399

Index

1,2-Ethanedithiol (EDT)– CM efficiencies 131– PbSe dots 1311,3-dipolar cycloaddition reactions 174–1763D printing technology 205–2064′,6-Diamidino-2-phenylindole (DAPI)

49–50

aActivation strain model (ASM)– deformed reactants 166– description 166– distortion/interaction model 166– double hydrogen atom transfer reaction

166–167– IRC 167aggregation/agglomeration– finite-size objects 297–298– steric and electrostatic hindrances 298Alder-ene reactions 173–174artificial molecular machines– 1H NMR spectra, EE-1H+ after 389– 1H NMR spectroscopic titration

experiments 393– EE-1H⋅PF6 and DB24 387–388– chemical equilibria and photochemical

reactions 390– concentration–time profiles 389–390– deprotonation, [ZZ-1H ⊂ DB24]+

ammonium center 391– description 387– development, supramolecular systems 388– examined axle and wheel components

392–393– light irradiation 388– nonsymmetric axle 391–392– photochemical and chemical stimulation

391

– photochemically and chemically controlled,DB24 through 3H+ 394

– photoirradiation, EE-1H+ 389– requirements 392– rotary and DNA-based linear motors 388– threading–dethreading kinetics 388ASM. See Activation strain model (ASM)asymmetric motors– bipolar electrodeposition 358– CABED and MWCNTs 359–360– centered and noncentered Pt deposits 360,

362– chemical microswimmers 363– CMTs with Ni patch 360– counterclockwise rotating microswimmer

362– linear motion, microswimmer 362– magnetic microswimmers 360– manipulation, nickel modified CMT

360–361– organic solvents 359– oxidation 358–359– platinum (Pt) 360asymmetry controlled motion– bubble-propelled swimmers 352–353, 355– diodes, AC electric field 355– magnetically propelled swimmers 355– particle 355–356– Salmonella bacterium 350, 355– self-electrophoretic swimmers 351, 355azobenzene– cis-azobenzene species 385– and naphthalene 385– artificial nanomachines 379– dendrimer D, all-trans form D and eosin, E

380–382– dendrimers 380

Discovering the Future of Molecular Sciences, First Edition. Edited by Bruno Pignataro.c© 2014 Wiley-VCH Verlag GmbH & Co. KGaA. Published 2014 by Wiley-VCH Verlag GmbH & Co. KGaA.

400 Index

azobenzene (contd.)

– EE-1H⋅PF6 and DB24, structure formulas387

– eosin extraction 382– eosin uptake and cis → trans isomerization

382–383– G0(t-Azo) and G1(t-Azo), structure formulas

384–385– G1(t-Azo) and G1(c-Azo), cyclam moieties

386– induced and reversible trans–cis

photoisomerization 379–380– kinetics, eosin release 383–384– light energy 379– pH value 382– photochemical experiments, metal

complexes 387

bBasic leucine zipper (bZIP) 39–40BET. See Brunauer–Emmett–Teller (BET)

surfacebioanalytes– carbohydrates (saccharides) 6– chemical structures 4, 6–7– genetic materials 6– intermediary metabolites 4– NTPs 4– recognition studies, ATP 4– sensor systems 6– transport pathways, glucose 6biological cell staining– α-CD.7 12–13– absorbance spectra 10– cell growth dynamics 13–14– cell proliferation and growth 12– colorimetric detection 9– colorless yeast cells 11– growth dynamics 12– prokaryotic Bacillus sp. and Pseudomonas sp.

bacteria 13–14– respiratory inhibitors 12– Zn(II)–DPA unit 10biological phosphates– chromogenic Zn(II) based metal receptors.

See biological cell staining– fluorescent Zn(II) based metal complexes.

