Molecular fragment shape variation index applied to intramolecular interaction studies

The fragment shape variation index approach is applied to intramolecular interactions involving C6 aromatic molecular fragments in the special case where the shape-modifying interactions are also caused primarily by other C6 aromatic fragments of the same molecule. This report is a part of a series of studies aimed at the detailed modeling of various components of intramolecular interactions among molecular fragments, including aromatic ring interactions, aromatic ring and non-aromatic conjugated and non-conjugated system interactions, and more general through-space and through-bond interactions. The ultimate purpose of these studies is a better understanding of the electron density shape modifying effects of intramolecular interactions.     

Holographic electron density shape theorem and its role in drug design and toxicological risk assessment

Each complete, boundaryless molecular electron density is fully determined by any nonzero volume piece of the electron density cloud. This inherent feature of molecules, called the "holographic" property of molecular electron densities, provides a strong foundation for the local, quantum chemical shape analysis of various functional groups, pharmacophores, and other local molecular moieties. A proof is presented for the relevant molecular shape theorem, the "holographic electron density shape theorem", and the role of this theorem in quantum chemical, quantitative shape-activity relations (QShAR) is discussed. The quantum chemical methods of molecular shape analysis can be extended to ab initio quality electron densities of macromolecules, such as proteins, as well as to local molecular moieties, such as functional groups or pharmacophores, based on the transferability and additivity of local, fuzzy density fragments and the associated local density matrixes within the framework of the ADMA (Adjustable Density Matrix Assembler) approach. In addition to new results on chemical bonding and the development of macromolecular force methods, the new methodologies are also applicable to QShAR studies in computer-aided drug discovery and in toxicological risk assessment.     

Effects of the CN and NH2 substitutions on the geometrical and optical properties of model vinylfluorenes,based on DFT calculations

A systematic study on the structural and photo-physical properties of model bifluorenevinylene compounds based on the density functional theory (DFT) and its time-dependent (TD-DFT) version is presented. The main aim of this work is to investigate the influence of substitution on bifluorenevinylene using strong electron acceptor CN or electron donor NH₂ groups on: (a) the optimal geometry, (b) torsional potentials and (c) photo-physical properties. Our results indicate that the substitution on the vinylene bridge, leads to the twisting of molecular fragment on the side of added group and are in good overall agreement with experiment. In the case of the amino mono-substituted bifluorenevinylene, the amino group leads to non-planarity at the non-substituted portion of the molecule. The chemical modification also have a pronounced impact on the electronic properties. The shape of the potential energy curves evaluated for the lowest vertically excited states is heavily dependent on the molecular conformation. Finally, we discuss how the structural and electronic information presented here can be useful in designing of novel optical materials as well as understanding of excitation–relaxation phenomena which may occur in various time-dependent optical experiments.     

Intramolecular interactions of L‐phenylalanine: Valence ionization spectra and orbital momentum distributions of its fragment molecules

Intramolecular interactions between fragments of L ‐phenylalanine, i.e., phenyl and alaninyl, have been investigated using dual space analysis (DSA) quantum mechanically. Valence space photoelectron spectra (PES), orbital energy topology and correlation diagram, as well as orbital momentum distributions (MDs) of L ‐phenylalanine, benzene and L ‐alanine are studied using density functional theory methods. While fully resolved experimental PES of L ‐phenylalanine is not yet available, our simulated PES reproduces major features of the experimental measurement. For benzene, the simulated orbital MDs for 1e_1g and 1a_2u orbitals also agree well with those measured using electron momentum spectra. Our theoretical models are then applied to reveal intramolecular interactions of the species on an orbital base, using DSA. Valence orbitals of L ‐phenylalanine can be essentially deduced into contributions from its fragments such as phenyl and alaninyl as well as their interactions. The fragment orbitals inherit properties of their parent species in energy and shape (ie., MDs). Phenylalanine orbitals show strong bonding in the energy range of 14‐20 eV, rather than outside of this region. This study presents a competent orbital based fragments‐in‐molecules picture in the valence space, which supports the fragment molecular orbital picture and building block principle in valence space. The optimized structures of the molecules are represented using the recently developed interactive 3D‐PDF technique. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

