Volume 230, Issue 5-7 - Special Issue: Dedicated to Professor Michael Springborg on the occasion of his 60th birthday / Jan-Ole Joswig

A method for the computation of electronic energies of stereoregular polymers is reviewed, using a formulation that makes use of Fourier-representation techniques and the Ewald procedure for accelerating the convergence of lattice sums. That method is in the present work extended to include the computation of electric polarization at an “uncoupled” approximation at the level of second-order perturbation theory based on Hartree–Fock wave functions, using the procedure of Blount and of Genkin and Mednis, as applied to polymers by Barbier, Delhalle, and André. The extension requires computation of the derivatives of Fock matrix elements with respect to the Bloch-wave parameter k , and an effficient numerical procedure for evaluating these derivatives is described here. The computational procedures are incorporated in the authors' ft-1d program, and the new features of that program are validated by reexamining the band structures of polyethylene and polysilane. The results are consistent with the older work on these systems, but exhibit more computational efficiency and greater achievable accuracy.

A brief review is given of how a constrained dipole oscillator strength distribution (DOSD) is constructed from experimental and possibly theoretical photoabsorption cross-sections with constraints provided by molar refractivity data and the Kuhn–Reiche–Thomas sum rule. Some recent refinements including the imposition of the correct high-energy behavior on the DOSD for homoatomic molecules are discussed and extended to the general molecular case. A sample application to pyridine is given.

The method of increments is applied to investigate the adsorption of a single water molecule inside and outside armchair carbon nanotubes with different curvature using density-fitting local coupled cluster with single and double excitations and perturbative triples treatment (DF-LCCSD(T)). The correlation contribution to the adsorption energy is expanded in terms of localized orbitals of both the water molecule and the nanotube. Results of this investigation show that the simultaneous correlation of groups of localized orbitals of the water molecule and of the carbon nanotube (i. e. inter-fragment two-body increments) is the major contribution to the attractive interaction. In contrast the individual correlation energy of localized orbitals of water molecule or carbon nanotube (i. e. one-body increments) is negligible. A detailed balance between the repulsive Hartree–Fock contribution and the attractive correlation contribution to the adsorption energy determines the ground-state structure of the water molecule inside the carbon nanotube. To elucidate this behavior benzene-based model systems are investigated with the same methods.

The application of conventional ab initio methods to large high-spin systems remains challenging because CPU time rapidly increases with the system size. The unrestricted elongation method performs stepwise electronic structure calculations for large high-spin systems and can reproduce the results of conventional methods, i.e., achieve a very small total energy error (∼ 10 – 9  a.u. per atom). Moreover, a polarizable continuum model (PCM) method is incorporated for the estimation of solvent effect and it is demonstrated that the unrestricted PCM-elongation method is accurate and efficient for performing electronic structure  calculations of large high-spin systems under solvent.

We introduce a hybrid Gaussian charge distribution model (HGM) that partitions the molecular electron density into overlapping spherical atomic domains. The semi-empirical HGM consists of atom-centered spherical Gaussian functions and discrete point charges, which are optimized to reproduce the electrostatic potential on the molecular surface as well as the number of electrons in atom-centered and certain off-atom-centered spherical regions as closely as possible. In contrast, our previous Gaussian charge distribution model [J. Chem. Phys. 129 , 014509 (2008)] contained only spherical Gaussian functions and was not required to reproduce the number of electrons in off-atom-centered regions. Variable van der Waals (vdW) radii fluctuating around the Bondi radii are derived from the HGM based on the isodensity contour concept and further employed to define the molecular cavity in our quantum mechanical/Poisson–Boltzmann/surface area model as well as the polarizable continuum model. The variable vdW radii produce more accurate solvation free energies for 31 neutral molecules than the Bondi radii for both continuum solvent models (CSM) consistently. Moreover, for H atoms, the linear dependence of the atomic radii on the atomic partial charges is identified.

