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The accuracy of a dispersion-corrected density functional theory method is validated against 241 experimental organic crystal structures from Acta Cryst. Section E.

This paper describes the validation of a dispersion-corrected density functional theory (d-DFT) method for the purpose of assessing the correctness of experimental organic crystal structures and enhancing the information content of purely experimental data. 241 experimental organic crystal structures from the August 2008 issue of Acta Cryst. Section E were energy-minimized in full, including unit-cell parameters. The differences between the experimental and the minimized crystal structures were subjected to statistical analysis. The r.m.s. Cartesian displacement excluding H atoms upon energy minimization with flexible unit-cell parameters is selected as a pertinent indicator of the correctness of a crystal structure. All 241 experimental crystal structures are reproduced very well: the average r.m.s. Cartesian displacement for the 241 crystal structures, including 16 disordered structures, is only 0.095 Å (0.084 Å for the 225 ordered structures). R.m.s. Cartesian displacements above 0.25 Å either indicate incorrect experimental crystal structures or reveal interesting structural features such as exceptionally large temperature effects, incorrectly modelled disorder or symmetry breaking H atoms. After validation, the method is applied to nine examples that are known to be ambiguous or subtly incorrect.

Although the dispersal of animals is influenced by a variety of factors, few studies have used a condition-dependent approach to assess it. The mechanisms underlying dispersal are thus poorly known in many species, especially in large mammals. We used 10 microsatellite loci to examine population density effects on sex-specific dispersal behavior in the American black bear, Ursus americanus. We tested whether dispersal increases with population density in both sexes. Fine-scale genetic structure was investigated in each of four sampling areas using Mantel tests and spatial autocorrelation analyses. Our results revealed male-biased dispersal pattern in low-density areas. As population density increased, females appeared to exhibit philopatry at smaller scales. Fine-scale genetic structure for males at higher densities may indicate reduced dispersal distances and delayed dispersal by subadults.

The major objective of this paper is to address a controversial binding sequence between nucleic acid bases (NABs) and C60 by investigating adsorptions of NABs and their cations on C60 fullerene with a variety of density functional theories including two novel hybrid meta-GGA functionals, M05-2x and M06-2x, as well as a dispersion-corrected density functional, PBE-D. The M05-2x/6-311++G** provides the same binding sequence as previously reported, guanine(G) > cytosine(C) > adenine (A) > thymine (T); however, M06-2x switches the binding strengths of A and C, and PBE-D eventually results in the following sequence, G>A>T>C, which is the same as the widely accepted hierarchy for the stacking of NABs on other carbon nanomaterials such as single-walled carbon nanotube and graphite. The results indicate that the questionable relative binding strength is due to insufficient electron correlation treatment with the M05-2x or even the M06-2x method. The binding energy of G@C60 obtained with the M06-2x/6-311++G(d,p) and the PBE-D/cc-pVDZ is −7.10 and −8.07 kcal/mol, respectively, and the latter is only slightly weaker than that predicted by the MP2/6-31G(d,p) (−8.10kca/mol). Thus, the PDE-D performs better than the M06-2x for the observed NAB@C60 π-stacked complexes. To discuss whether C60 could prevent NABs from radiation-induced damage, ionization potentials of NABs and C60, and frontier molecular orbitals of the complexes NABs@C60 and (NABs@C60)+ are also extensively investigated. These results revealed that when an electron escapes from the complexes, a hole was preferentially created in C60 for T and C complexes, while for G and A the hole delocalizes over the entire complex, rather than a localization on the C60 moiety. The interesting finding might open a new strategy for protecting DNA from radiation-induced damage and offer a new idea for designing C60-based antiradiation drugs.

Background

Goethite is a common and reactive mineral in the environment. The transport of contaminants and anaerobic respiration of microbes are significantly affected by adsorption and reduction reactions involving goethite. An understanding of the mineral-water interface of goethite is critical for determining the molecular-scale mechanisms of adsorption and reduction reactions. In this study, periodic density functional theory (DFT) calculations were performed on the mineral goethite and its (010) surface, using the Vienna Ab Initio Simulation Package (VASP).

