Biomedical subjects

Piotr Piecuch

Publications and source records attributed to Piotr Piecuch.

17 recordsLinked to original sources

PubMed2006

Efficient formulation and computer implementation of the active-space electron-attached and ionized equation-of-motion coupled-cluster methods.

The efficient, general-purpose implementations of the active-space electron-attached (EA) and ionized (IP) equation-of-motion coupled-cluster (EOMCC) methods including up to 3p-2h and 3h-2p excitations, called EA-EOMCCSDt and IP-EOMCCSDt, respectively, are discussed. The details of the algorithm that enables one to achieve a high degree of code vectorization for the active-space methods and the factorized forms of the EA- and IP-EOMCCSDt equations that maximize the benefits of using active orbitals in the process of selecting the dominant 3p-2h and 3h-2p excitations are presented. The results of benchmark calculations for the low-lying doublet and quartet states of the CH and SH radicals reveal that the active-space EA-EOMCCSDt and IP-EOMCCSDt methods are capable of producing results for the electronic excitations in open-shell systems that match the high accuracy of EA- and IP-EOMCC calculations with a full treatment of 3p-2h and 3h-2p excitations, even when the excited states of interest display a manifestly multideterminantal nature, with the costs that can be on the same order of those characterizing the basic EOMCC singles and doubles approach.

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PubMed2006

Theoretical characterization of end-on and side-on peroxide coordination in ligated Cu2O2 models.

The relative energetics of mu-eta1:eta1 (trans end-on) and mu-eta2:eta2 (side-on) peroxo isomers of Cu2O2 fragments supported by 0, 2, 4, and 6 ammonia ligands have been computed with various density functional, coupled-cluster, and multiconfigurational protocols. There is substantial disagreement between the different levels for most cases, although completely renormalized coupled-cluster methods appear to offer the most reliable predictions. The significant biradical character of the end-on peroxo isomer proves problematic for the density functionals, while the demands on active space size and the need to account for interactions between different states in second-order perturbation theory prove challenging for the multireference treatments. In the latter case, it proved impossible to achieve any convincing convergence.

Cations, Divalent↗

PubMed2006

Theoretical models on the Cu2O2 torture track: mechanistic implications for oxytyrosinase and small-molecule analogues.

Accurately describing the relative energetics of alternative bis(mu-oxo) and mu-eta2:eta2 peroxo isomers of Cu2O2 cores supported by 0, 2, 4, and 6 ammonia ligands is remarkably challenging for a wide variety of theoretical models, primarily owing to the difficulty of maintaining a balanced description of rapidly changing dynamical and nondynamical electron correlation effects and a varying degree of biradical character along the isomerization coordinate. The completely renormalized coupled-cluster level of theory including triple excitations and extremely efficient pure density functional levels of theory quantitatively agree with one another and also agree qualitatively with experimental results for Cu2O2 cores supported by analogous but larger ligands. Standard coupled-cluster methods, such as CCSD(T), are in most cases considerably less accurate and exhibit poor convergence in predicted relative energies. Hybrid density functionals significantly underestimate the stability of the bis(mu-oxo) form, with the magnitude of the error being directly proportional to the percentage Hartree-Fock exchange in the functional. Single-root CASPT2 multireference second-order perturbation theory, by contrast, significantly overestimates the stability of bis(mu-oxo) isomers. Implications of these results for modeling the mechanism of C-H bond activation by supported Cu2O2 cores, like that found in the active site of oxytyrosinase, are discussed.

Binding Sites↗

PubMed2006

Is the mechanism of the [2+2] cycloaddition of cyclopentyne to ethylene concerted or biradical? A completely renormalized coupled cluster study.

