Ensemble of transition state structures for the cis-trans isomerization of N-methylacetamide.

The cis-trans isomerization of N-methylacetamide (NMA), a model peptidic fragment, is studied theoretically in vacuo and in explicit water solvent at 300 K using the metadynamics technique. The computed cis-trans free energy difference is very similar for NMA(g) and NMA(aq), in agreement with experimental measurements of population ratios and theoretical studies at 0 K. By exploiting the flexibility in the definition of a pair of recently introduced collective variables (Branduardi, D.; Gervasio, F. L.; Parrinello, M. J. Chem. Phys. 2007, 126, 054103), an ensemble of transition state structures is generated at finite temperature for both NMA(g) and NMA(aq), as verified by computing committor distribution functions. Ensemble members of NMA(g) are shown to have correlated values of the backbone dihedral angle and a second dihedral angle involving the amide hydrogen atom. The dynamical character of these structures is preserved in the presence of solvent, whose influence on the committor functions can be modeled using effective friction/noise terms.

Solvent effects on charge spatial extent in DNA and implications for transfer.

To clarify the role played by water in facilitating long-range DNA charge transport, carefully designed, state-of-the-art, self-interaction corrected density-functional quantum mechanical and molecular mechanical (SIC-QM/MM) simulations are performed for the first time on two ionized adenine:thymine bridge models in explicit water solvent at finite temperature. For random solvent configurations, the charge is partially delocalized. However, a charge localization on different, well-separated adenines can be induced and is correlated with a restructuring of their first solvation shells. Thus, the importance of water in the mechanism of long-range charge transport is explicitly demonstrated, and the microscopic conditions for a charge localization are revealed.

Charge localization in stacked radical cation DNA base pairs and the benzene dimer studied by self-interaction corrected density-functional theory.

The incomplete cancellation of the electron self-interaction can be a serious shortcoming of density-functional theory especially when treating odd-electron systems. In this work, several popular and potentially viable correction schemes are applied in order to characterize the electronic structure of stacked molecular pairs, consisting of a neutral molecule and adjacent radical cation, as a function of separation distance. The unphysical sharing of the positive charge between adjacent molecules separated by 6-7 A is corrected for by applying a new empirical scheme proposed by VandeVondele and Sprik [Phys. Chem. Chem. Phys. 2005, 7, 1363] with a unique choice of parameters. This method is subsequently applied to characterize the electronic structure of two neighboring guanines excised from a canonical Arnott B-DNA structure and will be used in future investigations of certain model DNA fibers.

Ab initio and empirical model MD simulation studies of solvent effects on the properties of N-methylacetamide along a cis-trans isomerization pathway.

The properties of N-methylacetamide along a cis-trans isomerization pathway described by twisting about the C(O)-N bond are examined at finite temperature both in vacuo and in explicit water solvent. Two distinctly different theoretical descriptions, an ab initio (DFT-BLYP) and an empirical (CHARMM22) model, are studied in order to permit an assessment of the dominant forces active in the system. An analysis of the solvent structure at equilibrium and changes in solvation structure accompanying isomerization is, therefore, given for each model. Many-body polarization effects absent under CHARMM22 but present in the ab initio model are found to have a profound influence on the system. The electronic structure of the NMA molecule predicted by the ab initio method along the reaction coordinate is examined in order to shed further light on changes in peptide "partial-double" bond character [C(O)-N] as isomerization takes place. A new statistical-mechanical interpretation of the entropy change during a chemical reaction is presented to help interpret the thermochemistry of the simple reaction.

Structural correlations and motifs in liquid water at selected temperatures: ab initio and empirical model predictions.