Results

Calculations of the bulk mineral structure accurately reproduced the observed crystal structure and vibrational frequencies, suggesting that this computational methodology was suitable for modeling the goethite-water interface. Energy-minimized structures of bare, hydrated (one H2O layer) and solvated (three H2O layers) (010) surfaces were calculated for 1 × 1 and 3 × 3 unit cell slabs. A good correlation between the calculated and observed vibrational frequencies was found for the 1 × 1 solvated surface. However, differences between the 1 × 1 and 3 × 3 slab calculations indicated that larger models may be necessary to simulate the relaxation of water at the interface. Comparison of two hydrated surfaces with molecularly and dissociatively adsorbed H2O showed a significantly lower potential energy for the former.

Conclusion

Surface Fe-O and (Fe)O-H bond lengths are reported that may be useful in surface complexation models (SCM) of the goethite (010) surface. These bond lengths were found to change significantly as a function of solvation (i.e., addition of two extra H2O layers above the surface), indicating that this parameter should be carefully considered in future SCM studies of metal oxide-water interfaces.

In this work, we studied a copper complex-based dye, which is proposed for potential photovoltaic applications and is named Cu (I) biquinoline dye. Results of electron affinities and ionization potentials have been used for the correlation between different levels of calculation used in this study, which are based on The Density Functional Theory (DFT) and time-dependent (TD) DFT. Further, the maximum absorption wavelengths of our theoretical calculations were compared with the experimental data. It was found that the M06/LANL2DZ + DZVP level of calculation provides the best approximation. This level of calculation was used to find the optimized molecular structure and to predict the main molecular vibrations, the molecular orbitals energies, dipole moment, isotropic polarizability and the chemical reactivity parameters that arise from Conceptual DFT.

The normal mode spectrum for the four-coordinated heme compound Fe(II) octaethylporphyrin, Fe(OEP), has been determined by refining force constants to the experimental Fe vibrational density of states measured with nuclear resonance vibrational spectroscopy (NRVS). Convergence of the calculated spectrum to the data was achieved by first imposing D4 symmetry on the model structure as well as the force constants, progressively including different internal coordinates of motion, then allowing the true Ci (or S2) point group symmetry of the Ci1 Fe(OEP) crystal structure. The NRVS-refined normal modes are in good agreement with Raman and IR spectra at high frequencies. Prior density functional theory predictions for a model porphyrin are similar to the core modes computed with the best-fit force field, but significant differences between D4 and Ci modes underline the sensitivity of porphyrin Fe normal modes to structural details. Some differences between the Ci best fit and the NRVS data can be attributed to intermolecular contacts not included in the normal mode analysis.

Dispersion is well known to be important in biological systems, but the effect of electron correlation in such systems remains unclear. In order to assess the relationship between the structure of a protein and its electron correlation energy, we employed both full system Hartree-Fock (HF) and second-order Møller-Plesset perturbation (MP2) calculations in conjunction with the Polarizable Continuum Model (PCM) on the native structures of two proteins and their corresponding computer-generated decoy sets. Due to the expense of the MP2 calculation, we have utilized the fragment molecular orbital method (FMO) in this study. We show that the sum of the Hartree-Fock (HF) energy and force field (LJ6) derived dispersion energy (HF + LJ6) is well correlated with the energies obtained using second-order Møller-Plesset perturbation (MP2) theory. In one of the two examples studied the correlation energy as well as the empirical dispersive energy term was able to discriminate between native and decoy structures. On the other hand, for the second protein we studied, neither the correlation energy nor dispersion energy showed discrimination capabilities; however, the ab initio MP2 energy and the HF+LJ6 both ranked the native structure correctly. Furthermore, when we randomly scrambled the Lennard-Jones parameters, the correlation between the MP2 energy and the sum of the HF energy and dispersive energy (HF+LJ6) significantly drops, which indicates that the choice of Lennard-Jones parameters is important.

Based on the minimum shear criterion, a direct and simple method is proposed to calculate twinning elements from the experimentally determined twinning plane for Type I twins or the twinning direction for Type II twins. It is generic and applicable to any crystal structure.

The fundamental theory of crystal twinning has been long established, leading to a significant advance in understanding the nature of this physical phenomenon. However, there remains a substantial gap between the elaborate theory and the practical determination of twinning elements. This paper proposes a direct and simple method – valid for any crystal structure and based on the minimum shear criterion – to calculate various twinning elements from the experimentally determined twinning plane for Type I twins or the twinning direction for Type II twins. Without additional efforts, it is generally applicable to identify and predict possible twinning modes occurring in a variety of crystalline solids. Therefore, the present method is a promising tool to characterize twinning elements, especially for those materials with complex crystal structure.

