Effect of spin polarization for hydrogen adsorbed on Si(111)(1×1) surface: First‐principles calculations

The role of spin polarization on adsorption of atomic and molecular hydrogen on Si(111)(1×1) surface is examined by comparing the results of the local spin density approximation (LSD) and those of the local density approximation (LDA). A large improvement of the adsorption energies (around 0.8 eV/H) was found for the H atom adsorbed on Si(111)(1×1) surface. The inclusion of spin polarization reduces the overbinding between the H atom and the silicon surface and its effect is much more pronounced when the H atom is far away from the surface. Despite of the large changes in the adsorption energies, the main character of the potential energy surface of the H atom on Si(111)(1×1) surface is retained. An opposite effect is found in the charge‐density‐transfer map of LSD results as compared to LDA results for the H atom approaching the surface through the H3 path, in which the H atom loses electrons rather than gains electrons from the surface. The fact that the H atom tends to lose electrons in the silicon bulk has already been reported by the experimental studies for the behavior of the H atom in the p‐type silicon. For the molecular hydrogen on Si(111)(1×1) surface, the effect of the spin polarization is so small that it can be neglected. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 79: 47–55, 2000     

Quantum Chemical Investigation of Monostanna[n]cyclacenes

Semiempirical molecular orbital treatment at the level of PM3 type calculations has been performed on the Hückel-type monostannacyclacenes having tin atom at the fusion and periposition of arenoid rings. The effect of tin substitution is found to be moderately destabilizing, but it becomes less pronounced in larger systems. The heats of formation values of fusion- and peri-type monostannacyclacenes, in some cases, are more endothermic and, in some cases, less endothermic as compared to the cyclacenes having the same n (the number of arenoid rings) value. The frontier molecular orbital energies, cryptoannulenic effects, geometries, and dipole moments of these structures have also been examined.     

A classical trajectory study of the effect of reaction barrier height on the vibrational energy transfer efficiency in the Cl + HCl system

The effects of reaction barrier height and initial rotational excitation of the reactants on the overall rate of H atom exchange between atomic chlorine and HCl (v = 0) and on the 0 → 1 vibrational excitation of HCl via reactive and nonreactive collisions have been investigated using quasiclassical trajectory techniques. Two empirical LEPS potential energy surfaces were employed in the calculations having reaction barrier heights of 9.84 and 7.05 kcal mol^?1. Trajectory studies of planar collisions were carried out on each surface over a range of relative translational energies with the ground-state HCI collision partner given initial rotational excitation corresponding J = 0, 3, and 7. Initial molecular rotation was found to be relatively inefficient in promoting the H atom exchange; the computed rate coefficient for H atom exchange between Cl + HCl (v = 0, J = 7) was only 4 times larger than that for CI + HCI (v = 0, J = 0). The vibrational excitation rate coefficient exhibited a stronger dependence on initial molecular rotational excitation. The observed increase in the vibrational excitation rate coefficient with increasing initial molecular rotational excitation was due primarily to nonreactive intermolecular R → V energy transfer. The vibrational excitation rate coefficients increase with decreasing reaction barrier height.     

Ab initio Mechanism Study on the Reaction of Chlorine Atom with Formic Acid

The potential energy surface(PES) for the reaction of Cl atom with HCOOH is predicted using ab initio molecular orbital calculation methods at UQCIDS(T,full)6-311 G(3df,2p)//UMP2(full)/6-311 G(d,P) level of theory with zero-point vibrational energy (ZPVE) correction.The calculated results show that the reaction mechanism of Cl atom with formic acid is a C-site hydrogen abstraction reaction from cis-HOC(H)O molecule by Cl atom with a 3.73kJ/mol reaction barrier height,leading to the formation of cis-HOCO radical which will reacts with Cl atom or other molecules in such a reaction system.Because the reaction barrier height of O-site hydrogen abstraction reaction from cis-HOC(H)O molecule by Cl atom which leads to the formation of HCO2 radical is 67.95kJ/mol,it is a secondary reaction channel in experiment,This is in good agreement with the prediction based on the previous experiments.     