The mechanism of the [2+2] cycloaddition reaction of cyclopentyne to ethylene has been studied using the completely renormalized coupled cluster method with singles, doubles, and noniterative triples (CR-CCSD(T)). In agreement with the experimentally observed stereochemistry, the CR-CCSD(T) method favors the concerted pathway involving a [2+1] transition state, whereas the popular CCSD(T) method, which is often regarded as the "gold standard" of electronic structure theory, and low-order multireference methods support the less probable biradical mechanism. In addition, the CCSD(T) approach produces an erroneous description of some transition states and intermediates, particularly those which have a significant biradical character. The CR-CCSD(T) calculations indicate that the reaction is a highly exothermic (deltaG(r)298 = -68 kcal/mol), predominantly concerted process with a relatively low activation barrier on the order of 13-16 kcal/mol which permits its thermal occurrence.

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PubMed2005

Can a single-reference approach provide a balanced description of ground and excited states? A comparison of the completely renormalized equation-of-motion coupled-cluster method with multireference quasidegenerate perturbation theory near a conical intersection and along a photodissociation coordinate in ammonia.

We 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-of-motion 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.

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PubMed2005

Renormalized coupled-cluster methods exploiting left eigenstates of the similarity-transformed Hamiltonian.

Completely renormalized (CR) coupled-cluster (CC) approaches, such as CR-CCSD(T), in which one corrects the standard CC singles and doubles (CCSD) energy for the effects of triply (T) and other higher-than-doubly excited clusters [K. Kowalski and P. Piecuch, J. Chem. Phys. 113, 18 (2000)], are reformulated in terms of the left eigenstates Phimid R:L of the similarity-transformed Hamiltonian of CC theory. The resulting CR-CCSD(T)(L) or CR-CC(2,3) and other CR-CC(L) methods are derived from the new biorthogonal form of the method of moments of CC equations (MMCC) in which, in analogy to the original MMCC theory, one focuses on the noniterative corrections to standard CC energies that recover the exact, full configuration-interaction energies. One of the advantages of the biorthogonal MMCC theory, which will be further analyzed and extended to excited states in a separate paper, is a rigorous size extensivity of the basic ground-state CR-CC(L) approximations that result from it, which was slightly violated by the original CR-CCSD(T) and CR-CCSD(TQ) approaches. This includes the CR-CCSD(T)(L) or CR-CC(2,3) method discussed in this paper, in which one corrects the CCSD energy by the relatively inexpensive noniterative correction due to triples. Test calculations for bond breaking in HF, F(2), and H(2)O indicate that the noniterative CR-CCSD(T)(L) or CR-CC(2,3) approximation is very competitive with the standard CCSD(T) theory for nondegenerate closed-shell states, while being practically as accurate as the full CC approach with singles, doubles, and triples in the bond-breaking region. Calculations of the activation enthalpy for the thermal isomerizations of cyclopropane involving the trimethylene biradical as a transition state show that the noniterative CR-CCSD(T)(L) approximation is capable of providing activation enthalpies which perfectly agree with experiment.

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PubMed2005

Active-space equation-of-motion coupled-cluster methods for excited states of radicals and other open-shell systems: EA-EOMCCSDt and IP-EOMCCSDt.

The previously developed active-space coupled-cluster (CC) and equation-of-motion (EOM) CC methods are extended to radicals and other open-shell systems by combining them with the electron attached (EA) and ionized (IP) EOMCC approaches. As illustrated by the calculations for the CH and OH radicals, the resulting EA-EOMCCSDt and IP-EOMCCSDt theories are capable of providing a highly accurate description of the electronic spectra of radical systems, including excited states displaying a manifestly multideterminantal nature, with the low costs that are not much greater that those characterizing the standard EOMCC singles and doubles method.

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PubMed2005

Active-space coupled-cluster study of electronic states of Be3.

The active-space coupled-cluster (CC) and equation-of-motion (EOM) CC methods with all single and double excitations with triple excitations defined via active orbitals (CCSDt, EOMCCSDt), as implemented with TENSOR CONTRACTION ENGINE, are applied to the challenging Be3 system, which is characterized by a large number of low-lying excited states dominated by two-electron transitions and significant high-order correlation effects in the ground electronic state. It is demonstrated that the CCSDt and EOMCCSDt methods provide an excellent description of complicated electronic quasidegeneracies present in the Be3 cluster. Different strategies for defining triple excitations within the CCSDtEOMCCSDt approach are discussed.