See live cell imaging– types, water soluble receptors 6biomotors– Brownian motion and viscosity effects 349– energy rich biomolecules 349– examples 349–350– kinesin-modified surfaces 350

– polydimethylsiloxane (PDMS)microchambers 349

bipolar electrochemistry– ‘‘floating electrodes’’ 356– bypass current ibps and ibe 356–357– electrochemical reactions 357–358– imposed electric field E 357– industrial applications 356– motion generation. See Motion generation– polarization potential 357– spherical bipolar electrode exposed to

electric field 356–357– synthetized, asymmetric motors. See

Asymmetric motorsBissilylenes– categorization 244– isoelectronic structure 244– spacer-separated 245Bis(silylene) Co(I) complex 248– application 262–263– molecular structure 261– synthesis 261Bis(silylene)nickel complex– benzylzinc bromides and aryl halides

250–251– bromo-and chloro-derivatives 251– cross-coupling reaction 252, 254– disiloxane-like system 249– electron rich transition metal 249– Grignard reagents and aryl halides

252–253– organometallic zinc reagents 252– oxygen-bridged bis(silylene) nickel

complex 8 249–250– R1ZnX 252– recrystallization 249– transition metal 248Bis(silylene)titanium complexes– Fisher-and Schrock-type silylene 246– hafnium-silylene complex 247– molecular structures 247–248– Schrock-type silylene 247– Si-Ti-Si framework 248– Sila-Schrock-type complexes III 246– synthesis 247–248Bis(silylenyl)-substituted ferrocene cobalt

complex– arene and heteroarene moieties 262– bidentate σ-donor ligands 259– bis(silylene) Co(I) complex 39. See

Bis(silylene) Co(I) complex 39– bis(silylene) Co(I) complex 40 262– bissilylene 38 synthesis 259–260boronic acid receptors 23–25

Index 401

Brunauer–Emmett–Teller (BET) surface329

building block approach, POMs 197–198bulk semiconductors 117–118bZIP. See Basic leucine zipper (bZIP)

cCABED. See Capillary-assisted bipolar

electrodeposition (CABED)Cage specific force field (CSFF) 337Calcium pyrophosphate dihydrate disease

(CPPD) 4Capillary-assisted bipolar electrodeposition

(CABED) 359cell necrosis, streptolysin 9chemical motors– bubble propulsion mechanism 352–353– Ni/Au nanorod 350–351– polymerization-powered motors 352– Pt-CNT/Au/Ni/Au nanomotor 351–352– recorded current–voltage curves 351– rotational motion 352– self-electrophoresis mechanism, Pt/Au

nanorod 351– stable synthetic motors, similar

performances 350–365– strong speed enhancements 351–352CMPs. See Conjugated microporous polymers

(CMPs)COFs. See Covalent organic frameworks

(COFs)Conjugated microporous polymers (CMPs)

342continuous flow systems– linear flow reactor system 204– molybdenum blue family 204– NRS and iso-POTs 204– pump reactor system 204– representation, Na16 204–205– self-assembly processes 203copper-catalyzed aryl halide exchange

reactions– aromatic halides 284–285– arylcopper(III)-halide complex 288– C-halogen bond 285– copper-mediated aromatic fluorination

289–290– CuF2 mediated process 288– description 284–285– dioxane/pentanol 286– domino reactions 286–287– fluorination reaction 287–288– fluorine insertion methodologies 290–291

– intramolecular halide exchange reactions288–289

– neurodegenerative disorders 287– salts and diamine ligands 285–286covalent molecular mediators– di-functional ligands 304–305– interligands reactions 303–305Covalent organic frameworks (COFs) 329CSFF. See Cage specific force field (CSFF)

d3D printing technology 205–206dendrimers 380Density functional theory (DFT) 165, 336DGT. See Double group transfer (DGT)Diels–Alder reactions– cycloalkenones and cyclic dienes 176– cyclobutenone 177– pyramidal transition structure 179diol-containing bioanalytes 23–25DLS. See Dynamic light scattering (DLS)DNA binding domains– β sheet proteins 40– bZIP and HLH 39–40– HTH and homeodomains 36–37– ZFPs 37–39DNA recognition methods– B-form, dsDNA. 32– biomedical and chemical sciences 31– cellular processes 32– covalent interaction (alkylation agents) 48– drug design models 56– external electrostatic interaction 47– insertion, grooves 48–50– intercalation 47–48– metallo-DNA binders 50–52– nonnatural agents 31– polypyrroles and bis(benzamidine) minor

groove binders 52–56– structural and nanotechnological scaffold

31– TFs 33–46– Watson–Crick model 32Double group transfer (DGT)– activation strain analysis 171– AICD method 169–170– cyclic transition states 172– definition 168– NICS 169– symmetric planar six-membered ring

transition state 169– transition-state region 172Dynamic light scattering (DLS) 17

