The hydrogen bond is the most important of all directional intermolecular interactions. It is operative in determining molecular conformation, molecular aggregation, and the function of a vast number of chemical systems ranging from inorganic to biological. Research into hydrogen bonds experienced a stagnant period in the 1980s, but re-opened around 1990, and has been in rapid development since then. In terms of modern concepts, the hydrogen bond is understood as a very broad phenomenon, and it is accepted that there are open borders to other effects. There are dozens of different types of X-H.A hydrogen bonds that occur commonly in the condensed phases, and in addition there are innumerable less common ones. Dissociation energies span more than two orders of magnitude (about 0.2-40 kcal mol(-1)). Within this range, the nature of the interaction is not constant, but its electrostatic, covalent, and dispersion contributions vary in their relative weights. The hydrogen bond has broad transition regions that merge continuously with the covalent bond, the van der Waals interaction, the ionic interaction, and also the cation-pi interaction. All hydrogen bonds can be considered as incipient proton transfer reactions, and for strong hydrogen bonds, this reaction can be in a very advanced state. In this review, a coherent survey is given on all these matters.

The hydrogen bond in the solid state.

Relationships between the carbon-oxygen stretching frequencies of carboxylato complexes and the type of carboxylate coordination

The vibrational spectrum of a molecule is considered to be a unique physical property and is characteristic of the molecule. As such, the infrared spectrum can be used as a fingerprint for identification by the comparison of the spectrum from an “unknown” with previously recorded reference spectra. This is the basis of computer-based spectral searching. In the absence of a suitable reference database, it is possible to effect a basic interpretation of the spectrum from first principles, leading to characterization, and possibly even identification of an unknown sample. This first principles approach is based on the fact that structural features of the molecule, whether they are the backbone of the molecule or the functional groups attached to the molecule, produce characteristic and reproducible absorptions in the spectrum. This information can indicate whether there is backbone to the structure and, if so, whether the backbone consists of linear or branched chains. Next it is possible to determine if there is unsaturation and/or aromatic rings in the structure. Finally, it is possible to deduce whether specific functional groups are present. If detected, one is also able to determine local orientation of the group and its local environment and/or location in the structure. The origins of the sample, its prehistory, and the manner in which the sample is handled all have impact on the final result. Basic rules of interpretation exist and, if followed, a simple, first-pass interpretation leading to material characterization is possible. This article addresses these issues in a simple, logical fashion. Practical examples are included to help guide the reader through the basic concepts of infrared spectral interpretation.

