Local Minimum Energy Structures Research Articles

Inter-channel conversion between population-/coherence-channel dictates thermal transport in MAPbI3 crystals

Hybrid halide perovskites, with their favorable carrier recombination time and ultrashort phonon mean-free paths, are leading candidates for various energy conversion applications like photovoltaics and thermoelectrics. The origin of the ultralow thermal conductivity of the prototypical methylammonium lead triiodide (MAPbI3) is of intense research interest as it is critical for improving its energy conversion performance. So far, such an understanding remains elusive in the MAPbI3 above room temperatures (c-MAPbI3) despite numerous efforts due to its unstable phonon modes. Here, we report the discovery of several c-MAPbI3 local minimum energy structures that produce stable phonon dispersions to reveal an amorphous-like coherence-channel thermal transport mechanism in these crystals. Interestingly, an inter-channel conversion between the population- and coherence-channel of the phonons occurs when the c-MAPbI3 changes across these different structures at the same temperature. Such an effect is not yet observed in simple atomic crystals. Our work also shows that existing thermal transport intuitions based on the phonon gas model can be misleading in such hybrid crystals. Further, the dominance of the non-traditional coherence-channel of phonons will affect the interpretation of other phonon-mediated processes in MAPbI3 and other hybrid perovskites.

A look inside the black box: Using graph-theoretical descriptors to interpret a Continuous-Filter Convolutional Neural Network (CF-CNN) trained on the global and local minimum energy structures of neutral water clusters.

We describe a method for the post-hoc interpretation of a neural network (NN) trained on the global and local minima of neutral water clusters. We use the structures recently reported in a newly published database containing over 5 × 106 unique water cluster networks (H2O)N of size N = 3-30. The structural properties were first characterized using chemical descriptors derived from graph theory, identifying important trends in topology, connectivity, and polygon structure of the networks associated with the various minima. The code to generate the molecular graphs and compute the descriptors is available at https://github.com/exalearn/molecular-graph-descriptors, and the graphs are available alongside the original database at https://sites.uw.edu/wdbase/. A Continuous-Filter Convolutional Neural Network (CF-CNN) was trained on a subset of 500 000 networks to predict the potential energy, yielding a mean absolute error of 0.002 ± 0.002 kcal/mol per water molecule. Clusters of sizes not included in the training set exhibited errors of the same magnitude, indicating that the CF-CNN protocol accurately predicts energies of networks for both smaller and larger sizes than those used during training. The graph-theoretical descriptors were further employed to interpret the predictive power of the CF-CNN. Topological measures, such as the Wiener index, the average shortest path length, and the similarity index, suggested that all networks from the test set were within the range of values as the ones from the training set. The graph analysis suggests that larger errors appear when the mean degree and the number of polygons in the cluster lie further from the mean of the training set. This indicates that the structural space, and not just the chemical space, is an important factor to consider when designing training sets, as predictive errors can result when the structural composition is sufficiently different from the bulk of those in the training set. To this end, the developed descriptors are quite effective in explaining the results of the CF-CNN (a.k.a. the "black box") model.

A machine learning technique toward generating minimum energy structures of small boron clusters

AbstractThe search for a global minimum related to molecular electronic structure and chemical bonding has received wide attention based on some theoretical calculations at various levels of theory. Particle swarm optimization (PSO) algorithm and modified PSO have been used to predict the energetically stable/metastable states associated with a given chemical composition. Out of a variety of techniques such as genetic algorithm, basin hopping, simulated annealing, PSO, and so on, PSO is considered to be one of the most suitable methods due to its various advantages over others. We use a swarm‐intelligence based parallel code to improve a PSO algorithm in a multidimensional search space augmented by quantum chemical calculations on gas phase structures at 0 K without any symmetry constraint to obtain an optimal solution. Our currently employed code is interfaced with Gaussian software for single point energy calculations. The code developed here is shown to be efficient. Small population size (small cluster) in the multidimensional space is actually good enough to get better results with low computational cost than the typical larger population. But for larger systems also the analysis is possible. One can try with a large number of particles as well. We have also analyzed how arbitrary and random structures and the local minimum energy structures gravitate toward the target global minimum structure. At the same time, we compare our results with that obtained from other evolutionary techniques.

Assessing the stable conformations of ibuprofen in solution by means of Residual Dipolar Couplings

Detailing the conformational equilibria between global and local minimum energy structures of anti-inflammatory α-arylpropionic acids directly in solution is of the utmost importance for a better understanding of the structure-activity relationships, hence providing valuable clues for rational structure-based drug design studies. Here the conformational preferences of the widely used pharmaceutical ibuprofen were investigated in solution by NMR spectroscopy in weakly ordering phases. A thorough theoretical treatment of the anisotropic interactions that are relevant for NMR spectra led to a conformational model characterized by six pairs of symmetry-related conformers, in particular four couples of gauche structures, with a total probability of 93%, and 2 couples of trans structures, counting for the remaining 7%.