Static investigation of adsorption and hetero‐diffusion of copper,silver, and gold adatoms on the (111) surface

In this work, we have used the static molecular simulations combined with an interatomic potential derived from the embedded‐atom method to study the adsorption and hetero‐diffusion on the (111) surface of Cu, Ag, and Au adatoms by using LAMMPS code. The investigation is performed for six heterogeneous systems such as Ag/Au(111), Ag/Cu(111), Au/Ag(111), Au/Cu(111), Cu/Ag(111), and Cu/Au(111). First, we have investigated the relaxation trends and the bond lengths of the atoms in the systems. The calculation results show that, the top layer spacing between the first and second layers of the Au(111), Ag(111), and Cu(111) substrates is contracted. This contraction is found to be more important in the Au(111) substrate. On the other hand, the strong reduction of the binding length is found in Au/Cu(111) for the different adsorption sites. In addition, the binding, adsorption, and static activation energies for all studied systems were examined. The results indicated that the binding and adsorption energies reached their maximum values in the Au/Cu(111) and Au/Ag(111) systems, respectively. Moreover, the static activation barriers for hopping diffusion on the (111) surfaces are found to be low compared with those found in the (100) and (110) surfaces. Therefore, our calculations showed that the difference in energy between the hcp and fcc sites on the (111) surfaces is very small. Copyright © 2017 John Wiley & Sons, Ltd.     

Exploring the similarities between potential smoothing and simulated annealing

Simulated annealing and potential function smoothing are two widely used approaches for global energy optimization of molecular systems. Potential smoothing as implemented in the diffusion equation method has been applied to study partitioning of the potential energy surface (PES) for N‐Acetyl‐Ala‐Ala‐N‐Methylamide (CDAP) and the clustering of conformations on deformed surfaces. A deformable version of the united‐atom OPLS force field is described, and used to locate all local minima and conformational transition states on the CDAP surface. It is shown that the smoothing process clusters conformations in a manner consistent with the inherent structure of the undeformed PES. Smoothing deforms the original surface in three ways: structural shifting of individual minima, merging of adjacent minima, and energy crossings between unrelated minima. A master equation approach and explicit molecular dynamics trajectories are used to uncover similar features in the equilibrium probability distribution of CDAP minima as a function of temperature. Qualitative and quantitative correlations between the simulated annealing and potential smoothing approaches to enhanced conformational sampling are established. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 531–552, 2000     

Sampling potential energy surface of glycyl glycine peptide: Comparison of Metropolis Monte Carlo and stochastic dynamics

A comparative study was carried out to test the efficiency with which Metropolis Monte Carlo (MC) and stochastic dynamics (SD) sample the potential energy surface of the N-acetyl glycyl glycine methylamide peptide as defined by the united atom AMBER* force field. Boltzmann-weighted ensembles were generated with variations of all internal degrees of freedom (i.e., stretch, bend, and torsion) for a single N-acetyl glycyl glycine methylamide molecule at 300 K by 10⁸-step MC and 100-ns SD simulations. As expected, both methods gave the same final energetic results. However, convergence was found to be ∼10 times faster with MC than with SD as measured by comparisons of the populations of all symmetrically equivalent conformers. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1294–1299, 1998     

Domain‐Averaged Exchange‐Correlation Energies as a Physical Underpinning for Chemical Graphs

A novel solution to the problem of assigning a molecular graph to a collection of nuclei (i.e. how to draw a molecular structure) is presented. Molecules are universally understood as a set of nuclei linked by bonds, but establishing which nuclei are bonded and which are not is still an empirical matter. Our approach borrows techniques from quantum chemical topology, which showed for the first time the construction of chemical graphs from wave functions, shifting the focus on energetics. This new focus resolves issues surrounding previous topological analyses, in which domain‐averaged exchange‐correlation energies (V_xc), quantities defined in real space between each possible atom pair, hold the key. Exponential decay of V_xc in non‐metallic systems as the intercenter distance increases guarantees a well‐defined hierarchy for all possible V_xc values in a molecule. Herein, we show that extracting the set of atom pairs that display the largest V_xc values in the hierarchy is equivalent to retrieving the molecular graph itself. Notably, domain‐averaged exchange‐correlation energies are transferable, and they can be used to calculate bond strengths. Fine‐grained details resulted to be related to simple stereoelectronic effects. These ideas are demonstrated in a set of simple pilot molecules.     

Molecular states of atoms. I. Orbital energy parameters

Atomic valence state energies are analyzed to obtain values of orbital energy parameters that may be used in semiempirical molecular orbital calculations. Difficulty in defining the interaction between orbitals with non-integer electron populations is systematically avoided by distinguishing between a valence state and a molecular state of an atom, only the latter state having non-integer spin paired orbital occupancy. Application of the virial theorem to the molecular state enables a value for the orbital kinetic energy to be obtained from the valence state orbital energy parameters once an arbitrary configuration is defined as reference. The orbitals then are eigenfunctions of the atomic Fock operator for that reference molecular state and, with their energy parameters, may be employed as a fixed basis set for molecular orbital calculations.     

