Journal of Computational Chemistry

doi: 10.1002/jcc.23866pmid: N/A

A large‐scale global search of pentaatomic planar tetracoordinate silicon (ptSi) with 14 valence electrons is performed. A total of 129 molecular systems SiXnYmq (n+m=4; q=0,±1,‐2; X, Y=main group elements from H to Br) are considered, among which 50 systems possess a ptSi structure and 9 systems have the global minimum ptSi. On page 355 (DOI: 10.1002/jcc.23792), Jing Xu and Yi‐hong Ding propose two strategies to generalize the global 14e‐ptSi; 1) introducing the alkaline/alkaline‐earth elements and 2) breaking the peripheral bonding.

doi: 10.1002/jcc.23865pmid: N/A

The reflection of a methane molecule forms the non‐covalent cluster (CH4)2. The interactions between the molecules are represented by a spark while the water waves evoke the mutual perturbations of the two monomers. On page 361 (DOI: 10.1002/jcc.23798), Vícto r Duarte Alaniz, Tomás Rocha‐Rinza, and Gabriel Cuevas analyze hydrophobic interactions (HIs) within the methane dimer using Atoms in Molecules and Symmetry Adapted Perturbation Theory (SAPT). Mollier‐like diagrams are built to estimate the interaction energies and their SAPT components in hydrocarbon chains regardless of their size and number. This new approach might prove useful for studying intramolecular HIs and those in large systems where electronic structure or SAPT calculations are very expensive or prohibitive.

Xu, Jing; Ding, Yi‐hong

doi: 10.1002/jcc.23792pmid: 25430676

Designing and characterizing the compounds with exotic structures and bonding that seemingly contrast the traditional chemical rules are a never‐ending goal. Although the silicon chemistry is dominated by the tetrahedral picture, many examples with the planar tetracoordinate‐Si skeletons have been discovered, among which simple species usually contain the 17/18 valence electrons. In this work, we report hitherto the most extensive structural search for the pentaatomic ptSi with 14 valence electrons, that is, SiXnYmq (n + m = 4; q = 0, ±1, −2; X, Y = main group elements from H to Br). For 129 studied systems, 50 systems have the ptSi structure as the local minimum. Promisingly, nine systems, that is, Li3SiAs2−, HSiY3 (Y = Al/Ga), Ca3SiAl−, Mg4Si2−, C2LiSi, Si3Y2 (Y = Li/Na/K), each have the global minimum ptSi. The former six systems represent the first prediction. Interestingly, in HSiY3 (Y = Al/Ga), the H‐atom is only bonded to the ptSi‐center via a localized 2c–2e σ bond. This sharply contradicts the known pentaatomic planar‐centered systems, in which the ligands are actively involved in the ligand–ligand bonding besides being bonded to the planar center. Therefore, we proposed here that to generalize the 14e‐ptSi, two strategies can be applied as (1) introducing the alkaline/alkaline‐earth elements and (2) breaking the peripheral bonding. In light of the very limited global ptSi examples, the presently designed six systems with 14e are expected to enrich the exotic ptSi chemistry and welcome future laboratory confirmation. © 2014 Wiley Periodicals, Inc.

Duarte Alaniz, Víctor; Rocha‐Rinza, Tomás; Cuevas, Gabriel

doi: 10.1002/jcc.23798pmid: 25470384

Hydrophobic Interactions (HIs) are important in many phenomena of molecular recognition in chemistry and biology. Still, the relevance of HIs is sometimes difficult to evaluate particularly in large systems and intramolecular interactions. We put forward a method to estimate the magnitude and the different contributions of a given HI of the C···C, HC···H, and H···H type through (i) the analysis of the electron density in the intermolecular region for eleven relative orientations of the methane dimer and (ii) the subsequent decomposition of the corresponding interaction energy in physically significant contributions using Symmetry Adapted Perturbation Theory (SAPT). Strong correlations were found between the topological properties of ρ(r) calculated at intermolecular bond critical points and EintSAPT plus its different contributions with the C···C distance of the considered orientations of (CH4)2. These correlations were used to construct Mollier‐like diagrams of EintSAPT and its components as a function of the separation between two carbons and the orientation of the groups bonded to these atoms. The ethane dimer and tert‐butylcyclohexane are used as representative examples of this new approach. Overall, we anticipate that this new method might prove useful in the study of both intramolecular and intermolecular HIs particularly of those within large systems wherein SAPT or electronic structure calculations are computationally expensive or even prohibitive. © 2014 Wiley Periodicals, Inc.

