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.

I. Introduction: Conceptual vs Fundamental andComputational Aspects of DFT1793II. Fundamental and Computational Aspects of DFT 1795A. The Basics of DFT: The Hohenberg−KohnTheorems1795B. DFT as a Tool for Calculating Atomic andMolecular Properties: The Kohn−ShamEquations1796C. Electronic Chemical Potential andElectronegativity: Bridging Computational andConceptual DFT1797III. DFT-Based Concepts and Principles 1798A. General Scheme: Nalewajski’s ChargeSensitivity Analysis1798B. Concepts and Their Calculation 18001. Electronegativity and the ElectronicChemical Potential18002. Global Hardness and Softness 18023. The Electronic Fukui Function, LocalSoftness, and Softness Kernel18074. Local Hardness and Hardness Kernel 18135. The Molecular Shape FunctionsSimilarity 18146. The Nuclear Fukui Function and ItsDerivatives18167. Spin-Polarized Generalizations 18198. Solvent Effects 18209. Time Evolution of Reactivity Indices 1821C. Principles 18221. Sanderson’s Electronegativity EqualizationPrinciple18222. Pearson’s Hard and Soft Acids andBases Principle18253. The Maximum Hardness Principle 1829IV. Applications 1833A. Atoms and Functional Groups 1833B. Molecular Properties 18381. Dipole Moment, Hardness, Softness, andRelated Properties18382. Conformation 18403. Aromaticity 1840C. Reactivity 18421. Introduction 18422. Comparison of Intramolecular ReactivitySequences18443. Comparison of Intermolecular ReactivitySequences18494. Excited States 1857D. Clusters and Catalysis 1858V. Conclusions 1860VI. Glossary of Most Important Symbols andAcronyms1860VII. Acknowledgments 1861VIII. Note Added in Proof 1862IX. References 1865

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Conceptual density functional theory.

"Chemists familiar with conventional quantum mechanics will applaud and benefit greatly from this particularly instructive, thorough and clearly written exposition of density functional theory: its basis, concepts, terms, implementation, and performance in diverse applications. Users of DFT for structure, energy, and molecular property computations, as well as reaction mechanism studies, are guided to the optimum choices of the most effective methods. Well done!" Paul von RaguE Schleyer "A conspicuous hole in the computational chemist's library is nicely filled by this book, which provides a wide-ranging and pragmatic view of the subject.[...It] should justifiably become the favorite text on the subject for practioneers who aim to use DFT to solve chemical problems." J. F. Stanton, J. Am. Chem. Soc. "The authors' aim is to guide the chemist through basic theoretical and related technical aspects of DFT at an easy-to-understand theoretical level. They succeed admirably." P. C. H. Mitchell, Appl. Organomet. Chem. "The authors have done an excellent service to the chemical community. [...] A Chemist's Guide to Density Functional Theory is exactly what the title suggests. It should be an invaluable source of insight and knowledge for many chemists using DFT approaches to solve chemical problems." M. Kaupp, Angew. Chem.

A Chemist's Guide to Density Functional Theory

Computational studies of proteins based on empirical force fields represent a powerful tool to obtain structure-function relationships at an atomic level, and are central in current efforts to solve the protein folding problem. The results from studies applying these tools are, however, dependent on the quality of the force fields used. In particular, accurate treatment of the peptide backbone is crucial to achieve representative conformational distributions in simulation studies. To improve the treatment of the peptide backbone, quantum mechanical (QM) and molecular mechanical (MM) calculations were undertaken on the alanine, glycine, and proline dipeptides, and the results from these calculations were combined with molecular dynamics (MD) simulations of proteins in crystal and aqueous environments. QM potential energy maps of the alanine and glycine dipeptides at the LMP2/cc-pVxZ//MP2/6-31G* levels, where x = D, T, and Q, were determined, and are compared to available QM studies on these molecules. The LMP2/cc-pVQZ//MP2/6-31G* energy surfaces for all three dipeptides were then used to improve the MM treatment of the dipeptides. These improvements included additional parameter optimization via Monte Carlo simulated annealing and extension of the potential energy function to contain peptide backbone phi, psi dihedral crossterms or a phi, psi grid-based energy correction term. Simultaneously, MD simulations of up to seven proteins in their crystalline environments were used to validate the force field enhancements. Comparison with QM and crystallographic data showed that an additional optimization of the phi, psi dihedral parameters along with the grid-based energy correction were required to yield significant improvements over the CHARMM22 force field. However, systematic deviations in the treatment of phi and psi in the helical and sheet regions were evident. Accordingly, empirical adjustments were made to the grid-based energy correction for alanine and glycine to account for these systematic differences. These adjustments lead to greater deviations from QM data for the two dipeptides but also yielded improved agreement with experimental crystallographic data. These improvements enhance the quality of the CHARMM force field in treating proteins. This extension of the potential energy function is anticipated to facilitate improved treatment of biological macromolecules via MM approaches in general.

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations.

This ebook is the first authorized digital version of Kernighan and Ritchie's 1988 classic, The C Programming Language (2nd Ed.). One of the best-selling programming books published in the last fifty years, "K&R" has been called everything from the "bible" to "a landmark in computer science" and it has influenced generations of programmers. Available now for all leading ebook platforms, this concise and beautifully written text is a "must-have" reference for every serious programmers digital library.

