X‐Shaped Polycyclic Aromatic Hydrocarbons: Optical Properties and Tunable Assembly Ability

Although a number of synthetic methodologies have been developed to prepare stable polycyclic aromatic hydrocarbons (PAHs), much less research has been devoted to functionalizing the peripheries of molecules to tune the self‐assembly ability or introduce functional groups without altering their photophysical properties. Herein, we report twisted “X”‐shaped molecules prepared through annulation of hexacene with benzoanthracene on the zigzag edge, and an investigation of their photophysical properties and self‐assembly properties. The shape‐complementary “X”‐shaped molecules prefer to dimerize, while the π‐extension would lead to one‐dimensional π‐stacking. Our findings give some insights into the design of stable PAHs without disturbing the electronic structures.     

Conjugated Oligomers and Polymers Sheathed with Designer Side Chains

Conjugated polymers (CPs) are often referred to as molecular wires because of their quasi one‐dimensional electronic wavefunctions delocalized along the polymer chains. However, in the solid state, CPs tend to self‐assemble through π‐stacking, which greatly attenuates the one‐dimensional nature. By molecular design, CPs can be molecularly insulated just like electric power cords, resulting in so‐called “insulated” molecular wires (IMWs). In this Focus Review, we will discuss their unique photophysical, electronic, and mechanical properties which originate from the absence of π‐stacking.     

molSimplify: A toolkit for automating discovery in inorganic chemistry

We present an automated, open source toolkit for the first‐principles screening and discovery of new inorganic molecules and intermolecular complexes. Challenges remain in the automatic generation of candidate inorganic molecule structures due to the high variability in coordination and bonding, which we overcome through a divide‐and‐conquer tactic that flexibly combines force‐field preoptimization of organic fragments with alignment to first‐principles‐trained metal‐ligand distances. Exploration of chemical space is enabled through random generation of ligands and intermolecular complexes from large chemical databases. We validate the generated structures with the root mean squared (RMS) gradients evaluated from density functional theory (DFT), which are around 0.02 Ha/au across a large 150 molecule test set. Comparison of molSimplify results to full optimization with the universal force field reveals that RMS DFT gradients are improved by 40%. Seamless generation of input files, preparation and execution of electronic structure calculations, and post‐processing for each generated structure aids interpretation of underlying chemical and energetic trends. © 2016 Wiley Periodicals, Inc.     

Investigation of the Electronic Structure of Alkyl Allyl Radicals

The electronic structure of the homologous series of CH₃(CH₂)_nCHCHCH₂ (n = 0÷5) allyl all radicals is studied. The obtained spin density distribution is used to determine the fragment serving as the radical center. The delocalization of spin density over the basin of the radical center is shown to be responsible for two free valencies associated with two classical canonical structures (the conjugated fragment). The conjugation phenomenon is studied and electronic parameters are determined for the “standard” conjugated fragment CHCHCH₂.     

Semiempirical implementation of strictly localized geminals for analysis of molecular electronic structure

Approximate electronic trial wave function taken as the antisymmetrized product of strictly localized geminals (APSLG) is implemented for semiempirical analysis of molecular electronic structure of “organic” compounds and for calculations of their heats of formation. This resulted in an O(N)‐scaling method. Using the MINDO/3 form of the semiempirical Hamiltonian with reparameterized β_AB values in combination with the APSLG form of the wave function yields the computational procedure BF'98. Calculations on the heats formation and the equilibrium geometries for a wide range of molecules show that the APSLG‐MINDO/3 approach is more favorable than its self‐consistent field‐based counterpart. Also, the APSLG formalism allows to interpret molecular electronic wave function in chemically sensible terms. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 752–764, 2001     

Protein-Templated Fragment Ligations—From Molecular Recognition to Drug Discovery

Protein-templated fragment ligation is a novel concept to support drug discovery and can help to improve the efficacy of protein ligands. Protein-templated fragment ligations are chemical reactions between small molecules (“fragments”) utilizing a protein's surface as a reaction vessel to catalyze the formation of a protein ligand with increased binding affinity. The approach exploits the molecular recognition of reactive small-molecule fragments by proteins both for ligand assembly and for the identification of bioactive fragment combinations. In this way, chemical synthesis and bioassay are integrated in one single step. This Review discusses the biophysical basis of reversible and irreversible fragment ligations and gives an overview of the available methods to detect protein-templated ligation products. The chemical scope and recent applications as well as future potential of the concept in drug discovery are reviewed.     

