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

Structural studies have paved the avenue to a deeper understanding of aquaporins (AQPs), small ancient proteins providing efficient transmembrane pathways for water, small uncharged solutes such as glycerol, and possibly gas molecules. Despite the numerous studies, their roles in health and disease remain to be fully disclosed. The recent discovery of AuIII complexes as potent and selective inhibitors of aquaglyceroporin isoforms paves the way to their possible therapeutic application. The binding of the selective human AQP3 inhibitor, the cationic complex [Au(bipy)Cl2]+ (Aubipy), to the protein channel has been investigated here by means of a multi-level theoretical workflow that includes QM, MD and QM/MM approaches. The hydroxo complex was identified as the prevalent form of Aubipy in physiological media and its binding to AQP3 studied by MD. Both non-covalent and coordinative Aubipy–AQP3 adducts were simulated to probe their role in the modulation of water channel functionality. The electronic structures of representative Aubipy–AQP3 adducts were then analysed to unveil the role played by the metal moiety in their stabilisation. This study spotlights the overall importance of three key aspects for AQP3 inhibition: 1) water speciation of the AuIII complex, 2) stability of non-covalent adducts and 3) conformational changes induced within the pore by the coordinative binding of AuIII. The obtained results are expected to orient future developments in the design of isoform-selective AuIII inhibitors.

/pdf/a-multi-level-theoretical-study-to-disclose-the-binding-3rx1gg45yn.pdf

A Multi-Level Theoretical Study to Disclose the Binding Mechanisms of Gold(III)-Bipyridyl Compounds as Selective Aquaglyceroporin Inhibitors.

Lennard-Jones was among the earliest to stress the dominant role played by the exclusion principle in chemistry and was the first to exploit the properties of the same-spin pair density to demonstrate the most probable spatial distribution of a given number of electron pairs. This paper demonstrates that a related distribution function, the conditional probability for same-spin electrons, is so successful in recovering the geometrical models associated with differing numbers of electron pairs, as suggested by the work of Lennard-Jones and subsequently adopted as the basis for the VSEPR model, that we propose that it be called the Lennard-Jones function, or LJF. The maxima in LJF show where the density of the other electrons is most likely to be found, relative to a fixed position of a same-spin reference electron. The digonal, trigonal, tetrahedral, bipyramidal, and octahedral patterns of maxima obtained in such displays demonstrate that these are the most probable arrangements for corresponding numbers o...

The Lennard-Jones Function: A Quantitative Description of the Spatial Correlation of Electrons As Determined by the Exclusion Principle

A Theoretical Study of the Proton-Bound Ammonia Dimer

G-quadruplexes are higher-order four-stranded structures formed from repetitive guanine-containing tracts in nucleic acids. They comprise a core of stacked guanine-quartets linked by loops of length and sequence that vary with the context in which the quadruplex sequence occurs. Such sequences can be found in a number of genomic environments; at the telomeric ends of eukaryotic chromosomes, in promoter regions, in untranslated sequences and in open reading frames. Quadruplex formation can inhibit telomere maintenance, transcription and translation, especially when enhanced by quadruplex-binding small molecules, and quadruplex targeting is currently of considerable interest. The available experimental structural data shows that quadruplexes can have high conformational flexibility, especially in loop regions, which has hampered attempts to use high-throughput docking to find quadruplex-binding small-molecules with new scaffolds or to optimize existing ones with structure-based design methods. An approach to overcome the challenge of quadruplex conformational flexibility is presented here, which uses a combined multiple molecular dynamics and sampling approach. Two test small molecules have been used, RHPS4 and pyridostatin, which themselves have contrasting degrees of conformational flexibility.

Small-molecule G-quadruplex interactions: Systematic exploration of conformational space using multiple molecular dynamics

The experimental electron density of the only known example of a four-membered Ga(I) N-heterocyclic carbene analogue has been determined by multipole modeling of 90 K X-ray diffraction data and compared to theoretical data. In order to obtain a satisfactory model, it is necessary to modify the radial dependency of the core electrons of Ga using two separate scaling parameters for s,p- and d-electrons. Evidence for significant lone-pair density on Ga is found in the electron density and derived properties despite the partial positive charge of this atom. Static deformation density and molecular electrostatic potential clearly show a directional lone pair on Ga, whereas the Laplacian of the total electron density does not; this feature is, however, present in the Laplacian of the valence-only density. The Ga center also acts as an acceptor in four intramolecular C–H···Ga contacts, whose nature is probed by density properties. Substantial covalent character is apparent in the Ga–N bonds, but no sign of donation from filled N p-orbitals to empty Ga p-orbitals is found, whereas π-delocalization over the organic ligand is evident. This study highlights the utility of experimental charge density analysis as a technique to investigate the unusual bonding and electronic characteristics of low oxidation state/low coordinate p-block complexes.

James Alexis Platts

Papers

A Multi-Level Theoretical Study to Disclose the Binding Mechanisms of Gold(III)-Bipyridyl Compounds as Selective Aquaglyceroporin Inhibitors.

The Lennard-Jones Function: A Quantitative Description of the Spatial Correlation of Electrons As Determined by the Exclusion Principle

A Theoretical Study of the Proton-Bound Ammonia Dimer

Small-molecule G-quadruplex interactions: Systematic exploration of conformational space using multiple molecular dynamics

Experimental charge density analysis of a gallium(I) N-heterocyclic carbene analogue.