/pdf/interpretation-of-infrared-spectra-a-practical-approach-5ewm5vzugi.pdf

Interpretation of Infrared Spectra, A Practical Approach

Series Preface.Preface.Acronyms, Abbreviations and Symbols.About the Author.1. Introduction.1.1 Electromagnetic Radiation.1.2 Infrared Absorptions.1.3 Normal Modes of Vibration.1.4 Complicating Factors.1.4.1 Overtone and Combination Bands.1.4.2 Fermi Resonance.1.4.3 Coupling.1.4.4 Vibration-Rotation Bands.References.2. Experimental Methods.2.1 Introduction.2.2 Dispersive Infrared Spectrometers.2.3 Fourier-Transform Infrared Spectrometers.2.3.1 Michelson Interferometers.2.3.2 Sources and Detectors.2.3.3 Fourier-Transformation.2.3.4 Moving Mirrors.2.3.5 Signal-Averaging.2.3.6 Advantages.2.3.7 Computers.2.3.8 Spectra.2.4 Transmission Methods.2.4.1 Liquids and Solutions.2.4.2 Solids.2.4.3 Gases.2.4.4 Pathlength Calibration.2.5 Reflectance Methods.2.5.1 Attenuated Total Reflectance Spectroscopy.2.5.2 Specular Reflectance Spectroscopy.2.5.3 Diffuse Reflectance Spectroscopy.2.5.4 Photoacoustic Spectroscopy.2.6 Microsampling Methods.2.7 Chromatography-Infrared Spectroscopy.2.8 Thermal Analysis-Infrared Spectroscopy.2.9 Other Techniques.References.3. Spectral Analysis.3.1 Introduction.3.2 Group Frequencies.3.2.1 Mid-Infrared Region.3.2.2 Near-Infrared Region.3.2.3 Far-Infrared Region.3.3 Identification.3.4 Hydrogen Bonding.3.5 Spectrum Manipulation.3.5.1 Baseline Correction.3.5.2 Smoothing.3.5.3 Difference Spectra.3.5.4 Derivatives.3.5.5 Deconvolution.3.5.6 Curve-Fitting.3.6 Concentration.3.7 Simple Quantitative Analysis.3.7.1 Analysis of Liquid Samples.3.7.2 Analysis of Solid Samples.3.8 Multi-Component Analysis.3.9 Calibration Methods.References.4. Organic Molecules.4.1 Introduction.4.2 Aliphatic Hydrocarbons.4.3 Aromatic Compounds.4.4 Oxygen-Containing Compounds.4.4.1 Alcohols and Phenols.4.4.2 Ethers.4.4.3 Aldehydes and Ketones.4.4.4 Esters.4.4.5 Carboxylic Acids and Anhydrides.4.5 Nitrogen-Containing Compounds.4.5.1 Amines.4.5.2 Amides.4.6 Halogen-Containing Compounds.4.7 Heterocyclic Compounds.4.8 Boron Compounds.4.9 Silicon Compounds.4.10 Phosphorus Compounds.4.11 Sulfur Compounds.4.12 Near-Infrared Spectra.4.13 Identification.References.5. Inorganic Molecules.5.1 Introduction.5.2 General Considerations.5.3 Normal Modes of Vibration.5.4 Coordination Compounds.5.5 Isomerism.5.6 Metal Carbonyls.5.7 Organometallic Compounds.5.8 Minerals.References.6. Polymers.6.1 Introduction.6.2 Identification.6.3 Polymerization.6.4 Structure.6.5 Surfaces.6.6 Degradation.References.7. Biological Applications.7.1 Introduction.7.2 Lipids.7.3 Proteins and Peptides.7.4 Nucleic Acids.7.5 Disease Diagnosis.7.6 Microbial Cells.7.7 Plants.7.8 Clinical Chemistry.References.8. Industrial and Environmental Applications.8.1 Introduction.8.2 Pharmaceutical Applications.8.3 Food Science.8.4 Agricultural Applications.8.5 Pulp and Paper Industries.8.6 Paint Industry.8.7 Environmental Applications.References.Responses to Self-Assessment Questions.Bibliography.Glossary of Terms.SI Units and Physical Constants.Periodic Table.Index.