Summary

We present experimental results and theoretical simulations of the adsorption behavior of the metal–organic precursor Co2(CO)8 on SiO2 surfaces after application of two different pretreatment steps, namely by air plasma cleaning or a focused electron beam pre-irradiation. We observe a spontaneous dissociation of the precursor molecules as well as autodeposition of cobalt on the pretreated SiO2 surfaces. We also find that the differences in metal content and relative stability of these deposits depend on the pretreatment conditions of the substrate. Transport measurements of these deposits are also presented. We are led to assume that the degree of passivation of the SiO2 surface by hydroxyl groups is an important controlling factor in the dissociation process. Our calculations of various slab settings, using dispersion-corrected density functional theory, support this assumption. We observe physisorption of the precursor molecule on a fully hydroxylated SiO2 surface (untreated surface) and chemisorption on a partially hydroxylated SiO2 surface (pretreated surface) with a spontaneous dissociation of the precursor molecule. In view of these calculations, we discuss the origin of this dissociation and the subsequent autocatalysis.

A physical theory explaining the anisotropic dispersion of water and solutes in biological tissues is introduced based on the phenomena of Taylor dispersion, in which highly diffusive solutes cycle between flowing and stagnant regions in the tissue, enhancing dispersion in the direction of microvascular flow. An effective diffusion equation is derived, for which the coefficient of dispersion in the axial direction (direction of capillary orientation) depends on the molecular diffusion coefficient, tissue perfusion, and vessel density. This analysis provides a homogenization that represents three-dimensional transport in capillary beds as an effectively one-dimensional phenomenon. The derived dispersion equation may be used to simulate the transport of solutes in tissues, such as in pharmacokinetic modeling. In addition, the analysis provides a physically based hypothesis for explaining dispersion anisotropy observed in diffusion-weighted imaging (DWI) and diffusion-tensor magnetic resonance imaging (DTMRI) and suggests a means of obtaining quantitative functional information on capillary vessel density from measurements of dispersion coefficients. It is shown that a failure to account for flow-mediated dispersion in vascular tissues may lead to misinterpretations of imaging data and significant overestimates of directional bias in molecular diffusivity in biological tissues. Measurement of the ratio of axial to transverse diffusivity may be combined with an independent measurement of perfusion to provide an estimate of capillary vessel density in the tissue.

The title compound, C13H10BrNO2, exists as an enol–imine form in the crystal and adopts an E configuration with respect to the C=N double bond. The mol­ecule is close to planar, with a dihedral angle of 6.88 (14)° between the aromatic rings. Intra­molecular O—H⋯N and O—H⋯O hydrogen bonds generate S(6) and S(5) ring motifs, respectively. The crystal structure is stabilized by inter­molecular O—H⋯O hydrogen-bond inter­actions, forming R 2 2(10) and R 2 2(20) chains along [100]. ab initio Hartree–Fock (HF), density-functional theory (DFT) and semi-empirical (AM1 and PM3) calculations and full-geometry optimizations were also performed. Although there are some discrepancies between the experimental and calculated parameters, caused presumably by the O—H⋯O hydrogen-bond inter­actions, there is an acceptable general agreement between them.

In this work we studied three dyes which are proposed for potential photovoltaic applications and named Dye7, Dye7-2t and Dye7-3t. The Density Functional Theory (DFT) was utilized, using the M05-2X hybrid meta-GGA functional and the 6–31+G(d,p) basis set. This level of calculation was used to find the optimized molecular structure and to predict the main molecular vibrations, the absorption and emission spectra, the molecular orbitals energies, dipole moment, isotropic polarizability and the chemical reactivity parameters that arise from Conceptual DFT. Also, the pKa values were calculated with the semi-empirical PM6 method.