Anisotropy analysis of the surface stress in Ag stepped surfaces with the modified embedded atom method

The surface stresses in Ag stepped surfaces (910), (710), (510), (410), (310), (210), (320), (430) and (540) have been calculated by using the modified embedded atom method (MEAM). The surface stresses in the surface plane τ_xx (along the step edge) and τ_yy (normal to the step edge) have similar orders of magnitude as the surface energy. For surfaces having the (100) and (110) terraces, the change of τ_xx and τ_yy is very small and the variation of the surface energy is smooth. The stress τ_zz (normal to the surface plane) is always tensile in the unrelaxed state. The linear variation of the change in surface energy per unit change in elastic strain , and (i.e. τ_xx ? γ, τ_yy ? γ and τ_zz) with the angle α between the (hk0) and (100) planes has a turning point corresponding to the (210) surface. The anisotropic ratio in the stepped surface having the (110) terrace is larger than that having the (100) terrace, and the wider the (110) terrace or the narrower the (100) terrace, the larger the ratio τ_yy/τ_xx. Copyright © 2006 John Wiley & Sons, Ltd.     

Density functional studies of LiN and LiN+ (N = 2–30) clusters: Structure,binding and charge distribution

Density functional calculations using B3LYP/6‐311G method have been carried out for small to medium‐sized lithium clusters (Li_N, N = 2–30). The optimized geometries of neutral and singly charged clusters, their binding energies, ionization potential, electron affinity, chemical potential, softness, hardness, highest occupied molecular orbital and lowest unoccupied molecular orbital (HOMO–LUMO) gap, and static dipole polarizability have been investigated systematically. In addition, we study the distribution of partial charges in detail using natural population analysis (NPA) in small‐sized clusters (Li_N, N = 2–10), both neutral and cationic, and demonstrate the correlation between symmetry and charge. Uniform distribution of charges in cationic clusters confirms them to be energetically more favorable than the neutral counterparts. Whenever possible, results have been compared with available data. An excellent agreement in every case supports new results as reliable predictions. A careful study of optimized geometries shows that Li₉ is derivable from bulk Li structure, i.e., body centered cubic cell, and higher clusters have optimized shapes derived from this. Further, the turnover form two to three dimensional structure occurs at cluster size N = 6. The quantity α^1/3 (α = polarizability) per atom is found to be broadly proportional to softness (per atom) as well as inverse ionization potential (per atom). The present work forms a sound basis for further study of large‐sized clusters as well as other atomic clusters. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Electrostatic Energies in the 1,4‐Dichlorobenzene Polymorph Crystals: the Role of Charge Density Overlap Effects in Crystal Packing Analysis

Electrostatic and polarization energies for the three known polymorphic crystal structures of 1,4‐dichlorobenzene, as well as for one particularly stable virtual crystal structure generated by computer search, were calculated by a new accurate numerical integration method over static molecular charge densities obtained from high level ab initio molecular‐orbital calculations. Results are compared with those from standard empirical atom‐atom force fields. The new electrostatic energies, which include charge density overlap (penetration) effects, are seen to be much larger than and sometimes of opposite sign to those derived from point‐charge models. None of the four polymorphs is substantially more stable than the others on electrostatic‐energy grounds. Molecule‐molecule electrostatic energies have been calculated for the more important molecular pairs in each of the four structures; trends are found to be very different from those indicated by point‐charge energies or by total energies estimated with a parametric atom‐atom force field. Conclusions based exclusively on analysis of intermolecular atom contacts and point‐charge electrostatics may need to be modified in the light of the new kind of calculation.     

