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.

Time-resolved resonance Raman spectroscopic studies on the triplet excited state of fluoranil

Perfluoro substituted organic compounds have attracted attention owing to their unique structure and reactivity induced by the perfluoro effect. Fluoranil, a perfluoro derivative of p-benzoquinone, is the subject of this paper. Although the perfluoro effect in the ground state seems to have been well understood there is no information available about such effects on the excited state. Here, the time-resolved resonance Raman spectra of the triplet excited state of fluoranil are reported along with the Raman excitation profiles (REPs) of the various vibrational modes. The vibrational spectral analyses have been carried out by analogy with the fluoranil ground state, triplet benzoquinone, and triplet chloranil vibrational spectral assignments. Also, the assignments are further supported by the calculated frequencies using ab initio theoretical methods. It is observed that for fluoranil in the triplet excited state, due to the perfluoro effect, the structure is considerably less distorted than benzoquinone and also the electron delocalization in the pi* antibonding orbital is less than that of triplet excited state of benzoquinone.

Energy Hyperspace for Stacking Interaction in AU/AU Dinucleotide Step: Dispersion-Corrected Density Functional Theory Study

Double helical structures of DNA and RNA are mostly determined by base pair stacking interactions, which give them the base sequence-directed features, such as small roll values for the purine-pyrimidine steps. Earlier attempts to characterize stacking interactions were mostly restricted to calculations on fiber diffraction geometries or optimized structure using ab initio calculations lacking variation in geometry to comment on rather unusual large roll values observed in AU/AU base pair step in crystal structures of RNA double helices. We have generated stacking energy hyperspace by modeling geometries with variations along the important degrees of freedom, roll, and slide, which were chosen via statistical analysis as maximally sequence dependent. Corresponding energy contours were constructed by several quantum chemical methods including dispersion corrections. This analysis established the most suitable methods for stacked base pair systems despite the limitation imparted by number of atom in a base pair step to employ very high level of theory. All the methods predict negative roll value and near-zero slide to be most favorable for the purine-pyrimidine steps, in agreement with Calladine's steric clash based rule. Successive base pairs in RNA are always linked by sugar-phosphate backbone with C3-endo sugars and this demands C1-C1 distance of about 5.4 angstrom along the chains. Consideration of an energy penalty term for deviation of C1-C1 distance from the mean value, to the recent DFT-D functionals, specifically B97X-D appears to predict reliable energy contour for AU/AU step. Such distance-based penalty improves energy contours for the other purine-pyrimidine sequences also. (c) 2013 Wiley Periodicals, Inc. Biopolymers 101: 107-120, 2014.

Improved quasiparticle wave functions and mean field for G(0)W(0) calculations: Initialization with the COHSEX operator

The GW approximation to the electron self-energy has become a standard method for ab initio calculation of excited-state properties of condensed-matter systems. In many calculations, the G W self-energy operator, E, is taken to be diagonal in the density functional theory (DFT) Kohn-Sham basis within the G0 W0 scheme. However, there are known situations in which this diagonal Go Wo approximation starting from DFT is inadequate. We present two schemes to resolve such problems. The first, which we called sc-COHSEX-PG W, involves construction of an improved mean field using the static limit of GW, known as COHSEX (Coulomb hole and screened exchange), which is significantly simpler to treat than GW W. In this scheme, frequency-dependent self energy E(N), is constructed and taken to be diagonal in the COHSEX orbitals after the system is solved self-consistently within this formalism. The second method is called off diagonal-COHSEX G W (od-COHSEX-PG W). In this method, one does not self-consistently change the mean-field starting point but diagonalizes the COHSEX Hamiltonian within the Kohn-Sham basis to obtain quasiparticle wave functions and uses the resulting orbitals to construct the G W E in the diagonal form. We apply both methods to a molecular system, silane, and to two bulk systems, Si and Ge under pressure. For silane, both methods give good quasiparticle wave functions and energies. Both methods give good band gaps for bulk silicon and maintain good agreement with experiment. Further, the sc-COHSEX-PGW method solves the qualitatively incorrect DFT mean-field starting point (having a band overlap) in bulk Ge under pressure.

The X-C center dot center dot center dot pi (X = F, Cl, Br, CN) Carbon Bond

High-level ab initio calculations have been used to study the interactions between the CH3 group of CH3X (X = F, Cl, Br, CN) molecules and pi-electrons. These interactions are important because of the abundance of both the CH3 groups and pi-electrons in biological systems. Complexes between C2H4/C2H2 and CH3X molecules have been used as model systems. Various theoretical methods such as atoms in molecules theory, reduced density gradient analysis, and natural bond orbital analysis have been used to discern these interactions. These analyses show that the interaction of the p-electrons with the CH3X molecules leads to the formation of X-C...p carbon bonds. Similar complexes with other tetrel molecules, SiH3X and GeH3X, have also been considered.