We report self-assembly and phase transition behavior of lower diamondoid molecules and their primary derivatives using molecular dynamics (MD) simulation and density functional theory (DFT) calculations. Two lower diamondoids (adamantane and diamantane), three adamantane derivatives (amantadine, memantine and rimantadine) and two artificial molecules (ADM•Na and DIM•Na) are studied separately in 125-molecule simulation systems. We performed DFT calculations to optimize their molecular geometries and obtained atomic electronic charges for the corresponding MD simulation, by which we predicted self-assembly structures and simulation trajectories for the seven different diamondoids and derivatives. Our radial distribution function and structure factor studies showed clear phase transitions and self-assemblies for the seven diamondoids and derivatives.

The explicit polarization (X-Pol) method has been examined using ab initio molecular orbital theory and density functional theory. The X-Pol potential was designed to provide a novel theoretical framework for developing next-generation force fields for biomolecular simulations. Importantly, the X-Pol potential is a general method, which can be employed with any level of electronic structure theory. The present study illustrates the implementation of the X-Pol method using ab initio Hartree—Fock theory and hybrid density functional theory. The computational results are illustrated by considering a set of bimolecular complexes of small organic molecules and ions with water. The computed interaction energies and hydrogen bond geometries are in good accord with CCSD(T) calculations and B3LYP/aug-cc-pVDZ optimizations.

The title compound, C13H10Cl2O2, is a mixed derivative of orthocarbonic acid. The non-crystallographic symmetry of the mol­ecule is close to C 2v. The aromatic residues are oriented in a syn conformation with respect to the Cl atoms. The least-squares planes through the phenyl rings enclose an angle of 36.11 (10)°. The C—O bonds at the central carbon are relatively short, and the O—C—O and Cl—C—Cl angles are smaller than the tetra­hedral angle. These metrical peculiarities including a mol­ecular symmetry close to C 2v are also observed in density functional theory (DFT) calculations, thus ruling out the decisive influence of inter­molecular forces in the crystal structure. Accordingly, only few and weak inter­molecular inter­actions are found. At distances smaller than the sum of the van der Waals radii, only two attractive inter­actions are detected: a weak C—H⋯O and a weak C—H⋯Cl hydrogen bond to one of the two potential acceptor atoms each.

The reliable prediction of molecular properties is a vital task of computational chemistry. In recent years, density functional theory (DFT) has become a popular method for calculating molecular properties for a vast array of systems varying in size from small organic molecules to large biological compounds such as proteins. In this work we assess the ability of many DFT methods to accurately determine atomic and molecular properties for small molecules containing elements commonly found in proteins, DNA, and RNA. These properties include bond lengths, bond angles, ground state vibrational frequencies, electron affinities, ionization potentials, heats of formation, hydrogen bond interaction energies, conformational energies, and reaction barrier heights. Calculations are carried out with the 3-21G*, 6-31G*, 3-21+G*, 6-31+G*, 6-31++G*, cc-pVxZ, and aug-cc-pVxZ (x=D,T) basis sets, while bond distance and bond angle calculations are also done using the cc-pVQZ and aug-cc-pVQZ basis sets. Members of the popular functional classes, namely, LSDA, GGA, meta-GGA, hybrid-GGA, and hybrid-meta-GGA, are considered in this work. For the purpose of comparison, Hartree-Fock (HF) and second order many-body perturbation (MP2) methods are also assessed in terms of their ability to determine these physical properties. Ultimately, it is observed that the split valence bases of the 6-31G variety provide accuracies similar to those of the more computationally expensive Dunning type basis sets. Another conclusion from this survey is that the hybrid-meta-GGA functionals are typically among the most accurate functionals for all of the properties examined in this work.

We have investigated the structures and stabilities of four different adenine quartets with alkali and halide ions in the gas phase and in water, using dispersion-corrected density functional theory at the BLYP-D/TZ2P level. First, we examine the empty quartets and how they interact with alkali cations and halide anions with formation of adenine quartet–ion complexes. Second, we examine the interaction in a stack, in which a planar adenine quartet interacts with a cation or anion in the periphery as well as in the center of the quartet. Interestingly, for the latter situation, we find that both cations and anions can stabilize a planar adenine quartet in a stack.

Electronic supplementary material

The online version of this article (doi:10.1007/s00775-009-0611-8) contains supplementary material, which is available to authorized users.