402 Index

eECD. See Electron capture dissociation (ECD)ECL. See Electrogenerated chemiluminescence

(ECL)EDA. See Energy decomposition analysis

(EDA)T. See Electronic energy transfer (EET)I

EISA. See Evaporation induced self-assembly(EISA)

electrochemical motors– asymmetry, controlled motion. See

Asymmetry controlled motion– bipolar electrochemistry. See Bipolar

electrochemistry– chemical. See Chemical motors– externally powered motion. See Externally

powered motion– inspiration, biomotors. See BiomotorsElectrogenerated chemiluminescence (ECL)

368–369Electron capture dissociation (ECD) 79Electron transfer dissociation (ETD) 79electronic coherence, EET– ‘‘quantumness’’ degree 95– 2DPE. See two-dimensional photon echo

(2DPE)– biological light-harvesting systems and

energy transport 95–96– distant and weakly interacting pigments 96– expectation value 94– interference concept 94– random fluctuations, double slit experiment

94–95Electronic energy transfer (EET)– description 91– different regimes 92–93– electronic coherence. See Electronic

coherence, EET– examples, energy migration 91–92– Forster theory 91–92– intermediate coupling regime 93–94– LHCs 93– new chromophores 93– occupation probability. See Occupation

probability– quantum coherence. See quantum

coherence– strong coupling limit 92Electrospray-ionization mass spectrometry

(ESI-MS)– and hetero-nuclear NMR 191– isopolytungstates and isopolyniobates 194– Palladium-based systems 195

– structural architecture 194energy conversion– photoreduction. See Photoreduction– water oxidation, molecular catalysts

226–228– water splitting 225Energy decomposition analysis (EDA)

167–168energy migration. See occupation probabilityESI-MS. See Electrospray-ionization mass

spectrometry (ESI-MS)ETD. See Electron transfer dissociation (ETD)1,2-Ethanedithiol (EDT)– CM efficiencies 131– PbSe dots 131Evaporation induced self-assembly (EISA)

311–313externally powered motion– alternative swimmers 353– bacteria’s flagella 353– electric field-driven 354–355– electrowetting 355– magnetic rigid helical motors 354

fFACS. See Fluorescence-activated cell sorting

(FACS)FDM. See Filter diagonalization method

(FDM)FEP. See Fluorinated ethylene propylene (FEP)Filter diagonalization mxethod (FDM)– vs. FT drops 85–86– parameter estimator method 85– resolution level 86– signal processing 85Fluorescence-activated cell sorting (FACS)

19Fluorinated ethylene propylene (FEP) 148fluorogenic and chromogenic supramolecular

sensors– artificial systems design 3– bioanalytes 4–6– Boolean logic 26– boronic acid receptors 23–25– chromogenic, visual detection 4– fluorescent and colorimetric receptors 4– geometric and electronic features 3– metal complexes, biological phosphates

6–14– molecular recognition 3– vesicles, bioanalytes 14–23FMO. See Fukui’s frontier molecular orbital

(FMO)

Index 403

Fourier transform ion cyclotron resonancemass spectrometer (FT-ICR MS)

– activation and dissociation reactions 70– data acquisition 71– optimum cell performance 70– ParaCell 71– transient signal 71– trapping field 71– types, ICR cells 70Fourier transform mass spectrometry (FTMS)– current-based ion detector 67– data acquisition speed 82– destructive ion collisions 68– harmonic (sinusoidal) transient signals 69– high-performance data acquisition systems

