A complete set of intermolecular potential functions has been developed for use in computer simulations of proteins in their native environment. Parameters are reported for 25 peptide residues as well as the common neutral and charged terminal groups. The potential functions have the simple Coulomb plus Lennard-Jones form and are compatible with the widely used models for water, TIP4P, TIP3P, and SPC. The parameters were obtained and tested primarily in conjunction with Monte Carlo statistical mechanics simulations of 36 pure organic liquids and numerous aqueous solutions of organic ions representative of subunits in the side chains and backbones of proteins. Bond stretch, angle bend, and torsional terms have been adopted from the AMBER united-atom force field. As reported here, further testing has involved studies of conformational energy surfaces and optimizations of the crystal structures for four cyclic hexapeptides and a cyclic pentapeptide. The average root-mean-square deviation from the X-ray structures of the crystals is only 0.17 A for the atomic positions and 3% for the unit cell volumes. A more critical test was then provided by performing energy minimizations for the complete crystal of the protein crambin, including 182 water molecules that were initially placed via a Monte Carlo simulation. The resultant root-mean-square deviation for the non-hydrogen atoms is still ca. 0.2 A and the variation in the errors for charged, polar, and nonpolar residues is small. Improvement is apparent over the AMBER united-atom force field which has previously been demonstrated to be superior to many alternatives. Computer simulations are undoubtedly destined to became an increasingly important means for investigating the structures and dynamics of biomolecular systems.' At the heart of such theoretical calculations are the force fields that describe the interatomic interactions and the mechanics of deformations of the molecules.* There is also little doubt that there will be a continual evolution in force fields with added complexity and improved performance paralleling the availability of computer resources. Our own efforts in this area over the last few years have resulted in the OPLS potential functions for proteins whose development and performance are summarized here. These potential functions have a simple form and they have been parametrized directly to reproduce experimental thermodynamic and structural data on fluids. Consequently, they are computationally efficient and their description of proteins in solution or crystalline environments should be superior to many alterantives that have been developed with limited condensed-phase data. The latter point is pursued here primarily through calculations on the crystal structures for four cyclic hexapeptides, a cyclic pentapeptide, and the protein crambin. Improvements are apparent in comparison to the AMBER united-atom force field3 which has previously been shown to be superior to many alternative^.^ (1) Beveridge, D. L., Jorgensen, W. L., Eds. Ann. N.Y. Acad. Sci. 1986, 482. ( 2 ) For reviews, see: (a) Levitt, M. Annu. Reu. Biophys. Eioeng. 1982, 11, 251. (b) McCammon, J. A. Rep. Prog. Phys. 1984, 47, 1. (3) Weiner, S. J.; Kollman, P. A.; Case, D. A,; Singh, U. C.; Ghio, C.; Alagona, G.; Profeta, S.; Weiner, P. J. Am. Chem. SOC. 1984, 106, 765. Parametrization The peptide residues of proteins contain readily identifiable organic subunits such as amides, hydrocarbons, alcohols, thioethers, etc. In view of this and since data are available on the corresponding pure organic liquids, our approach to developing a force field for proteins was to build it up from parameters demonstrated to yield good descriptions of organic liquids. U1timately, the force field would need to treat both intramolecular terms for bond stretches, angle bends, and torsions, as well as the intermolecular and intramolecular nonbonded interactions. The latter are generally accepted to be the most difficult part of the problem and have been our focus.3 A simple, computationally efficient form was chosen to represent the nonbonded interactions through Coulomb and Lennard-Jones terms interacting between sites centered on nuclei (eq 1). Thus, the intermolecular inter-

The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin.

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.

Nitrogen doping has been an effective way to tailor the properties of graphene and render its potential use for various applications. Three common bonding configurations are normally obtained when doping nitrogen into the graphene: pyridinic N, pyrrolic N, and graphitic N. This paper reviews nitrogen-doped graphene, including various synthesis methods to introduce N doping and various characterization techniques for the examination of various N bonding configurations. Potential applications of N-graphene are also reviewed on the basis of experimental and theoretical studies.

https://s3-eu-west-1.amazonaws.com/pfigshare-u-files/1431849/NitrogenReviewonRecentProgressinNitrogenDopedGrapheneSynthesisCharacterizationandItsPotentialApplications.pdf

Review on Recent Progress in Nitrogen-Doped Graphene: Synthesis, Characterization, and Its Potential Applications

Tetrathiafulvalenes, oligoacenenes, and their buckminsterfullerene derivatives: the brick and mortar of organic electronics.

