Influenza fusion peptide is critical for mediating the fusion of viral and host cell membranes during viral entry. The interaction of monomeric influenza fusion peptide with membranes is studied with replica exchange molecular dynamics simulations using a new implicit membrane model to effectively reach microsecond to millisecond time scales. The conformational sampling of the fusion peptide was studied as a function of different N- and C-termini, including an experimental construct with an additional C-terminal tag, as well as a function of protonation of acidic residues. It is found that the influenza fusion peptide mostly adopts helical structures with a pronounced kink at residues 11−13 with both N-terminal and C-terminal helices oriented mostly parallel to the membrane surface. A charged C-terminus and the presence of a charge C-terminal tag significantly alters the conformational sampling of the fusion peptide and results in more diverse conformational ensembles that include obliquely inserted N-terminal peptide structures. Protonation of acidic residues also affects the conformational sampling, however, based on pKa shift estimates the overall effect of pH = 5 on the conformational sampling of the influenza fusion peptide appears to be only minor.

1 aPanahi, Afra1 aFeig, Michael uhttps://icer.msu.edu/research/publications/conformational-sampling-influenza-fusion-peptide-membrane-bilayers-function01129nas a2200157 4500008004100000245011900041210006900160260001200229300001000241490000800251520054300259100001800802700002200820700001700842856011200859 2010 eng d00aConformational Sampling of S- and R-Warfarin in Polar Solvents: Implications for Stereoselective Complex Formation0 aConformational Sampling of S and RWarfarin in Polar Solvents Imp c06/2010 a41-510 v9493 aMolecular dynamics simulations of the open side chain conformation of ionic and neutral S- and R-warfarin in aqueous solvent and acetonitrile are described. In all cases, warfarin is found to sample a broad conformational ensemble with major and minor states due to torsional degrees of freedom associated with its side chain. Thermodynamics and kinetics of transitions between these states are analyzed from the simulations and interpreted in the context of stereoselective interactions in biological and non-biological complexes.

1 aFeig, Michael1 aGebreyohannes, K.1 aMcGuffin, V. uhttps://icer.msu.edu/research/publications/conformational-sampling-s-r-warfarin-polar-solvents-implications01184nas a2200157 4500008004100000245009900041210006900140260001200209300001200221490000800233520062000241100000500861700002200866700001900888856011900907 2009 eng d00aCenter-of-Mass Problem in Truncated Configuration Interaction and Coupled-Cluster Calculations0 aCenterofMass Problem in Truncated Configuration Interaction and c08/2009 a334-3390 v6793 aThe problem of center-of-mass (CM) contaminations in ab initio nuclear structure calculations using configuration interaction (CI) and coupled-cluster (CC) approaches is analyzed. A rigorous and quantitative scheme for diagnosing the CM contamination of intrinsic observables is proposed and applied to ground-state calculations for 4He and 16O. The CI and CC calculations for 16O based on model spaces defined via a truncation of the single-particle basis lead to sizable CM contaminations, while the importance-truncated no-core shell model based on the NmaxΩ space is virtually free of CM contaminations.

1 a1 aGour, Jeffrey, R.1 aPiecuch, Piotr uhttps://icer.msu.edu/research/publications/center-mass-problem-truncated-configuration-interaction-coupled-cluster01289nas a2200205 4500008004100000245006500041210006500106260001200171300001100183490000800194520066500202100001800867700001900885700002000904700001600924700001100940700001800951700002000969856009400989 2009 eng d00aConstraints on the Density Dependence of the Symmetry Energy0 aConstraints on the Density Dependence of the Symmetry Energy c03/2009 a1227010 v1023 aCollisions involving {112Sn} and {124Sn} nuclei have been simulated with the improved quantum molecular dynamics transport model. The results of the calculations reproduce isospin diffusion data from two different observables and the ratios of neutron and proton spectra. By comparing these data to calculations performed over a range of symmetry energies at saturation density and different representations of the density dependence of the symmetry energy, constraints on the density dependence of the symmetry energy at subnormal density are obtained. The results from the present work are compared to constraints put forward in other recent analyses.