88– magnetic field gradients 67– multiple periodical measurements 69– non-FT signal processing methods 88– petroleomics-grade platform 81– reproducible ion oscillations 69– resolving power and mass accuracy 67–68– signal processing, transients 85– time-domain signal processing 69FT-ICR MS. See Fourier transform ion

cyclotron resonance mass spectrometer(FT-ICR MS)

FTMS. See Fourier transform massspectrometry (FTMS)

Fukui’s frontier molecular orbital (FMO) 165

gGrand canonical Monte Carlo (GCMC)

simulations 336–337

hN′-2-Hydroxyethylpiperazine-N′-2

ethanesulfonic acid (HEPES) 12halide exchange reactions– aryl halides 275–276– catalytic cycle 277– copper-catalyzed aryl halide exchange

reactions 284–290– electron-deficient haloarenes 276– Finkelstein reaction 276– haloarene compounds 275–276– nickel-based methodologies. See

Nickel-based methodologies– organometallic compounds 275– palladium-catalyzed aryl halide exchange

reactions 280– pseudohalides 277– single-electron transfer 277

Hard and soft acid and base (HSAB) theories165

HCPs. See Hyper-cross-linked polymers(HCPs)

heat transfer– 1-methyl-imidazole and diethyl sulfate 140– contourplot 141– ortho-bromophenyllithium 141– surface-to-volume ratios 140Helix-loop-helix (HLH) 39–40Helix-turn-helix (HTH) 36–37Hexamethyl tetramine (HTMA) 199–200high-resolution MS– composition analysis, complex mixtures

76–77– crude oils (petroleum) and complex

petroleum fractions 73– intact proteins 78– mass scale calibration method 77– middle-down and top-down proteomics 84– molecular antibodies 78– petroleomics 73– proteoforms 83– proteomics 83–84– SOD 77– solution phase protein-ligand interactions

78HLH. See Helix-loop-helix (HLH)HTMA. See Hexamethyl tetramine (HTMA)hydrothermal and ionic thermal synthesis

200N′-2-Hydroxyethylpiperazine-N′-2

ethanesulfonic acid (HEPES), 1.439–441Hyper-cross-linked polymers (HCPs) 342

iInfrared multiphoton dissociation (IRMPD)

81Intrinsic reaction coordinate (IRC) 167ionic liquids– POM-ILs 231–233– properties 231–232IRC. See Intrinsic reaction coordinate (IRC)IRMPD. See Infrared multiphoton dissociation

(IRMPD)

lLangmuir-Blodgett deposition method

310–311lead chalcogenides 120–121ligand exchange and film studies– absorption spectra 130–131– CM threshold 131–132– dipole–dipole interactions 131

404 Index

ligand exchange and film studies (contd.)– EDT 130– halide treatments 133– hydrazine and methylamine 131– mobility 131–133– structural and optical changes 130– transient absorption data 131–132Lipopolysaccharides (LPS)– Gram–ve bacteria 6–7– microbial inducers, inflammation 6– PDA based chromatic vesicles 20–21– types 6live cell imaging– dipicolylamine (DPA) ligand 7– fluorescent chemical receptors 7– FRET 8– site-specific imaging, nucleoside

polyphosphates 8–9– xanthene type chemosensor 1 7LPSs. See Lipopolysaccharides (LPS) 4

mmass analyzers– FT-ICR MS. See Fourier transform ion

cyclotron resonance mass spectrometer(FT-ICR MS)

– orbitrap FTMS. See Orbitrap mass analyzersMass spectrometry (MS)– analytical characteristics 63–64– electric and magnetic fields 63– intra-and intermolecular complexity

63–64– ionization 63– isotopic distribution 65– monoisotopic analysis 67– petroleomics 65– protein dynamic range, plasma 65– protein measurements 65–66– resolution/resolving power 63mass transfer– convection and diffusion 138– Friedel–Crafts aminoalkylation 140– interdigital micromixers 139– micromixers 140– Reynolds number 138Metal-organic frameworks (MOFs) 329metallo-DNA binders– bifunctional DNA cross-linkers 51– chemotherapeutics 52– cytotoxic pathway, cisplatin 51– electrodes, platinum 50– platinum ammine complexes 51– platinum-based chemotherapeutics 52– Pt(IV) prodrugs 52

