Molecular structure does not easily identify the intricate noncovalent interactions that govern many areas of biology and chemistry, including design of new materials and drugs. We develop an approach to detect noncovalent interactions in real space, based on the electron density and its derivatives. Our approach reveals the underlying chemistry that compliments the covalent structure. It provides a rich representation of van der Waals interactions, hydrogen bonds, and steric repulsion in small molecules, molecular complexes, and solids. Most importantly, the method, requiring only knowledge of the atomic coordinates, is efficient and applicable to large systems, such as proteins or DNA. Across these applications, a view of nonbonded interactions emerges as continuous surfaces rather than close contacts between atom pairs, offering rich insight into the design of new and improved ligands.

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Revealing noncovalent interactions.

In the last few years the analysis of molecular crystal structures using tools based on Hirshfeld surfaces has rapidly gained in popularity. This approach represents an attempt to venture beyond the current paradigm—internuclear distances and angles, crystal packing diagrams with molecules represented via various models, and the identification of close contacts deemed to be important—and to view molecules as “organic wholes”, thereby fundamentally altering the discussion of intermolecular interactions through an unbiased identification of all close contacts.

Hirshfeld surface analysis

Noncovalent interactions hold the key to understanding many chemical, biological, and technological problems. Describing these noncovalent interactions accurately, including their positions in real space, constitutes a first step in the process of decoupling the complex balance of forces that define noncovalent interactions. Because of the size of macromolecules, the most common approach has been to assign van der Waals interactions (vdW), steric clashes (SC), and hydrogen bonds (HBs) based on pairwise distances between atoms according to their vdW radii. We recently developed an alternative perspective, derived from the electronic density: the non-covalent interactions (NCI) index [J. Am. Chem. Soc. 2010, 132, 6498]. This index has the dual advantages of being generally transferable to diverse chemical applications and being very fast to compute, since it can be calculated from promolecular densities. Thus, NCI analysis is applicable to large systems, including proteins and DNA, where analysis of noncova...

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NCIPLOT: A Program for Plotting Noncovalent Interaction Regions

There is a special reason for reviewing this book at this time: it is the 50th edition of a compendium that is known and used frequently in most chemical and physical laboratories in many parts of the world. Surely, a publication that has been published for 56 years, withstanding the vagaries of science in this century, must have had something to offer. There is another reason: while the book is a standard fixture in most chemical and physical laboratories, including those in medical centers, it is not as frequently seen in the laboratories of physician's offices (those either in solo or group practice). I believe that the Handbook can be useful in those laboratories. One of the reasons, among others, is that the various basic items of information it offers may be helpful in new tests, either physical or chemical, which are continuously being published. The basic information may relate

Handbook of Chemistry and Physics

A new way of exploring packing modes and intermolecular interactions in molecular crystals is described, using Hirshfeld surfaces to partition crystal space. These molecular Hirshfeld surfaces, so named because they derive from Hirshfeld's stockholder partitioning, divide the crystal into regions where the electron distribution of a sum of spherical atoms for the molecule (the promolecule) dominates the corresponding sum over the crystal (the procrystal). These surfaces reflect intermolecular interactions in a novel visual manner, offering a previously unseen picture of molecular shape in a crystalline environment. Surface features characteristic of different types of intermolecular interactions can be identified, and such features can be revealed by colour coding distances from the surface to the nearest atom exterior or interior to the surface, or by functions of the principal surface curvatures. These simple devices provide a striking and immediate picture of the types of interactions present, and even reflect their relative strengths from molecule to molecule. A complementary two-dimensional mapping is also presented, which summarizes quantitatively the types of intermolecular contacts experienced by molecules in the bulk and presents this information in a convenient colour plot. This paper describes the use of these tools in the compilation of a pictorial glossary of intermolecular interactions, using identifiable patterns of interaction between small molecules to rationalize the often complex mix of interactions displayed by large molecules.

Novel tools for visualizing and exploring intermolecular interactions in molecular crystals.

