Modern Polymer Spect..

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~~ ~~ ~~~ ~ ~ ~~ 5.4 Polypeptides 277 Table 5-10. Comparison of some modes of ccl-poly( L-glutaniic acid) and q1-poly(L-alanine) with those of ccl-poly(L-alaniiie). Moded u1-PLAb ~I-PLGH' MII-PLA Observed Calculated Observed Calculated Observedd Calculatedb I 1658 1657iA) 1655 1655(El) 1653 1652 1657(A) 1655(El) 1667 1667(A) 1661 166O( El) I1 1545 1538(El) 1516 1519(A) 1 550 1510 1537(Ei) 1517(A) 1547 1540( Ei ) 1515(A) I11 1338 1345(El) 1278 1287iE2) 1270 1278(E1) 1265 1262(A) 1340 1296 1283 1 326(El) 12991 E2) 1287(Ei) 1263(A) 1346(E1 ) 1281 (E2) 1272(El) 1260( A) NCn s, C"CP s 1178(A) 1 167(El) 1118 1 l29(A) 1129(El) 1175(A) 1 169(EL) CN s. CNC" d V 909 910(A) 893 901 (€5 658 660(E1) 618 608(E1) 928 924 670 618 929( El) 922(A) 678(Ei) 626iE1) 909(A) 900(E1) 1 615(Ei) CO ib, C"CN d 528 537(A) 565 549(A) 536(A) NC'C d 528 522(El ) 515(E1) 518(E1) CO ob, Cb b Cb b CTP t 375 374(Ei) 366 367(A) 292 307(A) 260 264(A) 409 318 280 402(E1) 368(A) 334(A) 265(A) 376(A) 369(E1) 302jA) 274(A) a I, 11, 111. V: amide modes, in cm-'; s: stretch, b: bend, ib: in-plane bend, ob: out-of-plane bend, d: deformation, t: torsion. From [106]. From [139]. From [140]. Small changes in backbone structure, such as are represented by the aII-helix, also lead to predictable spectral changes, as seen from Table 5-10. The amide I mode, found about 10 cm-' higher in (putative [107]) qr-helices [140], is expected to be particularly affected because of the weaker hydrogen bond resulting from the tilted peptide group. The other higher-frequency modes do not change very much, but there are some possible characteristic changes in the low frequency region: the frequency order of the symmetry species of the CO ob, Cb b modes inverts, and the frequency separation between Cb b and C*Cb t is expected to decrease significantly in an. Thus, vibrational spectra can be sensitive to even very small changes in structure.
218 5 Vibratioid <strong>Spect</strong>roscopy oj Pollyeprides In addition to frequencies, dichroic properties can be altered by small structural changes. Since the peptide group in the uII-helix is more inclined to the helix axis than it is in the a,-helix, the DRs of amide modes are expected to differ significantly between the two structures. To calculate the DR of, for example, ainide I of an a-helix we need to know (?g/dQ~),, and (l@/?Q,),, which involves knowing the L,, and dc/dS, (see Eq. (5-5)). Since the L,r are known from the normal mode calculation and the d$/ciSl have been obtained from ab azirio calculations [63], it becomes possible to synthesize a band intensity profile for a given (even finite) ol-helix structure. Such a calculation has been done for the oll-helix and the a11-helix for amide I and aniide I1 by computing the IR intensity profiles for the two polarization components of these two bands [141]. The results show that the DRs are significantly different enough to pennit identification of these structures from this property. The ability to predict a band intensity profile opens up an important additional dimension in vibrational analysis. It means that we will be able to relate subtle spectral differences to small structural changes with a greater degree of confidence. Thus, it has been possible to confirm that an observed three-component contour of the amide I band of tropomyosin is indeed expected for a coiled-coil a-helix [142]. Extensions to understanding the normal modes of proteins become possible [ 1431. The systematic incorporation in an SDFF of dipoles and dipole fluxes to calculate IR intensities [ 1441 will finally bring to the vibrational analysis of polymeric niolecules the completeness and flexibility needed to make it a much more powerful structural tool. 5.4.2.3 3lo-Helix The 3lo-helix represents a different topology than the a-helix, being 4 - I rather than 5 - 1, and is therefore of importance in studying the vibrational dynamics of polypeptide helices. At present, its only clear identification has been in PAIB, so its characterization from this polypeptide may lack soine generality. On the other hand, the excellence of the experimental data [I 101 makes its vibrational analysis secure. Since the structure of PAIB has not been determined in detail by diffraction methods, the normal-mode studies [110] were based on a 310 structure obtained from conforniational analysis [l 1 11 (Figure 5-7). The vibrational studies compared experimental data with predictions for two helices, and the results clearly favored the 310- over the a-helix. The threefold screw symmetry of this structure results in El and E2 species modes reducing to doubly degenerate E species modes. The main chain force field was the same as that for oll-PLA, with additional force constants refined for the (CH3)2 group. Some inodes from the full analysis [110] are compared with those of q-PLA in Table 5-1 1. The observed amide I frequencies are slightly lower for the 3lo-helix than for the cq-helix because of the slightly stronger hydrogen bond (N...O = 2.83 A versus 2.86 A, respectively). The increased splitting is undoubtedly due to the different TDC interactions as a function of conformation. This probably also accounts for the large change in the A-E splitting of the aniide 11 modes. The nominal aniide 111 modes (they contain no CN s and NH ib dominates only in the 1312 cn-' mode!
