ADSORPTION OF HALOGENATED ORGANIC MOLECULES AND PHOTO-INDUCED CONSTRUCTION OF A COVALENTLY BONDED SECOND ORGANIC LAYER ON SILICON SURFACES SHAO YANXIA NATIONAL UNIVERSITY OF SINGAPORE 2009 ADSORPTION OF HALOGENATED ORGANIC MOLECULES AND PHOTO-INDUCED CONSTRUCTION OF A COVALENTLY BONDED SECOND ORGANIC LAYER ON SILICON SURFACES SHAO YANXIA (M.E., XI’AN JIAOTONG UNIVERSITY) A THESIS SUBMITTED FOR THE DEGREE OF DOCTOR OF PHILOSOPHY DEPARTMENT OF CHEMISTRY NATIONAL UNIVERSITY OF SINGAPORE 2009 Acknowledgement I would like to express my deepest gratitude to my supervisor, Professor Xu Guo Qin, for his invaluable advice and patient guidance during this research work. His passion for research and kindness to people will encourage me forever. I would also like to thank my co-supervisor, Associate Professor Ang Siau Gek, who has offered great support for the completion and development of this research work. My sincere thanks to my colleagues Dr. Zhang Yongping, Dr. Huang Haigou, Dr. Huang Jingyan, Dr. Yong Kian Soon, Dr. Ning Yuesheng, Dr. Cai Yinghui, Dr. Tang Haihua, Mr. Dong Dong, Mr. Wang Shuai, Mr. Tan Wee Boon, Mr. He Jinghui, Dr. Zhou Xuedong, Mr. Xiang Chaoli, Mr. Gu Feng, Ms. Wu Jihong, Ms. Zhao Aiqin, and Ms. Liu Yi, for their generous help, invaluable suggestions and discussions during my research work. Of course, I would like to appreciate my husband Zhang Xiaohua, who has provided me great support and encouragement. His solid knowledge in Latex programming saved a lot of time for me in writing this thesis. To my parents, my brother and his families, I am forever thankful for their everlasting encouragement and support. Last but not least, I must acknowledge the National University of Singapore for awarding me the research scholarship. Contents Summary vi List of publication ix List of Figures xii List of Tables xix Chapter Introduction 1.1 Background . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1.2 Geometry and electronic structures of Si surfaces . . . . . . . . . . . . . 1.2.1 The geometrical structure of Si(100)-2×1 . . . . . . . . . . . . . . 1.2.2 The electronic properties of Si(100)-2×1 . . . . . . . . . . . . . . 1.2.3 The atomic arrangement of Si(111)-7×7 . . . . . . . . . . . . . . 1.2.4 The electronic structure of Si(111)-7×7 . . . . . . . . . . . . . . . 1.3 Reaction mechanisms of organic molecules on silicon surfaces . . . . . . . 1.3.1 [2+2]-like cycloaddition . . . . . . . . . . . . . . . . . . . . . . . . 1.3.2 [4+2]-like cycloaddition . . . . . . . . . . . . . . . . . . . . . . . . 1.3.3 Dative bonding . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11 1.3.4 Ene-like reaction . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 1.3.5 Dissociative reaction . . . . . . . . . . . . . . . . . . . . . . . . . 13 1.4 Surface photochemistry of halogenated organic molecules . . . . . . . . . 15 i Contents 1.5 Objective and organization of this thesis . . . . . . . . . . . . . . . . . . Chapter Experimental 16 22 2.1 Surface analytical techniques . . . . . . . . . . . . . . . . . . . . . . . . . 22 2.1.1 High resolution electron energy loss spectroscopy . . . . . . . . . 22 2.1.2 X-ray photoelectron spectroscopy . . . . . . . . . . . . . . . . . . 25 2.1.3 Density functional theory calculations . . . . . . . . . . . . . . . . 27 2.2 Experimental procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . 29 2.2.1 Ultra-high vacuum systems . . . . . . . . . . . . . . . . . . . . . 29 2.2.2 Sample preparation . . . . . . . . . . . . . . . . . . . . . . . . . . 30 2.2.3 Pulsed laser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31 2.2.4 Organic molecules . . . . . . . . . . . . . . . . . . . . . . . . . . . 32 Chapter Fluoroacetonitrile and bromoacetonitrile adsorption on Si(100)2×1 39 3.1 [2+2]-like cycloaddition of fluoroacetonitrile on Si(100)-2×1 . . . . . . . . 40 3.1.1 High resolution electron energy loss spectroscopy . . . . . . . . . 