Resonance Energy Transfer

by Andrews, David L.; Demidov, Andrey A.

• ISBN13: 9780471987321
• ISBN10: 0471987328
• Edition: 1st
• Format: Hardcover
• Copyright: 1999-05-04
• Publisher: WILEY

Summary

Resonance Energy Transfer The resonance transfer of energy between molecules, or between sites within a large molecule, plays a central role in many areas of modern chemistry and physics. In biophysics, for example, this process defines the migration of excitation energy within photosynthetic systems (commonly the Frster mechanism). Another important area is in crystals, laser and other laser materials. Resonance Energy Transfer contains a large amount of cutting-edge research which has never before appeared in book form. It is the first comprehensive modern survey of the field, offering a broad, yet detailed view of the mechanisms of energy transfer. The broad range of applications of fluorescence and fluorescence energy transfer to studies in molecular biology and biotechnology ensures that resonance energy transfer will be a vital component of the new science and technology of the next millenium. This book is written for those working with materials, both experimentally and theoretically, as well as for biophysicists and biochemists interested in studying protein structure and dynamics. ISBN 0 471 987328 (Cloth) Foreword supplied by Professor Graham Fleming FRS, University of California, Berkeley, USA. Cover shows the Peripheral Light Harvesting Complex (LH2) of Rps.acidophila kindly supplied by Dr. Stephen M. Prince, University of Glasgow, UK.

Author Biography

David L. Andrews, School of Chemical Sciences, University of East Anglia, GB. Highly respected and has made major interesting contributions in the field. His works are very deep and illuminating. Professor Andrews has also published in condensed matter QED, though not to the same extent. One of his books has gone to a third edition, and another has been reprinted.

Table of Contents

Contributors	xvii
Preface	xxiii
Naturally Occurring Aminophosphonic and Aminophosphinic Acids	1	(32)
Przemyslaw Mastalerz
Pawel Kafarski
2-Aminoethanephosphonic acid (AEP, ciliatane)	2	(6)
Phosphonates metabolically related to 2-aminoethanephosphonic acid	8	(1)
Aminophosphonate antibiotics and related compounds	9	(1)
Antibiotic phosphonopeptides	10	(5)
Biosynthesis of the P--C bond	15	(2)
Biosynthesis of 2-aminoethanephosphonic acid and its N-methylated derivatives	17	(1)
Biosynthesis of bialaphos	18	(1)
Biodegradation of organophosphonates	18	(4)
The origin of aminophosphonates in nature	22	(1)
References	23	(10)
Synthesis of α-Aminoalkanephosphonic and α-Aminoalkanephosphinic Acids	33	(42)
Pawel Kafarski
Jerzy Zon
Aldehydes and ketones as substrates for the preparation of aminophosphonates	34	(16)
Amidolkylation of trivalent phosphorus compounds	34	(3)
Mannich-type condensation of amines with aldehydes and phosphorous or hypophosphorous acid	37	(1)
Kabachnik-Fields reaction	38	(3)
Hydrophosphonylation of imines	41	(3)
Hydrophosphonylation of other C=N bonds	44	(2)
Hydrophosphonylation of triazines	46	(1)
Hydrophosphonylation of aldehydes-hydroxyalkanephosphonates as substrates for the preparation of 1-aminoalkanephosphonates	47	(3)
Carboxylic acids as substrates for the synthesis of 1-aminoalkanephosphonic acids	50	(5)
1-Oxoalkanephosphonates as substrates	50	(3)
Phosphonoacetates as substrates	53	(1)
Replacement of amino acid carboxylic moieties by phosphonic groups	54	(1)
Nitriles as substrates	55	(1)
Phosphonylation of halogenoalkylamines and related compounds	56	(3)
Amination of alkanephosphonates and functionalized alkanephosphonates	59	(2)
Nucleophilic amination	59	(1)
Electrophilic amination	60	(1)
Alkylation of derivatives of dialkyl aminomethanephosphonates	61	(3)
Alkylation of Schiff bases	61	(1)
