A new density functional (DF) of the generalized gradient approximation (GGA) type for general chemistry applications termed B97-D is proposed. It is based on Becke's power-series ansatz from 1997 and is explicitly parameterized by including damped atom-pairwise dispersion corrections of the form C(6) x R(-6). A general computational scheme for the parameters used in this correction has been established and parameters for elements up to xenon and a scaling factor for the dispersion part for several common density functionals (BLYP, PBE, TPSS, B3LYP) are reported. The new functional is tested in comparison with other GGAs and the B3LYP hybrid functional on standard thermochemical benchmark sets, for 40 noncovalently bound complexes, including large stacked aromatic molecules and group II element clusters, and for the computation of molecular geometries. Further cross-validation tests were performed for organometallic reactions and other difficult problems for standard functionals. In summary, it is found that B97-D belongs to one of the most accurate general purpose GGAs, reaching, for example for the G97/2 set of heat of formations, a mean absolute deviation of only 3.8 kcal mol(-1). The performance for noncovalently bound systems including many pure van der Waals complexes is exceptionally good, reaching on the average CCSD(T) accuracy. The basic strategy in the development to restrict the density functional description to shorter electron correlation lengths scales and to describe situations with medium to large interatomic distances by damped C(6) x R(-6) terms seems to be very successful, as demonstrated for some notoriously difficult reactions. As an example, for the isomerization of larger branched to linear alkanes, B97-D is the only DF available that yields the right sign for the energy difference. From a practical point of view, the new functional seems to be quite robust and it is thus suggested as an efficient and accurate quantum chemical method for large systems where dispersion forces are of general importance.

Semiempirical GGA-type density functional constructed with a long-range dispersion correction.

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.

Combined quantum-mechanics/molecular-mechanics (QM/MM) approaches have become the method of choice for modeling reactions in biomolecular systems. Quantum-mechanical (QM) methods are required for describing chemical reactions and other electronic processes, such as charge transfer or electronic excitation. However, QM methods are restricted to systems of up to a few hundred atoms. However, the size and conformational complexity of biopolymers calls for methods capable of treating up to several 100,000 atoms and allowing for simulations over time scales of tens of nanoseconds. This is achieved by highly efficient, force-field-based molecular mechanics (MM) methods. Thus to model large biomolecules the logical approach is to combine the two techniques and to use a QM method for the chemically active region (e.g., substrates and co-factors in an enzymatic reaction) and an MM treatment for the surroundings (e.g., protein and solvent). The resulting schemes are commonly referred to as combined or hybrid QM/MM methods. They enable the modeling of reactive biomolecular systems at a reasonable computational effort while providing the necessary accuracy.

QM/MM Methods for Biomolecular Systems

Dispersion corrections to standard Kohn–Sham density functional theory (DFT) are reviewed. The focus is on computationally efficient methods for large systems that do not depend on virtual orbitals or rely on separated fragments. The recommended approaches (van der Waals density functional and DFT-D) are asymptotically correct and can be used in combination with standard or slightly modified (short-range) exchange–correlation functionals. The importance of the dispersion energy in intramolecular cases (conformational problems and thermochemistry) is highlighted. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 211-228 DOI: 10.1002/wcms.30

Density functional theory with London dispersion corrections

Introduction
PaDEL-Descriptor is a software for calculating molecular descriptors and fingerprints. The software currently calculates 797 descriptors (663 1D, 2D descriptors, and 134 3D descriptors) and 10 types of fingerprints. These descriptors and fingerprints are calculated mainly using The Chemistry Development Kit. Some additional descriptors and fingerprints were added, which include atom type electrotopological state descriptors, McGowan volume, molecular linear free energy relation descriptors, ring counts, count of chemical substructures identified by Laggner, and binary fingerprints and count of chemical substructures identified by Klekota and Roth.

Methods
PaDEL-Descriptor was developed using the Java language and consists of a library component and an interface component. The library component allows it to be easily integrated into quantitative structure activity relationship software to provide the descriptor calculation feature while the interface component allows it to be used as a standalone software. The software uses a Master/Worker pattern to take advantage of the multiple CPU cores that are present in most modern computers to speed up calculations of molecular descriptors.

Results
The software has several advantages over existing standalone molecular descriptor calculation software. It is free and open source, has both graphical user interface and command line interfaces, can work on all major platforms (Windows, Linux, MacOS), supports more than 90 different molecular file formats, and is multithreaded.