As modestly described by the authors in the Preface to the First Edition, this "is not an introductory programming manual; it assumes some familiarity with basic programming concepts like variables, assignment statements, loops, and functions. Nonetheless, a novice programmer should be able to read along and pick up the language, although access to a more knowledgeable colleague will help."

The C programming language

Although the existence of Cα−H···OC hydrogen bonds in protein structures recently has been established, little is known about their strength and, therefore, the relative importance of these interactions. We have discovered that similar interactions occur in N,N-dimethylformamide dimers. High level ab initio calculations (MP2/aug-cc-pTZV) yield electronic association energies (De) and association enthalpies (ΔH298) for four dimer geometries. These data provide a lower limit of De = −2.1 kcal mol-1 for the Cα−H···OC hydrogen bond. A linear correlation between C−H···O bond energies and gas-phase proton affinities is reported. The gas-phase anion proton affinity of a peptide Cα−H hydrogen was calculated (355 kcal mol-1) and used to estimate values of De = −4.0 ± 0.5 kcal mol-1 and ΔH298 = −3.0 ± 0.5 kcal mol-1 for the Cα−H···OC hydrogen bond. The magnitude of this interaction, roughly one-half the strength of the N−H···OC hydrogen bond, suggests that Cα−H···OC hydrogen bonding interactions represent a hithert...

How Strong Is the Cα−H···OC Hydrogen Bond?

Conformations of an important model system, the alanine dipeptide, have been calculated by using high-level, ab initio electronic structure theory. A Ramachandran plot, with the angle φ in the range −180° to 90° and the angle ψ in the range −60° to 180°, was generated by using density functional theory with the generalized-gradient BLYP functional and a polarized triple-ζ basis set (TZVP+). Six conformers, C7eq, C5, C7ax, β2, αL, and α‘, have been identified in this region of the Ramachandran plot. A second derivative (frequency) analysis showed that all conformers are stable at this level of theory. These structures were used as starting points for geometry optimizations at the MP2/aug-cc-pVDZ level. Single-point energies were calculated at the MP2/aug-cc-pVTZ and MP2/aug-cc-pVQZ levels at the final MP2/aug-cc-pVDZ structures and together with the MP2/aug-cc-pVDZ results were used in extrapolations to the complete basis set limit. The N−H···O, N−H···N, and C−H···O hydrogen bond interactions that are key ...

Conformational Study of the Alanine Dipeptide at the MP2 and DFT Levels

The structures of the dimers of formamide and N-methylacetamide have been calculated at the ab initio electronic structure theory level, 2nd order Miller-Plesset perturbation theory (MP2) with augmented correlation consistent basis sets. Five unique structures were optimized for the formamide dimers at the MP2/aug-cc-pVDZ and MP2/aug-cc-pVTZ levels. At the optimized geometries obtained with the aug-cc-pVTZ basis set, MP2 energies were evaluated with the aug-cc-pVQZ basis set allowing an extrapolation of the energies to the complete basis set limit. Four structures were found for the N-methylacetamide dimer at the MP2/aug-cc-pVDZ level and single point energies were calculated at the MP2/aug-cc-pVTZ level. In both systems, the basis set superposition error (BSSE) was estimated with the counterpoise method. The strength of the N-HiiiO=C bond has a mean value of 7.1 kcal/mol in the formamide dimers and a mean value of 8.6 kcal/mol in the N-methylacetamide dimers. The difference in hydrogen bond strengths is attributed to differences in basicity at the carbonyl oxygen receptor site. In several dimers C-HiiiO=C hydrogen bonds play an important role in stabilizing these intermolecular complexes increasing the interaction energy by 1.1 to 2.6 kcal/mol per interaction.

Strength of the NH···OC and CH···OC Bonds in Formamide and N-Methylacetamide Dimers

Antidiarrhoeal activity of Waltheria americana, Commelina coelestis and Alternanthera repens

The electron transfer (ET) reaction between carotenoids and the superoxide radical anion is found to be not only a viable process but also a very unique one. The nature of the O2˙− inverts the direction of the transfer, with respect to ET involving other ROS: the O2˙− becomes the electron donor and carotenoids (CAR) the electron acceptor. Therefore the “antioxidant” activity of CAR when reacting with O2˙− lies in their capacity to prevent the formation of oxidant ROS. This peculiar charge transfer is energetically feasible in non-polar environments but not in polar media. In addition the relative reactivity of CAR towards O2˙− is drastically different from their reactivity to other ROS. Asthaxanthin (ASTA) is predicted to be a better O2˙− quencher than LYC and the other CAR. The CAR + O2˙− reactions were found to be diffusion controlled. The agreement with available experimental data supports the density functional theory results from the present work.

Rubicelia Vargas

Papers

How Strong Is the Cα−H···OC Hydrogen Bond?

Conformational Study of the Alanine Dipeptide at the MP2 and DFT Levels

Strength of the NH···OC and CH···OC Bonds in Formamide and N-Methylacetamide Dimers

Antidiarrhoeal activity of Waltheria americana, Commelina coelestis and Alternanthera repens

Carotenoids can act as antioxidants by oxidizing the superoxide radical anion