A strategy to find minimal energy nanocluster structures

An unbiased strategy to search for the global and local minimal energy structures of free standing nanoclusters is presented. Our objectives are twofold: to find a diverse set of low lying local minima, as well as the global minimum. To do so, we use massively the fast inertial relaxation engine algorithm as an efficient local minimizer. This procedure turns out to be quite efficient to reach the global minimum, and also most of the local minima. We test the method with the Lennard–Jones (LJ) potential, for which an abundant literature does exist, and obtain novel results, which include a new local minimum for LJ₁₃, 10 new local minima for LJ₁₄, and thousands of new local minima for . Insights on how to choose the initial configurations, analyzing the effectiveness of the method in reaching low‐energy structures, including the global minimum, are developed as a function of the number of atoms of the cluster. Also, a novel characterization of the potential energy surface, analyzing properties of the local minima basins, is provided. The procedure constitutes a promising tool to generate a diverse set of cluster conformations, both two‐ and three‐dimensional, that can be used as an input for refinement by means of ab initio methods. © 2013 Wiley Periodicals, Inc.     

Structure Prediction for Crystalline Ca3SiBr2 using an Environment Dependent Potential

An environment dependent effective potential was employed in the structure prediction for the not-yet-synthesised compound Ca₃SiBr₂. Using a combination of global and local optimisation methods, nine local minima on the potential energy hypersurface with low energy values were determined. Subsequently, the energies of the corresponding configurations were recalculated using an ab-initio method. In order to estimate the stability of these structures, the regions of the energy landscape close to these minima were investigated with the threshold-algorithm. Combining all these results suggests that the title compound should be capable of existence and most probably crystallize in a NaCl-superstructure.     

Exploring the potential energy hypersurface of histamine monocation: Tautomerism in gas phase

The potential energy hypersurface of the histamine monocation is determined by ab initio methods at the STO -4G level using analytical gradient techniques. Three transition states and two minima have been found for the N_τ? H tautomer. One of the transition states connects the trans conformational region with a minimum gauche structure, where the proton of the ammonium group is approximately halfway between the N_π of the imidazole group and the N of the ammonium group, but nearer to the N_π. This minimum connects the potential energy surface of the N_τ? H tautomer with the imidazolium one. In the latter region, three transition states and two minima have been found. Critical points are discussed in relation with experimental data and histamine H₂ receptor models.     

Energy landscape study of water splitting and H2 evolution at a ruthenium(II) pincer complex

A bird's-eye view of the water splitting and H₂ generation at a ruthenium(II) pincer complex is presented. Using a combination of density functional theory and efficient algorithms for exploration of potential energy hypersurface (PES), a total of 197 local minima and 186 transition states are identified, and a new mechanism for water splitting and H₂ evolution via hydroxycarbonyl intermediates is presented. Furthermore, a global feature of the reaction PES, so-called potential energy landscape, is discussed on analyzing the obtained structures. As a result, the landscape is characterized by hierarchical structure, namely, PES consists of many “superbasins (SBs)” that are separated by relatively high energy barriers corresponding to bond breaking around Ru(II) center. Each SB involves a set of conformational isomers that can be interchanged with each other through relatively small barriers. To the best of our best knowledge, this is the first report on the quantum chemical computation of the hierarchical structure of PES for a realistic, catalytic reaction system.     

Ab initio and pseudopotential calculations on the singlet and triplet states of the disilyne isomers

Ab initio SCF as well as pseudopotential calculations were performed for determining equilibrium structures and relative stabilities of several disilyne isomers. For the singlet state there are only two structures, the bridged and the silavinylidene carbene, which correspond to minima on the energy hypersurface. The most stable of the six isomeric structures investigated is the bridged conformer in the ¹A₁ electronic state, followed by the silavinylidene carbene in the ¹A₁ and ³A₂ electronic states. Inclusion of electron correlation by MRD-CI calculations has no qualitative influence on the relative stabilities found in the SCF calculations.     