– single nucleotide polymorphism 52– transition metal complexes 50metamaterials 321micro flow chemistry– chemical reactions 137– chromatography effect 151– continuous-flow methodology 152– hazardous intermediates 140–145– heat transfer 140–141– high-temperature and high-pressure

processing 144–145– homogeneous catalysts 151– laboratory to production scale 157,

159–160– mass transfer. See mass transfer– microreactor clogging 154–158– microreactor technology 137– multiphase flow. See multiphase flow– multistep synthesis 152–154– organic synthetic process 138– Pd-catalyzed fluorination 149– photochemistry. See photochemistry– PTFE 138– reaction screening and optimization

protocols 157–158– recycling, enzyme 150– transesterification, ethyl butyrate 150– urea synthesis 137microreactor clogging– ACR 156–157– chemical industry 154– continuous-flow processing 155– Pd-catalyzed C–N cross-coupling reactions

154–155– surface imperfections 156– Teflon stack microreactor 155–156molecular cluster batteries 231–234molecular metal oxides– 3D printing technology 205–206– building block approach 197–198– complex architectures 192–194– continuous flow systems and networked

reactions 203–205– controlled-based oscillations 210–211– crystallization 192– definition 191– disassembly/reassembly processes 195– ESI-MS 194– hydrothermal and ionic thermal synthesis

200– instrumentation development 192– Mn-cubane core 194–195– novel building block libraries 198–199– Palladium-based systems 195

Index 405

– POMs. See Polyoxometalates (POMs)– porous keplerate nanocapsules 207–208– properties and novel phenomena 206– Sb-based heteropolytungstates 194– self-assembly process 192– shrink-wrapping effect 199–200– space filling representation 195–196– structural identification 194– synthetic approaches 196–197– TOF 194– transformation, POM structures 208–210– tungsten-based iso-POMs 194– wired-frame representation 191–192– XO3 and XO6 templated POMs 200–201motion generation– advantages 364–365– aqueous HQ solution 364– bipolar electrochemistry-induced water

splitting 365– cargo lifter, cargo and bipolar motor

367–368– description 363– dynamic bipolar self-regeneration 370– electrogenerated chemiluminescence (ECL)

368–369– GC bead levitation 366–367– glass capillary filled, zinc dendrites

370–371– glass tube filled, zinc macroswimmer

370–371– glassy carbon bead emitting ECL 369–370– H2 bubble production, cathodic pole 366– horizontal bipolar rotor, electric field 365– light emission 367–368– protons reduction coupled with HQ

oxidation 365– rotation of objects 366– synergetic reduction, H2O 369– translation motion induced, bubble

production 363–364– vertical rotor 365–366– zinc dendrites 370–371MS. See Mass spectrometry (MS)multiphase flow– biphasic liquid–liquid flow 142– bubbly/dispersed flow 143– gas–liquid reactions 142– liquid–liquid segmented flow 142–143– microreactors 142– Pd-catalyzed Mizoroki–Heck vinylation

143– water reactions 142Multiwall carbon nanotubes (MWCNTs) 359

nnanoparticle assemblies– aggregation/agglomeration 297–298– assembly/self-assembly 296–297– bubble deposition 313–314– catalysis/electrocatalysis 322– covalent molecular mediators 303–305– EISA 311–313– Langmuir-Blodgett deposition method

310–311– layer-by-layer deposition 308–310– linker-assisted syntheses 296– materials reinforcement 295– metamaterials 321– noncovalent vs. covalent interaction

305–306– noncovalent linker interactions and

self-assembly 299–300– plasmonics 314–319– pressure-driven assembly 314– super-spins/magnetic materials interaction