Density functional and molecular orbital study of physical process of inversion of nitrogen trifluoride (NF3) molecule

The physical process of the umbrella inversion of the nitrogen trifluoride molecule has been studied invoking the formalisms of the density functional theory, the frontier orbital theory, and the molecular orbital theory. An intuitive structure and dynamics of evolution of the transition state for the event of inversion is suggested. The physical process of dynamic evolution of the molecular conformations between the equilibrium (C_3v) shape and the planar (D_3h) transition state has been followed by a number of molecular orbital and density functional parameters like the total energy, the eigenvalues of the frontier orbitals, the highest occupied molecular orbital and lowest unoccupied molecular orbital, the (HOMO–LUMO) gap, the global hardness and softness, and the chemical potential. The molecular conformations are generated by deforming the ∠FNF angle through steps of 2° from its equilibrium value, and the cycle is continued till the planar transition state is reached, and the geometry of each conformation is optimized with respect to the length of the N? F bond. The geometry optimization demonstrates that the structural evolution entails an associated slow decrease in the length of the N? F bond. The dipole moment at the equilibrium form is small and that at the transition state is zero and shows a strange behavior with the evolution of conformations. As the molecular structure begins to distort from its equilibrium shape by opening of the ∠FNF angle, the dipole moment starts increasing very sharply, and the trend continues very near to the transition state but abruptly vanishes at the transition state. A rationale of the strange variation of dipole moment as a function of evolution of conformations could be obtained in terms of quantum mechanical hybridization of the lone pair on the N atom. The pattern of charge density reorganization as a function of geometry evolution is a continuous depletion of charge from the F center and piling up of charge on the N center. The continuous shortening of bond length and the pattern of variation of net charge densities on atomic sites with evolution of molecular conformations predicts that the bond moment would decrease continuously. The quantum mechanical hybridization of the lone pair of the central N atom shows that the percentage of s character of the lone‐pair hybrid on the N atom decreases at a very accelerated rate, and the lone pair at the transition state is accommodated in a pure p orbital. The result of the continued destruction of asymmetry of charge distribution in the lone pair on the central N atom due to the elimination of contribution of the s orbital with evolution of molecular conformations is the sharp decrease in lone‐pair moment. The decrease in bond moment is overcompensated by the sharp fall of its offsetting component, the lone‐pair moment, resulting in a net gain in dipole moment with the evolution of molecular geometry. Since the offsetting component decreases very sharply, the net effect is a sharp rise of dipole moment with the evolution of molecular conformations just before the transition state. The lone‐pair moment is zero by virtue of the symmetry of the pure p orbital, the lone pair of the central atom in the transition state, and the sum of the bond moments is zero by symmetry of the geometry. The barrier height is quite high at ～65.45 kcal/mol, which is close to values computed through more sophisticated methods. It is argued that an earlier suggestion regarding the development of high barrier value of NF₃ system seems to be misleading and confronting with the conclusions of the density functional theory. An analysis and a comparative study of the physical components of the one‐ and two‐center energy terms reveals that the pattern of the charge density reorganization has the principal role in deciding the origin and the magnitude of barrier of inversion of the molecule and the barrier originates not from a particular energetic effect localized in a particular region of the molecule, rather the barrier originates from a subtle interplay of one‐ and two‐center components of the total energy. The decomposed energy components show that the F?F nonbonded interaction and N? F bonded interaction favor the formation of transition state, while the one‐center energy terms prohibit the formation of the transition state. The barrier principally develops from the one‐center energy components. The profile of the HOMO is isomorphic and that of the LUMO is homomorphic with the potential energy curve for the physical process of the event of umbrella inversion of the molecule. The variation of the HOMO–LUMO gap, ?ε, the global hardness, η, and the softness, S, as a function of the reaction coordinates of angular deformation of NF₃ molecule are quite consistent with the predictions of the molecular orbital and the density functional theories in connection with the deformation of molecular geometry. The profiles of ?ε, η, and S, as a function of reaction coordinates, mimic the potential energy curve of the molecule. The eigenvalues of the frontier orbitals, and the ?ε, η, S parameters are found to be equally effective theoretical parameters, like the total energy, to monitor the physical process of the inversion of pyramidal molecules. The nature of the variation of the global hardness parameter between the equilibrium shape and the transition state form for the inversion is in accordance with the principle of maximum hardness (PMH). © 2002 John Wiley & Sons, Inc. Int J Quantum Chem, 2002     

Effect of n-alkyl and sulfonyl groups on the wetting properties of comblike poly(oxyethylene)s and stick-slip behavior

The influence of side chain length and sulfonyl moiety on the molecular structures and wettability behavior of poly(oxyethylene)s with alkyl sulfonyl side chains (CH(3)-nSE, n = 1, 2, 3, 4, 5, 6, 8, 10), where n is the number of the carbon atom in the n-alkyl side group, was investigated. CH(3)-nSEs having shorter side chains (n < 5) do not have ordered structures, and their surfaces were found to be more polar than those of CH(3)-nSEs having longer side chains (n ≥ 5). The CH(3)-nSEs having longer side chains show double-layered lamellar structures (n ≥ 5) with well-aligned side chains and low surface energies in the range 21.2-25.8 mN/m. Interestingly, stick-slip behavior was observed only on the surfaces of CH(3)-3SE and CH(3)-4SE when water was used as the test liquid. The surface deformation at the three-phase line was generated from interactions between water and sulfonyl groups, and the optimum side chain lengths were believed to cause the stick-slip behavior.     

