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