1063\/1.445869","volume":"79","year":"1983","journal-title":"J. Chem. Phys."},{"key":"2023062523342408000_c45","doi-asserted-by":"publisher","first-page":"521","DOI":"10.1080\/00268978200100411","volume":"45","year":"1982","journal-title":"Mol. Phys."},{"key":"2023062523342408000_c46","doi-asserted-by":"publisher","first-page":"327","DOI":"10.1016\/0021-9991(77)90098-5","volume":"23","year":"1977","journal-title":"J. Comput. Phys."},{"key":"2023062523342408000_c47","doi-asserted-by":"publisher","first-page":"435","DOI":"10.1021\/ct700301q","volume":"4","year":"2008","journal-title":"J. Chem. Theory Comput."},{"key":"2023062523342408000_c48","doi-asserted-by":"publisher","first-page":"8577","DOI":"10.1063\/1.470117","volume":"103","year":"1995","journal-title":"J. Chem. Phys."},{"key":"2023062523342408000_c49","doi-asserted-by":"publisher","first-page":"255","DOI":"10.1080\/00268978400101201","volume":"52","year":"1984","journal-title":"Mol. Phys."},{"key":"2023062523342408000_c50","doi-asserted-by":"publisher","first-page":"1695","DOI":"10.1103\/PhysRevA.31.1695","volume":"31","year":"1985","journal-title":"Phys. Rev. A"},{"key":"2023062523342408000_c51","doi-asserted-by":"publisher","first-page":"15765","DOI":"10.1021\/bi000714m","volume":"39","year":"2000","journal-title":"Biochemistry"},{"key":"2023062523342408000_c52","doi-asserted-by":"publisher","first-page":"127","DOI":"10.1023\/A:1018698002314","volume":"9","year":"1997","journal-title":"J. Biomol. NMR"},{"key":"2023062523342408000_c53","doi-asserted-by":"publisher","first-page":"9570","DOI":"10.1021\/bi010640u","volume":"40","year":"2001","journal-title":"Biochemistry"},{"key":"2023062523342408000_c54","doi-asserted-by":"publisher","first-page":"60","DOI":"10.1006\/jmrb.1995.1146","volume":"109","year":"1995","journal-title":"J. Magn. Reson. Ser. B"},{"key":"2023062523342408000_c55","doi-asserted-by":"publisher","first-page":"6380","DOI":"10.1021\/jp001268f","volume":"104","year":"2000","journal-title":"J. Phys. Chem. B"},{"key":"2023062523342408000_c56","doi-asserted-by":"publisher","first-page":"2271","DOI":"10.1063\/1.1488579","volume":"117","year":"2002","journal-title":"J. Chem. Phys."},{"key":"2023062523342408000_c57","doi-asserted-by":"publisher","first-page":"1874","DOI":"10.1039\/b313231p","volume":"6","year":"2004","journal-title":"Phys. Chem. Chem. Phys."},{"key":"2023062523342408000_c58","doi-asserted-by":"publisher","first-page":"144702","DOI":"10.1063\/1.3496466","volume":"133","year":"2010","journal-title":"J. Chem. Phys."},{"key":"2023062523342408000_c59","doi-asserted-by":"publisher","first-page":"456","DOI":"10.1038\/471456a","volume":"471","year":"2011","journal-title":"Nature (London)"},{"key":"2023062523342408000_c60","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1038\/nclimate1422","volume":"2","year":"2012","journal-title":"Nat. Clim. Change"},{"key":"2023062523342408000_c61","doi-asserted-by":"publisher","first-page":"4421","DOI":"10.1039\/b004345l","volume":"2","year":"2000","journal-title":"Phys. Chem. Chem. Phys."},{"key":"2023062523342408000_c62","doi-asserted-by":"publisher","first-page":"1079","DOI":"10.1016\/S0045-6535(02)00718-X","volume":"51","year":"2003","journal-title":"Chemosphere"},{"key":"2023062523342408000_c63","doi-asserted-by":"publisher","first-page":"1644","DOI":"10.1021\/ef049736y","volume":"19","year":"2005","journal-title":"Energy Fuel"},{"key":"2023062523342408000_c64","doi-asserted-by":"publisher","first-page":"775","DOI":"10.1016\/j.combustflame.2008.06.009","volume":"154","year":"2008","journal-title":"Combust. Flame"},{"key":"2023062523342408000_c65","doi-asserted-by":"publisher","first-page":"681","DOI":"10.1016\/j.proci.2008.07.023","volume":"32","year":"2009","journal-title":"Proc. Combust. Inst."},{"key":"2023062523342408000_c66","volume-title":"Chemistry; The Bile Acids","author":"Nair","year":"1971"},{"key":"2023062523342408000_c67","doi-asserted-by":"publisher","first-page":"9886","DOI":"10.1021\/jp072974k","volume":"111","year":"2007","journal-title":"J. Phys. Chem. B"},{"key":"2023062523342408000_c68","doi-asserted-by":"publisher","first-page":"12322","DOI":"10.1021\/la701749u","volume":"23","year":"2007","journal-title":"Langmuir"},{"key":"2023062523342408000_c69","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","volume":"14","year":"1996","journal-title":"J. Mol. Graphics"},{"key":"2023062523342408000_c70","doi-asserted-by":"publisher","first-page":"2005","DOI":"10.1021\/la052719w","volume":"22","year":"2006","journal-title":"Langmuir"}],"container-title":["The Journal of Chemical Physics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.aip.org\/aip\/jcp\/article-pdf\/doi\/10.1063\/1.4776196\/15458920\/044110_1_online.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.aip.org\/aip\/jcp\/article-pdf\/doi\/10.1063\/1.4776196\/15458920\/044110_1_online.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,25]],"date-time":"2023-06-25T23:34:29Z","timestamp":1687736069000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.aip.org\/jcp\/article\/138\/4\/044110\/193226\/The-generalized-identification-of-truly"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,1,28]]},"references-count":70,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2013,1,28]]}},"URL":"https:\/\/doi.org\/10.1063\/1.4776196","relation":{},"ISSN":["0021-9606","1089-7690"],"issn-type":[{"value":"0021-9606","type":"print"},{"value":"1089-7690","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2013,1,28]]},"published":{"date-parts":[[2013,1,28]]},"article-number":"044110"}}