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Modern Polymer Spectroscopy Edited
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Modern Polymer Spectroscopy Edited
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Preface For unfortunate reasons the
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However, theory and calculations yi
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Contents 1 Two-Dimensional Infrared
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Con ten t~ xi Index 5.2 Force Field
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Contributors M. Del Zoppo Dipartime
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1 Two-Dimensional Infrared (2D IR)
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1.2 Brick~qrorrnrl 3 . Figure 1-3.
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1.0 , Figure 1-6. The in-phtrse and
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1.2 Bcrckgroinizd 7 where AA (i~) i
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1.2 Background 9 1.2.5 Two-Dimensio
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1.3 Bnsic Properties of 20 IR Corre
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2D IR spectrometer coupled with a d
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1.5 Applirtrtions 15 Unlike a dispe
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\ '\ Melliyleiie 1'7- -3000 Posiliv
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11 Amorphous Crystalline ,...." I F
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1.5 Applications 21 / I 1430 Figure
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1.5 Appliccitioiis 23 Methylene Fig
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1.5 Ajqdicrrtions 25 3024 Figure 1-
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1.5 Applicutions 27 Furthermore. th
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1.7 Coizclirsions 29 derived in a s
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1.9 References 31 [9] Colthup, N. B
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2 Segmental Mobility of Liquid Crys
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SRMPLE/DETECTOR e3 ‘retardation
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2.4 Srvuc me-Dependenr Alignment 37
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2.5 Electric Field-Innductid Orirnt
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2.5 Electric Field-nclticetl Orient
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a -@ COWER SRHPLE ._ 2.5 Elec tric
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2.5 Electric Field-Itzduced Orienta
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2.5 Electric Field-IwrElrced Orient
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2.5 Electric Field-Im/irced Orientu
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2.5 Electric Field-Induced Orientli
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2.5 Electric Field-Induced Orientat
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2.5 Electric Field-Induced Orienfat
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2.5 Elrc tric Field-Iiidircwl Orim
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2500 2008 I s00 WRVtNdMRtR CM-I Fig
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-3.6 Aligmient OJ' Side- Clinin Liy
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~ polyester 2.6 Alignnient qf Side-
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I." 0.9 0.8 Figure 2-34. FTlR 0.7 p
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induced alignment of the investigat
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2.7 Orientation oj Liquid Ci:i,stal
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2.7 Orieritation of Liquid Ciysttrl
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0 8 18 16 1 a W u z a m a 0 Ln m Q
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2.7 Orientation oj Liquid Crystals
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2.7 Orientation of Liquid Crjvtals
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2.7 Orientatioiz of Liquid Crystals
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2.8 Conclusions 81 strain. As A0 is
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3. I0 Refcreiice.r 83 [I 71 Hoffina
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2.10 References 85 [92] Wiesner, U.
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t Order/Disorder in Chain Molecules
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onds which hold atoms together thro
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3.2 The Dyriamical Case qf Simll ar
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3.2 The Dyrinniical Case of Sinnll
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3.4 S11or.f- and Loizg-Rcrizye Vibr
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3.4 Slzort- and Loiig-Range Vibrati
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eyularity), e.g., 2. During the pol
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3.5 Towards Lnrger Molecules: From
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3.5 TOIIYW~ Laiyer Molertiles: Fvoi
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3.5 Towmu" Larger Molecules: F~om O
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1700 - CIO --- ca c 22 _- c 12 l l
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3.6 From Dynamics to Vibrational Sp
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3.6 Froin Dynaiiiics to T’ihratio
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3.7 The Case of Isotactic Polypropy
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3.7 The Cuse of Isotactic Polypvop.