1 aTsang, M., B.1 aZhang, Yingxun1 aDanielewicz, P.1 aFamiano, M.1 aLi, Z.1 aLynch, W., G.1 aSteiner, A., W. uhttps://icer.msu.edu/research/publications/constraints-density-dependence-symmetry-energy02156nas a2200181 4500008004100000245022700041210006900268260001200337490000800349520139600357100001401753700001601767700001501783700001401798700001901812700001801831856012501849 2008 eng d00aA Comparative Assessment of the Perturbative and Renormalized Coupled Cluster Theories with a Non-iterative Treatment of Triple Excitations for Thermochemical Kinetics, Including a Study of Basis Set and Core Correlation E0 aComparative Assessment of the Perturbative and Renormalized Coup c01/20080 v1283 aThe CCSD, CCSD(T), and CR-CC(2,3) coupled cluster methods, combined with five triple-zeta basis sets, namely, MG3S, aug-cc-pVTZ, aug-cc-pV(T+d)Z, aug-cc-pCVTZ, and aug-cc-pCV(T+d)Z, are tested against the DBH24 database of diverse reaction barrier heights. The calculations confirm that the inclusion of connected triple excitations is essential to achieving high accuracy for thermochemical kinetics. They show that various noniterative ways of incorporating connected triple excitations in coupled cluster theory, including the CCSD(T) approach, the full CR-CC(2,3) method, and approximate variants of CR-CC(2,3) similar to the triples corrections of the CCSD(2) approaches, are all about equally accurate for describing the effects of connected triply excited clusters in studies of activation barriers. The effect of freezing core electrons on the results of the CCSD, CCSD(T), and CR-CC(2,3) calculations for barrier heights is also examined. It is demonstrated that to include core correlation most reliably, a basis set including functions that correlate the core and that can treat core-valence correlation is required. On the other hand, the frozen-core approximation using valence-optimized basis sets that lead to relatively small computational costs of CCSD(T) and CR-CC(2,3) calculations can achieve almost as high accuracy as the analogous fully correlated calculations.

