Accurate and Computationally Efficient Prediction of Thermochemical Properties of Biomolecules Using the Generalized Connectivity-Based Hierarchy

Sengupta, Arkajyoti; Ramabhadran, Raghunath O.; Raghavachari, Krishnan

doi:10.1021/jp505544y

Cited by 14 publications

(18 citation statements)

References 96 publications

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“…Only a single MP2 calculation To test the accuracy of CBH to get extrapolated CCSD(T) energies, we included all the varied 27 nonaromatic molecules from our earlier test set for obtaining accurate enthalpies of formation 36,37,39 and added glucose (ring and open forms) and alanine dipeptide. 39 The 30 molecule test we assembled ( Figure 6) was further divided into test set A and test set B. Test set A has the 20 common organic molecules, and test set B contains the more challenging systems with ring strain, multiple heteroatoms, or biomolecules with internal hydrogen bonds.…”

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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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%

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

Ramabhadran

Raghavachari

2014

Acc. Chem. Res.

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“…To date, the standard CBH correction scheme has been benchmarked on closed-and open-shell, H,C,N,O,F,S,Clcontaining organic and biomolecules, both neutral and cationic with a wide variety of functional groups. 41,[45][46][47][48][49] Previous performance of CBH on the calculation of the heat of formation of a set of neutral organic molecules from Reference 41 is showcased in Table 4. Using the CBH-3 correction scheme, mean absolute deviations within chemical accuracy are achieved for many different low levels of theory.…”

Section: Performance Of Cbh For Thermochemistrymentioning

confidence: 99%

Applications of isodesmic‐type reactions for computational thermochemistry

Chan

Collins

Raghavachari

2020

WIREs Comput Mol Sci

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In computational thermochemistry, “isodesmic‐type” reactions play a significant role for obtaining accurate thermochemical quantities using low‐cost methods that can be applied to large systems. This review touches on some of the examples. For instance, a series of relative bond dissociation energies (BDEs) have been devised to calculate absolute BDEs with near‐chemical‐accuracy (~5 kJ mol−1) using density functional theory (DFT) methods. To facilitate the applicability of isodesmic‐type reactions, the connectivity‐based hierarchy (CBH) has been developed to automate the systematic generation of isodesmic‐type reaction schemes, and applied to large organic and biomolecular systems. The related netCBH scheme yields accurate reaction energies in complex organic reactions, achieving coupled‐cluster quality results at DFT cost. Isodesmic‐type reactions have been used to obtain heats of formation for medium‐sized fullerenes, with uncertainties of ~20 kJ mol−1 up to C180. In comparison, the literature C60 heat of formation has an uncertainty of 100 kJ mol−1. Importantly, it fills the gap in which heats of formation for those larger fullerenes are not available. These studies showcase how isodesmic‐type reactions propel the accuracy of quantum chemistry computations to a level that rivals or even betters modern experimental determinations, particularly for systems that are difficult to study experimentally. This article is categorized under: Structure and Mechanism > Reaction Mechanisms and Catalysis Electronic Structure Theory > Combined QM/MM Methods Theoretical and Physical Chemistry > Thermochemistry

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“…[46] Subsequent applications of CBH on biomolecules have shown that the heats of formation obtained with CBH-2 (vide infra) are in good agreement with computationally expensive Gaussian-n (Gn) and Weizmann-n (Wn) methods for most of the amino acids. [47,48] For a range of organic and bioorganic 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.…”

Section: Introductionmentioning

confidence: 70%

“…It yields accurate thermochemical properties using density functional theory (DFT) methods, as well as wavefunction‐based methods . Subsequent applications of CBH on biomolecules have shown that the heats of formation obtained with CBH‐2 ( vide infra ) are in good agreement with computationally expensive Gaussian‐ n (G n ) and Weizmann‐ n (W n ) methods for most of the amino acids . 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.…”

Section: Introductionmentioning

confidence: 86%

“…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, [45][46][47][48] and an accurate extrapolation to CCSD(T) energies. [49] Figure 1 represents the schematic working of CBH-2 for CCSD(T) extrapolation with 5,6-dimethyldec-3-yl radical as an example.…”

Section: Application Of Cbh-2 and Cbh-3 Schemes For Ccsd(t) Extrapolamentioning

confidence: 99%

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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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Accurate and Computationally Efficient Prediction of Thermochemical Properties of Biomolecules Using the Generalized Connectivity-Based Hierarchy

Cited by 14 publications

References 96 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

Applications of isodesmic‐type reactions for computational thermochemistry

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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