Infrared Spectroscopy: Fundamentals and Applications

IA Basic Concepts.- 1 The Importance of Hydrogen Bonds.- 1.1 Historical Perspective.- 1.2 The Importance of Hydrogen Bonds in Biological Structure and Function.- 1.3 The Role of the Water Molecules.- 1.4 Significance of Small Molecule Crystal Structural Studies.- 1.5 The Structural Approach.- 2 Definitions and Concepts.- 2.1 Definition of the Hydrogen Bond - Strong and Weak Bonds.- 2.2 Hydrogen-Bond Configurations: Two- and Three-Center Hydrogen Bonds Bifurcated and Tandem Bonds.- 2.3 Hydrogen Bonds Are Very Different from Covalent Bonds.- 2.4 The van der Waals Radii Cut-Off Criterion Is Not Useful.- 2.5 The Concept of the Hydrogen-Bond Structure.- 2.6 The Importance of ? and ? Cooperativity.- 2.7 Homo-, Anti- and Heterodromic Patterns.- 2.8 Hydrogen Bond Flip-Flop Disorder: Conformational and Configurational.- 2.9 Proton-Deficient Hydrogen Bonds.- 2.10 The Excluded Region.- 2.11 The Hydrophobic Effect.- 3 Experimental Studies of Hydrogen Bonding.- 3.1 Infrared Spectroscopy and Gas Electron Diffraction.- 3.2 X-Ray and Neutron Crystal Structure Analysis.- 3.3 Treatment of Hydrogen Atoms in Neutron Diffraction Studies.- 3.4 Charge Density and Hydrogen-Bond Energies.- 3.5 Neutron Powder Diffraction.- 3.6 Solid State NMR Spectroscopy.- 4 Theoretical Calculations of Hydrogen-Bond Geometries.- 4.1 Calculating Hydrogen-Bond Geometries.- 4.2 Ab-Initio Molecular Orbital Methods.- 4.3 Application to Hydrogen-Bonded Complexes.- 4.4 Semi-Empirical Molecular Orbital Methods.- 4.5 Empirical Force Field or Molecular Mechanics Methods.- 5 Effect of Hydrogen Bonding on Molecular Structure.- IB Hydrogen-Bond Geometry.- 6 The Importance of Small Molecule Structural Studies.- 6.1 Problems Associated with the Hydrogen-Bond Geometry.- 6.2 The Hydrogen Bond Can Be Described Statistically.- 6.3 The Problems of Measuring Hydrogen-Bond Lengths and Angles in Small Molecule Crystal Structures.- 7 Metrical Aspects of Two-Center Hydrogen Bonds.- 7.1 The Metrical Properties of O-H *** O Hydrogen Bonds.- 7.1.1 Very Strong and Strong OH *** O Hydrogen Bonds Occur with Oxyanions, Acid Salts, Acid Hydrates, and Carboxylic Acids.- 7.1.2 OH *** O Hydrogen Bonds in the Ices and High Hydrates.- 7.1.3 Carbohydrates Provide the Best Data for OH ... O Hydrogen Bonds: Evidence for the Cooperative Effect.- 7.2 N-H *** O Hydrogen Bonds.- 7.3 N-H *** N Hydrogen Bonds.- 7.4 O-H *** N Hydrogen Bonds.- 7.5 Sequences in Lengths of Two-Center Hydrogen Bonds.- 7.6 H/D Isotope Effect.- 8 Metrical Aspects of Three- and Four-Center Hydrogen Bonds.- 8.1 Three-Center Hydrogen Bonds.- 8.2 Four-Center Hydrogen Bonds.- 9 Intramolecular Hydrogen Bonds.- 10 Weak Hydrogen-Bonding Interactions Formed by C-H Groups as Donors and Aromatic Rings as Acceptors.- 11 Halides and Halogen Atoms as Hydrogen-Bond Acceptors.- 12 Hydrogen-Bond Acceptor Geometries.- II Hydrogen Bonding in Small Biological Molecules.- 13 Hydrogen Bonding in Carbohydrates.- 13.1 Sugar Alcohols (Alditols) as Model Cooperative Hydrogen-Bonded Structures.- 13.2 Influence of Hydrogen Bonding on Configuration and Conformation in Cyclic Monosaccharides.- 13.3 Rules to Describe Hydrogen-Bonding Patterns in Monosaccharides.- 13.4 The Water Molecules Link Hydrogen-Bond Chains into Nets in the Hydrated Monosaccharide Crystal Structures.- 13.5 The Disaccharide Crystal Structures Provide an Important Source of Data About Hydrogen-Bonding Patterns in Polysaccharides.- 13.6 Hydrogen Bonding in the Tri- and Tetrasaccharides Is More Complex and Less Well Defined.- 13.7 The Hydrogen Bonding in Polysaccharide Fiber Structures Is Poorly Defined.- 14 Hydrogen Bonding in Amino Acids and Peptides: Predominance of Zwitterions.- 15 Purines and Pyrimidines.- 15.1 Bases Are Planar and Each Contains Several Different Hydrogen-Bonding Donor and Acceptor Groups.- 15.2 Many Tautomeric Forms Are Feasible But Not Observed.- 15.3 ?-Bond Cooperativity Enhances Hydrogen-Bonding Forces.- 15.4 General, Non-Base-Pairing Hydrogen Bonds.- 16 Base Pairing in the Purine and Pyrimidine Crystal Structures.- 16.1 Base-Pair Configurations with Purine and Pyrimidine Homo-Association.