Bonded Atom Pairs Research Articles

Computational prediction of MOFs with the potential to improve the efficiency of industrial CO2 capture

Capturing and storing carbon dioxide produced during industrial production operations has become a global focus in terms of energy conservation and emission reduction, especially for high-emission sources such as coal-fired power plants. In this study, the high-throughput Grand Canonical Monte Carlo (HT-GCMC) simulation method was used to assess the performance of 4,188 MOFs that were carefully selected from a comprehensive pool of 10,143 CoRE-MOFs using specific criteria. Exploratory data analysis for the population demonstratedthe effect of structural properties and isosteric enthalpy on MOFs’ adsorption performance. 90 MOFs were identified as superior adsorbents that show a strong adsorption performance when screening based on four filter criteria considered important for improving industrial economic efficiency. As the desorption pressure was increased, numerous MOFs maintained their potential and met the four screening conditions. This implies that there is room to increase the desorption pressure, which suggests a potential energy saving in practical applications. HT-GCMC was applied to calculate the adsorption properties of the 90 potential MOFs using various industrial CO2 concentration levels and showed the versatility of these MOFs for use in various industrial CO2 separation schemes. In addition, the adsorption mechanism of potential MOFs was analyzed, revealing specific numerical ranges for Qst and structural characteristics that correlate with their performance. Character analysis of 90 potential MOFs revealed that the elements O, N, Zn, and Cu have the highest content; C-O, Cu-O, C-N, and Cu-N are the bonded atom pairs most commonly seen in these 90 potential MOFs.

The effect of molecular dynamics sampling on the calculated observable gas-phase structures.

In this study, we compare the performance of various ab initio molecular dynamics (MD) sampling methods for the calculation of the observable vibrationally-averaged gas-phase structures of benzene, naphthalene and anthracene molecules. Nose-Hoover (NH), canonical and quantum generalized-Langevin-equation (GLE) thermostats as well as the a posteriori quantum correction to the classical trajectories have been tested and compared to the accurate path-integral molecular dynamics (PIMD), static anharmonic vibrational calculations as well as to the experimental gas electron diffraction data. Classical sampling methods neglecting quantum effects (NH and canonical GLE thermostats) dramatically underestimate vibrational amplitudes for the bonded atom pairs, both C-H and C-C, the resulting radial distribution functions exhibit nonphysically narrow peaks. This deficiency is almost completely removed by taking the quantum effects on the nuclei into account. The quantum GLE thermostat and a posteriori correction to the canonical GLE and NH thermostatted trajectories capture most vibrational quantum effects and closely reproduce computationally expensive PIMD and experimental radial distribution functions. These methods are both computationally feasible and accurate and are therefore recommended for calculations of the observable gas-phase structures. A good performance of the quantum GLE thermostat for the gas-phase calculations is encouraging since its parameters have been originally fitted for the condensed-phase calculations. Very accurate molecular structures can be predicted by combining the equilibrium geometry obtained at a high level of electronic structure theory with vibrational amplitudes and corrections calculated using MD driven by a lower level of electronic structure theory.

Mesomeric effect on the structural and electronic properties of 4-(2-tert-butyl-4-methylphenoxy)phthalonitrile

The molecular and crystal structures of the title compound, C19H18N2O, were determined and characterized by single crystal X-ray diffraction and spectroscopic methods. Details of the molecular geometry imply that there is a mesomeric effect between the electron-withdrawing N atoms of nitrile substituents and electron-donating O atom. Formally, single central O–Car bond lengths are considerably different from each other. O–Car distance to phthalonitrile ring is shorter than the other O–Car distance due to mesomeric effect under discussion. In addition to structural and spectral evidences, possible results from mesomerism of the compound were investigated by topological analysis on the electronic properties using quantum theory of atoms in molecules (QTAIM) approach. It is inferred from topological analysis that the nitrile group in para position has slightly stronger mesomeric effect than that in meta position due to diffusive double charge separation property during meta mesomerism of the compound. Mesomeric effect revealing itself by differences in delocalization indices between certain bonded atom pairs results in considerable decrease in aromaticity of phthalonitrile ring.