Triisopropylsilylethynyl‐Functionalized Graphene‐Like Fragment Semiconductors: Synthesis,Crystal Packing,and Density Functional Theory Calculations

Tri‐isopropylsilylethynyl (TIPS)‐functionalized polycyclic aromatic hydrocarbon (PAH) molecules incorporate structural components of graphene nanoribbons and represent a family of model molecules that form organic crystal semiconductors for electronic devices. Here, we report a series of TIPS‐functionalized PAHs and discuss their electronic properties and crystal packing features. We observe that these soluble compounds easily form one‐dimensional (1 D) packing arrangements and allow a direct evolution of the π stacking by varying the geometric shape. We find that the aspect ratio between length and width plays an important role on crystal packing. Our result indicates that when the PAH molecules have zigzag edges, these can provide enough volume for the molecules to rotate and reorient, alleviating the unfavorable electrostatic interactions found in perfectly cofacial π–π stacking. Density functional theory calculations were carried out to provide insights into how the molecular geometric shape influences the electronic structure and transport properties. The calculations indicate that, among the compounds studied here, “brick‐layer” stacks provide the highest hole mobility.     

A Periodic System of Supramolecular Elements

Chemistry “beyond the molecule” is based on weak, noncovalent, and reversible interactions. As a consequence of these bonds being weak, structural organization by folding and self‐assembly can only be fully exploited with larger molecules that can provide multiple binding sites. Such “supramolecules” can now be synthesized and their folding into desired conformations predicted. A new level of chemistry can now be realized through the creation of non‐natural entities composed of molecular building blocks with defined secondary structures. Herein we define these building blocks as “supramolecular elements”. We anticipate that further research on such large molecules will reveal construction principles dictated by recurring motifs that govern structure formation through folding and self‐assembly. These principles are comparable to the organization of atoms in the Periodic Table of Chemical Elements and may lead to the establishment of a Periodic System of Supramolecular Elements.     

Equivalent potential of water for electronic structure of asparagine

The equivalent potential of water for the electronic structure of asparagine(Asn) is constructed by using the first‐principles, all‐electron, ab initio calculation. The process is composed of three steps. The first step is to determine the geometric structure of Asn+nH₂O system with a minimum energy. The second step is to calculate the electronic structure of Asn with the potential of water molecules by using the self‐consistent cluster‐embedding (SCCE) method, based on the result obtained in the first step. The last step is to calculate the electronic structure of Asn with the potential of dipole after replacing water molecules with dipoles. The results show that the major effect of water molecules on Asn' electronic structure be raising the occupied electronic states by 0.034 Ry on average and narrowing energy gap by 0.91%. The effect of water on the electronic structure of Asn can be well simulated by using dipole potential. The obtained equivalent potential can be applied directly to the electronic structure calculation of protein in solution by using the SCCE method. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Structure-based fragment hopping for lead optimization using predocked fragment database

In this work, we describe a structure-based de novo optimization process, called "LeadOp" (short for lead optimization), that decomposes a compound into fragments of different molecular components either by chemical or user-defined rules. Each fragment is evaluated through a predocked fragment database that ranks fragments according to specific fragment-receptor binding interactions, replacing fragments that contribution the least to binding and finally reassembling the fragments to form a new ligand. The fundamental idea is to replace "bad" fragments of a ligand with "good" fragments while leaving the core of the ligand intact, thus improving the compound's activity. The molecular fragments were selected from a collection of 27,417 conformers that are the fragments of compounds in the DrugBank database. The collection of molecular fragments are docked to the target's binding site and evaluated using group efficiency (calculated binding affinity divided by the number of heavy atoms), and the "strongest" binder is selected. The LeadOp method was tested with two biomolecular systems: mutant B-Raf kinase and human 5-lipoxygenase. The LeadOp methodology was able to optimize the query molecules and systematically developed improved analogs for each of our example systems.     

Rapid sampling of all‐atom peptides using a library‐based polymer‐growth approach

We adapted existing polymer growth strategies for equilibrium sampling of peptides described by modern atomistic forcefields with a simple uniform dielectric solvent. The main novel feature of our approach is the use of precalculated statistical libraries of molecular fragments. A molecule is sampled by combining fragment configurations—of single residues in this study—which are stored in the libraries. Ensembles generated from the independent libraries are reweighted to conform with the Boltzmann‐factor distribution of the forcefield describing the full molecule. In this way, high‐quality equilibrium sampling of small peptides (4–8 residues) typically requires less than one hour of single‐processor wallclock time and can be significantly faster than Langevin simulations. Furthermore, approximate, clash‐free ensembles can be generated for larger peptides (up to 32 residues in this study) in less than a minute of single‐processor computing. We discuss possible applications of our growth procedure to free energy calculation, fragment assembly protein‐structure prediction protocols, and to “multi‐resolution” sampling. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

Synthesis of novel asymmetric dendritic‐linear‐dendritic block copolymers via “living” anionic polymerization of ethylene oxide initiated by dendritic macroinitiators