- 16.2 Base-Pair Configurations with Purine-Pyrimidine Hetero-Association: the Watson-Crick Base-Pairs.- 16.3 Base Pairs Can Combine to Form Triplets and Quadruplets.- 17 Hydrogen Bonding in the Crystal Structures of the Nucleosides and Nucleotides.- 17.1 Conformational and Hydrogen-Bonding Characteristics of the Nucleosides and Nucleotides.- 17.2 A Selection of Cyclic Hydrogen-Bonding Patterns Formed in Nucleoside and Nucleotide Crystal Structures.- 17.3 General Hydrogen-Bonding Patterns in Nucleoside and Nucleotide Crystal Structures.- III Hydrogen Bonding in Biological Macromolecules.- 18 O-H *** O Hydrogen Bonding in Crystal Structures of Cyclic and Linear Oligoamyloses: Cyclodextrins, Maltotriose, and Maltohexaose.- 18.1 The Cyclodextrins and Their Inclusion Complexes.- 18.2 Crystal Packing Patterns of Cyclodextrins Are Determined by Hydrogen Bonding.- 18.3 Cyclodextrins as Model Compounds to Study Hydrogen-Bonding Networks.- 18.4 Cooperative, Homodromic, and Antidromic Hydrogen-Bonding Patterns in the ?-Cyclodextrin Hydrates.- 18.5 Homodromic and Antidromic O-H *** O Hydrogen-Bonding Systems Analyzed Theoretically.- 18.6 Intramolecular Hydrogen Bonds in the ?-Cyclodextrin Molecule are Variable - the Induced-Fit Hypothesis.- 18.7 Flip-Flop Hydrogen Bonds in ?-Cyclodextrin * 11 H2O.- 18.8 From Flip-Flop Disorder to Ordered Homodromic Arrangements at Low lbmperature: The Importance of the Cooperative Effect.- 18.9 Maltohexaose Polyiodide and Maltotriose - Double and Single Left-Handed Helices With and Without Intramolecular O(2) *** O(3?) Hydrogen Bonds.- 19 Hydrogen Bonding in Proteins.- 19.1 Geometry of Secondary-Structure Elements: Helix, Pleated Sheet, and Turn.- 19.2 Hydrogen-Bond Analysis in Protein Crystal Structures.- 19.3 Hydrogen-Bonding Patterns in the Secondary Structure Elements.- 19.4 Hydrogen-Bonding Patterns Involving Side-Chains.- 19.5 Internal Water Molecules as Integral Part of Protein Structures.- 19.6 Metrical Analysis of Hydrogen Bonds in Proteins.- 19.7 Nonsecondary-Structure Hydrogen-Bond Geometry Between Main-Chains, Side-Chains and Water Molecules.- 19.8 Three-Center (Bifurcated) Bonds in Proteins.- 19.9 Neutron Diffraction Studies on Proteins Give Insight into Local Hydrogen-Bonding Flexibility.- 19.10 Site-Directed Mutagenesis Gives New Insight into Protein Thermal Stability and Strength of Hydrogen Bonds.- 20 The Role of Hydrogen Bonding in the Structure and Function of the Nucleic Acids.- 20.1 Hydrogen Bonding in Nucleic Acids is Essential for Life.- 20.2 The Structure of DNA and RNA Double Helices is Determined by Watson-Crick Base-Pair Geometry.- 20.3 Systematic and Accidental Base-Pair Mismatches: "Wobbling" and Mutations.- 20.4 Noncomplementary Base Pairs Have a Structural Role in tRNA.- 20.5 Homopolynucleotide Complexes Are Stabilized by a Variety of Base-Base Hydrogen Bonds - Three-Center (Bifurcated) Hydrogen Bonds in A-Tracts.- 20.6 Specific Protein-Nucleic Acid Recognition Involves Hydrogen Bonding.- IV Hydrogen Bonding by the Water Molecule.- 21 Hydrogen-Bonding Patterns in Water, Ices, the Hydrate Inclusion Compounds, and the Hydrate Layer Structures.- 21.1 Liquid Water and the Ices.- 21.2 The Hydrate Inclusion Compounds.- 21.3 Hydrate Layer Structures.- 22 Hydrates of Small Biological Molecules: Carbohydrates, Amino Acids, Peptides, Purines, Pyrimidines, Nucleosides and Nucleotides.- 23 Hydration of Proteins.- 23.1 Characterization of "Bound Water" at Protein Surfaces - the First Hydration Shell.- 23.2 Sites of Hydration in Proteins.- 23.3 Metrics of Water Hydrogen Bonding to Proteins.- 23.4 Ordered Water Molecules at Protein Surfaces - Clusters and Pentagons.- 24 Hydration of Nucleic Acids.- 24.1 Two Water Layers Around the DNA Double Helix.- 24.2 Crystallographically Determined Hydration Sites in A-, B-, Z-DNA. A Statistical Analysis.- 24.3 Hydration Motifs in Double Helical Nucleic Acids.- 24.3.1 Sequence-Independent Motifs.- 24.3.2 Sequence-Dependent Motifs.- 24.4 DNA Hydration and Structural Transitions Are Correlated: Some Hypotheses.- 25 The Role of Three-Center Hydrogen Bonds in the Dynamics of Hydration and of Structure Transition.- References.- Refcodes.