Alkylation of other derivatives of aminomethanephosphonic acid	62	(2)
Hydrogenation of N-acyl-α, β-dehydroaminophosphonates	64	(1)
Other methods	64	(3)
Hydrolytic cleavage of carbon-phosphorus bond	67	(1)
References	67	(8)
Synthesis of Aminoalkanephosphonic and Aminoalkanephosphinic Acids with the Amino Substituent in other than the α-Position	75	(28)
Valery P. Kukhar
Synthesis of ω-aminophosphonates by addition of amines to unsaturated phosphonates	76	(2)
Introduction of the amino function by ketophosphonate transformation	78	(4)
Formation of the amino function in phosphonates by reduction of nitrogen-containing groups	82	(1)
Syntheses of aminophosphonates by the Arbuzov and Michaelis--Becker reactions	83	(2)
Synthesis of aminoalkanephosphonic acids by Curtius and Hofmann rearrangements	85	(1)
Syntheses of aminophosphonates by the carbanion approach	86	(2)
Miscellaneous reactions leading to aminophosphonates	88	(4)
Arenephosphonic acids containing an amino function in the ring	92	(2)
Nitrogen heterocycles with a phosphonic (or phosphinic) acid residue	94	(5)
References	99	(4)
α-Amino Acid Analogues Bearing Side-Chain C-P Linkages	103	(24)
Sharon Lall
Robert Engel
Introduction	103	(1)
Syntheses and biological significance	104	(1)
Analogues of biological α-amino acids	104	(11)
Structures of interest	104	(2)
Syntheses of analogues of phosphinothricin	106	(3)
Other potentially useful analogues of phosphinothricin	109	(1)
Analogues of glutamic and aspartic acid--structure	110	(1)
Analogues of glutamic and aspartic acid--syntheses and biology	110	(5)
Analogues of amino acid phosphate esters	115	(4)
Biology and structure	115	(1)
Analogues of amino acid phosphate esters--synthesis	116	(3)
Other α-amino acids containing a C-P bond in the side-chain	119	(1)
Analogues of phosphatidylserine	120	(1)
Consideration for future studies	121	(1)
References	122	(5)
Asymmetric Synthesis of Aminophosphonic and Aminophosphinic Acids	127	(46)
Valery P. Kukhar
Enantioselective C--C Bond forming reactions	128	(15)
Chiral `glycine' synthons--chirality in the nitrogen residue	128	(9)
Chiral `glycine' synthons--chirality in the phosphorus residue	137	(2)
Catalyzed C--C bond formation reaction leading to chiral aminophosphonates	139	(1)
Miscellaneous C--C bond formation reactions leading to chiral aminophosphonates	140	(3)
Enantioselective C--P bond forming reactions	143	(11)
Addition of hydrophosphonyl compounds to imines	143	(5)
Three-component Kabachnik--Fields reaction	148	(3)
Catalytic addition of hydrophosphonyl compounds to C=N bonds	151	(1)
Miscellaneous reactions for stereoselective C--P bond formation	152	(2)
Stereoselective C--N bond formation	154	(10)
Steroselective C--H bond forming reactions	164	(3)
Conclusions	167	(1)
References	168	(5)
Synthesis of Phosphono-and Phosphinopeptides	173	(32)
Pawel Kafarski
Barbara Lejcczak
Protection of the amino group	174	(2)
Protection of the phosphonic moiety	176	(2)
Synthesis of phosphono-and phosphinopeptides containing P-terminal aminophosphonate	178	(5)
Preparation of diastereomeric phosphonodipeptides containing P-terminal aminophosphonate	183	(1)
Phosphonodepsipeptides containing P-terminal hydroxyphosphonate	183	(1)
Peptides containing a phosphonic or phosphinic moiety in the side-chain	184	(3)
Peptides containing a phosphonamide or phosphinamide bond	187	(4)
Phosphonodepsipeptides containing a phosphonoester moiety	191	(2)
Phosphinopeptide nucleic acids	193	(1)
Phosphinopeptides in which a phosphinic acid replaces a dipeptidyl fragment of the peptide chain	194	(2)
Peptides in which a PH2 group replaces the NH2 moiety	196	(1)
References	196	(9)
Column Chromatography of Aminophosphonic Acids and Phosphonopeptides	205	(12)
S. V. Galushko
Introduction	205	(1)
Separation of phosphonopeptides using column liquid chromatography	206	(1)
