Anisotropic magnetic couplings and structure-driven canted to collinear transitions in Sr2IrO4 by magnetically constrained noncollinear DFT

We study the canted magnetic state in Sr2IrO4 using fully relativistic density functional theory (DFT) including an on-site Hubbard U correction. A complete magnetic phase diagram with respect to the tetragonal distortion and the rotation of IrO6 octahedra is constructed, revealing the presence of two types of canted to collinear magnetic transitions: a spin-flop transition with increasing tetragonal distortion and a complete quenching of the basal weak ferromagnetic moment below a critical octahedral rotation. Moreover, we put forward a scheme to study the anisotropic magnetic couplings by mapping magnetically constrained noncollinear DFT onto a general spin Hamiltonian. This procedure allows for the simultaneous account and direct control of the lattice, spin, and orbital interactions within a fully ab initio scheme. We compute the isotropic, single site anisotropy and Dzyaloshinskii-Moriya (DM) coupling parameters, and clarify that the origin of the canted magnetic state in Sr2IrO4 arises from the structural distortions and the competition between isotropic exchange and DM interactions.

X-Ha center dot center dot center dot C hydrogen bonds in n-alkane-HX (X = F, OH) complexes are stronger than C-Ha <-X hydrogen bonds

Computational study of X-Ha <-C and C-Ha <-X hydrogen bonds in n-alkane-HX complexes (X =F,OH, alkane =propane, butane, pentane) has been carried out in this work. Ab initio and density functional theories were used for this study. For n-alkane-H2O complexes both Oa <-H-C and O-Ha <-C hydrogen bonded complex have been found, while for n-alkane-HF complexes, our attempt to optimize Fa <-H-C H-bond was not successful. Like most of the hydrogen bonded systems, strong correlation between binding energy and stretching frequency of H-F and O-H stretching mode was observed. The values of electron density and Laplacian of electron density are within the accepted range for hydrogen bonds. In all these cases, X-Ha <-C hydrogen bonds are found to be stronger than C-Ha <-X hydrogen bonds.

Rational molecular dynamics scheme for predicting optimum concentration loading of nano-additive in phase change materials

The present study deals with the diffusion and phase transition behaviour of paraffin reinforced with carbon nano-additives namely graphene oxide (GO) and surface functionalized single walled carbon nanotubes (SWCNT). Bulk disordered systems of paraffin hydrocarbons impregnated with carbon nano-additives have been generated in realistic equilibrium conformations for potential application as latent heat storage systems. Ab initio molecular dynamics(MD) in conjugation with COMPASS forcefield has been implemented using periodic boundary conditions. The proposed scheme allows determination of optimum nano-additive loading for improving thermo-physical properties through analysis of mass, thermal and transport properties; and assists in determination of composite behaviour and related performance from microscopic point of view. It was observed that nanocomposites containing 7.8% surface functionalised SWCNT and 55% GO loading corresponds to best latent heat storage system. The propounded methodology could serve as a by-pass route for economically taxing and iterative experimental procedures required to attain the optimum composition for best performance. The results also hint at the large unexplored potential of ab-initio classical MD techniques for predicting performance of new nanocomposites for potential phase change material applications. (C) 2015 Author(s).

Time-Resolved Resonance Raman Spectroscopic Studies on the Radical Anions of Menaquinone and Naphthoquinone

Quinones and their radical ion intermediates have been much studied by vibrational spectroscopy to understand their structure-function relationships in various biological processes. In this paper, we present a comprehensive analysis of vibrational spectra in the structure-sensitive region of both the naphthoquinone (NQ) and 2-methyl-1,4-naphthoquinone (MQ, menaquinone) radical anions using time-resolved resonance Raman and ab initio studies. Specific vibrational mode assignments have been made to all the vibrational frequencies recorded in the experiment. It is observed that the carbonyl and C-C stretching frequencies show considerable coupling in NQ and MQ radical anions. Further, the asymmetric substitution present in MQ with respect to NQ shows important signatures in the radical anion spectrum. It is concluded that assignments of vibrational frequencies of asymmetrically substituted quinones must take into consideration the influence of asymmetry on structure and reactivity.