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3.8 Density of Vibrational States a
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3.8 Dtvz.sit,v of L’ihrntioizal S
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3.8 Driisity of Vibratioiid StLitrs
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3 9 Mouiiiq ToIvmds Rerrlitv: From
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3.9 Moving Towards Reality: From Or
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3.9 Moving Towards Reality: Froin O
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3.10 Wlmt Do We Learn from Cnlcailc
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+ 3.11 A Very Siriiple Ccrse: Latti
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3 I1 A Yey) Siiiiple Case: LLittice
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3.11 A Vq> Siiiiplc Crrw: Luttice D
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Figure 3-22. Sample eigenvectors in
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3.12 CIS-trans Opening @the Double
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3.13 Defect Modes cis Structtrr.al
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3.13 Defect Mo&s cis Structurcil Pr
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0 3.14 Case Studies N 0 d - Y N o m
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3.14 Case Studies 147 OC 60 58 57.
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3.14 Case Studies 149 GI A V E N U
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3.14 Case Studies 15 1 correspond t
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3.14 Case Studies 153 (I10 + 200) +
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3.14 Case Studies 155 1500 1480 146
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3.14 Case Studies 157 the molecular
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17E (ir 1, R): (iii) z = 4, t = 1,
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3.16 Stnictural Znlioi~zogeneity an
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3.1 7 Fermi Resonancrs 163 stants.
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3.1 7 Femi Resorinnces 165 2 L 1 29
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lowing. The CHl-bending mode 6 [cer
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3.17 Ferini Re.sonrriire.s 169 a Fi
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3. I7 Fernii Resoiiances 17 1 terin
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3.18 Band Broadening and Confonnati
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3.18 Bmd Brourleiziriy md Cmforrnat
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3.18 Band Bvoaderiing arid Conjonna
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3.18 Band Broadening and Confornmti
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3.19 A Worked E.utinple 181 pre-mel
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3.19 A Wovh-ecl E.uanzple 183
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3.19 A Worked Example 185 19 5°C 2
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3.19 A Workrd Example 187 Figure 3-
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3.19 A Worked E.rcnniplr 189 LAM I
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3.19 A Worked E.xuniple 191 Figure
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3.19 A Worked E.vnn~yle 193 Figure
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3.19 A Worked E.vnrqde 195 009.1 00
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3.19 A Worked Example 197 existence
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3.1 9 A Worked Example 199 The soli
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3.20 References 201 very important,
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3.20 References 203 [41] M. Gussoni
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3.20 Refeeveiicrs 205 [I 171 P. Jon
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4 Vibrational Spectroscopy of Intac
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4.3 Georrietvy oj Intuct Po1vniev.r
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1'45 4.4 Geometric Chunges I?zditce
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4.4 Geometric Chmges Iiid~lrcecl bj
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4 5 Mer1iodolog.v of Raiii~11 Studi
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4.7 Poly(p-pheiq.lene) 217 with an
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4.7 Pol)~(p-pheiz~~lene) 219 ENERGY
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is worthwhile pointing out that the
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~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ 801 Table 4-3
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4.7 Poly(y-phenylene) 225 Figure 4-
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Page 254 and 255: 5 Vibrational Spectroscopy of Polyp
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Page 268 and 269: Table 5-2. Some amide modes of four
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Page 276 and 277: I 5.4 Polypeptides 261 )I .- + $ 80
Page 278 and 279: 1226M 1222s (1 1165W 1167s (1 1120V
Page 280 and 281: 135s 9 1 Ms1i 122Wbr 147 NH ob(37)
Page 282 and 283: 5.4 Polypeptides 267 glycine residu
Page 284 and 285: 5.4 Polypeptides 269 Raman bands in
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Page 288 and 289: Frequency (cm-'1 100% b 700 500 300
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Page 296 and 297: Table 5-12. Aniide mode frequencies
Page 298 and 299: 1351 Lifson, S., Stern, P. S., J. C
Page 300 and 301: 5.6 Refeverices 285 [130] Tiffany,
Page 302 and 303: Index Amide modes 249 Amorphous pol
Page 304 and 305: Step-scan FTIR spectroscopy 14,34 -
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