40 3.1.2 X-ray photoelectron spectroscopy . . . . . . . . . . . . . . . . . . 41 3.1.3 Density functional theory calculations . . . . . . . . . . . . . . . . 43 3.2 Ene-like reaction of bromoacetonitrile attachment on Si(100)-2×1 . . . . 44 3.2.1 High resolution electron energy loss spectroscopy . . . . . . . . . 44 3.2.2 X-ray photoelectron spectroscopy . . . . . . . . . . . . . . . . . . 45 3.2.3 Density functional theory calculations . . . . . . . . . . . . . . . . 48 3.3 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49 ii Contents 3.3.1 The bonding configurations of fluoroacetonitrile on the Si(100)2×1 surface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49 3.3.2 The attachment of bromoacetonitrile on the Si(100)-2×1 surface . 50 3.3.3 The reaction mechanisms of fluoroacetonitrile and bromoacetonitrile on the Si(100)-2×1 surface . . . . . . . . . . . . . . . . . . . 50 3.4 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51 Chapter Chloroacetonitrile and propargyl chloride attachment on Si(100)2×1 69 4.1 Coexistence of [2+2]-like cycloaddition and ene-like reaction of chloroacetonitrile on Si(100)-2×1 . . . . . . . . . . . . . . . . . . . . . . . . . . . 70 4.1.1 High resolution electron energy loss spectroscopy . . . . . . . . . 70 4.1.2 X-ray photoelectron spectroscopy . . . . . . . . . . . . . . . . . . 72 4.1.3 Density functional theory calculations . . . . . . . . . . . . . . . . 75 4.2 Dissociative reaction of propargyl chloride on Si(100)-2×1 . . . . . . . . 76 4.2.1 High resolution electron energy loss spectroscopy . . . . . . . . . 76 4.2.2 X-ray photoelectron spectroscopy . . . . . . . . . . . . . . . . . . 77 4.2.3 Density functional theory calculations . . . . . . . . . . . . . . . . 79 4.3 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80 4.3.1 Combination of the [2+2]-like cycloaddition and ene-like reaction at chloroacetonitrile/Si(100)-2×1 surface . . . . . . . . . . . . . . 80 4.3.2 Dissociation of propargyl chloride on Si(100)-2×1 . . . . . . . . . 81 4.3.3 Adsorption behaviors of chloroacetonitrile and propargyl chloride on Si(100)-2×1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82 4.4 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83 Chapter Photo-induced secondary attachment of 3-chloro-1-propanol iii Contents on Si(100)-2×1 99 5.1 Dissociation of 3-chloro-1-propanol on Si(100)-2×1 . . . . . . . . . . . . . 100 5.1.1 High resolution electron energy loss spectroscopy . . . . . . . . . 100 5.1.2 X-ray photoelectron spectroscopy . . . . . . . . . . . . . . . . . . 101 5.1.3 Density functional theory calculations . . . . . . . . . . . . . . . . 103 5.2 Photochemistry of the chemisorbed 3-chloro-1-propanol on Si(100)-2×1 . 104 5.2.1 High resolution electron energy loss spectroscopy . . . . . . . . . 105 5.2.2 X-ray photoelectron spectroscopy . . . . . . . . . . . . . . . . . . 105 5.3 Photo-induced secondary attachment of 3-chloro-1-propanol layer on Si(100)2×1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107 5.3.1 High resolution electron energy loss spectroscopy . . . . . . . . . 108 5.3.2 X-ray photoelectron spectroscopy . . . . . . . . . . . . . . . . . . 109 5.4 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111 Chapter Laser-induced cyano group attachment onto the 3-chloro-1propanol modified Si(111)-7×7 131 6.1 Attachment of 3-chloro-1-propanol on Si(111)-7×7 . . . . . . . . . . . . . 132 6.1.1 High resolution electron energy loss spectroscopy . . . . . . . . . 132 6.1.2 X-ray photoelectron spectroscopy . . . . . . . . . . . . . . . . . . 133 6.2 d3 -acetonitrile attached onto 3-chloro-1-propanol modified Si(111)-7×7 by photon irradiation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134 6.2.1 High resolution electron energy loss spectroscopy . . . . . . . . . 135 6.2.2 X-ray photoelectron spectroscopy . . . . . . . . . . . . . . . . . . 