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PubMed2005

Extension of renormalized coupled-cluster methods including triple excitations to excited electronic states of open-shell molecules.

The general-purpose open-shell implementation of the completely renormalized equation-of-motion coupled-cluster approach with singles, doubles, and noniterative triples [CR-EOMCCSD(T)] is reported. Benchmark calculations for the low-lying doublet and quartet states of the CH radical show that the CR-EOMCCSD(T) method is capable of providing a highly accurate description of ground and excited states of open-shell molecules. This includes states with strong double excitation character, for which the conventional EOMCCSD approach fails.

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PubMed2005

Comparison of low-order multireference many-body perturbation theories.

Tests 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.

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PubMed2005

The X1Sigmag+, B1Deltag, and B' 1Sigmag+ states of C2: a comparison of renormalized coupled-cluster and multireference methods with full configuration interaction benchmarks.

Unusual 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.

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PubMed2005

Balancing dynamic and nondynamic correlation for diradical and aromatic transition states: a renormalized coupled-cluster study of the cope rearrangement of 1,5-hexadiene.

Single-reference coupled-cluster calculations employing the completely renormalized CCSD(T) (CR-CCSD(T)) approach have been used to examine the mechanism of the Cope rearrangement of 1,5-hexadiene. In agreement with multireference perturbation theory, the CR-CCSD(T) method favors the concerted mechanism of the Cope rearrangement involving an aromatic transition state. The CCSD(T) approach, which is often regarded as the "gold standard" of electronic structure theory, seems to fail in this case, favoring pathways through diradical structures.

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PubMed2005

Extensive generalization of renormalized coupled-cluster methods.

The recently developed completely renormalized (CR) coupled-cluster (CC) methods with singles, doubles, and noniterative triples or triples and quadruples [CR-CCSD(T) or CR-CCSD(TQ), respectively], which are based on the method of moments of CC equations (MMCC) [K. Kowalski and P. Piecuch, J. Chem. Phys. 113, 18 (2000)], eliminate the failures of the standard CCSD(T) and CCSD(TQ) methods at larger internuclear separations, but they are not rigorously size extensive. Although the departure from strict size extensivity of the CR-CCSD(T) and CR-CCSD(TQ) methods is small, it is important to examine the possibility of formulating the improved CR-CC methods, which are as effective in breaking chemical bonds as the existing CR-CCSD(T) and CR-CCSD(TQ) approaches, which are as easy to use as the CR-CCSD(T) and CR-CCSD(TQ) methods, and which can be made rigorously size extensive. This may be particularly useful for the applications of CR-CC methods and other MMCC approaches in calculations of potential energy surfaces of large many-electron systems and van der Waals molecules, where the additive separability of energies in the noninteracting limit is very important. In this paper, we propose different types of CR-CC approximations, termed the locally renormalized (LR) CCSD(T) and CCSD(TQ) methods, which become rigorously size extensive if the orbitals are localized on nointeracting fragments. The LR-CCSD(T) and LR-CCSD(TQ) methods rely on the form of the energy expression in terms of the generalized moments of CC equations, derived in this work, termed the numerator-denominator-connected MMCC expansion. The size extensivity and excellent performance of the LR-CCSD(T) and LR-CCSD(TQ) methods are illustrated numerically by showing the results for the dimers of stretched HF and LiH molecules and bond breaking in HF and H2O.

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PubMed2005

Where does the planar-to-nonplanar turnover occur in small gold clusters?