Construction of a Shape-Diverse Fragment Set: Design,Synthesis and Screen against Aurora-A Kinase

Historically, chemists have explored chemical space in a highly uneven and unsystematic manner. As an example, the shape diversity of existing fragment sets does not generally reflect that of all theoretically possible fragments. To assess experimentally the added value of increased three dimensionality, a shape-diverse fragment set was designed and collated. The set was assembled by both using commercially available fragments and harnessing unified synthetic approaches to sp³-rich molecular scaffolds. The resulting set of 80 fragments was highly three-dimensional, and its shape diversity was significantly enriched by twenty synthesised fragments. The fragment set was screened by high-throughput protein crystallography against Aurora-A kinase, revealing four hits that targeted the binding site of allosteric regulators. In the longer term, it is envisaged that the fragment set could be screened against a range of functionally diverse proteins, allowing the added value of more shape-diverse screening collections to be more fully assessed.     

Lessons for fragment library design: analysis of output from multiple screening campaigns

Over the past 8 years, we have developed, refined and applied a fragment based discovery approach to a range of protein targets. Here we report computational analyses of various aspects of our fragment library and the results obtained for fragment screening. We reinforce the finding of others that the experimentally observed hit rate for screening fragments can be related to a computationally defined druggability index for the target. In general, the physicochemical properties of the fragment hits display the same profile as the library, as is expected for a truly diverse library which probes the relevant chemical space. An analysis of the fragment hits against various protein classes has shown that the physicochemical properties of the fragments are complementary to the properties of the target binding site. The effectiveness of some fragments appears to be achieved by an appropriate mix of pharmacophore features and enhanced aromaticity, with hydrophobic interactions playing an important role. The analysis emphasizes that it is possible to identify small fragments that are specific for different binding sites. To conclude, we discuss how the results could inform further development and improvement of our fragment library. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

On the importance of the "density per particle" (shape function) in the density functional theory

The central role of the shape function sigma(r) from the density functional theory (DFT), the ratio of the electron density rho(r) and the number of electrons N of the system (density per particle), is investigated. Moreover, its relationship with DFT based reactivity indices is established. In the first part, it is shown that an estimate for the chemical hardness can be obtained from the long range behavior of the shape function and its derivative with respect to the number of electrons at a fixed external potential. Next, the energy of the system is minimized with the constraint that the shape function should integrate to unity; the associated Lagrange multiplier is shown to be related to the electronic chemical potential micro of the system. Finally, the importance of the shape function for both molecular structure, reactivity, and similarity is outlined.     

Molecular weight determination of bulk polymer surfaces by static secondary ion mass spectrometry

The determination of molecular weights at surfaces of bulk polymer materials can be accomplished by static secondary ion mass spectrometry (SIMS) via fragments originating from repeat units and end groups. The intensity ratio of these fragments depends on the polymer chain length as seen for bisphenol-A-polycarbonate and perfluorinated polyethers (Krytox). A kinetic model of fragment ion formation explains the molecular weight dependent fragment intensities and links them to properties of the molecular weight distribution. In the most simple case one obtains the number average molecular weight <M_n> at the surface. This technique can be used for the determination of the molecular weight at bulk polymer surfaces such as a CD-ROM made from polycarbonate by injection molding.     

Group electronegativity and Fukui function studies of the substituent effects in aromatic and inorganic systems

The group electronegativities (GE ) of molecular fragments, including the environmental contributions due to both the electrostatic interactions and electron distribution relaxation, and the Fukui function (FF ) indices of the charge sensitivity analysis (CSA ) are correlated with the known substituent effects in molecular systems. The semiempirical CSA in the atoms-in-molecules (AIM ) resolution has been applied to substituted benzenes and square platinum complexes treated as illustrative examples. The calculated FF indices and GE are both shown to constitute adequate reactivity criteria that qualitatively reproduce the known substituent effects. The FF index (second-order property) is found to be a more sensitive detector of the substituent influence than is the corresponding GE parameter (first-order property). © 1992 John Wiley & Sons, Inc.     