Conclusion
PaDEL-Descriptor is a useful addition to the currently available molecular descriptor calculation software. The software can be downloaded at http://padel.nus.edu.sg/software/padeldescriptor. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011

https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.21707

PaDEL‐descriptor: An open source software to calculate molecular descriptors and fingerprints

The removal of a fluorine atom from its central position in a cubiclike Li14F13+ cluster creates an F‐center vacancy that may or may not be occupied by the remaining odd electron. The topology exhibited by the electron density in Li14F12+, the F‐center cluster, enables one to make a clear distinction between the two possible forms that the odd electron can assume. If it possesses a separate identity, then a local maximum in the electron density will be found within the vacancy and the F‐center will behave quantum mechanically as an open system, bounded by a surface of local zero flux in the gradient vector field of the electron density. If, however, the density of the odd electron is primarily delocalized onto the neighboring ions, then a cage critical point, a local minimum in the density, will be found at the center of the vacancy. Without an associated local maximum, the vacancy has no boundary and is undefined. Self‐consistent field (SCF) calculations with geometry optimization of the Li14F13+ cluster...

Characterization of an F‐center in an alkali halide cluster

The syntheses of five new heteroleptic iridium complexes [Ir(L1–4)2(Diobpy)]PF6 (where Diobpy = 4,4′-dioctylamido-2,2′-bipyridine) and [Ir(L3)2(bpy)]PF6 (where L = para-substituted 2,3-diphenylquinoxaline cyclometalating ligands; bpy = 2,2′-bipyridine) are described. The structures of [Ir(L3)2(Diobpy)]PF6 and [Ir(L3)2(bpy)]PF6 show that the complexes each adopt a distorted octahedral geometry with the expected trans-N, cis-C arrangement of the cyclometalated ligands. Electrochemical studies confirmed subtle perturbation of the IrIII/IV redox couple as a function of ligand variation. Luminescence studies showed the significant contribution of 3MLCT to the phosphorescent character with predictable and modestly tunable emission wavelengths between 618 and 636 nm. DFT studies provided approximate qualitative descriptions of the HOMO {located over the Ir(5d) center (11–42%) and the phenylquinoxaline ligand (54–87%)} and LUMO {located over the ancillary bipyridine ligands (ca. 93%)} energy levels of the five co...

Using Substituted Cyclometalated Quinoxaline Ligands To Finely Tune the Luminescence Properties of Iridium(III) Complexes

The experimental electron density distributions (EDD) in tetrafluorophthalonitrile and tetrafluoroisophthalonitrile have been determined from a multipole refinement with use of accurate X-ray diffraction data collected at 100 K. As hydrogen atoms pose a serious challenge to a successful X-ray based EDD determination due to their diminishing diffraction power, the absence of any such atoms in the studied complexes is an important advantage. The experimental EDD is compared with theoretical densities resulting from high-level ab initio and DFT calculations using the atoms in molecules theory. Topological analysis of the electron density was used to compare the two different isomers and to estimate the similarity of identical functional groups in different crystalline environments. Comparison with theoretical results reveals subtle differences in C−F bonds. The experimental molecular electrostatic potential satisfactorily explains the observed differences in the patterns of weak intermolecular interactions.

Experimental and theoretical charge density studies of tetrafluorophthalonitrile and tetrafluoroisophthalonitrile

The experimental electron density distribution in taurine, 2-aminoethane sulfonic acid, 1, has been determined from high-resolution X-ray diffraction data collected at a temperature of 100 K. Taurine crystallizes as a zwitterion in the monoclinic space group P2 1 /c. Topological analysis of the experimental electron density and a comparison with high-level theoretical gas-phase calculations show that the crystal environment has a significant influence on the electronic configuration of the sulfonate moiety in 1. which in the crystal is more delocalized than in the gas phase. This crystal effect is mainly due to hydrogen bonding.

Experimental and theoretical charge density study of the neurotransmitter taurine.

Platinum containing compounds are promising antitumor agents, but must enter cells before reaching their main biological target, namely DNA. Their distribution within the body, and hence their activity is to a large extent determined by their lipophilicity, thus there is a strong interest to develop computational methods to predict this important property. This study analyses accuracy of five methods, namely ALOGPS, KOWWIN, CLOGP and two quantum chemical approaches, to predict octanol/water partition coefficients (log P) for sets of 43 and 12 Pt(II) complexes, collected from the literature and measured by the authors, respectively. All methods gave generally poor results with mean absolute error (MAE) of between 0.8 and 3 log units for prediction of new compounds. Extension of the ALOGPS program with data from the literature set resulted in the best prediction ability, MAE = 0.46, for the measured molecules. The program was also able to correctly predict errors in calculated log P values. It is freely available for interactive use at http://www.vcclab.org.

/pdf/calculation-of-lipophilicity-for-pt-ii-complexes-47eg7ealb4.pdf

James Alexis Platts

Papers

Characterization of an F‐center in an alkali halide cluster

Using Substituted Cyclometalated Quinoxaline Ligands To Finely Tune the Luminescence Properties of Iridium(III) Complexes

Experimental and theoretical charge density studies of tetrafluorophthalonitrile and tetrafluoroisophthalonitrile

Experimental and theoretical charge density study of the neurotransmitter taurine.

Calculation of lipophilicity for Pt(II) complexes: experimental comparison of several methods