Sugar–salt and sugar–salt–water complexes: structure and dynamics of glucose–KNO3–(H2O)n

Molecular dynamics (MD) simulations are carried out for the complex of glucose with KNO(3) and for complexes of the type glucose-KNO(3)-(H(2)O)(n), for n < or = 11. Structure and dynamic properties of the systems are explored. The MD simulations are carried out using primarily the DL_POLY/OPLS force field, and global and local minimum energy structures of some of the systems are compared with ab initio calculations. The main findings include: (1) complexation with KNO(3) leads to an "inverse anomeric effect", with the beta-glucose complex more stable than the alpha-glucose by approximately 1.74 kcal mol(-1); (2) as temperature is increased to 600 K, the KNO(3) remains undissociated in the 1 : 1 complex, with the K(+) hooked to the equilibrium site, and the NO(3)(-) bound to it, undergoing large-amplitude bending/torsional motions; (3) for n > or = 3 water molecules added to the system, charge separation into K(+) and NO(3)(-) ions takes place; (4) for the sugar-water system with n = 11 water molecules all hydroxyl groups are hydrated with the glucose adopting a surface position, indicative of a surfactant property of the sugar; and (5) comparison of DL_POLY with MP2/TZP structure predictions indicates that the empirical force field predicts global and local minimum structures reasonably well, but errs in giving the energy rankings of the different minima. The implications of the results on the effects of salts on saccharides are discussed.

Theoretical Analysis of Diamond Mechanosynthesis. Part I. Stability of C&lt;SUB&gt;2&lt;/SUB&gt; Mediated Growth of Nanocrystalline Diamond C(110) Surface

A theoretical investigation of the chemical vapor deposition (CVD) growth on clean diamond C(110) surfaces from carbon dimer precursors shows that isolated deposited C2 dimers appear stable at room temperature, but a second carbon dimer subsequently chemisorbed in close vicinity to the first can adopt one of 19 local energy minima, five of which require barriers � 0.5 eV to reach the global minimum and, thus, constitute stabilized defects. Three chemisorbed C2 dimers can adopt one of 35 local minimum energy structures, 10 of which are stable defects located in deep potential energy wells. The number of potential defects increases with the number of deposited carbon dimers, which suggests an isolated rather than clustered growth mechanism in CVD on bare diamond C(110). These results also provide information regarding outcomes of the misplacement of a carbon dimer and establish constraints on the required dimerplacement positional precision that would be needed to avoid the formation of stable defects during diamond surface growth.

Dodecahedral clathrate structures and magic numbers in alkali cation microhydration clusters.

Using global geometry optimization based on our specialized version of Genetic Algorithms, we have examined the global and most important local minimum energy structures of water microsolvation clusters of potassium and cesium cations within the common TIP4P/OPLS model. Together with our earlier results on the corresponding sodium case, this work constitutes a first step towards a theoretical elucidation of "magic numbers" of solvating molecules and proposed special structures occurring in these systems. In particular, the actual role of dodecahedral cage structures is examined. Within the present model, they do not occur in sodium microsolvation, in agreement with the absence of the magic number 20 for this system. For potassium and cesium microsolvation, dodecahedral cages do occur but their actual structures are far from ideal and their importance appears to be overrated. We offer simple explanations for structural features and trends, and for magic numbers smaller than 20.

Structure and stability of the N-hydroxyurea dimer: Post-Hartree–Fock quantum mechanical study

The potential energy surface (PES) search of the N-hydroxyurea dimer was searched with second-order Møller–Plesset perturbation theory (MP2) and the 6-31G(d,p) basis set. Eight local minimum energy structures have been found. Four of them have relatively strong (ΔE∼−10 to −13 kcal/mol) intermolecular interactions and the others are moderately strongly interacting species (ΔE∼−3 to −7 kcal/mol). Final estimation of interaction energies was performed using the larger 6-311G(df,pd) and 6-311G(2df,2pd) basis sets. The predicted interaction energies are ΔE=−14.26 kcal/mol and −3.43 kcal/mol for the strongest and the weakest interacting forms of the studied complex, respectively, at the MP2/6-311G(2df,2pd)//MP2/6-31G(d,p) level of theory. The self-consistent field (SCF) interaction energy decomposition indicates the important influence of the deformation term magnitude on ΔE(SCF). The calculated electron correlation contribution to ΔE(MP2) depends on the geometry of the system and varies from −0.5 to −5 kcal/mol. The estimated influence of water on the stability (free energy of hydration) of N-hydroxyurea dimers using the self-consistent isodensity polarized continuum (SCI-PCM) model of solvation varies from ∼−11 kcal/mol to ∼−21 kcal/mol. The forms predicted to be more strongly interacting species in gas phase are less influenced by hydration than the more weakly interacting ones.

A Comparison of Calculated and Experimental Geometries for Crowded polycyclic Aromatic Hydrocarbons and their Metabolites

It has become useful to consider the subclass of PAHs with a crowded bay region because of similar biological activity within the subclass. Crowding in the bay region of a polycyclic aromatic hydrocarbon results in a twisted molecular geometry. The purpose of this study is to help gauge the utility of various computational methods for determining the molecular geometry of molecules in this subclass and their metabolites. The results from semi-empirical methods AM1 and PM3, ab initio Hartree-Fock methods and density functional methods will be compared to experimentally determined geometries for crowded PAHs. It will be seen that excellent geometries for all local minimum energy structures are obtained from semi-empirical methods. More exact and computationally extensive methods yield equivalent or somewhat better results only with good basis sets. However, methods disagree on the relative energies of the isomers of diol-epoxides.