The calculation of electron localization and delocalization indices at the Hartree–Fock, density functional and post-Hartree–Fock levels of theory

 Localization, λ(A), and delocalization indices, δ(A,B), as defined in the atoms in molecules theory, are a convenient tool for the analysis of molecular electronic structure from an electron-pair perspective. These indices can be calculated at any level of theory, provided that first- and second-order electron densities are available. In particular, calculations at the Hartree–Fock (HF) and configuration interaction (CI) levels have been previously reported for many molecules. However, λ(A) and δ(A,B) cannot be calculated exactly in the framework of Kohn–Sham (KS) density functional theory (DFT), where the electron-pair density is not defined. As a practical workaround, one can derive a HF-like electron-pair density from the KS orbitals and calculate approximate localization and delocalization indices at the DFT level. Recently, several calculations using this approach have been reported. Here we present HF, CI and approximate DFT calculations of λ(A) and δ(A,B) values for a number of molecules. Furthermore, we also perform approximate CI calculations using the HF formalism to obtain the electron-pair density. In general, the approximate DFT and CI results are closer to the HF results than to the CI ones. Indeed, the approximate calculations take into account Coulomb electron correlation effects on the first-order electron density but not on the electron-pair density. In summary, approximate DFT and CI localization and delocalization indices are easy to calculate and can be useful in the analysis of molecular electronic structure; however, one should take into account that this approximation increases systematically the delocalization between covalently bonded atoms, with respect to the exact CI results. Received: 13 February 2002 / Accepted: 24 April 2002 / Published online: 18 June 2002     

A configuration analysis for fragment interaction

We propose a modified version of configuration analysis (CA) for the fragment interaction in conjunction with Kitaura’s fragment molecular orbital (FMO) scheme. The proposal is abbreviated as CAFI. The MO sets of fragments are merged and then orthonormalized by the use of a weighted Löwdin orthonormalization. The energy calculation is performed with the concurrent electron relaxation functional (CERF). The relaxation energy is obtained in an orbital-wise fashion and is distinguished as the charge-transfer and the polarization. The utility of CAFI is demonstrated through test calculations on hydrogen-bonding systems.     

Stability and reactivities based on moment analysis

The truncated expansion of a function ¦x¦ is used to obtain the total Hückel -electron energy partitioned into various sums, in terms of moments as well as molecular fragments. The additivity is in general satisfactory for acyclic and cyclic systems, which exhibit a regularity called the generalized Hückel rule which indicates whether a fragment plays the role of stabilization or of destabilization. A unified treatment based on the energy partitioning is proposed for rationalizing aromaticity, reactivities and bond lengths of conjugated hydrocarbons. The relationships between molecular properties and topology can be deduced from inspecting, enumerating or summing the relative contributions of various fragments. Also known as: Yuan-sun Kiang     

Degradation of gas phase decabromodiphenyl ether by resonant interaction with low-energy electrons

Resonance electron attachment in a series of brominated phenyl ethers, including decabromodiphenyl ether (DBDE), was investigated in the gas phase by means of electron transmission spectroscopy (ETS) and dissociative electron attachment spectroscopy (DEAS). Attachment of thermal electrons to DBDE leads to various dissociative decay channels of the temporary molecular anion. In contrast to other bromophenyl ethers, the bromide anion is not the most intense negative fragment. The neutral counterparts of the observed [Br(2)](-) and [C(6)Br(4)O](-) anion fragments are ascribed to the closed-shell species octabromodibenzofuran and hexabromobenzene, respectively, although their formation implies complex atomic rearrangements. Density functional theory calculations are employed to evaluate electron affinities, thermodynamic energy thresholds for production of the anion fragments observed in the DEA spectra and the proton affinities of the corresponding neutral radicals. Since DBDE is one of the most widespread organic pollutants, the present gas-phase DEA study can provide indications on the reaction mechanisms which occur in vivo and cause injuries to living cells.     