Theoretical study of helical structure caused by chirality of cysteine dimer

In this work we report a theoretical study of the helix structure and chiral discrimination on the interactions between the chiral cysteine–cysteine. Two reasonable geometries on the potential energy hypersurface of the cysteine–cysteine system are considered with the global minimum. Accurate geometric structures, relative stabilities, harmonic vibrational frequencies, and infrared (IR) intensities were investigated. To take into account the water solvation effect, the Onsager model within the self‐consistent reaction field (SCRF) method and the polarized continuum (PCM) method were used to evaluate the interaction energy, ΔG_solv at the same level employed in the gas phase. The results indicate that the polarity of the solvent plays an important role in the structures and relative stabilities of different isomers. Computational results indicate that the global minimum should be conformer I regardless of whether in the gas phase or in aqueous solution, which differs from previous theoretical reports. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Density functional complete study of hydrogen bonding between the water molecule and the hydroxyl radical (H2O · HO)

The hydrogen bonding complexes formed between the H₂O and OH radical have been completely investigated for the first time in this study using density functional theory (DFT). A larger basis set 6‐311++G(2d,2p) has been employed in conjunction with a hybrid density functional method, namely, UB3LYP/6‐311++G(2d,2p). The two degenerate components of the OH radical ²Π ground electronic state give rise to independent states upon interaction with the water molecule, with hydrogen bonding occurring between the oxygen atom of H₂O and the hydrogen atom of the OH radical. Another hydrogen bond occurs between one of the H atoms of H₂O and the O atom of the OH radical. The extensive calculation reveals that there is still more hydrogen bonding form found first in this investigation, in which two or three hydrogen bonds occur at the same time. The optimized geometry parameter and interaction energy for various isomers at the present level of theory was estimated. The infrared (IR) spectrum frequencies, IR intensities, and vibrational frequency shifts are reported. The estimates of the H₂O · OH complex's vibrational modes and predicted IR spectra for these structures are also made. It should be noted that a total of 10 stationary points have been confirmed to be genuine minima and transition states on the potential energy hypersurface of the H₂O · HO system. Among them, four genuine minima were located. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

Conformational analysis of X3PNP(O)X2 and (X3PNPX3)+ for X = H,F, Cl,CH3 by the pcilo method

Conformational energy maps have been calculated, using the PCILO method, for X₃PNP(O)X₂ and (X₃PNPX₃)⁺ for X = H, F, Cl, CH₃ as a function of the PNP angle. In H₃PNP(O)H₂ the global energy minimum corresponds to the eclipsed conformation of the H₃P and P(O)H₂ fragments for all PNP angles, while in Cl₃PNP(O)Cl₂, the global minimum always has Cl₃P and P(O)C1₂ staggered: the global minimum in F₃PNP(O)F₂ corresponds to eclipsed F₃P and P(O)F₂ fragments at low PNP angles and staggered fragments at high PNP angles: in (CH₃))₃PNPO(CH₃)₂ the global minimum conformation is very sensitive to ∠ PNP. Subordinate energy minima occur for all X₃PNP(O)X₂, species: in particular, there are two local conformational minima for Cl₃PNP(O)Cl₂ at the optimum value of ∠ PNP, and the relative energies of the three stable conformations are in good agreement with those derivable from the ³¹P NMR spectrum of this compound. In (X₃PNPX₃)⁺ the global minimum, usually the sole minimum on the conformational energy surface, is always close to the eclipsed conformation: free rotation of the X₃P groups relative to one another is approached in each (X₃PNPX₃)⁺ ion as ∠PNP approaches 180°. The conformations of the transition states for the equilibria between energy minima are reported with their relative energies, for X₃PNP(O)X₂ (X = H, F. Cl, CH₃) and for (Cl₃PNPCl₃)⁺     

On the investigation of the low-energy conformational space of molecules

A new perspective on traditional energy minimization problems is provided by a connection between statistical thermodynamics and combinatorial optimization (finding the minimum of a function depending on many variables). The joint use of a new method for uncovering the global minimum of intramolecular potential energy functions, based on following the asymptotic behavior of a system of stochastic differential equations, and an iterative-improvement technique, whereby a search for relative minima is made by carrying out local quasi-Newton minimizations starting from many distinct points of the energy hypersurface, proved most effective for investigating the low-energy conformational space of molecules.     

