Visualization of Molecular Orbitals and the Related Electron Densities

When plotting different orbitals with consistent contour values, one can create illusions about the relative extension of charge distributions. We suggest that the comparison is not biased when plots reproduce the same fraction of the total charge. We have developed an algorithm and software that facilitate this type of visualization. We propose superimposing molecules and associated orbitals, and creating cross-sections by selecting a particular part of the orbital limited by pre-defined planes

Valence and Dipole-Bound Anions of the Most Stable Tautomers of Guanine

Anionic states of guanine, which is the only nucleic acid base of which the anions have not yet been studied in either photoelectron spectroscopic (PES) or Rydberg electron transfer (RET) experiments, have been characterized for the four most stable tautomers of neutral guanine using a broad spectrum of electronic structure methods from the density functional theory, with the B3LYP exchange−correlation functional, to the coupled-cluster method, with single, double, and perturbative triple excitations. Both valence and dipole-bound anionic states were addressed. We identified some of the difficulties facing future PES or RET experiments on the anion of guanine. Even if guanine is successfully transferred to the gas phase without thermal decomposition, it is critical to have the canonical amino−oxo (G) and both amino−hydroxy (GH and GHN7H) tautomers in the beam, not only the most stable, a noncanonical, amino−oxo tautomer (GN7H), as the latter does not support an adiabatically bound anionic state. We also suggested a scheme for enrichment of gas-phase guanine with the canonical tautomer, which is not the most stable in the gas phase, but which is of main interest due to its biological relevance. The tautomers G, GN7H, and GHN7H support vertically bound valence anionic states with the CCSD(T) value of vertical detachment energy of +0.58, +0.21, and +0.39 eV, respectively. These anionic states are, however, adiabatically unbound and thus metastable. The vertical electronic stability of these valence anionic states is accompanied by serious “buckling” of the molecular skeleton. The G and GHN7H tautomers support dipole-bound states with the CCSD(T) values of adiabatic electron affinity of 65 and 36 meV, respectively. A contribution from higher-than-second-order correlation terms represents, respectively, 48 and 68% of the total vertical electron detachment energy determined at the CCSD(T) level

Insights into Multi-Objective Design of Metal–Organic Frameworks

Metal–organic frameworks (MOFs) are a highly versatile class of crystalline porous materials. In recent years, many diverse MOF materials have been experimentally realized, exhibiting a wide range of underlying topologies. In this work, we guide material design efforts by identifying the most promising MOF topologies for achieving high surface area frameworks. High surface area is one of the most targeted properties of MOF materials for adsorption applications, and we focus on evaluating the achievable surface area (gravimetric, volumetric, and a composite function) within each topological class by means of multiobjective optimization, illustrating that researchers can focus on a few select topologies to achieve a particular balance between gravimetric and volumetric surface area

Optimization-Based Design of Metal–Organic Framework Materials

Metal–organic frameworks (MOFs) are a class of porous materials constructed from metal or metal oxide building blocks connected by organic linkers. MOFs are highly tunable structures that can in theory be custom designed to meet the specific pore geometry and chemistry required for a given application such as methane storage or carbon capture. However, due to the sheer number of potential materials, identification of optimal MOF structures is a significant challenge. In this contribution we describe an automated technique for MOF design based on mathematical optimization. Optimization is performed on linkers represented by abstract space-filling shapes, in order to generalize the desirable geometric parameters describing linkers, and optimal shapes are projected to real molecules to illustrate realistic MOFs exhibiting the calculated properties. Six examined topologies of MOF and two distinct geometrical pore properties relevant to guest adsorption phenomena are explored. We demonstrate that the optimal shapes of linkers depend on both the topology and the property of interest and moreover that synthetically challenging linkers are not necessary to achieve the most promising candidate materials

How Do the Partitioning Properties of Polyhalogenated POPs Change When Chlorine Is Replaced with Bromine?