Fermionic natural occupation numbers do not only obey Pauli's exclusion principle but are even stronger restricted by so-called generalized Pauli constraints. Whenever given natural occupation numbers lie on the boundary of the allowed region the corresponding N -fermion quantum state has a significantly simpler structure. We recall the recently proposed natural extension of the Hartree–Fock ansatz based on this structural simplification. This variational ansatz is tested for the lithium atom. Intriguingly, the underlying mathematical structure yields universal geometrical bounds on the correlation energy reconstructed by this ansatz.

A quasi-analytical theoretical method is devised, and implemented in the Crystal program, for calculation of the direct “proper” piezoelectric tensor of periodic systems including both the clamped-nuclei electronic and nuclear relaxation contributions. It is based on using the analytical Coupled-Perturbed-Hartree–Fock/Kohn–Sham (CPHF/KS) procedure to obtain dipole derivatives with respect to lattice deformations as well as internal coordinates. The sole numerical step required involves building the Hessian matrix through differentiation of analytical energy gradients. Two prototypical piezoelectric, non-ferroelectric, crystals, namely ZnO and α -quartz, are used to demonstrate the accuracy and computational efficiency of our new scheme, which significantly improves upon the commonly used numerical Berry phase approach.

The errors in atomization energies ( AE ) of molecules have long been used to measure the errors of wavefunction or density functional methods for electronic structure calculations. In particular, the G3 set of Pople and collaborators (for sp -bonded molecules from the first rows of the periodic table) has become a standard benchmark for such methods. But the mean absolute error of AE tends to increase with increasing number N at of atoms in a molecule. In fact, AE is an extensive variable, which diverges as N at  →∞. Here, as did Savin and Johnson 2015, we define an intensive atomization energy, IAE  =  AE / N at or atomization energy per atom, which tends to the finite cohesive energy (per atom) of a large cluster or solid ( N at  →∞). We find that the mean absolute error of the G3 molecular IAE from accurate density functionals remains close to 1 kcal/mol as the average molecular size increases. This makes it possible to estimate in advance the magnitude of the error in AE for a molecule similar to most of those in the G3 set. It also allows us identify the G3 “outlying molecules”, and to more directly compare the accuracy of a given functional for different kinds of molecules (such as those containing transition-metal atoms) to that for G3-type molecules, by removing the otherwise-uncontrolled size factor. Finally, we point out that the familiar concept of “chemical accuracy” needs to be qualified.

This work started as a (biased) review of the state of the art of the Davydov/Scott model for energy transfer in proteins via the propagation of amide I excitations and of how this initial quantum stage may lead to protein conformational changes. It is not a traditional review because certain results reported in the literature have been complemented by extra simulations which revealed, for instance, a new class of possible states for the amide I excitation, here designated as double discrete breathers. The issue of the thermal stability of the Davydov soliton is discussed, as well as the deeper question of how to simulate the non-equilibrium regime of a mixed quantum-classical system at finite temperature. While an exact answer to the latter question is not yet available, a specific formalism that is able to reproduce the correct canonical ensemble is described. Finally, the question of how a quantum amide I excitation can generate of the specific protein conformational changes known to be associated with function is also explored. Indeed, computer simulations indicate that a local action can lead to reproducible conformational changes. The paper ends with a discussion of some of the open questions that plague/stimulate this field and with a suggestion for an experiment to test the basic assumption of the Davydov/Scott model.

By using density-functional tight-binding method we have calculated the electronic structure of graphene quantum dot (GQD)-fullerene hybrid systems and explored the efficacy of their use in designing solar cells. We have shown that the electronic energy levels of the nanohybrids can be tuned either by varying the size of the quantum dots or by proper functionalization of the quantum dot (QD). The GQD-fullerene nanohybrids form type-I or type-II band energy alignment depending upon the size of the GQD. Thus, hybrid systems with smaller sized QDs form type-II band energy alignment while those of larger GQDs form type-I alignment. The type-II band alignment confirms the spatial charge separation for the systems and thus the rate of recombination of charge carriers will be low. The value of ΔG i.e. the difference in energy between the LUMO of the donor (GQD) and LUMO of the acceptor (fullerene) which measures the rate of electron injection from the donor to the acceptor is also large for the nanohybrids with smaller GQDs. So, we suggest that GQD-fullerene nanocomposites with smaller GQD will be a suitable system for photovoltaic devices. We also show that the type-II band energy alignment for the nanohybrids with larger QDs can be achieved through the functionalization of the GQD with electron donating group such as -NH 2 .