Several levels of theory, including both Gaussian-based and plane wave density functional theory (DFT), second-order perturbation theory (MP2), and coupled cluster methods (CCSD(T)), are employed to study Au6 and Au8 clusters. All methods predict that the lowest energy isomer of Au6 is planar. For Au8, both DFT methods predict that the two lowest isomers are planar. In contrast, both MP2 and CCSD(T) predict the lowest Au8 isomers to be nonplanar.

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PubMed2004

Combined coupled-cluster and many-body perturbation theories.

Various approximations combining coupled-cluster (CC) and many-body perturbation theories have been derived and implemented into the parallel execution programs that take into account the spin, spatial (real Abelian), and permutation symmetries and that are applicable to closed- and open-shell molecules. The implemented models range from the CCSD(T), CCSD[T], CCSD(2)(T), CCSD(2)(TQ), and CCSDT(2)(Q) methods to the completely renormalized (CR) CCSD(T) and CCSD[T] approaches, where CCSD (CCSDT) stands for the CC method with connected single and double (single, double, and triple) cluster operators, and subscripted or parenthesized 2, T, and Q indicate the perturbation order or the excitation ranks of the cluster operators included in the corrections. The derivation and computer implementation have been automated by the algebraic and symbolic manipulation program TENSOR CONTRACTION ENGINE (TCE). The TCE-synthesized subroutines generate the tensors with the highest excitation rank in a blockwise manner so that they need not be stored in their entirety, while enabling the efficient reuse of other precalculated intermediate tensors defined by prioritizing the memory optimization as well as operation minimization. Consequently, the overall storage requirements for the corrections due to connected triple and quadruple cluster operators scale as O(n(4)) and O(n(6)), respectively (n being a measure of the system size). For systems with modest multireference character of their wave functions, we found that the order of accuracy is CCSD<CR-CCSD(T) approximately CCSD(2)(T) approximately CCSD(T)<CCSDT approximately CCSD(2)(TQ)<CCSDT(2)(Q), whereas CR-CCSD(T) is more effective in cases of larger quasidegeneracy. The operation costs of the TCE-generated CCSD(2)(TQ) and CCSDT(2)(Q) codes scale as rather steep O(n(9)), while the TCE-generated CCSD(T), CCSD(2)(T), and CR-CCSD(T) codes are near operation minimum [a noniterative O(n(7))]. The perturbative correction part of the CCSD(T)/cc-pVDZ calculations for azulene exhibited a 45-fold speedup upon a 64-fold increase in the number of processors from 8 to 512.

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PubMed2004

New coupled-cluster methods with singles, doubles, and noniterative triples for high accuracy calculations of excited electronic states.

The single-reference ab initio methods for high accuracy calculations of potential energy surfaces (PESs) of excited electronic states, termed the completely renormalized equation-of-motion coupled-cluster approaches with singles, doubles, and noniterative triples [CR-EOMCCSD(T)], are developed. In the CR-EOMCCSD(T) methods, which are based on the formalism of the method of moments of coupled-cluster equations, the suitably designed corrections due to triple excitations are added, in a state-selective manner, to the excited-state energies obtained in the standard equation-of-motion coupled-cluster calculations with singles and doubles (EOMCCSD). It is demonstrated that the CR-EOMCCSD(T) approaches, which can be regarded as the excited-state analogs of the ground-state CR-CCSD(T) theory, provide a highly accurate description of excited states dominated by double excitations, excited states displaying a manifestly multireference character, and PESs of excited states along bond breaking coordinates with the ease of the ground-state CCSD(T) or CR-CCSD(T) calculations. The performance of the CR-EOMCCSD(T) methods is illustrated by the results of calculations for the excited states of CH+, HF, N2, C2, and ozone.

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PubMed2003

Exactness of two-body cluster expansions in many-body quantum theory.

The Horn-Weinstein formula and the variational principle, combined with numerical results for a few many-electron systems, are used to provide support for a conjecture that the exact ground-state wave function for a Hamiltonian system containing up to two-body terms may be represented by an exponential cluster expansion employing a finite two-body operator.

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