319–320– synthesis methods 298–314– synthesis pathways and applications

295–296– template assisted synthesis 306–307– water treatment/photodegradation

322–323Networked reactor system (NRS) 204nickel-based methodologies– aryl chlorides and bromides 278–279– biaryl side products 279–280– bromoarenes 278– bromobenzenes 278– halogen exchange, aryl iodides 279– HMPA 278NICS. See Nucleus independent chemical

shifts (NICS)Nitrophenyl-phosphates (NPPs) 9noncovalent linker interactions– electrostatic interactions 299–300– hydrogen bonding 300–301– hydrophobic and π-π stacking interactions

301–303NPPs. See Nitrophenyl-phosphates (NPPs)NRS. See Networked reactor system (NRS)NTPs. See Nucleoside triphosphates (NTPs)nucleophilic substitutions and additions– bimolecular (SN2) reaction 179–180– nucleophilic additions to arynes 180–181Nucleoside triphosphates (NTPs) 6–7Nucleus independent chemical shifts (NICS)

169

406 Index

ooccupation probability– advantages 96– characteristic damped oscillating behavior

100– cross-correlation functions (i≠j) 98– dephasing-assisted transport 97– donor and acceptor mix, delocalized states

99–100– excitation energy, incoherently and

irreversibly 99– Haken–Strobl model 96– intermediate coupling regime 96– phonon antenna concept 97– probability 98– simple molecular dimer, Heitler–London

approximation 97Orbitrap mass analyzers– axial motion frequencies, ion 73– configurations, high-resolution MS 73–74– ion trapping and periodic motion 72– parameters 72– signal stability 73– working principle 73–75organic cages– [2+3] cage synthesized, Doonan group

335–336– [4+6] and [2+3] cages, molecular structures

333, 335– applications 338– connolly surface area, N2 probe radius

332–334– Cooper research group 331–332– large cavity volumes, guest molecules 331– molecular packing motifs 331– molecular stick models, covalent cages

(CC1–CC10) 332– N2 sorption/desorption isotherms

333–334– salicylbisimine 333– simulation 336–338– solvent accessible surface area, N2 probe

radius 335organic molecules– Calix[n]arenes 330– crystal structure, 4TMSEBP 331– Cucurbit[n]urils 330– TPP 331Oxygen-bridged bissilylene 249– benzylzinc bromides and aryl halide

250–251– oxygen-bridged bis(silylene) nickel complex

7 250– synthesis 249

ppalladium-catalyzed aryl halide exchange

reactions– aromatic fluorination 282–288– aryl halides/pseudohalides 284– aryl triflates to aryl bromides 280–281– arylpalladium (II) complexes 282– C-halogen reductive elimination 280– C–F reductive elimination 283– C–H functionalization 282–283– electron-deficient aryl chlorides 280– electrophilic halogenating reagent 282– fluoroarene formation 281–282– late-stage fluorination 282–284– organometallic palladium complexes 284– potassium fluoride 281PDMS. See Polydimethylsiloxane (PDMS)

microchamberspericyclic reactions– 1,3-dipolar cycloaddition reactions

174–176– Alder-ene reactions 173–174– DGT 168–173– Diels–Alder reactions 176–179photocatalysis– cluster-support interactions 225– Keggin and Dawson anions 225– sunlight-driven POM 222–225– UV-light 221photochemistry– continuous-flow synthesis 148– FEP 149– glass microreactors 147– photochemical microreactors 147– photoredox catalysis 148photoluminescence 126photoreduction– CO2 activation 229–231– H2-generation 229Photovoltaics (PVs)– AM1.5 reference spectrum 115–116– and QE 126–127– bulk semiconductors 117–118– carrier dynamics 121– carrier multiplication 121– electron–hole pairs 116– lead chalcogenides 120–121– ligand exchange and film studies 130–133– photocurrent 117– photoluminescence 126– pump-probe 124–126– relaxation. See relaxation mechanisms– second generation devices 115– semiconductor quantum dots 118–120

Index 407

– Shockley–Queisser (S-Q) limit 116– single-junction silicon devices 115– thermodynamic efficiency calculation 116– third generation 115PIMs. See Polymers of intrinsic microporosity