Chiral recognition of aminophosphonic acids	207	(6)
Derivatization of aminophosphonic acids for HPLC analysis	213	(1)
Derivatization of aminophosphonic acids for gas chromatographic analysis	214	(1)
Optimization and problem solving	215	(1)
References	215	(2)
Physical Properties and NMR-Spectroscopic Characterization of Aminophosphonates and Aminophosphinates	217	(68)
Gerhard Hagele
Introduction	217	(2)
The 1H-NMR spectrum of α-N-phenylamino-α-phenylmethanephosphonic acid diethyl ester	219	(14)
The aromatic region	219	(3)
The-CHP-NH-skeleton	222	(1)
The alkoxy region	223	(3)
Aromatic ring current effects and molecular structure	226	(7)
1H-, 19F-and 31 P-NMR spectra of aromatic substitutents Ar1 and Ar2 and related fragments in α-N-arylamino-α-arylmethanephosphonic acid diethyl esters	233	(1)
Increasing complexity by sterically demanding aromatic substituents in Ar1 or Ar2	234	(8)
The 1-naphthyl group attached to the CHP unit	234	(3)
The 2-naphthyl group attached to the CHP unit	237	(2)
The 9-anthryl group attached to the CHP unit	239	(1)
The 1-naphthyl group attached to the NH unit	240	(2)
Sterically overcrowded aminophosphonates	242	(4)
Variations of 1H-NMR spectra from-CHP-NH-fragments with substituent pattern, temperature, solvent and protonation	246	(14)
α-N-(4-fluorophenyl)amino-α-phenylmethanephosphonic acid diethyl ester	246	(5)
Classification of-CHP-NH-spectra	251	(1)
Attempts to interpret the results	251	(2)
Conformational analysis of α-N-(4-trifluoromethylphenyl)amino-α-phenylmethanephosphonic acid diethyl ester	253	(6)
Bulky aromatic substituents in Ar1 and Ar2	259	(1)
Heterocyclic aminophosphonates	260	(2)
Aromatic ring current effects in an isomeric pair of naphthyl-substituted aminophosphonates	262	(3)
Bifunctional aminophosphonates	265	(4)
Structural considerations	265	(1)
The CHP-skeleton of bifunctional aminophosphonates	265	(2)
The P(O) (OCH3)2 groups from bifunctional aminophosphonates	267	(2)
Aminophosphinates	269	(7)
Solid state and molecular modelling of P-[α-N-(4-fluorophenyl)-amino-α-phenylmethyl]-P-(methyl) phosphinic acid n-butyl ester (2.1-D1)	271	(3)
The 1H-NMR spectrum of P-[α-N-(4-fluorophenyl) amino-α-phenyl-methyl]-P-(methyl)phosphinic acid n-butyl ester (2.1-D1)	274	(2)
Some comments on phosphonic and phosphinic acids	276	(4)
References	280	(5)
Structure and Stability Constants of Metal Complexes in Solution	285	(42)
Tamas Kiss
Istvan Lazar
Introduction	285	(1)
Phosphonic derivatives of amino acids and related compounds	286	(11)
Acid-base chemistry	286	(1)
Metal-binding capabilities	287	(10)
Phosphono derivatives of dipeptides	297	(1)
Open-chain aminopolyphosphonates	298	(8)
Macrocyclic aminophosphonates and aminophosphinates	306	(15)
Acid-base chemistry	309	(3)
Metal complex formation	312	(5)
Biomedical applications	317	(1)
MRI contrast enhancement materials	317	(2)
Diagnostic use of fluorescent complexes	319	(1)
Paramagnetic complexes as shift reagents	320	(1)
Determination of intracellular metal ion concentration	320	(1)
Radioimmunoassay techniques	320	(1)
Determination of pH	321	(1)
Acknowledgements	321	(1)
References	321	(6)
X-Ray Crystallographic Studies	327	(36)
Nick Choi
Mary McPartlin
Introduction	327	(18)
Mono(aminophosphonic) and mono (aminophosphinic) acids	345	(4)
N-Acylated aminophosphonic and aminophosphinic acids	349	(2)
Diphosphonic and diphosphinic acids	351	(1)
Triphosphonic acids	351	(1)
Tetraphosphonic and tetraphosphinic acids	352	(7)
References	359	(4)
Mass Spectrometry and Gas Chromatography-Mass Spectrometry of Aminoalkanephosphonic Acids	363	(44)
Zbigniew H. Kudzin
M. Sochaki
Introduction	363	(1)
Derivatization of aminophosphonic acids and related compounds for GC and GC/MS	364	(8)
Mass spectrometric characterization of derivatized aminoalkanephosphonic acids and related copounds	372	(13)