Design and Evaluation of Bonded Atom Pair Descriptors

Atom pairs have been among the first systematically derived fragment-type topological descriptors and have been one of the origins of two-dimensional fingerprint searching. These descriptors continue to be popular and widely used to this date. Herein we introduce a new type of atom pair descriptors, bonded atom pairs, that exclusively capture short-range atom environment information and, thus, depart in their design from other topological descriptors that enumerate bond paths of varying length. Bonded atom pairs combine different types of structural information including element type, hybridization state, aliphatic/aromatic character, and cyclic/acyclic arrangement. Systematic design led to a set of 117 bonded atom pairs, all of which exist in synthetic compounds. A further expanded bonded atom pair set accounting for specific halogen atoms and including a total of 159 descriptors is also provided. Atom pair distribution and frequency analysis in sets of compounds having different selectivity reveals that both conventional and bonded atom pairs capture complementary structural information. In similarity searching, bonded atom pairs meet or exceed the performance of standard atom pairs and structural fragment fingerprints. The complementary nature of structural information captured by atom pairs of different design is also reflected by individual search calculations. Taken together, our findings indicate that bonded atom pairs extend the current repertoire of topological molecular descriptors.

A simple approach to electronic charge induction in atomistic simulations

A scheme is presented for periodically updating atom-centered partial charges due to changing local electric fields that arise during the course of a molecular simulation. The effects of electrostatic induction, due to polarization of the local electron density of bonded atom pairs, are realized through the approximation of the bond polarizability tensor as being cylindrically symmetric and directed along the bond axis, with negligible lateral polarizability. This simplification allows the reduction of polarization effects to a scalar bond ‘polarization parameter’, and subsequent partitioning of the local electron density into charge modifiers located at atom centers. The induced charges assigned to each atom are determined self-consistently. This simplification permits a reasonable approximation of both the magnitude and direction of molecular dipole moments and of molecular polarizabilities in the case of small-molecule fluorocarbons. The model is extended to the calculation of atom-centered partial atomic charges for two conformations of poly(vinylidenefluoride). The proposed method fits well into the framework of established atomistic simulation techniques based on Coulombic nonbonded atomic interactions.

Calculation of the cartesian components of average internuclear displacements in CO 2 and CS 2 from the force fields in natural curvilinear internal coordinates

The Cartesian components of average internuclear distances for bonded atom pairs in CO 2 and CS 2 were calculated by a perturbation heory of second-order in a large temperature interval from spectroscopic force fields expanded in a power series of natural curvilinear internal coordinates. It is shown that the harmonic pattern of the linear term <Δ Z> makes a significant contribution to the average internuclear distance. The temperature dependence of average distance parameters under various definitions was estimated and discussed.

Can X-ray data distinguish bonding effects from vibrational smearing?

The frequent practice of combining X-ray and neutron diffraction for distinguishing vibrational smearing from charge deformation due to chemical bonding is neither necessary nor completely satisfactory. The two effects occur principally in distinct regions of real and reciprocal space. They can be distinguished by X-ray data alone provided these extend to reciprocal radii d* > 2 Å- 1 and provided the refinement program allows explicitly for the bonding deformation. The success of this separation can be tested by comparison of the vibration ellipsoids of bonded atom pairs, which should have equal amplitudes in the bond direction. Application of this 'rigid-bond' test to four recent refinements using the charge deformation model shows the vibration parameters to be largely unbiased, as those from parallel spherical-atom refinements are not. Hydrogen vibration parameters cannot be derived from X-ray data because of large deformation densities at the nuclei; nor do they satisfy the rigid-bond postulate.

On an empirical rule for the mean amplitudes of bonded atom pairs

It has been shown on empirical grounds that the bond stretching mean amplitude of a molecule which corresponds to the highest stretching frequency is in general very close to the minimum value allowed by vibrational frequencies for certain types of molecules. By using the theory of molecular vibrations, this has been shown to have close relation to the empirical knowledge that the normal mode of a stretching vibration has essentially no dependence on the bending coordinates when a stretching and a bending vibration occur in the same symmetry species.

The Mean Amplitudes of Thermal Vibrations in Polyatomic Molecules. II. An Approximate Method for Calculating Mean Square Amplitudes

A simple method of the calculation of the mean amplitudes of both directly bonded atom pairs and nonbonded ones is proposed by approximating the function cothx by 1/x+x/4. The enumeration of the L matrix, the most time-consuming procedure, is replaced by the calculation of the inverse matrix F−1 from the potential energy matrix. The formulae obtained are applicable with reasonable accuracy (4 percent) to almost all the cases except the atom pairs having higher frequencies than 1200 cm−1. For the latter cases modified formulas are presented by using hyperbolic cotangent function. It is also revealed that, if some allowance be made for the errors of the mean amplitudes, a definite value can be assigned to the mean amplitude of a given pair of atoms, without referring to the structure of the other part of the molecule. Reliable values of the mean amplitudes are computed for some typical atom pairs, by the use of the force constants of Urey-Bradley type obtained by the analysis of the vibrational spectra.