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

Electrostatic parameters in the Debye-Hiickel equations for activity coefficients and the relative partial molal enthalpies, internal energies, isochoric and isobaric heat capacities, volumes, comprcssibilities, and expansibilities of aqueous electrolytes have been computed for pressures and temperatures from l bar to 5 kb and 0° to 600°C. The calculations are based on the equation of state for H 20 derived by Keenan and others (1969) for pressures ~ a kilobar together with power functions of temperature and density (or pressure) obtained by regression analysis (Helgeson and Kirkham, l974a) of dielectric constant data (Oshry, ms; Owen and others, 1961; Heger, ms) and finite difference coefficients of isobaric thermal expansion and isothermal compressibility generated (Helgeson and Kirkham, l974a) from densities (Burnham, Holloway, and Davis, 1969) of H 20 at pressures > a kilobar. The Debye-Hiickel parameters are sensitive quasi-asymptotic functions of pressure and temperature, which may be monotonic or exhibit extrema, depending on the property. Changes in the dielectric constant and the Debye-Hiickel parameters with increasing temperature andfor decreasing pressure favor increasing mineral solubilities and extension of the applicability of DebyeHiickel theory to electrolytes with progressively higher concentrations. In the supercritical region, the absolute values of the limiting law parameters for the relative partial molal properties of electrolytes are of the order of 5 to > 1000 times larger than they are at 25°C and l bar.

Theoretical prediction of the thermodynamic behavior of aqueous electrolytes at high pressures and temperatures:II. Debye-Huckel parameters for activity coefficients and relative partial molal properties

A new formulation is presented of the static relative permittivity or dielectric constant of water and steam, including supercooled and supercritical states. The range is from 238 K to 873 K, at pressures up to 1200 MPa. The formulation is based on the ITS-90 temperature scale. It correlates a selected set of data from a recently published collection of all experimental data. The set includes new data in the liquid water and the steam regions that have not been part of earlier correlations. The physical basis for the formulation is the so-called g-factor in the form proposed by Harris and Alder. An empirical 12-parameter form for the g-factor as a function of the independent variables temperature and density is used. For the conversion of experimental pressures to densities, the newest formulation of the equation of state of water on the ITS-90, prepared by Wagner and Pruss, has been used. All experimental data are compared with the formulation. The reliability of the new formulation is assessed in all su...

A Formulation for the Static Permittivity of Water and Steam at Temperatures from 238 K to 873 K at Pressures up to 1200 MPa, Including Derivatives and Debye–Hückel Coefficients

The five-site transferable interaction potential (TIP5P) for water [M. W. Mahoney and W. L. Jorgensen, J. Chem. Phys. 112, 8910 (2000)] is most accurate at reproducing experimental data when used with a simple spherical cutoff for the long-ranged electrostatic interactions. When used with other methods for treating long-ranged interactions, the model is considerably less accurate. With small modifications, a new TIP5P-like potential can be made which is very accurate for liquid water when used with Ewald sums, a more physical and increasingly more commonly used method for treating long-ranged electrostatic interactions. The new model demonstrates a density maximum near 4 °C, like the TIP5P model, and otherwise is similar to the TIP5P model for thermodynamic, dielectric, and dynamical properties of liquid water over a range of temperatures and densities. An analysis of this and other commonly used water models reveals how the quadrupole moment of a model can influence the dielectric response of liquid water.

/pdf/a-reoptimization-of-the-five-site-water-potential-tip5p-for-1vvsh5nri6.pdf

A reoptimization of the five-site water potential (TIP5P) for use with Ewald sums

This paper examines and assesses predictive methods for the saturated hydraulic conductivity of soils. The soil definition is that of engineering. It is not that of soil science and agriculture, which corresponds to “top soil” in engineering. Most predictive methods were calibrated using laboratory permeability tests performed on either disturbed or intact specimens for which the test conditions were either measured or supposed to be known. The quality of predictive equations depends highly on the test quality. Without examining all the quality issues, the paper explains the 14 most important mistakes for tests in rigid-wall or flexible-wall permeameters. Then, it briefly presents 45 predictive methods, and in detail, those with some potential, such as the Kozeny-Carman equation. Afterwards, the data of hundreds of excellent quality tests, with none of the 14 mistakes, are used to assess the predictive methods with a potential. The relative performance of those methods is evaluated and presented in graphs. Three methods are found to work fairly well for non-plastic soils, two for plastic soils without fissures, and one for compacted plastic soils used for liners and covers. The paper discusses the effects of temperature and intrinsic anisotropy within the specimen, but not larger scale anisotropy within aquifers and aquitards.

Predicting the saturated hydraulic conductivity of soils: a review

IN this very remarkable book, Dr. Dorsey presents a series of nearly three hundred tables on the principal physical properties of water. The book continues the work commenced when the author was an associate editor of the International Critical Tables, for which he worked indefatigably. It is based, in respect of data obtained before 1923, mainly on these Tables; for more recent data, the literature has been exhaustively searched, much more than a thousand references being given, and good use has been made of other tables and monographs. The breadth of knowledge and the conscientiousness with which this enormous mass of data has been digested and put into perspective compel profound respect. Properties of Ordinary Water-Substance in all its Phases Water-vapor, Water and all the Ices. Compiled by N. Ernest Dorsey. (American Chemical Society, Monograph Series No. 81.) Pp. xxiv + 673. (New York: Reinhold Publishing Corporation; London: Chapman and Hall, Ltd., 1940.) 90s. net.

N. K. Adam

Papers

Properties of Ordinary Water-Substance in all its Phases