1 aZheng, J.1 aGour, J., R1 aLutz, J.J.1 aWloch, M.1 aPiecuch, Piotr1 aTruhlar, D.G. uhttps://icer.msu.edu/research/publications/comparative-assessment-perturbative-renormalized-coupled-cluster-theories-non00743nas a2200205 4500008004100000245010000041210006900141300001400210490000800224653002200232653001800254653002100272653002300293100002100316700001900337700002000356700001800376700001900394856012400413 2008 eng d00aCosmological Shocks in Adaptive Mesh Refinement Simulations and the Acceleration of Cosmic Rays0 aCosmological Shocks in Adaptive Mesh Refinement Simulations and a1063-10770 v68910acosmology: theory10ahydrodynamics10aISM: Cosmic Rays10amethods: numerical1 aSkillman, S., W.1 aO'Shea, B., W.1 aHallman, E., J.1 aBurns, J., O.1 aNorman, M., L. uhttps://icer.msu.edu/research/publications/cosmological-shocks-adaptive-mesh-refinement-simulations-acceleration-cosmic03686nas a2200145 4500008004100000245018100041210006900222260001200291300001200303490000800315520305800323100001403381700001903395856012603414 2007 eng d00aComputational Investigation of the Conrotatory and Disrotatory Isomerization Channels of Bicyclo[1.1.0]butane to Buta-1,3-diene: A Completely Renormalized Coupled-Cluster Study0 aComputational Investigation of the Conrotatory and Disrotatory I c01/2007 a734-7420 v1113 aThe conrotatory and disrotatory mechanisms of the isomerization of bicyclo[1.1.0]butane to trans-buta-1,3-diene have been computationally investigated with the CASSCF, MCQDPT2, (U)B3LYP, CCSD(T), CR-CCSD(T), and CR-CC(2,3) approaches. The coupled-cluster (CC) methods, including the CC approach with singles, doubles, and noniterative triples (CCSD(T)), and its completely renormalized (CR) extensions called CR-CCSD(T) and CR-CC(2,3), and the density functional theory B3LYP approach do an excellent job of correctly predicting the activation barrier for the conrotatory pathway, which corresponds to a weakly biradical transition state (TS), producing values within experimental error bars. In particular, the recently developed CR-CC(2,3) method gives 40.8 or 41.1 kcal/mol, in perfect agreement with the experimental value of 40.6 ± 2.5 kcal/mol. The complete-active-space self-consistent-field (CASSCF) approach and the second-order multireference perturbation theory (MCQDPT2) are less accurate in describing the conrotatory barrier than CR-CC(2,3). The higher energy disrotatory pathway, which has not been characterized experimentally and which involves a strongly biradical TS, poses a great challenge for many methods. CCSD(T) fails, predicting the activation barrier for the disrotatory pathway significantly below the conrotatory barrier, contradicting the experimental result that the conrotatory pathway describes the mechanism. The strongly biradical character of the disrotatory TS, spin contamination, and the proximity of singlet and triplet potential energy surfaces cause difficulties for B3LYP, which does not link this TS with gauche-buta-1,3-diene. No such difficulties occur in the CASSCF calculations, which offer a proper description of the structure of the disrotatory TS that links it with the reactant and product molecules. The CR-CC(2,3) approach, which accurately balances dynamical and nondynamical correlations in systems containing closed-shell and biradical structures, predicts the activation enthalpy for the disrotatory mechanism of 66 kcal/mol. CR-CCSD(T) gives 69 kcal/mol. In agreement with experiment and earlier multireference configuration interaction calculations of Nguyen and Gordon, CR-CCSD(T) and CR-CC(2,3) favor the conrotatory mechanism. The CASSCF, MCQDPT2, and B3LYP methods correctly place the disrotatory barrier above the conrotatory one, but, on the basis of a comparison with the accurate CR-CC(2,3) results, they underestimate the activation energy for the disrotatory pathway. All CC approaches employed in this study produce very good estimates of the enthalpy of isomerization of bicyclo[1.1.0]butane into buta-1,3-diene, the experimental value of which is −25.9 ± 0.4 kcal/mol, giving about −28 kcal/mol, when trans-buta-1,3-diene is used as a product, and −25 kcal/mol, when the nearly isoenergetic gauche-buta-1,3-diene rotamer is used as a product. The CC reaction enthalpies are more accurate than those obtained with CASSCF, MCQDPT2, and B3LYP.

1 aKinal, A.1 aPiecuch, Piotr uhttps://icer.msu.edu/computational-investigation-conrotatory-and-disrotatory-isomerization-channels-bicyclo110butane-buta01210nas a2200193 4500008004100000245008000041210006900121260001200190300001200202490000700214520059600221100001400817700001600831700001400847700002100861700001800882700001900900856009700919 2007 eng d00aCoupled-Cluster and Configuration-Interaction Calculations for Heavy Nuclei0 aCoupledCluster and ConfigurationInteraction Calculations for Hea c03/2007 a4 pages0 v983 aWe compare coupled-cluster (CC) and configuration-interaction (CI) results for 56Ni obtained in the pf-shell basis, focusing on practical CC approximations that can be applied to systems with dozens or hundreds of correlated fermions. The weight of the reference state and the strength of correlation effects are controlled by the gap between the f7/2 orbit and the f5/2, p3/2, p1/2 orbits. Independent of the gap, the CC method with 1p-1h and 2p-2h clusters and a noniterative treatment of 3p-3h clusters is as accurate as the more demanding CI approach truncated at the 4p-4h level.