136 6.3 Grafting of benzonitrile onto the interface of 3-chloro-1-propanol/Si(111)7×7 by laser irradiation . . . . . . . . . . . . . . . . . . . . . . . . . . . 139 iv Contents 6.3.1 X-ray photoelectron spectroscopy . . . . . . . . . . . . . . . . . . 140 6.4 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143 Chapter Conclusion 158 Reference 161 v Summary Summary Advanced surface analytical techniques, including high resolution electron energy loss spectroscopy (HREELS) and X-ray photoelectron spectroscopy (XPS), together with density functional theory (DFT) calculations were used to investigate the reaction mechanism of unsaturated halogenated organic molecules on Si(100)-2×1 and Si(111)-7×7 surfaces. On the basis of fundamental understanding of silicon surface chemistry of halogenated organic molecules, a second covalently bonded organic layer was grafted by introducing photons. Fluoroacetonitrile (N≡C-CH2 -F) and bromoacetonitrile (N≡C-CH2 -Br) were chosen as typical molecules to understand the selectivity and competition of bifunctional molecules on the Si(100)-2×1 surface. A [2+2]-like cycloadduct is formed at the fluoroacetonitrile / Si(100)-2×1 interface, evidenced by the appearance of the N=C stretching mode (1620 cm−1 ) and the retention of the C-F stretching mode (1040 cm−1 ) in the chemisorbed EELS spectrum. Meanwhile, the significant binding energy downshift of 1.6 eV (N1s) and 1.9 eV (C1s) in the XPS spectrum for the chemisorbed molecules also supports the formation of [2+2]-like cycloadduct. Bromoacetonitrile adsorbs on the Si(100)-2×1 surface through the ene-like reaction with the C-Br bond dissociation to form Si-N=C=CH2 -like and Si-Br linkages. These structures are strongly suggested by the appearance of the characteristic vibrational peaks at 2054 cm−1 (N=C=C asymmetric stretching) and 660 cm−1 (N=C=C bending) in the chemisorbed EELS spectrum, as well as by significant chemical downshifts of N1s (1.7 eV), Br3d5/2 (1.0 eV), and C1s (1.6 eV) in the XPS investigations. The different reaction mechanisms of these two molecules are due to their individual different halogen substitution groups. vi Summary Chloroacetonitrile (N≡C-CH2 -Cl) chemisorbs on the Si(100)-2×1 surface through the ene-like reaction and [2+2]-like cycloaddition to form Si-N=C=CH2 -like and SiN=C(CH2 -Cl)-Si-like species, which are evidenced by the appearance of the N=C=C asymmetric stretching (2051 cm−1 ), N=C=C symmetric stretching (1148 cm−1 ), and N=C stretching (1630 cm−1 ) modes in the EELS spectrum for chemisorbed molecules. Concurrently, the XPS results and DFT calculations also suggest the coexistence of enelike reaction and [2+2]-like cycloaddition upon the chemisorption of chloroacetonitrile on the Si(100)-2×1 surface. The EELS and XPS results, together with the DFT calculation, confirm that propargyl chloride (Cl-C1 H2 -C2 ≡C3 H) dissociatively adsorbs onto the Si(100)-2×1 surface with the C-Cl bond cleavage to form Si-C1 H2 -C2 ≡C3 H-like and Si-Cl-like species. The large downshift of Cl2p3/2 (1.1 eV) and C1 1s (2.6 eV) in the chemisorbed XPS spectrum strongly demonstrates the occurrence of the C-Cl dissociative reaction on Si(100)-2×1. 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Reaction mechanisms of organic molecules on silicon surfaces As described in Section 1.2, the buckled dimer of Si(100)-2×1 and the adjacent adatom-rest atom pair on Si(111)-7×7 can act as reactive sites in the adsorption reaction between organic molecules and silicon surfaces Functionalization of Si surfaces with organic molecules depends on the detailed understanding of the reaction mechanisms of functional... possibilities of employing the C-X bonds to control the adsorption reaction pathways, and successfully constructed a second chemically attached Cl-containing organic layer on the Si surfaces viii Publications List of Publications 1 Chemisorption mechanisms of halogenated acetonitrile on Si(100)-2×1 surfaceeffect of different halogen substitution groups Shao, Yan