Generalized generalized gradient approximation: An improved density-functional theory for accurate orbital eigenvalues

The generalized gradient approximation (GGA) for the exchange functional in conjunction with accurate expressions for the correlation functional have led to numerous applications in which density-functional theory (DFT) provides structures, bond energies, and reaction activation energies in excellent agreement with the most accurate ab initio calculations and with the experiment. However, the orbital energies that arise from the Kohn-Sham auxiliary equations of DFT may differ by a factor of 2 from the ionization potentials, indicating that excitation energies and properties involving sums over excited states (nonlinear-optical properties, van der Waals attraction) may be in serious error.mWe propose herein a generalization of the GGA in which the changes in the functionals due to virtual changes in the orbitals are allowed to differ from the functional used to map the exact density onto the exact energy. Using the simplest version of this generalized GGA we show that orbital energies are within ∼5% of the correct values and the long-range behavior has the correct form

Lancifodilactone G : insights about an unusually stable enol

From quantum mechanics calculations we confirm that the naturally occurring enol lancifodilactone G is stable over the keto form (by 2.6 kcal/mol in water), the only known stable aliphatic enol (devoid of conjugated or bulky aromatics and lacking a 1,3-diketone structural motif known to stabilize enols). We determine architectural elements responsible for the enol stabilization and find a mechanism for keto-enol conversion in solution. In addition, we correct previously reported computational results that were performed on the misinterpreted structure demonstrating that the enol form of this natural product is more stable than previously thought

Molecular mechanics and molecular dynamics analysis of Drexler-Merkle gears and neon pump

Over the past two years at the Materials and Process Simulation Center, we have been developing simulation approaches for studying the molecular nanomachine designs pioneered by Drexler and Merkle. These nanomachine designs, such as planetary gears and neon pump, are described with atomistic details and involve up to 10 000 atoms. With the Dreiding and universal force fields, we have optimized the structures of the two planetary gear designs and the neon pump. At the Fourth Foresight conference, we reported rotational impulse dynamics studies of the first and second generation designs of planetary gears undergoing very high-frequency rotational motions. We will explore stability of these designs in the lower frequency regimes which require long time simulations. We will report the molecular mechanics and molecular dynamics simulations performed on these model systems. We explore the following modes in these studies: (1) impulse mode; (2) constant angular velocity - perpetual rotation; (3) constant torque - acceleration from rest

The electronic structure of pyrazine. Configuration interaction calculations using an extended basis

Extensive ab initio double zeta basis set configuration interaction calculations have been carried out on the nπ^∗ and ππ^∗ states of pyrazine as well as on the low‐lying n and π cations. The calculations corroborate the validity of the valence bond (VB) model for the interaction of lone pair excitations proposed earlier by Wadt and Goddard. Good agreement (errors of ∼0.2 eV) with experiment is obtained (except for the higher‐lying 1ππ∗ states that possess significant ionic character). The calculations indicate that the order of increasing ionization potentials is ^2A_g(n), 2B_(1g)(π), 2B_(1u)(n), and ^2B_(2g)(π). The forbidden 1 ^1B_(2g)(nπ^∗) state is predicted to be 1.30 eV above the allowed 1^ 1B_(3u)(nπ^∗) state. Finally, the calculations indicate that the adiabatic excitation energies to the 1^ 3B_1(nπ^∗) and 1^ 3A_1(ππ^∗) states in pyridine should be nearly degenerate at ∼3.6 eV

Predictions of structural elements for the binding of Hin recombinase with the hix site of DNA

Molecular dynamics simulations were coupled with experimental data from biochemistry and genetics to generate a theoretical structure for the binding domain of Hin recombinase complexed with the hix site of DNA. The theoretical model explains the observed sequence specificity of Hin recombinase and leads to a number of testable predictions concerning altered sequence selectivity for various mutants of protein and DNA. Combining molecular dynamics simulations with constraints based on current knowledge of protein structure leads to a theoretical structure of the binding domain of Hin recombinase with the hix site of DNA. The model offers a mechanistic explanation of the presently known characteristics of Hin and predicts the effects of specific mutations of both protein and DNA. The predictions can be tested by currently feasible experiments that should lead to refinements in and improvements on the current theoretical model. Because current experimental and theoretical methods are all limited to providing only partial information about protein-DNA interactions, we believe that this approach of basing molecular simulations on experimental knowledge and using the results of these simulations to design new, more precise experimental tests will be of general utility. These results provide additional evidence for the generality of the helix-turn-helix motif in DNA recognition and stabilization of proteins on DNA

