A summary of the technical advances that are incorporated in the fourth major release of the Q-Chem quantum chemistry program is provided, covering approximately the last seven years. These include developments in density functional theory methods and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster and perturbation theories, methods for electronically excited and openshell species, tools for treating extended environments, algorithms for walking on potential surfaces, analysis tools, energy and electron transfer modelling, parallel computing capabilities, and graphical user interfaces. In addition, a selection of example case studies that illustrate these capabilities is given. These include extensive benchmarks of the comparative accuracy of modern density functionals for bonded and non-bonded interactions, tests of attenuated second order Møller-Plesset (MP2) methods for intermolecular interactions, a variety of parallel performance benchmarks, and tests of the accuracy of implicit solvation models. Some specific chemical examples include calculations on the strongly correlated Cr 2 dimer, exploring zeolitecatalysed ethane dehydrogenation, energy decomposition analysis of a charged ter-molecular complex arising from glycerol photoionisation, and natural transition orbitals for a Frenkel exciton state in a nine-unit model of a self-assembling nanotube.Keywords quantum chemistry, software, electronic structure theory, density functional theory, electron correlation, computational modelling, Q-Chem Disciplines Chemistry CommentsThis article is from Molecular Physics: An International Journal at the Interface Between Chemistry and Physics 113 (2015): 184, doi:10.1080/00268976.2014. RightsWorks produced by employees of the U.S. Government as part of their official duties are not copyrighted within the U.S. The content of this document is not copyrighted. Authors 185A summary of the technical advances that are incorporated in the fourth major release of the Q-CHEM quantum chemistry program is provided, covering approximately the last seven years. These include developments in density functional theory methods and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster and perturbation theories, methods for electronically excited and open-shell species, tools for treating extended environments, algorithms for walking on potential surfaces, analysis tools, energy and electron transfer modelling, parallel computing capabilities, and graphical user interfaces. In addition, a selection of example case studies that illustrate these capabilities is given. These include extensive benchmarks of the comparative accuracy of modern density functionals for bonded and non-bonded interactions, tests of attenuated second order Møller-Plesset (MP2) methods for intermolecular interactions, a variety of parallel performance benchmarks, and tests of the accuracy of implicit solvation models. Some specific chemical examples include calculations on the strongly corre...

Molecular dynamics simulations reveal substructures within the liquid-ordered phase of lipid bilayers. These substructures, identified in a 10 μsec all-atom trajectory of liquid-ordered/liquid-disordered coexistence (Lo/Ld), are composed of saturated hydrocarbon chains packed with local hexagonal order, and separated by interstitial regions enriched in cholesterol and unsaturated chains. Lipid hydrocarbon chain order parameters calculated from the Lo phase are in excellent agreement with 2H NMR measurements; the local hexagonal packing is also consistent with 1H-MAS NMR spectra of the Lo phase, NMR diffusion experiments, and small angle X-ray- and neutron scattering. The balance of cholesterol-rich to local hexagonal order is proposed to control the partitioning of membrane components into the Lo regions. The latter have been frequently associated with formation of so-called rafts, platforms in the plasma membranes of cells that facilitate interaction between components of signaling pathways.

One way to reduce the computational cost of electronic structure calculations is to use auxiliary basis expansions to approximate four-center integrals in terms of two-and three-center integrals, usually by using the variationally optimum Coulomb metric to determine the expansion coefficients. However, the long-range decay behavior of the auxiliary basis expansion coefficients has not been characterized. We find that this decay can be surprisingly slow. Numerical experiments on linear alkanes and a toy model both show that the decay can be as slow as 1͞r in the distance between the auxiliary function and the fitted charge distribution. The Coulomb metric fitting equations also involve divergent matrix elements for extended systems treated with periodic boundary conditions. An attenuated Coulomb metric that is short-range can eliminate these oddities without substantially degrading calculated relative energies. The sparsity of the fit coefficients is assessed on simple hydrocarbon molecules and shows quite early onset of linear growth in the number of significant coefficients with system size using the attenuated Coulomb metric. Hence it is possible to design linear scaling auxiliary basis methods without additional approximations to treat large systems.linear scaling ͉ resolution of the identity ͉ density fitting E lectronic structure calculations are normally performed by using basis set expansions to allow approximations to the Schrödinger equation to be expressed as algebraic rather than differential equations. Molecular electronic structure calculations (1) of either the density functional theory or wave-function type typically use standardized atom-centered basis sets, {͉ ͘}, whose functions are fixed linear combinations of Gaussian functions. With Gaussian basis functions, two-electron matrix elements,can be efficiently evaluated (2), normally with g(r 1 , r 2 ) ϭ ͉r 1 Ϫ r 2 ͉ Ϫ1 for Coulomb interactions. There are formally O(N 4 ) of these integrals for an atomic orbital basis set of size N. However, for a given choice of basis set, the number of nonnegligible integrals grows as only O(N 2 ) with increases in the size of the molecule. This growth arises from the rapid (Gaussian) decay of the amplitude of the product charge distribution ͉ ͘ ϵ (r 1 ) (r 1 ) with separation of the basis function centers. In density functional theory calculations, even this reduced bottleneck can be overcome for construction of the Coulomb matrix, J ϭ ͚ ͗ ͉ ͘P , from the density matrix by use of linearscaling fast multipole (3-5) and tree code methods (6).However, for a molecule of fixed size, increasing the number of basis functions per atom, n, does inexorably lead to O(n 4 ) growth in the number of significant integrals. This growth follows directly from the fact that the number of nonnegligible product charge distributions, ͉ ͘, grows as O(n 2 ). As a result, the use of large (high-quality) basis expansions is computationally costly. This article revisits perhaps the most practical way around this ''basis set quality'' bo...