Effect of Structural Modification on the Quantum-Size Effect in II-VI Semiconducting Nanocrystals

The electronic structure of group II-VI semiconductors in the stable wurtzite form is analyzed using state-of-the-art ab initio approaches to extract a simple and chemically transparent tight-binding model. This model can be used to understand the variation in the bandgap with size, for nanoclusters of these compounds. Results complement similar information already available for same systems in the zinc blende structure. A comparison with all available experimental data on quantum size effects in group II-VI semiconductor nanoclusters establishes a remarkable agreement between theory and experiment in both structure types, thereby verifying the predictive ability of our approach. The significant dependence of the quantum size effect on the structure type suggests that the experimental bandgap change at a given size compared to the bulk bandgap, may be used to indicate the structural form of the nanoclusters, particularly in the small size limit, where broadening of diffraction features often make it difficult to unambiguously determine the structure.

Studies involving electrostatic potential of valinomycin

The electrostatic potential of valinomycin in various conformations as obtained by the crystal structures (uncomplexed, complexed) and theoretical considerations have been evaluated and compared. The potential energy profiles along the æ axis of the bracelet-like structures show a systematic variation from the uncomplexed to the complexed structure. This type of conformational change and the potential variation are probably associated with different states of ion transport, like the capture and release of ions by the ionophore. Also, the asymmetry of the molecule due to D-HyIV on one side and L-Lac on the other side is reflected in the potential values along the Z-axis, the magnitude of which, is considerable in the uncomplexed structure. The evaluation of the potential at the ab-initio level on smaller fragments indicate that the order of liganding capacity of oxygen is amide ether ester. Also, the inductive effects due to alkyl substitution is negligible as evidenced by the potential studies on the substituted amides and esters.

Systematic variation in bond lengths of peptides

The lengths of the carbonyl as well as of the adjacent C-N and C-C bonds in peptides are shown to vary systematically with the central C-N bond length. Results of ab initio calculations on N-methylacetamide and its Li+, Na+ and Mg2+ complexes are also discussed.

Experimental and Theoretical Charge Density Analysis of Polymorphic Structures: The Case of Coumarin 314 Dye

Experimental charge density distributions in two known conformational polymorphs (orange and yellow) of coumarin 314 dye are analyzed based on multipole modeling of X-ray diffraction data collected at 100 K. The experimental results are compared with the charge densities derived from multipole modeling of theoretical structure factors obtained from periodic quantum calculation with density functional theory (DFT) method and B3LYP/6-31G(d,p) level of theory. The presence of disorder at the carbonyl oxygen atom of ethoxycarbonyl group in the yellow form, which was not identified earlier, is addressed here. The investigationof intermolecular interactions, based on Hirshfeld surface analysis and topological properties via quantum theory of atoms in molecule and total electrostatic interaction energies, revealed significant differences between the polymorphs. The differences of electrostatic nature in these two polymorphic forms were unveiled via construction of three-dimensional deformation electrostatic potential maps plotted over the molecular surfaces. The lattice energies evaluated from ab initio calculations on the two polymorphic forms indicate that the yellow form is likely to be the most favorable thermodynamically. The dipole moments derived from experimental and theoretical charge densities and also from Lorentz tensor approach are compared with the single-molecule dipole moments. In each case, the differences of dipole moments between the polymorphs are identified.

Growth Mechanism of Cadmium Sulfide Nanocrystals

We investigate the growth kinetics of CdS nanocrystals in the quantum confinement regime using time-resolved small-angle X-ray scattering. In contrast to earlier reports for similar systems, we establish that the growth kinetics in this case follows the Lifshitz-Slyozov-Wagner theory, for not only growth of the average diameter of the nanocrystals but also the time dependence of the size distribution and the temperature dependence of the rate constant. This is the first rigorous example of the coarsening process in the quantum confinement (< 5 nm)regime. Ab initio studies for the reaction pathways provide a microscopic understanding of this finding.

Asynchronous behaviour in some three-atom linear concerted radical-exchange reactions

A few simple three-atom thermoneutral radical exchange reactions (i.e. A + BC --> AB + C) are examined by ab initio SCF methods. Emphasis is laid on the detailed analysis of density matrices rather than on energetics. Results reveal that the sum of the bond orders of the breaking and forming bonds is not conserved to unity, due to development of free valence on the migrating atom 'B' in the transition state. Bond orders, free valence and spin densities on the atoms are calculated. The present analysis shows that the bond-cleavage process is always more advanced than the bond-formation process in the transition state. Further analysis shows a development of the negative spin density on the migrating atom 'B' in the transition state. The depletion of the alpha-spin density on the radical site "A" in the reactant during the reaction lags behind the growth of the alpha-spin density on the terminal atom "C" of the reactant bond, 'B-C' in the transition state. But all these processes are completed simultaneously at the end of the reaction. Hence, the reactions are asynchronous but kinetically concerted in most cases.