Information about the mobility and the partitioning properties of brominated persistent organic pollutants, the environmental levels of which are sometimes higher than those of the chlorinated analogues, is limited. We estimated n-octanol/water (log KOW), n-octanol/air (log KOA), and air/water (log KAW) partition coefficients for 1436 chloro- and bromo-analogues of dibenzo-p-dioxins, dibenzofurans, biphenyls, naphthalenes, diphenyl ethers, and benzenes by employing quantitative structure−property relationship (QSPR) techniques. The searches for similar partitioning patterns were performed by means of two-dimensional cluster analysis. Five classes of compounds were identified. Each of the class is characterized by similar partition coefficients and, in consequence, similar environmental properties. Finally the data was fitted into a simple multimedia model involving the partitioning map. In addition, we found that the changes in the partition coefficients upon the replacement of chlorine with bromine were constant: 0.11, 0.31, and −0.21 per bromine atom for log KOW, log KOA, and log KAW, respectively. On the basis of this observation, a method for rapid estimation of changes in the partition coefficient upon chlorine−bromine substitution was proposed

pyIAST: Ideal Adsorbed Solution Theory (IAST) Python Package

Ideal adsorbed solution theory (IAST) is a widely-used thermodynamic framework to readily predict mixed-gas adsorption isotherms from a set of pure-component adsorption isotherms. We present an open-source, user-friendly Python package, pyIAST, to perform IAST calculations for an arbitrary number of components. pyIAST supports several common analytical models to characterize the pure-component isotherms from experimental or simulated data. Alternatively, pyIAST can use numerical quadrature to compute the spreading pressure for IAST calculations by interpolating the pure-component isotherm data. pyIAST can also perform reverse IAST calculations, where one seeks the required gas phase composition to yield a desired adsorbed phase composition

Chemical Hieroglyphs: Abstract Depiction of Complex Void Space Topology of Nanoporous Materials

In general, most porous materials are so complex that structural information cannot be easily observed with 3D visualization tools. To address this problem, we have developed a special abstract 2D representation to depict all important topological features and geometrical parameters. Our approach involves reducing these structures based on symmetry and perceived building blocks to a compressed, graph representation that allows for quick structure analysis, classification, and comparison

History and Utility of Zeolite Framework-Type Discovery from a Data-Science Perspective

Mature applications such as fluid catalytic cracking and hydrocracking rely critically on early zeolite structures. With a data-driven approach, we find that the discovery of exceptional zeolite framework types around the new millennium was spurred by exciting new utilization routes. The promising processes have yet not been successfully implemented (“valley of death” effect), mainly because of the lack of thermal stability of the crystals. This foreshadows limited deployability of recent zeolite discoveries that were achieved by novel crystal synthesis routes

Cylindrical Projection of Electrostatic Potential and Image Analysis Tools for Damaged DNA: The Substitution of Thymine with Thymine Glycol

Changes of electrostatic potential around the DNA molecule resulting from chemical modifications of nucleotides may play a role in enzymatic recognition of damaged sites. Effects of chemical modifications of nucleotides on the structure of DNA have been characterized through electronic structure computations. Quantum mechanical structural optimizations of fragments of five pairs of nucleotides with thymine or thymine glycol were performed at the density functional level of theory with a B3LYP exchange-correlation functional and 6-31G(d,p) basis sets. The electrostatic potential (EP) around DNA fragments was projected on a cylindrical surface around the double helix. The 2D maps of EP of intact and damaged DNA fragments were compared using image analysis methods to identify and measure modifications of the EP that result from the occurrence of thymine glycol. It was found that distortions of phosphate groups and displacements of the accompanying countercations by up to ∼0.5 Å along the axis of DNA are clearly reflected in the EP maps. Modifications of the EP in the major groove of DNA near the damaged site are also reported

Discovery of Most Stable Structures of Neutral and Anionic Phenylalanine through Automated Scanning of Tautomeric and Conformational Spaces

We have developed a software tool for combinatorial generation of tautomers and conformers of small molecules. We have demonstrated it by performing a systematic search for the most stable structures of neutral and anionic phenylalanine (Phe) using electronic structure methods. For the neutral canonical tautomer we found out that the conformers <i>with</i> and <i>without</i> the intramolecular (O)­H···NH₂ hydrogen bond are similarly stable, within the error bars of our method. A unique IR signature of the conformer without the hydrogen bond has been identified. We also considered anions of Phe, both valence type and dipole-bound. We have found out that tautomers resulting from proton transfer from the carboxylic OH to the phenyl ring do support valence anions that are vertically strongly bound, with electron vertical detachment energies (VDE) in a range of 3.2–3.5 eV. The most stable conformer of these valence anions remains adiabatically unbound with respect to the canonical neutral by only 2.17 kcal/mol at the CCSD­(T)/aug-cc-pVDZ level. On the basis of our past experience with valence anions of nucleic acid bases, we suggest that the valence anions of Phe identified in this report can be observed experimentally. The most stable conformer of canonical Phe is characterized by an adiabatic electron affinity of 53 meV (a dipole-bound state)