(PIMs)Pincer-type bis(silylene) complexes– catalytic applications 252– C-H borylation, benzene 257, 260– chemical shift 255– chemical transformations 254– ECE vs. bis-silylene SiCSi pincer arene

complexes 254–255– iridium and rhodium complexes 257, 259– model compounds 257–258– molecular structure, bis(silylene) iridium

complex 257, 260– SiCSi ligand 26 synthesis 254–255– Silyl(silylene)palladium complex. See

Silyl(silylene)palladium complexplasmonics– ‘hot spots’ 315– plasmon resonance wave 315– plasmonic nanostructures 316– sensoric 317–318– signal amplification/SERS 318–319Polydiacetylene (PDA)– biological phosphate 15–20– colorimetric response (CR) 18– emission intensities 18– functionalized liposome (LP-11) 19– liposome chip to pyrophosphate 19–20– LPS 20–21– oligonucleotides and nucleic acids 21–23– polymeric system 15– receptor modified diacetylene monomers

17– structural and chromatic properties 15–16Polydimethylsiloxane (PDMS) microchambers

349Polymers of intrinsic microporosity (PIMs)– and molecular sensors 338– insoluble networks/soluble polymers 339– porous amorphous polymers structures

342Polyoxometalate ionic liquids (POM-ILs)– applications– bulky cations 231, 232– catalysis and materials science 233– conductivity mechanism 232– physicochemical properties 232– redox-active electrolytes 233– tetraalkylphosphonium cations 232

Polyoxometalates (POMs). See molecularmetal oxides

– ε-Keggin 202–203– 3D POMOF materials 202– applications, energy 221– aqueous acidic solutions 218– building block approach 201– condensation reaction 217–218– controlled-based oscillations 210–211– description 193– energy conversion 225–231– ionic liquids, catalysis and energy storage

231–234– isopolyoxometalate 217– lacunary polyoxotungstate clusters

218–219– molecular tubes and inorganic cells

208–210– novel templates 200–201– photocatalysis. See photocatalysis– photochemistry 219–220– photovoltaics. See photovoltaics– redox chemistry 219– SC–SC transformations 202– sunlight-driven. See sunlight-driven

POMPolypyrroles and bis(benzamidine) minor

groove binders– discovery, genetic origin 53– distamycin A with DNA 53– DNA recognition, polyamide hairpins

53–54– energy transfer 56– hairpin polyamides 55– pharmacological properties 55– slow kinetics 55– TMR 54Polytetrafluoroethylene (PTFE)– continuous-flow synthesis 148– microreactor solutions 138POM-ILs. See Polyoxometalate ionic liquids

(POM-ILs)porous amorphous molecular materials– BET surface areas 339–340– control and tuning 339– description 338– PIMs 339– scrambling reactions and freeze-drying. See

Scrambling reactions andfreeze-drying

porous keplerate nanocapsules– chemical adaptability 208– enzymatic reactions 207– internal ligands 207

408 Index

porous keplerate nanocapsules (contd.)– Keplerate-type nanospheres sizing 207– nanosponge capsules 208– plethora, structural motifs 208porous organic molecular crystals– organic cages. See Organic cages– organic molecules. See Organic moleculespump-probe experiments– CB and VB 125–126– on quantum dots 125– TA representation 124–125– technique 104– THz electric field 125PVs. See Photovoltaics (PVs)

qQE. See Quantum efficiency (QE)quantum coherence– 2DES methods 100–101– biological complexes 104– eigenstate description 101–102– Fenna-Matthews-Olson (FMO) complex

103– MEH-PPV, chloroform at room temperature

101– pump-probe anisotropy experiments 102– technological advances, spectroscopy 100– TTAD 102–103Quantum efficiency (QE)– CM threshold 126–127– electron–hole recombination 127– experimental considerations 129–130– TRPL data 128– yield 128–129

rreaction barriers– ASM 166–167– atom-economy 165– EDA 167–168– FMO 165– hard and soft acid and base (HSAB) theories

165– nucleophilic substitutions and additions

179–181– pericyclic reactions 168–179– reaction pathways 165– unimolecular processes 181–183relaxation mechanisms– Ec-dependent Auger relaxation 123–124– AR 121–122– biexciton decay component 126– direct band gap, AR 122– lead chalcogenides 123