1 aHoroi, M.1 aGour, J., R1 aWloch, M.1 aLodriguito, M.D.1 aBrown, B., A.1 aPiecuch, Piotr uhttps://icer.msu.edu/coupled-cluster-and-configuration-interaction-calculations-heavy-nuclei01203nas a2200205 4500008004100000245005500041210005300096260001200149300001300161490000700174520063000181100001400811700001900825700001700844700001600861700001500877700001400892700001900906856007200925 2007 eng d00aCoupled-Cluster Theory for Three-Body Hamiltonians0 aCoupledCluster Theory for ThreeBody Hamiltonians c09/2007 a11 pages0 v763 aWe derive coupled-cluster equations for three-body Hamiltonians. The equations for the one- and two-body cluster amplitudes are presented in a factorized form that leads to an efficient numerical implementation. We employ low-momentum two- and three-nucleon interactions and calculate the binding energy of 4He. The results show that the main contribution of the three-nucleon interaction stems from its density-dependent zero-, one-, and two-body terms that result from the normal ordering of the Hamiltonian in coupled-cluster theory. The residual three-body terms that remain after normal ordering can be neglected.

1 aHagen, G.1 aPapenbrock, T.1 aDean, D., J.1 aSchwenk, A.1 aNHogga, A.1 aWloch, M.1 aPiecuch, Piotr uhttps://icer.msu.edu/coupled-cluster-theory-three-body-hamiltonians00864nas a2200193 4500008004100000245003800041210003800079300001400117490000700131520031100138653006000449100001900509700001700528700001600545700001400561700002600575700001400601856005500615 2006 eng d00aCoupled Cluster Theory for Nuclei0 aCoupled Cluster Theory for Nuclei a5338-53450 v203 aThis presentation focuses on some of the recent developments in low-energy nuclear structure theory, with emphasis on applications of coupled-cluster theory. We report on results for ground and excited states in 4He and 16O, and about extensions of coupled-cluster theory to treat three-body forces.

10aNuclear structure; light nuclei; coupled-cluster theory1 aPapenbrock, T.1 aDean, D., J.1 aGour, J., R1 aHagen, G.1 aHjorth-Jensen}, M., {1 aWloch, M. uhttps://icer.msu.edu/coupled-cluster-theory-nuclei01833nas a2200181 4500008004100000245006500041210006400106260001100170300001300181490000700194520127600201100001901477700001601496700002601512700001401538700001701552856008201569 2006 eng d00aCoupled-Cluster Calculations for Valence Systems around 16 O0 aCoupledCluster Calculations for Valence Systems around 16 O c8/2006 a18 pages0 v743 aWe study the ground and low-lying excited states of 15O, 17O, 15N, and 17F using modern two-body nucleon-nucleon interactions and the suitably designed variants of the ab initio equation-of-motion coupled-cluster theory aimed at an accurate description of systems with valence particles and holes. A number of properties of 15O, 17O, 15N, and 17F, including ways the energies of ground and excited states of valence systems around 16O change as functions of the number of nucleons, are correctly reproduced by the equation-of-motion coupled-cluster calculations performed in up to eight major-oscillator shells. Certain disagreements with experiment are in part because of the degrees of freedom such as three-body interactions not accounted for in our effective two-body Hamiltonians. In particular, the calculated binding energies of 15O/15N and 17O/17F enable us to rationalize the discrepancy between the experimental and recently published [Phys. Rev. Lett. 94, 212501 (2005)] equation-of-motion coupled-cluster excitation energies for the Jπ=3- state of 16O. Our calculations demonstrate the feasibility of the equation-of-motion coupled-cluster methods to deal with valence systems around closed-shell nuclei and to provide results for systems beyond A=16.