The cytochrome P450 (CYP) enzymes are important in many areas, including pharmaceutical development. Subtle changes in the electronic structure of the active species, Compound I, have been postulated previously to account partly for the experimentally observed differences in reactivity between isoforms. Current predictive models of CYP metabolism typically assume an identical Compound I in all isoforms. Here we present a method to calculate the electronic structure and to estimate the Fe–O bond enthalpy of Compound I, and apply it to several human and bacterial CYP isoforms. Conformational flexibility is accounted for by sampling large numbers of structures from molecular dynamics simulations, which are subsequently optimized with density functional theory (B3LYP) based quantum mechanics/molecular mechanics. The observed differences in Compound I between human isoforms are small: They are generally smaller than the spread of values obtained for the same isoform starting from different initial structures. Hence, it is unlikely that the variation in activity between human isoforms is due to differences in the electronic structure of Compound I. A larger difference in electronic structure is observed between the human isoforms and P450cam and may be explained by the slightly different hydrogen-bonding environment surrounding the cysteinyl sulfur. The presence of substrate in the active site of all isoforms studied appears to cause a slight decrease in the Fe–O bond enthalpy, apparently due to displacement of water out of the active site, suggesting that Compound I is less stable in the presence of substrate.

Prolyl-leucyl-glycinamide (PLG) is a unique endogenous peptide that modulates dopamine receptor subtypes of the D2 receptor family within the CNS. We seek to elucidate the structural basis and molecular mechanism by which PLG and its analogues modulate dopamine receptors, toward the development of new therapeutics to treat Parkinson's disease, tardive dyskinesia and schizophrenia. As a first step toward establishing a validated protocol for accurate computational modeling of PLG and associated peptidomimetic analogues, we evaluated the accuracy of density functional theory (DFT), wavefunction theory (WFT), and molecular mechanics (MM) calculations for PLG and for a library of structurally related small molecules. We first tested twelve local and nonlocal density functionals, Hartree-Fock (HF) theory, four “semiempirical” methods of the neglect of diatomic differential overlap (NDDO) type, and one self-consistent-charge nonorthogonal tight-binding (SCC-DFTB) method as implemented in two software suites, against coupled-cluster benchmark geometries for 4-methylthiazolidine, a small molecule that comprises key structural features present in our PLG analogue library. DFT and HF calculations were done with the MG3S augmented polarized triple-zeta basis set. We find that for 4-methylthiazolidine bond distances, DFT significantly outperforms NDDO, and both SCC-DFTB versions we evaluated perform worse than HF theory and are less accurate than 83% of the density functionals tested. The top five functionals for 4-methylthiazolidine were M05-2X, mPW1PW, B97-2, M06-2X, and PBEh, with mean unsigned errors (MUEs) in bond length of 0.0017, 0.0020, 0.0023, 0.0025 and 0.0027 Å, respectively. The widely used B3LYP functional ranked 11th out of twelve functionals evaluated, slightly below SCC-DFTB, and is significantly less accurate for 4-methylthiazolidine bond distances (MUE = 0.0095 Å) than the best local functional (M06-L, MUE = 0.0030 Å), which is far less computationally costly. Based on that initial analysis, we obtained new M05-2X benchmark geometric parameters for PLG and a library of eleven peptidomimetic derivatives, which we in turn used to examine the accuracy of thirty-four popular molecular mechanics (MM) force fields, four NDDO approaches, and SCC-DFTB for the full compound structures. Here, we found that ∼70% of the MM force fields tested superior to the best semiempirical and SCC-DFTB codings. Moreover, AMBER-type force fields proved most accurate among MM methods for this class of small-molecule peptidomimetics; the AMBER-type methods comprised eight out of the top ten molecular mechanics options we tested.

In this work, we make use of a model chemistry within Density Functional Theory (DFT) recently presented, which is called M05-2X, to calculate the molecular structure of the flavonoid Rutin, as well as to predict the infrared (IR) and ultraviolet (UV-Vis) spectra, the dipole moment and polarizability, the free energy of solvation in different solvents as an indication of solubility, the HOMO and LUMO orbitals, and the chemical reactivity parameters that arise from Conceptual DFT. The calculated values are compared with the available experimental data for this molecule as a means of validation of the used model chemistry.