Hydrogen andPbdefects at the(111)Si−SiO2interface: Anab initiocluster study

Employing {ital ab initio} density functional methods and atomistic cluster models, we investigate the properties of P{sub b} defects and their interactions with hydrogen at the (111)Si-SiO{sub 2} interface. Our calculated hyperfine parameters agree quantitatively with experiments indicating that the P{sub b} defect is a silicon dangling bond at the silicon side of the interface. We calculate the local minimum energy structures for one and two hydrogen atoms interacting with the P{sub b} defect. From these calculations, we derive reaction energies for H{sub 2} adsorption and H desorption. Comparing our results to experimentally derived activation barriers, we suggest different atomistic mechanisms for the observed reactions. {copyright} {ital 1999} {ital The American Physical Society}

Molecular Arrangement Simulation of Pentacosadiynoic Acid Langmuir-Blodgett Films

A simulation of the molecular arrangement of 10,12-pentacosadiynoic acid (PDA) Langmuir-Blodgett (LB) films has been carried out. The PDA molecules were optimized to local minimum energy structures by the molecular mechanics technique using Allinger's MM2 force field. The optimized molecules were arranged in the close-packed structures in a two-dimensional area where the closest atomic distances of the contacting molecules were restricted by the Van der Waals radii. The simulation results showed successful agreement with the reported experimental data.

Conformation of hexadecylphosphocholine, an anticancer drug, by molecular dynamics and NMR methods

The conformation of hexadecylphosphocholine (HPC) and its interaction with model membranes prepared from dipalmitoylphosphatidylcholine (DPPC) have been investigated by molecular dynamics (MD) and NMR methods. The results of MD studies indicate that in the global minimum energy structure, the phosphocholine head group of the drug is bent at τ 18 and τ 19, while the hexadecyl chain is nearly extended. In the two-dimensional nuclear Overhauser effect (NOE) experiments, intramolecular NOEs have been observed between the N-methyl moieties of the head group and the methylene protons of the alkyl chain. Such a folding of the molecule is seen in several of the local minimum energy structures computed by MD simulations. The interaction of HPC with DPPC as studied by 31P NMR shows a strong interaction between head groups of the two molecules.

Aromatic van der Waals Clusters: Structure and Nonrigidity

More than a dozen cases of nonrigid van der Waals clusters are presented and discussed to demonstrate that cluster nonrigidity is a general phenomenon in all weakly bound systems. The interplay of structure and nonrigidity complicates cluster research and mandates a dynamical approach to cluster properties in which multiple stable configurations coexist and interconvert, and large amplitude nuclear motions are the rule rather than the exception. Empirical potential energy surface calculations are employed to yield physical insight into the structure and dynamics of nonrigid clusters, and molecular symmetry group theory is applied to analyze spectroscopic manifestations of cluster nonrigidity. Empirical potentials of various forms are successful in predicting most cluster structures, as well as estimating the potential surface barrier heights hindering the interconversion between different local minimum-energy structures. Such calculational approaches also emphasize the importance of large amplitude motion...

Framework silica structures generated using simulated annealing with a potential energy function based on an H6Si2O7 molecule

A simulated annealing technique was used to search for global and local minimum energy structures of a potential energy model for silica. The model is based on ab initio SCF MO calculations on the disilicic acid molecule, H6Si2O7. Starting with 4 SiO2 units, with the atoms randomly distributed in the unit cell, 23 distinct silica tetrahedral framework structures were found, with a variety of space group symmetries and cell dimensions. Despite the assumption of P 1 space group symmetry for the starting structure, only 7 of the local minimum energy structures were found to possess triclinic symmetry with the remainder exhibiting symmetries ranging from P c to $$I\bar 42d$$ to within 0.001 A. Although the interaction potential for the disilicic acid molecule has a single minimum energy SiO bond length and SiOSi angle, the local minimum energy structures exhibit angles that range between 105° and 180° and bond lengths that range between 1.55 and 1.68 A. The correlation observed for coesite and the other silica polymorphs between SiO bond length and fs(O) is reproduced. The generated structures show a wide variety of coordination sequences, ring sizes and framework densities, the later ranging from 19.8 to 35.5 Si/1000 A3. The energies of these structures correlate with their framework densities, particularly for higher energy structures.

Ab initio SCF molecular dynamics: Exploring the potential energy surface of small silicon clusters

AbstractA few classical nuclear trajectories at finite temperature have been calculated from ab initio SCF energy gradients. They have been used as an alternative means to search for local minimum energy structures on the Born–Oppenheimer surfaces for some elemental silicon clusters. The approach is found to be beneficial in yielding different structures of silicon clusters. In other cases, the trajectories stay trapped in only one region of the phase space.