Mass spectrometric characterization of O,O-substituted aminoalkanephosphonic acids	372	(1)
Mass spectrometric characterization of TMS-derivatives of aminoalkanephosphonates	372	(2)
Mass spectrometric characterization of O,O-dialkyl derivatives of aminoalkanephosphonates	374	(2)
Mass spectrometric characterization of O,O-dialkyl 1-(N-acylamino)-alkanephosphonates	376	(1)
Mass spectrometric characterization of O,O-dialkyl 1-(N-formylamino)-alkanephosphonates	377	(2)
Mass spectrometric characterization of O,O-dialkyl 1-(N-acetylamino)-alkanephosphonates	379	(1)
Mass Spectrometic Characterization of O,O-Dialkyl 1-(N-trifluoroacetylamino)-alkanephosphonates	379	(3)
Mass spectrometric characterization of other types of N-acylaminoalkanephosphonates	382	(1)
Chemical ionization mass spectrometry of O,O-dialkyl 1-(N-acylamino)alkanephosphonates	382	(3)
Mass spectrometric characterization of underivatized aminoalkanephosphonic acids, partly protected aminoalkanephosphonic acids and related derivatives	385	(10)
Mass spectra of underivatized aminoalkanephosphonic acids	385	(1)
Chemical ionization mass spectra of aminoalkanephosphonic acids	385	(3)
Fast atom bombardment mass spectra of amino-and guanidino-alkanephosphonic acids	388	(2)
Mass spectra of N-acylaminoalkanephosphonic acids	390	(5)
Mass spectrometric characterization of phosphonopetides	395	(9)
EI mass spectra of protected phosphonopeptides	397	(2)
FAB mass spectra of protected phosphonopeptides	399	(2)
FAB mass spectra of unprotected phosphonopeptides	401	(3)
References	404	(3)
The Biological Activity of Phosphono-and Phosphinopeptides	407	(36)
Pawel Kafarski
Barbara Lejczak
Antibacterial phosphonopeptides	408	(3)
Inhibition of proteases	411	(16)
Inhibitors of serine proteases	412	(5)
Inhibitors of metalloproteases	417	(8)
Inhibitors of aspartic proteases	425	(1)
Inhibitors of cysteine proteases	426	(1)
Inhibitors of β-lactamase	427	(1)
Inhibitors of ligases	427	(1)
Inhibitors of phosphotyrosyl-dependent signal transduction	428	(3)
Analogues of methotrexate	431	(3)
Other actvities	434	(1)
Catalytic antibodies (abzymes)	434	(1)
References	435	(8)
Aminophosphonic and Aminophosphinic Acids and their Derivatives as Agrochemicals	443	(40)
Harry R. Hudson
Introduction	443	(1)
Commercially available agrochemicals and their analogues	444	(10)
Glyphosate	445	(4)
Glufosinate and Bilanafos	449	(5)
Related Aminocarbonylphosphonic Acids	454	(1)
Biologically active aminophosphonic and aminophosphinic acids as candidate agrochemicals	454	(20)
Introduction	454	(1)
Plant-growth Regulators and Herbicides	455	(1)
Aminoalkane-phosphonic and-phosphinic acids	455	(3)
Aminocycloalkyl-phosphonic acids and-phosphine oxides	458	(1)
N-Arylaminoalkyl-phosphonates,-phosphinates, and-phosphine oxides	458	(1)
Amino(aryl)alkyl-phosphonic and-phosphinic acids	459	(2)
Phosphono-and phosphinopeptides	461	(1)
N-Phosphonoacetylamines, guanidino derivatives, and isoxazole-substituted aminoethylphosphonates	462	(1)
Aminomethylenebisphosphonic acids	463	(2)
Fungicides	465	(1)
Introduction	465	(1)
N-(ω-Guanidinoalkyl)-and N-(ω-aminoalkyl)-aminoalkane-phosphonic and-phosphinic acids	466	(1)
Aminoalkane-phosphonic and-phosphinic acids	467	(2)
Amino(aryl)alkyl-phosphonic and-phosphinic acids	469	(1)
Phosphonopeptides	470	(1)
Insecticides and related compounds	471	(1)
Summary and Prospects	472	(2)
Acknowledgement	474	(1)
References	474	(9)
Neuroactive Aminophosphinic and Aminophosphinic Acid Derivatives	483	(54)
David Jane
Introduction	483	(1)
Ionotropic glutamate receptors	484	(21)
Introduction	484	(2)
The NMDA receptor complex	486	(1)
NMDA receptor subtypes	487	(1)
NMDA recepter agonists	488	(2)
Competitive NMDA receptor antagonists	490	(4)
Radioligands for the glutamate recognition site of the NMDA receptor	494	(1)
Molecular modelling studies	494	(1)