A variety of two-dimensional materials have been reported in recent years, yet single-element systems such as graphene and black phosphorus have remained rare. Boron analogues have been predicted, as boron atoms possess a short covalent radius and the flexibility to adopt sp2 hybridization, features that favour the formation of two-dimensional allotropes, and one example of such a borophene material has been reported recently. Here, we present a parallel experimental work showing that two-dimensional boron sheets can be grown epitaxially on a Ag(111) substrate. Two types of boron sheet, a β12 sheet and a χ3 sheet, both exhibiting a triangular lattice but with different arrangements of periodic holes, are observed by scanning tunnelling microscopy. Density functional theory simulations agree well with experiments, and indicate that both sheets are planar without obvious vertical undulations. The boron sheets are quite inert to oxidization and interact only weakly with their substrate. We envisage that such boron sheets may find applications in electronic devices in the future. A variety of two-dimensional materials have been reported in the past few years, yet single-element systems—such as graphene and black phosphorus—have remained rare. 2D allotropes of boron have long been predicted and recently investigated. Two boron sheets have now been grown on a Ag(111) surface by molecule beam epitaxy that exhibit significant chemical stability against oxidation.

Experimental realization of two-dimensional boron sheets

A reduced HOMO−LUMO gap, which is defined as the HOMO−LUMO energy separation of a molecule divided by that of the hypothetical polyene reference, can be used as an index of kinetic stability for a variety of polycyclic aromatic hydrocarbons (PAHs). The reduced HOMO−LUMO gap < 1.00 indicates that the HOMO contributes to the decrease in the topological resonance energy. In general, PAHs with reduced HOMO−LUMO gaps < 1.30 are chemically very reactive. Fully benzenoid hydrocarbons are kinetically very stable with very large reduced HOMO−LUMO gaps. Many of the PAH molecules with large reduced HOMO−LUMO gaps are closed-shell substructures of nonmetallic one-dimensional benzenoid polymers.

Reduced HOMO−LUMO Gap as an Index of Kinetic Stability for Polycyclic Aromatic Hydrocarbons

A very simple but general index of kinetic stability, T, is proposed for π-electron systems, which is defined as a highest occupied molecular orbital (HOMO)- lowest unoccupied molecular orbital (LUMO) energy separation multiplied by the number of conjugated atoms. This new index can be justified by relating it to the approximate form of the superdelocalizability, an index of chemical reactivity defined by Fukui et al. It is best suited for predicting the kinetic stability of fullerenes. All isolable fullerene isomers have T values larger than 13.

Weighted HOMO-LUMO energy separation as an index of kinetic stability for fullerenes

Resonance energies of nonbenzenoid hydrocarbons.

For isolated-pentagon isomers of fullerenes with up to 90 carbon atoms, the HOMO–LUMO energy
 separation is closely associated with the chemical reactivity at the most reactive site of the molecule. To be
 exact, the T value correlates very well with the minimum bond resonance energy (min BRE). Here, the T value
 is the HOMO–LUMO energy separation multiplied by the number of carbon atoms, and the min BRE is the
 minimum bond resonance energy in the molecule. This correlation explicitly shows that an isolated-pentagon
 fullerene isomer with chemically reactive substructures in general has a small HOMO–LUMO gap energy.

Correlation found between the HOMO–LUMO energy separation and the chemical reactivity at the most reactive site for isolated-pentagon isomers of fullerenes

Jun-ichi Aihara

Papers

Reduced HOMO−LUMO Gap as an Index of Kinetic Stability for Polycyclic Aromatic Hydrocarbons

Weighted HOMO-LUMO energy separation as an index of kinetic stability for fullerenes

Resonance energies of nonbenzenoid hydrocarbons.

Correlation found between the HOMO–LUMO energy separation and the chemical reactivity at the most reactive site for isolated-pentagon isomers of fullerenes

Nucleus-independent chemical shifts and local aromaticities in large polycyclic aromatic hydrocarbons