Revisiting small clusters of water molecules

The geometries and relative energies of small clusters of water molecules, (H₂O)_n with 4 ⩽ n ⩽ 8, are reported. For each value of n we have considered the conformations corresponding to the lowest-energy minimum and those in nearby relative minima. Thus we report on six tetramers, four pentamers, six hexanlers, four heptamers, and eigth octamers. The geometrical conformations have been obtained using the Metropolis Monte Carlo method as a minimization technique, where the interaction energy is computed with the MCY potential plus three- and four-body corrections previously discussed. All the reported structures for a given cluster size are found to be close in energy. For the lowest conformation the geometry was optimized with ab initio SCF computations using energy gradients. Our results are compared with previous theoretical studies. We discuss the convergence of the interaction potential for liquid water when expressed in terms of a many-body series expansion.     

Hydrogen bond: Second order effects on potentials calculated by CNDO/2 method

Second order perturbation theory (SOP) has been used to introduce electronic correlation effects on CNDP/2 calculated quantities like stabilization energy, proton potential curves, intermolecular dependence on distance and orientation. The HCHO…H₂O' model has been studied. The SOP energy as a function of the R_O…O' distance introduces changes in the potential minima which amount to 14% of the CNDO/2 value and in the asymmetry of the potential energy curve. For the proton curve, an extra stabilization energy of 4 kcal/mole at the minimum is found as well as changes in the shape of the potential curve. Effects on orientation dependence are also reported.     

On the structural and electronic properties of poly(dicarbon monofluoride): solid-state semi-empirical INDO study

Three-dimensional semi-empirical quantum chemical calculations of the structural and electronic properties of the fluorine intercalated graphite compound poly(dicarbon monofluoride)—(C₂F)_n have been performed for several possible stacking sequences of puckered trans-cyclohexane chair layers. Such basic structure consisting from carbon hexagons in chair conformation has been confirmed. Furthermore, based on the geometry optimization, 12 structural sequences have been found to provide a local minima on the potential hypersurface, from which four are considerably more stable and one can assume their statistical distribution in the real poly(dicarbon monofluoride). This is also indicated by comparison with recent Kα XES spectra. In such arrangement the maximal entropy contribution leads to the minimum Gibbs energy of the system. Band structure calculations show that the most stable sequences have insulating properties, which implies that the real poly(carbon monofluoride) behaves as an insulator. The conductive properties of some less stable sequences result from particular interlayer interactions.     

N2O in small para‐hydrogen clusters: Structures and energetics

We present the minimum‐energy structures and energetics of clusters of the linear N₂O molecule with small numbers of para‐hydrogen molecules with pairwise additive potentials. Interaction energies of (p‐H₂)–N₂O and (p‐H₂)–(p‐H₂) complexes were calculated by averaging the corresponding full‐dimensional potentials over the H₂ angular coordinates. The averaged (p‐H₂)–N₂O potential has three minima corresponding to the T‐shaped and the linear (p‐H₂)–ONN and (p‐H₂)–NNO structures. Optimization of the minimum‐energy structures was performed using a Genetic Algorithm. It was found that p‐H₂ molecules fill three solvation rings around the N₂O axis, each of them containing up to five p‐H₂ molecules, followed by accumulation of two p‐H₂ molecules at the oxygen and nitrogen ends. The first solvation shell is completed at N = 17. The calculated chemical potential oscillates with cluster size up to the completed first solvation shell. These results are consistent with the available experimental measurements. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

Investigation of isomerization pathways in monosaccharides. Computer modeling of the hybrid conformations of hexapyranose rings

The method of Wiberg and Boyd was used to determine the pathways for the interconversion of the 3,4-anhydropyranose ring in methyl-2,6-di-O-acetyl-3,4-anhydro--DL (6,6-²H₂) derivatives of talopyranoside (1) and galactopyranoside (2). Stationary points were found on the potential surface. The E₀+¹H₀ and⁰H_1def conformations are global minima in 1. Three local minima are found near the boat conformation B_2.5 and^2.5B. Two saddle points are also found near these conformations. The¹H₀ and⁰H_1def conformations are also global minima in 2. Only one local minimum and two saddle points were found, as in the case of 1, near the B_2.5 and^2.5B conformations. The interconversion barriers in 1 and 2 were calculated. The physical factors affecting the ring conformation in these compounds were discussed.Institute of Physics, Belarus Academy of Sciences. Translated from Zhurnal Strukturnoi Khimii, Vol. 34, No. 2, pp. 112–118, March–April, 1993.     

