We present results for the structural and vibrational properties of the water molecule, water dimer, and liquid water at the experimental equilibrium density, as obtained with several van der Waals density functionals. The functional form originally proposed by Dion et al. [ Phys. Rev. Lett. 2004 , 92 , 246401 ], with an appropriately chosen local exchange functional, yields a description of the liquid superior to that of the semilocal functional PBE. In particular, a specific choice of the local exchange functional (optB88) fitted to quantum chemistry calculations yields the best agreement with experimental results for pair correlation functions although it is slightly inferior to other van der Waals functionals in describing infrared spectra. When using optB88, liquid water displays a hydrogen-bonded network less tightly bound than when using the PBE approximation. The performance of optB88 is definitely inferior to that of the PBE0 hybrid functional for the isolated molecule but only moderately so for the liquid. However, the computational cost of optB88 is much less than that of hybrid functionals; therefore the use of optB88 appears to be a sensible alternative to calculations implying the evaluation of the Fock operator, in cases when simulations of large systems are required.

Noncovalent interactions are quite important in biological structure-function relationships. To study the pairwise interaction of aromatic amino acids (phenylalanine, tyrosine, tryptophan) with anionic amino acids (aspartic and glutamic acids), small molecule mimics (benzene, phenol or indole interacting with formate) were used at the MP2 level of theory. The overall energy associated with an anion-quadrupole interaction is substantial (-9.5 kcal/mol for a benzene-formate planar dimer at van der Waals contact distance), indicating the electropositive ring edge of an aromatic group can interact with an anion. Deconvolution of the long-range coplanar interaction energy into fractional contributions from charge-quadrupole interactions, higher-order electrostatic interactions, and polarization terms was achieved. The charge-quadrupole term contributes between 30 to 45% of the total MP2 benzene-formate interaction; most of the rest of the interaction arises from polarization contributions. Additional studies of the Protein Data Bank (PDB Select) show that nearly planar aromatic-anionic amino acid pairs occur more often than expected from a random angular distribution, while axial aromatic-anionic pairs occur less often than expected; this demonstrates the biological relevance of the anion-quadrupole interaction. While water may mitigate the strength of these interactions, they may be numerous in a typical protein structure, so their cumulative effect could be substantial.

Tailoring optical response using periodic nanostructures is one of the key issues in the current research on functional composite materials. [1][2][3][4][5] The anomalous light transmission through metallic films that have a regular array of submicrometer holes [3][4][5][6] has stimulated much interest. This interest stems from both the underlying physics and also the perceived potential for applications in nanophotonics, [7] quantum-information processing, [8] nanolithography, [9] and surface-enhanced Raman scattering.[10]Extraordinary transmission of light through an optically opaque metal film perforated with a 2D array of subwavelength holes was first reported by Ebbesen et al. [5] This unusual phenomenon can be understood as a result of diffractive coupling to evanescent surface plasmon polaritons (SPPs) that leads to a strong concentration of light at the metal surface, which then weakly tunnels through the holes in the film, reradiating by the inverse process on the exit side. [4,[11][12][13] In order to explore the SPP properties of microstructured metal films, extensive efforts have been made to study their spectral response and dependence on geometrical parameters, such as the type of lattice symmetry, metal film thickness, and adjacent dielectric media. [14] Recent studies show that the hole shape has a significant effect on the optical transmission. [15][16][17][18][19] Nearly all the metallic films studied have been on a flat substrate and the hole arrays were made using focused ion-beam milling, [5,15,17,19] and electron-beam lithography [8] or interferometric lithography combined with reactive ion etching. [16,18] Here we use nanosphere lithography [20] as the sample production technique. This approach has several advantages over the conventional lithographic and machining techniques, including the relative ease of casting large, high-quality, ordered nanomaterials and the low cost of implementation. Ordered arrays of gold half shells and nanocaps have been constructed by controlled gold vapor deposition with thicknesses less than 20 nm by using a 2D colloidal crystal (CC) as a substrate. [21,22] Baumberg's group has fabricated metallic nanocavity arrays by electrodeposition within the pores of CC templates and observed the excitation of the SPPs in metallic cavities that led to rich features in reflectivity spectra.[23] Very recently, Landström et al. have shown that the transmission spectra through a metal film formed on a 2D CC substrate are quite similar to those observed through subwavelength hole arrays in metal films. [24] In this communication, we report a study on the infrared transmission properties of gold films patterned on 2D CCs. The fabricated metallodielectric structures have a strong surface corrugation as well as a 2D periodic pore array. We show that the SPPs on these curved surfaces display unusual dispersion properties, compared to those of metal films on flat substrates studied before. The dielectric property of the template spheres is also found to have a substantial effect o...

We present a simplified implementation of the non-local van der Waals correlation functional introduced by Dion et al. [Phys. Rev. Lett. 92, 246401 (2004)] and reformulated by Román-Pérez et al. [Phys. Rev. Lett. 103, 096102 (2009)]. The proposed numerical approach removes the logarithmic singularity of the kernel function. Complete expressions of the self-consistent correlation potential and of the stress tensor are given. Combined with various choices of exchange functionals, five versions of van der Waals density functionals are implemented. Applications to the computation of the interaction energy of the benzene-water complex and to the computation of the equilibrium cell parameters of the benzene crystal are presented. As an example of crystal structure calculation involving a mixture of hydrogen bonding and dispersion interactions, we compute the equilibrium structure of two polymorphs of aspirin (2-acetoxybenzoic acid, C(9)H(8)O(4)) in the P2(1)/c monoclinic structure.