GIBBS: isothermal-isobaric thermodynamics of solids from energy curves using a quasi-harmonic Debye model

We make use of the Quantum Theory of Atoms in Molecules (QTAM) to partition the total energy of a many-electron system into intra- and interatomic terms, by explicitly computing both the one- and two-electron contributions. While the general scheme is formally equivalent to that by Bader et al., we focus on the separation and computation of the atomic self-energies and all the interaction terms. The partition is ultimately performed within the density matrices, in analogy with McWeeny's Theory of Electronic Separability, and then carried onto the energy. It is intimately linked with the atomistic picture of the chemical bond, not only allowing the separation of different two-body contributions (point-charge-like, multipolar, total Coulomb, exchange, correlation, ...) to the interaction between a pair of atoms but also including an effective many-body contribution to the binding (self-energy, formally one-body) due to the deformation of the atoms within the many-electron system as compared to the free atoms. Many qualitative ideas about the chemical bond can be quantified using this scheme.

Interacting Quantum Atoms: A Correlated Energy Decomposition Scheme Based on the Quantum Theory of Atoms in Molecules

We have recently developed a non-empirical Debye-like model for the inclusion of thermal effects in the equation of state (EOS) of solids. This model allows the calculation of many thermodynamical properties from the E-V relationship. We report the results of a theoretical investigation that explores the EOS of two ionic solids: MgF2 and Al2O3. The interionic interactions are modelized using either the ab initio Perturbed Ion (aiPI) method or the electron gas formalism along with aiPI electronic wavefunctions, which are allowed to relax with crystal strains. Our EOS results are in overall good agreement with experimental data. Other thermodynamic properties behave in the same way, although Gruneisen constant and related quantities have significant errors. This may be caused by numerical inaccuracies on the high order derivatives needed for its calculation.

Thermodynamical properties of solids from microscopic theory : applications to mgf2 and al2o3

We present a detailed investigation of observable properties associated with the relative stability of the rocksalt ( B1) and cesium chloride (B2) phases in the AX (A5Li, Na, K, Rb, Cs; X5F, Cl, Br, I! crystal family. Thermodynamic B1!B2 transition pressures and DY 5Y (B2)2Y (B1) differences in total energies, volumes, and bulk moduli at zero and transition pressures are computed following a localized Hartree-Fock method. The arrangement of the data in clear trends is shown to be mainly dominated by the cation atomic number. This behavior is well interpreted in terms of a variety of microscopic arguments that emerge from ~i! the evaluation of the energy Hessian at the B1 and B2 points and ~ii! the decomposition of the energy and pressure in anionic and cationic classical and quantum-mechanical contributions.

First-principles study of the rocksalt–cesium chloride relative phase stability in alkali halides

Electron gas interionic potentials (EGIP) have been developed to determine the equation of state (EOS) of the cubic (C1) and orthorhombic (C23) polymorphs of ${\mathrm{SrF}}_{2},$ including the thermal effects by means of a quasiharmonic Debye model. The zero pressure cell parameter ${(a}_{0}),$ lattice energy ${(E}_{\mathrm{latt}}),$ and bulk modulus ${(B}_{0})$ of the C1 phase are computed with errors smaller than 1.2%, 1.2%, and 7.1%, respectively. The predicted EOS is in good agreement with the observed data and satisfies the universal Vinet EOS. For the C23 phase, the optimized zero-$p$ cell parameters a, b, and c and the six fractional coordinates are reported and the pressure dependence of ${a/a}_{0},$ ${b/b}_{0},$ and ${c/c}_{0}$ explored by fitting independent modified Vinet EOS's to the computed data. The analysis reveals a greater compressibility of the C23 phase along the b and c axes than along the a direction. Our calculation predicts the $\mathrm{C}1\ensuremath{\rightleftharpoons}\mathrm{C}23$ equilibrium to occur at ${p}_{\mathrm{tr}}=3.92$ GPa, which is between the observed values for the $\mathrm{C}\stackrel{\ensuremath{\rightarrow}}{1}\mathrm{C}23$ ${(p}_{\mathrm{tr}}=5.0$ GPa) and $\mathrm{C}23\ensuremath{\rightarrow}\mathrm{C}1$ ${(p}_{\mathrm{tr}}=1.7$ GPa) phase transitions.

Evelio Francisco

Papers

GIBBS: isothermal-isobaric thermodynamics of solids from energy curves using a quasi-harmonic Debye model

Interacting Quantum Atoms: A Correlated Energy Decomposition Scheme Based on the Quantum Theory of Atoms in Molecules

Thermodynamical properties of solids from microscopic theory : applications to mgf2 and al2o3

First-principles study of the rocksalt–cesium chloride relative phase stability in alkali halides

Atomistic simulation of Sr F 2 polymorphs