A non-empirical study of the hydrogen bond between peptide units
TL;DR: A detailed study of hydrogen bonding in the linear dimers of formamide has been performed in a non-empirical SCF framework as mentioned in this paper, where the stabilization energy was studied as a function of the distance between the monomers and a decomposition of the energy into the coulomb, exchange and polarization and charge transfer contributions.
Abstract: A detailed study of hydrogen bonding in the linear dimers of formamide has been performed in a non-empirical SCF framework. The stabilization energy is studied as a function of the distance between the monomers and a decomposition of the energy into the coulomb, exchange and polarization and charge transfer contributions is given as well as a study of the underlying changes in the electron distribution. The angular displacements around the carbonyl oxygen are studied in the antiparallel dimer and show a very shallow minimum. The effects of hydrogen bonding on the NH stretching are satisfactorily accounted for.
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17 Jul 1991
TL;DR: In this article, the van der Waals Radii cut-off criterion is used to define the strong and weak hydrogen-bond configurations, as well as the relationship between two-center and three-center hydrogen bonds.
Abstract: 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.
2,739 citations
TL;DR: In this paper, a model that relies on the knowledge of the molecular electrostatic potential, which is derived from a molecular wave function by using the usual methods for calculating the mean expectation value of an operator, is discussed.
Abstract: Publisher Summary This chapter discusses a model that relies on the knowledge of the molecular electrostatic potential, which is derived from a molecular wavefunction by using the usual methods for calculating the mean expectation value of an operator. In its basic premises the model employs quantum mechanics, with only the approximations necessary in molecular quantal calculations. The model is also discussed regarding its relationships with the Hellmann–Feynman theorem. The electrostatic potential V itself is examined in order to show how the electrostatic potential reflects the characteristics of the electronic distribution of a molecule and then the reliability of V is discussed as a reactivity index. The shape of the electrostatic potential and its relationship to the electronic molecular structure is discussed with the aid of various examples. One of them includes the glycine tautomers and the corresponding anion example. The chapter also discusses the electrostatic molecular potential in terms of local group contributions.
1,116 citations
TL;DR: Fragmentation Methods: A Route to Accurate Calculations on Large Systems Mark S. Gordon,* Dmitri G. Fedorov, Spencer R. Pruitt, and Lyudmila V. Slipchenko.
Abstract: Fragmentation Methods: A Route to Accurate Calculations on Large Systems Mark S. Gordon,* Dmitri G. Fedorov, Spencer R. Pruitt, and Lyudmila V. Slipchenko Department of Chemistry and Ames Laboratory, Iowa State University, Ames Iowa 50011, United States Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
938 citations
696 citations
TL;DR: In this article, a reduced variational space method is presented for analyzing hydrogen bonding interactions in terms of Coulomb and exchange, polarizability, and charge-transfer components, which relies on the use of SCF optimized monomer orbitais in dimer calculations.
388 citations
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TL;DR: In this paper, an analysis in quantitative form is given in terms of breakdowns of the electronic population into partial and total ''gross atomic populations'' and ''overlap populations'' for molecules.
Abstract: With increasing availability of good all‐electron LCAO MO (LCAO molecular orbital) wave functions for molecules, a systematic procedure for obtaining maximum insight from such data has become desirable. An analysis in quantitative form is given here in terms of breakdowns of the electronic population into partial and total ``gross atomic populations,'' or into partial and total ``net atomic populations'' together with ``overlap populations.'' ``Gross atomic populations'' distribute the electrons almost perfectly among the various AOs (atomic orbitals) of the various atoms in the molecule. From these numbers, a definite figure is obtained for the amount of promotion (e.g., from 2s to 2p) in each atom; and also for the gross charge Q on each atom if the bonds are polar. The total overlap population for any pair of atoms in a molecule is in general made up of positive and negative contributions. If the total overlap population between two atoms is positive, they are bonded; if negative, they are antibonded. Tables of gross atomic populations and overlap populations, also gross atomic charges Q, computed from SCF (self‐consistent field) LCAO‐MO data on CO and H2O, are given. The amount of s‐p promotion is found to be nearly the same for the O atom in CO and in H2O (0.14 electron in CO and 0.15e in H2O). For the C atom in CO it is 0.50e. For the N atom in N2 it is 0.26e according to calculations by Scherr. In spite of very strong polarity in the π bonds in CO, the σ and π overlap populations are very similar to those in N2. In CO the total overlap population for the π electrons is about twice that for the σ electrons. The most easily ionized electrons of CO are in an MO such that its gross atomic population is 94% localized on the carbon atom; these electrons account for the (weak) electron donor properties of CO. A comparison between changes of bond lengths observed on removal of an electron from one or another MO of CO and H2, and corresponding changes in computed overlap populations, shows good correlation. Several other points of interest are discussed.
9,238 citations
4,691 citations
TL;DR: In this article, a systematisches Storungsverfahren entwickelt, in which homoopolaren and van der Waalsschen Kraftwirkungen in einheitlichem Zusammenhang umfast and die fruheren Untersuchungen zur chemischen Bindung als erste Naherung enthalt.
Abstract: Es wird ein systematisches Storungsverfahren entwickelt, welches die homoopolaren und die van der Waalsschen Kraftwirkungen in einheitlichem Zusammenhang umfast und die fruheren Untersuchungen zur chemischen Bindung als erste Naherung enthalt. Das Verfahren wird zur Bestimmung der van der Waalsschen Konstanten des atomaren Wasserstoffs angewandt.
530 citations
TL;DR: In this paper, the authors used a Gaussian orbital basis set to calculate the hydrogen-bond energy and the most stable structure of the dimeric H2O system using the LCAO MO SCF method.
Abstract: The hydrogen‐bond energy and the most stable structure of the dimeric H2O system are calculated by the LCAO MO SCF method using a medium‐sized Gaussian orbital basis set. The most stable structure, found by a limited variation of the interatomic coordinates, is a linear hydrogen bond (stabilization energy 12.6 kcal mole−1) with an H···O distance of 1.72 A, and with the hydrogen‐acceptor molecule almost freely rotating around its molecular axis. The stretching of the proton donor O–H bond is calculated to be 0.12 A. A population anaysis near the energy minimum shows that the change in the population is distributed not only in the O···H–O fragment, but also delocalized into the neighboring O–H bonds. Hydrogen bonds of dimeric H2O other than the linear structure (cyclic and bifurcated) are also examined.
226 citations