The Predicted Binding Site and Dynamics of Peptide Inhibitors to the Methuselah GPCR from Drosophila melanogaster

Peptide inhibitors of Methuselah (Mth), a G protein-coupled receptor (GPCR), were reported that can extend the life span of Drosophila melanogaster. Mth is a class B GPCR, which is characterized by a large, N-terminal ectodomain that is often involved with ligand recognition. The crystal structure of the Mth ectodomain, which binds to the peptide inhibitors with high affinity, was previously determined. Here we report the predicted structures for RWR motif peptides in complex with the Mth ectodomain. We studied representatives of both Pro-class and Arg-class RWR motif peptides and identified ectodomain residues Asp139, Phe130, Asp127, and Asp78 as critical in ligand binding. To validate these structures, we predicted the effects of various ligand mutations on the structure and binding to Mth. The binding of five mutant peptides to Mth was characterized experimentally by surface plasmon resonance, revealing measured affinities that are consistent with predictions. The electron density map calculated from our MD structure compares well with the experimental map of a previously determined peptide/Mth crystal structure and could be useful in refining the current low-resolution data. The elucidation of the ligand binding site may be useful in analyzing likely binding sites in other class B GPCRs

Ab initio effective potentials for use in molecular quantum mechanics

We have investigated the method of effective potentials for replacing the core electrons in molecular calculations. The effective potential has been formulated in a way which simplifies computations while producing wave functions of ab initio quality. The effective potential is expressed in an analytic form which (i) represents the actual ab initio nonlocal potential (as defined by the matrix elements for a given basis set) and (ii) permits efficient computations of the effective-potential integrals (by incorporating the properties of Gaussian basis functions). To minimize the number of basis functions required in the molecular calculations, we define a new ab initio effective potential derived from modified Hartree-Fock valence orbitals whose core character has been removed. The effective-potential method as formulated becomes a very strong and reliable tool in attempting calculations on very large molecules. Applications to Li, Na, and K are presented

Shock-induced consolidation and spallation of Cu nanopowders

A useful synthesis technique, shock synthesis of bulk nanomaterials from nanopowders, is explored here with molecular dynamics simulations. We choose nanoporous Cu (∼11 nm in grain size and 6% porosity) as a representative system, and perform consolidation and spallation simulations. The spallation simulations characterize the consolidated nanopowders in terms of spall strength and damage mechanisms. The impactor is full density Cu, and the impact velocity (u_i) ranges from 0.2 to 2 km s^(−1). We present detailed analysis of consolidation and spallation processes, including atomic-level structure and wave propagation features. The critical values of u_i are identified for the onset plasticity at the contact points (0.2 km s^(−1)) and complete void collapse (0.5 km s^(−1)). Void collapse involves dislocations, lattice rotation, shearing/friction, heating, and microkinetic energy. Plasticity initiated at the contact points and its propagation play a key role in void collapse at low u_i, while the pronounced, grain-wise deformation may contribute as well at high u_i. The grain structure gives rise to nonplanar shock response at nanometer scales. Bulk nanomaterials from ultrafine nanopowders (∼10 nm) can be synthesized with shock waves. For spallation, grain boundary (GB) or GB triple junction damage prevails, while we also observe intragranular voids as a result of GB plasticity

Configuration interaction studies of the excited states of water

We report the results of extensive configuration interaction studies on 16 excited states of water. These states can be accurately described as corresponding to excitation from one of the highest two molecular orbitals (1b_1 or 3a_1) of the ground state into either the 3s or one of the three 3p Rydberg orbitals. The results provide the most accurate and consistent treatment of these states to date (within 0.1 eV for all known transitions) and form a reliable basis for the assignment of the photon and electron impact spectra of H_2O

Shock Induced Decomposition and Sensitivity of Energetic Materials by ReaxFF Molecular Dynamics

We develop strain-driven compression-expansion technique using molecular dynamics (MD) with reactive force fields (ReaxFF) to study the impact sensitivity of energetic materials. It has been applied to simulation of 1,3,5-trinitrohexahydro-s-triazine (RDX) crystal subjected to high-rate compression typical at the detonation front. The obtained results show that at lower compression ratio x = 1-V/V040%) all molecules decompose very quickly. We have observed both primary and secondary reactions during the decomposition process as well as production of various intermediates (NO2, NO, HONO, OH) and final products (H2O, N2, CO, CO2). The results of strain-driven compression-expansion modeling are in a good agreement with previous ReaxFF-MD shock simulations in RDX. Proposed approach might be useful for a quick test of sensitivity of energetic materials under conditions of high strain rate loading