Particle size is generally considered to be the primary factor in design of nanocrystal photocatalyst, because the reduction of particle size increases the number of active sites. However, the benefit from the size reduction can be canceled by a higher electron-hole recombination rate due to the confined space in sphere-shaped nanoparticles. Here we report a mechanistic study on a novel nanobelt structure that overcomes the drawback of sphere-shaped nanoparticles. Single-crystalline anatase TiO2 nanobelts with two dominant surfaces of (101) facet exhibit enhanced photocatalytic activity than the nanosphere counterparts with an identical crystal phase and similar specific surface area. The ab initio density functional theory (DFT) calculations show that the exposed (101) facet of the nanobelts yields an enhanced reactivity with molecular O2, facilitating the generation of superoxide radical. Moreover, the nanobelts exhibit a lower electron-hole recombination rate than the nanospheres due to the following three reasons: (i) greater charge mobility in the nanobelts, which is enabled along the longitudinal dimension of the crystals; (ii) fewer localized states near the band edges and in the bandgap due to less unpassivated surface states in the nanobelts; and (iii) enhanced charge separation due to trapping of photogenerated electrons by chemisorbed molecular O2 on the (101) facet. Our results suggest that the photocatalysis efficiency of nanocrystals can be significantly improved by tailoring the shape and the surface structure of nanocrystals, which provides a new concept for rational design and development of high-performance photocatalysts.

Phononic and magnonic dispersions of a linear array of periodic alternating Ni80Fe20 and bottom anti-reflective coating nanostripes on a Si substrate have been measured using Brillouin light scattering. The observed phononic gaps are considerably larger than those of laterally patterned multi-component crystals previously reported, mainly a consequence of the high elastic and density contrasts between the stripe materials. Additionally, the phonon hybridization bandgap has an unusual origin in the hybridization and avoided crossing of the zone-folded Rayleigh and pseudo-Sezawa waves. The magnonic band structure features near-dispersionless branches, with unusual vortex-like dynamic magnetization profiles, some of which lie below the highly-dispersive fundamental mode branch. Finite element calculations of the phononic and magnonic dispersions of the magphonic crystal accord well with experimental data.

The study aims to present a detailed theoretical investigation of noncovalent intermolecular interactions between different π–π stacking nitrogen substituted phenothiazine derivatives by applying second-order Møller-Plesset perturbation (MP2), density functional (DFT) and semiempirical theories. The conformational stability of these molecular systems is mainly given by the dispersion-type electron correlation effects. The density functional tight-binding (DFTB) method applied for dimer structures are compared with the results obtained by the higher level theoretical methods. Additionally, the optimal configuration of the investigated supramolecular systems and their self-assembling properties are discussed.

The determination of out-of-plane density profiles of a confined molecular liquid by synchrotron X-ray reflectivity is presented.

An X-ray reflectivity theory on the determination of the density profile of a molecular liquid under nanometre confinement is presented. The confinement geometry acts like an X-ray interferometer, which consists of two opposing atomically flat single-crystal mica membranes with an intervening thin liquid film of variable thickness. The X-rays reflected from the parallel crystal planes (of known structure) and the layered liquid in between them (of unknown structure) interfere with one another, making X-ray reflectivity highly sensitive to the liquid’s density profile along the confinement direction. An expression for the reflected intensity as a function of momentum transfer is given. The total structure factor intensity for the liquid-filled confinement device is derived as a sum of contributions from the inner and outer crystal terminations. The method presented readily distinguishes the confined liquid from the liquid adsorbed on the outer mica surfaces. It is illustrated for the molecular liquid tetrakis(trimethyl)siloxysilane, confined by two mica surfaces at a distance of 8.6 nm.

γ-Al2O3 is a porous metal oxide and described as a defective spinel with some cationic vacancies. In this work, we calculate the electronic density of states and band structure for the bulk of this material. The calculations are performed within the density functional theory using the full potential augmented plan waves plus local orbital method, as embodied in the WIEN2k code. We show that the modified Becke-Johnson exchange potential, as a semi-local method, can predict the bandgap in better agreement with the experiment even compared to the accurate but much more expensive green function method. Moreover, our electronic structure analysis indicates that the character of the valence band maximum mainly originates from the p orbital of those oxygen atoms that are close to the vacancy. The charge density results show that the polarization of the oxygen electron cloud is directed toward aluminum cations, which cause Al and O atoms to be tightly connected by a strong dipole bond.