Extrapolation to the Gold-Standard in Quantum Chemistry: Computationally Efficient and Accurate CCSD(T) Energies for Large Molecules Using an Automated Thermochemical Hierarchy

Ramabhadran, Raghunath O.; Raghavachari, Krishnan

doi:10.1021/ct400465q

Cited by 74 publications

(123 citation statements)

References 140 publications

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“…41 To illustrate the use of CBH as a fragment-based method, we hereafter loosely use the phrase "fragments" to allude to the "reference molecules" in the CBH scheme (i.e., both primary and derivative subsystems).…”

Section: A New Concept In Fragment-based Methods As a Results Of Its Mmentioning

confidence: 99%

“…Yet, sub-kilocalorie per mole accuracy is achieved with the ring form and the open form (Table 2), thus showcasing the success of our method. More detailed insights on the individual performance of some of the other molecules in the test set, extrapolated CCSD energies, and the poor performance with the CBH-1 rung (thus testifying the need for appropriate error cancellation from CBH-2 and higher rungs) are given in ref 41. It should also be emphasized here that the current formulation of CBH as a fragment-based method is applicable only for energetic minima on the potential energy surface since the fragment energies are constant and do not vary as the geometry of the parent molecule changes.…”

Section: A New Concept In Fragment-based Methods As a Results Of Its Mmentioning

confidence: 99%

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The Successful Merger of Theoretical Thermochemistry with Fragment-Based Methods in Quantum Chemistry

Ramabhadran

Raghavachari

2014

Acc. Chem. Res.

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CONSPECTUS: Quantum chemistry and electronic structure theory have proven to be essential tools to the experimental chemist, in terms of both a priori predictions that pave the way for designing new experiments and rationalizing experimental observations a posteriori. Translating the well-established success of electronic structure theory in obtaining the structures and energies of small chemical systems to increasingly larger molecules is an exciting and ongoing central theme of research in quantum chemistry. However, the prohibitive computational scaling of highly accurate ab initio electronic structure methods poses a fundamental challenge to this research endeavor. This scenario necessitates an indirect fragment-based approach wherein a large molecule is divided into small fragments and is subsequently reassembled to compute its energy accurately. In our quest to further reduce the computational expense associated with the fragment-based methods and overall enhance the applicability of electronic structure methods to large molecules, we realized that the broad ideas involved in a different area, theoretical thermochemistry, are transferable to the area of fragment-based methods. This Account focuses on the effective merger of these two disparate frontiers in quantum chemistry and how new concepts inspired by theoretical thermochemistry significantly reduce the total number of electronic structure calculations needed to be performed as part of a fragment-based method without any appreciable loss of accuracy. Throughout, the generalized connectivity based hierarchy (CBH), which we developed to solve a long-standing problem in theoretical thermochemistry, serves as the linchpin in this merger. The accuracy of our method is based on two strong foundations: (a) the apt utilization of systematic and sophisticated error-canceling schemes via CBH that result in an optimal cutting scheme at any given level of fragmentation and (b) the use of a less expensive second layer of electronic structure method to recover all the missing long-range interactions in the parent large molecule. Overall, the work featured here dramatically decreases the computational expense and empowers the execution of very accurate ab initio calculations (gold-standard CCSD(T)) on large molecules and thereby facilitates sophisticated electronic structure applications to a wide range of important chemical problems.

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Section: A New Concept In Fragment-based Methods As a Results Of Its Mmentioning

confidence: 99%

Section: A New Concept In Fragment-based Methods As a Results Of Its Mmentioning

confidence: 99%

The Successful Merger of Theoretical Thermochemistry with Fragment-Based Methods in Quantum Chemistry

Ramabhadran

Raghavachari

2014

Acc. Chem. Res.

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“…CCSD(T) is generally considered as “gold standard” . By comparing Table with Table S2 (Supporting Information), we can see that the performance of the single‐point‐energy calculations at the CCSD level [without (T)] is actually not that close to those at the CCSD(T) level.…”

Section: Resultsmentioning

confidence: 99%

Ab initio path‐integral calculations of kinetic and equilibrium isotope effects on base‐catalyzed RNA transphosphorylation models