Geometry changes induced by negative hyperconjugative interactions involving carbonyl and thiocarbonyl groups

MNDO geometry optimizations have been carried out on a series of acyclic and cyclic unsymmetrically disubstituted carbonyl and thiocarbonyl compounds. The C=X unit shows a consistent and often sizeable tilt towards one of the substituents, following the order O > Snot, vert, similarN > C > B. Reference ab initio calculations and available experimental results support the MNDO results. The effect, which is particularly dramatic in small rings, is attributed primarily to favorable negative hyperconjugative interaction between the lone pair on X and a low lying adjacent σ* orbital. Such an interaction can lead to highly distorted structures, including perhaps to a planar molecule with an inverted sp2 carbon center.

Vibrational analysis of boldine hydrochloride using QM/MM approach

A complete vibrational analysis was performed on the molecular structure of boldine hydrochloride using QM/MM method. The equilibrium geometry, harmonic vibrational frequencies and infrared intensities were calculated by QM/MM method with B3LYP/6-31G(d) and universal force field (UFF) combination using ONIOM code. We found the geometry obtained by the QM/MM method to be very accurate, and we can use this rapid method in place of time consuming ab initio methods for large molecules. A detailed interpretation of the infrared spectra of boldine hydrochloride is reported. The scaled theoretical wave numbers are in perfect agreement with the experimental values. The FT-IR spectra of boldine hydrochloride in the region 4000-500 cm(-1) were recorded in CsI (solid phase) and in chloroform with concentration 5 and 10 mg/ml.

Size-Dependent Tuning of Mn2+ d Emission in Mn2+-Doped CdS Nanocrystals: Bulk vs Surface

We show that the characteristic Mn2+ d emission color from Mn2+-doped CdS nanocrystals can be tuned over as much as 40 nm, in contrast to what should be expected from such a nearly localized d-d transition. This is achieved surprisingly by a fine-tuning of the host particle diameter from 1.9 to 2.6 nm, thereby changing the overall emission color from red to yellow. Systematic experiments in conjunction with state-of-the-art ab initio calculations with full geometry optimization establish that Mn2+ ions residing at surface/subsurface regions have a distorted tetrahedral coordination resulting in a larger ligand field splitting. Consequently, these near-surface Mn2+ species exhibit a lower Mn2+ d emission energy, compared to those residing at the core of the nanocrystal with an undisturbed tetrahedral coordination. The origin of the tunability of the observed Mn2+ emission is the variation of emission contributions arising from Mn2+ doped at the core, subsurface, and surface of the host. Our findings provide a unique and easy method to identify the location of an emitting Mn2+ ion in the nanocrystal, which would be otherwise very difficult to decipher.

The influence of lone-pair repulsions on C–C bond lengths: a critical evaluation of the experimental and theoretical evidence

X-Ray structural data, as well as semiempirical and ab initio molecular orbital calculations, reveal no systematic and substantial difference between the C–C bond lengths of cis and trans 1,2-diketones. Additional results on various conformations of 1,2-diimines and 1,2-dithiones follow the same pattern. Therefore, lone-pair repulsions cannot be implicated in the observed lengthening of C–C bonds in isatin and several related molecules. Conjugation in these systems occurs peripherally avoiding the participation of the central C–C bond. Negative hyperconjugative interaction between the oxygen lone pairs and the adjacent C–C σ* orbital is suggested to be the principal reason for the relatively long C–C bond in diketones. This effect is found in both the cis and trans conformations.

Conformational Studies of Some Alpha-substituted Acetones CH3COCH2XCH3 Where X=CH2, O Or S And Phenacyl Sulfide

Both semiempirical and ab initio calculations are reported for conformational studies of a series of alpha-substituted acetones CH3COCH2XCH3 where X = CH2, O or S and of phenacyl sulfide PhCOCH2SCH3. For conformational studies in the lowest triplet state of these molecules, the MINDO/3 method was employed in the unrestricted Hartree-Fock frame. Results reveal that rotation around a bond alpha to the carbonyl group is more favourable than that around the beta bond. The preferred conformations in the lowest triplet state are nearly the same as in the ground state.