On the basis of the first principle density functional theory (DFT) the stability, the electronic structure and the hydrogen adsorption of a metal functionalized monolayer of AGNR-O (armchair graphene nanoribbons) have been studied. The AGNR-O and AGNR-OH structures were decorated with different metal atoms, M = Ca, Mg, Ti. Ca and Mg as decorating metals were found to be superior to the transition metals due to small cohesive energies (no clustering) and the capability of binding multiple hydrogen molecules. The binding of up to four hydrogen molecules to the alkaline earth and transition metal atoms has been investigated. For the alkaline earth metal atoms the binding energy per H 2 molecule is almost independent from the number of adsorbed H 2 molecules. An increase in the adsorption energy by a factor of six or even more, from 0.07 eV/H 2 for “naked” nanoribbons to 0.35 eV/H 2 or to 0.69 eV/H 2 for AGNR-O structures has been observed. This different hydrogen binding energy is due to different construction of the AGNR-O edges. The AGNR edge terminations influence the binding energies of the M/AGNR and consequently the H 2 binding energies on M/AGNR. If the binding energy between the metal atoms and AGNR is not very strong, then H 2 could bind much stronger to the M/AGNR. This could be a possible route to 10 wt % hydrogen storage capacity.

Carbon nanotubes (CNTs)/Al interface interaction is critical to the mechanical properties of CNT-reinforced Al matrix composites. In this study, the effect of different defects (oxygen and carbon adatoms, n-type N substitution and p-type B substitution) on the interactions between a (5, 5) CNT and an Al (111) surface is studied based on first-principles total energy calculations. It is found that the defects can enhance the interaction between the CNT and Al (111) surface in different degree due to the different valence electron configurations of the interfacial defect atoms, as well as the different influences of the defects on the electronic structures of the CNT. The results are helpful for the improvement of the interfacial interactions between CNTs and Al matrix via the introduction of the defects at the interface to enhance the mechanical properties of CNT-reinforced Al matrix composites.

Sophorolipids contain hydrophilic head groups at the ends of a long hydrophobic tail. As a result, sophorolipids can self assemble into variety of structures in water. Atomistic self assembly simulations of sophorolipids are performed in water. Two sophorolipids, oleic acid sophorolipid and linolenic acid sophorolipid, differing in number of double bonds in the hydrophobic tail are considered for this study. Long time self assembly simulations are performed considering 1:3 lipid to water ratio by weight for both oleic and linolenic acid sophorolipids. In addition to 1:3 ratio, long time self assembly simulations are also performed with 1:1 and 1:2 ratios for linolenic acid sophorolipids. Distinctions in structural arrangements of sophorolipid molecules in the self assembled configuration for all the systems are investigated. The present study aims to provide structural insight into the different self assembled configurations of sophorolipids in water.

We have investigated the role of a specific gate residue, LEU362, located at the side-door of the pnbCE enzyme, on the thermal stability and structural flexibility of the enzyme. pnbCE is a bacterial carboxylesterase enzyme from Bacillus subtilis , which has a structural resemblance as well as similar catalytic behavior to the mammalian carboxylesterases. Mutations at the side-door residue 362 of pnbCE are known to alter the catalytic activity of this enzyme. Using molecular dynamics simulations at several temperatures, we have studied the mechanism through which mutations at position 362 of pnbCE affect the structure and dynamics of this enzyme. We have identified two coil residues, SER218 and GLN276, whose interactions with residue 362 in wild-type and mutant pnbCE enzymes control the dynamics of the side-door domain of pnbCE. A hydrogen bond between the GLN276 and ARG362 residues in the arginine substituted (L362R) pnbCE mutant enzyme appears to be responsible for locking the side-door domain region of the L362R enzyme, thus lowering the catalytic rates of the L362R mutant pnbCE enzyme compared to the wild-type. Similarly, a hydrogen bond formed between SER218 and ARG362 in L362R provides thermal stability to the arginine substituted mutant enzyme. This hydrogen bond is not as prevalent in the wild-type or other mutated pnbCE's, making them more prone to structural fluctuations upon increasing temperature. A trade-off between thermal stability of pnbCE and flexibility of the side-door domain region appears to be a best compromise for effectively controlling the catalytic properties of mutated pnbCE enzymes.