Conformational analysis of the antimalarial agent quinine

Quinine, an active antimalarial compound, is one of the most abundant constituents extracted from the bark ofCinchona trees. The activity differences among structurally related molecules appear to depend on the absolute stereochemistry of some functional groups, a result that has stimulated a detailed conformational analysis of these molecules of biological interest. In the present study the potential energy surface (PES) for the antimalarial agent quinine (C₂₀H₂₄O₂N₂) has been comprehensively investigated using the molecular mechanics (MM) and quantum mechanical semiem-pirical AM1 and PM3 methods. Six distinct minimum-energy structures are located on the multidimensional PES and also characterized as true minima through harmonic frequency analysis. The relative stabilities and thermodynamic properties are reported. The coexistence of different conformers is discussed for the first time in the literature based on the calculated transition-state (TS) structures connecting the six minima located on the PES for the quinine molecule. The theoretical results reported in the present study are in agreement with the experimental proposal, based on NMR data, that there are two possible forms for the quinine molecule in solution.     

Potential energy curves and photochemical cis-trans isomerism in styrene

Cis-trans photoisomerism of styrene is investigated from a theoretical point of view. Curves of the potential energy as a function of the rotation angle (ω) around the ethylenic bond were obtained for the ground state and a few excited states by the CIPSI PCILO method. The potential surface of the lowest excited singlet is found to have both an absolute minimum at ω = π/2 and a small relative minimum at ω = 0. These findings are consistent with the singlet mechanism for the direct cis-trans photoconversion. The origin of the two energy minima in the S₁ potential surface is explained in terms of weights of the local excitations in the zero-order wavefunction.     

Structure and stability of X4Y4H4 (XY=CC,BN)

Ab initio calculations have been carried out to study the structures and relative stabilities of the planar eight‐membered ring B₄N₄H₄ and its isoelectronic species C₈H₄ at the HF/6‐31G*, MP2/6‐31G*, MP2/6‐311G**, and MP4SDQ/6‐31G* levels. The analyses of Milliken population, vibration frequencies, π‐molecular orbital components, and orbital energy levels were used to evaluate the relative stabilities of these two similar systems. The homodesmotic reactions were also taken to be a useful index of relative stability for X₄Y₄H₄ (XY=CC, BN) and gave the resonance energies with MP4SDQ/6‐31G* of C₈H₄ (?37.2 kcal/mol) < B₄N₄H₄ (?29.2 kcal/mol). Furthermore, we calculated the thermodynamic functions of these reactions to discuss the influence of temperature. It is concluded that B₄N₄H₄ may exist in theory and could be a little more stable than C₈H₄. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 82: 293–298, 2001     

Stationary points on the potential energy surface of O2−HF and O2−H2O

The determination of minima and saddle points on the potential energy surfaces of the hydrogen bonded species O₂^?HF and O₂^?H₂O is performed with unrestricted Hartree-Fock calculations. Geometries, electron density distributions, and relative energies for every stationary point are reported. Only one true minimum is found for O₂^?HF and for O₂^?H₂O, and this approximately corresponds to a structure where the partially positive hydrogen atom is located along one of the superoxide ion electron lone-pair directions. Calculated ΔH, ΔS, and ΔG values for the reaction between O₂^? and H₂O are in good agreement with experimental data.     

A Rechargeable Hydrogen Battery Based on Ru Catalysis

Apart from energy generation, the storage and liberation of energy are among the major problems in establishing a sustainable energy supply chain. Herein we report the development of a rechargeable H₂ battery which is based on the principle of the Ru‐catalyzed hydrogenation of CO₂ to formic acid (charging process) and the Ru‐catalyzed decomposition of formic acid to CO₂ and H₂ (discharging process). Both processes are driven by the same catalyst at elevated temperature either under pressure (charging process) or pressure‐free conditions (discharging process). Up to five charging–discharging cycles were performed without decrease of storage capacity. The resulting CO₂/H₂ mixture is free of CO and can be employed directly in fuel‐cell technology.