α-Synuclein (α-syn) membrane interactions are implicated in the pathogenesis of Parkinson's disease. Fluorescence and neutron reflectometry (NR) measurements reveal that α-syn penetrates ∼9-14 Å into the outer leaflet of the bilayer, with a substantial portion of the membrane-bound polypeptide extending into the aqueous solvent. For the first time, to our knowledge, we used NR to obtain direct quantitative evidence of α-syn-induced membrane thinning. To examine the effect of specific residues on membrane penetration depths, we used a series of W4-containing N-terminal peptides. We identified that the first 15 residues (P15) nearly recapitulate the features of the full-length protein (i.e., partition constants, molecular mobility, and insertion of the W4 side chain into the bilayer), and found that as few as the first four N-terminal residues are sufficient for vesicle binding. Although at least one imperfect amphipathic repeat sequence (KAKEGV) is required for α-helical formation, secondary structural formation has little effect on membrane affinity. To develop an N-terminal α-syn model for bilayer interactions, we performed molecular-dynamics simulations of the P15 peptide submerged in a bilayer. The simulation results are highly consistent with experimental data indicating a broad low-energy region (8.5-14.5 Å) for W4 insertion.

Two modifications of the resolution of the identity (RI)/density fitting (DF) approximations are presented. First, we apply linear scaling and J-engine techniques to speed up traditional DF. Second, we develop an algorithm that produces local, accurate fits with effort that scales linearly with system size. The fits produced are continuous, differentiable, well-defined, and do not require preset fitting domains. This metric-independent technique for producing a priori local fits is shown to be accurate and robust even for large systems. Timings are presented for linear scaling RI/DF calculations on large one-, two-, and three-dimensional carbon systems.

We model the triplet-triplet energy transfer experiments from the Closs group [G. L. Closs et al, JACS, 110, p. 2652 (1988)] using a combination of Marcus theory and either Boys or Edmiston-Ruedenberg localized diabatization. We show that relative and absolute rates of electronic excitation transfer may be computed successfully, as we find βcalc = 2.8 per C-C bond, compared with the experimental value βexp = 2.6, for the case where both donor and acceptor occupy equatorial positions on a rigid cyclohexane bridge. This work highlights the power of using localized diabatization methods as a tool for modeling non-equilibrium processes.

Articles you may be interested inRelativistic coupled-cluster calculations on XeF6: Delicate interplay between electron-correlation and basis-set effects Divide-and-conquer-based linear-scaling approach for traditional and renormalized coupled cluster methods with single, double, and noniterative triple excitations Transferability in the natural linear-scaled coupled-cluster effective Hamiltonian approach: Applications to dynamic polarizabilities and dispersion coefficients A natural linear scaling coupled-cluster methodWe demonstrate near linear scaling of a new algorithm for computing smooth local coupled-cluster singles-doubles ͑LCCSD͒ correlation energies of quantum mechanical systems. The theory behind our approach has been described previously, ͓J. Subotnik and M. Head-Gordon, J. Chem. Phys. 123, 064108 ͑2005͔͒, and requires appropriately multiplying standard iterative amplitude equations by a bump function, creating local amplitude equations ͑which are smooth according to the implicit function theorem͒. Here, we provide an example that this theory works in practice: we show that our algorithm leads to smooth potential energy surfaces and yields large computational savings. As an example, we apply our LCCSD approach to measure the post-MP2 correction to the energetic gap between two different alanine tetrapeptide conformations.

The unique properties of the individual lipids that compose biological membranes together determine the energetics of the surface. The energetics of the surface in turn govern the formation of membrane structures and membrane reshaping processes, and will thus underlie cellular-scale models of viral fusion, vesicle-dependent transport, and lateral organization relevant to signaling. The spontaneous curvature, to the best of our knowledge, is always assumed to be additive. The letter describes observations from simulations of unexpected non-additive compositional curvature energetics of two lipids essential to the plasma membrane: sphingomyelin and cholesterol. A model is developed that connects molecular interactions to curvature stress, and which explains the role of local composition. Cholesterol is shown to lower the number of effective Kuhn segments of saturated acyl chains, reducing lateral pressure below the neutral surface of bending and favoring positive curvature. The effect is not observed for unsaturated (flexible) acyl chains. Likewise, hydrogen bonding between sphingomyelin lipids leads to positive curvature, but only at sufficient concentration, below which the lipid prefers negative curvature.