The electric dipole moment, polarizability, first and second dipole hyperpolarizability of HOF were determined via finite-field calculations with ab initio calculations of high predictive potential. Basis set sensibility and method dependence were systematically studied. We relied on a systematic sequence of prepared basis sets of Gaussian-type functions (GTF). A very large purpose-oriented, HOF-specific basis set yields CCSD(T) values ( SCF results in parentheses) for the property invariants: μ /ea 0  = 0.7374 (0.8503), α ̅/e 2 a 0 2 E h −1  = 11.77 (11.22), Δα /e 2 a 0 2 E h −1  = 5.95 (8.50), β ̅/e 3 a 0 3 E h −2  =− 13.8 (− 16.5) and γ ̅/e 4 a 0 4 E h −3  = 1099 (620).

The conformation and vibration analysis of 2-, 3- and 4-pyridinecarbonyl chlorides have been computed using B3LYP hybrid density functional with 6-311++G** basis set. All structures have been fully optimized, and the optimized geometries, dipole moments, infrared vibrational frequencies and relative energies are reported. From the computations, 2-pyridinecarbonyl chloride is predicted to exist predominantly in trans conformation, while the 3-pyridinecarbonyl chloride is predicted to exist predominantly in cis conformation with the trans-cis rotational barrier of 4.63 and 5.48 kcal/mol respectively. The two equivalent planar structures of 4-pyridinecarbonyl chloride are separated by an energy barrier of 4.55 kcal/mol. The effect of solvents on the conformational stability have been examined for nine different solvents (heptane, chloroform, THF, dichloroethane, acetone, ethanol, methanol, DSMO and water). The Integral Equation Formalism version of Polarized Continuum model (IEF-PCM) used for all solution phase computations. The trans conformer of 2-pyridinecarbonyl chloride and the cis conformer of 3-pyridinecarbonyl chloride which are more stable in gas phase remain the stable confomers in solution, but the stability decreases as the dielectric constant of the solvent increases. The variation of relative energies, dipole moments, solvation energies as function of the dielectric constant of solvents has been investigated.

Structural and physical properties such as some spectral features of α -L rhamno-indigo and β -L rhamno-indigo molecules are presented in this paper. Results are compared with those of 5,5'-dichloro-indigo N- β -glycosidic 4-amino-4,6-didesoxyglucose (Akashine A) that exhibits a strong inhibitory activity against various human tumor cell lines. Density functional theory (DFT) using B3LYP functional and 6-31G+(d,p), 6-311+G(2d,p) and cc-pvdz as basis sets was applied to perform these studies. Calculations were carried out both in gas phase and with DMSO as an implicit solvent. Gauge including atomic orbitals (GIAO) approach was used to calculate 1 H NMR chemical shifts and Time dependent density functional theory (TD-DFT) calculations were performed to determine the electronic transitions and their nature within the molecules. Moreover, stabilization energies of intra and intermolecular interactions were determined using NBO analyses. Local reactivity descriptors were computed to give insight in the nature of reactive sites. Overall, it has been shown that the nature of the glycosidic linkages has a significant influence on the molecular properties.

We present a DFT approach for precise estimation of the intermolecular effects on the experimental and calculated 13 C NMR shifts for a series of 5-spiro-2,4-dithiohydantoins ( 1 – 5 ), both in solid state and in solution. It has been found that the used B3LYP/6-31+ G ** method gives very good agreement with the experimental structural and the NMR parameters, provided the intermolecular hydrogen bonds are properly considered. For correct description of the experimental NMR shifts in solid state we have initially used the isolated-molecule and the cluster approaches for GIAO calculations of the NMR shifts, followed by periodic boundary condition calculations of the structure and the nuclear magnetic shielding constants by the GIPAW method implemented in the Quantum Espresso code. The best agreement with the experimental solid state data is obtained for the optimized small cluster (a trimer of molecules) in the calculations using the atom-centered orbitals. Excellent agreement between the 13 C CPMAS NMR and the GIPAW calculated shift is obtained for fully relaxed bulk structures of compounds 1 – 5 . This has been used as a final verification of the proposed solid state structure of compound 5 whose crystal structure is unknown yet.