1 aPiecuch, Piotr1 aGour, J., R1 aHjorth-Jensen}, M., {1 aWloch, M.1 aDean, D., J. uhttps://icer.msu.edu/coupled-cluster-calculations-valence-systems-around-16-o01855nas a2200181 4500008004100000245006400041210006300105260001200168300001100180490000700191520130200198100001601500700001901516700002601535700001401561700001701575856008101592 2006 eng d00aCoupled-cluster calculations for valence systems around O160 aCoupledcluster calculations for valence systems around O16 c08/2006 a0243100 v743 aWe study the ground and low-lying excited states of {15O,} {17O,} {15N,} and {17F} using modern two-body nucleon-nucleon interactions and the suitably designed variants of the ab initio equation-of-motion coupled-cluster theory aimed at an accurate description of systems with valence particles and holes. A number of properties of {15O,} {17O,} {15N,} and {17F,} including ways the energies of ground and excited states of valence systems around {16O} change as functions of the number of nucleons, are correctly reproduced by the equation-of-motion coupled-cluster calculations performed in up to eight major-oscillator shells. Certain disagreements with experiment are in part because of the degrees of freedom such as three-body interactions not accounted for in our effective two-body Hamiltonians. In particular, the calculated binding energies of {15O/15N} and {17O/17F} enable us to rationalize the discrepancy between the experimental and recently published {[Phys.} Rev. Lett. 94, 212501 (2005)] equation-of-motion coupled-cluster excitation energies for the Jπ=3- state of {16O.} Our calculations demonstrate the feasibility of the equation-of-motion coupled-cluster methods to deal with valence systems around closed-shell nuclei and to provide results for systems beyond A=16.

1 aGour, J., R1 aPiecuch, Piotr1 aHjorth-Jensen}, M., {1 aWloch, M.1 aDean, D., J. uhttps://icer.msu.edu/coupled-cluster-calculations-valence-systems-around-o1600328nam a2200109 4500008004100000020001800041245003800059210003700097260002000134490000700154856005700161 2006 eng d a1-59454-989-300aCoupled-Cluster Theory for Nuclei0 aCoupledCluster Theory for Nuclei bNova Publishers0 v20 uhttps://icer.msu.edu/coupled-cluster-theory-nuclei-001552nas a2200169 4500008004100000245026000041210006900301260001200370300001600382490000800398520078000406100001901186700001501205700001801220700002301238856012101261 2005 eng d00aCan a Single-Reference Approach Provide a Balanced Description of Ground and Excited States? A Comparison of the Completely Renormalized Equation-of-the-Motion Coupled-Cluster Method with Multi-Reference Quasi-Degenerate Perturbation Theory Near a Conical0 aCan a SingleReference Approach Provide a Balanced Description of c11/2005 a11643-116460 v1093 aWe calculated the two lowest electronically adiabatic potential energy surfaces of ammonia in the region of the conical intersection and at a sequence of geometries along which one of the N-H bonds is broken. We employed both a multireference (MR) method and a single-reference (SR) method. The MR calculations are based on multiconfiguration quasidegenerate perturbation theory (MC-QDPT) with a 6-311+G(3df,3pd) basis set. The SR calculations, carried out with the same basis, employ the completely renormalized equation-ofmotion coupled-cluster method with singles and doubles, and a noniterative treatment of triples, denoted CR-EOMCCSD(T). At 91 geometries used for comparison, including geometries near a conical intersection, the surfaces agree to 7% on average.

1 aPiecuch, Piotr1 aNangia, S.1 aTruhlar, D.G.1 aMcGuire}, M., J. { uhttps://icer.msu.edu/research/publications/can-single-reference-approach-provide-balanced-description-ground-excited01534nas a2200265 4500008004100000245007500041210006900116260001500185300001200200490000800212520073300220100001900953700002000972700001600992700001301008700001701021700001401038700002201052700001801074700001401092700001701106700001301123700001701136856011501153 2005 eng d00aComparison of Low-Order Multireference Many-Body Perturbation Theories0 aComparison of LowOrder Multireference ManyBody Perturbation Theo c04/01/2005 a9 pages0 v1223 aTests have been made to benchmark and assess the relative accuracies of low-order multireference perturbation theories as compared to coupled cluster (CC) and full configuration interaction (FCI) methods. Test calculations include the ground and some excited states of the Be, H(2), BeH(2), CH(2), and SiH(2) systems. Comparisons with FCI and CC calculations show that in most cases the effective valence shell Hamiltonian (H(v)) method is more accurate than other low-order multireference perturbation theories, although none of the perturbative methods is as accurate as the CC approximations. We also briefly discuss some of the basic differences among the multireference perturbation theories considered in this work.