Exploiting space‐group symmetry in fragment‐based molecular crystal calculations

Recent developments in fragment‐based methods make it increasingly feasible to use high‐level ab initio electronic structure techniques to molecular crystals. Such studies remain computationally demanding, however. Here, we describe a straightforward algorithm for exploiting space‐group symmetry in fragment‐based methods which often provides computational speed‐ups of several fold or more. This algorithm does not require a priori specification of the space group or symmetry operators. Rather, the symmetrically equivalent fragments are identified automatically by aligning the individual fragments along their principle axes of inertia and testing for equivalence with other fragments. The symmetry operators relating equivalent fragments can then be worked out easily. Implementation of this algorithm for computing energies, nuclear gradients with respect to both atomic coordinates and lattice parameters, and the nuclear hessian is described. © 2014 Wiley Periodicals, Inc.     

Automated site-directed drug design: The generation of a basic set of fragments to be used for automated structure assembly

Summary If a method is to be developed to assemble putative ligands structures in site-directed drug design, from molecular graphs generated in the site, then basic building blocks are needed. Structure assembly is a combinatoric process that needs to be optimised if it is to be tractable. What has to be determined is whether small molecular fragments can have transferable properties from one molecule to another. In this paper we determine all possible combinations of 3-, 4- and 5-atom aliphatic fragments from a small set of atoms H, C, N, O, F or Cl. The frequency of occurrence of these candidate fragments is searched for in the Cambridge Structural Database. A similar analysis is performed on charged fragments. A more restricted search is carried out for P and S and aromatic structures. A basic set of fragments can be derived that have a significant frequency in known crystal structures. The transferability of fragment properties is discussed in subsequent papers.     

Complete sets of structure fragments for interpreting IR spectra using IR databases

This paper studies the possibility of revealing various fragments (not given beforehand) in a structure by analyzing the structures selected from the database as a result of a retrieval by the IR spectrum of the compound; the fragments range from those with two nodes (e.g., C=O, C=C) to those with some limited number of connected nodes. It is shown that complete fragment sets reflecting the composition of the selected compound (fragment compositions) contain the information about the set of bonded fragments of the compound. Various factors affecting analysis of the compiled list of fragments are considered using a particular example. Different techniques for revealing structural information are discussed. Scientific and Technical Center of Chemical Informatics, Novosibirsk Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences. Translated fromZhurnal Strukturnoi Khimii, Vol. 37, No. 2, pp. 368–378, March–April, 1996. Translated by L. Smolina     

Empty-level structure and reactive species produced by dissociative electron attachment to tert-butyl peroxybenzoate

The energy and nature of the gas-phase temporary anion states of tert-butylperoxybenzoate in the 0-6 eV energy range are determined for the first time by means of electron transmission spectroscopy (ETS) and appropriate theoretical calculations. The first anion state, associated with electron capture into a delocalized π* MO with mainly ring and carbonyl character, is found to lie close to zero energy, i.e., sizably more stable (about 2 eV) than the ground (σ*) anion state of saturated peroxides. Dissociative decay channels of the unstable parent molecular anions are detected with dissociative attachment spectroscopy (DEAS), as a function of the incident electron energy, in the 0-14 eV energy range. A large DEA cross-section, with maxima at zero energy, 0.7 and 1.3 eV, is found for production of the (m/e = 121) PhCOO(-) anion fragment, together with the corresponding tert-butoxy neutral radical, following cleavage of the O-O bond. Although with much smaller intensities, a variety of other negative currents are observed and assigned to the corresponding anion fragments with the support of density functional theory calculations.     

Spectral and luminescent properties of hydroxyazomethines of indoline spiropyrans

Spectral and luminescent properties of novel bifunctional compounds 1–3 based on indole spiropyrans and hydroxyazomethines have been studied in comparison with the properties of the model compounds 5’-substituted spiropyrans and azomethines in organic solvents and PMMA films at 293 and 77 K. Luminescence of compounds 1–3 is due to the presence of the azomethine fragment conjugated with the indoline ring of the spiropyran moiety and determining the long-wavelength absorption band of 1–3. Depending on the solvent, temperature, and the substituent, various combinations of the structures of the chromophore fragments are observed in 1–3: the imine or amine form of the azomethine fragment and the spirocyclic or merocyanine form of the spiropyran fragment.