Metal hydrides exhibit interesting properties as hosts for Eu(II) containing luminescent compounds due to the nephelauxetic effect and the strong ligand field of the hydride anion. In order to elucidate the lattice site symmetry of europium dopants, Q-band and X-band electron paramagnetic resonance (EPR) spectra were collected on LiMH 3  : Eu 2+ and LiMD 3  : Eu 2+ (M = Sr, Ba) powders with europium concentrations between 0.0037 and 0.27 mol %. They show well resolved hyperfine splitting in the central part of the spectra due to magnetic electron spin-nuclear spin coupling of 151 Eu and 153 Eu, and are in good agreement with simulated spectra based upon cubic site symmetry. Spin Hamiltonian parameters were extracted by spectral analysis and are reported. Low intensity rhombic spectra contributions could be assigned to small amounts of MH 2  : Eu 2+ or the respective deuterides as impurities in the samples. The results of this EPR investigation and size considerations suggest that europium is divalent and occupies the alkaline earth metal (M) positions in LiMH 3  : Eu 2+ and LiMD 3  : Eu 2+ (M = Sr, Ba).

Mn adsorption on the GaAs(111)–(1×1)B surface electronic and magnetic properties are investigated using first principles total energy calculations within the periodic spin polarized density functional theory. Results show that one Mn atom adsorption on top of the surface drives to an interstitial Mn atom. The interstitial atom is bonded to three first monolayer As atoms forming a chain-like structure. This stable structure has a ferromagnetic behavior with a Mn magnetic moment of ∼ 3.98 μ B . The Mn coverage increase yields a stable structure with the creation of an interstitial Mn layer, which in turn gives rise to a GaMnAs like alloy at the surface. The layer displays a ferromagnetic characteristic with magnetic moment of ∼ 4.40 μ B . A surface formation energy analysis of all these stable structures shows that one Mn interstitial monolayer and a Mn interstitial atom may coexist. Density of states shows that there is an important contribution of the Mn atoms to the occupied and unoccupied states. The DOS of one Mn monolayer is metallic with the most important contribution around the Fermi level coming from the Ga-p and Mn-d orbitals.

The unbiased density functional-based Birmingham Cluster Genetic Algorithm is employed to locate the global minima of all neutral and mono-ionic silver-gold octamer clusters. Structural, energetic and electronic trends are determined across the series, in order to clarify the role of composition and charge on the position of the 2D–3D transition in ultrasmall coinage metal systems. Our calculations indicate a preference for three dimensional structures at high silver concentrations, which varies significantly with charge. The minimum in composition dependent mixing energies is independent of the charge, however, with a preference for the maximally mixed clusters, Ag 4 Au 4 ν for all charge states ν . The sensitivity of isomeric preference to ν is found to be greater for electron-rich and electron-deficient clusters, implying a complexity of unambiguous determination of cluster motifs in related experiments. Vertical ionization potentials and detachment energies are calculated to probe electronic behaviour, providing numerical predictions for future spectroscopic studies.

We characterize, by means of the definition of a generalized distance, the differences and similarities between binary nanoclusters. To define analytically, and to compute numerically this distance, we have generalized an original concept that was introduced for pure clusters. Since the diversity of cluster conformations grows exponentially with their size, and becomes even larger when the cluster atoms are of more than one species, we limit our attention to small ones. Thus, to illustrate and analyze our distance definition we characterize the Lennard-Jones (LJ) minimum energy conformations of two- and three-dimensional (2D and 3D) binary clusters, for 5 ≤  N  ≤ 12, where N is the number of atoms of the cluster. In addition, when varying the LJ potential parameters, we find that the number of minima decreases as the range of the potential of one of the species is increased, and confirm that minimal energy conformations adopt a well defined core-shell configuration.