Chen, Siyan; Yi, Shasha; Gao, Wenmei; Zuo, Chuncheng; Hu, Zhonghan

doi: 10.1002/jcc.23808pmid: 25487650

We comprehensively illustrate a general process of fitting all‐atom molecular mechanics force field (FF) parameters based on quantum mechanical calculations and experimental thermodynamic data. For common organic molecules with free dihedral rotations, this FF format is comprised of the usual bond stretching, angle bending, proper and improper dihedral rotation, and 1–4 scaling pair interactions. An extra format of 1–n scaling pair interaction is introduced when a specific intramolecular rotation is strongly hindered. We detail how the preferred order of fitting all intramolecular FF parameters can be determined by systematically generating characteristic configurations. The intermolecular Van der Waals parameters are initially taken from the literature data but adjusted to obtain a better agreement between the molecular dynamics (MD) simulation results and the experimental observations if necessary. By randomly choosing the molecular configurations from MD simulation and comparing their energies computed from FF parameters and quantum mechanics, the FF parameters can be verified self‐consistently. Using an example of a platform chemical 3‐hydroxypropionic acid, we detail the comparison between the new fitting parameters and the existing FF parameters. In particular, the introduced systematic approach has been applied to obtain the dihedral angle potential and 1–n scaling pair interaction parameters for 48 organic molecules with different functionality. We suggest that this procedure might be used to obtain better dihedral and 1–n interaction potentials when they are not available in the current widely used FF. © 2014 Wiley Periodicals, Inc.

Muz, İskender; Canko, Osman; Atiş, Murat; Kamil Yıldırım, Erdem

doi: 10.1002/jcc.23812pmid: 25514852

The global minimum structures of AlB3H2n (n = 0–6) clusters are determined using the stochastic search method at the B3LYP/6–31G level of theory. These initially specified geometries are recalculated using B3LYP and CCSD(T) methods using the 6–311++G** basis set. The structural and electronic properties of the two lowest‐lying isomers are presented. The structural parameters obtained for aluminum borohydride are compared with the experimental and theoretical results. The H2 fragmentation energies of the most stable isomers are investigated. Chemical bonding analyses for the global minimum of AlB3H2n (n = 0–6) clusters are performed using the adaptive natural density partitioning method. © 2014 Wiley Periodicals, Inc.

Dubaj, Tibor; Cibulková, Zuzana; Šimon, Peter

doi: 10.1002/jcc.23813pmid: 25523237

The parameters obtained from a kinetic analysis of thermoanalytical data often exhibit a conversion‐dependent behavior. A novel incremental isoconversional method able to deal with this phenomenon is proposed. The kinetic model is directly fitted to the experimental data using nonlinear orthogonal least squares procedure. The data are processed without transformations, so their error distribution is preserved. As the objective function is based on a maximum likelihood approach, reliable uncertainties of the parameters can be estimated. In contrast to other methods, the activation energy and the pre‐exponential factor are treated as equally important kinetic parameters and are estimated simultaneously. Validity of the method is verified on simulated data, including a dataset with local nonlinearity in the temperature variation. A practical application on the nonisothermal cold crystallization of polyethylene terephthalate is presented. © 2014 Wiley Periodicals, Inc.

D'Alessando, Maira; Amadei, Andrea; Stener, Mauro; Aschi, Massimiliano

doi: 10.1002/jcc.23814pmid: 25537730

Essential Dynamics (ED) is a powerful tool for analyzing molecular dynamics (MD) simulations and it is widely adopted for conformational analysis of large molecular systems such as, for example, proteins and nucleic acids. In this study, we extend the use of ED to the study of clusters of arbitrary size constituted by weakly interacting particles, for example, atomic clusters and supramolecular systems. The key feature of the method we present is the identification of the relevant atomic‐molecular clusters to be analyzed by ED for extracting the information of interest. The application of this computational approach allows a straightforward and unbiased conformational study of the local microstructures in liquids, as emerged from semiclassical MD simulations. The good performance of the method is demonstrated by calculating typical observables of liquid water, that is, NMR, NEXAFS O1s, and IR spectra, known to be rather sensitive both to the presence and to the conformational features of hydrogen‐bonded clusters. © 2014 Wiley Periodicals, Inc.

Xia, Kelin; Feng, Xin; Tong, Yiying; Wei, Guo Wei

doi: 10.1002/jcc.23816pmid: 25523342

Persistent homology is a relatively new tool often used for qualitative analysis of intrinsic topological features in images and data originated from scientific and engineering applications. In this article, we report novel quantitative predictions of the energy and stability of fullerene molecules, the very first attempt in using persistent homology in this context. The ground‐state structures of a series of small fullerene molecules are first investigated with the standard Vietoris–Rips complex. We decipher all the barcodes, including both short‐lived local bars and long‐lived global bars arising from topological invariants, and associate them with fullerene structural details. Using accumulated bar lengths, we build quantitative models to correlate local and global Betti‐2 bars, respectively with the heat of formation and total curvature energies of fullerenes. It is found that the heat of formation energy is related to the local hexagonal cavities of small fullerenes, while the total curvature energies of fullerene isomers are associated with their sphericities, which are measured by the lengths of their long‐lived Betti‐2 bars. Excellent correlation coefficients (>0.94) between persistent homology predictions and those of quantum or curvature analysis have been observed. A correlation matrix based filtration is introduced to further verify our findings. © 2014 Wiley Periodicals, Inc.