In order to optimize the growth conditions for tungstate crystals, the structural evolution of ditungstate Na 2 W 2 O 7 from the crystalline to molten states during heating has been investigated by in-situ high temperature Raman spectroscopic technique. The experimental temperature-dependent Raman spectra showed that Na 2 W 2 O 7 crystal has not undergone any solid-state phase transformations during heating process from 298 to 1013 K. In contrast to crystalline Na 2 W 2 O 7 , in which [WO 4 ] tetrahedra and [WO 6 ] octahedra coexist, the tungsten-oxygen groups in molten Na 2 W 2 O 7 have the form of (W 2 O 7 ) 2À anion composed of two [WO 4 ] by sharing their corner oxygen atoms. To validate the structural evolution of Na 2 W 2 O 7 above, Raman activity of vibrations of Na 2 W 2 O 7 crystal and its melt were calculated using density functional theory (DFT) and compared with the in-situ Raman spectra of Na 2 W 2 O 7 . A non-crystalline phase and an intermediate state of Na 2 W 2 O 7 were obtained by rapid quenching and relatively slow cooling of the homogeneous melt, respectively.

R67 dihydrofolate reductase (DHFR) is a novel protein that possesses 222 symmetry. A single active site pore traverses the length of the homotetramer. Although the 222 symmetry implies that four symmetry-related binding sites should exist for each substrate as well as each cofactor, isothermal titration calorimetry (ITC) studies indicate only two molecules bind. Three possible combinations include two dihydrofolate molecules, two NADPH molecules, or one substrate with one cofactor. The latter is the productive ternary complex. To evaluate the roles of A36, Y46, T51, G64, and V66 residues in binding and catalysis, a site-directed mutagenesis approach was employed. One mutation per gene produces four mutations per active site pore, which often result in large cumulative effects. Conservative mutations at these positions either eliminate the ability of the gene to confer trimethoprim resistance or have no effect on catalysis. This result, in conjunction with previous mutagenesis studies on K32, K33, S65, Q67, I68, and Y69 [Strader, M. B., et al. (2001) Biochemistry 40, 11344-11352; Hicks, S. N., et al. (2003) Biochemistry 42, 10569-10578; Park, H., et al. (1997) Protein Eng. 10, 1415-1424], allows mapping of the active site surface. Residues for which conservative mutations have large effects on binding and catalysis include K32, Q67, I68, and Y69. These residues form a stripe that establishes the ligand binding surface. Residues that accommodate conservative mutations that do not greatly affect catalysis include K33, Y46, T51, S65, and V66. Isothermal titration calorimetry studies were also conducted on many of the mutants described above to determine the enthalpy of folate binding to the R67 DHFR.NADPH complex. A linear correlation between this DeltaH value and log k(cat)/K(m) is observed. Since structural tightness appears to be correlated with the exothermicity of the binding interaction, this leads to the hypothesis that enthalpy-driven formation of the ternary complex in these R67 DHFR variants plays a strong role in catalysis. Use of the alternate cofactor, NADH, extends this correlation, indicating preorganization of the ternary complex determines the efficiency of the reaction. This hypothesis is consistent with data suggesting R67 DHFR uses an endo transition state (where the nicotinamide ring of cofactor overlaps the more bulky side of the substrate's pteridine ring).

Temperature‐dependent Raman spectra of K2MonO3n+1 (n = 1, 2, 3) crystals up to and above their melting points were recorded, and their vibration modes in solid and molten states were assigned. Basic structural units and the corresponding cluster forms in molten dipotassium monomolybdates, dimolybdates, and trimolybdates were studied by in situ high‐temperature Raman spectroscopic studies together with theoretical calculations, including density functional theory and quantum chemistry ab initio calculation. Anion units of [MoO4]2−, [Mo2O7]2−, and [Mo3O10]2− were shown to principally exist in molten K2MoO4, K2Mo2O7, and K2Mo3O10, respectively. The mechanisms of the microstructural evolution of K2MonO3n+1 (n = 1, 2, 3) crystals while being melted are schematically illustrated. Copyright © 2016 John Wiley & Sons, Ltd.

Various spectroscopic properties of Yb3+-doped Y2SiO5 crystal have been extensively investigated due to its promising application in quantum information processing. However, the local structure, electronic structure of Yb3+:Y2SiO5 crystal, and its optical and magnetic properties have not been comprehensively studied from a theoretical viewpoint. In this work, the geometric and electronic structures of Yb3+ that replaces two crystallographic Y3+ sites in the Y2SiO5 crystal are first obtained by the method of density functional theory (DFT). Then, the optical, electron paramagnetic resonance (EPR), and optically detected magnetic resonance (ODMR) spectra for 171Yb3+ (nuclear spin I = 1/2) at such two sites are simultaneously calculated in the framework of the complete diagonalization (of energy) matrix (CDM) based on the optimized local structure around 171Yb3+ ion by DFT. The various calculated spectroscopic properties by such combined theoretical approach are consistent with the experimental ones, which demonstrates that CDM is effective and particularly suitable for calculating hyperfine A -tensors under zero, low, and intermediate magnetic field. More importantly, based on the obtained accurate hyperfine structure of 171Yb3+ in Y2SiO5 crystal, the possible “clock transitions”, which can enhance the optical coherence time, can be assigned or predicted by the present approach. This study successfully explains the spectroscopic properties of 171Yb3+-doped Y2SiO5 and provides a feasible method to design and search for practical rare-earth-doped quantum information materials for the community.