To gain further insight into liquid water's structure and explore the role of different physical forces underlying the interaction between water molecules, the radial and angular structure of water is probed as a function of temperature for a carefully selected set of theoretical models. Simulations are performed with empirical rigid, empirical polarizable, empirical flexible with classical and quantum nuclei, and ab initio models with classical nuclei at 300 and 353 K and quantum nuclei at 300 K. The predicted radial distribution functions, spatial maps, and angular distributions of the neighboring water molecules are consistent with a model of liquid water in which water molecules are tetrahedrally coordinated. In addition, three-dimensional joint distribution functions are introduced and analyzed. By comparison of the functions obtained for hexagonal ice to those of liquid water, several thermally disordered, ice-like cluster structures are identified in the fluid.

Isomerization of a peptidic fragment studied theoretically in vacuum and in explicit water solvent at finite temperature.

The cis-trans isomerization of N-methylacetamide, a molecular model of the polypeptide chain, is examined via umbrella sampling Car-Parrinello MD and classical MD, in both gas and solution phases at 300 K. A new analysis of the C(O)-N bond interconversion and a full examination of the solvent shell structure are presented.

A solid-state spectral effect in eclipsed tetracyanonickelates: X-ray crystal structure, polarized specular reflectance spectroscopy, and ZINDO modeling of Sr[Ni(CN)4].5H2O, Rb2[Ni(CN)4].H2O, and Na2[Ni(CN)4].3H2O.

Crystal structures of three Ni(CN)(4)(2)(-) salts all with eclipsed ligands and varying axial stacking arrangements are presented. The absorption spectra of all three salts show a slight red shift in the x,y-polarizations and a large red shift in their z-polarizations upon crystallization from solution. Semiempirical ZINDO calculations provide a good model of the solid state, even with only a three-molecule segment, allowing reproduction of the red-shifting and intensity increase upon crystallization found experimentally. The modified nickel beta(s,p) bonding parameter of -5 found appropriate for Ni coordination in our previous studies of single Ni(CN)(4)(2-) planes and a helically stacked Cs(2)[Ni(CN)(4)].H(2)O crystal was changed to -3 for the more parallel-stacked Ni(CN)(4)(2-) planes in this case, while beta(d) was retained at -41. Crystal data are as follows: Na(2)[Ni(CN)(4)].3H(2)O, triclinic space group P1, a = 7.2980(10) A, b = 8.8620(10) A, c = 15.132(2) A, alpha = 89.311(5) degrees, beta = 87.326(5) degrees, gamma = 83.772(6) degrees, V = 971.8(2) A(3), T = 100 K, Z = 4, R = 0.024, R(w) = 0.064; Sr[Ni(CN)(4)].5H(2)O, monoclinic space group C2/m, a = 10.356(2) A, b = 15.272(3) A, c = 7.1331(10) A, beta = 98.548(12) degrees, V = 1115.6(3) A(3), T = 100 K, Z = 4, R = 0.024, R(w) = 0.059; Rb(2)[Ni(CN)(4)].1.05H(2)O, triclinic space group P1, a = 8.6020(10) A, b = 9.6930(10) A, c = 12.006(2) A, alpha = 92.621(6) degrees, beta = 94.263(6) degrees, gamma = 111.795(10) degrees, V = 924.0(2) A(3), T = 100 K, Z = 4, R = 0.034, R(w) = 0.067.

ZINDO calculations of the ground state and electronic transitions in the tetracyanonickelate Ion, Ni(CN)(4)(2-).

ZINDO semiempirical calculations on the Ni(CN)(4)(2-) ion were performed, and ground-state energies for all 41 valence-orbital-based MOs and orbital transition components of the two lowest energy fully allowed electronic transitions are reported. Gaussian 94 was used to calculate ground-state energies as a comparison. The ground-state energies using ZINDO compare much more favorably with those found through ab initio techniques than with those from a reported INDO calculation. The found electronic transitions agree substantially with earlier assignments with the exception that several orbital transitions are required to adequately model the lowest energy allowed x,y-polarized experimental transition. Calculation parameters were optimized to give excellent agreement with experiment and may serve well for more complex arrangements of this ion.