Design of symmetric TIM barrel proteins from first principles

Background: Computational protein design is a rapidly maturing field within structural biology, with the goal of designing proteins with custom structures and functions. Such proteins could find widespread medical and industrial applications. Here, we have adapted algorithms from the Rosetta software suite to design much larger proteins, based on ideal geometric and topological criteria. Furthermore, we have developed techniques to incorporate symmetry into designed structures. For our first design attempt, we targeted the (alpha/beta)(8) TIM barrel scaffold. We gained novel insights into TIM barrel folding mechanisms from studying natural TIM barrel structures, and from analyzing previous TIM barrel design attempts. Methods: Computational protein design and analysis was performed using the Rosetta software suite and custom scripts. Genes encoding all designed proteins were synthesized and cloned on the pET20-b vector. Standard circular dichroism and gel chromatographic experiments were performed to determine protein biophysical characteristics. 1D NMR and 2D HSQC experiments were performed to determine protein structural characteristics. Results: Extensive protein design simulations coupled with ab initio modeling yielded several all-atom models of ideal, 4-fold symmetric TIM barrels. Four such models were experimentally characterized. The best designed structure (Symmetrin-1) contained a polar, histidine-rich pore, forming an extensive hydrogen bonding network. Symmetrin-1 was easily expressed and readily soluble. It showed circular dichroism spectra characteristic of well-folded alpha/beta proteins. Temperature melting experiments revealed cooperative and reversible unfolding, with a T-m of 44 degrees C and a Gibbs free energy of unfolding (Delta G degrees) of 8.0 kJ/mol. Urea denaturing experiments confirmed these observations, revealing a C-m of 1.6 M and a Delta G degrees of 8.3 kJ/mol. Symmetrin-1 adopted a monomeric conformation, with an apparent molecular weight of 32.12 kDa, and displayed well resolved 1D-NMR spectra. However, the HSQC spectrum revealed somewhat molten characteristics. Conclusions: Despite the detection of molten characteristics, the creation of a soluble, cooperatively folding protein represents an advancement over previous attempts at TIM barrel design. Strategies to further improve Symmetrin-1 are elaborated. Our techniques may be used to create other large, internally symmetric proteins.

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.

A comparative study of the energetics, structures, and mechanisms of the HCN H HNC and LiCN <-> LiNC isomerizations

The potential energy surfaces of the HCN<->HNC and LiCN<->LiNC isomerization processes were determined by ab initio theory using fully optimized triple-zeta double polarization types of basis sets. Both the MP2 corrections and the QCISD level of calculations were performed to correct for the electron correlation. Results show that electron correlation has a considerable influence on the energetics and structures. Analysis of the intramolecular bond rearrangement processes reveals that, in both cases, H (or Li+) migrates in an almost elliptic path in the plane of the molecule. In HCN<->HNC, the migrating hydrogen interacts with the in-plane pi,pi* orbitals of CN, leading to a decrease in the C-N bond order. In LiCN<->LiNC, Li+ does not interact with the corresponding pi,pi* orbitals of CN.

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.

Design, Synthesis, and DNA Binding Properties of Photoisomerizable Azobenzene−Distamycin Conjugates: An Experimental and Computational Study

Here, we present the synthesis, photochemical, and DNA binding properties of three photoisomerizable azobenzene−distamycin conjugates in which two distamycin units were linked via electron-rich alkoxy or electron-withdrawing carboxamido moieties with the azobenzene core. Like parent distamycin A, these molecules also demonstrated AT-specific DNA binding. Duplex DNA binding abilities of these conjugates were found to depend upon the nature and length of the spacer, the location of protonatable residues, and the isomeric state of the conjugate. The changes in the duplex DNA binding efficiency of the individual conjugates in the dark and with their respective photoirradiated forms were examined by circular dichroism, thermal denaturation of DNA, and Hoechst displacement assay with poly[d(A-T).d(T-A)] DNA in 150 mM NaCl buffer. Computational structural analyses of the uncomplexed ligands using ab initio HF and MP2 theory and molecular docking studies involving the conjugates with duplex d[(GC(AT)10CG)]2 DNA were performed to rationalize the nature of binding of these conjugates.

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.

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.