Fast and accurate grid representations for atom‐based docking with partner flexibility

Macromolecular docking methods can broadly be divided into geometric and atom‐based methods. Geometric methods use fast algorithms that operate on simplified, grid‐like molecular representations, while atom‐based methods are more realistic and flexible, but far less efficient. Here, a hybrid approach of grid‐based and atom‐based docking is presented, combining precalculated grid potentials with neighbor lists for fast and accurate calculation of atom‐based intermolecular energies and forces. The grid representation is compatible with simultaneous multibody docking and can tolerate considerable protein flexibility. When implemented in our docking method ATTRACT, grid‐based docking was found to be ∼35x faster. With the OPLSX forcefield instead of the ATTRACT coarse‐grained forcefield, the average speed improvement was >100x. Grid‐based representations may allow atom‐based docking methods to explore large conformational spaces with many degrees of freedom, such as multiple macromolecules including flexibility. This increases the domain of biological problems to which docking methods can be applied. © 2017 Wiley Periodicals, Inc.     

The mass spectra of 1-arylanthra-9,10-quinones

The mass spectra of 1-phenylanthra-9,10-quinone and 20 substituted l-phenylanthraquinones having alkyl methoxyl, nitro and halogen substituents in the o-, m- and p-positions of the phenyl ring have been measured. The spectra are discussed with particular reference to the loss from the molecular ion of a hydrogen atom and of the substituent.     

Effect of Bulky Functional Groups on Donor and Acceptor Interactions and their Photoluminescence Properties

Material designs that use donor and acceptor units are often found in organic optoelectronic devices. Molecular level insight into the interactions between donors and acceptors are crucial for understanding how such interactions can modify the optical properties of the organic optoelectronic materials. In this paper, tris(4-(tert-butyl)phenyl)amine (pTPA) was synthesized as a donor in order to compare with unmodified triphenylamine (TPA) in a donor–acceptor system by having 2,4,6-triphenyl-1,3,5-triazine (TRZ) as an acceptor. Dimerization of donors and acceptors occurred in solvent when the concentration of solute is high. At 0 K, using a polarizable continuum model, the nitrogen atom of TPA is found to stack on top of the center of triazine of TRZ, whereas such alignment is offset in pTPA and TRZ. We attributed such alignment in TPA-TRZ as the result of attractive interactions between partial localization of 2p_z electrons at the nitrogen atom of TPA and the π deficiency of triazine in TPA-TRZ. By taking into account random motions of the solvent effect at 300 K in quantum molecular dynamics and classical molecular dynamics simulations to interpret the marked difference in emission spectra between TPA-TRZ and pTPA-TRZ, it was revealed that the attractive interaction between pTPA and TRZ in toluene is weaker than TPA and TRZ. Because of the weaker attractive interaction between pTPA and TRZ in toluene, the dimers adopted numerous ground state conformations resulting in broad emission bands superimposed with multiple small Gaussian peaks. This is in contrast to TPA-TRZ which has only one dominant dimer conformation. This study demonstrates that the strength of intermolecular interactions between donors and acceptors should be taken into consideration in designing supramolecular structures.     

Study of chemical bonding in H2 and HF molecules: Wave function and density functional theory (DFT) parameters approach

Balint Kurti's Fourier grid Hamiltonian method is employed to obtain the molecular wave function and equilibrium bond length for H₂ and HF molecules. The density functional theory parameter, namely, the chemical hardness (η) value, was determined for some diatomic hydride molecules using this wave function and the results are found to be in good agreement with the values obtained from the ab initio HF–SCF method. A new formula for chemical hardness (η=1/2Dr, where D is the proportionality constant and r is the internuclear distance) is introduced in binding energy and change of hardness equations to determine the chemical hardness and chemical potential values for different bond lengths. The binding energy and change of hardness values are calculated for H₂, H, H, HF, HF⁺, and HF⁻ molecules and the bond stability is discussed. Finally, the concept of an atom in a molecule is examined in the context of DFT parameters and comparison is made between an atom in a molecule and the isolated atom. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 76: 662–669, 2000