Ground state and low lying isomer structures of (Bi 2 O 3 ) n clusters with n  = 6 − 9 were determined by first-principle calculations. These calculations were performed with the LCGTO-ADFT method as implemented in the deMon2k program. Initial structures from Born–Oppenheimer molecular dynamics trajectories were selected as starting points for local geometry optimizations. The optimized structures where identified as minimum structures by frequency analysis. Furthermore, the structural relation between the clusters is presented. This work shows for the (Bi 2 O 3 ) 8 cluster a higher stability then for the other clusters.

A first principles density functional theory calculation has been carried out to study the energetics and structural properties of substituted polyhedral oligomeric silsesquioxane (POSS) as a function of the POSS cage size. The substitution of Si atom in the POSS molecules has been performed in three different ways, namely (i) both Si and an adjacent H atom are replaced by an Al atom, (ii) only a Si atom is replaced by an Al atom, and (iii) a Si atom is replaced by an Al and a Na/K atom. For the first and third kind of substitution, the net spin state is the same (i.e. closed shell), while the structures corresponding to the second kind of substitution are characterized by an excess spin (i.e. open shell). The structures of substituted POSS for the first and second kind of substitution are greatly distorted and always energetically less stable than the parent structure, while for the third kind of substitution, the stability depends on the cage size of POSS molecule, as also shown in a previous work (Asaduzzaman et al. [1]).

We report first principle study of Nowotny Chimney Ladder silicide Os 2 Si 3 , calculated using the full-potential augmented plane-wave method based on the density functional theory. Thus, total energies and energy gap values were determined within the local density and conjugate gradient approximations, using also their correction called: the modified Becke-Johnson potential, in order to treat the exchange-correlation potential energy. Our results show that this compound exhibits semiconducting character with a direct gap at the Γ point of the Brillouin zone, which is confirmed by other experimental and theoretical works. Results on band structures, density of states, and charge-density distributions are presented. In addition, we performed calculations of optical properties by determining the complex dielectric function from which are derived the other parameters.

In this communication we calculate the TPI cross-section for pump-probe scheme in Au, Ag and Na neutral clusters in high refractive index environment. The pump photon energy is chosen to be close to the surface plasmon (SP) energy of considered clusters. Since the interband transition energy in Ag and Na exceeds the SP resonance energy, the main contribution into the TPI in these clusters comes from the interband transitions. In Au clusters the interband transition threshold is very close to SP resonance, and the SP assisted TPI cross-section is attenuated. The calculations are performed by separating the coordinates of electrons corresponding to the collective oscillations and the individual motion that allows to take into account the resonance contribution of excited SP oscillations. It is shown that the ionization cross section increases by two orders of magnitude if the energy of the pump photon matches the surface plasmon energy in the Ag and Na cluster.

Previously we have determined the lowest-energy structures and full vibrational spectra of Cu N with N up to 150 atoms by means of an unbiased-structure-optimization approach combined with the analytical formulas of the embedded-atom total-energy method and the harmonic superposition approximation. Here, we extend the earlier T  = 0 studies to T  ≠ 0 and present the equilibrium thermodynamic properties of copper clusters with N from 2 to 150. Thereby, we calculate the Helmholtz free energy quantum mechanically and examine it as a function of temperature and cluster size. It is shown, that the impact of entropic effects on the stability of the copper clusters is rather small for temperatures less than 300 K, which is about the bulk Debye temperature. For larger temperatures, the influence of the vibrational entropy on the cluster stability becomes stronger so that with increasing temperature the stability of some clusters (most often low-symmetrical) is increased and that of others (most often high-symmetrical) is reduced. For the first time, we demonstrate the existence of new magic copper clusters at elevated temperatures. These have the sizes 80, 88, 104, and 125 and will be called the temperature-dependent magic clusters.

Detecting and quantifying geometric features in large series of cluster structures is in the focus of the present paper. Three so-called similarity functions that have been presented earlier are compared and their ability to point to highly symmetric clusters is shown. These functions quantify the similarity between different cluster structures or between a cluster and bulk structures. As an example, we have chosen a continuous series of Lennard–Jones cluster structures with 350 to 1000 atoms. The similarity functions of these systems are compared to other descriptions of relative stability, cluster shape and shell building and are found to be very useful and reliable.