– multiexciton decay dynamics 123– multiple excited carriers 121– nanocrystals 123– Poisson statistics 122–123– quantum dots 126

sSaccharomyces cerevisiae (yeast cells) 11scrambling reactions and freeze-drying– amorphous CC1 and CC3 synthesis

341–342– gas sorption analysis 340– HCPs, CMPs and PIMs 342–343– novel methods 340– OMIMs 343– simulation methodology 343– synthesis 340– topologies and sizes 342semiconductor quantum dots– Bohr radius 118– long-chain organic ligands 119–120– optical absorption spectrum 119– surface passivation 119shrink-wrapping effect– polyhedral representation 199– TEA/HTMA 199–200Silylenes– iron complexes 263–267– N-heterocyclic silylenes (NHSi’s) 243– stabilization 243–244– synthesis and catalytic applications

246–263– transition metal complexes 245–246Silylene iron complexes– π-back bonding donation 263– 29Si NMR chemical shifts 264– complexes 46 and 47 synthesis 263–264– Fe-hydrido complexes 267– hydrosilylation, ketones 265–266– N-donor coordination 263– NHSi transition 263– Si–Fe bond lengths 265– synthesis, complex 45 263–264Silyl(silylene)palladium complex 29, 255– molecular structure 256– synthesis 255–256SOD. See Superoxide dismutase (SOD)sunlight-driven POM– harvesting, metal substitution 223–224– structurally adaptive systems 222–223– visible-light photocatalysis 224–225Superoxide dismutase (SOD) 77Surface enhanced Raman Scattering (SERS)

318

Index 409

tTandem mass spectrometry– ECD 79– electronic subsystems, molecular functional

group 81– ion activation and dissociation methods 79– IRMPD 81– molecular structure analysis 79TEA. See Triethanolamine (TEA)template assisted synthesis 306–307Tetramethyl rhodamine (TMR) 54Tetramethyl rhodamine (TMR),

2.1075–1078TFs. See Transcription factors (TFs)TMR. See Tetramethyl rhodamine (TMR)Transcription factors (TFs)– biochemical interaction 33– cellular genome 34– chemical strategies 42– conjugation, DNA binding peptides 45–46– DNA binding domains. See DNA binding

domains– gene expression 33– high-affinity sequence-specific complex

41–42– protein folding 42– proteins vs. nucleic acids 40–41– recognition process 35– residue grafting 44–45– structure, nucleobases 34– synthetic modification, bZIP 43–44– thermodynamic factors 41Triethanolamine (TEA) 199–200Two-dimensional photon echo (2DPE)– advantages 105– coherent mechanisms 108– contour plot, spectra amplitude 109– cross-peaks 106–107– cryptophytes 106– electronic absorption spectrum, PC645

106–107– experimental 2DPE spectra, MEH-PPV

108–109– frequency-resolved pump-probe

spectroscopy 105

– intrachain energy transfer, two adjacentsites 108

– light-matter interactions 105– local oscillator (LO) 104–105– nuclear coherences 109– PC645 antenna protein determination

106–107– pump-probe technique 104– spectrum for PC645 recorded 106–107– vibrational modes 110

uUltra-high-performance liquid

chromatography (UHPLC) 82

vVesicles, bioanalytes– biomolecular sensing 14– cell membrane 14– fluorescence based 14– PDA based chromatic vesicles 15–23

wwater oxidation– Dawson anions, ionic liquids 227–228– polyoxoniobate water splitting 227– POM-WOCs stability 228– Ru-and Co-polyoxometalates 226–227water splitting 225water treatment/photodegradation 322–323Watson–Crick model 32Wide-angle X-ray scattering (WAXS) 343

xxanthene type chemosensor 1 7XO3 and XO6 templated POMs 200– ball-and-stick representations 200–201– polyhedral representation 201–202– polyoxotungstate chemistry 201– pyramidal geometry 200

zZinc finger proteins (ZFPs) 37–39