The first synthesis of asymmetric dendritic‐linear‐dendritic ABC block copolymers, that contain a linear B block and dissimilar A and C dendritic fragments is reported. Third generation poly(benzyl ether) monodendrons having benzyl alcohol moiety at their “focal” point were activated by quantitative titration with organometallic anions and the resulting alkoxides were used as initiators in the “living” ring‐opening polymerization of ethylene oxide. The reaction proceeded in controlled fashion at 40–50 °C affording linear‐dendritic AB block copolymers with predictable molecular weights (M_w = 6000–13,000) and narrow molecular weight distributions (M_w/M_n = 1.02–1.04). The propagation process was monitored by size‐exclusion chromatography with multiple detection. The resulting “living” copolymers were terminated by reaction either with HCl/tetrahydrofuran or with a reactive monodendron that differed from the initiating dendron not only in size, but also in chemical composition. The asymmetric triblock copolymers follow a peculiar structure‐induced self‐assembly pattern in block‐selective solvents as evidenced by size‐exclusion chromatography in combination with multi‐angle light scattering. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 5136–5148, 2007     

A general approach for atom-type assignment and the interconversion of molecular structure files

In molecular modeling projects which require use of several different computer programs, one encounters problems in sharing data between programs. One difficult problem is the conversion of atom types from one program's definition to another. A second problem is the conversion of a polymer, such as a protein or polynucleotide molecule, from a “general” program, which understands molecules as a collection of atoms, to a “polymer” program, which understands molecules as a collection of molecular fragments stored in some library. We describe here a new method by which atom types are deduced from the environment of each atom. We use the Daylight Chemical Information Systems library of programs to deduce the atom types based only on the atomic symbol, connectivity and formal charge of each atom in the molecule. We also describe a method by which the polypeptide nature and sequence of a molecule can be deduced from minimal information about the atoms in the molecule. We have written a computer program which demonstrates this method. This program deduces atom types for AMBER, GRIN/GRID, CHARMm, and ALOGP. It will also produce input files for the AMBER/PREP fragment library preparation program.     

Automated site-directed drug design: An assessment of the transferability of atomic residual charges (CNDO) for molecular fragments

Summary In this paper a database of atomic residual charges has been constructed for all the molecular fragments defined previously in a combinatorial search of the Cambridge Structural Database. The charges generated for the atoms in each fragment are compared with charges calculated for whole molecules containing those fragments. The fragment atomic charges lie within 1 S.D. of the mean for 68%, and within 2 S.D. for 91%, of the atoms whose charges were computed for whole molecules. The actual charges on any atom are strongly influenced by the adjacent connected atoms. There is a large spread of atomic residual charge within the fragments database.     

Enzymatic Synthesis of a DNA Triblock Copolymer that is Composed of Natural and Unnatural Nucleotides

DNA molecules have come under the spotlight as potential templates for the fabrication of nanoscale products, such as molecular‐scale electronic or photonic devices. Herein, we report an enhanced approach for the synthesis of oligoblock copolymer‐type DNA by using the Klenow fragment exonuclease minus of E. coli DNA polymerase I (KF^?) in a multi‐step reaction with natural and unnatural nucleotides. First, we confirmed the applicability of unnatural nucleotides with 7‐deaza‐nucleosides—which was expected because they were non‐metalized nucleotides—on the unique polymerization process known as the “strand‐slippage model”. Because the length of the DNA sequence could be controlled by tuning the reaction time, analogous to a living polymerization reaction on this process, stepwise polymerization provided DNA block copolymers with natural and unnatural bases. AFM images showed that this DNA block copolymer could be metalized sequence‐selectively. This approach could expand the utility of DNA as a template.     

Are water–aromatic complexes always stabilized due to π–H interactions? LMP2 study

Eight complexes of various aromatic molecules with water have been studied theoretically at the local Møller–Plesset 2nd order theory (LMP2)/aug‐cc‐pVTZ(‐f)//LMP2/6‐31+G* level of theory. Two types of complexes can be formed, depending on the electronic structure of aromatic molecules. Donor hydrocarbons form A‐type complexes, while aromatics bearing electron‐withdrawing substituents form B‐type complexes. A‐type complexes are stabilized due to π–H interactions with the OH bond pointing to the aromatic molecule plane, while B‐type complexes have geometry with the oxygen atom pointing to the aromatic molecule plane stabilized by the interaction of highest occupied molecular orbital (HOMO) of water molecule with π* orbitals of the aromatics. It has been found that a (? HOMO–lowest unoccupied molecular orbital (LUMO)/2 value of aromatic molecule, which can be called “molecular electronegativity,” is useful to predict the type of complex formed by aromatic molecule and water. Aromatic hydrocarbons with “molecular electronegativity” of <0.15 tend to form A‐type complexes, while aromatic molecules with “molecular electronegativity” of <0.15 a.u. form B‐type complexes. The binding energy of water–aromatic complexes undergoes a minimum in the area of switching from A‐type to B type complexes, which can be rationalize in terms of frontier orbital interactions. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005