Xia; Dong, Dong.; Wang, Shuai; Ang, Siau Gek;... formation of single bond between inter-3-chloro-1-propanol molecules on Si(100)2×1 surface by photon irradiation Shao, Yan Xia; Cai, Ying Hui; Wang, Shuai; Dong, Dong; Ang, Siau Gek; Xu, Guo Qin In preparation ix Publications 5 Photo- induced Construction of a Second Covalently Bonded d3 -Acetonitrile Layer on 3-Chloro-1-Propanol Modified Si(111)-7×7 Surface Shao, Yan Xia; Cai, Ying Hui; Dong, Dong; Ang,... the monochromatic radiation was employed to activate surface chemical modification and provide direct photopatterning of specific functional groups on surfaces [51–53] Cai and coworkers successfully constructed a second covalently bonded organic layer on Si(111)-7×7 through laser irradiation [54] In this study, halogenated organic molecules were chosen due to the high photodissociation cross section of. .. Si surfaces has attracted a great deal of attention in past thirty years for a variety of present and potential applications in biosensors, molecular devices, high throughput combinatoric analysis, optoelectronic devices, nonlinear optical materials, and microelectronics [1, 5–14] The binding of organic molecules (mono-, bi-, and multi-functional) onto Si surfaces can be achieved through one or a combination... the carbon-halogen (C-X) bonds [55–60] The purpose of this study is to investigate the reaction of halogenated organic molecules on Si surfaces and to build up a second covalently bonded organic molecules layer on Si surfaces through laser irradiation The modified Si surfaces with enhanced multi-functionality are expected to be more useful in biosensors, optoelectronic devices, and microelectronics applications... reflection Fourier transform infrared (MIRFTIR) spectroscopy, TPD, and DFT calculations [160] Later, Mui et al and Cao et al systematically studied the adsorption mechanisms of primary, secondary, and tertiary alkylamines on Si(100)-2×1 with XPS, UPS, FTIR, and STM [40, 161, 162] It was found that only tertiary alkylamines attach to silicon surfaces through a dative bonding process Recently, Tao and coworkers... that methyl methacrylate may form dative bonds on silicon surfaces at the initial stage of adsorption [152, 163] 1.3.4 Ene-like reaction The ene-like reaction mechanism, which involves a αC-H bond dissociation, emerged a few years ago and has been experimentally and theoretically investigated [9, 41–43, 45, 164] due to its important role in exploring adsorption pathways on semiconductor and metal surfaces. .. the dative bonding reaction to pyridine (containing a lone pair of electron and acting as an electron-donor in the surface reaction) on silicon surfaces, which demonstrated the coexistence of dative -bonded state and [4+2]-like cycloadduct at liquid nitrogen temperature [38, 73] The dative -bonded state is the final surface species for some simple molecules, as 11 Chapter 1 well as the precursor state... In order to saturate all the dangling bonds in the dimer layer, the rest atoms in the above rest atom layer must occupy stacking fault sites within one of the subunits, resulting in the formation of faulted and unfaulted regions in this layer At the topmost layer (adatom layer) , there are twelve adatoms and each silicon atom is back -bonded to three underlying rest atoms These adatoms can be further . ADSORPTION OF HALOGENATED ORGANIC MOLECULES AND PHOTO- INDUCED CONSTRUCTION OF A COVALENTLY BONDED SECOND ORGANIC LAYER ON SILICON SURFACES SHAO YANXIA NATIONAL UNIVERSITY OF SINGAPORE 2009 ADSORPTION. SINGAPORE 2009 ADSORPTION OF HALOGENATED ORGANIC MOLECULES AND PHOTO- INDUCED CONSTRUCTION OF A COVALENTLY BONDED SECOND ORGANIC LAYER ON SILICON SURFACES SHAO YANXIA (M.E., XI’AN JIAOTONG UNIVERSITY) A THESIS. mech- anism of unsaturated halogenated organic molecules on Si(100)-2×1 and Si(111 )-7×7 surfaces. On the basis of fundamental understanding of silicon surface chemistry of halogenated organic molecules,