1 aPiecuch, Piotr1 aChaudhuri, R.K.1 aFreed, K.F.1 aHose, G.1 aKowalski, K.1 aWloch, M.1 aChattopadhyay, S.1 aMukherjee, D.1 aRolik, R.1 aSzabados, A.1 aToth, G.1 aSurjan, P.R. uhttps://icer.msu.edu/research/publications/comparison-low-order-multireference-many-body-perturbation-theories01895nas a2200133 4500008004100000245012300041210006900164260001400233490000800247520134500255100001901600700001901619856012301638 2005 eng d00aA Comparison of Renormalized Coupled-Cluster and Multireference Methods with Full Configuration Interaction Benchmarks0 aComparison of Renormalized CoupledCluster and Multireference Met c3/22/20050 v1223 aUnusual bonding and electronic near degeneracies make the lowest-lying singlet states of the C2 molecule particularly challenging for electronic structure theory. Here we compare two alternative approaches to modeling bond-breaking reactions and excited states: sophisticated multireference configuration interaction and multireference perturbation theory methods, and a more "black box," single-reference approach, the completely renormalized coupled-cluster method. These approximate methods are assessed in light of their ability to reproduce the full configuration interaction potential energy curves for the X1Sigmag+, B1Deltag, and B' 1Sigmag+ states of C2, which are numerically exact solutions of the electronic Schrodinger equation within the space spanned by a 6-31G* basis set. Both the multireference methods and the completely renormalized coupled-cluster approach provide dramatic improvements over the standard single-reference methods. The multireference methods are nearly as reliable for this challenging test case as for simpler reactions which break only single bonds. The completely renormalized coupled-cluster approach has difficulty for large internuclear separations R in this case, but over the wide range of R=1.0-2.0 A, it compares favorably with the more complicated multireference methods.

1 aPiecuch, Piotr1 aSherrill, C.D. uhttps://icer.msu.edu/comparison-renormalized-coupled-cluster-and-multireference-methods-full-configuration-interaction00768nas a2200169 4500008004100000245007500041210006900116260002500185520018800210100001900398700001700417700002200434700001700456700001900473700001400492856009200506 2005 eng d00aCoupled Cluster Approaches to Nuclei, Ground States and Excited States0 aCoupled Cluster Approaches to Nuclei Ground States and Excited S aPaestum, Italyc20053 aWe present recent coupled-cluster studies of nuclei, with an emphasis on ground state and excited states of closed shell nuclei. Perspectives for future studies are delineated.

1 aPiecuch, Piotr1 aDean, D., J.1 aJhorth-Jensen, M.1 aKowalski, K.1 aPapenbrock, T.1 aWloch, M. uhttps://icer.msu.edu/coupled-cluster-approaches-nuclei-ground-states-and-excited-states01444nas a2200109 4500008004100000245013100041210006900172260001100241490000700252520095200259856012301211 2005 eng d00aCoupled-Cluster Calculations for Ground and Excited States of Closed- and Open-Shell Nuclei Using Methods of Quantum Chemistry0 aCoupledCluster Calculations for Ground and Excited States of Clo c7/20050 v313 aWe discuss large-scale ab initio calculations of ground and excited states of 16O and preliminary calculations for 15O and 17O using coupled-cluster methods and algorithms developed in quantum chemistry. By using realistic two-body interactions and the renormalized form of the Hamiltonian obtained with a no-core G-matrix approach, we are able to obtain the virtually converged results for 16O and promising results for 15O and 17O at the level of two-body interactions. The calculated properties other than binding and excitation energies include charge radius and charge form factor. The relatively low costs of coupled-cluster calculations, which are characterized by the low-order polynomial scaling with the system size, enable us to probe large model spaces with up to seven or eight major oscillator shells, for which nontruncated shell-model calculations for nuclei with A = 15–17 active particles are presently not possible.

uhttps://icer.msu.edu/coupled-cluster-calculations-ground-and-excited-states-closed-and-open-shell-nuclei-using-methods