Wong

York

2014

J Comput Chem

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Detailed understandings of the reaction mechanisms of RNA catalysis in various environments can have profound importance for many applications, ranging from the design of new biotechnologies to the unraveling of the evolutionary origin of life. An integral step in the nucleolytic RNA catalysis is self-cleavage of RNA strands by 2′-O-transphosphorylation. Key to elucidating a reaction mechanism is determining the molecular structure and bonding characteristics of transition state. A direct and powerful probe of transition state is measuring isotope effects on biochemical reactions, particularly if we can reproduce isotope effect values from quantum calculations. This paper significantly extends the scope of our previous joint experimental and theoretical work in examining isotope effects on enzymatic and non-enzymatic 2′-O-transphosphorylation reaction models that mimic reactions catalyzed by RNA enzymes (ribozymes), and protein enzymes such as ribonuclease A (RNase A). Native reactions are studied, as well as reactions with thio substitutions representing chemical modifications often used in experiments to probe mechanism. Here, we report and compare results from eight levels of electronic-structure calculations for constructing the potential energy surfaces in kinetic and equilibrium isotope effects (KIE and EIE) computations, including a “gold-standard” coupled-cluster level of theory [CCSD(T)]. In addition to the widely-used Bigeleisen equation for estimating KIE and EIE values, internuclear anharmonicity and quantum tunneling effects were also computed using our recently-developed ab initio path-integral method, i.e., automated integration-free path-integral (AIF-PI) method. The results of this work establish an important set of benchmarks that serve to guide calculations of KIE and EIE for RNA catalysis.

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“…At CBH‐3, the immediate chemical environments of all the heavy atom bonds are preserved. As the name suggests, at higher level of rungs a greater chemical environment (and a geometry more similar to parent molecule) is preserved, and results in accurate thermochemistry, and an accurate extrapolation to CCSD(T) energies …”

Section: Methodology and Comparison With Other Fragment‐based Methodsmentioning

confidence: 99%

“…For a range of organic and bio‐organic molecules in these studies, it was observed that the MP2 and CCSD(T) reaction energies were in close agreement for CBH‐2 reaction schemes. This allowed the use of MP2 energy and CCSD(T) energies of fragments to extrapolate to the CCSD(T) energy of the target molecule . For the sake of brevity, the method is only discussed briefly in the methodology section, while complete details of the method can be found in the previous work, and a recent review .…”

Section: Introductionmentioning

confidence: 99%

Breaking a bottleneck: Accurate extrapolation to “gold standard” CCSD(T) energies for large open shell organic radicals at reduced computational cost

2015

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Open Shell organic radicals are principal species involved in many diverse areas such as combustion, photochemistry, and polymer chemistry. Computational studies of such species with an accurate method like coupled-cluster with single and double and perturbative triple (CCSD(T)) may be restricted to systems of modest size due to the steep computational scaling of the method. Herein, we assess the accuracy of extrapolated CCSD(T) energies determined using the connectivity-based hierarchy (CBH) method on medium to large sized radicals. In our method, an MP2 calculation on the target radical is coupled with CCSD(T) energies of fragments determined uniquely by our hierarchy to perform accurate extrapolations. A careful assessment is done with a robust CBH-rad49 test set comprising of 49 diverse cyclic and acyclic radicals with a variety of functional groups. We demonstrate that the extrapolation method with CBH-2 or CBH-3 is sufficient to obtain sub-kcal accuracy. ROMP2 and PMP2 calculations with both Pople-style and Dunning-style basis-sets resulted in mean absolute errors for CCSD(T) extrapolation (full CCSD(T)-extrapolated CCSD(T)) within 0.5 kcal/mol. Further speedup for such CCSD(T) extrapolations are obtained with ROHF-based RI-MP2 calculations. Challenging systems with (a) high ring strain, (b) delocalized character, and (c) spin contamination are identified and analyzed in detail. Finally, we apply our extrapolation method on 10 larger radicals containing 10-15 heavy atoms, where accurate CCSD(T) energies are obtained at a fractional cost of full CCSD(T) calculations.

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Extrapolation to the Gold-Standard in Quantum Chemistry: Computationally Efficient and Accurate CCSD(T) Energies for Large Molecules Using an Automated Thermochemical Hierarchy

Cited by 74 publications

References 140 publications

The Successful Merger of Theoretical Thermochemistry with Fragment-Based Methods in Quantum Chemistry

The Successful Merger of Theoretical Thermochemistry with Fragment-Based Methods in Quantum Chemistry

Ab initio path‐integral calculations of kinetic and equilibrium isotope effects on base‐catalyzed RNA transphosphorylation models

Breaking a bottleneck: Accurate extrapolation to “gold standard” CCSD(T) energies for large open shell organic radicals at reduced computational cost

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