Hydrogen Bonding in Biological Structures

Inorganic molecules (ions) and ligands are classified into diatomic, triatomic, four-atomic, five-atomic, six-atomic, and seven-atomic types, and their normal modes of vibration are illustrated and the corresponding vibrational frequencies are listed for each type. Molecules of other types are grouped into compounds of boron, carbon, silicon, nitrogen, phosphorus, and sulfur, and the structures and infrared (IR)/Raman spectra of select examples are shown for each group. Group frequency charts including band assignments are shown for phosphorus and sulfur compounds. Other group frequency charts include hydrogen stretching frequencies, halogen stretching frequencies, oxygen stretching and bending frequencies, inorganic ions, and metal complexes containing simple coordinating ligands.


Keywords:

inorganic compounds;
coordination compounds;
diatomic molecules (ligands);
triatomic molecules (ligands);
four-atomic molecules (ligands);
five-atomic molecules (ligands);
six-atomic molecules (ligands);
seven-atomic molecules (ligands);
boron compounds;
carbon compounds;
silicon compounds;
nitrogen compounds;
phosphorus compounds;
sulfur compounds;
group frequency charts

/pdf/infrared-and-raman-spectra-of-inorganic-and-coordination-45cjzo0tny.pdf

Infrared and Raman Spectra of Inorganic and Coordination Compounds

Infrared spectra of inorganic and coordination compounds

Infrared and Raman spectra of inorganic and coordination compounds

Part 1 Basic Theory.- Historical Background of Raman Spectroscopy Energy Units and Molecular Spectra Vibration of a Diatomic Molecule Origin of Raman Spectra Factors Determining Vibrational Frequencies Vibrations of Polyatomic Molecules Selection Rules for Infrared and Raman Spectra Raman Versus infrared Spectroscopy Depolarisation Ratios The Concept of Symmetry Point Symmetry Elements The Character Table Classification of Nominal Vibrations by Symmetry Point Group Selection Rules Resonance Raman Spectra Space Group Symmetry Normal Vibrations in a Crystal Selection Rules for Solids (Factor Group) Polarised Raman Spectra of Single Crystals Normal Co-ordinate Analysis Band Assignments and Isotopic Shifts. Part 2 Instrumentation and Experimental Techniques: Major Components Excitation Sources Sample Illumination and Scattered Light Collection Monochromator or Spectograph Detection System Instrument Calibration Sampling Techniques Depolarisation Ratios Raman Difference Spectroscopy. Part 3 Special Techniques: Nonlinear Raman Spectroscopy Time-Resolved (IR2) Spectroscopy Matrix Isolation Raman Spectroscopy High Pressure Raman Spectroscopy Surface Enhanced Raman Spectroscopy Raman Spectroelectrochemistry Raman Microscopy FT-Raman Spectroscopy New Raman Techniques. Part 4 Applications: Applications to Structural Chemistry Applications to Biochemistry, Biology, and Medicine Solid State Application of Raman Spectroscopy Industrial Applications Appendices Chapter References Subject Index.

Kazuo Nakamoto

Papers

Infrared and Raman Spectra of Inorganic and Coordination Compounds

Infrared spectra of inorganic and coordination compounds

Infrared and Raman spectra of inorganic and coordination compounds

Introductory Raman spectroscopy

Stretching Frequencies as a Function of Distances in Hydrogen Bonds