Subtype selectivity of competitive NMDA receptor antagonists	495	(1)
Antagonists binding to the glycine co-agonist site of the NMDA receptor	496	(1)
Therapeutic applications of NMDA receptor antagonists	497	(1)
AMPA and kainate receptors	498	(3)
AMPA and kainate receptor agonists	501	(1)
AMPA and kainate receptor antagonists	501	(3)
Therapeutic utility of AMPA and kainate antagonists	504	(1)
Metabotropic glutamate receptors	505	(11)
Introduction	505	(3)
Group I selective agonists and antagonists	508	(2)
Group II selective agonists and antagonists	510	(1)
Group III selective agonists and antagonists	511	(4)
The QUIS effect	515	(1)
Phospholipase D coupled mGlu receptors	516	(1)
Therapeutic utility of mGlu receptor agonists and antagonists	516	(1)
Gaba receptor pharmacology	516	(9)
Introduction	516	(1)
GABAB receptor agonists and antagonists	517	(4)
GABAC receptor agonists and antagonists	521	(2)
GABA uptake inhibitors	523	(1)
Antagonists of the strychnine-sensitive glycine receptor	524	(1)
Concluding remarks	525	(1)
Acknowledgements	525	(1)
References	526	(11)
Aminophosphonic and Aminophosphinic Acid Derivatives in the Design of Transition State Analogue Inhibitors: Biomedical Opportunities and Limitations	537	(22)
Jozef Oleksyszyn
Proteolytic Enzymes: classification, mechanism of the proteolysis and implication for the design of transition analogue inhibitors	539	(2)
Drug development	541	(3)
Proteolytic enzymes as targets for drug design	544	(2)
Serine proteinases as targets for drug design. Biomedical opportunities for derivatives of α-aminoalkylphosphonic acid diphenyl esters	546	(3)
Human neutrophil elastase (HNE)	549	(1)
Dipeptidyl peptidase IV (DPP IV/D26)	550	(2)
Human heart chymase	552	(1)
Human cytomegalovirus protease	553	(1)
Granzymes	553	(2)
Proteolytic enzymes from larvae of the fire ant, Solenopsis invicta	555	(1)
References	556	(3)
Aminophosphonic and Aminophosphinic Acids in the Design and Synthesis of HIV Protease Inhibitors	559	(20)
Anusch Peyman
Introduction	559	(2)
Linear Inhibitors of HIV protease	561	(4)
C2-Symmetric Inhibitors of HIV protease	565	(8)
Non-peptide inhibitors of HIV protease	573	(2)
Conclusions	575	(1)
References	575	(4)
Aminophosphonic Acid Derivatives as Antithrombotic Agents	579	(18)
Donovan St. C. Green
Emmanuel Skordalakes
Michael F. Scully
John J. Deadman
Introduction	579	(2)
Studies of the Mechanism of Inhibition of Thrombin by Peptidylphosphonates	581	(2)
Routes to Dialkyl and Diaryl α-Aminophosphonates as Precursors for Thrombin Inhibitors	583	(1)
Tripeptidylphosphonates as Thrombin Inhibitors	584	(2)
Determination of Ki and Mechanism of Inhibition of Thrombin	586	(1)
Kinetics of the Slow Binding Phase (k2, k-2, and ki,) of Thrombin Inhibition by Z-Dpa-Pro-MpgP (OPH)2	586	(1)
Fitting generated values for A0 (initial absorbance), Vo (initial velocity), and Vs (final steady state velocity)	587	(2)
Specificity of Z-Dpa-Pro-MpgP (OPh)2 for Thrombin	589	(1)
Analysis of the Interaction of Z-D-Dpa-Pro-MpgP (OPh)2 with Human Thrombin by Crystallography	590	(2)
O,O-Dialkyl Dipeptidyl-ψ-(carboxy) benzylphosphonates as Novel Thrombin Inhibitors	592	(2)
Conclusions	594	(1)
References	594	(3)
Aminophosphonic and Aminophosphinic Acid Derivatives as Inhibitors of Human Collagenase	597	(24)
Roger Markwell
Human collagenase (MMP-1) and the matrix metalloproteinase (MMP) family	597	(1)
Potential therapeutic indications for MMP inhibitors	598	(1)
Structural characterisation of the MMP's	598	(1)
Design of collagenase inhibitors	599	(1)
Aminophosphonic acid derivatives as collagenase inhibitors	600	(6)
Proposed binding of an aminophosphonic acid inhibitor to collagenase (MMP-1)	606	(3)
Aminophosphinic acid derivatives as collagenase inhibitors	609	(6)
Comparison of aminophosphonic acid based inhibitors with other structural types	615	(2)
References	617	(4)
Index	621